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Sample records for asymmetrical endonuclease double

  1. How quantum entanglement in DNA synchronizes double-strand breakage by type II restriction endonucleases.

    Science.gov (United States)

    Kurian, P; Dunston, G; Lindesay, J

    2016-02-21

    Macroscopic quantum effects in living systems have been studied widely in pursuit of fundamental explanations for biological energy transport and sensing. While it is known that type II endonucleases, the largest class of restriction enzymes, induce DNA double-strand breaks by attacking phosphodiester bonds, the mechanism by which simultaneous cutting is coordinated between the catalytic centers remains unclear. We propose a quantum mechanical model for collective electronic behavior in the DNA helix, where dipole-dipole oscillations are quantized through boundary conditions imposed by the enzyme. Zero-point modes of coherent oscillations would provide the energy required for double-strand breakage. Such quanta may be preserved in the presence of thermal noise by the enzyme's displacement of water surrounding the DNA recognition sequence. The enzyme thus serves as a decoherence shield. Palindromic mirror symmetry of the enzyme-DNA complex should conserve parity, because symmetric bond-breaking ceases when the symmetry of the complex is violated or when physiological parameters are perturbed from optima. Persistent correlations in DNA across longer spatial separations-a possible signature of quantum entanglement-may be explained by such a mechanism. PMID:26682627

  2. Bound states in a hyperbolic asymmetric double-well

    Energy Technology Data Exchange (ETDEWEB)

    Hartmann, R. R., E-mail: richard.hartmann@dlsu.edu.ph [Physics Department, De La Salle University, 2401 Taft Avenue, Manila (Philippines)

    2014-01-15

    We report a new class of hyperbolic asymmetric double-well whose bound state wavefunctions can be expressed in terms of confluent Heun functions. An analytic procedure is used to obtain the energy eigenvalues and the criterion for the potential to support bound states is discussed.

  3. Asymmetric double-well potential for single-atom interferometry

    International Nuclear Information System (INIS)

    We consider the evolution of a single-atom wave function in a time-dependent double-well interferometer in the presence of a spatially asymmetric potential. We examine a case where a single trapping potential is split into an asymmetric double well and then recombined again. The interferometer involves a measurement of the first excited state population as a sensitive measure of the asymmetric potential. Based on a two-mode approximation a Bloch vector model provides a simple and satisfactory description of the dynamical evolution. We discuss the roles of adiabaticity and asymmetry in the double-well interferometer. The Bloch model allows us to account for the effects of asymmetry on the excited state population throughout the interferometric process and to choose the appropriate splitting, holding, and recombination periods in order to maximize the output signal. We also compare the outcomes of the Bloch vector model with the results of numerical simulations of the multistate time-dependent Schroedinger equation

  4. An asymmetric relativistic model for classical double radio sources

    CERN Document Server

    Arshakian, T G

    2000-01-01

    There is substantial observational evidence against the symmetric relativistic model of FRII radio sources. An asymmetric relativistic model is proposed which takes account of both relativistic effects and intrinsic/environmental asymmetries to explain the structural asymmetries of their radio lobes. A key parameter of the model is the jet-side of the double sources, which is estimated for 80% of the FRII sources in the 3CRR complete sample. Statistical analyses of the properties of these sources show that the asymmetric model is in agreement with a wide range of observational data, and that the relativistic and intrinsic asymmetry effects are of comparable importance. Intrinsic/environmental asymmetry effects are more important at high radio luminosities and small physical scales. The mean translational speed of the lobes is found to be 0.11c, consistent with the speeds found from spectral ageing arguments. According to a Gaussian model, the standard deviation of lobe speeds is 0.04c. The results are in agre...

  5. Pentamode metamaterials with asymmetric double-cone elements

    International Nuclear Information System (INIS)

    Pentamode metamaterials are a very interesting set of artificial solids. They are difficult to compress but flow easily, hence imitating somehow the behaviours of liquids. In this paper, three-dimensional (3D) pentamode metamaterials based on the asymmetric double-cone element (ADCE) are proposed. The ADCE is composed by two connected truncated cones with different thin diameters. The phonon band structures of the ADCEs pentamode metamaterials are numerically analysed by using the finite element method (FEM). Besides the single phonon mode, the complete 3D band gaps are also found in the phonon band structures. Here, the influence of the degree of asymmetry of ADCE to the figure of merit (FOM), which is the ratio of bulk modulus and shear modulus, is discussed. The FOM can be increased by 21–30% (at FOM ≥ 103) when the degree of asymmetry m ranges from 0.4 to 0.6. (paper)

  6. Independently tunable double Fano resonances in asymmetric MIM waveguide structure.

    Science.gov (United States)

    Qi, Jiwei; Chen, Zongqiang; Chen, Jing; Li, Yudong; Qiang, Wu; Xu, Jingjun; Sun, Qian

    2014-06-16

    In this paper, an asymmetric plasmonic structure composed of a MIM (metal-insulator-metal) waveguide and a rectangular cavity is reported, which can support double Fano resonances originating from two different mechanisms. One of Fano resonance originates from the interference between a horizontal and a vertical resonance in the rectangular cavity. And the other is induced by the asymmetry of the plasmonic structure. Just because the double Fano resonances originate from two different mechanisms, each Fano resonance can be well tuned independently by changing the parameters of the rectangular cavity. And during the tuning process, the FOMs (figure of merit) of both the Fano resonances can keep unchanged almost with large values, both larger than 650. Such, the transmission spectra of the plasmonic structure can be well modulated to form transmission window with the position and the full width at half maximum (FWHM) can be tuned freely, which is useful for the applications in sensors, nonlinear and slow-light devices. PMID:24977564

  7. Strand-specific contacts and divalent metal ion regulate double-strand break formation by the GIY-YIG homing endonuclease I-BmoI.

    Science.gov (United States)

    Carter, Jonathan M; Friedrich, Nancy C; Kleinstiver, Benjamin; Edgell, David R

    2007-11-23

    GIY-YIG homing endonucleases are modular enzymes consisting of a well-defined N-terminal catalytic domain connected to a variable C-terminal DNA-binding domain. Previous studies have revealed that the role of the DNA-binding domain is to recognize and bind intronless DNA substrate, positioning the N-terminal catalytic domain such that it is poised to generate a staggered double-strand break by an unknown mechanism. Interactions of the N-terminal catalytic domain with intronless substrate are therefore a critical step in the reaction pathway but have been difficult to define. Here, we have taken advantage of the reduced activity of I-BmoI, an isoschizomer of the well-studied bacteriophage T4 homing endonuclease I-TevI, to examine double-strand break formation by I-BmoI. We present evidence demonstrating that I-BmoI generates a double-strand break by two sequential but chemically independent nicking reactions where divalent metal ion is a limiting factor in top-strand nicking. We also show by in-gel footprinting that contacts by the I-BmoI catalytic domain induce significant minor groove DNA distortions that occur independently of bottom-strand nicking. Bottom-strand contacts are critical for accurate top-strand nicking, whereas top-strand contacts have little influence on the accuracy of bottom-strand nicking. We discuss our results in the context of current models of GIY-YIG endonuclease function, with emphasis on the role of divalent metal ion and strand-specific contacts in regulating the activity of a single active site to generate a staggered double-strand break. PMID:17936302

  8. The Application of The Double Queue Asymmetric Gated Service Polling Control Theory in Intelligent Traffic System

    Directory of Open Access Journals (Sweden)

    Zhao Yi Fan

    2016-01-01

    Full Text Available paper presents a new use of double queues asymmetric gated service polling system in the intelligent traffic light control system.Usually there are more vehicles in main road than minor road,so there are more green light time be needed in the main road.From the computer simulation and theory analysis,we can find that the application of double queues asymmetric gated service polling theory in intelligent traffic system can balance intersections load and set suitable passing time for vehicles to assure the roads open.

  9. Simultaneous measurements of plasma flow and ion temperature using the asymmetric double probe

    International Nuclear Information System (INIS)

    The asymmetric double probe method is extended to measure not only the ion temperature but also plasma flow in the tokamak edge plasma under a strong magnetic field. The plasma flow or the Mach number is determined by the ratio of ion saturation currents of the double probe pins, where the axes of the cylindrical pins are oriented perpendicular to the magnetic field and face up-or downstream. An experiment was performed in the JFT-2M tokamak. (author)

  10. Tunneling and energy splitting in an asymmetric double-well potential

    International Nuclear Information System (INIS)

    An asymmetric double-well potential is considered, assuming that the minima of the wells are quadratic with a frequency ω and the difference of the minima is close to a multiple of hω. A WKB wave function is constructed on both sides of the local maximum between the wells, by matching the WKB function to the exact wave functions near the classical turning points. The continuities of the wave function and its first derivative at the local maximum then give the energy-level splitting formula, which not only reproduces the instanton result for a symmetric potential, but also elucidates the appearance of resonances of tunneling in the asymmetric potential

  11. Current-phase relation of a ballistic asymmetric double superconductor-normal-metal-superconductor junction

    International Nuclear Information System (INIS)

    The zero-temperature current-phase (I-φ) relation (CPR) of a mesoscopic, ballistic, and asymmetrically stacked, double superconductor-normal-metal-superconduc tor (SNS) junction is studied. Here φ is the phase difference between the two superconducting end-electrodes. The lack of configuration symmetry in such asymmetric SNSNS junctions forbids a simple choice of values for the phase φ2 of the middle superconductor. We propose to determine the values of φ2 by equating the currents in the two normal regions. Two features in the CPR are found. First, the CPR of the asymmetric junction has a cutoff feature, whose origin is best demonstrated in the long middle superconductor (large L2) cases, when the critical current of the double SNS junction is bounded by the SNS junction that has the longer normal region. This cutoff feature is more pronounced for longer L2 and for higher degree of junction asymmetry. Second, in regions other than the cutoff region, the CPR of the asymmetric junction deviates only within a few percent from the CPR of the symmetric junction which has the same total length LTotal in the normal regions and the same L2. This is in contrast with the greater sensitivity the CPR has to the changes in LTotal or L2. (orig.)

  12. Electron Transport through Magnetic Superlattices with Asymmetric Double-Barrier Units in Graphene

    International Nuclear Information System (INIS)

    We investigate the transport properties through magnetic superlattices with asymmetric double-barrier units in monolayer graphene. In N-periodic asymmetric double-barrier units, there is (N − 1)-fold resonant peak splitting for transmission, but the splitting is (2N − 1)-fold in N-periodic symmetric units. The transmission depends not only on the value of incident wavevectors but also on the value and the direction of transverse wavevectors. This renders the structure's efficient wavevector filters. In addition, the conductance of standard electrons with a parabolic energy spectrum is suppressed more strongly than that of Dirac electrons, whereas the resonances are more pronounced for Dirac electrons than for standard ones. (condensed matter: electronic structure, electrical, magnetic, and optical properties)

  13. Dynamic control of coherent pulses via Fano-type interference in asymmetric double quantum wells

    International Nuclear Information System (INIS)

    We study the temporal and spatial dynamics of two light pulses, a probe and a switch, propagating through an asymmetric double quantum well where tunneling-induced quantum interference may be observed. When such an interference takes place, in the absence of the switch, the quantum well is transparent to the probe which propagates over sufficiently long distances at very small group velocities. In the presence of a relatively strong switch, however, the probe pulse is absorbed due to the quenching of tunneling-induced quantum interference. The probe may be made to vanish even when switch and probe are somewhat delayed with respect to one another. Conversely, our asymmetric double quantum well may be rendered either opaque or transparent to the switch pulse. Such a probe-switch 'reciprocity' can be used to devise a versatile all-optical quantum interference-based solid-state switch for optical communication devices

  14. Lateral current density fronts in asymmetric double-barrier resonant-tunneling structures

    OpenAIRE

    Rodin, Pavel; Schoell, Eckehard

    2003-01-01

    We present a theoretical analysis and numerical simulations of lateral current density fronts in bistable resonant-tunneling diodes with Z-shaped current-voltage characteristics. The bistability is due to the charge accumulation in the quantum well of the double-barrier structure. We focus on asymmetric structures in the regime of sequential incoherent tunneling and study the dependence of the bistability range, the front velocity and the front width on the structure parameters. We propose a ...

  15. Enhanced refractive index without absorption in four-level asymmetrical double semiconductor quantum well

    Science.gov (United States)

    Kang, Chengxian; Wang, Zhiping; Yu, Benli

    2016-03-01

    We investigate the absorptive-dispersive properties of a weak probe field in a four-level asymmetrical double semiconductor quantum well. It is found that the enhanced refraction index without absorption can be easily controlled via adjusting properly the corresponding parameters of the system. Our scheme may provide some new possibilities for technological applications in dispersion compensation and solid-state quantum communication for quantum information processing.

  16. Strongly confined tunnel-coupled one-dimensional electron systems from an asymmetric double quantum well

    Science.gov (United States)

    Buchholz, S. S.; Fischer, S. F.; Kunze, U.; Schuh, D.; Abstreiter, G.

    2008-03-01

    Vertically stacked quantum point contacts (QPCs) are prepared by atomic force microscope (AFM) lithography from an asymmetric GaAs/AlGaAs double quantum well (DQW) heterostructure. Top- and back-gate voltages are used to tune the tunnel-coupled QPCs, and back-gate bias cooling is employed to investigate coupled and decoupled one-dimensional (1D) modes. Parity dependent mode coupling is invoked by the particular asymmetry in the vertical DQW confinement.

  17. Concerted Electronic and Nuclear Fluxes During Coherent Tunnelling in Asymmetric Double-Well Potentials.

    Science.gov (United States)

    Bredtmann, Timm; Manz, Jörn; Zhao, Jian-Ming

    2016-05-19

    The quantum theory of concerted electronic and nuclear fluxes (CENFs) during coherent periodic tunnelling from reactants (R) to products (P) and back to R in molecules with asymmetric double-well potentials is developed. The results are deduced from the solution of the time-dependent Schrödinger equation as a coherent superposition of two eigenstates; here, these are the two states of the lowest tunnelling doublet. This allows the periodic time evolutions of the resulting electronic and nuclear probability densities (EPDs and NPDs) as well as the CENFs to be expressed in terms of simple sinusodial functions. These analytical results reveal various phenomena during coherent tunnelling in asymmetric double-well potentials, e.g., all EPDs and NPDs as well as all CENFs are synchronous. Distortion of the symmetric reference to a system with an asymmetric double-well potential breaks the spatial symmetry of the EPDs and NPDs, but, surprisingly, the symmetry of the CENFs is conserved. Exemplary application to the Cope rearrangement of semibullvalene shows that tunnelling of the ideal symmetric system can be suppressed by asymmetries induced by rather small external electric fields. The amplitude for the half tunnelling, half nontunnelling border is as low as 0.218 × 10(-8) V/cm. At the same time, the delocalized eigenstates of the symmetric reference, which can be regarded as Schrödinger's cat-type states representing R and P with equal probabilities, get localized at one or the other minima of the asymmetric double-well potential, representing either R or P. PMID:26799383

  18. Independently tunable double electromagenetically induced transparency-like resonances in asymmetric plasmonic waveguide resonator system

    Science.gov (United States)

    Yu, Da-Ming; Wang, Ling-Ling; Lin, Qi; Zhai, Xiang; Li, Hong-Ju; Xia, Sheng-Xuan

    2016-05-01

    Double electromagnetically induced transparency (EIT)-like resonances are numerically achieved by detuning and bright-dark coupling in an asymmetric plasmonic waveguide resonator system. The transmission properties of the system are simulated by the finite-difference time-domain (FDTD) method. Just because double EIT-like resonances originate from different mechanisms, a single EIT-like resonance can be well tuned independently, namely, one induced transparency window can be tuned in the horizontal direction while the other one is nearly invariable. The present design idea will be applicable in highly integrated optical circuits. Moreover, the formation of double EIT-like resonances may play a guiding role when designing plasmonic devices.

  19. Asymmetric double quantum well structure as a tunable detector in the far-infrared range

    CERN Document Server

    Shin, U; Park, M J; Lee, S J

    1999-01-01

    The eigenvalues and the wave functions of GaAs/Al sub x Ga sub 1 sub - sub x As asymmetric double quantum well structure have been calculated by using of complex energy method. Based on theoretical calculations, tuning ranges from 9 to 14 mu m are predicted for the proposed asymmetric coupled-quantum-well structure. In addition we calculated the energy eigenvalues and the wave functions of an electron in GaAs/Al sub x Ga sub 1 sub - sub x As single quantum well structure (including delta-perturbation). the variation in E sub 1 , the ground state energy eigenvalue of the electron, depends on the strength and position of the perturbation within the well.

  20. Optical absorption in asymmetric double quantum wells driven by two intense terahertz fields

    International Nuclear Information System (INIS)

    Optical absorption is investigated for asymmetric double quantum wells driven by a resonant terahertz field and a varied terahertz field, both polarized along the growth direction. Rich nonlinear dynamics of the replica peak and the Autler-Townes splitting of various dressed states are systematically studied in undoped asymmetric double quantum wells by taking account of multiple factors, such as the frequency of the varied terahertz field and the strength of the resonant terahertz field. Each electron subband splits into two dressed states when the resonant terahertz field is applied in the absence of the varied terahertz field, the optical absorption spectrum shows the first-order Autler-Townes splitting of the electron subbands. When a varied terahertz field is added into the resonant system, the replica peak and the second-order Autler-Townes splitting of the dressed states near the band edge respectively emerge when the varied terahertz field is non-resonant and resonant with these dressed states. When the strength of the resonant terahertz field is increased, the first-order Autler-Townes double peaks and the replica peak in the optical absorption spectrum shift with the shifts of the dressed states. The presented results have potential applications in electro-optical devices

  1. Optical absorption in asymmetric double quantum wells driven by two intense terahertz fields

    Institute of Scientific and Technical Information of China (English)

    Wu Hong-Wei; Mi Xian-Wu

    2013-01-01

    Optical absorption is investigated for asymmetric double quantum wells driven by a resonant terahertz field and a varied terahertz field,both polarized along the growth direction.Rich nonlinear dynamics of the replica peak and the Autler-Townes splitting of various dressed states are systematically studied in undoped asymmetric double quantum wells by taking account of multiple factors,such as the frequency of the varied terahertz field and the strength of the resonant terahertz field.Each electron subband splits into two dressed states when the resonant terahertz field is applied in the absence of the varied terahertz field,the optical absorption spectrum shows the first-order Autler-Townes splitting of the electron subbands.When a varied terahertz field is added into the resonant system,the replica peak and the second-order Autler-Townes splitting of the dressed states near the band edge respectively emerge when the varied terahertz field is non-resonant and resonant with these dressed states.Wben the strength of the resonant terahertz field is increased,the first-order Autler-Townes double peaks and the replica peak in the optical absorption spectrum shift with the shifts of the dressed states.The presented results have potential applications in electro-optical devices.

  2. Gain of intersubband Raman lasing in modulation-doped asymmetric coupled double quantum wells

    Science.gov (United States)

    Maung, S. M.; Katayama, S.

    2004-03-01

    A microscopic theory is developed for the laser gain due to stimulated intersubband electronic Raman effect pumped by CO 2 laser in modulation-doped asymmetric coupled double quantum wells. We focus on the charge density excitation mechanism for electronic Raman scattering, taking into account the coupling between intersubband plasmons and LO phonons. Numerical simulations for the temporal variation of stimulated Stokes photon density, subband populations and output Raman laser power are carried out by using the self-consistent conventional rate equations with stimulated Raman gain coefficient.

  3. Optical toroidal dipolar response by an asymmetric double-bar metamaterial

    CERN Document Server

    Dong, Zheng-Gao; Rho, Junsuk; Li, Jia-Qi; Lu, Changgui; Yin, Xiaobo; Zhang, X; 10.1063/1.4757613

    2012-01-01

    We demonstrate that the toroidal dipolar response can be realized in the optical regime by designing a feasible nanostructured metamaterial, comprising asymmetric double-bar magnetic resonators assembled into a toroid-like configuration. It is confirmed numerically that an optical toroidal dipolar moment dominates over other moments. This response is characterized by a strong confinement of an E-field component at the toroid center, oriented perpendicular to the H-vortex plane. The resonance-enhanced optical toroidal response can provide an experimental avenue for various interesting optical phenomena associated with the elusive toroidal moment.

  4. Dispersive properties of tunnelling-induced transparency in an asymmetric double quantum well

    Institute of Scientific and Technical Information of China (English)

    苏雪梅; 卓仲畅; 王立军; 高锦岳

    2002-01-01

    We have investigated the dispersive properties of tunnelling-induced transparency in asymmetric double quantumwell structures where two excited states are coupled by resonant tunnelling through a thin barrier in a three-levelsystem of electronic subbands. The intersubband transitions exhibit high dispersion at zero absorption, which leads tothe slow light velocity in this medium as compared with that in vacuum (c=3× 108). The group velocity in a specificGaAs/AlGaAs sample is calculated to be vg=c/4.30. This structure can be used to compensate for the dispersion andenergy loss in fibre optical communications.

  5. Controllable optical bistability and multistability in asymmetric double quantum wells via spontaneously generated coherence

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Yuan; Deng, Li [Department of Applied Physics, East China Jiaotong University, Nanchang, 330013 (China); Chen, Aixi, E-mail: aixichen@ecjtu.jx.cn [Department of Applied Physics, East China Jiaotong University, Nanchang, 330013 (China); Institute for Quantum Computing, University of Waterloo, Ontario N2L 3G1 (Canada)

    2015-02-15

    We investigate the nonlinear optical phenomena of the optical bistability and multistability via spontaneously generated coherence in an asymmetric double quantum well structure coupled by a weak probe field and a controlling field. It is shown that the threshold and hysteresis cycle of the optical bistability can be conveniently controlled only by adjusting the intensity of the SGC or the controlling field. Moreover, switching between optical bistability and multistability can be achieved. These studies may have practical significance for the preparation of optical bistable switching device.

  6. Condensate Splitting in an Asymmetric Double Well for Atom Chip Based Sensors

    International Nuclear Information System (INIS)

    We report on the adiabatic splitting of a Bose-Einstein condensate of 87Rb atoms by an asymmetric double-well potential located above the edge of a perpendicularly magnetized TbGdFeCo film atom chip. By controlling the barrier height and double-well asymmetry, the sensitivity of the axial splitting process is investigated through observation of the fractional atom distribution between the left and right wells. This process constitutes a novel sensor for which we infer a single shot sensitivity to gravity fields of δg/g≅2x10-4. From a simple analytic model, we propose improvements to chip-based gravity detectors using this demonstrated methodology

  7. Asymmetric and double-cathode-pad wire chambers for the LHCb muon system

    CERN Document Server

    Kachtchouk, A; Riegler, W; Schmidt, B; Schneider, T; Souvorov, V

    2005-01-01

    We present results from two types of Multi-Wire Proportional Chambers (MWPCs) with wire pitch of 1.5 mm and cathode–cathode distance of 5 mm intended for triggering purposes in the LHCb experiment. Both prototypes use cathode readout because this allows arbitrary segmentation in order to achieve the required granularity. One MWPC prototype uses a symmetric wire–cathode distance (2.5/2.5 mm) with double cathode readout, which doubles the signal compared to reading only one cathode. The second prototype uses an asymmetric wire–cathode distance (1.25/3.75 mm) with single cathode readout which also doubles the signal and in addition reduces the width of the induced charge distribution and therefore reduces the crosstalk for small cathode pads. We also performed a dedicated optimization of readout traces and guard traces in order to reduce the pad–pad crosstalk. Both prototypes show a few hundred volts of operating plateau defined as the region with 99% efficiency in a 20 ns time window. Close to the plate...

  8. Asymmetric voltage behavior of the tunnel magnetoresistance in double barrier magnetic tunnel junctions

    KAUST Repository

    Useinov, Arthur

    2012-06-01

    In this paper, we study the value of the tunnel magnetoresistance (TMR) as a function of the applied voltage in double barrier magnetic tunnel junctions (DMTJs) with the left and right ferromagnetic (FM) layers being pinned and numerically estimate the possible difference of the TMR curves for negative and positive voltages in the homojunctions (equal barriers and electrodes). DMTJs are modeled as two single barrier junctions connected in series with consecutive tunneling (CST). We investigated the asymmetric voltage behavior of the TMR for the CST in the range of a general theoretical model. Significant asymmetries of the experimental curves, which arise due to different annealing regimes, are mostly explained by different heights of the tunnel barriers and asymmetries of spin polarizations in magnetic layers. © (2012) Trans Tech Publications.

  9. Theory of Intersubband Raman Laser in Modulation-doped Asymmetric Coupled Double Quantum Wells

    Science.gov (United States)

    Maung, S. M.; Katayama, S.

    2004-09-01

    A microscopic theory is developed for the laser gain due to stimulated intersubband electronic Raman scattering pumped by CO2 laser in modulation-doped GaAs/AlGaAs asymmetric coupled double quantum wells (ACDQWs). Based on the charge-density-excitation (CDE) mechanism, the formula for electronic Raman scattering cross-section is given, taking into account the coupling between intersubband plasmon and optical phonons including GaAs confined LO phonons and interface phonons. Stimulated Raman gain factor is then derived from the cross-section. The optimization of Raman gain, the gain saturation and threshold condition are also discussed. Numerical analysis for temporal variation of stimulated Stokes photon density, subband populations and output Raman laser power is carried out by using the self-consistent conventional rate equations. The theory can predict the presence or lack of coupled modes in lasing in agreement with the recent experimental results.

  10. Output voltage calculations in double barrier magnetic tunnel junctions with asymmetric voltage behavior

    KAUST Repository

    Useinov, Arthur

    2011-10-22

    In this paper we study the asymmetric voltage behavior (AVB) of the tunnel magnetoresistance (TMR) for single and double barrier magnetic tunnel junctions (MTJs) in range of a quasi-classical free electron model. Numerical calculations of the TMR-V curves, output voltages and I-V characteristics for negative and positive values of applied voltages were carried out using MTJs with CoFeB/MgO interfaces as an example. Asymmetry of the experimental TMR-V curves is explained by different values of the minority and majority Fermi wave vectors for the left and right sides of the tunnel barrier, which arises due to different annealing regimes. Electron tunneling in DMTJs was simulated in two ways: (i) Coherent tunneling, where the DMTJ is modeled as one tunnel system and (ii) consecutive tunneling, where the DMTJ is modeled by two single barrier junctions connected in series. © 2012 Elsevier B.V. All rights reserved.

  11. Phase control of light propagation via Fano interference in asymmetric double quantum wells

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Wen-Xing, E-mail: wenxingyang2@126.com [Department of Physics, Southeast University, Nanjing 210096 (China); Institute of Photonics Technologies, National Tsing-Hua University, Hsinchu 300, Taiwan (China); Lu, Jia-Wei; Zhou, Zhi-Kang; Yang, Long [Department of Physics, Southeast University, Nanjing 210096 (China); Lee, Ray-Kuang [Institute of Photonics Technologies, National Tsing-Hua University, Hsinchu 300, Taiwan (China)

    2014-05-28

    We investigate the light propagation and dynamical control of a weak pulsed probe field in asymmetric double quantum wells via Fano interference, which is caused by tunneling from the excited subbands to the same continuum. Our results show that the system can produce anomalous and normal dispersion regions with negligible absorption by choosing appropriate coupling strength of the tunneling and the Fano interference. Interesting enough, the dispersion can be switched between normal and anomalous by adjusting the relative phase between the pulsed probe and coherent control fields owing to the existence of the perfectly Fano interference. Thus, the relative phase can be regarded as a switch to manipulate light propagation with subluminal or superluminal. The temporal and spatial dynamics of the pulsed probe field with hyperbolic secant envelope are analyzed.

  12. Large Scale Synthesis of NiCo Layered Double Hydroxides for Superior Asymmetric Electrochemical Capacitor

    Science.gov (United States)

    Li, Ruchun; Hu, Zhaoxia; Shao, Xiaofeng; Cheng, Pengpeng; Li, Shoushou; Yu, Wendan; Lin, Worong; Yuan, Dingsheng

    2016-01-01

    We report a new environmentally-friendly synthetic strategy for large-scale preparation of 16 nm-ultrathin NiCo based layered double hydroxides (LDH). The Ni50Co50-LDH electrode exhibited excellent specific capacitance of 1537 F g-1 at 0.5 A g-1 and 1181 F g-1 even at current density as high as 10 A g-1, which 50% cobalt doped enhances the electrical conductivity and porous and ultrathin structure is helpful with electrolyte diffusion to improve the material utilization. An asymmetric ultracapacitor was assembled with the N-doped graphitic ordered mesoporous carbon as negative electrode and the NiCo LDH as positive electrode. The device achieves a high energy density of 33.7 Wh kg-1 (at power density of 551 W kg-1) with a 1.5 V operating voltage.

  13. Two kinds of double Fano resonances induced by an asymmetric MIM waveguide structure

    Science.gov (United States)

    Zhang, Bing-Hua; Wang, Ling-Ling; Li, Hong-Ju; Zhai, Xiang; Xia, Sheng-Xuan

    2016-06-01

    Asymmetric plasmonic waveguides with a shoulder-coupled rectangle cavity are proposed and investigated numerically by using the finite-difference time-domain (FDTD) method. The symmetry breaking of the structure results in a new discrete mode supported by the cavity. The extreme interference between two discrete states and an intrinsic wide continuous state gives rise to novel double Fano resonances with symmetric and anti-symmetric configurations. Coupled-mode theory (CMT) further confirms that two Fano profiles originate from the different coupling conditions of the cavity modes with the waveguides. Moreover, the sensing characters are performed. The Fano responses with the higher sensitivity and figure of merit (FOM) up to 57 are realized. Undoubtedly, the studied structure will play an important role in the nano-integrated plasmonic devices for optical switching and sensing.

  14. Phase control of light propagation via Fano interference in asymmetric double quantum wells

    International Nuclear Information System (INIS)

    We investigate the light propagation and dynamical control of a weak pulsed probe field in asymmetric double quantum wells via Fano interference, which is caused by tunneling from the excited subbands to the same continuum. Our results show that the system can produce anomalous and normal dispersion regions with negligible absorption by choosing appropriate coupling strength of the tunneling and the Fano interference. Interesting enough, the dispersion can be switched between normal and anomalous by adjusting the relative phase between the pulsed probe and coherent control fields owing to the existence of the perfectly Fano interference. Thus, the relative phase can be regarded as a switch to manipulate light propagation with subluminal or superluminal. The temporal and spatial dynamics of the pulsed probe field with hyperbolic secant envelope are analyzed.

  15. Tunable multi-band chiral metamaterials based on double-layered asymmetric split ring resonators

    Science.gov (United States)

    Jia, Xiuli; Wang, Xiaoou; Meng, Qingxin; Zhou, Zhongxiang

    2016-07-01

    We have numerically demonstrated chiral metamaterials based on double-layered asymmetric Au film with hollow out design of split ring resonators on either side of the polyimide. Multiple electric dipoles and magnetic dipoles resulted from parallel and antiparallel currents between the eight split ring resonators. Multi-band circular dichroism is found in the visible frequency regime by studying the transmission properties. Huge optical activity and the induced multi-band negative refractive index are obtained at resonance by calculating the optical activity and ellipticity of the transmitted E-fields. Chirality parameter and effective refractive index are retrieved to illustrate the tunable optical properties of the metamaterials. The underlying mechanisms for the observed circular dichroism are analyzed. These metamaterials would offer flexible electromagnetic applications in the infrared and visible regime.

  16. Applications of repaired endonucleases

    International Nuclear Information System (INIS)

    The possibilities of using antimutagenously various endonucleases are discussed. Since mutageniety of excision repair is considerably lower than the repair in the replication moment or after thereof the intensification of the excision repair of premutation disorders can suppress mutagenesis. Experimental aproaches of using repair endonucleases for sounding premutation changes are described. The optimal object has been chosen for endonuclear sounding of premutation DNA disorders following an ionizing radiation action

  17. Catalytic asymmetric synthesis of spirocyclic azlactones by a double Michael-addition approach.

    Science.gov (United States)

    Weber, Manuel; Frey, Wolfgang; Peters, René

    2013-06-17

    Spirocyclic azlactones are shown to be useful precursors of cyclic quaternary amino acids, such as the constrained cyclohexane analogues of phenylalanine. These compounds are of interest as building blocks for the synthesis of artificial peptide analogues with controlled folds in the peptide backbone. They were prepared in the present study by a step- and atom-economic catalytic asymmetric tandem approach, requiring two steps starting from N-benzoyl glycine and divinylketones. The key of this protocol is the enantioselective formation of the azlactone spirocycles, which involves a PdII-catalyzed double 1,4-addition of an in situ generated azlactone intermediate to the dienone (a formal [5+1] cycloaddition). As the catalyst, a planar chiral ferrocene bispalladacycle was used. Mechanistic studies suggest a monometallic reaction pathway. Although the diastereoselectivity was found to be moderate, the enantioselectivity is usually high for the formation of the azlactone spirocycles, which contain up to three contiguous stereocenters. Spectroscopic studies have shown that the spirocycles often prefer a twist over a chair conformation of the cyclohexanone moiety. PMID:23613333

  18. Simulations of Cyclic Voltammetry for Electric Double Layers in Asymmetric Electrolytes: A Generalized Modified Poisson-Nernst-Planck Model

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Hainan; Thiele, Alexander; Pilon, Laurent [UCLA

    2013-11-15

    This paper presents a generalized modified Poisson–Nernst–Planck (MPNP) model derived from first principles based on excess chemical potential and Langmuir activity coefficient to simulate electric double-layer dynamics in asymmetric electrolytes. The model accounts simultaneously for (1) asymmetric electrolytes with (2) multiple ion species, (3) finite ion sizes, and (4) Stern and diffuse layers along with Ohmic potential drop in the electrode. It was used to simulate cyclic voltammetry (CV) measurements for binary asymmetric electrolytes. The results demonstrated that the current density increased significantly with decreasing ion diameter and/or increasing valency |zi| of either ion species. By contrast, the ion diffusion coefficients affected the CV curves and capacitance only at large scan rates. Dimensional analysis was also performed, and 11 dimensionless numbers were identified to govern the CV measurements of the electric double layer in binary asymmetric electrolytes between two identical planar electrodes of finite thickness. A self-similar behavior was identified for the electric double-layer integral capacitance estimated from CV measurement simulations. Two regimes were identified by comparing the half cycle period τCV and the “RC time scale” τRC corresponding to the characteristic time of ions’ electrodiffusion. For τRC ← τCV, quasi-equilibrium conditions prevailed and the capacitance was diffusion-independent while for τRC → τCV, the capacitance was diffusion-limited. The effect of the electrode was captured by the dimensionless electrode electrical conductivity representing the ratio of characteristic times associated with charge transport in the electrolyte and that in the electrode. The model developed here will be useful for simulating and designing various practical electrochemical, colloidal, and biological systems for a wide range of applications.

  19. Structure-specific endonucleases

    DEFF Research Database (Denmark)

    Minocherhomji, Sheroy; Hickson, Ian D

    2014-01-01

    Fragile sites are conserved loci predisposed to form breaks in metaphase chromosomes. The inherent instability of these loci is associated with chromosomal rearrangements in cancers and is a feature of cells from patients with chromosomal instability syndromes. One class of fragile sites, the com......, leading to the formation of ultra-fine anaphase bridges (UFBs) and micronuclei. We discuss recent developments in the CFS field; in particular, the role of DNA structure-specific endonucleases in promoting cleavage at CFSs....

  20. A site-specific endonuclease encoded by a typical archaeal intron

    DEFF Research Database (Denmark)

    Dalgaard, Jacob; Garrett, Roger Antony; Belfort, Malene

    1993-01-01

    The protein encoded by the archaeal intron in the 23S rRNA gene of the hyperthermophile Desulfurococcus mobilis is a double-strand DNase that, like group I intron homing endonucleases, is capable of cleaving an intronless allele of the gene. This enzyme, I-Dmo I, is unusual among the intron endon...... of endonucleases and intron core elements and are consistent with the invasive potential of endonuclease genes....

  1. Theory of Raman Lasing due to Coupled Intersubband Plasmon-Phonon Modes in Asymmetric Coupled Double Quantum Wells

    Science.gov (United States)

    Maung, S. M.; Katayama, S.

    2005-06-01

    A theory of Raman laser gain due to coupled intersubband (ISB) plasmon-optical phonon modes in asymmetric coupled double quantum wells (ACDQWs) is presented. Based on the charge-density-excitations (CDE) mechanism, we take into account the electron-electron and electron-phonon (confined LO phonon and interface (IF) phonons) interactions in the scattering cross-section. For Al0.35Ga0.65As/GaAs ACDQWs the calculated coupled mode energies which are responsible for the lasing Stokes emission are well consistent with recent experiments.

  2. Intense laser effects on the optical properties of asymmetric GaAs double quantum dots under applied electric field

    Science.gov (United States)

    Bejan, Doina; Niculescu, Ecaterina Cornelia

    2016-06-01

    We investigated the combined effects of a non-resonant intense laser field and a static electric field on the electronic structure and the nonlinear optical properties (absorption, optical rectification) of a GaAs asymmetric double quantum dot under a strong probe field excitation. The calculations were performed within the compact density-matrix formalism under steady state conditions using the effective mass approximation. Our results show that: (i) the electronic structure and optical properties are sensitive to the dressed potential; (ii) under applied electric fields, an increase of the laser intensity induces a redshift of the optical absorption and rectification spectra; (iii) the augment of the electric field strength leads to a blueshift of the spectra; (iv) for high electric fields the optical spectra show a shoulder-like feature, related with the occurrence of an anti-crossing between the two first excited levels.

  3. A Novel Method for Calculation of Strain Energy Release Rate of Asymmetric Double Cantilever Laminated Composite Beams

    Science.gov (United States)

    Shokrieh, M. M.; Zeinedini, A.

    2014-06-01

    In this research, a novel data reduction method for calculation of the strain energy release rate ( SERR) of asymmetric double cantilever beams ( ADCB) is presented. For this purpose the elastic beam theory ( EBT) is modified and the new method is called as the modified elastic beam theory ( MEBT). Also, the ADCB specimens are modeled using ABAQUS/Standard software. Then, the initiation of delamination of ADCB specimens is modeled using the virtual crack closure technique ( VCCT). Furthermore, magnitudes of the SERR for different samples are also calculated by an available data reduction method, called modified beam theory ( MBT). Using the hand lay-up method, different laminated composite samples are manufactured by E-glass/epoxy unidirectional plies. In order to measure the SERR, all samples are tested using an experimental setup. The results determined by the new data reduction method ( MEBT) show good agreements with the results of the VCCT and the MBT.

  4. Kinetic analysis of the thermal isomerisation pathways in an asymmetric double azobenzene switch

    NARCIS (Netherlands)

    Robertus, Jort; Reker, Siebren F.; Pijper, Thomas C.; Deuzeman, Albert; Browne, Wesley R.; Feringa, Ben L.

    2012-01-01

    Here we report a photochemical and kinetic study of the thermal relaxation reaction of a double azobenzene system, in which two azobenzene photochromic units are connected via a phenyl ring. Upon UV irradiation, three thermally unstable isomers are formed. Kinetic studies using arrayed H-1-NMR spect

  5. Shifted one-parameter supersymmetric family of quartic asymmetric double-well potentials

    International Nuclear Information System (INIS)

    Extending our previous work (Rosu, 2014), we define supersymmetric partner potentials through a particular Riccati solution of the form F(x)=(x−c)2−1, where c is a real shift parameter, and work out the quartic double-well family of one-parameter isospectral potentials obtained by using the corresponding general Riccati solution. For these parametric double well potentials, we study how the localization properties of the two wells depend on the parameter of the potentials for various values of the shifting parameter. We also consider the supersymmetric parametric family of the first double-well potential in the Razavy chain of double well potentials corresponding to F(x)=1/2 sinh2x−2((1+√(2))sinh2x)/((1+√(2))cosh2x+1) , both unshifted and shifted, to test and compare the localization properties. - Highlights: • Quartic one-parameter DWs with an additional shift parameter are introduced. • Anomalous localization feature of their zero modes is confirmed at different shifts. • Razavy one-parameter DWs are also introduced and shown not to have this feature

  6. A noniterative asymmetric triple excitation correction for the density-fitted coupled-cluster singles and doubles method: Preliminary applications

    Science.gov (United States)

    Bozkaya, Uǧur

    2016-04-01

    An efficient implementation of the asymmetric triples correction for the coupled-cluster singles and doubles [ΛCCSD(T)] method [S. A. Kucharski and R. J. Bartlett, J. Chem. Phys. 108, 5243 (1998); T. D. Crawford and J. F. Stanton, Int. J. Quantum Chem. 70, 601 (1998)] with the density-fitting [DF-ΛCCSD(T)] approach is presented. The computational time for the DF-ΛCCSD(T) method is compared with that of ΛCCSD(T). Our results demonstrate that the DF-ΛCCSD(T) method provide substantially lower computational costs than ΛCCSD(T). Further application results show that the ΛCCSD(T) and DF-ΛCCSD(T) methods are very beneficial for the study of single bond breaking problems as well as noncovalent interactions and transition states. We conclude that ΛCCSD(T) and DF-ΛCCSD(T) are very promising for the study of challenging chemical systems, where the coupled-cluster singles and doubles with perturbative triples method fails.

  7. Asymmetric effects on the optical properties of double-quantum well systems

    Science.gov (United States)

    Silotia, Poonam; Batra, Kriti; Prasad, Vinod

    2014-02-01

    Linear, nonlinear, and total absorption coefficient and refractive index changes of double-quantum well (DQW) systems are studied theoretically in the presence of external static electric field applied along the growth direction. The analytical expression for the linear and nonlinear optical properties is obtained using density matrix method. Emphasis is laid on the effect of asymmetry in the shapes of DQW system on optical properties. Some interesting results are obtained and explained.

  8. Ultrathin nanoflakes of cobalt-manganese layered double hydroxide with high reversibility for asymmetric supercapacitor

    Science.gov (United States)

    Jagadale, Ajay D.; Guan, Guoqing; Li, Xiumin; Du, Xiao; Ma, Xuli; Hao, Xiaogang; Abudula, Abuliti

    2016-02-01

    CoMn LDH electrode is successfully prepared via facile and cost-effective electrodeposition method. The effect of Co2+/Mn2+ molar ratio on supercapacitive performance is systematically investigated. It is found that the presence of Mn(OH)6 unit in CoMn LDH offers an excellent reversibility as well as highly electrochemical activity for supercapacitor application. The CoMn LDH film with a Co2+/Mn2+ molar ratio of 9:1 loaded on Ni foam electrode exhibits the maximum specific capacitance of 1062.6 F/g at the current density of 0.7 A/g with an excellent cyclic stability of 96.3% over 5000 CD cycles. It indicates that CoMn LDH nanoflakes loaded on Ni foam can minimize the lattice mismatch which leads to an excellent cyclic stability. The asymmetric supercapacitor assembled with CoMn LDH/Ni foam and AC electrodes shows an excellent cyclic life of 84.2% and an energy density of 4.4 Wh/kg with a power density of 2500 W/kg.

  9. Broadband Absorption Enhancement in Thin Film Solar Cells Using Asymmetric Double-Sided Pyramid Gratings

    Science.gov (United States)

    Alshal, Mohamed A.; Allam, Nageh K.

    2016-07-01

    A design for a highly efficient modified grating crystalline silicon (c-Si) thin film solar cell is demonstrated and analyzed using the two-dimensional (2-D) finite element method. The suggested grating has a double-sided pyramidal structure. The incorporation of the modified grating in a c-Si thin film solar cell offers a promising route to harvest light into the few micrometers active layer. Furthermore, a layer of silicon nitride is used as an antireflection coating (ARC). Additionally, the light trapping through the suggested design is significantly enhanced by the asymmetry of the top and bottom pyramids. The effects of the thickness of the active layer and facet angle of the pyramid on the spectral absorption, ultimate efficiency (η), and short-circuit current density (J sc) are investigated. The numerical results showed 87.9% efficiency improvement over the conventional thin film c-Si solar cell counterpart without gratings.

  10. Endonuclease activity in E. coli against photoalkylated DNA

    International Nuclear Information System (INIS)

    Photoalkylation, the ultraviolet irradiation (wavelength > 305 nm) of DNA in the presence of isopropanol and the free radical photoinitiator di-tert-butylperoxide, causes a variety of base alterations. These include 8-(2-hydroxy-2-propyl)guanine, 8-(2-hydroxy-2-propyl)adenine and thymine dimers. The authors have found a endonuclease activity in E. coli directed against photoalkylated DNA. This activity converts photoalkylated superhelical PM2 phage DNA to the nicked form, as measured by a nitrocellulose filter binding assay. Enzyme activities were compared between crude extracts of mutant strain BW9051 (xth-), lacking in exonuclease III activity, and strain BW434 (xth-, nth-), deficient in both exonuclease III and endonuclease III. The endonuclease level in the double mutant against substrate photoalkylated DNA was under 20% of the activity in the E. coli strain lacking only exonuclease III. This was paralleled by a similar finding of deficient activity in the double mutant against partially depurinated PM2 DNA. Irradiation of the DNA substrate in the absence of isopropanol did not affect the activity in either strain. These studies suggest that the enzyme activity against photoalkylated DNA is endonuclease III and that the substrate photoproduct is neither a 8-(2-hydroxy-2-propyl)purine nor a thymine dimer

  11. Low frequency noise in asymmetric double barrier magnetic tunnel junctions with a top thin MgO layer

    Science.gov (United States)

    Guo, Hui-Qiang; Tang, Wei-Yue; Liu, Liang; Wei, Jian; Li, Da-Lai; Feng, Jia-Feng; Han, Xiu-Feng

    2015-07-01

    Low frequency noise has been investigated at room temperature for asymmetric double barrier magnetic tunnel junctions (DBMTJs), where the coupling between the top and middle CoFeB layers is antiferromagnetic with a 0.8-nm thin top MgO barrier of the CoFeB/MgO/CoFe/CoFeB/MgO/CoFeB DBMTJ. At enough large bias, 1/f noise dominates the voltage noise power spectra in the low frequency region, and is conventionally characterized by the Hooge parameter αmag. With increasing external field, the top and bottom ferromagnetic layers are aligned by the field, and then the middle free layer rotates from antiparallel state (antiferromagnetic coupling between top and middle ferromagnetic layers) to parallel state. In this rotation process αmag and magnetoresistance-sensitivity-product show a linear dependence, consistent with the fluctuation dissipation relation. With the magnetic field applied at different angles (θ) to the easy axis of the free layer, the linear dependence persists while the intercept of the linear fit satisfies a cos(θ) dependence, similar to that for the magnetoresistance, suggesting intrinsic relation between magnetic losses and magnetoresistance. Project supported by the National Basic Research Program of China (Grant Nos. 2011CBA00106, 2012CB927400, 2010CB934401, and 2014AA032904), the National High Technology Research and Development Program of China (Grant No. 2014AA032904), and the National Natural Science Foundation of China (Grant Nos. 11434014 and 11104252).

  12. Nonmonotonous electron mobility due to structurally induced resonant coupling of subband states in an asymmetric double quantum well

    Energy Technology Data Exchange (ETDEWEB)

    Nayak, R. K.; Das, S.; Panda, A. K.; Sahu, T., E-mail: tsahu-bu@rediffmail.com [Department of Electronics and Communication Engineering, National Institute of Science and Technology, Palur Hills, Berhampur-761 008, Odisha (India)

    2015-11-15

    We show that sharp nonmonotic variation of low temperature electron mobility μ can be achieved in GaAs/Al{sub x}Ga{sub 1-x}As barrier delta-doped double quantum well structure due to quantum mechanical transfer of subband electron wave functions within the wells. We vary the potential profile of the coupled structure as a function of the doping concentration in order to bring the subbands into resonance such that the subband energy levels anticross and the eigen states of the coupled structure equally share both the wells thereby giving rise to a dip in mobility. When the wells are of equal widths, the dip in mobility occurs under symmetric doping of the side barriers. In case of unequal well widths, the resonance can be obtained by suitable asymmetric variation of the doping concentrations. The dip in mobility becomes sharp and also the wavy nature of mobility takes a rectangular shape by increasing the barrier width. We show that the dip in mobility at resonance is governed by the interface roughness scattering through step like changes in the subband mobilities. It is also gratifying to show that the drop in mobility at the onset of occupation of second subband is substantially supressed through the quantum mechanical transfer of subband wave functions between the wells. Our results can be utilized for performance enhancement of coupled quantum well devices.

  13. Nonmonotonous electron mobility due to structurally induced resonant coupling of subband states in an asymmetric double quantum well

    International Nuclear Information System (INIS)

    We show that sharp nonmonotic variation of low temperature electron mobility μ can be achieved in GaAs/AlxGa1-xAs barrier delta-doped double quantum well structure due to quantum mechanical transfer of subband electron wave functions within the wells. We vary the potential profile of the coupled structure as a function of the doping concentration in order to bring the subbands into resonance such that the subband energy levels anticross and the eigen states of the coupled structure equally share both the wells thereby giving rise to a dip in mobility. When the wells are of equal widths, the dip in mobility occurs under symmetric doping of the side barriers. In case of unequal well widths, the resonance can be obtained by suitable asymmetric variation of the doping concentrations. The dip in mobility becomes sharp and also the wavy nature of mobility takes a rectangular shape by increasing the barrier width. We show that the dip in mobility at resonance is governed by the interface roughness scattering through step like changes in the subband mobilities. It is also gratifying to show that the drop in mobility at the onset of occupation of second subband is substantially supressed through the quantum mechanical transfer of subband wave functions between the wells. Our results can be utilized for performance enhancement of coupled quantum well devices

  14. Homing endonuclease structure and function.

    Science.gov (United States)

    Stoddard, Barry L

    2005-02-01

    Homing endonucleases are encoded by open reading frames that are embedded within group I, group II and archael introns, as well as inteins (intervening sequences that are spliced and excised post-translationally). These enzymes initiate transfer of those elements (and themselves) by generating strand breaks in cognate alleles that lack the intervening sequence, as well as in additional ectopic sites that broaden the range of intron and intein mobility. Homing endonucleases can be divided into several unique families that are remarkable in several respects: they display extremely high DNA-binding specificities which arise from long DNA target sites (14-40 bp), they are tolerant of a variety of sequence variations in these sites, and they display disparate DNA cleavage mechanisms. A significant number of homing endonucleases also act as maturases (highly specific cofactors for the RNA splicing reactions of their cognate introns). Of the known homing group I endonuclease families, two (HNH and His-Cys box enzymes) appear to be diverged from a common ancestral nuclease. While crystal structures of several representatives of the LAGLIDADG endonuclease family have been determined, only structures of single members of the HNH (I-HmuI), His-Cys box (I-PpoI) and GIY-YIG (I-TevI) families have been elucidated. These studies provide an important source of information for structure-function relationships in those families, and are the centerpiece of this review. Finally, homing endonucleases are significant targets for redesign and selection experiments, in hopes of generating novel DNA binding and cutting reagents for a variety of genomic applications. PMID:16336743

  15. Double coupling: modeling subjectivity and asymmetric organization in social-ecological systems

    Directory of Open Access Journals (Sweden)

    David Manuel-Navarrete

    2015-09-01

    Full Text Available Social-ecological organization is a multidimensional phenomenon that combines material and symbolic processes. However, the coupling between social and ecological subsystem is often conceptualized as purely material, thus reducing the symbolic dimension to its behavioral and actionable expressions. In this paper I conceptualize social-ecological systems as doubly coupled. On the one hand, material expressions of socio-cultural processes affect and are affected by ecological dynamics. On the other hand, coupled social-ecological material dynamics are concurrently coupled with subjective dynamics via coding, decoding, personal experience, and human agency. This second coupling operates across two organizationally heterogeneous dimensions: material and symbolic. Although resilience thinking builds on the recognition of organizational asymmetry between living and nonliving systems, it has overlooked the equivalent asymmetry between ecological and socio-cultural subsystems. Three guiding concepts are proposed to formalize double coupling. The first one, social-ecological asymmetry, expands on past seminal work on ecological self-organization to incorporate reflexivity and subjectivity in social-ecological modeling. Organizational asymmetry is based in the distinction between social rules, which are symbolically produced and changed through human agents' reflexivity and purpose, and biophysical rules, which are determined by functional relations between ecological components. The second guiding concept, conscious power, brings to the fore human agents' distinctive capacity to produce our own subjective identity and the consequences of this capacity for social-ecological organization. The third concept, congruence between subjective and objective dynamics, redefines sustainability as contingent on congruent relations between material and symbolic processes. Social-ecological theories and analyses based on these three guiding concepts would support the

  16. Analyzing the forces binding a restriction endonuclease to DNA using a synthetic nanopore

    OpenAIRE

    Dorvel, B.; Sigalov, G.; Zhao, Q.; Comer, J.; Dimitrov, V; Mirsaidov, U.; Aksimentiev, A.; Timp, G.

    2009-01-01

    Restriction endonucleases are used prevalently in recombinant DNA technology because they bind so stably to a specific target sequence and, in the presence of cofactors, cleave double-helical DNA specifically at a target sequence at a high rate. Using synthetic nanopores along with molecular dynamics (MD), we have analyzed with atomic resolution how a prototypical restriction endonuclease, EcoRI, binds to the DNA target sequence—GAATTC—in the absence of a Mg2+ ion cofactor. We have previously...

  17. Measurements of ion temperature and flow velocity using symmetric and asymmetric double probes in the boundary plasma of the JFT-2M tokamak

    International Nuclear Information System (INIS)

    The radial profiles of the ion temperature as well as the flow velocity have been measured by using rotatable symmetric and asymmetric double probes in the boundary plasma of the JFT-2M tokamak. It has been found that the ion temperature is higher than the electron temperature by a factor of about 10, and the flow velocity is 0.2-0.3 of the ion sound velocity in the SOL for both ohmic and NB injection heating. These data can help to determine the cross-field thermal diffusivity in tokamak boundary plasma. (author)

  18. 810-nm InGaA1As/A1GaAs double quantum well semiconductor lasers with asymmetric waveguide structures

    Institute of Scientific and Technical Information of China (English)

    Lin Li; Guojun Liu; Zhanguo Li; Mei Li; Xiaohua Wang; Hui Li; Chunming Wan

    2008-01-01

    @@ The 810-nm InGaA1As/A1GaAs double quantum well (QW) semiconductor lasers with asymmetric waveguide structures, grown by molecular beam epitaxy, show high quantum efficiency and high-power conversion efficiency at continuous-wave (CW) power output. The threshold current density and slope efficiency of the device are 180 A/cm2 and 1.3 W/A, respectively. The internal loss and the internal quantum efficiency are 1.7 cm-1 and 93%, respectively. The 70% maximum power conversion efficiency is achieved with narrow far-field patterns.

  19. Influence of applied electric field on the absorption coefficient and subband distances in asymmetrical AIN/GaN coupled double quantum wells

    Institute of Scientific and Technical Information of China (English)

    Cen Long-Bin; Shen Bo; qin Zhi-Xin; Zhang Guo-Yi

    2009-01-01

    The influence of applied electric fields on the absorption coefficient and subband distances in asymmetrical AlN/GaN coupled double quantum wells (CDQWs) has been investigated by solving Schrodinger and Poisson equations self-consistently. It is found that the absorption coefficient of the intersubband transition (ISBT) between the ground state and the third excited state (1odd -2even) can be equal to zero when the electric fields are applied in asymmetrical A1N/GaN CDQWs,which is related to applied electric fields induced symmetry recovery of these states. Meanwhile,the energy distances between 1odd -2even and 1even - 2even subbands have different relationships from each other with the increase of applied electric fields due to the different polarization-induced potential drops between the lett and the right wells. The results indicate that an electrical-optical modulator operated within the opto-communication wavelength range can be realized in spite of the strong polarization-induced electric fields in asymmetrical AIN/GaN CDQWs.

  20. Analytical model for an asymmetric double-gate MOSFET with gate-oxide thickness and flat-band voltage variations in the subthreshold region

    Science.gov (United States)

    Shin, Yong Hyeon; Yun, Ilgu

    2016-06-01

    This paper proposes an analytical model for an asymmetric double-gate metal-oxide-semiconductor field-effect transistor (DG MOSFET) with varying gate-oxide thickness (tox) and flat-band voltage (Vfb) in the subthreshold region. Since such variations cannot be completely avoided, the modeling of their behaviors is essential. The analytical model is developed by solving a 2D Poisson equation with a varying channel doping concentration (NA). To solve the 2D Poisson equation of the asymmetric DG MOSFET, a perturbation method is used to separate the solution of the channel potential into basic and perturbed terms. Since the basic terms can be regarded as the equations derived from a general symmetric doped DG MOSFET, the conventional analytical model is adopted. In addition, a solution related to the perturbed terms for the asymmetric structures is obtained using Fourier series. Based on the obtained channel potential, the electrical characteristics of the drive current (IDS) are expressed in the analytical model. The prediction of the electrical characteristics by the analytical model shows excellent agreement when compared with commercially available 2D numerical device simulation results with respect to not only tox and Vfb variations but also channel length and NA variations.

  1. Single-stranded endonuclease activity in the excretory--secretory products of Trichinella spiralis and Trichinella pseudospiralis

    OpenAIRE

    Mak, C.; Chung, YYY; Ko, RCC

    2000-01-01

    A novel acidic extracellular single-stranded endonuclease was demonstrated for the first time in the excretory-secretory (E-S) products of 2 species of Trichinella. Unlike the double-stranded endonuclease reported earlier, the single-stranded molecule is divalent cation independent and is detected in both T. spiralis and T. pseudospiralis E-S products. It hydrolysed single-stranded DNA and RNA at comparable rates. The single-stranded endonuclease was sensitive to inhibition by Zn2+ and to hig...

  2. Conserved Endonuclease Function of Hantavirus L Polymerase

    Directory of Open Access Journals (Sweden)

    Sylvia Rothenberger

    2016-05-01

    Full Text Available Hantaviruses are important emerging pathogens belonging to the Bunyaviridae family. Like other segmented negative strand RNA viruses, the RNA-dependent RNA polymerase (RdRp also known as L protein of hantaviruses lacks an intrinsic “capping activity”. Hantaviruses therefore employ a “cap snatching” strategy acquiring short 5′ RNA sequences bearing 5′cap structures by endonucleolytic cleavage from host cell transcripts. The viral endonuclease activity implicated in cap snatching of hantaviruses has been mapped to the N-terminal domain of the L protein. Using a combination of molecular modeling and structure–function analysis we confirm and extend these findings providing evidence for high conservation of the L endonuclease between Old and New World hantaviruses. Recombinant hantavirus L endonuclease showed catalytic activity and a defined cation preference shared by other viral endonucleases. Based on the previously reported remarkably high activity of hantavirus L endonuclease, we established a cell-based assay for the hantavirus endonuclase function. The robustness of the assay and its high-throughput compatible format makes it suitable for small molecule drug screens to identify novel inhibitors of hantavirus endonuclease. Based on the high degree of similarity to RdRp endonucleases, some candidate inhibitors may be broadly active against hantaviruses and other emerging human pathogenic Bunyaviruses.

  3. Conserved Endonuclease Function of Hantavirus L Polymerase.

    Science.gov (United States)

    Rothenberger, Sylvia; Torriani, Giulia; Johansson, Maria U; Kunz, Stefan; Engler, Olivier

    2016-01-01

    Hantaviruses are important emerging pathogens belonging to the Bunyaviridae family. Like other segmented negative strand RNA viruses, the RNA-dependent RNA polymerase (RdRp) also known as L protein of hantaviruses lacks an intrinsic "capping activity". Hantaviruses therefore employ a "cap snatching" strategy acquiring short 5' RNA sequences bearing 5'cap structures by endonucleolytic cleavage from host cell transcripts. The viral endonuclease activity implicated in cap snatching of hantaviruses has been mapped to the N-terminal domain of the L protein. Using a combination of molecular modeling and structure-function analysis we confirm and extend these findings providing evidence for high conservation of the L endonuclease between Old and New World hantaviruses. Recombinant hantavirus L endonuclease showed catalytic activity and a defined cation preference shared by other viral endonucleases. Based on the previously reported remarkably high activity of hantavirus L endonuclease, we established a cell-based assay for the hantavirus endonuclase function. The robustness of the assay and its high-throughput compatible format makes it suitable for small molecule drug screens to identify novel inhibitors of hantavirus endonuclease. Based on the high degree of similarity to RdRp endonucleases, some candidate inhibitors may be broadly active against hantaviruses and other emerging human pathogenic Bunyaviruses. PMID:27144576

  4. Visualizing phosphodiester-bond hydrolysis by an endonuclease

    DEFF Research Database (Denmark)

    Molina, Rafael; Stella, Stefano; Redondo, Pilar;

    2015-01-01

    The enzymatic hydrolysis of DNA phosphodiester bonds has been widely studied, but the chemical reaction has not yet been observed. Here we follow the generation of a DNA double-strand break (DSB) by the Desulfurococcus mobilis homing endonuclease I-DmoI, trapping sequential stages of a two...... third metal ion has a crucial role, triggering the consecutive hydrolysis of the targeted phosphodiester bonds in the DNA strands and leaving its position once the DSB is generated. The multiple structures show the orchestrated conformational changes in the protein residues, nucleotides and metals...

  5. Position dependence of the particle density in a double-chain section of a linear network in a totally asymmetric simple exclusion process

    Science.gov (United States)

    Pesheva, N. C.; Brankov, J. G.

    2013-06-01

    We report here results on the study of the totally asymmetric simple exclusion process, defined on an open network, consisting of head and tail simple-chain segments with a double-chain section inserted in between. Results of numerical simulations for relatively short chains reveal an interesting feature of the network. When the current through the system takes its maximum value, a simple translation of the double-chain section forward or backward along the network leads to a sharp change in the shape of the density profiles in the parallel chains, thus affecting the total number of particles in that part of the network. In the symmetric case of equal injection and ejection rates α=β>1/2 and equal lengths of the head and tail sections, the density profiles in the two parallel chains are almost linear, characteristic of the coexistence line (shock phase). Upon moving the section forward (backward), their shape changes to the one typical for the high- (low-) density phases of a simple chain. The total bulk density of particles in a section with a large number of parallel chains is evaluated too. The observed effect might have interesting implications for the traffic flow control as well as for biological transport processes in living cells. An explanation of this phenomenon is offered in terms of a finite-size dependence of the effective injection and ejection rates at the ends of the double-chain section.

