bluuebunny/crossref_metadata_2025 huggingface dataset:
The reaction of N2O with phenylium ions C6(H,D)5+: An integrated experimental and theoretical mechanistic study
Authors: Giordana Anna , Ghigo Giovanni , Tonachini Glauco , Ascenzi Daniela , Tosi Paolo , Guella Graziano
Published: July 2009

The reaction of N2O (known to be an O atom donor under several conditions) with the phenyl cation is studied by experimental and theoretical methods. Phenyl cation (or phenylium), C6H5+, and its perdeuterated derivative C6D5+ are produced either by electron impact or by atmospheric pressure chemical ionization of adequate neutral precursors, and product mass spectra are measured in a guided ion beam tandem mass spectrometer. The ions C5(H,D)5+, C6(H,D)5O+, and C3(H,D)3+ are experimentally detected as the most relevant reaction products. In addition, the detection of the adduct (C6H5⋅N2O)+, which is collisionally stabilized in the scattering cell of the mass spectrometer, is reported here for the first time. The reaction pathways, which could bring about the formation of the mentioned ions, are then explored extensively by density functional theory and, for the more promising pathways, by CASPT2/CASSCF calculations. The two reacting species (1) form initially a phenoxydiazonium adduct, C6H5ON2+ (2a), by involving the empty in-plane hybrid C orbital of phenylium. The alternative attack to the ring π system to produce an epoxidic adduct 2c is ruled out on the basis of the energetics. Then, 2a loses N2 quite easily, thus affording the phenoxyl cation 3. This is only the first of several C6H5O+ isomers (4–6 and 8–12), which can stem from 3 upon different cleavages and formations of C–C bond and/or H shifts. As regards the formation of C5H5+, among several conceivable pathways, a direct CO extrusion from 3 is discarded, while others appear to be viable to different extents, depending on the initial energy of the system. The easiest CO loss is from 4, with formation of the cyclopentadienyl cation 7. Formation of C3H3+ is generally hindered and its detection depends again on the availability of some extra initial energy.
Electronic energy states in Si-doped MgO for exoelectron emission
Authors: Ho S. , Nobuki S. , Uemura N. , Mori S. , Miyake T. , Suzuki K. , Mikami Y. , Shiiki M. , Kubo S.
Published: July 2009

A generalized analytical method to determine the density of energy states of electron emission source (EES) is devised by using a thermal excitation and emission model for an exoelectron in the MgO layer and the emission time constants of the exoelectron extracted from experimental stochastic distributions of discharge delay time. When applied to Si-doped MgO, the emission time constant of the exoelectron from the Si EES becomes shorter at high temperature and at short time intervals due to thermal excitation. The density of energy states of the Si EES DSi(E) shows the main peak at 736 meV, a satellite peak at 601 meV, and broad energy structures over the range of 586–896 meV. The effective number of Si EES is 5.5 times larger than that in purified MgO. The excitation energy in a Si-doped MgO cluster with a crystal structure is obtained to be 0.83 eV by using the symmetry-adapted-cluster configuration interaction method and the Si EES contributes to exoelectron emission. The thermal excitation is governed by the transition from the Si–O bound state and the Mg edge state to the antisymmetrical edge states and the extended surface state. The excitation energy in an MgO cluster with a Si-doped atom inside and a nearest oxygen vacancy taking account of structural relaxation is calculated to be 0.75 eV, which shows good agreement with the main peak in DSi(E). The excitation energies of 0.64, 0.73, and 0.78 eV are also obtained in an MgO cluster with a Si-doped atom at the surface and a nearest oxygen vacancy. The first excitation energy corresponds with the satellite peak. The broad energy structures of DSi(E) are caused by the dependence of excitation energy on the position of Si-doped atoms inside and at the surface of the MgO cluster, and on the interatomic distance of Si–O due to structural relaxation. The energy structures can be also attributed to the thermal excitation to the various symmetrical Mg edge states and the surface states. When the number of complex structures of the Si EES with adjacent oxygen vacancies increases, oxygen vacancies are generated from the complex structures and the increase in the electron traps degrades electron emission rate. Therefore, the number of complex structures has an optimum value that leads to the maximum effective number of Si EES.
Thermodynamic limit for the Mallows model on Sn
Authors: Starr Shannon
Published: July 2009

The Mallows model on Sn is a probability distribution on permutations, qd(π,e)/Pn(q), where d(π,e) is the distance between π and the identity element, relative to the Coxeter generators. Equivalently, it is the number of inversions: pairs (i,j) where 1≤iπj. Analyzing the normalization Pn(q), Diaconis and Ram calculated the mean and variance of d(π,e) in the Mallows model, which suggests that the appropriate n→∞ limit has qn scaling as 1−β/n. We calculate the distribution of the empirical measure in this limit, u(x,y)dxdy=limn→∞(1/n)∑i=1nδ(i,πi). Treating it as a mean-field problem, analogous to the Curie–Weiss model, the self-consistent mean-field equations are (∂2/∂x∂y)ln u(x,y)=2βu(x,y), which is an integrable partial differential equation, known as the hyperbolic Liouville equation. The explicit solution also gives a new proof of formulas for the blocking measures in the weakly asymmetric exclusion process and the ground state of the Uq(sl2)-symmetric XXZ ferromagnet.
Current oscillation originating from negative differential resistance in one-dimensional halogen-bridged nickel compounds
Authors: Kishida Hideo , Ito Takafumi , Nakamura Arao , Takaishi Shinya , Yamashita Masahiro
Published: July 2009

