bluuebunny/crossref_metadata_2025 huggingface dataset:
Propagation of tsunami‐driven gravity waves into the thermosphere and ionosphere
Authors: Hickey M. P. , Schubert G. , Walterscheid R. L.
Published: August 2009

Recent observations have revealed large F‐region electron density perturbations (∼100%) and total electron content (TEC) perturbations (∼30%) that appear to be correlated with tsunamis. The characteristic speed and horizontal wavelength of the disturbances are ∼200 m/s and ∼400 km. We describe numerical simulations using our spectral full‐wave model (SFWM) of the upward propagation of a spectrum of gravity waves forced by a tsunami, and the interaction of these waves with the F‐region ionosphere. The SFWM describes the propagation of linear, steady‐state acoustic‐gravity waves in a nonisothermal atmosphere with the inclusion of eddy and molecular diffusion of heat and momentum, ion drag, Coriolis force, and height‐dependent mean winds. The tsunami is modeled as a deformation of our model lower boundary traveling at the shallow water wave speed of 200 m/s with a maximum vertical displacement of 50 cm and described by a modified Airy function in the horizontal direction. The derived vertical velocity spectrum at the surface describes the forcing at the lower boundary of the SFWM. A steady‐state 1‐D ionospheric perturbation model is used to calculate the electron density and TEC perturbations. The molecular diffusion strongly damps the waves in the topside (>300‐km altitude) ionosphere. In spite of this, the F‐region response is large, with vertical displacements of ∼2 to 5 km and electron density perturbations of ∼100%. Mean winds have a profound effect on the ability of the waves to propagate into the F‐region ionosphere.
Measurements of stray antenna capacitance in the STEREO/WAVES instrument: Comparison of the radio frequency voltage spectrum with models of the galactic nonthermal continuum spectrum
Authors: Eastwood J. P. , Bale S. D. , Maksimovic M. , Zouganelis I. , Goetz K. , Kaiser M. L. , Bougeret J.‐L.
Published: August 2009

The STEREO/WAVES instrument is designed to measure interplanetary radio emission and in situ plasma waves in the solar wind. The instrument uses three orthogonal monopole electric antennas as its sensor system in both a pseudodipole and monopole mode. At high radio frequencies, the capacitance of the antennas determines the system gain. Here we estimate the stray capacitance in the antenna system by comparing the measured voltage spectrum with a model of the galactic continuum spectrum, which is the instrument background at high frequencies. Together with the antenna free‐space capacitance, these measurements provide an absolute calibration of the STEREO/WAVES experiment at radio frequencies, a prerequisite for quantitative studies of solar and astrophysical radio emission.
Replication of Association Between a Common Variant Near Melanocortin‐4 Receptor Gene and Obesity‐related Traits in Asian Sikhs
Authors: Been Latonya F. , Nath Swapan K. , Ralhan Sarju K. , Wander Gurpreet S. , Mehra Narinder K. , Singh Jairup , Mulvihill John J. , Sanghera Dharambir K.
Published: August 2009

Recent genome‐wide association studies (GWAS) in Asian Indians reported strong associations of variants near melanocortin‐4 receptor (MC4R) and MLX interacting protein‐like (MLXIPL) genes with insulin resistance and several obesity‐related quantitative traits (QTs). Here, we evaluated the association of two variants (rs12970134 and rs4450508) near MC4R and a nonsynonymous (Gln241His) variant (rs3812316) in MLXIPL gene with type 2 diabetes (T2D) and obesity‐related QTs in our case–control cohort (n = 1,528; 745 T2D cases and 783 controls) from a Sikh population from North India. We have successfully replicated the association of MC4R (rs12970134) with BMI (P = 0.0005), total weight (WT) (P = 0.001), and waist circumference (WC) (P = 0.001). These associations remained significant after controlling for multiple testing by applying Bonferroni's correction. However, our data did not confirm the association of rs3812316 in the MLXIPL gene with triglyceride (TG) levels. These observations demonstrate that the genetic variation in MC4R locus can have a moderate contribution in the regional fat deposition and development of central obesity in Asian Indians.
Vibrationally Mediated Photodissociation
Authors: Rosenwaks Salman
Published: August 2009

Vibrationally Mediated Photodissociation (VMP) deals with the influence of vibrational excitation of the ground electronic state of a molecule on its dissociation following excitation of this state to a higher electronic state. Aimed at students and academics, this is the first book devoted to the effect of vibrational pre-excitation on molecular dynamics in the gas phase. In particular, it deals with the influence of this excitation on the dissociation of molecules (ie: on the branching ratio between the dissociation products and its dependence on the vibrational state being excited). The effect in the gas phase has been extensively studied, both theoretically and experimentally and encompasses diverse areas of chemical physics. This monograph presents the methodology of VMP, using state-of-the-art specific examples. Overviews of earlier works are included as well, to serve as a background for current research. Wherever appropriate, original works are quoted, including the original drawings. The contents include a brief review of theoretical and experimental methods relevant to VMP and specific examples. Also included are a bibliography, author and subject index. From the description of the motivation, the approach, the execution of the experiment and the analysis of the results of the specific examples, the reader will get a comprehensive understanding of the field. The book is aimed at senior undergraduate and graduate students of chemistry and physics. It serves as an introduction to VMP for beginners and as a literature guide to those acquainted with the subject but not necessarily working on VMP.
Inorganic Rings and Polymers of the p-Block Elements
Authors: Chivers Tristram , Manners Ian
Published: August 2009