  6. Why Public Employment Services Always Fail. Double-sided Asymmetric Information and the Replacement of Low-skill Workers in six European Countries

    DEFF Research Database (Denmark)

    Larsen, Christian Albrekt; Vesan, Patrik

    2012-01-01

    It has been a general finding across Europe that very few job matches are facilitated by public employment services (PES).The article explains this failure by highlighting the existence of a double-sided asymmetric information problem on the labour market. It is argued that although a PES...... potentially reduces search costs, both employers and employees have strong incentives not to use PES. The reason is that employers try to avoid the ‘worst’ employees, and employees try to avoid the ‘worst’ employers. Therefore these services get caught in a low-end equilibrium that is almost impossible to...... escape. The mechanisms leading to this low-end equilibrium are illustrated by means of qualitative interviews with 40 private employers in six European countries....

  7. Detection of DNA double-strand breaks in synchronous cultures of CHO cells by means of asymmetric field inversion gel electrophoresis

    International Nuclear Information System (INIS)

    A pulsed field gel electrophoresis technique, asymmetric field inversion gel electrophoresis (AFIGE), was used to evaluate induction by X-rays of DNA damage in CHO cells. The fraction of DNA activity released from the plug (FAR) was used as a measure for the amount of radiation-induced DNA damage, predominantly DNA double-strand breaks (dsb) (Stamato and Denko 1990), and was determined at various stages of growth and phases of the cell cycle in a range of doses between zero and 70 Gy. It is concluded that caution needs to be exercised before differences observed in the FAR between different cell lines or between various phases of the cell cycle after exposure to a given dose of radiation are interpreted as suggesting differences in the induction of DNA dsb. (author)

  8. Effect of asymmetrical double-pockets and gate-drain underlap on Schottky barrier tunneling FET: Ambipolar conduction vs. high frequency performance

    Science.gov (United States)

    Shaker, Ahmed; Ossaimee, Mahmoud; Zekry, A.

    2016-08-01

    In this paper, a proposed structure based on asymmetrical double pockets SB-TFET with gate-drain underlap is presented. 2D extensive modeling and simulation, using Silvaco TCAD, were carried out to study the effect of both underlap length and pockets' doping on the transistor performance. It was found that the underlap from the drain side suppresses the ambipolar conduction and doesn't enhance the high-frequency characteristics. The enhancement of the high-frequency characteristics could be realized by increasing the doping of the drain pocket over the doping of the source pocket. An optimum choice was found which gives the conditions of minimum ambipolar conduction, maximum ON current and maximum cut-off frequency. These enhancements render the device more competitive as a nanometer transistor.

  9. Endonuclease V cleaves at inosines in RNA.

    Science.gov (United States)

    Vik, Erik Sebastian; Nawaz, Meh Sameen; Strøm Andersen, Pernille; Fladeby, Cathrine; Bjørås, Magnar; Dalhus, Bjørn; Alseth, Ingrun

    2013-01-01

    Endonuclease V orthologues are highly conserved proteins found in all kingdoms of life. While the prokaryotic enzymes are DNA repair proteins for removal of deaminated adenosine (inosine) from the genome, no clear role for the eukaryotic counterparts has hitherto been described. Here we report that human endonuclease V (ENDOV) and also Escherichia coli endonuclease V are highly active ribonucleases specific for inosine in RNA. Inosines are normal residues in certain RNAs introduced by specific deaminases. Adenosine-to-inosine editing is essential for proper function of these transcripts and defects are linked to various human disease. Here we show that human ENDOV cleaves an RNA substrate containing inosine in a position corresponding to a biologically important site for deamination in the Gabra-3 transcript of the GABA(A) neurotransmitter. Further, human ENDOV specifically incises transfer RNAs with inosine in the wobble position. This previously unknown RNA incision activity may suggest a role for endonuclease V in normal RNA metabolism. PMID:23912683

  10. Phase transfer and point-spread function of the human eye determined by a new asymmetric double-pass method.

    OpenAIRE

    Navarro, Rafael; M. A. Losada

    1995-01-01

    A recent study has shown that the double-pass method provides a good estimate of the ocular modulation transfer function (MTF) but that it does not yield the phase transfer function (PTF) [J. Opt. Soc. Am. A 12, 195 (1995)]. Therefore, one cannot recover the true retinal point-spread function (PSF). We present a modification of the double-pass method to overcome this problem. The key is to break the symmetry between the two passes. By using an unexpanded Gaussian input beam, we produce ...

  11. Endonuclease IV (nfo) mutant of Escherichia coli.

    OpenAIRE

    Cunningham, R P; Saporito, S M; Spitzer, S G; Weiss, B

    1986-01-01

    A cloned gene, designated nfo, caused overproduction of an EDTA-resistant endonuclease specific for apurinic-apyrimidinic sites in DNA. The sedimentation coefficient of the enzyme was similar to that of endonuclease IV. An insertion mutation was constructed in vitro and transferred from a plasmid to the Escherichia coli chromosome. nfo mutants had an increased sensitivity to the alkylating agents methyl methanesulfonate and mitomycin C and to the oxidants tert-butyl hydroperoxide and bleomyci...

  12. Massively parallel characterization of restriction endonucleases

    OpenAIRE

    Kamps-Hughes, Nick; Quimby, Aine; Zhu, Zhenyu; Johnson, Eric A.

    2013-01-01

    Restriction endonucleases are highly specific in recognizing the particular DNA sequence they act on. However, their activity is affected by sequence context, enzyme concentration and buffer composition. Changes in these factors may lead to either ineffective cleavage at the cognate restriction site or relaxed specificity allowing cleavage of degenerate ‘star’ sites. Additionally, uncharacterized restriction endonucleases and engineered variants present novel activities. Traditionally, restri...

  13. A ligation-independent cloning method using nicking DNA endonuclease.

    Science.gov (United States)

    Yang, Jie; Zhang, Zhihong; Zhang, Xin A; Luo, Qingming

    2010-11-01

    Using nicking DNA endonuclease (NiDE), we developed a novel technique to clone DNA fragments into plasmids. We created a NiDE cassette consisting of two inverted NiDE substrate sites sandwiching an asymmetric four-base sequence, and NiDE cleavage resulted in 14-base single-stranded termini at both ends of the vector and insert. This method can therefore be used as a ligation-independent cloning strategy to generate recombinant constructs rapidly. In addition, we designed and constructed a simple and specific vector from an Escherichia coli plasmid back-bone to complement this cloning method. By cloning cDNAs into this modified vector, we confirmed the predicted feasibility and applicability of this cloning method. PMID:21091446

  14. Structure of bacteriophage T4 endonuclease II mutant E118A, a tetrameric GIY-YIG enzyme.

    Science.gov (United States)

    Andersson, C Evalena; Lagerbäck, Pernilla; Carlson, Karin

    2010-04-01

    Coliphage T4 endonuclease II (EndoII), encoded by gene denA, is a small (16 kDa, 136 aa) enzyme belonging to the GIY-YIG family of endonucleases, which lacks a C-terminal domain corresponding to that providing most of the binding energy in the structurally characterized GIY-YIG endonucleases, I-TevI and UvrC. In vivo, it is involved in degradation of host DNA, permitting scavenging of host-derived nucleotides for phage DNA synthesis. EndoII primarily catalyzes single-stranded nicking of DNA; 5- to 10-fold less frequently double-stranded breaks are produced. The Glu118Ala mutant of EndoII was crystallized in space group P2(1) with four monomers in the asymmetric unit. The fold of the EndoII monomer is similar to that of the catalytic domains of UvrC and I-TevI. In contrast to these enzymes, EndoII forms a striking X-shaped tetrameric structure composed as a dimer of dimers, with a protruding hairpin domain not present in UvrC or I-TevI providing most of the dimerization and tetramerization interfaces. A bound phosphate ion in one of the four active sites of EndoII likely mimics the scissile phosphate in a true substrate complex. In silico docking experiments showed that a protruding loop containing a nuclease-associated modular domain 3 element is likely to be involved in substrate binding, as well as residues forming a separate nucleic acid binding surface adjacent to the active site. The positioning of these sites within the EndoII primary dimer suggests that the substrate would bind to a primary EndoII dimer diagonally over the active sites, requiring significant distortion of the enzyme or the substrate DNA, or both, for simultaneous nicking of both DNA strands. The scarcity of potential nucleic acid binding residues between the active sites indicates that EndoII may bind its substrate inefficiently across the two sites in the dimer, offering a plausible explanation for the catalytic preponderance of single-strand nicks. Mutations analyzed in earlier functional

  15. Purification, crystallization, X-ray diffraction analysis and phasing of an engineered single-chain PvuII restriction endonuclease

    International Nuclear Information System (INIS)

    PvuII is the first type II restriction endonuclease to be converted from its wild-type homodimeric form into an enzymatically active single-chain variant. The enzyme was crystallized and phasing was successfully performed by molecular replacement. The restriction endonuclease PvuII from Proteus vulgaris has been converted from its wild-type homodimeric form into the enzymatically active single-chain variant scPvuII by tandemly joining the two subunits through the peptide linker Gly-Ser-Gly-Gly. scPvuII, which is suitable for the development of programmed restriction endonucleases for highly specific DNA cleavage, was purified and crystallized. The crystals diffract to a resolution of 2.35 Å and belong to space group P42, with unit-cell parameters a = b = 101.92, c = 100.28 Å and two molecules per asymmetric unit. Phasing was successfully performed by molecular replacement

  16. Linear and nonlinear optical properties in an asymmetric double quantum well under intense laser field: Effects of applied electric and magnetic fields

    Science.gov (United States)

    Yesilgul, U.; Al, E. B.; Martínez-Orozco, J. C.; Restrepo, R. L.; Mora-Ramos, M. E.; Duque, C. A.; Ungan, F.; Kasapoglu, E.

    2016-08-01

    In the present study, the effects of electric and magnetic fields on the linear and third-order nonlinear optical absorption coefficients and relative change of the refractive index in asymmetric GaAs/GaAlAs double quantum wells under intense laser fields are theoretically investigated. The electric field is oriented along the growth direction of the heterostructure while the magnetic field is taken in-plane. The intense laser field is linear polarization along the growth direction. Our calculations are made using the effective-mass approximation and the compact density-matrix approach. Intense laser effects on the system are investigated with the use of the Floquet method with the consequent change in the confinement potential of heterostructures. Our results show that the increase of the electric and magnetic fields blue-shifts the peak positions of the total absorption coefficient and of the total refractive index while the increase of the intense laser field firstly blue-shifts the peak positions and later results in their red-shifting.

  17. Purification and Characterization of Thermotoga maritima Endonuclease IV, a Thermostable Apurinic/Apyrimidinic Endonuclease and 3′-Repair Diesterase

    OpenAIRE

    Haas, Brian J.; Sandigursky, Margarita; Tainer, John A.; Franklin, William A.; Cunningham, Richard P.

    1999-01-01

    An endonuclease IV homolog was identified as the product of a conceptual open reading frame in the genome of the hyperthermophilic bacterium Thermotoga maritima. The T. maritima endonuclease IV gene encodes a 287-amino-acid protein with 32% sequence identity to Escherichia coli endonuclease IV. The gene was cloned, and the expressed protein was purified and shown to have enzymatic activities that are characteristic of the endonuclease IV family of DNA repair enzymes, including apurinic/apyrim...

  18. Divalent metal ion differentially regulates the sequential nicking reactions of the GIY-YIG homing endonuclease I-BmoI.

    Directory of Open Access Journals (Sweden)

    Benjamin P Kleinstiver

    Full Text Available Homing endonucleases are site-specific DNA endonucleases that function as mobile genetic elements by introducing double-strand breaks or nicks at defined locations. Of the major families of homing endonucleases, the modular GIY-YIG endonucleases are least understood in terms of mechanism. The GIY-YIG homing endonuclease I-BmoI generates a double-strand break by sequential nicking reactions during which the single active site of the GIY-YIG nuclease domain must undergo a substantial reorganization. Here, we show that divalent metal ion plays a significant role in regulating the two independent nicking reactions by I-BmoI. Rate constant determination for each nicking reaction revealed that limiting divalent metal ion has a greater impact on the second strand than the first strand nicking reaction. We also show that substrate mutations within the I-BmoI cleavage site can modulate the first strand nicking reaction over a 314-fold range. Additionally, in-gel DNA footprinting with mutant substrates and modeling of an I-BmoI-substrate complex suggest that amino acid contacts to a critical GC-2 base pair are required to induce a bottom-strand distortion that likely directs conformational changes for reaction progress. Collectively, our data implies mechanistic roles for divalent metal ion and substrate bases, suggesting that divalent metal ion facilitates the re-positioning of the GIY-YIG nuclease domain between sequential nicking reactions.

  19. Efficient fdCas9 Synthetic Endonuclease with Improved Specificity for Precise Genome Engineering

    KAUST Repository

    Aouida, Mustapha

    2015-07-30

    The Cas9 endonuclease is used for genome editing applications in diverse eukaryotic species. A high frequency of off-target activity has been reported in many cell types, limiting its applications to genome engineering, especially in genomic medicine. Here, we generated a synthetic chimeric protein between the catalytic domain of the FokI endonuclease and the catalytically inactive Cas9 protein (fdCas9). A pair of guide RNAs (gRNAs) that bind to sense and antisense strands with a defined spacer sequence range can be used to form a catalytically active dimeric fdCas9 protein and generate double-strand breaks (DSBs) within the spacer sequence. Our data demonstrate an improved catalytic activity of the fdCas9 endonuclease, with a spacer range of 15–39 nucleotides, on surrogate reporters and genomic targets. Furthermore, we observed no detectable fdCas9 activity at known Cas9 off-target sites. Taken together, our data suggest that the fdCas9 endonuclease variant is a superior platform for genome editing applications in eukaryotic systems including mammalian cells.

  20. Double-diffusive natural convection in an asymmetric trapezoidal enclosure: unsteady behavior in the laminar and the turbulent-flow regime

    Energy Technology Data Exchange (ETDEWEB)

    Papanicolaou, E.; Belessiotis, V. [Demokritos National Center for Scientific Research, Attiki (Greece). Solar and Other Energy Systems Lab.

    2005-01-01

    In the present work the natural convective heat and mass transfer in an asymmetric, trapezoidal enclosure is studied numerically. Such a configuration is encountered in greenhouse-type solar stills, where natural convection in the enclosed humid air due to vertical temperature and concentration gradients between the saline water and the transparent cover, plays a decisive role. In this double-diffusion problem, the relative magnitude of the thermal and the concentration (or solutal) Rayleigh numbers, expressed by their ratio N is a key parameter. The two-dimensional flow equations, expressed here in a stream function-vorticity ({psi} - {omega}) formulation, along with the energy and concentration equations are solved. Due to the large values of the Rayleigh numbers encountered under realistic conditions (10{sup 7} {<=} Ra {<=} 10{sup 10}), mostly turbulent flow conditions prevail. A two-equation, low-Reynolds number turbulence model has thus been selected and a curvilinear coordinate system is employed, allowing for better matching of the computational grid to the enclosure geometry. The numerical solutions yield a multi-cellular flow field, with the number of cells depending on the Rayleigh number for a fixed Lewis number and geometry. For a positive value of N (N = 1) the solution is qualitatively similar to the case with only thermal buoyancy present (N = 0). However, for negative values (N=-1), more complex unsteady phenomena arise, having a different nature in the laminar and the turbulent flow regime, which are both investigated. Correlations for the mean convective heat and mass transfer coefficients are obtained for a wide range of Rayleigh numbers, and comparisons are made for the different values of N, showing lower values and different rate of increase with Ra for N = -1. (author)

  1. Comparison of the cleavage of pyrimidine dimers by the bacteriophage T4 and Micrococcus luteus uv-specific endonucleases

    International Nuclear Information System (INIS)

    A comparison was made of the activity of the uv-specific endonucleases of bacteriophage T4 (T4 endonuclease V) and of Micrococcus luteus on ultraviolet light-irradiated DNA substrates of defined sequence. The two enzyms cleave DNA at the site of pyrimidine dimers with the same frequency. The products of the cleavage reaction are the same. The pyrimidine dimer DNA-glycosylase activity of both enzymes is more active on double-stranded DNA than it is on single-stranded DNA

  2. Endonuclease III (nth) mutants of Escherichia coli.

    OpenAIRE

    Cunningham, R P; Weiss, B

    1985-01-01

    Two strains that overproduce endonuclease III were found in a colony bank containing hybrid ColE1-Escherichia coli plasmids. The enzyme was identified in crude extracts by the degradation of partially depyrimidinated DNA in the presence of EDTA, by its sedimentation velocity, and by its associated thymine glycol-DNA glycosylase activity. An insertion mutation was produced by cloning the kanamycin-resistance gene of Tn5 into the plasmid copy of the nth gene. The mutation was then transferred t...

  3. Crystal Structure of the Homing Endonuclease I-CvuI Provides a New Template for Genome Modification

    DEFF Research Database (Denmark)

    Molina, Rafael; Redondo, Pilar; López-Méndez, Blanca;

    2015-01-01

    Homing endonucleases recognize and generate a DNA double-strand break, which has been used to promote gene targeting. These enzymes recognize long DNA stretches; they are highly sequence-specific enzymes and display a very low frequency of cleavage even in complete genomes. Although a large number...... of homing endonucleases have been identified, the landscape of possible target sequences is still very limited to cover the complexity of the whole eukaryotic genome. Therefore, the finding and molecular analysis of homing endonucleases identified but not yet characterized may widen the landscape of...... enzyme widely used in genome engineering. To characterize the enzyme cleavage mechanism, we have solved the I-CvuI DNA structures in the presence of non-catalytic (Ca(2+)) and catalytic ions (Mg(2+)). We have also analyzed the metal dependence of DNA cleavage using Mg(2+) ions at different concentrations...

  4. Shade avoidance 6 encodes an Arabidopsis flap endonuclease required for maintenance of genome integrity and development.

    Science.gov (United States)

    Zhang, Yijuan; Wen, Chunhong; Liu, Songbai; Zheng, Li; Shen, Binghui; Tao, Yi

    2016-02-18

    Flap endonuclease-1 (FEN1) belongs to the Rad2 family of structure-specific nucleases. It is required for several DNA metabolic pathways, including DNA replication and DNA damage repair. Here, we have identified a shade avoidance mutant, sav6, which reduces the mRNA splicing efficiency of SAV6. We have demonstrated that SAV6 is an FEN1 homologue that shows double-flap endonuclease and gap-dependent endonuclease activity, but lacks exonuclease activity. sav6 mutants are hypersensitive to DNA damage induced by ultraviolet (UV)-C radiation and reagents that induce double-stranded DNA breaks, but exhibit normal responses to chemicals that block DNA replication. Signalling components that respond to DNA damage are constitutively activated in sav6 mutants. These data indicate that SAV6 is required for DNA damage repair and the maintenance of genome integrity. Mutant sav6 plants also show reduced root apical meristem (RAM) size and defective quiescent centre (QC) development. The expression of SMR7, a cell cycle regulatory gene, and ERF115 and PSK5, regulators of QC division, is increased in sav6 mutants. Their constitutive induction is likely due to the elevated DNA damage responses in sav6 and may lead to defects in the development of the RAM and QC. Therefore, SAV6 assures proper root development through maintenance of genome integrity. PMID:26721386

  5. Yeast redoxyendonuclease, a DNA repair enzyme similar to Escherichia coli endonuclease III

    International Nuclear Information System (INIS)

    A DNA repair endonuclease (redoxyendonuclease) was isolated from bakers' yeast (Saccharomyces cerevisiae). The enzyme has been purified by a series of column chromatography steps and cleaves OsO4-damaged, double-stranded DNA at sites of thymine glycol and heavily UV-irradiated DNA at sites of cytosine, thymine, and guanine photoproducts. The base specificity and mechanism of phosphodiester bond cleavage for the yeast redoxyendonuclease appear to be identical with those of Escherichia coli endonuclease III when thymine glycol containing, end-labeled DNA fragments of defined sequence are employed as substrates. Yeast redoxyendonuclease has an apparent molecular size of 38,000-42,000 daltons and is active in the absence of divalent metal cations. The identification of such an enzyme in yeast may be of value in the elucidation of the biochemical basis for radiation sensitivity in certain yeast mutants

  6. Design and analysis of site-specific single-strand nicking endonucleases for gene correction.

    Science.gov (United States)

    Metzger, Michael J; Certo, Michael T

    2014-01-01

    Single-strand nicking endonucleases ("nickases") have been shown to induce homology-mediated gene correction with reduced toxicity of DNA double-strand break-producing enzymes, and nickases have been engineered from both homing endonuclease and FokI-based scaffolds. We describe the strategies used to engineer these site-specific nickases as well as the in vitro methods used to confirm their activity and specificity. Additionally, we describe the Traffic Light Reporter system, which uses a flow cytometric assay to simultaneously detect both gene repair and mutagenic nonhomologous end-joining outcomes at a single targeted site in mammalian cells. With these methods, novel nickases can be designed and tested for use in gene correction with novel target sites. PMID:24557907

  7. Asymmetric GaAs n-type double δ-doped quantum wells as a source of intersubband-related nonlinear optical response: Effects of an applied electric field

    International Nuclear Information System (INIS)

    In this work, the conduction band electron states and the associated intersubband-related linear and nonlinear optical absorption coefficient and relative refractive index change are calculated for an asymmetric double n-type δ-doped quantum well in a GaAs-matrix. The effects of an external applied static electric field are included. Values of the two-dimensional impurities density (N2d) of each single δ-doped quantum well are taken to vary within the range of 1.0×1012 to 7.0×1012 cm−2, consistent with the experimental data growth regime. The optical responses are reported as a function of the δ-doped impurities density and the applied electric field. It is shown that single electron states and the related optical quantities are significantly affected by the structural asymmetry of the double δ-doped quantum well system. In addition, a brief comparison with the free-carrier-related optical response is presented. -- Highlights: • Nonlinear optics in asymmetric double n-type δ-doped quantum well in a GaAs-matrix. • The system is considered under external applied electric field in growth direction. • The 2D impurity density is consistent with the experimental data growth regime. • The optical quantities are significantly affected by the structural asymmetry of the system

  8. Asymmetric GaAs n-type double δ-doped quantum wells as a source of intersubband-related nonlinear optical response: Effects of an applied electric field

    Energy Technology Data Exchange (ETDEWEB)

    Rodríguez-Magdaleno, K.A.; Martínez-Orozco, J.C.; Rodríguez-Vargas, I. [Unidad Académica de Física, Universidad Autónoma de Zacatecas, Calz. Solidaridad Esq. Paseo a La Bufa S/N. C.P. 98060 Zacatecas (Mexico); Mora-Ramos, M.E. [Facultad de Ciencias, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, CP 62209 Cuernavaca, Morelos (Mexico); Física Teórica y Aplicada, Escuela de Ingeniería de Antioquia, AA 7516 Medellín (Colombia); Grupo de Materia Condensada-UdeA, Instituto de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín (Colombia); Duque, C.A., E-mail: cduque@fisica.udea.edu.co [Grupo de Materia Condensada-UdeA, Instituto de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín (Colombia)

    2014-03-15

    In this work, the conduction band electron states and the associated intersubband-related linear and nonlinear optical absorption coefficient and relative refractive index change are calculated for an asymmetric double n-type δ-doped quantum well in a GaAs-matrix. The effects of an external applied static electric field are included. Values of the two-dimensional impurities density (N{sub 2d}) of each single δ-doped quantum well are taken to vary within the range of 1.0×10{sup 12} to 7.0×10{sup 12} cm{sup −2}, consistent with the experimental data growth regime. The optical responses are reported as a function of the δ-doped impurities density and the applied electric field. It is shown that single electron states and the related optical quantities are significantly affected by the structural asymmetry of the double δ-doped quantum well system. In addition, a brief comparison with the free-carrier-related optical response is presented. -- Highlights: • Nonlinear optics in asymmetric double n-type δ-doped quantum well in a GaAs-matrix. • The system is considered under external applied electric field in growth direction. • The 2D impurity density is consistent with the experimental data growth regime. • The optical quantities are significantly affected by the structural asymmetry of the system.

  9. Neutron diffraction studies of a high resolution double crystal (+n,-m) setting containing Si(220) and Si(311) bent perfect crystals in symmetric and fully asymmetric diffraction geometry, respectively

    International Nuclear Information System (INIS)

    In this paper studies of neutron diffraction properties of the double crystal (+n,-m) setting containing Si(220) and Si(311) bent perfect crystals (BPC) in symmetric and fully asymmetric diffraction (FAD) geometry with the output beam expansion (OBE), respectively, are presented. Namely, our attention was focused on the properties of the FAD geometry of the BPC Si(311) crystal slab. It has been found that after a beam expansion this FAD geometry can provide a monochromatic beam of a rather large cross-section and of very small divergence with some possible application use.

  10. Selection of a remote cleavage site by I-tevI, the td intron-encoded endonuclease.

    Science.gov (United States)

    Bryk, M; Belisle, M; Mueller, J E; Belfort, M

    1995-03-24

    I-TevI, a double-strand DNA endonuclease involved in the mobility of the td intron of phage T4, is highly unusual in that it binds and cleaves intronless td alleles (td homing sites) in a site-specific but sequence-tolerant manner. The endonuclease binds to sequences flanking the intron insertion site and near the remote cleavage site, located 23 and 25 nucleotides away on the top and bottom strands, respectively. Mapping studies indicate that I-TevI has both sequence and distance sensors that function during cut-site selection. Although I-TevI cleavage of many insertion and deletion variants of the homing site is impaired, double-strand breaks are generated at positions that collectively span two turns of the helix, indicating that the interaction is extraordinarily flexible. However, the endonuclease does exhibit spacing preferences between its binding domains, and sequence preferences near the cleavage site, with the G:C pair at -23 implicated as a cleavage determinant. Furthermore, I-TevI appears to function through interactions across the minor groove at the cleavage site, as it does at the intron insertion site, and to be capable of cleaving sequentially, first on the bottom and then on the top strand. These properties of I-TevI are incorporated in a model wherein the endonuclease effects distant cleavage via a flexible hinge. PMID:7707369

  11. Restriction endonuclease EcaI from Enterobacter cloacae

    OpenAIRE

    Hobom, G.; Schwarz, E; Melzer, M.; Mayer, H

    1981-01-01

    Restriction endonuclease EcaI obtained from Enterobacter cloacae DSM30056 recognizes the group of heptanucleotide palindromes 5′-G[unk]G-T-N-A-C-C-3′, and on cleavage (arrow) produces fragments with 5′-terminal pentanucleotide extensions. It is identical in specificity with restriction endonuclease BstEII from Bacillus stearothermophilus ET.

  12. Yeast structural gene (APN1) for the major apurinic endonuclease: homology to Escherichia coli endonuclease IV.

    OpenAIRE

    Popoff, S C; Spira, A I; Johnson, A. W.; Demple, B

    1990-01-01

    DNA damage generated by oxygen radicals includes base-free apurinic/apyrimidinic (AP) sites and strand breaks that bear deoxyribose fragments. The yeast Saccharomyces cerevisiae repairs such DNA lesions by using a single major enzyme. We have cloned the yeast structural gene (APN1) encoding this AP endonuclease/3'-repair diesterase by immunological screening of a yeast genomic DNA expression library in lambda gt11. Gene disruption experiments confirm that the Apn1 protein accounts for greater...

  13. Mechanism of action of Micrococcus luteus γ-endonuclease

    International Nuclear Information System (INIS)

    Micrococcus luteus extracts contain γ-endonuclease, a Mg2+-independent endonuclease that cleaves γ-irradiated DNA. This enzyme has been purified approximately 1000-fold, and the purified enzyme was used to study its substrate specificity and mechanism of action. γ-Endonuclease cleaves DNA containing either thymine glycols, urea residues, or apurinic sites but not undamaged DNA or DNA containing reduced apurinic sites. The enzyme has both N-glycosylase activity that releases thymine glycol residues from OsO4-treated DNA and an associated apurinic endonuclease activity. The location and nature of the cleavage site produced has been determined with DNA sequencing techniques. γ-Endonuclease cleaves DNA containing thymine glycols or apurinic sites immediately 3' to the damaged or missing base. Cleavage results in a 5'-phosphate terminus and a 3' baseless sugar residue. Cleavage sites can be converted to primers for DNA polymerase I by subsequent treatment with Escherichia coli exonuclease III. The mechanism of action of γ-endonuclease and its substrate specificity are very similar to those identified for E. coli endonuclease III

  14. Structures of Cas9 Endonucleases Reveal RNA-Mediated Conformational Activation

    OpenAIRE

    Jinek, Martin; Jiang, Fuguo; Taylor, David W.; Sternberg, Samuel H.; Kaya, Emine; MA, ENBO; Anders, Carolin; Hauer, Michael; Zhou, Kaihong; Lin, Steven; Kaplan, Matias; Anthony T Iavarone; Charpentier, Emmanuelle; Nogales, Eva; Doudna, Jennifer A.

    2014-01-01

    Type II CRISPR (clustered regularly interspaced short palindromic repeats)–Cas (CRISPR-associated) systems use an RNA-guided DNA endonuclease, Cas9, to generate double-strand breaks in invasive DNA during an adaptive bacterial immune response. Cas9 has been harnessed as a powerful tool for genome editing and gene regulation in many eukaryotic organisms. We report 2.6 and 2.2 angstrom resolution crystal structures of two major Cas9 enzyme subtypes, revealing the structural core shared by all C...

  15. Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease

    OpenAIRE

    Anders, Carolin; Niewoehner, Ole; Duerst, Alessia; Jinek, Martin

    2014-01-01

    The CRISPR-associated protein Cas9 is an RNA-guided endonuclease that cleaves double-stranded DNAs bearing sequences complementary to a 20-nucleotide segment in the guide RNA 1,2 . Cas9 has emerged as a versatile molecular tool for genome editing and gene expression control 3 . RNA-guided DNA recognition and cleavage strictly require the presence of a protospacer adjacent motif (PAM) in the target DNA 1,4-6 . Here, we report a crystal structure of Streptococcus pyogenes Cas9 complexed with a ...

  16. Nonlinear optical rectification and optical absorption in GaAs-Ga1-xAlxAs asymmetric double quantum wells: Combined effects of applied electric and magnetic fields and hydrostatic pressure

    International Nuclear Information System (INIS)

    The intersubband electron-related nonlinear optical absorption and nonlinear optical rectification in GaAs-Ga1-xAlxAs asymmetric double quantum wells are studied, under the influence of combined or independent applied electric and magnetic fields as well as hydrostatic pressure. The outcome of the density matrix formalism and the effective mass, and parabolic-band approximations have been considered as main theoretical tools for the description. It is obtained that under particular geometrical conditions, with or without electric and/or magnetic field strength, the optical rectification is null and, simultaneously, in such circumstances the optical absorption has a relative maximum. It is also detected that the influence of the hydrostatic pressure leads to increasing or decreasing behaviors of the nonlinear optical absorption in dependence of the particular regime of pressure values considered, with significant distinction of the cases of opposite electric field orientations. - Highlights: → Maxima of the NOA correspond to zero in the NOR. → Electric fields can couple the double quantum wells. → Hydrostatic pressure can couple the double quantum wells. → NOA can increase/decrease with hydrostatic pressure. → Overlap between wave functions depends on the magnetic field.

  17. Nonlinear optical rectification and optical absorption in GaAs-Ga{sub 1-x}Al{sub x}As asymmetric double quantum wells: Combined effects of applied electric and magnetic fields and hydrostatic pressure

    Energy Technology Data Exchange (ETDEWEB)

    Karabulut, I. [Department of Physics, Selcuk University, Konya 42075 (Turkey); Mora-Ramos, M.E. [Facultad de Ciencias, Universidad Autonoma del Estado de Morelos, Ave. Universidad 1001, CP 62209, Cuernavaca, Morelos (Mexico); Duque, C.A., E-mail: cduque_echeverri@yahoo.e [Instituto de Fisica, Universidad de Antioquia, AA 1226, Medellin (Colombia)

    2011-07-15

    The intersubband electron-related nonlinear optical absorption and nonlinear optical rectification in GaAs-Ga{sub 1-x}Al{sub x}As asymmetric double quantum wells are studied, under the influence of combined or independent applied electric and magnetic fields as well as hydrostatic pressure. The outcome of the density matrix formalism and the effective mass, and parabolic-band approximations have been considered as main theoretical tools for the description. It is obtained that under particular geometrical conditions, with or without electric and/or magnetic field strength, the optical rectification is null and, simultaneously, in such circumstances the optical absorption has a relative maximum. It is also detected that the influence of the hydrostatic pressure leads to increasing or decreasing behaviors of the nonlinear optical absorption in dependence of the particular regime of pressure values considered, with significant distinction of the cases of opposite electric field orientations. - Highlights: {yields} Maxima of the NOA correspond to zero in the NOR. {yields} Electric fields can couple the double quantum wells. {yields} Hydrostatic pressure can couple the double quantum wells. {yields} NOA can increase/decrease with hydrostatic pressure. {yields} Overlap between wave functions depends on the magnetic field.

  18. Crystallization and preliminary X-ray analysis of flap endonuclease 1 (FEN1) from Desulfurococcus amylolyticus

    International Nuclear Information System (INIS)

    Flap endonuclease 1 from D. amylolyticus was expressed, purified and crystallized by the sitting-drop vapour-diffusion method. X-ray diffraction data were collected to 2.00 Å resolution. Flap endonuclease 1 (FEN1) is a structure-specific nuclease that removes 5′-overhanging flaps in DNA repair and removes the RNA/DNA primer during maturation of the Okazaki fragment in lagging-strand DNA replication. FEN1 from the hyperthermophilic archaeon Desulfurococcus amylolyticus was expressed in Escherichia coli, purified and crystallized using the sitting-drop vapour-diffusion method with monoammonium dihydrogen phosphate as the precipitant at pH 8.3. X-ray diffraction data were collected to 2.00 Å resolution. The space group of the crystal was determined as the primitive hexagonal space group P321, with unit-cell parameters a = b = 103.76, c = 84.58 Å. The crystal contained one molecule in the asymmetric unit

  19. Developing a programmed restriction endonuclease for highly specific DNA cleavage

    OpenAIRE

    Eisenschmidt, Kristin; Lanio, Thomas; Simoncsits, András; Jeltsch, Albert; Pingoud, Vera; Wende, Wolfgang; Pingoud, Alfred

    2005-01-01

    Specific cleavage of large DNA molecules at few sites, necessary for the analysis of genomic DNA or for targeting individual genes in complex genomes, requires endonucleases of extremely high specificity. Restriction endonucleases (REase) that recognize DNA sequences of 4–8 bp are not sufficiently specific for this purpose. In principle, the specificity of REases can be extended by fusion to sequence recognition modules, e.g. specific DNA-binding domains or triple-helix forming oligonucleotid...

  20. Dynamic characteristics of double-barrier nanostructures with asymmetric barriers of finite height and widths in a strong ac electric field

    Energy Technology Data Exchange (ETDEWEB)

    Chuenkov, V. A., E-mail: v.a.chuenkov@mail.ru [Russian Academy of Sciences, Lebedev Physical Institute (Russian Federation)

    2013-12-15

    The theory of the interaction of a monoenergetic flow of injected electrons with a strong high-frequency ac electric field in resonant-tunneling diode (RTD) structures with asymmetric barriers of finite height and width is generalized. In the quasi-classical approximation, electron wavefunctions and tunneling functions in the quantum well and barriers are found. Analytical expressions for polarization currents in RTDs are derived in both the general case and in a number of limiting cases. It is shown that the polarization currents and radiation power in RTDs with asymmetric barriers strongly depend on the ratio of the probabilities of electron tunneling through the emitter and collector barriers. In the quantum mode, when δ = ε − ε{sub r} = ħω ≪ Γ (ε is the energy of electrons injected in the RTD, ħ is Planck’s constant, ω is the ac field frequency, ε{sub r} and Γ are the energy and width of the resonance level, respectively), the active polarization current in a field of E ≈ 2.8ħω/ea (e is the electron charge and a is the quantum-well width) reaches a maximum equal in magnitude to 84% of the direct resonant current, if the probability of electron tunneling through the emitter barrier is much higher than that through the collector barrier. The radiation-generation power at frequencies of ω = 10{sup 12}–10{sup 13} s{sup −1} can reach 10{sup 5}–10{sup 6} W/cm{sup 2} in this case.

  1. Endonucleases: new tools to edit the mouse genome.

    Science.gov (United States)

    Wijshake, Tobias; Baker, Darren J; van de Sluis, Bart

    2014-10-01

    Mouse transgenesis has been instrumental in determining the function of genes in the pathophysiology of human diseases and modification of genes by homologous recombination in mouse embryonic stem cells remains a widely used technology. However, this approach harbors a number of disadvantages, as it is time-consuming and quite laborious. Over the last decade a number of new genome editing technologies have been developed, including zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeats/CRISPR-associated (CRISPR/Cas). These systems are characterized by a designed DNA binding protein or RNA sequence fused or co-expressed with a non-specific endonuclease, respectively. The engineered DNA binding protein or RNA sequence guides the nuclease to a specific target sequence in the genome to induce a double strand break. The subsequent activation of the DNA repair machinery then enables the introduction of gene modifications at the target site, such as gene disruption, correction or insertion. Nuclease-mediated genome editing has numerous advantages over conventional gene targeting, including increased efficiency in gene editing, reduced generation time of mutant mice, and the ability to mutagenize multiple genes simultaneously. Although nuclease-driven modifications in the genome are a powerful tool to generate mutant mice, there are concerns about off-target cleavage, especially when using the CRISPR/Cas system. Here, we describe the basic principles of these new strategies in mouse genome manipulation, their inherent advantages, and their potential disadvantages compared to current technologies used to study gene function in mouse models. This article is part of a Special Issue entitled: From Genome to Function. PMID:24794718

  2. The actions of restriction endonucleases on lampbrush chromosomes.

    Science.gov (United States)

    Gould, D C; Callan, H G; Thomas, C A

    1976-07-01

    Lampbrush chromosomes from oocytes of Notophthalmus viridescens were dispersed in media containing restriction endonucleases isolated from Haemophilus and E. coli. These endonucleases cleave duplex DNAs at specific palindromic sequences of nucleotides, and several sensitive sites occur per micron of DNA. The overwhelming majority of the lateral loops of lampbrush chromosomes are extensively fragmented by these endonucleases, but an occasional pair of loops is refractory. A notable example of loops showing this refractory property are the giant loops on chromosome II in the presence of Hae. These loops, whose DNA-containing axes are several hundred micra long, are sensitive to other nucleases such as EcoB, endonuclease I and pancreatic DNase I; their refractory behavior towards Hae therefore indicates that the sequence sensitive to this particular endonuclease is systematically absent. This anomalous property can be comprehended if it be assumed that the axial DNA of the giant loops consists of tandem repeats of a sequence which happens not to include the sensitive site. PMID:987047

  3. Asymmetric collider

    International Nuclear Information System (INIS)

    The study of CP violation in beauty decay is one of the key challenges facing high energy physics. Much work has not yielded a definitive answer how this study might best be performed. However, one clear conclusion is that new accelerator facilities are needed. Proposals include experiments at asymmetric electron-positron colliders and in fixed-target and collider modes at LHC and SSC. Fixed-target and collider experiments at existing accelerators, while they might succeed in a first observation of the effect, will not be adequate to study it thoroughly. Giomataris has emphasized the potential of a new approach to the study of beauty CP violation: the asymmetric proton collider. Such a collider might be realized by the construction of a small storage ring intersecting an existing or soon-to-exist large synchrotron, or by arranging collisions between a large synchrotron and its injector. An experiment at such a collider can combine the advantages of fixed-target-like spectrometer geometry, facilitating triggering, particle identification and the instrumentation of a large acceptance, while the increased √s can provide a factor > 100 increase in beauty-production cross section compared to Tevatron or HERA fixed-target. Beams crossing at a non-zero angle can provide a small interaction region, permitting a first-level decay-vertex trigger to be implemented. To achieve large √s with a large Lorentz boost and high luminosity, the most favorable venue is the high-energy booster (HEB) at the SSC Laboratory, though the CERN SPS and Fermilab Tevatron are also worth considering

  4. Nonlinear absorption coefficient and relative refraction index change for an asymmetrical double δ-doped quantum well in GaAs with a Schottky barrier potential

    International Nuclear Information System (INIS)

    In this work we are reporting the energy level spectrum for a quantum system consisting of an n-type double δ-doped quantum well with a Schottky barrier potential in a Gallium Arsenide matrix. The calculated states are taken as the basis for the evaluation of the linear and third-order nonlinear contributions to the optical absorption coefficient and to the relative refractive index change, making particular use of the asymmetry of the potential profile. These optical properties are then reported as a function of the Schottky barrier height (SBH) and the separation distance between the δ-doped quantum wells. Also, the effects of the application of hydrostatic pressure are studied. The results show that the amplitudes of the resonant peaks are of the same order of magnitude of those obtained in the case of single δ-doped field effect transistors; but tailoring the asymmetry of the confining potential profile allows the control the resonant peak positions

  5. Nonlinear absorption coefficient and relative refraction index change for an asymmetrical double δ-doped quantum well in GaAs with a Schottky barrier potential

    Energy Technology Data Exchange (ETDEWEB)

    Rojas-Briseño, J.G.; Martínez-Orozco, J.C.; Rodríguez-Vargas, I. [Unidad Académica de Física, Universidad Autónoma de Zacatecas, Calzada Solidaridad esquina con Paseo la Bufa S/N, C.P. 98060, Zacatecas, Zac. (Mexico); Mora-Ramos, M.E. [Facultad de Ciencias, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, CP 62209, Cuernavaca, Morelos (Mexico); Instituto de Física, Universidad de Antioquia, AA 1226, Medellín (Colombia); Duque, C.A., E-mail: cduque@fisica.udea.edu.co [Instituto de Física, Universidad de Antioquia, AA 1226, Medellín (Colombia)

    2013-09-01

    In this work we are reporting the energy level spectrum for a quantum system consisting of an n-type double δ-doped quantum well with a Schottky barrier potential in a Gallium Arsenide matrix. The calculated states are taken as the basis for the evaluation of the linear and third-order nonlinear contributions to the optical absorption coefficient and to the relative refractive index change, making particular use of the asymmetry of the potential profile. These optical properties are then reported as a function of the Schottky barrier height (SBH) and the separation distance between the δ-doped quantum wells. Also, the effects of the application of hydrostatic pressure are studied. The results show that the amplitudes of the resonant peaks are of the same order of magnitude of those obtained in the case of single δ-doped field effect transistors; but tailoring the asymmetry of the confining potential profile allows the control the resonant peak positions.

  6. Endonuclease domain of non-LTR retrotransposons: loss-of-function mutants and modeling of the R2Bm endonuclease

    OpenAIRE

    Govindaraju, Aruna; Cortez, Jeremy D.; Reveal, Brad; Shawn M. Christensen

    2016-01-01

    Non-LTR retrotransposons are an important class of mobile elements that insert into host DNA by target-primed reverse transcription (TPRT). Non-LTR retrotransposons must bind to their mRNA, recognize and cleave their target DNA, and perform TPRT at the site of DNA cleavage. As DNA binding and cleavage are such central parts of the integration reaction, a better understanding of the endonuclease encoded by non-LTR retrotransposons is needed. This paper explores the R2 endonuclease domain from ...

  7. Biomass-Derived Nitrogen-Doped Carbon Nanofiber Network: A Facile Template for Decoration of Ultrathin Nickel-Cobalt Layered Double Hydroxide Nanosheets as High-Performance Asymmetric Supercapacitor Electrode.

    Science.gov (United States)

    Lai, Feili; Miao, Yue-E; Zuo, Lizeng; Lu, Hengyi; Huang, Yunpeng; Liu, Tianxi

    2016-06-01

    The development of biomass-based energy storage devices is an emerging trend to reduce the ever-increasing consumption of non-renewable resources. Here, nitrogen-doped carbonized bacterial cellulose (CBC-N) nanofibers are obtained by one-step carbonization of polyaniline coated bacterial cellulose (BC) nanofibers, which not only display excellent capacitive performance as the supercapacitor electrode, but also act as 3D bio-template for further deposition of ultrathin nickel-cobalt layered double hydroxide (Ni-Co LDH) nanosheets. The as-obtained CBC-N@LDH composite electrodes exhibit significantly enhanced specific capacitance (1949.5 F g(-1) at a discharge current density of 1 A g(-1) , based on active materials), high capacitance retention of 54.7% even at a high discharge current density of 10 A g(-1) and excellent cycling stability of 74.4% retention after 5000 cycles. Furthermore, asymmetric supercapacitors (ASCs) are constructed using CBC-N@LDH composites as positive electrode materials and CBC-N nanofibers as negative electrode materials. By virtue of the intrinsic pseudocapacitive characteristics of CBC-N@LDH composites and 3D nitrogen-doped carbon nanofiber networks, the developed ASC exhibits high energy density of 36.3 Wh kg(-1) at the power density of 800.2 W kg(-1) . Therefore, this work presents a novel protocol for the large-scale production of biomass-derived high-performance electrode materials in practical supercapacitor applications. PMID:27135301

  8. SegG endonuclease promotes marker exclusion and mediates co-conversion from a distant cleavage site.

    Science.gov (United States)

    Liu, Qingqing; Belle, Archana; Shub, David A; Belfort, Marlene; Edgell, David R

    2003-11-14

    Bacteriophages T2 and T4 are closely related T-even phages. However, T4 genetic markers predominate in the progeny of mixed infections, a phenomenon termed marker exclusion. One region previously mapped where the frequency of T2 markers in the progeny is extremely low is located around gene 32. Here, we describe SegG, a GIY-YIG family endonuclease adjacent to gene 32 of phage T4 that is absent from phage T2. In co-infections with T2 and T4, cleavage in T2 gene 32 by T4-encoded SegG initiates a gene conversion event that results in replacement of T2 gene 32 markers with the corresponding T4 sequence. Interestingly, segG inheritance is limited, apparently because of the physical separation of its cleavage and insertion sites, which are 332 base-pairs apart. This contrasts with efficient inheritance of the phage T4 td group I intron and its endonuclease, I-TevI, for which the distance separating the I-TevI cleavage site and td insertion site is 23 base-pairs. Furthermore, we show that co-conversion tracts generated by repair of SegG and I-TevI double-strand breaks contribute to the localized exclusion of T2 markers. Our results demonstrate that the endonuclease activities of SegG and I-TevI promote the spread of these two endonucleases to progeny phage, consistent with their role as selfish genetic elements, and also provide a mechanism by which the genetic contribution of T2 markers to progeny phage is reduced. PMID:14596796

  9. Endonucleases induced TRAIL-insensitive apoptosis in ovarian carcinoma cells

    International Nuclear Information System (INIS)

    TRAIL induced apoptosis of tumor cells is currently entering phase II clinical settings, despite the fact that not all tumor types are sensitive to TRAIL. TRAIL resistance in ovarian carcinomas can be caused by a blockade upstream of the caspase 3 signaling cascade. We explored the ability of restriction endonucleases to directly digest DNA in vivo, thereby circumventing the caspase cascade. For this purpose, we delivered enzymatically active endonucleases via the cationic amphiphilic lipid SAINT-18®:DOPE to both TRAIL-sensitive and insensitive ovarian carcinoma cells (OVCAR and SKOV-3, respectively). Functional nuclear localization after delivery of various endonucleases (BfiI, PvuII and NucA) was indicated by confocal microscopy and genomic cleavage analysis. For PvuII, analysis of mitochondrial damage demonstrated extensive apoptosis both in SKOV-3 and OVCAR. This study clearly demonstrates that cellular delivery of restriction endonucleases holds promise to serve as a novel therapeutic tool for the treatment of resistant ovarian carcinomas.

  10. Cleavage of guanine-modified DNA by restriction endonucleases

    Czech Academy of Sciences Publication Activity Database

    Slavíčková, Michaela; Boháčová, Soňa; Perlíková, Pavla; Hocek, Michal

    Praha : Czech Chemical Society, 2015. s. 139. [Liblice 2015. Advances in Organic , Bioorganic and Pharmaceutical Chemistry /50./. 06.11.2015-08.11.2015, Olomouc] R&D Projects: GA ČR GA14-04289S Institutional support: RVO:61388963 Keywords : base-modified DNA * restriction endonucleases Subject RIV: CC - Organic Chemistry

  11. Crystallization and preliminary crystallographic analysis of the catalytic domain of human flap endonuclease 1 in complex with a nicked DNA product: use of a DPCS kit for efficient protein–DNA complex crystallization

    International Nuclear Information System (INIS)

    Human flap endonuclease 1 complexed with nicked DNA has been crystallized. A diffraction data set was collected to a resolution of 2.75 Å. Flap endonuclease 1 (FEN1) is a structure-specific nuclease that removes the RNA/DNA primer associated with Okazaki fragments in DNA replication. Here, crystals of the complex between the catalytic domain of human FEN1 and a DNA product have been obtained. For efficient crystallization screening, a DNA–protein complex crystallization screening (DPCS) kit was designed based on commercial crystallization kits. The crystal was found to belong to space group P21, with unit-cell parameters a = 61.0, b = 101.3, c = 106.4 Å, β = 106.4°. The asymmetric unit is predicted to contain two complexes in the crystallographic asymmetric unit. A diffraction data set was collected to a resolution of 2.75 Å

  12. Purification and characterization of the x-ray endonuclease of Escherichia coli

    International Nuclear Information System (INIS)

    This work concerns the purification and characterization of the x-ray endonuclease of E. coli. The x-ray endonuclease was purified by chromatography on DNA-agarose, Sephadex gel filtration, hydroxylapatite chromatography, and phosphocellulose chromatography. Parallel assays on modified DNA and oligonucleotide substances established that the x-ray endonuclease was active on DNA contain in apurinic and apyrimidinic sites, thymine glycol and urea residues, and undefined lesions produced by UV and X radiation. Characterization of the x-ray endonuclease by gel filtration gave a molecular weight of about 25,000 dalton while SDS-polyacrylamide gel electrophoresis of the most purified preparations showed a single band corresponding to a molecular weight of about 13,000 daltons. Analysis of DNA substrates following x-ray endonuclease treatment showed that the x-ray endonuclease nicked at the 3' side of a base lesion to yield 3'OH and 5'PO termini. Analysis of the acid/alcohol soluble products of the digestion of specifically modified synthetic poly dT:dA by the x-ray endonuclease showed this enzyme to have DNA glycosylase activities that released both thymine glycol and urea residues from DNA. Inhibitor studies showed the thymine-glycol endonuclease activity was inhibited by NEM while the AP endonuclease was not. NEM was also shown to inhibit endonuclease activity on UV-irradiated DNA, X-irradiated DNA, and urea-containing DNA

  13. Endonuclease activities in extracts of Micrococcus luteus that act on γ-irradiated DNA

    International Nuclear Information System (INIS)

    Several protein fractions containing endonuclease activity against γ-irradiated DNA (γ-endonuclease) were isolated from M.luteus. The crude extract was eluted on a phosphocellulose column and chromatographed on TEAE cellulose and subsequently on hydroxypatite. Five peaks of γ-endonuclease were obtained from each preparation. Repeated experiments showed comparable chromatographic behaviour of the fractions. There was no detectable activity of U.V.-endonuclease in the fractions with γ-endonuclease but a small contamination of endonuclease against unirradiated DNA and against DNA with apurinic sites. The γ-endonuclease was stimulated by, but was not dependent on, magnesium. Several tests for endonuclease activity have been used: the analysis of strand breaks in calf-thymus DNA or in PM2 DNA, and the determination of end-groups formed by endonuclease, either 3'OH end-groups or phosphomonoester end groups. From the results obtained it can be assumed that the strand breaks induced by the γ-endonuclease carry 3'OH and 5' phosphate end groups. (author)

  14. Sequence specificity of DNA cleavage by Micrococcus luteus γ endonuclease

    International Nuclear Information System (INIS)

    DNA fragments of defined sequence have been used to determine the sites of cleavage by γ-endonuclease activity in extracts prepared from Micrococcus luteus. End-labeled DNA restriction fragments of pBR322 DNA that had been irradiated under nitrogen in the presence of potassium iodide or t-butanol were treated with M. luteus γ endonuclease and analyzed on irradiated DNA preferentially at the positions of cytosines and thymines. DNA cleavage occurred immediately to the 3' side of pyrimidines in irradiated DNA and resulted in fragments that terminate in a 5'-phosphoryl group. These studies indicate that both altered cytosines and thymines may be important DNA lesions requiring repair after exposure to γ radiation

  15. Asymmetric Ashes

    Science.gov (United States)

    2006-11-01

    that oscillate in certain directions. Reflection or scattering of light favours certain orientations of the electric and magnetic fields over others. This is why polarising sunglasses can filter out the glint of sunlight reflected off a pond. When light scatters through the expanding debris of a supernova, it retains information about the orientation of the scattering layers. If the supernova is spherically symmetric, all orientations will be present equally and will average out, so there will be no net polarisation. If, however, the gas shell is not round, a slight net polarisation will be imprinted on the light. This is what broad-band polarimetry can accomplish. If additional spectral information is available ('spectro-polarimetry'), one can determine whether the asymmetry is in the continuum light or in some spectral lines. In the case of the Type Ia supernovae, the astronomers found that the continuum polarisation is very small so that the overall shape of the explosion is crudely spherical. But the much larger polarization in strongly blue-shifted spectral lines evidences the presence, in the outer regions, of fast moving clumps with peculiar chemical composition. "Our study reveals that explosions of Type Ia supernovae are really three-dimensional phenomena," says Dietrich Baade. "The outer regions of the blast cloud is asymmetric, with different materials found in 'clumps', while the inner regions are smooth." "This study was possible because polarimetry could unfold its full strength thanks to the light-collecting power of the Very Large Telescope and the very precise calibration of the FORS instrument," he adds. The research team first spotted this asymmetry in 2003, as part of the same observational campaign (ESO PR 23/03 and ESO PR Photo 26/05). The new, more extensive results show that the degree of polarisation and, hence, the asphericity, correlates with the intrinsic brightness of the explosion. The brighter the supernova, the smoother, or less clumpy

  16. Identification of leptospiral isolates by bacterial restriction endonuclease analysis (Brenda

    Directory of Open Access Journals (Sweden)

    Venkatesha M

    2001-01-01

    Full Text Available DNA samples from 19 reference serovars belonging to 19 different serogroups of Leptospira interrogans and two serovars belonging to Leptospira biflexa were examined by bacterial restriction endonuclease analysis using EcoR I and Hae III enzymes. All the serovars gave unique restriction patterns that differed from each other. DNA from 10 local isolates digested with these enzymes produced patterns which on comparison with the standard patterns produced by reference strains could be identified to serovar level.

  17. Human repair endonuclease incises DNA at cytosine photoproducts

    International Nuclear Information System (INIS)

    The nature of DNA damage by uvB and uvC irradiation was investigated using a defined sequence of human DNA. A UV-irradiated, 3'-end-labeled, 92 base pair sequence from the human alphoid segment was incubated with a purified human lymphoblast endonuclease that incises DNA at non-dimer photoproducts. Analysis by polyacrylamide gel electrophoresis identified all sites of endonucleolytic incision as cytosines. These were found in regions of the DNA sequence lacking adjacent pyrimidines and therefore are neither cyclobutane pyrimidine dimers nor 6-4'-pyrimidines. Incision at cytosine photoproducts was not detected at loci corresponding to alkali-labile sites in either control or irradiated substrates. This demonstrates that the bands detected after the enzymic reactions were not the result of DNA strand breaks, base loss sites or ring-opened cytosines. The optimal wavelengths for formation of cytosine photoproducts are 270-295 nm, similar to those associated with maximal tumor yields in animal ultraviolet carcinogenesis studies. Irradiation by monochromatic 254 nm light resulted in reduced cytosine photoproduct formation. This human UV endonuclease has an apparently identical substrate specificity to E. coli endonuclease III. Both the human and bacterial enzymes incise cytosine moieties in UV irradiated DNA and modified thymines in oxidized DNA

  18. Induction of DNA double-strand breaks by restriction enzymes in X-ray-sensitive mutant Chinese hamster ovary cells measured by pulsed-field gel electrophoresis

    International Nuclear Information System (INIS)

    This investigation was designed to determine whether the cytotoxic effects of different restriction endonucleases are related to the number and type of DNA double-strand breaks (DSBs) they produce. Chinese hamster ovary (CHO) K1 and xrs-5 cells, a radiosensitive mutant of CHO K1, were exposed to restriction endonucleases HaeIII, HinfI, PvuII and BamHI by electroporation. These enzymes represent both blunt and sticky end cutters with differing recognition sequence lengths. The number of DSBs was measured by pulsed-field gel electrophoresis (PFGE). Two forms of PFGE were employed: asymmetric field-inversion gel electrophoresis (AFIGE) for measuring the kinetics of DNA breaks by enzyme digestion and clamped homogeneous gel electrophoresis (CHEF) for examining the size distributions of damaged DNA. The amount of DNA damage induced by exposure to all four restriction enzymes was significantly greater in xrs-5 compared to CHO K1 cells, consistent with the reported DSB repair deficiency in these cells. Since restriction endonucleases produce DSBs alone as opposed to the various types of DNA damage induced by X rays, these results confirm that the repair defect in this mutant involves the rejoining of DSBs. Although the cutting frequency was directly related to the length of the recognition sequence for four restriction enzymes, there was no simple correlation between the cytotoxic effect and the amount of DNA damage produced by each enzyme in either cell line. This finding suggests that the type or nature of the cutting sequence itself may play a role in restriction enzyme-induced cell killing. 32 refs., 6 figs., 3 tabs

  19. Importance of a single base pair for discrimination between intron-containing and intronless alleles by endonuclease I-BmoI.

    Science.gov (United States)

    Edgell, David R; Stanger, Matthew J; Belfort, Marlene

    2003-05-27

    Homing endonucleases initiate mobility of their host group I introns by binding to and cleaving lengthy recognition sequences that are typically centered on the intron insertion site (IS) of intronless alleles. Because the intron interrupts the endonucleases' recognition sequence, intron-containing alleles are immune to cleavage by their own endonuclease. I-TevI and I-BmoI are related GIY-YIG endonucleases that bind a homologous stretch of thymidylate synthase (TS)-encoding DNA but use different strategies to distinguish intronless from intron-containing substrates. I-TevI discriminates between substrates at the level of DNA binding, as its recognition sequence is centered on the intron IS. I-BmoI, in contrast, possesses a very asymmetric recognition sequence with respect to the intron IS, binds both intron-containing and intronless TS-encoding substrates, but efficiently cleaves only intronless substrate. Here, we show that I-BmoI is extremely tolerant of multiple substitutions around its cleavage sites and has a low specific activity. However, a single G-C base pair, at position -2 of a 39-base pair recognition sequence, is a major determinant for cleavage efficiency and distinguishes intronless from intron-containing alleles. Strikingly, this G-C base pair is universally conserved in phylogenetically diverse TS-coding sequences; this finding suggests that I-BmoI has evolved exquisite cleavage requirements to maximize the potential to spread to variant intronless alleles, while minimizing cleavage at its own intron-containing allele. PMID:12781137

  20. AP-endonuclease activity in thymocytes of normal and irradiated rats

    International Nuclear Information System (INIS)

    Using the viscosimetric method we established that AP-endonuclease activity is strongly pronounced in the chromatin fraction of rat thymocytes. A 1.7-fold increase of the AP-endonuclease activity was observed 1.5 h following irradiation (9 Gy) in the chromatin fraction, and a 2-fold increase, 4 h after irradiation, in both the chromatin and the nuclear fractions of thymocytes. The authors discuss the role of various endonucleases involved in the secondary postirradiation DNA degradation

  1. Biochemical characterization of a thermostable HNH endonuclease from deep-sea thermophilic bacteriophage GVE2.

    Science.gov (United States)

    Zhang, Likui; Huang, Yanchao; Xu, Dandan; Yang, Lixiang; Qian, Kaicheng; Chang, Guozhu; Gong, Yong; Zhou, Xiaojian; Ma, Kesen

    2016-09-01

    His-Asn-His (HNH) proteins are a very common family of small nucleic acid-binding proteins that are generally associated with endonuclease activity and are found in all kingdoms of life. Although HNH endonucleases from mesophiles have been widely investigated, the biochemical functions of HNH endonucleases from thermophilic bacteriophages remain unknown. Here, we characterized the biochemical properties of a thermostable HNH endonuclease from deep-sea thermophilic bacteriophage GVE2. The recombinant GVE2 HNH endonuclease exhibited non-specific cleavage activity at high temperature. The optimal temperature of the GVE2 HNH endonuclease for cleaving DNA was 60-65 °C, and the enzyme retained its DNA cleavage activity even after heating at 100 °C for 30 min, suggesting the enzyme is a thermostable endonuclease. The GVE2 HNH endonuclease cleaved DNA over a wide pH spectrum, ranging from 5.5 to 9.0, and the optimal pH for the enzyme activity was 8.0-9.0. Furthermore, the GVE2 HNH endonuclease activity was dependent on a divalent metal ion. While the enzyme is inactive in the presence of Cu(2+), the GVE2 HNH endonuclease displayed cleavage activity of varied efficiency with Mn(2+), Mg(2+), Ca(2+), Fe(2+), Co(2+), Zn(2+), and Ni(2+). The GVE2 HNH endonuclease activity was inhibited by NaCl. This study provides the basis for determining the role of this endonuclease in life cycle of the bacteriophage GVE2 and suggests the potential application of the enzyme in molecular biology and biotechnology. PMID:27131500

  2. Neisseria gonorrhoeae FA1090 Carries Genes Encoding Two Classes of Vsr Endonucleases

    OpenAIRE

    Kwiatek, Agnieszka; Łuczkiewicz, Maciej; Bandyra, Katarzyna; Stein, Daniel C.; Piekarowicz, Andrzej

    2010-01-01

    A very short patch repair system prevents mutations resulting from deamination of 5-methylcytosine to thymine. The Vsr endonuclease is the key enzyme of this system, providing sequence specificity. We identified two genes encoding Vsr endonucleases V.NgoAXIII and V.NgoAXIV from Neisseria gonorrhoeae FA1090 based on DNA sequence similarity to genes encoding Vsr endonucleases from other bacteria. After expression of the gonococcal genes in Escherichia coli, the proteins were biochemically chara...

