WorldWideScience

Sample records for asymmetrical endonuclease double

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

    Science.gov (United States)

    Kurian, P; Dunston, G; Lindesay, J

    2016-02-21

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

  2. Regulated restriction endonuclease expression: A novel, radiomimetic model of DNA double strand break induction

    Energy Technology Data Exchange (ETDEWEB)

    Radany, E.H.; Pu, A.T. [Univ. of Michigan School of Medicine, Ann Arbor, MI (United States)

    1997-10-01

    Exposure of mammalian cells to ionizing radiations (IR) produces a plethora of damages in DNA and non-DNA targets. Although DNA double strand breaks (DSB) are thought to be the critical lesion generated by IR with respect to conventional cytotoxicity, it is clear that signaling events regulating cellular responses to IR arise from multiple other lesions in addition to these. The authors are interested in identifying cellular signaling events that derive from DSB specifically, as well as the distal effects (e.g., repair, apoptosis, cell cycle delay) of such signaling. Although electroporation of restriction enzymes might afford an approach to such studies, serious concerns would be raised by the non-uniformity of enzyme transfer and general disruption of the intracellular environment (with the possibility of associated signaling processes) when using this method. The authors have established a radiomimetic model for DSB induction, based upon expression of a hybrid steroid hormone receptor: this system is subject to tight, rapid postranslational regulation of endonuclease activity via addition or withdrawl of the cognate hormone ligand. In preliminary experiments, The authors have demonstrated ligand dose and exposure time-dependent cytotoxicity and DSB induction (the latter assayed by PFGE). Cytogenetic characterization of this system, as well as studies of the interaction between enzyme- and IR-generated DSB are in progress. RNA differential display and subtractive enrichment cloning approaches will ultimately be used to identify genes whose expression changes as a consequence of isolated DSB induction.

  3. ERCC1-XPF endonuclease facilitates DNA double-strand break repair.

    Science.gov (United States)

    Ahmad, Anwaar; Robinson, Andria Rasile; Duensing, Anette; van Drunen, Ellen; Beverloo, H Berna; Weisberg, David B; Hasty, Paul; Hoeijmakers, Jan H J; Niedernhofer, Laura J

    2008-08-01

    ERCC1-XPF endonuclease is required for nucleotide excision repair (NER) of helix-distorting DNA lesions. However, mutations in ERCC1 or XPF in humans or mice cause a more severe phenotype than absence of NER, prompting a search for novel repair activities of the nuclease. In Saccharomyces cerevisiae, orthologs of ERCC1-XPF (Rad10-Rad1) participate in the repair of double-strand breaks (DSBs). Rad10-Rad1 contributes to two error-prone DSB repair pathways: microhomology-mediated end joining (a Ku86-independent mechanism) and single-strand annealing. To determine if ERCC1-XPF participates in DSB repair in mammals, mutant cells and mice were screened for sensitivity to gamma irradiation. ERCC1-XPF-deficient fibroblasts were hypersensitive to gamma irradiation, and gammaH2AX foci, a marker of DSBs, persisted in irradiated mutant cells, consistent with a defect in DSB repair. Mutant mice were also hypersensitive to irradiation, establishing an essential role for ERCC1-XPF in protecting against DSBs in vivo. Mice defective in both ERCC1-XPF and Ku86 were not viable. However, Ercc1(-/-) Ku86(-/-) fibroblasts were hypersensitive to gamma irradiation compared to single mutants and accumulated significantly greater chromosomal aberrations. Finally, in vitro repair of DSBs with 3' overhangs led to large deletions in the absence of ERCC1-XPF. These data support the conclusion that, as in yeast, ERCC1-XPF facilitates DSB repair via an end-joining mechanism that is Ku86 independent.

  4. Synthetic lethal targeting of DNA double strand break repair deficient cells by human apurinic/apyrimidinic endonuclease (APE1) inhibitors

    OpenAIRE

    Sultana, Rebeka; McNeill, Daniel R.; Abbotts, Rachel; Mohammed, Mohammed Z.; Zdzienicka, Małgorzata Z.; Qutob, Haitham; Seedhouse, Claire; Charles A. Laughton; Fischer, Peter M.; Patel, Poulam M.; Wilson, David M.; Madhusudan, Srinivasan

    2012-01-01

    An apurinic/apyrimidinic (AP) site is an obligatory cytotoxic intermediate in DNA Base Excision Repair (BER) that is processed by human AP endonuclease 1 (APE1). APE1 is essential for BER and an emerging drug target in cancer. We have isolated novel small molecule inhibitors of APE1. In the current study we have investigated the ability of APE1 inhibitors to induce synthetic lethality in a panel of DNA double strand break (DSB) repair deficient and proficient cells; a) Chine...

  5. The structure-specific endonuclease Mus81 contributes to replication restart by generating double-strand DNA breaks.

    Science.gov (United States)

    Hanada, Katsuhiro; Budzowska, Magda; Davies, Sally L; van Drunen, Ellen; Onizawa, Hideo; Beverloo, H Berna; Maas, Alex; Essers, Jeroen; Hickson, Ian D; Kanaar, Roland

    2007-11-01

    Faithful duplication of the genome requires structure-specific endonucleases such as the RuvABC complex in Escherichia coli. These enzymes help to resolve problems at replication forks that have been disrupted by DNA damage in the template. Much less is known about the identities of these enzymes in mammalian cells. Mus81 is the catalytic component of a eukaryotic structure-specific endonuclease that preferentially cleaves branched DNA substrates reminiscent of replication and recombination intermediates. Here we explore the mechanisms by which Mus81 maintains chromosomal stability. We found that Mus81 is involved in the formation of double-strand DNA breaks in response to the inhibition of replication. Moreover, in the absence of chromosome processing by Mus81, recovery of stalled DNA replication forks is attenuated and chromosomal aberrations arise. We suggest that Mus81 suppresses chromosomal instability by converting potentially detrimental replication-associated DNA structures into intermediates that are more amenable to DNA repair.

  6. ERCC1-XPF Endonuclease Facilitates DNA Double-Strand Break Repair▿ †

    Science.gov (United States)

    Ahmad, Anwaar; Robinson, Andria Rasile; Duensing, Anette; van Drunen, Ellen; Beverloo, H. Berna; Weisberg, David B.; Hasty, Paul; Hoeijmakers, Jan H. J.; Niedernhofer, Laura J.

    2008-01-01

    ERCC1-XPF endonuclease is required for nucleotide excision repair (NER) of helix-distorting DNA lesions. However, mutations in ERCC1 or XPF in humans or mice cause a more severe phenotype than absence of NER, prompting a search for novel repair activities of the nuclease. In Saccharomyces cerevisiae, orthologs of ERCC1-XPF (Rad10-Rad1) participate in the repair of double-strand breaks (DSBs). Rad10-Rad1 contributes to two error-prone DSB repair pathways: microhomology-mediated end joining (a Ku86-independent mechanism) and single-strand annealing. To determine if ERCC1-XPF participates in DSB repair in mammals, mutant cells and mice were screened for sensitivity to gamma irradiation. ERCC1-XPF-deficient fibroblasts were hypersensitive to gamma irradiation, and γH2AX foci, a marker of DSBs, persisted in irradiated mutant cells, consistent with a defect in DSB repair. Mutant mice were also hypersensitive to irradiation, establishing an essential role for ERCC1-XPF in protecting against DSBs in vivo. Mice defective in both ERCC1-XPF and Ku86 were not viable. However, Ercc1−/− Ku86−/− fibroblasts were hypersensitive to gamma irradiation compared to single mutants and accumulated significantly greater chromosomal aberrations. Finally, in vitro repair of DSBs with 3′ overhangs led to large deletions in the absence of ERCC1-XPF. These data support the conclusion that, as in yeast, ERCC1-XPF facilitates DSB repair via an end-joining mechanism that is Ku86 independent. PMID:18541667

  7. Bound states in a hyperbolic asymmetric double-well

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-01-15

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

  8. ERCC1-XPF endonuclease facilitates DNA double-strand break repair

    NARCIS (Netherlands)

    R.A. Ahmad (Riris); A.R. Robinson (Andria Rasile); A. Duensing (Anette); E. van Drunen (Ellen); H.B. Beverloo (Berna); D.B. Weisberg (David); P. Hasty (Paul); J.H.J. Hoeijmakers (Jan); L.J. Niedernhofer (Laura)

    2008-01-01

    textabstractERCC1-XPF endonuclease is required for nucleotide excision repair (NER) of helix-distorting DNA lesions. However, mutations in ERCC1 or XPF in humans or mice cause a more severe phenotype than absence of NER, prompting a search for novel repair activities of the nuclease. In Saccharomyce

  9. Transmission of asymmetric coupling double-ring resonator

    Science.gov (United States)

    Zhao, C. Y.; Tan, W. H.

    2015-02-01

    Based on the asymmetry between waveguide and double ring, the transmission and phase characteristics of coupled double-ring resonators are analyzed systemically. It is shown that the initial detuning determines the shape of transmission spectrum. The transmission spectrum of all-optical analog to electromagnetic inducted transparency (EIT) is controlled by tuning the asymmetric coupled parameter and loss. With the increasing of asymmetric coupled parameter, the transmission spectrum changes from EIT-like profile to Lorenz profile. The EIT-like transmission spectrum results from the interference between two Lorenz profiles. With the increasing of the loss, the transmission spectrum full frequency width at half-maximum broadens and its peak declines. The detuning and loss also make significant influences on the phase profile.

  10. J0316+4328: a Probable "Asymmetric Double" Lens

    CERN Document Server

    Boyce, E R; Browne, I W A; Stroman, W J; Jackson, N J

    2007-01-01

    We report a probable gravitational lens J0316+4328, one of 19 candidate asymmetric double lenses (2 images at a high flux density ratio) from CLASS. Observations with the Very Large Array (VLA), MERLIN and the Very Long Baseline Array (VLBA) imply that J0316+4328 is a lens with high confidence. It has 2 images separated by 0.40", with 6 GHz flux densities of 62 mJy and 3.2 mJy. The flux density ratio of ~19 (constant over the frequency range 6-22 GHz) is the largest for any 2 image gravitational lens. High resolution optical imaging and deeper VLBI maps should confirm the lensing interpretation and provide inputs to detailed lens models. The unique configuration will give strong constraints on the lens galaxy's mass profile.

  11. 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.

  12. Synthetic lethal targeting of DNA double strand break repair deficient cells by human apurinic/apyrimidinic endonuclease (APE1) inhibitors

    Science.gov (United States)

    Sultana, Rebeka; McNeill, Daniel R.; Abbotts, Rachel; Mohammed, Mohammed Z.; Zdzienicka, Małgorzata Z.; Qutob, Haitham; Seedhouse, Claire; Laughton, Charles A.; Fischer, Peter M.; Patel, Poulam M.; Wilson, David M.; Madhusudan, Srinivasan

    2013-01-01

    An apurinic/apyrimidinic (AP) site is an obligatory cytotoxic intermediate in DNA Base Excision Repair (BER) that is processed by human AP endonuclease 1 (APE1). APE1 is essential for BER and an emerging drug target in cancer. We have isolated novel small molecule inhibitors of APE1. In the current study we have investigated the ability of APE1 inhibitors to induce synthetic lethality in a panel of DNA double strand break (DSB) repair deficient and proficient cells; a) Chinese hamster (CH) cells: BRCA2 deficient (V-C8), ATM deficient (V-E5), wild type (V79) and BRCA2 revertant (V-C8(Rev1)). b) Human cancer cells: BRCA1 deficient (MDA-MB-436), BRCA1 proficient (MCF-7), BRCA2 deficient (CAPAN-1 and HeLa SilenciX cells), BRCA2 proficient (PANC1 and control SilenciX cells). We also tested synthetic lethality (SL) in CH ovary cells expressing a dominant–negative form of APE1 (E8 cells) using ATM inhibitors and DNA-PKcs inhibitors (DSB inhibitors). APE1 inhibitors are synthetically lethal in BRCA and ATM deficient cells. APE1 inhibition resulted in accumulation of DNA DSBs and G2/M cell cycle arrest. Synthetic lethality was also demonstrated in CH cells expressing a dominant–negative form of APE1 treated with ATM or DNA-PKcs inhibitors. We conclude that APE1 is a promising synthetic lethality target in cancer. PMID:22377908

  13. Structures of an asymmetrically coupled double-well superlattice by double-crystal X-ray diffraction

    Institute of Scientific and Technical Information of China (English)

    马文全; 庄岩; 王玉田; 江德生

    1997-01-01

    An asymmetrically coupled ( GaAs/AlAs/GaAs/AlAs)/GaAs(001) double-well supperlattice isstudied by HRDCD (high resolution double-crystal X-ray diffractometry).The intensity of satellite peaks is modulated by wave packet of different sublayers.In the course of simulation,the satellite peaks in the vicinity of the node points of wave packet are very informative for precise determination of sublayer thickness and for improving accuracy.

  14. Asymmetric double split-ring metamaterials absorber in the terahertz region

    Science.gov (United States)

    Jun, He; Li, Qingmei; Shen, Jingling

    2012-12-01

    We present the simulation of an asymmetric double split-ring metamaterials absorber in terahertz region. The device consists of a metal/dielectric-spacer/metal structure allowing us select absorption by varying the asymmetric characteristics. When the two gaps are gradually away from the center in opposite direction, a giant amplitude modulation is observed at the fundamental inductive-capacitive (LC) resonance and the resonant frequencies are observed to red shifting. Besides, increasing the thickness of dielectric-spacer, the peak absorption can be changed. This theoretical simulation will be good reference for the follow experiments, and these asymmetric metamaterials absorbers is expected to be used as cloaking materials.

  15. 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.

  16. 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.

  17. Mode mixing in asymmetric double trench photonic crystal waveguides

    CERN Document Server

    Vlasov, Y A; McNab, S J; Vlasov, Yu. A.

    2003-01-01

    e investigate both experimentally and theoretically the waveguiding properties of a novel double trench waveguide where a conventional single-mode strip waveguide is embedded in a two dimensional photonic crystal (PhC) slab formed in silicon on insulator (SOI) wafers. We demonstrate that the bandwidth for relatively low-loss (50dB/cm) waveguiding is significantly expanded to 250nm covering almost all the photonic band gap owing to nearly linear dispersion of the TE-like waveguiding mode. The flat transmission spectrum however is interrupted by numerous narrow stop bands. We found that these stop bands can be attributed to anti-crossing between TE-like (positive parity) and TM-like (negative parity) modes. This effect is a direct result of the strong asymmetry of the waveguides that have an upper cladding of air and lower cladding of oxide. To our knowledge this is the first demonstration of the effects of cladding asymmetry on the transmission characteristics of the PhC slab waveguides.

  18. 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.

  19. The structure-specific endonuclease Mus81-Eme1 promotes conversion of interstrand DNA crosslinks into double-strands breaks

    NARCIS (Netherlands)

    K. Hanada (Katsuhiro); M. Budzowska (Magdalena); M. Modesti (Mauro); A. Maas (Alex); C. Wyman (Claire); J. Essers (Jeroen); R. Kanaar (Roland)

    2006-01-01

    textabstractRepair of interstrand crosslinks (ICLs) requires multiple-strand incisions to separate the two covalently attached strands of DNA. It is unclear how these incisions are generated. DNA double-strand breaks (DSBs) have been identified as intermediates in ICL repair, but enzymes responsible

  20. 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.

  1. 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.

  2. Enhancement of multisubband electron mobility in asymmetrically doped coupled double quantum well structure

    Energy Technology Data Exchange (ETDEWEB)

    Das, S.; Nayak, R.K.; Sahu, T., E-mail: tsahu_bu@rediffmail.com; Panda, A.K.

    2015-11-01

    We study the effect of coupling of subband wave functions on the multisubband electron mobility in a barrier delta doped GaAs/Al{sub x}Ga{sub 1−x}As asymmetric double quantum well structure. We use selfconsistent solution of the coupled Schrödinger equation and Poisson's equation to calculate the subband wave functions and energy levels. The low temperature mobility is considered by using scatterings due to ionized impurities, interface roughness and alloy disorder. We show that variation of the width of the central barrier considerably affect the interplay of different scattering mechanisms on electron mobility through intersubband effects. Under single subband occupancy, the mobility increases with decrease in the barrier width as functions of doping concentration as well as function of well width. However, in case of double subband occupancy, effect of intersubband interaction yields opposite trend, i.e., increase in mobility with increase in barrier width. It is gratifying to show that in case of asymmetric variation of well widths the mobility shows nonmonotonic behavior which varies with change in the width of the central barrier under double subband occupancy.

  3. 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.

  4. 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.

  5. The structure-specific endonuclease Ercc1-Xpf is required to resolve DNA interstrand cross-link-induced double-strand breaks.

    Science.gov (United States)

    Niedernhofer, Laura J; Odijk, Hanny; Budzowska, Magda; van Drunen, Ellen; Maas, Alex; Theil, Arjan F; de Wit, Jan; Jaspers, N G J; Beverloo, H Berna; Hoeijmakers, Jan H J; Kanaar, Roland

    2004-07-01

    Interstrand cross-links (ICLs) are an extremely toxic class of DNA damage incurred during normal metabolism or cancer chemotherapy. ICLs covalently tether both strands of duplex DNA, preventing the strand unwinding that is essential for polymerase access. The mechanism of ICL repair in mammalian cells is poorly understood. However, genetic data implicate the Ercc1-Xpf endonuclease and proteins required for homologous recombination-mediated double-strand break (DSB) repair. To examine the role of Ercc1-Xpf in ICL repair, we monitored the phosphorylation of histone variant H2AX (gamma-H2AX). The phosphoprotein accumulates at DSBs, forming foci that can be detected by immunostaining. Treatment of wild-type cells with mitomycin C (MMC) induced gamma-H2AX foci and increased the amount of DSBs detected by pulsed-field gel electrophoresis. Surprisingly, gamma-H2AX foci were also induced in Ercc1(-/-) cells by MMC treatment. Thus, DSBs occur after cross-link damage via an Ercc1-independent mechanism. Instead, ICL-induced DSB formation required cell cycle progression into S phase, suggesting that DSBs are an intermediate of ICL repair that form during DNA replication. In Ercc1(-/-) cells, MMC-induced gamma-H2AX foci persisted at least 48 h longer than in wild-type cells, demonstrating that Ercc1 is required for the resolution of cross-link-induced DSBs. MMC triggered sister chromatid exchanges in wild-type cells but chromatid fusions in Ercc1(-/-) and Xpf mutant cells, indicating that in their absence, repair of DSBs is prevented. Collectively, these data support a role for Ercc1-Xpf in processing ICL-induced DSBs so that these cytotoxic intermediates can be repaired by homologous recombination.

  6. Tunneling-Induced Transient Gain in an Asymmetric Double Quantum Well

    Institute of Scientific and Technical Information of China (English)

    XU Wei-Hua; WU Jin-Hui; GAO Jin-Yue

    2004-01-01

    @@ We investigate the transient behaviour of a weak probe in asymmetric double quantum well structures, where two excited states are coupled by resonant tunnelling through a thin barrier in a three-level system of electronic subbands. There is no external coherent coupling field applied, and we find that probe gain can be achieved during the transient process, which is induced by the coherent coupling of the upper states via the resonant tunnelling.We show that the transient behaviour of the probe depends on the coupling strength and the dephasing rate and can be tuned by changing the width of the tunnelling barrier.

  7. Electromagnetically induced transparency in an asymmetric double quantum well under non-resonant, intense laser fields

    Science.gov (United States)

    Niculescu, E. C.

    2017-02-01

    Electromagnetically induced transparency in an asymmetric double quantum well subjected to a non-resonant, intense laser field is theoretically investigated. We found that the energy levels configuration could be switched between a Λ-type and a ladder-type scheme by varying the non-resonant radiation intensity. This effect is due to the laser-induced electron tunneling between the wells and it allows a substantial flexibility in the manipulation of the optical properties. The dependence of the susceptibilities on the control field Rabi frequency, intensity of the nonresonant laser, and the control field detuning for both configurations are discussed and compared.

  8. Two-dimensional analytical models for asymmetric fully depleted double-gate strained silicon MOSFETs

    Institute of Scientific and Technical Information of China (English)

    Liu Hong-Xia; Li Jin; Li Bin; Cao Lei; Yuan Bo

    2011-01-01

    This paper develops the simple and accurate two-dimensional analytical models for new asymmetric double-gate fully depleted strained-Si MOSFET. The models mainly include the analytical equations of the surface potential, surface electric field and threshold voltage, which are derived by solving two dimensional Poisson equation in strained-Si layer.The models are verified by numerical simulation. Besides offering the physical insight into device physics in the model,the new structure also provides the basic designing guidance for further immunity of short channel effect and drain-induced barrier-lowering of CMOS-based devices in nanometre scale.

  9. 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.

  10. 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.

  11. 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.

  12. Structure of a double-domain phosphagen kinase reveals an asymmetric arrangement of the tandem domains.

    Science.gov (United States)

    Wang, Zhiming; Qiao, Zhu; Ye, Sheng; Zhang, Rongguang

    2015-04-01

    Tandem duplications and fusions of single genes have led to magnificent expansions in the divergence of protein structures and functions over evolutionary timescales. One of the possible results is polydomain enzymes with interdomain cooperativities, few examples of which have been structurally characterized at the full-length level to explore their innate synergistic mechanisms. This work reports the crystal structures of a double-domain phosphagen kinase in both apo and ligand-bound states, revealing a novel asymmetric L-shaped arrangement of the two domains. Unexpectedly, the interdomain connections are not based on a flexible hinge linker but on a rigid secondary-structure element: a long α-helix that tethers the tandem domains in relatively fixed positions. Besides the connective helix, the two domains also contact each other directly and form an interdomain interface in which hydrogen bonds and hydrophobic interactions further stabilize the L-shaped domain arrangement. Molecular-dynamics simulations show that the interface is generally stable, suggesting that the asymmetric domain arrangement crystallographically observed in the present study is not a conformational state simply restrained by crystal-packing forces. It is possible that the asymmetrically arranged tandem domains could provide a structural basis for further studies of the interdomain synergy.

  13. Tapping natural reservoirs of homing endonucleases for targeted gene modification

    OpenAIRE

    2011-01-01

    Homing endonucleases mobilize their own genes by generating double-strand breaks at individual target sites within potential host DNA. Because of their high specificity, these proteins are used for “genome editing” in higher eukaryotes. However, alteration of homing endonuclease specificity is quite challenging. Here we describe the identification and phylogenetic analysis of over 200 naturally occurring LAGLIDADG homing endonucleases (LHEs). Biochemical and structural characterization of end...

  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. 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.

  17. 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.

  18. 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.

  19. 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.

  20. Asymmetric Cyclopropanation Catalyzed by Four Stereoisomers of a Copper-(Schiff-base) Complex with Double Chiral Centers

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Four stereoisomers of a copper-(Schiff-base) complex with double chiral centers were applied to catalyze the asymmetric cyclopropanation. Two of the stereoisomers were also efficient catalysts affording high enantiomeric excess of up to 91.8%. A mechanism that predicts the observed results accurately was proposed.

  1. 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

  2. Effects of electromagnetic fields on the nonlinear optical properties of asymmetric double quantum well under intense laser field

    Science.gov (United States)

    Yesilgul, U.; Sari, H.; Ungan, F.; Martínez-Orozco, J. C.; Restrepo, R. L.; Mora-Ramos, M. E.; Duque, C. A.; Sökmen, I.

    2017-03-01

    In this study, the effects of electric and magnetic fields on the optical rectification and second and third harmonic generation in asymmetric double quantum well under the intense non-resonant laser field is theoretically investigated. We calculate the optical rectification and second and third harmonic generation within the compact density-matrix approach. The theoretical findings show that the influence of electric, magnetic, and intense laser fields leads to significant changes in the coefficients of nonlinear optical rectification, second and third harmonic generation.

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

    DEFF Research Database (Denmark)

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

    1993-01-01

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

  4. Asymmetric electron energy sharing in electron-impact double ionization of helium

    Science.gov (United States)

    Silenou Mengoue, M.; Tetchou Nganso, H. M.

    2016-12-01

    We present the fully fivefold differential cross sections (FDCSs) for (e ,3 e ) processes in helium within the first Born approximation. The calculation is performed for a coplanar geometry in which the incident electron is fast (˜6 keV), the momentum transfer is small (0.24 a.u.), and for an asymmetric energy sharing between both slow ejected electrons at excess energy of 20 eV. Two cases have been considered: E1=15 eV, E2=5 eV and E1=8 eV, E2=12 eV. While waiting for new theoretical and experimental results for confrontations, in particular for asymmetric energy sharing, our results clearly demonstrate that, for the same incident energy, the same momentum transfer and the same excess energy, the (e ,3 e ) process in helium with asymmetric energy sharing between ejected electrons is more likely than the case with symmetric energy sharing. The two- and three-dimensional representation of the FDCSs covering all possible values of the angle of ejections are presented and discussed. The theoretical cross sections are calculated by using a compact-kernel-integral-equation approach associated with the Jacobi matrix method to calculate a three-body wave function and which leads to a full convergence in terms of the basis size.

  5. 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.

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

    DEFF Research Database (Denmark)

    Larsen, Christian Albrekt; Vesan, Patrik

    2012-01-01

    It has been a general finding across Europe that very few job matches are facilitated by public employment services (PES).The article explains this failure by highlighting the existence of a double-sided asymmetric information problem on the labour market. It is argued that although a PES...

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

    Science.gov (United States)

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

    2016-02-01

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

  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.

    2016-11-01

    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. Drain Current Models for Single-Gate Mosfets & Undoped Symmetric & Asymmetric Double-Gate SOI Mosfets And Quantum Mechanical Effects: A Review

    Directory of Open Access Journals (Sweden)

    SUBHA SUBRAMANIAM

    2013-01-01

    Full Text Available In this paper modeling framework for single gate conventional planar MOSFET and double gate (DG MOSFETS are reviewed. MOS Modeling can be done by either analytical modeling or compact modeling. Single gate MOSFET technology has been the choice of mainstream digital circuits for VLSI as well as for other high frequency application in the low GHZ range. The major single gate MOS modeling methods are reviewed and compared. First generation to fifth generation MOS models like BSIM & PSP are compared. The use of multiple gates has emerged as a new technology to replace the conventional planar MOSFET when itsfeature size is scaled to the sub 22nm regime. Double Gate devices seem to be attractive alternatives as they can effectively reduce the short channel effects and yield higher current drive. DGFETS are classified as Symmetric Double Gate FETs (SDGFET and Asymmetric Double Gate FETs (ADGFET. This paper covers the fundamentals of SDGFETs and ADGFETs. Drain current models for single gate MOSFETs, SDGFETs and ADGFETs are reviewed. In the Double gate MOS era the dominating quantum mechanical effects which has to be considered in two dimensional modeling are also discussed. The comparisons of drain current models for Symmetric and Asymmetric Double gate MOSFETs are done and shown with the results like limitations of the models. A brief summary of the review work is provided. The result shows a greater demand in the field of Asymmetric Double gate modeling which can be extended for circuits like SRAM and RF amplifier design. Thepremier quantum mechanical effects which should be included in model development for below 22nm devices are listed.

  10. 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.

  11. 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.

  12. 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

  13. Prediction of simultaneously large and opposite generalized Goos-Hänchen shifts for TE and TM light beams in an asymmetric double-prism configuration.

    Science.gov (United States)

    Li, Chun-Fang; Wang, Qi

    2004-05-01

    It is predicted that large and opposite generalized Goos-Hänchen (GGH) shifts may occur simultaneously for TE and TM light beams upon reflection from an asymmetric double-prism configuration when the angle of incidence is below but near the critical angle for total reflection, which may lead to interesting applications in optical devices and integrated optics. Numerical simulations show that the magnitude of the GGH shift can be of the order of beam's width.

  14. A Series of Soliton-like and Double-like Periodic Solutions of a (2+1)-Dimensional Asymmetric Nizhnik-Novikov-Vesselov Equation

    Institute of Scientific and Technical Information of China (English)

    CHENYong; WANGQi; LIBiao

    2004-01-01

    We generalize the algebraic method presented by Fan [J.Phys. A: Math. Gen. 36 (2003) 7009)] to uniformly construct a series of soliton-like solutions and double-like periodic solutions for nonlinear partial differential equations (NPDE). As an application of the method, we choose a (2+1)-dimensional asymmetric Nizhnik Novikov Vesselov equation and successfully construct new and more general solutions including a series of nontraveling wave and coefficient functions'soliton-like solutions, double-like periodic and trigonometric-like function solutions.

  15. A Series of Soliton-like and Double-like Periodic Solutions of a (2+1)-Dimensional Asymmetric Nizhnik-Novikov-Vesselov Equation

    Institute of Scientific and Technical Information of China (English)

    CHEN Yong; WANG Qi; LI Biao

    2004-01-01

    We generalize the algebraic method presented by Fan [J. Phys. A: Math. Gen. 36 (2003) 7009)] to uniformly construct a series of soliton-like solutions and double-like periodic solutions for nonlinear partial differential equations(NPDE). As an application of the method, we choose a (2+1)-dimensional asymmetric Nizhnik-Novikov-Vesselov equation and successfully construct new and more general solutions including a series of nontraveling wave and coefficient functions' soliton-like solutions, double-like periodic and trigonometric-like function solutions.

  16. The site-specific deoxyribonuclease from Bacillus pumilus (endonuclease R.Bpu1387).

    Science.gov (United States)

    Ikawa, S; Shibata, T; Ando, T

    1976-12-01

    A new site-specific endonuclease (DNase) was isolated from the cells of Bacillus pumilus AHU 1387 strain. This enzyme (endonuclease R.Bpu 1387) introduced double-stranded scissions at unique sites on DNA's of coli phage lambda, lambdadvl, coli phage T7, Bacillus phage phi105C, Bacillus phage SP10, and Simian Virus 40, in the presence of magnesium ion. The activity was stimulated by the presence of NaCl.

  17. Type I restriction endonucleases are true catalytic enzymes.

    Science.gov (United States)

    Bianco, Piero R; Xu, Cuiling; Chi, Min

    2009-06-01

    Type I restriction endonucleases are intriguing, multifunctional complexes that restrict DNA randomly, at sites distant from the target sequence. Restriction at distant sites is facilitated by ATP hydrolysis-dependent, translocation of double-stranded DNA towards the stationary enzyme bound at the recognition sequence. Following restriction, the enzymes are thought to remain associated with the DNA at the target site, hydrolyzing copious amounts of ATP. As a result, for the past 35 years type I restriction endonucleases could only be loosely classified as enzymes since they functioned stoichiometrically relative to DNA. To further understand enzyme mechanism, a detailed analysis of DNA cleavage by the EcoR124I holoenzyme was done. We demonstrate for the first time that type I restriction endonucleases are not stoichiometric but are instead catalytic with respect to DNA. Further, the mechanism involves formation of a dimer of holoenzymes, with each monomer bound to a target sequence and, following cleavage, each dissociates in an intact form to bind and restrict subsequent DNA molecules. Therefore, type I restriction endonucleases, like their type II counterparts, are true enzymes. The conclusion that type I restriction enzymes are catalytic relative to DNA has important implications for the in vivo function of these previously enigmatic enzymes.

  18. 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.

  19. The asymmetric reactions of mean and volatility of stock returns to domestic and international information based on a four-regime double-threshold GARCH model

    Science.gov (United States)

    Chen, Cathy W. S.; Yang, Ming Jing; Gerlach, Richard; Jim Lo, H.

    2006-07-01

    In this paper, we investigate the asymmetric reactions of mean and volatility of stock returns in five major markets to their own local news and the US information via linear and nonlinear models. We introduce a four-regime Double-Threshold GARCH (DTGARCH) model, which allows asymmetry in both the conditional mean and variance equations simultaneously by employing two threshold variables, to analyze the stock markets’ reactions to different types of information (good/bad news) generated from the domestic markets and the US stock market. By applying the four-regime DTGARCH model, this study finds that the interaction between the information of domestic and US stock markets leads to the asymmetric reactions of stock returns and their variability. In addition, this research also finds that the positive autocorrelation reported in the previous studies of financial markets may in fact be mis-specified, and actually due to the local market's positive response to the US stock market.

  20. 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.

  1. 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.

  2. Problem-Solving Test: Restriction Endonuclease Mapping

    Science.gov (United States)

    Szeberenyi, Jozsef

    2011-01-01

    The term "restriction endonuclease mapping" covers a number of related techniques used to identify specific restriction enzyme recognition sites on small DNA molecules. A method for restriction endonuclease mapping of a 1,000-basepair (bp)-long DNA molecule is described in the fictitious experiment of this test. The most important fact needed to…

  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. 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.

  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. 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....... This third metal ion has a crucial role, triggering the consecutive hydrolysis of the targeted phosphodiester bonds in the DNA strands and leaving its position once the DSB is generated. The multiple structures show the orchestrated conformational changes in the protein residues, nucleotides and metals...