Ring systems represent a very important branch of organic chemistry. Benzene is perhaps the pre-eminent example and provides the benchmark for the so-called aromatic character of cyclic systems. Cycloalkanes are another prominent class of organic compounds and these saturated ring systems form a homologous series known as alicyclics. Materials that are constructed from organic polymers such as polythene, polystyrene, polyisoprene (natural rubber) and polyvinyl chloride are common features of our daily lives. Most of these and related organic polymers are generated from acyclic precursors by free radical, anionic, cationic or organometallic polymerisation processes or by condensation reactions. The focus of this book is monocyclic inorganic ring systems of the p-block elements and the polymers that are, in many cases derived from them. Bicyclic or polycyclic arrangements are considered when they are closely related to those of monocyclic systems. Inorganic heterocycles that are more accurately described as coordination complexes of chelating inorganic ligands are included only when they are directly related to an inorganic homocycle or heterocycle by the replacement of one p-block element by a more metallic p-block element. After a short introductory chapter, the first half of the book is comprised of seven chapters that deal with the fundamentals of the subject intended for undergraduates or researchers who are unfamiliar with the topic, covering the following areas: - synthetic methods - characterisation techniques - delocalisation in inorganic rings - paramagnetic inorganic rings - inorganic macrocycles - ligand chemistry - inorganic polymers (general concepts including, synthesis, structure and bonding, characterisation methods, properties and applications) The final four chapters discuss in detail the chemistry of inorganic homo- and hetero-cycles involving the elements of groups 13-16 (the p-block elements). The focus is on relating the early seminal contributions to the field with exciting new developments. From the fundamental standpoint, novel structures and new bonding concepts are highlighted, in addition to synthetic approaches. This is the first book that addresses both the fundamental and applied aspects of inorganic ring systems through an emphasis of their use as precursors to inorganic polymers and other useful materials (e.g. semiconductors and ceramics). The book is intended primarily for senior undergraduates and graduate students in inorganic chemistry, as well research workers in the field of inorganic ring systems and polymers. At the undergraduate level it serves as a supplementary text to the more general inorganic chemistry text books and at the graduate level it would be the text of choice for a course in the area of inorganic rings and polymers.
Evolution of vertebrate glucokinase regulatory protein from a bacterial N-acetylmuramate 6-phosphate etherase
Authors: Veiga-da-Cunha Maria , Sokolova Tatiana , Opperdoes Fred , Van Schaftingen Emile
Published: August 2009

Mammalian GKRP [GK (glucokinase) regulatory protein], a fructose 6-phosphate and fructose 1-phosphate sensitive inhibitor of GK, appears to have resulted from the duplication of a gene similar to bacterial N-acetylmuramate 6-phosphate etherase MurQ. In the present study, we show that several genomes of primitive eukaryotes encode a GKRP-like protein with two MurQ repeats. Recombinant Haemophilus influenzae MurQ and the GKRP homologue of the amoeboflagellate Naegleria gruberi both behaved as excellent N-acetylmuramate 6-phosphate etherases, with Kcat values (83 and 20 s−1) at least as high as that reported for Escherichia coli MurQ. In contrast, rat and Xenopus GKRP displayed much lower etherase activities (Kcat=0.08 and 0.05 s−1 respectively). The etherase activity of rat GKRP was inhibited by ligands (fructose 6-phosphate, fructose 1-phosphate and sorbitol 6-phosphate) known to regulate its interaction with GK and by mutations affecting the binding of these phosphate esters. This indicated that these phosphate esters all bind to a single regulatory site, which evolved from the original catalytic site. Sorbitol 6-phosphate and other phosphate esters also inhibited the etherase activity of Xenopus GKRP, but did not affect its ability to inhibit GK. Thus, unlike what was previously thought, Xenopus GKRP has a binding site for phosphate esters, but this site is uncoupled from the GK-binding site. Taken together, these data indicate that duplication of the murQ gene led to a eukaryotic-type etherase, which subsequently evolved to GKRP by acquiring a new binding specificity while losing most of its etherase activity.
Enhancement of transport from drops by steady and modulated electric fields
Authors: Christov C. I. , Homsy G. M.
Published: August 2009

We consider the problem of transport of heat or mass from circulating droplets that are both settling and subject to an axial electric field. The electric field can be either steady or oscillatory in time and drives an electrohydrodynamic flow, called the Taylor circulation, which augments the Hadamard circulation caused by steady translation. The problem is governed by four dimensionless groups: the Peclet number Pe, the dimensionless amplitudes of both the steady and unsteady electric field, and the dimensionless frequency ω of the modulation. The convective diffusion equation is solved numerically by an efficient finite-difference scheme that allows a wide range of parameters—in particular, very large Peclet numbers—to be covered. The results are characterized by the asymptotic rate of extraction of heat or mass from the droplet, which is found to be exponential in time. The enhancement factor, defined as the ratio of this rate to that of a stagnant drop, is studied as a function of parameters. For steady drops, we find that transport remains diffusion controlled, but the enhancement factor is significantly higher with the Taylor flow than without. For modulated electric field the enhancement factor is not a simple function of parameters and exhibits spectral “resonant peaks” at particular values of ω for which the enhancement factor is extremely large. Movies of the simulations are used to study the underlying time-periodic spatial structures of the concentration field (so-called strange eigenmodes) and the complex time dependence that is responsible for these resonances.
Bethe ansatz approach to quench dynamics in the Richardson model
Authors: Faribault Alexandre , Calabrese Pasquale , Caux Jean-Sébastien
Published: August 2009