We demonstrate current oscillation phenomena using the negative differential resistance in a one-dimensional halogen-bridged nickel compound, [Ni(chxn)2Br]Br2 (chxn=cyclohexanediamine). By attaching external resistors and a capacitor to a [Ni(chxn)2Br]Br2 sample, we obtain stable current oscillation at 90 K. The oscillation and its period are explained by a simple model.
Current densities of MgB2 wires by combined ex situ/in situ process
Authors: Kováč P. , Reissner M. , Melišek T. , Hušek I. , Mohammad S.
Published: July 2009

SiC doped MgB2/Ti/Cu wires have been made by powder-in-tube technique using precursor prepared by mixing of MgB2 (ex situ) with Mg, B (in situ) in variable ex situ/in situ ratio. Wires containing 0%, 23%, 50%, 70%, and 100% of MgB2 powder were two axially rolled to 1.2 mm and annealed in Ar at temperatures 700–850 °C/0.5 h. Increased critical current density [Jc(μ0H) performance] has been measured for 23% and 50% of added MgB2, which is attributed to improved grain connectivity combined with more effective grain boundaries acting as pinning centers. This novel process utilizes the advantages of both techniques: lower MgB2 porosity typical ex situ and better grain connectivity and effective C-substitution through SiC addition obtained by in situ.
Time and temperature dependence of surface relief grating formation in polymers containing azobenzene groups with different dipole moment
Authors: Veer Padmanabh U. , Pietsch Ullrich , Saphiannikova Marina
Published: July 2009

We present the results of time and temperature dependent deformation of two azobenzene materials with different dipole moment during the process of surface relief grating formation. The effect of chromophore orientation on grating formation in these films was studied in situ using continuous and pulselike exposure techniques at various temperatures up to the glass transition temperature of the respective polymer material. The results obtained for high dipole moment pDR1M and low dipole moment pMEA were compared in terms of the rate of the grating formation and related to the quantities as relaxation of the chromophores in the absence of the inscribing light and induced stress due to the chromophore orientation. The parameters obtained from the simulation data can be well explained considering viscoelastic material model. The experimental findings can be explained by assuming the interaction of azochromophores with polarized light leading to the orientation anisotropy of the azobenzene macromolecules, thereby generating a mechanical stress.
Einstein relation in hopping transport of organic semiconductors
Authors: Li Ling , Meller Gregor , Kosina Hans
Published: July 2009

The ratio between mobility and diffusion parameters (Einstein relation) in organic semiconductors has been a debating issue in the recent years. In this paper we developed an analytical model based on hopping transport theory and the Gaussian density of states. The validity of Einstein relation in organic semiconductors is discussed. It is shown that the classic Einstein relation is invalid for organic semiconductors, even for the carrier concentration for experimental purpose.
Effect of Mg2+ content on the dielectric properties of Ba0.65−xSr0.35MgxTiO3 ceramics
Authors: Xu Shiguo , Qu Yuanfang , Zhang Chen
Published: July 2009

The Ba0.65−xSr0.35MgxTiO3 ceramics was prepared by conventional solid method. The effects of the Mg2+ content on the crystal structure and dielectric properties of Ba0.65−xSr0.35MgxTiO3 ceramics were investigated. The results show that as the Mg2+ content increases, the influence of Mg2+ on the crystal structure of Ba0.65−xSr0.35MgxTiO3 ceramics undergoes three different stages, which orderly are the in situ synthesis of the A site, then the replacement on the B site and at last the replacement on the A site. As a result, the Curie peak and the loss peak of Ba0.65−xSr0.35MgxTiO3 ceramics gradually decrease first with X from 0 to 2.5 mol % and increase afterward with X above 2.5 mol %.
Spectra and energy levels of Yb3+ in AlN
Authors: Koubaa T. , Dammak M. , Kammoun M. , Jadwisienczak W. M. , Lozykowski H. J. , Anders A.
Published: July 2009

We report on the crystal-field energy levels calculation of Yb3+ ions in an AlN host using crystal-field theory. Cathodoluminescence spectra of AlN grown by molecular beam epitaxy on Si (0001) substrate and doped by implantation with ytterbium (Yb) ions were critically examined assuming that Yb3+ ions are involved in different sites. The comparison between the emission spectra of Yb3+ ions in the GaN and AlN indicates the presence of some similarities between the lattice locations of Yb3+ ions in these hosts. We demonstrate that assuming the existence of a substitutional YbAl(Ga) site and a VN-Yb complex defect in AlN (GaN) lattice, a good agreement between the measured and calculated energy values of Yb3+ ion transition lines can be obtained. Furthermore, we have investigated the Zeeman g∥ and g⊥ parameters for the Yb3+ ion in an Al substitutional site as well as in the VN-Yb complex using the perturbation theory.
Photoluminescence from Si-capped GeSn nanodots on Si substrates formed using an ultrathin SiO2 film technique
Authors: Nakamura Yoshiaki , Fujinoki Norihiko , Ichikawa Masakazu
Published: July 2009

We observed strong 1.5 μm photoluminescence (PL) from Si-capped Ge1−xSnx nanodots on Si (001) substrates formed using ultrathin SiO2 films. The lack of the quantum size effect in the PL revealed that the PL came from Si capping layers with radiative defects and not from the nanodots. The PL intensities were strongly enhanced when the Sn composition x increased in Ge1−xSnx nanodots or the nanodot size decreased. These results indicate that the formation of the radiative defects in Si is strongly correlated with the nanodot structures such as its geometry and strain states. This study demonstrates a new formation technique for light-emitting Si structures with high controllability and compatibility with Si technology.
Doppler reflectometer system in the stellarator TJ-II
Authors: Happel T. , Estrada T. , Blanco E. , Tribaldos V. , Cappa A. , Bustos A.
Published: July 2009