  7. A Numerical Investigation of the Strain Effect on Saturation Optical Intensity in Electroabsorption Modulators Based on Asymmetric Intra-step-barrier Coupled Double Strained Quantum Wells

    Science.gov (United States)

    Abedi, Kambiz

    2011-12-01

    In this paper, the strain effect on saturation optical intensity in electroabsorption modulators (EAMs) based on asymmetric intra-step-barrier coupled double strained quantum well (AICD-SQWs) active region is theoretically investigated and compared with intra-step quantum well (IQW) structure. For this purpose, the thermionic emission and tunneling escape processes are taken into account and the escape times of photogenerated carriers are calculated. Then, the electroabsorption coefficient is calculated for different well strains for TE input light polarization. Finally, the saturation optical intensity of electroabsorption modulators with AICD-SQW structures in comparison with IQW structure is evaluated. Numerical results show that the tensile strain of well has the most significant effect on the saturation optical intensity of electroabsorption modulators with AICD-SQW structures due to reduction in escape times.

  8. 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.

  9. Specific fragments of phi X174 deoxyribonucleic acid produced by a restriction enzyme from Haemophilus aegyptius, endonuclease Z.

    Science.gov (United States)

    Middleton, J H; Edgell, M H; Hutchison, C A

    1972-07-01

    A restriction-like enzyme has been purified from Haemophilus aegyptius. This nuclease, endonuclease Z, produces a rapid decrease in the viscosity of native calf thymus and H. influenzae deoxyribonucleic acids (DNA), but does not degrade homologous DNA. The specificity of endonuclease Z is different from that of the similar endonuclease isolated from H. influenzae (endonuclease R). The purified enzyme cleaves the double-stranded replicative form DNA of bacteriophage phiX174 (phiX174 RF DNA) into at least 11 specific limit fragments whose molecular sizes have been estimated by gel electrophoresis. The position of these fragments with respect to the genetic map of phiX174 can be determined by using the genetic assay for small fragments of phiX174 DNA.

  10. Size asymmetric hard spheres as a convenient model for the capacitance of the electrical double layer of an ionic liquid.

    Science.gov (United States)

    Lamperski, Stanisław; Sosnowska, Joanna; Bhuiyan, Lutful Bari; Henderson, Douglas

    2014-01-07

    Even though ionic liquids are composed of nonspherical ions, it is shown here that the general features of the capacitance of an electrical double layer can be obtained using a charged hard sphere model. We have shown in our earlier studies that at high electrolyte concentrations or large magnitudes of the electrode charge density the fact that the ions have a finite size, and are not point ions, cause the capacitance near the potential of zero charge to increase and change from a minimum to a maximum as the ionic concentration is increased and to decrease as the magnitude of the electrode charge density increases. Here, we show that the asymmetry of the capacitance of an ionic liquid can be explained qualitatively by using spherical ions of different size without attempting to introduce the ionic shape in a detailed manner. This means that the general features of the capacitance of the double layer of an ionic liquid can be studied without using a complex model, although the study of the density or charge profiles of an ionic fluid would require one. However, this is often unnecessary in the analysis of many experiments.

  11. Substrate recognition and catalysis by flap endonucleases and related enzymes.

    Science.gov (United States)

    Tomlinson, Christopher G; Atack, John M; Chapados, Brian; Tainer, John A; Grasby, Jane A

    2010-04-01

    FENs (flap endonucleases) and related FEN-like enzymes [EXO-1 (exonuclease-1), GEN-1 (gap endonuclease 1) and XPG (xeroderma pigmentosum complementation group G)] are a family of bivalent-metal-ion-dependent nucleases that catalyse structure-specific hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair and recombination. In the case of FENs, the ability to catalyse reactions on a variety of substrates has been rationalized as a result of combined functional and structural studies. Analyses of FENs also exemplify controversies regarding the two-metal-ion mechanism. However, kinetic studies of T5FEN (bacteriophage T5 FEN) reveal that a two-metal-ion-like mechanism for chemical catalysis is plausible. Consideration of the metallobiochemistry and the positioning of substrate in metal-free structures has led to the proposal that the duplex termini of substrates are unpaired in the catalytically active form and that FENs and related enzymes may recognize breathing duplex termini within more complex structures. An outstanding issue in FEN catalysis is the role played by the intermediate (I) domain arch or clamp. It has been proposed that FENs thread the 5'-portion of their substrates through this arch, which is wide enough to accommodate single-stranded, but not double-stranded, DNA. However, FENs exhibit gap endonuclease activity acting upon substrates that have a region of 5'-duplex. Moreover, the action of other FEN family members such as GEN-1, proposed to target Holliday junctions without termini, appears incompatible with a threading mechanism. An alterative is that the I domain is used as a clamp. A future challenge is to clarify the role of this domain in FENs and related enzymes.

  12. Phage T4 mobE promotes trans homing of the defunct homing endonuclease I-TevIII.

    Science.gov (United States)

    Wilson, Gavin W; Edgell, David R

    2009-11-01

    Homing endonucleases are site-specific DNA endonucleases that typically function as mobile genetic elements by introducing a double-strand break (DSB) in genomes that lack the endonuclease, resulting in a unidirectional gene conversion event that mobilizes the homing endonuclease gene and flanking DNA. Here, we characterize phage T4-encoded mobE, a predicted free-standing HNH family homing endonuclease. We show that mobE is promoterless and dependent on upstream transcription for expression, and that an internal intrinsic terminator regulates mobE transcript levels. Crucially, in vivo mapping experiments revealed a MobE-dependent, strand-specific nick in the non-coding strand of the nrdB gene of phage T2. An internal deletion of the predicted HNH catalytic motif of MobE abolishes nicking, and reduces high-frequency inheritance of mobE. Sequence polymorphisms of progeny phage that inherit mobE are consistent with DSB repair pathways. Significantly, we found that mobility of the neighboring I-TevIII, a defunct homing endonuclease encoded within a group I intron interrupting the nrdB gene of phage T4, was dependent on an intact mobE gene. Thus, our data indicate that the stagnant nrdB intron and I-TevIII are mobilized in trans as a consequence of a MobE-dependent gene conversion event, facilitating persistence of genetic elements that have no inherent means of promoting their own mobility.

  13. 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.

  14. Regulation of Apoptotic Endonucleases by EndoG

    Science.gov (United States)

    Zhdanov, Dmitry D.; Fahmi, Tariq; Wang, Xiaoying; Apostolov, Eugene O.; Sokolov, Nikolai N.; Javadov, Sabzali

    2015-01-01

    Cells contain several apoptotic endonucleases, which appear to act simultaneously before and after cell death by destroying the host cell DNA. It is largely unknown how the endonucleases are being induced and whether they can regulate each other. This study was performed to determine whether apoptotic mitochondrial endonuclease G (EndoG) can regulate expression of other apoptotic endonucleases. The study showed that overexpression of mature EndoG in kidney tubular epithelial NRK-52E cells can increase expression of caspase-activated DNase (CAD) and four endonucleases that belong to DNase I group including DNase I, DNase X, DNase IL2, and DNase γ, but not endonucleases of the DNase 2 group. The induction of DNase I-type endonucleases was associated with DNA degradation in promoter/exon 1 regions of the endonuclease genes. These results together with findings on colocalization of immunostained endonucleases and TUNEL suggest that DNA fragmentation after EndoG overexpression was caused by DNase I endonucleases and CAD in addition to EndoG itself. Overall, these data provide first evidence for the existence of the integral network of apoptotic endonucleases regulated by EndoG. PMID:25849439

  15. 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.

  16. 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...

  17. 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.

  18. 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.

  19. A new restriction endonuclease from Spirulina platensis.

    OpenAIRE

    Kawamura, M; Sakakibara, M; Watanabe, T; Kita, K.; Hiraoka, N; Obayashi, A; Takagi, M; Yano, K

    1986-01-01

    Three restriction endonucleases, Sp1I, Sp1II and Sp1III have been purified partially from Spirulina platensis subspecies siamese and named. Sp1I cleaves bacteriophage lambda DNA at one site, phi X 174 RF DNA at two sites, but does not cleave pBR322 DNA. This enzyme recognizes the sequence 5'CGTACG3' 3'GCATCG5' and cuts the site indicated by the arrows. Sp1II is an isoschizomer of Tth111I and Sp1III is an isoschizomer of HaeIII.

  20. Homing endonucleases: from genetic anomalies to programmable genomic clippers.

    Science.gov (United States)

    Belfort, Marlene; Bonocora, Richard P

    2014-01-01

    Homing endonucleases are strong drivers of genetic exchange and horizontal transfer of both their own genes and their local genetic environment. The mechanisms that govern the function and evolution of these genetic oddities have been well documented over the past few decades at the genetic, biochemical, and structural levels. This wealth of information has led to the manipulation and reprogramming of the endonucleases and to their exploitation in genome editing for use as therapeutic agents, for insect vector control and in agriculture. In this chapter we summarize the molecular properties of homing endonucleases and discuss their strengths and weaknesses in genome editing as compared to other site-specific nucleases such as zinc finger endonucleases, TALEN, and CRISPR-derived endonucleases.

  1. 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.

  2. PCR-based bioprospecting for homing endonucleases in fungal mitochondrial rRNA genes.

    Science.gov (United States)

    Hafez, Mohamed; Guha, Tuhin Kumar; Shen, Chen; Sethuraman, Jyothi; Hausner, Georg

    2014-01-01

    Fungal mitochondrial genomes act as "reservoirs" for homing endonucleases. These enzymes with their DNA site-specific cleavage activities are attractive tools for genome editing and gene therapy applications. Bioprospecting and characterization of naturally occurring homing endonucleases offers an alternative to synthesizing artificial endonucleases. Here, we describe methods for PCR-based screening of fungal mitochondrial rRNA genes for homing endonuclease encoding sequences, and we also provide protocols for the purification and biochemical characterization of putative native homing endonucleases.

  3. Thermodynamics of DNA target site recognition by homing endonucleases

    OpenAIRE

    Eastberg, Jennifer H.; Smith, Audrey McConnell; Zhao, Lei; Ashworth, Justin; Shen, Betty W.; Stoddard, Barry L.

    2007-01-01

    The thermodynamic profiles of target site recognition have been surveyed for homing endonucleases from various structural families. Similar to DNA-binding proteins that recognize shorter target sites, homing endonucleases display a narrow range of binding free energies and affinities, mediated by structural interactions that balance the magnitude of enthalpic and entropic forces. While the balance of ΔH and TΔS are not strongly correlated with the overall extent of DNA bending, unfavorable ΔH...

  4. 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.

  5. Interacting asymmetric double Rydberg series: the Ba 8snl(l = 5) + 5f{sub j}n'l' case

    Energy Technology Data Exchange (ETDEWEB)

    Cohen, S [Atomic and Molecular Physics Laboratory, Physics Department, University of Ioannina, GR-45110 Ioannina (Greece); Camus, P [Laboratoire Aime Cotton , Centre National de la Recherche Scientifique II, Batiment 505, Campus d' Orsay, 91405 Orsay Cedex (France); Bolovinos, A [Atomic and Molecular Physics Laboratory, Physics Department, University of Ioannina, GR-45110 Ioannina (Greece)

    2005-01-28

    The 8snl double Rydberg states of barium with l = 5 and n = 12-15 are populated by employing an isolated core excitation (ICE) scheme in conjunction with the Stark switching technique. The recorded spectra show strong configuration interaction with three adjacent 5f{sub j}n'l' series. One of the latter series is converging to the 5f{sub 5/2} ionization limit and the other two to the higher lying 5f{sub 7/2} one. A multichannel quantum defect theory (MQDT) analysis reveals the presence of low-lying members of double Rydberg series converging to higher ionization thresholds and determining the configuration mixing. At least two perturbers, affecting energy level positions, are identified while a comparison between experimental and fitted excitation profiles points towards the presence of a third one. Finally, theoretical calculations of the 8snl(l = 5) series members quantum defects demonstrate the onset of mutual penetration between the two excited electrons. Nevertheless, the most important quantum defect contributions stem from exchange and polarization effects and thus long-range interactions alone are insufficient for a proper description of the double Rydberg states involved.

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

    Science.gov (United States)

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

    2014-10-01

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

  7. 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.

  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. In vivo disruption of latent HSV by designer endonuclease therapy.

    Science.gov (United States)

    Aubert, Martine; Madden, Emily A; Loprieno, Michelle; DeSilva Feelixge, Harshana S; Stensland, Laurence; Huang, Meei-Li; Greninger, Alexander L; Roychoudhury, Pavitra; Niyonzima, Nixon; Nguyen, Thuy; Magaret, Amalia; Galleto, Roman; Stone, Daniel; Jerome, Keith R

    2016-09-08

    A large portion of the global population carries latent herpes simplex virus (HSV), which can periodically reactivate, resulting in asymptomatic shedding or formation of ulcerative lesions. Current anti-HSV drugs do not eliminate latent virus from sensory neurons where HSV resides, and therefore do not eliminate the risk of transmission or recurrent disease. Here, we report the ability of HSV-specific endonucleases to induce mutations of essential HSV genes both in cultured neurons and in latently infected mice. In neurons, viral genomes are susceptible to endonuclease-mediated mutagenesis, regardless of the time of treatment after HSV infection, suggesting that both HSV lytic and latent forms can be targeted. Mutagenesis frequency after endonuclease exposure can be increased nearly 2-fold by treatment with a histone deacetylase (HDAC) inhibitor. Using a mouse model of latent HSV infection, we demonstrate that a targeted endonuclease can be delivered to viral latency sites via an adeno-associated virus (AAV) vector, where it is able to induce mutation of latent HSV genomes. These data provide the first proof-of-principle to our knowledge for the use of a targeted endonuclease as an antiviral agent to treat an established latent viral infection in vivo.

  11. Thermodynamics of DNA target site recognition by homing endonucleases

    Science.gov (United States)

    Eastberg, Jennifer H.; Smith, Audrey McConnell; Zhao, Lei; Ashworth, Justin; Shen, Betty W.; Stoddard, Barry L.

    2007-01-01

    The thermodynamic profiles of target site recognition have been surveyed for homing endonucleases from various structural families. Similar to DNA-binding proteins that recognize shorter target sites, homing endonucleases display a narrow range of binding free energies and affinities, mediated by structural interactions that balance the magnitude of enthalpic and entropic forces. While the balance of ΔH and TΔS are not strongly correlated with the overall extent of DNA bending, unfavorable ΔHbinding is associated with unstacking of individual base steps in the target site. The effects of deleterious basepair substitutions in the optimal target sites of two LAGLIDADG homing endonucleases, and the subsequent effect of redesigning one of those endonucleases to accommodate that DNA sequence change, were also measured. The substitution of base-specific hydrogen bonds in a wild-type endonuclease/DNA complex with hydrophobic van der Waals contacts in a redesigned complex reduced the ability to discriminate between sites, due to nonspecific ΔSbinding. PMID:17947319

  12. Genetic and biochemical characterization of human AP endonuclease 1 mutants deficient in nucleotide incision repair activity.

    Directory of Open Access Journals (Sweden)

    Aurore Gelin

    Full Text Available BACKGROUND: Human apurinic/apyrimidinic endonuclease 1 (APE1 is a key DNA repair enzyme involved in both base excision repair (BER and nucleotide incision repair (NIR pathways. In the BER pathway, APE1 cleaves DNA at AP sites and 3'-blocking moieties generated by DNA glycosylases. In the NIR pathway, APE1 incises DNA 5' to a number of oxidatively damaged bases. At present, physiological relevance of the NIR pathway is fairly well established in E. coli, but has yet to be elucidated in human cells. METHODOLOGY/PRINCIPAL FINDING: We identified amino acid residues in the APE1 protein that affect its function in either the BER or NIR pathway. Biochemical characterization of APE1 carrying single K98A, R185A, D308A and double K98A/R185A amino acid substitutions revealed that all mutants exhibited greatly reduced NIR and 3'-->5' exonuclease activities, but were capable of performing BER functions to some extent. Expression of the APE1 mutants deficient in the NIR and exonuclease activities reduced the sensitivity of AP endonuclease-deficient E. coli xth nfo strain to an alkylating agent, methylmethanesulfonate, suggesting that our APE1 mutants are able to repair AP sites. Finally, the human NIR pathway was fully reconstituted in vitro using the purified APE1, human flap endonuclease 1, DNA polymerase beta and DNA ligase I proteins, thus establishing the minimal set of proteins required for a functional NIR pathway in human cells. CONCLUSION/SIGNIFICANCE: Taken together, these data further substantiate the role of NIR as a distinct and separable function of APE1 that is essential for processing of potentially lethal oxidative DNA lesions.

  13. Double electromagnetically induced transparency phenomenon in an asymmetric N-type semiconductor quantum well%非对称半导体双量子阱中的双电磁感应透明现象

    Institute of Scientific and Technical Information of China (English)

    张蔚曦; 张愉; 金慧

    2016-01-01

    The characteristics of optical absorption in an asymmetric four-level N-type semiconductor quantum well with the cross-coupling longitude-optical phonons (CCLOP) relaxation were studied. In the linear range, it shows that the electromagnetically induced transparency (EIT) relies on the coherence control of the optical fields and the CCLOP relaxation. Especially, there exhibits a double-EIT when the transition frequency between the hole and anti-bonding states is rather large. Interestingly, there appears a near-perfect double-EIT phenomenon when increasing the CCLOP relaxation. It is expected that these results may exhibit some potential applications in the all-optical switching and other optical information engineering related issues.%对在交叉耦合纵波光学声子(Cross-coupling Longitude-optical Phonons,简称CCLOP)弛豫时四能级非对称N型半导体量子阱系统的光吸收特性进行了研究。研究表明,在线性范围内,在该系统中能够实现电磁感应透明效应(Electromagnetically Induced Transparency,简称EIT),并且这种EIT效应依赖于光场与系统的谐振控制和CCLOP 弛豫;尤其是当空穴态和反键态之间的跃迁频率较大时,系统会出现双EIT现象。有趣的是,当CCLOP弛豫增大时,将出现近乎完美的双EIT现象。研究结果在全光开关和其他的光信息工程中有着潜在的应用。

  14. 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.

  15. Bme585 I [5'-CCCGC(4/6)-3'], a new isoschizomer of restriction endonuclease Fau I, isolated from a strain of Bacillus mesentericus.

    Science.gov (United States)

    Davalieva, Katarina; Ziberovski, Jugoslav; Efremov, Georgi D

    2004-01-01

    Bme585 I is a new member of the restriction endonuclease type IIS family. It was partially purified from the heterothrophic, mesophilic bacterial strain Bacillus mesentericus 585 by ammonium sulphate precipitation and phosphocellulose column chromatography. Bme585 I is a monomeric protein with a molecular mass of 62 kD. The enzyme is active over a broad pH range from 7.0 to 8.8, has a temperature optimum of 37 degrees C and tolerance of NaCl in reaction buffer from 0 to 400 mM. Bme585 I recognizes the asymmetric sequence 5'-CCCGC(4/6)-3' and is therefore an isoschizomer of restriction endonuclease Fau I.

  16. DNA structural elements required for ERCC1-XPF endonuclease activity

    NARCIS (Netherlands)

    W.L. de Laat (Wouter); E. Appeldoorn (Esther); J.H.J. Hoeijmakers (Jan); N.G.J. Jaspers (Nicolaas)

    1998-01-01

    textabstractThe heterodimeric complex ERCC1-XPF is a structure-specific endonuclease responsible for the 5' incision during mammalian nucleotide excision repair (NER). Additionally, ERCC1-XPF is thought to function in the repair of interstrand DNA cross-links and, by analogy to the

  17. Interplay between structure-specific endonucleases for crossover control during Caenorhabditis elegans meiosis.

    Directory of Open Access Journals (Sweden)

    Takamune T Saito

    Full Text Available The number and distribution of crossover events are tightly regulated at prophase of meiosis I. The resolution of Holliday junctions by structure-specific endonucleases, including MUS-81, SLX-1, XPF-1 and GEN-1, is one of the main mechanisms proposed for crossover formation. However, how these nucleases coordinately resolve Holliday junctions is still unclear. Here we identify both the functional overlap and differences between these four nucleases regarding their roles in crossover formation and control in the Caenorhabditis elegans germline. We show that MUS-81, XPF-1 and SLX-1, but not GEN-1, can bind to HIM-18/SLX4, a key scaffold for nucleases. Analysis of synthetic mitotic defects revealed that MUS-81 and SLX-1, but not XPF-1 and GEN-1, have overlapping roles with the Bloom syndrome helicase ortholog, HIM-6, supporting their in vivo roles in processing recombination intermediates. Taking advantage of the ease of genetic analysis and high-resolution imaging afforded by C. elegans, we examined crossover designation, frequency, distribution and chromosomal morphology in single, double, triple and quadruple mutants of the structure-specific endonucleases. This revealed that XPF-1 functions redundantly with MUS-81 and SLX-1 in executing crossover formation during meiotic double-strand break repair. Analysis of crossover distribution revealed that SLX-1 is required for crossover suppression at the center region of the autosomes. Finally, analysis of chromosome morphology in oocytes at late meiosis I stages uncovered that SLX-1 and XPF-1 promote meiotic chromosomal stability by preventing formation of chromosomal abnormalities. We propose a model in which coordinate action between structure-specific nucleases at different chromosome domains, namely MUS-81, SLX-1 and XPF-1 at the arms and SLX-1 at the center region, exerts positive and negative regulatory roles, respectively, for crossover control during C. elegans meiosis.

  18. 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

  19. 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

  20. 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.

  1. Crystallization and preliminary X-ray diffraction analysis of restriction endonuclease EcoRII

    Science.gov (United States)

    Karpova, E. A.; Meehan, E.; Pusey, M. L.; Chen, L.

    1999-01-01

    Crystals of the restriction endonuclease EcoRII have been obtained by the vapor-diffusion technique in the presence of ammonium sulfate or polyethylene glycol. The best crystals were grown with ammonium sulfate as a precipitant. Crystals with dimensions of up to 0.6 x 0. 6 x 0.6 mm have been observed. The crystals diffract to about 4.0 A resolution at a cryo-temperature of 100 K using a rotating-anode X-ray source and a Rigaku R-AXIS IV imaging-plate detector. The space group has been determined to be either I23 or I2(1)3, with unit-cell parameters a = b = c = 160.3 A, alpha = beta = gamma = 90 degrees. The crystal asymmetric unit contains two protein molecules, and self-rotation function analysis shows a pseudo-twofold symmetry relating the two monomers. Attempts to improve the resolution of crystal diffraction and to search for heavy-atom derivatives are under way.

  2. Three structure-selective endonucleases are essential in the absence of BLM helicase in Drosophila.

    Science.gov (United States)

    Andersen, Sabrina L; Kuo, H Kenny; Savukoski, Daniel; Brodsky, Michael H; Sekelsky, Jeff

    2011-10-01

    DNA repair mechanisms in mitotically proliferating cells avoid generating crossovers, which can contribute to genome instability. Most models for the production of crossovers involve an intermediate with one or more four-stranded Holliday junctions (HJs), which are resolved into duplex molecules through cleavage by specialized endonucleases. In vitro studies have implicated three nuclear enzymes in HJ resolution: MUS81-EME1/Mms4, GEN1/Yen1, and SLX4-SLX1. The Bloom syndrome helicase, BLM, plays key roles in preventing mitotic crossover, either by blocking the formation of HJ intermediates or by removing HJs without cleavage. Saccharomyces cerevisiae mutants that lack Sgs1 (the BLM ortholog) and either Mus81-Mms4 or Slx4-Slx1 are inviable, but mutants that lack Sgs1 and Yen1 are viable. The current view is that Yen1 serves primarily as a backup to Mus81-Mms4. Previous studies with Drosophila melanogaster showed that, as in yeast, loss of both DmBLM and MUS81 or MUS312 (the ortholog of SLX4) is lethal. We have now recovered and analyzed mutations in Drosophila Gen. As in yeast, there is some redundancy between Gen and mus81; however, in contrast to the case in yeast, GEN plays a more predominant role in responding to DNA damage than MUS81-MMS4. Furthermore, loss of DmBLM and GEN leads to lethality early in development. We present a comparison of phenotypes occurring in double mutants that lack DmBLM and either MUS81, GEN, or MUS312, including chromosome instability and deficiencies in cell proliferation. Our studies of synthetic lethality provide insights into the multiple functions of DmBLM and how various endonucleases may function when DmBLM is absent.

  3. Three structure-selective endonucleases are essential in the absence of BLM helicase in Drosophila.

    Directory of Open Access Journals (Sweden)

    Sabrina L Andersen

    2011-10-01

    Full Text Available DNA repair mechanisms in mitotically proliferating cells avoid generating crossovers, which can contribute to genome instability. Most models for the production of crossovers involve an intermediate with one or more four-stranded Holliday junctions (HJs, which are resolved into duplex molecules through cleavage by specialized endonucleases. In vitro studies have implicated three nuclear enzymes in HJ resolution: MUS81-EME1/Mms4, GEN1/Yen1, and SLX4-SLX1. The Bloom syndrome helicase, BLM, plays key roles in preventing mitotic crossover, either by blocking the formation of HJ intermediates or by removing HJs without cleavage. Saccharomyces cerevisiae mutants that lack Sgs1 (the BLM ortholog and either Mus81-Mms4 or Slx4-Slx1 are inviable, but mutants that lack Sgs1 and Yen1 are viable. The current view is that Yen1 serves primarily as a backup to Mus81-Mms4. Previous studies with Drosophila melanogaster showed that, as in yeast, loss of both DmBLM and MUS81 or MUS312 (the ortholog of SLX4 is lethal. We have now recovered and analyzed mutations in Drosophila Gen. As in yeast, there is some redundancy between Gen and mus81; however, in contrast to the case in yeast, GEN plays a more predominant role in responding to DNA damage than MUS81-MMS4. Furthermore, loss of DmBLM and GEN leads to lethality early in development. We present a comparison of phenotypes occurring in double mutants that lack DmBLM and either MUS81, GEN, or MUS312, including chromosome instability and deficiencies in cell proliferation. Our studies of synthetic lethality provide insights into the multiple functions of DmBLM and how various endonucleases may function when DmBLM is absent.

  4. Research on construction optimization of asymmetric double-arch section in Jiaozhou Bay Subsea Tunnel%胶州湾海底隧道不对称双连拱断面施工优化分析

    Institute of Scientific and Technical Information of China (English)

    王凯; 张成平; 王梦恕

    2012-01-01

    以青岛胶州湾海底隧道中的不对称双连拱隧道为工程背景,选取主隧道与匝道交叉口段的典型断面建立数值计算模型,针对不同的施工开挖顺序和掘进进尺制订了4种施工方案,并采用有限差分软件FLAC3D进行动态施工的三维数值模拟,计算分析并比较各方案的地表沉降、拱顶沉降和支护结构位移以及围岩应力和支护结构应力的分布情况,明确不对称双连拱隧道施工中结构变形及应力的最不利位置.分析结果表明,先施工中导洞再施工匝道断面右导洞并采用小进尺的施工方案更有利于控制围岩的稳定性,并据此提出了合理的施工方案建议.%Aiming at the asymmetric double-arch tunnel engineering that lies at Jiaozhou Bay in Qingdao, the section located in the intersection between main tunnel and ramb tunnel is chosen as a typical cross section and a three-dimensional model for numerical analysis. Four construction schemes are constituted according to different construction sequences and different digging lengths. Then these schemes are simulated with FLAC3D program. By analyzing ground surface settlement, vault settlement values, displacement of supporting structure, principle stress in surrounding rock, as well as principle stress in supporting structure, the most disadvantage position of structural deformation and stress during construction is determined. It concludes that the surrounding rock deformation could be better controlled by using of the construction sequence that first middle drift and then right hole of ramb tunnel, and the reasonable construction scheme is suggested.

  5. 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.

  6. 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.

  7. The population genetics of using homing endonuclease genes in vector and pest management.

    Science.gov (United States)

    Deredec, Anne; Burt, Austin; Godfray, H C J

    2008-08-01

    Homing endonuclease genes (HEGs) encode proteins that in the heterozygous state cause double-strand breaks in the homologous chromosome at the precise position opposite the HEG. If the double-strand break is repaired using the homologous chromosome, the HEG becomes homozygous, and this represents a powerful genetic drive mechanism that might be used as a tool in managing vector or pest populations. HEGs may be used to decrease population fitness to drive down population densities (possibly causing local extinction) or, in disease vectors, to knock out a gene required for pathogen transmission. The relative advantages of HEGs that target viability or fecundity, that are active in one sex or both, and whose target is expressed before or after homing are explored. The conditions under which escape mutants arise are also analyzed. A different strategy is to place HEGs on the Y chromosome that cause one or more breaks on the X chromosome and so disrupt sex ratio. This strategy can cause severe sex-ratio biases with efficiencies that depend on the details of sperm competition and zygote mortality. This strategy is probably less susceptible to escape mutants, especially when multiple X shredders are used.

  8. 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.

  9. Home and away- the evolutionary dynamics of homing endonucleases

    Directory of Open Access Journals (Sweden)

    Barzel Adi

    2011-11-01

    Full Text Available Abstract Background Homing endonucleases (HEases are a large and diverse group of site-specific DNAases. They reside within self-splicing introns and inteins, and promote their horizontal dissemination. In recent years, HEases have been the focus of extensive research due to their promising potential use in gene targeting procedures for the treatment of genetic diseases and for the genetic engineering of crop, animal models and cell lines. Results Using mathematical analysis and computational modeling, we present here a novel account for the evolution and population dynamics of HEase genes (HEGs. We describe HEGs as paradoxical selfish elements whose long-term persistence in a single population relies on low transmission rates and a positive correlation between transmission efficiency and toxicity. Conclusion Plausible conditions allow HEGs to sustain at high frequency through long evolutionary periods, with the endonuclease frequency being either at equilibrium or periodically oscillating. The predictions of our model may prove important not only for evolutionary theory but also for gene therapy and bio-engineering applications of HEases.

  10. 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.

  11. 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.

  12. 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.

  13. Targeting DNA double-strand breaks with TAL effector nucleases.

    Science.gov (United States)

    Christian, Michelle; Cermak, Tomas; Doyle, Erin L; Schmidt, Clarice; Zhang, Feng; Hummel, Aaron; Bogdanove, Adam J; Voytas, Daniel F

    2010-10-01

    Engineered nucleases that cleave specific DNA sequences in vivo are valuable reagents for targeted mutagenesis. Here we report a new class of sequence-specific nucleases created by fusing transcription activator-like effectors (TALEs) to the catalytic domain of the FokI endonuclease. Both native and custom TALE-nuclease fusions direct DNA double-strand breaks to specific, targeted sites.

  14. 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

  15. 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.

  16. 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.

  17. 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

  18. Early endonuclease-mediated evasion of RNA sensing ensures efficient coronavirus replication

    Science.gov (United States)

    Kindler, Eveline; Gil-Cruz, Cristina; Spanier, Julia; Li, Yize; Wilhelm, Jochen; Rabouw, Huib H.; Züst, Roland; Marti, Sabrina; Habjan, Matthias; Cervantes-Barragan, Luisa; Elliot, Ruth; Karl, Nadja; Gaughan, Christina; Silverman, Robert H.; Keller, Markus; Ludewig, Burkhard; Bergmann, Cornelia C.; Ziebuhr, John; Kalinke, Ulrich

    2017-01-01

    Coronaviruses are of veterinary and medical importance and include highly pathogenic zoonotic viruses, such as SARS-CoV and MERS-CoV. They are known to efficiently evade early innate immune responses, manifesting in almost negligible expression of type-I interferons (IFN-I). This evasion strategy suggests an evolutionary conserved viral function that has evolved to prevent RNA-based sensing of infection in vertebrate hosts. Here we show that the coronavirus endonuclease (EndoU) activity is key to prevent early induction of double-stranded RNA (dsRNA) host cell responses. Replication of EndoU-deficient coronaviruses is greatly attenuated in vivo and severely restricted in primary cells even during the early phase of the infection. In macrophages we found immediate induction of IFN-I expression and RNase L-mediated breakdown of ribosomal RNA. Accordingly, EndoU-deficient viruses can retain replication only in cells that are deficient in IFN-I expression or sensing, and in cells lacking both RNase L and PKR. Collectively our results demonstrate that the coronavirus EndoU efficiently prevents simultaneous activation of host cell dsRNA sensors, such as Mda5, OAS and PKR. The localization of the EndoU activity at the site of viral RNA synthesis–within the replicase complex—suggests that coronaviruses have evolved a viral RNA decay pathway to evade early innate and intrinsic antiviral host cell responses. PMID:28158275

  19. 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.

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

    Directory of Open Access Journals (Sweden)

    Juan Reguera

    2016-06-01

    Full Text Available 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.

  1. 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.

  2. Cofactor requirement of HpyAV restriction endonuclease.

    Directory of Open Access Journals (Sweden)

    Siu-Hong Chan

    Full Text Available BACKGROUND: Helicobacter pylori is the etiologic agent of common gastritis and a risk factor for gastric cancer. It is also one of the richest sources of Type II restriction-modification (R-M systems in microorganisms. PRINCIPAL FINDINGS: We have cloned, expressed and purified a new restriction endonuclease HpyAV from H. pylori strain 26695. We determined the HpyAV DNA recognition sequence and cleavage site as CCTTC 6/5. In addition, we found that HpyAV has a unique metal ion requirement: its cleavage activity is higher with transition metal ions than in Mg(++. The special metal ion requirement of HpyAV can be attributed to the presence of a HNH catalytic site similar to ColE9 nuclease instead of the canonical PD-X-D/EXK catalytic site found in many other REases. Site-directed mutagenesis was carried out to verify the catalytic residues of HpyAV. Mutation of the conserved metal-binding Asn311 and His320 to alanine eliminated cleavage activity. HpyAV variant H295A displayed approximately 1% of wt activity. CONCLUSIONS/SIGNIFICANCE: Some HNH-type endonucleases have unique metal ion cofactor requirement for optimal activities. Homology modeling and site-directed mutagenesis confirmed that HpyAV is a member of the HNH nuclease family. The identification of catalytic residues in HpyAV paved the way for further engineering of the metal binding site. A survey of sequenced microbial genomes uncovered 10 putative R-M systems that show high sequence similarity to the HpyAV system, suggesting lateral transfer of a prototypic HpyAV-like R-M system among these microorganisms.