By instantaneously changing a global parameter in an extended quantum system, an initially equilibrated state will afterwards undergo a complex nonequilibrium unitary evolution whose description is extremely challenging. A nonperturbative method giving a controlled error in the long time limit remained highly desirable to understand general features of the quench induced quantum dynamics. In this paper we show how integrability (via the algebraic Bethe ansatz) gives one numerical access, in a nearly exact manner, to the dynamics resulting from a global interaction quench of an ensemble of fermions with pairing interactions (Richardson’s model). This possibility is deeply linked to the specific structure of this particular integrable model which gives simple expressions for the scalar product of eigenstates of two different Hamiltonians. We show how, despite the fact that a sudden quench can create excitations at any frequency, a drastic truncation of the Hilbert space can be carried out therefore allowing access to large systems. The small truncation error which results does not change with time and consequently the method grants access to a controlled description of the long time behavior which is a hard to reach limit with other numerical approaches.
Quantitative nanoscale monitoring the effect of annealing process on the morphology and optical properties of poly(3-hexylthiophene)/[6,6]-phenyl C61-butyric acid methyl ester thin film used in photovoltaic devices
Authors: Huang Yu-Ching , Chuang Shang-Yu , Wu Ming-Chung , Chen Hsuen-Li , Chen Chun-Wei , Su Wei-Fang
Published: August 2009

We have studied the nanoscale changes in morphology and optical properties during annealing for bulk-heterojunction poly(3-hexylthiophene) (P3HT) and [6,6]-phenyl C61-butyric acid methyl ester (PCBM) composite film. Thermal atomic force microscopy was used to monitor the morphology evolution of the film in situ quantitatively, which showed a migration and aggregation of PCBM with increasing temperature. Scanning near-field microscopy was used to investigate the quantitative changes in absorption behavior of the film in nanoscale with increasing annealing time at 140 °C, which indicated that the extent of absorption of the film was increased with increasing annealing time. However, a large PCBM aggregate (1 μm) was formed after the film annealed at 140 °C for 1 h. The aggregate interrupted the bicontinous morphology of the film and further affected the absorption behavior in nanoscale. Furthermore, the refractive index and extinction coefficient of the films increased after annealed 30 min at 140 °C, but decreased after an extended annealing for 60 min. The increase in optical properties indicated the film achieving a highly ordered structure upon heating. The results suggested that an optimized annealing process was at 140 °C for 30 min. Finally, devices with different annealing times at 140 °C were fabricated and evaluated. The highest charge mobility and power conversion efficiency of the device were fabricated as suggested annealing conditions. The nanoscale monitoring of the P3HT/PCBM film has been found to be very useful to determine the optimized annealing conditions for high efficiency photovoltaic device.
Defect structure in Mg-doped LiNbO3: Revisited study
Authors: Abdi F. , Aillerie M. , Bourson P. , Fontana M. D.
Published: August 2009

We present and discuss the mechanism of incorporation of Mg ions in congruent lithium niobate where we assume the coexistence of both lithium and niobium vacancies induced for charge compensation. This model is supported by the site spectroscopy afforded by Raman scattering data. The dependence of the concentration of various intrinsic defects, derived from this description is then compared with corresponding experimental data. In particular this comparison shows that the Li and vacancy contents as well as the crystal density show similar behaviors versus Mg concentration, which reinforces the validity of our description.
Acoustic levitator for structure measurements on low temperature liquid droplets
Authors: Weber J. K. R. , Rey C. A. , Neuefeind J. , Benmore C. J.
Published: August 2009

A single-axis acoustic levitator was constructed and used to levitate liquid and solid drops of 1–3 mm in diameter at temperatures in the range −40 to +40 °C. The levitator comprised (i) two acoustic transducers mounted on a rigid vertical support that was bolted to an optical breadboard, (ii) an acoustic power supply that controlled acoustic intensity, relative phase of the drive to the transducers, and could modulate the acoustic forces at frequencies up to 1 kHz, (iii) a video camera, and (iv) a system for providing a stream of controlled temperature gas flow over the sample. The acoustic transducers were operated at their resonant frequency of ∼22 kHz and could produce sound pressure levels of up to 160 dB. The force applied by the acoustic field could be modulated to excite oscillations in the sample. Sample temperature was controlled using a modified Cryostream Plus and measured using thermocouples and an infrared thermal imager. The levitator was installed at x-ray beamline 11 ID-C at the Advanced Photon Source and used to investigate the structure of supercooled liquids.
Relativistic laser piston model: Ponderomotive ion acceleration in dense plasmas using ultraintense laser pulses
Authors: Schlegel T. , Naumova N. , Tikhonchuk V. T. , Labaune C. , Sokolov I. V. , Mourou G.
Published: August 2009