A Doppler reflectometer system has recently been installed in the stellarator TJ-II. The system is optimized for the Q-band (33–50 GHz) and the high-curvature plasmas produced in TJ-II. The launch angle of the microwave beam can be controlled by a steerable mirror to obtain angles between ±20° enabling the measurement of perpendicular wave numbers in the range of 3–15 cm−1. The available angular range allows for comparisons between positive and negative values and additionally for calibration of the system. Localization and k⊥-estimation is done via the three-dimensional ray/beam-tracing code TRUBA. First measured spectra and radial profiles of the perpendicular velocity of plasma density fluctuations are presented.
Radiation pressure excitation and cooling of a cryogenic micro-mechanical systems cavity
Authors: Siciliani de Cumis Mario , Farsi Alessandro , Marino Francesco , D’Arrigo Giuseppe , Marin Francesco , Cataliotti Francesco Saverio , Rimini Emanuele
Published: July 2009

We describe an experiment achieving radiation pressure excitation and cooling of a mechanical mode in a cryogenic Fabry–Perot cavity with a micromechanical oscillator [micro-electro-mechanical systems (MEMS)] as end mirror. The response function to periodic modulations of the intracavity power provides an independent measurement of the effective modal mass allowing an accurate estimate of the mode temperature from the corresponding displacement noise spectrum. We also obtained optical cooling of the MEMS fundamental mode at 110 kHz from 11 to 4.4 K, limited only by the optical Finesse and the mechanical quality of the system. These results represent a step toward the observation of quantum optomechanical effects and motivate further experiments with improved performances of the MEMS samples.
Modeling of capillary Z-pinch recombination pumping of boron extreme ultraviolet laser
Authors: Vrba P. , Bobrova N. A. , Sasorov P. V. , Vrbova M. , Hubner J.
Published: July 2009

Computer modeling of fast capillary discharge is performed to investigate a new laser active medium created by excited hydrogenlike boron ions leading to lasing at 26.23 nm. Recombination excitation of the boron ions is expected in the undercooled pinching plasma created during the expansion phase of the pinch. Plasma dynamics is described by the magnetohydrodynamic code NPINCH and the plasma ion kinetics is evaluated according to the FLY code. Results of simulations for capillary filled with boron are reported and compared with previous results achieved for nitrogen filled capillary. In both cases, the same nonablative capillary with radius of 1.6 mm is presumed and the current pulse with 50 kA peak value and 1012 A s−1 current slope are taken into account. Evaluated pressure optimized gains are 1.04 and 0.11 cm−1 are found for boron and nitrogen filled capillary, respectively. Capillary wall ablation is then also assayed.
Virial theorem in the Kohn–Sham density-functional theory formalism: Accurate calculation of the atomic quantum theory of atoms in molecules energies
Authors: Rodríguez Juan I. , Ayers Paul W. , Götz Andreas W. , Castillo-Alvarado F. L.
Published: July 2009

A new approach for computing the atom-in-molecule [quantum theory of atoms in molecule (QTAIM)] energies in Kohn–Sham density-functional theory is presented and tested by computing QTAIM energies for a set of representative molecules. In the new approach, the contribution for the correlation-kinetic energy (Tc) is computed using the density-functional theory virial relation. Based on our calculations, it is shown that the conventional approach where atomic energies are computed using only the noninteracting part of the kinetic energy might be in error by hundreds of kJ/mol.
Clarification and extension of the optical reciprocity theorem
Authors: Xie H. Y. , Leung P. T. , Tsai D. P.
Published: July 2009

Clarifications on the optical reciprocity theorem are provided by explicitly proving the equivalence between the Lorentz lemma and the symmetry of the Green dyadic for the electromagnetic wave equation. This is achieved by explicitly including the surface term in the former so that different boundary conditions can be considered as required in the formulation of the latter. In addition, we shall also extend the theorem to include anisotropic magnetic materials with a nonlocal response, leading to a result which will be useful for the study of materials possessing such properties such as certain types of metamaterials.
Raman spectral signatures as conformational probes of gas phase flexible molecules
Authors: Golan Amir , Mayorkas Nitzan , Rosenwaks Salman , Bar Ilana
Published: July 2009

A novel application of ionization-loss stimulated Raman spectroscopy (ILSRS) for monitoring the spectral features of four conformers of a gas phase flexible molecule is reported. The Raman spectral signatures of four conformers of 2-phenylethylamine are well matched by the results of density functional theory calculations, showing bands uniquely identifying the structures. The measurement of spectral signatures by ILSRS in an extended spectral range, with a conventional laser source, is instrumental in facilitating the unraveling of intra- and intermolecular interactions that are significant in biological structure and activity.
Electrowetting propulsion of water-floating objects
Authors: Chung Sang Kug , Ryu Kyungjoo , Cho Sung Kwon
Published: July 2009

This letter describes a propulsion principle along with experimental verification of this principle by which an air-to-water interface vertically oscillated by ac electrowetting generates a quasisteady, “streaming” flow that can be utilized to propel water-floating objects. This propulsion does not require any mechanical moving parts. Using a centimeter-sized boat whose outer surfaces were covered with microfabricated electrowetting electrodes, linear, and rotational motions of the boat were achieved up to maximum speeds of 5 mm/s and 20 rpm, respectively. By combining the above two motions, the boat was successfully propelled and steered along a curvilinear pathline. A potential application of this principle is to propel and maneuver various water-floating mini/microrobots and boats used for water/air quality monitoring or surveillance/security purposes.
Sunlight-style color-temperature tunable organic light-emitting diode
Authors: Jou Jwo-Huei , Wu Ming-Hsuan , Shen Shih-Ming , Wang Hsi-Ching , Chen Sun-Zen , Chen Szu-Hao , Lin Chuen-Ren , Hsieh Yueh-Lin
Published: July 2009