  3. II-Q restriction endonucleases--new class of type II enzymes.

    Science.gov (United States)

    Degtyarev, S K; Rechkunova, N I; Kolyhalov, A A; Dedkov, V S; Zhilkin, P A

    1990-10-11

    Unique restriction endonucleases Bpu 10l and Bsil have been isolated from Bacillus pumilas and Bacillus sphaericus, respectively. The recognition sequences and cleavage points of these enzymes have been determinated as 5'-CC1TNAGC-3'/3'-GGANT1CG-5' for Bpu 10l and 5'-C1TCGTG-3'/3'-GAGCA1C-5' for Bsil. Restriction endonucleases Bpu 10l and Bsil represent a new class of enzymes which recognize non-palindromic nucleotide sequences and hydrolize DNA within the recognition sequence. Bpu 10l and Bsil recognition sequences may be regarded as quasipalindromic and the enzymes may be designated as type II-Q restriction endonucleases.

  4. Identification of a new restriction endonuclease R.NciII, from Neisseria cinerea.

    Science.gov (United States)

    Piekarowicz, A

    1994-01-01

    Site-specific restriction endonuclease R. Nci II has been purified from Neisseria cinerea strain 32615. The enzyme recognizes the sequence 5' GATC 3' and its activity is inhibited by the presence of methylated adenine residue within the recognition sequence.

  5. DNase γ Is the Effector Endonuclease for Internucleosomal DNA Fragmentation in Necrosis

    Science.gov (United States)

    Mizuta, Ryushin; Araki, Shinsuke; Furukawa, Makoto; Furukawa, Yuki; Ebara, Syota; Shiokawa, Daisuke; Hayashi, Katsuhiko; Tanuma, Sei-ichi; Kitamura, Daisuke

    2013-01-01

    Apoptosis and necrosis, two major forms of cell death, can be distinguished morphologically and biochemically. Internucleosomal DNA fragmentation (INDF) is a biochemical hallmark of apoptosis, and caspase-activated DNase (CAD), also known as DNA fragmentation factor 40 kDa (DFF40), is one of the major effector endonucleases. DNase γ, a Mg2+/Ca2+-dependent endonuclease, is also known to generate INDF but its role among other apoptosis-associated endonucleases in cell death is unclear. Here we show that (i) INDF occurs even during necrosis in cell lines, primary cells, and in tissues of mice in vivo, and (ii) DNase γ, but not CAD, is the effector endonuclease for INDF in cells undergoing necrosis. These results document a previously unappreciated role for INDF in necrosis and define its molecular basis. PMID:24312463

  6. DNase γ is the effector endonuclease for internucleosomal DNA fragmentation in necrosis.

    Directory of Open Access Journals (Sweden)

    Ryushin Mizuta

    Full Text Available Apoptosis and necrosis, two major forms of cell death, can be distinguished morphologically and biochemically. Internucleosomal DNA fragmentation (INDF is a biochemical hallmark of apoptosis, and caspase-activated DNase (CAD, also known as DNA fragmentation factor 40 kDa (DFF40, is one of the major effector endonucleases. DNase γ, a Mg(2+/Ca(2+-dependent endonuclease, is also known to generate INDF but its role among other apoptosis-associated endonucleases in cell death is unclear. Here we show that (i INDF occurs even during necrosis in cell lines, primary cells, and in tissues of mice in vivo, and (ii DNase γ, but not CAD, is the effector endonuclease for INDF in cells undergoing necrosis. These results document a previously unappreciated role for INDF in necrosis and define its molecular basis.

  7. 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....

  8. Fractured genes: a novel genomic arrangement involving new split inteins and a new homing endonuclease family.

    Science.gov (United States)

    Dassa, Bareket; London, Nir; Stoddard, Barry L; Schueler-Furman, Ora; Pietrokovski, Shmuel

    2009-05-01

    Inteins are genetic elements, inserted in-frame into protein-coding genes, whose products catalyze their removal from the protein precursor via a protein-splicing reaction. Intein domains can be split into two fragments and still ligate their flanks by a trans-protein-splicing reaction. A bioinformatic analysis of environmental metagenomic data revealed 26 different loci with a novel genomic arrangement. In each locus, a conserved enzyme coding region is broken in two by a split intein, with a free-standing endonuclease gene inserted in between. Eight types of DNA synthesis and repair enzymes have this 'fractured' organization. The new types of naturally split-inteins were analyzed in comparison to known split-inteins. Some loci include apparent gene control elements brought in with the endonuclease gene. A newly predicted homing endonuclease family, related to very-short patch repair (Vsr) endonucleases, was found in half of the loci. These putative homing endonucleases also appear in group-I introns, and as stand-alone inserts in the absence of surrounding intervening sequences. The new fractured genes organization appears to be present mainly in phage, shows how endonucleases can integrate into inteins, and may represent a missing link in the evolution of gene breaking in general, and in the creation of split-inteins in particular.

  9. The metabolic enhancer piracetam attenuates mitochondrion-specific endonuclease G translocation and oxidative DNA fragmentation.

    Science.gov (United States)

    Gupta, Sonam; Verma, Dinesh Kumar; Biswas, Joyshree; Rama Raju, K Siva; Joshi, Neeraj; Wahajuddin; Singh, Sarika

    2014-08-01

    This study was performed to investigate the involvement of mitochondrion-specific endonuclease G in piracetam (P)-induced protective mechanisms. Studies have shown the antiapoptotic effects of piracetam but the mechanism of action of piracetam is still an enigma. To assess the involvement of endonuclease G in piracetam-induced protective effects, astrocyte glial cells were treated with lipopolysaccharide (LPS) and piracetam. LPS treatment caused significantly decreased viability, mitochondrial activity, oxidative stress, chromatin condensation, and DNA fragmentation, which were attenuated by piracetam cotreatment. Cotreatment of astrocytes with piracetam showed its significantly time-dependent absorption as observed with high-performance liquid chromatography. Astrocytes treated with piracetam alone showed enhanced mitochondrial membrane potential (MMP) in comparison to control astrocytes. However, in LPS-treated cells no significant alteration in MMP was observed in comparison to control cells. Protein and mRNA levels of the terminal executor of the caspase-mediated pathway, caspase-3, were not altered significantly in LPS or LPS + piracetam-treated astrocytes, whereas endonuclease G was significantly translocated to the nucleus in LPS-treated astrocytes. Piracetam cotreatment attenuated the LPS-induced endonuclease G translocation. In conclusion this study indicates that LPS treatment of astrocytes caused decreased viability, oxidative stress, mitochondrial dysfunction, chromatin condensation, DNA damage, and translocation of endonuclease G to the nucleus, which was inhibited by piracetam cotreatment, confirming that the mitochondrion-specific endonuclease G is one of the factors involved in piracetam-induced protective mechanisms.

  10. 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↓.

  11. Characterization and expression of the mouse endonuclease G gene.

    Science.gov (United States)

    Prats, E; Noël, M; Létourneau, J; Tiranti, V; Vaqué, J; Debón, R; Zeviani, M; Cornudella, L; Ruiz-Carrillo, A

    1997-09-01

    Endonuclease G (Endo G) is a nuclease of prokaryotic lineage found in the mitochondria of vertebrates that has been suggested to play a role in mitochondrial DNA (mtDNA) replication. We have isolated and sequenced the entire mouse endo G gene, determined the limits of the mRNA, and mapped the promoter region. The coding sequence of the single copy gene is interrupted by two introns and analysis of the transcripts does not support a model by which more than one Endo G isoform could be produced by alternative splicing. We have also characterized a full-length human Endo G cDNA and comparison at the protein level of the human, bovine, and murine nucleases indicates a high degree of conservation except in the respective mitochondrial targeting signals. Endo G is ubiquitously expressed and the steady-state levels of its mRNA vary by a factor greater than seven between different tissues. The relationship between the mtDNA copy number and Endo G mRNA levels is not strictly proportional but tissues richer in mtDNA have higher amounts of the mRNA and vice versa.

  12. 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.

  13. Asymmetrical field emitter

    Science.gov (United States)

    Fleming, J.G.; Smith, B.K.

    1995-10-10

    A method is disclosed for providing a field emitter with an asymmetrical emitter structure having a very sharp tip in close proximity to its gate. One preferred embodiment of the present invention includes an asymmetrical emitter and a gate. The emitter having a tip and a side is coupled to a substrate. The gate is connected to a step in the substrate. The step has a top surface and a side wall that is substantially parallel to the side of the emitter. The tip of the emitter is in close proximity to the gate. The emitter is at an emitter potential, and the gate is at a gate potential such that with the two potentials at appropriate values, electrons are emitted from the emitter. In one embodiment, the gate is separated from the emitter by an oxide layer, and the emitter is etched anisotropically to form its tip and its asymmetrical structure. 17 figs.

  14. Altered endoribonuclease activity of apurinic/apyrimidinic endonuclease 1 variants identified in the human population.

    Directory of Open Access Journals (Sweden)

    Wan Cheol Kim

    Full Text Available Apurinic/apyrimidinic endonuclease 1 (APE1 is the major mammalian enzyme in the DNA base excision repair pathway and cleaves the DNA phosphodiester backbone immediately 5' to abasic sites. APE1 also has 3'-5' DNA exonuclease and 3' DNA phosphodiesterase activities, and regulates transcription factor DNA binding through its redox regulatory function. The human APE1 has recently been shown to endonucleolytically cleave single-stranded regions of RNA. Towards understanding the biological significance of the endoribonuclease activity of APE1, we examined eight different amino acid substitution variants of APE1 previously identified in the human population. Our study shows that six APE1 variants, D148E, Q51H, I64V, G241R, R237A, and G306A, exhibit a 76-85% reduction in endoribonuclease activity against a specific coding region of the c-myc RNA, yet fully retain the ability to cleave apurinic/apyrimidinic DNA. We found that two APE1 variants, L104R and E126D, exhibit a unique RNase inhibitor-resistant endoribonuclease activity, where the proteins cleave c-myc RNA 3' of specific single-stranded guanosine residues. Expression of L104R and E126D APE1 variants in bacterial Origami cells leads to a 60-80% reduction in colony formation and a 1.5-fold increase in cell doubling time, whereas the other variants, which exhibit diminished endoribonuclease activity, had no effect. These data indicate that two human APE1 variants exhibit a unique endoribonuclease activity, which correlates with their ability to induce cytotoxicity or slow down growth in bacterial cells and supports the notion of their biological functionality.

  15. Altered endoribonuclease activity of apurinic/apyrimidinic endonuclease 1 variants identified in the human population.

    Science.gov (United States)

    Kim, Wan Cheol; Ma, Conan; Li, Wai-Ming; Chohan, Manbir; Wilson, David M; Lee, Chow H

    2014-01-01

    Apurinic/apyrimidinic endonuclease 1 (APE1) is the major mammalian enzyme in the DNA base excision repair pathway and cleaves the DNA phosphodiester backbone immediately 5' to abasic sites. APE1 also has 3'-5' DNA exonuclease and 3' DNA phosphodiesterase activities, and regulates transcription factor DNA binding through its redox regulatory function. The human APE1 has recently been shown to endonucleolytically cleave single-stranded regions of RNA. Towards understanding the biological significance of the endoribonuclease activity of APE1, we examined eight different amino acid substitution variants of APE1 previously identified in the human population. Our study shows that six APE1 variants, D148E, Q51H, I64V, G241R, R237A, and G306A, exhibit a 76-85% reduction in endoribonuclease activity against a specific coding region of the c-myc RNA, yet fully retain the ability to cleave apurinic/apyrimidinic DNA. We found that two APE1 variants, L104R and E126D, exhibit a unique RNase inhibitor-resistant endoribonuclease activity, where the proteins cleave c-myc RNA 3' of specific single-stranded guanosine residues. Expression of L104R and E126D APE1 variants in bacterial Origami cells leads to a 60-80% reduction in colony formation and a 1.5-fold increase in cell doubling time, whereas the other variants, which exhibit diminished endoribonuclease activity, had no effect. These data indicate that two human APE1 variants exhibit a unique endoribonuclease activity, which correlates with their ability to induce cytotoxicity or slow down growth in bacterial cells and supports the notion of their biological functionality.

  16. Mutations that extend the specificity of the endonuclease activity of lambda terminase.

    Science.gov (United States)

    Arens, J S; Hang, Q; Hwang, Y; Tuma, B; Max, S; Feiss, M

    1999-01-01

    Terminase, an enzyme encoded by the Nu1 and A genes of bacteriophage lambda, is crucial for packaging concatemeric DNA into virions. cosN, a 22-bp segment, is the site on the virus chromosome where terminase introduces staggered nicks to cut the concatemer to generate unit-length virion chromosomes. Although cosN is rotationally symmetric, mutations in cosN have asymmetric effects. The cosN G2C mutation (a G-to-C change at position 2) in the left half of cosN reduces the phage yield 10-fold, whereas the symmetric mutation cosN C11G, in the right half of cosN, does not affect the burst size. The reduction in phage yield caused by cosN G2C is correlated with a defect in cos cleavage. Three suppressors of the cosN G2C mutation, A-E515G, A-N509K, and A-R504C, have been isolated that restore the yield of lambda cosN G2C to the wild-type level. The suppressors are missense mutations that alter amino acids located near an ATPase domain of gpA. lambda A-E515G, A-N509K, and A-R504C phages, which are cosN+, also had wild-type burst sizes. In vitro cos cleavage experiments on cosN G2C C11G DNA showed that the rate of cleavage for A-E515G terminase is three- to fourfold higher than for wild-type terminase. The A-E515G mutation changes residue 515 of gpA from glutamic acid to glycine. Uncharged polar and hydrophobic residues at position 515 suppressed the growth defect of lambda cosN G2C C11G. In contrast, basic (K, R) and acidic (E, D) residues at position 515 failed to suppress the growth defect of lambda cosN G2C C11G. In a lambda cosN+ background, all amino acids tested at position 515 were functional. These results suggest that A-E515G plays an indirect role in extending the specificity of the endonuclease activity of lambda terminase.

  17. 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

  18. 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.

  19. 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.

  20. The structure-specific endonuclease Ercc1–Xpf is required for targeted gene replacement in embryonic stem cells

    Science.gov (United States)

    Niedernhofer, Laura J.; Essers, Jeroen; Weeda, Geert; Beverloo, Berna; de Wit, Jan; Muijtjens, Manja; Odijk, Hanny; Hoeijmakers, Jan H.J.; Kanaar, Roland

    2001-01-01

    The Ercc1–Xpf heterodimer, a highly conserved structure-specific endonuclease, functions in multiple DNA repair pathways that are pivotal for maintaining genome stability, including nucleotide excision repair, interstrand crosslink repair and homologous recombination. Ercc1–Xpf incises double-stranded DNA at double-strand/single-strand junctions, making it an ideal enzyme for processing DNA structures that contain partially unwound strands. Here we demonstrate that although Ercc1 is dispensable for recombination between sister chromatids, it is essential for targeted gene replacement in mouse embryonic stem cells. Surprisingly, the role of Ercc1–Xpf in gene targeting is distinct from its previously identified role in removing nonhomologous termini from recombination intermediates because it was required irrespective of whether the ends of the DNA targeting constructs were heterologous or homologous to the genomic locus. Our observations have implications for the mechanism of gene targeting in mammalian cells and define a new role for Ercc1–Xpf in mammalian homologous recombination. We propose a model for the mechanism of targeted gene replacement that invokes a role for Ercc1–Xpf in making the recipient genomic locus receptive for gene replacement. PMID:11707424

  1. Electrostatic-Induced Assembly of Graphene-Encapsulated Carbon@Nickel-Aluminum Layered Double Hydroxide Core-Shell Spheres Hybrid Structure for High-Energy and High-Power-Density Asymmetric Supercapacitor.

    Science.gov (United States)

    Wu, Shuxing; Hui, Kwan San; Hui, Kwun Nam; Kim, Kwang Ho

    2017-01-18

    Achieving high energy density while retaining high power density is difficult in electrical double-layer capacitors and in pseudocapacitors considering the origin of different charge storage mechanisms. Rational structural design became an appealing strategy in circumventing these trade-offs between energy and power densities. A hybrid structure consists of chemically converted graphene-encapsulated carbon@nickel-aluminum layered double hydroxide core-shell spheres as spacers among graphene layers (G-CLS) used as an advanced electrode to achieve high energy density while retaining high power density for high-performance supercapacitors. The merits of the proposed architecture are as follows: (1) CLS act as spacers to avoid the close restacking of graphene; (2) highly conductive carbon sphere and graphene preserve the mechanical integrity and improve the electrical conductivity of LDHs hybrid. Thus, the proposed hybrid structure can simultaneously achieve high electrical double-layer capacitance and pseudocapacitance resulting in the overall highly active electrode. The G-CLS electrode exhibited high specific capacitance (1710.5 F g(-1) at 1 A g(-1)) under three-electrode tests. An ASC fabricated using the G-CLS as positive electrode and reduced graphite oxide as negative electrode demonstrated remarkable electrochemical performance. The ASC device operated at 1.4 V and delivered a high energy density of 35.5 Wh kg(-1) at a 670.7 W kg(-1) power density at 1 A g(-1) with an excellent rate capability as well as a robust long-term cycling stability of up to 10 000 cycles.

  2. Multiplex, rapid and sensitive isothermal detection of nucleic-acid sequence by endonuclease restriction-mediated real-time multiple cross displacement amplification

    Directory of Open Access Journals (Sweden)

    Yi eWang

    2016-05-01

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

  3. 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-in...

  4. 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.

  5. Asymmetric extractions in orthodontics

    OpenAIRE

    Camilo Aquino Melgaço; Mônica Tirre de Souza Araújo

    2012-01-01

    INTRODUCTION: Extraction decisions are extremely important in during treatment planning. In addition to the extraction decision orthodontists have to choose what tooth should be extracted for the best solution of the problem and the esthetic/functional benefit of the patient. OBJECTIVE: This article aims at reviewing the literature relating the advantages, disadvantages and clinical implications of asymmetric extractions to orthodontics. METHODS: Keywords were selected in English and Portugue...

  6. Asymmetric Evolutionary Games.

    Directory of Open Access Journals (Sweden)

    Alex McAvoy

    2015-08-01

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

  7. Asymmetric extractions in orthodontics

    Directory of Open Access Journals (Sweden)

    Camilo Aquino Melgaço

    2012-04-01

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

  8. 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.

  9. 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.

  10. 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.

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

    Science.gov (United States)

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

    1989-01-01

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

  12. 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.

  13. Gelatinases, endonuclease and Vascular Endothelial Growth Factor during development and regression of swine luteal tissue

    Directory of Open Access Journals (Sweden)

    Bacci Maria

    2006-11-01

    Full Text Available Abstract Background The development and regression of corpus luteum (CL is characterized by an intense angiogenesis and angioregression accompanied by luteal tissue and extracellular matrix (ECM remodelling. Vascular Endothelial Growth Factor (VEGF is the main regulator of angiogenesis, promoting endothelial cell mitosis and differentiation. After the formation of neovascular tubes, the remodelling of ECM is essential for the correct development of CL, particularly by the action of specific class of proteolytic enzymes known as matrix metalloproteinases (MMPs. During luteal regression, characterized by an apoptotic process and successively by an intense ECM and luteal degradation, the activation of Ca++/Mg++-dependent endonucleases and MMPs activity are required. The levels of expression and activity of VEGF, MMP-2 and -9, and Ca++/Mg++-dependent endonucleases throughout the oestrous cycle and at pregnancy were analyzed. Results Different patterns of VEGF, MMPs and Ca++/Mg++-dependent endonuclease were observed in swine CL during different luteal phases and at pregnancy. Immediately after ovulation, the highest levels of VEGF mRNA/protein and MMP-9 activity were detected. On days 5–14 after ovulation, VEGF expression and MMP-2 and -9 activities are at basal levels, while Ca++/Mg++-dependent endonuclease levels increased significantly in relation to day 1. Only at luteolysis (day 17, Ca++/Mg++-dependent endonuclease and MMP-2 spontaneous activity increased significantly. At pregnancy, high levels of MMP-9 and VEGF were observed. Conclusion Our findings, obtained from a precisely controlled in vivo model of CL development and regression, allow us to determine relationships among VEGF, MMPs and endonucleases during angiogenesis and angioregression. Thus, CL provides a very interesting model for studying factors involved in vascular remodelling.

  14. ASYMMETRICAL COUPLING DOUBLE QUANTUM WELL INTERMIXING INDUCED BY COMBINATORIAL PROTON IMPLANTATION%组合注入质子导致不对称耦合双量子阱界面混合效应研究

    Institute of Scientific and Technical Information of China (English)

    缪中林; 陈平平; 蔡炜颖; 李志锋; 袁先漳; 刘平; 史国良; 徐文兰; 陆卫; 陈昌明; 朱德彰; 潘浩昌; 胡军; 李明乾

    2001-01-01

    用分子束外延系统(MBE)生长了GaAs/AlGaAs不对称耦合双量子阱(ACDQW),采用组合注入质子的方法,在同一块衬底上获得了不同注入剂量的GaAs/AlGaAs不对称耦合双量子阱单元,没有经过快速热退火的过程,在常温下测量了不同注入剂量量子阱单元的显微光荧光谱和光调制反射光谱,发现了各区域子带间跃迁能量最大变化范围达到81meV.由于样品未作高温热退火处理,为此由Al组分误差函数模型推导的扩散长度要大大高于扩散系数公式.耦合量子阱的界面混合效应对于质子注入非常敏感.%With combinatorial proton implantation, we obtained several areas with different implantation doses in single wafer of GaAs/AlGaAs asymmetry coupling double quantum well grown by MBE, and studied the optical characteristics with photoluminescence (PL) and photo-modulated reflectance(PR). Without rapid thermal annealing, maximum transition energy shift 81 meV was obtained in single wafer. The diffusion lengths of Al component calculated from error function were larger than that calculated from coefficient of diffusion formula. The interface effect of double quantum well is sensitive to proton implantation.

  15. 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.

  16. 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

  17. 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

  18. Asymmetric flow networks

    OpenAIRE

    Olaizola Ortega, María Norma; Valenciano Llovera, Federico

    2012-01-01

    This paper provides a new model of network formation that bridges the gap between the two benchmark models by Bala and Goyal, the one-way flow model, and the two-way flow model, and includes both as particular extreme cases. As in both benchmark models, in what we call an "asymmetric flow" network a link can be initiated unilaterally by any player with any other, and the flow through a link towards the player who supports it is perfect. Unlike those models, in the opposite direction there is ...

  19. 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.

  20. Double injection/single detection asymmetric flow injection manifold for spectrophotometric determination of ascorbic acid and uric acid: Selection the optimal conditions by MCDM approach based on different criteria weighting methods

    Science.gov (United States)

    Boroumand, Samira; Chamjangali, Mansour Arab; Bagherian, Ghadamali

    2017-03-01

    A simple and sensitive double injection/single detector flow injection analysis (FIA) method is proposed for the simultaneous kinetic determination of ascorbic acid (AA) and uric acid (UA). This method is based upon the difference between the rates of the AA and UA reactions with Fe3 + in the presence of 1, 10-phenanthroline (phen). The absorbance of Fe2 +/1, 10-phenanthroline (Fe-phen) complex obtained as the product was measured spectrophotometrically at 510 nm. To reach a good accuracy in the differential kinetic determination via the mathematical manipulations of the transient signals, different criteria were considered in the selection of the optimum conditions. The multi criteria decision making (MCDM) approach was applied for the selection of the optimum conditions. The importance weights of the evaluation criteria were determined using the analytic hierarchy process, entropy method, and compromised weighting (CW). The experimental conditions (alternatives) were ranked by the technique for order preference by similarity to an ideal solution. Under the selected optimum conditions, the obtained analytical signals were linear in the ranges of 0.50-5.00 and 0.50-4.00 mg L- 1 for AA and UA, respectively. The 3σ detection limits were 0.07 mg L- 1 for AA and 0.12 mg L- 1 for UA. The relative standard deviations for four replicate determinations of AA and UA were 2.03% and 3.30% respectively. The method was also applied for the analysis of analytes in the blood serum, Vitamine C tablets, and tap water with satisfactory results.

  1. 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...

  2. T7 Endonuclease I Mediates Error Correction in Artificial Gene Synthesis.

    Science.gov (United States)

    Sequeira, Ana Filipa; Guerreiro, Catarina I P D; Vincentelli, Renaud; Fontes, Carlos M G A

    2016-09-01

    Efficacy of de novo gene synthesis largely depends on the quality of overlapping oligonucleotides used as template for PCR assembly. The error rate associated with current gene synthesis protocols limits the efficient and accurate production of synthetic genes, both in the small and large scales. Here, we analysed the ability of different endonuclease enzymes, which specifically recognize and cleave DNA mismatches resulting from incorrect impairments between DNA strands, to remove mutations accumulated in synthetic genes. The gfp gene, which encodes the green fluorescent protein, was artificially synthesized using an integrated protocol including an enzymatic mismatch cleavage step (EMC) following gene assembly. Functional and sequence analysis of resulting artificial genes revealed that number of deletions, insertions and substitutions was strongly reduced when T7 endonuclease I was used for mutation removal. This method diminished mutation frequency by eightfold relative to gene synthesis not incorporating an error correction step. Overall, EMC using T7 endonuclease I improved the population of error-free synthetic genes, resulting in an error frequency of 0.43 errors per 1 kb. Taken together, data presented here reveal that incorporation of a mutation-removal step including T7 endonuclease I can effectively improve the fidelity of artificial gene synthesis.

  3. 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

  4. Efficient targeting of a SCID gene by an engineered single-chain homing endonuclease.

    Science.gov (United States)

    Grizot, Sylvestre; Smith, Julianne; Daboussi, Fayza; Prieto, Jesús; Redondo, Pilar; Merino, Nekane; Villate, Maider; Thomas, Séverine; Lemaire, Laetitia; Montoya, Guillermo; Blanco, Francisco J; Pâques, Frédéric; Duchateau, Philippe

    2009-09-01

    Sequence-specific endonucleases recognizing long target sequences are emerging as powerful tools for genome engineering. These endonucleases could be used to correct deleterious mutations or to inactivate viruses, in a new approach to molecular medicine. However, such applications are highly demanding in terms of safety. Mutations in the human RAG1 gene cause severe combined immunodeficiency (SCID). Using the I-CreI dimeric LAGLIDADG meganuclease as a scaffold, we describe here the engineering of a series of endonucleases cleaving the human RAG1 gene, including obligate heterodimers and single-chain molecules. We show that a novel single-chain design, in which two different monomers are linked to form a single molecule, can induce high levels of recombination while safeguarding more effectively against potential genotoxicity. We provide here the first demonstration that an engineered meganuclease can induce targeted recombination at an endogenous locus in up to 6% of transfected human cells. These properties rank this new generation of endonucleases among the best molecular scissors available for genome surgery strategies, potentially avoiding the deleterious effects of previous gene therapy approaches.

  5. 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-

  6. 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

  7. 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.

  8. Seamless gene tagging by endonuclease-driven homologous recombination.

    Directory of Open Access Journals (Sweden)

    Anton Khmelinskii

    Full Text Available Gene tagging facilitates systematic genomic and proteomic analyses but chromosomal tagging typically disrupts gene regulatory sequences. Here we describe a seamless gene tagging approach that preserves endogenous gene regulation and is potentially applicable in any species with efficient DNA double-strand break repair by homologous recombination. We implement seamless tagging in Saccharomyces cerevisiae and demonstrate its application for protein tagging while preserving simultaneously upstream and downstream gene regulatory elements. Seamless tagging is compatible with high-throughput strain construction using synthetic genetic arrays (SGA, enables functional analysis of transcription antisense to open reading frames and should facilitate systematic and minimally-invasive analysis of gene functions.

  9. 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.

  10. Families of asymmetric periodic solutions in the restricted four-body problem

    Science.gov (United States)

    Papadakis, K. E.

    2016-12-01

    Very recently, we presented five of the basic families of the network of periodic orbits of the restricted four-body problem which are simple, i.e. one intersection with the horizontal x-axis at the half period, symmetric with respect to the same axis and asymmetric with respect to the vertical y-axis. In the present work, using these families, we found series of asymmetric critical orbits for various values of the primaries m2 and m3. From these critical orbits we calculate and present five new families of simple periodic orbits which are asymmetric with respect to both the x- and y-axis. Additionally, we describe a grid method in the (x0, dot{x}0) plane and we obtain initial conditions for new asymmetric double-periodic orbits. We determine ten families of asymmetric double-periodic orbits from the bifurcations of the previous five asymmetric families using the special generating horizontally critical periodic orbits. The stability of each calculated asymmetric periodic orbit is also studied. Characteristic curves as well as stability diagrams of these families are illustrated. In the last section we present the evolution of the five basic families of simple asymmetric periodic orbits when the primaries are the Sun the Jupiter and the 2797 Teucer Asteroid.

  11. Additive Effects on Asymmetric Catalysis.

    Science.gov (United States)

    Hong, Liang; Sun, Wangsheng; Yang, Dongxu; Li, Guofeng; Wang, Rui

    2016-03-23

    This review highlights a number of additives that can be used to make asymmetric reactions perfect. Without changing other reaction conditions, simply adding additives can lead to improved asymmetric catalysis, such as reduced reaction time, improved yield, or/and increased selectivity.

  12. Effect of multifunctional protein YB-1 on the AP site cleavage by AP endonuclease 1 and tyrosyl phosphodiesterase 1

    Directory of Open Access Journals (Sweden)

    Ovchinnikov L. P.

    2012-07-01

    Full Text Available Apurinic/apyrimidinic sites (AP sites which represent one of the most abundantly generated DNA lesions in the cell are generally repaired by base excision repair (BER pathway. Multifunctional protein YB-1 is known to participate in cellular response to genotoxic stress and was shown to interact with several components of BER – DNA glycosylases NTH1, NEIL2, DNA polymerase and DNA ligase III. Therefore, it is of great interest to investigate the influence of YB-1 on one of the major BER enzymes, responsible for AP site cleavage, AP endonuclease APE1, and on tyrosyl phosphodiesterase Tdp1, participating in APE1 independent pathway of AP site repair. Aim. Effect of multifunctional protein YB-1 on the AP site cleavage by the activities of APE1 and Tdp1 was studied. Methods. Gel-mobility shift assays and enzyme activity tests. Results. YB-1 was shown to inhibit the cleavage of AP site located in single-stranded DNA by both APE1 and Tdp1. Stimulation of APE1 activity on protruding double-stranded DNA in the presence of YB-1 was observed, whereas no effect on Tdp1-mediated cleavage of AP site in double-stranded DNA was found. Conclusions. YB-1 can modulate the repair of AP sites in DNA by both positively stimulating APE1 during the classic BER of AP sites and avoiding a possible generation of doublestrand breaks, arising from the cleavage of single-stranded portion of DNA substrate already used by different DNA-processing pathway

  13. The asymmetric sandwich theorem

    CERN Document Server

    Simons, Stephen

    2011-01-01

    We discuss the asymmetric sandwich theorem, a generalization of the Hahn-Banach theorem. As applications, we derive various results on the existence of linear functionals that include bivariate, trivariate and quadrivariate generalizations of the Fenchel duality theorem. Most of the results are about affine functions defined on convex subsets of vector spaces, rather than linear functions defined on vector spaces. We consider both results that use a simple boundedness hypothesis (as in Rockafellar's version of the Fenchel duality theorem) and also results that use Baire's theorem (as in the Robinson-Attouch-Brezis version of the Fenchel duality theorem). This paper also contains some new results about metrizable topological vector spaces that are not necessarily locally convex.

  14. 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.

  15. 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.

  16. Asymmetric responses of international stock markets to trading volume

    Science.gov (United States)

    Gerlach, Richard; Chen, Cathy W. S.; Lin, Doris S. Y.; Huang, Ming-Hsiang

    2006-02-01

    The major goal of this paper is to examine the hypothesis that stock returns and return volatility are asymmetric, threshold nonlinear, functions of change in trading volume. A minor goal is to examine whether return spillover effects also display such asymmetry. Employing a double-threshold GARCH model with trading volume as a threshold variable, we find strong evidence supporting this hypothesis in five international market return series. Asymmetric causality tests lend further support to our trading volume threshold model and conclusions. Specifically, an increase in volume is positively associated, while decreasing volume is negatively associated, with the major price index in four of the five markets. The volatility of each series also displays an asymmetric reaction, four of the markets display higher volatility following increases in trading volume. Using posterior odds ratio, the proposed threshold model is strongly favored in three of the five markets, compared to a US news double threshold GARCH model and a symmetric GARCH model. We also find significant nonlinear asymmetric return spillover effects from the US market.

  17. 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.

  18. Quantitation and analysis of the formation of HO-endonuclease stimulated chromosomal translocations by single-strand annealing in Saccharomyces cerevisiae.