Laser ponderomotive force at superhigh intensities provides an efficient ion acceleration in bulk dense targets and evacuates a channel enabling further laser beam propagation. The developed quasistationary model of a laser piston—a double layer structure supported by the radiation pressure—predicts the general parameters of the acceleration process in homogeneous and inhomogeneous overdense plasmas. Particle-in-cell simulations confirm the estimated characteristics in a wide range of laser intensities and ion densities and show advantages of circularly polarized laser pulses. Two nonstationary effects are identified in the simulations. First, oscillations of the piston velocity and of the thickness of the ion charge separation layer broaden the energy spectrum of accelerated ions. Second, the electrons accelerated toward the incoming laser wave emit strong high-frequency radiation, enabling a cooling effect, which helps to sustain high charge neutrality in the piston and to maintain an efficient ion acceleration.
Spontaneous high-speed transport of subnanoliter water droplet on gradient nanotextured surfaces
Authors: Khoo Hwa Seng , Tseng Fan-Gang
Published: August 2009

We present water droplets that undergo spontaneous self-directed motion upon contact with a chemically patterned nanotextured surface with wedge-shaped gradient. The surface exhibits two distinct wetting properties and low hysteresis. The droplet velocity depends on the droplet position and gradient angle. A wide range of droplet volume can be transported and a droplet velocity as high as 0.5 m/s has been achieved herein. Ascension of water droplets with all-round acclivity and a subnanoliter droplet movement were also demonstrated. We conclude that it is the combination of surface tension gradient and nanowetting actuation that governs the droplet motion.
Analytic gradients for the state-specific multireference coupled cluster singles and doubles model
Authors: Prochnow Eric , Evangelista Francesco A. , Schaefer Henry F. , Allen Wesley D. , Gauss Jürgen
Published: August 2009

The general theory of analytic energy gradients is presented for the state-specific multireference coupled cluster method introduced by Mukherjee and co-workers [Mol. Phys. 94, 157 (1998)], together with an implementation within the singles and doubles approximation, restricted to two closed-shell determinants and Hartree–Fock orbitals. Expressions for the energy gradient are derived based on a Lagrangian formalism and cast in a density-matrix notation suitable for implementation in standard quantum-chemical program packages. In the present implementation, we exploit a decomposition of the multireference coupled cluster gradient expressions, i.e., lambda equations and the corresponding density matrices, into a so-called single-reference part for each reference determinant and a coupling term. Our implementation exhibits the proper scaling, i.e., O(dN6) with d as the number of reference determinants and N as the number of orbitals, and it is thus suitable for large-scale applications. The applicability of our multireference coupled cluster gradients is illustrated by computations for the equilibrium geometry of the 2,6-isomers of pyridyne and the pyridynium cation. The results are compared to those from single-reference coupled cluster calculations and are discussed with respect to the future perspectives of multireference coupled cluster theory.
Photovoltaic cells fabricated utilizing core-shell CdSe/ZnSe quantum dot/multiwalled carbon nanotube heterostructures
Authors: Li Fushan , Son Dong Ick , Kim Tae Whan , Ryu Euidock , Kim Sang Wook , Lee Sun Kyun , Cho Yong Hoon
Published: August 2009

An efficient quenching of the photoluminescence spectrum was observed for the quantum dot (QD)-multiwalled carbon nanotubes (MWCNTs) nanocomposite. While the lifetime of the blue emission from ZnSe shell was significantly reduced, it did not exhibit any obvious change in the red emission from CdSe core-crystal. This difference revealed two competing charge transfer processes between the CdSe core-crystal, the ZnSe shell and the MWCNTs. Current-voltage measurements on devices fabricated utilizing CdSe QD-MWCNT nanocomposites showed photovoltaic (PV) effect under ultraviolet light illumination. Charge transfer mechanisms of the PV cells are described on the basis of the experimental results.
Dependence of anisotropic surface plasmon lifetimes of two-dimensional hole arrays on hole geometry
Authors: Hui K. C. , Wan J. T. K. , Xu J. B. , Ong H. C.
Published: August 2009

The dependences of surface plasmon lifetimes of two-dimensional Au hole arrays on aspect ratio, hole length, and depth have been studied by angle-dependent reflectivity. Long lifetimes can be obtained from the arrays by reducing the hole length and depth and increasing the aspect ratio. In addition, our results can be qualitatively discussed under the framework of coupled-charge model, indicating the interaction between holes can lead to an increase of surface plasmon lifetime. We believe such interaction can find applications in biosensing such as surface plasmon resonance spectroscopy.
Optimizing the hyperpolarizability tensor using external electromagnetic fields and nuclear placement
Authors: Watkins David S. , Kuzyk Mark G.
Published: August 2009

