bluuebunny/crossref_metadata_2025 huggingface dataset:
Cold and ultracold chemical reactions of F+HCl and F+DCl
Authors: Quéméner Goulven , Balakrishnan Naduvalath
Published: June 2008

We report quantum dynamics calculations of F(P2)+HCl(v,j)→HF(v′,j′)+Cl(P2) and F+DCl(v,j)→DF(v′,j′)+Cl reactions at cold and ultracold temperatures. The effect of rotational and vibrational excitations of the HCl molecule on the reactivity is investigated. It is found that, in the ultracold regime, vibrational excitation of the HCl molecule from v=0 to v=2 enhances the reactivity by four orders of magnitude. The rotational excitation from j=0 to j=1 decreases the reactivity while the rotational excitation from j=0 to j=2 increases the reactivity. The overall effect of rotational excitation was found to be much smaller than vibrational excitation. The reactivity of the F+DCl system is significantly lower than that of the F+HCl case indicating the importance of quantum tunneling at low energies. For both reactions, Feshbach resonances corresponding to F⋯ HCl or F⋯DCl triatomic states occur at low energies. We also explored the validity of the coupled-states approximation for cold collisions taking the F+HCl(v=0,j=0) reaction as an illustrative example. It is found that the coupled-states approximation is generally valid for the background scattering even at low energies but it is inadequate to accurately describe the rich resonances in the energy dependence of the cross section resulting from the decay of van der Waals complexes. It is further shown that the coupled-states approximation cannot be used for scattering in the Wigner threshold regime when the molecule is initially in a rotationally excited level.
Gaussian core model phase diagram and pair correlations in high Euclidean dimensions
Authors: Zachary Chase E. , Stillinger Frank H. , Torquato Salvatore
Published: June 2008

The physical properties of a classical many-particle system with interactions given by a repulsive Gaussian pair potential are extended to arbitrarily high Euclidean dimensions. The goals of this paper are to characterize the behavior of the pair correlation function g2 in various density regimes and to understand the phase properties of the Gaussian core model (GCM) as parametrized by dimension d. To this end, we explore the fluid (dilute and dense) and crystalline solid phases. For the dilute regime of the fluid phase, a cluster expansion of g2 in reciprocal temperature β is presented, the coefficients of which may be evaluated analytically due to the nature of the Gaussian potential. We present preliminary results concerning the convergence properties of this expansion. The analytical cluster expansion is related to numerical approximations for g2 in the dense fluid regime by utilizing hypernetted chain, Percus–Yevick, and mean-field closures to the Ornstein–Zernike equation. Based on the results of these comparisons, we provide evidence in support of a decorrelation principle for the GCM in high Euclidean dimensions. In the solid phase, we consider the behavior of the freezing temperature Tf(ρ) in the limit ρ→+∞ and show Tf(ρ)→0 in this limit for any d via a collective coordinate argument. Duality relations with respect to the energies of a lattice and its dual are then discussed, and these relations aid in the Maxwell double-tangent construction of phase coexistence regions between dual lattices based on lattice summation energies. The results from this analysis are used to draw conclusions about the ground-state structures of the GCM for a given dimension.
The effects of nonlinear series resonance on Ohmic and stochastic heating in capacitive discharges
Authors: Lieberman M. A. , Lichtenberg A. J. , Kawamura E. , Mussenbrock Thomas , Brinkmann Ralf Peter
Published: June 2008

The flow of electron and ion conduction currents across a nonlinear capacitive sheath to the electrode surface self-consistently sets the dc bias voltage across the sheath. We incorporate these currents into a model of a homogeneous capacitive sheath in order to determine the enhancement of the Ohmic and stochastic heating due to self-excitation of the nonlinear series resonance in an asymmetric capacitive discharge. At lower pressures, the series resonance can enhance both the Ohmic and stochastic heating by factors of 2–4, with the Ohmic heating tending to zero as the pressure decreases. The model was checked, for a particular set of parameters, by a particle-in-cell (PIC) simulation using the homogeneous sheath approximation, giving good agreement. With a self-consistent Child-law sheath, the PIC simulation showed increased heating, as expected, whether the series resonance is important or not.
The influence of electrostatic forces on the structure and dynamics of molecular ionic liquids
Authors: Schröder C. , Steinhauser O.
Published: June 2008