    Science.gov (United States)

    Liddell, Lauren; Manthey, Glenn; Pannunzio, Nicholas; Bailis, Adam

    2011-09-23

    Genetic variation is frequently mediated by genomic rearrangements that arise through interaction between dispersed repetitive elements present in every eukaryotic genome. This process is an important mechanism for generating diversity between and within organisms(1-3). The human genome consists of approximately 40% repetitive sequence of retrotransposon origin, including a variety of LINEs and SINEs(4). Exchange events between these repetitive elements can lead to genome rearrangements, including translocations, that can disrupt gene dosage and expression that can result in autoimmune and cardiovascular diseases(5), as well as cancer in humans(6-9). Exchange between repetitive elements occurs in a variety of ways. Exchange between sequences that share perfect (or near-perfect) homology occurs by a process called homologous recombination (HR). By contrast, non-homologous end joining (NHEJ) uses little-or-no sequence homology for exchange(10,11). The primary purpose of HR, in mitotic cells, is to repair double-strand breaks (DSBs) generated endogenously by aberrant DNA replication and oxidative lesions, or by exposure to ionizing radiation (IR), and other exogenous DNA damaging agents. In the assay described here, DSBs are simultaneously created bordering recombination substrates at two different chromosomal loci in diploid cells by a galactose-inducible HO-endonuclease (Figure 1). The repair of the broken chromosomes generates chromosomal translocations by single strand annealing (SSA), a process where homologous sequences adjacent to the chromosome ends are covalently joined subsequent to annealing. One of the substrates, his3-Δ3', contains a 3' truncated HIS3 allele and is located on one copy of chromosome XV at the native HIS3 locus. The second substrate, his3-Δ5', is located at the LEU2 locus on one copy of chromosome III, and contains a 5' truncated HIS3 allele. Both substrates are flanked by a HO endonuclease recognition site that can be targeted for

  19. 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...

  20. 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.

  1. Analysis of simian virus 40 DNA with the restriction enzyme of Haemophilus aegyptius, endonuclease Z.

    Science.gov (United States)

    Huang, E S; Newbold, J E; Pagano, J S

    1973-04-01

    Limited digestion of simian virus 40 (SV40) DNA from both small- and large- plaque strains with the restriction endonuclease Z from Haemophilus aegyptius yielded 10 specific fragments. The number of nucleotide pairs for each fragment, determined by co-electrophoresis with phiX174 RF fragments produced by endonuclease Z, ranges from 2,050 to 80. The difference in the pattern between the large- and small-plaque strains is the disappearance of one fragment containing approximately 255 nucleotide pairs and the appearance of a new fragment with 145 nucleotide pairs. This finding can be explained either by deletions or insertions totaling 110 nucleotide pairs. Complementary RNA synthesized in vitro from the adeno-SV40 hybrid virus, strain ND-1, hybridized preferentially to four of the fragments of SV40 DNA.

  2. Asymmetric Gepner Models (Revisited)

    CERN Document Server

    Gato-Rivera, B

    2010-01-01

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

  3. 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.

  4. 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.

  5. 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.

  6. Three Structure-Selective Endonucleases Are Essential in the Absence of BLM Helicase in Drosophila

    OpenAIRE

    Sabrina L Andersen; H Kenny Kuo; Daniel Savukoski; Brodsky, Michael H.; Jeff Sekelsky

    2011-01-01

    DNA repair mechanisms in mitotically proliferating cells avoid generating crossovers, which can contribute to genome instability. Most models for the production of crossovers involve an intermediate with one or more four-stranded Holliday junctions (HJs), which are resolved into duplex molecules through cleavage by specialized endonucleases. In vitro studies have implicated three nuclear enzymes in HJ resolution: MUS81-EME1/Mms4, GEN1/Yen1, and SLX4-SLX1. The Bloom syndrome helicase, BLM, pla...

  7. 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.

  8. Site specific endonucleases for human genome mapping. Final report, April 1, 1992--March 31, 1994

    Energy Technology Data Exchange (ETDEWEB)

    Knoche, K.; Selman, S.; Hung, L. [and others

    1994-06-01

    Current large scale genome mapping methodology suffers from a lack of tools for generating specific DNA fragments in the megabase size range. While technology such as pulsed field gel electrophoresis can resolve DNA fragments greater than 10 megabases in size, current methods for cleaving mammalian DNA using bacterial restriction enzymes are incapable of producing such fragments. Though several multidimensional approaches are underway to overcome this limitation, there currently is no single step procedure to generate specific DNA fragments in the 2-100 megabase size range. In order to overcome these limitations, we proposed to develop a family of site-specific endonucleases capable of generating DNA fragments in the 2-100 megabase size range in a single step. Additionally, we proposed to accomplish this by relaxing the specificity of a very-rare cutting intron-encoded endonucleases, I-Ppo I, and potentially using the process as a model for development of other enzymes. Our research has uncovered a great deal of information about intron-encoded endonucleases. We have found that I-Ppo I has a remarkable ability to tolerate degeneracy within its recognition sequence, and we have shown that the recognition sequence is larger than 15 base pairs. These findings suggest that a detailed study of the mechanism by which intron-encoded endonucleases recognize their target sequences should provide new sights into DNA-protein interactions; this had led to a continuation of the study of I-Ppo I in Dr. Raines` laboratory and we expect a more detailed understanding of the mechanism of I-Ppo I action to result.

  9. Chromosomal context and epigenetic mechanisms control the efficacy of genome editing by rare-cutting designer endonucleases.

    Science.gov (United States)

    Daboussi, Fayza; Zaslavskiy, Mikhail; Poirot, Laurent; Loperfido, Mariana; Gouble, Agnès; Guyot, Valerie; Leduc, Sophie; Galetto, Roman; Grizot, Sylvestre; Oficjalska, Danusia; Perez, Christophe; Delacôte, Fabien; Dupuy, Aurélie; Chion-Sotinel, Isabelle; Le Clerre, Diane; Lebuhotel, Céline; Danos, Olivier; Lemaire, Frédéric; Oussedik, Kahina; Cédrone, Frédéric; Epinat, Jean-Charles; Smith, Julianne; Yáñez-Muñoz, Rafael J; Dickson, George; Popplewell, Linda; Koo, Taeyoung; VandenDriessche, Thierry; Chuah, Marinee K; Duclert, Aymeric; Duchateau, Philippe; Pâques, Frédéric

    2012-07-01

    The ability to specifically engineer the genome of living cells at precise locations using rare-cutting designer endonucleases has broad implications for biotechnology and medicine, particularly for functional genomics, transgenics and gene therapy. However, the potential impact of chromosomal context and epigenetics on designer endonuclease-mediated genome editing is poorly understood. To address this question, we conducted a comprehensive analysis on the efficacy of 37 endonucleases derived from the quintessential I-CreI meganuclease that were specifically designed to cleave 39 different genomic targets. The analysis revealed that the efficiency of targeted mutagenesis at a given chromosomal locus is predictive of that of homologous gene targeting. Consequently, a strong genome-wide correlation was apparent between the efficiency of targeted mutagenesis (≤ 0.1% to ≈ 6%) with that of homologous gene targeting (≤ 0.1% to ≈ 15%). In contrast, the efficiency of targeted mutagenesis or homologous gene targeting at a given chromosomal locus does not correlate with the activity of individual endonucleases on transiently transfected substrates. Finally, we demonstrate that chromatin accessibility modulates the efficacy of rare-cutting endonucleases, accounting for strong position effects. Thus, chromosomal context and epigenetic mechanisms may play a major role in the efficiency rare-cutting endonuclease-induced genome engineering.

  10. 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 life....

  11. 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.

  12. 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

  13. 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.

  14. Asymmetric cation-binding catalysis

    DEFF Research Database (Denmark)

    Oliveira, Maria Teresa; Lee, Jiwoong

    2017-01-01

    and KCN, are selectively bound to the catalyst, providing exceptionally high enantioselectivities for kinetic resolutions, elimination reactions (fluoride base), and Strecker synthesis (cyanide nucleophile). Asymmetric cation-binding catalysis was recently expanded to silicon-based reagents, enabling...... solvents, thus increasing their applicability in synthesis. The expansion of this concept to chiral polyethers led to the emergence of asymmetric cation-binding catalysis, where chiral counter anions are generated from metal salts, particularly using BINOL-based polyethers. Alkali metal salts, namely KF...

  15. Asymmetric tandem organic solar cells

    Science.gov (United States)

    Howells, Thomas J.

    Organic photovoltaics (OPVs) is an area that has attracted much attention recently as a potential low cost, sustainable source of energy with a good potential for full-scale commercialisation. Understanding the factors that determine the efficiency of such cells is therefore a high priority, as well as developing ways to boost efficiency to commercially-useful levels. In addition to an intensive search for new materials, significant effort has been spent on ways to squeeze more performance out of existing materials, such as multijunction cells. This thesis investigates double junction tandem cells in the context of small molecule organic materials. . Two different organic electron donor materials, boron subphthalocyanine chloride (SubPc) and aluminium phthalocyanine chloride (ClAlPc) were used as donors in heterojunctions with C60 to create tandem cells for this thesis. These materials have been previously used for solar cells and the absorption spectra of the donor materials complement each other, making them good candidates for tandem cell architectures. The design of the recombination layer between the cells is considered first, with silver nanoparticles demonstrated to work well as recombination centres for charges from the front and back sub-cells, necessary to avoid a charge build-up at the interface. The growth conditions for the nanoparticles are optimised, with the tandem cells outperforming the single heterojunction architecture. Optical modelling is considered as a method to improve the understanding of thin film solar cells, where interference effects from the reflective aluminium electrode are important in determining the magnitude of absorption a cell can achieve. The use of such modelling is first demonstrated in hybrid solar cells based on a SubPc donor with a titanium oxide (TiOx) acceptor; this system is ideal for observing the effects of interference as only the SubPc layer has significant absorption. The modelling is then applied to tandem cells

  16. 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.

  17. Arabidopsis ZDP DNA 3'-phosphatase and ARP endonuclease function in 8-oxoG repair initiated by FPG and OGG1 DNA glycosylases.

    Science.gov (United States)

    Córdoba-Cañero, Dolores; Roldán-Arjona, Teresa; Ariza, Rafael R

    2014-09-01

    Oxidation of guanine in DNA generates 7,8-dihydro-8-oxoguanine (8-oxoG), an ubiquitous lesion with mutagenic properties. 8-oxoG is primarily removed by DNA glycosylases distributed in two families, typified by bacterial Fpg proteins and eukaryotic Ogg1 proteins. Interestingly, plants possess both Fpg and Ogg1 homologs but their relative contributions to 8-oxoG repair remain uncertain. In this work we used Arabidopsis cell-free extracts to monitor 8-oxoG repair in wild-type and mutant plants. We found that both FPG and OGG1 catalyze excision of 8-oxoG in Arabidopsis cell extracts by a DNA glycosylase/lyase mechanism, and generate repair intermediates with blocked 3'-termini. An increase in oxidative damage is detected in both nuclear and mitochondrial DNA from double fpg ogg1 mutants, but not in single mutants, which suggests that a single deficiency in one of these DNA glycosylases may be compensated by the other. We also found that the DNA 3'-phosphatase ZDP (zinc finger DNA 3'-phosphoesterase) and the AP(apurinic/apyirmidinic) endonuclease ARP(apurinic endonuclease redox protein) are required in the 8-oxoG repair pathway to process the 3'-blocking ends generated by FPG and OGG1. Furthermore, deficiencies in ZDP and/or ARP decrease germination ability after seed deteriorating conditions. Altogether, our results suggest that Arabidopsis cells use both FPG and OGG1 to repair 8-oxoG in a pathway that requires ZDP and ARP in downstream steps.

  18. 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.

  19. 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

  20. Nonlinear effects in asymmetric catalysis.

    Science.gov (United States)

    Satyanarayana, Tummanapalli; Abraham, Susan; Kagan, Henri B

    2009-01-01

    There is a need for the preparation of enantiomerically pure compounds for various applications. An efficient approach to achieve this goal is asymmetric catalysis. The chiral catalyst is usually prepared from a chiral auxiliary, which itself is derived from a natural product or by resolution of a racemic precursor. The use of non-enantiopure chiral auxiliaries in asymmetric catalysis seems unattractive to preparative chemists, since the anticipated enantiomeric excess (ee) of the reaction product should be proportional to the ee value of the chiral auxiliary (linearity). In fact, some deviation from linearity may arise. Such nonlinear effects can be rich in mechanistic information and can be synthetically useful (asymmetric amplification). This Review documents the advances made during the last decade in the use of nonlinear effects in the area of organometallic and organic catalysis.

  1. 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.

  2. 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...

  3. Human SLX4 is a Holliday junction resolvase subunit that binds multiple DNA repair/recombination endonucleases.

    Science.gov (United States)

    Fekairi, Samira; Scaglione, Sarah; Chahwan, Charly; Taylor, Ewan R; Tissier, Agnès; Coulon, Stéphane; Dong, Meng-Qiu; Ruse, Cristian; Yates, John R; Russell, Paul; Fuchs, Robert P; McGowan, Clare H; Gaillard, Pierre-Henri L

    2009-07-10

    Structure-specific endonucleases resolve DNA secondary structures generated during DNA repair and recombination. The yeast 5' flap endonuclease Slx1-Slx4 has received particular attention with the finding that Slx4 has Slx1-independent key functions in genome maintenance. Although Slx1 is a highly conserved protein in eukaryotes, no orthologs of Slx4 were reported other than in fungi. Here we report the identification of Slx4 orthologs in metazoa, including fly MUS312, essential for meiotic recombination, and human BTBD12, an ATM/ATR checkpoint kinase substrate. Human SLX1-SLX4 displays robust Holliday junction resolvase activity in addition to 5' flap endonuclease activity. Depletion of SLX1 and SLX4 results in 53BP1 foci accumulation and H2AX phosphorylation as well as cellular hypersensitivity to MMS. Furthermore, we show that SLX4 binds the XPF(ERCC4) and MUS81 subunits of the XPF-ERCC1 and MUS81-EME1 endonucleases and is required for DNA interstrand crosslink repair. We propose that SLX4 acts as a docking platform for multiple structure-specific endonucleases.

  4. Identification of a uniquely immunodominant, cross-reacting site in the human immunodeficiency virus endonuclease protein.

    Science.gov (United States)

    Björling, E; Utter, G; Stålhandske, P; Norrby, E; Chiodi, F

    1991-01-01

    One of the features of the life cycle of retroviruses is insertion of the proviral DNA into host chromosomes. A protein encoded by the 3' end of the pol gene of the virus genome has been shown to possess endonuclease activity (D. P. Grandgenett, A. C. Vora, and R. D. Schiff, Virology 89:119-132, 1978), which is necessary for DNA integration. Sera from the majority of human immunodeficiency virus (HIV)-infected individuals react with endonuclease protein p31 in serological tests (J. S. Allan, J. E. Coligan, T.-H. Lee, F. Barin, P. J. Kanki, S. M'Boup, M. F. McLane, J. E. Groopman, and M. Essex, Blood 69:331-333, 1987; E. F. Lillehoj, F. H. R. Salazar, R. J. Mervis, M. G. Raum, H. W. Chan, N. Ahmad, and S. Venkatesan, J. Virol. 62:3053-3058, 1988; K. S. Steimer, K. W. Higgins, M. A. Powers, J. C. Stephans, A. Gyenes, G. George-Nascimento, P. A. Liciw, P. J. Barr, R. A. Hallewell, and R. Sanchez-Pescador, J. Virol. 58:9-16, 1986). It is not known, however, which part of the protein represents the target(s) for antibody response. To study this, we synthesized peptides and used them in an enzyme-linked immunosorbent assay system to map the reactivity of human immunodeficiency virus type 1 (HIV-1) antibody-positive sera to the different regions of the HIV endonuclease. A uniquely antigenic, HIV-1- and HIV-2-cross-reacting site was identified in the central part of this protein from Phe-663 to Trp-670. PMID:2072463

  5. Geographically diverse Australian isolates of Melissococcus pluton exhibit minimal genotypic diversity by restriction endonuclease analysis.

    Science.gov (United States)

    Djordjevic, S P; Smith, L A; Forbes, W A; Hornitzky, M A

    1999-04-15

    Melissococcus pluton, the causative agent of European foulbrood is an economically significant disease of honey bees (Apis mellifera) across most regions of the world and is prevalent throughout most states of Australia. 49 Isolates of M. pluton recovered from diseased colonies or honey samples in New South Wales, Queensland, South Australia, Tasmania and Victoria were compared using SDS-PAGE, Western immunoblotting and restriction endonuclease analyses. DNA profiles of all 49 geographically diverse isolates showed remarkably similar AluI profiles although four isolates (one each from Queensland, South Australia, New South Wales and Victoria) displayed minor profile variations compared to AluI patterns of all other isolates. DNA from a subset of the 49 Australian and three isolates from the United Kingdom were digested separately with the restriction endonucleases CfoI, RsaI and DraI. Restriction endonuclease fragment patterns generated using these enzymes were also similar although minor variations were noted. SDS-PAGE of whole cell proteins from 13 of the 49 isolates from different states of Australia, including the four isolates which displayed minor profile variations (AluI) produced indistinguishable patterns. Major immunoreactive proteins of approximate molecular masses of 21, 24, 28, 30, 36, 40, 44, 56, 60, 71, 79 and 95 kDa were observed in immunoblots of whole cell lysates of 22 of the 49 isolates and reacted with rabbit hyperimmune antibodies raised against M. pluton whole cells. Neither SDS-PAGE or immunoblotting was capable of distinguishing differences between geographically diverse isolates of M. pluton. Collectively these data confirm that Australian isolates of M. pluton are genetically homogeneous and that this species may be clonal. Plasmid DNA was not detected in whole cell DNA profiles of any isolate resolved using agarose gel electrophoresis.

  6. Structural and functional studies of the restriction endonuclease BpuJI

    OpenAIRE

    Sukackaitė, Rasa

    2009-01-01

    Type II restriction endonucleases recognize specific DNA sequences and cleave DNA at fixed positions within or close to this sequence. BpuJI recognizes the 5’-CCCGT sequence, but in contrast to other enzymes its cleavage site is very variable. This study shows that BpuJI is a dimer in solution and consists of two separate domains. The N-domain binds to the target sequence as a monomer, while the C-domain is responsible for nuclease activity and dimerization. The nuclease activity is repressed...

  7. 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

  8. Improving performance of resonant tunneling devices in asymmetric structures

    Science.gov (United States)

    Shi, Jun-jie; Sanders, Barry C.; Pan, Shao-hua; Goldys, E. M.

    2001-06-01

    Based on the global coherent tunneling model, we present a self-consistent calculation and show that structural asymmetry of double barrier resonant tunneling structures (DBRTSs) significantly modifies the current-voltage characteristics compared to the symmetric structures. Within the framework of the dielectric continuum model, we further investigate the phonon-assisted tunneling (PAT) current in symmetric and asymmetric DBRTSs. Both the interface modes and the confined bulk-like longitudinal-optical phonons are considered. The results indicate that the four higher-frequency interface phonon modes (especially the one which has the largest electron-phonon interaction at either interface of the emitter barrier) dominate the PAT processes. We show that a suitably designed asymmetric structure can produce much larger peak current and absolute value of the negative differential conductivity than its commonly used symmetric counterpart.

  9. Asymmetric Organocatalytic Reactions of α,β-Unsaturated Cyclic Ketones

    Directory of Open Access Journals (Sweden)

    Giuseppe Bartoli

    2011-03-01

    Full Text Available The 1,4-conjugate addition of nucleophiles to α,β-unsaturated carbonyl compounds represents one fundamental bond-forming reaction in organic synthesis. The development of effective organocatalysts for the enantioselective conjugate addition of malonate, nitroalkane and other carbon and heteroatom nucleophiles to cycloenones constitutes an important research field and has been explored in recent years. At the same time, asymmetric Diels-Alder reactions have been developed and often a mechanism has been demonstrated to be a double addition rather than synchronous. This review aims to cover literature up to the end of 2010, describing all the different organocatalytic asymmetric 1,4-conjugate additions even if they are listed as transfer hydrogenation, cycloadditions or desymmetrization of aromatic compounds.

  10. Synthesis of Asymmetric Propanetriol Analogues

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

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

  11. Catalytic Asymmetric Bromocyclization of Polyenes.

    Science.gov (United States)

    Samanta, Ramesh C; Yamamoto, Hisashi

    2017-02-01

    The first catalytic asymmetric bromonium ion-induced polyene cyclization has been achieved by using a chiral BINOL-derived thiophosphoramide catalyst and 1,3-dibromo-5,5-dimethylhydantoin as an electrophilic bromine source. Bromocyclization products are obtained in high yields, with good enantiomeric ratios and high diastereoselectivity, and are abundantly found as scaffolds in natural products.

  12. 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.

  13. 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.

  14. 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.

  15. Crimean–Congo hemorrhagic fever virus nucleoprotein reveals endonuclease activity in bunyaviruses

    Science.gov (United States)

    Guo, Yu; Wang, Wenming; Ji, Wei; Deng, Maping; Sun, Yuna; Zhou, Honggang; Yang, Cheng; Deng, Fei; Wang, Hualin; Hu, Zhihong; Lou, Zhiyong; Rao, Zihe

    2012-01-01

    Crimean–Congo hemorrhagic fever virus (CCHFV), a virus with high mortality in humans, is a member of the genus Nairovirus in the family Bunyaviridae, and is a causative agent of severe hemorrhagic fever (HF). It is classified as a biosafety level 4 pathogen and a potential bioterrorism agent due to its aerosol infectivity and its ability to cause HF outbreaks with high case fatality (∼30%). However, little is known about the structural features and function of nucleoproteins (NPs) in the Bunyaviridae, especially in CCHFV. Here we report a 2.3-Å resolution crystal structure of the CCHFV nucleoprotein. The protein has a racket-shaped overall structure with distinct “head” and “stalk” domains and differs significantly with NPs reported so far from other negative-sense single-stranded RNA viruses. Furthermore, CCHFV NP shows a distinct metal-dependent DNA-specific endonuclease activity. Single residue mutations in the predicted active site resulted in a significant reduction in the observed endonuclease activity. Our results present a new folding mechanism and function for a negative-strand RNA virus nucleoprotein, extend our structural insight into bunyavirus NPs, and provide a potential target for antiviral drug development to treat CCHFV infection. PMID:22421137

  16. Characterization of mitochondrial DNA in various Candida species: isolation, restriction endonuclease analysis, size, and base composition.

    Science.gov (United States)

    Su, C S; Meyer, S A

    1991-01-01

    A practical and effective method for the extraction of mitochondrial DNA from Candida species was developed. Zymolyase was used to induce yeast protoplasts, and mitochondrial DNA was extracted from DNase I-treated mitochondrial preparations. Restriction endonuclease analyses of mitochondrial DNAs from 19 isolates representing seven species of Candida (C. albicans, C. kefyr, C. lusitaniae, C. maltosa, C. parapsilosis, C. shehatae, and C. tropicalis) and Lodderomyces elongisporus revealed different cleavage patterns that appeared to be specific for the species. Few common restriction fragments were evident. The genome sizes of the mitochondrial DNAs ranged from 26.4 to 51.4 kilobase pairs, and the guanine-plus-cytosine contents ranged from 20.7 to 36.8 mol%. There was no correlation between the base compositions of nuclear and mitochondrial DNAs. Eight isolates of C. parapsilosis, including the type culture, and an ascosporogenous strain of L. elongisporus, which was once proposed as the teleomorph of C. parapsilosis, had similar mitochondrial DNA molecular sizes (30.2 and 28.8 kilobase pairs); however, restriction endonuclease patterns of these organisms were distinct. These data provide additional support for discrimination of these two species. The results of our experiments demonstrate that mitochondrial DNA analyses may provide useful criteria for the differentiation of yeast species.

  17. 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.

  18. 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.

  19. A kinetic and structural investigation of DNA-Based asymmetric catalysis using first-generation ligands

    NARCIS (Netherlands)

    Rosati, Fiora; Boersma, Arnold J.; Klijn, Jaap E.; Meetsma, Auke; Feringa, Ben L.; Roelfes, Gerard

    2009-01-01

    The recently developed concept of DNA-based asymmetric catalysis involves the transfer of chirality from the DNA double helix in reactions using a noncovalently bound catalyst. To date, two generations of DNA-based catalysts have been reported that differ in the design of the ligand for the metal. H

  20. 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.

  1. 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; Reis, Ana Beatriz de Bragança Dos; Albano, Rodolpho Mattos; Da-Cruz, Alda Maria; Bello, Alexandre Ribeiro

    2016-05-01

    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.

  2. 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

  3. 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...

  4. 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...

  5. 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.

  6. 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.

  7. 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.

  8. Asymmetrical Γ-Source Inverters

    DEFF Research Database (Denmark)

    Wei, Mo; Poh Chiang, Loh; Blaabjerg, Frede

    2014-01-01

    , inverters with coupled transformers have been introduced, but they usually lead to high turns ratio, and hence many winding turns, at high gain. An alternative would then be the asymmetrical Γ-source inverters proposed in this paper, whose gain is raised by lowering their turns ratio toward unity. The input...... current drawn by the proposed inverters is smoother and, hence, more adaptable by the source. Theories and experimental results have been presented in this paper for validating the concepts proposed....

  9. Up-down asymmetric tokamaks

    CERN Document Server

    Ball, Justin

    2016-01-01

    Bulk toroidal rotation has proven capable of stabilising both dangerous MHD modes and turbulence. In this thesis, we explore a method to drive rotation in large tokamaks: up-down asymmetry in the magnetic equilibrium. We seek to maximise this rotation by finding optimal up-down asymmetric flux surface shapes. First, we use the ideal MHD model to show that low order external shaping (e.g. elongation) is best for creating up-down asymmetric flux surfaces throughout the device. Then, we calculate realistic up-down asymmetric equilibria for input into nonlinear gyrokinetic turbulence analysis. Analytic gyrokinetics shows that, in the limit of fast shaping effects, a poloidal tilt of the flux surface shaping has little effect on turbulent transport. Since up-down symmetric surfaces do not transport momentum, this invariance to tilt implies that devices with mirror symmetry about any line in the poloidal plane will drive minimal rotation. Accordingly, further analytic investigation suggests that non-mirror symmetri...

  10. Evolution of I-SceI Homing Endonucleases with Increased DNA Recognition Site Specificity

    Energy Technology Data Exchange (ETDEWEB)

    Joshi, Rakesh; Ho, Kwok Ki; Tenney, Kristen; Chen, Jui-Hui; Golden, Barbara L.; Gimble, Frederick S. (UIUC); (Purdue)

    2013-09-18

    Elucidating how homing endonucleases undergo changes in recognition site specificity will facilitate efforts to engineer proteins for gene therapy applications. I-SceI is a monomeric homing endonuclease that recognizes and cleaves within an 18-bp target. It tolerates limited degeneracy in its target sequence, including substitution of a C:G{sub +4} base pair for the wild-type A:T{sub +4} base pair. Libraries encoding randomized amino acids at I-SceI residue positions that contact or are proximal to A:T{sub +4} were used in conjunction with a bacterial one-hybrid system to select I-SceI derivatives that bind to recognition sites containing either the A:T{sub +4} or the C:G{sub +4} base pairs. As expected, isolates encoding wild-type residues at the randomized positions were selected using either target sequence. All I-SceI proteins isolated using the C:G{sub +4} recognition site included small side-chain substitutions at G100 and either contained (K86R/G100T, K86R/G100S and K86R/G100C) or lacked (G100A, G100T) a K86R substitution. Interestingly, the binding affinities of the selected variants for the wild-type A:T{sub +4} target are 4- to 11-fold lower than that of wild-type I-SceI, whereas those for the C:G{sub +4} target are similar. The increased specificity of the mutant proteins is also evident in binding experiments in vivo. These differences in binding affinities account for the observed -36-fold difference in target preference between the K86R/G100T and wild-type proteins in DNA cleavage assays. An X-ray crystal structure of the K86R/G100T mutant protein bound to a DNA duplex containing the C:G{sub +4} substitution suggests how sequence specificity of a homing enzyme can increase. This biochemical and structural analysis defines one pathway by which site specificity is augmented for a homing endonuclease.

  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. 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...

  13. 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.

  14. Expansion of CAG triplet repeats by human DNA polymerases λ and β in vitro, is regulated by flap endonuclease 1 and DNA ligase 1.

    Science.gov (United States)

    Crespan, Emmanuele; Hübscher, Ulrich; Maga, Giovanni

    2015-05-01

    Huntington's disease (HD) is a neurological genetic disorder caused by the expansion of the CAG trinucleotide repeats (TNR) in the N-terminal region of coding sequence of the Huntingtin's (HTT) gene. This results in the addition of a poly-glutamine tract within the Huntingtin protein, resulting in its pathological form. The mechanism by which TRN expansion takes place is not yet fully understood. We have recently shown that DNA polymerase (Pol) β can promote the microhomology-mediated end joining and triplet expansion of a substrate mimicking a double strand break in the TNR region of the HTT gene. Here we show that TNR expansion is dependent on the structure of the DNA substrate, as well as on the two essential Pol β co-factors: flap endonuclease 1 (Fen1) and DNA ligase 1 (Lig1). We found that Fen1 significantly stimulated TNR expansion by Pol β, but not by the related enzyme Pol λ, and subsequent ligation of the DNA products by Lig1. Interestingly, the deletion of N-terminal domains of Pol λ, resulted in an enzyme which displayed properties more similar to Pol β, suggesting a possible evolutionary mechanism. These results may suggest a novel mechanism for somatic TNR expansion in HD.

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

    Science.gov (United States)

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

    2015-10-07

    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.

  16. 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.

  17. 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.

  18. 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.

  19. Role of Magnesium Ions in DNA Recognition by the EcoRV Restriction Endonuclease

    Energy Technology Data Exchange (ETDEWEB)

    Zahran, Mai [ORNL; Berezniak, Tomasz [University of Heidelberg; Imhof, Petra [University of Heidelberg; Smith, Jeremy C [ORNL

    2011-01-01

    The restriction endonuclease EcoRV binds two magnesium ions. One of these ions, Mg2+A, binds to the phosphate group where the cleavage occurs and is required for catalysis, but the role of the other ion, Mg2+B is debated. Here, multiple independent molecular dynamics simulations suggest that Mg2+B is crucial for achieving a tightly bound protein DNA complex and stabilizing a conformation that allows cleavage. In the absence of Mg2+B in all simulations the protein DNA hydrogen bond network is significantly disrupted and the sharp kink at the central base pair step of the DNA, which is observed in the two-metal complex, is not present. Also, the active site residues rearrange in such a way that the formation of a nucleophile, required for DNA hydrolysis, is unlikely.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-11-10

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

  1. Digital detection of endonuclease mediated gene disruption in the HIV provirus

    Science.gov (United States)

    Sedlak, Ruth Hall; Liang, Shu; Niyonzima, Nixon; De Silva Feelixge, Harshana S.; Roychoudhury, Pavitra; Greninger, Alexander L.; Weber, Nicholas D.; Boissel, Sandrine; Scharenberg, Andrew M.; Cheng, Anqi; Magaret, Amalia; Bumgarner, Roger; Stone, Daniel; Jerome, Keith R.

    2016-01-01

    Genome editing by designer nucleases is a rapidly evolving technology utilized in a highly diverse set of research fields. Among all fields, the T7 endonuclease mismatch cleavage assay, or Surveyor assay, is the most commonly used tool to assess genomic editing by designer nucleases. This assay, while relatively easy to perform, provides only a semi-quantitative measure of mutation efficiency that lacks sensitivity and accuracy. We demonstrate a simple droplet digital PCR assay that quickly quantitates a range of indel mutations with detection as low as 0.02% mutant in a wild type background and precision (≤6%CV) and accuracy superior to either mismatch cleavage assay or clonal sequencing when compared to next-generation sequencing. The precision and simplicity of this assay will facilitate comparison of gene editing approaches and their optimization, accelerating progress in this rapidly-moving field. PMID:26829887

  2. 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.

  3. 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.

  4. 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)

    SONG GaoGuang; YAO Lu; HUANG Cheng; XIE Xin; TAN Xin; YANG XinLin

    2009-01-01

    Aqueous nanoparticle suspension of fullerene and its derivatives are currently attracting much atten-tion. To determine the effects of aqueous nanoparticle suspension of a mono-methanophosphonate fuIlerene and bis-methanophosphonate fuIlerene (denoted as n-MMPF and n-BMPF, respectively) on the activities of ONA 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. Addi-tion 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 mmool/L, did not reverse inhibition of n-BMPF, implying that this inhibition probably is not corre-lated to ROS. These results suggested that aqueous nano-fullerenee might act as inhibitors of DNA restrictive endonucleases.

  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. A synthetic homing endonuclease-based gene drive system in the human malaria mosquito.