We investigate the effects of an external electric and magnetic field on the first hyperpolarizability tensor of a quantum system, such as a molecule or nanoparticle, whose nonlinear response is well below the fundamental limit. We find that the intrinsic hyperpolarizability is optimized when the applied electric and magnetic fields are comparable to the internal molecular fields. Indeed, the nonlinear response is just as large for an electron in the presence of the external field without the nuclei as it is for an electron bound to a molecule and in the presence of the applied field. We find that all combinations of fields and molecular structures that optimize the largest diagonal component of the intrinsic hyperpolarizability share the same universal properties: The three-level ansatz is obeyed, the normalized transition moment to the dominant state is about 0.76, the ratio of the two dominant excited state energies is about 0.48, the electron density tends toward being one-dimensional, and the intrinsic hyperpolarizability is less than 0.71. Thus, strategies for optimizing the hyperpolarizability should focus on ways to achieve these universal properties. On the other hand, when βxxy is optimized, the three level ansatz appears to hold for a pair of degenerate states. In this case, the energy ratio between the pairs of degenerate states is 0.42 and the normalized transition moment to the pair of dominant states is 0.87. Most importantly, the intrinsic hyperpolarizability is 0.9, the largest ever calculated for a system described by a potential energy function.
Optoacoustic response of a single submicronic gold particle revealed by the picosecond ultrasonics technique
Authors: Guillet Yannick , Rossignol Clément , Audoin Bertrand , Calbris Gaëtan , Ravaine Serge
Published: August 2009

The optoacoustic response of a single submicron (430 nm) gold particle embedded in a silica thin film is experimentally revealed by femtosecond pump-probe experiments. A semianalytical model is developed to calculate the transient reflectivity accounting for optical index changes in both media and for particle and film surface displacements. The displacement of the particle-film interface turns out to be the major contribution to the measured signal. The amplitude of the acoustical component of the transient reflectivity is modulated by the depth at which the particle is buried in the film.
Strong photoluminescence at 1.53 μm from GaSb/AlGaSb multiple quantum wells grown on Si substrate
Authors: Nguyen D. H. , Park J. , Noh Y. K. , Kim M. D. , Lee D. , Oh J. E.
Published: August 2009

Strong photoluminescence at 1.53 μm was obtained from a GaSb/Al0.4Ga0.6Sb multiple-quantum-well sample grown on Si substrate, indicating greatly reduced defects by InSb quantum-dot layers that terminate dislocations. The carrier lifetime of 1.4 ns, comparable to typical InP-based quantum wells, and its independence on excitation power indicates the low defect density. Due to the wide well width and tensile strain, photoluminescence was dominated by the light hole-electron transition at low temperature. However, the heavy hole-electron transition was dominant at room temperature due to the proximity of energy levels and higher density of states for the heavy hole transition.
Sarcoptic mange in southern hairy-nosed wombats (Lasiorhinus latifrons): distribution and prevalence in the Murraylands of South Australia
Authors: Ruykys Laura , Taggart David A. , Breed William G. , Schultz David
Published: August 2009

This study examined the history, prevalence and distribution of sarcoptic mange in southern hairy-nosed wombats (Lasiorhinus latifrons) in the Murraylands, South Australia. Results from a survey suggested that there had been a long history of sporadic mange outbreaks, with 43% of 85 respondents indicating that they had seen diseased animals. There was a concentration of positive sightings (59%) in the vicinity of one town, Swan Reach. A total of 67 wombats was also caught on three pastoral properties; 0% (n = 21), 4% (n = 21) and 76% (n = 23) were found to have mange at each respective site. Diseased wombats presented with erythema, parakeratosis and alopecia and had lower median condition, subcutaneous fat and higher bone prominence scores than healthy animals. Severely diseased adult wombats had an average bodyweight that was 9.86 kg lower than those without mange. Infected animals suffered higher mortality, with a rate of ~37% in eight months on one property. It is suggested that mange may have a significant effect on southern hairy-nosed wombats and outbreaks could result in the decline and/or possible extinction of small, isolated populations. Population management initiatives, including suspending culling quotas in infected populations, should thus be considered.
Reproduction in the northern brown bandicoot (Isoodon macrourus) in the Australian Wet Tropics
Authors: Vernes Karl , Pope Lisa Claire
Published: August 2009

We investigated timing of reproduction in a wild population of northern brown bandicoots (Isoodon macrourus) in the Australian Wet Tropics. Almost all births occurred during the late dry season and early wet season, and most adult females (78–96%) were carrying pouch young during those times. Litter sizes ranged from 1 to 6 pouch young (mean = 3.1) and was not influenced by season. Adult males had significantly larger testes in the late dry and early wet seasons, corresponding with the peak in births. Daylength was the only environmental factor that predicted the presence of a litter; when daylength exceeded 12 h, more than 70% of captured females were carrying pouch young, and most (94%) births were estimated to have occurred on days with >12 h of daylight. Various environmental factors have been proposed as a cue for breeding in I. macrourus, with daylength though to be the primary cue initiating breeding in temperate Australia, but temperature and rainfall thought to be more important in the tropics. Our data suggest that in the Australian Wet Tropics, increasing daylength in the late dry season acts as the primary cue for breeding.
Faecal DNA analysis enables genetic monitoring of the species recovery program for an arid-dwelling marsupial
Authors: Smith Steve , McRae Peter , Hughes Jane
Published: August 2009

