bluuebunny/crossref_metadata_2025 huggingface dataset:
Computation of correlation functions and wave function projections in the context of quantum trajectory dynamics
Authors: Garashchuk Sophya
Published: April 2007

The de Broglie-Bohm formulation of the Schrödinger equation implies conservation of the wave function probability density associated with each quantum trajectory in closed systems. This conservation property greatly simplifies numerical implementations of the quantum trajectory dynamics and increases its accuracy. The reconstruction of a wave function, however, becomes expensive or inaccurate as it requires fitting or interpolation procedures. In this paper we present a method of computing wave packet correlation functions and wave function projections, which typically contain all the desired information about dynamics, without the full knowledge of the wave function by making quadratic expansions of the wave function phase and amplitude near each trajectory similar to expansions used in semiclassical methods. Computation of the quantities of interest in this procedure is linear with respect to the number of trajectories. The introduced approximations are consistent with approximate quantum potential dynamics method. The projection technique is applied to model chemical systems and to the H+H2 exchange reaction in three dimensions.
Renner-Teller/Jahn-Teller intersections along the collinear axes of polyatomic molecules: C2H2+ as a case study
Authors: Halász G. J. , Vibók Á. , Hoffman D. K. , Kouri D. J. , Baer M.
Published: April 2007

Recently we discussed the Renner-Teller effect in triatomic molecules [J. Chem. Phys. 125, 094102 (2006)]. In that article the main message is that the Renner-Teller phenomenon, just like the Jahn-Teller phenomenon, is a topological effect. Now we extend this study to a tetra-atomic system, namely, the C2H2+ ion, for which topological effects are revealed when one atom surrounds the triatom axis or when two atoms surround (at a time) the two-atom axis. The present study not only supports the findings of the previous study, in particular, the crucial role played by the topological D matrix for diabatization, but it also reveals new features which are expected to be more and more pronounced the larger the original collinear molecule. As already implied, shifting away two atoms from the collinear molecular axis does not necessarily abolish the ability of the remaining two atoms to form topological effects. Moreover, the study indicates that when the two hydrogens are shifted away, the CC axis produces two kinds of topological effects: (1) a Renner-Teller effect (characterized by a topological phase of 2π) which is revealed when the two hydrogens surround, rigidly, this axis (as mentioned above), and (2) a Jahn-Teller effect (characterized by a topological phase of π) which is revealed when one of the hydrogens surrounds this axis while the other hydrogen is clamped to its position.
On the study of collective dynamics in supercooled liquids through the statistics of the isoconfigurational ensemble
Authors: Widmer-Cooper Asaph , Harrowell Peter
Published: April 2007

The use of the isoconfigurational ensemble to explore structure-dynamic correlations in supercooled liquids is examined. The statistical error of the dynamic propensity and its spatial distribution are determined. The authors present the spatial distribution of the particle non-Gaussian parameter as a measure of the intermittency with which particles exhibit their propensity for motion. The ensemble average of the direction of particle motion is introduced to establish the anisotropy of the dynamic propensity.
Simple fabrication technique for rapid prototyping of seamless cylindrical microchannels in polymer substrates
Authors: Perry Hannah , Greiner Cherry , Georgakoudi Irene , Cronin-Golomb Mark , Omenetto Fiorenzo G.
Published: April 2007

This article presents a simple and novel method for the fabrication of cylindrical microchannels in polymer or biopolymer substrates. This process results in highly regular, cylindrical microchannels, suitable both to the transport of liquid and the transmission of light. This method eliminates issues associated with positioning tolerances characteristic of conventional fabrication techniques, such as soft lithography. Such devices hold great promise in the field of biomedical engineering by providing a true cylindrical profile for microflow studies and vascular modeling, as well as the ability to optically analyze injected biological samples. An evaluation of these devices is performed by real time optical imaging of blood flow.
Measurement of the partial photoionization cross sections and asymmetry parameters of S atoms in the photon energy range 10.0–30.0eV using constant-ionic-state spectroscopy
Authors: Innocenti Fabrizio , Zuin Lucia , Costa Maria L. , Dias Antonio A. , Morris Alan , Stranges Stefano , Dyke John M.
Published: April 2007

The partial photoionization cross sections and asymmetry parameters of S atoms have been measured using constant-ionic-state (CIS) spectroscopy in the photon energy range 10.0–30.0eV. The ionizations investigated in these CIS experiments are the (3p)−1 ionizations S+(S4)←S(P3), S+(D2)←S(P3), and S+(P2)←S(P3). For the first time Rydberg series which converge to the fourth ionization limit have been observed and assignments of these series have been proposed. These correspond to excitations to Rydberg states that are parts of series which converge to the fourth ionization limit, S+(P4)←S(P3) (3s)−1, and autoionize to the lower S+(S4), S+(D2), or S+(P2) states. For each series observed in the CIS spectra photoelectron angular distribution studies, combined with other evidence, has allowed the angular momentum character of the free electron on autoionization to be determined.
High-speed GaAs metal gate semiconductor field effect transistor structure grown on a composite Ge∕GexSi1−x∕Si substrate
Authors: Luo Guang-Li , Hsieh Yen-Chang , Chang Edward Yi , Pilkuhn M. H. , Chien Chao-Hsin , Yang Tsung-Hsi , Cheng Chao-Ching , Chang Chun-Yen
Published: April 2007