  3. Adenosine Triphosphate Stimulates Aquifex aeolicus MutL Endonuclease Activity

    OpenAIRE

    Jerome Mauris; Thomas C Evans

    2009-01-01

    BACKGROUND: Human PMS2 (hPMS2) homologues act to nick 5' and 3' to misincorporated nucleotides during mismatch repair in organisms that lack MutH. Mn(++) was previously found to stimulate the endonuclease activity of these homologues. ATP was required for the nicking activity of hPMS2 and yPMS1, but was reported to inhibit bacterial MutL proteins from Thermus thermophilus and Aquifex aeolicus that displayed homology to hPMS2. Mutational analysis has identified the DQHA(X)(2)E(X)(4)E motif pre...

  4. Adenosine triphosphate stimulates Aquifex aeolicus MutL endonuclease activity.

    Directory of Open Access Journals (Sweden)

    Jerome Mauris

    Full Text Available BACKGROUND: Human PMS2 (hPMS2 homologues act to nick 5' and 3' to misincorporated nucleotides during mismatch repair in organisms that lack MutH. Mn(++ was previously found to stimulate the endonuclease activity of these homologues. ATP was required for the nicking activity of hPMS2 and yPMS1, but was reported to inhibit bacterial MutL proteins from Thermus thermophilus and Aquifex aeolicus that displayed homology to hPMS2. Mutational analysis has identified the DQHA(X(2E(X(4E motif present in the C-terminus of PMS2 homologues as important for endonuclease activity. METHODOLOGIES/PRINCIPAL FINDINGS: We examined the effect ATP had on the Mn(++ induced nicking of supercoiled pBR322 by full-length and mutant A. aeolicus MutL (Aae MutL proteins. Assays were single time point, enzyme titration experiments or reaction time courses. The maximum velocity for MutL nicking was determined to be 1.6+/-0.08x10(-5 s(-1 and 4.2+/-0.3x10(-5 s(-1 in the absence and presence of ATP, respectively. AMPPNP stimulated the nicking activity to a similar extent as ATP. A truncated Aae MutL protein composed of only the C-terminal 123 amino acid residues was found to nick supercoiled DNA. Furthermore, mutations in the conserved C-terminal DQHA(X(2E(X(4E and CPHGRP motifs were shown to abolish Aae MutL endonuclease activity. CONCLUSIONS: ATP stimulated the Mn(++ induced endonuclease activity of Aae MutL. Experiments utilizing AMPPNP implied that the stimulation did not require ATP hydrolysis. A mutation in the DQHA(X(2E(X(4E motif of Aae MutL further supported the role of this region in endonclease activity. For the first time, to our knowledge, we demonstrate that changing the histidine residue in the conserved CPHGRP motif abolishes endonucleolytic activity of a hPMS2 homologue. Finally, the C-terminal 123 amino acid residues of Aae MutL were sufficient to display Mn(++ induced nicking activity.

  5. Crystal structure of an avian influenza polymerase PA[subscript N] reveals an endonuclease active site

    Energy Technology Data Exchange (ETDEWEB)

    Yuan, Puwei; Bartlam, Mark; Lou, Zhiyong; Chen, Shoudeng; Zhou, Jie; He, Xiaojing; Lv, Zongyang; Ge, Ruowen; Li, Xuemei; Deng, Tao; Fodor, Ervin; Rao, Zihe; Liu, Yingfang; (NU Sinapore); (Nankai); (Oxford); (Chinese Aca. Sci.); (Tsinghua)

    2009-11-10

    The heterotrimeric influenza virus polymerase, containing the PA, PB1 and PB2 proteins, catalyses viral RNA replication and transcription in the nucleus of infected cells. PB1 holds the polymerase active site and reportedly harbours endonuclease activity, whereas PB2 is responsible for cap binding. The PA amino terminus is understood to be the major functional part of the PA protein and has been implicated in several roles, including endonuclease and protease activities as well as viral RNA/complementary RNA promoter binding. Here we report the 2.2 angstrom (A) crystal structure of the N-terminal 197 residues of PA, termed PA(N), from an avian influenza H5N1 virus. The PA(N) structure has an alpha/beta architecture and reveals a bound magnesium ion coordinated by a motif similar to the (P)DX(N)(D/E)XK motif characteristic of many endonucleases. Structural comparisons and mutagenesis analysis of the motif identified in PA(N) provide further evidence that PA(N) holds an endonuclease active site. Furthermore, functional analysis with in vivo ribonucleoprotein reconstitution and direct in vitro endonuclease assays strongly suggest that PA(N) holds the endonuclease active site and has critical roles in endonuclease activity of the influenza virus polymerase, rather than PB1. The high conservation of this endonuclease active site among influenza strains indicates that PA(N) is an important target for the design of new anti-influenza therapeutics.

  6. Structural stability and endonuclease activity of a PI-SceI GFP-fusion protein

    Directory of Open Access Journals (Sweden)

    Alireza G. Senejani, J. Peter Gogarten

    2007-01-01

    Full Text Available Homing endonucleases are site-specific and rare cutting endonucleases often encoded by intron or intein containing genes. They lead to the rapid spread of the genetic element that hosts them by a process termed 'homing'; and ultimately the allele containing the element will be fixed in the population. PI-SceI, an endonuclease encoded as a protein insert or intein within the yeast V-ATPase catalytic subunit encoding gene (vma1, is among the best characterized homing endonucleases. The structures of the Sce VMA1 intein and of the intein bound to its target site are known. Extensive biochemical studies performed on the PI-SceI enzyme provide information useful to recognize critical amino acids involved in self-splicing and endonuclease functions of the protein. Here we describe an insertion of the Green Fluorescence Protein (GFP into a loop which is located between the endonuclease and splicing domains of the Sce VMA1 intein. The GFP is functional and the additional GFP domain does not prevent intein excision and endonuclease activity. However, the endonuclease activity of the newly engineered protein was different from the wild-type protein in that it required the presence of Mn2+ and not Mg2+ metal cations for activity.

  7. Cleavage of phosphorothioated DNA and methylated DNA by the type IV restriction endonuclease ScoMcrA.

    Directory of Open Access Journals (Sweden)

    Guang Liu

    Full Text Available Many taxonomically diverse prokaryotes enzymatically modify their DNA by replacing a non-bridging oxygen with a sulfur atom at specific sequences. The biological implications of this DNA S-modification (phosphorothioation were unknown. We observed that simultaneous expression of the dndA-E gene cluster from Streptomyces lividans 66, which is responsible for the DNA S-modification, and the putative Streptomyces coelicolor A(32 Type IV methyl-dependent restriction endonuclease ScoA3McrA (Sco4631 leads to cell death in the same host. A His-tagged derivative of ScoA3McrA cleaved S-modified DNA and also Dcm-methylated DNA in vitro near the respective modification sites. Double-strand cleavage occurred 16-28 nucleotides away from the phosphorothioate links. DNase I footprinting demonstrated binding of ScoA3McrA to the Dcm methylation site, but no clear binding could be detected at the S-modified site under cleavage conditions. This is the first report of in vitro endonuclease activity of a McrA homologue and also the first demonstration of an enzyme that specifically cleaves S-modified DNA.

  8. Fragment-Based Identification of Influenza Endonuclease Inhibitors.

    Science.gov (United States)

    Credille, Cy V; Chen, Yao; Cohen, Seth M

    2016-07-14

    The influenza virus is responsible for millions of cases of severe illness annually. Yearly variance in the effectiveness of vaccination, coupled with emerging drug resistance, necessitates the development of new drugs to treat influenza infections. One attractive target is the RNA-dependent RNA polymerase PA subunit. Herein we report the development of inhibitors of influenza PA endonuclease derived from lead compounds identified from a metal-binding pharmacophore (MBP) library screen. Pyromeconic acid and derivatives thereof were found to be potent inhibitors of endonuclease. Guided by modeling and previously reported structural data, several sublibraries of molecules were elaborated from the MBP hits. Structure-activity relationships were established, and more potent molecules were designed and synthesized using fragment growth and fragment merging strategies. This approach ultimately resulted in the development of a lead compound with an IC50 value of 14 nM, which displayed an EC50 value of 2.1 μM against H1N1 influenza virus in MDCK cells. PMID:27291165

  9. Sequence specificity of DNA cleavage by Micrococcus luteus gamma endonuclease

    International Nuclear Information System (INIS)

    Gamma irradiation induces the formation of lesions in DNA that are cleaved by an endonuclease activity in Micrococcus luteus extract. DNA fragments of defined sequence an DNA sequencing techniques were used to determine the sites of cleavage by this activity. /sup 32/P end-labelled DNA restriction fragments were gamma irradiated under N/sub 2/ and in the presence of KI (conditions which maximize the enzyme sensitive site to strand break ratio), treated with M. luteus extract, and analyzed by electrophoresis on denaturing polyacrylamide gels. Irradiated DNA was preferentially cleaved by the extract at sites of cytosine and thymine. Little or no cleavage was observed at purines. Scission of 3' end-labelled DNA at altered pyrimidines resulted in fragments that had electrophoretic mobilities similar to those of DNA fragments that were phosphorylated at the 5' terminus. The presence of a 5' phosphate was confirmed by a change in electrophoretic mobility after phosphatase treatment of the fragments. The sites of endonucleolytic cleavage by M. luteus extract were compared to those of the purified Escherichia coli endonuclease III, which has been shown to be active against x-irradiated DNA. Preliminary results from velocity sedimentation studies indicate that these two enzyme preparations differ in specificity

  10. Inteins, introns, and homing endonucleases: recent revelations about the life cycle of parasitic genetic elements

    Directory of Open Access Journals (Sweden)

    Hilario Elena

    2006-11-01

    Full Text Available Abstract Self splicing introns and inteins that rely on a homing endonuclease for propagation are parasitic genetic elements. Their life-cycle and evolutionary fate has been described through the homing cycle. According to this model the homing endonuclease is selected for function only during the spreading phase of the parasite. This phase ends when the parasitic element is fixed in the population. Upon fixation the homing endonuclease is no longer under selection, and its activity is lost through random processes. Recent analyses of these parasitic elements with functional homing endonucleases suggest that this model in its most simple form is not always applicable. Apparently, functioning homing endonuclease can persist over long evolutionary times in populations and species that are thought to be asexual or nearly asexual. Here we review these recent findings and discuss their implications. Reasons for the long-term persistence of a functional homing endonuclease include: More recombination (sexual and as a result of gene transfer than previously assumed for these organisms; complex population structures that prevent the element from being fixed; a balance between active spreading of the homing endonuclease and a decrease in fitness caused by the parasite in the host organism; or a function of the homing endonuclease that increases the fitness of the host organism and results in purifying selection for the homing endonuclease activity, even after fixation in a local population. In the future, more detailed studies of the population dynamics of the activity and regulation of homing endonucleases are needed to decide between these possibilities, and to determine their relative contributions to the long term survival of parasitic genes within a population. Two outstanding publications on the amoeba Naegleria group I intron (Wikmark et al. BMC Evol Biol 2006, 6:39 and the PRP8 inteins in ascomycetes (Butler et al.BMC Evol Biol 2006, 6:42 provide

  11. DNA interrogation by the CRISPR RNA-guided endonuclease Cas9

    Science.gov (United States)

    Sternberg, Samuel H.; Redding, Sy; Jinek, Martin; Greene, Eric C.; Doudna, Jennifer A.

    2014-03-01

    The clustered regularly interspaced short palindromic repeats (CRISPR)-associated enzyme Cas9 is an RNA-guided endonuclease that uses RNA-DNA base-pairing to target foreign DNA in bacteria. Cas9-guide RNA complexes are also effective genome engineering agents in animals and plants. Here we use single-molecule and bulk biochemical experiments to determine how Cas9-RNA interrogates DNA to find specific cleavage sites. We show that both binding and cleavage of DNA by Cas9-RNA require recognition of a short trinucleotide protospacer adjacent motif (PAM). Non-target DNA binding affinity scales with PAM density, and sequences fully complementary to the guide RNA but lacking a nearby PAM are ignored by Cas9-RNA. Competition assays provide evidence that DNA strand separation and RNA-DNA heteroduplex formation initiate at the PAM and proceed directionally towards the distal end of the target sequence. Furthermore, PAM interactions trigger Cas9 catalytic activity. These results reveal how Cas9 uses PAM recognition to quickly identify potential target sites while scanning large DNA molecules, and to regulate scission of double-stranded DNA.

  12. I-TevI, the endonuclease encoded by the mobile td intron, recognizes binding and cleavage domains on its DNA target.

    OpenAIRE

    Bell-Pedersen, D; Quirk, S M; Bryk, M; Belfort, M

    1991-01-01

    Mobility of the phage T4 td intron depends on activity of an intron-encoded endonuclease (I-TevI), which cleaves a homologous intronless (delta In) target gene. The double-strand break initiates a recombination event that leads to intron transfer. We found previously that I-TevI cleaves td delta In target DNA 23-26 nucleotides upstream of the intron insertion site. DNase I-footprinting experiments and gel-shift assays indicate that I-TevI makes primary contacts around the intron insertion sit...

  13. Human RECQL5beta stimulates flap endonuclease 1

    DEFF Research Database (Denmark)

    Speina, Elzbieta; Dawut, Lale; Hedayati, Mohammad;

    2010-01-01

    Human RECQL5 is a member of the RecQ helicase family which is implicated in genome maintenance. Five human members of the family have been identified; three of them, BLM, WRN and RECQL4 are associated with elevated cancer risk. RECQL1 and RECQL5 have not been linked to any human disorder yet; cells...... devoid of RECQL1 and RECQL5 display increased chromosomal instability. Here, we report the physical and functional interaction of the large isomer of RECQL5, RECQL5beta, with the human flap endonuclease 1, FEN1, which plays a critical role in DNA replication, recombination and repair. RECQL5beta...... dramatically stimulates the rate of FEN1 cleavage of flap DNA substrates. Moreover, we show that RECQL5beta and FEN1 interact physically and co-localize in the nucleus in response to DNA damage. Our findings, together with the previous literature on WRN, BLM and RECQL4's stimulation of FEN1, suggests...

  14. New ruthenium catalysts for asymmetric hydrogenation

    OpenAIRE

    Diaz Valenzuela, Maria Belen

    2007-01-01

    A review on catalytic asymmetric hydrogenation of C=O double bonds is presented in the first chapter. Noyori’s pioneering research on ruthenium complexes containing both phosphine and diamine ligands using [i superscript]PrOH and [t superscript]BuOK is described, this system gave impressive highly chemeo-selectivity for C=O bonds and extremely high enantioselectivity for a range of acetophenone derivatives. Numerous groups have been inspired by Noyori’s catalyst of the ty...

  15. Substrate specificity of Micrococcus luteus uv endonuclease and its overlap with DNA photolyase activity

    International Nuclear Information System (INIS)

    The action of an endonuclease from Micrococcus luteus that operates on uv damage in DNA overlaps with that of DNA photolyase from yeast: homo- and heterocyclobutane dipyrimidines in DNA are substrates for both enzymes, but pyrimidine adducts or the spore photoproduct in DNA are not. As expected from this overlap, the action of the two enzymes is mutually interfering: single-strand nicks introduced by the endonuclease effectively preclude photoreactivation; conversely, formation of a photolyase-cyclobutane dipyrimidine complex can prevent nicking by the endonuclease

  16. The Asymmetric Leximin Solution

    OpenAIRE

    Driesen, Bram W.

    2012-01-01

    In this article we define and characterize a class of asymmetric leximin solutions, that contains both the symmetric leximin solution of Imai[5] and the two-person asymmetric Kalai-Smorodinsky solution of Dubra [3] as special cases. Solutions in this class combine three attractive features: they are defined on the entire domain of convex n-person bargaining problems, they generally yield Pareto efficient solution outcomes, and asymmetries among bargainers are captured by a single parameter ve...

  17. Asymmetric WIMP dark matter

    OpenAIRE

    Graesser, Michael L.; Shoemaker, Ian M.; Vecchi, Luca

    2011-01-01

    In existing dark matter models with global symmetries the relic abundance of dark matter is either equal to that of anti-dark matter (thermal WIMP), or vastly larger, with essentially no remaining anti-dark matter (asymmetric dark matter). By exploring the consequences of a primordial asymmetry on the coupled dark matter and anti-dark matter Boltzmann equations we find large regions of parameter space that interpolate between these two extremes. Interestingly, this new asymmetric WIMP framewo...

  18. Binding of T4 endonuclease V to deoxyribonucleic acid irradiated with ultraviolet light

    International Nuclear Information System (INIS)

    Endonuclease V of bacteriophage T4 binds to uv-irradiated deoxyribonucleic acid (DNA) but not to unirradiated DNA. We have developed an assay to detect this binding, based on the retention of enzyme - DNA complexes on nitrocellulose filters. The amount of complex retained, ascertained by using radioactive DNA, is a measure of T4 endonuclease V activity. From our data we conclude that (1) T4 endonuclease V binds to uv-irradiated DNA but not to DNA that has been previously incised by the endonuclease, (2) equilibrium between the free and complexed form of the enzyme is attained under our reaction conditions, (3) dissociation of enzyme - DNA complexes is retarded by sodium cyanide, and (4) retention of enzyme - DNA complexes on nitrocellulose filters is enhanced by high concentrations of saline-citrate

  19. Highly Selective and Sensitive Electrochemiluminescence Biosensor for p53 DNA Sequence Based on Nicking Endonuclease Assisted Target Recycling and Hyperbranched Rolling Circle Amplification.

    Science.gov (United States)

    Yang, Linlin; Tao, Yingzhou; Yue, Guiyin; Li, Ruibao; Qiu, Bin; Guo, Longhua; Lin, Zhenyu; Yang, Huang-Hao

    2016-05-17

    An ultrasensitive and specific electrochemiluminescence (ECL) biosensor has been designed for the p53 DNA sequence, which is based on cascade signal amplification of nicking endonuclease assisted target recycling and hyperbranched rolling circle amplification (HRCA). First of all, biotin modified hairpin capture DNA (HP) probe was immobilized on the surface of streptavidin magnespheres paramagnetic particles (PMPs). Target DNA hybridized with the loop portion of the HP probe, therefore unfolding HP to form a double-stranded DNA (dsDNA) containing the specific nicking site of the nicking endonuclease. Then, the nicking endonuclease recognized the specific nicking site and cleaved the HP into two pieces, liberating target DNA and the complementary sequence piece for the padlock probe. The intact target DNA would initiate the next cycle of hybridization and cleavage, thereby releasing multiple complementary sequences for the padlock probes. The liberated complementary sequences hybridized with the padlock probes, subsequently inducing the HRCA reaction and generating numerous dsDNA segments. Herein, Ru(phen)3(2+) was embedded into dsDNA and worked as ECL signal reporter. The reaction products were eventually pretreated by dialysis tube with the cutoff membrane to remove the residual Ru(phen)3(2+) in the solution for the following ECL measurements. Using this cascade amplification strategy, an ultrasensitive p53 DNA sequence detection method was developed with a wide linear range from 0.05 to 100 fM and a low detection limit of 0.02 fM. Moreover, this cascade amplified ECL biosensor had specific recognition capacity for noncomplementary and single- and double-base mismatched DNA. The proposed ECL biosensor might have a great potential in biomedical research and clinic analysis. PMID:27086663

  20. Characterization of Borrelia burgdorferi isolates by restriction endonuclease analysis and DNA hybridization.

    OpenAIRE

    LeFebvre, R B; Perng, G C; Johnson, R C

    1989-01-01

    Genomes of several Borrelia burgdorferi isolates from North America and Europe were characterized by restriction endonuclease analysis and DNA hybridization using labeled B. burgdorferi whole-cell DNA (strain ATCC 35210). Several different restriction and homology patterns were observed among these isolates, indicating genotypic heterogeneity within this genus and species. It was concluded from this study that restriction endonuclease analysis of B. burgdorferi whole-cell DNA may be a reliabl...

  1. Unambiguous typing of canine adenovirus isolates by deoxyribonucleic acid restriction-endonuclease analysis.

    OpenAIRE

    Assaf, R; Marsolais, G; Yelle, J; Hamelin, C

    1983-01-01

    Viral deoxyribonucleic acid extracted from a limited number of cells infected with canine adenovirus type 1 or type 2 was cleaved with several restriction endonucleases. Agarose gel electrophoresis of the limit digests showed stable differences between the canine adenovirus type 1 and type 2 cleavage patterns. Rapid and accurate typing of large numbers of clinical isolates may thus be done by deoxyribonucleic acid restriction-endonuclease analysis.

  2. Cloning and characterization of a wheat homologue of apurinic/apyrimidinic endonuclease Ape1L.

    Directory of Open Access Journals (Sweden)

    Botagoz Joldybayeva

    Full Text Available BACKGROUND: Apurinic/apyrimidinic (AP endonucleases are key DNA repair enzymes involved in the base excision repair (BER pathway. In BER, an AP endonuclease cleaves DNA at AP sites and 3'-blocking moieties generated by DNA glycosylases and/or oxidative damage. A Triticum aestivum cDNA encoding for a putative homologue of ExoIII family AP endonucleases which includes E. coli Xth, human APE1 and Arabidopsis thaliana AtApe1L has been isolated and its protein product purified and characterized. METHODOLOGY/PRINCIPAL FINDINGS: We report that the putative wheat AP endonuclease, referred here as TaApe1L, contains AP endonuclease, 3'-repair phosphodiesterase, 3'-phosphatase and 3' → 5' exonuclease activities. Surprisingly, in contrast to bacterial and human AP endonucleases, addition of Mg(2+ and Ca(2+ (5-10 mM to the reaction mixture inhibited TaApe1L whereas the presence of Mn(2+, Co(2+ and Fe(2+ cations (0.1-1.0 mM strongly stimulated all its DNA repair activities. Optimization of the reaction conditions revealed that the wheat enzyme requires low divalent cation concentration (0.1 mM, mildly acidic pH (6-7, low ionic strength (20 mM KCl and has a temperature optimum at around 20 °C. The steady-state kinetic parameters of enzymatic reactions indicate that TaApe1L removes 3'-blocking sugar-phosphate and 3'-phosphate groups with good efficiency (kcat/KM = 630 and 485 μM(-1 · min(-1, respectively but possesses a very weak AP endonuclease activity as compared to the human homologue, APE1. CONCLUSIONS/SIGNIFICANCE: Taken together, these data establish the DNA substrate specificity of the wheat AP endonuclease and suggest its possible role in the repair of DNA damage generated by endogenous and environmental factors.

  3. Studies on rat liver nuclear DNA damaged by chemical carcinogen (3'-Me DAB) and AP DNA endonuclease. II. Kinetic properties of AP DNA endonucleases in rat liver chromatin.

    OpenAIRE

    Y. S. Kim; Kim, J. W.; Lee, S. E.; Oh, S.H.(Department of Physics, Duke University, Durham, NC, United States)

    1990-01-01

    An experiment was designed to investigate the reaction mechanism of AP (apurinic or apyrimidinic) DNA endonucleases (APcI, APcII, APcIII) purified from rat liver chromatin. Sulfhydryl compounds (2-mercaptoethanol, dithiothreitol) brought about optimal activities of AP DNA endonucleases and N-ethylmaleimide or HgCl2 inhibited the enzyme activities, indicating the presence of sulfhydryl group at or near the active sites of the enzymes. Mg2+ was essential and 4mM of Mg2+ was sufficient for the o...

  4. Alteration of the Specificity of PstⅠRestriction Endonuclease

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    The influence of factors on the substrate-specificity of Pst Ⅰ restriction endonuclease has been studied with the method of electrophoresis. The results show that, the specificity of Pst Ⅰ almost can not be influenced by the single alteration of the concentration of Tris*HCl, Mg2+ or Na+ in the reaction system, but it can be altered by the reduction of any two of them. The specificity can not be altered by the single alteration of pH or the replacement of Mg2+ with Mn2+. The addition of glycerol or dimethylsulphoxide (DMSO) to the reaction system results in the relaxation of the substrate-specificity of Pst Ⅰ , but dimethylmethylformide, glycol and ethyl alcohol can not bring about the alteration of Pst Ⅰ specificity. Through the method of cloning and sequencing, the nucleotides of No.1 and 6 in the recognition sequence of Pst Ⅰ have changed (1C→A or 6G→T). Used with the enzyme analysis of an artificially synthetic DNA segment containing a special sequence, the nucleotides of No.1 and 6 have both changed (1C→A and 6G→T). The recognition sequence of Pst Ⅰ is speculated to be changed from CTGCA↓G to TGCA↓.

  5. Properties of an endonuclease activity in Micrococcus luteus acting on γ-irradiated DNA and on apurinic DNA

    International Nuclear Information System (INIS)

    A protein fraction from Micrococcus luteus with endonuclease activity against γ-irradiated DNA was isolated and characterized. An additional activity on apurinic sites could not be separated, either by sucrose gradient sedimentation or by gel filtration through Sephadex G 100. From gel filtration, a molecular weight of about 25 000 was calculated for both endonuclease activities. The endonuclease activity against γ-irradiated DNA was stimulated five-fold with 5 mM Mg++, whereas that against apurinic sites was less dependent on the Mg++ concentration. 100 mM KCl inhibited the γ-ray endonuclease, but not the apurinic endonuclease activity. In γ-irradiated DNA the protein recognized 1.65 endonuclease sensitive sites per radiation-induced single-strand break, among which are 0.45 alkali labile lesions in the nucleotide strand. The was evaluated resulting in a Ksub(m)-value of 73 nM. (author)

  6. Zinc finger as distance determinant in the flexible linker of intron endonuclease I-TevI.

    Science.gov (United States)

    Dean, Amy B; Stanger, Matt J; Dansereau, John T; Van Roey, Patrick; Derbyshire, Victoria; Belfort, Marlene

    2002-06-25

    I-TevI, the phage T4 td intron-encoded endonuclease, recognizes a lengthy DNA target and initiates intron mobility by introducing a double-strand break in the homing site. The enzyme uses both sequence and distance determinants to cleave the DNA 23-25 bp upstream of the intron insertion site. I-TevI consists of an N-terminal catalytic domain and a C-terminal DNA-binding domain separated by a long, flexible linker. The DNA-binding domain consists of three subdomains: a zinc finger, a minor-groove binding alpha-helix, and a helix-turn-helix. In this study, a mutational analysis was undertaken to assess the roles of these subdomains in substrate binding and cleavage. Surprisingly, the zinc finger is not required for DNA binding or catalysis. Rather, the zinc finger is a component of the linker and directs the catalytic domain to cleave the homing site at a fixed distance from the intron insertion site. When the cleavage site (CS) is shifted outside a given range, wild-type I-TevI defaults to the fixed distance, whereas zinc-finger mutants have lost the distance determinant and search out the displaced cleavage sequences. Although counterintuitive, a protein containing a 19-aa deletion of the zinc finger can extend further than can wild-type I-TevI to cleave a distant CS sequence, and a Cys-to-Ala mutant of the ligands for zinc, nominally a longer protein, can retract to cleave at a closer CS sequence. Models are presented for the novel function of the zinc finger, as a molecular constraint, whereby intramolecular protein-protein interactions position the catalytic domain by "catalytic clamp" and/or "linker-organizer" mechanisms. PMID:12077294

  7. Asymmetric ion trap

    International Nuclear Information System (INIS)

    An ion trap having two end cap electrodes disposed asymmetrically about a center of a ring electrode is disclosed. The inner surface of the end cap electrodes are conformed to an asymmetric pair of equipotential lines of the harmonic formed by the application of voltages to the electrodes. The asymmetry of the end cap electrodes allows ejection of charged species through the closer of the two electrodes which in turn allows for simultaneously detecting anions and cations expelled from the ion trap through the use of two detectors charged with opposite polarity. 4 figs

  8. Site-directed mutagenesis of the T4 endonuclease V gene: role of lysine-130

    International Nuclear Information System (INIS)

    The DNA sequence of the bacteriophage T4 denV gene which encodes the DNA repair enzyme endonuclease V was previously constructed behind the hybrid lambda promoter OLPR in a plasmid vector. The OLPR-denV sequence was subcloned in M13mp18 and used as template to construct site-specific mutations in the denV structural gene in order to investigate structure/function relationships between the primary structure of the protein and its various DNA binding and catalytic activities. The Lys-130 residue of the wild-type endonuclease V has been postulated to be associated with its apurinic endonuclease (AP-endonuclease) activity. The codon for Lys-130 was changed to His-130 or Gly-130, and each denV sequence was subcloned into a pEMBL expression vector. These plasmids were transformed into repair-deficient Escherichia coli (uvrA recA), and the following parameters were examined for cells or cell extracts: expression and accumulation of endonuclease V protein (K-130, H-130, or G-130); survival after UV irradiation; dimer-specific DNA binding; and kinetics of phosphodiester bond scission at pyrimidine dimer sites, dimer-specific N-glycosylase activity, and AP-endonuclease activity. The enzyme's intracellular accumulation was significantly decreased for G-130 and slightly decreased for H-130 despite normal levels of denV-specific mRNA for each mutant. On a molar basis, the endonuclease V gene products generally gave parallel levels of each of the catalytic and binding functions with K-130 greater than H-130 greater than G-130 much greater than control denV-

  9. Asymmetric reactions in continuous flow

    Directory of Open Access Journals (Sweden)

    Xiao Yin Mak

    2009-04-01

    Full Text Available An overview of asymmetric synthesis in continuous flow and microreactors is presented in this review. Applications of homogeneous and heterogeneous asymmetric catalysis as well as biocatalysis in flow are discussed.

  10. Multiplex, Rapid, and Sensitive Isothermal Detection of Nucleic-Acid Sequence by Endonuclease Restriction-Mediated Real-Time Multiple Cross Displacement Amplification

    Science.gov (United States)

    Wang, Yi; Wang, Yan; Zhang, Lu; Liu, Dongxin; Luo, Lijuan; Li, Hua; Cao, Xiaolong; Liu, Kai; Xu, Jianguo; Ye, Changyun

    2016-01-01

    We have devised a novel isothermal amplification technology, termed endonuclease restriction-mediated real-time multiple cross displacement amplification (ET-MCDA), which facilitated multiplex, rapid, specific and sensitive detection of nucleic-acid sequences at a constant temperature. The ET-MCDA integrated multiple cross displacement amplification strategy, restriction endonuclease cleavage and real-time fluorescence detection technique. In the ET-MCDA system, the functional cross primer E-CP1 or E-CP2 was constructed by adding a short sequence at the 5′ end of CP1 or CP2, respectively, and the new E-CP1 or E-CP2 primer was labeled at the 5′ end with a fluorophore and in the middle with a dark quencher. The restriction endonuclease Nb.BsrDI specifically recognized the short sequence and digested the newly synthesized double-stranded terminal sequences (5′ end short sequences and their complementary sequences), which released the quenching, resulting on a gain of fluorescence signal. Thus, the ET-MCDA allowed real-time detection of single or multiple targets in only a single reaction, and the positive results were observed in as short as 12 min, detecting down to 3.125 fg of genomic DNA per tube. Moreover, the analytical specificity and the practical application of the ET-MCDA were also successfully evaluated in this study. Here, we provided the details on the novel ET-MCDA technique and expounded the basic ET-MCDA amplification mechanism. PMID:27242766

  11. DNA binding and cleavage by the HNH homing endonuclease I-HmuI.

    Science.gov (United States)

    Shen, Betty W; Landthaler, Markus; Shub, David A; Stoddard, Barry L

    2004-09-01

    The structure of I-HmuI, which represents the last family of homing endonucleases without a defining crystallographic structure, has been determined in complex with its DNA target. A series of diverse protein structural domains and motifs, contacting sequential stretches of nucleotide bases, are distributed along the DNA target. I-HmuI contains an N-terminal domain with a DNA-binding surface found in the I-PpoI homing endonuclease and an associated HNH/N active site found in the bacterial colicins, and a C-terminal DNA-binding domain previously observed in the I-TevI homing endonuclease. The combination and exchange of these features between protein families indicates that the genetic mobility associated with homing endonucleases extends to the level of independent structural domains. I-HmuI provides an unambiguous structural connection between the His-Cys box endonucleases and the bacterial colicins, supporting the hypothesis that these enzymes diverged from a common ancestral nuclease. PMID:15313606

  12. Enhancement effect of asymmetry on the thermal conductivity of double-stranded chain systems

    International Nuclear Information System (INIS)

    Using nonequilibrium molecular dynamics simulations, we study the thermal conductivity of asymmetric double chains. We couple two different single chains through interchain coupling to build three kinds of asymmetric double-stranded chain system: intrachain interaction, external potential, and mass asymmetric double chains. It is reported that asymmetry is helpful in improving the thermal conductivity of the system. We first propose double-heat flux channels to explain the influence of asymmetric structures on the thermal conductivity. The phonon spectral behaviour and finite size effect are also included. (general)

  13. Comparison of genomes of malignant catarrhal fever-associated herpesviruses by restriction endonuclease analysis.

    Science.gov (United States)

    Shih, L M; Zee, Y C; Castro, A E

    1989-01-01

    The restriction endonuclease DNA cleavage patterns of eight isolates of malignant catarrhal fever-associated herpesviruses were examined using the restriction endonucleases HindIII and EcoRI. The eight viruses could be assigned to two distinct groups. Virus isolates from a blue wildebeest, a sika deer and an ibex had restriction endonuclease DNA cleavage patterns that were in general similar to each other. The restriction pattern of these three viruses was distinct from the other five. Of these five, four were isolated from a greater kudu, a white tailed wildebeest, a white bearded wildebeest, and a cape hartebeest. The fifth isolate C500, was isolated from a domestic cow with malignant catarrhal fever. These five viruses had similar DNA cleavage patterns. PMID:2558629

  14. The identification and optimization of a N-hydroxy urea series of flap endonuclease 1 inhibitors.

    Science.gov (United States)

    Tumey, L Nathan; Bom, David; Huck, Bayard; Gleason, Elizabeth; Wang, Jianmin; Silver, Daniel; Brunden, Kurt; Boozer, Sherry; Rundlett, Stephen; Sherf, Bruce; Murphy, Steven; Dent, Tom; Leventhal, Christina; Bailey, Andrew; Harrington, John; Bennani, Youssef L

    2005-01-17

    Flap endonuclease-1 (FEN1) is a key enzyme involved in base excision repair (BER), a primary pathway utilized by mammalian cells to repair DNA damage. Sensitization to DNA damaging agents is a potential method for the improvement of the therapeutic window of traditional chemotherapeutics. In this paper, we describe the identification and SAR of a series of low nanomolar FEN1 inhibitors. Over 1000-fold specificity was achieved against a related endonuclease, xeroderma pigmentosum G (XPG). Two compounds from this series significantly potentiate the action of methyl methanesulfonate (MMS) and temozolamide in a bladder cancer cell line (T24). To our knowledge, these are the most potent endonuclease inhibitors reported to date. PMID:15603939

  15. Asymmetric information and economics

    Science.gov (United States)

    Frieden, B. Roy; Hawkins, Raymond J.

    2010-01-01

    We present an expression of the economic concept of asymmetric information with which it is possible to derive the dynamical laws of an economy. To illustrate the utility of this approach we show how the assumption of optimal information flow leads to a general class of investment strategies including the well-known Q theory of Tobin. Novel consequences of this formalism include a natural definition of market efficiency and an uncertainty principle relating capital stock and investment flow.

  16. Asymmetric Organocatalytic Cycloadditions

    DEFF Research Database (Denmark)

    Mose, Rasmus

    2016-01-01

    were pioneered by Otto Paul Hermann Diels and Kurt Alder who discovered what later became known as the Diels Alder reaction. The Diels Alder reaction is a [4+2] cycloaddition in which a π4 component reacts with a π2 component via a cyclic transition state to generate a 6 membered ring. This reaction...... reactions constitute the first organocatalytic asymmetric higher order cycloadditions and a rational for the periselectivity and stereoselectivity is provided based on experimental and computational investigations....

  17. Asymmetric extractions in orthodontics

    Directory of Open Access Journals (Sweden)

    Camilo Aquino Melgaço

    2012-04-01

    Full Text Available INTRODUCTION: Extraction decisions are extremely important in during treatment planning. In addition to the extraction decision orthodontists have to choose what tooth should be extracted for the best solution of the problem and the esthetic/functional benefit of the patient. OBJECTIVE: This article aims at reviewing the literature relating the advantages, disadvantages and clinical implications of asymmetric extractions to orthodontics. METHODS: Keywords were selected in English and Portuguese and the EndNote 9 program was used for data base search in PubMed, Web of Science (WSc and LILACS. The selected articles were case reports, original articles and prospective or retrospective case-control studies concerning asymmetrical extractions of permanent teeth for the treatment of malocclusions. CONCLUSION: According to the literature reviewed asymmetric extractions can make some specific treatment mechanics easier. Cases finished with first permanent molars in Class II or III relationship in one or both sides seem not to cause esthetic or functional problems. However, diagnosis knowledge and mechanics control are essential for treatment success.

  18. Asymmetric Evolutionary Games.

    Science.gov (United States)

    McAvoy, Alex; Hauert, Christoph

    2015-08-01

    Evolutionary game theory is a powerful framework for studying evolution in populations of interacting individuals. A common assumption in evolutionary game theory is that interactions are symmetric, which means that the players are distinguished by only their strategies. In nature, however, the microscopic interactions between players are nearly always asymmetric due to environmental effects, differing baseline characteristics, and other possible sources of heterogeneity. To model these phenomena, we introduce into evolutionary game theory two broad classes of asymmetric interactions: ecological and genotypic. Ecological asymmetry results from variation in the environments of the players, while genotypic asymmetry is a consequence of the players having differing baseline genotypes. We develop a theory of these forms of asymmetry for games in structured populations and use the classical social dilemmas, the Prisoner's Dilemma and the Snowdrift Game, for illustrations. Interestingly, asymmetric games reveal essential differences between models of genetic evolution based on reproduction and models of cultural evolution based on imitation that are not apparent in symmetric games. PMID:26308326

  19. I-TevI, the endonuclease encoded by the mobile td intron, recognizes binding and cleavage domains on its DNA target.

    Science.gov (United States)

    Bell-Pedersen, D; Quirk, S M; Bryk, M; Belfort, M

    1991-09-01

    Mobility of the phage T4 td intron depends on activity of an intron-encoded endonuclease (I-TevI), which cleaves a homologous intronless (delta In) target gene. The double-strand break initiates a recombination event that leads to intron transfer. We found previously that I-TevI cleaves td delta In target DNA 23-26 nucleotides upstream of the intron insertion site. DNase I-footprinting experiments and gel-shift assays indicate that I-TevI makes primary contacts around the intron insertion site. A synthetic DNA duplex spanning the insertion site but lacking the cleavage site was shown to bind I-TevI specifically, and when cloned, to direct cleavage into vector sequences. The behavior of the cloned duplex and that of deletion and insertion mutants support a primary role for sequences surrounding the insertion site in directing I-TevI binding, conferring cleavage ability, and determining cleavage polarity. On the other hand, sequences around the cleavage site were shown to influence cleavage efficiency and cut-site selection. The role of cleavage-site sequences in determining cleavage distance argues against a strict "ruler" mechanism for cleavage by I-TevI. The complex nature of the homing site recognized by this unusual type of endonuclease is considered in the context of intron spread. PMID:1881913

  20. Asymmetric transmission: a generic property of two-dimensional periodic patterns

    International Nuclear Information System (INIS)

    Asymmetric transmission of circularly polarized waves is a well-established property of lossy, anisotropic, two-dimensionally chiral patterns. Here we show that asymmetric transmission can be observed for oblique incidence onto any lossy periodically structured plane. Our results greatly expand the range of natural and artificial materials in which directionally asymmetric transmission can be expected, making it a cornerstone electromagnetic effect rather than a curiosity of planar chiral metamaterials. Prime candidates for asymmetric transmission at oblique incidence are rectangular arrays of plasmonic spheres or semiconductor quantum dots, lossy double-periodic gratings and planar metamaterial structures

  1. Efficient fdCas9 Synthetic Endonuclease with Improved Specificity for Precise Genome Engineering

    OpenAIRE

    Aouida, Mustapha; Eid, Ayman; Ali, Zahir; Cradick, Thomas; Lee, Ciaran; Deshmukh, Harshavardhan; Atef, Ahmed; AbuSamra, Dina; Gadhoum, Samah Zeineb; Merzaban, Jasmeen; Bao, Gang; Mahfouz, Magdy

    2015-01-01

    The Cas9 endonuclease is used for genome editing applications in diverse eukaryotic species. A high frequency of off-target activity has been reported in many cell types, limiting its applications to genome engineering, especially in genomic medicine. Here, we generated a synthetic chimeric protein between the catalytic domain of the FokI endonuclease and the catalytically inactive Cas9 protein (fdCas9). A pair of guide RNAs (gRNAs) that bind to sense and antisense strands with a defined spac...

  2. The use of thioglycolate to distinguish between 3' AP (apurinic/apyrimidinic) endonucleases and AP lyases.

    OpenAIRE

    Bricteux-Grégoire, S; Verly, W G

    1989-01-01

    Addition of thioglycolate and DEAE-Sephadex chromatography were used to analyze the cleavage of the C(3')-O-P bond 3' to AP (apurinic/apyrimidinic) sites in DNA and to distinguish between a mechanism of hydrolysis (which would allow the nicking enzyme to be called 3' AP endonuclease) or beta-elimination (so that the nicking enzyme should be called AP lyase). For this purpose, DNA labelled in the AP sites was first cleaved by rat-liver AP endonuclease, then with the 3' nicking catalyst in the ...

  3. Escherichia coli endonuclease VIII: cloning, sequencing, and overexpression of the nei structural gene and characterization of nei and nei nth mutants.

    OpenAIRE

    Jiang, D.; Hatahet, Z; Blaisdell, J O; Melamede, R J; Wallace, S S

    1997-01-01

    Escherichia coli possesses two DNA glycosylase/apurinic lyase activities with overlapping substrate specificities, endonuclease III and endonuclease VIII, that recognize and remove oxidized pyrimidines from DNA. Endonuclease III is encoded by the nth gene. Endonuclease VIII has now been purified to apparent homogeneity, and the gene, nei, has been cloned by using reverse genetics. The gene nei is located at 16 min on the E. coli chromosome and encodes a 263-amino-acid protein which shows sign...

  4. Continuous microfluidic fabrication of synthetic asymmetric vesicles.

    Science.gov (United States)

    Lu, Li; Schertzer, Jeffrey W; Chiarot, Paul R

    2015-09-01

    We report on a novel microfluidic strategy for the continuous fabrication of monodisperse asymmetric vesicles with customized membrane composition, size, and luminal content. The microfluidic device encompasses a triangular post region and two flow-focusing regions. The major steps involved in the vesicle fabrication process include: (1) forming highly uniform water emulsions in an oil/inner-leaflet-lipid solution, (2) replacing the inner-leaflet-lipid solution with an outer-leaflet-lipid solution inside the microchannel network, (3) forming water-in-oil-in-water double emulsions, and (4) extracting excess oil/outer-leaflet-lipid solution from the double emulsions. Bilayer membrane asymmetry and unilamellarity are evaluated using a fluorescence quenching assay and a transmembrane protein insertion assay, respectively. Our approach addresses many of the deficiencies found in existing technologies for building vesicles, and yields strong membrane asymmetry. The ability to create and sustain membrane asymmetry is an important feature, as it is a characteristic of nearly all natural membranes. Over 80% of the vesicles remain stable for at least 6 weeks and the membrane asymmetry is maintained for over 30 hours. The asymmetric vesicles built using this strategy are collected off-chip and hold the potential to be used as model systems in membrane biology or as vehicles for drug delivery. PMID:26220822

  5. Facilitated Asymmetric Exclusion

    OpenAIRE

    Gabel, Alan; Krapivsky, P. L.; Redner, S.

    2010-01-01

    We introduce a class of facilitated asymmetric exclusion processes in which particles are pushed by neighbors from behind. For the simplest version in which a particle can hop to its vacant right neighbor only if its left neighbor is occupied, we determine the steady state current and the distribution of cluster sizes on a ring. We show that an initial density downstep develops into a rarefaction wave that can have a jump discontinuity at the leading edge, while an upstep results in a shock w...

  6. Asymmetric synthesis v.4

    CERN Document Server

    Morrison, James

    1984-01-01

    Asymmetric Synthesis, Volume 4: The Chiral Carbon Pool and Chiral Sulfur, Nitrogen, Phosphorus, and Silicon Centers describes the practical methods of obtaining chiral fragments. Divided into five chapters, this book specifically examines initial chiral transmission and extension. The opening chapter describes the so-called chiral carbon pool, the readily available chiral carbon fragments used as building blocks in synthesis. This chapter also provides a list of 375 chiral building blocks, along with their commercial sources, approximate prices, and methods of synthesis. Schemes involving

  7. Specific action of T4 endonuclease V on damaged DNA in xeroderma pigmentosum cells in vivo

    International Nuclear Information System (INIS)

    The specific action of T4 endonuclease V on damaged DNA in xeroderma pigmentosum cells was examined using an in vivo assay system with hemagglutinating virus of Japan (Sendai virus) inactivated by uv light. A clear dose response was observed between the level of uv-induced unscheduled DNA synthesis of xeroderma pigmentosum cells and the amount of T4 endonuclease V activity added. The T4 enzyme was unstable in human cells, and its half-life was 3 hr. Fractions derived from an extract of Escherichia coli infected with T4v1, a mutant defective in the endonuclease V gene, showed no ability to restore the uv-induced unscheduled DNA synthesis of xeroderma pigmentosum cells. However, fractions derived from an extract of T4D-infected E. coli with endonuclease V activity were effective. The T4 enzyme was effective in xeroderma pigmentosum cells on DNA damaged by uv light but not in cells damaged by 4-nitroquinoline 1-oxide. The results of these experiments show that the T4 enzyme has a specific action on human cell DNA in vivo. Treatment with the T4 enzyme increased the survival of group A xeroderma pigmentosum cells after uv irradiation

  8. Distance determination by GIY-YIG intron endonucleases: discrimination between repression and cleavage functions.

    Science.gov (United States)

    Liu, Qingqing; Derbyshire, Victoria; Belfort, Marlene; Edgell, David R

    2006-01-01

    GIY-YIG homing endonucleases are modular proteins, with conserved N-terminal catalytic domains connected by linkers to C-terminal DNA-binding domains. I-TevI, the T4 phage GIY-YIG intron endonuclease, functions both in promoting td intron homing, and in acting as a transcriptional autorepressor. Repression is achieved by binding to an operator, which is cleaved at 100-fold reduced efficiency relative to the intronless homing site. The linker includes a zinc finger, which functions in distance determination, to constrain the catalytic domain to cleave the homing site at a fixed position. Here we show that I-BmoI, a related GIY-YIG endonuclease lacking a zinc finger, also possesses some cleavage distance discrimination. Furthermore, hybrid endonucleases constructed by swapping the domains of I-BmoI and I-TevI are active, precise and demonstrate that features other than the zinc finger facilitate distance determination. Most importantly, I-TevI zinc finger mutants cleave the operator more efficiently than the homing site, the converse of wild-type protein. These results are consistent with the zinc finger acting as a measuring device, directing efficient cleavage of the homing site to promote intron mobility, while reducing cleavage at the operator to ensure transcriptional autorepression and phage viability. PMID:16582101

  9. Molecular Recognition of DNA Damage Sites by Apurinic/Apyrimidinic Endonucleases

    Energy Technology Data Exchange (ETDEWEB)

    Braun, W. A.

    2005-07-28

    The DNA repair/redox factor AP endonuclease 1 (APE1) is a multifunctional protein which is known to to be essential for DNA repair activity in human cells. Structural/functional analyses of the APE activity is thus been an important research field to assess cellular defense mechanisms against ionizing radiation.

  10. The identification and optimization of 2,4-diketobutyric acids as flap endonuclease 1 inhibitors.

    Science.gov (United States)

    Tumey, L Nathan; Huck, Bayard; Gleason, Elizabeth; Wang, Jianmin; Silver, Daniel; Brunden, Kurt; Boozer, Sherry; Rundlett, Stephen; Sherf, Bruce; Murphy, Steven; Bailey, Andrew; Dent, Tom; Leventhal, Christina; Harrington, John; Bennani, Youssef L

    2004-10-01

    There have been several recent reports of chemopotentiation via inhibition of DNA repair processes. Flap endonuclease 1 (FEN1) is a key enzyme involved in base excision repair (BER), a primary pathway utilized by mammalian cells to repair DNA damage. In this report, we describe the identification and SAR of a series of 2,4-diketobutyric acid FEN1 inhibitors. PMID:15341951

  11. Cleavage and protection of locked nucleic acid-modified DNA by restriction endonucleases

    DEFF Research Database (Denmark)

    Crouzier, Lucile; Dubois, Camille; Wengel, Jesper;

    2012-01-01

    Locked nucleic acid (LNA) is one of the most prominent nucleic acid analogues reported so far. We herein for the first time report cleavage by restriction endonuclease of LNA-modified DNA oligonucleotides. The experiments revealed that RsaI is an efficient enzyme capable of recognizing and cleaving...

  12. Structural studies on metal-containing enzymes. T4 endonuclease VII and D. gigas formate dehydrogenase

    NARCIS (Netherlands)

    Raaijmakers, H.C.A.

    2001-01-01

    Many biological processes require metal ions, and many of these metal-ion functions involve metalloproteins. The metal ions in metalloproteins are often critical to the protein's function, structure, or stability. This thesis focuses on two of these proteins, bacteriophage T4 endonuclease VII (EndoV

  13. Use of Multiple Restriction Endonucleases for the Enhanced Differentiation of Candida albicans Strains

    OpenAIRE

    Cunningham, M. J.

    2011-01-01

    Using multiple endonuclease restriction enzymes it was possible to distinguish 31 patterns among 33 epidemiologi-cally independent Candida albicans from the oral cavity. This degree of discrimination required the use of three restriction enzymes.Keywords - Candida albicans, RFLP, Electrophoretic patterns, Epidemiology.

  14. Endonuclease modified comet assay for oxidative DNA damage induced by detection of genetic toxiants

    Institute of Scientific and Technical Information of China (English)

    赵健

    2014-01-01

    Objective The aim of this study was to investigate the use of the lesion-specific endonucleases-modifiedcomet assay for analysis of DNA,oxidation in cell lines.Methods DNA breaks and oxidative damage were evaluated by normal alkaline and formamidopyrimidine-DNAglycosylase(FPG)modified comet assays.Cytotoxicity was assessed by MTT method.The human bronchial epi-

  15. Endonuclease activity from tobacco nuclei specific for ultraviolet radiation-damaged DNA

    International Nuclear Information System (INIS)

    Endonuclease activity specific for UV damaged DNA was isolated from tobacco leaf nuclei and detected by relaxation of supercoiled pUC 19 plasmid DNA. The activity did not require divalent cations or ATP. It acted on photoproducts induced by as little as 24 J m−2 of UV-C (primarily 254 nm) radiation. but not on photoproducts produced by UV-B (290–320 nm) radiation in the presence of acetophenone and a N2 atmosphere or by UV-A (320–400 nm) radiation in the presence of 4′-methoxy-methyltrioxsalen in a N2 atmosphere and not on the products of OsO4 oxidation of the DNA. Using end-labeled DNA of defined sequence, it was possible to identify sites in UV-C-irradiated DNA that were cut by the endonuclease preparation: most sites were assocrated with pyrimidine pairs. Cleavage by the tobacco endonuclease was not eliminated by treatment with Escherichia coli photolyase and light, suggesting that the endonuclease did not recognize cyclobutadipyrimidines. (author)

  16. Structural aspects of catalytic mechanisms of endonucleases and their binding to nucleic acids

    Energy Technology Data Exchange (ETDEWEB)

    Zhukhlistova, N. E.; Balaev, V. V.; Lyashenko, A. V.; Lashkov, A. A., E-mail: alashkov83@gmail.com [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)

    2012-05-15

    Endonucleases (EC 3.1) are enzymes of the hydrolase class that catalyze the hydrolytic cleavage of deoxyribonucleic and ribonucleic acids at any region of the polynucleotide chain. Endonucleases are widely used both in biotechnological processes and in veterinary medicine as antiviral agents. Medical applications of endonucleases in human cancer therapy hold promise. The results of X-ray diffraction studies of the spatial organization of endonucleases and their complexes and the mechanism of their action are analyzed and generalized. An analysis of the structural studies of this class of enzymes showed that the specific binding of enzymes to nucleic acids is characterized by interactions with nitrogen bases and the nucleotide backbone, whereas the nonspecific binding of enzymes is generally characterized by interactions only with the nucleic-acid backbone. It should be taken into account that the specificity can be modulated by metal ions and certain low-molecular-weight organic compounds. To test the hypotheses about specific and nonspecific nucleic-acid-binding proteins, it is necessary to perform additional studies of atomic-resolution three-dimensional structures of enzyme-nucleic-acid complexes by methods of structural biology.

  17. Asymmetric quantum cloning machines

    International Nuclear Information System (INIS)

    A family of asymmetric cloning machines for quantum bits and N-dimensional quantum states is introduced. These machines produce two approximate copies of a single quantum state that emerge from two distinct channels. In particular, an asymmetric Pauli cloning machine is defined that makes two imperfect copies of a quantum bit, while the overall input-to-output operation for each copy is a Pauli channel. A no-cloning inequality is derived, characterizing the impossibility of copying imposed by quantum mechanics. If p and p' are the probabilities of the depolarizing channels associated with the two outputs, the domain in (√p,√p')-space located inside a particular ellipse representing close-to-perfect cloning is forbidden. This ellipse tends to a circle when copying an N-dimensional state with N→∞, which has a simple semi-classical interpretation. The symmetric Pauli cloning machines are then used to provide an upper bound on the quantum capacity of the Pauli channel of probabilities px, py and pz. The capacity is proven to be vanishing if (√px, √py, √pz) lies outside an ellipsoid whose pole coincides with the depolarizing channel that underlies the universal cloning machine. Finally, the tradeoff between the quality of the two copies is shown to result from a complementarity akin to Heisenberg uncertainty principle. (author)

  18. Asymmetric inclusion process

    Science.gov (United States)

    Reuveni, Shlomi; Eliazar, Iddo; Yechiali, Uri

    2011-10-01

    We introduce and explore the asymmetric inclusion process (ASIP), an exactly solvable bosonic counterpart of the fermionic asymmetric exclusion process (ASEP). In both processes, random events cause particles to propagate unidirectionally along a one-dimensional lattice of n sites. In the ASEP, particles are subject to exclusion interactions, whereas in the ASIP, particles are subject to inclusion interactions that coalesce them into inseparable clusters. We study the dynamics of the ASIP, derive evolution equations for the mean and probability generating function (PGF) of the sites’ occupancy vector, obtain explicit results for the above mean at steady state, and describe an iterative scheme for the computation of the PGF at steady state. We further obtain explicit results for the load distribution in steady state, with the load being the total number of particles present in all lattice sites. Finally, we address the problem of load optimization, and solve it under various criteria. The ASIP model establishes bridges between statistical physics and queueing theory as it represents a tandem array of queueing systems with (unlimited) batch service, and a tandem array of growth-collapse processes.

  19. Enhancement effect of asymmetry on the thermal conductivity of double-stranded chain systems

    Institute of Scientific and Technical Information of China (English)

    Zhang Mao-Ping; Zhong Wei-Rong; Ai Bao-Quan

    2011-01-01

    Using nonequilibrium molecular dynamics simulations,we study the thermal conductivity of asymmetric double chains.We couple two different single chains through interchain coupling to build three kinds of asymmetric doublestranded chain system:intrachain interaction,external potential,and mass asymmetric double chains.It is reported that asymmetry is helpful in improving the thermal conductivity of the system.We first propose double-heat flux channels to explain the influence of asymmetric structures on the thermal conductivity.The phonon spectral behaviour and finite size effect are also included.

  20. Alternative Asymmetric Stochastic Volatility Models

    NARCIS (Netherlands)

    M. Asai (Manabu); M.J. McAleer (Michael)

    2010-01-01

    textabstractThe stochastic volatility model usually incorporates asymmetric effects by introducing the negative correlation between the innovations in returns and volatility. In this paper, we propose a new asymmetric stochastic volatility model, based on the leverage and size effects. The model is

  1. Engineered Asymmetric Synthetic Vesicles

    Science.gov (United States)

    Lu, Li; Chiarot, Paul

    2013-11-01

    Synthetic vesicles are small, fluid-filled spheres that are enclosed by a bilayer of lipid molecules. They can be used as models for investigating membrane biology and as delivery vehicles for pharmaceuticals. In practice, it is difficult to simultaneously control membrane asymmetry, unilamellarity, vesicle size, vesicle-to-vesicle uniformity, and luminal content. Membrane asymmetry, where each leaflet of the bilayer is composed of different lipids, is of particular importance as it is a feature of most natural membranes. In this study, we leverage microfluidic technology to build asymmetric vesicles at high-throughput. We use the precise flow control offered by microfluidic devices to make highly uniform emulsions, with controlled internal content, that serve as templates to build the synthetic vesicles. Flow focusing, dielectrophoretic steering, and interfacial lipid self-assembly are critical procedures performed on-chip to produce the vesicles. Fluorescent and confocal microscopy are used to evaluate the vesicle characteristics.

  2. Asymmetric black dyonic holes

    Directory of Open Access Journals (Sweden)

    I. Cabrera-Munguia

    2015-04-01

    Full Text Available A 6-parametric asymptotically flat exact solution, describing a two-body system of asymmetric black dyons, is studied. The system consists of two unequal counterrotating Kerr–Newman black holes, endowed with electric and magnetic charges which are equal but opposite in sign, separated by a massless strut. The Smarr formula is generalized in order to take into account their contribution to the mass. The expressions for the horizon half-length parameters σ1 and σ2, as functions of the Komar parameters and of the coordinate distance, are displayed, and the thermodynamic properties of the two-body system are studied. Furthermore, the seven physical parameters satisfy a simple algebraic relation which can be understood as a dynamical scenario, in which the physical properties of one body are affected by the ones of the other body.

  3. Asymmetric twin Dark Matter

    International Nuclear Information System (INIS)

    We study a natural implementation of Asymmetric Dark Matter in Twin Higgs models. The mirroring of the Standard Model strong sector suggests that a twin baryon with mass around 5 GeV is a natural Dark Matter candidate once a twin baryon number asymmetry comparable to the SM asymmetry is generated. We explore twin baryon Dark Matter in two different scenarios, one with minimal content in the twin sector and one with a complete copy of the SM, including a light twin photon. The essential requirements for successful thermal history are presented, and in doing so we address some of the cosmological issues common to many Twin Higgs models. The required interactions we introduce predict signatures at direct detection experiments and at the LHC

  4. Organizing for Asymmetric Collaboration

    DEFF Research Database (Denmark)

    Nielsen, Jørn Flohr; Sørensen, Henrik B.

    meet each other. On the contrary, we assume that asymmetry is both important and normal; moreover, asymmetry should be considered to be more complex than economists indicate with their concept of asymmetric information. Thus, the aim of the paper is to explore how asymmetries related to partners......  The vision of new organizational forms consists of less-organized networks and alliances between organizations, in which collaborative capabilities are assumed to be crucial (Miles et al., 2005). The path to such new forms may go through fragile cooperative efforts. Despite the good will of many......' different motives and different situational factors appear in an interorganizational setting. We classify interfaces according to the symmetry/asymmetry in the respective parent organizations' resources, commitment, and control of representatives and indicate how  classification schemes can be used to...

  5. Annihilating Asymmetric Dark Matter

    CERN Document Server

    Bell, Nicole F; Shoemaker, Ian M

    2014-01-01

    The relic abundance of particle and antiparticle dark matter (DM) need not be vastly different in thermal asymmetric dark matter (ADM) models. By considering the effect of a primordial asymmetry on the thermal Boltzmann evolution of coupled DM and anti-DM, we derive the requisite annihilation cross section. This is used in conjunction with CMB and Fermi-LAT gamma-ray data to impose a limit on the number density of anti-DM particles surviving thermal freeze-out. When the extended gamma-ray emission from the Galactic Center is reanalyzed in a thermal ADM framework, we find that annihilation into $\\tau$ leptons prefer anti-DM number densities 1-4$\\%$ that of DM while the $b$-quark channel prefers 50-100$\\%$.

  6. Conserved structural chemistry for incision activity in structurally non-homologous apurinic/apyrimidinic endonuclease APE1 and endonuclease IV DNA repair enzymes.

    Energy Technology Data Exchange (ETDEWEB)

    Tsutakawa, Susan E.; Shin, David S.; Mol, Clifford D.; Izum, Tadahide; Arvai, Andrew S.; Mantha, Anil K.; Szczesny, Bartosz; Ivanov, Ivaylo N.; Hosfield, David J.; Maiti, Buddhadev; Pique, Mike E.; Frankel, Kenneth A.; Hitomi, Kenichi; Cunningham, Richard P.; Mitra, Sankar; Tainer, John A.