The vast majority of molecular dynamics simulations are based on nonpolarizable force fields with fixed partial charges for all atoms. The traditional way to obtain these charges are quantum-mechanical calculations performed prior to simulation. Unfortunately, the set of the partial charges heavily relies on the method and the basis set used. Therefore, investigations of the influence of charge variation on simulation data are necessary in order to validate various charge sets. This paper elucidates the consequences of different charge sets on the structure and dynamics of the ionic liquid: 1-ethyl-3-methyl-imidazolium dicyanoamide. The structural features seem to be more or less independent of the partial charge set pointing to a dominance of shape force as modeled by Lennard–Jones parameters. This can be seen in the radial distribution and orientational correlation functions. The role of electrostatic forces comes in when studying dynamical properties. Here, significant deviations between different charge sets can be observed. Overall, dynamics seems to be governed by viscosity. In fact, all dynamical parameters presented in this work can be converted from one charge set to another by viscosity scaling.
Predictive simulations of ITER including neutral beam driven toroidal rotation
Authors: Halpern Federico D. , Kritz Arnold H. , Bateman Glenn , Pankin Alexei Y. , Budny Robert V. , McCune Douglas C.
Published: June 2008

Predictive simulations of ITER [R. Aymar et al., Plasma Phys. Control. Fusion 44, 519 (2002)], discharges are carried out for the 15MA high confinement mode (H-mode) scenario using PTRANSP, the predictive version of the TRANSP code. The thermal and toroidal momentum transport equations are evolved using turbulent and neoclassical transport models. A predictive model is used to compute the temperature and width of the H-mode pedestal. The ITER simulations are carried out for neutral beam injection (NBI) heated plasmas, for ion cyclotron resonant frequency (ICRF) heated plasmas, and for plasmas heated with a mix of NBI and ICRF. It is shown that neutral beam injection drives toroidal rotation that improves the confinement and fusion power production in ITER. The scaling of fusion power with respect to the input power and to the pedestal temperature is studied. It is observed that, in simulations carried out using the momentum transport diffusivity computed using the GLF23 model [R. Waltz et al., Phys. Plasmas 4, 2482 (1997)], the fusion power increases with increasing injected beam power and central rotation frequency. It is found that the ITER target fusion power of 500MW is produced with 20MW of NBI power when the pedestal temperature is 3.5keV.
A molecular spectroscopic view of surface plasmon enhanced resonance Raman scattering
Authors: Kelley Anne Myers
Published: June 2008

The enhancement of resonance Raman scattering by coupling to the plasmon resonance of a metal nanoparticle is developed by treating the molecule-metal interaction as transition dipole coupling between the molecular electronic transition and the much stronger optical transition of the nanoparticle. A density matrix treatment accounts for coupling of both transitions to the electromagnetic field, near-resonant energy transfer between the molecule-excited and nanoparticle-excited states, and dephasing processes. This fully quantum mechanical approach reproduces the interference effects observed in extinction spectra of J-aggregated dyes adsorbed to metal nanoparticles and makes testable predictions for surface-enhanced resonance Raman excitation profiles.
Detailed study of fine and hyperfine structures in rotational spectra of the free fluoroformyloxyl radical FCO2⋅
Authors: Kolesniková Lucie , Varga Juraj , Beckers Helmut , Šimečková Marie , Zelinger Zdeněk , Stříteská Lucie Nová , Kania Patrik , Willner Helge , Urban Štěpán
Published: June 2008

More than 160 new hyperfine components of rotational transitions of the free fluoroformyloxyl radical FCO2⋅ have been measured using the Prague millimeter wave high resolution spectrometer. The frequencies of these transitions together with the previously measured data were analyzed in detail and precise values of magnetic hyperfine and fine parameters were obtained. These new parameters significantly improve the values of previously determined hyperfine parameters which were rather unreliable. The new fine and hyperfine parameters obtained in this study are compatible with those of the simultaneously electron paramagnetic resonance study. Besides that, significantly improved ground state rotational and centrifugal distortion constants of the fluoroformyloxyl radical were derived.
Folding mechanisms of individual β-hairpins in a Gō model of Pin1 WW domain by all-atom molecular dynamics simulations
Authors: Luo Zhonglin , Ding Jiandong , Zhou Yaoqi
Published: June 2008