    Science.gov (United States)

    Windbichler, Nikolai; Menichelli, Miriam; Papathanos, Philippos Aris; Thyme, Summer B; Li, Hui; Ulge, Umut Y; Hovde, Blake T; Baker, David; Monnat, Raymond J; Burt, Austin; Crisanti, Andrea

    2011-05-12

    Genetic methods of manipulating or eradicating disease vector populations have long been discussed as an attractive alternative to existing control measures because of their potential advantages in terms of effectiveness and species specificity. The development of genetically engineered malaria-resistant mosquitoes has shown, as a proof of principle, the possibility of targeting the mosquito's ability to serve as a disease vector. The translation of these achievements into control measures requires an effective technology to spread a genetic modification from laboratory mosquitoes to field populations. We have suggested previously that homing endonuclease genes (HEGs), a class of simple selfish genetic elements, could be exploited for this purpose. Here we demonstrate that a synthetic genetic element, consisting of mosquito regulatory regions and the homing endonuclease gene I-SceI, can substantially increase its transmission to the progeny in transgenic mosquitoes of the human malaria vector Anopheles gambiae. We show that the I-SceI element is able to invade receptive mosquito cage populations rapidly, validating mathematical models for the transmission dynamics of HEGs. Molecular analyses confirm that expression of I-SceI in the male germline induces high rates of site-specific chromosomal cleavage and gene conversion, which results in the gain of the I-SceI gene, and underlies the observed genetic drive. These findings demonstrate a new mechanism by which genetic control measures can be implemented. Our results also show in principle how sequence-specific genetic drive elements like HEGs could be used to take the step from the genetic engineering of individuals to the genetic engineering of populations.

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

    Institute of Scientific and Technical Information of China (English)

    刘金毅; 赵晓娟; 孟雁; 沈洁; 薛越强; 史顺娣; 蔡有余

    2001-01-01

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

  8. Nonlinear Dynamics in Double Square Well Potential

    CERN Document Server

    Khomeriki, Ramaz; Ruffo, Stefano; Wimberger, Sandro; 10.1007/s11232-007-0096-y

    2009-01-01

    Considering the coherent nonlinear dynamics in double square well potential we find the example of coexistence of Josephson oscillations with a self-trapping regime. This macroscopic bistability is explained by proving analytically the simultaneous existence of symmetric, antisymmetric and asymmetric stationary solutions of the associated Gross-Pitaevskii equation. The effect is illustrated and confirmed by numerical simulations. This property allows to make suggestions on possible experiments using Bose-Einstein condensates in engineered optical lattices or weakly coupled optical waveguide arrays.

  9. Asymmetric Schiff bases derived from diaminomaleonitrile and their metal complexes

    Science.gov (United States)

    Yang, Jianjie; Shi, Rufei; Zhou, Pei; Qiu, Qiming; Li, Hui

    2016-02-01

    Asymmetric Schiff bases, due to its asymmetric structure, can be used as asymmetric catalyst, antibacterial, and mimic molecules during simulate biological processes, etc. In recent years, research on synthesis and properties of asymmetric Schiff bases have become an increase interest of chemists. This review summarizes asymmetric Schiff bases derived from diaminomaleonitrile (DAMN) and DAMN-based asymmetric Schiff bases metal complexes. Applications of DAMN-based asymmetric Schiff bases are also discussed in this review.

  10. 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.

  11. The asymmetric Goos-H\\"anchen effect

    OpenAIRE

    Araujo, Manoel P.; Carvalho, Silvânia A.; De Leo, Stefano

    2013-01-01

    We show in which conditions optical gaussian beams, propagating throughout an homogeneous dielectric right angle prism, present an asymmetric Goos-H\\"anchen (GH) effect. This asymmetric behavior is seen for incidence at critical angles and happens in the propagation direction of the outgoing beam. The asymmetric GH effect can be also seen as an amplification of the standard GH shift. Due to the fact that it only depends on the ratio between the wavelength and the minimal waist size of the inc...

  12. Review of Composite Asymmetric Spur Gear

    OpenAIRE

    Sandeep C. Dhaduti; Dr. S. G. Sarganachari

    2015-01-01

    Gears made from composite materials are widely used in many power and motion transmission applications. Due to lower weight to stiffness ratio, composite gears may be replaced by conventional material gears in power transmission systems. Design of gears with asymmetric teeth enables to increase load capacity, reduce weight, size and vibration level. This article includes a summary of asymmetric gear design parameters, new developments of asymmetric spur gear and their ...

  13. The asymmetric Goos-H\\"anchen effect

    CERN Document Server

    Araujo, Manoel P; De Leo, Stefano

    2014-01-01

    We show in which conditions optical gaussian beams, propagating throughout an homogeneous dielectric right angle prism, present an asymmetric Goos-H\\"anchen (GH) effect. This asymmetric behavior is seen for incidence at critical angles and happens in the propagation direction of the outgoing beam. The asymmetric GH effect can be also seen as an amplification of the standard GH shift. Due to the fact that it only depends on the ratio between the wavelength and the minimal waist size of the incoming gaussian beam, it can be also used to determine one of these parameters. Multiple peaks interference is an additional phenomenon seen in the presence of such asymmetric effects.

  14. Thin lenses of asymmetric power

    Directory of Open Access Journals (Sweden)

    W. F. Harris

    2009-12-01

    Full Text Available It is generally supposed that thin systems, including refracting surfaces and thin lenses, have powers that are necessarily symmetric.  In other words they have powers which can be represented assymmetric dioptric power matrices and in the familar spherocylindrical form used in optometry and ophthalmology.  This paper shows that this is not correct and that it is indeed possible for a thin system to have a power that is not symmetric and which cannot be expressed in spherocylindrical form.  Thin systems of asymmetric power are illustratedby means of a thin lens that is modelled with small prisms and is chosen to have a dioptric power ma-trix that is antisymmetric.  Similar models can be devised for a thin system whose dioptric power matrix is any  2 2 ×  matrix.  Thus any power, symmetric, asymmetric or antisymmetric, is possible for a thin system.  In this sense our understanding of the power of thin systems is now complete.

  15. 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.

  16. 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.

  17. Double supergeometry

    CERN Document Server

    Cederwall, Martin

    2016-01-01

    A geometry of superspace corresponding to double field theory is developed, with type II supergravity in D=10 as the main example. The formalism is based on an orthosymplectic extension OSp(d,d|2s) of the continuous T-duality group. Covariance under generalised super-diffeomorphisms is manifest. Ordinary superspace is obtained as a solution of the orthosymplectic section condition. A systematic study of curved superspace Bianchi identities is performed, and a relation to a double pure spinor superfield cohomology is established. A Ramond-Ramond superfield is constructed as an infinite-dimensional orthosymplectic spinor. Such objects in minimal orbits under the OSp supergroup ("pure spinors") define super-sections.

  18. 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

  19. Asymmetric catalysis : ligand design and microwave acceleration

    OpenAIRE

    Bremberg, Ulf

    2000-01-01

    This thesis deals partly with the design and synthesis ofligands for use in asymmetric catalysis, and partly with theapplication of microwave heating on metal-based asymmetriccatalytic reactions. Enantiomerically pure pyridyl alcohols and bipyridylalcohols were synthesized from the chiral pool for future usein asymmetric catalysis. Lithiated pyridines were reacted withseveral chiral electrophiles, yielding diastereomeric mixturesthat could be separated without the use of resolutiontechniques....

  20. 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...

  1. 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. I...

  2. The Catalytic Asymmetric Intramolecular Stetter Reaction.

    Science.gov (United States)

    de Alaniz, Javier Read; Rovis, Tomislav

    2009-05-01

    This account chronicles our efforts at the development of a catalytic asymmetric Stetter reaction using chiral triazolium salts as small molecule organic catalysts. Advances in the mechanistically related azolium-catalyzed asymmetric benzoin reaction are discussed, particularly as they apply to catalyst design. A chronological treatise of reaction discovery, catalyst optimization and reactivity extension follows.

  3. Characterization of the restriction enzyme-like endonuclease encoded by the Entamoeba histolytica non-long terminal repeat retrotransposon EhLINE1.

    Science.gov (United States)

    Yadav, Vijay Pal; Mandal, Prabhat Kumar; Rao, Desirazu N; Bhattacharya, Sudha

    2009-12-01

    The genome of the human pathogen Entamoeba histolytica, a primitive protist, contains non-long terminal repeat retrotransposable elements called EhLINEs. These encode reverse transcriptase and endonuclease required for retrotransposition. The endonuclease shows sequence similarity with bacterial restriction endonucleases. Here we report the salient enzymatic features of one such endonuclease. The kinetics of an EhLINE1-encoded endonuclease catalyzed reaction, determined under steady-state and single-turnover conditions, revealed a significant burst phase followed by a slower steady-state phase, indicating that release of product could be the slower step in this reaction. For circular supercoiled DNA the K(m) was 2.6 x 10(-8) M and the k(cat) was 1.6 x 10(-2) sec(-1). For linear E. histolytica DNA substrate the K(m) and k(cat) values were 1.3 x 10(-8) M and 2.2 x 10(-4) sec(-1) respectively. Single-turnover reaction kinetics suggested a noncooperative mode of hydrolysis. The enzyme behaved as a monomer. While Mg(2+) was required for activity, 60% activity was seen with Mn(2+) and none with other divalent metal ions. Substitution of PDX(12-14)D (a metal-binding motif) with PAX(12-14)D caused local conformational change in the protein tertiary structure, which could contribute to reduced enzyme activity in the mutated protein. The protein underwent conformational change upon the addition of DNA, which is consistent with the known behavior of restriction endonucleases. The similarities with bacterial restriction endonucleases suggest that the EhLINE1-encoded endonuclease was possibly acquired from bacteria through horizontal gene transfer. The loss of strict sequence specificity for nicking may have been subsequently selected to facilitate spread of the retrotransposon to intergenic regions of the E. histolytica genome.

  4. Restriction enzyme body doubles and PCR cloning: on the general use of type IIs restriction enzymes for cloning.

    Science.gov (United States)

    Tóth, Eszter; Huszár, Krisztina; Bencsura, Petra; Kulcsár, Péter István; Vodicska, Barbara; Nyeste, Antal; Welker, Zsombor; Tóth, Szilvia; Welker, Ervin

    2014-01-01

    The procedure described here allows the cloning of PCR fragments containing a recognition site of the restriction endonuclease (Type IIP) used for cloning in the sequence of the insert. A Type IIS endonuclease--a Body Double of the Type IIP enzyme--is used to generate the same protruding palindrome. Thus, the insert can be cloned to the Type IIP site of the vector without digesting the PCR product with the same Type IIP enzyme. We achieve this by incorporating the recognition site of a Type IIS restriction enzyme that cleaves the DNA outside of its recognition site in the PCR primer in such a way that the cutting positions straddle the desired overhang sequence. Digestion of the PCR product by the Body Double generates the required overhang. Hitherto the use of Type IIS restriction enzymes in cloning reactions has only been used for special applications, the approach presented here makes Type IIS enzymes as useful as Type IIP enzymes for general cloning purposes. To assist in finding Body Double enzymes, we summarised the available Type IIS enzymes which are potentially useful for Body Double cloning and created an online program (http://group.szbk.u-szeged.hu/welkergr/body_double/index.html) for the selection of suitable Body Double enzymes and the design of the appropriate primers.

  5. 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...

  6. 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.

  7. Double Imbalance

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The government has been introducing a string of policies to stabilize the economy and cushion the impact of the global eco-nomic slowdown since October.These policies are generally deemed"timely"and"necessary,"but not a long-term cure for problems in China’s economy.Renowned economist Wu Jinglian says the country must address its"double imbalance"and further reform its economic growth mode.He made his comments at the First Annual Global Management Forum on December 6 in Shanghai.Excerptsf ollow:

  8. Single-molecule FRET unveils induced-fit mechanism for substrate selectivity in flap endonuclease 1

    Science.gov (United States)

    Rashid, Fahad; Harris, Paul D; Zaher, Manal S; Sobhy, Mohamed A; Joudeh, Luay I; Yan, Chunli; Piwonski, Hubert; Tsutakawa, Susan E; Ivanov, Ivaylo; Tainer, John A; Habuchi, Satoshi; Hamdan, Samir M

    2017-01-01

    Human flap endonuclease 1 (FEN1) and related structure-specific 5’nucleases precisely identify and incise aberrant DNA structures during replication, repair and recombination to avoid genomic instability. Yet, it is unclear how the 5’nuclease mechanisms of DNA distortion and protein ordering robustly mediate efficient and accurate substrate recognition and catalytic selectivity. Here, single-molecule sub-millisecond and millisecond analyses of FEN1 reveal a protein-DNA induced-fit mechanism that efficiently verifies substrate and suppresses off-target cleavage. FEN1 sculpts DNA with diffusion-limited kinetics to test DNA substrate. This DNA distortion mutually ‘locks’ protein and DNA conformation and enables substrate verification with extreme precision. Strikingly, FEN1 never misses cleavage of its cognate substrate while blocking probable formation of catalytically competent interactions with noncognate substrates and fostering their pre-incision dissociation. These findings establish FEN1 has practically perfect precision and that separate control of induced-fit substrate recognition sets up the catalytic selectivity of the nuclease active site for genome stability. DOI: http://dx.doi.org/10.7554/eLife.21884.001 PMID:28230529

  9. 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.

  10. [The resistance of the DNA of cyanophage LPP-3 to the action of different restriction endonucleases].

    Science.gov (United States)

    Mendzhul, M I; Syrchin, S A; Rebentish, B A; Averkiev, A A; Busakhina, I V

    1993-01-01

    Data on the study of structure peculiarities of cyanophage LPP-3 DNA are presented in the work. The length of cyanophage DNA calculated by means of the enzymatic hydrolysis by restrictases is 40 +/- 3.5 thou. pairs of bases. Cyanophage LPP-3 DNA was hydrolysed by more than 50 different restrictases. As a result of screening it was found out that the great number of restrictases, which recognized hexanucleotide sequences did not hydrolyze DNA of cyanophage LPP-3. A considerable deviation of the number of the observed sites of restriction from their theoretically expected number for restrictases Hae III and Cfr 131 was established. Restrictases-isoschisomeres with different sensitivity to the methylation of the recognition sites--Msp I, Hpa II and Sau 3A, MboI and DpnI were used to check the availability of methylated bases in LPP-3 DNA. Absence of methylated adenine in the site GATC and methylated cytosine in the second position of the site CCGG were established. The results obtained permit supposing that the expressed counterselection by the sites of recognition of many restriction endonucleases takes place in cyanophage LPP-3 DNA. It is supposed that apparently, this method of protection of its genome in LPP-3 is one of most important but the inconsiderable percentage of site-specific methylation of the virus DNA cannot be completely excluded.

  11. 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.

  12. The Vsr endonuclease of Escherichia coli: an efficient DNA repair enzyme and a potent mutagen.

    Science.gov (United States)

    Macintyre, G; Doiron, K M; Cupples, C G

    1997-01-01

    The Vsr endonuclease of Escherichia coli initiates the repair of T/G mismatches caused by deamination of 5-methylcytosine to thymine. In this paper, we examine the capacity of Vsr to prevent CG-to-TA mutations in cells with increased transcription of the cytosine methylase gene (dcm). We find that sufficient Vsr is produced by a single chromosomal copy of vsr to prevent mutagenesis. We also investigate the cause of the transition and frameshift mutations in cells overproducing Vsr. Neither the absence of the dcm methylase nor its overproduction affects Vsr-stimulated mutagenesis. However, addition of mutS, mutL, or mutH on multicopy plasmids has a significant effect: mutL or mutH decreases the number of mutations, while mutS stimulates mutagenesis. The mut-containing plasmids have the same effect in cells treated with 2-aminopurine and in cells made defective in DNA proofreading, two experimental situations known to cause transition and frameshift mutations by saturating mismatch repair. PMID:9324251

  13. Single-molecule FRET unveils induced-fit mechanism for substrate selectivity in flap endonuclease 1

    KAUST Repository

    Rashid, Fahad

    2017-02-23

    Human flap endonuclease 1 (FEN1) and related structure-specific 5\\'nucleases precisely identify and incise aberrant DNA structures during replication, repair and recombination to avoid genomic instability. Yet, it is unclear how the 5\\'nuclease mechanisms of DNA distortion and protein ordering robustly mediate efficient and accurate substrate recognition and catalytic selectivity. Here, single-molecule sub-millisecond and millisecond analyses of FEN1 reveal a protein-DNA induced-fit mechanism that efficiently verifies substrate and suppresses off-target cleavage. FEN1 sculpts DNA with diffusion-limited kinetics to test DNA substrate. This DNA distortion mutually \\'locks\\' protein and DNA conformation and enables substrate verification with extreme precision. Strikingly, FEN1 never misses cleavage of its cognate substrate while blocking probable formation of catalytically competent interactions with noncognate substrates and fostering their pre-incision dissociation. These findings establish FEN1 has practically perfect precision and that separate control of induced-fit substrate recognition sets up the catalytic selectivity of the nuclease active site for genome stability.

  14. 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

  15. 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.

  16. 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.

  17. 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.

  18. Enantioselective synthesis of (thiolan-2-yl)diphenylmethanol and its application in asymmetric, catalytic sulfur ylide-mediated epoxidation.

    Science.gov (United States)

    Wu, Hsin-Yi; Chang, Chih-Wei; Chein, Rong-Jie

    2013-06-07

    This work describes an expeditious and efficient preparation of enantiopure (thiolan-2-yl)diphenylmethanol (2) featuring a double nucleophilic substitution and Shi epoxidation as key steps. One of the applications of its benzyl ether derivative to asymmetric sulfur ylide-mediated epoxidation with up to 92% ee (14 examples) was also demonstrated herein.

  19. 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.

  20. 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.

  1. 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.

  2. Bunyaviridae RNA polymerases (L-protein have an N-terminal, influenza-like endonuclease domain, essential for viral cap-dependent transcription.

    Directory of Open Access Journals (Sweden)

    Juan Reguera

    Full Text Available Bunyaviruses are a large family of segmented RNA viruses which, like influenza virus, use a cap-snatching mechanism for transcription whereby short capped primers derived by endonucleolytic cleavage of host mRNAs are used by the viral RNA-dependent RNA polymerase (L-protein to transcribe viral mRNAs. It was recently shown that the cap-snatching endonuclease of influenza virus resides in a discrete N-terminal domain of the PA polymerase subunit. Here we structurally and functionally characterize a similar endonuclease in La Crosse orthobunyavirus (LACV L-protein. We expressed N-terminal fragments of the LACV L-protein and found that residues 1-180 have metal binding and divalent cation dependent nuclease activity analogous to that of influenza virus endonuclease. The 2.2 A resolution X-ray crystal structure of the domain confirms that LACV and influenza endonucleases have similar overall folds and identical two metal binding active sites. The in vitro activity of the LACV endonuclease could be abolished by point mutations in the active site or by binding 2,4-dioxo-4-phenylbutanoic acid (DPBA, a known influenza virus endonuclease inhibitor. A crystal structure with bound DPBA shows the inhibitor chelating two active site manganese ions. The essential role of this endonuclease in cap-dependent transcription was demonstrated by the loss of transcriptional activity in a RNP reconstitution system in cells upon making the same point mutations in the context of the full-length LACV L-protein. Using structure based sequence alignments we show that a similar endonuclease almost certainly exists at the N-terminus of L-proteins or PA polymerase subunits of essentially all known negative strand and cap-snatching segmented RNA viruses including arenaviruses (2 segments, bunyaviruses (3 segments, tenuiviruses (4-6 segments, and orthomyxoviruses (6-8 segments. This correspondence, together with the well-known mapping of the conserved polymerase motifs to the

  3. A new restriction endonuclease-based method for highly-specific detection of DNA targets from methicillin-resistant Staphylococcus aureus.

    Directory of Open Access Journals (Sweden)

    Maria W Smith

    Full Text Available PCR multiplexing has proven to be challenging, and thus has provided limited means for pathogen genotyping. We developed a new approach for analysis of PCR amplicons based on restriction endonuclease digestion. The first stage of the restriction enzyme assay is hybridization of a target DNA to immobilized complementary oligonucleotide probes that carry a molecular marker, horseradish peroxidase (HRP. At the second stage, a target-specific restriction enzyme is added, cleaving the target-probe duplex at the corresponding restriction site and releasing the HRP marker into solution, where it is quantified colorimetrically. The assay was tested for detection of the methicillin-resistant Staphylococcus aureus (MRSA pathogen, using the mecA gene as a target. Calibration curves indicated that the limit of detection for both target oligonucleotide and PCR amplicon was approximately 1 nM. Sequences of target oligonucleotides were altered to demonstrate that (i any mutation of the restriction site reduced the signal to zero; (ii double and triple point mutations of sequences flanking the restriction site reduced restriction to 50-80% of the positive control; and (iii a minimum of a 16-bp target-probe dsDNA hybrid was required for significant cleavage. Further experiments showed that the assay could detect the mecA amplicon from an unpurified PCR mixture with detection limits similar to those with standard fluorescence-based qPCR. Furthermore, addition of a large excess of heterologous genomic DNA did not affect amplicon detection. Specificity of the assay is very high because it involves two biorecognition steps. The proposed assay is low-cost and can be completed in less than 1 hour. Thus, we have demonstrated an efficient new approach for pathogen detection and amplicon genotyping in conjunction with various end-point and qPCR applications. The restriction enzyme assay may also be used for parallel analysis of multiple different amplicons from the same

  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. Endonuclease restriction-mediated real-time polymerase chain reaction: a novel technique for rapid, sensitive and quantitative detection of nucleic-acid sequence

    Directory of Open Access Journals (Sweden)

    Yi Wang

    2016-07-01

    Full Text Available The article reported a novel methodology for real-time PCR analysis of nucleic acids, termed endonuclease restriction-mediated real-time polymerase chain reaction (ET-PCR. Just like PCR, ET-PCR only required one pair of primers. A short sequence (Ss, which was recognized by restriction enzyme BstUI, was attached to the 5’ end of the forward (F or reverse (R PCR primer, and the new F or R primer was named EF or ER. EF/ER was labeled at the 5’ end with a reporter dye and in the middle with a quenching dye. BstUI cleaves the newly synthesized double-stranded terminal sequences (5’ end recognition sequences and their complementary sequences during the extension phase, which separates the reporter molecule from the quenching dye, leading to a gain of fluorescence signal. This process is repeated in each amplification cycle and unaffected the exponential synthesis of the PCR amplification. ET-PCR allowed real-time analysis of single or multiple targets in a single vessel, and provided the reproducible quantitation of nucleic acids. positive results were generated in a relatively short period. The analytical sensitivity and specificity of ETR-PCR were successfully evaluated, detecting down to 250 fg of genomic DNA per tube of target pathogen DNA examined, and the positive results were generated in a relatively short period. Moreover, the practical application of ET-PCR for simultaneous detection of multiple target pathogens was also demonstrated in artificially contaminated blood samples. In conclusion, due to the technique’s simplicity of design, reproducible data and low contamination risk, ET-PCR assay is an appealing alternative to conventional approaches currently used for real-time nucleic acid analysis.

  6. 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.

  7. Asymmetric stem cell division: lessons from Drosophila.

    Science.gov (United States)

    Wu, Pao-Shu; Egger, Boris; Brand, Andrea H

    2008-06-01

    Asymmetric cell division is an important and conserved strategy in the generation of cellular diversity during animal development. Many of our insights into the underlying mechanisms of asymmetric cell division have been gained from Drosophila, including the establishment of polarity, orientation of mitotic spindles and segregation of cell fate determinants. Recent studies are also beginning to reveal the connection between the misregulation of asymmetric cell division and cancer. What we are learning from Drosophila as a model system has implication both for stem cell biology and also cancer research.

  8. On-chip asymmetric microcavity optomechanics.

    Science.gov (United States)

    Soltani, Soheil; Hudnut, Alexa W; Armani, Andrea M

    2016-12-26

    High quality factor (Q) optical resonators have enabled rapid growth in the field of cavity-enhanced, radiation pressure-induced optomechanics. However, because research has focused on axisymmetric devices, the observed regenerative excited mechanical modes are similar. In the present work, a strategy for fabricating high-Q whispering gallery mode microcavities with varying degrees of asymmetry is developed and demonstrated. Due to the combination of high optical Q and asymmetric device design, two previously unobserved modes, the asymmetric cantilever and asymmetric crown mode, are demonstrated with sub-mW thresholds for onset of oscillations. The experimental results are in good agreement with computational modeling predictions.

  9. Regenerating a symmetry in asymmetric dark matter.

    Science.gov (United States)

    Buckley, Matthew R; Profumo, Stefano

    2012-01-06

    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.

  10. Absolute Asymmetric Synthesis Using A Cocrystal Approach

    Institute of Scientific and Technical Information of China (English)

    H.Koshima

    2007-01-01

    1 Results Absolute asymmetric synthesis by means of solid-state reaction of chiral crystals self-assembled from achiral molecules is an attractive and promising methodology for asymmetric synthesis because it is not necessary to employ any external chiral source like a chiral catalyst.In order to design reliably absolute asymmetric syntheses in the solid state,it is inevitable to prepare and predict the formation of chiral crystals from achiral compounds.We have prepared a number of chiral cocrystals co...

  11. 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.

  12. Enantiopure sulfoxides: recent applications in asymmetric synthesis.

    Science.gov (United States)

    Carreño, M Carmen; Hernández-Torres, Gloria; Ribagorda, María; Urbano, Antonio

    2009-11-07

    Sulfoxides are nowadays recognised as powerful chiral auxiliaries that may participate in a wide range of asymmetric reactions. Their high configurational stability, the existence of several efficient methods allowing the access to both configurations as well as their synthetic versatility are characteristic features offering a tremendous potential to develop new applications. Significant recent advances leading to high asymmetric inductions in carbon-carbon and carbon-oxygen bond forming reactions, and applications of homochiral sulfoxides to atroposelective synthesis and asymmetric catalysis are discussed. New uses of sulfoxides in the design of chiroptical switches are also shown.

  13. Stereoselective Synthesis of trans-Olefins by the Copper-Mediated SN2′ Reaction of Vinyl Oxazines with Grignard Reagents. Asymmetric Synthesis of D-threo-Sphingosines

    OpenAIRE

    Singh, Om V; Han, Hyunsoo

    2007-01-01

    The SN2′ reaction of 6-vinyl-5,6-dihydro-4H-[1,3]oxazines with Grignard reagents in the presence of CuCN was studied, and high trans selectivity for the formation of double bond was observed with a variety of RMgX. The SN2′ reaction, coupled with regioselective asymmetric aminohydroxylation reaction, provided a highly efficient route for the asymmetric synthesis of D-threo-N-acetylsphingosine.

  14. 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.

  15. Asymmetric dark matter bound state

    Science.gov (United States)

    Bi, Xiao-Jun; Kang, Zhaofeng; Ko, P.; Li, Jinmian; Li, Tianjun

    2017-02-01

    We propose an interesting framework for asymmetric scalar dark matter (ADM), which has novel collider phenomenology in terms of an unstable ADM bound state (ADMonium) produced via Higgs portals. ADMonium is a natural consequence of the basic features of ADM: the (complex scalar) ADM is charged under a dark local U (1 )d symmetry which is broken at a low scale and provides a light gauge boson X . The dark gauge coupling is strong and then ADM can annihilate away into X -pair effectively. Therefore, the ADM can form a bound state due to its large self-interaction via X mediation. To explore the collider signature of ADMonium, we propose that ADM has a two-Higgs doublet portal. The ADMonium can have a sizable mixing with the heavier Higgs boson, which admits a large cross section of ADMonium production associated with b b ¯. The resulting signature at the LHC depends on the decays of X . In this paper we consider a case of particular interest: p p →b b ¯ +ADMonium followed by ADMonium→2 X →2 e+e- where the electrons are identified as (un)converted photons. It may provide a competitive explanation to heavy di-photon resonance searches at the LHC.

  16. 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.

  17. 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...

  18. 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.

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

    Science.gov (United States)

    Wallat, Gregor D; Huang, Qinfeng; Wang, Wenjian; Dong, Haohao; Ly, Hinh; Liang, Yuying; Dong, Changjiang

    2014-01-01

    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.

  20. A novel asymmetric synthesis of cinacalcet hydrochloride

    OpenAIRE

    Arava, Veera R; Laxminarasimhulu Gorentla; Pramod K. Dubey

    2012-01-01

    A novel route to asymmetric synthesis of cinacalcet hydrochloride by the application of (R)-tert-butanesulfinamide and regioselective N-alkylation of the naphthyl ethyl sulfinamide intermediate is described.

  1. A novel asymmetric synthesis of cinacalcet hydrochloride

    Directory of Open Access Journals (Sweden)

    Veera R. Arava

    2012-08-01

    Full Text Available A novel route to asymmetric synthesis of cinacalcet hydrochloride by the application of (R-tert-butanesulfinamide and regioselective N-alkylation of the naphthyl ethyl sulfinamide intermediate is described.

  2. A novel asymmetric synthesis of cinacalcet hydrochloride

    Science.gov (United States)

    Gorentla, Laxminarasimhulu; Dubey, Pramod K

    2012-01-01

    Summary A novel route to asymmetric synthesis of cinacalcet hydrochloride by the application of (R)-tert-butanesulfinamide and regioselective N-alkylation of the naphthyl ethyl sulfinamide intermediate is described. PMID:23019473

  3. Catalytic Asymmetric Synthesis of Phosphine Boronates

    NARCIS (Netherlands)

    Hornillos, Valentin; Vila, Carlos; Otten, Edwin; Feringa, Ben L.

    2015-01-01

    The first catalytic enantioselective synthesis of ambiphilic phosphine boronate esters is presented. The asymmetric boration of ,-unsaturated phosphine oxides catalyzed by a copper bisphosphine complex affords optically active organoboronate esters that bear a vicinal phosphine oxide group in good y

  4. Asymmetric Swiss-cheese brane-worlds

    CERN Document Server

    Gergely, L A; K\\'{e}p\\'{\\i}r\\'{o}, Ibolya

    2006-01-01

    We consider Swiss-cheese brane universes embedded asymmetrically into the bulk. Neither the junction conditions between the Schwarzschild spheres and the sorrounding Friedmann brane regions with cosmological constant $\\Lambda $, nor the evolution of the scale factor are changed with respect to the symmetric case. The universe expands and decelerates forever. The asymmetry however has a drastic influence on the evolution of the cosmological fluid. Instead of the two branches of the symmetric case, in the asymmetric case four branches emerge. Moreover, the future pressure singularity arising in the symmetric case only for huge values of $\\Lambda $ becomes quite generic in the asymmetric case. Such pressure singularities emerge also when $\\Lambda=0$ is set. Then they are due entirely to the asymmetric embedding. For generic values of $\\Lambda $ we introduce a critical value of a suitably defined asymmetry parameter, which separates Swiss-cheese cosmologies with and without pressure singularities.

  5. Congenital asymmetric crying face: a case report

    Directory of Open Access Journals (Sweden)

    Semra Kara

    2011-12-01

    Full Text Available Congenital asymmetric crying face is an anomalia caused by unilateral absence or weakness of depressor anguli oris muscle The major finding of the disease is the absence or weakness in the outer and lower movement of the commissure during crying. The other expression muscles are normal and the face is symmetric at rest. The asymmetry in congenital asymmetric crying face is most evident during infancy but decreases by age. Congenital asymmetric crying face can be associated with cervicofacial, musclebone, respiratory, genitourinary and central nervous system anomalia. It is diagnosed by physical examination. This paper presents a six days old infant with Congenital asymmetric crying face and discusses the case in terms of diagnosis and disease features.

  6. 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.

  7. Total sequence decomposition distinguishes functional modules, "molegos" in apurinic/apyrimidinic endonucleases

    Directory of Open Access Journals (Sweden)

    Braun Werner

    2002-11-01

    Full Text Available Abstract Background Total sequence decomposition, using the web-based MASIA tool, identifies areas of conservation in aligned protein sequences. By structurally annotating these motifs, the sequence can be parsed into individual building blocks, molecular legos ("molegos", that can eventually be related to function. Here, the approach is applied to the apurinic/apyrimidinic endonuclease (APE DNA repair proteins, essential enzymes that have been highly conserved throughout evolution. The APEs, DNase-1 and inositol 5'-polyphosphate phosphatases (IPP form a superfamily that catalyze metal ion based phosphorolysis, but recognize different substrates. Results MASIA decomposition of APE yielded 12 sequence motifs, 10 of which are also structurally conserved within the family and are designated as molegos. The 12 motifs include all the residues known to be essential for DNA cleavage by APE. Five of these molegos are sequentially and structurally conserved in DNase-1 and the IPP family. Correcting the sequence alignment to match the residues at the ends of two of the molegos that are absolutely conserved in each of the three families greatly improved the local structural alignment of APEs, DNase-1 and synaptojanin. Comparing substrate/product binding of molegos common to DNase-1 showed that those distinctive for APEs are not directly involved in cleavage, but establish protein-DNA interactions 3' to the abasic site. These additional bonds enhance both specific binding to damaged DNA and the processivity of APE1. Conclusion A modular approach can improve structurally predictive alignments of homologous proteins with low sequence identity and reveal residues peripheral to the traditional "active site" that control the specificity of enzymatic activity.

  8. 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.

  9. 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

  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

    2016-04-08

    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. DOES VOLATILITY RESPOND ASYMMETRIC TO PAST SHOCKS?

    OpenAIRE

    Claudiu Botoc

    2014-01-01

    The main aim of the paper is to examine if the stock market volatility exhibits asymmetric or an asymmetric response to past shocks, for certain CEE countries (Romania,Hungary, Bulgaria, Poland) over the period May 2004 - September 2014. For the stock marketsfrom East Europe the results are in line with the symmetric volatility, i.e. volatility is similaraffected by both positive and negative returns with the same magnitude. For the stock marketsfrom Central Europe the results are consistent ...