We demonstrate a man-made lighting device of organic light-emitting diode (OLED) capable of yielding a sunlight-style illumination with various daylight chromaticities, whose color temperature ranges between 2300 and 8200 K, fully covering those of the entire daylight at different times and regions. The OLED employs a device architecture capable of simultaneously generating all the emissions required to form a series of daylight chromaticities. The wide color-temperature span may be attributed to that the recombination core therein can easily be shifted along the different emissive zones simply by varying the applied voltage via the use of a thin carrier-modulating layer.
First-principles study on ferromagnetism in nitrogen-doped In2O3
Authors: Guan L. X. , Tao J. G. , Huan C. H. A. , Kuo J. L. , Wang L.
Published: July 2009

We report stable room temperature ferromagnetism in nitrogen doped In2O3 (N–In2O3) based on density functional theory. Our investigation on the electronic and magnetic properties of N–In2O3 suggests that N dopant introduces spin-polarized hole states in the band gap generating a total magnetic moment of 1.0μB per N, which is mainly localized on the doped N atoms. The ferromagnetic interaction in N–In2O3 system is mainly driven by the occurrence of coupling chains between a first N (N1)-2p to a second N (N2)-2p via a bridging In 5p and 4d orbitals.
Polarization control of 1.6 μm vertical-cavity surface-emitting lasers using InAs quantum dashes on InP(001)
Authors: Lamy J. M. , Paranthoen C. , Levallois C. , Nakkar A. , Folliot H. , Gauthier J. P. , Dehaese O. , Le Corre A. , Loualiche S.
Published: July 2009

The authors report the demonstration of a polarization-controlled vertical-cavity surface-emitting laser (VCSEL), emitting at the telecommunication wavelength. VCSELs are based on an active medium constituted of well elongated InAs quantum dashes (QDHs) nanostructures grown on conventional (001) oriented InP substrate. QDHs present important optical polarization anisotropies according to the [11¯0] crystallographic orientation. Inserted into a VCSEL microcavity, QDH VCSELs show a continuous wave laser operation at 1.6 μm, at room temperature, with a reduced 13 kW/cm2 optical excitation density threshold. The QDH VCSEL output laser polarization is fixed along the same [11¯0] direction. Power and temperature dependant measurements do not show any polarization instabilities and switching on all QDH VCSELs. A polarization extinction ratio as high as 30 dB is deduced from experiments.
Observation of hole accumulation at the interface of an undoped InGaN/GaN heterostructure
Authors: Chen D. J. , Xue J. J. , Liu B. , Lu H. , Xie Z. L. , Han P. , Zhang R. , Zheng Y. D. , Kong Y. C. , Zhou J. J.
Published: July 2009

A pronounced hump structure at about −5 V in the high-frequency capacitance-voltage (C-V) curve of an undoped InGaN/GaN heterostructure is observed and this hump weakens gradually with decreasing measurement frequency, indicating the occurrence of an inversion behavior in the InGaN/GaN heterostructure. The inversion behavior in the C-V curve is attributed to hole accumulation at the heterointerface where a hole well is formed due to the strong piezoelectric polarization effect in the InGaN/GaN heterostructure. The acceptor traps related to Ga vacancies in the InGaN layer are thought to be the source of the minority carriers. The theoretical calculation of band diagram of the InGaN/GaN heterostructure confirms the formation of the hole well at the heterointerface and supports the behavior of hole accumulation under negative bias voltage.
Electronic transport characteristics of electrolyte-gated conducting polyaniline nanowire field-effect transistors
Authors: Lee Seung-Yong , Choi Gyoung-Rin , Lim Hyuneui , Lee Kyung-Mi , Lee Sang-Kwon
Published: July 2009

We investigate the electronic transport characteristics of an electrolyte-gated conducting polyaniline (PANI) nanowire field-effect transistor (FET) assembled between two Au electrodes on SiO2/Si substrate using nanochannel-assisted chemical oxidative polymerization. This is the first demonstration that the current-voltage characteristics for a PANI nanowire FET exhibit significant hysteresis, which is typically greater on the positive sweep of the potential than on the negative sweep. We suggest that this hysteresis is due to changes in the PANI structure and the effects of Coulombic repulsion in PANI nanowires on oxidation process. We also present degradation properties of PANI nanowire FETs with electrochemical gate potential.
Harvesting magnetic energy using extensional vibration of laminated magnetoelectric plates
Authors: Zhang C. L. , Yang J. S. , Chen W. Q.
Published: July 2009

Magnetically forced extensional vibrations of laminated plates with piezoelectric and piezomagnetic layers are analyzed theoretically. It is shown that such a structure can be used to harvest magnetic energy and convert it to electric energy. The output power and the energy conversion efficiency are calculated. The load dependence of the magnetoelectric coupling coefficient is also obtained.
Resistance switching in a single-crystalline NiO thin film grown on a Pt0.8Ir0.2 electrode
Authors: Kawai Masanori , Ito Kimihiko , Shimakawa Yuichi
Published: July 2009