    2013-03-22

    Non-coding apurinic/apyrimidinic (AP) sites in DNA form spontaneously and as DNA base excision repair intermediates are the most common toxic and mutagenic in vivo DNA lesion. For repair, AP sites must be processed by 5' AP endonucleases in initial stages of base repair. Human APE1 and bacterial Nfo represent the two conserved 5' AP endonuclease families in the biosphere; they both recognize AP sites and incise the phosphodiester backbone 5' to the lesion, yet they lack similar structures and metal ion requirements. Here, we determined and analyzed crystal structures of a 2.4 ? resolution APE1-DNA product complex with Mg(2+) and a 0.92 Nfo with three metal ions. Structural and biochemical comparisons of these two evolutionarily distinct enzymes characterize key APE1 catalytic residues that are potentially functionally similar to Nfo active site components, as further tested and supported by computational analyses. We observe a magnesium-water cluster in the APE1 active site, with only Glu-96 forming the direct protein coordination to the Mg(2+). Despite differences in structure and metal requirements of APE1 and Nfo, comparison of their active site structures surprisingly reveals strong geometric conservation of the catalytic reaction, with APE1 catalytic side chains positioned analogously to Nfo metal positions, suggesting surprising functional equivalence between Nfo metal ions and APE1 residues. The finding that APE1 residues are positioned to substitute for Nfo metal ions is supported by the impact of mutations on activity. Collectively, the results illuminate the activities of residues, metal ions, and active site features for abasic site endonucleases.

  7. High performance of junctionless MOSFET with asymmetric gate

    Science.gov (United States)

    Wang, Ying; Tang, Yan; Sun, Ling-ling; Cao, Fei

    2016-09-01

    In this work, we propose a junctionless MOSFET with asymmetric gates (AG-JL MOSFET). This device is a double gate structure with a lateral offset between the gate, and this leads to different characteristic than a conventional double gate structure. Specifically, the asymmetric gate modulates the effective channel length depending on whether the device is in the ON or OFF state, which this leads to more ideal device characteristics. A comprehensive device performance comparison including the ION/IOFF ratio, subthreshold slope (SS), and drain-induced barrier lowering (DIBL) between the proposed device and a conventional device is presented. The proposed device exhibits superior performance when compared a conventional device, and results show that it is also less sensitive to process variations.

  8. Analytical approach to soliton ratchets in asymmetric potentials

    OpenAIRE

    Rodríguez Quintero, Niurka; Sánchez-Rey, Bernardo; Salerno, Mario

    2004-01-01

    We use soliton perturbation theory and collective coordinate ansatz to investigate the mechanism of soliton ratchets in a driven and damped asymmetric double sine-Gordon equation. We show that, at the second order of the perturbation scheme, the soliton internal vibrations can couple {\\it effectively}, in presence of damping, to the motion of the center of mass, giving rise to transport. An analytical expression for the mean velocity of the soliton is derived. The results of our analysis conf...

  9. Rapid single step subcloning procedure by combined action of type II and type IIs endonucleases with ligase

    OpenAIRE

    Klingenspor Martin; Fromme Tobias

    2007-01-01

    Abstract Background The subcloning of a DNA fragment from an entry vector into a destination vector is a routinely performed task in molecular biology labs. Results We here present a novel benchtop procedure to achieve rapid recombination into any destination vector of choice with the sole requirement of an endonuclease recognition site. The method relies on a specifically designed entry vector and the combined action of type II and type IIs endonucleases with ligase. The formulation leads to...

  10. Permeabilization of ultraviolet-irradiated Chinese hamster cells with polyethylene glycol and introduction of ultraviolet endonuclease from Micrococcus luteus.

    OpenAIRE

    Yarosh, D B; Setlow, R B

    1981-01-01

    Chinese hamster V-79 cells were made permeable by treatment with polyethylene glycol and then incubated with a Micrococcus luteus extract containing ultraviolet-specific endonuclease activity. This treatment introduced nicks in irradiated, but not in unirradiated, deoxyribonucleic acid. The nicks remained open for at least 3 h; there was no loss of endonuclease-sensitive sites, and no excision of dimers as measured by chromatography was detected. In addition, there was no increase in ultravio...

  11. UVI31+ is a DNA endonuclease that dynamically localizes to chloroplast pyrenoids in C. reinhardtii.

    Directory of Open Access Journals (Sweden)

    Manish Shukla

    Full Text Available UVI31+ is an evolutionarily conserved BolA family protein. In this study we examine the presence, localization and possible functions of this protein in the context of a unicellular alga, Chlamydomonas reinhardtii. UVI31+ in C. reinhardtii exhibits DNA endonuclease activity and is induced upon UV stress. Further, UVI31+ that normally localizes to the cell wall and pyrenoid regions gets redistributed into punctate foci within the whole chloroplast, away from the pyrenoid, upon UV stress. The observed induction upon UV-stress as well as the endonuclease activity suggests plausible role of this protein in DNA repair. We have also observed that UV31+ is induced in C. reinhardtii grown in dark conditions, whereby the protein localization is enhanced in the pyrenoid. Biomolecular interaction between the purified pyrenoids and UVI31+ studied by NMR demonstrates the involvement of the disordered loop domain of the protein in its interaction.

  12. Does quantum entanglement in DNA synchronize the catalytic centers of type II restriction endonucleases?

    CERN Document Server

    Kurian, P; Lindesay, J

    2014-01-01

    Several living systems have been examined for their apparent optimization of structure and function for quantum behavior at biological length scales. Orthodox type II endonucleases, the largest class of restriction enzymes, recognize four-to-eight base pair sequences of palindromic DNA, cut both strands symmetrically, and act without an external metabolite such as ATP. While it is known that these enzymes induce strand breaks by attacking phosphodiester bonds, what remains unclear is the mechanism by which cutting occurs in concert at the catalytic centers. Previous studies indicate the primacy of intimate DNA contacts made by the specifically bound enzyme in coordinating the two synchronized cuts. We propose that collective electronic behavior in the DNA helix generates coherent oscillations, quantized through boundary conditions imposed by the endonuclease, that provide the energy required to break two phosphodiester bonds. Such quanta may be preserved in the presence of thermal noise and electromagnetic in...

  13. Metal rolling - Asymmetrical rolling process

    Science.gov (United States)

    Alexa, V.; Raţiu, S.; Kiss, I.

    2016-02-01

    The development of theory and practice related to the asymmetric longitudinal rolling process is based on the general theory of metalworking by pressure and symmetric rolling theory, to which a large number of scientists brought their contribution. The rolling of metal materials was a serious problem throughout history, either economically or technically, because the plating technologies enabled the consumption of raw materials (scarce and expensive) to be reduced, while improving the mechanical properties. Knowing the force parameters related to asymmetric rolling leads to the optimization of energy and raw material consumption. This paper presents data on symmetric rolling process, in order to comparatively highlight the particularities of the asymmetric process.

  14. Related homing endonucleases I-BmoI and I-TevI use different strategies to cleave homologous recognition sites.

    Science.gov (United States)

    Edgell, D R; Shub, D A

    2001-07-01

    A typical homing endonuclease initiates mobility of its group I intron by recognizing DNA both upstream and downstream of the intron insertion site of intronless alleles, preventing the endonuclease from binding and cleaving its own intron-containing allele. Here, we describe a GIY-YIG family homing endonuclease, I-BmoI, that possesses an unusual recognition sequence, encompassing 1 base pair upstream but 38 base pairs downstream of the intron insertion site. I-BmoI binds intron-containing and intronless substrates with equal affinity but can nevertheless discriminate between the two for cleavage. I-BmoI is encoded by a group I intron that interrupts the thymidylate synthase (TS) gene (thyA) of Bacillus mojavensis s87-18. This intron resembles one inserted 21 nucleotides further downstream in a homologous TS gene (td) of Escherichia coli phage T4. I-TevI, the T4 td intron-encoded GIY-YIG endonuclease, is very similar to I-BmoI, but each endonuclease gene is inserted within a different position of its respective intron. Remarkably, I-TevI and I-BmoI bind a homologous stretch of TS-encoding DNA and cleave their intronless substrates in very similar positions. Our results suggest that each endonuclease has independently evolved the ability to distinguish intron-containing from intronless alleles while maintaining the same conserved recognition sequence centered on DNA-encoding active site residues of TS. PMID:11416170

  15. Structure determination and biochemical characterization of a putative HNH endonuclease from Geobacter metallireducens GS-15.

    Directory of Open Access Journals (Sweden)

    Shuang-yong Xu

    Full Text Available The crystal structure of a putative HNH endonuclease, Gmet_0936 protein from Geobacter metallireducens GS-15, has been determined at 2.6 Å resolution using single-wavelength anomalous dispersion method. The structure contains a two-stranded anti-parallel β-sheet that are surrounded by two helices on each face, and reveals a Zn ion bound in each monomer, coordinated by residues Cys38, Cys41, Cys73, and Cys76, which likely plays an important structural role in stabilizing the overall conformation. Structural homologs of Gmet_0936 include Hpy99I endonuclease, phage T4 endonuclease VII, and other HNH endonucleases, with these enzymes sharing 15-20% amino acid sequence identity. An overlay of Gmet_0936 and Hpy99I structures shows that most of the secondary structure elements, catalytic residues as well as the zinc binding site (zinc ribbon are conserved. However, Gmet_0936 lacks the N-terminal domain of Hpy99I, which mediates DNA binding as well as dimerization. Purified Gmet_0936 forms dimers in solution and a dimer of the protein is observed in the crystal, but with a different mode of dimerization as compared to Hpy99I. Gmet_0936 and its N77H variant show a weak DNA binding activity in a DNA mobility shift assay and a weak Mn²⁺-dependent nicking activity on supercoiled plasmids in low pH buffers. The preferred substrate appears to be acid and heat-treated DNA with AP sites, suggesting Gmet_0936 may be a DNA repair enzyme.

  16. Endonuclease G is a novel determinant of cardiac hypertrophy and mitochondrial function

    Czech Academy of Sciences Publication Activity Database

    McDermott-Roe, Ch.; Ye, J.; Ahmed, R.; Sun, X. M.; Serafín, A.; Ware, J.; Bottolo, L.; Muckett, P.; Caňas, X.; Zhang, J.; Rowe, G. C.; Buchan, R.; Lu, H.; Braithwaite, A.; Mancini, M.; Hauton, D.; Martí, R.; García-Arumí, E.; Hubner, N.; Jacob, H.; Serikawa, T.; Zídek, Václav; Papoušek, František; Kolář, František; Cardona, M.; Ruiz-Meana, M.; García-Dorado, D.; Comella, J. X.; Felkin, L. E.; Barton, P. J. R.; Arany, Z.; Pravenec, Michal; Petretto, E.; Sanchis, D.; Cook, S.A.

    2011-01-01

    Roč. 478, č. 7367 (2011), s. 114-118. ISSN 0028-0836 R&D Projects: GA MŠk(CZ) 1M0520; GA ČR(CZ) GA301/08/0166 Institutional research plan: CEZ:AV0Z50110509 Keywords : left ventricular hypertrophy * endonuclease G * mitochondrial dysfunction Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 36.280, year: 2011

  17. RsaI: a new sequence-specific endonuclease activity from Rhodopseudomonas sphaeroides.

    OpenAIRE

    Lynn, S P; Cohen, L K; Kaplan, S; Gardner, J F

    1980-01-01

    A new type II sequence-specific endonuclease, RsaI, has been identified from Rhodopseudomonas sphaeroides strain 28/5. An RsaI purification scheme that yields enzyme which is free of contaminating exonuclease and phosphatase activities after a single column fractionation has been developed. The enzyme recognized the tetranucleotide sequence 5'-GTAC-3' and cleaved between the T and A, thereby generating flush ends. RsaI should be extremely useful in deoxyribonucleic acid sequencing experiments.

  18. Mitochondrial Targeted Endonuclease III DNA Repair Enzyme Protects against Ventilator Induced Lung Injury in Mice

    OpenAIRE

    Masahiro Hashizume; Marc Mouner; Joshua M. Chouteau; Gorodnya, Olena M.; Ruchko, Mykhaylo V.; Wilson, Glenn L.; Gillespie, Mark N.; Parker, James C.

    2014-01-01

    The mitochondrial targeted DNA repair enzyme, 8-oxoguanine DNA glycosylase 1, was previously reported to protect against mitochondrial DNA (mtDNA) damage and ventilator induced lung injury (VILI). In the present study we determined whether mitochondrial targeted endonuclease III (EndoIII) which cleaves oxidized pyrimidines rather than purines from damaged DNA would also protect the lung. Minimal injury from 1 h ventilation at 40 cmH2O peak inflation pressure (PIP) was reversed by EndoIII pret...

  19. A ribonucleoprotein complex protects the interleukin-6 mRNA from degradation by distinct herpesviral endonucleases.

    Directory of Open Access Journals (Sweden)

    Mandy Muller

    2015-05-01

    Full Text Available During lytic Kaposi's sarcoma-associated herpesvirus (KSHV infection, the viral endonuclease SOX promotes widespread degradation of cytoplasmic messenger RNA (mRNA. However, select mRNAs escape SOX-induced cleavage and remain robustly expressed. Prominent among these is interleukin-6 (IL-6, a growth factor important for survival of KSHV infected B cells. IL-6 escape is notable because it contains a sequence within its 3' untranslated region (UTR that can confer protection when transferred to a SOX-targeted mRNA, and thus overrides the endonuclease targeting mechanism. Here, we pursued how this protective RNA element functions to maintain mRNA stability. Using affinity purification and mass spectrometry, we identified a set of proteins that associate specifically with the protective element. Although multiple proteins contributed to the escape mechanism, depletion of nucleolin (NCL most severely impacted protection. NCL was re-localized out of the nucleolus during lytic KSHV infection, and its presence in the cytoplasm was required for protection. After loading onto the IL-6 3' UTR, NCL differentially bound to the translation initiation factor eIF4H. Disrupting this interaction, or depleting eIF4H, reinstated SOX targeting of the RNA, suggesting that interactions between proteins bound to distant regions of the mRNA are important for escape. Finally, we found that the IL-6 3' UTR was also protected against mRNA degradation by the vhs endonuclease encoded by herpes simplex virus, despite the fact that its mechanism of mRNA targeting is distinct from SOX. These findings highlight how a multitude of RNA-protein interactions can impact endonuclease targeting, and identify new features underlying the regulation of the IL-6 mRNA.

  20. A ribonucleoprotein complex protects the interleukin-6 mRNA from degradation by distinct herpesviral endonucleases.

    Science.gov (United States)

    Muller, Mandy; Hutin, Stephanie; Marigold, Oliver; Li, Kathy H; Burlingame, Al; Glaunsinger, Britt A

    2015-05-01

    During lytic Kaposi's sarcoma-associated herpesvirus (KSHV) infection, the viral endonuclease SOX promotes widespread degradation of cytoplasmic messenger RNA (mRNA). However, select mRNAs escape SOX-induced cleavage and remain robustly expressed. Prominent among these is interleukin-6 (IL-6), a growth factor important for survival of KSHV infected B cells. IL-6 escape is notable because it contains a sequence within its 3' untranslated region (UTR) that can confer protection when transferred to a SOX-targeted mRNA, and thus overrides the endonuclease targeting mechanism. Here, we pursued how this protective RNA element functions to maintain mRNA stability. Using affinity purification and mass spectrometry, we identified a set of proteins that associate specifically with the protective element. Although multiple proteins contributed to the escape mechanism, depletion of nucleolin (NCL) most severely impacted protection. NCL was re-localized out of the nucleolus during lytic KSHV infection, and its presence in the cytoplasm was required for protection. After loading onto the IL-6 3' UTR, NCL differentially bound to the translation initiation factor eIF4H. Disrupting this interaction, or depleting eIF4H, reinstated SOX targeting of the RNA, suggesting that interactions between proteins bound to distant regions of the mRNA are important for escape. Finally, we found that the IL-6 3' UTR was also protected against mRNA degradation by the vhs endonuclease encoded by herpes simplex virus, despite the fact that its mechanism of mRNA targeting is distinct from SOX. These findings highlight how a multitude of RNA-protein interactions can impact endonuclease targeting, and identify new features underlying the regulation of the IL-6 mRNA. PMID:25965334

  1. Modulation of the DNA scanning activity of the Micrococcus luteus UV endonuclease

    International Nuclear Information System (INIS)

    Micrococcus luteus UV endonuclease incises DNA at the sites of ultraviolet (UV) light-induced pyrimidine dimers. The mechanism of incision has been previously shown to be a glycosylic bond cleavage at the 5'-pyrimidine of the dimer followed by an apyrimidine endonuclease activity which cleaves the phosphodiester backbone between the pyrimidines. The process by which M. luteus UV endonuclease locates pyrimidine dimers within a population of UV-irradiated plasmids was shown to occur, in vitro, by a processive or sliding mechanism on non-target DNA as opposed to a distributive or random hit mechanism. Form I plasmid DNA containing 25 dimers per molecule was incubated with M. luteus UV endonuclease in time course reactions. The three topological forms of plasmid DNA generated were analyzed by agarose gel electrophoresis. When the enzyme encounters a pyrimidine dimer, it is significantly more likely to make only the glycosylase cleavage as opposed to making both the glycosylic and phosphodiester bond cleavages. Thus, plasmids are accumulated with many alkaline-labile sites relative to single-stranded breaks. In addition, reactions were performed at both pH 8.0 and pH 6.0, in the absence of NaCl, as well as 25,100, and 250 mM NaCl. The efficiency of the DNA scanning reaction was shown to be dependent on both the ionic strength and pH of the reaction. At low ionic strengths, the reaction was shown to proceed by a processive mechanism and shifted to a distributive mechanism as the ionic strength of the reaction increased. Processivity at pH 8.0 is shown to be more sensitive to increases in ionic strength than reactions performed at pH 6.0

  2. Asymmetric Gepner Models (Revisited)

    CERN Document Server

    Gato-Rivera, B

    2010-01-01

    We reconsider a class of heterotic string theories studied in 1989, based on tensor products of N=2 minimal models with asymmetric simple current invariants. We extend this analysis from (2,2) and (1,2) spectra to (0,2) spectra with SO(10) broken to the Standard Model. In the latter case the spectrum must contain fractionally charged particles. We find that in nearly all cases at least some of them are massless. However, we identify a large subclass where the fractional charges are at worst half-integer, and often vector-like. The number of families is very often reduced in comparison to the 1989 results, but there are no new tensor combinations yielding three families. All tensor combinations turn out to fall into two classes: those where the number of families is always divisible by three, and those where it is never divisible by three. We find an empirical rule to determine the class, which appears to extend beyond minimal N=2 tensor products. We observe that distributions of physical quantities such as th...

  3. Investigation of the salicylaldehyde thiosemicarbazone scaffold for inhibition of influenza virus PA endonuclease.

    Science.gov (United States)

    Rogolino, Dominga; Bacchi, Alessia; De Luca, Laura; Rispoli, Gabriele; Sechi, Mario; Stevaert, Annelies; Naesens, Lieve; Carcelli, Mauro

    2015-10-01

    The influenza virus PA endonuclease is an attractive target for the development of novel anti-influenza virus therapeutics, which are urgently needed because of the emergence of drug-resistant viral strains. Reported PA inhibitors are assumed to chelate the divalent metal ion(s) (Mg²⁺ or Mn²⁺) in the enzyme's catalytic site, which is located in the N-terminal part of PA (PA-Nter). In the present work, a series of salicylaldehyde thiosemicarbazone derivatives have been synthesized and evaluated for their ability to inhibit the PA-Nter catalytic activity. Compounds 1-6 have been evaluated against influenza virus, both in enzymatic assays with influenza virus PA-Nter and in virus yield assays in MDCK cells. In order to establish a structure-activity relationship, the hydrazone analogue of the most active thiosemicarbazone has also been evaluated. Since chelation may represent a mode of action of such class of molecules, we studied the interaction of two of them, one with and one without biological activity versus the PA enzyme, towards Mg²⁺, the ion that is probably involved in the endonuclease activity of the heterotrimeric influenza polymerase complex. The crystal structure of the magnesium complex of the o-vanillin thiosemicarbazone ligand 1 is also described. Moreover, docking studies of PA endonuclease with compounds 1 and 2 were performed, to further analyse the possible mechanism of action of this class of inhibitors. PMID:26323352

  4. Real-time quantitative nicking endonuclease-mediated isothermal amplification with small molecular beacons.

    Science.gov (United States)

    Xu, Wentao; Wang, Chenguang; Zhu, Pengyu; Guo, Tianxiao; Xu, Yuancong; Huang, Kunlun; Luo, Yunbo

    2016-04-21

    Techniques of isothermal amplification have recently made great strides, and have generated significant interest in the field of point-of-care detection. Nicking endonuclease-mediated isothermal amplification (NEMA) is an example of simple isothermal technology. In this paper, a real-time quantitative nicking endonuclease-mediated isothermal amplification with small molecular beacons (SMB-NEMA) of improved specificity and sensitivity is described. First, we optimized the prohibition of de novo synthesis by choosing Nt·BstNBI endonuclease. Second, the whole genome was successfully amplified with Nt·BstNBI (6 U), betaine (1 M) and trehalose (60 mM) for the first time. Third, we achieved 10 pg sensitivity for the first time after adding a small molecular beacon that spontaneously undergoes a conformational change when hybridizing to target, and the practical test validated the assay's application. The small molecular beacon has a similar melting temperature to the reaction temperature, but is approximately 10 bp shorter than the length of a traditional molecular beacon. A new threshold regulation was also established for isothermal conditions. Finally, we established a thermodynamic model for designing small molecular beacons. This multistate model is more correct than the traditional algorithm. This theoretical and practical basis will help us to monitor SMB-NEMA in a quantitative way. In summary, our SMB-NEMA method allows the simple, specific and sensitive assessment of isothermal DNA quantification. PMID:27027375

  5. Experimental evidence of resonant tunneling via localized DQW states in an asymmetric triple barrier structure

    Science.gov (United States)

    Velásquez, Rober

    2003-04-01

    In this work we report on field-induced features appearing in the tunneling current traces of a biased asymmetric triple barrier resonant tunneling device in the presence of an in-plane magnetic field. A theoretical model that satisfactorily explains the origin of these features is discussed. The reported data evidences the localized nature of the quantum states in thin layer asymmetric double-quantum-well structures.

  6. Magnetically Modified Asymmetric Supercapacitors Project

    Data.gov (United States)

    National Aeronautics and Space Administration — This Small Business Innovation Research Phase I project is for the development of an asymmetric supercapacitor that will have improved energy density and cycle...

  7. Active Matter on Asymmetric Substrates

    OpenAIRE

    Reichhardt, C. J. Olson; Drocco, J.; Mai, T.; Wan, M. B.; Reichhardt, C.

    2011-01-01

    For collections of particles in a thermal bath interacting with an asymmetric substrate, it is possible for a ratchet effect to occur where the particles undergo a net dc motion in response to an ac forcing. Ratchet effects have been demonstrated in a variety of systems including colloids as well as magnetic vortices in type-II superconductors. Here we examine the case of active matter or self-driven particles interacting with asymmetric substrates. Active matter systems include self-motile c...

  8. Mobile Termination with Asymmetric Networks

    OpenAIRE

    Dewenter, Ralf; Haucap, Justus

    2003-01-01

    This paper examines mobile termination fees and their regulation when networks are asymmetric in size. It is demonstrated that with consumer ignorance about the exact termination rates (a) a mobile network?s termination rate is the higher the smaller the network?s size (as measured through its subscriber base) and (b) asymmetric regulation of only the larger operators in a market will, ce-teris paribus, induce the smaller operators to increase their termination rates. The results are supporte...

  9. Multicatalyst system in asymmetric catalysis

    CERN Document Server

    Zhou, Jian

    2014-01-01

    This book introduces multi-catalyst systems by describing their mechanism and advantages in asymmetric catalysis.  Helps organic chemists perform more efficient catalysis with step-by-step methods  Overviews new concepts and progress for greener and economic catalytic reactions  Covers topics of interest in asymmetric catalysis including bifunctional catalysis, cooperative catalysis, multimetallic catalysis, and novel tandem reactions   Has applications for pharmaceuticals, agrochemicals, materials, and flavour and fragrance

  10. Asymmetric Dark Matter from Leptogenesis

    OpenAIRE

    Falkowski, Adam; Ruderman, Joshua T.; Volansky, Tomer

    2011-01-01

    We present a new realization of asymmetric dark matter in which the dark matter and lepton asymmetries are generated simultaneously through two-sector leptogenesis. The right-handed neutrinos couple both to the Standard Model and to a hidden sector where the dark matter resides. This framework explains the lepton asymmetry, dark matter abundance and neutrino masses all at once. In contrast to previous realizations of asymmetric dark matter, the model allows for a wide range of dark matter mas...

  11. What can pestiviral endonucleases teach us about innate immunotolerance?

    Science.gov (United States)

    Lussi, Carmela; Schweizer, Matthias

    2016-06-01

    Pestiviruses including bovine viral diarrhea virus (BVDV), border disease virus (BDV) and classical swine fever virus (CSFV), occur worldwide and are important pathogens of livestock. A large part of their success can be attributed to the induction of central immunotolerance including B- and T-cells upon fetal infection leading to the generation of persistently infected (PI) animals. In the past few years, it became evident that evasion of innate immunity is a central element to induce and maintain persistent infection. Hence, the viral non-structural protease N(pro) heads the transcription factor IRF-3 for proteasomal degradation, whereas an extracellularly secreted, soluble form of the envelope glycoprotein E(rns) degrades immunostimulatory viral single- and double-stranded RNA, which makes this RNase unique among viral endoribonucleases. We propose that these pestiviral interferon (IFN) antagonists maintain a state of innate immunotolerance mainly pertaining its viral nucleic acids, in contrast to the well-established immunotolerance of the adaptive immune system, which is mainly targeted at proteins. In particular, the unique extension of 'self' to include the viral genome by degrading immunostimulatory viral RNA by E(rns) is reminiscent of various host nucleases that are important to prevent inappropriate IFN activation by the host's own nucleic acids in autoimmune diseases such as Aicardi-Goutières syndrome or systemic lupus erythematosus. This mechanism of "innate tolerance" might thus provide a new facet to the role of extracellular RNases in the sustained prevention of the body's own immunostimulatory RNA to act as a danger-associated molecular pattern that is relevant across various species. PMID:27021825

  12. Asymmetric Flexible Supercapacitor Stack

    Directory of Open Access Journals (Sweden)

    Leela Mohana Reddy A

    2008-01-01

    Full Text Available AbstractElectrical double layer supercapacitor is very significant in the field of electrical energy storage which can be the solution for the current revolution in the electronic devices like mobile phones, camera flashes which needs flexible and miniaturized energy storage device with all non-aqueous components. The multiwalled carbon nanotubes (MWNTs have been synthesized by catalytic chemical vapor deposition technique over hydrogen decrepitated Mischmetal (Mm based AB3alloy hydride. The polymer dispersed MWNTs have been obtained by insitu polymerization and the metal oxide/MWNTs were synthesized by sol-gel method. Morphological characterizations of polymer dispersed MWNTs have been carried out using scanning electron microscopy (SEM, transmission electron microscopy (TEM and HRTEM. An assymetric double supercapacitor stack has been fabricated using polymer/MWNTs and metal oxide/MWNTs coated over flexible carbon fabric as electrodes and nafion®membrane as a solid electrolyte. Electrochemical performance of the supercapacitor stack has been investigated using cyclic voltammetry, galvanostatic charge-discharge, and electrochemical impedance spectroscopy.

  13. Asymmetric Gepner models (revisited)

    Energy Technology Data Exchange (ETDEWEB)

    Gato-Rivera, B. [NIKHEF Theory Group, Kruislaan 409, 1098 SJ Amsterdam (Netherlands)] [Instituto de Fisica Fundamental, CSIC, Serrano 123, Madrid 28006 (Spain); Schellekens, A.N., E-mail: t58@nikhef.n [NIKHEF Theory Group, Kruislaan 409, 1098 SJ Amsterdam (Netherlands)] [Instituto de Fisica Fundamental, CSIC, Serrano 123, Madrid 28006 (Spain)] [IMAPP, Radboud Universiteit, Nijmegen (Netherlands)

    2010-12-11

    We reconsider a class of heterotic string theories studied in 1989, based on tensor products of N=2 minimal models with asymmetric simple current invariants. We extend this analysis from (2,2) and (1,2) spectra to (0,2) spectra with SO(10) broken to the Standard Model. In the latter case the spectrum must contain fractionally charged particles. We find that in nearly all cases at least some of them are massless. However, we identify a large subclass where the fractional charges are at worst half-integer, and often vector-like. The number of families is very often reduced in comparison to the 1989 results, but there are no new tensor combinations yielding three families. All tensor combinations turn out to fall into two classes: those where the number of families is always divisible by three, and those where it is never divisible by three. We find an empirical rule to determine the class, which appears to extend beyond minimal N=2 tensor products. We observe that distributions of physical quantities such as the number of families, singlets and mirrors have an interesting tendency towards smaller values as the gauge groups approaches the Standard Model. We compare our results with an analogous class of free fermionic models. This displays similar features, but with less resolution. Finally we present a complete scan of the three family models based on the triply-exceptional combination (1,16{sup *},16{sup *},16{sup *}) identified originally by Gepner. We find 1220 distinct three family spectra in this case, forming 610 mirror pairs. About half of them have the gauge group SU(3)xSU(2){sub L}xSU(2){sub R}xU(1){sup 5}, the theoretical minimum, and many others are trinification models.

  14. Mm19, a Mycoplasma meleagridis Major Surface Nuclease that Is Related to the RE_AlwI Superfamily of Endonucleases.

    Science.gov (United States)

    Yacoub, Elhem; Ben Abdelmoumen Mardassi, Boutheina

    2016-01-01

    Mycoplasma meleagridis infection is widespread in turkeys, causing poor growth and feathering, airsacculitis, osteodystrophy, and reduction in hatchability. Like most mycoplasma species, M. meleagridis is characterized by its inability to synthesize purine and pyrimidine nucleotides de novo. Consistent with this intrinsic deficiency, we here report the cloning, expression, and characterization of a M. meleagridis gene sequence encoding a major surface nuclease, referred to as Mm19. Mm19 consists of a 1941-bp ORF encoding a 646-amino-acid polypeptide with a predicted molecular mass of 74,825 kDa. BLASTP analysis revealed a significant match with the catalytic/dimerization domain of type II restriction enzymes of the RE_AlwI superfamily. This finding is consistent with the genomic location of Mm19 sequence, which dispalys characteristics of a typical type II restriction-modification locus. Like intact M. meleagridis cells, the E. coli-expressed Mm19 fusion product was found to exhibit a nuclease activity against plasmid DNA, double-stranded DNA, single-stranded DNA, and RNA. The Mm19-associated nuclease activity was consistently enhanced with Mg2+ divalent cations, a hallmark of type II restriction enzymes. A rabbit hyperimmune antiserum raised against the bacterially expressed Mm19 strongly reacted with M. meleagridis intact cells and fully neutralized the surface-bound nuclease activity. Collectively, the results show that M. meleagridis expresses a strong surface-bound nuclease activity, which is the product of a single gene sequence that is related to the RE_AlwI superfamily of endonucleases. PMID:27010566

  15. Hydroxamic acids in asymmetric synthesis.

    Science.gov (United States)

    Li, Zhi; Yamamoto, Hisashi

    2013-02-19

    Metal-catalyzed stereoselective reactions are a central theme in organic chemistry research. In these reactions, the stereoselection is achieved predominantly by introducing chiral ligands at the metal catalyst's center. For decades, researchers have sought better chiral ligands for asymmetric catalysis and have made great progress. Nevertheless, to achieve optimal stereoselectivity and to catalyze new reactions, new chiral ligands are needed. Because of their high metal affinity, hydroxamic acids play major roles across a broad spectrum of fields from biochemistry to metal extraction. Dr. K. Barry Sharpless first revealed their potential as chiral ligands for asymmetric synthesis in 1977: He published the chiral vanadium-hydroxamic-acid-catalyzed, enantioselective epoxidation of allylic alcohols before his discovery of Sharpless asymmetric epoxidation, which uses the titanium-tartrate complex as the chiral reagent. However, researchers have reported few highly enantioselective reactions using metal-hydroxamic acid as catalysts since then. This Account summarizes our research on metal-catalyzed asymmetric epoxidation using hydroxamic acids as chiral ligands. We designed and synthesized a series of new hydroxamic acids, most notably the C2-symmetric bis-hydroxamic acid (BHA) family. V-BHA-catalyzed epoxidation of allylic and homoallylic alcohols achieved higher activity and stereoselectivity than Sharpless asymmetric epoxidation in many cases. Changing the metal species led to a series of unprecedented asymmetric epoxidation reactions, such as (i) single olefins and sulfides with Mo-BHA, (ii) homoallylic and bishomoallylic alcohols with Zr- and Hf-BHA, and (iii) N-alkenyl sulfonamides and N-sulfonyl imines with Hf-BHA. These reactions produce uniquely functionalized chiral epoxides with good yields and enantioselectivities. PMID:23157425

  16. Molecular dynamics simulations of deoxyribonucleic acids and repair enzyme T4 endonuclease V

    International Nuclear Information System (INIS)

    This report describes the results of molecular dynamics (MD) simulation of deoxyribonucleic acids (DNA) and specific repair enzyme T4 endonuclease V. Namely research described here is focused on the examination of specific recognition process, in which this repair enzyme recognizes the damaged site on the DNA molecule-thymine dimer (TD). TD is frequent DNA damage induced by UV radiation in sun light and unless properly repaired it may be mutagenic or lethal for cell, and is also considered among the major causes of skin cancer. T4 endonuclease V is a DNA specific repair enzyme from bacteriophage T4 that catalyzes the first reaction step of TD repair pathway. MD simulations of three molecules - native DNA dodecamer (12 base pairs), DNA of the same sequence of nucleotides as native one but with TD, and repair enzyme T4 endonuclease V - were performed for 1 ns individually for each molecule. Simulations were analyzed to determine the role of electrostatic interaction in the recognition process. It is found that electrostatic energies calculated for amino acids of the enzyme have positive values of around +15 kcal/mol. The electrostatic energy of TD site has negative value of approximately -9 kcal/mol, different from the nearly neutral value of the respective thymines site of the native DNA. The electrostatic interaction of TD site with surrounding water environment differs from the electrostatic interaction of other nucleotides. Differences found between TD site and respective thymines site of native DNA indicate that the electrostatic energy is an important factor contributing to proper recognition of TD site during scanning process in which enzyme scans the DNA. In addition to the electrostatic energy, the important factor in recognition process might be structural complementarity of enzyme and bent DNA with TD. There is significant kink formed around TD site, that is not observed in native DNA. (author)

  17. Asymmetric counterpropagating fronts without flow.

    Science.gov (United States)

    Andrade-Silva, I; Clerc, M G; Odent, V

    2015-06-01

    Out-of-equilibrium systems exhibit domain walls between different states. These walls, depending on the type of connected states, can display rich spatiotemporal dynamics. In this Rapid Communication, we investigate the asymmetrical counterpropagation of fronts in an in-plane-switching cell filled with a nematic liquid crystal. Experimentally, we characterize the different front shapes and propagation speeds. These fronts present dissimilar elastic deformations that are responsible for their asymmetric speeds. Theoretically, using a phenomenological model, we describe the observed dynamics with fair agreement. PMID:26172647

  18. Incompressibility of asymmetric nuclear matter

    OpenAIRE

    Chen, Lie-Wen; Cai, Bao-Jun; Shen, Chun; Ko, Che Ming; Xu, Jun; Li, Bao-An(Department of Physics and Astronomy, Texas A&M University-Commerce, Commerce, TX, 75429-3011, USA)

    2009-01-01

    The incompressibility $K_sat(\\delta)$ of isospin asymmetric nuclear matter at its saturation density. Our results show that in the expansion of $K_sat(\\delta)$ in powers of isospin asymmetry $\\delta$, i.e., $K_sat(\\delta )$=K_{0}+K_{sat,2}\\delta^{2}+K_{sat,4}\\delta^{4}+O(\\delta^{6})$, the magnitude of the 4th-order K_{sat,4} parameter is generally small. The 2nd-order K_{sat,2} parameter thus essentially characterizes the isospin dependence of the incompressibility of asymmetric nuclear matte...

  19. Asymmetric interference in molecular photoprocesses

    International Nuclear Information System (INIS)

    For the first time, the Coulomb continuum effects in asymmetric molecular interference have been studied analytically in photoionization, photorecombination, bremsstrahlung and Compton ionization. Simple, closed-form factors describe the interference not only in monochromatic photoprocesses, but also in the continuous photoelectron spectra generated by attosecond x-ray pulses with a frequency-dependent phase and broad bandwidth. Using HeH2+ molecular ion as an example, we show how the plane wave interference pattern is strongly modified by the two-centre Coulomb continuum. Asymmetric Coulomb continuum introduces qualitative changes in a photoionization process

  20. Asymmetric Baxter-King filter

    OpenAIRE

    Buss, Ginters

    2011-01-01

    The paper proposes an extension of the symmetric Baxter-King band pass filter to an asymmetric Baxter-King filter. The optimal correction scheme of the ideal filter weights is the same as in the symmetric version, i.e, cut the ideal filter at the appropriate length and add a constant to all filter weights to ensure zero weight on zero frequency. Since the symmetric Baxter-King filter is unable to extract the desired signal at the very ends of the series, the extension to an asymmetric filter...

  1. Forces between asymmetric polymer brushes

    OpenAIRE

    Shim, D.F.K.; Cates, M. E.

    1990-01-01

    We study the equilibrium compression of asymmetric polymer brushes grafted on flat plates, under athermal and theta solvent conditions, using a lattice self-consistent field (SCF) approach. We find that the separation d between two plates coated asymmetrically with brushes of type 1 and 2, as a function of the force F, obeys the "bisection rule", d(F) = (d1(F) + d 2(F)) /2 where d1(F)and d 2(F) are the corresponding separations for the symmetric brushes of type 1 and 2 respectively.The bisect...

  2. Research on asymmetric "Jerusalem" unit

    Institute of Scientific and Technical Information of China (English)

    Jun Lu; Jianbo Wang

    2009-01-01

    An asymmetric Jerusalem unit and the frequency selective surface(FSS)structure composed of such units are designed.The transmittance of the designed FSS structure is calculated by mode-matching method and compared with the test results.The comparison results show that the FSS center frequency of the asymmetric structure unit drifts little with the variation of the incident angles of the electromagnetic waves and keeps relatively stable.The research offers a new choice for the application of FSS under the large scanning angle of electromagnetic waves.

  3. Photoalkylated DNA and ultraviolet-irradiated DNA are incised at cytosines by endonuclease III.

    OpenAIRE

    Weiss, R B; Duker, N J

    1986-01-01

    Photoalkylation, the ultraviolet irradiation of DNA with isopropanol and di-tert-butylperoxide, causes a variety of base alterations. These include 8-(2-hydroxy-2-propyl)guanines, 8-(2-hydroxy-2-propyl)adenines and thymine dimers. An E. coli endonuclease against photoalkylated DNA was assayed by conversion of superhelical PM2 phage DNA to the nicked form. Enzyme activities were compared between extracts of strain BW9109 (xth-), lacking exonuclease III activity, and strain BW434 (xth-,nth-), d...

  4. DNA interrogation by the CRISPR RNA-guided endonuclease Cas9

    OpenAIRE

    Sternberg, Samuel H.; Redding, Sy; Jinek, Martin; Greene, Eric C.; Doudna, Jennifer A.

    2014-01-01

    The CRISPR-associated enzyme Cas9 is an RNA-guided endonuclease that uses RNA:DNA base-pairing to target foreign DNA in bacteria. Cas9:guide RNA complexes are also effective genome engineering agents in animals and plants. Here we use single-molecule and bulk biochemical experiments to determine how Cas9:RNA interrogates DNA to find specific cleavage sites. We show that both binding and cleavage of DNA by Cas9:RNA require recognition of a short trinucleotide protospacer adjacent motif (PAM). ...

  5. The endonuclease VIII-like proteins: new targets in the treatment of ischemic stroke?

    Directory of Open Access Journals (Sweden)

    Long-Xiu Yang

    2015-01-01

    Full Text Available Oxidative deoxyribonucleic acid (DNA damage is one of the major causes of neuronal injury in ischemia. The endonuclease VIII-like (NEIL DNA glycosylases have a specific role in recognition and removal of oxidative DNA damage. The NEIL family includes NEIL1, NEIL2, and NEIL3, that differ in substrate specificity, catalytic efficiency, and subcellular/tissue distribution. This opens for a situation-dependent phenotype in their absence. In this review, we will discuss the current knowledge on the involvement of the NEILs in ischemic stroke and discuss the potential of these enzymes to serve as new targets in the treatment of ischemic stroke.

  6. Identification of potential influenza virus endonuclease inhibitors through virtual screening based on the 3D-QSAR model.

    Science.gov (United States)

    Kim, J; Lee, C; Chong, Y

    2009-01-01

    Influenza endonucleases have appeared as an attractive target of antiviral therapy for influenza infection. With the purpose of designing a novel antiviral agent with enhanced biological activities against influenza endonuclease, a three-dimensional quantitative structure-activity relationships (3D-QSAR) model was generated based on 34 influenza endonuclease inhibitors. The comparative molecular similarity index analysis (CoMSIA) with a steric, electrostatic and hydrophobic (SEH) model showed the best correlative and predictive capability (q(2) = 0.763, r(2) = 0.969 and F = 174.785), which provided a pharmacophore composed of the electronegative moiety as well as the bulky hydrophobic group. The CoMSIA model was used as a pharmacophore query in the UNITY search of the ChemDiv compound library to give virtual active compounds. The 3D-QSAR model was then used to predict the activity of the selected compounds, which identified three compounds as the most likely inhibitor candidates. PMID:19343586

  7. Catalytic asymmetric umpolung reactions of imines.

    Science.gov (United States)

    Wu, Yongwei; Hu, Lin; Li, Zhe; Deng, Li

    2015-07-23

    The carbon-nitrogen double bonds in imines are fundamentally important functional groups in organic chemistry. This is largely due to the fact that imines act as electrophiles towards carbon nucleophiles in reactions that form carbon-carbon bonds, thereby serving as one of the most widely used precursors for the formation of amines in both synthetic and biosynthetic settings. If the carbon atom of the imine could be rendered electron-rich, the imine could react as a nucleophile instead of as an electrophile. Such a reversal in the electronic characteristics of the imine functionality would facilitate the development of new chemical transformations that convert imines into amines via carbon-carbon bond-forming reactions with carbon electrophiles, thereby creating new opportunities for the efficient synthesis of amines. The development of asymmetric umpolung reactions of imines (in which the imines act as nucleophiles) remains uncharted territory, in spite of the far-reaching impact such reactions would have in organic synthesis. Here we report the discovery and development of new chiral phase-transfer catalysts that promote the highly efficient asymmetric umpolung reactions of imines with the carbon electrophile enals. These catalysts mediate the deprotonation of imines and direct the 2-azaallyl anions thus formed to react with enals in a highly chemoselective, regioselective, diastereoselective and enantioselective fashion. The reaction tolerates a broad range of imines and enals, and can be carried out in high yield with as little as 0.01 mole per cent catalyst with a moisture- and air-tolerant operational protocol. These umpolung reactions provide a conceptually new and practical approach to chiral amino compounds. PMID:26201597

  8. A new label-free and turn-on strategy for endonuclease detection using a DNA-silver nanocluster probe.

    Science.gov (United States)

    Tian, Xue; Kong, Xiang-Juan; Zhu, Zi-Mao; Chen, Ting-Ting; Chu, Xia

    2015-01-01

    Endonuclease plays a vital role in a variety of biological processes and the assay of endonuclease activity and inhibitors is of high importance in the fields ranging from biotechnology to pharmacology. Howerer, traditional techniques usually suffer from time intensive, laborious, and cost-expensive. This work aims to develop a facile and sensitive method for endonuclease activity assay by making use of the fluorescence enhancement effect when DNA-silver nanoclusters (DNA-Ag NCs) are in proximity to guanine-rich DNA sequences. The system mainly consists of block DNA (B-DNA), G-DNA and Ag-DNA. B-DNA serves as the substrate of the endonuclease (S1 nuclease as the model enzyme). G-DNA, which is predesigned entirely complementary to B strand, contains a guanine-rich overhang sequence and hybridization part at the 5'-end. Ag-DNA involves a sequence for Ag NCs synthesis and a sequence complementary to the hybridization part of the G-DNA. In the "off" state, B-DNA plays the role as a blocker that inhibit the proximity between Ag NCs and guanine-rich DNA sequences, resulting in a low fluorescence readout. However, if S1 nuclease is introduced into the system, B-DNA was cleaved into mono- or short-oligonucleotides fragments, which could not hybridize with G-DNA. As a result, the subsequent addition of DNA-Ag NCs could bring guanine-rich DNA sequences close to the Ag NCs, accompanied by a significant fluorescence enhancement. Therefore, endonuclease activity could be successfully quantified by monitoring the variation in fluorescence intensity. In addition, this approach can also be applied for inhibitor screening of endonuclease. This label-free and turn-on fluorescent assays employing the mechanism proposed here for the detection of nuclease and inhibitors turn out to be sensitive, selective, and convenient. PMID:25281081

  9. JET and COMPASS asymmetrical disruptions

    Czech Academy of Sciences Publication Activity Database

    Gerasimov, S.N.; Abreu, P.; Baruzzo, M.; Drozdov, V.; Dvornova, A.; Havlíček, Josef; Hender, T.C.; Hronová-Bilyková, Olena; Kruezi, U.; Li, X.; Markovič, Tomáš; Pánek, Radomír; Rubinacci, G.; Tsalas, M.; Ventre, S.; Villone, F.; Zakharov, L.E.

    2015-01-01

    Roč. 55, č. 11 (2015), s. 113006-113006. ISSN 0029-5515 R&D Projects: GA MŠk(CZ) LM2011021 Institutional support: RVO:61389021 Keywords : tokamak * asymmetrical disruption * JET * COMPASS Subject RIV: BL - Plasma and Gas Discharge Physics Impact factor: 3.062, year: 2014

  10. Synthesis of Asymmetric Propanetriol Analogues

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    From natural tartaric acid, (R)-2-benzyloxy-3-(2-tetrahydropyranyloxy) propanol 3 was designed and synthesized, and (R)-2-benzyloxy-3-(4-methoxybenzyloxy) propanol 7 was prepared in a new method. They can be used as chiral synthons of lysophosphatidic acid and other compounds with asymmetric propanetriol backbone.

  11. Asymmetrical Switch Costs in Children

    Science.gov (United States)

    Ellefson, Michelle R.; Shapiron, Laura R.; Chater, Nick

    2006-01-01

    Switching between tasks produces decreases in performance as compared to repeating the same task. Asymmetrical switch costs occur when switching between two tasks of unequal difficulty. This asymmetry occurs because the cost is greater when switching to the less difficult task than when switching to the more difficult task. Various theories about…

  12. Asymmetric Synthesis via Chiral Aziridines

    DEFF Research Database (Denmark)

    Tanner, David Ackland; Harden, Adrian; Wyatt, Paul; Andersson, Pher G.; Johansson, Fredrik

    1996-01-01

    A series of chiral bis(aziridines) has been synthesised and evaluated as chelating ligands for a variety of asymmetric transformations mediated by metals [Os (dihydroxylation), Pd (allylic alkylation) Cu (cyclopropanation and aziridination, Li (1,2-addition of organolithiums to imines)]. In the...

  13. Identification of a novel site specific endonuclease produced by Mycoplasma fermentans: discovery while characterizing DNA binding proteins in T lymphocyte cell lines.

    OpenAIRE

    Halden, N F; Wolf, J B; Leonard, W J

    1989-01-01

    We have discovered a new restriction endonuclease, MfeI, in nuclear extracts from T cells contaminated with Mycoplasma fermentans. This endonuclease was identified while studying proteins binding to the interleukin-2 receptor alpha chain gene promoter. MfeI cuts at the recognition sequence C'AATTG generating EcoRI compatible cohesive ends. Potential applications are discussed.

  14. African swine fever virus AP endonuclease is a redox-sensitive enzyme that repairs alkylating and oxidative damage to DNA

    OpenAIRE

    Redrejo-Rodríguez, Modesto; Alexander A Ishchenko; Saparbaev, Murat K.; Salas, María L.; Salas, José

    2009-01-01

    African swine fever virus (ASFV) encodes an AP endonuclease (pE296R) which is essential for virus growth in swine macrophages. We show here that the DNA repair functions of pE296R (AP endonucleolytic, 3′ → 5′ exonuclease, 3′-diesterase and nucleotide incision repair (NIR) activities) and DNA binding are inhibited by reducing agents. Protein pE296R contains one intramolecular disulfide bond, whose disruption by reducing agents might perturb the interaction of the viral AP endonuclease with the...

  15. Optical mapping of a rice B AC clone using restriction endonuclease and imaging with fluorescent microscopy at single molecule level

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    A method of constructing restriction map by optical mapping and single molecule fluorescent microscopy is described. DNA molecules were aligned and adsorbed on a glass coverslip surface by a mbdified "molecular combing"technique, and then the surface-immobilized DNAs were cleaved in situ with a restriction endonuclease. Individual DNA molecules digested by the endonuclease EcoR I were observable with fluorescent microscopy. Using optical mapping, a physical map of a rice bacterial artificial chromosome clone was constructed. This method will facilitate genomic mapping and tracing the dynamic process in real time at a single molecule level with fluorescence microscopy.

  16. Permeabilization of ultraviolet-irradiated chinese hamster cells with polyethylene glycol and introduction of ultraviolet endonuclease from Micrococcus luteus

    International Nuclear Information System (INIS)

    Chinese hamster V-79 cells were made permeable by treatment with polyethylene glycol and then incubated with a Micrococcus luteus extract containing ultraviolet-specific endonuclease activity. This treatment introduced nicks in irradiated, but not in unirradiated, deoxyribonucleic acid. The nicks remained open for at least 3 h; there was no loss of endonuclease-sensitive sites, and no excision of dimers as measured by chromatography was detected. In addition, there was no increase in ultraviolet resistance in treated cells. This suggests that the absence of a significant amount of excision repair in rodent cells is due to the lack of both incision and excision capacity

  17. Characterization of DNA binding activities of over-expressed kpnI restriction endonuclease and modification methylase

    OpenAIRE

    Chandrashekaran, Siddamadappa; Babu, Padmanabhan; Nagaraja, Valakunja

    1999-01-01

    The genes encoding the KpnI restriction endonuclease and methyltransferase from Klebsiella pneumoniae have been cloned and expressed in Escherchia coli using a two plasmid strategy. The gene for KpnI methylase with its promoter was cloned and expressed in pACYC184. Even though the methylase clone is in a low copy number plasmid pACMK, high level expression of methylase is achieved. A hyper-expressing clone of KpnI endonuclease, pETRK was engineered by cloning the R gene into the T7 expression...

  18. Intron-encoded homing endonuclease I-TevI also functions as a transcriptional autorepressor.

    Science.gov (United States)

    Edgell, David R; Derbyshire, Victoria; Van Roey, Patrick; LaBonne, Stephen; Stanger, Matthew J; Li, Zhong; Boyd, Thomas M; Shub, David A; Belfort, Marlene

    2004-10-01

    Customary binding sites of intron-encoded homing endonucleases lie within cognate intronless alleles, at the so-called homing sites. Here, we describe a novel, high-affinity binding site for I-TevI endonuclease, encoded within the group I td intron of phage T4. This site is an operator that overlaps the T4 late promoter, which drives I-TevI expression from within the td intron. I-TevI binds the operator and homing sites with equal affinity, and functions as a transcriptional autorepressor. Distinct sequence and spacing requirements of the catalytic domain result in reduced cleavage activity on operator DNA. Crystallographic studies showed that the overall interactions of the DNA-binding domain with the operator and homing sites are similar, but have some different hydrogen-bonding contacts. We present a model in which the flexibility in protein-DNA interactions allows I-TevI to bind variant intronless alleles to promote intron mobility while facilitating its function in autorepression, and thereby persistence in its host. PMID:15361856

  19. Atypical myxomatosis--virus isolation, experimental infection of rabbits and restriction endonuclease analysis of the isolate.

    Science.gov (United States)

    Psikal, I; Smíd, B; Rodák, L; Valícek, L; Bendová, J

    2003-08-01

    Atypical form of myxomatosis, which caused non-lethal and clinically mild disease in domestic rabbits 1 month after immunization with a commercially available vaccine MXT, is described. The isolated myxoma virus designated as Litovel 2 (Li-2) did not induce systemic disease following subcutaneous and intradermal applications in susceptible experimental rabbits but led to the immune response demonstrated by ELISA. No severe disease was induced in those Li-2 inoculated rabbits by challenge with the virulent strains Lausanne (Lu) or Sanar (SA), while the control animals showed nodular form of myxomatosis with lethal course of the illness. Restriction fragment length polymorphism (RFLP) of genomic DNA with KpnI and BamHI endonucleases was used for genetic characterization of the Li-2 isolate, the vaccine strain MXT and both virulent strains Lu and SA, respectively. In general, RFLP analysis has shown to be informative for inferring genetic relatedness between myxoma viruses. Based on restriction endonuclease DNA fragment size distribution, it was evident that the pathogenic strain SA is genetically related to the reference strain Lu and the isolate Li-2 is more related, but not identical, to the vaccination strain MXT. PMID:14628995

  20. Key Players in I-DmoI Endonuclease Catalysis Revealed from Structure and Dynamics.

    Science.gov (United States)

    Molina, Rafael; Besker, Neva; Marcaida, Maria Jose; Montoya, Guillermo; Prieto, Jesús; D'Abramo, Marco

    2016-05-20

    Homing endonucleases, such as I-DmoI, specifically recognize and cleave long DNA target sequences (∼20 bp) and are potentially powerful tools for genome manipulation. However, inefficient and off-target DNA cleavage seriously limits specific editing in complex genomes. One approach to overcome these limitations is to unambiguously identify the key structural players involved in catalysis. Here, we report the E117A I-DmoI mutant crystal structure at 2.2 Å resolution that, together with the wt and Q42A/K120M constructs, is combined with computational approaches to shed light on protein cleavage activity. The cleavage mechanism was related both to key structural effects, such as the position of water molecules and ions participating in the cleavage reaction, and to dynamical effects related to protein behavior. In particular, we found that the protein perturbation pattern significantly changes between cleaved and noncleaved DNA strands when the ions and water molecules are correctly positioned for the nucleophilic attack that initiates the cleavage reaction, in line with experimental enzymatic activity. The proposed approach paves the way for an effective, general, and reliable procedure to analyze the enzymatic activity of endonucleases from a very limited data set, i.e., structure and dynamics. PMID:26909878

  1. Identification and characterization of inhibitors of human apurinic/apyrimidinic endonuclease APE1.

    Directory of Open Access Journals (Sweden)

    Anton Simeonov

    Full Text Available APE1 is the major nuclease for excising abasic (AP sites and particular 3'-obstructive termini from DNA, and is an integral participant in the base excision repair (BER pathway. BER capacity plays a prominent role in dictating responsiveness to agents that generate oxidative or alkylation DNA damage, as well as certain chain-terminating nucleoside analogs and 5-fluorouracil. We describe within the development of a robust, 1536-well automated screening assay that employs a deoxyoligonucleotide substrate operating in the red-shifted fluorescence spectral region to identify APE1 endonuclease inhibitors. This AP site incision assay was used in a titration-based high-throughput screen of the Library of Pharmacologically Active Compounds (LOPAC(1280, a collection of well-characterized, drug-like molecules representing all major target classes. Prioritized hits were authenticated and characterized via two high-throughput screening assays -- a Thiazole Orange fluorophore-DNA displacement test and an E. coli endonuclease IV counterscreen -- and a conventional, gel-based radiotracer incision assay. The top, validated compounds, i.e. 6-hydroxy-DL-DOPA, Reactive Blue 2 and myricetin, were shown to inhibit AP site cleavage activity of whole cell protein extracts from HEK 293T and HeLa cell lines, and to enhance the cytotoxic and genotoxic potency of the alkylating agent methylmethane sulfonate. The studies herein report on the identification of novel, small molecule APE1-targeted bioactive inhibitor probes, which represent initial chemotypes towards the development of potential pharmaceuticals.

  2. Selfhealing of asymmetric Bessel-like modes

    DEFF Research Database (Denmark)

    Israelsen, Stine Møller; Rishøj, Lars Søgaard; Rottwitt, Karsten

    2014-01-01

    We numerically investigate asymmetric Bessel-like modes in an aircladding fiber. The selfhealing ability of asymmetric Bessel-like modes is demonstrated and quantified including the angular dependency of this ability.......We numerically investigate asymmetric Bessel-like modes in an aircladding fiber. The selfhealing ability of asymmetric Bessel-like modes is demonstrated and quantified including the angular dependency of this ability....

  3. Excision repair of gamma-ray-induced alkali-stable DNA lesions with the help of γ-endonuclease from Micrococcus luteus

    International Nuclear Information System (INIS)

    γ-endonuclease Y, an enzyme that hydrolyses phosphodiester bonds at alkali-stable lesions in γ-irradiated (N2, tris buffer) DNA, has been partially purified from Micrococcus luteus. The enzyme has a molecular weight of about 19 000, induces single-strand breaks with 3'OH-5'PO4 termini and contains endonuclease activity towards DNA treated with 7-bromomethylbenz(a)anthracene. γ-endonuclease Y induces breaks in OsO4-treated poly(dA-dT) and apparently is specific towards γ-ray-induced base lesions of the t' type. The complete excision repair of γ-endonuclease Y substrate sites has been performed in vitro by γ-endonuclease Y, DNA polymerase and ligase. (author)

  4. Cyclodextrins in Asymmetric and Stereospecific Synthesis

    Directory of Open Access Journals (Sweden)

    Fliur Macaev

    2015-09-01

    Full Text Available Since their discovery, cyclodextrins have widely been used as green and easily available alternatives to promoters or catalysts of different chemical reactions in water. This review covers the research and application of cyclodextrins and their derivatives in asymmetric and stereospecific syntheses, with their division into three main groups: (1 cyclodextrins promoting asymmetric and stereospecific catalysis in water; (2 cyclodextrins’ complexes with transition metals as asymmetric and stereospecific catalysts; and (3 cyclodextrins’ non-metallic derivatives as asymmetric and stereospecific catalysts. The scope of this review is to systematize existing information on the contribution of cyclodextrins to asymmetric and stereospecific synthesis and, thus, to facilitate further development in this direction.

  5. Ion pumping in nanochannels using an asymmetric electrode array

    OpenAIRE

    Sparreboom, W.; Cucu, C.F.; Eijkel, J.C.T.; Berg, van den, T.J.T.P.; Locascio, L.E.; Gaitan, M.; Paegel, B.M.; Ross, D J; Vreeland, W. N.

    2008-01-01

    We demonstrate an ion pump, consisting of a nanochannel with an AC driven asymmetric electrode array. Our system enables us to actively pump ions using a low driving voltage. In all experiments the electrical double layers are overlapping. Via viscous coupling ion pumping is accompanied by liquid pumping. Actuation below 500 mV at 10 Hz results in a liquid velocity of ~10 μm/s, corresponding to an electrical ion current of ~400 fA. Finite element simulations support the experimental data.

  6. Stable walking with asymmetric legs

    International Nuclear Information System (INIS)

    Asymmetric leg function is often an undesired side-effect in artificial legged systems and may reflect functional deficits or variations in the mechanical construction. It can also be found in legged locomotion in humans and animals such as after an accident or in specific gait patterns. So far, it is not clear to what extent differences in the leg function of contralateral limbs can be tolerated during walking or running. Here, we address this issue using a bipedal spring-mass model for simulating walking with compliant legs. With the help of the model, we show that considerable differences between contralateral legs can be tolerated and may even provide advantages to the robustness of the system dynamics. A better understanding of the mechanisms and potential benefits of asymmetric leg operation may help to guide the development of artificial limbs or the design novel therapeutic concepts and rehabilitation strategies.

  7. Catalytic domain structure and hypothesis for function of GIY-YIG intron endonuclease I-TevI.

    Science.gov (United States)

    Van Roey, Patrick; Meehan, Lisa; Kowalski, Joseph C; Belfort, Marlene; Derbyshire, Victoria

    2002-11-01

    I-TevI, a member of the GIY-YIG family of homing endonucleases, consists of an N-terminal catalytic domain and a C-terminal DNA-binding domain joined by a flexible linker. The GIY-YIG motif is in the N-terminal domain of I-TevI, which corresponds to a phylogenetically widespread catalytic cartridge that is often associated with mobile genetic elements. The crystal structure of the catalytic domain of I-TevI, the first of any GIY-YIG endonuclease, reveals a novel alpha/beta-fold with a central three-stranded antiparallel beta-sheet flanked by three helices. The most conserved and putative catalytic residues are located on a shallow, concave surface and include a metal coordination site. Similarities in the three-dimensional arrangement of the catalytically important residues and the cation-binding site with those of the His-Cys box endonuclease I-PpoI suggest the possibility of mechanistic relationships among these different families of homing endonucleases despite completely different folds. PMID:12379841

  8. Ultraviolet-endonuclease activity in cell extracts of Saccharomyces cerevisiae mutants defective in excision of pyrimidine dimers

    International Nuclear Information System (INIS)

    Cell-free extracts of ultraviolet-sensitive mutants of Saccharomyces cerevisiae defective in excision of pyrimidine dimers, rad1, rad2, rad3, rad4, rad10, and rad16, as well as the extracts of the wild-type strain RAD+, display ultraviolet-endonuclease activity

  9. A newly discovered Bordetella species carries a transcriptionally active CRISPR-Cas with a small Cas9 endonuclease

    Science.gov (United States)

    The Cas9 endonuclease of the Type II-a clustered regularly interspersed short palindromic repeats (CRISPR), of Streptococcus pyogenes (SpCas9) has been adapted as a widely used tool for genome editing and genome engineering. Herein, we describe a gene encoding a novel Cas9 ortholog (BpsuCas9) and th...

