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Sample records for asymmetrical endonuclease double

  1. Vertical asymmetric double quantum dots

    Science.gov (United States)

    Roßbach, R.; Reischle, M.; Beirne, G. J.; Schweizer, H.; Jetter, M.; Michler, P.

    2007-01-01

    Two layers of differently sized self-assembled InP-quantum dots (QDs) separated by a GaInP spacer layer with varying thickness were grown by metal organic vapor phase epitaxy (MOVPE). Photoluminescence measurements of the QD ensembles and of individual asymmetric double QDS show coupling due to the tunnelling of carriers.

  2. 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.

  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. 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

  5. Double-stranded endonuclease activity in Bacillus halodurans clustered regularly interspaced short palindromic repeats (CRISPR)-associated Cas2 protein.

    Science.gov (United States)

    Nam, Ki Hyun; Ding, Fran; Haitjema, Charles; Huang, Qingqiu; DeLisa, Matthew P; Ke, Ailong

    2012-10-19

    The CRISPR (clustered regularly interspaced short palindromic repeats) system is a prokaryotic RNA-based adaptive immune system against extrachromosomal genetic elements. Cas2 is a universally conserved core CRISPR-associated protein required for the acquisition of new spacers for CRISPR adaptation. It was previously characterized as an endoribonuclease with preference for single-stranded (ss)RNA. Here, we show using crystallography, mutagenesis, and isothermal titration calorimetry that the Bacillus halodurans Cas2 (Bha_Cas2) from the subtype I-C/Dvulg CRISPR instead possesses metal-dependent endonuclease activity against double-stranded (ds)DNA. This activity is consistent with its putative function in producing new spacers for insertion into the 5'-end of the CRISPR locus. Mutagenesis and isothermal titration calorimetry studies revealed that a single divalent metal ion (Mg(2+) or Mn(2+)), coordinated by a symmetric Asp pair in the Bha_Cas2 dimer, is involved in the catalysis. We envision that a pH-dependent conformational change switches Cas2 into a metal-binding competent conformation for catalysis. We further propose that the distinct substrate preferences among Cas2 proteins may be determined by the sequence and structure in the β1-α1 loop.

  6. 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.

  7. Manipulative Properties of Asymmetric Double Quantum Dots via Laser and Gate Voltage

    Institute of Scientific and Technical Information of China (English)

    ZHAO Shun-Cai; LIU Zheng-Dong

    2009-01-01

    We present a density matrix approach for the theoretical description of an asymmetric double quantum dot (QD) system. The results show that the properties of gain, absorption and dispersion of the double QD system, the population of the state with one hole in one dot and an electron in another dot transferred by tunneling can be manipulated by a laser pulse or gate voltage. Our scheme may demonstrate the possibility of electro-optical manipulation of quantum systems.

  8. 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

  9. Double images encryption method with resistance against the specific attack based on an asymmetric algorithm.

    Science.gov (United States)

    Wang, Xiaogang; Zhao, Daomu

    2012-05-21

    A double-image encryption technique that based on an asymmetric algorithm is proposed. In this method, the encryption process is different from the decryption and the encrypting keys are also different from the decrypting keys. In the nonlinear encryption process, the images are encoded into an amplitude cyphertext, and two phase-only masks (POMs) generated based on phase truncation are kept as keys for decryption. By using the classical double random phase encoding (DRPE) system, the primary images can be collected by an intensity detector that located at the output plane. Three random POMs that applied in the asymmetric encryption can be safely applied as public keys. Simulation results are presented to demonstrate the validity and security of the proposed protocol.

  10. 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)

  11. 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

  12. 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.

  13. 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

  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. Site-specific DNA double-strand break generated by I-SceI endonuclease enhances ectopic homologous recombination in Pyricularia oryzae.

    Science.gov (United States)

    Arazoe, Takayuki; Younomaru, Tetsuya; Ohsato, Shuichi; Kimura, Makoto; Arie, Tsutomu; Kuwata, Shigeru

    2014-03-01

    To evaluate the contribution of DNA double-strand breaks (DSBs) to somatic homologous recombination (HR) in Pyricularia oryzae, we established a novel detection/selection system of DSBs-mediated ectopic HR. This system consists of donor and recipient nonfunctional yellow fluorescent protein (YFP)/blasticidin S deaminase (BSD) fusion genes and the yeast endonuclease I-SceI gene as a recipient-specific DSB inducer. The system enables to detect and select ectopic HR events by the restoration of YFP fluorescence and blasticidin S resistance. The transformed lines with donor and recipient showed low frequencies of endogenous ectopic HR (> 2.1%). Compared with spontaneous HR, c. 20-fold increases in HR and absolute frequency of HR as high as 40% were obtained by integration of I-SceI gene, indicating that I-SceI-mediated DSB was efficiently repaired via ectopic HR. Furthermore, to validate the impact of DSB on targeted gene replacement (TGR), the transformed lines with a recipient gene were transfected with an exogenous donor plasmid in combination with the DSB inducer. TGR events were not observed without the DSB inducer, whereas hundreds of colonies resulting from TGR events were obtained with the DSB inducer. These results clearly demonstrated that the introduction of site-specific DSB promotes ectopic HR repair in P. oryzae. PMID:24517488

  16. 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.

  17. 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

  18. 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.

  19. 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.

  20. Asymmetric Quantum Transport in a Double-Stranded Kronig-Penney Model

    Science.gov (United States)

    Cheon, Taksu; Poghosyan, Sergey S.

    2015-06-01

    We introduce a double-stranded Kronig-Penney model and analyze its transport properties. Asymmetric fluxes between two strands with suddenly alternating localization patterns are found as the energy is varied. The zero-size limit of the internal lines connecting two strands is examined using quantum graph vertices with four edges. We also consider a two-dimensional Kronig-Penney lattice with two types of alternating layer with δ and δ' connections, and show the existence of energy bands in which the quantum flux can flow only in selected directions.

  1. 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.

  2. 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.

  3. Endonuclease-based Method for Detecting the Sequence Specific DNA Binding Protein on Double-stranded DNA Microarray

    Institute of Scientific and Technical Information of China (English)

    Yun Fei BAI; Qin Yu GE; Tong Xiang LI; Jin Ke WANG; Quan Jun LIU; Zu Hong LU

    2005-01-01

    The double-stranded DNA (dsDNA) probe contains two different protein binding sites.One is for DNA- binding proteins to be detected and the other is for a DNA restriction enzyme.The two sites were arranged together with no base interval. The working principle of the capturing dsDNA probe is described as follows: the capturing probe can be cut with the DNA restriction enzyme (such as EcoR I) to cause a sticky terminal, if the probe is not bound with a target protein, and the sticky terminal can be extended and labeled with Cy3-dUTP by DNA polymerase. When the probe is bound with a target protein, the probe is not capable to be cut by the restriction enzyme because of space obstruction. The amount of the target DNA binding proteins can be measured according to the variations of fluorescent signals of the corresponding probes.

  4. 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

  5. Alkylation base damage is converted into repairable double-strand breaks and complex intermediates in G2 cells lacking AP endonuclease.

    Directory of Open Access Journals (Sweden)

    Wenjian Ma

    2011-04-01

    Full Text Available DNA double-strand breaks (DSBs are potent sources of genome instability. While there is considerable genetic and molecular information about the disposition of direct DSBs and breaks that arise during replication, relatively little is known about DSBs derived during processing of single-strand lesions, especially for the case of single-strand breaks (SSBs with 3'-blocked termini generated in vivo. Using our recently developed assay for detecting end-processing at random DSBs in budding yeast, we show that single-strand lesions produced by the alkylating agent methyl methanesulfonate (MMS can generate DSBs in G2-arrested cells, i.e., S-phase independent. These derived DSBs were observed in apn1/2 endonuclease mutants and resulted from aborted base excision repair leading to 3' blocked single-strand breaks following the creation of abasic (AP sites. DSB formation was reduced by additional mutations that affect processing of AP sites including ntg1, ntg2, and, unexpectedly, ogg1, or by a lack of AP sites due to deletion of the MAG1 glycosylase gene. Similar to direct DSBs, the derived DSBs were subject to MRX (Mre11, Rad50, Xrs2-determined resection and relied upon the recombinational repair genes RAD51, RAD52, as well as on the MCD1 cohesin gene, for repair. In addition, we identified a novel DNA intermediate, detected as slow-moving chromosomal DNA (SMD in pulsed field electrophoresis gels shortly after MMS exposure in apn1/2 cells. The SMD requires nicked AP sites, but is independent of resection/recombination processes, suggesting that it is a novel structure generated during processing of 3'-blocked SSBs. Collectively, this study provides new insights into the potential consequences of alkylation base damage in vivo, including creation of novel structures as well as generation and repair of DSBs in nonreplicating cells.

  6. 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...

  7. Experimental demonstration of sharp Fano resonance in optical metamaterials composed of asymmetric double bars.

    Science.gov (United States)

    Moritake, Yuto; Kanamori, Yoshiaki; Hane, Kazuhiro

    2014-07-01

    We experimentally demonstrated Fano resonance in metamaterials composed of asymmetric double bars (ADBs) in the optical region. ADB metamaterials were fabricated by a lift-off method, and the optical spectra were measured. Around a wavelength of 1100 nm, measured optical spectra clearly showed sharp Fano resonance due to weak asymmetry of the ADB structures. The highest-quality factor (Q-factor) of the Fano resonance was 7.34. Calculated spectra showed the same tendency as the experimental spectra. Moreover, in a Fano resonant condition, out of phase of induced current flowing along each bar was revealed by electromagnetic field calculations. These antiphase currents decreased radiative loss of the Fano mode, resulting in a high Q-factor of the Fano resonance in ADB metamaterials. As the degree of asymmetry became small, the Q-factor decreased, and the Fano resonance disappeared because the effect of Joule loss became significant. PMID:24978806

  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. 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.

  10. 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.

  11. Experimental demonstration of sharp Fano resonance in optical metamaterials composed of asymmetric double bars.

    Science.gov (United States)

    Moritake, Yuto; Kanamori, Yoshiaki; Hane, Kazuhiro

    2014-07-01

    We experimentally demonstrated Fano resonance in metamaterials composed of asymmetric double bars (ADBs) in the optical region. ADB metamaterials were fabricated by a lift-off method, and the optical spectra were measured. Around a wavelength of 1100 nm, measured optical spectra clearly showed sharp Fano resonance due to weak asymmetry of the ADB structures. The highest-quality factor (Q-factor) of the Fano resonance was 7.34. Calculated spectra showed the same tendency as the experimental spectra. Moreover, in a Fano resonant condition, out of phase of induced current flowing along each bar was revealed by electromagnetic field calculations. These antiphase currents decreased radiative loss of the Fano mode, resulting in a high Q-factor of the Fano resonance in ADB metamaterials. As the degree of asymmetry became small, the Q-factor decreased, and the Fano resonance disappeared because the effect of Joule loss became significant.

  12. 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.

  13. 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.

  14. 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.

  15. Dynamical behaviors of an exciton in an asymmetric double coupled quantum dot

    Institute of Scientific and Technical Information of China (English)

    LIU Can-de; LIU Wen; LI Feng-ling; WU Da-peng; SU Xi-yu

    2006-01-01

    Dynamical behaviors of an exciton in an asymmetric double coupled quantum dot and an altematingcurrent (ac) electric field have been analyzed based on the two-level approximation theory,and the conditions under which dynamical localization occurs are obtained.It shows that when the amplitude of the ac electric field is small,the Coulomb interaction plays an important role.The dynamical behaviors of the exciton are mainly confined in the low-level subspace.When the ratio of the field intensity to frequency is the root of Bessel function,electron and hole are localized in one dot,and they can be divided with the increasing amplitude of the ac electric field.

  16. 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.

  17. 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

  18. 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

  19. Study of different routes to develop asymmetric double decker silsesquioxane (DDSQ)

    Science.gov (United States)

    Attanayake, Gayanthi Kumari

    Silsesquioxane cages can be considered as well-defined nanosized molecules (1-3 nm) and have attracted widening interests due to their possible use as components of resourceful inorganic/organic hybrid materials, as well as their applications in optics, catalysis, polymers and electronics. Double-decker silsesquioxane (DDSQ) nanoparticles have attracted much attention recently due to the ease of which these particles can be incorporated into polymeric materials and their unique capability to reinforce polymers.These systems are of high interest to scientists, due to their unique chemical and physical properties (solubility, non-flammability, oxidation resistance, and very good dielectric properties). For example, the United States Air Force and NASA use DDSQ incorporated polymers as thermoset material and flame retardants. This thesis discussed mainly three projects. One project centered on the research to improve and optimize the synthetic routes for a large scale synthesis of DDSQ functionalized oligoimides. These procedures offer the opportunity to combine several synthetic steps into a single reaction vessel, thereby cutting processing time and costs. The second project discussed is on the synthesis of a novel (phenylethynyl)phenyl DDSQ oligomer that can be used for high temperature application. This oligomer was successfully synthesized through a one pot route with 70% yield by avoiding the tedious separation techniques, fractional distillations and Kugelroher distillation. This novel oligomer will be characterized using TGA (Thermal Gravimetric Analysis) and DSC (Differential Scanning Calorimetry) for future studies. Another novel synthetic approach towards the synthesis of (phenylethynyl)phenyl DDSQ oligomers is also discussed. This new approach was based on Pd-catalyzed silylation of aryl halides. Even though Pd-catalyzed silylation of aryl halides was successful for the T7(iBu) cage, this chemistry was not applicable for DDSQ-H cage. The main project was

  20. 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.

  1. Optimal inverter logic gate using 10-nm double gate-all-around (DGAA transistor with asymmetric channel width

    Directory of Open Access Journals (Sweden)

    Myunghwan Ryu

    2016-01-01

    Full Text Available We investigate the electrical characteristics of a double-gate-all-around (DGAA transistor with an asymmetric channel width using three-dimensional device simulation. The DGAA structure creates a silicon nanotube field-effect transistor (NTFET with a core-shell gate architecture, which can solve the problem of loss of gate controllability of the channel and provides improved short-channel behavior. The channel width asymmetry is analyzed on both sides of the terminals of the transistors, i.e., source and drain. In addition, we consider both n-type and p-type DGAA FETs, which are essential to forming a unit logic cell, the inverter. Simulation results reveal that, according to the carrier types, the location of the asymmetry has a different effect on the electrical properties of the devices. Thus, we propose the N/P DGAA FET structure with an asymmetric channel width to form the optimal inverter. Various electrical metrics are analyzed to investigate the benefits of the optimal inverter structure over the conventional inverter structure. Simulation results show that 27% delay and 15% leakage power improvement are enabled in the optimum structure.

  2. 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.

  3. ESTIMATION OF THE POPULATION MEDIAN OF SYMMETRIC AND ASYMMETRIC DISTRIBUTIONS USING DOUBLE ROBUST EXTREME RANKED SET SAMPLING

    Directory of Open Access Journals (Sweden)

    Amer Ibrahim Al-Omari

    2010-09-01

    Full Text Available Double robust extreme ranked set sampling (DRERSS and its properties for estimating the population median are suggested. The performance of DRERSS with respect to simple random sampling (SRS, ranked set sampling (RSS, and extreme ranked set sampling (ERSS schemes is considered. Real data set that consist of heights of 346 students are used to evaluate the DRERSS method. It is found that when the underlying distribution is symmetric, the DRERSS estimators are unbiased of the population median. When the sample size is odd, DRERSS is efficient than SRS, ERSS, and RSS. When the sample size is even, DRERSS is more efficient than RSS and ERSS if the underlying distribution is symmetric, and for asymmetric distributions, DRERSS is more efficient than RSS and ERSS for based on the same number of measured units.

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

    Energy Technology Data Exchange (ETDEWEB)

    Rosu, Haret C., E-mail: hcr@ipicyt.edu.mx [IPICYT, Instituto Potosino de Investigacion Cientifica y Tecnologica, Camino a la presa San José 2055, Col. Lomas 4a Sección, 78216 San Luis Potosí, S.L.P. (Mexico); Mancas, Stefan C., E-mail: mancass@erau.edu [Department of Mathematics, Embry-Riddle Aeronautical University, Daytona Beach, FL 32114-3900 (United States); Chen, Pisin, E-mail: pisinchen@phys.ntu.edu.tw [Leung Center for Cosmology and Particle Astrophysics (LeCosPA) and Department of Physics, National Taiwan University, Taipei 10617, Taiwan (China)

    2014-10-15

    Extending our previous work (Rosu, 2014), we define supersymmetric partner potentials through a particular Riccati solution of the form F(x)=(x−c){sup 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.

  5. 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

  6. 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.

  7. 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-metal-...

  8. 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.

  9. Impact of Lateral Straggle on the Analog/RF Performance of Asymmetric Gate Stack Double Gate MOSFET

    Science.gov (United States)

    Sivaram, Gollamudi Sai; Chakraborty, Shramana; Das, Rahul; Dasgupta, Arpan; Kundu, Atanu; Sarkar, Chandan K.

    2016-09-01

    This paper presents a systematic comparative study of Analog and RF performances of an underlapped double gate (U-DG) NMOSFET with Gate Stack (GS) for varying straggle lengths. Asymmetric underlap devices (A-U-DG) have been proposed as one of the remedies for reducing Short Channel Effects (SCE's) with the underlap being present towards the source for sub 20 nm devices. However, the Source to Drain (S/D) implant lateral diffusion leads to a variation in the effective underlap length. This paper investigates the impact of variation of straggle length on the Analog and RF parameters of the device. The RF performance is analyzed by considering the intrinsic capacitances (Cgd, Cgs), intrinsic resistances (Rgd, Rgs), transport delay (τm), inductance (Lsd), cutoff frequency (fT), and the maximum frequency of oscillations (fmax). The circuit performance of the devices are also studied. It is seen that the Analog and RF performances of the devices are improved by optimizing the S/D lateral straggle.

  10. 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.

  11. 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

  12. 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...

  13. Diversity of Endonuclease V: From DNA Repair to RNA Editing

    Directory of Open Access Journals (Sweden)

    Isao Kuraoka

    2015-09-01

    Full Text Available Deamination of adenine occurs in DNA, RNA, and their precursors via a hydrolytic reaction and a nitrosative reaction. The generated deaminated products are potentially mutagenic because of their structural similarity to natural bases, which in turn leads to erroneous nucleotide pairing and subsequent disruption of cellular metabolism. Incorporation of deaminated precursors into the nucleic acid strand occurs during nucleotide synthesis by DNA and RNA polymerases or base modification by DNA- and/or RNA-editing enzymes during cellular functions. In such cases, removal of deaminated products from DNA and RNA by a nuclease might be required depending on the cellular function. One such enzyme, endonuclease V, recognizes deoxyinosine and cleaves 3' end of the damaged base in double-stranded DNA through an alternative excision repair mechanism in Escherichia coli, whereas in Homo sapiens, it recognizes and cleaves inosine in single-stranded RNA. However, to explore the role of endonuclease V in vivo, a detailed analysis of cell biology is required. Based on recent reports and developments on endonuclease V, we discuss the potential functions of endonuclease V in DNA repair and RNA metabolism.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. Bias-tunable IR photodetector based on asymmetrically doped GaAs/AlGaAs double-quantum-well nanomaterial for remote temperature sensing

    Science.gov (United States)

    Zhang, Xiang; Mitin, Vladimir; Choi, Jae Kyu; Sablon, Kimberly; Sergeev, Andrei

    2016-05-01

    We designed, fabricated, and characterized multi-color IR photodetectors with asymmetrical doping of GaAs/AlGaAs double quantum wells (DQW). We measured and analyzed spectral and noise characteristics to evaluate feasibility of these photodetectors for remote temperature sensing at liquid nitrogen temperatures. The bias voltage controls the charge distribution between the two wells in a DQW unit and provides effective tuning of IR induced electron transitions. We have found that the responsivity of our devices is symmetrical and weakly dependent on the bias voltage because the doping asymmetry compensates the effect of dopant migration in the growth direction. At the same time, the asymmetrical doping strongly enhances the selectivity and tunability of spectral characteristics by bias voltage. Multicolor detection of our QWIP is realized by varying the bias voltage. Maximum detection wavelength moves from 7.5 μm to 11.1 μm by switching applied bias from -5 V to 4 V. Modeling shows significant dependence of the photocurrent ratio on the object temperature regardless of its emissivity and geometrical factors. We also experimentally investigated the feasibility of our devices for remote temperature sensing by measuring the photocurrent as a response to blackbody radiation with the temperature from 300°C to 1000°C in the range of bias voltages from -5 V to 5 V. The agreement between modelling and experimental results demonstrates that our QWIP based on asymmetrically doped GaAs/AlGaAs DQW nanomaterial is capable of remote temperature sensing. By optimizing the physical design and varying the doping level of quantum wells, we can generalize this approach to higher temperature measurements. In addition, continuous variation of bias voltage provides fast collection of large amounts of photocurrent data at various biases and improves the accuracy of remote temperature measurements via appropriate algorithm of signal processing.

  19. Explicit Compact Surface-Potential and Drain-Current Models for Generic Asymmetric Double-Gate Metal-Oxide-Semiconductor Field-Effect Transistors

    Science.gov (United States)

    Zhu, Zhaomin; Zhou, Xing; Chandrasekaran, Karthik; Rustagi, Subhash C.; See, Guan Huei

    2007-04-01

    In this paper, explicit surface potentials for undoped asymmetric-double-gate (a-DG) metal-oxide-semiconductor field-effect transistors (MOSFETs) suitable for compact model development are presented for the first time. The model is physically derived from Poisson’s equation in each region of operation and adopted in a unified regional approach. The proposed model is physically scalable with oxide/channel thicknesses and has been verified with generic implicit solutions for independent gate biases as well as for different gate/oxide materials. The model is extendable to silicon-on-insulator (SOI) and symmetric-DG (s-DG) MOSFETs. Finally, a continuous, explicit drain-current equation has been derived on the basis of the developed explicit surface-potential solutions.

  20. 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.

  1. 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....

  2. 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...

  3. Crystallization and preliminary X-ray diffraction analysis on the homing endonuclease I-Dmo-I in complex with its target DNA

    Energy Technology Data Exchange (ETDEWEB)

    Redondo, Pilar [Macromolecular Crystallography Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Centre (CNIO), c/Melchor Fdez. Almagro 3, 28029 Madrid (Spain); Prieto, Jesús; Ramos, Elena; Blanco, Francisco J. [NMR Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Centre (CNIO), c/Melchor Fdez. Almagro 3, 28029 Madrid (Spain); Montoya, Guillermo, E-mail: gmontoya@cnio.es [Macromolecular Crystallography Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Centre (CNIO), c/Melchor Fdez. Almagro 3, 28029 Madrid (Spain)

    2007-12-01

    I-Dmo-I is a well characterized homing endonuclease from the archaeon Desulfurococcus mobilis. The enzyme was cloned and overexpressed in Escherichia coli. Crystallization experiments of I-Dmo-I in complex with its DNA target in the presence of Ca{sup 2+} and Mg{sup 2+} yielded crystals that were suitable for X-ray diffraction analysis. Homing endonucleases are highly specific DNA-cleaving enzymes that recognize long stretches of base pairs. The availability of these enzymes has opened novel perspectives for genome engineering in a wide range of fields, including gene therapy, by taking advantage of the homologous gene-targeting enhancement induced by a double-strand break. I-Dmo-I is a well characterized homing endonuclease from the archaeon Desulfurococcus mobilis. The enzyme was cloned and overexpressed in Escherichia coli. Crystallization experiments of I-Dmo-I in complex with its DNA target in the presence of Ca{sup 2+} and Mg{sup 2+} yielded crystals that were suitable for X-ray diffraction analysis. The crystals belonged to the monoclinic space group P2{sub 1}, with unit-cell parameters a = 106.75, b = 70.18, c = 106.85 Å, α = γ = 90, β = 119.93°. The self-rotation function and the Matthews coefficient suggested the presence of three protein–DNA complexes per asymmetric unit. The crystals diffracted to a resolution limit of 2.6 Å using synchrotron radiation at the Swiss Light Source (SLS) and the European Synchrotron Radiation Facility (ESRF)

  4. 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

  5. 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.

  6. 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

  7. 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

  8. 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...

  9. 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.

  10. 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.

  11. 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 numbe...

  12. 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.

  13. 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.

  14. Genome-wide analysis reveals specificities of Cpf1 endonucleases in human cells.

    Science.gov (United States)

    Kim, Daesik; Kim, Jungeun; Hur, Junho K; Been, Kyung Wook; Yoon, Sun-Heui; Kim, Jin-Soo

    2016-08-01

    Programmable clustered regularly interspaced short palindromic repeats (CRISPR) Cpf1 endonucleases are single-RNA-guided (crRNA) enzymes that recognize thymidine-rich protospacer-adjacent motif (PAM) sequences and produce cohesive double-stranded breaks (DSBs). Genome editing with CRISPR-Cpf1 endonucleases could provide an alternative to CRISPR-Cas9 endonucleases, but the determinants of targeting specificity are not well understood. Using mismatched crRNAs we found that Cpf1 could tolerate single or double mismatches in the 3' PAM-distal region, but not in the 5' PAM-proximal region. Genome-wide analysis of cleavage sites in vitro for eight Cpf1 nucleases using Digenome-seq revealed that there were 6 (LbCpf1) and 12 (AsCpf1) cleavage sites per crRNA in the human genome, fewer than are present for Cas9 nucleases (>90). Most Cpf1 off-target cleavage sites did not produce mutations in cells. We found mismatches in either the 3' PAM-distal region or in the PAM sequence of 12 off-target sites that were validated in vivo. Off-target effects were completely abrogated by using preassembled, recombinant Cpf1 ribonucleoproteins.

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

    Energy Technology Data Exchange (ETDEWEB)

    Gossett, J.; Lee, K.; Cunningham, R.P.; Doetsch, P.W.

    1988-04-05

    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 OsO/sub 4/-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.

  16. Expression, purification and crystallization of two endonuclease III enzymes from Deinococcus radiodurans.

    Science.gov (United States)

    Sarre, Aili; Ökvist, Mats; Klar, Tobias; Moe, Elin; Timmins, Joanna

    2014-12-01

    Endonuclease III is a bifunctional DNA glycosylase that removes a wide range of oxidized bases in DNA. Deinococcus radiodurans is an extreme radiation-resistant and desiccation-resistant bacterium and possesses three genes encoding endonuclease III enzymes in its genome: DR2438 (EndoIII-1), DR0289 (EndoIII-2) and DR0982 (EndoIII-3). Here, EndoIII-1 and an N-terminally truncated form of EndoIII-3 (EndoIII-3Δ76) have been expressed, purified and crystallized, and preliminary X-ray crystallographic analyses have been performed to 2.15 and 1.31 Å resolution, respectively. The EndoIII-1 crystals belonged to the monoclinic space group C2, with unit-cell parameters a = 181.38, b = 38.56, c = 37.09 Å, β = 89.34° and one molecule per asymmetric unit. The EndoIII-3Δ76 crystals also belonged to the monoclinic space group C2, but with unit-cell parameters a = 91.47, b = 40.53, c = 72.47 Å, β = 102.53° and one molecule per asymmetric unit. The EndoIII-1 structure was determined by molecular replacement, while the truncated EndoIII-3Δ76 structure was determined by single-wavelength anomalous dispersion phasing. Refinement of the structures is in progress.