This paper examines the folding mechanism of an individual β-hairpin in the presence of other hairpins by using an off-lattice model of a small triple-stranded antiparallel β-sheet protein, Pin1 WW domain. The turn zipper model and the hydrophobic collapse model originally developed for a single β-hairpin in literature is confirmed to be useful in describing β-hairpins in model Pin1 WW domain. We find that the mechanism for folding a specific hairpin is independent of whether it folds first or second, but the formation process are significantly dependent on temperature. More specifically, β1-β2 hairpin folds via the turn zipper model at a low temperature and the hydrophobic collapse model at a high temperature, while the folding of β2-β3 hairpin follows the turn zipper model at both temperatures. The change in folding mechanisms is interpreted by the interplay between contact stability (enthalpy) and loop lengths (entropy), the effect of which is temperature dependent.
Cell-to-cell communication: Time and length scales of ligand internalization in cultures of suspended cells
Authors: Berezhkovskii Alexander M. , Coppey Mathieu , Sealfon Stuart C. , Shvartsman Stanislav
Published: June 2008

A problem of cell-to-cell communication by diffusible ligands is analyzed for the case when cells are distributed in three dimensions and diffusible ligands are secreted by cells and reversibly bind to cell surface receptors. Following its binding to a receptor, the ligand can either dissociate and be released back in the medium or be absorbed by the cell in a process that is called internalization. Using an effective medium approximation, we derive analytical expressions that characterize the time and length scales associated with the ligand trajectories leading to internalization. We discuss the applicability of our approximation and illustrate the application of our results to a specific cellular system.
Structure and bonding of the MCN molecules, M=Cu,Ag,Au,Rg
Authors: Zaleski-Ejgierd Patryk , Patzschke Michael , Pyykkö Pekka
Published: June 2008

High-precision calculations are reported for the title series with M=Cu, Ag, Au, using CCSD(T) with the latest pseudopotentials and basis sets up to cc-pVQZ. The bond lengths for M=Cu, Ag, Au agree with experiment within better than 1pm. The role of deep-core excitations is studied. The second-order spin-orbit effects are evaluated at the density functional theory level, including M=Rg. A qualitative bonding analysis suggests multiple M–C bonding. The calculated vibrational frequencies are expected to be more accurate than the available experimental estimates. The M–C bond lengths obey Cu<Rg<Au<Ag.
Stability of HfO2/SiOx/Si surficial films at ultralow oxygen activity
Authors: Jud E. , Tang M. , Chiang Y.-M.
Published: June 2008

HfO 2 / SiO x / Si layer structures have been fabricated using atomic layer deposition and subsequently annealed at partial oxygen pressures close to the equilibrium pressure of bulk SiO2. These ultralow oxygen partial pressures at around 10−40 atm have been achieved by a solid state buffer method. An interfacial SiOx layer with an approximate thickness of 1 nm is shown to be part of the equilibrium configuration of HfO2 on Si even at an oxygen activity eight orders of magnitude below the equilibrium pressure of bulk SiO2. Elimination of the silica-rich interfacial layer in any process permitting approach toward thermodynamic equilibrium seems highly improbable. By comparison with the case of pure SiOx on Si, it is shown that HfO2 acts as a “surfactant” to SiOx leading to a smooth film structure, while the pure SiOx on Si exhibits island formation under the same conditions. Furthermore, the oxidation state of Si in SiOx and the silicate composition at the HfO2/SiOx interface can be tailored by the partial oxygen pressure.
Alternating current susceptibility calculations for thin-film superconductors with regions of different critical-current densities
Authors: Navau C. , Sanchez A. , Del-Valle N. , Chen D.-X.
Published: June 2008

We present calculations of the alternating current (ac) susceptibility in rectangular thin-film type-II superconductors, based on the critical-state model and on the minimization of magnetic energy. First, we simulate a homogeneous superconductor and give an analytical approximate expression for both real and imaginary parts of the ac susceptibility as a function of the amplitude of the ac applied field. Second, ac susceptibility is calculated in a superconductor composed by two parts connected by a region of lower critical-current density. We find two peaks can appear in the imaginary ac susceptibility although, because of the strong demagnetizing fields, these peaks overlap in some cases. Detailed explanations of the imaginary part of the ac susceptibility are given.
High-coercivity SmCo5 thin films deposited on glass substrates
Authors: Zhang L. N. , Chen J. S. , Ding J. , Hu J. F.
Published: June 2008