A single-crystalline NiO thin film was grown epitaxially on an atomically flat Pt0.8Ir0.2 bottom electrode layer grown epitaxially on a SrTiO3(100) substrate. The memory cells of the single-crystalline NiO thin film with Pt top electrodes showed unipolar resistance switching behaviors. The result demonstrates that a unipolar resistance switching is not a characteristic phenomenon in the polycrystalline NiO but it can also occur in the single-crystalline NiO.
The Scintillating Grid Illusion: Influence of Size, Shape, and Orientation of the Luminance Patches
Authors: Qian Kun , Yamada Yuki , Kawabe Takahiro , Miura Kayo
Published: July 2009

The scintillating grid illusion refers to the illusory perception of black spots on luminance patches at the intersections of a grey grid on a black background. We examined how spatial parameters of luminance patches modulated the strength of the illusion. In experiment 1, we controlled the size and shape of the luminance patches. For the largest-size conditions tested, we found a significant reduction in the strength of the illusion with squares when compared to circles or diamonds. In experiment 2, we controlled the orientation of quadrangle patches and confirmed a significantly larger reduction in the strength of the illusion when the edge orientations of quadrangle patches were vertical and horizontal (square) than when they were oblique (diamond). To explore the relationship between orientation processing and scintillating grid illusion, we controlled, in experiment 3, the global orientation of the display; the strength of the illusion with diamonds was significantly weaker when it was rotated by 45° than when it was not rotated. These results indicate that it is not only the difference of edge orientation of luminance patches, but also the orientation with respect to the grid that determines the strength of the illusion.
Biosynthesis of the salinosporamide A polyketide synthase substrate chloroethylmalonyl-coenzyme A from
S
-adenosyl-
l
-methionine
Authors: Eustáquio Alessandra S. , McGlinchey Ryan P. , Liu Yuan , Hazzard Christopher , Beer Laura L. , Florova Galina , Alhamadsheh Mamoun M. , Lechner Anna , Kale Andrew J. , Kobayashi Yoshihisa , Reynolds Kevin A. , Moore Bradley S.
Published: July 2009

Polyketides are among the major classes of bioactive natural products used to treat microbial infections, cancer, and other diseases. Here we describe a pathway to chloroethylmalonyl-CoA as a polyketide synthase building block in the biosynthesis of salinosporamide A, a marine microbial metabolite whose chlorine atom is crucial for potent proteasome inhibition and anticancer activity.
S
-adenosyl-
l
-methionine (SAM) is converted to 5′-chloro-5′-deoxyadenosine (5′-ClDA) in a reaction catalyzed by a SAM-dependent chlorinase as previously reported. By using a combination of gene deletions, biochemical analyses, and chemical complementation experiments with putative intermediates, we now provide evidence that 5′-ClDA is converted to chloroethylmalonyl-CoA in a 7-step route via the penultimate intermediate 4-chlorocrotonyl-CoA. Because halogenation often increases the bioactivity of drugs, the availability of a halogenated polyketide building block may be useful in molecular engineering approaches toward polyketide scaffolds.
Identification of the functional core of the influenza A virus A/M2 proton-selective ion channel
Authors: Ma Chunlong , Polishchuk Alexei L. , Ohigashi Yuki , Stouffer Amanda L. , Schön Arne , Magavern Emma , Jing Xianghong , Lear James D. , Freire Ernesto , Lamb Robert A. , DeGrado William F. , Pinto Lawrence H.
Published: July 2009

The influenza A virus M2 protein (A/M2) is a homotetrameric pH-activated proton transporter/channel that mediates acidification of the interior of endosomally encapsulated virus. This 97-residue protein has a single transmembrane (TM) helix, which associates to form homotetramers that bind the anti-influenza drug amantadine. However, the minimal fragment required for assembly and proton transport in cellular membranes has not been defined. Therefore, the conductance properties of truncation mutants expressed in
Xenopus
oocytes were examined. A short fragment spanning residues 21–61, M2(21-61), was inserted into the cytoplasmic membrane and had specific, amantadine-sensitive proton transport activity indistinguishable from that of full-length A/M2; an epitope-tagged version of an even shorter fragment, M2(21-51)-FLAG, had specific activity within a factor of 2 of the full-length protein. Furthermore, synthetic fragments including a peptide spanning residues 22–46 were found to transport protons into liposomes in an amantadine-sensitive manner. In addition, the functionally important His-37 residue pK
a
values are highly perturbed in the tetrameric form of the protein, a property conserved in the TM peptide and full-length A/M2 in both micelles and bilayers. These data demonstrate that the determinants for folding, drug binding, and proton translocation are packaged in a remarkably small peptide that can now be studied with confidence.
Channelrhodopsin-2 is a leaky proton pump
Authors: Feldbauer Katrin , Zimmermann Dirk , Pintschovius Verena , Spitz Julia , Bamann Christian , Bamberg Ernst
Published: July 2009

Since its discovery, the light-gated cation channel Channelrhodopsin-2 (ChR2) has proven to be a long-sought tool for the noninvasive, light-activated control of neural cells in culture and in living animals. Although ChR2 is widely used in neurobiological applications, little is known about its molecular mechanism. In this work, the unitary conductance of ChR2 was determined for different cations, for example 40 fS at 200 mM NaCl and −60 mV, using noise analysis. The kinetics of the ion channel obtained by noise analysis is in excellent agreement with the photocurrent kinetics obtained by voltage-clamp and time-resolved spectroscopy. The inward rectification of the channel could be explained by the single channel parameters. ChR2 represents an ion channel with a 7 transmembrane helix motif, even though the sequence homology of its essential amino acids to those of the light-driven H
+
pump bacteriorhodopsin (bR) is high. Here, we also show that when ChR2 is expressed in electrofused giant HEK293 cells or reconstituted on planar lipid membranes, it can indeed act as an outwardly driven H
+
pump, demonstrating that ChR2 is bifunctional, and in-line with other microbial rhodopsins, a H
+
pump but with a leak that shows ion channel properties.
Differential RNA silencing suppression activity of NS1 proteins from different influenza A virus strains
Authors: de Vries Walter , Haasnoot Joost , Fouchier Ron , de Haan Peter , Berkhout Ben
Published: July 2009