  17. 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.

  18. 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.

  19. A highly efficient ADH-coupled NADH-recycling system for the asymmetric bioreduction of carbon-carbon double bonds using enoate reductases.

    Science.gov (United States)

    Tauber, Katharina; Hall, Melanie; Kroutil, Wolfgang; Fabian, Walter M F; Faber, Kurt; Glueck, Silvia M

    2011-06-01

    The asymmetric bioreduction of activated alkenes catalyzed by flavin-dependent enoate reductases from the OYE-family represents a powerful method for the production of optically active compounds. For its preparative-scale application, efficient and economic NADH-recycling is crucial. A novel enzyme-coupled NADH-recycling system is proposed based on the concurrent oxidation of a sacrificial sec-alcohol catalyzed by an alcohol dehydrogenase (ADH-A). Due to the highly favorable position of the equilibrium of ene-reduction versus alcohol-oxidation, the cosubstrate is only required in slight excess.

  20. 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...

  1. 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...

  2. 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.

  3. 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...

  4. Copper(II) coordination chain complex with the 2,5-bis(2-pyridyl)-1,3,4-thiadiazole ligand and an asymmetric μ2-1,1-azido double-bridged: Synthesis, crystal structure and magnetic properties

    Science.gov (United States)

    Laachir, Abdelhakim; Guesmi, Salaheddine; Saadi, Mohamed; El Ammari, Lahcen; Mentré, Olivier; Vezin, Hervé; Colis, Silviu; Bentiss, Fouad

    2016-11-01

    A new asymmetric μ2-1,1-azido double bridged cooper (II), with 2,5-bis(2-pyridyl)-1,3,4-thiadiazole (L), has been synthesized and characterized using single crystal X-ray diffraction, FT-IR, UV-Visible spectroscopic and magnetic measurements. The asymmetric unit of the title compound contains half molecule of formula, C12H8CuN10S, which crystallizes in the triclinic system, space group P 1 bar , with a = 6.5916 (4)Å, b = 10.6905 (7) Å, c = 11.5037 (7) Å, α = 106.508 (3)°, β = 105.538 (3)°, γ = 90.233 (4)°, V = 745.99 (8) Å3 and Z = 2. The structure consists of two [CuN5] prismatic polyhedra linked together by edge-sharing to build up a [Cu2N8] dimer arranged in chain. The connectivity along the chain is performed by Nsbnd N edge sharing between dimers. In the crystal, the molecules are linked together by Csbnd H⋯N hydrogen bonds and by π---π interactions between parallel pyridyl rings of neighboring molecules. The interpretation of FT-IR and UV-Vis spectra is consistent with the crystal structure determined by X-ray diffraction. The magnetic properties of the complex confirm the picture of an alternated … Cu-J1-Cu ….J2 … Cu-J1-Cu … magnetic chains. We found in the dimers weak antiferromagnetic exchange interactions J1/k = -5.9 (1) k and between them J2/k = -2.3 k.

  5. Restriction endonucleases digesting DNA in PCR buffer

    Institute of Scientific and Technical Information of China (English)

    LIU Xue-dong; ZHENG Dong; ZHOU Yan-na; MAO Wei-wei; MA Jian-zhang

    2005-01-01

    Six commonly used restriction endonucleases (Res) (Acc I, Ban II, EcoR I, Hind III, Sac I, Sca I) were tested for their ability to directly digest DNA completely in the Polymerase Chain Reaction (PCR) buffers. The results showed that: with the requirement for additional magnesium supplemented as activator, Res, except EcoR I appeared star activity, completely digested unmethylated lambda DNA after overnight incubation in PCR buffer and functioned as equally well as in recommended Restriction Enzyme Buffer provided with each enzyme; all Res tested completely digested PCR products in PCR buffer, it implied digestion of PCR products may often be performed directly in the PCR tube without the requirement for any precipitation or purification steps; and the concentration of MgCl2 from 2.5 mmol·L-1 to 10 mmol·L-1 did not significantly affect activity of Res in PCR buffer. This simplified method for RE digestion of PCR products could have applications in restriction fragment length polymorphism (RFLP) analysis and single-stranded conformational polymorphism (SSCP) analysis of large PCR products. However, usage of this procedure for cloning applications needs further data.

  6. 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

  7. 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.

  8. Leishmania (Viannia panamensis expresses a nuclease with molecular and biochemical features similar to the Endonuclease G of higher eukaryotes*

    Directory of Open Access Journals (Sweden)

    Miguel A Toro-Londoño

    2011-06-01

    Full Text Available Objective: To characterize the molecular and biochemical features of the Endonuclease G of Leishmania (Viannia panamensis. Methods: The gene of the putative L. (V. panamensis Endonuclease G was amplified, cloned, and sequenced. The recombinant protein was produced in a heterologous expression system and biochemical assays were run to determine its ion, temperature, and pH preferences. Results: The L. (V. panamensis rENDOG has biochemical features similar to those found in other trypanosomatids and higher eukaryotes. In addition, phylogenetic analysis revealed a possible evolutionary relationship with metazoan ENDOG. Conclusions: L. (V. panamensis has a gene that codifies an ENDOG homologous to those of higher organisms. This enzyme can be produced in Escherichia coli and is able to degrade covalently closed circular double-stranded DNA. It has a magnesium preference, can be inhibited by potassium, and is able to function within a wide temperature and pH range.

  9. Leishmania (Viannia panamensis expresses a nuclease with molecular and biochemical features similar to the Endonuclease G of higher eukaryotes

    Directory of Open Access Journals (Sweden)

    Miguel A. Toro-Londoño

    2011-06-01

    Full Text Available Objective: To characterize the molecular and biochemical features of the Endonuclease G of Leishmania (Viannia panamensis.Methods: The gene of the putative L. (V. panamensis Endonuclease G was amplified, cloned, and sequenced. The recombinant protein was produced in a heterologous expression system and biochemical assays were run to determine its ion, temperature, and pH preferences.Results: The L. (V. panamensis rENDOG has biochemical features similar to those found in other trypanosomatids and higher eukaryotes. In addition, phylogenetic analysis revealed a possible evolutionary relationship with metazoan ENDOG.Conclusions: L. (V. panamensis has a gene that codifies an ENDOG homologous to those of higher organisms. This enzyme can be produced in Escherichia coli and is able to degrade covalently closed circular double-stranded DNA. It has a magnesium preference, can be inhibited by potassium, and is able to function within a wide temperature and pH range.

  10. 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

  11. 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

  12. Creation of a novel telomere-cutting endonuclease based on the EN domain of telomere-specific non-long terminal repeat retrotransposon, TRAS1

    Directory of Open Access Journals (Sweden)

    Yoshitake Kazutoshi

    2010-04-01

    Full Text Available Abstract Background The ends of chromosomes, termed telomeres consist of repetitive DNA. The telomeric sequences shorten with cell division and, when telomeres are critically abbreviated, cells stop proliferating. However, in cancer cells, by the expression of telomerase which elongates telomeres, the cells can continue proliferating. Many approaches for telomere shortening have been pursued in the past, but to our knowledge, cutting telomeres in vivo has not so far been demonstrated. In addition, there is lack of information on the cellular effects of telomere shortening in human cells. Results Here, we created novel chimeric endonucleases to cut telomeres by fusing the endonuclease domain (TRAS1EN of the silkworm's telomere specific non-long terminal repeat retrotransposon TRAS1 to the human telomere-binding protein, TRF1. An in vitro assay demonstrated that the TRAS1EN-TRF1 chimeric endonucleases (T-EN and EN-T cut the human (TTAGGGn repeats specifically. The concentration of TRAS1EN-TRF1 chimeric endonucleases necessary for the cleavage of (TTAGGGn repeats was about 40-fold lower than that of TRAS1EN alone. When TRAS1EN-TRF1 endonucleases were introduced into human U2OS cancer cells using adenovirus vectors, the enzymes localized at telomeres of nuclei, cleaved and shortened the telomeric DNA by double-strand breaks. When human U2OS and HFL-1 fibroblast cells were infected with EN-T recombinant adenovirus, their cellular proliferation was suppressed for about 2 weeks after infection. In contrast, the TRAS1EN mutant (H258A chimeric endonuclease fused with TRF1 (ENmut-T did not show the suppression effect. The EN-T recombinant adenovirus induced telomere shortening in U2OS cells, activated the p53-dependent pathway and caused the senescence associated cellular responses, while the ENmut-T construct did not show such effects. Conclusions A novel TRAS1EN-TRF1 chimeric endonuclease (EN-T cuts the human telomeric repeats (TTAGGGn specifically in

  13. 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

  14. 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

  15. Asymmetric transmission: a generic property of lossy periodic interfaces

    CERN Document Server

    Plum, E; Zheludev, N I

    2010-01-01

    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.

  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. Simulation of Chaos in Asymmetric Nonlinear Chua's Circuit

    Institute of Scientific and Technical Information of China (English)

    WANG Yu-fei; QIAO Shu-tong; JIANG Jian-guo

    2008-01-01

    In order to describe practical chaotic systems exactly, we presented a simple modified Chua's circuit,which contains an asymmetric nonlinear resistive element. Mathematical analysis was made, and simulation study was performed by MATLAB. By varying the value of linear resistor in the circuit, rich variety dynamical behaviors were observed, such as DC equilibrium point, Hopf bifurcation, period-doubling bifurcation,single-scroll strange attractor, periodic windows, and asymmetric double-scroll strange attractor. The extreme sensitivity in the state trajectory with respect to the initial conditions was exhibited; the special characteristic of asymmetric nonlinear Chua's circuit was found also.

  18. Computational redesign of endonuclease DNA binding and cleavage specificity

    Science.gov (United States)

    Ashworth, Justin; Havranek, James J.; Duarte, Carlos M.; Sussman, Django; Monnat, Raymond J.; Stoddard, Barry L.; Baker, David

    2006-06-01

    The reprogramming of DNA-binding specificity is an important challenge for computational protein design that tests current understanding of protein-DNA recognition, and has considerable practical relevance for biotechnology and medicine. Here we describe the computational redesign of the cleavage specificity of the intron-encoded homing endonuclease I-MsoI using a physically realistic atomic-level forcefield. Using an in silico screen, we identified single base-pair substitutions predicted to disrupt binding by the wild-type enzyme, and then optimized the identities and conformations of clusters of amino acids around each of these unfavourable substitutions using Monte Carlo sampling. A redesigned enzyme that was predicted to display altered target site specificity, while maintaining wild-type binding affinity, was experimentally characterized. The redesigned enzyme binds and cleaves the redesigned recognition site ~10,000 times more effectively than does the wild-type enzyme, with a level of target discrimination comparable to the original endonuclease. Determination of the structure of the redesigned nuclease-recognition site complex by X-ray crystallography confirms the accuracy of the computationally predicted interface. These results suggest that computational protein design methods can have an important role in the creation of novel highly specific endonucleases for gene therapy and other applications.

  19. 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

  20. 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

  1. 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...

  2. 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...

  3. 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.

  4. Nucleosomes Inhibit Cas9 Endonuclease Activity in Vitro.

    Science.gov (United States)

    Hinz, John M; Laughery, Marian F; Wyrick, John J

    2015-12-01

    During Cas9 genome editing in eukaryotic cells, the bacterial Cas9 enzyme cleaves DNA targets within chromatin. To understand how chromatin affects Cas9 targeting, we characterized Cas9 activity on nucleosome substrates in vitro. We find that Cas9 endonuclease activity is strongly inhibited when its target site is located within the nucleosome core. In contrast, the nucleosome structure does not affect Cas9 activity at a target site within the adjacent linker DNA. Analysis of target sites that partially overlap with the nucleosome edge indicates that the accessibility of the protospacer-adjacent motif (PAM) is the critical determinant of Cas9 activity on a nucleosome.

  5. 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.

  6. 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.

  7. Structural and biochemical basis for development of influenza virus inhibitors targeting the PA endonuclease.

    Directory of Open Access Journals (Sweden)

    Rebecca M DuBois

    Full Text Available Emerging influenza viruses are a serious threat to human health because of their pandemic potential. A promising target for the development of novel anti-influenza therapeutics is the PA protein, whose endonuclease activity is essential for viral replication. Translation of viral mRNAs by the host ribosome requires mRNA capping for recognition and binding, and the necessary mRNA caps are cleaved or "snatched" from host pre-mRNAs by the PA endonuclease. The structure-based development of inhibitors that target PA endonuclease is now possible with the recent crystal structure of the PA catalytic domain. In this study, we sought to understand the molecular mechanism of inhibition by several compounds that are known or predicted to block endonuclease-dependent polymerase activity. Using an in vitro endonuclease activity assay, we show that these compounds block the enzymatic activity of the isolated PA endonuclease domain. Using X-ray crystallography, we show how these inhibitors coordinate the two-metal endonuclease active site and engage the active site residues. Two structures also reveal an induced-fit mode of inhibitor binding. The structures allow a molecular understanding of the structure-activity relationship of several known influenza inhibitors and the mechanism of drug resistance by a PA mutation. Taken together, our data reveal new strategies for structure-based design and optimization of PA endonuclease inhibitors.

  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. 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...

  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. Comparative Structural and Functional Analysis of Bunyavirus and Arenavirus Cap-Snatching Endonucleases

    Science.gov (United States)

    Reguera, Juan; Gerlach, Piotr; Rosenthal, Maria; Gaudon, Stephanie; Coscia, Francesca; Günther, Stephan; Cusack, Stephen

    2016-01-01

    Segmented negative strand RNA viruses of the arena-, bunya- and orthomyxovirus families uniquely carry out viral mRNA transcription by the cap-snatching mechanism. This involves cleavage of host mRNAs close to their capped 5′ end by an endonuclease (EN) domain located in the N-terminal region of the viral polymerase. We present the structure of the cap-snatching EN of Hantaan virus, a bunyavirus belonging to hantavirus genus. Hantaan EN has an active site configuration, including a metal co-ordinating histidine, and nuclease activity similar to the previously reported La Crosse virus and Influenza virus ENs (orthobunyavirus and orthomyxovirus respectively), but is more active in cleaving a double stranded RNA substrate. In contrast, Lassa arenavirus EN has only acidic metal co-ordinating residues. We present three high resolution structures of Lassa virus EN with different bound ion configurations and show in comparative biophysical and biochemical experiments with Hantaan, La Crosse and influenza ENs that the isolated Lassa EN is essentially inactive. The results are discussed in the light of EN activation mechanisms revealed by recent structures of full-length influenza virus polymerase. PMID:27304209

  12. Comparative Structural and Functional Analysis of Bunyavirus and Arenavirus Cap-Snatching Endonucleases.

    Science.gov (United States)

    Reguera, Juan; Gerlach, Piotr; Rosenthal, Maria; Gaudon, Stephanie; Coscia, Francesca; Günther, Stephan; Cusack, Stephen

    2016-06-01

    Segmented negative strand RNA viruses of the arena-, bunya- and orthomyxovirus families uniquely carry out viral mRNA transcription by the cap-snatching mechanism. This involves cleavage of host mRNAs close to their capped 5' end by an endonuclease (EN) domain located in the N-terminal region of the viral polymerase. We present the structure of the cap-snatching EN of Hantaan virus, a bunyavirus belonging to hantavirus genus. Hantaan EN has an active site configuration, including a metal co-ordinating histidine, and nuclease activity similar to the previously reported La Crosse virus and Influenza virus ENs (orthobunyavirus and orthomyxovirus respectively), but is more active in cleaving a double stranded RNA substrate. In contrast, Lassa arenavirus EN has only acidic metal co-ordinating residues. We present three high resolution structures of Lassa virus EN with different bound ion configurations and show in comparative biophysical and biochemical experiments with Hantaan, La Crosse and influenza ENs that the isolated Lassa EN is essentially inactive. The results are discussed in the light of EN activation mechanisms revealed by recent structures of full-length influenza virus polymerase. PMID:27304209

  13. 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.

  14. RecA-dependent programmable endonuclease Ref cleaves DNA in two distinct steps.

    Science.gov (United States)

    Ronayne, Erin A; Cox, Michael M

    2014-04-01

    The bacteriophage P1 recombination enhancement function (Ref) protein is a RecA-dependent programmable endonuclease. Ref targets displacement loops formed when an oligonucleotide is bound by a RecA filament and invades homologous double-stranded DNA sequences. Mechanistic details of this reaction have been explored, revealing that (i) Ref is nickase, cleaving the two target strands of a displacement loop sequentially, (ii) the two strands are cleaved in a prescribed order, with the paired strand cut first and (iii) the two cleavage events have different requirements. Cutting the paired strand is rapid, does not require RecA-mediated ATP hydrolysis and is promoted even by Ref active site variant H153A. The displaced strand is cleaved much more slowly, requires RecA-mediated ATP hydrolysis and does not occur with Ref H153A. The two cleavage events are also affected differently by solution conditions. We postulate that the second cleavage (displaced strand) is limited by some activity of RecA protein.

  15. RESTRICTION ENDONUCLEASE ANALYSIS OF MITOCHONDRIAL DNA FROM HUMAN LUNG ADENOCARCINOMA CELL LINE SPC-A-1

    Institute of Scientific and Technical Information of China (English)

    HU Yide; QIAN Guisheng; CHEN Weizhong; LI Shuping; WANG Guansong; MAO Baoling

    1999-01-01

    Objective: To understand the role of mitochondrial DNA (mtDNA) in carcinogenesis. Methods: single-step method was used to isolate the mtDNA from human lung adenocarcinoma cell line SPC-A-1. The mtDNA was analyzed by restriction fragment length polymorphism (RFLP) with 11 kinds of restriction endonuclease, which were Pvu Ⅱ, Xho Ⅰ, Pst Ⅰ, EcoR Ⅰ,BstE Ⅱ, Hind Ⅲ, Hpa Ⅰ, Bcl Ⅰ, EcoR Ⅴ, Sca Ⅰ and Xba Ⅰ.Restriction map of mtDNA from SPC-A-1 cell was obtained by the single and double-digestion method.Results: It was found that no variation at 32 restrictionsites could be detected in the coding region of mtDNA from SPC-A-1 cell line. But a new site was found at nucleotide 16276 (EcoR Ⅴ) within the noncoding region.Conclusion: These results indicate that the primary structure of gene coding region of mtDNA isolated from SPC-A-1 cell is highly stable. While the major variation of nucleotide is probably located in the noncoding region.

  16. 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...

  17. Mitochondrial endonuclease G mediates breakdown of paternal mitochondria upon fertilization.

    Science.gov (United States)

    Zhou, Qinghua; Li, Haimin; Li, Hanzeng; Nakagawa, Akihisa; Lin, Jason L J; Lee, Eui-Seung; Harry, Brian L; Skeen-Gaar, Riley Robert; Suehiro, Yuji; William, Donna; Mitani, Shohei; Yuan, Hanna S; Kang, Byung-Ho; Xue, Ding

    2016-07-22

    Mitochondria are inherited maternally in most animals, but the mechanisms of selective paternal mitochondrial elimination (PME) are unknown. While examining fertilization in Caenorhabditis elegans, we observed that paternal mitochondria rapidly lose their inner membrane integrity. CPS-6, a mitochondrial endonuclease G, serves as a paternal mitochondrial factor that is critical for PME. We found that CPS-6 relocates from the intermembrane space of paternal mitochondria to the matrix after fertilization to degrade mitochondrial DNA. It acts with maternal autophagy and proteasome machineries to promote PME. Loss of cps-6 delays breakdown of mitochondrial inner membranes, autophagosome enclosure of paternal mitochondria, and PME. Delayed removal of paternal mitochondria causes increased embryonic lethality, demonstrating that PME is important for normal animal development. Thus, CPS-6 functions as a paternal mitochondrial degradation factor during animal development.

  18. Human RECQL5beta stimulates flap endonuclease 1

    DEFF Research Database (Denmark)

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

    2010-01-01

    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...... that the ability of RecQ helicases to stimulate FEN1 may be a general feature of this class of enzymes. This could indicate a common role for the RecQ helicases in the processing of oxidative DNA damage....

  19. 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.

  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. 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...... LNA-modified DNA oligonucleotides. Furthermore, introduction of LNA nucleotides protects against cleavage by the restriction endonucleases PvuII, PstI, SacI, KpnI and EcoRI....

  2. Asymmetrical international attitudes

    NARCIS (Netherlands)

    Van Oudenhoven, JP; Askevis-Leherpeux, F; Hannover, B; Jaarsma, R; Dardenne, B

    2002-01-01

    In general, attitudes towards nations have a fair amount of reciprocity: nations either like each other are relatively indifferent to each other or dislike each other Sometimes, however international attitudes are asymmetrical. In this study, we use social identity theory in order to explain asymmet

  3. An asymmetric Kadison's inequality

    CERN Document Server

    Bourin, Jean-Christophe

    2010-01-01

    Some inequalities for positive linear maps on matrix algebras are given, especially asymmetric extensions of Kadison's inequality and several operator versions of Chebyshev's inequality. We also discuss well-known results around the matrix geometric mean and connect it with complex interpolation.

  4. 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.

  5. Asymmetric catalysis with helical polymers

    NARCIS (Netherlands)

    Megens, Rik P.; Roelfes, Gerard

    2011-01-01

    Inspired by nature, the use of helical biopolymer catalysts has emerged over the last years as a new approach to asymmetric catalysis. In this Concept article the various approaches and designs and their application in asymmetric catalysis will be discussed.

  6. 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↓.

  7. Effects of Dimerization of Serratia marcescens Endonuclease on Water Dynamics.

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Chuanying; Beck, Brian W.; Krause, Kurt; Weksberg, Tiffany E.; Pettitt, Bernard M.

    2007-02-15

    The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. The dynamics and structure of Serratia marcescens endonuclease and its neighboring solvent are investigated by molecular dynamics (MD). Comparisons are made with structural and biochemical experiments. The dimer form is physiologic and functions more processively than the monomer. We previously found a channel formed by connected clusters of waters from the active site to the dimer interface. Here, we show that dimerization clearly changes correlations in the water structure and dynamics in the active site not seen in the monomer. Our results indicate that water at the active sites of the dimer is less affected compared with bulk solvent than in the monomer where it has much slower characteristic relaxation times. Given that water is a required participant in the reaction, this gives a clear advantage to dimerization in the absence of an apparent ability to use both active sites simultaneously.

  8. 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)

  9. 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.

  10. 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....

  11. Asymmetric total synthesis of vindoline.

    Science.gov (United States)

    Kato, Daisuke; Sasaki, Yoshikazu; Boger, Dale L

    2010-03-24

    A concise asymmetric total synthesis of (-)-vindoline (1) is detailed based on a tandem intramolecular [4+2]/[3+2] cycloaddition cascade of a 1,3,4-oxadiazole inspired by the natural product structure, in which the tether linking the initiating dienophile and oxadiazole bears a chiral substituent that controls the facial selectivity of the initiating Diels-Alder reaction and sets absolute stereochemistry of the remaining six stereocenters in the cascade cycloadduct. This key reaction introduces three rings and four C-C bonds central to the pentacyclic ring system setting all six stereocenters and introducing essentially all the functionality found in the natural product in a single step. Implementation of the approach also required the development of a unique ring expansion reaction to provide a six-membered ring suitably functionalized for introduction of the Delta (6, 7)-double bond found in the core structure of vindoline and defined our use of a protected hydroxymethyl group as the substituent used to control the stereochemical course of the cycloaddition cascade.

  12. Differential regulation of the cellular response to DNA double-strand breaks in G1

    DEFF Research Database (Denmark)

    Barlow, Jacqueline H; Lisby, Michael; Rothstein, Rodney

    2008-01-01

    Double-strand breaks (DSBs) are potentially lethal DNA lesions that can be repaired by either homologous recombination (HR) or nonhomologous end-joining (NHEJ). We show that DSBs induced by ionizing radiation (IR) are efficiently processed for HR and bound by Rfa1 during G1, while endonuclease...

  13. 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

  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. Endonuclease-rolling circle amplification-based method for sensitive analysis of DNA-binding protein

    Institute of Scientific and Technical Information of China (English)

    Min Li Li; Dong Rui Zhou; Hong Zhao; Jin Ke Wang; Zu Hong Lu

    2009-01-01

    A sensitive approach for the qualitative detection of DNA-binding protein on the microarray was developed. DNA complexes in which a partial duplex region is formed from a biotin-primer and a circle single strand DNA (ssDNA) were spotted on a microarray. The endonuclease recognition site (ERS) and the DNA-binding sites (DBS) were arranged side by side within the duplex region. The working principle of the detection system is described as follows: when the DNA-binding protein capture the DBS, the endonuclease could not attach to the ERS, and the immobilized primer in the DNA complex could be extended along the circle ssDNA by rolling circle amplification (RCA). When no protein protects the DBS, the ERS could be attacked by the endonuclease and subsequently no rolling circle amplification occurs. Thereby we can detect the sequence specific DNA-binding activity with high-sensitivity due to the signal amplification of RCA.

  16. N-acylhydrazone inhibitors of influenza virus PA endonuclease with versatile metal binding modes

    Science.gov (United States)

    Carcelli, Mauro; Rogolino, Dominga; Gatti, Anna; de Luca, Laura; Sechi, Mario; Kumar, Gyanendra; White, Stephen W.; Stevaert, Annelies; Naesens, Lieve

    2016-08-01

    Influenza virus PA endonuclease has recently emerged as an attractive target for the development of novel antiviral therapeutics. This is an enzyme with divalent metal ion(s) (Mg2+ or Mn2+) in its catalytic site: chelation of these metal cofactors is an attractive strategy to inhibit enzymatic activity. Here we report the activity of a series of N-acylhydrazones in an enzymatic assay with PA-Nter endonuclease, as well as in cell-based influenza vRNP reconstitution and virus yield assays. Several N-acylhydrazones were found to have promising anti-influenza activity in the low micromolar concentration range and good selectivity. Computational docking studies are carried on to investigate the key features that determine inhibition of the endonuclease enzyme by N-acylhydrazones. Moreover, we here describe the crystal structure of PA-Nter in complex with one of the most active inhibitors, revealing its interactions within the protein’s active site.