  10. Chromosomal aberrations induced by the restriction endonucleases Alu I and Bam HI: comparison with X-rays

    International Nuclear Information System (INIS)

    Dose-effect relationships for the frequencies of polycentric chromosomes induced by the restriction endonucleases Alu I and Bam HI and by X-rays in Chinese hamster ovary (CHO) cells were analyzed and compared. 1 Gy of X-rays produce the same frequency of polycentric chromosomes as 2 units Alu I and 7.9 units Bam HI. (author)

  11. Asymmetrically coupled directed percolation systems

    OpenAIRE

    Noh, Jae Dong; Park, Hyunggyu

    2005-01-01

    We introduce a dynamical model of coupled directed percolation systems with two particle species. The two species $A$ and $B$ are coupled asymmetrically in that $A$ particles branch $B$ particles whereas $B$ particles prey on $A$ particles. This model may describe epidemic spreading controlled by reactive immunization agents. We study nonequilibrium phase transitions with focused attention to the multicritical point where both species undergo the absorbing phase transition simultaneously. In ...

  12. Asymmetric information and macroeconomic dynamics

    Science.gov (United States)

    Hawkins, Raymond J.; Aoki, Masanao; Roy Frieden, B.

    2010-09-01

    We show how macroeconomic dynamics can be derived from asymmetric information. As an illustration of the utility of this approach we derive the equilibrium density, non-equilibrium densities and the equation of motion for the response to a demand shock for productivity in a simple economy. Novel consequences of this approach include a natural incorporation of time dependence into macroeconomics and a common information-theoretic basis for economics and other fields seeking to link micro-dynamics and macro-observables.

  13. Entrepreneurship, Asymmetric Information and Unemployment

    OpenAIRE

    Robin Boadway; Nicolas Marceau; Maurice Marchand; Marianne Vigneault

    1998-01-01

    We examine how three sources of asymmetric information affect the supply of entrepreneurs and unemployment. In the first case, banks cannot observe entrepreneurs' risk of failure so ration credit. This increases the number of entrepreneurs and the level of unemployment. In the second case, firms cannot observe workers' effort so offer a wage above the market clearing one. This results in unemployment and too few entrepreneurs. The final case arises when firms cannot observe workers' abilities...

  14. Asymmetric Microscopic Driving Behavior Theory

    OpenAIRE

    Yeo, Hwasoo

    2008-01-01

    Numerous theories on traffic have been developed as traffic congestion gains more and more interest in our daily life. To model traffic phenomena, many traffic theorists have adopted theories from other fields such as fluid mechanics and thermodynamics. However, their efforts to model the traffic at a microscopic level have not been successful yet. Therefore, to overcome the limitations of the existing theories we propose a microscopic asymmetric traffic theory based on analysis of individual...

  15. Effciency Concern under Asymmetric Information

    OpenAIRE

    Winschel, Evguenia; Zahn, Philipp

    2012-01-01

    Experimental evidence from simple distribution games supports the view that some individuals have a concern for the effciency of allocations. This motive could be important for the implementation of economic policy proposals. In a typical lab experiment, however, individuals have much more information available than outside the lab. We conduct a lab experiment to test whether asymmetric information influences prosocial behavior in a simple non-strategic interaction. In our setting, a dictator...

  16. Two-domain structure of the td intron-encoded endonuclease I-TevI correlates with the two-domain configuration of the homing site.

    Science.gov (United States)

    Derbyshire, V; Kowalski, J C; Dansereau, J T; Hauer, C R; Belfort, M

    1997-02-01

    I-TevI, the T4 td intron-encoded endonuclease, catalyzes the first step in intron homing by making a double-strand break in the intronless allele within a sequence designated the homing site. The 28 kDa enzyme, which interacts with the homing site over a span of 37 bp, binds as a monomer, contacting two domains of the substrate. In this study, limited proteolysis experiments indicate that I-TevI consists of two domains that behave as discrete physical entities as judged by a number of functional and structural criteria. Overexpression clones for each domain were constructed and the proteins were purified. The carboxy-terminal domain has DNA-binding activity coincident with the primary binding region of the homing site and binds with the same affinity as the full-length enzyme. The isolated amino-terminal domain, contains the conserved GIY-YIG motif, consistent with its being the catalytic domain. Furthermore, site-directed mutagenesis of a conserved arginine residue within the extended motif rendered the full-length protein catalytically inactive, although DNA-binding was maintained. This is the first evidence that the GIY-YIG motif is important for catalytic activity. An enzyme with an N-terminal catalytic domain and a C-terminal DNA-binding domain connected by a flexible linker is in accord with the bipartite structure of the homing site. PMID:9048944

  17. Novel repair activities of AlkA (3-methyladenine DNA glycosylase II) and endonuclease VIII for xanthine and oxanine, guanine lesions induced by nitric oxide and nitrous acid

    Science.gov (United States)

    Terato, Hiroaki; Masaoka, Aya; Asagoshi, Kenjiro; Honsho, Akiko; Ohyama, Yoshihiko; Suzuki, Toshinori; Yamada, Masaki; Makino, Keisuke; Yamamoto, Kazuo; Ide, Hiroshi

    2002-01-01

    Nitrosation of guanine in DNA by nitrogen oxides such as nitric oxide (NO) and nitrous acid leads to formation of xanthine (Xan) and oxanine (Oxa), potentially cytotoxic and mutagenic lesions. In the present study, we have examined the repair capacity of DNA N-glycosylases from Escherichia coli for Xan and Oxa. The nicking assay with the defined substrates containing Xan and Oxa revealed that AlkA [in combination with endonuclease (Endo) IV] and Endo VIII recognized Xan in the tested enzymes. The activity (Vmax/Km) of AlkA for Xan was 5-fold lower than that for 7-methylguanine, and that of Endo VIII was 50-fold lower than that for thymine glycol. The activity of AlkA and Endo VIII for Xan was further substantiated by the release of [3H]Xan from the substrate. The treatment of E.coli with N-methyl-N′-nitro-N-nitrosoguanidine increased the Xan-excising activity in the cell extract from alkA+ but not alkA– strains. The alkA and nei (the Endo VIII gene) double mutant, but not the single mutants, exhibited increased sensitivity to nitrous acid relative to the wild type strain. AlkA and Endo VIII also exhibited excision activity for Oxa, but the activity was much lower than that for Xan. PMID:12434002

  18. H. pylori-Induced DNA Strand Breaks Are Introduced by Nucleotide Excision Repair Endonucleases and Promote NF-κB Target Gene Expression

    Directory of Open Access Journals (Sweden)

    Mara L. Hartung

    2015-10-01

    Full Text Available The human bacterial pathogen Helicobacter pylori exhibits genotoxic properties that promote gastric carcinogenesis. H. pylori introduces DNA double strand breaks (DSBs in epithelial cells that trigger host cell DNA repair efforts. Here, we show that H. pylori-induced DSBs are repaired via error-prone, potentially mutagenic non-homologous end-joining. A genome-wide screen for factors contributing to DSB induction revealed a critical role for the H. pylori type IV secretion system (T4SS. Inhibition of transcription, as well as NF-κB/RelA-specific RNAi, abrogates DSB formation. DSB induction further requires β1-integrin signaling. DSBs are introduced by the nucleotide excision repair endonucleases XPF and XPG, which, together with RelA, are recruited to chromatin in a highly coordinated, T4SS-dependent manner. Interestingly, XPF/XPG-mediated DNA DSBs promote NF-κB target gene transactivation and host cell survival. In summary, H. pylori induces XPF/XPG-mediated DNA damage through activation of the T4SS/β1-integrin signaling axis, which promotes NF-κB target gene expression and host cell survival.

  19. The study of responses to 'model' DNA breaks induced by restriction endonucleases in cells and cell-free systems: achievements and difficulties

    International Nuclear Information System (INIS)

    The use of restriction endonucleases (RE) as a means of implicating DNA double-strand breaks (dsb) in cellular responses is reviewed. The introduction of RE into cells leads to many of the responses known to be characteristic of radiation damage -cell killing, chromosomal aberration, oncogenic transformation, gene mutation and amplification. Additionally, radiosensitive cell lines are hypersensitive to RE, including those from the human disorder ataxia-telangiectasia. However, quantitation of response and comparisons of the effectiveness of different RE are difficult, partly because of unknown activity and lifetime of RE in the cell. Re-induced dsb have also been used to reveal molecular mechanisms of repair and misrepair at specific sites in DNA. Dsb have been implicated in recombination processes including those leading to illegitimate rejoining (formation of deletions and rearrangements) at short sequence features in DNA. Also model dsb act as a signal to activate other cellular processes, which may influence or indirectly cause some responses, including cell death. In these signalling responses the detailed chemistry at the break site may not be very important, perhaps explaining why there is considerable overlap in responses to RE and to ionizing radiations. (author)

  20. Lucanthone and its derivative hycanthone inhibit apurinic endonuclease-1 (APE1) by direct protein binding

    Energy Technology Data Exchange (ETDEWEB)

    Naidu, M.; Naidu, M.; Agarwal, R.; Pena, L.A.; Cunha, L.; Mezei, M.; Shen, M.; Wilson, D.M.; Liu, Y.; Sanchez, Z.; Chaudhary, P.; Wilson, S.H.; Waring, M.J.

    2011-09-15

    Lucanthone and hycanthone are thioxanthenone DNA intercalators used in the 1980s as antitumor agents. Lucanthone is in Phase I clinical trial, whereas hycanthone was pulled out of Phase II trials. Their potential mechanism of action includes DNA intercalation, inhibition of nucleic acid biosyntheses, and inhibition of enzymes like topoisomerases and the dual function base excision repair enzyme apurinic endonuclease 1 (APE1). Lucanthone inhibits the endonuclease activity of APE1, without affecting its redox activity. Our goal was to decipher the precise mechanism of APE1 inhibition as a prerequisite towards development of improved therapeutics that can counteract higher APE1 activity often seen in tumors. The IC{sub 50} values for inhibition of APE1 incision of depurinated plasmid DNA by lucanthone and hycanthone were 5 {mu}M and 80 nM, respectively. The K{sub D} values (affinity constants) for APE1, as determined by BIACORE binding studies, were 89 nM for lucanthone/10 nM for hycanthone. APE1 structures reveal a hydrophobic pocket where hydrophobic small molecules like thioxanthenones can bind, and our modeling studies confirmed such docking. Circular dichroism spectra uncovered change in the helical structure of APE1 in the presence of lucanthone/hycanthone, and notably, this effect was decreased (Phe266Ala or Phe266Cys or Trp280Leu) or abolished (Phe266Ala/Trp280Ala) when hydrophobic site mutants were employed. Reduced inhibition by lucanthone of the diminished endonuclease activity of hydrophobic mutant proteins (as compared to wild type APE1) supports that binding of lucanthone to the hydrophobic pocket dictates APE1 inhibition. The DNA binding capacity of APE1 was marginally inhibited by lucanthone, and not at all by hycanthone, supporting our hypothesis that thioxanthenones inhibit APE1, predominantly, by direct interaction. Finally, lucanthone-induced degradation was drastically reduced in the presence of short and long lived free radical scavengers, e

  1. Asymmetric Wettability Directs Leidenfrost Droplets

    Energy Technology Data Exchange (ETDEWEB)

    Agapov, Rebecca L [ORNL; Boreyko, Jonathan B [ORNL; Briggs, Dayrl P [ORNL; Srijanto, Bernadeta R [ORNL; Retterer, Scott T [ORNL; Collier, Pat [ORNL; Lavrik, Nickolay V [ORNL

    2014-01-01

    Leidenfrost phenomena on nano- and microstructured surfaces are of great importance for increasing control over heat transfer in high power density systems utilizing boiling phenomena. They also provide an elegant means to direct droplet motion in a variety of recently emerging fluidic systems. Here, we report the fabrication and characterization of tilted nanopillar arrays (TNPAs) that exhibit directional Leidenfrost water droplets under dynamic conditions, namely on impact with Weber numbers 40 at T 325 C. The batch fabrication of the TNPAs was achieved by glancing-angle anisotropic reactive ion etching of a thermally dewet platinum mask, with mean pillar diameters of 100 nm and heights of 200-500 nm. In contrast to previously implemented macro- and microscopic Leidenfrost ratchets, our TNPAs induce no preferential directional movement of Leidenfrost droplets under conditions approaching steady-state film boiling, suggesting that the observed droplet directionality is not a result of asymmetric vapor flow. Using high-speed imaging, phase diagrams were constructed for the boiling behavior upon impact for droplets falling onto TNPAs, straight nanopillar arrays, and smooth silicon surfaces. The asymmetric impact and directional trajectory of droplets was exclusive to the TNPAs for impacts corresponding to the transition boiling regime, revealing that asymmetric wettability upon impact is the mechanism for the droplet directionality.

  2. Alternative nucleophilic substrates for the endonuclease activities of human immunodeficiency virus type 1 integrase

    Energy Technology Data Exchange (ETDEWEB)

    Ealy, Julie B. [Department of Medicine, Penn State College of Medicine, Milton S. Hershey Medical Center, 500 University Drive, PO Box 850, Mail Services H036, Hershey, PA 17033 (United States); Department of Chemistry, Penn State Lehigh Valley, 2809 E. Saucon Valley Road, Center Valley, PA 18034 (United States); Sudol, Malgorzata [Department of Medicine, Penn State College of Medicine, Milton S. Hershey Medical Center, 500 University Drive, PO Box 850, Mail Services H036, Hershey, PA 17033 (United States); Krzeminski, Jacek; Amin, Shantu [Department of Pharmacology, Penn State College of Medicine, Milton S. Hershey Medical Center, 500 University Drive, Hershey, PA 17033 (United States); Katzman, Michael, E-mail: mkatzman@psu.edu [Department of Medicine, Penn State College of Medicine, Milton S. Hershey Medical Center, 500 University Drive, PO Box 850, Mail Services H036, Hershey, PA 17033 (United States); Department of Microbiology and Immunology, Penn State College of Medicine, Milton S. Hershey Medical Center, 500 University Drive, Hershey, PA 17033 (United States)

    2012-11-10

    Retroviral integrase can use water or some small alcohols as the attacking nucleophile to nick DNA. To characterize the range of compounds that human immunodeficiency virus type 1 integrase can accommodate for its endonuclease activities, we tested 45 potential electron donors (having varied size and number or spacing of nucleophilic groups) as substrates during site-specific nicking at viral DNA ends and during nonspecific nicking reactions. We found that integrase used 22 of the 45 compounds to nick DNA, but not all active compounds were used for both activities. In particular, 13 compounds were used for site-specific and nonspecific nicking, 5 only for site-specific nicking, and 4 only for nonspecific nicking; 23 other compounds were not used for either activity. Thus, integrase can accommodate a large number of nucleophilic substrates but has selective requirements for its different activities, underscoring its dynamic properties and providing new information for modeling and understanding integrase.

  3. Alternative nucleophilic substrates for the endonuclease activities of human immunodeficiency virus type 1 integrase

    International Nuclear Information System (INIS)

    Retroviral integrase can use water or some small alcohols as the attacking nucleophile to nick DNA. To characterize the range of compounds that human immunodeficiency virus type 1 integrase can accommodate for its endonuclease activities, we tested 45 potential electron donors (having varied size and number or spacing of nucleophilic groups) as substrates during site-specific nicking at viral DNA ends and during nonspecific nicking reactions. We found that integrase used 22 of the 45 compounds to nick DNA, but not all active compounds were used for both activities. In particular, 13 compounds were used for site-specific and nonspecific nicking, 5 only for site-specific nicking, and 4 only for nonspecific nicking; 23 other compounds were not used for either activity. Thus, integrase can accommodate a large number of nucleophilic substrates but has selective requirements for its different activities, underscoring its dynamic properties and providing new information for modeling and understanding integrase.

  4. Micrococcus luteus correndonucleases. II. Mechanism of action of two endonucleases specific for DNA containing pyrimidine dimers

    International Nuclear Information System (INIS)

    Py--Py correndonucleases I and II from Micrococcus luteus act exclusively on thymine-thymine, cytosine-cytosine, and thymine-cytosine cyclobutyl dimers in DNA, catalyzing incision 5' to the damage and generating 3'-hydroxyl and 5'-phosphoryl termini. Both enzymes initiate excision of pyrimidine dimers in vitro by correxonucleases and DNA polymerase I. The respective incised DNAs, however, differ in their ability to act as substrate for phage T4 polynucleotide ligase or bacterial alkaline phosphatase, suggesting that each endonuclease is specific for a conformationally unique site. The possibility that their respective action generates termini which represent different degrees of single strandedness is suggested by the unequal protection by Escherichia coli binding protein from the hydrolytic action of exonuclease VII

  5. Sequential and Multistep Substrate Interrogation Provides the Scaffold for Specificity in Human Flap Endonuclease 1

    KAUST Repository

    Sobhy, M.

    2013-06-06

    Human flap endonuclease 1 (FEN1), one of the structure-specific 5\\' nucleases, is integral in replication, repair, and recombination of cellular DNA. The 5\\' nucleases share significant unifying features yet cleave diverse substrates at similar positions relative to 5\\' end junctions. Using single-molecule Förster resonance energy transfer, we find a multistep mechanism that verifies all substrate features before inducing the intermediary-DNA bending step that is believed to unify 5\\' nuclease mechanisms. This is achieved by coordinating threading of the 5\\' flap of a nick junction into the conserved capped-helical gateway, overseeing the active site, and bending by binding at the base of the junction. We propose that this sequential and multistep substrate recognition process allows different 5\\' nucleases to recognize different substrates and restrict the induction of DNA bending to the last common step. Such mechanisms would also ensure the protection ofDNA junctions from nonspecific bending and cleavage. 2013 The Authors.

  6. Cyanobacterial ribosomal RNA genes with multiple, endonuclease-encoding group I introns

    Directory of Open Access Journals (Sweden)

    Turner Seán

    2007-09-01

    Full Text Available Abstract Background Group I introns are one of the four major classes of introns as defined by their distinct splicing mechanisms. Because they catalyze their own removal from precursor transcripts, group I introns are referred to as autocatalytic introns. Group I introns are common in fungal and protist nuclear ribosomal RNA genes and in organellar genomes. In contrast, they are rare in all other organisms and genomes, including bacteria. Results Here we report five group I introns, each containing a LAGLIDADG homing endonuclease gene (HEG, in large subunit (LSU rRNA genes of cyanobacteria. Three of the introns are located in the LSU gene of Synechococcus sp. C9, and the other two are in the LSU gene of Synechococcus lividus strain C1. Phylogenetic analyses show that these introns and their HEGs are closely related to introns and HEGs located at homologous insertion sites in organellar and bacterial rDNA genes. We also present a compilation of group I introns with homing endonuclease genes in bacteria. Conclusion We have discovered multiple HEG-containing group I introns in a single bacterial gene. To our knowledge, these are the first cases of multiple group I introns in the same bacterial gene (multiple group I introns have been reported in at least one phage gene and one prophage gene. The HEGs each contain one copy of the LAGLIDADG motif and presumably function as homodimers. Phylogenetic analysis, in conjunction with their patchy taxonomic distribution, suggests that these intron-HEG elements have been transferred horizontally among organelles and bacteria. However, the mode of transfer and the nature of the biological connections among the intron-containing organisms are unknown.

  7. EXPRESSION AND DELETION ANALYSIS OF EcoRII ENDONUCLEASE AND METHYLASE GENE

    Institute of Scientific and Technical Information of China (English)

    刘金毅; 赵晓娟; 孟雁; 沈洁; 薛越强; 史顺娣; 蔡有余

    2001-01-01

    Objective. To clone complete EcoRII restriction endonuclease gene (ecoRllR) and methyltransferase gene(ecoRllM) in one ector and to analyze the coordinating expression of this whole R-M system.Methods. Unidirectional deletion subclones were constructed with ExolII. ecoRllR/M genes were preliminari-ly located in the cloned fragment according to the enzyme activities of subclones. Exact deletion sites were deter-mined by sequencing, and transcriptional start sites were determined by S1 mapping.Results. The DNA fragment which was cloned into pBluescript SK + contained intact ecoRIlR gene andecoRllM gene, anc two transcriptional start sites of ecoRllR gene were determined. 132bp to 458bp from 3' endof ecoRllR gene ar.e indispensable to enzyme activities and deletion of 202bp from 3' end of ecoRllM gene madeenzyme lose the capability in DNA protection to resist specific cut with EcoRII endonuclease (EcoRII. R). Dele-tion of the coding ar d flanking sequences of one gene did not affect the expression of the other gene, and the recombi-nants only containing ecoRllR gene appeared to be lethal to dcm+ host.Conclusion. scoRllM gene linking closely to ecoRIIR gene is very important for the existence of the R-M sys-tem in process of evolution, but the key to control EcoRlI R-M order may not exist in transcriptional level .``Liu Jmy,Corresponding author.

  8. Inhibition of DNA restrictive endonucleases by aqueous nanoparticle suspension of methanophosphonate fullerene derivatives and its mechanisms

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Aqueous nanoparticle suspension of fullerene and its derivatives are currently attracting much attention. To determine the effects of aqueous nanoparticle suspension of a mono-methanophosphonate fullerene and bis-methanophosphonate fullerene (denoted as n-MMPF and n-BMPF, respectively) on the activities of DNA restrictive endonucleases, plasmid pEGFP-N1 was cleaved at a single but differently restrictive site by EcoR I, BamH I, and isozymes Cfr9 I and Xma I, respectively. Both n-MMPF and n-BMPF inhibited the activity of EcoR I, while n-BMPF exhibited stronger inhibition than n-MMPF. Addition of n-BMPF into reaction mixtures inhibited the activities of all the four enzymes, and IC50 values for EcoR I, BamH I, Cfr9 I and Xma I were 4.3, >30, 11.7 and 8.3 μmol/L, respectively. When EcoR I was completely inhibited by n-BMPF, addition of excess amounts of pEGFP-N1 could not produce the product linear plasmid; however, increase of EcoR I amounts antagonized EcoR I inhibition of n-BMPF. Two scavengers of reactive oxygen species (ROS), mannitol and sodium azide at the concentrations of 2-10 mmol/L, did not reverse inhibition of n-BMPF, implying that this inhibition probably is not correlated to ROS. These results suggested that aqueous nano-fullerenes might act as inhibitors of DNA restrictive endonucleases.

  9. Distinct facilitated diffusion mechanisms by E. coli Type II restriction endonucleases.

    Science.gov (United States)

    Pollak, Adam J; Chin, Aaron T; Reich, Norbert O

    2014-11-18

    The passive search by proteins for particular DNA sequences involving nonspecific DNA is essential for gene regulation, DNA repair, phage defense, and diverse epigenetic processes. Distinct mechanisms contribute to these searches, and it remains unresolved as to which mechanism or blend of mechanisms best suits a particular protein and, more importantly, its biological role. To address this, we compare the translocation properties of two well-studied bacterial restriction endonucleases (ENases), EcoRI and EcoRV. These dimeric, magnesium-dependent enzymes hydrolyze related sites (EcoRI ENase, 5'-GAATTC-3'; EcoRV ENase, 5'-GATATC-3'), leaving overhangs and blunt DNA segments, respectively. Here, we demonstrate that the extensive sliding by EcoRI ENase, involving sliding up to ∼600 bp prior to dissociating from the DNA, contrasts with a larger reliance on hopping mechanism(s) by EcoRV ENase. The mechanism displayed by EcoRI ENase results in a highly thorough search of DNA, whereas the EcoRV ENase mechanism results in an extended, yet less rigorous, interrogation of DNA sequence space. We describe how these mechanistic distinctions are complemented by other aspects of these endonucleases, such as the 10-fold higher in vivo concentrations of EcoRI ENase compared to that of EcoRV ENase. Further, we hypothesize that the highly diverse enzyme arsenal that bacteria employ against foreign DNA involves seemingly similar enzymes that rely on distinct but complementary search mechanisms. Our comparative approach reveals how different proteins utilize distinct site-locating strategies. PMID:25350874

  10. Incompressibility of asymmetric nuclear matter

    International Nuclear Information System (INIS)

    Using an isospin- and momentum-dependent modified Gogny (MDI) interaction, the Skyrme-Hartree-Fock (SHF) approach, and a phenomenological modified Skyrme-like (MSL) model, we have studied the incompressibility Ksat(δ) of isospin asymmetric nuclear matter at its saturation density. Our results show that in the expansion of Ksat(δ) in powers of isospin asymmetry δ, i.e., Ksat(δ) = K0 + Ksat,2δ2 + Ksat,4δ4 + O(δ6), the magnitude of the 4th-order Ksat,4 parameter is generally small. The 2nd-order Ksat,2 parameter thus essentially characterizes the isospin dependence of the incompressibility of asymmetric nuclear matter at saturation density. Furthermore, the Ksat,2 can be expressed as Ksat,2 = Ksym – 6L – J0/K0 L in terms of the slope parameter L and the curvature parameter Ksym of the symmetry energy and the third-order derivative parameter J0 of the energy of symmetric nuclear matter at saturation density, and we find the higher order J0 contribution to Ksat,2 generally cannot be neglected. Also, we have found a linear correlation between Ksym and L as well as between J0/K0 and K0. Using these correlations together with the empirical constraints on K0 and L, the nuclear symmetry energy Esym(ρ0) at normal nuclear density, and the nucleon effective mass, we have obtained an estimated value of Ksat,2 = -370 ± 120 MeV for the 2nd-order parameter in the isospin asymmetry expansion of the incompressibility of asymmetric nuclear matter at its saturation density. (author)

  11. Asymmetric Information and Consumer Demand

    OpenAIRE

    Ismagilova G. N.; Danilina E. I.; Gafurov I. R.; Ismagilov R. I.; Safiullin L. N.

    2014-01-01

    In the paper study the peculiarities of the formation the consumer demand for durable goods, the so-called «experience goods» in markets with asymmetric information. In the known literature sources studying of the demand is based on the assumption that at the moment of the purchase of goods and services people know exactly what price they are willing to pay for them and what utility they are going to obtain using those goods and services. Consider the signal model in which the initial price a...

  12. Transient Stability During Asymmetrical Faults

    OpenAIRE

    Couturier, Nicolas

    2015-01-01

    This research project has been conducted at RTE in order to study the transient stability after asymmetrical faults. When three-phase short-circuits occur in a network, almost all the electrical power is lost on the relevant line(s). Among all short-circuit types, it is the most drastic event and the issue has to be solved very quickly. But oddly, it is also the easiest problem to solve mathematically speaking. This comes from the fact that the system stays balanced, and equations can be simp...

  13. Phase equilibria in asymmetric mixtures

    International Nuclear Information System (INIS)

    The simplified version of the Perturbed Hard-Chain Theory (SPHCT) is used to compute the phase equilibria and Henry's constants for mixtures in which the molecules are highly asymmetric both in shape and in the intermolecular potential. These mixtures include binary systems such as CO2/hydrocarbons and hydrocarbons/hydrocarbons, which are of particular interest for the oil industry. For this type of mixtures a single parameter (which is calculated from available experimental data of liquid-vapor equilibrium) is introduced. The approach yields results which compare well with the experimental behavior reported in the literature (Author)

  14. Tripartite fully asymmetric universal quantum cloning

    International Nuclear Information System (INIS)

    Full text: We investigate the universal asymmetric cloning of states in a Hilbert space of arbitrary dimension d. We derive the class of optimal and fully asymmetric universal 1 → 3 cloners, which produce three copies, each having a different fidelity. A simple parametric expression for the maximum achievable cloning fidelity triplets will be provided. As a side-product, we also prove the optimality of the 1 → 2 asymmetric cloning machines that have been proposed in the literature. (author)

  15. Enhanced Asymmetric Bilinear Model for Face Recognition

    OpenAIRE

    Wenjuan Gong; Weishan Zhang; Jordi Gonzàlez; Yan Ren; Zhen Li

    2015-01-01

    Bilinear models have been successfully applied to separate two factors, for example, pose variances and different identities in face recognition problems. Asymmetric model is a type of bilinear model which models a system in the most concise way. But seldom there are works exploring the applications of asymmetric bilinear model on face recognition problem with illumination changes. In this work, we propose enhanced asymmetric model for illumination-robust face recognition. Instead of initiali...

  16. On new phenomena of photon from modified double slit experiment

    OpenAIRE

    Liu, Haisheng

    2010-01-01

    A modified double slit experiment of light was implemented. In the experiment, a spatial shape filter is used to manipulate the shape of cross section of laser beam. When this modified laser beam was shined on the double slit, the intensity distribution of laser beam on double slit is asymmetrical. In this way, the laser light was directed to pass through only one or two slits of double slit in different sections. So the which-way information is predetermined before the photons pass through t...

  17. Aberrations in asymmetrical electron lenses

    International Nuclear Information System (INIS)

    Starting from well established knowledge in light-optics we explore the question if electron-optical aberration can be improved in asymmetrical electron lenses. We show that spherical as well as chromatic aberration coefficients are reduced in asymmetric electrostatic einzel lenses when the center electrode is moved away from the center position towards the entrance electrode. Relative improvements up to 40% for both the chromatic and the spherical aberration coefficients can be obtained. We use analytical and numerical calculations to confirm this result for exemplary cases of a lens with fixed length and working distance. The agreement of the two calculation methods is very good. We then derive an estimate for the electron-optical aberration coefficients from light-optics. The derived expressions for chromatic and spherical aberrations are somewhat simpler than the ones derived from electron-optics as they involve integrals only over the electrostatic potential, not over the electron paths. The estimated formulas still agree well with the electron optical calculations. Overall, we are tempted to suggest that the enormous knowledge base of light optics can provide considerable guidance for electron-optical applications. -- Highlights: ► Develops the analogy between light and electron optics in aberration calculations. ► Optimized spherical and chromatic aberrations for an electrostatic einzel lens. ► Comparison between analytic and numerical aberration calculations.

  18. Aberrations in asymmetrical electron lenses.

    Science.gov (United States)

    Fitzgerald, J P S; Word, R C; Könenkamp, R

    2012-08-01

    Starting from well established knowledge in light-optics we explore the question if electron-optical aberration can be improved in asymmetrical electron lenses. We show that spherical as well as chromatic aberration coefficients are reduced in asymmetric electrostatic einzel lenses when the center electrode is moved away from the center position towards the entrance electrode. Relative improvements up to 40% for both the chromatic and the spherical aberration coefficients can be obtained. We use analytical and numerical calculations to confirm this result for exemplary cases of a lens with fixed length and working distance. The agreement of the two calculation methods is very good. We then derive an estimate for the electron-optical aberration coefficients from light-optics. The derived expressions for chromatic and spherical aberrations are somewhat simpler than the ones derived from electron-optics as they involve integrals only over the electrostatic potential, not over the electron paths. The estimated formulas still agree well with the electron optical calculations. Overall, we are tempted to suggest that the enormous knowledge base of light optics can provide considerable guidance for electron-optical applications. PMID:22206603

  19. Excitons in asymmetric quantum wells

    Science.gov (United States)

    Grigoryev, P. S.; Kurdyubov, A. S.; Kuznetsova, M. S.; Ignatiev, I. V.; Efimov, Yu. P.; Eliseev, S. A.; Petrov, V. V.; Lovtcius, V. A.; Shapochkin, P. Yu.

    2016-09-01

    Resonance dielectric response of excitons is studied for the high-quality InGaAs/GaAs heterostructures with wide asymmetric quantum wells (QWs). To highlight effects of the QW asymmetry, we have grown and studied several heterostructures with nominally square QWs as well as with triangle-like QWs. Several quantum confined exciton states are experimentally observed as narrow exciton resonances. A standard approach for the phenomenological analysis of the profiles is generalized by introducing different phase shifts for the light waves reflected from the QWs at different exciton resonances. Good agreement of the phenomenological fit to the experimentally observed exciton spectra for high-quality structures allowed us to reliably obtain parameters of the exciton resonances: the exciton transition energies, the radiative broadenings, and the phase shifts. A direct numerical solution of the Schrödinger equation for the heavy-hole excitons in asymmetric QWs is used for microscopic modeling of the exciton resonances. Remarkable agreement with the experiment is achieved when the effect of indium segregation is taken into account. The segregation results in a modification of the potential profile, in particular, in an asymmetry of the nominally square QWs.

  20. ASYMMETRIC SOLAR POLAR FIELD REVERSALS

    International Nuclear Information System (INIS)

    The solar polar fields reverse because magnetic flux from decaying sunspots moves toward the poles, with a preponderance of flux from the trailing spots. If there is a strong asymmetry, in the sense that most activity is in the northern hemisphere, then that excess flux will move toward the north pole and reverse that pole first. If there is more activity in the south later on, then that flux will help to reverse the south pole. In this way, two humps in the solar activity and a corresponding difference in the time of reversals develop (in the ideal case). Such a difference was originally noted in the very first observation of polar field reversal just after the maximum of the strongly asymmetric solar cycle 19, when the southern hemisphere was most active before sunspot maximum and the south pole duly reversed first, followed by the northern hemisphere more than a year later, when that hemisphere became most active. Solar cycles since then have had the opposite asymmetry, with the northern hemisphere being most active before solar maximum. We show that polar field reversals for these cycles have all happened in the north first, as expected. This is especially noteworthy for the present solar cycle 24. We suggest that the association of two or more peaks of solar activity when separated by hemispheres with correspondingly different times of polar field reversals is a general feature of the cycle, and that asymmetric polar field reversals are simply a consequence of the asymmetry of solar activity.

  1. Asymmetric Laguerre-Gaussian beams

    Science.gov (United States)

    Kovalev, A. A.; Kotlyar, V. V.; Porfirev, A. P.

    2016-06-01

    We introduce a family of asymmetric Laguerre-Gaussian (aLG) laser beams. The beams have been derived via a complex-valued shift of conventional LG beams in the Cartesian plane. While propagating in a uniform medium, the first bright ring of the aLG beam becomes less asymmetric and the energy is redistributed toward peripheral diffraction rings. The projection of the orbital angular momentum (OAM) onto the optical axis is calculated. The OAM is shown to grow quadratically with increasing asymmetry parameter of the aLG beam, which equals the ratio of the shift to the waist radius. Conditions for the OAM becoming equal to the topological charge have been derived. For aLG beams with zero radial index, we have deduced an expression to define the intensity maximum coordinates and shown the crescent-shaped intensity pattern to rotate during propagation. Results of the experimental generation and rotation of aLG beams agree well with theoretical predictions.

  2. Asymmetric Wettability Directs Leidenfrost Droplets

    Science.gov (United States)

    Agapov, Rebecca; Boreyko, Jonathan; Briggs, Dayrl; Srijanto, Bernadeta; Retterer, Scott; Collier, C. Patrick; Lavrik, Nickolay

    2014-03-01

    Exploration of Leidenfrost droplets on nano- and microstructured surfaces are of great importance for increasing control over heat transfer in high power density systems using boiling phenomena. They also provide an elegant way to direct droplet motion in a variety of emerging fluidic systems. Here, we report the fabrication and characterization of tilted nanopillar arrays (TNPAs) that exhibit directional Leidenfrost water droplets under dynamic conditions. The batch fabrication of the TNPAs was achieved by glancing-angle anisotropic reactive ion etching of a thermally dewet platinum mask. In contrast to previously implemented macro- and microscopic Leidenfrost ratchets, our TNPAs induce no preferential directional movement of Leidenfrost droplets under conditions approaching steady-state film boiling. This suggests that the observed droplet directionality is not a result of asymmetric vapor flow. Phase diagrams were constructed for the boiling behavior upon droplet impact onto TNPAs, straight nanopillar arrays, and smooth silicon surfaces. Asymmetric wettability and directional trajectory of droplets was exclusive to the TNPAs for impacts corresponding to the transition boiling regime, revealing this to be the mechanism for the droplet directionality. This work was conducted at the Center for Nanophase Materials Sciences, which is sponsored at Oak Ridge National Lab by the Division of Scientific User Facilities, US Dept. of Energy.

  3. Active matter on asymmetric substrates

    Science.gov (United States)

    Olson Reichhardt, C. J.; Drocco, J.; Mai, T.; Wan, M. B.; Reichhardt, C.

    2011-10-01

    For collections of particles in a thermal bath interacting with an asymmetric substrate, it is possible for a ratchet effect to occur where the particles undergo a net dc motion in response to an ac forcing. Ratchet effects have been demonstrated in a variety of systems including colloids as well as magnetic vortices in type-II superconductors. Here we examine the case of active matter or self-driven particles interacting with asymmetric substrates. Active matter systems include self-motile colloidal particles undergoing catalysis, swimming bacteria, artificial swimmers, crawling cells, and motor proteins. We show that a ratchet effect can arise in this type of system even in the absence of ac forcing. The directed motion occurs for certain particle-substrate interaction rules and its magnitude depends on the amount of time the particles spend swimming in one direction before turning and swimming in a new direction. For strictly Brownian particles there is no ratchet effect. If the particles reflect off the barriers or scatter from the barriers according to Snell's law there is no ratchet effect; however, if the particles can align with the barriers or move along the barriers, directed motion arises. We also find that under certain motion rules, particles accumulate along the walls of the container in agreement with experiment. We also examine pattern formation for synchronized particle motion. We discuss possible applications of this system for self-assembly, extracting work, and sorting as well as future directions such as considering collective interactions and flocking models.

  4. Some Remarks on Asymmetric Syntheses from Recent Studies

    OpenAIRE

    Baba, Naomichi

    1990-01-01

    Some asymmetric syntheses were presented here and discussed briefly including NADH model reactions, phase transfer-catalyzed asymmetric epoxidation, enantiotopic group-selective hydrolysis of a malonic anhydride with alkoxide anion, intramolecular acid-catalyzed lactonizations, catalytic asymmetric Diels-Alder synthesis, asymmetric aldol condensation, chiral homoallyl alcohol synthesis, asymmetric addition of diethylzinc to aldehyde, kinetic resolution of racemic hydroperoxides and binaphthol...

  5. Rapid single step subcloning procedure by combined action of type II and type IIs endonucleases with ligase

    Directory of Open Access Journals (Sweden)

    Klingenspor Martin

    2007-11-01

    Full Text Available Abstract Background The subcloning of a DNA fragment from an entry vector into a destination vector is a routinely performed task in molecular biology labs. Results We here present a novel benchtop procedure to achieve rapid recombination into any destination vector of choice with the sole requirement of an endonuclease recognition site. The method relies on a specifically designed entry vector and the combined action of type II and type IIs endonucleases with ligase. The formulation leads to accumulation of a single stable cloning product representing the desired insert carrying destination vector. Conclusion The described method provides a fast single step procedure for routine subcloning from an entry vector into a series of destination vectors with the same restriction enzyme recognition site.

  6. An analysis of the repair processes in ultraviolet-irradiated Micrococcus luteus using purified ultraviolet-endonuclease

    International Nuclear Information System (INIS)

    The measurement of the frequency of endonucleolytic incisions in ultraviolet-irradiated DNA serves as the test for the presence of pyrimidine dimers. In accordance with this approach, the lysates of three Micrococcus luteus strains containing radioactively labeled chromosomes were treated with purified M. luteus ultraviolet-endonuclease to trace segregation of dimers amongst parental and newly synthesized DNA and their removal during postreplication and excision DNA repair. A considerable proportion of the dimers in all strains tested proved to be insensitive to the action of exogenous incising enzyme. The use of chloramphenicol as an inhibitor of postirradiation protein synthesis in combination with ultraviolet-endonuclease treatment of DNA allowed to reveal at least two alternative pathways of postreplication repair: constitutively active recombinational pathway and inducible nonrecombinational one. (Auth.)

  7. Biological significance of facilitated diffusion in protein-DNA interactions. Applications to T4 endonuclease V-initiated DNA repair

    International Nuclear Information System (INIS)

    Facilitated diffusion along nontarget DNA is employed by numerous DNA-interactive proteins to locate specific targets. Until now, the biological significance of DNA scanning has remained elusive. T4 endonuclease V is a DNA repair enzyme which scans nontarget DNA and processively incises DNA at the site of pyrimidine dimers which are produced by exposure to ultraviolet (UV) light. In this study we tested the hypothesis that there exists a direct correlation between the degree of processivity of wild type and mutant endonuclease V molecules and the degree of enhanced UV resistance which is conferred to repair-deficient Eshcerichia coli. This was accomplished by first creating a series of endonuclease V mutants whose in vitro catalytic activities were shown to be very similar to that of the wild type enzyme. However, when the mechanisms by which these enzymes search nontarget DNA for its substrate were analyzed in vitro and in vivo, the mutants displayed varying degrees of nontarget DNA scanning ranging from being nearly as processive as wild type to randomly incising dimers within the DNA population. The ability of these altered endonuclease V molecules to enhance UV survival in DNA repair-deficient E. coli then was assessed. The degree of enhanced UV survival was directly correlated with the level of facilitated diffusion. This is the first conclusive evidence directly relating a reduction of in vivo facilitated diffusion with a change in an observed phenotype. These results support the assertion that the mechanisms which DNA-interactive proteins employ in locating their target sites are of biological significance

  8. An investigation of enzootic Glasser's disease in a specific-pathogen-free grower-finisher facility using restriction endonuclease analysis

    OpenAIRE

    Smart, Nonie L.; Hurnik, Daniel; MacInnes, Janet I.

    1993-01-01

    Enzootic Glassers's disease was investigated to study the epidemiology of the disease strains on a farm where it presented a problem. Restriction endonuclease fingerprinting (REF) analysis technique was used, as all strains of Haemophilus parasuis are biochemically similar and many strains are biochemically untypable. After young weaned pigs were moved from farm A to farm B, Glasser's disease routinely occurred despite the use of antibiotics and a commercial bacterin. Isolates were taken from...

  9. Coincidence of cleavage sites of intron endonuclease I-TevI and critical sequences of the host thymidylate synthase gene.

    Science.gov (United States)

    Edgell, David R; Stanger, Matthew J; Belfort, Marlene

    2004-11-01

    To maximize spread of their host intron or intein, many homing endonucleases recognize nucleotides that code for important and conserved amino acid residues of the target gene. Here, we examine the cleavage requirements for I-TevI, which binds a stretch of thymidylate synthase (TS) DNA that codes for functionally critical residues in the TS active site. Using an in vitro selection scheme, we identified two base-pairs in the I-TevI cleavage site region as important for cleavage efficiency. These were confirmed by comparison of I-TevI cleavage efficiencies on mutant and on wild-type substrates. We also showed that nicking of the bottom strand by I-TevI is not affected by mutation of residues surrounding the bottom-strand cleavage site, unlike other homing endonucleases. One of these two base-pairs is universally conserved in all TS sequences, and is identical with a previously identified cleavage determinant of I-BmoI, a related GIY-YIG endonuclease that binds a homologous stretch of TS-encoding DNA. The other base-pair is conserved only in a subset of TS genes that includes the I-TevI, but not the I-BmoI, target sequence. Both the I-TevI and I-BmoI cleavage site requirements correspond to functionally critical residues involved in an extensive hydrogen bond network within the TS active site. Remarkably, these cleavage requirements correlate with TS phylogeny in bacteria, suggesting that each endonuclease has individually adapted to efficiently cleave distinct TS substrates. PMID:15491609

  10. Differentiation of Neisseria gonorrhoeae from other Neisseria species by use of the restriction endonuclease HaeIII.

    OpenAIRE

    Torres, A. R. de; Li, M K; Ward, D C; Edberg, S C

    1984-01-01

    We used the restriction endonuclease HaeIII to differentiate Neisseria gonorrhoeae from other Neisseria species and Branhamella catarrhalis. A total of 16 clinical isolates and four American Type Culture Collection strains of N. gonorrhoeae were resistant to HaeIII digestion, whereas 17 isolates and four American Type Culture Collection strains from eight different bacterial species were susceptible. This resistance was not caused by an enzyme inhibitor. We propose that protection of the HaeI...

  11. CHIP has a protective role against oxidative stress-induced cell death through specific regulation of Endonuclease G

    OpenAIRE

    Lee, J.S.; Seo, T W; Yi, J. H.; K. S. Shin; Yoo, S. J.

    2013-01-01

    Oxidative stress is implicated in carcinogenesis, aging, and neurodegenerative diseases. The E3 ligase C terminus of Hsc-70 interacting protein (CHIP) has a protective role against various stresses by targeting damaged proteins for proteasomal degradation, and thus maintains protein quality control. However, the detailed mechanism by which CHIP protects cells from oxidative stress has not been demonstrated. Here, we show that depletion of CHIP led to elevated Endonuclease G (EndoG) levels and...

  12. Purification, properties, and sequence specificity of SslI, a new type II restriction endonuclease from Streptococcus salivarius subsp. thermophilus.

    Science.gov (United States)

    Benbadis, L; Garel, J R; Hartley, D L

    1991-01-01

    SslI, a type II restriction endonuclease, was purified from Streptococcus salivarius subsp. thermophilus strain BSN 45. SslI is an isoschizomer of BstNI. SslI activity was maximum at pH 8.8, 0 to 50 mM NaCl, 2 to 8 mM Mg2+, and 42 degrees C. Activity against phage DNA in vitro was demonstrated. Images PMID:1785940

  13. Two Distinctive Binding Modes of Endonuclease Inhibitors to the N-Terminal Region of Influenza Virus Polymerase Acidic Subunit.

    Science.gov (United States)

    Fudo, Satoshi; Yamamoto, Norio; Nukaga, Michiyoshi; Odagiri, Takato; Tashiro, Masato; Hoshino, Tyuji

    2016-05-10

    Influenza viruses are global threat to humans, and the development of new antiviral agents are still demanded to prepare for pandemics and to overcome the emerging resistance to the current drugs. Influenza polymerase acidic protein N-terminal domain (PAN) has endonuclease activity and is one of the appropriate targets for novel antiviral agents. First, we performed X-ray cocrystal analysis on the complex structures of PAN with two endonuclease inhibitors. The protein crystallization and the inhibitor soaking were done at pH 5.8. The binding modes of the two inhibitors were different from a common binding mode previously reported for the other influenza virus endonuclease inhibitors. We additionally clarified the complex structures of PAN with the same two endonuclease inhibitors at pH 7.0. In one of the crystal structures, an additional inhibitor molecule, which chelated to the two metal ions in the active site, was observed. On the basis of the crystal structures at pH 7.0, we carried out 100 ns molecular dynamics (MD) simulations for both of the complexes. The analysis of simulation results suggested that the binding mode of each inhibitor to PAN was stable in spite of the partial deviation of the simulation structure from the crystal one. Furthermore, crystal structure analysis and MD simulation were performed for PAN in complex with an inhibitor, which was already reported to have a high compound potency for comparison. The findings on the presence of multiple binding sites at around the PAN substrate-binding pocket will provide a hint for enhancing the binding affinity of inhibitors. PMID:27088785

  14. A Comparative Study on the Recovery of EcoRI Endonuclease from Two Different Genetically Modified Strains of Escherichia coli

    OpenAIRE

    Tamerler, Candan; Önsan, Z İlsen; Kirdar, Betül

    2001-01-01

    A laboratory scale procedure developed for the purification of EcoRI restriction endonuclease was applied to two different Escherichia coli} strains, E. coli 294 and E. coli M5248, which are genetically modified to overproduce the enzyme. The purification method consisted of three successive chromatographic steps including phosphocellulose and hydroxyapatite columns and further fractionation in a second phosphocellulose column. It was shown that the second phosphocellulose separ...

  15. Mean velocities measured with the double pulse technique

    Directory of Open Access Journals (Sweden)

    E. Nielsen

    2004-11-01

    Full Text Available It was recently observed that double-pulse measurements of the mean velocities of a wide asymmetric spectrum are a function of the time lag between the pulses (Uspensky et al., 2004. Here we demonstrate that the observed relationship probably is influenced by the measurement technique in a way that is consistent with theoretical prediction. It is further shown that for small time lags the double pulse velocity is a good approximation to the mean Doppler velo-city.

  16. Cas5d processes pre-crRNA and is a member of a larger family of CRISPR RNA endonucleases

    Science.gov (United States)

    Garside, Erin L.; Schellenberg, Matthew J.; Gesner, Emily M.; Bonanno, Jeffrey B.; Sauder, J. Michael; Burley, Stephen K.; Almo, Steven C.; Mehta, Garima; MacMillan, Andrew M.

    2012-01-01

    Small RNAs derived from clustered, regularly interspaced, short palindromic repeat (CRISPR) loci in bacteria and archaea are involved in an adaptable and heritable gene-silencing pathway. Resistance to invasive genetic material is conferred by the incorporation of short DNA sequences derived from this material into the genome as CRISPR spacer elements separated by short repeat sequences. Processing of long primary transcripts (pre-crRNAs) containing these repeats by a CRISPR-associated (Cas) RNA endonuclease generates the mature effector RNAs that target foreign nucleic acid for degradation. Here we describe functional studies of a Cas5d ortholog, and high-resolution structural studies of a second Cas5d family member, demonstrating that Cas5d is a sequence-specific RNA endonuclease that cleaves CRISPR repeats and is thus responsible for processing of pre-crRNA. Analysis of the structural homology of Cas5d with the previously characterized Cse3 protein allows us to model the interaction of Cas5d with its RNA substrate and conclude that it is a member of a larger family of CRISPR RNA endonucleases. PMID:23006625

  17. Structural and functional analysis of the symmetrical Type I restriction endonuclease R.EcoR124I(NT.

    Directory of Open Access Journals (Sweden)

    James E Taylor

    Full Text Available Type I restriction-modification (RM systems are comprised of two multi-subunit enzymes, the methyltransferase (∼160 kDa, responsible for methylation of DNA, and the restriction endonuclease (∼400 kDa, responsible for DNA cleavage. Both enzymes share a number of subunits. An engineered RM system, EcoR124I(NT, based on the N-terminal domain of the specificity subunit of EcoR124I was constructed that recognises the symmetrical sequence GAAN(7TTC and is active as a methyltransferase. Here, we investigate the restriction endonuclease activity of R. EcoR124I(NTin vitro and the subunit assembly of the multi-subunit enzyme. Finally, using small-angle neutron scattering and selective deuteration, we present a low-resolution structural model of the endonuclease and locate the motor subunits within the multi-subunit enzyme. We show that the covalent linkage between the two target recognition domains of the specificity subunit is not required for subunit assembly or enzyme activity, and discuss the implications for the evolution of Type I enzymes.

  18. Condensation on Slippery Asymmetric Bumps

    CERN Document Server

    Park, Kyoo-Chul; He, Neil; Aizenberg, Joanna

    2015-01-01

    Bumps are omnipresent from human skin to the geological structures on planets, which offer distinct advantages in numerous phenomena including structural color, drag reduction, and extreme wettability. Although the topographical parameters of bumps such as radius of curvature of convex regions significantly influence various phenomena including anti-reflective structures and contact time of impacting droplets, the effect of the detailed bump topography on growth and transport of condensates have not been clearly understood. Inspired by the millimetric bumps of the Namib Desert beetle, here we report the identified role of radius of curvature and width of bumps with homogeneous surface wettability in growth rate, coalescence and transport of water droplets. Further rational design of asymmetric convex topography and synergetic combination with slippery coating simultaneously enable self-transport, leading to unseen five-fold higher growth rate and an order of magnitude faster shedding time of droplets compared...

  19. Asymmetric diffusion of cosmic rays

    CERN Document Server

    Medvedev, Mikhail V

    2015-01-01

    Cosmic ray propagation is diffusive because of pitch angle scattering by waves. We demonstrate that if the high-amplitude magnetohydrodynamic turbulence with $\\tilde B/\\langle B\\rangle \\sim 1$ is present on top of the mean field gradient, the diffusion becomes asymmetric. As an example, we consider the vertical transport of cosmic rays in our Galaxy propagating away from a point-like source. We solve this diffusion problem analytically using a one-dimensional Markov chain analysis. We obtained that the cosmic ray density markedly differs from the standard diffusion prediction and has a sizable effect on their distribution throughout the galaxy. The equation for the continuous limit is also derived, which shows limitations of the convection-diffusion equation.

  20. New asymmetric quantum codes over Fq

    Science.gov (United States)

    Ma, Yuena; Feng, Xiaoyi; Xu, Gen

    2016-07-01

    Two families of new asymmetric quantum codes are constructed in this paper. The first family is the asymmetric quantum codes with length n=qm-1 over Fq, where qge 5 is a prime power. The second one is the asymmetric quantum codes with length n=3m-1. These asymmetric quantum codes are derived from the CSS construction and pairs of nested BCH codes. Moreover, let the defining set T1=T2^{-q}, then the real Z-distance of our asymmetric quantum codes are much larger than δ _max+1, where δ _max is the maximal designed distance of dual-containing narrow-sense BCH code, and the parameters presented here have better than the ones available in the literature.

  1. Digital doubles

    OpenAIRE

    Lewis, Chara; Mojsiewicz, Kristin; Pettican, Anneké

    2010-01-01

    Replication of the self and engagement with liminal spaces has informed our collaborative practice. 3D body scanning, processing and digital printing proffered new methods of engagement as yet uncharted to capture ourselves faithfully. (http://www.brassart.org.uk) Test body scans suggested the potential to reveal public and private aspects of ‘the self’ – representing both the physiological and psychological aspects of a subject. Digitised Doubles was a practice led enquiry ...

  2. The proapoptotic protein BNIP3 interacts with VDAC to induce mitochondrial release of endonuclease G.

    Directory of Open Access Journals (Sweden)

    Xiaosha Zhang

    Full Text Available BNIP3 is a proapoptotic protein that induces cell death through a mitochondria-mediated pathway. We reported previously that mitochondrial localization of BNIP3 and translocation of EndoG from mitochondria to the nucleus are critical steps of the BNIP3 pathway. It is not clear, however, that how BNIP3 interacts with mitochondria. Here we show that expression of BNIP3 resulted in mitochondrial release and nuclear translocation of EndoG. Incubation of a recombinant GST-BNIP3 protein with freshly isolated mitochondria led to the integration of BNIP3 into mitochondria, reduction in the levels of EndoG in mitochondria and the presence of EndoG in the supernatant that was able to cleave chromatin DNA. Co-immunoprecipitation and mass spectrometry analysis reveals that BNIP3 interacted with the voltage-dependent anion channel (VDAC to increase opening probabilities of mitochondrial permeability transition (PT pores and induce mitochondrial release of EndoG. Blocking VDAC with a VDAC antibody largely abolished mitochondrial localization of BNIP3 and prevented EndoG release. Together, the data identify VDAC as an interacting partner of BNIP3 and support endonuclease G as a mediator of the BNIP3 pathway.

  3. Redox-responsive zinc finger fidelity switch in homing endonuclease and intron promiscuity in oxidative stress.

    Science.gov (United States)

    Robbins, Justin B; Smith, Dorie; Belfort, Marlene

    2011-02-01

    It is well understood how mobile introns home to allelic sites, but how they are stimulated to transpose to ectopic locations on an evolutionary timescale is unclear. Here we show that a group I intron can move to degenerate sites under oxidizing conditions. The phage T4 td intron endonuclease, I-TevI, is responsible for this infidelity. We demonstrate that I-TevI, which promotes mobility and is subject to autorepression and translational control, is also regulated posttranslationally by a redox mechanism. Redox regulation is exercised by a zinc finger (ZF) in a linker that connects the catalytic domain of I-TevI to the DNA binding domain. Four cysteines coordinate Zn(2+) in the ZF, which ensures that I-TevI cleaves its DNA substrate at a fixed distance, 23-25 nucleotides upstream of the intron insertion site. We show that the fidelity of I-TevI cleavage is controlled by redox-responsive Zn(2+) cycling. When the ZF is mutated, or after exposure of the wild-type I-TevI to H(2)O(2), intron homing to degenerate sites is increased, likely because of indiscriminate DNA cleavage. These results suggest a mechanism for rapid intron dispersal, joining recent descriptions of the activation of biomolecular processes by oxidative stress through cysteine chemistry. PMID:21256016

  4. P1 Ref Endonuclease: A Molecular Mechanism for Phage-Enhanced Antibiotic Lethality.

    Science.gov (United States)

    Ronayne, Erin A; Wan, Y C Serena; Boudreau, Beth A; Landick, Robert; Cox, Michael M

    2016-01-01

    Ref is an HNH superfamily endonuclease that only cleaves DNA to which RecA protein is bound. The enigmatic physiological function of this unusual enzyme is defined here. Lysogenization by bacteriophage P1 renders E. coli more sensitive to the DNA-damaging antibiotic ciprofloxacin, an example of a phenomenon termed phage-antibiotic synergy (PAS). The complementary effect of phage P1 is uniquely traced to the P1-encoded gene ref. Ref is a P1 function that amplifies the lytic cycle under conditions when the bacterial SOS response is induced due to DNA damage. The effect of Ref is multifaceted. DNA binding by Ref interferes with normal DNA metabolism, and the nuclease activity of Ref enhances genome degradation. Ref also inhibits cell division independently of the SOS response. Ref gene expression is toxic to E. coli in the absence of other P1 functions, both alone and in combination with antibiotics. The RecA proteins of human pathogens Neisseria gonorrhoeae and Staphylococcus aureus serve as cofactors for Ref-mediated DNA cleavage. Ref is especially toxic during the bacterial SOS response and the limited growth of stationary phase cultures, targeting aspects of bacterial physiology that are closely associated with the development of bacterial pathogen persistence. PMID:26765929

  5. P1 Ref Endonuclease: A Molecular Mechanism for Phage-Enhanced Antibiotic Lethality.

    Directory of Open Access Journals (Sweden)

    Erin A Ronayne

    2016-01-01

    Full Text Available Ref is an HNH superfamily endonuclease that only cleaves DNA to which RecA protein is bound. The enigmatic physiological function of this unusual enzyme is defined here. Lysogenization by bacteriophage P1 renders E. coli more sensitive to the DNA-damaging antibiotic ciprofloxacin, an example of a phenomenon termed phage-antibiotic synergy (PAS. The complementary effect of phage P1 is uniquely traced to the P1-encoded gene ref. Ref is a P1 function that amplifies the lytic cycle under conditions when the bacterial SOS response is induced due to DNA damage. The effect of Ref is multifaceted. DNA binding by Ref interferes with normal DNA metabolism, and the nuclease activity of Ref enhances genome degradation. Ref also inhibits cell division independently of the SOS response. Ref gene expression is toxic to E. coli in the absence of other P1 functions, both alone and in combination with antibiotics. The RecA proteins of human pathogens Neisseria gonorrhoeae and Staphylococcus aureus serve as cofactors for Ref-mediated DNA cleavage. Ref is especially toxic during the bacterial SOS response and the limited growth of stationary phase cultures, targeting aspects of bacterial physiology that are closely associated with the development of bacterial pathogen persistence.

  6. Role of Endonuclease G in Exogenous DNA Stability in HeLa Cells.

    Science.gov (United States)

    Misic, V; El-Mogy, M; Haj-Ahmad, Y

    2016-02-01

    Endonuclease G (EndoG) is a well-conserved mitochondrial-nuclear nuclease with dual lethal and vital roles in the cell. The aim of our study was to examine whether EndoG exerts its nuclease activity on exogenous DNA substrates such as plasmid DNA (pDNA), considering their importance in gene therapy applications. The effects of EndoG knockdown on pDNA stability and levels of encoded reporter gene expression were evaluated in the cervical carcinoma HeLa cells. Transfection of pDNA vectors encoding short-hairpin RNAs (shRNAs) reduced levels of EndoG mRNA in HeLa cells. In physiological circumstances, EndoG knockdown did not have an effect on the stability of pDNA or the levels of encoded transgene expression as measured over a four-day time course. However, when endogenous expression of EndoG was induced by an extrinsic stimulus, targeting of EndoG by shRNA improved the perceived stability and transgene expression of pDNA vectors. Therefore, EndoG is not a mediator of exogenous DNA clearance, but in non-physiological circumstances, it may nonspecifically cleave intracellular DNA regardless of its origin. These findings make it unlikely that targeting of EndoG is a viable strategy for improving the duration and level of transgene expression from nonviral DNA vectors in gene therapy efforts. PMID:27260396

  7. Mutagenesis of Genes for Starch Debranching Enzyme Isoforms in Pea by Zinc-Finger Endonucleases

    International Nuclear Information System (INIS)

    Starch debranching enzymes in plants are divided into two groups based on their ability to hydrolyze different substrates. The first group, pullulanases, hydrolyze α-1,6-glucosidic linkages in substrates such as pullulan, amylopectin and glycogen. The second group of debranching enzymes, isoamylases, hydrolyze glycogen and amylopectin and are not active on pullulan. Three isoforms of isoamylase and a pullulanase have been isolated from a cDNA library of Pisum sativum. These isoamylases have been characterized following their heterologous expression in E. coli. Based on the DNA sequence that encodes these debranching enzymes, a specific mutagenesis targeting these enzymes will be attempted. The technique involves the homologous recombination of DNA mediated by zinc-finger endonucleases. Vectors will be constructed to include a fragment that will modify these genes. Using this technique, it is hoped that null mutants for each enzyme will be created and the exact role of these enzymes for the synthesis and degradation of starch in plants will be elucidated. (author)

  8. Thermodynamics of Damaged DNA Binding and Catalysis by Human AP Endonuclease 1.

    Science.gov (United States)

    Miroshnikova, A D; Kuznetsova, A A; Kuznetsov, N A; Fedorova, O S

    2016-01-01

    Apurinic/apyrimidinic (AP) endonucleases play an important role in DNA repair and initiation of AP site elimination. One of the most topical problems in the field of DNA repair is to understand the mechanism of the enzymatic process involving the human enzyme APE1 that provides recognition of AP sites and efficient cleavage of the 5'-phosphodiester bond. In this study, a thermodynamic analysis of the interaction between APE1 and a DNA substrate containing a stable AP site analog lacking the C1' hydroxyl group (F site) was performed. Based on stopped-flow kinetic data at different temperatures, the steps of DNA binding, catalysis, and DNA product release were characterized. The changes in the standard Gibbs energy, enthalpy, and entropy of sequential specific steps of the repair process were determined. The thermodynamic analysis of the data suggests that the initial step of the DNA substrate binding includes formation of non-specific contacts between the enzyme binding surface and DNA, as well as insertion of the amino acid residues Arg177 and Met270 into the duplex, which results in the removal of "crystalline" water molecules from DNA grooves. The second binding step involves the F site flipping-out process and formation of specific contacts between the enzyme active site and the everted 5'-phosphate-2'-deoxyribose residue. It was shown that non-specific interactions between the binding surfaces of the enzyme and DNA provide the main contribution into the thermodynamic parameters of the DNA product release step. PMID:27099790

  9. 5' End-independent RNase J1 endonuclease cleavage of Bacillus subtilis model RNA.