In this study we used a low-pressure metal organic vapor phase epitaxy method to investigate the growth of GaAs metal gate semiconductor field effect transistor (MESFET) structures on a Si substrate. The buffer layer between the Si substrate and the grown GaAs epitaxial layers was a composite Ge∕Si0.05Ge0.95∕Si0.1Ge0.9 metamorphic layer. We used transmission electron microscopy to observe the microstructures formed in the grown GaAs∕Ge∕SixGe1−x∕Si material and atomic force microscopy to analyze the surface morphology and the formation of antiphase domains in the GaAs epitaxial layers. The measured Hall electron mobility in the channel layer of a MESFET structure grown on a 6° misoriented Si substrate was 2015 cm2 V−1 s−1 with a carrier concentration of 5.0×1017 cm−3. The MESFET device fabricated on this sample exhibited good current-voltage characteristics.
Rough surface adhesion in the presence of capillary condensation
Authors: DelRio Frank W. , Dunn Martin L. , Phinney Leslie M. , Bourdon Chris J. , de Boer Maarten P.
Published: April 2007

Capillary condensation of water can have a significant effect on rough surface adhesion. To explore this phenomenon between micromachined surfaces, the authors perform microcantilever experiments as a function of surface roughness and relative humidity (RH). Below a threshold RH, the adhesion is mainly due to van der Waals forces across extensive noncontacting areas. Above the threshold RH, the adhesion jumps due to capillary condensation and increases towards the upper limit of Γ=144mJ∕m2. A detailed model based on the measured surface topography qualitatively agrees with the experimental data only when the topographic correlations between the upper and lower surfaces are considered.
Writing mesoscale patterns in block copolymer thin films through channel flow of a nonsolvent fluid
Authors: Pelletier Vincent , Adamson Douglas H. , Register Richard A. , Chaikin Paul M.
Published: April 2007

The authors demonstrate how a nonsolvent fluid, flowing over the surface of a block copolymer thin film in a complex path defined by a channel, can locally tailor the alignment of cylindrical microdomains. The cylinders have a periodicity of ∼30nm, while the mesoscale pattern has a millimeter length scale. A diverging-converging channel is employed to measure alignment quality over a range of applied stresses in a single experiment; the results are compared with analogous measurements where the stress is applied through a controlled-stress rheometer, and can be satisfactorily described by a melting-recrystallization model.
Low-voltage operation of ferroelectric poly(vinylidene fluoride-trifluoroethylene) copolymer capacitors and metal-ferroelectric-insulator-semiconductor diodes
Authors: Fujisaki Sumiko , Ishiwara Hiroshi , Fujisaki Yoshihisa
Published: April 2007

Exceptionally low-voltage operation of organic ferroelectric capacitors and diodes was demonstrated. Ferroelectric polyvinylidene fluoride-trifluoroethylene [P(VDF-TrFE)] thin films were prepared by the solvent-cast method. Metal-ferroelectric-metal capacitors with 60-nm-thick P(VDF-TrFE) films exhibited well-saturated hysteresis curves whose coercive voltage (Vc) and remanent polarization (Pr) were 2.0V and 11.9μC∕cm2, respectively. The authors also fabricated metal-ferroelectric-insulator-semiconductor diodes with 100-nm-thick P(VDF-TrFE) films. Rectangular-shaped capacitance-voltage (C-V) hysteresis loops were obtained with a voltage sweep range narrower than 5V. The maximum memory window of 4.7V was achieved.
Ground-state properties and hardness of high density BC6N phases originating from diamond structure
Authors: Luo Xiaoguang , Guo Xiaoju , Liu Zhongyuan , He Julong , Yu Dongli , Tian Yongjun , Wang Hui-Tian
Published: April 2007

We report two possible metastable high density BC6N phases originating from the diamond structure. The ground-state properties of the BC6N phases are calculated using first-principles density-functional methods and the Vickers hardness is estimated using a semiempirical microscopic model. The calculated results show that two BC6N phases are semiconductors with Vickers hardness about 79–80GPa, indicating that the zinc-blende-like BC6N compounds are superhard material and have larger hardness than cubic BC2N and cubic boron nitride.
Ultraviolet and visible photoresponse properties of n-ZnO∕p-Si heterojunction
Authors: Mridha S. , Basak D.
Published: April 2007

A n-ZnO∕p-Si thin film heterojunction has been fabricated by a low cost sol-gel technique. The wavelength dependent photoresponse properties of the heterojunction is investigated in detail by studying the effect of light illumination on current-voltage (I-V) characteristics, photocurrent, and photocapacitance spectra at room temperature. It shows good diode characteristics with IF∕IR=3.4×103 at 4V and reverse leakage current density of 7.6×10−5Acm−2 at −5V. From the photocurrent spectra, it is observed that the visible photons are absorbed in the depleted p-Si under reverse bias conditions, while ultraviolet (UV) photons are absorbed in the depleted n-ZnO under positive bias conditions. This indicates that such a sol-gel n-ZnO∕p-Si thin film heterojunction can be used to sense both UV and visible photons though the photoresponse for UV is much slower than that of visible. The photocapacitance measurements suggest the presence of a shallow defect level in the sol-gel derived ZnO film which acts as an electron trap at ∼0.16eV below the conduction band.
Effect of substitution of Nd3+ for Bi3+ on the dielectric properties and structures of SrBi2−χNdχNb2O9 bismuth layer-structured ceramics
Authors: Sun Lin , Feng Chude , Chen Lidong , Huang Shiming
Published: April 2007