  17. RNA-dependent DNA endonuclease Cas9 of the CRISPR system: Holy Grail of genome editing?

    Science.gov (United States)

    Gasiunas, Giedrius; Siksnys, Virginijus

    2013-11-01

    Tailor-made nucleases for precise genome modification, such as zinc finger or TALE nucleases, currently represent the state-of-the-art for genome editing. These nucleases combine a programmable protein module which guides the enzyme to the target site with a nuclease domain which cuts DNA at the addressed site. Reprogramming of these nucleases to cut genomes at specific locations requires major protein engineering efforts. RNA-guided DNA endonuclease Cas9 of the type II (clustered regularly interspaced short palindromic repeat) CRISPR-Cas system uses CRISPR RNA (crRNA) as a guide to locate the DNA target and the Cas9 protein to cut DNA. Easy programmability of the Cas9 endonuclease using customizable RNAs brings unprecedented flexibility and versatility for targeted genome modification. We highlight the potential of the Cas9 RNA-guided DNA endonuclease as a novel tool for genome surgery, and discuss possible constraints and future prospects.

  18. Mutagenic scan of the H-N-H motif of colicin E9: implications for the mechanistic enzymology of colicins, homing enzymes and apoptotic endonucleases

    Science.gov (United States)

    Walker, David C.; Georgiou, Theonie; Pommer, Ansgar J.; Walker, Daniel; Moore, Geoffrey R.; Kleanthous, Colin; James, Richard

    2002-01-01

    Colicin E9 is a microbial toxin that kills bacteria through random degradation of chromosomal DNA. Within the active site of the cytotoxic endonuclease domain of colicin E9 (the E9 DNase) is a 32 amino acid motif found in the H-N-H group of homing endonucleases. Crystal structures of the E9 DNase have implicated several conserved residues of the H-N-H motif in the mechanism of DNA hydrolysis. We have used mutagenesis to test the involvement of these key residues in colicin toxicity, metal ion binding and catalysis. Our data show, for the first time, that the H-N-H motif is the site of DNA binding and that Mg2+-dependent cleavage of double-stranded DNA is responsible for bacterial cell death. We demonstrate that more active site residues are required for catalysis in the presence of Mg2+ ions than transition metals, consistent with the recent hypothesis that the E9 DNase hydrolyses DNA by two distinct, cation-dependent catalytic mechanisms. The roles of individual amino acids within the H-N-H motif are discussed in the context of the available structural information on this and related DNases and we address the possible mechanistic similarities between caspase-activated DNases, responsible for the degradation of chromatin in eukaryotic apoptosis, and H-N-H DNases. PMID:12136104

  19. A novel label-free fluorescence strategy for methyltransferase activity assay based on dsDNA-templated copper nanoparticles coupled with an endonuclease-assisted signal transduction system.

    Science.gov (United States)

    Lai, Q Q; Liu, M D; Gu, C C; Nie, H G; Xu, X J; Li, Z H; Yang, Z; Huang, S M

    2016-02-21

    Evaluating DNA methyltransferase (MTase) activity has received considerable attention due to its significance in the fields of early cancer clinical diagnostics and drug discovery. Herein, we proposed a novel label-free fluorescence method for MTase activity assay by coupling double-stranded DNA (dsDNA)-templated copper nanoparticles (CuNPs) with an endonuclease-assisted signal transduction system. In this strategy, dsDNA molecules were first methylated by DNA adenine methylation (Dam) MTase and then cleaved by the methylation-sensitive restriction endonuclease DpnI. The cleaved DNA fragments could not act as efficient templates for the formation of fluorescent CuNPs and thus no fluorescence signal was produced. Under optimized experimental conditions, the developed strategy exhibited a sensitive fluorescence response to Dam MTase activity. This strategy was also demonstrated to provide an excellent platform to the inhibitor screening for Dam MTase. These results demonstrated the great potential for the practical applications of the proposed strategy for Dam MTase activity assay. PMID:26764536

  20. 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)

  1. 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.

  2. 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...

  3. The effects of addition of mononucleotides on Sma nuc endonuclease activity.

    Science.gov (United States)

    Romanova, Julia; Filimonova, Maria

    2012-01-01

    Examination of the effects of mononucleotides on Sma nuc endonuclease originated from Gram negative bacterium Serratia marcescens displayed that any mononucleotide produced by Sma nuc during hydrolysis of DNA or RNA may regulate the enzyme activity affecting the RNase activity without pronounced influence on the activity towards DNA. The type of carbohydrate residue in mononucleotides does not affect the regulation. In contrast, the effects depend on the type of bases in nucleotides. AMP or dAMP was classified as a competitive inhibitor of partial type. GMP, UMP, and CMP were found to be uncompetitive inhibitors that suggest a specific site(s) for the nucleotide(s) binding in Sma nuc endonuclease.

  4. 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

  5. The mitochondrial LSU rRNA group II intron of Ustilago maydis encodes an active homing endonuclease likely involved in intron mobility.

    Directory of Open Access Journals (Sweden)

    Anja Pfeifer

    Full Text Available BACKGROUND: The a2 mating type locus gene lga2 is critical for uniparental mitochondrial DNA inheritance during sexual development of Ustilago maydis. Specifically, the absence of lga2 results in biparental inheritance, along with efficient transfer of intronic regions in the large subunit rRNA gene between parental molecules. However, the underlying role of the predicted LAGLIDADG homing endonuclease gene I-UmaI located within the group II intron LRII1 has remained unresolved. METHODOLOGY/PRINCIPAL FINDINGS: We have investigated the enzymatic activity of I-UmaI in vitro based on expression of a tagged full-length and a naturally occurring mutant derivative, which harbors only the N-terminal LAGLIDADG domain. This confirmed Mg²⁺-dependent endonuclease activity and cleavage at the LRII1 insertion site to generate four base pair extensions with 3' overhangs. Specifically, I-UmaI recognizes an asymmetric DNA sequence with a minimum length of 14 base pairs (5'-GACGGGAAGACCCT-3' and tolerates subtle base pair substitutions within the homing site. Enzymatic analysis of the mutant variant indicated a correlation between the activity in vitro and intron homing. Bioinformatic analyses revealed that putatively functional or former functional I-UmaI homologs are confined to a few members within the Ustilaginales and Agaricales, including the phylogenetically distant species Lentinula edodes, and are linked to group II introns inserted into homologous positions in the LSU rDNA. CONCLUSIONS/SIGNIFICANCE: The present data provide strong evidence that intron homing efficiently operates under conditions of biparental inheritance in U. maydis. Conversely, uniparental inheritance may be critical to restrict the transmission of mobile introns. Bioinformatic analyses suggest that I-UmaI-associated introns have been acquired independently in distant taxa and are more widespread than anticipated from available genomic data.

  6. 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.

  7. Phase-transfer-catalysed asymmetric synthesis of tetrasubstituted allenes

    Science.gov (United States)

    Hashimoto, Takuya; Sakata, Kazuki; Tamakuni, Fumiko; Dutton, Mark J.; Maruoka, Keiji

    2013-03-01

    Allenes are molecules based on three carbons connected by two cumulated carbon-carbon double bonds. Given their axially chiral nature and unique reactivity, substituted allenes have a variety of applications in organic chemistry as key synthetic intermediates and directly as part of biologically active compounds. Although the demands for these motivated many endeavours to make axially chiral, substituted allenes by exercising asymmetric catalysis, the catalytic asymmetric synthesis of fully substituted ones (tetrasubstituted allenes) remained largely an unsolved issue. The fundamental obstacle to solving this conundrum is the lack of a simple synthetic transformation that provides tetrasubstituted allenes in the action of catalysis. We report herein a strategy to overcome this issue by the use of a phase-transfer-catalysed asymmetric functionalization of 1-alkylallene-1,3-dicarboxylates with N-arylsulfonyl imines and benzylic and allylic bromides.

  8. 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.

  9. 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.

  10. Crystal structure of the primary piRNA biogenesis factor Zucchini reveals similarity to the bacterial PLD endonuclease Nuc.

    Science.gov (United States)

    Voigt, Franka; Reuter, Michael; Kasaruho, Anisa; Schulz, Eike C; Pillai, Ramesh S; Barabas, Orsolya

    2012-12-01

    Piwi-interacting RNAs (piRNAs) are a gonad-specific class of small RNAs that associate with the Piwi clade of Argonaute proteins and play a key role in transposon silencing in animals. Since biogenesis of piRNAs is independent of the double-stranded RNA-processing enzyme Dicer, an alternative nuclease that can process single-stranded RNA transcripts has been long sought. A Phospholipase D-like protein, Zucchini, that is essential for piRNA processing has been proposed to be a nuclease acting in piRNA biogenesis. Here we describe the crystal structure of Zucchini from Drosophila melanogaster and show that it is very similar to the bacterial endonuclease, Nuc. The structure also reveals that homodimerization induces major conformational changes assembling the active site. The active site is situated on the dimer interface at the bottom of a narrow groove that can likely accommodate single-stranded nucleic acid substrates. Furthermore, biophysical analysis identifies protein segments essential for dimerization and provides insights into regulation of Zucchini's activity. PMID:23086923

  11. Crystal structure of the primary piRNA biogenesis factor Zucchini reveals similarity to the bacterial PLD endonuclease Nuc.

    Science.gov (United States)

    Voigt, Franka; Reuter, Michael; Kasaruho, Anisa; Schulz, Eike C; Pillai, Ramesh S; Barabas, Orsolya

    2012-12-01

    Piwi-interacting RNAs (piRNAs) are a gonad-specific class of small RNAs that associate with the Piwi clade of Argonaute proteins and play a key role in transposon silencing in animals. Since biogenesis of piRNAs is independent of the double-stranded RNA-processing enzyme Dicer, an alternative nuclease that can process single-stranded RNA transcripts has been long sought. A Phospholipase D-like protein, Zucchini, that is essential for piRNA processing has been proposed to be a nuclease acting in piRNA biogenesis. Here we describe the crystal structure of Zucchini from Drosophila melanogaster and show that it is very similar to the bacterial endonuclease, Nuc. The structure also reveals that homodimerization induces major conformational changes assembling the active site. The active site is situated on the dimer interface at the bottom of a narrow groove that can likely accommodate single-stranded nucleic acid substrates. Furthermore, biophysical analysis identifies protein segments essential for dimerization and provides insights into regulation of Zucchini's activity.

  12. 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

  13. 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

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

    DEFF Research Database (Denmark)

    Molina, Rafael; Besker, Neva; Marcaida, Maria Jose;

    2016-01-01

    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 th...

  15. 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.

  16. Arthrobacter luteus restriction endonuclease cleavage map of X174 RF DNA

    NARCIS (Netherlands)

    Vereijken, J.M.; Mansfeld, A.D.M. van; Baas, P.D.; Jansz, H.S.

    1975-01-01

    Cleavage of X174 RF DNA with the restriction endonuclease from Arthrobacter luteus (Alu I) produces 23 fragments of approximately 24–1100 base pairs in length. The order of most of these fragments has been established by digestion of Haemophilus influenzae Rd (Hind II) and Haemophilus aegyptius (Hae

  17. 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

  18. 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-

  19. 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.

  20. Watermarking in gyrator domain using an asymmetric cryptosystem

    Science.gov (United States)

    Vashisth, Sunanda; Yadav, A. K.; Singh, Hukun; Singh, Kehar

    2015-06-01

    A watermarking scheme is proposed based on optical asymmetric cryptography using double random phase encoding in the gyrator transform domain. It is based on the phase and amplitude truncation during the encryption process. The scheme is validated through computer simulations showing the scheme's sensitivity to decryption keys and orders of the gyrator transform. The occlusion and noise attacks have also been analysed. The proposed scheme is significantly resistant to both these attacks.

  1. 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...

  2. 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.

  3. 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...

  4. 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

  5. On Asymmetric Quantum MDS Codes

    CERN Document Server

    Ezerman, Martianus Frederic; Ling, San

    2010-01-01

    Assuming the validity of the MDS Conjecture, the weight distribution of all MDS codes is known. Using a recently-established characterization of asymmetric quantum error-correcting codes, linear MDS codes can be used to construct asymmetric quantum MDS codes with $d_{z} \\geq d_{x}\\geq 2$ for all possible values of length $n$ for which linear MDS codes over $\\F_{q}$ are known to exist.

  6. 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...

  7. 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.

  8. 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.

  9. 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.

  10. 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...

  11. 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...

  12. 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.

  13. The Effects of Addition of Mononucleotides on Sma nuc Endonuclease Activity

    Directory of Open Access Journals (Sweden)

    Julia Romanova

    2012-01-01

    Full Text Available Examination of the effects of mononucleotides on Sma nuc endonuclease originated from Gram negative bacterium Serratia marcescens displayed that any mononucleotide produced by Sma nuc during hydrolysis of DNA or RNA may regulate the enzyme activity affecting the RNase activity without pronounced influence on the activity towards DNA. The type of carbohydrate residue in mononucleotides does not affect the regulation. In contrast, the effects depend on the type of bases in nucleotides. AMP or dAMP was classified as a competitive inhibitor of partial type. GMP, UMP, and CMP were found to be uncompetitive inhibitors that suggest a specific site(s for the nucleotide(s binding in Sma nuc endonuclease.

  14. 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...

  15. 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.

  16. 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

  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. Human papillomavirus DNA from warts for typing by endonuclease restriction patterns: purification by alkaline plasmid methods.

    Science.gov (United States)

    Chinami, M; Tanikawa, E; Hachisuka, H; Sasai, Y; Shingu, M

    1990-01-01

    The alkaline plasmid DNA extraction method of Birnboim and Doly was applied for the isolation of human papillomavirus (HPV) from warts. Tissue from common and plantar warts was digested with proteinase K, and the extrachromosomal circular covalently-closed form of HPV-DNA was rapidly extracted by alkaline sodium dodecyl sulphate and phenol-chloroform treatment. Recovery of HPV-DNA from the tissue was sufficient for determination of endonuclease restriction patterns by agarose gel electrophoresis.

  19. Metal-chelating 2-hydroxyphenyl amide pharmacophore for inhibition of influenza virus endonuclease.

    Science.gov (United States)

    Carcelli, Mauro; Rogolino, Dominga; Bacchi, Alessia; Rispoli, Gabriele; Fisicaro, Emilia; Compari, Carlotta; Sechi, Mario; Stevaert, Annelies; Naesens, Lieve

    2014-01-01

    The influenza virus PA endonuclease is an attractive target for development of novel anti-influenza virus therapeutics. Reported PA inhibitors chelate the divalent metal ion(s) in the enzyme's catalytic site, which is located in the N-terminal part of PA (PA-Nter). In this work, a series of 2-hydroxybenzamide-based compounds have been synthesized and biologically evaluated in order to identify the essential pharmacophoric motif, which could be involved in functional sequestration of the metal ions (probably Mg(2+)) in the catalytic site of PA. By using HL(1), H2L(2), and HL(3) as model ligands with Mg(2+) ions, we isolated and fully characterized a series of complexes and tested them for inhibitory activity toward PA-Nter endonuclease. H2L(2) and the corresponding Mg(2+) complex showed an interesting inhibition of the endonuclease activity. The crystal structures of the uncomplexed HL(1) and H2L(2) and of the isolated magnesium complex [Mg(L(3))2(MeOH)2]·2MeOH were solved by X-ray diffraction analysis. Furthermore, the speciation models for HL(1), H2L(2), and HL(3) with Mg(2+) were obtained, and the formation constants of the complexes were measured. Preliminary docking calculations were conducted to investigate the interactions of the title compounds with essential amino acids in the PA-Nter active site. These findings supported the "two-metal" coordination of divalent ions by a donor triad atoms chemotype as a powerful strategy to develop more potent PA endonuclease inhibitors.

  20. 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.

  1. 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

  2. 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

  3. 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

  4. Asymmetric distances for binary embeddings.

    Science.gov (United States)

    Gordo, Albert; Perronnin, Florent; Gong, Yunchao; Lazebnik, Svetlana

    2014-01-01

    In large-scale query-by-example retrieval, embedding image signatures in a binary space offers two benefits: data compression and search efficiency. While most embedding algorithms binarize both query and database signatures, it has been noted that this is not strictly a requirement. Indeed, asymmetric schemes that binarize the database signatures but not the query still enjoy the same two benefits but may provide superior accuracy. In this work, we propose two general asymmetric distances that are applicable to a wide variety of embedding techniques including locality sensitive hashing (LSH), locality sensitive binary codes (LSBC), spectral hashing (SH), PCA embedding (PCAE), PCAE with random rotations (PCAE-RR), and PCAE with iterative quantization (PCAE-ITQ). We experiment on four public benchmarks containing up to 1M images and show that the proposed asymmetric distances consistently lead to large improvements over the symmetric Hamming distance for all binary embedding techniques.

  5. Complementary specificity of restriction endonucleases of Diplococcus pneumoniae with respect to DNA methylation. [Haemophilus influenzae, Escherichia coli, Paramecium aurelia

    Energy Technology Data Exchange (ETDEWEB)

    Lacks, S.; Greenberg, B.

    1977-01-01

    Restriction endonucleases Dpn I and Dpn II are produced by two distinct strains of Diplococcus pneumoniae. The two enzymes show complementary specificity with respect to methylation of sites in DNA. From the identity of its cleavage site with that of Mbo I, it appears that Dpn II cleaves at the unmodified sequence 5'-G-A-T-C-3'. Dpn I cleaves at the same sequence when the adenine residue is methylated. Both enzymes produce only double-strand breaks in susceptible DNA. Their susceptibility to Dpn I and not Dpn II shows that essentially all the G-A-T-C sequences are methylated in DNA from the pneumococcal strain that produces Dpn II as well as in DNA from Hemophilus influenzae and Escherichia coli. In the dam-3 mutant of E. coli none of these sequences appear to be methylated. Residual adenine methylation in the dam-3 mutant DNA most likely occurs at different sites. Different but characteristic degrees of methylation at G-A-T-C sites are found in the DNA of bacterial viruses grown in E. coli. DNAs from mammalian cells and viruses are not methylated at this sequence. Mitochondrial DNA from Paramecium aurelia is not methylated, but a small proportion of G-A-T-C sequences in the macronuclear DNA of this eukaryote appear to be methylated. Possible roles of sequence-specific methylation in the accommodation of plasmids, in the replication of DNA, in the regulation of gene function and in the restriction of viral infection are discussed.

  6. 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

  7. Asymmetric Synthesis via Chiral Aziridines

    DEFF Research Database (Denmark)

    Tanner, David Ackland; Harden, Adrian; Wyatt, Paul;

    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 b......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...

  8. Ideal 3D asymmetric concentrator

    Energy Technology Data Exchange (ETDEWEB)

    Garcia-Botella, Angel [Departamento Fisica Aplicada a los Recursos Naturales, Universidad Politecnica de Madrid, E.T.S.I. de Montes, Ciudad Universitaria s/n, 28040 Madrid (Spain); Fernandez-Balbuena, Antonio Alvarez; Vazquez, Daniel; Bernabeu, Eusebio [Departamento de Optica, Universidad Complutense de Madrid, Fac. CC. Fisicas, Ciudad Universitaria s/n, 28040 Madrid (Spain)

    2009-01-15

    Nonimaging optics is a field devoted to the design of optical components for applications such as solar concentration or illumination. In this field, many different techniques have been used for producing reflective and refractive optical devices, including reverse engineering techniques. In this paper we apply photometric field theory and elliptic ray bundles method to study 3D asymmetric - without rotational or translational symmetry - concentrators, which can be useful components for nontracking solar applications. We study the one-sheet hyperbolic concentrator and we demonstrate its behaviour as ideal 3D asymmetric concentrator. (author)

  9. 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...

  10. 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...

  11. 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.

  12. Rad10 exhibits lesion-dependent genetic requirements for recruitment to DNA double-strand breaks in Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Moore, Destaye M; Karlin, Justin; González-Barrera, Sergio;

    2009-01-01

    . Here we show that yeast strains expressing fluorescently labeled Rad10 protein (Rad10-YFP) form foci in response to double-strand breaks (DSBs) induced by a site-specific restriction enzyme, I-SceI or by ionizing radiation (IR). Additionally, for endonuclease-induced DSBs, Rad10-YFP localization to DSB...

  13. NMR detection of slow conformational dynamics in an endonuclease toxin

    Energy Technology Data Exchange (ETDEWEB)

    Whittaker, Sara B.-M.; Boetzel, Ruth; MacDonald, Colin [University of East Anglia, School of Chemical Sciences (United Kingdom); Lian Luyun [Leicester University, Biological NMR Centre (United Kingdom); Pommer, Ansgar J. [University of East Anglia, School of Biological Sciences (United Kingdom); Reilly, Ann; James, Richard; Kleanthous, Colin [Leicester University, Biological NMR Centre (United Kingdom); Moore, Geoffrey R. [University of East Anglia, School of Chemical Sciences (United Kingdom)

    1998-07-15

    The cytotoxic activity of the secreted bacterial toxin colicin E9 is due to a non-specific DNase housed in the C-terminus of the protein. Double-resonance and triple-resonance NMR studies of the 134-amino acid{sup 15} N- and {sup 13}C/{sup 15}N-labelled DNase domain are presented. Extensive conformational heterogeneity was evident from the presence of far more resonances than expected based on the amino acid sequence of the DNase, and from the appearance of chemical exchange cross-peaks in TOCSY and NOESY spectra. EXSY spectra were recorded to confirm that slow chemical exchange was occurring. Unambiguous sequence-specific resonance assignments are presented for one region of the protein, Pro{sup 65}-Asn{sup 72}, which exists in two slowly exchanging conformers based on the identification of chemical exchange cross-peaks in 3D {sup 1}H-{sup 1}H-{sup 15}N EXSY-HSQC, NOESY-HSQC and TOCSY-HSQC spectra, together with C{sup {alpha}} and C{sup {beta}} chemical shifts measured in triple-resonance spectra and sequential NH NOEs. The rates of conformational exchange for backbone amide resonances in this stretch of amino acids, and for the indole NH of either Trp{sup 22} or Trp{sup 58}, were determined from the intensity variation of the appropriate diagonal and chemical exchange cross-peaks recorded in 3D{sup 1} H-{sup 1}H-{sup 15}N NOESY-HSQC spectra. The data fitted a model in which this region of the DNase has two conformers, N{sub A} and N{sub B}, which interchange at 15 {sup o}C with a forward rate constant of 1.61 {+-} 0.5 s{sup -1} and a backward rate constant of 1.05 {+-} 0.5 s{sup -1}. Demonstration of this conformational equilibrium has led to a reappraisal of a previously proposed kinetic scheme describing the interaction of E9 DNase with immunity proteins [Wallis et al. (1995) Biochemistry, 34, 13743-13750 and 13751-13759]. The revised scheme is consistent with the specific inhibitor protein for the E9 DNase, Im9, associating with both the N{sub A} and N{sub B

  14. 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.

  15. 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…

  16. 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....

  17. Double Trouble

    NARCIS (Netherlands)

    Elsaesser, Thomas; Kievit, Robert; Simons, Jan

    1994-01-01

    Double Trouble highlights the career of Dutch scriptwriter and television producer Chiem van Houweninge, well-known for his long-running TV comedy series and as author of episodes for TV detective series. Double Trouble gives Van Houweninge's own views on writing and filming in television prime impo

  18. Asymmetric Multilevel Diversity Coding and Asymmetric Gaussian Multiple Descriptions

    CERN Document Server

    Mohajer, Soheil; Diggavi, Suhas N

    2009-01-01

    We consider the asymmetric multilevel diversity (A-MLD) coding problem, where a set of $2^K-1$ information sources, ordered in a decreasing level of importance, is encoded into $K$ messages (or descriptions). There are $2^K-1$ decoders, each of which has access to a non-empty subset of the encoded messages. Each decoder is required to reproduce the information sources up to a certain importance level depending on the combination of descriptions available to it. We obtain a single letter characterization of the achievable rate region for the 3-description problem. In contrast to symmetric multilevel diversity coding, source-separation coding is not sufficient in the asymmetric case, and ideas akin to network coding need to be used strategically. Based on the intuitions gained in treating the A-MLD problem, we derive inner and outer bounds for the rate region of the asymmetric Gaussian multiple description (MD) problem with three descriptions. Both the inner and outer bounds have a similar geometric structure t...

  19. 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). ...

  20. 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 ......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...

  1. 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.

  2. 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.

  3. 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.

  4. Terahertz metamaterial with asymmetric transmission

    CERN Document Server

    Singh, R; Menzel, C; Rockstuhl, C; Azad, A K; Cheville, R A; Lederer, F; Zhang, W; Zheludev, N I

    2009-01-01

    We show for the first time that a planar metamaterial, an array of coupled metal split-ring resonators with a unit cell lacking mirror symmetry, exhibits asymmetric transmission of terahertz radiation propagating through it in opposite directions. This intriguing effect, that is compatible with Lorentz reciprocity and time-reversal, depends on a directional difference in conversion efficiency of the incident circularly polarized wave into one of opposite handedness, that is only possible in lossy low-symmetry planar chiral metamaterials. We show that asymmetric transmission is linked to excitation of enantiomerically sensitive plasmons, these are induced charge-field excitations that depend on the mutual handedness of incident wave and metamaterial pattern. Various bands of positive, negative and zero phase and group velocities have been identified indicating the opportunity to develop polarization sensitive negative index and slow light media based on such metamaterials.

  5. 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.

  6. 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.

  7. 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...

  8. 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...

  9. 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.

  10. 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.

  11. 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...

  12. Functional complementation of Leishmania (Leishmania) amazonensis AP endonuclease gene (lamap) in Escherichia coli mutant strains challenged with DNA damage agents

    Science.gov (United States)

    Verissimo-Villela, Erika; Kitahara-Oliveira, Milene Yoko; dos Reis, Ana Beatriz de Bragança; Albano, Rodolpho Mattos; Da-Cruz, Alda Maria; Bello, Alexandre Ribeiro

    2016-01-01

    During its life cycle Leishmania spp. face several stress conditions that can cause DNA damages. Base Excision Repair plays an important role in DNA maintenance and it is one of the most conserved mechanisms in all living organisms. DNA repair in trypanosomatids has been reported only for Old World Leishmania species. Here the AP endonuclease from Leishmania (L.) amazonensis was cloned, expressed in Escherichia coli mutants defective on the DNA repair machinery, that were submitted to different stress conditions, showing ability to survive in comparison to the triple null mutant parental strain BW535. Phylogenetic and multiple sequence analyses also confirmed that LAMAP belongs to the AP endonuclease class of proteins. PMID:27223868

  13. 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...

  14. 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.

  15. 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.