    Science.gov (United States)

    Deikus, Gintaras; Bechhofer, David H

    2011-10-01

    Bacillus subtilis trp leader RNA is a small (140-nucleotide) RNA that results from attenuation of trp operon transcription upon binding of the regulatory TRAP complex. Previously, endonucleolytic cleavage by ribonuclease RNase J1 in a 3'-proximal, single-stranded region was shown to be critical for initiation of trp leader RNA decay. RNase J1 is a dual-specificity enzyme, with both 5' exonucleolytic and endonucleolytic activities. Here, we provide in vivo and in vitro evidence that RNase J1 accesses its internal target site on trp leader RNA in a 5' end-independent manner. This has important implications for the role of RNase J1 in RNA decay. We also tested the involvement in trp leader RNA decay of the more recently discovered endonuclease RNase Y. Half-lives of several trp leader RNA constructs, which were designed to probe pathways of endonucleolytic versus exonucleolytic decay, were measured in an RNase Y-deficient mutant. Remarkably, the half-lives of these constructs were indistinguishable from their half-lives in an RNase J1-deficient mutant. These results suggest that lowering RNase Y concentration may affect RNA decay indirectly via an effect on RNase J1, which is thought to exist with RNase Y in a degradosome complex. To generalize our findings with trp leader RNA to other RNAs, we show that the mechanism of trp leader RNA decay is not dependent on TRAP binding. PMID:21862575

  10. Micrococcus luteus correndonucleases. I. Resolution and purification of two endonucleases specific for DNA containing pyrimidine dimers

    International Nuclear Information System (INIS)

    Five peaks of endonuclease activity showing a preference for ultraviolet-damaged DNA have been chromatographically identified from extracts of Micrococcus luteus. They are numerically designated as I to V in order of their elution from phosphocellulose (Whatman P-11) columns. The first two of these peaks have been highly purified by a combination of gel filtration and affinity chromatography and are catalytically homogeneous judging from their effect on transforming DNAs. Peak I, which has an isoelectric point of 4.7, is heat-stable, requires high ionic strength for optimal activity, acts with equal facility on ultraviolet-irradiated native and denatured DNA, and has been designated as Py--Py correndonuclease I. Peak II which has a pI value of 8.7, is heat-labile, is inhibited by high ionic strength, acts on ultraviolet-irradiated native but not denatured DNA, and has been designated as Py--Py correndonuclease II. Both enzymes are inhibited by Ca2+ and Zn2+, do not show any cofactor or sulfhydryl requirement, act optimally between pH 7.0 and 7.4, and have molecular weights between 11,000 and 15,000. Py--Py correndonuclease I requires a dose about 1.6 times that for Py--Py correndonuclease II for incision saturation of irradiated phiX174 RFI DNA

  11. Mitochondrial Targeted Endonuclease III DNA Repair Enzyme Protects against Ventilator Induced Lung Injury in Mice

    Directory of Open Access Journals (Sweden)

    Masahiro Hashizume

    2014-08-01

    Full Text Available The mitochondrial targeted DNA repair enzyme, 8-oxoguanine DNA glycosylase 1, was previously reported to protect against mitochondrial DNA (mtDNA damage and ventilator induced lung injury (VILI. In the present study we determined whether mitochondrial targeted endonuclease III (EndoIII which cleaves oxidized pyrimidines rather than purines from damaged DNA would also protect the lung. Minimal injury from 1 h ventilation at 40 cmH2O peak inflation pressure (PIP was reversed by EndoIII pretreatment. Moderate lung injury due to ventilation for 2 h at 40 cmH2O PIP produced a 25-fold increase in total extravascular albumin space, a 60% increase in W/D weight ratio, and marked increases in MIP-2 and IL-6. Oxidative mtDNA damage and decreases in the total tissue glutathione (GSH and the GSH/GSSH ratio also occurred. All of these indices of injury were attenuated by mitochondrial targeted EndoIII. Massive lung injury caused by 2 h ventilation at 50 cmH2O PIP was not attenuated by EndoIII pretreatment, but all untreated mice died prior to completing the two hour ventilation protocol, whereas all EndoIII-treated mice lived for the duration of ventilation. Thus, mitochondrial targeted DNA repair enzymes were protective against mild and moderate lung damage and they enhanced survival in the most severely injured group.

  12. Mitochondrial Targeted Endonuclease III DNA Repair Enzyme Protects against Ventilator Induced Lung Injury in Mice.

    Science.gov (United States)

    Hashizume, Masahiro; Mouner, Marc; Chouteau, Joshua M; Gorodnya, Olena M; Ruchko, Mykhaylo V; Wilson, Glenn L; Gillespie, Mark N; Parker, James C

    2014-01-01

    The mitochondrial targeted DNA repair enzyme, 8-oxoguanine DNA glycosylase 1, was previously reported to protect against mitochondrial DNA (mtDNA) damage and ventilator induced lung injury (VILI). In the present study we determined whether mitochondrial targeted endonuclease III (EndoIII) which cleaves oxidized pyrimidines rather than purines from damaged DNA would also protect the lung. Minimal injury from 1 h ventilation at 40 cmH2O peak inflation pressure (PIP) was reversed by EndoIII pretreatment. Moderate lung injury due to ventilation for 2 h at 40 cmH2O PIP produced a 25-fold increase in total extravascular albumin space, a 60% increase in W/D weight ratio, and marked increases in MIP-2 and IL-6. Oxidative mtDNA damage and decreases in the total tissue glutathione (GSH) and the GSH/GSSH ratio also occurred. All of these indices of injury were attenuated by mitochondrial targeted EndoIII. Massive lung injury caused by 2 h ventilation at 50 cmH2O PIP was not attenuated by EndoIII pretreatment, but all untreated mice died prior to completing the two hour ventilation protocol, whereas all EndoIII-treated mice lived for the duration of ventilation. Thus, mitochondrial targeted DNA repair enzymes were protective against mild and moderate lung damage and they enhanced survival in the most severely injured group. PMID:25153040

  13. Mechanisms of DNA Packaging by Large Double-Stranded DNA Viruses.

    Science.gov (United States)

    Rao, Venigalla B; Feiss, Michael

    2015-11-01

    Translocation of viral double-stranded DNA (dsDNA) into the icosahedral prohead shell is catalyzed by TerL, a motor protein that has ATPase, endonuclease, and translocase activities. TerL, following endonucleolytic cleavage of immature viral DNA concatemer recognized by TerS, assembles into a pentameric ring motor on the prohead's portal vertex and uses ATP hydrolysis energy for DNA translocation. TerL's N-terminal ATPase is connected by a hinge to the C-terminal endonuclease. Inchworm models propose that modest domain motions accompanying ATP hydrolysis are amplified, through changes in electrostatic interactions, into larger movements of the C-terminal domain bound to DNA. In phage ϕ29, four of the five TerL subunits sequentially hydrolyze ATP, each powering translocation of 2.5 bp. After one viral genome is encapsidated, the internal pressure signals termination of packaging and ejection of the motor. Current focus is on the structures of packaging complexes and the dynamics of TerL during DNA packaging, endonuclease regulation, and motor mechanics. PMID:26958920

  14. High-resolution structure of the N-terminal endonuclease domain of the Lassa virus L polymerase in complex with magnesium ions.

    Directory of Open Access Journals (Sweden)

    Gregor D Wallat

    Full Text Available Lassa virus (LASV causes deadly hemorrhagic fever disease for which there are no vaccines and limited treatments. LASV-encoded L polymerase is required for viral RNA replication and transcription. The functional domains of L-a large protein of 2218 amino acid residues-are largely undefined, except for the centrally located RNA-dependent RNA polymerase (RdRP motif. Recent structural and functional analyses of the N-terminal region of the L protein from lymphocytic choriomeningitis virus (LCMV, which is in the same Arenaviridae family as LASV, have identified an endonuclease domain that presumably cleaves the cap structures of host mRNAs in order to initiate viral transcription. Here we present a high-resolution crystal structure of the N-terminal 173-aa region of the LASV L protein (LASV L173 in complex with magnesium ions at 1.72 Å. The structure is highly homologous to other known viral endonucleases of arena- (LCMV NL1, orthomyxo- (influenza virus PA, and bunyaviruses (La Crosse virus NL1. Although the catalytic residues (D89, E102 and K122 are highly conserved among the known viral endonucleases, LASV L endonuclease structure shows some notable differences. Our data collected from in vitro endonuclease assays and a reporter-based LASV minigenome transcriptional assay in mammalian cells confirm structural prediction of LASV L173 as an active endonuclease. The high-resolution structure of the LASV L endonuclease domain in complex with magnesium ions should aid the development of antivirals against lethal Lassa hemorrhagic fever.

  15. Regenerating a symmetry in asymmetric dark matter.

    Science.gov (United States)

    Buckley, Matthew R; Profumo, Stefano

    2012-01-01

    Asymmetric dark matter theories generically allow for mass terms that lead to particle-antiparticle mixing. Over the age of the Universe, dark matter can thus oscillate from a purely asymmetric configuration into a symmetric mix of particles and antiparticles, allowing for pair-annihilation processes. Additionally, requiring efficient depletion of the primordial thermal (symmetric) component generically entails large annihilation rates. We show that unless some symmetry completely forbids dark matter particle-antiparticle mixing, asymmetric dark matter is effectively ruled out for a large range of masses, for almost any oscillation time scale shorter than the age of the Universe. PMID:22304253

  16. Modelling asymmetric growth in crowded plant communities

    DEFF Research Database (Denmark)

    Damgaard, Christian

    2010-01-01

    A class of models that may be used to quantify the effect of size-asymmetric competition in crowded plant communities by estimating a community specific degree of size-asymmetric growth for each species in the community is suggested. The model consists of two parts: an individual size......-asymmetric growth part, where growth is assumed to be proportional to a power function of the size of the individual, and a term that reduces the relative growth rate as a decreasing function of the individual plant size and the competitive interactions from other plants in the neighbourhood....

  17. Asymmetric warfare and the will to win

    OpenAIRE

    Quinn, Matthew D.

    2001-01-01

    This thesis explores the will to win in asymmetric war. Asymmetric war, in which one side has an overwhelming advantage over its opponent, will likely be the war of the future for the United States in the post-Cold War uni-polar world. To win an asymmetric war, the individual and then the masses must be motivated to fight and, ultimately, the will to win must be cultivated and sustained for victory. Religion is a highly effective motivat or for both the individual and the masses. This motiva...

  18. Chiral Aminophosphines as Catalysts for Enantioselective Double-Michael Indoline Syntheses

    Directory of Open Access Journals (Sweden)

    Ohyun Kwon

    2012-05-01

    Full Text Available The bisphosphine-catalyzed double-Michael addition of dinucleophiles to electron-deficient acetylenes is an efficient process for the synthesis of many nitrogen-containing heterocycles. Because the resulting heterocycles contain at least one stereogenic center, this double-Michael reaction would be even more useful if an asymmetric variant of the reaction were to be developed. Aminophosphines can also facilitate the double-Michael reaction and chiral amines are more readily available in Nature and synthetically; therefore, in this study we prepared several new chiral aminophosphines. When employed in the asymmetric double-Michael reaction between ortho-tosylamidophenyl malonate and 3-butyn-2-one, the chiral aminophosphines produced indolines in excellent yields with moderate asymmetric induction.

  19. Asymmetric Information and Consumer Demand

    Directory of Open Access Journals (Sweden)

    Ismagilova G. N.

    2014-11-01

    Full Text Available In the paper study the peculiarities of the formation the consumer demand for durable goods, the so-called «experience goods» in markets with asymmetric information. In the known literature sources studying of the demand is based on the assumption that at the moment of the purchase of goods and services people know exactly what price they are willing to pay for them and what utility they are going to obtain using those goods and services. Consider the signal model in which the initial price and advertising expenditures are the signals of the quality influencing the formation of the demand for new goods offered by the company of unknown quality through consumer behavior. The basis of this model is the study of producers by consumers, acquisition of knowledge, information about price and quality, as well as their use in order to determine the market share of high-quality goods and low-quality goods in the asymmetry of information.

  20. Chaos suppression through asymmetric coupling

    Science.gov (United States)

    Bragard, J.; Vidal, G.; Mancini, H.; Mendoza, C.; Boccaletti, S.

    2007-12-01

    We study pairs of identical coupled chaotic oscillators. In particular, we have used Roessler (in the funnel and no funnel regimes), Lorenz, and four-dimensional chaotic Lotka-Volterra models. In all four of these cases, a pair of identical oscillators is asymmetrically coupled. The main result of the numerical simulations is that in all cases, specific values of coupling strength and asymmetry exist that render the two oscillators periodic and synchronized. The values of the coupling strength for which this phenomenon occurs is well below the previously known value for complete synchronization. We have found that this behavior exists for all the chaotic oscillators that we have used in the analysis. We postulate that this behavior is presumably generic to all chaotic oscillators. In order to complete the study, we have tested the robustness of this phenomenon of chaos suppression versus the addition of some Gaussian noise. We found that chaos suppression is robust for the addition of finite noise level. Finally, we propose some extension to this research.

  1. Why Do Nucleosomes Unwrap Asymmetrically?

    Science.gov (United States)

    de Bruin, Lennart; Tompitak, Marco; Eslami-Mossallam, Behrouz; Schiessel, Helmut

    2016-07-01

    Nucleosomes, DNA spools with a protein core, engage about three-quarters of eukaryotic DNA and play a critical role in chromosomal processes, ranging from gene regulation, recombination, and replication to chromosome condensation. For more than a decade, micromanipulation experiments where nucleosomes are put under tension, as well as the theoretical interpretations of these experiments, have deepened our understanding of the stability and dynamics of nucleosomes. Here we give a theoretical explanation for a surprising new experimental finding: nucleosomes wrapped onto the 601 positioning sequence (the sequence used in most laboratories) respond highly asymmetrically to external forces by always unwrapping from the same end. Using a computational nucleosome model, we show that this asymmetry can be explained by differences in the DNA mechanics of two very short stretches on the wrapped DNA portion. Our finding suggests that the physical properties of nucleosomes, here the response to forces, can be tuned locally by the choice of the underlying base-pair sequence. This leads to a new view of nucleosomes: a physically highly varied set of DNA-protein complexes whose properties can be tuned on evolutionary time scales to their specific function in the genomic context. PMID:26991771

  2. Twin Higgs Asymmetric Dark Matter.

    Science.gov (United States)

    García García, Isabel; Lasenby, Robert; March-Russell, John

    2015-09-18

    We study asymmetric dark matter (ADM) in the context of the minimal (fraternal) twin Higgs solution to the little hierarchy problem, with a twin sector with gauged SU(3)^{'}×SU(2)^{'}, a twin Higgs doublet, and only third-generation twin fermions. Naturalness requires the QCD^{'} scale Λ_{QCD}^{'}≃0.5-20  GeV, and that t^{'} is heavy. We focus on the light b^{'} quark regime, m_{b^{'}}≲Λ_{QCD}^{'}, where QCD^{'} is characterized by a single scale Λ_{QCD}^{'} with no light pions. A twin baryon number asymmetry leads to a successful dark matter (DM) candidate: the spin-3/2 twin baryon, Δ^{'}∼b^{'}b^{'}b^{'}, with a dynamically determined mass (∼5Λ_{QCD}^{'}) in the preferred range for the DM-to-baryon ratio Ω_{DM}/Ω_{baryon}≃5. Gauging the U(1)^{'} group leads to twin atoms (Δ^{'}-τ^{'}[over ¯] bound states) that are successful ADM candidates in significant regions of parameter space, sometimes with observable changes to DM halo properties. Direct detection signatures satisfy current bounds, at times modified by dark form factors. PMID:26430985

  3. Twin Higgs Asymmetric Dark Matter

    CERN Document Server

    García, Isabel García; March-Russell, John

    2015-01-01

    We study Asymmetric Dark Matter (ADM) in the context of the minimal (Fraternal) Twin Higgs solution to the little hierarchy problem, with a twin sector with gauged $SU(3)' \\times SU(2)'$, a twin Higgs, and only third generation twin fermions. Naturalness requires the QCD$^\\prime$ scale $\\Lambda'_{\\rm QCD} \\simeq 0.5 - 20 \\ {\\rm GeV}$, and $t'$ to be heavy. We focus on the light $b'$ quark regime, $m_{b'} \\lesssim \\Lambda'_{\\rm QCD}$, where QCD$^\\prime$ is characterised by a single scale $\\Lambda'_{\\rm QCD}$ with no light pions. A twin baryon number asymmetry leads to a successful DM candidate: the spin-3/2 twin baryon, $\\Delta' \\sim b'b'b'$, with a dynamically determined mass ($\\sim 5 \\Lambda'_{\\rm QCD}$) in the preferred range for the DM-to-baryon ratio $\\Omega_{\\rm DM}/\\Omega_{\\rm baryon} \\simeq 5$. Gauging the $U(1)'$ group leads to twin atoms ($\\Delta'$ - $\\bar {\\tau'}$ bound states) that are successful ADM candidates in significant regions of parameter space, sometimes with observable changes to DM halo ...

  4. Lithium Titanate Confined in Carbon Nanopores for Asymmetric Supercapacitors.

    Science.gov (United States)

    Zhao, Enbo; Qin, Chuanli; Jung, Hong-Ryun; Berdichevsky, Gene; Nese, Alper; Marder, Seth; Yushin, Gleb

    2016-04-26

    Porous carbons suffer from low specific capacitance, while intercalation-type active materials suffer from limited rate when used in asymmetric supercapacitors. We demonstrate that nanoconfinement of intercalation-type lithium titanate (Li4Ti5O12) nanoparticles in carbon nanopores yielded nanocomposite materials that offer both high ion storage density and rapid ion transport through open and interconnected pore channels. The use of titanate increased both the gravimetric and volumetric capacity of porous carbons by more than an order of magnitude. High electrical conductivity of carbon and the small size of titanate crystals allowed the composite electrodes to achieve characteristic charge and discharge times comparable to that of the electric double-layer capacitors. The proposed composite synthesis methodology is simple, scalable, and applicable for a broad range of active intercalation materials, while the produced composite powders are compatible with commercial electrode fabrication processes. PMID:26950509

  5. Generation of infrared entangled light in asymmetric semiconductor quantum wells

    Science.gov (United States)

    Lü, Xin-You; Wu, Jing; Zheng, Li-Li; Huang, Pei

    2010-12-01

    We proposed a scheme to achieve two-mode CV entanglement with the frequencies of entangled modes in the infrared range in an asymmetric semiconductor double-quantum-wells (DQW), where the required quantum coherence is obtained by inducing the corresponding intersubband transitions (ISBTs) with a classical field. By numerically simulating the dynamics of system, we show that the entanglement period can be prolonged via enhancing the intensity of classical field, and the generation of entanglement doesn't depend intensively on the initial condition of system in our scheme. Moreover, we also show that a bipartite entanglement amplifier can be realized in our scheme. The present research provides an efficient approach to achieve infrared entangled light in the semiconductor nanostructure, which may have significant impact on the progress of solid-state quantum information theory.

  6. Asymmetric electroresistance of cluster glass state in manganites

    KAUST Repository

    Lourembam, James

    2014-03-31

    We report the electrostatic modulation of transport in strained Pr0.65(Ca0.75Sr0.25)0.35MnO3 thin films grown on SrTiO3 by gating with ionic liquid in electric double layer transistors (EDLT). In such manganite films with strong phase separation, a cluster glass magnetic state emerges at low temperatures with a spin freezing temperature of about 99 K, which is accompanied by the reentrant insulating state with high resistance below 30 K. In the EDLT, we observe bipolar and asymmetric modulation of the channel resistance, as well as an enhanced electroresistance up to 200% at positive gate bias. Our results provide insights on the carrier-density-dependent correlated electron physics of cluster glass systems.

  7. Development of a nicking endonuclease-assisted method for the purification of minicircles.

    Science.gov (United States)

    Alves, Cláudia P A; Šimčíková, Michaela; Brito, Liliana; Monteiro, Gabriel A; Prazeres, Duarte Miguel F

    2016-04-22

    Minicircle (MC) DNA vectors are able to generate a high-level transgene expression in vivo, which is superior to the one afforded by conventional plasmids. MC vectors are produced by replicating a parental plasmid (PP) and promoting its recombination in Escherichia coli. This generates a MC with the expression cassette, and a miniplasmid (MP) with the replication segment. Unfortunately, wider use of MC vectors is hampered by difficulties in isolating the target MCs from their MP counterpart. In this proof-of-concept study, a reproducible process is described to improve the purification of supercoiled (sc) MCs that combines an in vitro enzymatic relaxation of sc MP impurities with topoisomer separation and RNA clearance by hydrophobic interaction chromatography (HIC) step. At the early stage of vector design, a site for the nicking endonuclease Nb.BbvCI was strategically placed in the MP part of the PP backbone. A process was then established that involves E. coli culture and recombination of PPs into target MC, cell harvesting and alkaline lysis, precipitation with isopropanol and ammonium sulfate and diafiltration/concentration by microfiltration. Next, an in vitro digestion step was carried out with Nb.BbvCI to nick of one of the strands of the MPs and of non-recombined PPs by Nb.BbvCI. As a result, sc MPs and non-recombined PPs were converted into the corresponding open circular (oc) forms whereas sc MCs remain unaffected. Finally, sc MC was isolated from oc DNA molecules (oc MPs, oc MC) and RNA by performing HIC with a phenyl-Sepharose column using a series of elution steps with decreasing ammonium sulfate concentrations. On the basis of agarose gel electrophoresis analysis, the sc MC-containing fractions were determined to be virtually free from nucleic acid impurities. PMID:27016116

  8. Cell-Autonomous Progeroid Changes in Conditional Mouse Models for Repair Endonuclease XPG Deficiency

    Science.gov (United States)

    Vermeij, Wilbert P.; Tresini, Maria; Weymaere, Michael; Menoni, Hervé; Brandt, Renata M. C.; de Waard, Monique C.; Botter, Sander M.; Sarker, Altaf H.; Jaspers, Nicolaas G. J.; van der Horst, Gijsbertus T. J.; Cooper, Priscilla K.; Hoeijmakers, Jan H. J.; van der Pluijm, Ingrid

    2014-01-01

    As part of the Nucleotide Excision Repair (NER) process, the endonuclease XPG is involved in repair of helix-distorting DNA lesions, but the protein has also been implicated in several other DNA repair systems, complicating genotype-phenotype relationship in XPG patients. Defects in XPG can cause either the cancer-prone condition xeroderma pigmentosum (XP) alone, or XP combined with the severe neurodevelopmental disorder Cockayne Syndrome (CS), or the infantile lethal cerebro-oculo-facio-skeletal (COFS) syndrome, characterized by dramatic growth failure, progressive neurodevelopmental abnormalities and greatly reduced life expectancy. Here, we present a novel (conditional) Xpg−/− mouse model which -in a C57BL6/FVB F1 hybrid genetic background- displays many progeroid features, including cessation of growth, loss of subcutaneous fat, kyphosis, osteoporosis, retinal photoreceptor loss, liver aging, extensive neurodegeneration, and a short lifespan of 4–5 months. We show that deletion of XPG specifically in the liver reproduces the progeroid features in the liver, yet abolishes the effect on growth or lifespan. In addition, specific XPG deletion in neurons and glia of the forebrain creates a progressive neurodegenerative phenotype that shows many characteristics of human XPG deficiency. Our findings therefore exclude that both the liver as well as the neurological phenotype are a secondary consequence of derailment in other cell types, organs or tissues (e.g. vascular abnormalities) and support a cell-autonomous origin caused by the DNA repair defect itself. In addition they allow the dissection of the complex aging process in tissue- and cell-type-specific components. Moreover, our data highlight the critical importance of genetic background in mouse aging studies, establish the Xpg−/− mouse as a valid model for the severe form of human XPG patients and segmental accelerated aging, and strengthen the link between DNA damage and aging. PMID:25299392

  9. Cell-autonomous progeroid changes in conditional mouse models for repair endonuclease XPG deficiency.

    Directory of Open Access Journals (Sweden)

    Sander Barnhoorn

    2014-10-01

    Full Text Available As part of the Nucleotide Excision Repair (NER process, the endonuclease XPG is involved in repair of helix-distorting DNA lesions, but the protein has also been implicated in several other DNA repair systems, complicating genotype-phenotype relationship in XPG patients. Defects in XPG can cause either the cancer-prone condition xeroderma pigmentosum (XP alone, or XP combined with the severe neurodevelopmental disorder Cockayne Syndrome (CS, or the infantile lethal cerebro-oculo-facio-skeletal (COFS syndrome, characterized by dramatic growth failure, progressive neurodevelopmental abnormalities and greatly reduced life expectancy. Here, we present a novel (conditional Xpg-/- mouse model which -in a C57BL6/FVB F1 hybrid genetic background- displays many progeroid features, including cessation of growth, loss of subcutaneous fat, kyphosis, osteoporosis, retinal photoreceptor loss, liver aging, extensive neurodegeneration, and a short lifespan of 4-5 months. We show that deletion of XPG specifically in the liver reproduces the progeroid features in the liver, yet abolishes the effect on growth or lifespan. In addition, specific XPG deletion in neurons and glia of the forebrain creates a progressive neurodegenerative phenotype that shows many characteristics of human XPG deficiency. Our findings therefore exclude that both the liver as well as the neurological phenotype are a secondary consequence of derailment in other cell types, organs or tissues (e.g. vascular abnormalities and support a cell-autonomous origin caused by the DNA repair defect itself. In addition they allow the dissection of the complex aging process in tissue- and cell-type-specific components. Moreover, our data highlight the critical importance of genetic background in mouse aging studies, establish the Xpg-/- mouse as a valid model for the severe form of human XPG patients and segmental accelerated aging, and strengthen the link between DNA damage and aging.

  10. Atomic structure of the DNA repair [4Fe-4S] enzyme endonuclease III.

    Science.gov (United States)

    Kuo, C F; McRee, D E; Fisher, C L; O'Handley, S F; Cunningham, R P; Tainer, J A

    1992-10-16

    The crystal structure of the DNA repair enzyme endonuclease III, which recognizes and cleaves DNA at damaged bases, has been solved to 2.0 angstrom resolution with an R factor of 0.185. This iron-sulfur [4Fe-4S] enzyme is elongated and bilobal with a deep cleft separating two similarly sized domains: a novel, sequence-continuous, six-helix domain (residues 22 to 132) and a Greek-key, four-helix domain formed by the amino-terminal and three carboxyl-terminal helices (residues 1 to 21 and 133 to 211) together with the [4Fe-4S] cluster. The cluster is bound entirely within the carboxyl-terminal loop with a ligation pattern (Cys-X6-Cys-X2-Cys-X5-Cys) distinct from all other known [4Fe-4S] proteins. Sequence conservation and the positive electrostatic potential of conserved regions identify a surface suitable for binding duplex B-DNA across the long axis of the enzyme, matching a 46 angstrom length of protected DNA. The primary role of the [4Fe-4S] cluster appears to involve positioning conserved basic residues for interaction with the DNA phosphate backbone. The crystallographically identified inhibitor binding region, which recognizes the damaged base thymine glycol, is a seven-residue beta-hairpin (residues 113 to 119). Location and side chain orientation at the base of the inhibitor binding site implicate Glu112 in the N-glycosylase mechanism and Lys120 in the beta-elimination mechanism. Overall, the structure reveals an unusual fold and a new biological function for [4Fe-4S] clusters and provides a structural basis for studying recognition of damaged DNA and the N-glycosylase and apurinic/apyrimidinic-lyase mechanisms. PMID:1411536

  11. AP endonuclease knockdown enhances methyl methanesulfonate hypersensitivity of DNA polymerase β knockout mouse embryonic fibroblasts

    International Nuclear Information System (INIS)

    Apurinic/apyrimidinic (AP) endonuclease (Apex) is required for base excision repair (BER), which is the major mechanism of repair for small DNA lesions such as alkylated bases. Apex incises the DNA strand at an AP site to leave 3'-OH and 5'-deoxyribose phosphate (5'-dRp) termini. DNA polymerase β (PolB) plays a dominant role in single nucleotide (Sn-) BER by incorporating a nucleotide and removing 5'-dRp. Methyl methanesulfonate (MMS)-induced damage is repaired by Sn-BER, and thus mouse embryonic fibroblasts (MEFs) deficient in PolB show significantly increased sensitivity to MMS. However, the survival curve for PolB-knockout MEFs (PolBKOs) has a shoulder, and increased sensitivity is only apparent at relatively high MMS concentrations. In this study, we prepared Apex-knockdown/PolB-knockout MEFs (AKDBKOs) to examine whether BER is related to the apparent resistance of PolBKOs at low MMS concentrations. The viability of PolBKOs immediately after MMS treatment was significantly lower than that of wild-type MEFs, but there was essentially no effect of Apex-knockdown on cell viability in the presence or absence of PolB. In contrast, relative counts of MEFs after repair were decreased by Apex knockdown. Parental PolBKOs showed especially high sensitivity at >1.5 mM MMS, suggesting that PolBKOs have another repair mechanism in addition to PolB-dependent Sn-BER, and that the back-up mechanism is unable to repair damage induced by high MMS concentrations. Interestingly, AKDBKOs were hypersensitive to MMS in a relative cell growth assay, suggesting that MMS-induced damage in PolB-knockout MEFs is repaired by Apex-dependent repair mechanisms, presumably including long-patch BER. (author)

  12. Asymmetric dense matter in holographic QCD

    Directory of Open Access Journals (Sweden)

    Shin Ik Jae

    2012-02-01

    Full Text Available We study asymmetric dense matter in holographic QCD.We construct asymmetric dense matter by considering two quark flavor branes with dierent quark masses in a D4/D6/D6 model. To calculate the symmetry energy in nuclear matter, we consider two quarks with equal masses and observe that the symmetry energy increases with the total charge showing the stiff dependence. This behavior is universal in the sense that the result is independent of parameters in the model. We also study strange (or hyperon matter with one light and one intermediate mass quarks. In addition to the vacuum properties of asymmetric matter, we calculate meson masses in asymmetric dense matter and discuss our results in the light of in-medium kaon masses.

  13. Massless sunset diagrams in finite asymmetric volumes

    CERN Document Server

    Niedermayer, Ferenc

    2016-01-01

    In this paper we present methods to compute massless sunset diagrams in finite asymmetric volumes in the framework of dimensional regularization and lattice regularization. We also consider 1-loop sums in both regularizations.

  14. Worst Asymmetrical Short-Circuit Current

    DEFF Research Database (Denmark)

    Arana Aristi, Iván; Holmstrøm, O; Grastrup, L;

    2010-01-01

    In a typical power plant, the production scenario and the short-circuit time were found for the worst asymmetrical short-circuit current. Then, a sensitivity analysis on the missing generator values was realized in order to minimize the uncertainty of the results. Afterward the worst asymmetrical...... short-circuit current was analyzed in order to compare the results with the allowable DC current component based in the IEC. Finally the normal operating condition for the power plant was modeled....

  15. Renewable resource management under asymmetric information

    DEFF Research Database (Denmark)

    Jensen, Frank; Andersen, Peder; Nielsen, Max

    Asymmetric information between fishermen and the regulator is important within fisheries. The regulator may have less information about stock sizes, prices, costs, effort, productivity and catches than fishermen. With asymmetric information, a strong analytical tool is principal-agent analysis. In......-productivity agents receive an information rent. The information rent is equivalent to the total incentive cost. The incentive costs arise as we want to reveal the agent's type....

  16. An asymmetric pericyclic cascade approach to oxindoles

    OpenAIRE

    Richmond, Edward

    2014-01-01

    The research in this thesis describes an asymmetric pericyclic cascade approach to the synthesis of a range of enantioenriched oxindoles using enantiopure oxazolidine derived nitrones and disubstituted ketenes. Chapter 1 aims to place this work in the context of the literature, describing other commonly employed or state-of-the-art asymmetric approaches to oxindoles and related compounds. Examples of where these approaches have been used successfully in the total synthesis of related indol...

  17. Asymmetric Federalism in Russia: Cure or Poison?

    OpenAIRE

    Jorge Martinez-Vazquez

    2003-01-01

    In the early years of its existence, the Russian Federation adopted a system of differential treatment of its regions in order to cope with the great degree of diversity present in them. This paper examines the Russian Federation’s asymmetric federalism by evaluating the system’s role, significance and effects on the Federation’s development. The study incorporates a detailed description of the asymmetric federalism over time along with the benefits and costs incurred by its implementation. I...

  18. Asymmetric Membrane Osmotic Capsules for Terbutaline Sulphate

    OpenAIRE

    Gobade, N. G.; Marina Koland; K H Harish

    2012-01-01

    The aim of the present study was to design an asymmetric membrane capsule, an osmotic pump-based drug delivery system of ethyl cellulose for controlled release of terbutaline sulphate. asymmetric membrane capsules contains pore-forming water soluble additive, sorbitol in different concentrations in the capsule shell membrane, which after coming in contact with water, dissolves, resulting in an in situ formation of a microporous structure. The terbutaline sulphate is a β-adrenoreceptor agonist...

  19. Asymmetric septal hypertrophy and hypothyroidism in children.

    OpenAIRE

    Altman, D I; Murray, J.; Milner, S.; Dansky, R; Levin, S. E.

    1985-01-01

    Any echocardiographic study of two children with hypothyroidism demonstrated the presence of asymmetric septal hypertrophy. One child died aged 11 months, and pronounced thickening of the interventricular septum was confirmed at necropsy. There was also hypertrophy of the left ventricular free wall. Histological examination showed only slight muscle fibre disarray, but there was striking vacuolation and hypertrophy of muscle fibres. In the second case, a child aged five years, the asymmetric ...

  20. Dominant mutations in S. cerevisiae PMS1 identify the Mlh1-Pms1 endonuclease active site and an exonuclease 1-independent mismatch repair pathway.

    Directory of Open Access Journals (Sweden)

    Catherine E Smith

    2013-10-01

    Full Text Available Lynch syndrome (hereditary nonpolypsis colorectal cancer or HNPCC is a common cancer predisposition syndrome. Predisposition to cancer in this syndrome results from increased accumulation of mutations due to defective mismatch repair (MMR caused by a mutation in one of the mismatch repair genes MLH1, MSH2, MSH6 or PMS2/scPMS1. To better understand the function of Mlh1-Pms1 in MMR, we used Saccharomyces cerevisiae to identify six pms1 mutations (pms1-G683E, pms1-C817R, pms1-C848S, pms1-H850R, pms1-H703A and pms1-E707A that were weakly dominant in wild-type cells, which surprisingly caused a strong MMR defect when present on low copy plasmids in an exo1Δ mutant. Molecular modeling showed these mutations caused amino acid substitutions in the metal coordination pocket of the Pms1 endonuclease active site and biochemical studies showed that they inactivated the endonuclease activity. This model of Mlh1-Pms1 suggested that the Mlh1-FERC motif contributes to the endonuclease active site. Consistent with this, the mlh1-E767stp mutation caused both MMR and endonuclease defects similar to those caused by the dominant pms1 mutations whereas mutations affecting the predicted metal coordinating residue Mlh1-C769 had no effect. These studies establish that the Mlh1-Pms1 endonuclease is required for MMR in a previously uncharacterized Exo1-independent MMR pathway.

  1. Altered target site specificity variants of the I-PpoI His-Cys box homing endonuclease

    OpenAIRE

    Eklund, Jennifer L.; Ulge, Umut Y.; Eastberg, Jennifer; Monnat, Raymond J.

    2007-01-01

    We used a yeast one-hybrid assay to isolate and characterize variants of the eukaryotic homing endonuclease I-PpoI that were able to bind a mutant, cleavage-resistant I-PpoI target or ‘homing’ site DNA in vivo. Native I-PpoI recognizes and cleaves a semi-palindromic 15-bp target site with high specificity in vivo and in vitro. This target site is present in the 28S or equivalent large subunit rDNA genes of all eukaryotes. I-PpoI variants able to bind mutant target site DNA had from 1 to 8 ami...

  2. Structure and specificity of the RNA-guided endonuclease Cas9 during DNA interrogation, target binding and cleavage

    OpenAIRE

    Josephs, Eric A.; Kocak, D. Dewran; Fitzgibbon, Christopher J.; McMenemy, Joshua; Gersbach, Charles A; Marszalek, Piotr E.

    2015-01-01

    CRISPR-associated endonuclease Cas9 cuts DNA at variable target sites designated by a Cas9-bound RNA molecule. Cas9's ability to be directed by single ‘guide RNA’ molecules to target nearly any sequence has been recently exploited for a number of emerging biological and medical applications. Therefore, understanding the nature of Cas9's off-target activity is of paramount importance for its practical use. Using atomic force microscopy (AFM), we directly resolve individual Cas9 and nuclease-in...

  3. Cas5d processes pre-crRNA and is a member of a larger family of CRISPR RNA endonucleases

    OpenAIRE

    Garside, Erin L.; Schellenberg, Matthew J.; Gesner, Emily M.; Bonanno, Jeffrey B.; Sauder, J. Michael; Burley, Stephen K.; Almo, Steven C.; Mehta, Garima; MacMillan, Andrew M.

    2012-01-01

    A detailed functional analysis of the CRISPR-associated Thermus thermophilus Cas5d protein identifies it as a sequence-specific pre-crRNA processing endonuclease. High-resolution X-ray structural studies of a second Cas5d ortholog highlight similarities with previously characterized CRISPR processing enzymes. A combination of structural and functional analyses based on these results allow a modeling of the interaction of Cas5d with its RNA substrate and suggest that it is a member of a larger...

  4. Genomic DNA restriction endonuclease from Pasteurella multocida isolated from Indonesia, katha strain and reference strains and analysed by PFGE

    Directory of Open Access Journals (Sweden)

    Supar

    2003-10-01

    Full Text Available Pasteurella multocida strains are the causative disease agents of wide range of domestic and wild animals in Indonesia. The most important serotypes are associated with Hemorrhagic septicaemic (HS diseases in cattle and buffaloes, cholera in ducks and chickens. The HS disease associated with P. multocia in large ruminants in Indonesia is controled by killed whole cell vaccines produced by the use of P. multocida Katha strains. There is no discriminatory data of the molecular biology technique has been applied to investigate P. multocida isolates from different geographic locations in Indonesia. The purpose of this studies were to observe the genetic diversity among P. multocida isolated from various geograpic locations and compared with Katha vaccine strain and other reference strains. A total samples of 38 isolates and strains of P. multocida were analysed by means of pulsed-field gel electrophoresis (PFGE. Each sample was grown in nutrient broth, cells were separeted by centrifugation. Whole cell pellet was mixed with agarose and then prepared agarose plugs. The genomic DNA of each sample was digested in situ (plug with either restriction endonuclease of ApaI and/or BamHI. The digested genomic DNA of each sample was analysed by PFGE, the genomic DNA restricted profile of each sample was compared with others. The use of ApaI restriction endonuclease digestion and analysed by PFGE, demonstrated that 34 out of 38 P. multocia samples could be differentiated into 16 ApaI types, whereas based on the BamHI digestion of these samples were differentiated into 20 BamHI types. Genomic DNA restriction pattern of Indonesian P. multocida isolates originated from cattle and buffaloes associated with haemorrhagic septicaemic diseases demonstrated different pattern to those of vaccine Katha strain, poultry strains as well as the reference strains currenly kept at Balitvet Culture Collection (BCC unit. Two P. multocida isolates derived from ducks with cholera

  5. Measuring motion on DNA by the type I restriction endonuclease EcoR124I using triplex displacement

    OpenAIRE

    Firman, Keith; Szczelkun, Mark D.

    2000-01-01

    The type I restriction enzyme EcoR124I cleaves DNA following extensive linear translocation dependent upon ATP hydrolysis. Using protein-directed displacement of a DNA triplex, we have determined the kinetics of one-dimensional motion without the necessity of measuring DNA or ATP hydrolysis. The triplex was pre-formed specifically on linear DNA, 4370 bp from an EcoR124I site, and then incubated with endonuclease. Upon ATP addition, a distinct lag phase was observed before the triplex-forming ...

  6. Next-generation sequencing of multiple individuals per barcoded library by deconvolution of sequenced amplicons using endonuclease fragment analysis

    DEFF Research Database (Denmark)

    Andersen, Jeppe D; Pereira, Vania; Pietroni, Carlotta;

    2014-01-01

    The simultaneous sequencing of samples from multiple individuals increases the efficiency of next-generation sequencing (NGS) while also reducing costs. Here we describe a novel and simple approach for sequencing DNA from multiple individuals per barcode. Our strategy relies on the endonuclease...... digestion of PCR amplicons prior to library preparation, creating a specific fragment pattern for each individual that can be resolved after sequencing. By using both barcodes and restriction fragment patterns, we demonstrate the ability to sequence the human melanocortin 1 receptor (MC1R) genes from 72...... individuals using only 24 barcoded libraries....

  7. Crystal structure of the R-protein of the multisubunit ATP-dependent restriction endonuclease NgoAVII

    OpenAIRE

    Tamulaitiene, Giedre; Silanskas, Arunas; Grazulis, Saulius; Zaremba, Mindaugas; Siksnys, Virginijus

    2014-01-01

    The restriction endonuclease (REase) NgoAVII is composed of two proteins, R.NgoAVII and N.NgoAVII, and shares features of both Type II restriction enzymes and Type I/III ATP-dependent restriction enzymes (see accompanying paper Zaremba et al., 2014). Here we present crystal structures of the R.NgoAVII apo-protein and the R.NgoAVII C-terminal domain bound to a specific DNA. R.NgoAVII is composed of two domains: an N-terminal nucleolytic PLD domain; and a C-terminal B3-like DNA-binding domain i...

  8. Crystal Structure of the R-Protein of the Multisubunit ATP-Dependent Restriction Endonuclease NgoAVII

    OpenAIRE

    Tamulaitiene, G.; Silanskas, A.; Grazulis, S.; Zaremba, M.; Siksnys, V.

    2014-01-01

    The restriction endonuclease (REase) NgoAVII iscomposed of two proteins, R.NgoAVII and N.NgoAVII,and shares features of both Type II restriction en-zymes and Type I/III ATP-dependent restriction en-zymes (see accompanying paper Zaremba et al.,2014). Here we present crystal structures of theR.NgoAVII apo-protein and the R.NgoAVII C-terminaldomain bound to a specific DNA. R.NgoAVII is com-posed of two domains: an N-terminal nucleolytic PLDdomain; and a C-terminal B3-like DNA-binding do-main ide...

  9. Properties of avian sarcoma-leukosis virus pp32-related pol-endonucleases produced in Escherichia coli.

    OpenAIRE

    Terry, R; Soltis, D A; Katzman, M; Cobrinik, D; Leis, J; Skalka, A M

    1988-01-01

    The gag-pol precursor protein of the avian sarcoma-leukosis virus is processed into three known pol-encoded mature polypeptides; the 95- and 63-kilodalton (kDa) beta and alpha subunits, respectively, of reverse transcriptase and the 32-kDa pp32 protein. The pp32 protein possesses DNA endonuclease activity and is produced from the precursor by two proteolytic cleavage events, one of which removes 4.1 kDa of protein from the C terminus. A 36-kDa protein (p36pol) which retains this C-terminal se...

  10. Mutants of the Base Excision Repair Glycosylase, Endonuclease III: DNA Charge Transport as a First Step in Lesion Detection

    OpenAIRE

    Romano, Christine A.; Sontz, Pamela A.; Barton, Jacqueline K.

    2011-01-01

    Endonuclease III (EndoIII) is a base excision repair glycosylase that targets damaged pyrimidines and contains a [4Fe-4S] cluster. We have proposed a model where BER proteins that contain redox-active [4Fe-4S] clusters utilize DNA charge transport (CT) as a first step in the detection of DNA lesions. Here, several mutants of EndoIII were prepared to probe their efficiency of DNA/protein charge transport. Cyclic voltammetry experiments on DNA-modified electrodes show that aromatic residues F30...

  11. Fatigue in asymmetric-field-driven ferroelectric thin films

    International Nuclear Information System (INIS)

    The polarization fatigue problems in asymmetric-field-driven ferroelectric thin films is investigated in present Letter. The refreshment of fatigue induced by the application of asymmetric voltage to the top and bottom electrodes is modeled by asymmetric Schottky voltage barrier of a quantum well structure. The fatigue behavior under various asymmetric driving voltages and asymmetric driving pulses have been studied. Theoretical calculations are shown to be in agreement with experimental results

  12. Restoration of ultraviolet-induced unscheduled DNA synthesis of xeroderma pigmentosum cells by the concomitant treatment with bacteriophage T4 endonuclease V and HVJ (Sendai virus)

    International Nuclear Information System (INIS)

    Ultraviolet (uv)-induced unscheduled DNA synthesis of xeroderma pigmentosum cells, belonging to complementation groups, A, B, C, D, and E, was restored to the normal level by concomitant treatment of the cells with T4 endonuclease V and uv-inactivated HVJ (Sendai virus). The present results suggest that T4 endonuclease molecules were inserted effectively into the cells by the interaction of HVJ with the cell membranes, the enzyme was functional on human chromosomal DNA which had been damaged by uv irradiation in the viable cells, all the studied groups of xeroderma pigmentosum (variant was not tested) were defective in the first step (incision) of excision repair

  13. Oxidative stress alters base excision repair pathway and increases apoptotic response in Apurinic/apyrimidinic endonuclease 1/Redox factor-1 haploinsufficient mice

    OpenAIRE

    Unnikrishnan, Archana; Raffoul, Julian J.; Patel, Hiral V.; Prychitko, Thomas M.; Anyangwe, Njwen; Meira, Lisiane B.; Friedberg, Errol C.; Cabelof, Diane C.; Heydari, Ahmad R.

    2009-01-01

    Apurinic/apyrimidinic endonuclease 1/redox factor-1 (APE1/Ref-1) is the redox regulator of multiple stress-inducible transcription factors, such as NF-κB, and the major 5’-endonuclease in base excision repair (BER). We utilized mice containing heterozygous gene-targeted deletion of APE1/Ref-1 (Apex+/-) to determine the impact of APE1/Ref-1 haploinsufficiency on the processing of oxidative DNA damage induced by 2-nitropropane (2-NP) in the liver tissue of mice. APE1/Ref-1 haploinsufficiency re...

  14. Role of the tryptophan residue in the vicinity of the catalytic center of exonuclease III family AP endonucleases: AP site recognition mechanism

    OpenAIRE

    Kaneda, Kohichi; Sekiguchi, Junichi; Shida, Toshio

    2006-01-01

    The mechanisms by which AP endonucleases recognize AP sites have not yet been determined. Based on our previous study with Escherichia coli exonuclease III (ExoIII), the ExoIII family AP endonucleases probably recognize the DNA-pocket formed at an AP site. The indole ring of a conserved tryptophan residue in the vicinity of the catalytic site presumably intercalates into this pocket. To test this hypothesis, we constructed a series of mutants of ExoIII and human APE1. Trp-212 of ExoIII and Tr...

  15. Microinjection of Micrococcus luteus UV-endonuclease restores UV-induced unscheduled DNA synthesis in cells of 9 xeroderma pigmentosum complementation groups.

    OpenAIRE

    Jonge, A.J.R.; Vermeulen, Wim; Keijzer, W.; Hoeijmakers, Jan; Bootsma, Dirk

    1985-01-01

    textabstractThe UV-induced unscheduled DNA synthesis (UDS) in cultured cells of excision-deficient xeroderma pigmentosum (XP) complementation groups A through I was assayed after injection of Micrococcus luteus UV-endonuclease using glass microneedles. In all complementation groups a restoration of the UV-induced UDS, in some cells to the repair-proficient human level, was observed. Another prokaryotic DNA-repair enzyme, T4 endonuclease V, restored the UV-induced UDS in a similar way after mi...

  16. Control of apoptosis by asymmetric cell division.

    Science.gov (United States)

    Hatzold, Julia; Conradt, Barbara

    2008-04-01

    Asymmetric cell division and apoptosis (programmed cell death) are two fundamental processes that are important for the development and function of multicellular organisms. We have found that the processes of asymmetric cell division and apoptosis can be functionally linked. Specifically, we show that asymmetric cell division in the nematode Caenorhabditis elegans is mediated by a pathway involving three genes, dnj-11 MIDA1, ces-2 HLF, and ces-1 Snail, that directly control the enzymatic machinery responsible for apoptosis. Interestingly, the MIDA1-like protein GlsA of the alga Volvox carteri, as well as the Snail-related proteins Snail, Escargot, and Worniu of Drosophila melanogaster, have previously been implicated in asymmetric cell division. Therefore, C. elegans dnj-11 MIDA1, ces-2 HLF, and ces-1 Snail may be components of a pathway involved in asymmetric cell division that is conserved throughout the plant and animal kingdoms. Furthermore, based on our results, we propose that this pathway directly controls the apoptotic fate in C. elegans, and possibly other animals as well. PMID:18399720

  17. NMR characterization of the interaction of the endonuclease domain of MutL with divalent metal ions and ATP.

    Science.gov (United States)

    Mizushima, Ryota; Kim, Ju Yaen; Suetake, Isao; Tanaka, Hiroaki; Takai, Tomoyo; Kamiya, Narutoshi; Takano, Yu; Mishima, Yuichi; Tajima, Shoji; Goto, Yuji; Fukui, Kenji; Lee, Young-Ho

    2014-01-01

    MutL is a multi-domain protein comprising an N-terminal ATPase domain (NTD) and C-terminal dimerization domain (CTD), connected with flexible linker regions, that plays a key role in DNA mismatch repair. To expand understanding of the regulation mechanism underlying MutL endonuclease activity, our NMR-based study investigated interactions between the CTD of MutL, derived from the hyperthermophilic bacterium Aquifex aeolicus (aqMutL-CTD), and putative binding molecules. Chemical shift perturbation analysis with the model structure of aqMutL-CTD and circular dichroism results revealed that tight Zn(2+) binding increased thermal stability without changing secondary structures to function at high temperatures. Peak intensity analysis exploiting the paramagnetic relaxation enhancement effect indicated the binding site for Mn(2+), which shared binding sites for Zn(2+). The coexistence of these two metal ions appears to be important for the function of MutL. Chemical shift perturbation analysis revealed a novel ATP binding site in aqMutL-CTD. A docking simulation incorporating the chemical shift perturbation data provided a putative scheme for the intermolecular interactions between aqMutL-CTD and ATP. We proposed a simple and understandable mechanical model for the regulation of MutL endonuclease activity in MMR based on the relative concentrations of ATP and CTD through ATP binding-regulated interdomain interactions between CTD and NTD. PMID:24901533

  18. NMR characterization of the interaction of the endonuclease domain of MutL with divalent metal ions and ATP.

    Directory of Open Access Journals (Sweden)

    Ryota Mizushima

    Full Text Available MutL is a multi-domain protein comprising an N-terminal ATPase domain (NTD and C-terminal dimerization domain (CTD, connected with flexible linker regions, that plays a key role in DNA mismatch repair. To expand understanding of the regulation mechanism underlying MutL endonuclease activity, our NMR-based study investigated interactions between the CTD of MutL, derived from the hyperthermophilic bacterium Aquifex aeolicus (aqMutL-CTD, and putative binding molecules. Chemical shift perturbation analysis with the model structure of aqMutL-CTD and circular dichroism results revealed that tight Zn(2+ binding increased thermal stability without changing secondary structures to function at high temperatures. Peak intensity analysis exploiting the paramagnetic relaxation enhancement effect indicated the binding site for Mn(2+, which shared binding sites for Zn(2+. The coexistence of these two metal ions appears to be important for the function of MutL. Chemical shift perturbation analysis revealed a novel ATP binding site in aqMutL-CTD. A docking simulation incorporating the chemical shift perturbation data provided a putative scheme for the intermolecular interactions between aqMutL-CTD and ATP. We proposed a simple and understandable mechanical model for the regulation of MutL endonuclease activity in MMR based on the relative concentrations of ATP and CTD through ATP binding-regulated interdomain interactions between CTD and NTD.

  19. Intertwined structure of the DNA-binding domain of intron endonuclease I-TevI with its substrate.

    Science.gov (United States)

    Van Roey, P; Waddling, C A; Fox, K M; Belfort, M; Derbyshire, V

    2001-07-16

    I-TevI is a site-specific, sequence-tolerant intron endonuclease. The crystal structure of the DNA-binding domain of I-TevI complexed with the 20 bp primary binding region of its DNA target reveals an unusually extended structure composed of three subdomains: a Zn finger, an elongated segment containing a minor groove-binding alpha-helix, and a helix-turn-helix. The protein wraps around the DNA, mostly following the minor groove, contacting the phosphate backbone along the full length of the duplex. Surprisingly, while the minor groove-binding helix and the helix-turn- helix subdomain make hydrophobic contacts, the few base-specific hydrogen bonds occur in segments that lack secondary structure and flank the intron insertion site. The multiple base-specific interactions over a long segment of the substrate are consistent with the observed high site specificity in spite of sequence tolerance, while the modular composition of the domain is pertinent to the evolution of homing endonucleases. PMID:11447104

  20. A Mismatch EndoNuclease Array-Based Methodology (MENA for Identifying Known SNPs or Novel Point Mutations

    Directory of Open Access Journals (Sweden)

    Josep M. Comeron

    2016-04-01

    Full Text Available Accurate and rapid identification or confirmation of single nucleotide polymorphisms (SNPs, point mutations and other human genomic variation facilitates understanding the genetic basis of disease. We have developed a new methodology (called MENA (Mismatch EndoNuclease Array pairing DNA mismatch endonuclease enzymology with tiling microarray hybridization in order to genotype both known point mutations (such as SNPs as well as identify previously undiscovered point mutations and small indels. We show that our assay can rapidly genotype known SNPs in a human genomic DNA sample with 99% accuracy, in addition to identifying novel point mutations and small indels with a false discovery rate as low as 10%. Our technology provides a platform for a variety of applications, including: (1 genotyping known SNPs as well as confirming newly discovered SNPs from whole genome sequencing analyses; (2 identifying novel point mutations and indels in any genomic region from any organism for which genome sequence information is available; and (3 screening panels of genes associated with particular diseases and disorders in patient samples to identify causative mutations. As a proof of principle for using MENA to discover novel mutations, we report identification of a novel allele of the beethoven (btv gene in Drosophila, which encodes a ciliary cytoplasmic dynein motor protein important for auditory mechanosensation.

  1. Computational study of hydration at the TD damaged site of DNA in complex with repair enzyme T4 endonuclease V

    International Nuclear Information System (INIS)

    An analysis of the distribution of water around DNA surface focusing on the role of the distribution of water molecules in the proper recognition of damaged site by repair enzyme T4 Endonuclease V was performed. The native DNA dodecamer, dodecamer with the thymine dimer (TD) and complex of DNA and part of repair enzyme T4 Endonuclease V were examined throughout the 500 ps of molecular dynamics simulation. During simulation the number of water molecules close to the DNA atoms and the residence time were calculated. There is an increase in number of water molecules lying in the close vicinity to TD if compared with those lying close to two native thymines (TT). Densely populated area with water molecules around TD is one of the factors detected by enzyme during scanning process. The residence time was found higher for molecule of the complex and the six water molecules were found occupying the stabile positions between the TD and catalytic center close to atoms P, C3' and N3. These molecules originate water mediated hydrogen bond network that contribute to the stability of complex required for the onset of repair process. (author)

  2. Structural insights of the ssDNA binding site in the multifunctional endonuclease AtBFN2 from Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Tsung-Fu Yu

    Full Text Available The multi S1/P1 nuclease AtBFN2 (EC 3.1.30.1 encoded by the Arabidopsis thaliana At1g68290 gene is a glycoprotein that digests RNA, ssDNA, and dsDNA. AtBFN2 depends on three zinc ions for cleaving DNA and RNA at 3'-OH to yield 5'-nucleotides. In addition, AtBFN2's enzymatic activity is strongly glycan dependent. Plant Zn(2+-dependent endonucleases present a unique fold, and belong to the Phospholipase C (PLC/P1 nuclease superfamily. In this work, we present the first complete, ligand-free, AtBFN2 crystal structure, along with sulfate, phosphate and ssDNA co-crystal structures. With these, we were able to provide better insight into the glycan structure and possible enzymatic mechanism. In comparison with other nucleases, the AtBFN2/ligand-free and AtBFN2/PO4 models suggest a similar, previously proposed, catalytic mechanism. Our data also confirm that the phosphate and vanadate can inhibit the enzyme activity by occupying the active site. More importantly, the AtBFN2/A5T structure reveals a novel and conserved secondary binding site, which seems to be important for plant Zn(2+-dependent endonucleases. Based on these findings, we propose a rational ssDNA binding model, in which the ssDNA wraps itself around the protein and the attached surface glycan, in turn, reinforces the binding complex.

  3. Endonucleolytic activity directed towards 8-(2-hydroxy-2-propyl) purines in double-stranded DNA.

    Science.gov (United States)

    Livneh, Z; Elad, D; Sperling, J

    1979-11-01

    Photoalkylation of circular covalently closed DNA from phage PM2 with isopropyl alcohol by using a free radical photoinitiator and UV light of lambda greater than 305 nm led to the specific 8-substitution of purine moieties in the DNA, yielding 8-(2-hydroxy-2-propyl)adenine and 8-(2-hydroxy-2-propyl)guanine as the only detectable damage in the DNA. Using this specifically photoalkylated DNA as a substrate, we discovered in extracts of Micrococcus luteus an endonucleolytic activity that is directed towards 8-(2-hydroxy-2-propyl) purines in DNA. The activity is not a combination of a DNA-glycosylase and an apurinic site endonuclease. It is not inhibited by single-stranded DNA, by UV- or gamma-irradiated single-stranded DNA, or by normal or depurinated double-stranded DNA. however, gamma- or UV-(254 nm) irradiated double-stranded DNAs to inhibit the activity, hinting at the possibility of a common type of lesion in these damaged DNAs. Divalent cations are not required for the incising activity, and it is fully active in 1 mM EDTA, whereas caffeine and ATP cause inhibition. Extracts of mutant M. luteus lacking pyrimidine-dimer-directed endonucleases were found to contain the endonucleolytic activity in levels comparable to those present in the wild type. After the incision, we could demonstrate the specific excision of the 8-alkylated purines from the damaged DNA. The special conformational consequences of the 8-alkylation of purines, at the nucleotide level, namely their nonregular syn conformation, suggest that it is the distortion in the DNA that is recognized by the endonuclease. PMID:293658

  4. The theory of double layers

    International Nuclear Information System (INIS)

    Numerical and in some degree laboratory experiments suggest the existence of at least two different kinds of time-independent double layers: a strictly monotonic transition of the electrostatic potential and a transition accompanied by a negative spike at the low potential side (ion acoustic DL). An interpretation of both is presented in terms of analytic BGK modes. The first class of DLs commonly observed in voltage- or beam-driven plasmas needs for its existence beam-type distributions satisfying a Bohm criterion. The potential drop is at least of the order of Tsub(e), and stability arguments favour currents which satisfy the Langmuir condition. The second class found in current-driven plasma simulations is correlated with ion holes. This latter kind of nonlinear wave-solutions is linearly based on the slow ion-acoustic mode and exists due to a vortex-like distortion of the ion distribution in the thermal range. During the growth of an ion hole which is triggered by ion-acoustic fluctuations, the partial reflection of streaming electrons causes different plasma states on both sides of the potential dip and makes the ion hole asymmetric giving rise to an effective potential drop. This implies that the amplitude of this second type of double layers has an upper limit of 1-2 Tsub(e) and presumes a temperature ratio of Tsub(e)/Tsub(i) > or approximately 3 in coincidence with the numerical results. (Auth.)

  5. Nanosheet-enhanced asymmetric induction of chiral α-amino acids in catalytic aldol reaction.

    Science.gov (United States)

    Zhao, Li-Wei; Shi, Hui-Min; Wang, Jiu-Zhao; He, Jing

    2012-11-26

    An efficient ligand design strategy towards boosting asymmetric induction was proposed, which simply employed inorganic nanosheets to modify α-amino acids and has been demonstrated to be effective in vanadium-catalyzed epoxidation of allylic alcohols. Here, the strategy was first extended to zinc-catalyzed asymmetric aldol reaction, a versatile bottom-up route to make complex functional compounds. Zinc, the second-most abundant transition metal in humans, is an environment-friendly catalytic center. The strategy was then further proved valid for organocatalyzed metal-free asymmetric catalysis, that is, α-amino acid catalyzed asymmetric aldol reaction. Visible improvement of enantioselectivity was experimentally achieved irrespective of whether the nanosheet-attached α-amino acids were applied as chiral ligands together with catalytic Zn(II) centers or as chiral catalysts alone. The layered double hydroxide nanosheet was clearly found by theoretical calculations to boost ee through both steric and H-bonding effects; this resembles the role of a huge and rigid substituent. PMID:23074138

  6. Asymmetric carbon nanotube–MnO2 two-ply yarn supercapacitors for wearable electronics

    International Nuclear Information System (INIS)

    Strong and flexible two-ply carbon nanotube yarn supercapacitors are electrical double layer capacitors that possess relatively low energy storage capacity. Pseudocapacitance metal oxides such as MnO2 are well known for their high electrochemical performance and can be coated on carbon nanotube yarns to significantly improve the performance of two-ply carbon nanotube yarn supercapacitors. We produced a high performance asymmetric two-ply yarn supercapacitor from as-spun CNT yarn and CNT@MnO2 composite yarn in aqueous electrolyte. The as-spun CNT yarn serves as negative electrode and the CNT@MnO2 composite yarn as positive electrode. This asymmetric architecture allows the operating potential window to be extended from 1.0 to 2.0 V and results in much higher energy and power densities than the reference symmetric two-ply yarn supercapacitors, reaching 42.0 Wh kg−1 at a lower power density of 483.7 W kg−1, and 28.02 Wh kg−1 at a higher power density of 19 250 W kg−1. The asymmetric supercapacitor can sustain cyclic charge–discharge and repeated folding/unfolding actions without suffering significant deterioration of specific capacitance. The combination of high strength, flexibility and electrochemical performance makes the asymmetric two-ply yarn supercapacitor a suitable power source for flexible electronic devices for applications that require high durability and wearer comfort. (paper)

  7. Asymmetric Magnon Excitation by Spontaneous Toroidal Ordering

    Science.gov (United States)

    Hayami, Satoru; Kusunose, Hiroaki; Motome, Yukitoshi

    2016-05-01

    The effects of spontaneous toroidal ordering on magnetic excitation are theoretically investigated for a localized spin model that includes a staggered Dzyaloshinsky-Moriya interaction and anisotropic exchange interactions, which arise from the antisymmetric spin-orbit coupling and the multiorbital correlation effect. We show that the model exhibits a Néel-type antiferromagnetic order, which simultaneously accompanies a ferroic toroidal order. We find that the occurrence of toroidal order modulates the magnon dispersion in an asymmetric way with respect to the wave number: a toroidal dipole order on the zigzag chain leads to a band-bottom shift, while a toroidal octupole order on the honeycomb lattice gives rise to a valley splitting. These asymmetric magnon excitations could be a source of unusual magnetic responses, such as nonreciprocal magnon transport. A variety of modulations are discussed while changing the lattice and magnetic symmetries. The implications regarding candidate materials for asymmetric magnon excitations are presented.