The NS1 gene of influenza A virus encodes a multi-functional protein that plays an important role in counteracting cellular antiviral mechanisms such as the interferon (IFN), protein kinase R and retinoic acid-inducible gene product I pathways. In addition, NS1 has recently been shown to have RNA interference (RNAi) or RNA silencing suppression (RSS) activity. This study analysed the IFN antagonistic activity of NS1 and the RSS activity for several influenza subtypes: H1N1, H3N2, H5N1 and H7N7. It was shown that the various NS1 proteins were capable of inhibiting the activation of an IFN-responsive promoter. However, differential RSS activity was measured among the NS1 variants. The NS1 protein of strain A/WSN/33 (H1N1) was most potent in suppressing short hairpin RNA-mediated gene silencing. In contrast, NS1 proteins of the highly pathogenic H5N1 strains A/VN/1194/04 and A/HK/156/97 were most potent in complementing the RSS function of the human immunodeficiency virus type 1 Tat protein. These results show that the ability of NS1 to suppress RNAi varies among influenza strains and is likely to contribute to differences in viral replication capacity and pathogenicity.
Comparison of 12 turkey hemorrhagic enteritis virus isolates allows prediction of genetic factors affecting virulence
Authors: Beach Nathan M. , Duncan Robert B. , Larsen Calvert T. , Meng Xiang-Jin , Sriranganathan Nammalwar , Pierson F. William
Published: July 2009

Turkey hemorrhagic enteritis virus (THEV) is a member of the genusSiadenovirusand causes disease in turkey poults characterized by splenomegaly, bloody diarrhoea and death. The mechanism responsible for intestinal lesion formation and mortality is not known, although there is strong evidence that it is immune-mediated. All strains of THEV are serologically indistinguishable, although there are naturally occurring avirulent strains of THEV that replicate efficiently in turkeys without the intestinal haemorrhage or mortality associated with more virulent strains. The purpose of this study was to determine which viral genes are involved in virulence. The full-length genome of an avirulent vaccine strain was sequenced and compared with the genome of a virulent field isolate from Israel that was sequenced in 1998. Comparison of the two 26.3 kb genomes revealed 49 nucleotide differences resulting in 14 putative amino acid changes within viral proteins. Sequencing of the regions surrounding the 14 missense mutations revealed variations inORF1,E3and the fiber (fib) knob domain in five additional strains with varying degrees of virulence. Complete sequences of these genes were determined in a total of 11 different strains of THEV. All strains had at least one missense mutation inORF1, and all but two of the strains had one missense mutation inE3. At least one missense mutation was found in the fiber knob domain in six out of seven virulent strains. Sequence variation ofORF1,E3andfibin strains of THEV with different phenotypes strongly indicates that these genes are the key factors affecting virulence.
Evaluation of smallpox vaccines using variola neutralization
Authors: Damon Inger K. , Davidson Whitni B. , Hughes Christine M. , Olson Victoria A. , Smith Scott K. , Holman Robert C. , Frey Sharon E. , Newman Frances , Belshe Robert B. , Yan Lihan , Karem Kevin
Published: July 2009

The search for a ‘third’-generation smallpox vaccine has resulted in the development and characterization of several vaccine candidates. A significant barrier to acceptance is the absence of challenge models showing induction of correlates of protective immunity against variola virus. In this light, virus neutralization provides one of few experimental methods to show specific ‘in vitro’ activity of vaccines against variola virus. Here, we provide characterization of the ability of a modified vaccinia virus Ankara vaccine to induce variola virus-neutralizing antibodies, and we provide comparison with the neutralization elicited by standard Dryvax vaccination.
Chlorella viruses prevent multiple infections by depolarizing the host membrane
Authors: Greiner Timo , Frohns Florian , Kang Ming , Van Etten James L. , Käsmann Anja , Moroni Anna , Hertel Brigitte , Thiel Gerhard
Published: July 2009

Previous experiments established that when the unicellular green alga Chlorella NC64A is inoculated with two viruses, usually only one virus replicates in a single cell. That is, the viruses mutually exclude one another. In the current study, we explore the possibility that virus-induced host membrane depolarization, at least partially caused by a virus-encoded K+ channel (Kcv), is involved in this mutual exclusion. Two chlorella viruses, PBCV-1 and NY-2A, were chosen for the study because (i) they can be distinguished by real-time PCR and (ii) they exhibit differential sensitivity to Cs+, a well-known K+ channel blocker. PBCV-1-induced host membrane depolarization, Kcv channel activity and plaque formation are only slightly affected by Cs+, whereas all three NY-2A-induced events are strongly inhibited by Cs+. The addition of one virus 5–15 min before the other results primarily in replication of the first virus. However, if virus NY-2A-induced membrane depolarization of the host is blocked by Cs+, PBCV-1 is not excluded. We conclude that virus-induced membrane depolarization is at least partially responsible for the exclusion phenomenon.
Detection of polyoma and corona viruses in bats of Canada
Authors: Misra Vikram , Dumonceaux Timothy , Dubois Jack , Willis Craig , Nadin-Davis Susan , Severini Alberto , Wandeler Alex , Lindsay Robbin , Artsob Harvey
Published: July 2009