  16. 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

  17. EENdb: a database and knowledge base of ZFNs and TALENs for endonuclease engineering.

    Science.gov (United States)

    Xiao, An; Wu, Yingdan; Yang, Zhipeng; Hu, Yingying; Wang, Weiye; Zhang, Yutian; Kong, Lei; Gao, Ge; Zhu, Zuoyan; Lin, Shuo; Zhang, Bo

    2013-01-01

    We report here the construction of engineered endonuclease database (EENdb) (http://eendb.zfgenetics.org/), a searchable database and knowledge base for customizable engineered endonucleases (EENs), including zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs). EENs are artificial nucleases designed to target and cleave specific DNA sequences. EENs have been shown to be a very useful genetic tool for targeted genome modification and have shown great potentials in the applications in basic research, clinical therapies and agricultural utilities, and they are specifically essential for reverse genetics research in species where no other gene targeting techniques are available. EENdb contains over 700 records of all the reported ZFNs and TALENs and related information, such as their target sequences, the peptide components [zinc finger protein-/transcription activator-like effector (TALE)-binding domains, FokI variants and linker peptide/framework], the efficiency and specificity of their activities. The database also lists EEN engineering tools and resources as well as information about forms and types of EENs, EEN screening and construction methods, detection methods for targeting efficiency and many other utilities. The aim of EENdb is to represent a central hub for EEN information and an integrated solution for EEN engineering. These studies may help to extract in-depth properties and common rules regarding ZFN or TALEN efficiency through comparison of the known ZFNs or TALENs.

  18. Decisive role of apurinic/apyrimidinic endonuclease/Ref-1 in initiation of cell death.

    Science.gov (United States)

    Cho, Kyoung Joo; Kim, Hyun Jeong; Park, Soo Chul; Kim, Hyun Woo; Kim, Gyung Whan

    2010-11-01

    The apurinic/apyrimidinic endonuclease/redox effector factor-1 (APE/Ref-1) is involved in the base excision repair of apurinic/apyrimidinic sites induced by oxidative DNA damage. APE/Ref-1 was decreased by kainic acid (KA) injury in a time-dependent manner at the level of proteins, not transcripts. We investigated whether alteration of APE/Ref-1 amounts would influence hippocampal cell fate, survival or death, after KA injury. Overexpression of APE/Ref-1 using adenovirus and restoration of APE small peptides significantly reduced KA-induced hippocampal cell death. Both silencing of APE/Ref-1 by siRNA and inhibition of endonuclease by an antibody significantly increased caspase-3 activity and apoptotic cell death triggered from the early time after exposure to KA. These findings suggest that cell death is initiated by reducing APE/Ref-1 protein and inhibiting its repair function in spite of enough protein amounts. In conclusion, APE/Ref-1 may be a regulator of cell death initiation, and APE small peptides could provide molecular mechanism-based therapies for neuroprotection in progressive excitotoxic neuronal damage.

  19. Polymerase-endonuclease amplification reaction (PEAR for large-scale enzymatic production of antisense oligonucleotides.

    Directory of Open Access Journals (Sweden)

    Xiaolong Wang

    Full Text Available Antisense oligonucleotides targeting microRNAs or their mRNA targets prove to be powerful tools for molecular biology research and may eventually emerge as new therapeutic agents. Synthetic oligonucleotides are often contaminated with highly homologous failure sequences. Synthesis of a certain oligonucleotide is difficult to scale up because it requires expensive equipment, hazardous chemicals and a tedious purification process. Here we report a novel thermocyclic reaction, polymerase-endonuclease amplification reaction (PEAR, for the amplification of oligonucleotides. A target oligonucleotide and a tandem repeated antisense probe are subjected to repeated cycles of denaturing, annealing, elongation and cleaving, in which thermostable DNA polymerase elongation and strand slipping generate duplex tandem repeats, and thermostable endonuclease (PspGI cleavage releases monomeric duplex oligonucleotides. Each round of PEAR achieves over 100-fold amplification. The product can be used in one more round of PEAR directly, and the process can be further repeated. In addition to avoiding dangerous materials and improved product purity, this reaction is easy to scale up and amenable to full automation. PEAR has the potential to be a useful tool for large-scale production of antisense oligonucleotide drugs.

  20. 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...

  1. Spontaneous baryogenesis from asymmetric inflaton

    Energy Technology Data Exchange (ETDEWEB)

    Takahashi, Fuminobu [Tohoku Univ., Sendai (Japan). Dept. of Physics; Tokyo Univ., Chiba (Japan). Kavli IPMU (WPI), UTIAS; Yamada, Masaki [Tokyo Univ., Chiba (Japan). Kavli IPMU (WPI), UTIAS; Tokyo Univ., Chiba (Japan). Inst. for Cosmic Ray Research; DESY Hamburg (Germany)

    2015-10-15

    We propose a variant scenario of spontaneous baryogenesis from asymmetric inflaton based on current-current interactions between the inflaton and matter fields with a non-zero B-L charge. When the inflaton starts to oscillate around the minimum after inflation, it may lead to excitation of a CP-odd component, which induces an effective chemical potential for the B-L number through the current-current interactions. We study concrete inflation models and show that the spontaneous baryogenesis scenario can be naturally implemented in the chaotic inflation in supergravity.

  2. Asymmetric Formal Synthesis of Azadirachtin.

    Science.gov (United States)

    Mori, Naoki; Kitahara, Takeshi; Mori, Kenji; Watanabe, Hidenori

    2015-12-01

    An asymmetric formal synthesis of azadirachtin, a potent insect antifeedant, was accomplished in 30 steps to Ley's synthetic intermediate (longest linear sequence). The synthesis features: 1) rapid access to the optically active right-hand segment starting from the known 5-hydroxymethyl-2-cyclopentenone scaffold; 2) construction of the B and E rings by a key intramolecular tandem radical cyclization; 3) formation of the hemiacetal moiety in the C ring through the α-oxidation of the six-membered lactone followed by methanolysis. PMID:26474211

  3. 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...

  4. 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

  5. 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.

  6. 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)

  7. 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...

  8. 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)

  9. 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

  10. 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...

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

    Directory of Open Access Journals (Sweden)

    Mamta D Naidu

    Full Text Available 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(50 values for inhibition of APE1 incision of depurinated plasmid DNA by lucanthone and hycanthone were 5 µM and 80 nM, respectively. The K(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

  12. 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.

  13. 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.

  14. 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.

  15. Atomic Structure and Biochemical Characterization of an RNA Endonuclease in the N Terminus of Andes Virus L Protein.

    Directory of Open Access Journals (Sweden)

    Yaiza Fernández-García

    2016-06-01

    Full Text Available Andes virus (ANDV is a human-pathogenic hantavirus. Hantaviruses presumably initiate their mRNA synthesis by using cap structures derived from host cell mRNAs, a mechanism called cap-snatching. A signature for a cap-snatching endonuclease is present in the N terminus of hantavirus L proteins. In this study, we aimed to solve the atomic structure of the ANDV endonuclease and characterize its biochemical features. However, the wild-type protein was refractory to expression in Escherichia coli, presumably due to toxic enzyme activity. To circumvent this problem, we introduced attenuating mutations in the domain that were previously shown to enhance L protein expression in mammalian cells. Using this approach, 13 mutant proteins encompassing ANDV L protein residues 1-200 were successfully expressed and purified. Protein stability and nuclease activity of the mutants was analyzed and the crystal structure of one mutant was solved to a resolution of 2.4 Å. Shape in solution was determined by small angle X-ray scattering. The ANDV endonuclease showed structural similarities to related enzymes of orthobunya-, arena-, and orthomyxoviruses, but also differences such as elongated shape and positively charged patches surrounding the active site. The enzyme was dependent on manganese, which is bound to the active site, most efficiently cleaved single-stranded RNA substrates, did not cleave DNA, and could be inhibited by known endonuclease inhibitors. The atomic structure in conjunction with stability and activity data for the 13 mutant enzymes facilitated inference of structure-function relationships in the protein. In conclusion, we solved the structure of a hantavirus cap-snatching endonuclease, elucidated its catalytic properties, and present a highly active mutant form, which allows for inhibitor screening.

  16. Atomic Structure and Biochemical Characterization of an RNA Endonuclease in the N Terminus of Andes Virus L Protein.

    Science.gov (United States)

    Fernández-García, Yaiza; Reguera, Juan; Busch, Carola; Witte, Gregor; Sánchez-Ramos, Oliberto; Betzel, Christian; Cusack, Stephen; Günther, Stephan; Reindl, Sophia

    2016-06-01

    Andes virus (ANDV) is a human-pathogenic hantavirus. Hantaviruses presumably initiate their mRNA synthesis by using cap structures derived from host cell mRNAs, a mechanism called cap-snatching. A signature for a cap-snatching endonuclease is present in the N terminus of hantavirus L proteins. In this study, we aimed to solve the atomic structure of the ANDV endonuclease and characterize its biochemical features. However, the wild-type protein was refractory to expression in Escherichia coli, presumably due to toxic enzyme activity. To circumvent this problem, we introduced attenuating mutations in the domain that were previously shown to enhance L protein expression in mammalian cells. Using this approach, 13 mutant proteins encompassing ANDV L protein residues 1-200 were successfully expressed and purified. Protein stability and nuclease activity of the mutants was analyzed and the crystal structure of one mutant was solved to a resolution of 2.4 Å. Shape in solution was determined by small angle X-ray scattering. The ANDV endonuclease showed structural similarities to related enzymes of orthobunya-, arena-, and orthomyxoviruses, but also differences such as elongated shape and positively charged patches surrounding the active site. The enzyme was dependent on manganese, which is bound to the active site, most efficiently cleaved single-stranded RNA substrates, did not cleave DNA, and could be inhibited by known endonuclease inhibitors. The atomic structure in conjunction with stability and activity data for the 13 mutant enzymes facilitated inference of structure-function relationships in the protein. In conclusion, we solved the structure of a hantavirus cap-snatching endonuclease, elucidated its catalytic properties, and present a highly active mutant form, which allows for inhibitor screening. PMID:27300328

  17. Restriction of a bacteriophage of Streptomyces albus G involving endonuclease SalI.

    Science.gov (United States)

    Chater, K F; Wilde, L C

    1976-11-01

    The bacteriophage Pa16, isolated from soil on Streptomyces albus G, was restricted when transferred from an alternative host back to S. albus G. Extracted unmodified Pa16 deoxyribonucleic acid was cleaved at a single site by a cell-free extract of S. albus G. Fractions cleaving Pal6 deoxyribonucleic acid contained the endonuclease SalI first described by J. Arrand, P. Myers, and R. J. Roberts (unpublished data). A mutant of S. albus G was isolated which was defective in both restriction and modification of Pal6. This mutant lacked SalI activity. It is concluded that SalI is the agent of restriction of Pal6 by S. albus G.

  18. Comparison of Mycoplasma ovipneumoniae isolates using bacterial restriction endonuclease DNA analysis and SDS-PAGE.

    Science.gov (United States)

    Mew, A J; Ionas, G; Clarke, J K; Robinson, A J; Marshall, R B

    1985-12-01

    Sixteen isolates of Mycoplasma ovipneumoniae recovered from the nasal tract or lungs of sheep from different flocks in New Zealand were examined by bacterial restriction endonuclease DNA analysis (BRENDA) using EcoR1 and by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE). All isolates gave BRENDA patterns which differed entirely from one another. Following 20 serial passages (corresponding to approximately 67 generations) of an isolate, no change was detected in the BRENDA pattern. When eight isolates were examined by SDS-PAGE most bands were common but, nevertheless, each isolate was unique in the sense that they differed from one another in one or more bands. The marked heterogeneity of patterns observed when strains of M. ovipneumoniae are compared by BRENDA, together with the stability of such patterns over many generations, will enable this approach to be used to study the epidemiology of individual strains of M. ovipneumoniae within a flock.

  19. Resolution of branched DNA substrates by T7 endonuclease I and its inhibition.

    Science.gov (United States)

    Lu, M; Guo, Q; Studier, F W; Kallenbach, N R

    1991-02-01

    Endonuclease I is a multipurpose enzyme implicated in the breakdown of host DNA, packaging of phage DNA, and recombination during the lytic cycle of bacteriophage T7. We investigate here some aspects of the substrate requirements for its activity in resolving branched intermediates similar to Holliday junctions (Holliday, R. (1964) Genet. Res. 5, 282-304) that arise in recombination. The enzyme is able to resolve branched substrates containing very short duplex arms: 4 base pairs suffice. It cleaves 5' to the branch, with a distinct preference for the non-crossover strands in Holliday-like model junctions. Ligands that interact strongly with the branch site can inhibit the enzyme, with KI values in the 10-50 microM range. PMID:1990002

  20. Primary processing of CRISPR RNA by the endonuclease Cas6 in Staphylococcus epidermidis.

    Science.gov (United States)

    Wakefield, Noelle; Rajan, Rakhi; Sontheimer, Erik J

    2015-10-01

    In many bacteria and archaea, an adaptive immune system (CRISPR-Cas) provides immunity against foreign genetic elements. This system uses CRISPR RNAs (crRNAs) derived from the CRISPR array, along with CRISPR-associated (Cas) proteins, to target foreign nucleic acids. In most CRISPR systems, endonucleolytic processing of crRNA precursors (pre-crRNAs) is essential for the pathway. Here we study the Cas6 endonuclease responsible for crRNA processing in the Type III-A CRISPR-Cas system from Staphylococcus epidermidis RP62a, a model for Type III-A CRISPR-Cas systems, and define substrate requirements for SeCas6 activity. We find that SeCas6 is necessary and sufficient for full-length crRNA biogenesis in vitro, and that it relies on both sequence and stem-loop structure in the 3' half of the CRISPR repeat for recognition and processing.

  1. 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.

  2. 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...

  3. 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

  4. 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.

  5. 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.

  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. Structural and functional characterization of two unusual endonuclease III enzymes from Deinococcus radiodurans.

    Science.gov (United States)

    Sarre, Aili; Ökvist, Mats; Klar, Tobias; Hall, David R; Smalås, Arne O; McSweeney, Sean; Timmins, Joanna; Moe, Elin

    2015-08-01

    While most bacteria possess a single gene encoding the bifunctional DNA glycosylase Endonuclease III (EndoIII) in their genomes, Deinococcus radiodurans possesses three: DR2438 (DrEndoIII1), DR0289 (DrEndoIII2) and DR0982 (DrEndoIII3). Here we have determined the crystal structures of DrEndoIII1 and an N-terminally truncated form of DrEndoIII3 (DrEndoIII3Δ76). We have also generated a homology model of DrEndoIII2 and measured activity of the three enzymes. All three structures consist of two all α-helical domains, one of which exhibits a [4Fe-4S] cluster and the other a HhH-motif, separated by a DNA binding cleft, similar to previously determined structures of endonuclease III from Escherichia coli and Geobacillus stearothermophilus. However, both DrEndoIII1 and DrEndoIII3 possess an extended HhH motif with extra helical features and an altered electrostatic surface potential. In addition, the DNA binding cleft of DrEndoIII3 seems to be less accessible for DNA interactions, while in DrEndoIII1 it seems to be more open. Analysis of the enzyme activities shows that DrEndoIII2 is most similar to the previously studied enzymes, while DrEndoIII1 seems to be more distant with a weaker activity towards substrate DNA containing either thymine glycol or an abasic site. DrEndoIII3 is the most distantly related enzyme and displays no detectable activity towards these substrates even though the suggested catalytic residues are conserved. Based on a comparative structural analysis, we suggest that the altered surface potential, shape of the substrate-binding pockets and specific amino acid substitutions close to the active site and in the DNA interacting loops may underlie the unexpected differences in activity.

  8. A case of asymmetrical monocephalus dipygus (tetrapus dibrachius) in a male Holstein calf in Iran

    Science.gov (United States)

    Marzban Abbasabadi, Behrokh; Ahmadzadeh, Aliakbar; Ramezanpour, Shahab; Hajati Ziabari, Amir Reza

    2016-01-01

    Dipygus is a teratological fetus with a double pelvis, genitals, and extremities. Congenital duplications in cattle are rare. Caudal duplication is more common in sheep and pigs while cranial duplications seem to be predominant in cattle. Asymmetric or parasitic conjoined twins consisting of an incomplete twin (parasite) attached to the body of a fully-developed twin (autosite). This report deals with a male Holstein calf with two extra limbs, in the pelvic region which were directed ventrally between the two normal hind limbs. The extra limbs were completely developed in one side and in other side just a bony mass were observed. So classification has been made as asymmetrical attached twins. The genital system was not affected and just one extra kidney-like structure was found. To the authors’ best knowledge, this is the first report of asymmetrical monocephalus dipygus (tetrapus dibrachius) in a male Holstein calf in Iran. PMID:27482365

  9. 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.

  10. 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...

  11. 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.

  12. 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 ...

  13. A mean-field theory on the differential capacitance of asymmetric ionic liquid electrolytes

    Science.gov (United States)

    Han, Yining; Huang, Shanghui; Yan, Tianying

    2014-07-01

    The size of ions significantly influences the electric double layer structure of room temperature ionic liquid (IL) electrolytes and their differential capacitance (Cd). In this study, we extended the mean-field theory (MFT) developed independently by Kornyshev (2007J. Phys. Chem. B 111 5545-57) and Kilic, Bazant, and Ajdari (2007 Phys. Rev. E 75 021502) (the KKBA MFT) to take into account the asymmetric 1:1 IL electrolytes by introducing an additional parameter ξ for the anion/cation volume ratio, besides the ionic compressibility γ in the KKBA MFT. The MFT of asymmetric ions becomes KKBA MFT upon ξ = 1, and further reduces to Gouy-Chapman theory in the γ → 0 limit. The result of the extended MFT demonstrates that the asymmetric ILs give rise to an asymmetric Cd, with the higher peak in Cd occurring at positive polarization for the smaller anionic size. At high potential, Cd decays asymptotically toward KKBA MFT characterized by γ for the negative polarization, and characterized by ξγ for the positive polarization, with inverse-square-root behavior. At low potential, around the potential of zero charge, the asymmetric ions cause a higher Cd, which exceeds that of Gouy-Chapman theory.

  14. 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.

  15. Microwave-induced inactivation of DNA-based hybrid catalyst in asymmetric catalysis.

    Science.gov (United States)

    Zhao, Hua; Shen, Kai

    2016-03-01

    DNA-based hybrid catalysts have gained strong interests in asymmetric reactions. However, to maintain the high enantioselectivity, these reactions are usually conducted at relatively low temperatures (e.g. DNA-based hybrid catalyst even at low temperatures (such as 5 °C). Circular dichroism (CD) spectra and gel electrophoresis of DNA suggest that microwave exposure degrades DNA molecules and disrupts DNA double-stranded structures, causing changes of DNA-metal ligand binding properties and thus poor DNA catalytic performance.

  16. 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

  17. Asymmetric dark matter in braneworld cosmology

    Energy Technology Data Exchange (ETDEWEB)

    Meehan, Michael T.; Whittingham, Ian B., E-mail: Michael.Meehan@my.jcu.edu.au, E-mail: Ian.Whittingham@jcu.edu.au [School of Engineering and Physical Sciences, James Cook University, Townsville, 4811 Australia (Australia)

    2014-06-01

    We investigate the effect of a braneworld expansion era on the relic density of asymmetric dark matter. We find that the enhanced expansion rate in the early universe predicted by the Randall-Sundrum II (RSII) model leads to earlier particle freeze-out and an enhanced relic density. This effect has been observed previously by Okada and Seto (2004) for symmetric dark matter models and here we extend their results to the case of asymmetric dark matter. We also discuss the enhanced asymmetric annihilation rate in the braneworld scenario and its implications for indirect detection experiments.

  18. 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.

  19. Asymmetric Dark Matter and Effective Operators

    CERN Document Server

    Buckley, Matthew R

    2011-01-01

    In order to annihilate in the early Universe to levels well below the measured dark matter density, asymmetric dark matter must possess large couplings to the Standard Model. In this paper, we consider effective operators which allow asymmetric dark matter to annihilate into quarks. In addition to a bound from requiring sufficient annihilation, the energy scale of such operators can be constrained by limits from direct detection and monojet searches at colliders. We show that the allowed parameter space for these operators is highly constrained, leading to non-trivial requirements that any model of asymmetric dark matter must satisfy.

  20. 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...

  1. 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

  2. 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...

  3. 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

  4. 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...

  5. 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.

  6. 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.

  7. The human homolog of Escherichia coli endonuclease V is a nucleolar protein with affinity for branched DNA structures.

    Directory of Open Access Journals (Sweden)

    Cathrine Fladeby

    Full Text Available Loss of amino groups from adenines in DNA results in the formation of hypoxanthine (Hx bases with miscoding properties. The primary enzyme in Escherichia coli for DNA repair initiation at deaminated adenine is endonuclease V (endoV, encoded by the nfi gene, which cleaves the second phosphodiester bond 3' of an Hx lesion. Endonuclease V orthologs are widespread in nature and belong to a family of highly conserved proteins. Whereas prokaryotic endoV enzymes are well characterized, the function of the eukaryotic homologs remains obscure. Here we describe the human endoV ortholog and show with bioinformatics and experimental analysis that a large number of transcript variants exist for the human endonuclease V gene (ENDOV, many of which are unlikely to be translated into functional protein. Full-length ENDOV is encoded by 8 evolutionary conserved exons covering the core region of the enzyme, in addition to one or more 3'-exons encoding an unstructured and poorly conserved C-terminus. In contrast to the E. coli enzyme, we find recombinant ENDOV neither to incise nor bind Hx-containing DNA. While both enzymes have strong affinity for several branched DNA substrates, cleavage is observed only with E. coli endoV. We find that ENDOV is localized in the cytoplasm and nucleoli of human cells. As nucleoli harbor the rRNA genes, this may suggest a role for the protein in rRNA gene transactions such as DNA replication or RNA transcription.

  8. 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.

  9. 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

  10. 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 ...

  11. 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.

  12. Force on an Asymmetric Capacitor

    CERN Document Server

    Bahder, T B; Bahder, Thomas B.; Fazi, Chris

    2002-01-01

    When a high voltage (~30 kV) is applied to a capacitor whose electrodes have different physical dimensions, the capacitor experiences a net force toward the smaller electrode (Biefeld-Brown effect). We have verified this effect by building four capacitors of different shapes. The effect may have applications to vehicle propulsion and dielectric pumps. We review the history of this effect briefly through the history of patents by Thomas Townsend Brown. At present, the physical basis for the Biefeld-Brown effect is not understood. The order of magnitude of the net force on the asymmetric capacitor is estimated assuming two different mechanisms of charge conduction between its electrodes: ballistic ionic wind and ionic drift. The calculations indicate that ionic wind is at least three orders of magnitude too small to explain the magnitude of the observed force on the capacitor. The ionic drift transport assumption leads to the correct order of magnitude for the force, however, it is difficult to see how ionic dr...

  13. 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

  14. Modeling of asymmetrical boost converters

    Directory of Open Access Journals (Sweden)

    Eliana Isabel Arango Zuluaga

    2014-03-01

    Full Text Available The asymmetrical interleaved dual boost (AIDB is a fifth-order DC/DC converter designed to interface photovoltaic (PV panels. The AIDB produces small current harmonics to the PV panels, reducing the power losses caused by the converter operation. Moreover, the AIDB provides a large voltage conversion ratio, which is required to step-up the PV voltage to the large dc-link voltage used in grid-connected inverters. To reject irradiance and load disturbances, the AIDB must be operated in a closed-loop and a dynamic model is required. Given that the AIDB converter operates in Discontinuous Conduction Mode (DCM, classical modeling approaches based on Continuous Conduction Mode (CCM are not valid. Moreover, classical DCM modeling techniques are not suitable for the AIDB converter. Therefore, this paper develops a novel mathematical model for the AIDB converter, which is suitable for control-pur-poses. The proposed model is based on the calculation of a diode current that is typically disregarded. Moreover, because the traditional correction to the second duty cycle reported in literature is not effective, a new equation is designed. The model accuracy is contrasted with circuital simulations in time and frequency domains, obtaining satisfactory results. Finally, the usefulness of the model in control applications is illustrated with an application example.

  15. 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

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. Asymmetric cryptography based on wavefront sensing.

    Science.gov (United States)

    Peng, Xiang; Wei, Hengzheng; Zhang, Peng

    2006-12-15

    A system of asymmetric cryptography based on wavefront sensing (ACWS) is proposed for the first time to our knowledge. One of the most significant features of the asymmetric cryptography is that a trapdoor one-way function is required and constructed by analogy to wavefront sensing, in which the public key may be derived from optical parameters, such as the wavelength or the focal length, while the private key may be obtained from a kind of regular point array. The ciphertext is generated by the encoded wavefront and represented with an irregular array. In such an ACWS system, the encryption key is not identical to the decryption key, which is another important feature of an asymmetric cryptographic system. The processes of asymmetric encryption and decryption are formulized mathematically and demonstrated with a set of numerical experiments.

  2. Oxidative Stress Impairs Cell Death by Repressing the Nuclease Activity of Mitochondrial Endonuclease G

    Directory of Open Access Journals (Sweden)

    Jason L.J. Lin

    2016-07-01

    Full Text Available Endonuclease G (EndoG is a mitochondrial protein that is released from mitochondria and relocated into the nucleus to promote chromosomal DNA fragmentation during apoptosis. Here, we show that oxidative stress causes cell-death defects in C. elegans through an EndoG-mediated cell-death pathway. In response to high reactive oxygen species (ROS levels, homodimeric CPS-6—the C. elegans homolog of EndoG—is dissociated into monomers with diminished nuclease activity. Conversely, the nuclease activity of CPS-6 is enhanced, and its dimeric structure is stabilized by its interaction with the worm AIF homolog, WAH-1, which shifts to disulfide cross-linked dimers under high ROS levels. CPS-6 thus acts as a ROS sensor to regulate the life and death of cells. Modulation of the EndoG dimer conformation could present an avenue for prevention and treatment of diseases resulting from oxidative stress.

  3. Suppression of oxidative phosphorylation in mouse embryonic fibroblast cells deficient in apurinic/apyrimidinic endonuclease

    Science.gov (United States)

    Suganya, Rangaswamy; Chakraborty, Anirban; Miriyala, Sumitra; Hazra, Tapas K.; Izumi, Tadahide

    2015-01-01

    The mammalian apurinic/apyrimidinic (AP) endonuclease 1 (APE1) is an essential DNA repair/gene regulatory protein. Decrease of APE1 in cells by inducible shRNA knockdown or by conditional gene knockout caused apoptosis. Here we succeeded in establishing a unique mouse embryonic fibroblast (MEF) line expressing APE1 at a level far lower than those achieved with shRNA knockdown. The cells, named MEFla (MEFlowAPE1), were hypersensitive to methyl methanesulfonate (MMS), and showed little activity for repairing AP-sites and MMS induced DNA damage. While these results were consistent with the essential role of APE1 in repair of AP sites, the MEFla cells grew normally and the basal activation of poly(ADP-ribose) polymerases in MEFla was lower than that in the wild-type MEF (MEFwt), indicating the low DNA damage stress in MEFla under the normal growth condition. Oxidative phosphorylation activity in MEFla was lower than in MEFwt, while the glycolysis rates in MEFla were higher than in MEFwt. In addition, we observed decreased intracellular oxidative stress in MEFla. These results suggest that cells with low APE1 reversibly suppress mitochondrial respiration and thereby reduce DNA damage stress and increases the cell viability. PMID:25645679

  4. 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.