Single phases of SrBi2−χNdχNb2O9 (χ=0, 0.1, 0.2, and 0.4) ceramics were prepared by the solid-state reaction method and studied by dielectric and Raman spectroscopy. The substitution of Nd3+ for Bi3+ induced a dielectric relaxation behavior for SrBi2−χNdχNb2O9 (χ=0.1, 0.2, and 0.4). When χ=0.4, the dielectric response of SrBi1.6Nd0.4Nb2O9 is characteristic of typical relaxor ferroelectrics, which could be attributed to the disorder induced by the Nd3+ substituting for Bi3+ in Bi2O2 layers. The dielectric relaxation of SrBi1.6Nd0.4Nb2O9 was fitted using the Vögel-Fulcher relationship, which indicates that SrBi1.6Nd0.4Nb2O9 is analogous to a spin glass with thermally activated polarization fluctuations above a static freezing temperature. Raman spectra of SrBi2−χNdχNb2O9 ceramics could indicate that the structural distortion of NbO6 octahedron decreases with the increase in Nd content, which results in the decrease in Tm for SrBi2−χNdχNb2O9 ceramics.
Thermal stability of Ohmic contacts to InN
Authors: Khanna Rohit , Gila B. P. , Stafford L. , Pearton S. J. , Ren F. , Kravchenko I. I. , Dabiran Amir , Osinsky A.
Published: April 2007

Ti ∕ Al ∕ Ni ∕ Au and Ti∕Al∕TiB2∕Ti∕Au Ohmic contacts on n-type InN were investigated as a function of annealing temperature. A minimum specific contact resistance of 1.6×10−6Ωcm−2 was obtained for the TiB2-based Ohmic contacts on n-type GaN with n∼1018cm−3 after annealing at 900°C. The minimum value with the Ni-based metallization was higher (6×10−6Ωcm2). The measurement temperature dependence of contact resistance was similar for both Ti∕Al∕TiB2∕Ti∕Au and Ti∕Al∕Ni∕Au, suggesting that the same transport mechanism was present in both types of contacts. The TiB2-based Ohmic contacts displayed superior thermal stability, suggesting that it is a superior diffusion barrier at these temperatures than Ni.
Atomic layer deposited Al2O3 for gate dielectric and passivation layer of single-walled carbon nanotube transistors
Authors: Kim S. K. , Xuan Y. , Ye P. D. , Mohammadi S. , Back J. H. , Shim Moonsub
Published: April 2007

High performance single-walled carbon nanotube field effect transistors (SWCNT-FETs) fabricated with thin atomic layer deposited (ALD) Al2O3 as gate dielectrics and passivation layer are demonstrated. A 1.5μm gate-length SWCNT-FETs with 15nm thick Al2O3 insulator shows a gate leakage current below 10−11A at −2.5V<Vg<+7V, a subthreshold swing of S∼105mV∕decade, and a maximum on current of −12μA at a reverse gate bias of −1V. Lack of hysteresis in IV characteristics and low low frequency noise indicate high quality oxide-nanotube interface achieved utilizing ALD Al2O3 as gate dielectrics and passivation layer.
Coherence properties of high-β elliptical semiconductor micropillar lasers
Authors: Ates S. , Ulrich S. M. , Michler P. , Reitzenstein S. , Löffler A. , Forchel A.
Published: April 2007

The authors report complementary investigations on the coherence properties of spontaneous and stimulated emission from (In,Ga)As∕GaAs quantum-dot-based high-quality semiconductor micropillar cavities. Low temperature microphotoluminescence measurements on an elliptically shaped micropillar revealed a clear polarization splitting (ΔE∼45μeV) of its fundamental mode. Full conformity is found with an oscillatory behavior observed in corresponding g(1)(τ) first-order field correlation measurements. In addition, power-dependent g(1)(τ) series on a single polarization component of the lasing mode have systematically revealed a strong coherence time increase from τc∼25to∼430ps, which traces the change of emission characteristics from thermal to coherent light.
Element-specific spin and orbital momentum dynamics of Fe∕Gd multilayers
Authors: Bartelt A. F. , Comin A. , Feng J. , Nasiatka J. R. , Eimüller T. , Ludescher B. , Schütz G. , Padmore H. A. , Young A. T. , Scholl A.
Published: April 2007

The role of orbital magnetism in the laser-induced demagnetization of Fe∕Gd multilayers was investigated using time-resolved x-ray magnetic circular dichroism at 2ps time resolution given by an x-ray streak camera. An ultrafast transfer of angular momentum from the spin via the orbital momentum to the lattice was observed which was characterized by rapidly thermalizing spin and orbital momenta. Strong interlayer exchange coupling between Fe and Gd led to a simultaneous demagnetization of both layers.
Observation of mass analyzed threshold ionization using synchrotron radiation on a new-style time of flight mass spectrometer
Authors: Zhang Song , Wang Yanmei , Cao Zhenzhou , Zhang Bing , Wang Sisheng , Kong Ruihong , Zhao Yujie , Shan Xiaobing , Sheng Liusi
Published: April 2007

We have developed an efficient and applicable apparatus that combines mass-analyzed threshold ionization (MATI) with continuous molecular-beam mass spectrometry using tunable vacuum ultraviolet synchrotron radiation at National Synchrotron Radiation Laboratory. The new design, in which the spoiling field and the pulsed ionization field are perpendicular to each other, can obtain efficiently the ionic spectra of molecule. The MATI spectra of Ar and N2 have been recorded in the energy region between 15.5 and 17.5eV to illustrate the feasibility of this scheme. With its unique features, the important experiment considerations are potentially a powerful tool for study of information of ionization energies and ionic states of complex organic compounds.
Trace metals and sulfur in soils and forage of a chronic wasting disease locus
Authors: McBride M. B.
Published: April 2007