Several instances of emerging diseases in humans appear to be caused by the spillover of viruses endemic to bats, either directly or through other animal intermediaries. The objective of this study was to detect, identify and characterize viruses in bats in the province of Manitoba and other regions of Canada. Bats were sampled from three sources: live-trapped Myotis lucifugus from Manitoba, rabies-negative Eptesicus fuscus, M. lucifugus, M. yumanensis, M. septentrionalis, M. californicus, M. evotis, Lasionycteris (L.) noctivagans and Lasiurus (Las.) cinereus, provided by the Centre of Expertise for Rabies of the Canadian Food Inspection Agency (CFIA), and L. noctivagans, Las. cinereus and Las. borealis collected from a wind farm in Manitoba. We attempted to isolate viruses from fresh tissue samples taken from trapped bats in cultured cells of bat, primate, rodent, porcine, ovine and avian origin. We also screened bat tissues by PCR using primers designed to amplify nucleic acids from members of certain families of viruses. We detected RNA of a group 1 coronavirus from M. lucifugus (3 of 31 animals) and DNA from an as-yet undescribed polyomavirus from female M. lucifugus (4 of 31 animals) and M. californicus (pooled tissues from two females).
Comparison of poliovirus recombinants: accumulation of point mutations provides further advantages
Authors: Savolainen-Kopra Carita , Samoilovich Elena , Kahelin Heidi , Hiekka Anna-Kaisa , Hovi Tapani , Roivainen Merja
Published: July 2009

The roles of recombination and accumulation of point mutations in the origin of new poliovirus (PV) characteristics have been hypothesized, but it is not known which are essential to evolution. We studied phenotypic differences between recombinant PV strains isolated from successive stool specimens of an oral PV vaccine recipient. The studied strains included three PV2/PV1 recombinants with increasing numbers of mutations in the VP1 gene, two of the three with an amino acid change I→T in the DE-loop of VP1, their putative PV1 parent and strains Sabin 1 and 2. Growth of these viruses was examined in three cell lines: colorectal adenocarcinoma, neuroblastoma and HeLa. The main observation was a higher growth rate between 4 and 6 h post-infection of the two recombinants with the I→T substitution. All recombinants grew at a higher rate than parental strains in the exponential phase of the replication cycle. In a temperature sensitivity test, the I→T-substituted recombinants replicated equally well at an elevated temperature. Complete genome sequencing of the three recombinants revealed 12 (3), 19 (3) and 27 (3) nucleotide (amino acid) differences from Sabin. Mutations were located in regions defining attenuation, temperature sensitivity, antigenicity and the cis-acting replicating element. The recombination site was in the 5′ end of 3D. In a competition assay, the most mutated recombinant beat parental Sabin in all three cell lines, strongly suggesting that this virus has an advantage. Two independent intertypic recombinants, PV3/PV1 and PV3/PV2, also showed similar growth advantages, but they also contained several point mutations. Thus, our data defend the hypothesis that accumulation of certain advantageous mutations plays a key role in gaining increased fitness.
SMAD proteins of oligodendroglial cells regulate transcription of JC virus early and late genes coordinately with the Tat protein of human immunodeficiency virus type 1
Authors: Stettner Michelle R. , Nance Jonas A. , Wright Clayton A. , Kinoshita Yayoi , Kim Woong-Ki , Morgello Susan , Rappaport Jay , Khalili Kamel , Gordon Jennifer , Johnson Edward M.
Published: July 2009

JC virus (JCV) is the aetiological agent of progressive multifocal leukoencephalopathy (PML), a fatal, demyelinating disease of the brain affecting people with AIDS. Although immunosuppression is involved in infection of the brain by JCV, a direct influence of human immunodeficiency virus type 1 (HIV-1) has also been established. The Tat protein of HIV-1 has been implicated in activation of the cytokine transforming growth factor (TGF)-βin HIV-1-infected cells and in stimulating JCV gene transcription and DNA replication in oligodendroglia, the primary central nervous system cell type infected by JCV in PML. This study demonstrated that Tat can cooperate with SMAD proteins, the intracellular effectors of TGF-β, at the JCV DNA control region (CR) to stimulate JCV gene transcription. Tat stimulated JCV early gene transcription in KG-1 oligodendroglial cells when expressed via transfection or added exogenously. Using chromatin immunoprecipitation, it was shown that exogenous Tat enhanced binding of SMAD2, -3 and -4 and their binding partner Fast1 to the JCV CR in living cells. When SMAD2, -3 and -4 were expressed together, Tat, expressed from plasmid pTat, stimulated transcription from both early and late gene promoters, with the early promoter exhibiting stimulation of >100-fold. Tat, SMAD4 and JCV large T-antigen were all visualized in oligodendroglial cells at the border of an active PML lesion in the cerebral frontal lobe. These results revealed a positive reinforcement system in which the SMAD mediators of the TGF-βsystem act cooperatively with Tat to stimulate JCV gene transcription.
A mutation in helicase motif IV of herpes simplex virus type 1 UL5 that results in reduced growth in vitro and lower virulence in a murine infection model is related to the predicted helicase structure
Authors: Biswas Subhajit , Miguel Ricardo Núñez , Sukla Soumi , Field Hugh J.
Published: July 2009