  5. 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

  6. Sequencing by ligation variation with endonuclease V digestion and deoxyinosine-containing query oligonucleotides

    Directory of Open Access Journals (Sweden)

    Ho Antoine

    2011-12-01

    Full Text Available Abstract Background Sequencing-by-ligation (SBL is one of several next-generation sequencing methods that has been developed for massive sequencing of DNA immobilized on arrayed beads (or other clonal amplicons. SBL has the advantage of being easy to implement and accessible to all because it can be performed with off-the-shelf reagents. However, SBL has the limitation of very short read lengths. Results To overcome the read length limitation, research groups have developed complex library preparation processes, which can be time-consuming, difficult, and result in low complexity libraries. Herein we describe a variation on traditional SBL protocols that extends the number of sequential bases that can be sequenced by using Endonuclease V to nick a query primer, thus leaving a ligatable end extended into the unknown sequence for further SBL cycles. To demonstrate the protocol, we constructed a known DNA sequence and utilized our SBL variation, cyclic SBL (cSBL, to resequence this region. Using our method, we were able to read thirteen contiguous bases in the 3' - 5' direction. Conclusions Combining this read length with sequencing in the 5' - 3' direction would allow a read length of over twenty bases on a single tage. Implementing mate-paired tags and this SBL variation could enable > 95% coverage of the genome.

  7. 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

  8. Inhibition of DNA restrictive endonucleases and Taq DNA polymerase by trimalonic acid C60

    Institute of Scientific and Technical Information of China (English)

    YANG XinLin; CHEN Zhe; MENG XianMei; LI Bo; TAN Xin

    2007-01-01

    Activities of trimalonic acid fullerene (TMA C60) on DNA restrictive enzymatic reaction were investigated by using two restrictive endonucleases Hind III and EcoR I and plasmid pEGFP-N1 with single restrictive site for both enzymes. Meanwhile,TMA C60 was also tested to clarify its effects on polymerase chain reaction (PCR) with the catalyst of Taq DNA polymerase and the template of plasmid pEGFP-N1. The products from restrictive reactions or PCR were detected by agarose gel electrophoresis. It was found that the product amounts from restrictive reactions or PCR decreased significantly with addition of TMA C60. The inhibition by TMA C60 was dose-dependent and IC50 values for reactions of Hind III,EcoR I and PCR were 16.3,6.0 and 6.0 μmol/L,respectively. Addition of two scavengers of reactive oxygen species (ROS),L-ascorbic acid-2-phosphate ester magnesium and sodium azide at the concentrations of 2―10 mmol/L did not antagonize the activities of TMA C60 against PCR and two restrictive reactions. However,increase of Taq DNA polymerase amounts in PCR system antagonized the activities of TMA C60. These data implied that TMA C60 was able to inhibit the activities of the three above-mentioned enzymes involved in DNA metabolism,and that this inhibition probably did not correlate to ROS.

  9. 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)

  10. 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.

  11. 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

  12. 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

  13. 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.

  14. 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

  15. 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.

  16. Adenomatous Polyposis Coli Interacts with Flap Endonuclease 1 to Block Its Nuclear Entry and Function

    Directory of Open Access Journals (Sweden)

    Aruna S. Jaiswal

    2012-06-01

    Full Text Available In previous studies, we found that adenomatous polyposis coli (APC blocks the base excision repair (BER pathway by interacting with 5′-flap endonuclease 1 (Fen1. In this study, we identify the molecular features that contribute to the formation and/or stabilization of the APC/Fen1 complex that determines the extent of BER inhibition, and the subsequent accumulation of DNA damage creates mutagenic lesions leading to transformation susceptibility. We show here that APC binds to the nuclear localization sequence of Fen1 (Lys365Lys366Lys367, which prevents entry of Fen1 into the nucleus and participation in Pol-β-directed long-patch BER. We also show that levels of the APC/Fen1 complex are higher in breast tumors than in the surrounding normal tissues. These studies demonstrate a novel role for APC in the suppression of Fen1 activity in the BER pathway and a new biomarker profile to be explored to identify individuals who may be susceptible to the development of mammary and other tumors.

  17. 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

  18. 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....

  19. 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...

  20. 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...

  1. 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...

  2. Novel strategies for asymmetric hydrogenation reactions

    OpenAIRE

    Chen, Dianjun

    2011-01-01

    This thesis describes two novel possibilities for asymmetric hydrogenation: enantioselective hydrogenation using chiral ionic liquid systems and metal-free hydrogenation with boranes. In the first part, asymmetric hydrogenation systems using chiral ionic liquids in combination with racemic rhodium catalyst are presented. Enantioselectivities up to 69% ee were achieved in homogeneous Rh-catalyzed hydrogenation with tropos ligand (BIPHEP, sulfonated BIPHEP) in a proline derived cation chiral io...

  3. 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 ...

  4. Apn1 AP-endonuclease is essential for the repair of oxidatively damaged DNA bases in yeast frataxin-deficient cells.

    Science.gov (United States)

    Lefevre, Sophie; Brossas, Caroline; Auchère, Françoise; Boggetto, Nicole; Camadro, Jean-Michel; Santos, Renata

    2012-09-15

    Frataxin deficiency results in mitochondrial dysfunction and oxidative stress and it is the cause of the hereditary neurodegenerative disease Friedreich ataxia (FA). Here, we present evidence that one of the pleiotropic effects of oxidative stress in frataxin-deficient yeast cells (Δyfh1 mutant) is damage to nuclear DNA and that repair requires the Apn1 AP-endonuclease of the base excision repair pathway. Major phenotypes of Δyfh1 cells are respiratory deficit, disturbed iron homeostasis and sensitivity to oxidants. These phenotypes are weak or absent under anaerobiosis. We show here that exposure of anaerobically grown Δyfh1 cells to oxygen leads to down-regulation of antioxidant defenses, increase in reactive oxygen species, delay in G1- and S-phases of the cell cycle and damage to mitochondrial and nuclear DNA. Nuclear DNA lesions in Δyfh1 cells are primarily caused by oxidized bases and single-strand breaks that can be detected 15-30 min after oxygen exposition. The Apn1 enzyme is essential for the repair of the DNA lesions in Δyfh1 cells. Compared with Δyfh1, the double Δyfh1Δapn1 mutant shows growth impairment, increased mutagenesis and extreme sensitivity to H(2)O(2). On the contrary, overexpression of the APN1 gene in Δyfh1 cells decreases spontaneous and induced mutagenesis. Our results show that frataxin deficiency in yeast cells leads to increased DNA base oxidation and requirement of Apn1 for repair, suggesting that DNA damage and repair could be important features in FA disease progression.

  5. Chemical display of pyrimidine bases flipped out by modification-dependent restriction endonucleases of MspJI and PvuRts1I families.

    Directory of Open Access Journals (Sweden)

    Evelina Zagorskaitė

    Full Text Available The epigenetic DNA modifications 5-methylcytosine (5mC and 5-hydroxymethylcytosine (5hmC in eukaryotes are recognized either in the context of double-stranded DNA (e.g., by the methyl-CpG binding domain of MeCP2, or in the flipped-out state (e.g., by the SRA domain of UHRF1. The SRA-like domains and the base-flipping mechanism for 5(hmC recognition are also shared by the recently discovered prokaryotic modification-dependent endonucleases of the MspJI and PvuRts1I families. Since the mechanism of modified cytosine recognition by many potential eukaryotic and prokaryotic 5(hmC "readers" is still unknown, a fast solution based method for the detection of extrahelical 5(hmC would be very useful. In the present study we tested base-flipping by MspJI- and PvuRts1I-like restriction enzymes using several solution-based methods, including fluorescence measurements of the cytosine analog pyrrolocytosine and chemical modification of extrahelical pyrimidines with chloroacetaldehyde and KMnO4. We find that only KMnO4 proved an efficient probe for the positive display of flipped out pyrimidines, albeit the method required either non-physiological pH (4.3 or a substitution of the target cytosine with thymine. Our results imply that DNA recognition mechanism of 5(hmC binding proteins should be tested using a combination of all available methods, as the lack of a positive signal in some assays does not exclude the base flipping mechanism.

  6. 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.

  7. Autophagy as a Survival Mechanism for Squamous Cell Carcinoma Cells in Endonuclease G-Mediated Apoptosis

    Science.gov (United States)

    Masui, Atsushi; Hamada, Masakazu; Kameyama, Hiroyasu; Wakabayashi, Ken; Takasu, Ayako; Imai, Tomoaki; Iwai, Soichi; Yura, Yoshiaki

    2016-01-01

    Safingol, L- threo-dihydrosphingosine, induces cell death in human oral squamous cell carcinoma (SCC) cells through an endonuclease G (endoG) -mediated pathway. We herein determined whether safingol induced apoptosis and autophagy in oral SCC cells. Safingol induced apoptotic cell death in oral SCC cells in a dose-dependent manner. In safingol-treated cells, microtubule-associated protein 1 light chain 3 (LC3)-I was changed to LC3-II and the cytoplasmic expression of LC3, amount of acidic vesicular organelles (AVOs) stained by acridine orange and autophagic vacuoles were increased, indicating the occurrence of autophagy. An inhibitor of autophagy, 3-methyladenine (3-MA), enhanced the suppressive effects of safingol on cell viability, and this was accompanied by an increase in the number of apoptotic cells and extent of nuclear fragmentation. The nuclear translocation of endoG was minimal at a low concentration of safingol, but markedly increased when combined with 3-MA. The suppressive effects of safingol and 3-MA on cell viability were reduced in endoG siRNA- transfected cells. The scavenging of reactive oxygen species (ROS) prevented cell death induced by the combinational treatment, whereas a pretreatment with a pan-caspase inhibitor z-VAD-fmk did not. These results indicated that safingol induced apoptosis and autophagy in SCC cells and that the suppression of autophagy by 3-MA enhanced apoptosis. Autophagy supports cell survival, but not cell death in the SCC cell system in which apoptosis occurs in an endoG-mediated manner. PMID:27658240

  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. DNA and Protein Requirements for Substrate Conformational Changes Necessary for Human Flap Endonuclease-1-catalyzed Reaction.

    Science.gov (United States)

    Algasaier, Sana I; Exell, Jack C; Bennet, Ian A; Thompson, Mark J; Gotham, Victoria J B; Shaw, Steven J; Craggs, Timothy D; Finger, L David; Grasby, Jane A

    2016-04-01

    Human flap endonuclease-1 (hFEN1) catalyzes the essential removal of single-stranded flaps arising at DNA junctions during replication and repair processes. hFEN1 biological function must be precisely controlled, and consequently, the protein relies on a combination of protein and substrate conformational changes as a prerequisite for reaction. These include substrate bending at the duplex-duplex junction and transfer of unpaired reacting duplex end into the active site. When present, 5'-flaps are thought to thread under the helical cap, limiting reaction to flaps with free 5'-terminiin vivo Here we monitored DNA bending by FRET and DNA unpairing using 2-aminopurine exciton pair CD to determine the DNA and protein requirements for these substrate conformational changes. Binding of DNA to hFEN1 in a bent conformation occurred independently of 5'-flap accommodation and did not require active site metal ions or the presence of conserved active site residues. More stringent requirements exist for transfer of the substrate to the active site. Placement of the scissile phosphate diester in the active site required the presence of divalent metal ions, a free 5'-flap (if present), a Watson-Crick base pair at the terminus of the reacting duplex, and the intact secondary structure of the enzyme helical cap. Optimal positioning of the scissile phosphate additionally required active site conserved residues Tyr(40), Asp(181), and Arg(100)and a reacting duplex 5'-phosphate. These studies suggest a FEN1 reaction mechanism where junctions are bound and 5'-flaps are threaded (when present), and finally the substrate is transferred onto active site metals initiating cleavage.

  11. [Development of new methods in asymmetric reactions and their applications].

    Science.gov (United States)

    Node, Manabu

    2002-01-01

    Several novel methods using chiral reagents and biocatalysts for asymmetric reactions are described. Among those reactions, asymmetric reduction via a novel tandem Michael addition/Meerwein-Ponndorf-Verley reduction of acyclic alpha,beta-unsaturated ketones using a chiral mercapto alcohol, asymmetric synthesis of allene-1,3-dicarboxylate via crystallization induced asymmetric transformation, and improved asymmetric nitroolefination of lactones and lactames at alpha-carbon using new chiral reagents were developed. In the reactions using biocatalysts, asymmetric dealkoxycarbonylation of bicyclic beta-keto diesters having sigma-symmetry with lipase or esterase to give optically active beta-keto esters, the asymmetric reduction of bicyclic 1,3-diketones having sigma-symmetry with Baker's yeast to give optically active keto alcohols, and the asymmetric aldol reaction of glycine with threonine aldolase were also developed. The above mentioned products were effectively utilized as chiral building blocks for the asymmetric synthesis of natural products and drugs.

  12. 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.

  13. The deal with diel: Temperature fluctuations, asymmetrical warming, and ubiquitous metals contaminants.

    Science.gov (United States)

    Hallman, Tyler A; Brooks, Marjorie L

    2015-11-01

    Climate projections over the next century include disproportionately warmer nighttime temperatures ("asymmetrical warming"). Cool nighttime temperatures lower metabolic rates of aquatic ectotherms. In contaminated waters, areas with cool nights may provide thermal refugia from high rates of daytime contaminant uptake. We exposed Cope's gray tree frogs (Hyla chrysoscelis), southern leopard frogs (Lithobates sphenocephalus), and spotted salamanders (Ambystoma maculatum) to five concentrations of a mixture of cadmium, copper, and lead under three to four temperature regimes, representing asymmetrical warming. At concentrations with intermediate toxicosis at test termination (96 h), temperature effects on acute toxicity or escape distance were evident in all study species. Asymmetrical warming (day:night, 22:20 °C; 22:22 °C) doubled or tripled mortality relative to overall cooler temperatures (20:20 °C) or cool nights (22:18 °C). Escape distances were 40-70% shorter under asymmetrical warming. Results suggest potentially grave ecological impacts from unexpected toxicosis under climate change.

  14. Renewable resource management under asymmetric information

    DEFF Research Database (Denmark)

    Jensen, Frank; Andersen, Peder; Nielsen, Max

    2013-01-01

    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 this paper, we study asymmetric information about productivity within a principal-agent framework and a tax on fishing effort is considered. It is shown that a second best optimum can be achieved if the effort tax is designed such that low-productivity agents rent is exhausted, while high-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....

  15. Dc SQUIDs with asymmetric shunt resistors

    Energy Technology Data Exchange (ETDEWEB)

    Rudolph, Matthias; Nagel, Joachim; Kemmler, Matthias; Koelle, Dieter; Kleiner, Reinhold [Physikalisches Institut - Experimentalphysik II and Center for Collective Quantum Phenomena in LISAplus, Universitaet Tuebingen (Germany); Meckbach, Johannes Maximilian; Ilin, Konstantin; Siegel, Michael [Institut fuer Mikro- und Nanoelektronische Systeme, Karlsruhe Institute of Technology, Karlsruhe (Germany)

    2013-07-01

    We have investigated asymmetrically shunted Nb/Al-AlO{sub x}/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{sup -1} = R{sub 1}{sup -1} + R{sub 2}{sup -1}, we shunted only one of the two Josephson junctions with R = R{sub 1,2}/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.

  16. 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.)

  17. 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.

  18. 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

  19. 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...

  20. 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...

  1. 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...

  2. 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...

  3. 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 ...

  4. 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...

  5. Homogeneous asymmetric catalysis in fragrance chemistry.

    Science.gov (United States)

    Ciappa, Alessandra; Bovo, Sara; Bertoldini, Matteo; Scrivanti, Alberto; Matteoli, Ugo

    2008-06-01

    Opposite enantiomers of a chiral fragrance may exhibit different olfactory activities making a synthesis in high enantiomeric purity commercially and scientifically interesting. Accordingly, the asymmetric synthesis of four chiral odorants, Fixolide, Phenoxanol, Citralis, and Citralis Nitrile, has been investigated with the aim to develop practically feasible processes. In the devised synthetic schemes, the key step that leads to the formation of the stereogenic center is the homogeneous asymmetric hydrogenation of a prochiral olefin. By an appropriate choice of the catalyst and the reaction conditions, Phenoxanol, Citralis, and Citralis Nitrile were obtained in high enantiomeric purity, and odor profiles of the single enantiomers were determined.

  6. Asymmetric catalysis with short-chain peptides.

    Science.gov (United States)

    Lewandowski, Bartosz; Wennemers, Helma

    2014-10-01

    Within this review article we describe recent developments in asymmetric catalysis with peptides. Numerous peptides have been established in the past two decades that catalyze a wide variety of transformations with high stereoselectivities and yields, as well as broad substrate scope. We highlight here catalytically active peptides, which have addressed challenges that had thus far remained elusive in asymmetric catalysis: enantioselective synthesis of atropoisomers and quaternary stereogenic centers, regioselective transformations of polyfunctional substrates, chemoselective transformations, catalysis in-flow and reactions in aqueous environments.

  7. Asymmetric counter propagation of domain walls

    Science.gov (United States)

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

    2016-07-01

    Far from equilibrium systems show different states and domain walls between them. These walls, depending on the type of connected equilibria, exhibit a rich spatiotemporal dynamics. Here, we investigate the asymmetrical counter propagation of domain walls in an in-plane-switching cell filled with a nematic liquid crystal. Experimentally, we characterize the shape and speed of the domain walls. Based on the molecular orientation, we infer that the counter propagative walls have different elastic deformations. These deformations are responsible of the asymmetric counter propagating fronts. Theoretically, based on symmetry arguments, we propose a simple bistable model under the influence of a nonlinear gradient, which qualitatively describes the observed dynamics.

  8. Asymmetric acoustic transmission in multiple frequency bands

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Hong-xiang, E-mail: jsdxshx@ujs.edu.cn [Research Center of Fluid Machinery Engineering and Technology, Jiangsu University, Zhenjiang 212013 (China); Laboratory of Modern Acoustics, Institute of Acoustics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093 (China); State Key Laboratory of Acoustics, Institute of Acoustics, Chinese Academy of Sciences, Beijing 100190 (China); Yuan, Shou-qi, E-mail: Shouqiy@ujs.edu.cn [Research Center of Fluid Machinery Engineering and Technology, Jiangsu University, Zhenjiang 212013 (China); Zhang, Shu-yi [Laboratory of Modern Acoustics, Institute of Acoustics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093 (China)

    2015-11-23

    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.

  9. Cell-sized asymmetric lipid vesicles facilitate the investigation of asymmetric membranes

    Science.gov (United States)

    Kamiya, Koki; Kawano, Ryuji; Osaki, Toshihisa; Akiyoshi, Kazunari; Takeuchi, Shoji

    2016-09-01

    Asymmetric lipid giant vesicles have been used to model the biochemical reactions in cell membranes. However, methods for producing asymmetric giant vesicles lead to the inclusion of an organic solvent layer that affects the mechanical and physical characteristics of the membrane. Here we describe the formation of asymmetric giant vesicles that include little organic solvent, and use them to investigate the dynamic responses of lipid molecules in the vesicle membrane. We formed the giant vesicles via the inhomogeneous break-up of a lipid microtube generated by applying a jet flow to an asymmetric planar lipid bilayer. The asymmetric giant vesicles showed a lipid flip-flop behaviour in the membrane, superficially similar to the lipid flip-flop activity observed in apoptotic cells. In vitro synthesis of membrane proteins into the asymmetric giant vesicles revealed that the lipid asymmetry in bilayer membranes improves the reconstitution ratio of membrane proteins. Our asymmetric giant vesicles will be useful in elucidating lipid–lipid and lipid–membrane protein interactions involved in the regulation of cellular functions.

  10. 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

  11. The NF1 gene contains hotspots for L1 endonuclease-dependent de novo insertion.

    Directory of Open Access Journals (Sweden)

    Katharina Wimmer

    2011-11-01

    Full Text Available Long interspersed (L1 and Alu elements are actively amplified in the human genome through retrotransposition of their RNA intermediates by the -100 still retrotranspositionally fully competent L1 elements. Retrotransposition can cause inherited disease if such an element is inserted near or within a functional gene. Using direct cDNA sequencing as the primary assay for comprehensive NF1 mutation analysis, we uncovered in 18 unrelated index patients splicing alterations not readily explained at the genomic level by an underlying point-mutation or deletion. Improved PCR protocols avoiding allelic drop-out of the mutant alleles uncovered insertions of fourteen Alu elements, three L1 elements, and one poly(T stretch to cause these splicing defects. Taken together, the 18 pathogenic L1 endonuclease-mediated de novo insertions represent the largest number of this type of mutations characterized in a single human gene. Our findings show that retrotransposon insertions account for as many as -0.4% of all NF1 mutations. Since altered splicing was the main effect of the inserted elements, the current finding was facilitated by the use of RNA-based mutation analysis protocols, resulting in improved detection compared to gDNA-based approaches. Six different insertions clustered in a relatively small 1.5-kb region (NF1 exons 21(16-23(18 within the 280-kb NF1 gene. Furthermore, three different specific integration sites, one of them located in this cluster region, were each used twice, i.e. NM_000267.3(NF1:c.1642-1_1642 in intron 14(10c, NM_000267.3(NF1:c.2835_2836 in exon 21(16, and NM_000267.3(NF1:c.4319_4320 in exon 33(25. Identification of three loci that each served twice as integration site for independent retrotransposition events as well as 1.5-kb cluster region harboring six independent insertions supports the notion of non-random insertion of retrotransposons in the human genome. Currently, little is known about which features make sites

  12. 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.

  13. 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.

  14. 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.

  15. Weak chaos in the asymmetric heavy top

    CERN Document Server

    Barrientos, M; Ranada, A F

    1995-01-01

    We consider the dynamics of the slightly asymmetric heavy top, a non-integrable system obtained from the Lagrange top by breaking the symmetry of its inertia tensor. It shows signs of weak chaos, which we study numerically. We argue that it is a good example for introducing students to non-integrability and chaos. (author)

  16. 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.

  17. Asymmetric Total Synthesis of (-)-Cladospolide B

    Institute of Scientific and Technical Information of China (English)

    WANG,Wen-Kuan; ZHANG,Ji-Yong; HE,Jin-Mei; TANG,Shi-Bing; WANG,Xiao-Lei; SHE,Xue-Gong; PAN,Xin-Fu

    2008-01-01

    An enantioselective total synthesis of (-)-cladospolide B was described.The key steps in this synthesis include (a) a Sharpless asymmetric dihydroxylation to elaborate syn diol at C-4 and C-5 positions;(b) a Mitsunobu esterification to reverse the configuration at C-11 from (S) to (R);and (c) a ring-closing metathesis to access the 12-membered macrocyclic ring.

  18. 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

  19. The Asymmetric Effects of Investor Sentiment

    DEFF Research Database (Denmark)

    Lutz, Chandler

    2016-01-01

    are asymmetric: During peak-to-trough periods of investor sentiment (sentiment contractions), high sentiment predicts low future returns for the cross section of speculative stocks and for the market overall, whereas the relationship between sentiment and future returns is positive but relatively weak during...... trough-to-peak episodes (sentiment expansions). Overall, these results match theories and anecdotal accounts of investor sentiment....

  20. 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.

  1. 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).

  2. Attentional Control and Asymmetric Associative Priming

    Science.gov (United States)

    Hutchison, Keith A.; Heap, Shelly J.; Neely, James H.; Thomas, Matthew A.

    2014-01-01

    Participants completed a battery of 3 attentional control (AC) tasks (OSPAN, antisaccade, and Stroop, as in Hutchison, 2007) and performed a lexical decision task with symmetrically associated (e.g., "sister-brother") and asymmetrically related primes and targets presented in both the forward (e.g., "atom-bomb") and backward…

  3. 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

  4. Asymmetric relationships between proteins shape genome evolution.

    NARCIS (Netherlands)

    Notebaart, R.A.; Kensche, P.R.; Huynen, M.A.; Dutilh, B.E.

    2009-01-01

    BACKGROUND: The relationships between proteins are often asymmetric: one protein (A) depends for its function on another protein (B), but the second protein does not depend on the first. In metabolic networks there are multiple pathways that converge into one central pathway. The enzymes in the conv

  5. 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

  6. 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...

  7. 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...

  8. 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...

  9. 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...

  10. 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

  11. 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

  12. 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.

  13. Functional significance of protein assemblies predicted by the crystal structure of the restriction endonuclease BsaWI.

    Science.gov (United States)

    Tamulaitis, Gintautas; Rutkauskas, Marius; Zaremba, Mindaugas; Grazulis, Saulius; Tamulaitiene, Giedre; Siksnys, Virginijus

    2015-09-18

    Type II restriction endonuclease BsaWI recognizes a degenerated sequence 5'-W/CCGGW-3' (W stands for A or T, '/' denotes the cleavage site). It belongs to a large family of restriction enzymes that contain a conserved CCGG tetranucleotide in their target sites. These enzymes are arranged as dimers or tetramers, and require binding of one, two or three DNA targets for their optimal catalytic activity. Here, we present a crystal structure and biochemical characterization of the restriction endonuclease BsaWI. BsaWI is arranged as an 'open' configuration dimer and binds a single DNA copy through a minor groove contacts. In the crystal primary BsaWI dimers form an indefinite linear chain via the C-terminal domain contacts implying possible higher order aggregates. We show that in solution BsaWI protein exists in a dimer-tetramer-oligomer equilibrium, but in the presence of specific DNA forms a tetramer bound to two target sites. Site-directed mutagenesis and kinetic experiments show that BsaWI is active as a tetramer and requires two target sites for optimal activity. We propose BsaWI mechanism that shares common features both with dimeric Ecl18kI/SgrAI and bona fide tetrameric NgoMIV/SfiI enzymes. PMID:26240380

  14. 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.

  15. 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.