Environmental context. Chronic wasting disease (CWD) and other ‘prion’ diseases tend to cluster geographically, a characteristic that may indicate environmental risk factors, yet the biogeochemical features of regions with high prion disease incidence have rarely been investigated. This study, presenting soil, water and forage trace element analyses for a CWD cluster in Wisconsin, suggests that trace metal toxicity is unlikely to be a disease factor, but further indicates that willow browse could present a risk for copper deficiency in deer owing to high foliar sulfur concentrations. As copper deficiency leads to impaired immune function, it is hypothesised that the risk for CWD could be increased in environments where deer browse willow heavily. Abstract. In an effort to determine whether incidence of chronic wasting disease (CWD) in wild cervids is linked to biogeochemical risk factors of affected regions, soils, plants and surface waters in the Mt Horeb, Wisconsin CWD cluster were sampled and analysed for trace metals as well as major elements. The results revealed normal (relatively low) levels of trace metals in the soils, water and most plants, with no evidence of widespread heavy metal contamination in this region. It was concluded that incidence of CWD in Mt Horeb is unlikely to be linked to abnormally high concentrations of potentially zootoxic metals, including Pb, Zn, Cd or Mn, in soils waters or forages of the region. However, shrub willow, a common browse plant in the area, had high S levels in its leaves compared with other potential forage plants. Bioaccumulation of S was species-specific, with one willow species in particular (Salix exigua) having high foliar S in comparison with other species both in controlled greenhouse experiments as well as in the field near Mt Horeb. The willow S concentrations in the Mt Horeb CWD locus, averaging in excess of 4500 mg kg–1 in 2003 and remaining high in 2004, were high enough to have contributed to hypocuprosis in deer, and possibly to have caused polioencephalomalacia (PEM). It is hypothesised that conditions favourable to intensive deer browsing on shrub willow may exist periodically in Mt Horeb, leading to hypocuprosis and increased susceptibility to CWD.
Integrated air-quality monitoring - combined use of measurements and models in monitoring programmes
Authors: Hertel Ole , Ellermann Thomas , Palmgren Finn , Berkowicz Ruwim , Løfstrøm Per , Frohn Lise Marie , Geels Camilla , Skjøth Carsten Ambelas , Brandt Jørgen , Christensen Jesper , Kemp Kåre , Ketzel Matthias
Published: April 2007

Environmental context. Optimisation of allocated resources, improved quality, and better understanding of processes – these are the main advantages of applying integrated monitoring (IM). The paper describes IM as a combination of air pollution measuring and modelling, and describes how it is implemented in air-quality management in Denmark. However, the IM concept may also be applied to follow air-quality levels in other countries that currently do not have a corresponding system. It may also be applied to the environmental monitoring of other compartments.
Abstract. Integrated air-quality monitoring (IM) is here defined as monitoring based on the combination of results of atmospheric measurements from usually fixed site stations, and results obtained from calculations with air-quality models. This paper outlines experience from the use of IM at the National Environmental Research Institute (NERI) within the two nationwide air-quality monitoring programmes for the Danish urban and rural environments, respectively. The measurements in these Danish monitoring programmes are used to determine actual levels and trends in pollutant concentrations and depositions of pollutants. The measurements are further used for process understanding, and for the development and validation of air-quality models. The results from the air-quality models are used in the interpretation of measurements, but they are also used to provide information about, for example, source apportionment. The model calculations are used to extend the geographical coverage of the monitoring, and to provide information about pollution loads at locations or regions that are not well covered by the limited number of measurement stations in the monitoring programmes. Finally, the air-quality models are applied to carry out scenario studies of future pollution loads, e.g. assessment of the effects of various emission reduction strategies. NERI operates and holds the overall responsibility for the Danish air-quality monitoring programmes. These monitoring programmes are designed to fulfil the Danish obligations in relation to the EU directives on air quality, as well as the Danish obligations in relation to the reporting of data to international organisations (EMEP, HELCOM, OSPARCOM, and WHO). The obtained results from the use of IM form the basis for the national assessment of the air pollution loads in relation to protection of the aquatic and terrestrial environment; in these assessments the use of IM plays a central role.
Organic complexation of copper in deep-sea hydrothermal vent systems
Authors: Sander Sylvia G. , Koschinsky Andrea , Massoth Gary , Stott Matthew , Hunter Keith A.
Published: April 2007

Environmental context. Deep-sea hydrothermal vents represent a natural habitat for many extremophile organisms able to cope with extreme physical and chemical conditions, including high loads of heavy metals and reduced gases. To date, no information is available on the level and role of organic complexation of metals in these systems, which will have consequences on the bioavailability and precipitation or mineralisation of metals. In this work, we give evidence for the presence of organic molecules, including thiols, capable of forming complexes with copper strong enough to compete against sulfide present at high levels in hydrothermal systems. Abstract. Here we report, for the first time, that strong organic complexation plays an important role in the chemical speciation of copper in hydrothermal vent systems including medium temperature outlets, diffuse vents with an adjacent hydrothermal biocommunity, and local mixing zone with seawater. Samples from three deep-sea hydrothermal vent areas show a wide concentration range of organic copper-binding ligands, up to 4000 nM, with very high conditional stability constants (log K′Cu′L = 12.48 to 13.46). Measurements were usually made using voltammetric methods after removal of sulfide species under ambient seawater conditions (pH 7.8), but binding still occurs at pH 4.5 and 2.1. The voltammetric behaviour of our hydrothermal samples is compared with that of glutathione (GSH) a known strong Cu-binding ligand, as a representative of an organic thiol. Our results provide compelling evidence for the presence of organic ligands, including thiols, which form complexes strong enough to play an important role in controlling the bioavailability and geochemical behaviour of metal ions around hydrothermal vents.
Resveratrol stimulates AMP kinase activity in neurons
Authors: Dasgupta Biplab , Milbrandt Jeffrey
Published: April 2007