The greater bilby, Macrotis lagotis, is a species of conservation significance in the arid and semiarid zones of Australia. A species recovery program has been underway since the mid-1990s but the incorporation of molecular genetic data within the program has been difficult due to the problems of obtaining regular, population-wide samples of this trap-shy and sparsely distributed species. In this study, we demonstrate that faecal pellets collected from around burrows in the dry, arid habitat of western Queensland provide a viable source for DNA extraction and analysis. Faecal DNA was used to generate population-level estimates of microsatellite and mtDNA diversity for comparison with previous estimates for the natural population derived from tissue samples. Data were used to assess both the reliability of faecal-derived genotypes and the extent of any diversity loss since the previous study. Microsatellite diversity recorded from eight polymorphic markers for the natural population (A = 4.31 ± 0.30, HE = 0.76 ± 0.03) was comparable with the previous study, indicating little change in genetic diversity for the natural population in the 10-year interim. Faecal genotypes generated for the recently reintroduced population matched the known number of founders as well as a known genotype, providing support for the reliability of the faecal DNA approach. The captive and reintroduced populations had significantly lower diversity levels than the natural population (A = 3.59 ± 0.28, HE = 0.68 ± 0.03; A = 3.57 ± 0.20, HE = 0.65 ± 0.03 respectively). Mitochondrial control region analysis, incorporating nested clade phylogeographic analysis (NCPA), agrees with earlier findings that populations of bilbies across the arid zone in Australia have only recently become fragmented, but the case for Queensland bilbies being strongly differentiated from other regions is diminished. Implications from this study include the need to further supplement the captive and reintroduced populations with additional out-bred individuals and that faecal DNA can be used effectively for ongoing monitoring and management of this species.
Patterns of praying mantid population density following cyclone disturbance in far north Queensland, Australia
Authors: O'Hanlon J. , Holwell G. I.
Published: August 2009

In 2006, Cyclone Larry passed over a large area of far north Queensland, Australia. Before the cyclone, data had been collected on the population density of two species of praying mantids. Follow-up surveys found that one species, Ciulfina klassi (Mantodea: Liturgusidae), decreased in density following Cyclone Larry whereas the congeneric C. rentzi appeared resilient to cyclone disturbance. The differing responses of these two species are most likely attributable to their respective habitats being affected differently by cyclone disturbance. Whereas dense rainforest may have buffered C. rentzi from the damaging effects of cyclones, C. klassi may have been more vulnerable as it inhabits more sparsely vegetated woodlands.
Coarse-grained modeling of allosteric regulation in protein receptors
Authors: Balabin Ilya A. , Yang Weitao , Beratan David N.
Published: August 2009

Allosteric regulation provides highly specific ligand recognition and signaling by transmembrane protein receptors. Unlike functions of protein molecular machines that rely on large-scale conformational transitions, signal transduction in receptors appears to be mediated by more subtle structural motions that are difficult to identify. We describe a theoretical model for allosteric regulation in receptors that addresses a fundamental riddle of signaling: What are the structural origins of the receptor agonism (specific signaling response to ligand binding)? The model suggests that different signaling pathways in bovine rhodopsin or human β
2
-adrenergic receptor can be mediated by specific structural motions in the receptors. We discuss implications for understanding the receptor agonism, particularly the recently observed “biased agonism” (selected activation of specific signaling pathways), and for developing rational structure-based drug-design strategies.
Scaling laws between population and facility densities
Authors: Um Jaegon , Son Seung-Woo , Lee Sung-Ik , Jeong Hawoong , Kim Beom Jun
Published: August 2009

When a new facility like a grocery store, a school, or a fire station is planned, its location should ideally be determined by the necessities of people who live nearby. Empirically, it has been found that there exists a positive correlation between facility and population densities. In the present work, we investigate the ideal relation between the population and the facility densities within the framework of an economic mechanism governing microdynamics. In previous studies based on the global optimization of facility positions in minimizing the overall travel distance between people and facilities, it was shown that the density of facility
D
and that of population ρ should follow a simple power law
D
∼ ρ
2/3
. In our empirical analysis, on the other hand, the power-law exponent α in
D
∼ ρ
α
is not a fixed value but spreads in a broad range depending on facility types. To explain this discrepancy in α, we propose a model based on economic mechanisms that mimic the competitive balance between the profit of the facilities and the social opportunity cost for populations. Through our simple, microscopically driven model, we show that commercial facilities driven by the profit of the facilities have α = 1, whereas public facilities driven by the social opportunity cost have α = 2/3. We simulate this model to find the optimal positions of facilities on a real U.S. map and show that the results are consistent with the empirical data.
Uncoupling CD21 and CD19 of the B-cell coreceptor
Authors: Barrington Robert A. , Schneider Thomas J. , Pitcher Lisa A. , Mempel Thorsten R. , Ma Minghe , Barteneva Natasha S. , Carroll Michael C.
Published: August 2009