  16. 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

  17. Charge Asymmetric Cosmic Rays as a probe of Flavor Violating Asymmetric Dark Matter

    DEFF Research Database (Denmark)

    Masina, Isabella; Sannino, Francesco

    2011-01-01

    The recently introduced cosmic sum rules combine the data from PAMELA and Fermi-LAT cosmic ray experiments in a way that permits to neatly investigate whether the experimentally observed lepton excesses violate charge symmetry. One can in a simple way determine universal properties of the unknown...... component of the cosmic rays. Here we attribute a potential charge asymmetry to the dark sector. In particular we provide models of asymmetric dark matter able to produce charge asymmetric cosmic rays. We consider spin zero, spin one and spin one-half decaying dark matter candidates. We show that lepton...... flavor violation and asymmetric dark matter are both required to have a charge asymmetry in the cosmic ray lepton excesses. Therefore, an experimental evidence of charge asymmetry in the cosmic ray lepton excesses implies that dark matter is asymmetric....

  18. 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.

  19. Frictional work in double-sided tablet compression.

    Science.gov (United States)

    Muñoz-Ruiz, A; Wihervaara, M; Hakkinen, M; Juslin, M; Paronen, P

    1997-04-01

    The aim of this study was to evaluate the friction during double-sided tablet compression. Dicalcium phosphate dihydrate and lactose were tabletted with a compaction simulator with symmetrical and asymmetrical double-sided sawtooth punch displacement profiles. The estimation of force transmission in a powder column was based on an exponential equation, including the material parameter consisting of both the friction coefficient and Poisson's ratio. This parameter was predetermined from a single-sided compression. A novel equation was derived from a previously presented equation for friction work in single-sided tablet compression. The basic assumption was drawn from the linearly decreasing movement of infinitely thin particle layers, which are produced as the compressing punch surface approaches the other punch. This calculation was also based on the assumption that the equilibrium point, where the particles do not move, is halfway between the punches in the symmetrical profile and at a distance proportional to the amplitudes of the asymmetrical upper and lower sawtooth profiles. The tensile strength of tablets compressed with single-double-sided profiles was identical, and thus the behavior of the materials studied under compression was independent of the compression profiles. The friction work values that were calculated with the proposed expression for double-sided profiles were close to the theoretical values, as estimated by calculations based on compressions with single-sided profiles. In conclusion, the novel mathematical expression opens new possibilities for the evaluation of friction in double-sided compression; for example, in rotary press tabletting. PMID:9109053

  20. 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...

  1. 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.

  2. 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

  3. 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.

  4. The Clustered, Regularly Interspaced, Short Palindromic Repeats-associated Endonuclease 9 (CRISPR/Cas9)-created MDM2 T309G Mutation Enhances Vitreous-induced Expression of MDM2 and Proliferation and Survival of Cells.

    Science.gov (United States)

    Duan, Yajian; Ma, Gaoen; Huang, Xionggao; D'Amore, Patricia A; Zhang, Feng; Lei, Hetian

    2016-07-29

    The G309 allele of SNPs in the mouse double minute (MDM2) promoter locus is associated with a higher risk of cancer and proliferative vitreoretinopathy (PVR), but whether SNP G309 contributes to the pathogenesis of PVR is to date unknown. The clustered regularly interspaced short palindromic repeats (CRISPR)-associated endonuclease (Cas) 9 from Streptococcus pyogenes (SpCas9) can be harnessed to manipulate a single or multiple nucleotides in mammalian cells. Here we delivered SpCas9 and guide RNAs using dual adeno-associated virus-derived vectors to target the MDM2 genomic locus together with a homologous repair template for creating the mutation of MDM2 T309G in human primary retinal pigment epithelial (hPRPE) cells whose genotype is MDM2 T309T. The next-generation sequencing results indicated that there was 42.51% MDM2 G309 in the edited hPRPE cells using adeno-associated viral CRISPR/Cas9. Our data showed that vitreous induced an increase in MDM2 and subsequent attenuation of p53 expression in MDM2 T309G hPRPE cells. Furthermore, our experimental results demonstrated that MDM2 T309G in hPRPE cells enhanced vitreous-induced cell proliferation and survival, suggesting that this SNP contributes to the pathogenesis of PVR.

  5. Complex group-I introns in nuclear SSU rDNA of red and green algae: evidence of homing-endonuclease pseudogenes in the Bangiophyceae

    DEFF Research Database (Denmark)

    Haugen, P; Huss, V A; Nielsen, Henrik;

    1999-01-01

    on the complementary strand. A comparison between related group-I introns in the Bangiophyceae revealed homing-endonuclease-like pseudogenes due to frame-shifts and deletions in Porphyra and Bangia. The Scenedesmus and Porphyra introns provide new insights into the evolution and possible novel functions of nuclear...

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

    NARCIS (Netherlands)

    A.J.R. de Jonge; W. Vermeulen (Wim); W. Keijzer; J.H.J. Hoeijmakers (Jan); D. 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

  7. Design of Asymmetric Peptide Bilayer Membranes.

    Science.gov (United States)

    Li, Sha; Mehta, Anil K; Sidorov, Anton N; Orlando, Thomas M; Jiang, Zhigang; Anthony, Neil R; Lynn, David G

    2016-03-16

    Energetic insights emerging from the structural characterization of peptide cross-β assemblies have enabled the design and construction of robust asymmetric bilayer peptide membranes. Two peptides differing only in their N-terminal residue, phosphotyrosine vs lysine, coassemble as stacks of antiparallel β-sheets with precisely patterned charged lattices stabilizing the bilayer leaflet interface. Either homogeneous or mixed leaflet composition is possible, and both create nanotubes with dense negative external and positive internal solvent exposed surfaces. Cross-seeding peptide solutions with a preassembled peptide nanotube seed leads to domains of different leaflet architecture within single nanotubes. Architectural control over these cross-β assemblies, both across the bilayer membrane and along the nanotube length, provides access to highly ordered asymmetric membranes for the further construction of functional mesoscale assemblies.

  8. δ Meson Effects on Asymmetric Nuclear Matter

    Science.gov (United States)

    Liu, B.; di Toro, M.; Greco, V.

    The impact of a δ meson field (the scalar-isovector channel) on asymmetric nuclear matter is studied within relativistic mean-field (RMF) models with both constant and density dependent (DD) nucleon-meson couplings. The Equation of State (EOS) for asymmetric nuclear matter and the neutron star properties by the different models are compared. We find that the δ-field in the constant coupling scheme leads to a larger repulsion in dense neutron-rich matter and to a definite splitting of proton and neutron effective masses, finally influencing the stability of the neutron stars. A broader analysis of possible δ-field effects is achieved considering also density dependent nucleon-meson coupling. A remarkable effect on the relation between mass and radius for the neutron stars is seen, showing a significant reduction of the radius along with a moderate mass reduction due to the increase of the effective δ coupling in high density regions.

  9. Enhancing molecule fluorescence with asymmetrical plasmonic antennas.

    Science.gov (United States)

    Lu, Guowei; Liu, Jie; Zhang, Tianyue; Shen, Hongming; Perriat, Pascal; Martini, Matteo; Tillement, Olivier; Gu, Ying; He, Yingbo; Wang, Yuwei; Gong, Qihuang

    2013-07-21

    We propose and justify by the finite-difference time-domain method an efficient strategy to enhance the spontaneous emission of a fluorophore with a multi-resonance plasmonic antenna. The custom-designed asymmetrical antenna consists of two plasmonic nanoparticles with different sizes and is able to couple efficiently to free space light through multiple localized surface plasmon resonances. This design simultaneously permits a large near-field excitation near the antenna as well as a high quantum efficiency, which results in an unusual and significant enhancement of the fluorescence of a single emitter. Such an asymmetrical antenna presents intrinsic advantages over single particle or dimer based antennas made using two identical nanostructures. This promising concept can be exploited in the large domain of light-matter interaction processes involving multiple frequencies.

  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. 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...

  12. 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.

  13. 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...

  14. 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...

  15. Selective Homogeneous Catalysis in Asymmetric Synthesis

    DEFF Research Database (Denmark)

    Fristrup, Peter

    The subject of this thesis is selectivity in homogeneous asymmetric transition metalcatalyzed reactions. Four different reactions within organic chemistry have been studied by kinetic measurements, computational chemistry (modelling) or both of them in parallel. A Hammett study was performed....... A thorough computational study succeeded in explaining the observed results, although other significant results were also obtained during this study. Finally, an intramolecular reaction was studied computationally, and the rate increase observed under phase transfer catalysis conditions could be related...

  16. 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

  17. 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...

  18. 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...

  19. 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...

  20. 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."

  1. 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,...

  2. Asymmetric Information – Adverse Selection Problem

    Directory of Open Access Journals (Sweden)

    Dumitru MARIN

    2007-01-01

    Full Text Available The present paper makes an introduction in the contract theory starting with the definitions of asymmetric information and some of the problems that generate: moral hazard and adverse selection. We provide an insight of the latest empirical studies in adverse selection in different markets. An adverse selection model, based on Rothchild and Stiglitz is also present to give a perspective of the theoretical framework.

  3. 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 ...

  4. Ultralong distance coupling between asymmetric resonant microcavities

    OpenAIRE

    Shu, Fang-Jie; Zou, Chang-Ling; Chen, Wen-Cong; Sun, Fang-Wen

    2013-01-01

    The ultralong distance coupling between two Asymmetric Resonant Microcavities (ARCs) is studied. Different from traditional short distance tunneling coupling between microcavities, the high efficient free space directional emission and excitation allow ultralong distance energy transfer between ARCs. In this paper, a novel unidirectional emission ARC, which shows directionality I40 = 0.54, is designed for materials of refractive index n = 2.0. Compared with regular whispering gallery microres...

  5. 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.

  6. 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...

  7. 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...

  8. Asymmetric nuclear matter equation of state

    Energy Technology Data Exchange (ETDEWEB)

    Bombaci, I.; Lombardo, U. (Dipartimento di Fisica, Universita di Catania, Corso Italia 57, Catania (Italy) Istituto Nazionale di Fisica Nucleare, Sezione di Catania, Corso Italia 57, I-95129 Catania (Italy))

    1991-11-01

    Systematic calculations of asymmetric nuclear matter have been performed in the framework of the Brueckner-Bethe-Goldstone approach in a wide range of both density and asymmetry parameter. The empirical parabolic law fulfilled by the binding energy per nucleon is confirmed by the present results in all the range of the asymmetry parameter values. The predominant role of the {sup 3}{ital S}{sub 1-}{sup 3}{ital D}{sub 1} component of the {ital NN} interaction is elucidated. A linear variation of the proton and neutron single-particle potentials is found as increasing the neutron excess; a deviation from the phenomenological potentials occurs for highly asymmetric matter as an effect of the self-consistency. The present calculations of the incompressibility predict a strong softening of the equation of state going from symmetric to asymmetric nuclear matter. The proton fraction in equilibrium with neutron matter has been determined from the beta-stability condition and its relevance to the superfluidity of neutron stars has been investigated.

  9. 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...

  10. 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.

  11. Traceless Synthesis of Asymmetrically Modified Bivalent Nucleosomes.

    Science.gov (United States)

    Lechner, Carolin C; Agashe, Ninad D; Fierz, Beat

    2016-02-18

    Nucleosomes carry extensive post-translational modifications (PTMs), which results in complex modification patterns that are involved in epigenetic signaling. Although two copies of each histone coexist in a nucleosome, they may not carry the same PTMs and are often differently modified (asymmetric). In bivalent domains, a chromatin signature prevalent in embryonic stem cells (ESCs), namely H3 methylated at lysine 4 (H3K4me3), coexists with H3K27me3 in asymmetric nucleosomes. We report a general, modular, and traceless method for producing asymmetrically modified nucleosomes. We further show that in bivalent nucleosomes, H3K4me3 inhibits the activity of the H3K27-specific lysine methyltransferase (KMT) polycomb repressive complex 2 (PRC2) solely on the same histone tail, whereas H3K27me3 stimulates PRC2 activity across tails, thereby partially overriding the H3K4me3-mediated repressive effect. To maintain bivalent domains in ESCs, PRC2 activity must thus be locally restricted or reversed.

  12. 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

  13. 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.

  14. MmoSTI restriction endonuclease, isolated from Morganella morganii infecting a tropical moth, Actias selene, cleaving 5'-|CCNGG-3' sequences.

    Science.gov (United States)

    Skowron, Marta A; Zebrowska, Joanna; Wegrzyn, Grzegorz; Skowron, Piotr M

    2016-02-01

    A type II restriction endonuclease, MmoSTI, from the pathogenic bacterium Morganella morganii infecting a tropical moth, Actias selene, has been detected and biochemically characterized, as a potential etiological differentiation factor. The described REase recognizes interrupted palindromes, i.e., 5'-CCNGG-3' sequences and cleaves DNA leaving 5-nucleotide (nt) long, single-stranded (ss), 5'-cohesive ends, which was determined by three complementary methods: (i) cleavage of custom and standard DNA substrates, (ii) run-off sequencing of cleavage products, and (iii) shotgun cloning and sequencing of bacteriophage lambda (λ) DNA digested with MmoSTI. MmoSTI, the first 5'-CCNGG-3' REase characterized from M. morganii, is a neoschizomer of ScrFI, which cleaves DNA leaving 1-nt long, ss, 5'-cohesive ends. It is a high-frequency cutter and can be isolated from easily cultured bacteria, thus it can potentially serve as a tool for DNA manipulations.

  15. Anticancer clinical utility of the apurinic/apyrimidinic endonuclease/redox factor-1 (APE/Ref-1).

    Science.gov (United States)

    Zhang, Ying; Wang, Jian

    2010-03-01

    Apurinic/apyrimidinic endonuclease/redox factor-1 (APE/Ref-1), as a type of multifunctional protein, plays an essential role in the base excision repair (BER) pathway, which is responsible for the repair of DNA caused by oxidative and alkylation damage. As importantly, APE/Ref-1 also functions as a redox factor maintaining transcription factors in an active reduced state. APE/Ref-1 stimulates the DNA-binding activity of numerous transcription factors that are involved in cancer promotion and progression, such as AP-1 (Fos/Jun), NF-kappaB, HIF-1alpha, p53, and others. Based on the structures and functions of APE1/Ref-1, we will provide an overview of its activities and explore the budding clinical use of this protein as a target in cancer treatment, and propose that APE/Ref-1 has a great potential for application in clinical research.

  16. Hold your horSSEs: controlling structure-selective endonucleases MUS81 and Yen1/GEN1

    Directory of Open Access Journals (Sweden)

    Miguel eGonzalez Blanco

    2015-07-01

    Full Text Available Repair of DNA lesions through homologous recombination promotes the establishment of stable chromosomal interactions. Multiple helicases, topoisomerases and structure-selective endonucleases (SSEs act upon recombining joint molecules (JMs to disengage chromosomal connections and safeguard chromosome segregation. Recent studies on two conserved SSEs -MUS81 and Yen1/GEN1- uncovered multiple layers of regulation that operate to carefully tailor JM-processing according to specific cellular needs. Temporal restriction of SSE function imposes a hierarchy in pathway usage that ensures efficient JM processing while minimizing reciprocal exchanges between the recombining DNAs. Whereas a conserved strategy of fine-tuning SSE functions exists in different model systems, the precise molecular mechanisms to implement it appear to be significantly different. Here, we summarize the current knowledge on the cellular switches that are in place to control MUS81 and Yen1/GEN1 functions.

  17. 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 ...

  18. 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.

  19. Chromosome doubling method

    Science.gov (United States)

    Kato, Akio

    2006-11-14

    The invention provides methods for chromosome doubling in plants. The technique overcomes the low yields of doubled progeny associated with the use of prior techniques for doubling chromosomes in plants such as grasses. The technique can be used in large scale applications and has been demonstrated to be highly effective in maize. Following treatment in accordance with the invention, plants remain amenable to self fertilization, thereby allowing the efficient isolation of doubled progeny plants.

  20. Synthetic Applications of Chiral Unsaturated Epoxy Alcohols Prepared by Sharpless Asymmetric Epoxidation

    Directory of Open Access Journals (Sweden)

    María Moreno

    2010-02-01

    Full Text Available An overview of the synthesis and applications of chiral 2,3-epoxy alcohols containing unsaturated chains is presented. One of the fundamental synthetic routes to these compounds is Sharpless asymmetric epoxidation, which is reliable, highly chemoselective and enables easy prediction of the product enantioselectivity. Thus, unsaturated epoxy alcohols are readily obtained by selective oxidation of the allylic double bond in the presence of other carbon-carbon double or triple bonds. The wide availability of epoxy alcohols with unsaturated chains, the versatility of the epoxy alcohol functionality (e.g. regio- and stereo-selective ring opening; oxidation; and reduction, and the arsenal of established alkene chemistries, make unsaturated epoxy alcohols powerful starting materials for the synthesis of complex targets such as biologically active molecules. The popularization of ring-closing metathesis has further increased their value, making them excellent precursors to cyclic compounds.

  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. Evidence for the Formation of Symmetric and Asymmetric DLPC-DAPC Lipid Bilayer Domains

    Directory of Open Access Journals (Sweden)

    Markus Ritter

    2013-07-01

    Full Text Available Background/Aims: We investigated if mixtures of the phosphatidylcholine (PC lipids 1,2-dilauroyl-sn-glycero-3-phosphocholine (C12:0 PC; DLPC and 1,2-diarachidoyl-sn-glycero-3-phosphocholine (C20:0 PC; DAPC, which differ by eight methylene groups in acyl chain length, lead to the spontaneous formation of distinct lipid rafts and asymmetric bilayers. Methods: The experiments were performed using Atomic Force Microscopy (AFM. Results: We show that DLPC and DAPC mixed at a molar ratio of 1:1 lead to the formation of single, double and triple bilayers with peaks at 6.14 ± 0.11, 13.27 ± 0.17 and 20.54 ± 0.46 nm, respectively (n=750. Within these formations discrete height steps of 0.92 nm can be resolved (n=422. Conclusion: The most frequently observed height steps value of 0.92 nm matches best with the calculated mean lipid hydrophobic thickness difference for asymmetric C12:0 PC and C20:0 PC lipid bilayers of 0.88 nm. This indicates the ability of DLPC and DAPC to form asymmetric lipid bilayers.

  3. DOUBLE-BOOST DC-AC CONVERTER WITH SLIDING-MODE CONTROL FOR PORTABLE AUDIO

    DEFF Research Database (Denmark)

    Bolten Maizonave, Gert; Andersen, Michael Andreas E.; Kjærgaard, Claus;

    2009-01-01

    The double-boost topology is studied for operation as a dc-ac converter and single stage audio amplifier. A sliding-mode controller is designed in order to achieve fast enough response for the whole audio frequency range. Symmetric, asymmetric and interleaved operation modes are analyzed....

  4. 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.

  5. 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.

  6. 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

  7. 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.

  8. 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.

  9. 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.

  10. Asymmetric chemical reactions by polarized quantum beams

    Science.gov (United States)

    Takahashi, Jun-Ichi; Kobayashi, Kensei

    One of the most attractive hypothesis for the origin of homochirality in terrestrial bio-organic compounds (L-amino acid and D-sugar dominant) is nominated as "Cosmic Scenario"; a chiral impulse from asymmetric excitation sources in space triggered asymmetric reactions on the surfaces of such space materials as meteorites or interstellar dusts prior to the existence of terrestrial life. 1) Effective asymmetric excitation sources in space are proposed as polarized quantum beams, such as circularly polarized light and spin polarized electrons. Circularly polarized light is emitted as synchrotron radiation from tightly captured electrons by intense magnetic field around neutron stars. In this case, either left-or right-handed polarized light can be observed depending on the direction of observation. On the other hand, spin polarized electrons is emitted as beta-ray in beta decay from radioactive nuclei or neutron fireballs in supernova explosion. 2) The spin of beta-ray electrons is longitudinally polarized due to parity non-conservation in the weak interaction. The helicity (the the projection of the spin onto the direction of kinetic momentum) of beta-ray electrons is universally negative (left-handed). For the purpose of verifying the asymmetric structure emergence in bio-organic compounds by polarized quantum beams, we are now carrying out laboratory simulations using circularly polarized light from synchrotron radiation facility or spin polarized electron beam from beta-ray radiation source. 3,4) The target samples are solid film or aqueous solution of racemic amino acids. 1) K.Kobayashi, K.Kaneko, J.Takahashi, Y.Takano, in Astrobiology: from simple molecules to primitive life; Ed. V.Basiuk; American Scientific Publisher: Valencia, 2008. 2) G.A.Gusev, T.Saito, V.A.Tsarev, A.V.Uryson, Origins Life Evol. Biosphere. 37, 259 (2007). 3) J.Takahashi, H.Shinojima, M.Seyama, Y.Ueno, T.Kaneko, K.Kobayashi, H.Mita, M.Adachi, M.Hosaka, M.Katoh, Int. J. Mol. Sci. 10, 3044

  11. 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.

  12. 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.

  13. The Asymmetric Effects of Investor Sentiment

    DEFF Research Database (Denmark)

    Lutz, Chandler

    2016-01-01

    are asymmetric: During peak-to-trough periods of investor sentiment (sentiment contractions), high sentiment predicts low future returns for the cross section of speculative stocks and for the market overall, whereas the relationship between sentiment and future returns is positive but relatively weak during......We use the returns on lottery-like stocks and a dynamic factor model to construct a novel index of investor sentiment. This new measure is highly correlated with other behavioral indicators, but more closely tracks speculative episodes. Our main new finding is that the effects of sentiment...... trough-to-peak episodes (sentiment expansions). Overall, these results match theories and anecdotal accounts of investor sentiment....

  14. 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.

  15. 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

  16. 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.

    2016-07-01

    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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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...

  2. 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.

  3. 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.

  4. 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

  5. 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.

  6. 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.

  7. 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...

  8. 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

  9. 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.

  10. Particle identification at an asymmetric B Factory

    International Nuclear Information System (INIS)

    Particle identification systems are an important component of any detector at a high-luminosity, asymmetric B Factory. In particular, excellent hadron identification is required to probe CP violation in B0 decays to CP eigenstates. The particle identification systems discussed below also provide help in separating leptons from hadrons at low momenta. We begin this chapter with a discussion of the physics motivation for providing particle identification, the inherent limitations due to interactions and decays in flight, and the requirements for hermiticity and angular coverage. A special feature of an asymmetric B Factory is the resulting asymmetry in the momentum distribution as a function of polar angle; this will also be quantified and discussed. In the next section the three primary candidates, time-of-flight (TOF), energy loss (dE/dx), and Cerenkov counters, both ring-imaging and threshold, will be briefly described and evaluated. Following this, one of the candidates, a long-drift Cerenkov ring-imaging device, is described in detail to provide a reference design. Design considerations for a fast RICH are then described. A detailed discussion of aerogel threshold counter designs and associated R ampersand D conclude the chapter. 56 refs., 64 figs., 13 tabs

  11. An asymmetric B factory based on PEP

    Energy Technology Data Exchange (ETDEWEB)

    1991-02-01

    In this report we describe a design for a high-luminosity Asymmetric B Factory to be built in the PEP tunnel on the SLAC site. This proposal, a collaborative effort SLAC, LBL, and LLNL, is the culmination of more than two years of effort aimed at the design and construction of an asymmetric e{sup +}e{sup {minus}} collider capable of achieving a luminosity of L = 3 {times} 10{sup 33} cm{sup {minus}2} s{sup {minus}1}. The configuration adopted utilizes two storage rings, and electron ring operating at 9 GeV and a positron ring at 3.1 GeV, each with a circumference of 2200 m. The high-energy ring is an upgrade of the PEP storage ring at SLAC; all PEP magnets and most power supplies will be reused. The upgrade consists primarily of replacing the PEP vacuum chamber and RF system with newly designed versions optimized for the high-current environment of the B Factory. The low-energy ring will be newly constructed and will be situated atop the high-energy ring in the PEP tunnel. Utilities already installed in the PEP tunnel are largely sufficient to operate the two B Factory storage rings.

  12. Asymmetric Twin Representation: the Transfer Matrix Symmetry

    Directory of Open Access Journals (Sweden)

    Anastasia Doikou

    2007-01-01

    Full Text Available The symmetry of the Hamiltonian describing the asymmetric twin model was partially studied in earlier works, and our aim here is to generalize these results for the open transfer matrix. In this spirit we first prove, that the so called boundary quantum algebra provides a symmetry for any generic - independent of the choice of model - open transfer matrix with a trivial left boundary. In addition it is shown that the boundary quantum algebra is the centralizer of the $B$ type Hecke algebra. We then focus on the asymmetric twin representation of the boundary Temperley-Lieb algebra. More precisely, by exploiting exchange relations dictated by the reflection equation we show that the transfer matrix with trivial boundary conditions enjoys the recognized $U_q(sl_2otimes U_i(sl_2$ symmetry. When a non-diagonal boundary is implemented the symmetry as expected is reduced, however again certain familiar boundary non-local charges turn out to commute with the corresponding transfer matrix.

  13. Asymmetric disassembly and robustness in declining networks.

    Science.gov (United States)

    Saavedra, Serguei; Reed-Tsochas, Felix; Uzzi, Brian

    2008-10-28

    Mechanisms that enable declining networks to avert structural collapse and performance degradation are not well understood. This knowledge gap reflects a shortage of data on declining networks and an emphasis on models of network growth. Analyzing >700,000 transactions between firms in the New York garment industry over 19 years, we tracked this network's decline and measured how its topology and global performance evolved. We find that favoring asymmetric (disassortative) links is key to preserving the topology and functionality of the declining network. Based on our findings, we tested a model of network decline that combines an asymmetric disassembly process for contraction with a preferential attachment process for regrowth. Our simulation results indicate that the model can explain robustness under decline even if the total population of nodes contracts by more than an order of magnitude, in line with our observations for the empirical network. These findings suggest that disassembly mechanisms are not simply assembly mechanisms in reverse and that our model is relevant to understanding the process of decline and collapse in a broad range of biological, technological, and financial networks.

  14. Instability of asymmetric continuous shaft system

    Science.gov (United States)

    Srinath, R.; Sarkar, Abhijit; Sekhar, A. S.

    2016-11-01

    In this work, the governing equation of asymmetric continuous shaft in inertial frame of reference is studied. In particular, determination of the parameter ranges for the stability or instability of the shaft response is the focus of the present work. The governing equations are a fourth-order coupled partial differential equations containing time dependent coefficients. The equations are non-dimensionalized in terms of two parameters related to the average moment of inertia and the difference of moments of inertia about the principal axes. Using the latter as the asymptotic parameter and employing modal superposition, a formal methodology based on perturbation methods is developed to ascertain the stability and instability characteristics. The methodology is applicable to shafts subjected to some of the classical boundary conditions viz. simply supported, cantilever, and fixed-fixed. Similar stability curves are obtained for each mode for these different boundary conditions. The novel non-dimensionalization scheme chosen leads to the stability boundaries as well as the loci of varying speeds to be in the form of straight lines. The intersection of these lines determine the stable and unstable speed ranges of different asymmetric shafts. The results are generalized for different material and geometric properties of the shaft.