  8. Dc SQUIDs with asymmetric shunt resistors

    International Nuclear Information System (INIS)

    We have investigated asymmetrically shunted Nb/Al-AlOx/Nb dc SQUIDs. Simulations based on the coupled Langevin equations predict that the optimum energy resolution ε, and thus also the noise performance of such an asymmetric SQUID, can be 3-4 times better than that of its symmetric counterpart. While keeping the total resistance R identical to a comparable symmetric SQUID with R-1 = R1-1 + R2-1, we shunted only one of the two Josephson junctions with R = R1,2/2. Both types of SQUIDs were characterized with respect to their transport and noise properties at temperature T = 4.2 K, and we compared the experimental results with numerical simulations. Experiments yielded ε ∼ 32 ℎ for an asymmetric SQUID with an inductance L = 22 pH, whereas a comparable symmetric device achieved ε = 110 ℎ.

  9. DNA SECURITY USING SYMMETRIC AND ASYMMETRIC CRYPTOGRAPHY

    Directory of Open Access Journals (Sweden)

    Radu Terec

    2011-01-01

    Full Text Available This paper presents alternative security methods based on DNA. From the available alternative security methods, symmetric DNA algorithms were developed and implemented. The first symmetric DNA algorithm was implemented in the Java language, while the second DNA algorithm was implemented in BioJava and MatLab. Comparisons have been made between the performances of different standard symmetrical algorithms and the DNA proposed algorithms. As a new step to enhance the security, an asymmetric key generation inside a DNA security algorithm is presented. The asymmetric key generation algorithm starts from a password phrase. The asymmetric DNA algorithm proposes a mechanism which makes use of more encryption technologies. Therefore, it is more reliable and more powerful than the OTP DNA symmetric algorithms.

  10. Asymmetric Composite Nanoparticles with Anisotropic Surface Functionalities

    Directory of Open Access Journals (Sweden)

    Donglu Shi

    2009-01-01

    Full Text Available Asymmetric inorganic/organic composite nanoparticles with anisotropic surface functionalities represent a new approach for creating smart materials, requiring the selective introduction of chemical groups to dual components of composite, respectively. Here, we report the synthesis of snowman-like asymmetric silica/polystyrene heterostructure with anisotropic functionalities via a chemical method, creating nanostructure possibly offering two-sided biologic accessibility through the chemical groups. Carboxyl group was introduced to polystyrene component of the snowman-like composites by miniemulsion polymerization of monomer on local surface of silica particles. Moreover, amino group was then grafted to remained silica surface through facile surface modification of the composite nanoparticles. The asymmetric shape of these composites was confirmed by TEM characterization. Moreover, characteristics of anisotropic surface functionalities were indicated by Zeta potential measurement and confocal laser microscopy after being labeled with fluorescent dyes. This structure could find potential use as carriers for biological applications.

  11. Asymmetric membrane osmotic capsules for terbutaline sulphate

    Directory of Open Access Journals (Sweden)

    N G Gobade

    2012-01-01

    Full Text Available The aim of the present study was to design an asymmetric membrane capsule, an osmotic pump-based drug delivery system of ethyl cellulose for controlled release of terbutaline sulphate. asymmetric membrane capsules contains pore-forming water soluble additive, sorbitol in different concentrations in the capsule shell membrane, which after coming in contact with water, dissolves, resulting in an in situ formation of a microporous structure. The terbutaline sulphate is a β-adrenoreceptor agonist widely used in the treatment of asthma. The oral dosage regimen of terbutaline sulphate is 5 mg twice or thrice daily, the plasma half-life is approximate 3-4 h and it produces GI irritation with extensive first pass metabolism. Hence, terbutaline sulphate was chosen as a model drug with an aim to develop controlled release system. Different formulations of ethyl cellulose were prepared by phase inversion technique using different concentrations of sorbitol as pore forming agent. It was found that the thickness of the prepared asymmetric membrane capsules was increased with increase in concentration of ethyl cellulose and pore forming agent, i.e. sorbitol. The dye release study in water and 10% sodium chloride solution indicates that, the asymmetric membrane capsules follow osmotic principle to release content. The pores formed due to sorbitol were confirmed by microscopic observation of transverse section of capsule membrane. Data of in vitro release study of terbutaline sulphate from asymmetric membrane capsules indicated that, the capsules prepared with 10% and 12.5% of ethyl cellulose and 25% of sorbitol released as much as 97.44% and 76.27% in 12 h, respectively with zero order release rate. Hence asymmetric membrane capsule of 10% ethyl cellulose and 25% of sorbitol is considered as optimum for controlled oral delivery of terbutaline sulphate.

  12. Asymmetric membrane osmotic capsules for terbutaline sulphate.

    Science.gov (United States)

    Gobade, N G; Koland, Marina; Harish, K H

    2012-01-01

    The aim of the present study was to design an asymmetric membrane capsule, an osmotic pump-based drug delivery system of ethyl cellulose for controlled release of terbutaline sulphate. asymmetric membrane capsules contains pore-forming water soluble additive, sorbitol in different concentrations in the capsule shell membrane, which after coming in contact with water, dissolves, resulting in an in situ formation of a microporous structure. The terbutaline sulphate is a β-adrenoreceptor agonist widely used in the treatment of asthma. The oral dosage regimen of terbutaline sulphate is 5 mg twice or thrice daily, the plasma half-life is approximate 3-4 h and it produces GI irritation with extensive first pass metabolism. Hence, terbutaline sulphate was chosen as a model drug with an aim to develop controlled release system. Different formulations of ethyl cellulose were prepared by phase inversion technique using different concentrations of sorbitol as pore forming agent. It was found that the thickness of the prepared asymmetric membrane capsules was increased with increase in concentration of ethyl cellulose and pore forming agent, i.e. sorbitol. The dye release study in water and 10% sodium chloride solution indicates that, the asymmetric membrane capsules follow osmotic principle to release content. The pores formed due to sorbitol were confirmed by microscopic observation of transverse section of capsule membrane. Data of in vitro release study of terbutaline sulphate from asymmetric membrane capsules indicated that, the capsules prepared with 10% and 12.5% of ethyl cellulose and 25% of sorbitol released as much as 97.44% and 76.27% in 12 h, respectively with zero order release rate. Hence asymmetric membrane capsule of 10% ethyl cellulose and 25% of sorbitol is considered as optimum for controlled oral delivery of terbutaline sulphate. PMID:23204625

  13. Repair of DNA double-strand breaks in Escherichia coli cells requires synthesis of proteins that can be induced by UV light

    International Nuclear Information System (INIS)

    The repair of DNA double-strand breaks in Escherichia coli cells irradiated with γ rays occurs only after new proteins are synthesized in response to damage introduced in the genome DNA. One protein whose synthesis is thus induced is the recA protein, and previous work has shown that recA- cells do not repair double-strand breaks. However, inducing recA protein by treating cells with nalidixic acid does not induce repair of double-strand breaks, so this repair requires more than the presence of the recA protein. When repair of double-strand breaks is blocked, the genome DNA is degraded by an endonuclease-like action. Evidence is presented to show that the inducible inhibition of DNA degradation after x-irradiation [Pollard, E.C. and Randall, E.P. (1973) Radiat. Res. 55, 265] is probably caused by the inducible repair of DNA double-strand breaks

  14. Algebraic Davis Decomposition and Asymmetric Doob Inequalities

    Science.gov (United States)

    Hong, Guixiang; Junge, Marius; Parcet, Javier

    2016-04-01

    In this paper we investigate asymmetric forms of Doob maximal inequality. The asymmetry is imposed by noncommutativity. Let {({M}, τ)} be a noncommutative probability space equipped with a filtration of von Neumann subalgebras {({M}_n)_{n ≥ 1}} , whose union {bigcup_{n≥1}{M}_n} is weak-* dense in {{M}} . Let {{E}_n} denote the corresponding family of conditional expectations. As an illustration for an asymmetric result, we prove that for {1 algebraic atomic description for the involved Hardy spaces. The latter results are new even for commutative von Neumann algebras.

  15. Improved DFIG Capability during Asymmetrical Grid Faults

    DEFF Research Database (Denmark)

    Zhou, Dao; Blaabjerg, Frede

    In the wind power application, different asymmetrical types of the grid fault can be categorized after the Y/d transformer, and the positive and negative components of a single-phase fault, phase-to-phase fault, and two-phase fault can be summarized. Due to the newly introduced negative and even......, the capability of a 2 MW DFIG to ride through asymmetrical grid faults can be estimated at the existing design of the power electronics converter. Finally, a control scheme aimed to improve the DFIG capability is proposed and the simulation results validate its feasibility....

  16. Hot and flowing, asymmetric nuclear matter

    International Nuclear Information System (INIS)

    We develop a consistent treatment for hot and flowing asymmetric nuclear matter. Using the mean-field theory, predictions of the σ- ω Walecka model at finite temperature are compared with the corresponding results of the Zimanyi-Moszlowski and the non-linear models. The statistical theory of grand-canonical potentials is incorporated to the formalism. We also describe the behavior, at finite temperature, of the asymmetric and flowing nuclear matter. As an application, we describe bulk properties of neutron and protoneutron stars by considering the Tolman-Oppenheimer-Volkoff equations. (author)

  17. Asymmetric acoustic transmission in multiple frequency bands

    International Nuclear Information System (INIS)

    We report both experimentally and numerically that the multi-band device of the asymmetric acoustic transmission is realized by placing two periodic gratings with different periods on both sides of two brass plates immersed in water. The asymmetric acoustic transmission can exist in four frequency bands below 1500 kHz, which arises from the interaction between various diffractions from the two gratings and Lamb modes in the brass plates immersed in water. The results indicate that the device has the advantages of multiple band, broader bandwidth, and simpler structure. Our finding should have great potential applications in ultrasonic devices

  18. A palmprint-based cryptosystem using double encryption

    Science.gov (United States)

    Kumar, Amioy; Kumar, Ajay

    2008-03-01

    We propose a novel cryptographic construct incorporating biometrics which insures a secure communication between two channels just by using Palmprint. The cryptosystem utilizes the advantages of both symmetric and asymmetric cryptographic approaches simultaneously; we denote it as double encryption. Any document in communication is first encrypted using symmetric cryptographic approach; the symmetric key involved is then encrypted using Asymmetric approach. Finally, the concept of fuzzy vault is explored to create a secure vault around the asymmetric key. We investigate the possible usage of palmprints in fuzzy vault to develop a user friendly and reliable crypto system. The experimental results from the proposed approach on the real palmprint images suggest its possible usage in an automated palmprint based key generation system.

  19. Asymmetric cryptosystem and software design based on two-step phase-shifting interferometry and elliptic curve algorithm

    Science.gov (United States)

    Fan, Desheng; Meng, Xiangfeng; Wang, Yurong; Yang, Xiulun; Peng, Xiang; He, Wenqi; Dong, Guoyan; Chen, Hongyi

    2013-11-01

    We propose an asymmetric cryptosystem based on two-step phase-shifting interferometry (PSI) and elliptic curve (EC) public-key cryptographic algorithm, in which one image is encrypted to two interferograms by double random-phase encoding (DRPE) in Fresnel domain and two-step PSI, and the session keys such as geometrical parameters and pseudo-random seeds, are asymmetrically encoded and decoded with the aid of EC algorithm. The receiver, who possesses the corresponding private key generated by EC algorithm, can successfully decipher the transmitted data using the extracted session keys. The utilization of EC asymmetric cryptosystem solves the problem of key management and dispatch, which is inevitable in the conventional optical symmetric cryptosystems. Not only computer simulation, but also software design and development are carried out to verify the feasibility of the proposed cryptosystem.

  20. BfiI, a restriction endonuclease from Bacillus firmus S8120, which recognizes the novel non-palindromic sequence 5'-ACTGGG(N)5/4-3'.

    OpenAIRE

    Vitkute, J; Maneliene, Z; Petrusyte, M; Janulaitis, A

    1998-01-01

    A new type IIS restriction endonuclease Bfi I hasbeen partially purified from Bacillus firmus S8120. Bfi I recognizes the non-palindromic hexanucleotide sequence 5'-ACTGGG(N)5/4-3' and makes a staggered cut at the fifth base pair downstream of the recognition sequence on the upper strand, producing a single base 3' protruding end.

  1. Application of spherical Ni(OH)2/CNTs composite electrode in asymmetric supercapacitor

    Institute of Scientific and Technical Information of China (English)

    WANG Xiao-feng; RUAN Dian-bo; YOU Zheng

    2006-01-01

    The composite electrodes consisting of carbon nanotubes and spherical Ni(OH)2 are developed by mixing nickel hydroxide, carbon nanotubes and carbonyl nickel powder together in 8-1-1 ratio. A maximum capacitance of 311 F/g is obtained for an electrode prepared with the precipitation process. In order to enhance energy density, an asymmetric type pseudo-capacitor/electric double layer capacitor is considered and its electrochemical properties are investigated. Values for the specific energy and maximum specific power of 25.8 W-h/kg and 2.8 kW/kg, respectively, are demonstrated for a cell voltage between 0 and 1.6 V. By using the modified cathode of a Ni(OH)2/carbon nanotube composite electrode, the asymmetric supercapacitor exhibits high energy density and stable power characteristics.

  2. Asymmetric Electrodes Constructed with PAN-Based Activated Carbon Fiber in Capacitive Deionization

    Directory of Open Access Journals (Sweden)

    Mingzhe Li

    2014-01-01

    Full Text Available Capacitive deionization (CDI method has drawn much attention for its low energy consumption, low pollution, and convenient manipulation. Activated carbon fibers (ACFs possess high adsorption ability and can be used as CDI electrode material. Herein, two kinds of PAN-based ACFs with different specific surface area (SSA were used for the CDI electrodes. The CDI performance was investigated; especially asymmetric electrodes’ effect was evaluated. The results demonstrated that PAN-based ACFs showed a high electrosorption rate (complete electrosorption in less than half an hour and moderate electrosorption capacity (up to 0.2 mmol/g. CDI experiments with asymmetric electrodes displayed a variation in electrosorption capacity between forward voltage and reverse voltage. It can be attributed to the electrical double layer (EDL overlap effect and inner pore potential; thus the ions with smaller hydrated ionic radius can be adsorbed more easily.

  3. Induction of Chromosomal Translocations in Mouse and Human Cells Using Site-Specific Endonucleases

    OpenAIRE

    Weinstock, David M.; Brunet, Erika; Jasin, Maria

    2008-01-01

    Reciprocal chromosomal translocations are early and essential events in the malignant transformation of several tumor types, yet the precise mechanisms that mediate translocation formation are poorly understood. We review here the development of approaches to induce and recover translocations between two targeted DNA double-strand breaks (DSBs) in mammalian chromosomes. Using mouse cells, we find that nonhomologous end-joining readily mediates translocation formation between two DSBs generate...

  4. Asymmetric cell division: a persistent issue?

    OpenAIRE

    Aakre, Christopher D.; Laub, Michael T.

    2012-01-01

    Heterogeneity within a clonal population of cells can increase survival in the face of environmental stress. In a recent issue of Science, Aldridge et al. (2012) demonstrate that cell division in mycobacteria is asymmetric, producing daughter cells that differ in size, growth rate, and susceptibility to antibiotics.

  5. Asymmetric demand for energy: A cointegration approach

    Science.gov (United States)

    Maclean, Thomas Frank

    1997-12-01

    This paper uses time series data in a study of the demand for energy. One goal is to compare the results from the traditional autoregressive distributed lag (ADL) model to the error correction model (ECM) using cointegration. The second goal is to determine if the demand elasticity is asymmetric with respect to increasing and decreasing prices. This paper discusses three topics that are important to the use of time series data. The first topic is the presence and consequences unit roots which are common in time series data. The second topic is the identification of cointegrated variables and the third topic is a development of the ECM. This results in a model that can be used in either a single equation or multivariate system context and it will estimate both long run and short run elasticities. Asymmetry theory and its implications are studied along with an investigation into competing methods of creating the asymmetric variables. Simulations provided evidence that the use of dummy variables results in biased estimates and that the cumulative difference method of Wolffram/Houck gives valid estimates. The results of the empirical part of the paper show that the short run estimates of the ADL model are like those of the error correction model, but the cointegration method's long run estimates are better since they are known to be consistent and asymptotically unbiased. Tests for asymmetry do not support the theory of asymmetric long run price elasticities; however there is evidence to support the presence of asymmetric demand in the short run.

  6. Leverage bounds with default and asymmetric information

    Czech Academy of Sciences Publication Activity Database

    Boháček, Radim

    2014. [2014 North American Summer Meeting of the Econometric Society. Minneapolis (US), 19.06.2014-22.06.2014] R&D Projects: GA ČR GA402/09/1340 Institutional support: RVO:67985998 Keywords : financial markets and the macroeconomy * asymmetric and private information * occupational choice Subject RIV: AH - Economics http://editorialexpress.com/conference/NASM2014/program/NASM2014.html

  7. Asymmetric Taxation under Incremental and Sequential Investment

    OpenAIRE

    Panteghini, Paolo

    2002-01-01

    This article discusses the effects of an asymmetric tax scheme on incremental and sequential investment strategies. The tax base is equal to the firm’s return, net of an imputation rate. When the firm’s return is less than this rate, however, no tax refunds are allowed. This scheme is neutral under both income and capital uncertainty.

  8. Beam-beam issues in asymmetric colliders

    Energy Technology Data Exchange (ETDEWEB)

    Furman, M.A.

    1992-07-01

    We discuss generic beam-beam issues for proposed asymmetric e{sup +}- e{sup -} colliders. We illustrate the issues by choosing, as examples, the proposals by Cornell University (CESR-B), KEK, and SLAC/LBL/LLNL (PEP-II).

  9. Catalytic asymmetric synthesis of mycocerosic acid

    NARCIS (Netherlands)

    ter Horst, B.; Feringa, B.L.; J. Minnaard, A.

    2007-01-01

    The first catalytic asymmetric total synthesis of mycocerosic acid was achieved via the application of iterative enantioselective 1,4-addition reactions and allows for the efficient construction of 1,3-polymethyl arrays with full stereocontrol; further exemplified by the synthesis of tetramethyl-dec

  10. Evidence of asymmetric top in 130Ba

    International Nuclear Information System (INIS)

    Introduced is a new relation connecting moment of inertia, Lipas parameter and asymmetric rotor model energies and put forward much closer trend in odd even staggering of quasi γ-band. A different view point regarding generation of quasi γ-band in 130Ba have been presented

  11. Asymmetric conditional volatility in international stock markets

    Science.gov (United States)

    Ferreira, Nuno B.; Menezes, Rui; Mendes, Diana A.

    2007-08-01

    Recent studies show that a negative shock in stock prices will generate more volatility than a positive shock of similar magnitude. The aim of this paper is to appraise the hypothesis under which the conditional mean and the conditional variance of stock returns are asymmetric functions of past information. We compare the results for the Portuguese Stock Market Index PSI 20 with six other Stock Market Indices, namely the SP 500, FTSE 100, DAX 30, CAC 40, ASE 20, and IBEX 35. In order to assess asymmetric volatility we use autoregressive conditional heteroskedasticity specifications known as TARCH and EGARCH. We also test for asymmetry after controlling for the effect of macroeconomic factors on stock market returns using TAR and M-TAR specifications within a VAR framework. Our results show that the conditional variance is an asymmetric function of past innovations raising proportionately more during market declines, a phenomenon known as the leverage effect. However, when we control for the effect of changes in macroeconomic variables, we find no significant evidence of asymmetric behaviour of the stock market returns. There are some signs that the Portuguese Stock Market tends to show somewhat less market efficiency than other markets since the effect of the shocks appear to take a longer time to dissipate.

  12. Detection loophole in asymmetric Bell experiments

    OpenAIRE

    Brunner, Nicolas; Gisin, Nicolas; Scarani, Valerio; Simon, Christoph

    2007-01-01

    The problem of closing the detection loophole with asymmetric systems, such as entangled atom-photon pairs, is addressed. We show that, for the Bell inequality I_3322, a minimal detection efficiency of 43% can be tolerated for one of the particles, if the other one is always detected. We also study the influence of noise and discuss the prospects of experimental implementation.

  13. Standards vs. labels with imperfect competition and asymmetric information

    DEFF Research Database (Denmark)

    Baltzer, Kenneth Thomas

    2012-01-01

    I demonstrate that providing information about product quality is not necessarily the best way to address asymmetric information problems when markets are imperfectly competitive. In a vertical differentiation model I show that a Minimum Quality Standard, which retains asymmetric information...

  14. Standards vs. labels with imperfect competition and asymmetric information

    DEFF Research Database (Denmark)

    Baltzer, Kenneth Thomas

    I demonstrate that providing information about product quality is not necessarily the best way to address asymmetric information problems when markets are imperfectly competitive. In a vertical dierentiation model I show that a Minimum Quality Standard, which retains asymmetric information...

  15. Asymmetric Bulkheads for Cylindrical Pressure Vessels

    Science.gov (United States)

    Ford, Donald B.

    2007-01-01

    Asymmetric bulkheads are proposed for the ends of vertically oriented cylindrical pressure vessels. These bulkheads, which would feature both convex and concave contours, would offer advantages over purely convex, purely concave, and flat bulkheads (see figure). Intended originally to be applied to large tanks that hold propellant liquids for launching spacecraft, the asymmetric-bulkhead concept may also be attractive for terrestrial pressure vessels for which there are requirements to maximize volumetric and mass efficiencies. A description of the relative advantages and disadvantages of prior symmetric bulkhead configurations is prerequisite to understanding the advantages of the proposed asymmetric configuration: In order to obtain adequate strength, flat bulkheads must be made thicker, relative to concave and convex bulkheads; the difference in thickness is such that, other things being equal, pressure vessels with flat bulkheads must be made heavier than ones with concave or convex bulkheads. Convex bulkhead designs increase overall tank lengths, thereby necessitating additional supporting structure for keeping tanks vertical. Concave bulkhead configurations increase tank lengths and detract from volumetric efficiency, even though they do not necessitate additional supporting structure. The shape of a bulkhead affects the proportion of residual fluid in a tank that is, the portion of fluid that unavoidably remains in the tank during outflow and hence cannot be used. In this regard, a flat bulkhead is disadvantageous in two respects: (1) It lacks a single low point for optimum placement of an outlet and (2) a vortex that forms at the outlet during outflow prevents a relatively large amount of fluid from leaving the tank. A concave bulkhead also lacks a single low point for optimum placement of an outlet. Like purely concave and purely convex bulkhead configurations, the proposed asymmetric bulkhead configurations would be more mass-efficient than is the flat

  16. Double-Strand Break Repair in Bacteriophage T4: Recombination Effects of 3′–5′ Exonuclease Mutations

    OpenAIRE

    Shcherbakov, Victor P; Kudryashova, E. A.; Shcherbakova, T. S.; Sizova, S. T.; Plugina, L. A.

    2006-01-01

    The role of 3′–5′ exonucleases in double-strand break (DSB)-promoted recombination was studied in crosses of bacteriophage T4, in which DSBs were induced site specifically within the rIIB gene by SegC endonuclease in the DNA of only one of the parents. Frequency of rII+ recombinants was measured in two-factor crosses of the type i × ets1, where ets1 designates an insertion in the rIIB gene carrying the cleavage site for SegC and i's are rIIB or rIIA point mutations located at various distance...

  17. Molecular analysis of plasmid DNA repair within ultraviolet-irradiated Escherichia coli. I. T4 endonuclease V-initiated excision repair

    International Nuclear Information System (INIS)

    The process by which DNA-interactive proteins locate specific sequences or target sites on cellular DNA within Escherichia coli is a poorly understood phenomenon. In this study, we present the first direct in vivo analysis of the interaction of a DNA repair enzyme, T4 endonuclease V, and its substrate, pyrimidine dimer-containing plasmid DNA, within UV-irradiated E. coli. A pyrimidine dimer represents a small target site within large domains of DNA. There are two possible paradigms by which endonuclease V could locate these small target sites: a processive mechanism in which the enzyme scans DNA for dimer sites or a distributive process in which dimers are located by random three-dimensional diffusion. In order to discriminate between these two possibilities in E. coli, an in vivo DNA repair assay was developed to study the kinetics of plasmid DNA repair and the dimer frequency (i.e. the number of dimer sites on a given plasmid molecule) in plasmid DNA as a function of time during repair. Our results demonstrate that the overall process of plasmid DNA repair initiated by T4 endonuclease V (expressed from a recombinant plasmid within repair-deficient E. coli) occurs by a processive mechanism. Furthermore, by reducing the temperature of the repair incubation, the endonuclease V-catalyzed incision step has been effectively decoupled from the subsequent steps including repair patch synthesis, ligation, and supercoiling. By this manipulation, it was determined that the overall processive mechanism is composed of two phases: a rapid processive endonuclease V-catalyzed incision reaction, followed by a slower processive mechanism, the ultimate product of which is the dimer-free supercoiled plasmid molecule

  18. A label-free DNA-templated silver nanocluster probe for fluorescence on-off detection of endonuclease activity and inhibition.

    Science.gov (United States)

    Qian, Yunxia; Zhang, Yaodong; Lu, Lu; Cai, Yanan

    2014-01-15

    Endonuclease cleavage of DNA plays an important role in biological and medicinal chemistry. This study aimed to develop a reliable and sensitive method for nuclease activity assay by combining the high specificity of DNA cleavage reactions with ultrahigh fluorescence turn-on abilities of guanine-rich (G-rich) DNA sequences in proximity to silver nanoclusters (Ag NCs). The DNA-templated Ag NC (DNA-Ag NC) probe with endonuclease recognition sequence consists of NC and a G-rich probe. The NC probe was designed by adding Ag NC nucleation sequence at the 5'-end. The G-rich probe is the complementary DNA sequence modified by adding a G-rich overhang sequence at the 3'-end. Thus, the fluorescence of DNA-Ag NC probe was activated because of DNA hybridization. When these DNA-Ag NC probes were exposed to the targeted endonucleases, specific DNA cleavages occurred, and pieces of G-rich DNA fragments separated from Ag NCs, resulting in fluorescence turn-off. The endonuclease activity was quantified by monitoring the change in the fluorescence intensity. Detection was demonstrated by assaying EcoRI activity. Under optimized conditions, the fluorescence reduction efficiency was linear with the EcoRI concentration in the range of 5.0×10(-4) U μL(-1) to 3.0×10(-3) U μL(-1), with a detection limit of 3.5×10(-4) U μL(-1), which is much better than or at least comparable with that in previous reports. The potential application of the proposed method for screening endonuclease inhibitors was also demonstrated. The presented assay protocol proved to be convenient, effective, sensitive, and easy in preparing the fluorescent probe. PMID:24001584

  19. Selective inhibition by methoxyamine of the apurinic/apyrimidinic endonuclease activity associated with pyrimidine dimer-DNA glycosylases from Micrococcus luteus and bacteriophage T4

    International Nuclear Information System (INIS)

    The UV endonucleases from Micrococcus luteus and bacteriophage T4 possess two catalytic activities specific for the site of cyclobutane pyrimidine dimers in UV-irradiated DNA: a DNA glycosylase that cleaves the 5'-glycosyl bond of the dimerized pyrimidines and an apurinic/apyrimidinic (AP) endonuclease that thereupon incises the phosphodiester bond 3' to the resulting apyrimidinic site. The authors have explored the potential use of methoxyamine, a chemical that reacts at neutral pH with AP sites in DNA, as a selective inhibitor of the AP endonuclease activities residing in the M. luteus and T4 enzymes. The presence of 50 mM methoxyamine during incubation of UV-treated, [3H]thymine-labeled poly(dA) x poly(dT) with either enzyme preparation was found to protect completely the irradiated copolymer from endonucleolytic attack at dimer sites, as assayed by yield of acid-soluble radioactivity. In contrast, the dimer-DNA glycosylase activity of each enzyme remained fully functional, as monitored retrospectively by release of free thymine after either photochemical-(5 kJ/m2, 254 nm) or photoenzymic- (Escherichia coli photolyase plus visible light) induced reversal of pyrimidine dimers in the UV-damaged substrate. The data demonstrate that the inhibition of the strand-incision reaction arises because of chemical modification of the AP sites and is not due to inactivation of the enzyme by methoxyamine. The results, combined with earlier findings for 5'-acting AP endonucleases, strongly suggest that methoxyamine is a highly specific inhibitor of virtually all AP endonucleases, irrespective of their modes of action, and may therefore prove useful in a wide variety of DNA repair studies

  20. [Is it reality that the endonuclease that cleaves pre-mRNA on polyadenylation has not been discovered?].

    Science.gov (United States)

    Zarudnaia, M I; Govorun, D N

    2001-01-01

    Specific cleavage of transcript by a complex of multisubunit proteins is the first stage of polyadenylation of eukaryotic pre-mRNAs. The main participant of this reaction--endonuclease--is not discovered yet. However it is known that proteins CPSF-30 (mammalian) and Yth 1p (yeast) are homologues of the drosofila protein clipper (CLP), which displays endoribonucleolytic activity. In the N-terminal region all three proteins contain five copies of CCCH zinc finger motif that are associated with nucleolytic activity in the case of CLP. Literature data on the three above-mentioned proteins has been analysed. The results of these works do not contradict the hypothesis that exactly CPSF-30 and its homologues are the actual nucleases that cleave pre-mRNA in the process of polyadenylation. PMID:12035497

  1. The DNA repair endonuclease XPG interacts directly and functionally with the WRN helicase defective in Werner syndrome

    Energy Technology Data Exchange (ETDEWEB)

    Trego, Kelly S.; Chernikova, Sophia B.; Davalos, Albert R.; Perry, J. Jefferson P.; Finger, L. David; Ng, Cliff; Tsai, Miaw-Sheue; Yannone, Steven M.; Tainer, John A.; Campisi, Judith; Cooper, Priscilla K.

    2011-04-20

    XPG is a structure-specific endonuclease required for nucleotide excision repair (NER). XPG incision defects result in the cancer-prone syndrome xeroderma pigmentosum, whereas truncating mutations of XPG cause the severe postnatal progeroid developmental disorder Cockayne syndrome. We show that XPG interacts directly with WRN protein, which is defective in the premature aging disorder Werner syndrome, and that the two proteins undergo similar sub-nuclear redistribution in S-phase and co-localize in nuclear foci. The co-localization was observed in mid- to late-S-phase, when WRN moves from nucleoli to nuclear foci that have been shown to contain protein markers of both stalled replication forks and telomeric proteins. We mapped the interaction between XPG and WRN to the C-terminal domains of each and show that interaction with the C-terminal domain of XPG strongly stimulates WRN helicase activity. WRN also possesses a competing DNA single-strand annealing activity that, combined with unwinding, has been shown to coordinate regression of model replication forks to form Holliday junction/chicken foot intermediate structures. We tested whether XPG stimulated WRN annealing activity and found that XPG itself has intrinsic strand annealing activity that requires the unstructured R- and C-terminal domains, but not the conserved catalytic core or endonuclease activity. Annealing by XPG is cooperative, rather than additive, with WRN annealing. Taken together, our results suggest a novel function for XPG in S-phase that is at least in part carried out coordinately with WRN, and which may contribute to the severity of the phenotypes that occur upon loss of XPG.

  2. Spin-polarized current in double quantum dots

    Institute of Scientific and Technical Information of China (English)

    Li Ai-Xian; Duan Su-Qing

    2012-01-01

    We analyze the transport through asymmetric double quantum dots with an inhomogeneous Zeeman splitting in the presence of crossed dc and ac magnetic fields.A strong spin-polarized current can be obtained by changing the dc magnetic field.It is mainly due to the resonant tunnelling.But for the ferromagnetic right electrode,the electron spin resonance also plays an important role in transport.We show that the double quantum dots with three-level mixing under crossed dc and ac magnetic fields can act not only as a bipolar spin filter but also as a spin inverter under suitable conditions.

  3. Slow conformational dynamics of an endonuclease persist in its complex with its natural protein inhibitor.

    OpenAIRE

    Whittaker, S. B.; Czisch, M.; Wechselberger, R.; Kaptein, R; Hemmings, A. M.; James, R.; Kleanthous, C; Moore, G. R.

    2000-01-01

    The bacterial toxin colicin E9 is secreted by producing Escherichia coli cells with its 9.5 kDa inhibitor protein Im9 bound tightly to its 14.5 kDa C-terminal DNase domain. Double- and triple-resonance NMR spectra of the isolated DNase domain uniformly labeled with 13C/15N bound to unlabeled Im9 contain more signals than expected for a single DNase conformer, consistent with the bound DNase being present in more than one form. The presence of chemical exchange cross peaks in 750 MHz 15N-1H-15...

  4. Dynamical Localization in an Asymmetric Two-Electron Quantum Dot Molecule by an Alternating-Current Electric Field

    Institute of Scientific and Technical Information of China (English)

    LIU Yu-Shen; CHEN Hao

    2004-01-01

    @@ We investigate the dynamics of two interacting electrons in an asymmetric double coupled quantum dot under an ac electric field. The numerical results demonstrate that dynamical localization and Rabi oscillation still exist in such a system under the stronger electron correlation. The two electrons can be regarded as a quasiparticle,which move together between two dots similarly to a boson. The dynamics of two electrons in such a quantum system are mainly confined in a Q subspace, which is constructed by two double-occupied states.

  5. Dual emission in asymmetric ``giant'' PbS/CdS/CdS core/shell/shell quantum dots

    Science.gov (United States)

    Zhao, Haiguang; Sirigu, Gianluca; Parisini, Andrea; Camellini, Andrea; Nicotra, Giuseppe; Rosei, Federico; Morandi, Vittorio; Zavelani-Rossi, Margherita; Vomiero, Alberto

    2016-02-01

    Semiconducting nanocrystals optically active in the infrared region of the electromagnetic spectrum enable exciting avenues in fundamental research and novel applications compatible with the infrared transparency windows of biosystems such as chemical and biological optical sensing, including nanoscale thermometry. In this context, quantum dots (QDs) with double color emission may represent ultra-accurate and self-calibrating nanosystems. We present the synthesis of giant core/shell/shell asymmetric QDs having a PbS/CdS zinc blende (Zb)/CdS wurtzite (Wz) structure with double color emission close to the near-infrared (NIR) region. We show that the double emission depends on the excitation condition and analyze the electron-hole distribution responsible for the independent and simultaneous radiative exciton recombination in the PbS core and in the CdS Wz shell, respectively. These results highlight the importance of the driving force leading to preferential crystal growth in asymmetric QDs, and provide a pathway for the rational control of the synthesis of double color emitting giant QDs, leading to the effective exploitation of visible/NIR transparency windows.Semiconducting nanocrystals optically active in the infrared region of the electromagnetic spectrum enable exciting avenues in fundamental research and novel applications compatible with the infrared transparency windows of biosystems such as chemical and biological optical sensing, including nanoscale thermometry. In this context, quantum dots (QDs) with double color emission may represent ultra-accurate and self-calibrating nanosystems. We present the synthesis of giant core/shell/shell asymmetric QDs having a PbS/CdS zinc blende (Zb)/CdS wurtzite (Wz) structure with double color emission close to the near-infrared (NIR) region. We show that the double emission depends on the excitation condition and analyze the electron-hole distribution responsible for the independent and simultaneous radiative exciton

  6. Flexible and Asymmetric Ligand in Constructing Coordinated Complexes: Synthesis, Crystal Structures and Fluorescent Characterization

    Directory of Open Access Journals (Sweden)

    Jianhua Lin

    2010-12-01

    Full Text Available Flexible and asymmetric ligand L [L = 1-((pyridin-3-ylmethyl-1H-benzotriazole], is used as a basic backbone to construct complicated metal-organic frameworks. Two new polymers, namely, [Ag2(L2(NO32]n (1 and [Ag(L(ClO4]n (2, were synthesized and characterized by X-ray structure analysis and fluorescent spectroscopy. The complex 1 gives an “S” type double helical conformation, whereas complex 2 exhibits a 1D zigzag configuration. Different anions affect the silver coordination geometry and crystal packing topology.

  7. Control of indirect exciton population in an asymmetric quantum dot molecule

    International Nuclear Information System (INIS)

    We analyze the problem of coherent population transfer to the indirect exciton state in an asymmetric double semiconductor quantum dot molecule that interacts with an external electromagnetic field. Using the controlled rotation method, we obtain analytical solutions of the time-dependent Schrödinger equation and determine closed-form conditions for the parameters of the applied field and the quantum system that lead to complete population transfer to the indirect exciton state, in the absence of decay effects. Then, by numerical solution of the relevant density matrix equations we study the influence of decay mechanisms to the efficiency of population transfer.

  8. Asymmetric fuel assembly for BWR type reactor

    International Nuclear Information System (INIS)

    A coolant turning introduction member is properly extended at coolant flow channels on the side of control rod of an inner frame for supporting the insertion of a water channel. With such a constitution, the thermal margin of the fuel rods can be made uniform over the entire region of the channel box by supplying coolants uniformly for an asymmetrical fuel assembly which can effectively suppress local peaking coefficient thereby enabling to improve performances at limit power. In addition, in the asymmetrical fuel assembly, a flow vane disposed to the outer frame plate of a spacer is increased in the size at coolant flow channels on the side of the control rod. Then, sufficient amount of coolants can surely be supplied to fuel rods at coolant flow channels on the side of the control rod. (N.H.)

  9. ON ASYMMETRIC DISTRIBUTIONS OF SATELLITE GALAXIES

    International Nuclear Information System (INIS)

    We demonstrate that the asymmetric distribution of M31 satellites cannot be produced by tides from the Milky Way as such effects are too weak. However, loosely bound associations and groups of satellites can fall into larger halos and give rise to asymmetries. We compute the survival times for such associations. We prove that the survival time is always shortest in Keplerian potentials, and can be ∼3 times longer in logarithmic potentials. We provide an analytical formula for the dispersal time in terms of the size and velocity dispersion of the infalling structure. We show that, if an association of ∼10 dwarfs fell into the M31 halo, its present aspect would be that of an asymmetric disk of satellites. We also discuss the case of cold substructure in the Andromeda II and Ursa Minor dwarfs

  10. Cosmological signatures of time-asymmetric gravity

    CERN Document Server

    Cortês, Marina; Smolin, Lee

    2016-01-01

    We develop the model proposed by Cort\\^es, Gomes & Smolin, to predict cosmological signatures of time-asymmetric extensions of general relativity they proposed recently. Within this class of models the equation of motion of chiral fermions is modified by a torsion term. This term leads to a dispersion law for neutrinos that associates a new time-varying energy with each particle. We find a new neutrino contribution to the Friedmann equation resulting from the torsion term in the Ashtekar connection. In this note we explore the phenomenology of this term and observational consequences for cosmological evolution. We show that constraints on the critical energy density will ordinarily render this term unobservably small, a maximum of order $10^{-25}$ of the neutrino energy density today. However, if the time-asymmetric dark energy is tuned to cancel the cosmological constant, the torsion effect may be a dark matter candidate.

  11. Effects of asymmetric sitting on spinal balance

    Science.gov (United States)

    Woo, Hee Soon; Oh, Jong Chi; Won, Sung Yoon

    2016-01-01

    [Purpose] To investigate the effects of two common asymmetric sitting positions on spinal balance. [Subjects and Methods] Thirty-seven healthy subjects in their twenties were enrolled and randomly divided into two groups. Asymmetric positions of resting the chin on a hand and crossing the legs were performed by each group for 1 hour. After 1 hour, the subjects lay in the supine position again and spinal imbalance was measured using a device. [Results] After 1 hour of resting with the chin on a hand, sagittal imbalance, coronal imbalance, pelvic obliquity and lordosis angle presented spinal imbalance worsening of 1 hour of crossing legs, sagittal imbalance, pelvic torsion showed in mainly learned spinal imbalance living. [Conclusion] Good posture could be an innate ability, however it through habits. So this study is meaningful from the perspective of the importance of good posture. PMID:27065291

  12. Mixtures of Shifted Asymmetric Laplace Distributions

    OpenAIRE

    Franczak, Brian C.; Browne, Ryan P.; McNicholas, Paul D.

    2012-01-01

    A mixture of shifted asymmetric Laplace distributions is introduced and used for clustering and classification. A variant of the EM algorithm is developed for parameter estimation by exploiting the relationship with the general inverse Gaussian distribution. This approach is mathematically elegant and relatively computationally straightforward. Our novel mixture modelling approach is demonstrated on both simulated and real data to illustrate clustering and classification applications. In thes...

  13. Competitive Price and Quality Under Asymmetric Information

    OpenAIRE

    Gerard J. Tellis; Birger Wernerfelt

    1987-01-01

    We present an analysis of equilibrium in markets with asymmetrically informed consumers. Some consumers know both price and quality of all sellers, whereas others know neither but may search among sellers. The equilibrium correlation between price and quality generally increases with the level of information in the market and can be negative when this level is sufficiently small. A meta-analysis of the available empirical studies strongly supports the model's predictions.

  14. Cosmological signatures of time-asymmetric gravity

    OpenAIRE

    Cortês, Marina; Liddle, Andrew R; Smolin, Lee

    2016-01-01

    We develop the model proposed by Cort\\^es, Gomes & Smolin, to predict cosmological signatures of time-asymmetric extensions of general relativity they proposed recently. Within this class of models the equation of motion of chiral fermions is modified by a torsion term. This term leads to a dispersion law for neutrinos that associates a new time-varying energy with each particle. We find a new neutrino contribution to the Friedmann equation resulting from the torsion term in the Ashtekar conn...

  15. Relative profit maximization in asymmetric oligopoly

    OpenAIRE

    Satoh, Atsuhiro; Tanaka, Yasuhito

    2014-01-01

    We analyze Bertrand and Cournot equilibria in an asymmetric oligopoly in which the firms produce differentiated substitutable goods and seek to maximize their relative profits instead of their absolute profits. Assuming linear demand functions and constant marginal costs we show the following results. If the marginal cost of a firm is lower (higher) than the average marginal cost over the industry, its output at the Bertrand equilibrium is larger (smaller) than that at the Cournot equilibrium...

  16. Asymmetric inheritance of cytoophidia in Schizosaccharomyces pombe

    OpenAIRE

    Jing Zhang; Lydia Hulme; Ji-Long Liu

    2014-01-01

    ABSTRACT A general view is that Schizosaccharomyces pombe undergoes symmetric cell division with two daughter cells inheriting equal shares of the content from the mother cell. Here we show that CTP synthase, a metabolic enzyme responsible for the de novo synthesis of the nucleotide CTP, can form filamentous cytoophidia in the cytoplasm and nucleus of S. pombe cells. Surprisingly, we observe that both cytoplasmic and nuclear cytoophidia are asymmetrically inherited during cell division. Our t...

  17. Interfacial properties of charge asymmetric ionic liquids

    OpenAIRE

    Alejandre, Jose; Bresme, Fernando; Gonzalez-Melchor, Minerva

    2009-01-01

    We report molecular dynamics simulations of the coexistence and interfacial properties of ionic liquids as a function of cation/anion, (z$_+$ : z$_-$) = (2:-1), (4:-1), charge asymmetry. Our results correct previous computations of the coexistence curve of (2:-1) charge asymmetric systems, obtained via the fine-lattice discretization method. In agreement with previous computations we report a reduction in the critical temperature and an increase in the critical density with charge asymmetry. ...

  18. Asymmetric directed polymers in random environments

    OpenAIRE

    Flores, Gregorio R. Moreno

    2010-01-01

    The model of Brownian Percolation has been introduced as an approximation of discrete last-passage percolation models close to the axis. It allowed to compute some explicit limits and prove fluctuation theorems for these, based on the relations between the Brownian percolation and random matrices. Here, we present two approaches that allow to treat discrete asymmetric models of directed polymers. In both cases, the behaviour is universal, meaning that the results do not depend on the precise ...

  19. Neuronal alignment on asymmetric textured surfaces

    OpenAIRE

    Beighley, Ross; Spedden, Elise; Sekeroglu, Koray; Atherton, Timothy; Demirel, Melik C.; Staii, Cristian

    2012-01-01

    Axonal growth and the formation of synaptic connections are key steps in the development of the nervous system. Here, we present experimental and theoretical results on axonal growth and interconnectivity in order to elucidate some of the basic rules that neuronal cells use for functional connections with one another. We demonstrate that a unidirectional nanotextured surface can bias axonal growth. We perform a systematic investigation of neuronal processes on asymmetric surfaces and quantify...

  20. On asymmetric collisions with large disruption parameters

    International Nuclear Information System (INIS)

    Collisions between a weak electron bunch and a strong positron bunch are studied within a flat model. Electrons are tracked through the transverse space charge field of the positron bunch, and it is shown that positrons in a storage ring may remain stable after asymmetric collisions with a weak electron bunch in spite of large values of the electron disruption parameter. The plasma oscillations that affect collisions with large disruption parameters may be suppressed by properly matching the electrons. 8 refs., 5 figs

  1. Asymmetric dark matter from hidden sector baryogenesis

    Energy Technology Data Exchange (ETDEWEB)

    Dutta, Bhaskar [Department of Physics and Astronomy, Mitchell Institute for Fundamental Physics, Texas A and M University, College Station, TX 77843 (United States); Kumar, Jason, E-mail: jkumar@hawaii.edu [Department of Physics and Astronomy, University of Hawai' i, Honolulu, HI 96822 (United States)

    2011-05-23

    We consider the production of asymmetric dark matter during hidden sector baryogenesis. We consider a particular supersymmetric model where the dark matter candidate has a number density approximately equal to the baryon number density, with a mass of the same scale as the b, c and {tau}. Both baryon asymmetry and dark matter are created at the same time in this model. We describe collider and direct detection signatures of this model.

  2. Trapdoor Privacy in Asymmetric Searchable Encryption Schemes

    OpenAIRE

    Delerue Arriaga, Afonso; TANG, QIANG; Ryan, Peter

    2014-01-01

    Asymmetric searchable encryption allows searches to be carried over ciphertexts, through delegation, and by means of trapdoors issued by the owner of the data. Public Key Encryption with Keyword Search (PEKS) is a primitive with such functionality that provides delegation of exact-match searches. As it is important that ciphertexts preserve data privacy, it is also important that trapdoors do not expose the user’s search criteria. The difficulty of formalizing a security model for trapdoor pr...

  3. Asymmetric deformation of contracting human gastrocnemius muscle

    OpenAIRE

    Kinugasa, Ryuta; Hodgson, John A.; Edgerton, V. Reggie; Sinha, Shantanu

    2011-01-01

    Muscle fiber deformation is related to its cellular structure, as well as its architectural arrangement within the musculoskeletal system. While playing an important role in aponeurosis displacement, and efficiency of force transmission to the tendon, such deformation also provides important clues about the underlying mechanical structure of the muscle. We hypothesized that muscle fiber cross section would deform asymmetrically to satisfy the observed constant volume of muscle during a contra...

  4. Interfacial properties of charge asymmetric ionic liquids

    OpenAIRE

    2009-01-01

    Abstract We report molecular dynamics simulations of the coexistence and interfacial properties of ionic liquids as a function of cation/anion, (z$_+$ : z$_-$) = (2:-1), (4:-1), charge asymmetry. Our results correct previous computations of the coexistence curve of (2:-1) charge asymmetric systems, obtained via the fine-lattice discretization method. In agreement with previous computations we report a reduction in the critical temperature and an increase in the critical density wit...

  5. Do Daily Retail Gasoline Prices adjust Asymmetrically?

    OpenAIRE

    Bettendorf, Leon; Geest, Stéphanie; Kuper, G.

    2005-01-01

    This paper analyzes adjustments in the Dutch retail gasoline prices. We estimate an error correction model on changes in the daily retail price for gasoline (taxes excluded) for the period 1996-2004 taking care of volatility clustering by estimating an EGARCH model. It turns out the volatility process is asymmetrical: an unexpected increase in the producer price has a larger effect on the variance of the producer price than an unexpected decrease. We do not find evidence for amount asymmetry,...

  6. OFFICER AND COMMANDER IN ASYMMETRIC WARFARE OPERATIONS

    OpenAIRE

    Giuseppe CAFORIO

    2013-01-01

    Starting from the data of a field research conducted among soldiers with asymmetric warfare experiences from nine different countries, the author seeks to identify and shed light on the various problems that officers with command responsibilities had to face during their missions. A picture emerges of feelings and experiences relating to their first impression upon arriving in the theatre, relations with local armed forces, relations with the local population and local authorities, relations ...

  7. Dust temperatures in asymmetric prestellar cores

    OpenAIRE

    Stamatellos, D.; Whitworth, A. P.

    2004-01-01

    We present 2D Monte Carlo radiative transfer simulations of flattened prestellar cores. We argue the importance of observing prestellar cores near the peak of their emission spectra, and we point out observable characteristic features on isophotal maps of asymmetric cores at FIR wavelengths that are indicative of the cores' density and temperature structure. These features are on scales 1/5 to 1/3 of the overall core size, and so high resolution observations are needed to observe them. Finall...

  8. Prospects for Asymmetric PNe with ALMA

    CERN Document Server

    Huggins, P J

    2010-01-01

    Millimeter and sub-millimeter observations have made fundamental contributions to our current understanding of the transition from AGB stars to white dwarfs. The approaching era of ALMA brings significantly enhanced observing capabilities at these wavelengths and promises to push back the frontiers in a number of ways. We examine the scientific prospects of this new era for PNe, with an emphasis on how developments may contribute to the goals of the asymmetric PNe community.

  9. Surface segregation of conformationally asymmetric polymer blends

    OpenAIRE

    Stepanow, Semjon; Fedorenko, Andrei A.

    2005-01-01

    We have generalized the Edwards' method of collective description of dense polymer systems in terms of effective potentials to polymer blends in the presence of a surface. With this method we have studied conformationally asymmetric athermic polymer blends in the presence of a hard wall to the first order in effective potentials. For polymers with the same gyration radius $R_g$ but different statistical segment lengths $l_{A}$ and $l_{B}$ the excess concentration of stiffer polymers at the su...

  10. Legal Dilemmas in Fighting Asymmetrical Conflicts

    Directory of Open Access Journals (Sweden)

    Pnina Sharvit Baruch

    2012-04-01

    Full Text Available What legal rules apply to armed confrontations against non-state elements in areas populated by civilians? What rules apply when the enemy does not honor the basic laws of warfare - does not distinguish itself from the local population, and even uses it for shelter and as a base of operations? This essay, which presents my position on the issue, refers to such confrontations as "asymmetrical conflicts."

  11. Venture Capital Contracting Under Asymmetric Information

    OpenAIRE

    Jeffrey Trester

    1993-01-01

    The author develops a model of venture capital contracting in which the entrepreneur and venture capitalist contract under symmetric information. A condition of asymmetric information may arise subsequent to the first contract. The author shows that this condition makes debt contracts infeasible and leads to the use of preferred equity contracts. The author notes that discussions of the relation between venture capital and capital structure are rare. This paper expands the literature by addre...

  12. Applications of Chiral Anions in Asymmetric Catalysis

    OpenAIRE

    Hamilton, Gregory Lawrence

    2011-01-01

    The synthesis of molecules with control over their three-dimensional configuration, known as absolute stereochemistry, is one of the highest goals of synthetic organic chemists. As is so often the case, we strive to reach the facility and efficiency with which Nature achieves this goal. Fortunately, the chemist's imagination allows us to envision nearly unlimited possibilities for new modes of catalysis. In this dissertation, I discuss one branch of asymmetric catalysis that has in a short ti...

  13. Asymmetric Reversal in Inhomogeneous Magnetic Heterostructures

    OpenAIRE

    Li, Zhi-Pan; Petracic, Oleg; Morales, Rafael; Olamit, Justin; Batlle, Xavier; Liu, Kai; Schuller, Ivan K.

    2006-01-01

    Asymmetric magnetization reversal is an unusual phenomenon in antiferromagnet/ferromagnet (AF/FM) exchange biased bilayers. We investigated this phenomenon in a simple model system experimentally and by simulation assuming inhomogeneously distributed interfacial AF moments. The results suggest that the observed asymmetry originates from the intrinsic broken symmetry of the system, which results in local incomplete domain walls parallel to the interface in reversal to negative saturation of th...

  14. The Cambridge Double Star Atlas

    Science.gov (United States)

    MacEvoy, Bruce; Tirion, Wil

    2015-12-01

    Preface; What are double stars?; The binary orbit; Double star dynamics; Stellar mass and the binary life cycle; The double star population; Detecting double stars; Double star catalogs; Telescope optics; Preparing to observe; Helpful accessories; Viewing challenges; Next steps; Appendices: target list; Useful formulas; Double star orbits; Double star catalogs; The Greek alphabet.

  15. Asymmetric threat data mining and knowledge discovery

    Science.gov (United States)

    Gilmore, John F.; Pagels, Michael A.; Palk, Justin

    2001-03-01

    Asymmetric threats differ from the conventional force-on- force military encounters that the Defense Department has historically been trained to engage. Terrorism by its nature is now an operational activity that is neither easily detected or countered as its very existence depends on small covert attacks exploiting the element of surprise. But terrorism does have defined forms, motivations, tactics and organizational structure. Exploiting a terrorism taxonomy provides the opportunity to discover and assess knowledge of terrorist operations. This paper describes the Asymmetric Threat Terrorist Assessment, Countering, and Knowledge (ATTACK) system. ATTACK has been developed to (a) data mine open source intelligence (OSINT) information from web-based newspaper sources, video news web casts, and actual terrorist web sites, (b) evaluate this information against a terrorism taxonomy, (c) exploit country/region specific social, economic, political, and religious knowledge, and (d) discover and predict potential terrorist activities and association links. Details of the asymmetric threat structure and the ATTACK system architecture are presented with results of an actual terrorist data mining and knowledge discovery test case shown.

  16. Multiple Traveling Salesmen in Asymmetric Metrics

    CERN Document Server

    Friggstad, Zachary

    2011-01-01

    We consider some generalizations of the Asymmetric Traveling Salesman Path problem. Suppose we have an asymmetric metric G = (V,A) with two distinguished nodes s,t. We are also given a positive integer k. The goal is to find k paths of minimum total cost from s to t whose union spans all nodes. We call this the k-Person Asymmetric Traveling Salesmen Path problem (k-ATSPP). Our main result for k-ATSPP is a bicriteria approximation that, for some parameter b >= 1 we may choose, finds between k and k + k/b paths of total length O(b log |V|) times the optimum value of an LP relaxation based on the Held-Karp relaxation for the Traveling Salesman problem. On one extreme this is an O(log |V|)-approximation that uses up to 2k paths and on the other it is an O(k log |V|)-approximation that uses exactly k paths. Next, we consider the case where we have k pairs of nodes (s_1,t_1), ..., (s_k,t_k). The goal is to find an s_i-t_i path for every pair such that each node of G lies on at least one of these paths. Simple appro...

  17. Asymmetric Conditional Volatility in International Stock Markets

    CERN Document Server

    Ferreira, N B; Menezes, R; Ferreira, Nuno B.; Mendes, Diana A.; Menezes, Rui

    2006-01-01

    Recent studies show that a negative shock in stock prices will generate more volatility than a positive shock of similar magnitude. The aim of this paper is to appraise the hypothesis under which the conditional mean and the conditional variance of stock returns are asymmetric functions of past information. We compare the results for the Portuguese Stock Market Index PSI 20 with six other Stock Market Indices, namely the S&P 500, FTSE100, DAX 30, CAC 40, ASE 20, and IBEX 35. In order to assess asymmetric volatility we use autoregressive conditional heteroskedasticity specifications known as TARCH and EGARCH. We also test for asymmetry after controlling for the effect of macroeconomic factors on stock market returns using TAR and M-TAR specifications within a VAR framework. Our results show that the conditional variance is an asymmetric function of past innovations raising proportionately more during market declines, a phenomenon known as the leverage effect. However, when we control for the effect of chan...

  18. Double outlet right ventricle

    Science.gov (United States)

    ... medlineplus.gov/ency/article/007328.htm Double outlet right ventricle To use the sharing features on this page, please enable JavaScript. Double outlet right ventricle (DORV) is a heart disease that is ...

  19. Exploring the decomposition pathways of iron asymmetric transfer hydrogenation catalysts.

    Science.gov (United States)

    Lagaditis, Paraskevi O; Sues, Peter E; Lough, Alan J; Morris, Robert H

    2015-07-21

    Our group has developed a series of iron-based asymmetric transfer hydrogenation (ATH) catalysts for the reduction of polar double bonds. The activation of the precatalysts as well as the catalytic mechanism have been thoroughly investigated, but the decomposition pathways of these systems are poorly understood. Herein, we report a study of the deactivation pathways for an iron ATH catalyst under catalytically relevant conditions. The decomposition pathways were examined using experimental techniques and density functional theory (DFT) calculations. The major decomposition products that formed, Fe(CO)((Et)2PCH2CH2CHCHNCH2CH2P(Et)2) (3a) and Fe(CO)((Et)2PCH2CH2C(Ph)C(Ph)NCH2CH2P(Et)2) (3b), had two amido donors as well as a C=C bond on the diamine backbone of the tetradentate ligand. These species were identified by NMR studies and one was isolated as a bimetallic complex with Ru(II)Cp*. Two minor iron hydride species also formed concurrently with 3a, as determined by NMR studies, one of which was isolated and contained a fully saturated ligand as well as a hydride ligand. None of the compounds that were isolated were found to be active ATH catalysts. PMID:25373607

  20. Double orifice mitral valve: A case report

    Directory of Open Access Journals (Sweden)

    Musić Ljilja

    2016-01-01

    Full Text Available Introduction. Double orifice mitrol valve (DOMV is a very rare congenital heart defect. Case report. We reported 20-year-old male referred to our center due to evaluation of his cardiologic status. He was operated on shortly after birth for a tracheoesophageal fistula. Accidentally, echocardiography examination at the age of 4 years revealed double orifice mitral valve (DOMV without the presence of mitral regurgitation, as well as mitral stenosis, with normal dimensions of all cardiac chambers. The patient was asymptomatic, even more he was a kick boxer. His physical finding was normal. Electrocardiography showed regular sinus rhythm, incomplete right bundle branch block. Transthoracic echocardiography (TTE examination revealed the normal size of the left atrial, mitral leaflets were slightly more redundant. The left and right heart chambers, aorta, tricuspid valve and pulmonary artery valve were normal. During TTE examination on a short axis view two asymmetric mitral orifices were seen as a double mitral orifice through which we registered normal flow, without regurgitation and mitral stenosis. Transesophageal echocardiography (TEE examination from the transgastric view at the level of mitral valve, showed 2 single asymmetric mitral orifices separated by fibrous tissue, mitral leaflet with a separate insertion of hordes for each orifice. Conclusion. The presented patient with DOMV is the only one recognized in our country. The case is interesting because during 16-year a follow-up period there were no functional changes despite the fact that he performed very demanded sport activities. This is very important because there is no information in the literature about that.

  1. Electrochemical study of aqueous asymmetric FeWO4/MnO2 supercapacitor

    Science.gov (United States)

    Goubard-Bretesché, Nicolas; Crosnier, Olivier; Buvat, Gaëtan; Favier, Frédéric; Brousse, Thierry

    2016-09-01

    The concept of an asymmetric FeWO4/MnO2 electrochemical capacitor cycled in a neutral aqueous electrolyte is presented for the first time. Commercially available cryptomelane-type MnO2 and synthesized nanocrystalline FeWO4 were used as positive and negative electrode materials, respectively. Prior to assembling the cell, the electrodes have been individually tested in a 5 M LiNO3 electrolyte solution to define both the adequate balance of active material in the supercapacitor and the proper working voltage window. Then, the full asymmetric device has been cycled between 0 and 1.4 V for over 40,000 cycles and subjected to accelerated ageing tests under floating conditions at different voltages, without any significant change on its electrochemical behavior. This remarkable stability shows the interest of developing full oxide-based asymmetric supercapacitors operating in non-toxic aqueous electrolytes that could compete with commercial carbon-based electrochemical double-layer capacitors.

  2. A Ca2+-induced mitochondrial permeability transition causes complete release of rat liver endonuclease G activity from its exclusive location within the mitochondrial intermembrane space. Identification of a novel endo-exonuclease activity residing within the mitochondrial matrix

    OpenAIRE

    Davies, Adrian M.; Hershman, Stuart; Stabley, Gabriel J.; Hoek, Jan B.; Peterson, Jason; Cahill, Alan

    2003-01-01

    Endonuclease G, a protein historically thought to be involved in mitochondrial DNA (mtDNA) replication, repair, recombination and degradation, has recently been reported to be involved in nuclear DNA degradation during the apoptotic process. As a result, its involvement in mtDNA homeostasis has been called into question and has necessitated detailed analyses of its precise location within the mitochondrion. Data is presented localizing rat liver endonuclease G activity exclusively to the mito...