  12. DNA Double-Strand Breaks,Potential Targets for HBV Integration

    Institute of Scientific and Technical Information of China (English)

    胡晓文; 林菊生; 谢琼慧; 任精华; 常莹; 吴文杰; 夏羽佳

    2010-01-01

    Hepatitis B virus(HBV)-induced hepatocellular carcinoma(HCC) is one of the most fre-quently occurring cancers.Hepadnaviral DNA integrations are considered to be essential agents which can promote the process of the hepatocarcinogenesis.More and more researches were designed to find the relationship of the two.In this study,we investigated whether HBV DNA integration occurred at sites of DNA double-strand breaks(DSBs),one of the most detrimental DNA damage.An 18-bp I-SceI homing endonuclease recognition site...

  13. 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.

  14. Physical mapping of BK virus DNA with SacI, MboII, and AluI restriction endonucleases.

    Science.gov (United States)

    Yang, R C; Wu, R

    1978-12-01

    A new restriction endonuclease, SacI from Streptomyces achromogenes cleaves BK virus (strain MM) DNA into 3 fragments, whereas MboII from Moraxella bovis and AluI from Arthrobacter luteus give 22 and 30 fragments, respectively. All these specific DNA fragments were ordered and mapped on the viral genome by two methods first, by the reciprocal digestion method using uniformly 32P-labeled DNA; and second, by the partial digestion technique using the single-end 32P-labeled DNA. This study, together with those reported earlier, defined the location of 90 cleavage sites on the BK virus DNA.

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

    Directory of Open Access Journals (Sweden)

    Supar

    2003-10-01

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

  16. Double Conditional Expectation

    Institute of Scientific and Technical Information of China (English)

    HU Di-he

    2004-01-01

    The concept of double conditional expectation is introduced. A series of properties for the double conditional expectation are obtained several convergence theorems and Jensen inequality are proved. Finally we discuss the special cases and application for double conditional expectation.

  17. 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

  18. Control of apoptosis by asymmetric cell division.

    Directory of Open Access Journals (Sweden)

    Julia Hatzold

    2008-04-01

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

  19. [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.

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

    Science.gov (United States)

    Su, Fenghua; Miao, Menghe

    2014-04-04

    Strong and flexible two-ply carbon nanotube yarn supercapacitors are electrical double layer capacitors that possess relatively low energy storage capacity. Pseudocapacitance metal oxides such as MnO₂ are well known for their high electrochemical performance and can be coated on carbon nanotube yarns to significantly improve the performance of two-ply carbon nanotube yarn supercapacitors. We produced a high performance asymmetric two-ply yarn supercapacitor from as-spun CNT yarn and CNT@Mn₂2 composite yarn in aqueous electrolyte. The as-spun CNT yarn serves as negative electrode and the CNT@MnO₂ composite yarn as positive electrode. This asymmetric architecture allows the operating potential window to be extended from 1.0 to 2.0 V and results in much higher energy and power densities than the reference symmetric two-ply yarn supercapacitors, reaching 42.0 Wh kg(-1) at a lower power density of 483.7 W kg(-1), and 28.02 Wh kg(-1) at a higher power density of 19,250 W kg(-1). The asymmetric supercapacitor can sustain cyclic charge-discharge and repeated folding/unfolding actions without suffering significant deterioration of specific capacitance. The combination of high strength, flexibility and electrochemical performance makes the asymmetric two-ply yarn supercapacitor a suitable power source for flexible electronic devices for applications that require high durability and wearer comfort.

  1. 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.

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

    Science.gov (United States)

    Comeron, Josep M.; Reed, Jordan; Christie, Matthew; Jacobs, Julia S.; Dierdorff, Jason; Eberl, Daniel F.; Manak, J. Robert

    2016-01-01

    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. PMID:27600073

  3. A simple, high sensitivity mutation screening using Ampligase mediated T7 endonuclease I and Surveyor nuclease with microfluidic capillary electrophoresis.

    Science.gov (United States)

    Huang, Mo Chao; Cheong, Wai Chye; Lim, Li Shi; Li, Mo-Huang

    2012-03-01

    Mutation and polymorphism detection is of increasing importance for a variety of medical applications, including identification of cancer biomarkers and genotyping for inherited genetic disorders. Among various mutation-screening technologies, enzyme mismatch cleavage (EMC) represents a great potential as an ideal scanning method for its simplicity and high efficiency, where the heteroduplex DNAs are recognized and cleaved into DNA fragments by mismatch-recognizing nucleases. Thereby, the enzymatic cleavage activities of the resolving nucleases play a critical role for the EMC sensitivity. In this study, we utilized the unique features of microfluidic capillary electrophoresis and de novo gene synthesis to explore the enzymatic properties of T7 endonuclease I and Surveyor nuclease for EMC. Homoduplex and HE DNAs with specific mismatches at desired positions were synthesized using PCR (polymerase chain reaction) gene synthesis. The effects of nonspecific cleavage, preference of mismatches, exonuclease activity, incubation time, and DNA loading capability were systematically examined. In addition, the utilization of a thermostable DNA ligase for real-time ligase mediation was investigated. Analysis of the experimental results has led to new insights into the enzymatic cleavage activities of T7 endonuclease I and Surveyor nuclease, and aided in optimizing EMC conditions, which enhance the sensitivity and efficiency in screening of unknown DNA variations.

  4. Isolation by restriction endonuclease digestion and base-specific affinity chromatography of rat-embryo DNA sequences disproportionately enriched in virogenic bromodeoxyuridine.

    Science.gov (United States)

    Schwartz, S A

    1981-02-01

    Control and bromodeoxyuridine-containing rat-embryo-cell DNA were digested by the restriction endonucleases Hpa II and Msp I and were subsequently analyzed by agarose-gel electrophoresis as well as DNA-affinity chromatography. By the former technique, it appeared that no substantial differences existed between the two DNA samples with respect to the amount or distribution of methylcytosine. On the other hand, it was obvious following base-specific DNA chromatography that the virogenic analog was markedly concentrated in particular nucleotide sequences which demonstrated a proportionately greater affinity for the (A-T)-specific adsorbent irrespective of digestion by either restriction endonuclease.

  5. 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.

  6. Asymmetric gear rectifies random robot motion

    Science.gov (United States)

    Li, He; Zhang, H. P.

    2013-06-01

    We experimentally study the dynamics of centimetric robots and their interactions with rotary gears through inelastic collisions. Under the impacts of self-propelled robots, a gear with symmetric teeth diffuses with no preferred direction of motion. An asymmetric gear, however, rectifies random motion of nearby robots which, in return, exert a torque on the gear and drive it into unidirectional motion. Rectification efficiency increases with the degree of gear asymmetry. Our work demonstrates that asymmetric environments can be used to rectify and extract energy from random motion of macroscopic self-propelled particles.

  7. 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.

  8. 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.

  9. 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.

  10. Integrated asymmetric vertical coupler pressure sensors

    Science.gov (United States)

    Kiyat, Isa; Kocabas, Askin; Akcag, Imran; Aydinli, Atilla

    2004-08-01

    Design and analysis of a novel pressure sensor based on a silicon-on-insulator asymmetric integrated vertical coupler is presented. The coupler is composed of a single mode low index waveguide and a thin silicon slab. Wavelength selective optical modulation of asymmetric vertical coupler is examined in detail. Its potential for sensing applications is highlighted as an integrated optical pressure sensor which can be realized by standard silicon micro-fabrication. Sensitivity of transmission of such couplers on refractive index change of silicon slab ensures that they are good candidates for applications requiring high sensitivities.

  11. Asymmetric localization in disordered Landau bands

    Energy Technology Data Exchange (ETDEWEB)

    Nita, M [Institute of Physics and Technology of Materials, PO Box MG7, Bucharest-Magurele (Romania); Aldea, A [Institute of Physics and Technology of Materials, PO Box MG7, Bucharest-Magurele (Romania); Zittartz, J [Institute of Theoretical Physics, Cologne University, 50937 Cologne (Germany)

    2007-06-06

    We show that, due to band mixing, the eigenstate localization within the disordered Landau bands gets an asymmetric structure: the degree of localization increases in the lower part of the band and decreases in the upper one. The calculation is performed for a two-dimensional lattice with the Anderson disorder potential and we prove that this effect is related to the upper shift of the extended states within the band and is enhanced by the disorder strength. The asymmetric localization and the energy shift disappear when the interband coupling is switched off.

  12. Asymmetric multiscale behavior in PM2.5 time series: Based on asymmetric MS-DFA

    Science.gov (United States)

    Zhang, Chen; Ni, Zhiwei; Ni, Liping

    2016-11-01

    Particulate matter with an aerodynamic diameter of 2.5 mm or less (PM2.5) is one of the most serious air pollution, considered most harmful for people by World Health Organisation. In this paper, we utilized the asymmetric multiscale detrended fluctuation analysis (A-MSDFA) method to explore the existence of asymmetric correlation properties for PM2.5 daily average concentration in two USA cities (Fresno and Los Angeles) and two Chinese cities (Hong Kong and Shanghai), and to assess the properties of these asymmetric correlations. The results show the existences of asymmetric correlations, and the degree of asymmetric for two USA cities is stronger than that of two Chinese cities. Further, most of the local exponent β(n) are smaller than 0.5, which indicates the existence of anti-persistent long-range correlation for PM2.5 time series in four cities. In addition, we reanalyze the asymmetric correlation by the A-MSDFA method with secant rolling windows of different sizes, which can investigate dynamic changes in the multiscale correlation for PM2.5 time series with changing window size. Whatever window sizes, the correlations are asymmetric and display smaller asymmetries at small scales and larger asymmetries at large scales. Moreover, the asymmetries become increasingly weaker with the increase of window sizes.

  13. Pulsatile flow in a compliant stenosed asymmetric model

    Science.gov (United States)

    Usmani, Abdullah Y.; Muralidhar, K.

    2016-12-01

    Time-varying velocity field in an asymmetric constricted tube is experimentally studied using a two-dimensional particle image velocimetry system. The geometry resembles a vascular disease which is characterized by arterial narrowing due to plaque deposition. The present study compares the nature of flow patterns in rigid and compliant asymmetric constricted tubes for a range of dimensionless parameters appearing in a human artery. A blood analogue fluid is employed along with a pump that mimics cardioflow conditions. The peak Reynolds number range is Re 300-800, while the Womersley number range considered in experiments is Wo 6-8. These values are based on the peak velocity in a straight rigid tube connected to the model, over a pulsation frequency range of 1.2-2.4 Hz. The medial-plane velocity distribution is used to investigate the nature of flow patterns. Temporal distribution of stream traces and hemodynamic factors including WSS, TAWSS and OSI at important phases of the pulsation cycle are discussed. The flow patterns obtained from PIV are compared to a limited extent against numerical simulation. Results show that the region downstream of the constriction is characterized by a high-velocity jet at the throat, while a recirculation zone, attached to the wall, evolves in time. Compliant models reveal large flow disturbances upstream during the retrograde flow. Wall shear stress values are lower in a compliant model as compared to the rigid. Cross-plane flow structures normal to the main flow direction are visible at select phases of the cycle. Positive values of largest Lyapunov exponent are realized for wall movement and are indicative of chaotic motion transferred from the flow to the wall. These exponents increase with Reynolds number as well as compliance. Period doubling is observed in wall displacement of highly compliant models, indicating possible triggering of hemodynamic events in a real artery that may cause fissure in the plaque deposits.

  14. 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.

  15. 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.

  16. THz operation of asymmetric-nanochannel devices

    NARCIS (Netherlands)

    Balocco, C.; Halsall, M.; Vinh, N. Q.; Song, A. M.

    2008-01-01

    The THz spectrum lies between microwaves and the mid-infrared, a region that remains largely unexplored mainly due to the bottleneck issue of lacking compact, solid state, emitters and detectors. Here, we report on a novel asymmetric-nanochannel device, known as the self-switching device, which can

  17. 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.

  18. Dynamic Conditional Correlations for Asymmetric Processes

    NARCIS (Netherlands)

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

    2010-01-01

    textabstractThe paper develops two Dynamic Conditional Correlation (DCC) models, namely the Wishart DCC (WDCC) model and the Matrix-Exponential Conditional Correlation (MECC) model. The paper applies the WDCC approach to the exponential GARCH (EGARCH) and GJR models to propose asymmetric DCC models.

  19. 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)

  20. Catalytic Asymmetric Synthesis of Phosphine Boronates.

    Science.gov (United States)

    Hornillos, Valentín; Vila, Carlos; Otten, Edwin; Feringa, Ben L

    2015-06-26

    The first catalytic enantioselective synthesis of ambiphilic phosphine boronate esters is presented. The asymmetric boration of α,β-unsaturated phosphine oxides catalyzed by a copper bisphosphine complex affords optically active organoboronate esters that bear a vicinal phosphine oxide group in good yields and high enantiomeric excess. The synthetic utility of the products is demonstrated through stereospecific transformations into multifunctional optically active compounds.

  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. Three dimensional force balance of asymmetric droplets

    Science.gov (United States)

    Kim, Yeseul; Lim, Su Jin; Cho, Kun; Weon, Byung Mook

    2016-11-01

    An equilibrium contact angle of a droplet is determined by a horizontal force balance among vapor, liquid, and solid, which is known as Young's law. Conventional wetting law is valid only for axis-symmetric droplets, whereas real droplets are often asymmetric. Here we show that three-dimensional geometry must be considered for a force balance for asymmetric droplets. By visualizing asymmetric droplets placed on a free-standing membrane in air with X-ray microscopy, we are able to identify that force balances in one side and in other side control pinning behaviors during evaporation of droplets. We find that X-ray microscopy is powerful for realizing the three-dimensional force balance, which would be essential in interpretation and manipulation of wetting, spreading, and drying dynamics for asymmetric droplets. This research was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (NRF-2016R1D1A1B01007133).

  3. Asymmetric Hydrogenation of 3-Substituted Pyridinium Salts

    NARCIS (Netherlands)

    Renom-Carrasco, Marc; Gajewski, Piotr; Pignataro, Luca; de Vries, Johannes G.; Piarulli, Umberto; Gennari, Cesare; Lefort, Laurent

    2016-01-01

    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 Et3N, a Rh-JosiPhos catalyst reduced a range of pyridinium salts with ee

  4. Nucleation Process in Asymmetric Nuclear Matter

    CERN Document Server

    Peres-Menezes, D

    1998-01-01

    An extended version of the non linear Walecka model, with rho mesons and eletromagnetic field is used to investigate the possibility of phase transitions in hot (warm) nuclear matter, giving rise to droplet formation. Surface properties of asymmetric nuclear matter as the droplet surface energy and its thickness are also examined.

  5. Integrated Optical Asymmetric Coupler Pressure Sensor

    Science.gov (United States)

    Kiyat, Isa; Kocabas, Coskun; Aydinli, Atilla

    2004-05-01

    Analysis of a novel pressure sensor based on a silicon-on-insulator (SOI) asymmetric vertical coupler is presented. The integrated optical component is a coupler composed of a single mode (SM) low index waveguide and a thin silicon slab. High sensitivities of about 0.14 rad.kPa-1 should be achieved.

  6. 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

  7. 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...

  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. 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....

  10. 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

  11. Stochastic induction of persister cells by HipA through (p)ppGpp-mediated activation of mRNA endonucleases

    DEFF Research Database (Denmark)

    Germain-Maisonneuve, Elsa; Roghanian, Mohammad; Gerdes, Kenn

    2015-01-01

    The model organism Escherichia coli codes for at least 11 type II toxin-antitoxin (TA) modules, all implicated in bacterial persistence (multidrug tolerance). Ten of these encode messenger RNA endonucleases (mRNases) inhibiting translation by catalytic degradation of mRNA, and the 11th module, hi...

  12. 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.

  13. Asymmetric magnetic reconnection with a flow shear and applications to the magnetopause

    Science.gov (United States)

    Doss, C. E.; Komar, C. M.; Cassak, P. A.; Wilder, F. D.; Eriksson, S.; Drake, J. F.

    2015-09-01

    We perform a systematic theoretical and numerical study of antiparallel two-dimensional magnetic reconnection with asymmetries in the plasma density and reconnecting magnetic field strength in addition to a bulk flow shear across the reconnection site in the plane of the reconnecting fields, which commonly occurs at planetary magnetospheres. We analytically predict the speed at which an isolated X line is convected by the flow, the reconnection rate, and the critical flow speed at which reconnection no longer takes place for arbitrary reconnecting magnetic field strengths, densities, and upstream flow speeds, and we confirm the results with two-fluid numerical simulations. The predictions and simulation results counter the prevailing model of reconnection at Earth's dayside magnetopause which says reconnection occurs with a stationary X line for sub-Alfvénic magnetosheath flow, reconnection occurs but the X line convects for magnetosheath flows between the Alfvén speed and double the Alfvén speed, and reconnection does not occur for magnetosheath flows greater than double the Alfvén speed. In particular, we find that X line motion is governed by momentum conservation from the upstream flows, which are weighted differently in asymmetric systems, so the X line convects for generic conditions including sub-Alfvénic upstream speeds. For the reconnection rate, as with symmetric reconnection, it drops with increasing flow shear and there is a cutoff speed above which reconnection is not predominant. However, while the cutoff condition for symmetric reconnection is that the difference in flows on the two sides of the reconnection site is twice the Alfvén speed, we find asymmetries cause the cutoff speed for asymmetric reconnection to be higher than twice the asymmetric form of the Alfvén speed. The stronger the asymmetries, the more the cutoff exceeds double the asymmetric Alfvén speed. This is due to the fact that in asymmetric reconnection, the plasma with the

  14. The double identity of linguistic doubling.

    Science.gov (United States)

    Berent, Iris; Bat-El, Outi; Brentari, Diane; Dupuis, Amanda; Vaknin-Nusbaum, Vered

    2016-11-29

    Does knowledge of language consist of abstract principles, or is it fully embodied in the sensorimotor system? To address this question, we investigate the double identity of doubling (e.g., slaflaf, or generally, XX; where X stands for a phonological constituent). Across languages, doubling is known to elicit conflicting preferences at different levels of linguistic analysis (phonology vs. morphology). Here, we show that these preferences are active in the brains of individual speakers, and they are demonstrably distinct from sensorimotor pressures. We first demonstrate that doubling in novel English words elicits divergent percepts: Viewed as meaningless (phonological) forms, doubling is disliked (e.g., slaflaf linguistic preferences doubly dissociate from sensorimotor demands: A single stimulus can elicit diverse percepts, yet these percepts are invariant across stimulus modality--for speech and signs. These conclusions are in line with the possibility that some linguistic principles are abstract, and they apply broadly across language modality.

  15. 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.

  16. 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.

  17. 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.

  18. Labeling of double-stranded DNA by ROX-dideoxycytosine triphosphate using terminal deoxynucleotidyl transferase and separation by capillary electrophoresis

    Energy Technology Data Exchange (ETDEWEB)

    Figeys, D.; Renborg, A.; Dovichi, N.J. (Univ. of Alberta, Edmonton, Alberta (Canada))

    1994-12-01

    Terminal transferase is used to add a single fluorescently labeled dideoxynucleotide to double-stranded DNA prepared by restriction endonuclease action on a bacteriophage. The product is separated by capillary electrophoresis with both hydroxypropylmethylcellulose and non-cross-linked polyacrylamide. The reaction products generate single peaks for each fragment with hydroxypropylmethylcellulose. However, the higher resolution separation produced by non-cross-linked polyacrylamide shows that the product contains two components for each restriction digest fragment. This labeling technique should be useful in restriction fragment length polymorphism studies. 9 refs., 2 figs.

  19. 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.

  20. 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.

  1. Dual emission in asymmetric ``giant'' PbS/CdS/CdS core/shell/shell quantum dots

    Science.gov (United States)

    Zhao, Haiguang; Sirigu, Gianluca; Parisini, Andrea; Camellini, Andrea; Nicotra, Giuseppe; Rosei, Federico; Morandi, Vittorio; Zavelani-Rossi, Margherita; Vomiero, Alberto

    2016-02-01

    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

  2. Critical behavior near the Mott transition in the half-filled asymmetric Hubbard model

    Energy Technology Data Exchange (ETDEWEB)

    Hoang, Anh-Tuan, E-mail: hatuan@iop.vast.ac.vn [Institute of Physics, Vietnam Academy of Science and Technology, Hanoi (Viet Nam); Le, Duc-Anh [Faculty of Physics, Hanoi National University of Education, Xuan Thuy 136, Cau Giay, Hanoi 10000 (Viet Nam)

    2016-03-15

    We study the half-filled asymmetric Hubbard model within the two-site dynamical mean field theory. At zero temperature, explicit expressions of the critical interaction U{sub c} for the Mott transition and the local self-energy are analytically derived. Critical behavior of the quasiparticle weights and the double occupancy are obtained analytically as functions of the on-site interaction U and the hopping asymmetry r. Our results are in good agreement with the ones obtained by much more sophisticated theory.

  3. Pulse generation and compression using an asymmetrical porous silicon-based Mach–Zehnder interferometer configuration

    Indian Academy of Sciences (India)

    SHU-WEN GUO; JIAN-WEI WU

    2016-12-01

    We propose an asymmetrical Mach–Zehnder interferometer (MZI) for efficient pulse generation and compression using porous silicon (PS) waveguide, fibre delay line and couplers. We show a pulse compression of about 0.4 ns at the output port with third-order super-Gaussian input pulse in ∼2 ns time duration and ∼40.3 W peak power level. Also, we show the possibility of obtaining compressed single- or double-pulse with judicious choice of various parameters like input peak power, delay time and input pulse width.

  4. 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.

  5. 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.

  6. Double orifice mitral valve: A case report

    Directory of Open Access Journals (Sweden)

    Musić Ljilja

    2016-01-01

    Full Text Available Introduction. Double orifice mitrol valve (DOMV is a very rare congenital heart defect. Case report. We reported 20-year-old male referred to our center due to evaluation of his cardiologic status. He was operated on shortly after birth for a tracheoesophageal fistula. Accidentally, echocardiography examination at the age of 4 years revealed double orifice mitral valve (DOMV without the presence of mitral regurgitation, as well as mitral stenosis, with normal dimensions of all cardiac chambers. The patient was asymptomatic, even more he was a kick boxer. His physical finding was normal. Electrocardiography showed regular sinus rhythm, incomplete right bundle branch block. Transthoracic echocardiography (TTE examination revealed the normal size of the left atrial, mitral leaflets were slightly more redundant. The left and right heart chambers, aorta, tricuspid valve and pulmonary artery valve were normal. During TTE examination on a short axis view two asymmetric mitral orifices were seen as a double mitral orifice through which we registered normal flow, without regurgitation and mitral stenosis. Transesophageal echocardiography (TEE examination from the transgastric view at the level of mitral valve, showed 2 single asymmetric mitral orifices separated by fibrous tissue, mitral leaflet with a separate insertion of hordes for each orifice. Conclusion. The presented patient with DOMV is the only one recognized in our country. The case is interesting because during 16-year a follow-up period there were no functional changes despite the fact that he performed very demanded sport activities. This is very important because there is no information in the literature about that.

  7. 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.

  8. 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.

  9. Asymmetric dark matter models in SO(10)

    Science.gov (United States)

    Nagata, Natsumi; Olive, Keith A.; Zheng, Jiaming

    2017-02-01

    We systematically study the possibilities for asymmetric dark matter in the context of non-supersymmetric SO(10) models of grand unification. Dark matter stability in SO(10) is guaranteed by a remnant Z2 symmetry which is preserved when the intermediate scale gauge subgroup of SO(10) is broken by a {126} dimensional representation. The asymmetry in the dark matter states is directly generated through the out-of-equilibrium decay of particles around the intermediate scale, or transferred from the baryon/lepton asymmetry generated in the Standard Model sector by leptogenesis. We systematically classify possible asymmetric dark matter candidates in terms of their quantum numbers, and derive the conditions for each case that the observed dark matter density is (mostly) explained by the asymmetry of dark matter particles.

  10. Asymmetric Dark Matter Models in SO(10)

    CERN Document Server

    Nagata, Natsumi; Zheng, Jiaming

    2016-01-01

    We systematically study the possibilities for asymmetric dark matter in the context of non-supersymmetric SO(10) models of grand unification. Dark matter stability in SO(10) is guaranteed by a remnant $\\mathbb{Z}_2$ symmetry which is preserved when the intermediate scale gauge subgroup of SO(10) is broken by a ${\\bf 126}$ dimensional representation. The asymmetry in the dark matter states is directly generated through the out-of-equilibrium decay of particles around the intermediate scale, or transferred from the baryon/lepton asymmetry generated in the Standard Model sector by leptogenesis. We systematically classify possible asymmetric dark matter candidates in terms of their quantum numbers, and derive the conditions for each case that the observed dark matter density is (mostly) explained by the asymmetry of dark matter particles.

  11. 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.

  12. Venture Capital Contracting Under Asymmetric Information

    OpenAIRE

    Jeffrey Trester

    1993-01-01

    The author develops a model of venture capital contracting in which the entrepreneur and venture capitalist contract under symmetric information. A condition of asymmetric information may arise subsequent to the first contract. The author shows that this condition makes debt contracts infeasible and leads to the use of preferred equity contracts. The author notes that discussions of the relation between venture capital and capital structure are rare. This paper expands the literature by addre...

  13. Fluorous Mixture Synthesis of Asymmetric Dendrimers

    Science.gov (United States)

    Jiang, Zhong-Xing; Yu, Yihua Bruce

    2010-01-01

    A divergent fluorous mixture synthesis (FMS) of asymmetric fluorinated dendrimers has been developed. Four generations of fluorinated dendrimers with the same fluorinated moiety were prepared with high efficiency, yield and purity. Comparison of the physicochemical properties of these dendrimers provided valuable information for their application and future optimization. This strategy has not only provided a practical method for the synthesis and purification of dendrimers, but also established the possibility of utilizing the same fluorinated moiety for FMS. PMID:20170088

  14. Asymmetric k-Center with Minimum Coverage

    DEFF Research Database (Denmark)

    Gørtz, Inge Li

    2008-01-01

    In this paper we give approximation algorithms and inapproximability results for various asymmetric k-center with minimum coverage problems. In the k-center with minimum coverage problem, each center is required to serve a minimum number of clients. These problems have been studied by Lim et al. [A....... Lim, B. Rodrigues, F. Wang, Z. Xu, k-center problems with minimum coverage, Theoret. Comput. Sci. 332 (1–3) (2005) 1–17] in the symmetric setting....

  15. New electric field in asymmetric magnetic reconnection.

    Science.gov (United States)

    Malakit, K; Shay, M A; Cassak, P A; Ruffolo, D

    2013-09-27

    We present a theory and numerical evidence for the existence of a previously unexplored in-plane electric field in collisionless asymmetric magnetic reconnection. This electric field, dubbed the "Larmor electric field," is associated with finite Larmor radius effects and is distinct from the known Hall electric field. Potentially, it could be an important indicator for the upcoming Magnetospheric Multiscale mission to locate reconnection sites as we expect it to appear on the magnetospheric side, pointing earthward, at the dayside magnetopause reconnection site.

  16. 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.

  17. 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.

  18. 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...

  19. 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...

  20. 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.

  1. SPECT using asymmetric pinholes with truncated projections

    Energy Technology Data Exchange (ETDEWEB)

    Lin Jianyu; Meikle, Steven R, E-mail: jianyu.lin@curtin.edu.au [Ramaciotti Imaging Centre, Brain and Mind Research Institute, University of Sydney (Australia)

    2011-07-07

    Tomographic systems employing truncated projections have been developed for parallel and fan beam collimation and for cone beam CT but the idea has not been extensively explored in pinhole single photon emission computed tomography (SPECT). In this paper, we explore the sampling requirements and system performance of SPECT systems with asymmetric pinhole collimators and truncated projections. We demonstrate that complete 3D sampling can be achieved by using multiple detectors with truncated asymmetric pinholes, offset axially from each other, and a spiral orbit. The use of truncated projections can be exploited in the design of pinhole SPECT systems by moving the pinholes closer to the subject, resulting in increased sensitivity and improved spatial resolution. Truncated and untruncated pinhole systems were evaluated using the contrast-to-noise ratio (CNR) calculated from the linearized local impulse response as a figure of merit. The CNR for the truncated pinhole system was up to 60% greater than that for the untruncated system at matched resolution for a source voxel near the centre of a uniform phantom and 30% greater at the edge. We conclude that an object can be reconstructed from asymmetric pinholes with truncated projections, which leads to potentially important design considerations and applications in single- and multi-pinhole SPECT.

  2. 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....

  3. 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.

  4. 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.

  5. 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.

  6. Correlation effects in double rydberg atoms

    Energy Technology Data Exchange (ETDEWEB)

    Camus, P. (Lab. Aime Cotton, Centre National de la Recherche Scientifique 2, 91 Orsay (France))

    1994-01-01

    The present review is devoted to the recent advances performed in alkaline-earth atoms by the selective laser preparation of autoionizing asymmetrical double Rydberg states which have, so far, not been observed in natural environments. Because the great amount of flexibility achieved by the sequential laser electron excitations, a wide choice of two-electron situations have been investigated and analyzed which exhibit spectral features due to long-range effects of the Coulomb electron-electron repulsion. To overcome the autoionization broadening of the lines, double Rydberg states with a non-core penetrating high-l outer electron were produced by combining temporal laser excitation technique with the electric-field switching method. The study of the spectral correlation signatures in N snl double Rydberg states versus l allow to understand their evolution from simple spectra (l [>=] 10) due to long-range dipole interaction to more complex data (l [<=] 7) induced by short-range multipole effects when two electrons start to influence more each other. (orig.).

  7. Structure of the EndoMS-DNA Complex as Mismatch Restriction Endonuclease.

    Science.gov (United States)

    Nakae, Setsu; Hijikata, Atsushi; Tsuji, Toshiyuki; Yonezawa, Kouki; Kouyama, Ken-Ichi; Mayanagi, Kouta; Ishino, Sonoko; Ishino, Yoshizumi; Shirai, Tsuyoshi

    2016-11-01

    Archaeal NucS nuclease was thought to degrade the single-stranded region of branched DNA, which contains flapped and splayed DNA. However, recent findings indicated that EndoMS, the orthologous enzyme of NucS, specifically cleaves double-stranded DNA (dsDNA) containing mismatched bases. In this study, we determined the structure of the EndoMS-DNA complex. The complex structure of the EndoMS dimer with dsDNA unexpectedly revealed that the mismatched bases were flipped out into binding sites, and the overall architecture most resembled that of restriction enzymes. The structure of the apo form was similar to the reported structure of Pyrococcus abyssi NucS, indicating that movement of the C-terminal domain from the resting state was required for activity. In addition, a model of the EndoMS-PCNA-DNA complex was preliminarily verified with electron microscopy. The structures strongly support the idea that EndoMS acts in a mismatch repair pathway.

  8. 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.

  9. Unintegrated double parton distributions

    CERN Document Server

    Golec-Biernat, K

    2016-01-01

    We present the construction of unintegrated double parton distribution functions which include dependence on transverse momenta of partons. We extend the formulation which was used to obtain the single unintegrated parton distributions from the standard, integrated parton distribution functions. Starting from the homogeneous part of the evolution equations for the integrated double parton distributions, we construct the unintegrated double parton distributions as the convolutions of the integrated double distributions and the splitting functions, multiplied by the Sudakov form factors. We show that there exist three domains of external hard scales which require three distinct forms of the unintegrated double distributions. The additional transverse momentum dependence which arises through the Sudakov form factors leads to non-trivial correlations in the parton momenta. We also discuss the non-homogeneous contribution to the unintegrated double parton distributions, which arises due to the splitting of a singl...

  10. 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.

  11. Endonuclease and helicase activities of bacteriophage lambda terminase: changing nearby residue 515 restores activity to the gpA K497D mutant enzyme.

    Science.gov (United States)

    Hwang, Y; Hang, J Q; Neagle, J; Duffy, C; Feiss, M

    2000-11-10

    Terminase, the DNA packaging enzyme of bacteriophage lambda, is a heteromultimer of gpNu1 and gpA subunits. In an earlier investigation, a lethal mutation changing gpA residue 497 from lysine to aspartic acid (K497D) was found to cause a mild change in the high-affinity ATPase that resides in gpA and a severe defect in the endonuclease activity of terminase. The K497D terminase efficiently sponsored packaging of mature lambda DNA into proheads. In the present work, K497D terminase was found to have a severe defect in the cohesive end separation, or helicase, activity. Plaque-forming pseudorevertants of lambda A K497D were found to carry mutations in A that suppressed the lethality of the A K497D mutation. The two suppressor mutations identified, A E515G and A E515K, affected residue 515, which is located near the putative P-loop of gpA. A codon substitution study of codon 515 showed that hydrophobic and basic residues suppress the K497D defect, but hydrophilic and acidic residues do not. The E515G change was demonstrated to reverse the endonuclease and helicase defects caused by the K497D change. Moreover, the gpA K497D E515G enzyme was found to have kinetic constants for the high-affinity ATPase center similar to those of the wild type enzyme, and the endonuclease activity of the K497D E515G enzyme was stimulated by ATP to an extent similar to the ATP stimulation of the endonuclease activity of the wild type enzyme.