  15. Properties of asymmetrically evolved community networks

    Institute of Scientific and Technical Information of China (English)

    Cui Di; Gao Zi-You; Zheng Jian-Feng

    2009-01-01

    This paper studies a simple asymmetrically evolved community network with a combination of preferential at-tachment and random properties. An important issue about community networks is to discover the different utility increments of two nodes, where the utility is introduced to investigate the asymmetrical effect of connecting two nodes. On the other hand, the connection of two nodes in community networks can be classified as two nodes belonging to the same or to different communities. The simulation results show that the model can reproduce a power-law utility distribution P(u)~ u-σ,σ=2+ 1/p, which can be obtained by using mean-field approximation methods. Furthermore, the model exhibits exponential behaviour with respect to small values of a parameter denoting the random effect in our model at the low-utility region and a power-law feature with respect to big values of this parameter at the high-utility region, which is in good agreement with theoretical analysis. This kind of community network can reproduce a unique utility distribution by theoretical and numerical analysis.

  16. An asymmetric B factory based on PEP

    International Nuclear Information System (INIS)

    In this report we describe a design for a high-luminosity Asymmetric B Factory to be built in the PEP tunnel on the SLAC site. This proposal, a collaborative effort SLAC, LBL, and LLNL, is the culmination of more than two years of effort aimed at the design and construction of an asymmetric e+e- collider capable of achieving a luminosity of L = 3 x 1033 cm-2 s-1. The configuration adopted utilizes two storage rings, and electron ring operating at 9 GeV and a positron ring at 3.1 GeV, each with a circumference of 2200 m. The high-energy ring is an upgrade of the PEP storage ring at SLAC; all PEP magnets and most power supplies will be reused. The upgrade consists primarily of replacing the PEP vacuum chamber and RF system with newly designed versions optimized for the high-current environment of the B Factory. The low-energy ring will be newly constructed and will be situated atop the high-energy ring in the PEP tunnel. Utilities already installed in the PEP tunnel are largely sufficient to operate the two B Factory storage rings

  17. Asymmetric transition disks: Vorticity or eccentricity?

    CERN Document Server

    Zsom, A; Ghanbari, J

    2013-01-01

    Context. Transition disks typically appear in resolved millimeter observations as giant dust rings surrounding their young host stars. More accurate observations with ALMA have shown several of these rings to be in fact asymmetric: they have lopsided shapes. It has been speculated that these rings act as dust traps, which would make them important laboratories for studying planet formation. It has been shown that an elongated giant vortex produced in a disk with a strong viscosity jump strikingly resembles the observed asymmetric rings. Aims. We aim to study a similar behavior for a disk in which a giant planet is embedded. However, a giant planet can induce two kinds of asymmetries: (1) a giant vortex, and (2) an eccentric disk. We studied under which conditions each of these can appear, and how one can observationally distinguish between them. This is important because only a vortex can trap particles both radially and azimuthally, while the eccentric ring can only trap particles in radial direction. Method...

  18. Asymmetric EPR entanglement in continuous variable systems

    International Nuclear Information System (INIS)

    Continuous variable entanglement can be produced in nonlinear systems or via the interference of squeezed states. In many optical systems such as parametric down conversion, the production of two perfectly symmetric subsystems is usually assumed when demonstrating the existence of entanglement. This symmetry simplifies the description of entanglement. However, asymmetry in entanglement may arise naturally in a real experiment, or be intentionally introduced in a given quantum information protocol. These asymmetries can emerge from having the output beams experience different losses and environmental contamination, or from the availability of non-identical input quantum states in quantum communication protocols. In this paper, we present a visualization of entanglement using quadrature amplitude plots of the twin beams. We quantitatively discuss the strength of asymmetric entanglement using EPR and inseparability criteria and theoretically show that the optimal beamsplitter ratio for entanglement is dependent on the asymmetries and may not be 50 : 50. To support this theory, we present experimental results showing one particular asymmetric entanglement where a 78 : 22 beamsplitter is optimal for observing entanglement. (paper)

  19. Stretchable Wire-Shaped Asymmetric Supercapacitors Based on Pristine and MnO2 Coated Carbon Nanotube Fibers.

    Science.gov (United States)

    Xu, Ping; Wei, Bingqing; Cao, Zeyuan; Zheng, Jie; Gong, Ke; Li, Faxue; Yu, Jianyong; Li, Qingwen; Lu, Weibang; Byun, Joon-Hyung; Kim, Byung-Sun; Yan, Yushan; Chou, Tsu-Wei

    2015-06-23

    While the emerging wire-shaped supercapacitors (WSS) have been demonstrated as promising energy storage devices to be implemented in smart textiles, challenges in achieving the combination of both high mechanical stretchability and excellent electrochemical performance still exist. Here, an asymmetric configuration is applied to the WSS, extending the potential window from 0.8 to 1.5 V, achieving tripled energy density and doubled power density compared to its asymmetric counterpart while accomplishing stretchability of up to 100% through the prestrainning-then-buckling approach. The stretchable asymmetric WSS constituted of MnO2/CNT hybrid fiber positive electrode, aerogel CNT fiber negative electrode and KOH-PVA electrolyte possesses a high specific capacitance of around 157.53 μF cm(-1) at 50 mV s(-1) and a high energy density varying from 17.26 to 46.59 nWh cm(-1) with the corresponding power density changing from 7.63 to 61.55 μW cm(-1). Remarkably, a cyclic tensile strain of up to 100% exerts negligible effects on the electrochemical performance of the stretchable asymmetric WSS. Moreover, after 10,000 galvanostatic charge-discharge cycles, the specific capacitance retains over 99%, demonstrating a long cyclic stability. PMID:25961131

  20. Project Half Double

    DEFF Research Database (Denmark)

    Ehlers, Michael; Adland, Karoline Thorp; Boston, Nicolai Elborough;

    Project Half Double has a clear mission to succeed in finding a project methodology that can increase the success rate of our projects while increasing the speed at which we generate new ideas and develop new products and services. Chaos and complexity should be seen as a basic condition...... activities carried out within the framework of the projects. The formal part of Project Half Double was initiated in June 2015. We started out by developing, refining and testing the Half Double methodology on seven pilot projects in the first phase of the project, which will end June 2016. The current...... organisations concerning project methodology and beyond. The many learning points from each pilot project show that Project Half Double has left its clear footprint in the pilot organisations, and that the Half Double methodology has evolved and developed very much during Project Half Double phase 1....

  1. 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...

  2. UNILATERAL INCOMPLETE DOUBLE URETER

    Directory of Open Access Journals (Sweden)

    Kaini

    2013-04-01

    Full Text Available ABSTRACT: Double ureter is a result of premature division of t he ureteric bud. The ureters may join in the lower third of their course and open thr ough a common orifice into the bladder. If they open independently into the bladder, the ureter draining the upper pelvis opens into the bladder below the opening of the other ureter. Patie nts with double ureter or double pelvis are more likely to develop urinary infection and calculi .

  3. The virion host shutoff endonuclease (UL41) of herpes simplex virus interacts with the cellular cap-binding complex eIF4F.

    Science.gov (United States)

    Page, Heidi G; Read, G Sullivan

    2010-07-01

    The herpes simplex virus Vhs endonuclease degrades host and viral mRNAs. Isolated Vhs cuts any RNA at many sites. Yet, within cells, it targets mRNAs and cuts at preferred sites, including regions of translation initiation. Previous studies have shown that Vhs binds the translation factors eIF4A and eIF4H. Here, we show that Vhs binds the cap-binding complex eIF4F. Association with eIF4F correlated with the ability of Vhs to bind eIF4A but not eIF4H. All Vhs proteins that degrade mRNAs associated with eIF4F. However, simply tethering an active endonuclease to eIF4F is not sufficient to degrade mRNAs. Binding to eIF4H may also be required.

  4. Restriction endonuclease analysis and mapping of the genomes of granulosis viruses isolated from Xestia c-nigrum and five other noctuid species.

    Science.gov (United States)

    Goto, C; Minobe, Y; Iizuka, T

    1992-06-01

    Restriction endonuclease analysis was performed on the genomic DNA of granulosis viruses isolated from noctuid species of six genera: Xestia c-nigrum, Autographa gamma, Hydraecia amurensis, Celaena leucostigma, Aletia pallens and Pseudaletia separata. All of the isolates gave very similar restriction endonuclease profiles with only minor variations. An isolate obtained from X. c-nigrum was chosen as the reference genotype, and a genomic library was constructed for this isolate using plasmid vectors. The genome was mapped using EcoRI, BamHI and BglII, and Southern hybridization; the size of the genome was estimated to be 179 kbp. Hybridization of labelled clones to fragments of other isolates revealed that genotypic variation among isolates resulted from changes in restriction sites, and from deletion or insertion of DNA. Comparative restriction mapping revealed that all of the isolates were variants of one virus, even though they originated from different host species. PMID:1607867

  5. Study on characteristics of double surface VOC emissions from dry flat-plate building materials

    Institute of Scientific and Technical Information of China (English)

    WANG Xinke; ZHANG Yinping; ZHAO Rongyi

    2006-01-01

    This paper sets up an analytic model of double surface emission of volatile organic compound (VOC) from dry, flat-plate building materials. Based on it, the influence of factors including air change rate, loading factor of materials in the room, mass diffusion coefficient, partition coefficient, convective mass transfer coefficient, thickness of materials, asymmetric convective flow and initial VOC concentration distribution in the building material on emission is discussed. The conditions for simplifying double surface emission into single surface emission are also discussed. The model is helpful to assess the double surface VOC emission from flat-plate building materials used in indoor furniture and space partition.

  6. Modeling interconnect corners under double patterning misalignment

    Science.gov (United States)

    Hyun, Daijoon; Shin, Youngsoo

    2016-03-01

    Publisher's Note: This paper, originally published on March 16th, was replaced with a corrected/revised version on March 28th. If you downloaded the original PDF but are unable to access the revision, please contact SPIE Digital Library Customer Service for assistance. Interconnect corners should accurately reflect the effect of misalingment in LELE double patterning process. Misalignment is usually considered separately from interconnect structure variations; this incurs too much pessimism and fails to reflect a large increase in total capacitance for asymmetric interconnect structure. We model interconnect corners by taking account of misalignment in conjunction with interconnect structure variations; we also characterize misalignment effect more accurately by handling metal pitch at both sides of a target metal independently. Identifying metal space at both sides of a target metal.

  7. Observing Double Stars

    Science.gov (United States)

    Genet, Russell M.; Fulton, B. J.; Bianco, Federica B.; Martinez, John; Baxter, John; Brewer, Mark; Carro, Joseph; Collins, Sarah; Estrada, Chris; Johnson, Jolyon; Salam, Akash; Wallen, Vera; Warren, Naomi; Smith, Thomas C.; Armstrong, James D.; McGaughey, Steve; Pye, John; Mohanan, Kakkala; Church, Rebecca

    2012-05-01

    Double stars have been systematically observed since William Herschel initiated his program in 1779. In 1803 he reported that, to his surprise, many of the systems he had been observing for a quarter century were gravitationally bound binary stars. In 1830 the first binary orbital solution was obtained, leading eventually to the determination of stellar masses. Double star observations have been a prolific field, with observations and discoveries - often made by students and amateurs - routinely published in a number of specialized journals such as the Journal of Double Star Observations. All published double star observations from Herschel's to the present have been incorporated in the Washington Double Star Catalog. In addition to reviewing the history of visual double stars, we discuss four observational technologies and illustrate these with our own observational results from both California and Hawaii on telescopes ranging from small SCTs to the 2-meter Faulkes Telescope North on Haleakala. Two of these technologies are visual observations aimed primarily at published "hands-on" student science education, and CCD observations of both bright and very faint doubles. The other two are recent technologies that have launched a double star renaissance. These are lucky imaging and speckle interferometry, both of which can use electron-multiplying CCD cameras to allow short (30 ms or less) exposures that are read out at high speed with very low noise. Analysis of thousands of high speed exposures allows normal seeing limitations to be overcome so very close doubles can be accurately measured.

  8. Saturated free fatty acids and apoptosis in microvascular mesangial cells: palmitate activates pro-apoptotic signaling involving caspase 9 and mitochondrial release of endonuclease G

    Directory of Open Access Journals (Sweden)

    Simonson Michael S

    2005-01-01

    Full Text Available Abstract Background In type 2 diabetes, free fatty acids (FFA accumulate in microvascular cells, but the phenotypic consequences of FFA accumulation in the microvasculature are incompletely understood. Here we investigated whether saturated FFA induce apoptosis in human microvascular mesangial cells and analyzed the signaling pathways involved. Methods Saturated and unsaturated FFA-albumin complexes were added to cultured human mesangial cells, after which the number of apoptotic cells were quantified and the signal transduction pathways involved were delineated. Results The saturated FFA palmitate and stearate were apoptotic unlike equivalent concentrations of the unsaturated FFA oleate and linoleate. Palmitate-induced apoptosis was potentiated by etomoxir, an inhibitor of mitochondrial β-oxidation, but was prevented by an activator of AMP-kinase, which increases fatty acid β-oxidation. Palmitate stimulated an intrinsic pathway of pro-apoptotic signaling as evidenced by increased mitochondrial release of cytochrome-c and activation of caspase 9. A caspase 9-selective inhibitor blocked caspase 3 activation but incompletely blocked apoptosis in response to palmitate, suggesting an additional caspase 9-independent pathway. Palmitate stimulated mitochondrial release of endonuclease G by a caspase 9-independent mechanism, thereby implicating endonuclease G in caspase 9-indpendent regulation of apoptosis by saturated FFA. We also observed that the unsaturated FFA oleate and linoleate prevented palmitate-induced mitochondrial release of both cytochrome-c and endonuclease G, which resulted in complete protection from palmitate-induced apoptosis. Conclusions Taken together, these results demonstrate that palmitate stimulates apoptosis by evoking an intrinsic pathway of proapoptotic signaling and identify mitochondrial release of endonuclease G as a key step in proapoptotic signaling by saturated FFA and in the anti-apoptotic actions of unsaturated FFA.

  9. 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 ...

  10. Iron-, Cobalt-, and Nickel-Catalyzed Asymmetric Transfer Hydrogenation and Asymmetric Hydrogenation of Ketones.

    Science.gov (United States)

    Li, Yan-Yun; Yu, Shen-Luan; Shen, Wei-Yi; Gao, Jing-Xing

    2015-09-15

    Chiral alcohols are important building blocks in the pharmaceutical and fine chemical industries. The enantioselective reduction of prochiral ketones catalyzed by transition metal complexes, especially asymmetric transfer hydrogenation (ATH) and asymmetric hydrogenation (AH), is one of the most efficient and practical methods for producing chiral alcohols. In both academic laboratories and industrial operations, catalysts based on noble metals such as ruthenium, rhodium, and iridium dominated the asymmetric reduction of ketones. However, the limited availability, high price, and toxicity of these critical metals demand their replacement with abundant, nonprecious, and biocommon metals. In this respect, the reactions catalyzed by first-row transition metals, which are more abundant and benign, have attracted more and more attention. As one of the most abundant metals on earth, iron is inexpensive, environmentally benign, and of low toxicity, and as such it is a fascinating alternative to the precious metals for catalysis and sustainable chemical manufacturing. However, iron catalysts have been undeveloped compared to other transition metals. Compared with the examples of iron-catalyzed asymmetric reduction, cobalt- and nickel-catalyzed ATH and AH of ketones are even seldom reported. In early 2004, we reported the first ATH of ketones with catalysts generated in situ from iron cluster complex and chiral PNNP ligand. Since then, we have devoted ourselves to the development of ATH and AH of ketones with iron, cobalt, and nickel catalysts containing novel chiral aminophosphine ligands. In our study, the iron catalyst containing chiral aminophosphine ligands, which are expected to control the stereochemistry at the metal atom, restrict the number of possible diastereoisomers, and effectively transfer chiral information, are successful catalysts for enantioselective reduction of ketones. Among these novel chiral aminophosphine ligands, 22-membered macrocycle P2N4

  11. A new convenient asymmetric approach to herbarumin Ⅲ

    Institute of Scientific and Technical Information of China (English)

    Xue Song Chen; Shi Jun Da; Li Hong Yang; Bo Yan Xu; Zhi Xiang Xie; Ying Li

    2007-01-01

    The asymmetric total synthesis of herbarumin Ⅲ 3, a naturally occurred phytotoxin, along with 8-epi-herbarumin Ⅲ 22, was succeeded in 12 steps from n-butyraldehyde based on Brown's asymmetric allylation, taking modified Julia olefination and Yamaguchi's macro-lactonization as key steps.

  12. Effects of Noise on Asymmetric Bidirectional Controlled Teleportation

    Science.gov (United States)

    Nie, Yi-you; Sang, Ming-huang

    2016-07-01

    We present a scheme for asymmetric bidirectional controlled teleportation via a six-qubit cluster state in noisy environments, which includes the phase-damping and amplitude-damping channels. We analytically derive the fidelities of the asymmetric bidirectional controlled teleportation process in these two noise channels. We show that the fidelities only depend on the initial state and the noisy rate.

  13. Asymmetric Catalytic Reactions Catalyzed by Chiral Titanium Complexes

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    @@ Chiral titanium complexes is very importance catalyst to asymmetric catalytic reactions. A series of catalytic systems based on titanium-chiral ligands complexes has been reported. This presentation will discuss some of our recent progress on asymmetric catalytic reactions catalyzed by chiral titanium complexes.

  14. Asymmetric Catalytic Reactions Catalyzed by Chiral Titanium Complexes

    Institute of Scientific and Technical Information of China (English)

    FENG; XiaoMing

    2001-01-01

    Chiral titanium complexes is very importance catalyst to asymmetric catalytic reactions. A series of catalytic systems based on titanium-chiral ligands complexes has been reported. This presentation will discuss some of our recent progress on asymmetric catalytic reactions catalyzed by chiral titanium complexes.  ……

  15. Asymmetric catalytic synthesis of the proposed structure of trocheliophorolide B.

    Science.gov (United States)

    Trost, Barry M; Quintard, Adrien

    2012-09-01

    A concise catalytic asymmetric synthesis of the proposed structure of trocheliophorolide B is reported. The synthetic sequence notably features an asymmetric acetaldehyde alkynylation, a Ru-catalyzed alder-ene reaction, and a Zn-ProPhenol ynone aldol condensation. Comparison with the reported data suggests a misassignment of the natural product structure.

  16. Asymmetric catalytic synthesis of the proposed structure of trocheliophorolide B

    OpenAIRE

    Trost, Barry M.; Quintard, Adrien

    2012-01-01

    A concise catalytic asymmetric synthesis of the proposed structure of Trocheliophorolide B is reported. The synthetic sequence notably features an asymmetric acetaldehyde alkynylation, Ru-catalyzed alder-ene reaction and Zn-ProPhenol ynone aldol condensation. Comparison with the reported data suggests a miss-assignment of the natural product structure.

  17. ASYMMETRIC HYDROSILYLATION CATALYZED BY POLYMER—SUPPORTED THIAZOLIDINE RHODIUM CATALYSTS

    Institute of Scientific and Technical Information of China (English)

    LEIYanohui; LIHong; 等

    1999-01-01

    Asymmetric hydrisilylation catalyzed by polymeric thiazolidine rhodium catalysts was conducted.Almost the same optical yields have been obtained when comb-shaped polymeric ligands and their corresponding monomer complexed rhodium cataltysts were used to asymmetric hydrosilylation of acetophenone.Optical yield of chiral 1-methylbenzyl alcohol reaches as high as 71.5%.Temperature dependence of enantioselective hydrosilylation of acetophenone was discussed.

  18. Extensive Taguchi's Quality Loss Function Based On Asymmetric tolerances

    Institute of Scientific and Technical Information of China (English)

    ZHU Wei; LI Yuan-sheng; LIU Feng

    2004-01-01

    If specification interval is asymmetric, basic specification is the target value of quality characteristics. In this paper Taguchi's quality loss function is applied to describe quality loss based on asymmetric tolerances. The measurement of quality loss which is caused by the deviation of quality characteristics from basic specification is further presented.

  19. Asymmetric group loans, non-assortative matching and adverse selection

    NARCIS (Netherlands)

    Gangopadhyay, Shubhashis; Lensink, Robert

    2014-01-01

    This paper shows that an asymmetric group debt contract, where one borrower co-signs for another, but not vice versa, leads to heterogeneous matching. The analysis suggests that micro finance organizations can achieve the first best by offering asymmetric group contracts. (C) 2014 Elsevier B.V. All

  20. Electron localization in an asymmetric double quantum well nanostructure (II): Improvement via Fano-type interference

    Energy Technology Data Exchange (ETDEWEB)

    Hamedi, H.R., E-mail: Hamid.r.Hamedi@gmail.com

    2014-10-01

    This letter explores the one dimensional (1D) and two-dimensional (2D) position dependent probe absorption spectrum in a four-subband semiconductor quantum-well (QW) system in presence of Fano-type interference. Compared with obtained results for the maximal detecting probability of electron in Hamedi (2014. Physica B 440, 83) which was 50%, in this paper, we show that the detecting probability and precision of electron localization in one period can be significantly improved and reaches to 100% at the origin of coordinates, through proper tuning the strength of Fano-type interference. Also, the influence of other controlling parameters on the localization behavior of the QW system is discussed. The obtained results may provide some new possibilities for technological applications in laser cooling or nanolithography via high-precision and high-resolution electron localization.

  1. Electron localization in an asymmetric double quantum well nanostructure (II): Improvement via Fano-type interference

    International Nuclear Information System (INIS)

    This letter explores the one dimensional (1D) and two-dimensional (2D) position dependent probe absorption spectrum in a four-subband semiconductor quantum-well (QW) system in presence of Fano-type interference. Compared with obtained results for the maximal detecting probability of electron in Hamedi (2014. Physica B 440, 83) which was 50%, in this paper, we show that the detecting probability and precision of electron localization in one period can be significantly improved and reaches to 100% at the origin of coordinates, through proper tuning the strength of Fano-type interference. Also, the influence of other controlling parameters on the localization behavior of the QW system is discussed. The obtained results may provide some new possibilities for technological applications in laser cooling or nanolithography via high-precision and high-resolution electron localization

  2. Isospin violating dark matter being asymmetric

    CERN Document Server

    Okada, Nobuchika

    2013-01-01

    The isospin violating dark matter (IVDM) scenario offers an interesting possibility to reconcile conflicting results among direct dark matter search experiments for a mass range around 10 GeV. We consider two simple renormalizable IVDM models with a complex scalar dark matter and a Dirac fermion dark matter, respectively, whose stability is ensured by the conservation of "dark matter number". Although both models successfully work as the IVDM scenario with destructive interference between effective couplings to proton and neutron, the dark matter annihilation cross section is found to exceed the cosmological/astrophysical upper bounds. Then, we propose a simple scenario to reconcile the IVDM scenario with the cosmological/astrophysical bounds, namely, the IVDM being asymmetric. Assuming a suitable amount of dark matter asymmetry has been generated in the early Universe, the annihilation cross section beyond the cosmological/astrophysical upper bound nicely works to dramatically reduce the anti-dark matter rel...

  3. Asymmetric morphology of the propagating jet

    Science.gov (United States)

    Hardee, Philip E.; Norman, Michael L.

    1990-12-01

    Simulations of slab jets propagating in constant atmospheres are reported for a range of jet velocities and Mach numbers. At early times, the jet maintains approximate axisymmetry within a backflowing cocoon. When the jet has penetrated farther into the external medium, the symmetry is broken by sideways oscillation and the leading edge of the jet moves about within a growing lobe. The oscillation results from nonlinear resonant amplification of the initial perturbation by the Kelvin-Helmholtz instability. Finally, the jet flaps chaotically within the growing lobe. The flapping is driven by turbulent vortices in the lobe. The basic picture of Scheuer's (1982) 'dentist's drill' model of the physical processes underlying asymmetric morphologies in radio galaxies is confirmed. The fluid motions in the lobe are found to govern the location of the drill bit. The morphology is time-dependent on relatively short time scales.

  4. Asymmetric Beam Combination for Optical Interferometry

    CERN Document Server

    Monnier, J D

    2001-01-01

    Optical interferometers increasingly use single-mode fibers as spatial filters to convert varying wavefront distortion into intensity fluctuations which can be monitored for accurate calibration of fringe amplitudes. Here I propose using an asymmetric coupler to allow the photometric intensities of each telescope beam to be measured at the same time as the fringe visibility, but without the need for dedicated photometric outputs, which reduce the light throughput in the interferometric channels. In the read-noise limited case often encountered in the infrared, I show that a 53% improvement in signal-to-noise ratio for the visibility amplitude measurement is achievable, when compared to a balanced coupler setup with 50% photometric taps (e.g., the FLUOR experiment). In the Poisson-noise limit appropriate for visible light, the improvement is reduced to only ~8%. This scheme also reduces the cost and complexity of the beam combination since fewer components and detectors are required, and can be extended to mor...

  5. Asymmetric Ferromagnet-Superconductor-Ferromagnet Switch

    Energy Technology Data Exchange (ETDEWEB)

    Cadden-Zimansky, P.; Bazaliy, Ya.B.; Litvak, L.M.; Jiang, J.S.; Pearson, J.; Gu, J.Y.; You, Chun-Yeol; Beasley, M.R.; Bader, S.D.

    2011-11-04

    In layered ferromagnet-superconductor-ferromagnet F{sub 1} /S/F{sub 2} structures, the critical temperature T{sub c} of the superconductors depends on the magnetic orientation of the ferromagnetic layers F{sub 1} and F{sub 2} relative to each other. So far, the experimentally observed magnitude of change in T{sub c} for structures utilizing weak ferromagnets has been 2 orders of magnitude smaller than is expected from calculations. We theoretically show that such a discrepancy can result from the asymmetry of F/S boundaries, and we test this possibility by performing experiments on structures where F{sub 1} and F{sub 2} are independently varied. Our experimental results indicate that asymmetric boundaries are not the source of the discrepancy. If boundary asymmetry is causing the suppressed magnitude of T{sub c} changes, it may only be possible to detect in structures with thinner ferromagnetic layers.

  6. Magnetoresistive system with concentric ferromagnetic asymmetric nanorings

    Energy Technology Data Exchange (ETDEWEB)

    Avila, J. I., E-mail: javila@ulg.ac.be; Tumelero, M. A.; Pasa, A. A.; Viegas, A. D. C. [Laboratório de Filmes Finos e Superfícies (LFFS), Departamento de Física, Universidade Federal de Santa Catarina, CP 476 Florianópolis (Brazil)

    2015-03-14

    A structure consisting of two concentric asymmetric nanorings, each displaying vortex remanent states, is studied with micromagnetic calculations. By orienting in suitable directions, both the asymmetry of the rings and a uniform magnetic field, the vortices chiralities can be switched from parallel to antiparallel, obtaining in this way the analogue of the ferromagnetic and antiferromagnetic configurations found in bar magnets pairs. Conditions on the thickness of single rings to obtain vortex states, as well as formulas for their remanent magnetization are given. The concentric ring structure enables the creation of magnetoresistive systems comprising the qualities of magnetic nanorings, such as low stray fields and high stability. A possible application is as contacts in spin injection in semiconductors, and estimations obtained here of magnetoresistance change for a cylindrical spin injection based device show significant variations comparable to linear geometries.