  3. Doubling rational normal curves

    OpenAIRE

    Notari, Roberto; Ojeda, Ignacio; Spreafico, Maria Luisa

    2008-01-01

    In this paper, we study double structures supported on rational normal curves. After recalling the general construction of double structures supported on a smooth curve described in \\cite{fer}, we specialize it to double structures on rational normal curves. To every double structure we associate a triple of integers $ (2r,g,n) $ where $ r $ is the degree of the support, $ n \\geq r $ is the dimension of the projective space containing the double curve, and $ g $ is the arithmetic genus of the...

  4. Double-double effect and coordination number

    International Nuclear Information System (INIS)

    The original method of interpretation together with its theoretical foundations is developed, making it possible to use location and direction of the double-double (tetrad) effect within the Ln and An series to determine the coordination number (CN) complexes of the f-block elements. The method is applied for potentiometric and radiometric equilibrium studies. It has been pointed and that the decisive factor for the direction of the double-double effect in the case of the Gibbs energy variations is a difference in the CN of the f-element ion between the reaction product complex and that for the reaction substrate the ''regular'' effect for a given tetrad is accompanied by decrease in the CN while the ''reverse'' effect by increase in the CN. (author). 122 refs, 5 tabs, 8 figs

  5. Novel repair activities of AlkA (3-methyladenine DNA glycosylase II) and endonuclease VIII for xanthine and oxanine, guanine lesions induced by nitric oxide and nitrous acid

    OpenAIRE

    Terato, Hiroaki; Masaoka, Aya; Asagoshi, Kenjiro; Honsho, Akiko; Ohyama, Yoshihiko; Suzuki, Toshinori; Yamada, Masaki; Makino, Keisuke; Yamamoto, Kazuo; Ide, Hiroshi

    2002-01-01

    Nitrosation of guanine in DNA by nitrogen oxides such as nitric oxide (NO) and nitrous acid leads to formation of xanthine (Xan) and oxanine (Oxa), potentially cytotoxic and mutagenic lesions. In the present study, we have examined the repair capacity of DNA N-glycosylases from Escherichia coli for Xan and Oxa. The nicking assay with the defined substrates containing Xan and Oxa revealed that AlkA [in combination with endonuclease (Endo) IV] and Endo VIII recognized Xan in the tested enzymes....

  6. Amino Acid Residues in the GIY-YIG Endonuclease II of Phage T4 Affecting Sequence Recognition and Binding as Well as Catalysis▿ †

    Science.gov (United States)

    Lagerbäck, Pernilla; Carlson, Karin

    2008-01-01

    Phage T4 endonuclease II (EndoII), a GIY-YIG endonuclease lacking a carboxy-terminal DNA-binding domain, was subjected to site-directed mutagenesis to investigate roles of individual amino acids in substrate recognition, binding, and catalysis. The structure of EndoII was modeled on that of UvrC. We found catalytic roles for residues in the putative catalytic surface (G49, R57, E118, and N130) similar to those described for I-TevI and UvrC; in addition, these residues were found to be important for substrate recognition and binding. The conserved glycine (G49) and arginine (R57) were essential for normal sequence recognition. Our results are in agreement with a role for these residues in forming the DNA-binding surface and exposing the substrate scissile bond at the active site. The conserved asparagine (N130) and an adjacent proline (P127) likely contribute to positioning the catalytic domain correctly. Enzymes in the EndoII subfamily of GIY-YIG endonucleases share a strongly conserved middle region (MR, residues 72 to 93, likely helical and possibly substituting for heterologous helices in I-TevI and UvrC) and a less strongly conserved N-terminal region (residues 12 to 24). Most of the conserved residues in these two regions appeared to contribute to binding strength without affecting the mode of substrate binding at the catalytic surface. EndoII K76, part of a conserved NUMOD3 DNA-binding motif of homing endonucleases found to overlap the MR, affected both sequence recognition and catalysis, suggesting a more direct involvement in positioning the substrate. Our data thus suggest roles for the MR and residues conserved in GIY-YIG enzymes in recognizing and binding the substrate. PMID:18539732

  7. Amino acid residues in the GIY-YIG endonuclease II of phage T4 affecting sequence recognition and binding as well as catalysis.

    Science.gov (United States)

    Lagerbäck, Pernilla; Carlson, Karin

    2008-08-01

    Phage T4 endonuclease II (EndoII), a GIY-YIG endonuclease lacking a carboxy-terminal DNA-binding domain, was subjected to site-directed mutagenesis to investigate roles of individual amino acids in substrate recognition, binding, and catalysis. The structure of EndoII was modeled on that of UvrC. We found catalytic roles for residues in the putative catalytic surface (G49, R57, E118, and N130) similar to those described for I-TevI and UvrC; in addition, these residues were found to be important for substrate recognition and binding. The conserved glycine (G49) and arginine (R57) were essential for normal sequence recognition. Our results are in agreement with a role for these residues in forming the DNA-binding surface and exposing the substrate scissile bond at the active site. The conserved asparagine (N130) and an adjacent proline (P127) likely contribute to positioning the catalytic domain correctly. Enzymes in the EndoII subfamily of GIY-YIG endonucleases share a strongly conserved middle region (MR, residues 72 to 93, likely helical and possibly substituting for heterologous helices in I-TevI and UvrC) and a less strongly conserved N-terminal region (residues 12 to 24). Most of the conserved residues in these two regions appeared to contribute to binding strength without affecting the mode of substrate binding at the catalytic surface. EndoII K76, part of a conserved NUMOD3 DNA-binding motif of homing endonucleases found to overlap the MR, affected both sequence recognition and catalysis, suggesting a more direct involvement in positioning the substrate. Our data thus suggest roles for the MR and residues conserved in GIY-YIG enzymes in recognizing and binding the substrate. PMID:18539732

  8. Delta-elimination by T4 endonuclease V at a thymine dimer site requires a secondary binding event and amino acid Glu-23.

    Science.gov (United States)

    Latham, K A; Lloyd, R S

    1995-07-11

    Endonuclease V from bacteriophage T4 is a well characterized enzyme that initiates the repair of ultraviolet light induced pyrimidine dimers. Scission of the phosphodiester backbone between the pyrimidines within a dimer, or 3' to an abasic (AP) site, occurs by a beta-elimination mechanism. In addition, high concentrations of endonuclease V have been reported to catalyze the cleavage of the C5'-O-P bond in a reaction referred to as delta-elimination. To better understand the enzymology of endonuclease V, the delta-elimination reaction of the enzyme has been investigated using an oligonucleotide containing a site-specific cis-syn cyclobutane thymine dimer. The slower kinetics of the delta-elimination reaction compared to beta-elimination and the ability of unlabeled dimer-containing DNA to compete more efficiently for delta-elimination than beta-elimination indicate that delta-elimination most likely occurs during a separate enzyme encounter with the incised DNA. Previous studies have shown that both the alpha-amino group of the N-terminus and the acidic residue Glu-23 are necessary for the N-glycosylase and AP lyase activities of endonuclease V. Experiments with T2P, E23Q, and E23D mutants, which are defective in pyrimidine dimer-specific nicking, demonstrated that delta-elimination requires Glu-23, but not the primary amine at the N-terminus. In fact, the T2P mutant was much more efficient at promoting delta-elimination than the wild-type enzyme. Besides lending further proof that delta-elimination requires a second encounter between enzyme and DNA, this result may reflect an enhanced binding of the T2P mutant to dimer-containing DNA. PMID:7612620

  9. Mutational analysis of the binding pockets of the diketo acid inhibitor L-742,001 in the influenza virus PA endonuclease.

    Science.gov (United States)

    Stevaert, Annelies; Dallocchio, Roberto; Dessì, Alessandro; Pala, Nicolino; Rogolino, Dominga; Sechi, Mario; Naesens, Lieve

    2013-10-01

    The influenza virus PA endonuclease, which cleaves capped host pre-mRNAs to initiate synthesis of viral mRNA, is a prime target for antiviral therapy. The diketo acid compound L-742,001 was previously identified as a potent inhibitor of the influenza virus endonuclease reaction, but information on its precise binding mode to PA or potential resistance profile is limited. Computer-assisted docking of L-742,001 into the crystal structure of inhibitor-free N-terminal PA (PA-Nter) indicated a binding orientation distinct from that seen in a recent crystallographic study with L-742,001-bound PA-Nter (R. M. DuBois et al., PLoS Pathog. 8:e1002830, 2012). A comprehensive mutational analysis was performed to determine which amino acid changes within the catalytic center of PA or its surrounding hydrophobic pockets alter the antiviral sensitivity to L-742,001 in cell culture. Marked (up to 20-fold) resistance to L-742,001 was observed for the H41A, I120T, and G81F/V/T mutant forms of PA. Two- to 3-fold resistance was seen for the T20A, L42T, and V122T mutants, and the R124Q and Y130A mutants were 3-fold more sensitive to L-742,001. Several mutations situated at noncatalytic sites in PA had no or only marginal impact on the enzymatic functionality of viral ribonucleoprotein complexes reconstituted in cell culture, consistent with the less conserved nature of these PA residues. Our data provide relevant insights into the binding mode of L-742,001 in the PA endonuclease active site. In addition, we predict some potential resistance sites that should be taken into account during optimization of PA endonuclease inhibitors toward tight binding in any of the hydrophobic pockets surrounding the catalytic center of the enzyme. PMID:23824822

  10. Enrichment of G2/M cell cycle phase in human pluripotent stem cells enhances HDR-mediated gene repair with customizable endonucleases

    OpenAIRE

    Diane Yang; Scavuzzo, Marissa A.; Jolanta Chmielowiec; Robert Sharp; Aleksandar Bajic; Malgorzata Borowiak

    2016-01-01

    Efficient gene editing is essential to fully utilize human pluripotent stem cells (hPSCs) in regenerative medicine. Custom endonuclease-based gene targeting involves two mechanisms of DNA repair: homology directed repair (HDR) and non-homologous end joining (NHEJ). HDR is the preferred mechanism for common applications such knock-in, knock-out or precise mutagenesis, but remains inefficient in hPSCs. Here, we demonstrate that synchronizing synchronizing hPSCs in G2/M with ABT phase increases ...

  11. Selective metal binding to Cys-78 within endonuclease V causes an inhibition of catalytic activities without altering nontarget and target DNA binding

    International Nuclear Information System (INIS)

    T4 endonuclease V is a pyrimidine dimer-specific DNA repair enzyme which has been previously shown not to require metal ions for either of its two catalytic activities or its DNA binding function. However, we have investigated whether the single cysteine within the enzyme was able to bind metal salts and influence the various activities of this repair enzyme. A series of metals (Hg2+, Ag+, Cu+) were shown to inactivate both endonuclease Vs pyrimidine dimer-specific DNA glycosylase activity and the subsequent apurinic nicking activity. The binding of metal to endonuclease V did not interfere with nontarget DNA scanning or pyrimidine dimer-specific binding. The Cys-78 codon within the endonuclease V gene was changed by oligonucleotide site-directed mutagenesis to Thr-78 and Ser-78 in order to determine whether the native cysteine was directly involved in the enzyme's DNA catalytic activities and whether the cysteine was primarily responsible for the metal binding. The mutant enzymes were able to confer enhanced ultraviolet light (UV) resistance to DNA repair-deficient Escherichia coli at levels equal to that conferred by the wild type enzyme. The C78T mutant enzyme was purified to homogeneity and shown to be catalytically active on pyrimidine dimer-containing DNA. The catalytic activities of the C78T mutant enzyme were demonstrated to be unaffected by the addition of Hg2+ or Ag+ at concentrations 1000-fold greater than that required to inhibit the wild type enzyme. These data suggest that the cysteine is not required for enzyme activity but that the binding of certain metals to that amino acid block DNA incision by either preventing a conformational change in the enzyme after it has bound to a pyrimidine dimer or sterically interfering with the active site residue's accessibility to the pyrimidine dimer

  12. Dynamics of atom tunnelling in a symmetric double well coupled to an asymmetric double well: The case of malonaldehyde

    Indian Academy of Sciences (India)

    S Ghosh; S P Bhattacharyya

    2012-01-01

    The quantum dynamics of intramolecular H-atom transfer in malonaldehyde is investigated with a model two-dimensional Hamiltonian constructed with the help of available ab initio theoretical data on the relevant portion of the potential energy surface. At zero temperature, the H-atom transfer takes place by tunnelling leading to cis-cis isomerization while the cis-trans channel remains closed. Local excitation of the cis-trans mode by an external field is predicted to quench cis-cis tunnelling isomerization while excitation of the cis-cis mode is found to enhance the isomerization by tunnelling.

  13. Intron-encoded endonuclease I-TevII binds across the minor groove and induces two distinct conformational changes in its DNA substrate.

    Science.gov (United States)

    Loizos, N; Silva, G H; Belfort, M

    1996-01-26

    I-TevII is the homing endonuclease encoded by the sunY intron of bacteriophage T4. The enzyme cleaves an intronless sunY gene near the exon I-exon II junction, thereby initiating intron homing into its cognate intronless allele. Specifically, I-TevII cleaves its DNA target 13 to 15 nucleotides (nt) downstream of the sunY intron insertion site, generating 2-nl 3'-OH extensions. Here, we present evidence that I-TevII makes predominantly minor groove contacts in two regions of its recognition sequence, as does I-TevI, the other homing endonuclease encoded by phage T4. Following cleavage, I-TevII was shown to remain bound to one of its DNA products, suggesting possible additional roles for the endonuclease in the mobility process. Interestingly, two distinct conformational changes were detected by gel analysis in the DNA substrate following binding by I-TevII, one occurring in the absence of Mg2+, the second being dependent on the presence of Mg2+. The Mg(2+)-induced distortion accompanies a nick in one strand, and may serve to bring the cleavage site on the other strand into proximity with the catalytic domain of the protein. PMID:8568886

  14. Asymmetric flows over symmetric surfaces: capacitive coupling in induced-charge electro-osmosis

    International Nuclear Information System (INIS)

    We report curious asymmetric induced-charge electro-osmotic (ICEO) flows over a symmetric, planar gate electrode under applied ac electric fields, whereas symmetric, counter-rotating rolls are expected. Furthermore, the asymmetric component of the flow is consistently directed towards the grounded electrode. We propose that capacitive coupling of the gate electrode to the microscope stage-a comparatively large equipotential surface that acts effectively as a ground-is responsible for this symmetry breaking. This stray capacitance drives the formation of a double layer whose zeta potential is proportional to the potential drop from the electrolyte directly above the gate electrode to the external stage. Therefore, the charge in this 'stray' double layer varies in phase with the driving field, resulting in a rectified, steady flow as with standard ICEO. We experimentally vary the stray capacitance, the electric potential of the stage and the location of the gate electrode, and find that the effect on the stray flow is qualitatively consistent with the predictions of the proposed mechanism. In the process, we demonstrate that capacitive coupling offers an additional means of manipulating fluid flow over a polarizable surface.

  15. Asymmetric-Structure Analysis of Carbon and Energy Markets

    Science.gov (United States)

    Xu, Wei; Cao, Guangxi

    2016-02-01

    This study aimed to investigate the asymmetric structure between the carbon and energy markets from two aspects of different trends (up or down) and volatility-transmission direction using asymmetric detrended cross-correlation analysis (DCCA) cross-correlation coefficient test, multifractal asymmetric DCCA (MF-ADCCA) method, asymmetric volatility-constrained correlation metric and time rate of information-flow approach. We sampled 1283 observations from January 2008 to December 2012 among pairs of carbon and energy markets for analysis. Empirical results show that the (1) asymmetric characteristic from the cross-correlation between carbon and returns in the energy markets is significant, (2) asymmetric cross-correlation between carbon and energy market price returns is persistent and multifractral and (3) volatility of the base assets of energy market returns is more influential to the base asset of the carbon market than that of the energy market.

  16. On the electron dynamics during island coalescence in asymmetric magnetic reconnection

    Energy Technology Data Exchange (ETDEWEB)

    Cazzola, E., E-mail: emanuele.cazzola@wis.kuleuven.be; Innocenti, M. E., E-mail: mariaelena.innocenti@wis.kuleuven.be; Lapenta, G., E-mail: giovanni.lapenta@wis.kuleuven.be [Center for Mathematical Plasma Astrophysics, Department of Mathematics, K.U. Leuven (University of Leuven), Celestijnenlaan 200B, B-3001 Leuven (Belgium); Markidis, S., E-mail: markidis@pdc.kth.se [PDC Center for High Performance Computing, KTH Royal Institute of Technology, Teknikringen 14, 10044 Stockholm (Sweden); Goldman, M. V., E-mail: martin.goldman@Colorado.edu; Newman, D. L., E-mail: david.newman@colorado.edu [Center for Integrated Plasma Studies, University of Colorado Boulder, Gamow Tower, Boulder, Colorado 80309-0390 (United States)

    2015-09-15

    We present an analysis of the electron dynamics during rapid island merging in asymmetric magnetic reconnection. We consider a doubly periodic system with two asymmetric transitions. The upper layer is an asymmetric Harris sheet of finite width perturbed initially to promote a single reconnection site. The lower layer is a tangential discontinuity that promotes the formation of many X-points, separated by rapidly merging islands. Across both layers, the magnetic field and the density have a strong jump, but the pressure is held constant. Our analysis focuses on the consequences of electron energization during island coalescence. We focus first on the parallel and perpendicular components of the electron temperature to establish the presence of possible anisotropies and non-gyrotropies. Thanks to the direct comparison between the two different layers simulated, we can distinguish three main types of behavior characteristic of three different regions of interest. The first type represents the regions where traditional asymmetric reconnections take place without involving island merging. The second type of regions instead shows reconnection events between two merging islands. Finally, the third regions identify the regions between two diverging island and where typical signature of reconnection is not observed. Electrons in these latter regions additionally show a flat-top distribution resulting from the saturation of a two-stream instability generated by the two interacting electron beams from the two nearest reconnection points. Finally, the analysis of agyrotropy shows the presence of a distinct double structure laying all over the lower side facing the higher magnetic field region. This structure becomes quadrupolar in the proximity of the regions of the third type. The distinguishing features found for the three types of regions investigated provide clear indicators to the recently launched Magnetospheric Multiscale NASA mission for investigating magnetopause

  17. Observation of asymmetric transverse voltage in granular high-T c superconductors

    International Nuclear Information System (INIS)

    This work reports the influence of the granularity on the transverse voltage as a function of the temperature, V XY(T), in polycrystalline samples of Bi2Sr2Ca0.8Pr0.2Cu2O8+δ composition. It is observed nonzero transverse voltage at zero external magnetic field in the vicinity of the superconducting transition while far away from it, both above and below, no such voltage was detected. Measurements of V XY(T) in both directions of magnetic field allowed to calculate the symmetric and asymmetric transverse voltages in the full range of the applied magnetic field studied (zero up to 9 T). The symmetric transverse voltage as a function of the temperature presents sign reversal of the Hall resistance and positive Hall voltage at normal state such as expected for hole-doped high critical temperature superconductors. On the other hand, the asymmetric component of V XY(T) shows a peak near the superconducting transition which has been recently reported in literature. V XY(T) curves measured in a sample with double superconducting transition, which was confirmed by ac-susceptibility measurements and hysteresis loops of the magneto-resistance, present two peaks in the asymmetric component. These peaks are related to the intergranular and intragranular transitions and can be explained within the framework of Josephson and Abrikosov vortices and anti-vortices motion. By comparing the temperature dependence of the asymmetric transverse voltage and the derivative of longitudinal voltage is possible to observe a specific relation between both transport properties, which is noted to be valid not only at zero applied magnetic field but also under applied field

  18. On the electron dynamics during island coalescence in asymmetric magnetic reconnection

    International Nuclear Information System (INIS)

    We present an analysis of the electron dynamics during rapid island merging in asymmetric magnetic reconnection. We consider a doubly periodic system with two asymmetric transitions. The upper layer is an asymmetric Harris sheet of finite width perturbed initially to promote a single reconnection site. The lower layer is a tangential discontinuity that promotes the formation of many X-points, separated by rapidly merging islands. Across both layers, the magnetic field and the density have a strong jump, but the pressure is held constant. Our analysis focuses on the consequences of electron energization during island coalescence. We focus first on the parallel and perpendicular components of the electron temperature to establish the presence of possible anisotropies and non-gyrotropies. Thanks to the direct comparison between the two different layers simulated, we can distinguish three main types of behavior characteristic of three different regions of interest. The first type represents the regions where traditional asymmetric reconnections take place without involving island merging. The second type of regions instead shows reconnection events between two merging islands. Finally, the third regions identify the regions between two diverging island and where typical signature of reconnection is not observed. Electrons in these latter regions additionally show a flat-top distribution resulting from the saturation of a two-stream instability generated by the two interacting electron beams from the two nearest reconnection points. Finally, the analysis of agyrotropy shows the presence of a distinct double structure laying all over the lower side facing the higher magnetic field region. This structure becomes quadrupolar in the proximity of the regions of the third type. The distinguishing features found for the three types of regions investigated provide clear indicators to the recently launched Magnetospheric Multiscale NASA mission for investigating magnetopause

  19. Nanotribology of Symmetric and Asymmetric Liquid Lubricants

    Directory of Open Access Journals (Sweden)

    Shinji Yamada

    2010-03-01

    Full Text Available When liquid molecules are confined in a narrow gap between smooth surfaces, their dynamic properties are completely different from those of the bulk. The molecular motions are highly restricted and the system exhibits solid-like responses when sheared slowly. This solidification behavior is very dependent on the molecular geometry (shape of liquids because the solidification is induced by the packing of molecules into ordered structures in confinement. This paper reviews the measurements of confined structures and friction of symmetric and asymmetric liquid lubricants using the surface forces apparatus. The results show subtle and complex friction mechanisms at the molecular scale.

  20. Analysis of Asymmetric Piezoelectric Composite Beam

    CERN Document Server

    Chen, J -S; Wu, K -C

    2008-01-01

    This paper deals with the vibration analysis of an asymmetric composite beam composed of glass a piezoelectric material. The Bernoulli's beam theory is adopted for mechanical deformations, and the electric potential field of the piezoelectric material is assumed such that the divergence-free requirement of the electrical displacements is satisfied. The accuracy of the analytic model is assessed by comparing the resonance frequencies obtained by the analytic model with those obtained by the finite element method. The model developed can be used as a tool for designing piezoelectric actuators such as micro-pumps.

  1. On asymmetric causal relationships in Petropolitics

    Directory of Open Access Journals (Sweden)

    Balan Feyza

    2016-01-01

    Full Text Available The aim of this paper is to examine whether the First Law of Petropolitics denominated by Friedman in 2006 is valid for OPEC countries. To do this, this paper analyses the relationship between political risk and oil supply by applying the asymmetric panel causality test suggested by Hatemi-J (2011 to these countries for the period 1984-2014. The results show that the First Law of Petropolitics is valid for Angola, Iraq, Kuwait, Libya, Nigeria, Qatar, Saudi Arabia, and the UAE, given that positive oil supply shocks significantly lead to negative political stability shocks, and negative oil supply shocks significantly lead to positive shocks in political stability.

  2. RHIC operation with asymmetric collisions in 2015

    Energy Technology Data Exchange (ETDEWEB)

    Liu, C. [Brookhaven National Lab. (BNL), Upton, NY (United States); Aschenauer, C. [Brookhaven National Lab. (BNL), Upton, NY (United States); Atoian, G. [Brookhaven National Lab. (BNL), Upton, NY (United States); Blaskiewicz, M. [Brookhaven National Lab. (BNL), Upton, NY (United States); Brown, K. A. [Brookhaven National Lab. (BNL), Upton, NY (United States); Bruno, D. [Brookhaven National Lab. (BNL), Upton, NY (United States); Connolly, R. [Brookhaven National Lab. (BNL), Upton, NY (United States); Ottavio, T. D. [Brookhaven National Lab. (BNL), Upton, NY (United States); Drees, K. A. [Brookhaven National Lab. (BNL), Upton, NY (United States); Fischer, W. [Brookhaven National Lab. (BNL), Upton, NY (United States); Gardner, C. J. [Brookhaven National Lab. (BNL), Upton, NY (United States); Gu, X. [Brookhaven National Lab. (BNL), Upton, NY (United States); Hayes, T. [Brookhaven National Lab. (BNL), Upton, NY (United States); Huang, H. [Brookhaven National Lab. (BNL), Upton, NY (United States); Laster, J. S. [Brookhaven National Lab. (BNL), Upton, NY (United States); Luo, Y. [Brookhaven National Lab. (BNL), Upton, NY (United States); Makdisi, Y. [Brookhaven National Lab. (BNL), Upton, NY (United States); Marr, G. [Brookhaven National Lab. (BNL), Upton, NY (United States); Marusic, A. [Brookhaven National Lab. (BNL), Upton, NY (United States); Meot, F. [Brookhaven National Lab. (BNL), Upton, NY (United States); Mernick, K. [Brookhaven National Lab. (BNL), Upton, NY (United States); Michnoff, R. [Brookhaven National Lab. (BNL), Upton, NY (United States); Minty, M. [Brookhaven National Lab. (BNL), Upton, NY (United States); Montag, C. [Brookhaven National Lab. (BNL), Upton, NY (United States); Morris, J. [Brookhaven National Lab. (BNL), Upton, NY (United States); Narayan, G. [Brookhaven National Lab. (BNL), Upton, NY (United States); Nayak, S. [Brookhaven National Lab. (BNL), Upton, NY (United States); Nemesure, S. [Brookhaven National Lab. (BNL), Upton, NY (United States); Pile, P. [Brookhaven National Lab. (BNL), Upton, NY (United States); Poblaguev, A. [Brookhaven National Lab. (BNL), Upton, NY (United States); Ranjbar, V. [Brookhaven National Lab. (BNL), Upton, NY (United States); Robert-Demolaize, G. [Brookhaven National Lab. (BNL), Upton, NY (United States); Roser, T. [Brookhaven National Lab. (BNL), Upton, NY (United States); Schmidke, B. [Brookhaven National Lab. (BNL), Upton, NY (United States); Schoefer, V. [Brookhaven National Lab. (BNL), Upton, NY (United States); Severino, F. [Brookhaven National Lab. (BNL), Upton, NY (United States); Shrey, T. [Brookhaven National Lab. (BNL), Upton, NY (United States); Smith, K. [Brookhaven National Lab. (BNL), Upton, NY (United States); Steski, D. [Brookhaven National Lab. (BNL), Upton, NY (United States); Tepikian, S. [Brookhaven National Lab. (BNL), Upton, NY (United States); Trbojevic, D. [Brookhaven National Lab. (BNL), Upton, NY (United States); Tsoupas, N. [Brookhaven National Lab. (BNL), Upton, NY (United States); Wang, G. [Brookhaven National Lab. (BNL), Upton, NY (United States); White, S. [Brookhaven National Lab. (BNL), Upton, NY (United States); Yip, K. [Brookhaven National Lab. (BNL), Upton, NY (United States); Zaltsman, A. [Brookhaven National Lab. (BNL), Upton, NY (United States); Zeno, K. [Brookhaven National Lab. (BNL), Upton, NY (United States); Zhang, S. Y. [Brookhaven National Lab. (BNL), Upton, NY (United States)

    2015-08-07

    To study low-x shadowing/saturation physics as well as other nuclear effects [1], [2], proton-gold (p-Au, for 5 weeks) and proton-Aluminum (p-Al, for 2 weeks) collisions were provided for experiments in 2015 at the Relativistic Heavy Ion Collider (RHIC), with polarized proton beam in the Blue ring and Au/Al beam in the Yellow ring. The special features of the asymmetric run in 2015 will be introduced. The operation experience will be reviewed as well in the report.

  3. OFFICER AND COMMANDER IN ASYMMETRIC WARFARE OPERATIONS

    Directory of Open Access Journals (Sweden)

    Giuseppe CAFORIO

    2013-01-01

    Full Text Available Starting from the data of a field research conducted among soldiers with asymmetric warfare experiences from nine different countries, the author seeks to identify and shed light on the various problems that officers with command responsibilities had to face during their missions. A picture emerges of feelings and experiences relating to their first impression upon arriving in the theatre, relations with local armed forces, relations with the local population and local authorities, relations with NGOs, relations with other armies, the impact of the rules of engagement (ROEs, training and education, and operational experiences. The paper ends with a discussion of the lessons learned.

  4. Asymmetric catalytic aziridination of cyclic enones.

    Science.gov (United States)

    De Vincentiis, Francesco; Bencivenni, Giorgio; Pesciaioli, Fabio; Mazzanti, Andrea; Bartoli, Giuseppe; Galzerano, Patrizia; Melchiorre, Paolo

    2010-07-01

    The first catalytic method for the asymmetric aziridination of cyclic enones is described. The presented organocatalytic strategy is based on the use of an easily available organocatalyst that is able to convert a wide range of cyclic enones into the desired aziridines with very high enantiomeric purity and good chemical yield. Such a method may very well open up new opportunities to stereoselectively prepare complex chiral molecules that possess an indane moiety, a framework that is found in a large number of bioactive and pharmaceutically important molecules. PMID:20512797

  5. Plasmonic photodetectors based on asymmetric nanogap electrodes

    Science.gov (United States)

    Ge, Junyu; Luo, Manlin; Zou, Wanghui; Peng, Wei; Duan, Huigao

    2016-08-01

    Hot electrons excited by plasmon resonance in nanostructure can be employed to enhance the properties of photodetectors, even when the photon energy is lower than the bandgap of the semiconductor. However, current research has seldom considered how to realize the efficient collection of hot electrons, which restricts the responsivity of the device. In this paper, a type of plasmonic photodetector based on asymmetric nanogap electrodes is proposed. Owing to this structure, the device achieves responsivities as high as 0.45 and 0.25 mA/W for wavelengths of 1310 and 1550 nm, respectively. These insights can aid the realization of efficient plasmon-enhanced photodetectors for infrared detection.

  6. Governor model for asymmetric deformed nuclei

    International Nuclear Information System (INIS)

    The governor model is extended to include the asymmetric shape of nuclei which allows a simultaneous analysis of the data for both the ground state and the γ-vibrational bands in deformed even-even nuclei. The rotationally invariant core is assumed to be a spheroid with an axis of symmetry parallel to the axis of rotation. The calculations are carried out under the assumption of no stretching. The static γ-deformation results are compared with the VMI(ARM) and Krutov values, and the calculated energies are in good agreement with the experimental data

  7. Plasma current resonance in asymmetric toroidal systems

    Energy Technology Data Exchange (ETDEWEB)

    Hazeltine, R. D. [Institute for Fusion Studies, University of Texas at Austin, Austin, Texas 78712 (United States); Catto, Peter J. [Plasma Science and Fusion Center, Massachusetts Institute of Technology, 167 Albany Street, Cambridge, Massachusetts 02139 (United States)

    2015-09-15

    The well-known singularity in the magnetic differential equation for plasma current in an asymmetric toroidal confinement system is resolved by including in the pressure tensor corrections stemming from finite Larmor radius. The result provides an estimate of the amplitude of spikes in the parallel current that occur on rational magnetic surfaces. Resolution of the singularity is shown to depend on both the ambipolarity condition—the requirement of zero surface-averaged radial current—and the form of the magnetic differential equation near the rational surface.

  8. Security-Preserving Asymmetric Protocol Encapsulation

    OpenAIRE

    Vaudenay, Serge; Phan, Raphael C-W

    2007-01-01

    Query-response based protocols between a client and a server such as SSL, TLS, SSH are asymmetric in the sense that the querying client and the responding server play different roles, and for which there is a need for two-way linkability between queries and responses within the protocol. We are motivated by the observation that though results exist in other related contexts, no provably secure scheme has been applied to the setting of client-server protocols, which differ from conventional co...

  9. Infinite dimensional mixed economies with asymmetric information

    CERN Document Server

    Bhowmik, Anuj

    2011-01-01

    In this paper, we study asymmetric information economies consisting of both non-negligible and negligible agents and having ordered Banach spaces as their commodity spaces. In answering a question of Herv\\'{e}s-Beloso and Moreno-Garc\\'{i}a, we establish a characterization of Walrasian expectations allocations by the veto power of the grand coalition. It is also shown that when an economy contains only negligible agents a Vind's type theorem on the private core with the exact feasibility can be restored. This solves a problem of Pesce.

  10. Chiral Diamine-catalyzed Asymmetric Aldol Reaction

    Institute of Scientific and Technical Information of China (English)

    LI Hui; XU Da-zhen; WU Lu-lu; WANG Yong-mei

    2012-01-01

    A highly efficient catalytic system composed of a simple and commercially available chiral primary diamine (1R,2R)-cyclohexane-1,2-diamine(6) and trifluoroacetic acid(TFA) was employed for asymmetric Aldol reaction in i-PrOH at room temperature.A loading of 10%(molar fraction) catalyst 6 with TFA as a cocatalyst could catalyze the Aldol reactions of various ketones or aldehydes with a series of aromatic aldehydes,furnishing Aldol products in moderate to high yields(up to >99%) with enantioselectivities of up to >99% and diastereoselectivities of up to 99:1.

  11. Quantum optics of lossy asymmetric beam splitters.

    Science.gov (United States)

    Uppu, Ravitej; Wolterink, Tom A W; Tentrup, Tristan B H; Pinkse, Pepijn W H

    2016-07-25

    We theoretically investigate quantum interference of two single photons at a lossy asymmetric beam splitter, the most general passive 2×2 optical circuit. The losses in the circuit result in a non-unitary scattering matrix with a non-trivial set of constraints on the elements of the scattering matrix. Our analysis using the noise operator formalism shows that the loss allows tunability of quantum interference to an extent not possible with a lossless beam splitter. Our theoretical studies support the experimental demonstrations of programmable quantum interference in highly multimodal systems such as opaque scattering media and multimode fibers. PMID:27464096

  12. Long-lived oscillons from asymmetric bubbles

    CERN Document Server

    Adib, A B; Almeida, C A S; Adib, Artur B.; Gleiser, Marcelo; Almeida, Carlos A. S.

    2002-01-01

    The possibility that extremely long-lived, time-dependent, and localized field configurations (``oscillons'') arise during the collapse of asymmetrical bubbles in 2+1 dimensional \\phi^4 models is investigated. It is found that oscillons can develop from a large spectrum of elliptically deformed bubbles. Moreover, it is found that such oscillons are: a) circularly symmetric; and b) stable against small arbitrary radial and angular perturbations. They may thus play an important role in the study of time-dependent nonperturbative configurations in field theory, with applications ranging from nonequilibrium statistical physics to early universe cosmology.

  13. Catalytic asymmetric formal synthesis of beraprost

    Science.gov (United States)

    Kobayashi, Yusuke; Kuramoto, Ryuta

    2015-01-01

    Summary The first catalytic asymmetric synthesis of the key intermediate for beraprost has been achieved through an enantioselective intramolecular oxa-Michael reaction of an α,β-unsaturated amide mediated by a newly developed benzothiadiazine catalyst. The Weinreb amide moiety and bromo substituent of the Michael adduct were utilized for the C–C bond formations to construct the scaffold. All four contiguous stereocenters of the tricyclic core were controlled via Rh-catalyzed stereoselective C–H insertion and the subsequent reduction from the convex face. PMID:26734111

  14. Sorting with Asymmetric Read and Write Costs

    OpenAIRE

    Blelloch, Guy E.; Fineman, Jeremy T.; Gibbons, Phillip B.; Gu, Yan; Shun, Julian

    2016-01-01

    Emerging memory technologies have a significant gap between the cost, both in time and in energy, of writing to memory versus reading from memory. In this paper we present models and algorithms that account for this difference, with a focus on write-efficient sorting algorithms. First, we consider the PRAM model with asymmetric write cost, and show that sorting can be performed in $O\\left(n\\right)$ writes, $O\\left(n \\log n\\right)$ reads, and logarithmic depth (parallel time). Next, we conside...

  15. Neuronal Alignment On Asymmetric Textured Surfaces

    CERN Document Server

    Beighley, Ross; Sekeroglu, Koray; Atherton, Timothy; Demirel, Melik C; Staii, Cristian

    2013-01-01

    Axonal growth and the formation of synaptic connections are key steps in the development of the nervous system. Here we present experimental and theoretical results on axonal growth and interconnectivity in order to elucidate some of the basic rules that neuronal cells use for functional connections with one another. We demonstrate that a unidirectional nanotextured surface can bias axonal growth. We perform a systematic investigation of neuronal processes on asymmetric surfaces and quantify the role that biomechanical surface cues play in neuronal growth. These results represent an important step towards engineering directed axonal growth for neuro-regeneration studies.

  16. Asymmetric Hydrogenation of 3-Substituted Pyridinium Salts.

    Science.gov (United States)

    Renom-Carrasco, Marc; Gajewski, Piotr; Pignataro, Luca; de Vries, Johannes G; Piarulli, Umberto; Gennari, Cesare; Lefort, Laurent

    2016-07-01

    The use of an equivalent amount of an organic base leads to high enantiomeric excess in the asymmetric hydrogenation of N-benzylated 3-substituted pyridinium salts into the corresponding piperidines. Indeed, in the presence of Et3 N, a Rh-JosiPhos catalyst reduced a range of pyridinium salts with ee values up to 90 %. The role of the base was elucidated with a mechanistic study involving the isolation of the various reaction intermediates and isotopic labeling experiments. Additionally, this study provided some evidence for an enantiodetermining step involving a dihydropyridine intermediate. PMID:27140832

  17. Quantum optics of lossy asymmetric beam splitters

    CERN Document Server

    Uppu, Ravitej; Tentrup, Tristan B H; Pinkse, Pepijn W H

    2016-01-01

    We theoretically investigate quantum interference of two single photons at a lossy asymmetric beam splitter, the most general passive 2$\\times$2 optical circuit. The losses in the circuit result in a non-unitary scattering matrix with a non-trivial set of constraints on the elements of the scattering matrix. Our analysis using the noise operator formalism shows that the loss allows tunability of quantum interference to an extent not possible with a lossless beam splitter. Our theoretical studies support the experimental demonstrations of programmable quantum interference in highly multimodal systems such as opaque scattering media and multimode fibers.

  18. Hydrodynamic attraction and repulsion between asymmetric rotors

    International Nuclear Information System (INIS)

    At low Reynolds numbers, the hydrodynamic interaction between dumbbells driven by an external rotating field can be attractive or repulsive. Dumbbells of dissimilar asymmetric shape or different coupling to the external field undergo conformational rearrangements that break the time-reversal symmetry. The parameter ranges leading to attraction or repulsion are explored numerically. The results of our simulations suggest that rotating fields may be a useful avenue for the assembly, disassembly and sorting of particles of different shapes, as well as for the study of collective micro-swimmers.

  19. Massless sunset diagrams in finite asymmetric volumes

    Science.gov (United States)

    Niedermayer, F.; Weisz, P.

    2016-06-01

    This paper discusses the methods and the results used in an accompanying paper describing the matching of effective chiral Lagrangians in dimensional and lattice regularizations. We present methods to compute 2-loop massless sunset diagrams in finite asymmetric volumes in the framework of these regularizations. We also consider 1-loop sums in both regularizations, extending the results of Hasenfratz and Leutwyler for the case of dimensional regularization and we introduce a new method to calculate precisely the expansion coefficients of the 1-loop lattice sums.

  20. Asymmetric Synthesis of Both Enantiomers of Disparlure

    Institute of Scientific and Technical Information of China (English)

    王志刚; 郑剑峰; 黄培强

    2012-01-01

    Starting from propargyl alcohol (12), and on the basis of Zhou's modified Sharpless asymmetric epoxidation, the sex pheromone of the Gypsy moth, disparlure (+)-8 and its enantiomer (-)-8 have been synthesized, each in six steps, with overall yields of 29% for (+)-8 and 27% for (-)-8 (ee〉98%). The use of the sequential coupling tactic renders the method flexible, which is applicable to the synthesis of other cis-epoxy pheromones.

  1. Dual emission in asymmetric "giant" PbS/CdS/CdS core/shell/shell quantum dots.

    Science.gov (United States)

    Zhao, Haiguang; Sirigu, Gianluca; Parisini, Andrea; Camellini, Andrea; Nicotra, Giuseppe; Rosei, Federico; Morandi, Vittorio; Zavelani-Rossi, Margherita; Vomiero, Alberto

    2016-02-21

    Semiconducting nanocrystals optically active in the infrared region of the electromagnetic spectrum enable exciting avenues in fundamental research and novel applications compatible with the infrared transparency windows of biosystems such as chemical and biological optical sensing, including nanoscale thermometry. In this context, quantum dots (QDs) with double color emission may represent ultra-accurate and self-calibrating nanosystems. We present the synthesis of giant core/shell/shell asymmetric QDs having a PbS/CdS zinc blende (Zb)/CdS wurtzite (Wz) structure with double color emission close to the near-infrared (NIR) region. We show that the double emission depends on the excitation condition and analyze the electron-hole distribution responsible for the independent and simultaneous radiative exciton recombination in the PbS core and in the CdS Wz shell, respectively. These results highlight the importance of the driving force leading to preferential crystal growth in asymmetric QDs, and provide a pathway for the rational control of the synthesis of double color emitting giant QDs, leading to the effective exploitation of visible/NIR transparency windows. PMID:26837955

  2. Asymmetric Dark Matter in the Shear--dominated Universe

    OpenAIRE

    Iminniyaz, Hoernisa

    2016-01-01

    We explore the relic abundance of asymmetric Dark Matter in shear--dominated universe in which it is assumed the universe is expanded anisotropically. The modified expansion rate leaves its imprint on the relic density of asymmetric Dark Matter particles if the asymmetric Dark Matter particles are decoupled in shear dominated era. We found the relic abundances for particle and anti--particle are increased. The particle and anti--particle abundances are almost in the same amount for appropriat...

  3. RELATIONSHIP OF TRANSVERSAL ASYMMETRIC FACE AND UNILATERAL POSTERIOR CROSSBITE

    OpenAIRE

    Indah Dwinursanty; Krisnawati Krisnawati; Maria Purbiati

    2006-01-01

    Unilateral posterior crossbite is commonly seen in mixed dentition, but it couldn’t be self corrected. If this condition is not treated properly, it could lead to asymmetric face. Asymmetric face with unilateral posterior crossbite could make the treatment process more difficult. The objective of this study is to find out the relationship between transversal skeletal asymmetry and unilateral posterior crossbite. Patients older than 13 years with skeletal asymmetric face, who had never undergo...

  4. Asymmetrical Sample Training Produces Asymmetrical Retention Functions in Feature-Present/Feature-Absent Matching in Pigeons

    Science.gov (United States)

    Grant, Douglas S.; Blatz, Craig W.

    2004-01-01

    Pigeons were trained in a matching task in which samples involved presentation of a white line on a green background (feature-present) or on an otherwise dark key (feature-absent). After asymmetrical training in which one group was initially trained with the feature-present sample and another was initially trained with the feature-absent sample,…

  5. Involvement of Hydrogen Peroxide in Safingol-Induced Endonuclease G-Mediated Apoptosis of Squamous Cell Carcinoma Cells

    Directory of Open Access Journals (Sweden)

    Masakazu Hamada

    2014-02-01

    Full Text Available Safingol, a L-threo-dihydrosphingosine, induced the nuclear translocation of a mitochondrial apoptogenic mediator—endonuclease G (endo G—and apoptosis of human oral squamous cell carcinoma (SCC cells. Upstream mediators remain largely unknown. The levels of hydrogen peroxide (H2O2 in cultured oral SCC cells were measured. Treatment with safingol increased intracellular H2O2 levels but not extracellular H2O2 levels, indicating the production of H2O2. The cell killing effect of safingol and H2O2 was diminished in the presence of reactive oxygen species (ROS scavenger N-acetyl-L-cysteine (NAC. Dual staining of cells with annexin V and propidium iodide (PI revealed that apoptotic cell death occurred by treatment with H2O2 and safingol. The number of apoptotic cells was reduced in the presence of NAC. In untreated cells, endo G distributed in the cytoplasm and an association of endo G with mitochondria was observed. After treatment with H2O2 and safingol, endo G was distributed to the nucleus and cytoplasm, indicating the nuclear translocation of the mitochondrial factor. NAC prevented the increase of apoptotic cells and the translocation of endo G. Knock down of endo G diminished the cell killing effect of H2O2 and safingol. These results suggest that H2O2 is involved in the endo G-mediated apoptosis of oral SCC cells by safingol.

  6. Crystal structure and MD simulation of mouse EndoV reveal wedge motif plasticity in this inosine-specific endonuclease

    Science.gov (United States)

    Nawaz, Meh Sameen; Vik, Erik Sebastian; Ronander, Mia Elise; Solvoll, Anne Marthe; Blicher, Pernille; Bjørås, Magnar; Alseth, Ingrun; Dalhus, Bjørn

    2016-04-01

    Endonuclease V (EndoV) is an enzyme with specificity for deaminated adenosine (inosine) in nucleic acids. EndoV from Escherichia coli (EcEndoV) acts both on inosines in DNA and RNA, whereas the human homolog cleaves only at inosines in RNA. Inosines in DNA are mutagenic and the role of EndoV in DNA repair is well established. In contrast, the biological function of EndoV in RNA processing is largely unexplored. Here we have characterized a second mammalian EndoV homolog, mouse EndoV (mEndoV), and show that mEndoV shares the same RNA selectivity as human EndoV (hEndoV). Mouse EndoV cleaves the same inosine-containing substrates as hEndoV, but with reduced efficiencies. The crystal structure of mEndoV reveals a conformation different from the hEndoV and prokaryotic EndoV structures, particularly for the conserved tyrosine in the wedge motif, suggesting that this strand separating element has some flexibility. Molecular dynamics simulations of mouse and human EndoV reveal alternative conformations for the invariant tyrosine. The configuration of the active site, on the other hand, is very similar between the prokaryotic and mammalian versions of EndoV.

  7. Intein-mediated purification of cytotoxic endonuclease I-TevI by insertional inactivation and pH-controllable splicing.

    Science.gov (United States)

    Wu, Wei; Wood, David W; Belfort, Georges; Derbyshire, Victoria; Belfort, Marlene

    2002-11-15

    An intein-mediated approach was developed for expression and affinity purification of a protein that is lethal to Escherichia coli. The protein, I-TevI, is an intron-encoded endonuclease. The approach involved the insertional inactivation of I-TevI with a controllable mini-intein placed in front of a cysteine required for splicing (an I-TevI::intein fusion). The purification was facilitated by a chitin-binding domain inserted into the mini-intein. Affinity purification of the I-TevI::intein fusion precursor on a chitin column was followed by pH-controllable splicing to restore the structure and function of I-TevI. To study the impact of the insertion context on I-TevI inactivation, the chimeric intein was inserted independently in front of seven cysteines of I-TevI. One of the seven intein integrants yielded I-TevI of high activity. This technique is, in principle, generalizable to the expression and purification of other cytotoxic proteins and is amenable to scale-up. PMID:12433989

  8. Using Group II Introns for Attenuating the In Vitro and In Vivo Expression of a Homing Endonuclease.

    Directory of Open Access Journals (Sweden)

    Tuhin Kumar Guha

    Full Text Available In Chaetomium thermophilum (DSM 1495 within the mitochondrial DNA (mtDNA small ribosomal subunit (rns gene a group IIA1 intron interrupts an open reading frame (ORF encoded within a group I intron (mS1247. This arrangement offers the opportunity to examine if the nested group II intron could be utilized as a regulatory element for the expression of the homing endonuclease (HEase. Constructs were generated where the codon-optimized ORF was interrupted with either the native group IIA1 intron or a group IIB type intron. This study showed that the expression of the HEase (in vivo in Escherichia coli can be regulated by manipulating the splicing efficiency of the HEase ORF-embedded group II introns. Exogenous magnesium chloride (MgCl2 stimulated the expression of a functional HEase but the addition of cobalt chloride (CoCl2 to growth media antagonized the expression of HEase activity. Ultimately the ability to attenuate HEase activity might be useful in precision genome engineering, minimizing off target activities, or where pathways have to be altered during a specific growth phase.

  9. Mutagenesis of genes for starch debranching enzyme isoforms in pea by means of zinc-finger endonucleases

    International Nuclear Information System (INIS)

    Starch debranching enzymes in plants are divided into two groups based on their ability to hydrolyse different substrates. The first group, pullulanases, hydrolyses α-1,6-glucosidic linkages in substrates such as pullulan, amylopectin and glycogen. The second group of debranching enzymes, isoamylases, hydrolyse glycogen and amylopectin and are not active on pullulan. Three isoforms of isoamylase and a pullulanase have been isolated from cDNA library of Pisum sativum. These isoamylases have been characterised based on the their heterologous expression in E coli. Based on the DNA sequence that encodes these debranching enzyme, a specific mutagenesis targeting at these DNA will be attempted. The method that will be employed are based on the techniques developed by Wright et al. (2005). This technique involves the homologous recombination of DNA that is mediated by zinc-finger endonucleases. Vectors will be constructed to include a fragment that will modify these genes. Microinjection technique will be used to insert these vectors into pollen which then will be fertilized. Using this technique, it is hoped that null mutant for each enzyme will be created and the exact role of these enzymes for the synthesis and degradation of starch in plants will be elucidate. (author)

  10. The elastic network model reveals a consistent picture on intrinsic functional dynamics of type II restriction endonucleases

    International Nuclear Information System (INIS)

    The vibrational dynamics of various type II restriction endonucleases, in complex with cognate/non-cognate DNA and in the apo form, are investigated with the elastic network model in order to reveal common functional mechanisms in this enzyme family. Scissor-like and tong-like motions observed in the slowest modes of all enzymes and their complexes point to common DNA recognition and cleavage mechanisms. Normal mode analysis further points out that the scissor-like motion has an important role in differentiating between cognate and non-cognate sequences at the recognition site, thus implying its catalytic relevance. Flexible regions observed around the DNA-binding site of the enzyme usually concentrate on the highly conserved β-strands, especially after DNA binding. These β-strands may have a structurally stabilizing role in functional dynamics for target site recognition and cleavage. In addition, hot spot residues based on high-frequency modes reveal possible communication pathways between the two distant cleavage sites in the enzyme family. Some of these hot spots also exist on the shortest path between the catalytic sites and are highly conserved

  11. In vivo characterization of the homing endonuclease within the polB gene in the halophilic archaeon Haloferax volcanii.

    Directory of Open Access Journals (Sweden)

    Adit Naor

    Full Text Available Inteins are parasitic genetic elements, analogous to introns that excise themselves at the protein level by self-splicing, allowing the formation of functional non-disrupted proteins. Many inteins contain a homing endonuclease (HEN gene, and rely on its activity for horizontal propagation. In the halophilic archaeon, Haloferax volcanii, the gene encoding DNA polymerase B (polB contains an intein with an annotated but uncharacterized HEN. Here we examine the activity of the polB HEN in vivo, within its natural archaeal host. We show that this HEN is highly active, and able to insert the intein into both a chromosomal target and an extra-chromosomal plasmid target, by gene conversion. We also demonstrate that the frequency of its incorporation depends on the length of the flanking homologous sequences around the target site, reflecting its dependence on the homologous recombination machinery. Although several evolutionary models predict that the presence of an intein involves a change in the fitness of the host organism, our results show that a strain deleted for the intein sequence shows no significant changes in growth rate compared to the wild type.

  12. In vivo characterization of the homing endonuclease within the polB gene in the halophilic archaeon Haloferax volcanii.

    Science.gov (United States)

    Naor, Adit; Lazary, Rona; Barzel, Adi; Papke, R Thane; Gophna, Uri

    2011-01-01

    Inteins are parasitic genetic elements, analogous to introns that excise themselves at the protein level by self-splicing, allowing the formation of functional non-disrupted proteins. Many inteins contain a homing endonuclease (HEN) gene, and rely on its activity for horizontal propagation. In the halophilic archaeon, Haloferax volcanii, the gene encoding DNA polymerase B (polB) contains an intein with an annotated but uncharacterized HEN. Here we examine the activity of the polB HEN in vivo, within its natural archaeal host. We show that this HEN is highly active, and able to insert the intein into both a chromosomal target and an extra-chromosomal plasmid target, by gene conversion. We also demonstrate that the frequency of its incorporation depends on the length of the flanking homologous sequences around the target site, reflecting its dependence on the homologous recombination machinery. Although several evolutionary models predict that the presence of an intein involves a change in the fitness of the host organism, our results show that a strain deleted for the intein sequence shows no significant changes in growth rate compared to the wild type. PMID:21283796

  13. Effects of mono- and divalent metal ions on DNA binding and catalysis of human apurinic/apyrimidinic endonuclease 1.

    Science.gov (United States)

    Miroshnikova, Anastasia D; Kuznetsova, Alexandra A; Vorobjev, Yuri N; Kuznetsov, Nikita A; Fedorova, Olga S

    2016-05-26

    Here, we used stopped-flow fluorescence techniques to conduct a comparative kinetic analysis of the conformational transitions in human apurinic/apyrimidinic endonuclease 1 (APE1) and in DNA containing an abasic site in the course of their interaction. Effects of monovalent (K(+)) and divalent (Mg(2+), Mn(2+), Ca(2+), Zn(2+), Cu(2+), and Ni(2+)) metal ions on DNA binding and catalytic stages were studied. It was shown that the first step of substrate binding (corresponding to formation of a primary enzyme-substrate complex) does not depend on the concentration (0.05-5.0 mM) or the nature of divalent metal ions. In contrast, the initial DNA binding efficiency significantly decreased at a high concentration (5-250 mM) of monovalent K(+) ions, indicating the involvement of electrostatic interactions in this stage. It was also shown that Cu(2+) ions abrogated the DNA binding ability of APE1, possibly, due to a strong interaction with DNA bases and the sugar-phosphate backbone. In the case of Ca(2+) ions, the catalytic activity of APE1 was lost completely with retention of binding potential. Thus, the enzymatic activity of APE1 is increased in the order Zn(2+) < Ni(2+) < Mn(2+) < Mg(2+). Circular dichroism spectra and calculation of the contact area between APE1 and DNA reveal that Mg(2+) ions stabilize the protein structure and the enzyme-substrate complex. PMID:27063150

  14. Autosomal-Recessive Mutations in the tRNA Splicing Endonuclease Subunit TSEN15 Cause Pontocerebellar Hypoplasia and Progressive Microcephaly.

    Science.gov (United States)

    Breuss, Martin W; Sultan, Tipu; James, Kiely N; Rosti, Rasim O; Scott, Eric; Musaev, Damir; Furia, Bansri; Reis, André; Sticht, Heinrich; Al-Owain, Mohammed; Alkuraya, Fowzan S; Reuter, Miriam S; Abou Jamra, Rami; Trotta, Christopher R; Gleeson, Joseph G

    2016-07-01

    The tRNA splicing endonuclease is a highly evolutionarily conserved protein complex, involved in the cleavage of intron-containing tRNAs. In human it consists of the catalytic subunits TSEN2 and TSEN34, as well as the non-catalytic TSEN54 and TSEN15. Recessive mutations in the corresponding genes of the first three are known to cause pontocerebellar hypoplasia (PCH) types 2A-C, 4, and 5. Here, we report three homozygous TSEN15 variants that cause a milder version of PCH2. The affected individuals showed progressive microcephaly, delayed developmental milestones, intellectual disability, and, in two out of four cases, epilepsy. None, however, displayed the central visual failure seen in PCH case subjects where other subunits of the TSEN are mutated, and only one was affected by the extensive motor defects that are typical in other forms of PCH2. The three amino acid substitutions impacted the protein level of TSEN15 and the stoichiometry of the interacting subunits in different ways, but all resulted in an almost complete loss of in vitro tRNA cleavage activity. Taken together, our results demonstrate that mutations in any known subunit of the TSEN complex can cause PCH and progressive microcephaly, emphasizing the importance of its function during brain development. PMID:27392077

  15. Isolation and properties of the acid site-specific endonuclease from mature eggs of the sea urchin Strongylocentrotus intermedius

    International Nuclear Information System (INIS)

    An acid site-specific endonuclease has been detected in mature sea urchin eggs and cells of embryos at early stages of differentiation. Fractionation with ammonium sulfate, followed by chromatography on columns with DEAE, phosphocellulose, and hydroxyapatite resulted in an 18,000-fold purification. The molecular weight of the enzyme was determined at ∼ 29,000, the optimum pH 5.5. The activity of the enzyme does not depend on divalent metal ions, EDTA, ATP, and tRNA, but it is modulated to a substantial degree by NaCl. The maximum rate of cleavage of the DNA supercoil (form I) is observed at 100 mM NaCl. Increasing the NaCl concentration to 350 mM only slightly lowers the rate of cleavage of form I, yielding form II, but entirely suppresses the accumulation of form III. Restriction analysis of the products of enzymatic hydrolysis of Co1E1 and pBR322 DNA showed that at the early stages of hydrolysis the enzyme exhibits pronounced specificity for definite sites, the number of which is 12 for Co1 E1 DNA and 8 sites for pBR322 DNA

  16. Lundep, a sand fly salivary endonuclease increases Leishmania parasite survival in neutrophils and inhibits XIIa contact activation in human plasma.

    Directory of Open Access Journals (Sweden)

    Andrezza C Chagas

    2014-02-01

    Full Text Available Neutrophils are the host's first line of defense against infections, and their extracellular traps (NET were recently shown to kill Leishmania parasites. Here we report a NET-destroying molecule (Lundep from the salivary glands of Lutzomyia longipalpis. Previous analysis of the sialotranscriptome of Lu. longipalpis showed the potential presence of an endonuclease. Indeed, not only was the cloned cDNA (Lundep shown to encode a highly active ss- and dsDNAse, but also the same activity was demonstrated to be secreted by salivary glands of female Lu. longipalpis. Lundep hydrolyzes both ss- and dsDNA with little sequence specificity with a calculated DNase activity of 300000 Kunitz units per mg of protein. Disruption of PMA (phorbol 12 myristate 13 acetate- or parasite-induced NETs by treatment with recombinant Lundep or salivary gland homogenates increases parasite survival in neutrophils. Furthermore, co-injection of recombinant Lundep with metacyclic promastigotes significantly exacerbates Leishmania infection in mice when compared with PBS alone or inactive (mutagenized Lundep. We hypothesize that Lundep helps the parasite to establish an infection by allowing it to escape from the leishmanicidal activity of NETs early after inoculation. Lundep may also assist blood meal intake by lowering the local viscosity caused by the release of host DNA and as an anticoagulant by inhibiting the intrinsic pathway of coagulation.

  17. Slow conformational dynamics of an endonuclease persist in its complex with its natural protein inhibitor.

    Science.gov (United States)

    Whittaker, S B; Czisch, M; Wechselberger, R; Kaptein, R; Hemmings, A M; James, R; Kleanthous, C; Moore, G R

    2000-04-01

    The bacterial toxin colicin E9 is secreted by producing Escherichia coli cells with its 9.5 kDa inhibitor protein Im9 bound tightly to its 14.5 kDa C-terminal DNase domain. Double- and triple-resonance NMR spectra of the isolated DNase domain uniformly labeled with 13C/15N bound to unlabeled Im9 contain more signals than expected for a single DNase conformer, consistent with the bound DNase being present in more than one form. The presence of chemical exchange cross peaks in 750 MHz 15N-1H-15N HSQC-NOESY-HSQC spectra for backbone NH groups of Asp20, Lys21, Trp22, Leu23, Lys69, and Asn70 showed that the bound DNase was in dynamic exchange. The rate of exchange from the major to the minor form was determined to be 1.1 +/- 0.2 s(-1) at 298 K. Previous NMR studies have shown that the free DNase interchanges between two conformers with a forward rate constant of 1.61 +/- 0.11 s(-1) at 288 K, and that the bound Im9 is fixed in one conformation. The NMR studies of the bound DNase show that Im9 binds similarly to both conformers of the DNase and that the buried Trp22 is involved in the dynamic process. For the free DNase, all NH groups within a 9 A radius of any point of the Trp22 ring exhibit heterogeneity suggesting that a rearrangement of the position of this side chain is connected with the conformational interchange. The possible functional significance of this feature of the DNase is discussed. PMID:10794413

  18. Quantity Discount Scheme in Supply Chain under Asymmetric Information

    Institute of Scientific and Technical Information of China (English)

    LI Ji-bin; PENG Zuo-he

    2007-01-01

    Quantity discount scheme plays an important role in supply chain management. The different quantity discount schemes under symmetric (full) information and asymmetric information, are analyzed by using principal-agent and optimal control theory. As a result, the research reveals that the optimal quantity discount solution under symmetric information is a special case of that under asymmetric information. At the same price, the critical value of quantity discount under asymmetric information is much lower than that under asymmetric information. Therefore, this leads to less cost for retailers and smaller profit for their supplier.

  19. Coherent Control of Tunneling in Double-Well Potentials

    CERN Document Server

    Song, Dae-Yup

    2011-01-01

    For an asymmetric double-well potential system, it is shown that, if the potential is quadratic until it reaches several times of the zero-point energies from the bottoms in each well, the energy eigenvalues of the low lying excited states of the double-well system must be close to the eigenvalues of the quadratic potentials. These eigenvalue structures suggest a method for the coherent control of the tunneling as well as realizing almost complete localization of the wave packet in one of the wells, by handling the double-well asymmetry. Numerical examples are included to indicate that the method could be useful also in a more general potential, and to propose experimental confirmations.

  20. The deconfinement phase transition in asymmetric matter

    International Nuclear Information System (INIS)

    We study the phase transition of asymmetric hadronic matter to a quark-gluon plasma within the framework of a simple two-phase model. The analysis is performed in a system with two conserved charges (baryon number and isospin) using the stability conditions on the free energy, the conservation laws and Gibbs' criteria for phase equilibrium. The EOS is obtained in a separate description for the hadronic phase and for the quark-gluon plasma. For the hadrons, a relativistic mean-field model calibrated to the properties of nuclear matter is used, and a bag-model type EOS is used for the quarks and gluons. The model is applied to the deconfinement phase transition that may occur in matter created in ultra-relativistic collisions of heavy ions. Based on the two-dimensional coexistence surface (binodal), various phase separation scenarios and the Maxwell construction through the mixed phase are discussed. In the framework of the two-phase model the phase transition in asymmetric matter is continuous (second-order by Ehrenfest's definition) in contrast to the discontinuous (first-order) transition of symmetric systems. (orig.)