  12. On Double Vector Bundles

    Institute of Scientific and Technical Information of China (English)

    Zhuo CHEN; Zhang Ju LIU; Yun He SHENG

    2014-01-01

    In this paper, we construct a category of short exact sequences of vector bundles and prove that it is equivalent to the category of double vector bundles. Moreover, operations on double vector bundles can be transferred to operations on the corresponding short exact sequences. In particular, we study the duality theory of double vector bundles in term of the corresponding short exact sequences. Examples including the jet bundle and the Atiyah algebroid are discussed.

  13. On Double Vector Bundles

    OpenAIRE

    Chen, Zhuo; Liu, Zhangju; Sheng, Yunhe

    2011-01-01

    In this paper, we construct a category of short exact sequences of vector bundles and prove that it is equivalent to the category of double vector bundles. Moreover, operations on double vector bundles can be transferred to operations on the corresponding short exact sequences. In particular, we study the duality theory of double vector bundles in term of the corresponding short exact sequences. Examples including the jet bundle and the Atiyah algebroid are discussed.

  14. 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 .

  15. Double-strand breaks at the target locus stimulate gene targeting in embryonic stem cells.

    Science.gov (United States)

    Smih, F; Rouet, P; Romanienko, P J; Jasin, M

    1995-01-01

    Double-strand breaks (DSBs) are recombinogenic lesions in chromosomal DNA in yeast, Drosophila and Caenorhabditis elegans. Recent studies in mammalian cells utilizing the I-Scel endonuclease have demonstrated that in some immortalized cell lines DSBs in chromosomal DNA are also recombinogenic. We have now tested embryonic stem (ES) cells, a non-transformed mouse cell line frequently used in gene targeting studies. We find that a DSB introduced by I-Scel stimulates gene targeting at a selectable neo locus at least 50-fold. The enhanced level of targeting is achieved by transient expression of the I-Scel endonuclease. In 97% of targeted clones a single base pair polymorphism in the transfected homologous fragment was incorporated into the target locus. Analysis of the targeted locus demonstrated that most of the homologous recombination events were 'two-sided', in contrast to previous studies in 3T3 cells in which 'one-sided' homologous events predominated. Thus ES cells may be more faithful in incorporating homologous fragments into their genome than other cells in culture. Images PMID:8559659

  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. Improved DFIG Capability during Asymmetrical Grid Faults

    DEFF Research Database (Denmark)

    Zhou, Dao; Blaabjerg, Frede

    2015-01-01

    the natural component of the Doubly-Fed Induction Generator (DFIG) stator flux during the fault period, their effects on the rotor voltage can be investigated. It is concluded that the phase-to-phase fault has the worst scenario due to its highest introduction of the negative stator flux. Afterwards......, the capability of a 2 MW DFIG to ride through asymmetrical grid faults can be estimated at the existing design of the power electronics converter. Finally, a control scheme aimed to improve the DFIG capability is proposed and the simulation results validate its feasibility....

  18. Resonance phenomena for asymmetric weakly nonlinear oscillator

    Institute of Scientific and Technical Information of China (English)

    钱定边

    2002-01-01

    We establish the coexistence of periodic solution and unbounded solution, the infinity of largeamplitude subharmonics for asymmetric weakly nonlinear oscillator x" + a2x+ - b2x- + h(x) = p(t) with h(±∞) - 0 and xh(x) → +∞(x →∞), assuming that M(τ ) has zeros which are all simple and M(τ ) 0respectively, where M(τ ) is a function related to the piecewise linear equation x" + a2x+ - b2x- = p(t).``

  19. Dynamic Conditional Correlations for Asymmetric Processes

    OpenAIRE

    Asai, Manabu; McAleer, Michael

    2011-01-01

    The paper develops two Dynamic Conditional Correlation (DCC) models, namely the Wishart DCC (wDCC) model. The paper applies the wDCC approach to the exponential GARCH (EGARCH) and GJR models to propose asymmetric DCC models. We use the standardized multivariate t-distribution to accommodate heavy-tailed errors. The paper presents an empirical example using the trivariate data of the Nikkei 225, Hang Seng and Straits Times Indices for estimating and forecasting the wDCC-EGARCH and wDCC-GJR mod...

  20. 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.

  1. 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.

  2. 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

  3. 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.

  4. Photoresponse of silicon with asymmetric area contacts

    Science.gov (United States)

    Rabbani, M. Golam; Sundararajan, Jency P.; Verma, Amit; Nekovei, Reza; Khader, Mahmoud M.; Darling, R. B.; Patil, Sunil R.

    2017-01-01

    We report on high performance metal-semiconductor-metal (MSM) photosensors based on asymmetric metal pad areas. The reported devices require a single-step metal deposition, and exhibit large photo response even under zero-bias. Moreover the devices offer fast and stable light switching behavior. Device fabrication and electrical characterization results are presented that are further analyzed with TCAD modeling and simulation. Device simulations show that contact asymmetry along with surface recombination and barrier lowering plays an important role in the MSM I-V characteristics.

  5. 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.

  6. 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.

  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. 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.

  9. 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.

  10. Asymmetric acoustic transmission in graded beam

    Science.gov (United States)

    Jing, Li; Wu, Jiu Hui; Guan, Dong; Lu, Kuan; Gao, Nansha; Songhua, Cao

    2016-12-01

    We demonstrate the dynamic effective material parameters and vibration performance of a graded beam. The structure of the beam was composed of several unit cells with different fill factors. The dispersion relations and energy band structures of each unit cell were calculated using the finite element method (FEM). The dynamic effective material parameters in each unit cell of the graded beam were determined by the dispersion relations and energy band structures. Longitudinal wave propagation was investigated using a numerical method and FEM. The results show that the graded beam allows asymmetric acoustic transmission over a wide range of frequencies.

  11. 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.

  12. An Asymmetric Block Dynamic Conditional Correlation Multivariate GARCH Model

    OpenAIRE

    Vargas, Gregorio A.

    2006-01-01

    The Block DCC model for determining dynamic correlations within and between groups of financial asset returns is extended to account for asymmetric effects. Simulation results show that the Asymmetric Block DCC model is competitive in in-sample forecasting and performs better than alternative DCC models in out-of-sample forecasting of conditional correlation in the presence of asymmetric effect between blocks of asset returns. Empirical results demonstrate that the model is able to capture ...

  13. Asymmetric joint multifractal analysis in Chinese stock markets

    Science.gov (United States)

    Chen, Yuwen; Zheng, Tingting

    2017-04-01

    In this paper, the asymmetric joint multifractal analysis method based on statistical physics is proposed to explore the asymmetric correlation between daily returns and trading volumes in Chinese stock markets. The result shows asymmetric multifractal correlations exist between return and trading volume in Chinese stock markets. Moreover, when the stock indexes are upward, the fluctuations of returns are always weaker than when they are downward, whether the trading volumes are more or less.

  14. Asymmetric Campaigning as a Rational Choice: Planning Considerations

    Science.gov (United States)

    2006-06-01

    Maslow identified five levels: survival, safety, belonging, esteem, and self-actualization. He presented his theory as a pyramid with five layers...to be sustained by actions of the asymmetric opponent. For the media-fed frenzy over constraints and protraction to continue, the asymmetric...lot of people. The reason for this is twofold. First, the actor needs sufficient support to exist and to sustain an asymmetric campaign. Second, the

  15. Trans-complementation by human apurinic endonuclease (Ape) of hypersensitivity to DNA damage and spontaneous mutator phenotype in apn1-yeast.

    Science.gov (United States)

    Wilson, D M; Bennett, R A; Marquis, J C; Ansari, P; Demple, B

    1995-01-01

    Abasic (AP) sites in DNA are potentially lethal and mutagenic. 'Class II' AP endonucleases initiate the repair of these and other DNA lesions. In yeast, the predominant enzyme of this type is Apn1, and its elimination sensitizes the cells to killing by simple alkylating agents or oxidants, and raises the rate of spontaneous mutation. We investigated the ability of the major human class II AP endonuclease, Ape, which is structurally unrelated to Apn1, to replace the yeast enzyme in vivo. Confocal immunomicroscopy studies indicate that approximately 25% of the Ape expressed in yeast is present in the nucleus. High-level Ape expression corresponding to approximately 7000 molecules per nucleus, equal to the normal Apn1 copy number, restored resistance to methyl methanesulfonate to near wild-type levels in Apn1-deficient (apn1-) yeast. Ape expression in apn1- yeast provided little protection against H2O2 challenges, consistent with the weak 3'-repair diesterase activity of the human enzyme. Ape expression at approximately 2000 molecules per nucleus reduced the spontaneous mutation rate of apn1- yeast to that seen for wild-type cells. Because Ape has a powerful AP endonuclease but weak 3'-diesterase activity, these findings indicate that endogenously generated AP sites can drive spontaneous mutagenesis. Images PMID:8559661

  16. 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.

  17. 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.

  18. Quantity Discount Scheme in Supply Chain under Asymmetric Information

    Institute of Scientific and Technical Information of China (English)

    LI Ji-bin; PENG Zuo-he

    2007-01-01

    Quantity discount scheme plays an important role in supply chain management. The different quantity discount schemes under symmetric (full) information and asymmetric information, are analyzed by using principal-agent and optimal control theory. As a result, the research reveals that the optimal quantity discount solution under symmetric information is a special case of that under asymmetric information. At the same price, the critical value of quantity discount under asymmetric information is much lower than that under asymmetric information. Therefore, this leads to less cost for retailers and smaller profit for their supplier.

  19. PAM-Dependent Target DNA Recognition and Cleavage by C2c1 CRISPR-Cas Endonuclease

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Hui; Gao, Pu; Rajashankar, Kanagalaghatta R.; Patel, Dinshaw J.

    2016-12-01

    C2c1 is a newly identified guide RNA-mediated type V-B CRISPR-Cas endonuclease that site-specifically targets and cleaves both strands of target DNA. We have determined crystal structures of Alicyclobacillus acidoterrestris C2c1 (AacC2c1) bound to sgRNA as a binary complex and to target DNAs as ternary complexes, thereby capturing catalytically competent conformations of AacC2c1 with both target and non-target DNA strands independently positioned within a single RuvC catalytic pocket. Moreover, C2c1-mediated cleavage results in a staggered seven-nucleotide break of target DNA. crRNA adopts a pre-ordered five-nucleotide A-form seed sequence in the binary complex, with release of an inserted tryptophan, facilitating zippering up of 20-bp guide RNA:target DNA heteroduplex on ternary complex formation. Notably, the PAM-interacting cleft adopts a “locked” conformation on ternary complex formation. Structural comparison of C2c1 ternary complexes with their Cas9 and Cpf1 counterparts highlights the diverse mechanisms adopted by these distinct CRISPR-Cas systems, thereby broadening and enhancing their applicability as genome editing tools.

  20. Involvement of hydrogen peroxide in safingol-induced endonuclease G-mediated apoptosis of squamous cell carcinoma cells.

    Science.gov (United States)

    Hamada, Masakazu; Wakabayashi, Ken; Masui, Atsushi; Iwai, Soichi; Imai, Tomoaki; Yura, Yoshiaki

    2014-02-17

    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.

  1. A comparative study of cold- and warm-adapted Endonucleases A using sequence analyses and molecular dynamics simulations

    Science.gov (United States)

    Michetti, Davide; Brandsdal, Bjørn Olav; Bon, Davide; Isaksen, Geir Villy; Tiberti, Matteo; Papaleo, Elena

    2017-01-01

    The psychrophilic and mesophilic endonucleases A (EndA) from Aliivibrio salmonicida (VsEndA) and Vibrio cholera (VcEndA) have been studied experimentally in terms of the biophysical properties related to thermal adaptation. The analyses of their static X-ray structures was no sufficient to rationalize the determinants of their adaptive traits at the molecular level. Thus, we used Molecular Dynamics (MD) simulations to compare the two proteins and unveil their structural and dynamical differences. Our simulations did not show a substantial increase in flexibility in the cold-adapted variant on the nanosecond time scale. The only exception is a more rigid C-terminal region in VcEndA, which is ascribable to a cluster of electrostatic interactions and hydrogen bonds, as also supported by MD simulations of the VsEndA mutant variant where the cluster of interactions was introduced. Moreover, we identified three additional amino acidic substitutions through multiple sequence alignment and the analyses of MD-based protein structure networks. In particular, T120V occurs in the proximity of the catalytic residue H80 and alters the interaction with the residue Y43, which belongs to the second coordination sphere of the Mg2+ ion. This makes T120V an amenable candidate for future experimental mutagenesis. PMID:28192428

  2. 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.

  3. 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.

  4. Loss of mitochondrial exo/endonuclease EXOG affects mitochondrial respiration and induces ROS-mediated cardiomyocyte hypertrophy.

    Science.gov (United States)

    Tigchelaar, Wardit; Yu, Hongjuan; de Jong, Anne Margreet; van Gilst, Wiek H; van der Harst, Pim; Westenbrink, B Daan; de Boer, Rudolf A; Silljé, Herman H W

    2015-01-15

    Recently, a locus at the mitochondrial exo/endonuclease EXOG gene, which has been implicated in mitochondrial DNA repair, was associated with cardiac function. The function of EXOG in cardiomyocytes is still elusive. Here we investigated the role of EXOG in mitochondrial function and hypertrophy in cardiomyocytes. Depletion of EXOG in primary neonatal rat ventricular cardiomyocytes (NRVCs) induced a marked increase in cardiomyocyte hypertrophy. Depletion of EXOG, however, did not result in loss of mitochondrial DNA integrity. Although EXOG depletion did not induce fetal gene expression and common hypertrophy pathways were not activated, a clear increase in ribosomal S6 phosphorylation was observed, which readily explains increased protein synthesis. With the use of a Seahorse flux analyzer, it was shown that the mitochondrial oxidative consumption rate (OCR) was increased 2.4-fold in EXOG-depleted NRVCs. Moreover, ATP-linked OCR was 5.2-fold higher. This increase was not explained by mitochondrial biogenesis or alterations in mitochondrial membrane potential. Western blotting confirmed normal levels of the oxidative phosphorylation (OXPHOS) complexes. The increased OCR was accompanied by a 5.4-fold increase in mitochondrial ROS levels. These increased ROS levels could be normalized with specific mitochondrial ROS scavengers (MitoTEMPO, mnSOD). Remarkably, scavenging of excess ROS strongly attenuated the hypertrophic response. In conclusion, loss of EXOG affects normal mitochondrial function resulting in increased mitochondrial respiration, excess ROS production, and cardiomyocyte hypertrophy.

  5. A T7 Endonuclease I Assay to Detect Talen-Mediated Targeted Mutation of HBV cccDNA.

    Science.gov (United States)

    Bloom, Kristie; Ely, Abdullah; Arbuthnot, Patrick

    2017-01-01

    Gene editing using designer nucleases is now widely used in many fields of molecular biology. The technology is being developed for the treatment of viral infections such as persistant hepatitis B virus (HBV). The replication intermediate of HBV comprising covalently closed circular DNA (cccDNA) is stable and resistant to available licensed antiviral agents. Advancing gene editing as a means of introducing targeted mutations into cccDNA thus potentially offers the means to cure infection by the virus. Essentially, targeted mutations are initiated by intracellular DNA cleavage, then error-prone nonhomologous end joining results in insertions and deletions (indels) at intended sites. Characterization of these mutations is crucial to confirm activity of potentially therapeutic nucleases. A convenient tool for evaluation of the efficiency of target cleavage is the single strand-specific endonuclease, T7EI. Assays employing this enzyme entail initial amplification of DNA encompassing the targeted region. Thereafter the amplicons are denatured and reannealed to allow hybridization between indel-containing and wild-type sequences. Heteroduplexes that contain mismatched regions are susceptible to action by T7EI and cleavage of the hybrid amplicons may be used as an indicator of efficiency of designer nucleases. The protocol described here provides a method of isolating cccDNA from transfected HepG2.2.15 cells and evaluation of the efficiency of mutation by a transcription activator-like effector nuclease that targets the surface open reading frame of HBV.

  6. [Effect of endonuclease G depletion on plasmid DNA uptake and levels of homologous recombination in hela cells].

    Science.gov (United States)

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

    2016-01-01

    Endonuclease G (EndoG) is a mitochondrial apoptosis regulator that also has roles outside of programmed cell death. It has been implicated as a defence DNase involved in the degradation of exogenous DNA after transfection of mammalian cells and in homologous recombination of viral and endogenous DNA. In this study, we looked at the effect of EndoG depletion on plasmid DNA uptake and the levels of homologous recombination in HeLa cells. We show that the proposed defence role of EndoG against uptake of non-viral DNA vectors does not extend to the cervical carcinoma HeLa cells, as targeting of EndoG expression by RNA interference failed to increase intracellular plasmid DNA levels. However, reducing EndoG levels in HeLa cells resulted in a statistically significant reduction of homologous recombination between two plasmid DNA substrates. These findings suggest that non-viral DNA vectors are also substrates for EndoG in its role in homologous recombination.

  7. 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

  8. Characterization of a new aberration of the human Y chromosome by banding methods and DNA restriction endonuclease analysis.

    Science.gov (United States)

    Schmid, M; Gall, H; Schempp, W; Weber, L; Schmidtke, J

    1981-01-01

    Comparative cytogenetic analyses were performed with ten different banding methods on a previously undescribed, inherited structural aberration of a Y chromosome, and the results compared with those of normal Y chromosomes occurring in the same family. The value of the individual staining techniques in investigations of Y chromosomal aberrations is emphasized. The aberrant Y chromosome analyzed can be formally derived from an isodicentric Y chromosome for the short arm with a very terminal long-arm breakpoint, in which the centromere, an entire short arm, and the proximal region on one long arm was lost. This interpretation was confirmed by determining the amount of the two Y-specific DNA sequences (2.1 and 3.4 kb in length) by means of Hae III restriction endonuclease analysis. The karyotype-phenotype correlations in the men with this aberrant Y chromosome, especially the fertility dysfunctions (oligoasthenoteratozoospermia, cryptozoospermia), are discussed. The possibility of the existence of fertility factors involved in the control of spermatogenesis within the quinacrine-bright heterochromatic region of the Y long arm is presented.

  9. Sensitive and specific colorimetric DNA detection by invasive reaction coupled with nicking endonuclease-assisted nanoparticles amplification.

    Science.gov (United States)

    Zou, Bingjie; Cao, Xiaomei; Wu, Haiping; Song, Qinxin; Wang, Jianping; Kajiyama, Tomoharu; Kambara, Hideki; Zhou, Guohua

    2015-04-15

    Colorimetric DNA detection is preferable to methods in clinical molecular diagnostics, because no expensive equipment is required. Although many gold nanoparticle-based colorimetric DNA detection strategies have been developed to analyze DNA sequences of interest, few of them can detect somatic mutations due to their insufficient specificity. In this study, we proposed a colorimetric DNA detection method by coupling invasive reaction with nicking endonuclease-assisted nanoparticles amplification (IR-NEANA). A target DNA firstly produces many flaps by invasive reaction. Then the flaps are converted to targets of nicking reaction-assisted nanoparticles amplification by ligation reaction to produce the color change of AuNPs, which can be observed by naked eyes. The detection limit of IR-NEANA was determined as 1pM. Most importantly, the specificity of the method is high enough to pick up as low as 1% mutant from a large amount of wild-type DNA backgrounds. The EGFR gene mutated at c.2573 T>G in 9 tissue samples from non-small cell lung cancer patients were successfully detected by using IR-NEANA, suggesting that our proposed method can be used to detect somatic mutations in biological samples.

  10. 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.

  11. In vivo characterization of the homing endonuclease within the polB gene in the halophilic archaeon Haloferax volcanii.

    Directory of Open Access Journals (Sweden)

    Adit Naor

    Full Text Available Inteins are parasitic genetic elements, analogous to introns that excise themselves at the protein level by self-splicing, allowing the formation of functional non-disrupted proteins. Many inteins contain a homing endonuclease (HEN gene, and rely on its activity for horizontal propagation. In the halophilic archaeon, Haloferax volcanii, the gene encoding DNA polymerase B (polB contains an intein with an annotated but uncharacterized HEN. Here we examine the activity of the polB HEN in vivo, within its natural archaeal host. We show that this HEN is highly active, and able to insert the intein into both a chromosomal target and an extra-chromosomal plasmid target, by gene conversion. We also demonstrate that the frequency of its incorporation depends on the length of the flanking homologous sequences around the target site, reflecting its dependence on the homologous recombination machinery. Although several evolutionary models predict that the presence of an intein involves a change in the fitness of the host organism, our results show that a strain deleted for the intein sequence shows no significant changes in growth rate compared to the wild type.

  12. 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.

  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. 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 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.

  15. Asymmetric DSL Technology of Signal Transmission

    Directory of Open Access Journals (Sweden)

    Dražen Kovačević

    2005-05-01

    Full Text Available Asymmetric flow of information is the key feature of theADSL (Asymmetric Digital Subscriber Loop technology, i.e.higher data transmission rate towards the user than from theuser towards the network. Characteristic is the short messagesending by the user with a certain request to the se!Ver. These!Ver responds to the request by a significantly longer messageof various electronic forms (data, digitized speech, pictures orvideo. Therefore, this technology is most often used by smalland medium users. ADSL is currently the only commerciallyavailable DSL technology which is still experiencing the breakthroughon the seiVice market. It enables faster access to theInternet, LAN (Local Area Network, videoconferencing, VoD(Video on Demand and interactive multimedia. In order tostandardize such se/Vices, the !TU (International TelecommunicationsUnion G. 992.1 (standardized DMT-discrete multi-tone line coding technology and ANSJ (American NationalStandards Institution Tl.413-95!98 are used for ADSL. DMT(Discrete Multi Tone, as the more popular one, uses the linecoding technique, which splits a certain frequency range intoseveral sub-channels. Most of these sub-channels are used forupstream and downstream transmission of speech and data,whereas some are used as pilot signals or kept in rese/Ve. Suchmodulation technique expands the frequency spectrum, allowingthe usage ofbroadband se/Vices per one pair of wires. In thisway the sharing of speech and data se/Vice transmission is realized.

  16. 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.

  17. Evolutionary stability in the asymmetric volunteer's dilemma.

    Directory of Open Access Journals (Sweden)

    Jun-Zhou He

    Full Text Available It is often assumed that in public goods games, contributors are either strong or weak players and each individual has an equal probability of exhibiting cooperation. It is difficult to explain why the public good is produced by strong individuals in some cooperation systems, and by weak individuals in others. Viewing the asymmetric volunteer's dilemma game as an evolutionary game, we find that whether the strong or the weak players produce the public good depends on the initial condition (i.e., phenotype or initial strategy of individuals. These different evolutionarily stable strategies (ESS associated with different initial conditions, can be interpreted as the production modes of public goods of different cooperation systems. A further analysis revealed that the strong player adopts a pure strategy but mixed strategies for the weak players to produce the public good, and that the probability of volunteering by weak players decreases with increasing group size or decreasing cost-benefit ratio. Our model shows that the defection probability of a "strong" player is greater than the "weak" players in the model of Diekmann (1993. This contradicts Selten's (1980 model that public goods can only be produced by a strong player, is not an evolutionarily stable strategy, and will therefore disappear over evolutionary time. Our public good model with ESS has thus extended previous interpretations that the public good can only be produced by strong players in an asymmetric game.

  18. At Low SNR Asymmetric Quantizers Are Better

    CERN Document Server

    Koch, Tobias

    2012-01-01

    We study the capacity of the discrete-time Gaussian channel when its output is quantized with a one-bit quantizer. We focus on the low signal-to-noise ratio (SNR) regime, where communication at very low spectral efficiencies takes place. In this regime a symmetric threshold quantizer is known to reduce channel capacity by 2/pi, i.e., to cause an asymptotic power loss of approximately two decibels. Here it is shown that this power loss can be entirely avoided by using asymmetric threshold quantizers and asymmetric signaling constellations. We prove that in order to avoid this power loss flash-signaling input-distributions are essential. Consequently, one-bit output quantization of the Gaussian channel reduces spectral efficiency. Threshold quantizers are not only asymptotically optimal: as we prove, at every fixed SNR, a threshold quantizer maximizes capacity among all one-bit output quantizers. The picture changes on the Rayleigh-fading channel. In the noncoherent case we show that a one-bit output quantizer ...

  19. 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.

  20. 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...

  1. 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.

  2. Survey of Reflection-Asymmetric Nuclear Deformations

    Science.gov (United States)

    Olsen, Erik; Cao, Yuchen; Nazarewicz, Witold; Schunck, Nicolas

    2016-09-01

    Due to spontaneous symmetry breaking it is possible for a nucleus to have a deformed shape in its ground state. It is theorized that atoms whose nuclei have reflection-asymmetric or pear-like deformations could have non-zero electric dipole moments (EDMs). Such a trait would be evidence of CP-violation, a feature that goes beyond the Standard Model of Physics. It is the purpose of this project to predict which nuclei exhibit a reflection-asymmetric deformation and which of those would be the best candidates for an EDM measuring experiment. Using nuclear Density Functional Theory along with the new computer code AxialHFB and massively parallel computing we calculated ground state nuclear properties for thousands of even-even nuclei across the nuclear chart: from light to superheavy and from stable to short-lived systems. Six different Energy Density Functionals (EDFs) were used to assess systematic errors in our calculations. These results are to be added to the website Massexplorer (http://massexplorer.frib.msu.edu/) which contains results from earlier mass table calculations and information on single quasiparticle energies.

  3. Double beta decay experiments

    CERN Document Server

    Barabash, A S

    2011-01-01

    The present status of double beta decay experiments is reviewed. The results of the most sensitive experiments are discussed. Proposals for future double beta decay experiments with a sensitivity to the $$ at the level of (0.01--0.1) eV are considered.

  4. 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

  5. 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.

  6. Effect of spacer dielectric engineering on Asymmetric Source Underlapped Double Gate MOSFET using Gate Stack

    Science.gov (United States)

    Chattopadhyay, Ankush; Dasgupta, Arpan; Das, Rahul; Kundu, Atanu; Sarkar, Chandan K.

    2017-01-01

    In this paper, the use of high-k spacers in a source underlapped nMOSFET is explored. The effects have been reported by varying the dielectric constant of the spacer from 3.9 to 22.5 and the study includes a comparison of analog parameters such as transconductance, transconductance generation factor, intrinsic gain, and RF parameters such as parasitic capacitances, resistances, and cut-off frequency. The RF parameters are calculated using the Non-Quasi Static (NQS) Approach which is required for sub 20 nm technology node. The device with high-k spacers features an improvement of 33% in DIBL, significantly increases the on current and reducing the off current by 60%. However, there is a slight compromise in the RF performance of the device, owing to an increase in intrinsic capacitance by about 0.35 fF. The Voltage Transfer Characteristics (VTC) and AC gain analysis of the circuit is also done in this paper. The circuit performance using single stage amplifier with the proposed device as the driver MOS has been analysed. High-k spacers also account for 19% improvement in small signal gain when used in a single stage amplifier circuit.

  7. Asymmetric Synthesis of (+)-(11 R,12S)-Mefloquine Hydrochloride

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The asymmetric synthesis of (+)-(11R,12S)-mefloquine hydrochloride, an antimalarial drug, was accomplished from commercially available 2-trifluoromethylaniline, ethyl 4,4,4-trifluoroacetoacetate and cyclopentanone in 7 steps with a 14% overall yield. The key steps were proline-catalyzed asymmetric direct aldol reaction and Beck-mann rearrangement. The absolute configuration was assigned by a Mosher's method.

  8. 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.

  9. 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.

  10. 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.

  11. 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.  ……

  12. 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.

  13. 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.

  14. 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

  15. Effect of asymmetric auxin application on Helianthus hypocotyl curvature

    Science.gov (United States)

    Migliaccio, F.; Rayle, D. L.

    1989-01-01

    Indole-3-acetic acid was applied asymmetrically to the hypocotyls of sunflower (Helianthus annuus L.) seedlings. After 5 hours on a clinostat, auxin gradients as small as 1 to 1.3 produced substantial (more than 60 degrees) hypocotyl curvature. This result suggests the asymmetric growth underlying hypocotyl gravitropism can be explained by lateral auxin redistribution.

  16. Selection of DC voltage magnitude using Fibonacci series for new hybrid asymmetrical multilevel inverter with minimum PIV

    Directory of Open Access Journals (Sweden)

    M.R. Banaei

    2014-09-01

    Full Text Available Multilevel inverters are suggested to obtain high quality output voltage. In this paper, a new hybrid configuration is proposed, obtained by cascading one four switches H-bridge cell with a family of multilevel inverters. In addition, by the use of specific sequence for value of DC sources named Fibonacci series, asymmetrical topology of proposed inverter is introduced. Main advantages are that proposed inverter has least Peak Inverse Voltage (PIV than other conventional multilevel converters in both symmetric and asymmetric modes. Also, this topology doubles the number of output levels using only one cascaded four switches H-bridge cell. The PCI-1716 DAQ using PC has been used to generate switching pulses in experimental results. For presenting valid performance of proposed configuration, simulation results carried out by MATLAB/SIMULINK software and the validity of the proposed multilevel inverter is verified by experimental results.

  17. Alkene selenenylation: A comprehensive analysis of relative reactivities, stereochemistry and asymmetric induction, and their comparisons with sulfenylation

    Directory of Open Access Journals (Sweden)

    Donna J. Nelson

    2011-06-01

    Full Text Available A broad perspective of various factors influencing alkene selenenylation has been developed by concurrent detailed analysis of key experimental and theoretical data, such as asymmetric induction, stereochemistry, relative reactivities, and comparison with that of alkene sulfenylation. Alkyl group branching α to the double bond was shown to have the greatest effect on alkene reactivity and the stereochemical outcome of corresponding addition reactions. This is in sharp contrast with other additions to alkenes, which depend more on the degree of substitution on C=C or upon substituent electronic effects. Electronic and steric effects influencing asymmetric induction, stereochemistry, regiochemistry, and relative reactivities in the addition of PhSeOTf to alkenes are compared and contrasted with those of PhSCl.

  18. Polyimides Derived from Novel Asymmetric Benzophenone Dianhydrides

    Science.gov (United States)

    Chuang, Chun-Hua (Inventor)

    2015-01-01

    This invention relates to the composition and processes for preparing thermoset polyimides derived from an asymmetric dianhydride, namely 2,3,3',4'-benzophenone dianhydride (a-BTDA) with at least one diamine, and a monofunctional terminal endcaps. The monofunctional terminating groups include 4-phenylethynylphthalic anhydride ester-acid derivatives, phenylethyl trimellitic anhydride (PETA) and its ester derivatives as well as 3-phenylethynylaniline. The process of polyimide composite comprises impregnating monomer reactants of dianhydride or its ester-acid derivatives, diamine and with monofunctional reactive endcaps into glass, carbon, quartz or synthetic fibers and fabrics, and then stack up into laminates and subsequently heated to between 150-375.degree. C. either at atmosphere or under pressure to promote the curing and crosslinking of the reactive endcaps to form a network of thermoset polyimides.

  19. Asymmetric quantum dialogue in noisy environment

    Science.gov (United States)

    Banerjee, Anindita; Shukla, Chitra; Thapliyal, Kishore; Pathak, Anirban; Panigrahi, Prasanta K.

    2017-02-01

    A notion of asymmetric quantum dialogue (AQD) is introduced. Conventional protocols of quantum dialogue are essentially symmetric as the users (Alice and Bob) can encode the same amount of classical information. In contrast, the proposed scheme for AQD provides different amount of communication powers to Alice and Bob. The proposed scheme offers an architecture, where the entangled state to be used and the encoding scheme to be shared between Alice and Bob depend on the amount of classical information they want to exchange with each other. The general structure for the AQD scheme has been obtained using a group theoretic structure of the operators introduced in Shukla et al. (Phys Lett A 377:518, 2013). The effect of different types of noises (e.g., amplitude damping and phase damping noise) on the proposed scheme is investigated, and it is shown that the proposed scheme for AQD is robust and it uses an optimized amount of quantum resources.

  20. 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.

  1. 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.

  2. Universality in freezing of an asymmetric drop

    Science.gov (United States)

    Ismail, Md Farhad; Waghmare, Prashant R.

    2016-12-01

    We present the evidence of universality in conical tip formation during the freezing of arbitrary-shaped sessile droplets. The focus is to demonstrate the relationship between this universality and the liquid drop shape. We observe that, in the case of asymmetric drops, this universal shape is achieved when the tip reconfigures by changing its location, which subsequently alters the frozen drop shape. The proposed "two-triangle" model quantifies the change in the tip configuration as a function of the asymmetry of the drop that shows a good agreement with the experimental evidence. Finally, based on the experimental and theoretical exercise, we propose the scaling dependence between the variations in the tip configuration and the asymmetry of the drop.

  3. Activation of carboxylic acids in asymmetric organocatalysis.

    Science.gov (United States)

    Monaco, Mattia Riccardo; Poladura, Belén; Diaz de Los Bernardos, Miriam; Leutzsch, Markus; Goddard, Richard; List, Benjamin

    2014-07-01

    Organocatalysis, catalysis using small organic molecules, has recently evolved into a general approach for asymmetric synthesis, complementing both metal catalysis and biocatalysis. Its success relies to a large extent upon the introduction of novel and generic activation modes. Remarkably though, while carboxylic acids have been used as catalyst directing groups in supramolecular transition-metal catalysis, a general and well-defined activation mode for this useful and abundant substance class is still lacking. Herein we propose the heterodimeric association of carboxylic acids with chiral phosphoric acid catalysts as a new activation principle for organocatalysis. This self-assembly increases both the acidity of the phosphoric acid catalyst and the reactivity of the carboxylic acid. To illustrate this principle, we apply our concept in a general and highly enantioselective catalytic aziridine-opening reaction with carboxylic acids as nucleophiles.