Complement receptors (CRs) CD21 and CD35 form a coreceptor with CD19 and CD81 on murine B cells that when coligated with the B-cell receptor lowers the threshold of activation by several orders of magnitude. This intrinsic signaling role is thought to explain the impaired humoral immunity of mice bearing deficiency in CRs. However, CRs have additional roles on B cells independent of CD19, such as transport of C3-coated immune complexes and regulation of C4 and C3 convertase. To test whether association of CR with CD19 is necessary for their intrinsic activation-enhancing role, knockin mice expressing mutant receptors, Cr2Δ/Δgfp, that bind C3 ligands but do not signal through CD19 were constructed. We found that uncoupling of CR and CD19 significantly diminishes survival of germinal center B cells and secondary antibody titers. However, B memory is less impaired relative to mice bearing a complete deficiency in CRs on B cells. These findings confirm the importance of interaction of CR and CD19 for coreceptor activity in humoral immunity but identify a role for CR in B-cell memory independent of CD19.
Galectin-3 negatively regulates TCR-mediated CD4+T-cell activation at the immunological synapse
Authors: Chen Huan-Yuan , Fermin Agnes , Vardhana Santosh , Weng I-Chun , Lo Kin Fong Robin , Chang En-Yuh , Maverakis Emanual , Yang Ri-Yao , Hsu Daniel K , Dustin Michael L. , Liu Fu-Tong
Published: August 2009

We have investigated the function of endogenous galectin-3 in T cells. Galectin-3-deficient (gal3−/−) CD4+T cells secreted more IFN-γ and IL-4 than gal3+/+CD4+T cells after T-cell receptor (TCR) engagement. Galectin-3 was recruited to the cytoplasmic side of the immunological synapse (IS) in activated T cells. In T cells stimulated on supported lipid bilayers, galectin-3 was primarily located at the peripheral supramolecular activation cluster (pSMAC). Gal3+/+T cells formed central SMAC on lipid bilayers less effectively and adhered to antigen-presenting cells less firmly than gal3−/−T cells, suggesting that galectin-3 destabilizes the IS. Galectin-3 expression was associated with lower levels of early signaling events and phosphotyrosine signals at the pSMAC. Additional data suggest that galectin-3 potentiates down-regulation of TCR in T cells. By yeast two-hybrid screening, we identified as a galectin-3-binding partner, Alix, which is known to be involved in protein transport and regulation of cell surface expression of certain receptors. Co-immunoprecipitation confirmed galectin-3-Alix association and immunofluorescence analysis demonstrated the translocation of Alix to the IS in activated T cells. We conclude that galectin-3 is an inhibitory regulator of T-cell activation and functions intracellularly by promoting TCR down-regulation, possibly through modulating Alix's function at the IS.
Targeting a bacterial stress response to enhance antibiotic action
Authors: Lee Samuel , Hinz Aaron , Bauerle Elizabeth , Angermeyer Angus , Juhaszova Katy , Kaneko Yukihiro , Singh Pradeep K. , Manoil Colin
Published: August 2009

This report describes the identification and analysis of a 2-component regulator of
Pseudomonas aeruginosa
that is a potential aminoglycoside antibiotic combination therapy target. The regulator, AmgRS, was identified in a screen of a comprehensive, defined transposon mutant library for functions whose inactivation increased tobramycin sensitivity. AmgRS mutations enhanced aminoglycoside action against bacteria grown planktonically and in antibiotic tolerant biofilms, against genetically resistant clinical isolates, and in lethal infections of mice. Drugs targeting AmgRS would thus be expected to enhance the clinical efficacy of aminoglycosides. Unexpectedly, the loss of AmgRS reduced virulence in the absence of antibiotics, indicating that its inactivation could protect against infection directly as well as by enhancing aminoglycoside action. Transcription profiling and phenotypic analysis suggested that AmgRS controls an adaptive response to membrane stress, which can be caused by aminoglycoside-induced translational misreading. These results help validate AmgRS as a potential antibiotic combination target for
P. aeruginosa
and indicate that fundamental stress responses may be a valuable general source of such targets.
Diameter-dependent bending dynamics of single-walled carbon nanotubes in liquids
Authors: Fakhri Nikta , Tsyboulski Dmitri A. , Cognet Laurent , Weisman R. Bruce , Pasquali Matteo
Published: August 2009

By relating nanotechnology to soft condensed matter, understanding the mechanics and dynamics of single-walled carbon nanotubes (SWCNTs) in fluids is crucial for both fundamental and applied science. Here, we study the Brownian bending dynamics of individual chirality-assigned SWCNTs in water by fluorescence microscopy. The bending stiffness scales as the cube of the nanotube diameter and the shape relaxation times agree with the semiflexible chain model. This suggests that SWCNTs may be the archetypal semiflexible filaments, highly suited to act as nanoprobes in complex fluids or biological systems.
Sustained transgene expression despite T lymphocyte responses in a clinical trial of rAAV1-AAT gene therapy
Authors: Brantly Mark L. , Chulay Jeffrey D. , Wang Lili , Mueller Christian , Humphries Margaret , Spencer L. Terry , Rouhani Farshid , Conlon Thomas J. , Calcedo Roberto , Betts Michael R. , Spencer Carolyn , Byrne Barry J. , Wilson James M. , Flotte Terence R.
Published: August 2009