  7. The Asymmetric Effects of Investor Sentiment

    DEFF Research Database (Denmark)

    Lutz, Chandler

    We use the returns on lottery-like stocks to construct a novel index for investor sentiment in the stock market. This new measure is closely related to previously developed sentiment indicators, but more accurately tracks speculative episodes over the sample period. Using our index, we find...... that the relationship between sentiment and returns is asymmetric: during bear markets, high sentiment predicts low future returns for the cross-section of speculative stocks and the market overall while the relationship during bull markets is weak and often insignificant. Thus, the results suggest that sophisticated...... investors only act as corrective force during certain time periods. We also show that our index predicts implied volatility, media pessimism, and mutual fund flows. Overall, our findings are consistent with both the theories and anecdotal accounts of investor sentiment in the stock market....

  8. The Asymmetric Predictive Effects of Investor Sentiment

    DEFF Research Database (Denmark)

    Lutz, Chandler

    We use the returns on lottery-like stocks to construct a novel index for investor sentiment in the stock market. This new measure is closely related to previously developed sentiment indicators, but more accurately tracks speculative episodes over the sample period. Using our index, we find...... that the relationship between sentiment and returns is asymmetric: during bear markets, high sentiment predicts low future returns for the cross-section of speculative stocks and the market overall while the relationship during bull markets is weak and often insignicant. Thus, the results suggest that sophisticated...... investors only act as corrective force during certain time periods. We also show that our index predicts implied volatility, media pessimism, and mutual fund flows. Overall, our findings are consistent with both the theories and anecdotal accounts of investor sentiment in the stock market....

  9. Asymmetric correlations on the Croatian equity market

    Directory of Open Access Journals (Sweden)

    Davor Kunovac

    2011-03-01

    Full Text Available This paper compares the equity market in Croatia in bad (bear or turbulent and good (bull, calm market conditions. The two market regimes are formally identifi ed under the Markov Regime Switching (MRS framework. The analysis conducted suggests that correlations between equity prices are more than twice as high during bear than in bull markets. This result holds both for the shares included in the CROBEX and for the relationship among various European equity indices.In the context of international diversifi cation the result suggests only a limited benefi t that foreign investors can count on when diversifying their portfolios by expanding to developing European markets. In addition, by evaluating a portfolio optimization model that takes asymmetric correlations into account in an out-of-sample exercise, this paper also illustrates the losses that may occur if the asymmetry is ignored in practice.

  10. Distributed Function Computation in Asymmetric Communication Scenarios

    CERN Document Server

    Agnihotri, Samar

    2009-01-01

    We consider the distributed function computation problem in asymmetric communication scenarios, where the sink computes some deterministic function of the data split among N correlated informants. The distributed function computation problem is addressed as a generalization of distributed source coding (DSC) problem. We are mainly interested in minimizing the number of informant bits required, in the worst-case, to allow the sink to exactly compute the function. We provide a constructive solution for this in terms of an interactive communication protocol and prove its optimality. The proposed protocol also allows us to compute the worst-case achievable rate-region for the computation of any function. We define two classes of functions: lossy and lossless. We show that, in general, the lossy functions can be computed at the sink with fewer number of informant bits than the DSC problem, while computation of the lossless functions requires as many informant bits as the DSC problem.

  11. Micropolarity Ramification of Asymmetric Merging Flow

    CERN Document Server

    Siddiqui, Abuzar Abid

    2016-01-01

    The steady, asymmetric and two-dimensional flow of viscous, incompressible micropolar fluid through a rectangular channel with a splitter (parallel to walls) was formulated and simulated numerically. The plane Poiseuille flow was considered far from upstream and downstream of the splitter. The geometric parameter that controls the position of splitter was defined as splitter position parameter. A numerical scheme that comprises a fourth order method followed by special finite-difference method was used to solve the boundary value problem. This numerical scheme transforms the governing equations to system of finite difference equations which we have solved by SOR iterative method. Moreover, the results obtained were further refined and upgraded by the Richardson extrapolation method. The results were compared on different grid sizes as well as with the existing results for symmetric flow of Newtonian fluids. The comparisons were satisfactory. The microrotation effects on the splitter plate were significantly h...

  12. Asymmetric pneumatization of the petrous apex.

    Science.gov (United States)

    Roland, P S; Meyerhoff, W L; Judge, L O; Mickey, B E

    1990-07-01

    Three patients with high-intensity MR signals from one petrous apex, but nonpathologic fine-cut computed tomography are reported. In two of the three patients, normal bone marrow within the petrous apex on one side is believed to have generated the high-intensity signal. In one of the three patients, the etiology of the MR image remains obscure, but may represent the earliest stages of petrous cholesterol granuloma or mucocele. We have reviewed 500 head CT scans performed for non-otologic reasons, in an attempt to establish the frequency of this finding. The literature on MR and CT imaging of the petrous apex and asymmetric pneumatization of the petrous apex is reviewed. PMID:2117735

  13. Asymmetric exclusion processes with shuffled dynamics

    International Nuclear Information System (INIS)

    The asymmetric simple exclusion process (ASEP) with periodic boundary conditions is investigated for shuffled dynamics. In this type of update, in each discrete timestep the particles are updated in a random sequence. Such an update is important for several applications, e.g., for certain models of pedestrian flow in two dimensions. For the ASEP with shuffled dynamics and a related truncated process exact results are obtained for deterministic motion (p = 1). Since the shuffled dynamics is intrinsically stochastic, also this case is nontrivial. For the case of stochastic motion (0 < p < 1) it is shown that, in contrast to all other updates studied previously, the ASEP with shuffled update does not have a product measure steady state. Approximative formulae for the steady-state distribution and fundamental diagram are derived that are in very good agreement with simulation data

  14. Chilly Dark Sectors and Asymmetric Reheating

    CERN Document Server

    Adshead, Peter; Shelton, Jessie

    2016-01-01

    In a broad class of theories, the relic abundance of dark matter is determined by interactions internal to a thermalized dark sector, with no direct involvement of the Standard Model (SM). We point out that these theories raise an immediate cosmological question: how was the dark sector initially populated in the early universe? Motivated in part by the difficulty of accommodating large amounts of entropy carried in dark radiation with cosmic microwave background measurements of the effective number of relativistic species at recombination, $N_{\\mathrm{eff}}$, we aim to establish which admissible cosmological histories can populate a thermal dark sector that never reaches thermal equilibrium with the SM. The minimal cosmological origin for such a dark sector is asymmetric reheating, when the same mechanism that populates the SM in the early universe also populates the dark sector at a lower temperature. Here we demonstrate that the resulting inevitable inflaton-mediated scattering between the dark sector and ...

  15. Asymmetric EPR entanglement in continuous variable systems

    CERN Document Server

    Wagner, Katherine; Armstrong, Seiji; Morizur, Jean-Francois; Lam, Ping Koy; Bachor, Hans-Albert

    2012-01-01

    Continuous variable entanglement can be produced in nonlinear systems or via interference of squeezed states. In many of optical systems, such as parametric down conversion or interference of optical squeezed states, production of two perfectly symmetric subsystems is usually used for demonstrating the existence of entanglement. This symmetry simplifies the description of the concept of entanglement. However, asymmetry in entanglement may arise naturally in a real experiment, or be intentionally introduced in a given quantum information protocol. These asymmetries can emerge from having the output beams experience different losses and environmental contamination, or from the availability of non-identical input quantum states in quantum communication protocols. In this paper, we present a visualisation of entanglement using quadrature amplitude plots of the twin beams. We quantitatively discuss the strength of asymmetric entanglement using EPR and inseparability criteria and theoretically show that the optimal...

  16. Evolution of Fano resonance based on symmetric/asymmetric plasmonic waveguide system and its application in nanosensor

    Science.gov (United States)

    Zhang, Yunyun; Li, Shilei; Zhang, Xinyuan; Chen, Yuanyuan; Wang, Lulu; Zhang, Yong; Yu, Li

    2016-07-01

    We proposed a plasmonic nanosensor based on Fano resonance in the symmetric and asymmetric plasmonic waveguide system, which comprises with a rectangular cavity and two slot cavities with the metal-dielectric-metal waveguide. Simulation results show that by symmetric/asymmetry rectangular cavity and regulating the rectangular cavity coupling with slot cavities, different waveguide modes can be excited. Due to the interaction of the waveguide mode, the transmission spectra possess single, double or multiple sharp asymmetrical profiles. Because of the different origins, these Fano resonances exhibit different dependence on the parameters of the structure and can be easily tuned. These characteristics offer flexibility to design the device. This nanosensor yields a sensitivity of ∼800 nm/RIU and a figure of merit of about ∼1.35×104, which can find widely applications in the plasmonic nano-sensing area.

  17. Dual doubled geometry

    NARCIS (Netherlands)

    Bergshoeff, Eric A.; Riccioni, Fabio; Alvarez-Gaumé, L.

    2011-01-01

    We probe doubled geometry with dual fundamental branes. i.e. solitons. Restricting ourselves first to solitonic branes with more than two transverse directions we find that the doubled geometry requires an effective wrapping rule for the solitonic branes which is dual to the wrapping rule for fundam

  18. 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.

  19. 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.

  20. 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.

  1. A Cladistic Analysis of Phenotypic Associations with Haplotypes Inferred from Restriction Endonuclease Mapping and DNA Sequence Data. III. Cladogram Estimation

    Science.gov (United States)

    Templeton, A. R.; Crandall, K. A.; Sing, C. F.

    1992-01-01

    We previously developed a cladistic approach to identify subsets of haplotypes defined by restriction endonuclease mapping or DNA sequencing that are associated with significant phenotypic deviations. Our approach was limited to segments of DNA in which little recombination occurs. In such cases, a cladogram can be constructed from the restriction site or sequence data that represents the evolutionary steps that interrelate the observed haplotypes. The cladogram is used to define a nested statistical design to identify mutational steps associated with significant phenotypic deviations. The central assumption behind this strategy is that any undetected mutation causing a phenotypic effect is embedded within the same evolutionary history that is represented by the cladogram. The power of this approach depends upon the confidence one has in the particular cladogram used to draw inferences. In this paper, we present a strategy for estimating the set of cladograms that are consistent with a particular sample of either restriction site or nucleotide sequence data and that includes the possibility of recombination. We first evaluate the limits of parsimony in constructing cladograms. Once these limits have been determined, we construct the set of parsimonious and nonparsimonious cladograms that is consistent with these limits. Our estimation procedure also identifies haplotypes that are candidates for being products of recombination. If recombination is extensive, our algorithm subdivides the DNA region into two or more subsections, each having little or no internal recombination. We apply this estimation procedure to three data sets to illustrate varying degrees of cladogram ambiguity and recombination. PMID:1385266

  2. NMR study of Ni2+ binding to the H-N-H endonuclease domain of colicin E9.

    Science.gov (United States)

    Hannan, J. P.; Whittaker, S. B.; Davy, S. L.; Kühlmann, U. C.; Pommer, A. J.; Hemmings, A. M.; James, R.; Kleanthous, C.; Moore, G. R.

    1999-01-01

    Ni2+ affinity columns are widely used for protein purification, but they carry the risk that Ni2+ ions may bind to the protein, either adventitiously or at a physiologically important site. Dialysis against ethylenediaminetetraacetic acid (EDTA) is normally used to remove metal ions bound adventitiously to proteins; however, this approach does not always work. Here we report that a bacterial endonuclease, the DNase domain of colicin E9, binds Ni2+ acquired from Ni2+ affinity columns, and appears to bind [Ni(EDTA)(H2O)n]2- at low ionic strength. NMR was used to detect the presence of both Ni2+ coordinated to amino acid side chains and [Ni(EDTA)(H2O)N]2-. Dialysis against > or =0.2 M NaCl was required to remove the [Ni(EDTA)(H2O)n]2-. The NMR procedure we have used to characterize the presence of Ni2+ and [Ni(EDTA)(H2O)n]2- should be applicable to other proteins where there is the possibility of binding paramagnetic metal ions that are present to expedite protein purification. In the present case, the binding of Ni2+ seems likely to be physiologically relevant, and the NMR data complement recent X-ray crystallographic evidence concerning the number of histidine ligands to bound Ni2+. PMID:10452617

  3. 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.

  4. 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.

  5. 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

  6. The Uve1 endonuclease is regulated by the white collar complex to protect cryptococcus neoformans from UV damage.

    Directory of Open Access Journals (Sweden)

    Surbhi Verma

    Full Text Available The pathogenic fungus Cryptococcus neoformans uses the Bwc1-Bwc2 photoreceptor complex to regulate mating in response to light, virulence and ultraviolet radiation tolerance. How the complex controls these functions is unclear. Here, we identify and characterize a gene in Cryptococcus, UVE1, whose mutation leads to a UV hypersensitive phenotype. The homologous gene in fission yeast Schizosaccharomyces pombe encodes an apurinic/apyrimidinic endonuclease acting in the UVDE-dependent excision repair (UVER pathway. C. neoformans UVE1 complements a S. pombe uvde knockout strain. UVE1 is photoregulated in a Bwc1-dependent manner in Cryptococcus, and in Neurospora crassa and Phycomyces blakesleeanus that are species that represent two other major lineages in the fungi. Overexpression of UVE1 in bwc1 mutants rescues their UV sensitivity phenotype and gel mobility shift experiments show binding of Bwc2 to the UVE1 promoter, indicating that UVE1 is a direct downstream target for the Bwc1-Bwc2 complex. Uve1-GFP fusions localize to the mitochondria. Repair of UV-induced damage to the mitochondria is delayed in the uve1 mutant strain. Thus, in C. neoformans UVE1 is a key gene regulated in response to light that is responsible for tolerance to UV stress for protection of the mitochondrial genome.

  7. 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

  8. The importance of the N-terminus of T7 endonuclease I in the interaction with DNA junctions.

    Science.gov (United States)

    Freeman, Alasdair D J; Déclais, Anne-Cécile; Lilley, David M J

    2013-01-23

    T7 endonuclease I is a dimeric nuclease that is selective for four-way DNA junctions. Previous crystallographic studies have found that the N-terminal 16 amino acids are not visible, neither in the presence nor in the absence of DNA. We have now investigated the effect of deleting the N-terminus completely or partially. N-terminal deleted enzyme binds more tightly to DNA junctions but cleaves them more slowly. While deletion of the N-terminus does not measurably affect the global structure of the complex, the presence of the peptide is required to generate a local opening at the center of the DNA junction that is observed by 2-aminopurine fluorescence. Complete deletion of the peptide leads to a cleavage rate that is 3 orders of magnitude slower and an activation enthalpy that is 3-fold higher, suggesting that the most important interaction of the peptide is with the reaction transition state. Taken together, these data point to an important role of the N-terminus in generating a central opening of the junction that is required for the cleavage reaction to proceed properly. In the absence of this, we find that a cruciform junction is no longer subject to bilateral cleavage, but instead, just one strand is cleaved. Thus, the N-terminus is required for a productive resolution of the junction.

  9. 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

  10. [Apoptotic endonuclease EndoG induces alternative splicing of telomerase catalytic subunit hTERT and death of tumor cells].

    Science.gov (United States)

    Zhdanov, D D; Vasina, D A; Orlova, V S; Gotovtseva, V Y; Bibikova, M V; Pokrovsky, V S; Pokrovskaya, M V; Aleksandrova, S S; Sokolov, N N

    2016-03-01

    Telomerase activity is known to be regulated by alternative splicing of its catalytic subunit hTERT (human Telomerase Reverse Transcriptase) mRNA. Induction of non-active spliced hTERT leads to inhibition of telomerase activity. However, very little is known about the mechanism of hTERT mRNA alternative splicing. The aim of this study was to determine the role of apoptotic endonuclease EndoG in alternative splicing of hTERT and telomerase activity. Strong correlation was found between expression of EndoG and hTERT splice-variants in 12 colon cancer cell lines. Overexpression of EndoG in СаСо-2 cells downregulated the expression of active full-length hTERT variant and upregulated non-active spliced variant. Reduction of full-length hTERT caused downregulation of telomerase activity, dramatically shortening of telomeres length during cell divisions, converting cells to the replicative senescence state, activation of apoptosis and finally cell death. These data indicated the participation of EndoG in alternative splicing of mRNA of telomerase catalytic subunit, regulation of telomerase activity and cell fate. PMID:27420614

  11. 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)

  12. 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

  13. Asymmetric effects of monetary policy in Brazil

    Directory of Open Access Journals (Sweden)

    Edilean Kleber da Silva Bejarano Aragón

    2009-06-01

    Full Text Available In this paper, we check whether the effects of monetary policy actions on output in Brazil are asymmetric. Therefore, we estimate Markov-switching models that allow positive and negative shocks to affect the growth rate of output in an asymmetric fashion in expansion and recession states. In general, results show that: i the real effects of negative monetary shocks are larger than those of positive shocks in an expansion; ii in a recession, the real effects of positive and negative shocks are the same; iii there is no evidence of asymmetry between the effects of countercyclical monetary policies; and iv it is not possible to assert that the effects of a positive (or negative shock are dependent upon the phase of the business cycle.Neste trabalho, examinamos se os efeitos das ações de política monetária sobre o produto são assimétricos no Brasil. Para isto, estimamos modelos Markov-switching que permitem que choques positivos e negativos afetem a taxa de crescimento do produto de forma assimétrica nos estados de expansão e recessão econômica. Em geral, os resultados mostram que: i os efeitos reais de choques monetários negativos são maiores do que os de choques positivos em uma expansão; ii em uma recessão, os efeitos reais de choques positivos e negativos são iguais; iii não há evidência de assimetria entre os efeitos de políticas monetárias contracíclicas; iv não se pode afirmar que os efeitos de choques positivos (ou negativos dependem da fase do ciclo econômico.

  14. Asymmetric facial skin viscoelasticity during climacteric aging

    Directory of Open Access Journals (Sweden)

    Piérard GE

    2014-04-01

    Full Text Available Gérald E Piérard,1 Trinh Hermanns-Lê,1 Ulysse Gaspard,2 Claudine Piérard-Franchimont11Laboratory of Skin Bioengineering and Imaging, Department of Clinical Sciences, University of Liège, 2Department of Gynecology and Obstetrics, University Hospital of Liège, Liège, BelgiumBackground: Climacteric skin aging affects certain biophysical characteristics of facial skin. The purpose of the present study was to assess the symmetric involvement of the cheeks in this stage of the aging process.Methods: Skin viscoelasticity was compared on both cheeks in premenopausal and post-menopausal women with indoor occupational activities somewhat limiting the influence of chronic sun exposure. Eighty-four healthy women comprising 36 premenopausal women and 48 early post-menopausal women off hormone replacement therapy were enrolled in two groups. The tensile characteristics of both cheeks were tested and compared in each group. A computerized suction device equipped with a 2 mm diameter hollow probe was used to derive viscoelasticity parameters during a five-cycle procedure of 2 seconds each. Skin unfolding, intrinsic distensibility, biological elasticity, and creep extension were measured.Results: Both biological elasticity and creep extension were asymmetric on the cheeks of the post-menopausal women. In contrast, these differences were more discrete in the premenopausal women.Conclusion: Facial skin viscoelasticity appeared to be asymmetric following menopause. The possibility of asymmetry should be taken into account in future studies of the effects of hormone replacement therapy and any antiaging procedure on the face in menopausal women.Keywords: climacteric aging, biomechanics, photoaging, skin unfolding, biological elasticity, skin tensile properties

  15. Algebraic Davis Decomposition and Asymmetric Doob Inequalities

    Science.gov (United States)

    Hong, Guixiang; Junge, Marius; Parcet, Javier

    2016-09-01

    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 < p < 2} and {x in L_p({M},τ)} one can find {a, b in L_p({M},τ)} and contractions {u_n, v_n in {M}} such that {E}_n(x) = a u_n + v_n b quad and quad max big{ |a|_p,|b|_p big} ≤ c_p |x|_p. Moreover, it turns out that {a u_n} and {v_n b} converge in the row/column Hardy spaces {{H}_p^r({M})} and {{H}_p^c({M})} respectively. In particular, this solves a problem posed by the Defant and Junge in 2004. In the case p = 1, our results establish a noncommutative form of the Davis celebrated theorem on the relation betwe en martingale maximal and square functions in L 1, whose noncommutative form has remained open for quite some time. Given {1 ≤ p ≤ 2}, we also provide new weak type maximal estimates, which imply in turn left/right almost uniform convergence of {{E}_n(x)} in row/column Hardy spaces. This improves the bilateral convergence known so far. Our approach is based on new forms of Davis martingale decomposition which are of independent interest, and an algebraic atomic description for the involved Hardy spaces. The latter results are new even for commutative von Neumann algebras.

  16. The evolution of cooperation in asymmetric systems

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Explaining the "Tragedy of the Commons" of the evolution of cooperation remains one of the greatest problems for both biology and social science.Asymmetrical interaction,which is one of the most important characteristics of cooperative systems,has not been sufficiently considered in the existing models of the evolution of cooperation.Considering the inequality in the number and payoff between the cooperative actors and recipients in cooperation systems,discriminative density-dependent interference competition will occur in limited dispersal systems.Our model and simulation show that the local but not the global stability of a cooperative interaction can be maintained if the utilization of common resource remains unsaturated,which can be achieved by density-dependent restraint or competition among the cooperative actors.More intense density dependent interference competition among the cooperative actors and the ready availability of the common resource,with a higher intrinsic contribution ratio of a cooperative actor to the recipient,will increase the probability of cooperation.The cooperation between the recipient and the cooperative actors can be transformed into conflict and,it oscillates chaotically with variations of the affecting factors under different environmental or ecological conditions.The higher initial relatedness(i.e.similar to kin or reciprocity relatedness),which is equivalent to intrinsic contribution ratio of a cooperative actor to the recipient,can be selected for by penalizing less cooperative or cheating actors but rewarding cooperative individuals in asymmetric systems.The initial relatedness is a pivot but not the aim of evolution of cooperation.This explains well the direct conflict observed in almost all cooperative systems.

  17. PEP-II: An asymmetric B factory

    International Nuclear Information System (INIS)

    In this report, the authors have described an updated conceptual design for the high-luminosity Asymmetric B Factory (PEP-II) to be built in the PEP tunnel culmination of more than four years of effort aimed at the design and construction of an asymmetric e+e- collider capable of achieving a luminosity of L = 3 x 1033 cm-2 s-1. All aspects of the conceptual design were scrutinized in March 1991 by a DOE technical review committee chaired by Dr. L. Edward Temple. The design was deemed feasible and capable of achieving its physics goals. Furthermore, the cost estimate, schedule, and management plan for the project were fully endorsed by the committee. This updated conceptual design report captures the technical progress since the March 1991 review and reflects the lower cost estimate corresponding to the improved design. Although the PEP-II design has continued to evolve, no technical scope changes have been made that invalidate the conclusion of the DOE review. The configuration adopted utilizes two storage rings, an electron ring operating at 9 GeV and a positron ring at 3.1 GeV, each with a circumference of 2200 m. The high-energy ring is an upgrade of the PEP storage ring at SLAC; all PEP magnets and most power supplies will be reused. The upgrade consists primarily of replacing the PEP vacuum chamber and RF system with newly designed versions optimized for the high-current environment of PEP-II. The low-energy ring will be newly constructed and will be situated atop the high-energy ring in the PEP tunnel. Utilities already installed in the PEP tunnel are largely sufficient to operate the two PEP-II storage rings

  18. Improvement of the beam quality of a broad-area diode laser using double feedback from two external mirrors

    DEFF Research Database (Denmark)

    Chi, M.; Bøgh, A.-S.; Thestrup, B.;

    2004-01-01

    In this letter, a symmetric double-feedback configuration, to improve the beam quality of broad-area diode lasers is demonstrated. With this configuration, a symmetric double-lobed far field can be obtained, and this configuration leads to good beam quality. The beam quality factor M-2 of a diode...... laser with the emitting area 1 mumx200 mum is improved by using both the asymmetric single feedback and the symmetric double feedback. M-2 values of 4.3 for the asymmetric single-feedback laser system and 3.3 for the symmetric double-feedback laser system are obtained, whereas the M-2 value...... of the freely running laser is 42. The far and the near fields are also measured and compared for the three conditions. (C) 2004 American Institute of Physics....

  19. Special Issue of "Asymmetric Synthesis"%Special Issue of "Asymmetric Synthesis"

    Institute of Scientific and Technical Information of China (English)

    2012-01-01

    Organic chemistry exploring the world at a molecu- lar level remains essential for our society in the 21st century. Asymmetric synthesis, particularly those em- ploying catalytic approach, is one of the most important research fields in organic synthesis providing chiral compounds in an enantiopure form. The latter is critical since the two enantiomers of one chiral compound, in many cases, have a different response in biological sys- tems. The huge markets of non-racemic chiral com- pounds as synthetic intermediates, pharmaceuticals,

  20. 位点特异性DNA内切酶在植物基因打靶中的应用%The application of site-specific DNA endonucleases in plant gene targeting

    Institute of Scientific and Technical Information of China (English)

    程强; 胥猛; 黄敏仁

    2012-01-01

    Gene targeting is a powerful tool for site-specific insertion, deletion and replacement of DNA in genome. Gene targeting technology in plants is far from routine due to the low frequency of homologous recombination that limits the study of gene function and molecular breeding. Recently, breakthrough has been made in the engineered DNA binding domains combined with zinc finger protein and transcription activator-like effector. Engineered DNA binding domain fusing endonucleases can specifically breaks the DNA double-strand, then generate site-directed mutagenesis and facilitate homologous recombination. In this review, we focus on the application of zinc finger nuclease and TAL effector nu-clease in site-directed mutagenesis and gene targeting of plant genome and analyze their existing problems.%基因打靶是在基因组指定位点插入、删除和替换DNA序列的技术.由于同源重组频率低,在植物中高效的基因打靶技术一直未被建立,制约了植物基因功能和分子育种的研究.近年来,人工设计的锌指蛋白和TAL效应因子DNA结合结构域实现了对全新DNA序列的识别.人工设计的DNA结合结构域连接核酸内切酶能在基因组指定位点创造双链DNA断裂,进而产生定点突变和促进同源重组.笔者重点介绍锌指核酸酶和TAL效应因子核酸酶在植物基因组定点突变和基因打靶中的研究进展,并对目前存在的问题进行分析.