  4. THz operation of asymmetric-nanochannel devices

    Science.gov (United States)

    Balocco, C.; Halsall, M.; Vinh, N. Q.; Song, A. M.

    2008-09-01

    The THz spectrum lies between microwaves and the mid-infrared, a region that remains largely unexplored mainly due to the bottleneck issue of lacking compact, solid state, emitters and detectors. Here, we report on a novel asymmetric-nanochannel device, known as the self-switching device, which can operate at frequencies up to 2.5 THz for temperature up to 150 K. This is, to our knowledge, not only the simplest diode but also the quickest acting electronic nanodevice reported to date. The radiation was generated by the free electron laser FELIX (Netherlands). The dependences of the device efficiency as a function of the electric bias, radiation intensity, radiation frequency and temperature are reported.

  5. Isospin dependent properties of asymmetric nuclear matter

    CERN Document Server

    Chowdhury, P Roy; Samanta, C

    2009-01-01

    The density dependence of nuclear symmetry energy is determined from a systematic study of the isospin dependent bulk properties of asymmetric nuclear matter using the isoscalar and the isovector components of density dependent M3Y interaction. The incompressibility $K_\\infty$ for the symmetric nuclear matter, the isospin dependent part $K_{asy}$ of the isobaric incompressibility and the slope $L$ are all in excellent agreement with the constraints recently extracted from measured isotopic dependence of the giant monopole resonances in even-A Sn isotopes, from the neutron skin thickness of nuclei and from analyses of experimental data on isospin diffusion and isotopic scaling in intermediate energy heavy-ion collisions. This work provides a fundamental basis for the understanding of nuclear matter under extreme conditions, and validates the important empirical constraints obtained from recent experimental data.

  6. 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 ...

  7. Spectral measurements of asymmetrically irradiated capsule backlighters

    Science.gov (United States)

    Keiter, P. A.; Drake, R. P.

    2016-11-01

    Capsule backlighters provide a quasi-continuum x-ray spectrum over a wide range of photon energies [J. F. Hansen et al., Rev. Sci. Instrum. 79, 013504 (2008)]. Ideally one irradiates the capsule backlighter symmetrically, however, in complex experimental geometries, this is not always possible. In recent experiments we irradiated capsule backlighters asymmetrically and measured the x-ray spectrum from multiple directions. We will present time-integrated spectra over the photon energy range of 2-13 keV and time-resolved spectra over the photon energy range of 2-3 keV. We will compare the spectra from different lines of sight to determine if the laser asymmetry results in an angular dependence in the x-ray emission.

  8. 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.

  9. 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...

  10. 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...

  11. Study on "double dawn

    Institute of Scientific and Technical Information of China (English)

    刘次沅; 李建科; 周晓陆

    1999-01-01

    The ancient record, "During the first year of King Yi, the day dawned twice at Zheng", has provided important clues to early Chinese chronicles. The astronomical conditions and visible area distributions related to such a "double dawn" event are discussed, and the precision and current problems in the calculations of ancient astronomical phenomena are shown. On such a basis, all the solar eclipses from 1000 BC to 840 BC are calculated and their associated "double dawn" features investigated. The conclusion that the "double dawn" was a solar eclipse occurring on April 21st, 899 BC is corfirmed to be the most reasonable.

  12. Scaffold of Asymmetric Organic Compounds - Magnetite Plaquettes

    Science.gov (United States)

    Chan, Q. H. S.; Zolensky, M. E.; Martinez, J.

    2015-01-01

    Life on Earth shows preference towards the set of organics with particular spatial configurations, this 'selectivity' is a crucial criterion for life. With only rare exceptions, life prefers the left- (L-) form over the right- (D-) form of amino acids, resulting in an L-enantiomeric excess (L-ee). Recent studies have shown Lee for alpha-methyl amino acids in some chondrites. Since these amino acids have limited terrestrial occurrence, the origin of their stereoselectivity is nonbiological, and it seems appropriate to conclude that chiral asymmetry, the molecular characteristic that is common to all terrestrial life form, has an abiotic origin. A possible abiotic mechanism that can produce chiral asymmetry in meteoritic amino acids is their formation with the presence of asymmetric catalysts, as mineral crystallization can produce spatially asymmetric structures. Magnetite is shown to be an effective catalyst for the formation of amino acids that are commonly found in chondrites. Magnetite 'plaquettes' (or 'platelets'), first described by Jedwab, show an interesting morphology of barrel-shaped stacks of magnetite disks with an apparent dislocation-induced spiral growth that seem to be connected at the center. A recent study by Singh et al. has shown that magnetites can self-assemble into helical superstructures. Such molecular asymmetry could be inherited by adsorbed organic molecules. In order to understand the distribution of 'spiral' magnetites in different meteorite classes, as well as to investigate their apparent spiral configurations and possible correlation to molecular asymmetry, we observed polished sections of carbonaceous chondrites (CC) using scanning electron microscope (SEM) imaging. The sections were also studied by electron backscattered diffraction (EBSD) in order to reconstruct the crystal orientation along the stack of magnetite disks.

  13. 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.

  14. Biotinylation of Deoxyguanosine at the Abasic Site in Double-Stranded Oligodeoxynucleotides

    Directory of Open Access Journals (Sweden)

    Chun Wu

    2016-01-01

    Full Text Available Biotinylation of deoxyguanosine at an abasic site in double-stranded oligodeoxynucleotides was studied. The biotinylation of deoxyguanosine is achieved by copper-catalyzed click reaction after the conjugation of the oligodeoxynucleotide with 2-oxohex-5-ynal. The biotinylation enables visualization of the biotinylated oligodeoxynucleotides by chemiluminescence on a nylon membrane. In order to investigate the biotinylated site, the biotinylated oligodeoxynucleotides were amplified by the DNA polymerase chain reaction. Replacement of guanine opposing the abasic site with adenine generated by the activity of the terminal deoxynucleotidyl transferase of DNA polymerase was detected by DNA sequencing analysis and restriction endonuclease digestion. This study suggests that 2-oxohex-5-ynal may be useful for the detection of the unpaired deoxyguanosine endogenously generated at abasic sites in genomic DNA.

  15. Apurinic/apyrimidinic endonuclease/redox factor-1 (APE1/Ref-1) redox function negatively regulates NRF2.

    Science.gov (United States)

    Fishel, Melissa L; Wu, Xue; Devlin, Cecilia M; Logsdon, Derek P; Jiang, Yanlin; Luo, Meihua; He, Ying; Yu, Zhangsheng; Tong, Yan; Lipking, Kelsey P; Maitra, Anirban; Rajeshkumar, N V; Scandura, Glenda; Kelley, Mark R; Ivan, Mircea

    2015-01-30

    Apurinic/apyrimidinic endonuclease/redox factor-1 (APE1/Ref-1) (henceforth referred to as Ref-1) is a multifunctional protein that in addition to its base excision DNA repair activity exerts redox control of multiple transcription factors, including nuclear factor κ-light chain enhancer of activated B cells (NF-κB), STAT3, activator protein-1 (AP-1), hypoxia-inducible factor-1 (HIF-1), and tumor protein 53 (p53). In recent years, Ref-1 has emerged as a promising therapeutic target in cancer, particularly in pancreatic ductal carcinoma. Although a significant amount of research has centered on Ref-1, no wide-ranging approach had been performed on the effects of Ref-1 inhibition and transcription factor activity perturbation. Starting with a broader approach, we identified a previously unsuspected effect on the nuclear factor erythroid-related factor 2 (NRF2), a critical regulator of cellular defenses against oxidative stress. Based on genetic and small molecule inhibitor-based methodologies, we demonstrated that repression of Ref-1 potently activates NRF2 and its downstream targets in a dose-dependent fashion, and that the redox, rather than the DNA repair function of Ref-1 is critical for this effect. Intriguingly, our results also indicate that this pathway does not involve reactive oxygen species. The link between Ref-1 and NRF2 appears to be present in all cells tested in vitro, noncancerous and cancerous, including patient-derived tumor samples. In particular, we focused on understanding the implications of the novel interaction between these two pathways in primary pancreatic ductal adenocarcinoma tumor cells and provide the first evidence that this mechanism has implications for overcoming the resistance against experimental drugs targeting Ref-1 activity, with clear translational implications.

  16. Engineered selective plant male sterility through pollen-specific expression of the EcoRI restriction endonuclease.

    Science.gov (United States)

    Millwood, Reginald J; Moon, Hong S; Poovaiah, Charleson R; Muthukumar, Balasubramaniam; Rice, John Hollis; Abercrombie, Jason M; Abercrombie, Laura L; Green, William Derek; Stewart, Charles Neal

    2016-05-01

    Unintended gene flow from transgenic plants via pollen, seed and vegetative propagation is a regulatory concern because of potential admixture in food and crop systems, as well as hybridization and introgression to wild and weedy relatives. Bioconfinement of transgenic pollen would help address some of these concerns and enable transgenic plant production for several crops where gene flow is an issue. Here, we demonstrate the expression of the restriction endonuclease EcoRI under the control of the tomato pollen-specific LAT52 promoter is an effective method for generating selective male sterility in Nicotiana tabacum (tobacco). Of nine transgenic events recovered, four events had very high bioconfinement with tightly controlled EcoRI expression in pollen and negligible-to-no expression other plant tissues. Transgenic plants had normal morphology wherein vegetative growth and reproductivity were similar to nontransgenic controls. In glasshouse experiments, transgenic lines were hand-crossed to both male-sterile and emasculated nontransgenic tobacco varieties. Progeny analysis of 16 000-40 000 seeds per transgenic line demonstrated five lines approached (>99.7%) or attained 100% bioconfinement for one or more generations. Bioconfinement was again demonstrated at or near 100% under field conditions where four transgenic lines were grown in close proximity to male-sterile tobacco, and 900-2100 seeds per male-sterile line were analysed for transgenes. Based upon these results, we conclude EcoRI-driven selective male sterility holds practical potential as a safe and reliable transgene bioconfinement strategy. Given the mechanism of male sterility, this method could be applicable to any plant species.

  17. An antisense RNA in a lytic cyanophage links psbA to a gene encoding a homing endonuclease.

    Science.gov (United States)

    Millard, Andrew D; Gierga, Gregor; Clokie, Martha R J; Evans, David J; Hess, Wolfgang R; Scanlan, David J

    2010-09-01

    Cyanophage genomes frequently possess the psbA gene, encoding the D1 polypeptide of photosystem II. This protein is believed to maintain host photosynthetic capacity during infection and enhance phage fitness under high-light conditions. Although the first documented cyanophage-encoded psbA gene contained a group I intron, this feature has not been widely reported since, despite a plethora of new sequences becoming available. In this study, we show that in cyanophage S-PM2, this intron is spliced during the entire infection cycle. Furthermore, we report the widespread occurrence of psbA introns in marine metagenomic libraries, and with psbA often adjacent to a homing endonuclease (HE). Bioinformatic analysis of the intergenic region between psbA and the adjacent HE gene F-CphI in S-PM2 showed the presence of an antisense RNA (asRNA) connecting these two separate genetic elements. The asRNA is co-regulated with psbA and F-CphI, suggesting its involvement with their expression. Analysis of scaffolds from global ocean survey datasets shows this asRNA to be commonly associated with the 3' end of cyanophage psbA genes, implying that this potential mechanism of regulating marine 'viral' photosynthesis is evolutionarily conserved. Although antisense transcription is commonly found in eukaryotic and increasingly also in prokaryotic organisms, there has been no indication for asRNAs in lytic phages so far. We propose that this asRNA also provides a means of preventing the formation of mobile group I introns within cyanophage psbA genes.

  18. Nuclear depletion of apurinic/apyrimidinic endonuclease 1 (Ape1/Ref-1) is an indicator of energy disruption in neurons.

    Science.gov (United States)

    Singh, Shilpee; Englander, Ella W

    2012-11-01

    Apurinic/apyrimidinic endonuclease 1 (Ape1/Ref-1) is a multifunctional protein critical for cellular survival. Its involvement in adaptive survival responses includes key roles in redox sensing, transcriptional regulation, and repair of DNA damage via the base excision repair (BER) pathway. Ape1 is abundant in most cell types and central in integrating the first BER step catalyzed by different DNA glycosylases. BER is the main process for removal of oxidative DNA lesions in postmitotic brain cells, and after ischemic brain injury preservation of Ape1 coincides with neuronal survival, while its loss has been associated with neuronal death. Here, we report that in cultured primary neurons, diminution of cellular ATP by either oligomycin or H(2)O(2) is accompanied by depletion of nuclear Ape1, while other BER proteins are unaffected and retain their nuclear localization under these conditions. Importantly, while H(2)O(2) induces γH2AX phosphorylation, indicative of chromatin rearrangements in response to DNA damage, oligomycin does not. Furthermore, despite comparable diminution of ATP content, H(2)O(2) and oligomycin differentially affect critical parameters of mitochondrial respiration that ultimately determine cellular ATP content. Taken together, our findings demonstrate that in neurons, nuclear compartmentalization of Ape1 depends on ATP and loss of nuclear Ape1 reflects disruption of neuronal energy homeostasis. Energy crisis is a hallmark of stroke and other ischemic/hypoxic brain injuries. In vivo studies have shown that Ape1 deficit precedes neuronal loss in injured brain regions. Thus, our findings bring to light the possibility that energy failure-induced Ape1 depletion triggers neuronal death in ischemic brain injuries.

  19. Reduced Nuclease Activity of Apurinic/Apyrimidinic Endonuclease (APE1) Variants on Nucleosomes: IDENTIFICATION OF ACCESS RESIDUES.

    Science.gov (United States)

    Hinz, John M; Mao, Peng; McNeill, Daniel R; Wilson, David M

    2015-08-21

    Non-coding apurinic/apyrimidinic (AP) sites are generated at high frequency in genomic DNA via spontaneous hydrolytic, damage-induced or enzyme-mediated base release. AP endonuclease 1 (APE1) is the predominant mammalian enzyme responsible for initiating removal of mutagenic and cytotoxic abasic lesions as part of the base excision repair (BER) pathway. We have examined here the ability of wild-type (WT) and a collection of variant/mutant APE1 proteins to cleave at an AP site within a nucleosome core particle. Our studies indicate that, in comparison to the WT protein and other variant/mutant enzymes, the incision activity of the tumor-associated variant R237C and the rare population variant G241R are uniquely hypersensitive to nucleosome complexes in the vicinity of the AP site. This defect appears to stem from an abnormal interaction of R237C and G241R with abasic DNA substrates, but is not simply due to a DNA binding defect, as the site-specific APE1 mutant Y128A, which displays markedly reduced AP-DNA complex stability, did not exhibit a similar hypersensitivity to nucleosome structures. Notably, this incision defect of R237C and G241R was observed on a pre-assembled DNA glycosylase·AP-DNA complex as well. Our results suggest that the BER enzyme, APE1, has acquired distinct surface residues that permit efficient processing of AP sites within the context of protein-DNA complexes independent of classic chromatin remodeling mechanisms.

  20. Redox regulation of apurinic/apyrimidinic endonuclease 1 activity in Long-Evans Cinnamon rats during spontaneous hepatitis.

    Science.gov (United States)

    Karmahapatra, Soumendra Krishna; Saha, Tapas; Adhikari, Sanjay; Woodrick, Jordan; Roy, Rabindra

    2014-03-01

    The Long-Evans Cinnamon (LEC) rat is an animal model for Wilson's disease. This animal is genetically predisposed to copper accumulation in the liver, increased oxidative stress, accumulation of DNA damage, and the spontaneous development of hepatocellular carcinoma. Thus, this animal model is useful for studying the relationship of endogenous DNA damage to spontaneous carcinogenesis. In this study, we have investigated the apurinic/apyrimidinic endonuclease 1 (APE1)-mediated excision repair of endogenous DNA damage, apurinic/apyrimidinic (AP)-sites, which is highly mutagenic and implicated in human cancer. We found that the activity was reduced in the liver extracts from the acute hepatitis period of LEC rats as compared with extracts from the age-matched Long-Evans Agouti rats. The acute hepatitis period had also a heightened oxidative stress condition as assessed by an increase in oxidized glutathione level and loss of enzyme activity of glyceraldehyde 3-phosphate dehydrogenase, a key redox-sensitive protein in cells. Interestingly, the activity reduction was not due to changes in protein expression but apparently by reversible protein oxidation as the addition of reducing agents to extracts of the liver from acute hepatitis period reactivated APE1 activity and thus, confirmed the oxidation-mediated loss of APE1 activity under increased oxidative stress. These findings show for the first time in an animal model that the repair mechanism of AP-sites is impaired by increased oxidative stress in acute hepatitis via redox regulation which contributed to the increased accumulation of mutagenic AP-sites in liver DNA.

  1. Differential interaction kinetics of a bipolar structure-specific endonuclease with DNA flaps revealed by single-molecule imaging.

    Directory of Open Access Journals (Sweden)

    Rachid Rezgui

    Full Text Available As DNA repair enzymes are essential for preserving genome integrity, understanding their substrate interaction dynamics and the regulation of their catalytic mechanisms is crucial. Using single-molecule imaging, we investigated the association and dissociation kinetics of the bipolar endonuclease NucS from Pyrococcus abyssi (Pab on 5' and 3'-flap structures under various experimental conditions. We show that association of the PabNucS with ssDNA flaps is largely controlled by diffusion in the NucS-DNA energy landscape and does not require a free 5' or 3' extremity. On the other hand, NucS dissociation is independent of the flap length and thus independent of sliding on the single-stranded portion of the flapped DNA substrates. Our kinetic measurements have revealed previously unnoticed asymmetry in dissociation kinetics from these substrates that is markedly modulated by the replication clamp PCNA. We propose that the replication clamp PCNA enhances the cleavage specificity of NucS proteins by accelerating NucS loading at the ssDNA/dsDNA junctions and by minimizing the nuclease interaction time with its DNA substrate. Our data are also consistent with marked reorganization of ssDNA and nuclease domains occurring during NucS catalysis, and indicate that NucS binds its substrate directly at the ssDNA-dsDNA junction and then threads the ssDNA extremity into the catalytic site. The powerful techniques used here for probing the dynamics of DNA-enzyme binding at the single-molecule have provided new insight regarding substrate specificity of NucS nucleases.

  2. Conformational dynamics of abasic DNA upon interactions with AP endonuclease 1 revealed by stopped-flow fluorescence analysis.

    Science.gov (United States)

    Kanazhevskaya, Lyubov Yu; Koval, Vladimir V; Vorobjev, Yury N; Fedorova, Olga S

    2012-02-14

    Apurinic/apyrimidinic (AP) sites are abundant DNA lesions arising from exposure to UV light, ionizing radiation, alkylating agents, and oxygen radicals. In human cells, AP endonuclease 1 (APE1) recognizes this mutagenic lesion and initiates its repair via a specific incision of the phosphodiester backbone 5' to the AP site. We have investigated a detailed mechanism of APE1 functioning using fluorescently labeled DNA substrates. A fluorescent adenine analogue, 2-aminopurine, was introduced into DNA substrates adjacent to the abasic site to serve as an on-site reporter of conformational transitions in DNA during the catalytic cycle. Application of a pre-steady-state stopped-flow technique allows us to observe changes in the fluorescence intensity corresponding to different stages of the process in real time. We also detected an intrinsic Trp fluorescence of the enzyme during interactions with 2-aPu-containing substrates. Our data have revealed a conformational flexibility of the abasic DNA being processed by APE1. Quantitative analysis of fluorescent traces has yielded a minimal kinetic scheme and appropriate rate constants consisting of four steps. The results obtained from stopped-flow data have shown a substantial influence of the 2-aPu base location on completion of certain reaction steps. Using detailed molecular dynamics simulations of the DNA substrates, we have attributed structural distortions of AP-DNA to realization of specific binding, effective locking, and incision of the damaged DNA. The findings allowed us to accurately discern the step that corresponds to insertion of specific APE1 amino acid residues into the abasic DNA void in the course of stabilization of the precatalytic complex.

  3. 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,

  4. Axially chiral imidodiphosphoric Acid catalyst for asymmetric sulfoxidation reaction: insights on asymmetric induction.

    Science.gov (United States)

    Jindal, Garima; Sunoj, Raghavan B

    2014-04-22

    Insights into chiral induction for an asymmetric sulfoxidation reaction involving a single oxygen atom transfer are gained through analyzing the stereocontrolling transition states. The fitting of the substrate into the chiral cavity of a new class of imidodiphosphoric Brønsted acids, as well as weak CH⋅⋅⋅π and CH⋅⋅⋅O noncovalent interactions, are identified as responsible for the observed chiral induction.

  5. Neutrinoless double beta decay

    Indian Academy of Sciences (India)

    Kai Zuber

    2012-10-01

    The physics potential of neutrinoless double beta decay is discussed. Furthermore, experimental considerations as well as the current status of experiments are presented. Finally, an outlook towards the future, work on nuclear matrix elements and alternative processes is given.

  6. Double conjoining vas deferens.

    Science.gov (United States)

    Gravesen, R G

    1980-03-01

    The importance of careful palpation of the scrotal contents and follow-up semen analysis when performing vasectomies is proved by this case report of a double vas deferens conjoining into a single vas.

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

    CERN Document Server

    Liu, Haisheng

    2010-01-01

    A modified double slit experiment of light was implemented. In the experiment, a spatial shape filter is used to manipulate the shape of cross section of laser beam. When this modified laser beam was shined on the double slit, the intensity distribution of laser beam on double slit is asymmetrical. In this way, the laser light was directed to pass through only one or two slits of double slit in different sections. So the which-way information is predetermined before the photons pass through the slits. At the same time, the visible interference pattern can be observed on a monitor screen after the double slit. A couple of new phenomena had been observed from this experiment. The results of this experiment raise questions about Wave-Particle Duality model of quantum theory, which is the foundation for the Copenhagen explanation that is generally regarded as the principal interpretation of quantum theory. As the observed properties from this experiment cannot be fully explained using the quantum theory, especial...

  8. UV-induced endonuclease III-sensitive sites at the mating type loci in Saccharomyces cerevisiae are repaired by nucleotide excision repair: RAD7 and RAD16 are not required for their removal from HML alpha.

    Science.gov (United States)

    Reed, S H; Boiteux, S; Waters, R

    1996-03-01

    Ultraviolet irradiation of DNA induces cyclobutane pyrimidine dimers (CPDs) 6-4'-(pyrimidine 2'-one) pyrimidines and pyrimidine hydrates. The dimer is the major photoproduct, and is specifically recognized by endonuclease V of phage T4. Pyrimidine hydrates represent a small fraction of the total photoproducts, and are substrates for endonuclease III of Escherichia coli. We used these enzymes to follow the fate of their substrates in the mating type loci of Saccharomyces cerevisiae. In a RAD strain, CPSs in the transcriptionally active MAT alpha locus are preferentially repaired relative to the inactive HML alpha locus, whilst repair of endonuclease III-sensitive sites is not preferential. The rad1, 2, 3 and 4 mutants, which lack factors that are essential for the incision step of nucleotide excision repair (NER), repair neither CPDs nor endonuclease III-sensitive sites, clearly showing that these lesions are repaired by by NER pathway. Previously it had been shown that the products of the RAD7 and RAD16 genes are required for the NER of CPDs from the HML alpha locus. We show that, in the same locus, these gene products are not needed for removal of endonuclease III-sensitive sites by the same mechanism. This indicates that the components required for NER differ depending on either the type of lesion encountered or on the specific location of the lesion within the genome.

  9. A nuclear localization signal and the C-terminal omega sequence in the Agrobacterium tumefaciens VirD2 endonuclease are important for tumor formation.

    OpenAIRE

    Shurvinton, C. E.; Hodges, L; Ream, W

    1992-01-01

    The T-DNA portion of the Agrobacterium tumefaciens tumor-inducing (Ti) plasmid integrates into plant nuclear DNA. Direct repeats define the T-DNA ends; transfer begins when the VirD2 endonuclease produces a site-specific nick in the right-hand border repeat and attaches to the 5' end of the nicked strand. Subsequent events generate linear single-stranded VirD2-bound DNA molecules that include the entire T-DNA (T-strands). VirD2 protein contains a nuclear localization signal (NLS) near the C t...

  10. 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

    The green alga Scenedesmus pupukensis and the red alga Porphyra spiralis contain large group-IC1 introns in their nuclear small subunit ribosomal RNA genes due to the presence of open reading frames at the 5' end of the introns. The putative 555 amino-acid Scenedesmus-encoded protein harbors...... a sequence motif resembling the bacterial S9 ribosomal proteins. The Porphyra intron self-splices in vitro, and generates both ligated exons and a full-length intron RNA circle. The Porphyra intron has an unusual structural organization by encoding a potential 149 amino-acid homing-endonuclease-like protein...

  11. Repercussions of DNA tracking by the type IC restriction endonuclease EcoR124I on linear, circular and catenated substrates.

    OpenAIRE

    Szczelkun, M.D.; Dillingham, M. S.; Janscak, P; Firman, K; Halford, S.E.

    1996-01-01

    Type I restriction endonucleases such as EcoR124I cleave DNA at undefined loci, distant from their recognition sequences, by a mechanism that involves the enzyme tracking along the DNA between recognition and cleavage sites. This mechanism was examined on plasmids that carried recognition sites for EcoR124I and recombination sites for resolvase, the latter to create DNA catenanes. Supercoiled substrates with either one or two restriction sites were linearized by EcoR124I at similar rates, alt...

  12. Genetic discrimination for three gynogenetic clones of silver carp Hypophthalmichthys molitrix, based on restriction endonuclease analysis of Nd5-Nd6 region of mitochondrial DNA

    Institute of Scientific and Technical Information of China (English)

    ZHOU Jianfeng; YE Yuzhen; WU Qingjiang

    2005-01-01

    Three artificial gynogenetic clones of silver carp were produced for the analysis of restriction enzyme digestion patterns of ND5-ND6 region from mtDNA of the clones. It is revealed that all intraclonal individuals shared completely the same digestion patterns but among interclonal individuals did not. The three clones were mixed and cultured in a pond together for two years, and restriction endonuclease digestion patterns of ND5-ND6 were used as genetic markers to assess the growth performance of each clone.

  13. Configuration of the catalytic GIY-YIG domain of intron endonuclease I-TevI: coincidence of computational and molecular findings.

    OpenAIRE

    Kowalski, J C; Belfort, M; Stapleton, M A; Holpert, M; Dansereau, J T; Pietrokovski, S; Baxter, S M; Derbyshire, V

    1999-01-01

    I-TevI is a member of the GIY-YIG family of homing endonucleases. It is folded into two structural and functional domains, an N-terminal catalytic domain and a C-terminal DNA-binding domain, separated by a flexible linker. In this study we have used genetic analyses, computational sequence analysis andNMR spectroscopy to define the configuration of theN-terminal domain and its relationship to the flexible linker. The catalytic domain is an alpha/beta structure contained within the first 92 am...

  14. The Dualism of Asymmetric Information in Agricultural Insurance

    Directory of Open Access Journals (Sweden)

    Xuemei Yang

    2013-07-01

    Full Text Available Asymmetric information objectively exists in the insurance market, especially in agricultural insurance, which has a great impact on the insurance contract and market operation. This paper designs two game models to analyse the dualism of asymmetric information in agricultural insurance and its reasons of forming. We find that, the particularity of agricultural production, the agricultural risk diversification and the benefits’ spillover of the agricultural insurance are the main causes of asymmetric information. Therefore, this paper puts forward that establishment of appropriate agricultural insurance mode, optimization of insurance policy design and increasing investment in science and technology, increasing farmers’ insurance consciousness and establishing supervision system

  15. Asymmetric Orbifolds, Noncommutative Geometry and Type I String Vacua

    CERN Document Server

    Blumenhagen, R; Körs, B; Lüst, Dieter; Blumenhagen, Ralph; Goerlich, Lars; Kors, Boris; Lust, Dieter

    2000-01-01

    We investigate the D-brane contents of asymmetric orbifolds. Using T-dualitywe find that the consistent description of open strings in asymmetric orbifoldsrequires to turn on background gauge fields on the D-branes. Hence open stringsand D-branes in generic asymmetric orbifolds necessarily lead to noncommutativegeometry. We derive the corresponding noncommutative geometry arising on suchD-branes with mixed Neumann-Dirichlet boundary conditions by applying anasymmetric rotation to ordinary D-branes with pure Dirichlet boundaryconditions. As a concrete application of our results we construct asymmetrictype I vacua requiring open strings with mixed boundary conditions for tadpolecancellation.

  16. Mechanisms of asymmetric cell divisions in Drosophila melanogaster neuroblasts

    Directory of Open Access Journals (Sweden)

    X Jiang

    2014-04-01

    Full Text Available Stem cells possess the properties of self-renewal and differentiation, and mainly rely on two strategies for division, including symmetric and asymmetric cell divisions. In this review, we summarize the latest progress on asymmetric cell divisions in Drosophila melanogaster neuroblasts (NBs, which focus on the establishment of cell polarity, mitotic spindle orientation, the asymmetric segregation of cell fate determinants as well as cell-cycle control. Here we also introduce five major cell fate determinants, including Numb, Prospero, Brat, Miranda, and Pon, which are thought to be unequally segregated to the ganglion mother cells (GMCs and play an important role in the formation of stem cell-derived tumors

  17. Generic approach for synthesizing asymmetric nanoparticles and nanoassemblies

    Science.gov (United States)

    Sun, Yugang; Hu, Yongxing

    2015-05-26

    A generic route for synthesis of asymmetric nanostructures. This approach utilizes submicron magnetic particles (Fe.sub.3O.sub.4--SiO.sub.2) as recyclable solid substrates for the assembly of asymmetric nanostructures and purification of the final product. Importantly, an additional SiO.sub.2 layer is employed as a mediation layer to allow for selective modification of target nanoparticles. The partially patched nanoparticles are used as building blocks for different kinds of complex asymmetric nanostructures that cannot be fabricated by conventional approaches. The potential applications such as ultra-sensitive substrates for surface enhanced Raman scattering (SERS) have been included.

  18. The experimental study of acoustic field in an asymmetric borehole

    Institute of Scientific and Technical Information of China (English)

    LINWeijun; ZHANGChengyu; ZHANGHailan; WANGXiuming

    2003-01-01

    The acoustic field in an asymmetric borehole was investigated by recording and comparing the waveforms with different offset in both axial symmetric borehole and axial asymmetric borehole. The two-dimensional spectrum in wave-number and frequency domain was also calculated and compared with the result of numeric simulation with 2.5-D finite difference method, and a consistent result was obtained. This work provides an accurate verification of our investigation of asymmetric borehole with 2.5-D finite difference method.

  19. High-Voltage, Asymmetric-Waveform Generator

    Science.gov (United States)

    Beegle, Luther W.; Duong, Tuan A.; Duong, Vu A.; Kanik, Isik

    2008-01-01

    The shapes of waveforms generated by commercially available analytical separation devices, such as some types of mass spectrometers and differential mobility spectrometers are, in general, inadequate and result in resolution degradation in output spectra. A waveform generator was designed that would be able to circumvent these shortcomings. It is capable of generating an asymmetric waveform, having a peak amplitude as large as 2 kV and frequency of several megahertz, which can be applied to a capacitive load. In the original intended application, the capacitive load would consist of the drift plates in a differential-mobility spectrometer. The main advantage to be gained by developing the proposed generator is that the shape of the waveform is made nearly optimum for various analytical devices requiring asymmetric-waveform such as differential-mobility spectrometers. In addition, this waveform generator could easily be adjusted to modify the waveform in accordance with changed operational requirements for differential-mobility spectrometers. The capacitive nature of the load is an important consideration in the design of the proposed waveform generator. For example, the design provision for shaping the output waveform is based partly on the principle that (1) the potential (V) on a capacitor is given by V=q/C, where C is the capacitance and q is the charge stored in the capacitor; and, hence (2) the rate of increase or decrease of the potential is similarly proportional to the charging or discharging current. The proposed waveform generator would comprise four functional blocks: a sine-wave generator, a buffer, a voltage shifter, and a high-voltage switch (see Figure 1). The sine-wave generator would include a pair of operational amplifiers in a feedback configuration, the parameters of which would be chosen to obtain a sinusoidal timing signal of the desired frequency. The buffer would introduce a slight delay (approximately equal to 20 ns) but would otherwise

  20. Influences of Resistor-Type Superconducting Fault Current Limiter on Power System Transient Stability with Asymmetrical Short-Circuit Faults

    Institute of Scientific and Technical Information of China (English)

    Xue-Ping Gu; Zhi-Long Yang

    2008-01-01

    The transient stability of a single machine to infinite-busbar power system with resistor- type superconducting fault current limiters (SFCL) is analyzed under asymmetrical short-circuit fault conditions. The SFCL is considered to introduce a resistance into the three-phase circuits when faults occur. Based on the power-angle curves for different short-circuit conditions of the single-line to ground, double-line to ground and line to line short-circuit faults, the influences of the SFCLs on transient stability are analyzed in detail. The time-domain simulation of transient stability is carried out to verify the analytical results.