A variant was selected from a clinical isolate of herpes simplex virus type 1 (HSV-1) during a single passage in the presence of a helicase–primase inhibitor (HPI) at eight times the IC50. The variant was approximately 40-fold resistant to the HPI BAY 57-1293 and it showed significantly reduced growth in tissue culture with a concomitant reduction in virulence in a murine infection model. The variant contained a single mutation (Asn342Lys) in the UL5 predicted functional helicase motif IV. The Asn342Lys mutation was transferred to a laboratory strain, PDK cl-1, and the recombinant acquired the expected resistance and reduced growth characteristics. Comparative modelling and docking studies predicted the Asn342 position to be physically distant from the HPI interaction pocket formed by UL5 and UL52 (primase). We suggest that this mutation results in steric/allosteric modification of the HPI-binding pocket, conferring an indirect resistance to the HPI. Slower growth and moderately reduced virulence suggest that this mutation might also interfere with the helicase–primase activity.
Analysis of Puumala hantavirus in a bank vole population in northern Finland: evidence for co-circulation of two genetic lineages and frequent reassortment between strains
Authors: Razzauti Maria , Plyusnina Angelina , Sironen Tarja , Henttonen Heikki , Plyusnin Alexander
Published: July 2009

In this study, for the first time, two distinct genetic lineages of Puumala virus (PUUV) were found within a small sampling area and within a single host genetic lineage (Ural mtDNA) at Pallasjärvi, northern Finland. Lung tissue samples of 171 bank voles (Myodes glareolus) trapped in September 1998 were screened for the presence of PUUV nucleocapsid antigen and 25 were found to be positive. Partial sequences of the PUUV small (S), medium (M) and large (L) genome segments were recovered from these samples using RT-PCR. Phylogenetic analysis revealed two genetic groups of PUUV sequences that belonged to the Finnish and north Scandinavian lineages. This presented a unique opportunity to study inter-lineage reassortment in PUUV; indeed, 32 % of the studied bank voles appeared to carry reassortant virus genomes. Thus, the frequency of inter-lineage reassortment in PUUV was comparable to that of intra-lineage reassortment observed previously (Razzauti, M., Plyusnina, A., Henttonen, H. & Plyusnin, A. (2008).J Gen Virol89, 1649–1660). Of six possible reassortant S/M/L combinations, only two were found at Pallasjärvi and, notably, in all reassortants, both S and L segments originated from the same genetic lineage, suggesting a non-random pattern for the reassortment. These findings are discussed in connection to PUUV evolution in Fennoscandia.
In vitro biology of fibropapilloma-associated turtle herpesvirus and host cells in Hawaiian green turtles (Chelonia mydas)
Authors: Work Thierry M. , Dagenais Julie , Balazs George H. , Schumacher Joanne , Lewis Teresa D. , Leong Jo-Ann C. , Casey Rufina N. , Casey James W.
Published: July 2009

Fibropapillomatosis (FP) of green turtles has a global distribution and causes debilitating tumours of the skin and internal organs in several species of marine turtles. FP is associated with a presently non-cultivable alphaherpesvirus Chelonid fibropapilloma-associated herpesvirus (CFPHV). Our aims were to employ quantitative PCR targeted to pol DNA of CFPHV to determine (i) if DNA sequesters by tumour size and/or cell type, (ii) whether subculturing of cells is a viable strategy for isolating CFPHV and (iii) whether CFPHV can be induced to a lytic growth cycle in vitro using chemical modulators of replication (CMRs), temperature variation or co-cultivation. Additional objectives included determining whether non-tumour and tumour cells behave differently in vitro and confirming the phenotype of cultured cells using cell-type-specific antigens. CFPHV pol DNA was preferentially concentrated in dermal fibroblasts of skin tumours and the amount of viral DNA per cell was independent of tumour size. Copy number of CFPHV pol DNA per cell rapidly decreased with cell doubling of tumour-derived fibroblasts in culture. Attempts to induce viral replication in known CFPHV-DNA-positive cells using temperature or CMR failed. No significant differences were seen in in vitro morphology or growth characteristics of fibroblasts from tumour cells and paired normal skin, nor from CFPHV pol-DNA-positive intestinal tumour cells. Tumour cells were confirmed as fibroblasts or keratinocytes by positive staining with anti-vimentin and anti-pancytokeratin antibodies, respectively. CFPHV continues to be refractory to in vitro cultivation.
Host specificity of the anti-interferon and anti-apoptosis activities of parainfluenza virus P/C gene products
Authors: Chambers Raychel , Takimoto Toru
Published: July 2009

Human parainfluenza virus type 1 (HPIV-1) and Sendai virus (SeV) are highly homologous in structure and sequence, whilst maintaining distinct host ranges. These viruses express accessory proteins from their P/C gene that are known to have activities against innate immunity. The accessory proteins expressed from the P/C gene of these viruses are different. In addition to the nested set of C proteins, SeV expresses V protein from edited P mRNA, which is not expressed by HPIV-1. This study evaluated the host specificity and role of the P/C gene products in anti-interferon (IFN) and anti-apoptosis activity by characterizing a recombinant SeV, rSeVhP, in which the SeV P/C gene was replaced with that of HPIV-1. Unlike SeV, rSeVhP infection strongly activated IFN regulatory transcription factor (IRF)-3 and nuclear factor-κB, resulting in an increased level of IFN-β induction compared with SeV in murine cells. In contrast, activation of IRF-3 was not observed in rSeVhP-infected human A549 cells. rSeVhPSV, which expressed SeV V protein from an inserted gene in rSeVhP, induced less IFN-β than rSeVhP, suggesting that V contributes to the suppression of IFN production in murine cells. Furthermore, rSeVhP induced apoptotic cell death in murine but not in A549 cells. These data indicate the functional difference in P/C gene products from SeV and HPIV-1 in antagonizing IFN induction and apoptosis, which is likely to be one of the major factors for pathogenicity in specific hosts.