Alpha-1 antitrypsin (AAT) deficiency is well-suited as a target for human gene transfer. We performed a phase 1, open-label, dose-escalation clinical trial of a recombinant adeno-associated virus (rAAV) vector expressing normal (M) AAT packaged into serotype 1 AAV capsids delivered by i.m. injection. Nine AAT-deficient subjects were enrolled sequentially in cohorts of 3 each at doses of 6.9 × 10
12
, 2.2 × 10
13
, and 6.0 × 10
13
vector genome particles per patient. Four subjects receiving AAT protein augmentation discontinued therapy 28 or 56 days before vector administration. Vector administration was well tolerated, with only mild local reactions and 1 unrelated serious adverse event (bacterial epididymitis). There were no changes in hematology or clinical chemistry parameters. M-specific AAT was expressed above background in all subjects in cohorts 2 and 3 and was sustained at levels 0.1% of normal for at least 1 year in the highest dosage level cohort, despite development of neutralizing antibody and IFN-γ enzyme-linked immunospot responses to AAV1 capsid at day 14 in all subjects. These findings suggest that immune responses to AAV capsid that develop after i.m. injection of a serotype 1 rAAV vector expressing AAT do not completely eliminate transduced cells in this context.
Structure–neurotoxicity relationships of amyloid β-protein oligomers
Authors: Ono Kenjiro , Condron Margaret M. , Teplow David B.
Published: August 2009

Amyloid β-protein (Aβ) oligomers may be the proximate neurotoxins in Alzheimer's disease (AD). “Oligomer” is an ill-defined term because many kinds have been reported and they often exist in rapid equilibrium with monomers and higher-order assemblies. We report here results of studies in which specific oligomers have been stabilized structurally, fractionated in pure form, and then studied by using a combination of CD spectroscopy, Thioflavin T fluorescence, EM, atomic force microscopy (AFM), and neurotoxicity assays. Aβ monomers were largely unstructured, but oligomers exhibited order-dependent increases in β-sheet content. EM and AFM data suggest that dimerization and subsequent monomer addition are processes in which significant and asymmetric monomer conformational changes occur. Oligomer secondary structure and order correlated directly with fibril nucleation activity. Neurotoxic activity increased disproportionately (order dependence >1) with oligomer order. The structure–activity correlations reported here significantly extend our understanding of the conformational dynamics, structure, and relative toxicity of pure Aβ oligomers of specific order.
ICP0 enables and monitors the function of D cyclins in herpes simplex virus 1 infected cells
Authors: Kalamvoki Maria , Roizman Bernard
Published: August 2009

The herpes simplex virus 1 ICP0 is a regulatory protein. Early in infection ICP0 localizes in ND10 bodies and performs two functions: As an E3 ligase in conjunction with E2 UbcH5a conjugating enzyme, it degrades the ND10 components PML and SP100. Concurrently, it suppresses the silencing of viral DNA by dispersing the HDAC1/CoREST/REST/LSD1 repressor complex. Subsequently, ICP0 is exported to the cytoplasm. In cells treated with HDAC inhibitors or transfected with irrelevant DNA, the export is delayed in a DNA dose-dependent fashion. Here, we follow up an observation that ICP0 binds cyclin D3 and that ICP0 mutants unable to bind cyclin D3 are not exported. Moreover, in infected cells cdk4 is activated, but cdk2 is not. We report that (
i
) cyclin D1, D2, or D3 colocalize with ND10 bodies and ICP0 early in infection and ultimately become incorporated into viral replication compartments, (
ii
) each of the D cyclins partially rescues ΔICP0 mutants, and (
iii
) inhibition of cdk4 by inhibitor I sequesters ICP0 in the nucleus. A key finding is that overexpression of cyclin D3 enables the transport of ICP0 to the cytoplasm. We conclude that (
i
) ICP0 facilitates the recruitment of cyclin D3 to the sites of viral DNA synthesis, (
ii
) until its functions are completed, ICP0 is retained in the nucleus, and (
iii
) a common signal that results in the export of ICP0 to the cytoplasm is the accumulation of a viral DNA-synthesis-dependent late protein.
Phytochromes are the sole photoreceptors for perceiving red/far-red light in rice
Authors: Takano Makoto , Inagaki Noritoshi , Xie Xianzhi , Kiyota Seiichiro , Baba-Kasai Akiko , Tanabata Takanari , Shinomura Tomoko
Published: August 2009

Phytochromes are believed to be solely responsible for red and far-red light perception, but this has never been definitively tested. To directly address this hypothesis, a phytochrome triple mutant (
phyAphyBphyC
) was generated in rice (
Oryza sativa
L. cv. Nipponbare) and its responses to red and far-red light were monitored. Since rice only has three phytochrome genes (
PHYA
,
PHYB
and
PHYC
), this mutant is completely lacking any phytochrome. Rice seedlings grown in the dark develop long coleoptiles while undergoing regular circumnutation. The phytochrome triple mutants also show this characteristic skotomorphogenesis, even under continuous red or far-red light. The morphology of the triple mutant seedlings grown under red or far-red light appears completely the same as etiolated seedlings, and they show no expression of the light-induced genes. This is direct evidence demonstrating that phytochromes are the sole photoreceptors for perceiving red and far-red light, at least during rice seedling establishment. Furthermore, the shape of the triple mutant plants was dramatically altered. Most remarkably, triple mutants extend their internodes even during the vegetative growth stage, which is a time during which wild-type rice plants never elongate their internodes. The triple mutants also flowered very early under long day conditions and set very few seeds due to incomplete male sterility. These data indicate that phytochromes play an important role in maximizing photosynthetic abilities during the vegetative growth stage in rice.