Resveratrol is a polyphenol produced by plants that has multiple beneficial activities similar to those associated with caloric restriction (CR), such as increased life span and delay in the onset of diseases associated with aging. CR improves neuronal health, and the global beneficial effects of CR have been postulated to be mediated by the nervous system. One key enzyme thought to be activated during CR is the AMP-activated kinase (AMPK), a sensor of cellular energy levels. AMPK is activated by increases in the cellular AMP:ATP ratio, whereupon it functions to help preserve cellular energy. In this regard, the regulation of dietary food intake by hypothalamic neurons is mediated by AMPK. The suppression of nonessential energy expenditure by activated AMPK along with the CR mimetic and neuroprotective properties of resveratrol led us to hypothesize that neuronal activation of AMPK could be an important component of resveratrol activity. Here, we show that resveratrol activated AMPK in Neuro2a cells and primary neurons
in vitro
as well as in the brain. Resveratrol and the AMPK-activating compound 5-aminoimidazole-4-carboxamide-1-β-
d
-ribofuranoside (AICAR) promoted robust neurite outgrowth in Neuro2a cells, which was blocked by genetic and pharmacologic inhibition of AMPK. Resveratrol also stimulated mitochondrial biogenesis in an AMPK-dependent manner. Resveratrol-stimulated AMPK activity in neurons depended on LKB1 activity but did not require the NAD-dependent protein deacetylase SIRT1 during this time frame. These findings suggest that neuronal activation of AMPK by resveratrol could affect neuronal energy homeostasis and contribute to the neuroprotective effects of resveratrol.
Accumulation of NFAT mediates IL-2 expression in memory, but not naïve, CD4+T cells
Authors: Dienz Oliver , Eaton Sheri M. , Krahl Troy J. , Diehl Sean , Charland Colette , Dodge John , Swain Susan L. , Budd Ralph C. , Haynes Laura , Rincon Mercedes
Published: April 2007

In contrast to naïve CD4+T cells, memory CD4+T cells rapidly express high levels of effector cytokines in response to antigen stimulation. The molecular mechanism for this specific behavior is not well understood. The nuclear factor of activated T cells (NFAT) family of transcription factors plays an important role in the transcription of many cytokine genes. Here we show that memory CD4+T cells rapidly induce NFAT-mediated transcription upon T cell receptor ligation whereas NFAT activation in naïve CD4+T cells requires longer periods of stimulation. The difference in kinetics correlates with the low levels of NFATc1 and NFATc2 proteins present in naïve CD4+T cells and their high levels in memory CD4+T cells. Accordingly, IL-2 expression requires NFAT activation only in memory CD4+T cells whereas it is NFAT-independent in naïve CD4+T cells. Thus, the accumulation of NFATc1 and NFATc2 in memory CD4+T cells represents a previously uncharacterized regulatory mechanism for the induction of early gene expression after antigen stimulation.
Bacteriophage N4 virion RNA polymerase interaction with its promoter DNA hairpin
Authors: Davydova Elena K. , Santangelo Thomas J. , Rothman-Denes Lucia B.
Published: April 2007

Bacteriophage N4 minivirion RNA polymerase (mini-vRNAP), the RNA polymerase (RNAP) domain of vRNAP, is a member of the T7-like RNAP family. Mini-vRNAP recognizes promoters that comprise conserved sequences and a 3-base loop–5-base pair (bp) stem DNA hairpin structure on single-stranded templates. Here, we defined the DNA structural and sequence requirements for mini-vRNAP promoter recognition. Mini-vRNAP binds a 20-nucleotide (nt) N4 P2 promoter deoxyoligonucleotide with high affinity (
K
d
= 2 nM) to form a salt-resistant complex. We show that mini-vRNAP interacts specifically with the central base of the hairpin loop (−11G) and a base at the stem (−8G) and that the guanine 6-keto and 7-imino groups at both positions are essential for binding and complex salt resistance. The major determinant (−11G), which must be presented to mini-vRNAP in the context of a hairpin loop, appears to interact with mini-vRNAP Trp-129. This interaction requires template single-strandedness at positions −2 and −1. Contacts with the promoter are disrupted when the RNA product becomes 11–12 nt long. This detailed description of vRNAP interaction with its promoter hairpin provides insights into RNAP–promoter interactions and explains how the injected vRNAP, which is present in one or two copies, recognizes its promoters on a single copy of the injected genome.
Disruption of innate immunity due to mitochondrial targeting of a picornaviral protease precursor
Authors: Yang Yan , Liang Yuqiong , Qu Lin , Chen Zeming , Yi MinKyung , Li Kui , Lemon Stanley M.
Published: April 2007

Mitochondrial antiviral signaling protein (MAVS) is an essential component of virus-activated signaling pathways that induce protective IFN responses. Its localization to the outer mitochondrial membrane suggests an important yet unexplained role for mitochondria in innate immunity. Here, we show that hepatitis A virus (HAV), a hepatotropic picornavirus, ablates type 1 IFN responses by targeting the 3ABC precursor of its 3C
pro
cysteine protease to mitochondria where it colocalizes with and cleaves MAVS, thereby disrupting activation of IRF3 through the MDA5 pathway. The 3ABC cleavage of MAVS requires both the protease activity of 3C
pro
and a transmembrane domain in 3A that directs 3ABC to mitochondria. Lacking this domain, mature 3C
pro
protease is incapable of MAVS proteolysis. HAV thus disrupts host signaling by a mechanism that parallels that of the serine NS3/4A protease of hepatitis C virus, but differs in its use of a stable, catalytically active polyprotein processing intermediate. The unique requirement for mitochondrial localization of 3ABC underscores the importance of mitochondria to host control of virus infections within the liver.
Molecular basis of coiled-coil formation
Authors: Steinmetz Michel O. , Jelesarov Ilian , Matousek William M. , Honnappa Srinivas , Jahnke Wolfgang , Missimer John H. , Frank Sabine , Alexandrescu Andrei T. , Kammerer Richard A.
Published: April 2007

Coiled coils have attracted considerable interest as design templates in a wide range of applications. Successful coiled-coil design strategies therefore require a detailed understanding of coiled-coil folding. One common feature shared by coiled coils is the presence of a short autonomous helical folding unit, termed “trigger sequence,” that is indispensable for folding. Detailed knowledge of trigger sequences at the molecular level is thus key to a general understanding of coiled-coil formation. Using a multidisciplinary approach, we identify and characterize here the molecular determinants that specify the helical conformation of the monomeric early folding intermediate of the GCN4 coiled coil. We demonstrate that a network of hydrogen-bonding and electrostatic interactions stabilize the trigger-sequence helix. This network is rearranged in the final dimeric coiled-coil structure, and its destabilization significantly slows down GCN4 leucine zipper folding. Our findings provide a general explanation for the molecular mechanism of coiled-coil formation.
An instrument for direct observations of seismic and normal-mode rotational oscillations of the Earth
Authors: Cowsik R.
Published: April 2007

The rotations around the vertical axis associated with the normal mode oscillations of the Earth and those induced by the seismic and other disturbances have been very difficult to observe directly. Such observations will provide additional information for 3D modeling of the Earth and for understanding earthquakes and other underground explosions. In this paper, we describe the design of an instrument capable of measuring the rotational motions associated with the seismic oscillations of the Earth, including the lowest frequency normal mode at ν ≈ 3.7 × 10
−4
Hz. The instrument consists of a torsion balance with a natural frequency of ν
0
≈ 1.6 × 10
−4
Hz, which is observed by an autocollimating optical lever of high angular resolution and dynamic range. Thermal noise limits the sensitivity of the apparatus to amplitudes of ≈ 1.5 × 10
−9
rad at the lowest frequency normal mode and the sensitivity improves as ν
−3/2
with increasing frequency. Further improvements in sensitivity by about two orders of magnitude may be achieved by operating the balance at cryogenic temperatures. Alternatively, the instrument can be made more robust with a reduced sensitivity by increasing ν
0
to ≈10
−2
Hz. This instrument thus complements the ongoing effort by Igel and others to study rotational motions using ring laser gyroscopes and constitutes a positive response to the clarion call for developments in rotation seismology by Igel, Lee, and Todorovska [H. Igel, W.H.K. Lee and M.I. Todorovska, AGU Fall Meeting 2006, Rotational Seismology Sessions: S22A,S23B,
Inauguration of the International Working Group on Rotational Seismology (IWGoRS)
].
The dynein light chain 8 binding motif of rabies virus phosphoprotein promotes efficient viral transcription
Authors: Tan Gene S. , Preuss Mirjam A. R. , Williams John C. , Schnell Matthias J.
Published: April 2007

Recent studies indicate that the interaction between rabies virus (RV) phosphoprotein and the dynein light chain 8 (LC8) is essential for RV pathogenesis. Through its association with the dynein motor complex, LC8 has been suggested as a molecular factor that links the viral ribonucleoprotein to the host cell transport system. Recent structural investigations, however, dispute this model. To understand the role of LC8 in RV pathogenesis, we generated recombinant RVs with or without the LC8 binding domain (LC8-BD) deleted from the RV phosphoprotein. Peripheral infection of adult mice showed that removal of the LC8-BD did not inhibit entry into the CNS, although it prevented onset of RV-induced CNS disease. However, deletion of the LC8-BD significantly attenuated viral transcription and replication in the CNS. Studies in RAG2 knockout (KO) mice infected with the same recombinant RVs confirmed this finding and indicated that the adaptive immune system is not a factor in the attenuation of viral replication early in the infection. In cell culture, the deletion of the LC8-BD greatly attenuated growth on neuronal cells whereas the growth pattern on nonneuronal cells remained unchanged. However, deletion of the LC8-BD did not affect production of RV virions. We provide evidence that removal of the LC8-BD decreases primary transcription. In this study, we propose that LC8 does not play a role in the retrograde axonal transport of RV and that the deletion of the LC8-BD impairs the infectivity of the virions by reducing early transcription and replication in neurons.
Environmental effects on parasitic disease transmission exemplified by schistosomiasis in western China
Authors: Liang Song , Seto Edmund Y. W. , Remais Justin V. , Zhong Bo , Yang Changhong , Hubbard Alan , Davis George M. , Gu Xueguang , Qiu Dongchuan , Spear Robert C.
Published: April 2007

Environmental effects on the transmission of many parasitic diseases are well recognized, but the role of specific factors like climate and agricultural practices in modulating transmission is seldom characterized quantitatively. Based on studies ofSchistosoma japonicumtransmission in irrigated agricultural environments in western China, a mathematical model was used to quantify environmental impacts on transmission intensity. The model was calibrated by using field data from intervention studies in three villages and simulated to predict the effects of alternative control options. Both the results of these interventions and earlier epidemiological findings confirm the central role of environmental factors, particularly those relating to snail habitat and agricultural and sanitation practices. Moreover, the findings indicate the inadequacy of current niclosamide-praziquantel strategies alone to achieve sustainable interruption of transmission in some endemic areas. More generally, the analysis suggests a village-specific index of transmission potential and how this potential is modulated by time-varying factors, including climatological variables, seasonal water-contact patterns, and irrigation practices. These time-variable factors, a village's internal potential, and its connectedness to its neighbors provide a framework for evaluating the likelihood of sustained schistosomiasis transmission and suggest an approach to quantifying the role of environmental factors for other parasitic diseases.
Vitellogenin, juvenile hormone, insulin signaling, and queen honey bee longevity
Authors: Corona Miguel , Velarde Rodrigo A. , Remolina Silvia , Moran-Lauter Adrienne , Wang Ying , Hughes Kimberly A. , Robinson Gene E.
Published: April 2007

In most animals, longevity is achieved at the expense of fertility, but queen honey bees do not show this tradeoff. Queens are both long-lived and fertile, whereas workers, derived from the same genome, are both relatively short-lived and normally sterile. It has been suggested, on the basis of results from workers, that vitellogenin (Vg), best known as a yolk protein synthesized in the abdominal fat body, acts as an antioxidant to promote longevity in queen bees. We explored this hypothesis, as well as related roles of insulin–IGF-1 signaling and juvenile hormone.
Vg
was expressed in thorax and head fat body cells in an age-dependent manner, with old queens showing much higher expression than workers. In contrast,
Vg
expression in worker head was much lower. Queens also were more resistant to oxidative stress than workers. These results support the hypothesis that caste-specific differences in
Vg
expression are involved in queen longevity. Consistent with predictions from
Drosophila
, old queens had lower head expression of
insulin-like peptide
and its putative receptors than did old workers. Juvenile hormone affected the expression of
Vg
and insulin–IGF-1 signaling genes in opposite directions. These results suggest that conserved and species-specific mechanisms interact to regulate queen bee longevity without sacrificing fecundity.
Derepression of the NC80 motif is critical for the photoactivation of
Arabidopsis
CRY2
Authors: Yu Xuhong , Shalitin Dror , Liu Xuanming , Maymon Maskit , Klejnot John , Yang Hongyun , Lopez Javier , Zhao Xiaoying , Bendehakkalu Krishnaprasad T. , Lin Chentao
Published: April 2007

Cryptochromes are blue light receptors that regulate photomorphogenesis in plants and the circadian clock in animals and plants.
Arabidopsis
cryptochrome 2 (CRY2) mediates blue light inhibition of hypocotyl elongation and photoperiodic control of floral initiation. CRY2 undergoes blue light-induced phosphorylation, which was hypothesized to be associated with CRY2 photoactivation. To further investigate how light activates CRY2, we analyzed the physiological activities and phosphorylation of various CRY2 fusion proteins in transgenic plants. Our results showed that an 80-residue motif, referred to as NC80, was sufficient to confer the physiological function of CRY2. The GUS-NC80 fusion protein expressed in transgenic plants is constitutively active but unphosphorylated, suggesting that the blue light-induced CRY2 phosphorylation causes a conformational change to derepress the NC80 motif. Consistent with this hypothesis, the CRY2 C-terminal tail was found to be required for the blue light-induced CRY2 phosphorylation but not for the CRY2 activity. We propose that the PHR domain and the C-terminal tail of the unphosphorylated CRY2 form a “closed” conformation to suppress the NC80 motif in the absence of light. In response to blue light, the C-terminal tail of CRY2 is phosphorylated and electrostatically repelled from the surface of the PHR domain to form an “open” conformation, resulting in derepression of the NC80 motif and signal transduction to trigger photomorphogenic responses.
Evolutionary dynamics of olfactory receptor genes inDrosophilaspecies
Authors: Nozawa Masafumi , Nei Masatoshi
Published: April 2007

Olfactory receptor (OR) genes are of vital importance for animals to find food, identify mates, and avoid dangers. In mammals, the number of OR genes is large and varies extensively among different orders, whereas, in insects, the extent of interspecific variation appears to be small, although only a few species have been studied. To understand the evolutionary changes of OR genes, we identified all OR genes from 12Drosophilaspecies, of which the evolutionary time is roughly equivalent to that of eutherian mammals. The results showed that all species examined have similar numbers (≈60) of functional OR genes. Phylogenetic analysis indicated that the ancestral species also had similar numbers of genes, but there were frequent gains and losses of genes that occurred in each evolutionary lineage. It appears that tandem duplication and random inactivation of duplicate genes are the major factors of gene number change. However, chromosomal rearrangements have contributed to the establishment of genome-wide distribution of OR genes. These results suggest that the repertoire of OR genes inDrosophilahas been quite stable compared with the mammalian genes. The difference in evolutionary pattern betweenDrosophilaand mammals can be explained partly by the differences of gene expression mechanisms and partly by the environmental and behavioral differences.
Real-time control of the energy landscape by force directs the folding of RNA molecules
Authors: Li Pan T. X. , Bustamante Carlos , Tinoco Ignacio
Published: April 2007

The rugged folding-energy landscapes of RNAs often display many competing minima. How do RNAs discriminate among competing conformations in their search for the native state? By using optical tweezers, we show that the folding-energy landscape can be manipulated to control the fate of an RNA: individual RNA molecules can be induced into either native or misfolding pathways by modulating the relaxation rate of applied force and even be redirected during the folding process to switch from misfolding to native folding pathways. Controlling folding pathways at the single-molecule level provides a way to survey the manifold of folding trajectories and intermediates, a capability that previously was available only to theoretical studies.
Three-dimensional structures of the flagellar dynein–microtubule complex by cryoelectron microscopy
Authors: Oda Toshiyuki , Hirokawa Nobutaka , Kikkawa Masahide
Published: April 2007

The outer dynein arms (ODAs) of the flagellar axoneme generate forces needed for flagellar beating. Elucidation of the mechanisms underlying the chemomechanical energy conversion by the dynein arms and their orchestrated movement in cilia/flagella is of great importance, but the nucleotide-dependent three-dimensional (3D) movement of dynein has not yet been observed. In this study, we establish a new method for reconstructing the 3D structure of the in vitro reconstituted ODA–microtubule complex and visualize nucleotide-dependent conformational changes using cryoelectron microscopy and image analysis. As the complex went from the rigor state to the relaxed state, the head domain of the β heavy chain shifted by 3.7 nm toward the B tubule and inclined 44° inwards. These observations suggest that there is a mechanism that converts head movement into the axonemal sliding motion.
Early endosomes associated with dynamic F-actin structures are required for late trafficking of H. pylori VacA toxin
Authors: Gauthier Nils C. , Monzo Pascale , Gonzalez Teresa , Doye Anne , Oldani Amanda , Gounon Pierre , Ricci Vittorio , Cormont Mireille , Boquet Patrice
Published: April 2007

Glycosylphosphatidylinositol-anchored proteins (GPI-APs) are endocytosed by a clathrin- independent pathway into vesicles named GPI-AP–enriched early endosomal compartments (GEECs). We recently showed that the vacuolating toxin VacA secreted by Helicobacter pylori is endocytosed into the GEECs (Gauthier, N.C., P. Monzo, V. Kaddai, A. Doye, V. Ricci, and P. Boquet. 2005. Mol. Biol. Cell. 16:4852–4866). Unlike GPI-APs that are mostly recycled back to the plasma membrane, VacA reaches early endosomes (EEs) and then late endosomes (LEs), where vacuolation occurs.

In this study, we used VacA to study the trafficking pathway between GEECs and LEs. We found that VacA routing from GEECs to LEs required polymerized actin. During this trafficking, VacA was transferred from GEECs to EEs associated with polymerized actin structures. The CD2-associated protein (CD2AP), a docking protein implicated in intracellular trafficking, bridged the filamentous actin (F-actin) structures with EEs containing VacA. CD2AP regulated those F-actin structures and was required to transfer VacA from GEECs to LEs. These results demonstrate that sorting from GEECs to LEs requires dynamic F-actin structures on EEs.
A signal from inside the peroxisome initiates its division by promoting the remodeling of the peroxisomal membrane
Authors: Guo Tong , Gregg Christopher , Boukh-Viner Tatiana , Kyryakov Pavlo , Goldberg Alexander , Bourque Simon , Banu Farhana , Haile Sandra , Milijevic Svetlana , San Karen Hung Yeung , Solomon Jonathan , Wong Vivianne , Titorenko Vladimir I.
Published: April 2007

We define the dynamics of spatial and temporal reorganization of the team of proteins and lipids serving peroxisome division. The peroxisome becomes competent for division only after it acquires the complete set of matrix proteins involved in lipid metabolism. Overloading the peroxisome with matrix proteins promotes the relocation of acyl-CoA oxidase (Aox), an enzyme of fatty acid β-oxidation, from the matrix to the membrane. The binding of Aox to Pex16p, a membrane-associated peroxin required for peroxisome biogenesis, initiates the biosynthesis of phosphatidic acid and diacylglycerol (DAG) in the membrane. The formation of these two lipids and the subsequent transbilayer movement of DAG initiate the assembly of a complex between the peroxins Pex10p and Pex19p, the dynamin-like GTPase Vps1p, and several actin cytoskeletal proteins on the peroxisomal surface. This protein team promotes membrane fission, thereby executing the terminal step of peroxisome division.
Sending proteins to dense core secretory granules: still a lot to sort out
Authors: Dikeakos Jimmy D. , Reudelhuber Timothy L.
Published: April 2007

The intracellular sorting of peptide hormone precursors to the dense core secretory granules (DCSGs) is essential for their bioactivation. Despite the fundamental importance of this cellular process, the nature of the sorting signals for entry of proteins into DCSGs remains a source of vigorous debate. This review highlights recent discoveries that are consistent with a model in which several protein domains, acting in a cell-specific fashion and at different steps in the sorting process, act in concert to regulate the entry of proteins into DCSGs.