Structural and magnetic properties of SmCo5 thin films grown on glass substrates with a Cr underlayer were investigated. The nanocrystalline SmCo5 film with a (112¯0) texture exhibited high in-plane intrinsic coercivity up to 26.5 kOe and a large in-plane magnetic anisotropy. The crystallinity of the SmCo5 layer plays an important role, which is strongly dependent on the texture and the morphology of the Cr underlayer. A smooth Cr underlayer with a (200) texture and a good crystallinity is desired for the SmCo5 film with a good magnetic performance. This work demonstrates a process to achieve high intrinsic coercivity and large in-plane magnetic anisotropy SmCo5 films on glass substrates deposited at a relatively low temperature (400 °C).
Three-dimensional confocal Raman imaging of volume holograms formed in ZrO2 nanoparticle-photopolymer composite materials
Authors: Chikama Katsumi , Mastubara Koutastu , Oyama Shigeki , Tomita Yasuo
Published: June 2008

We describe physicochemical microanalyses of plane-wave volume holograms recorded in ZrO2 nanoparticle-photopolymer composite films with approximately 50μm thickness. Transversal and longitudinal density distributions of compositions embedded in holograms are analyzed by a confocal scanning Raman microscope. Other microscopic measurements using an electron-probe microanalyzer and an atomic force microscope are also performed to examine hologram’s compositional and structural morphology near the surface. It is found that the induced density distributions of ZrO2 nanoparticles and the formed polymer are 180° out of phase with each other in holograms. This result shows a decisive evidence of the counterdiffusion of monomer molecules and ZrO2 nanoparticles in a film under two-beam holographic exposure. It is also found that when grating spacing is 5μm or longer, a relief structure of a few 10nm appears on a film’s surface and its height increases with the grating spacing. This result indicates a significance of the surface tension effect at shorter grating spacing and the imperfect compensation of local volume changes in the counterdiffusion process.
Impact of carbon concentration on 1∕f noise and random telegraph signal noise in SiGe:C heterojunction bipolar transistors
Authors: Raoult J. , Pascal F. , Delseny C. , Marin M. , Deen M. J.
Published: June 2008

The influence of carbon concentration on the low-frequency noise (LF noise) of Si∕SiGe:C∕Si heterojunction bipolar transistors (HBTs) is investigated. When carbon is incorporated into these HBTs, representative noise spectra of the input current spectral density SIB show significant generation-recombination (GR) components. On the other hand, for transistors without carbon incorporation, no GR components were observed. When only 1∕f noise component is observed, the 1∕f noise level is found to be independent of the carbon concentration and the associated figure of merit of the normalized noise magnitude KB has a very good value of ∼4×10−10μm2. In order to relate the 1∕f noise and the high-frequency performance of the transistor, we studied and modeled the figure of merit defined as the ratio fc∕fT (fc is the low-frequency corner frequency and fT the unity current-gain frequency). Then we performed a detailed analysis of the GR components associated with the presence of the carbon. We found that the observed Lorentzian spectra are associated with random telegraph signal (RTS) noise. However, no RTS noise was measured in carbon-free devices. It is believed that the RTS noise is due to electrically active defects formed by the addition of carbon, typically observed for concentrations above the bulk solid solubility limit in silicon. The RTS amplitude (ΔIB) is found to scale with the base current, to decrease exponentially with temperature, and to be independent of the carbon concentration. The mean pulse widths (tH,tL) of the RTS are found to decrease rapidly with bias voltage, as 1∕exp(qVBE∕kT) or stronger. Our results confirm that electrically active C-related defects are located in the base-emitter junction, and the RTS amplitude is explained by a model based on voltage barrier height fluctuations across the base-emitter junction induced by trapped carriers in the space charge region. The observed bias dependence of mean pulse widths seems to indicate that two capture processes are involved, electron and hole capture. These C-related defects behave like recombination centers with deep energy levels rather than electron or hole traps involving trapping-detrapping processes.
Quantitative measurement of piezoelectric coefficient of thin film using a scanning evanescent microwave microscope
Authors: Zhao Zhenli , Luo Zhenlin , Liu Chihui , Wu Wenbin , Gao Chen , Lu Yalin
Published: June 2008

This article describes a new approach to quantitatively measure the piezoelectric coefficients of thin films at the microscopic level using a scanning evanescent microwave microscope. This technique can resolve 10pm deformation caused by the piezoelectric effect and has the advantages of high scanning speed, large scanning area, submicron spatial resolution, and a simultaneous accessibility to many other related properties. Results from the test measurements on the longitudinal piezoelectric coefficient of PZT thin film agree well with those from other techniques listed in literatures.
Free energy and structure of calcium carbonate nanoparticles during early stages of crystallization
Authors: Quigley D. , Rodger P. M.
Published: June 2008

We introduce a metadynamics based scheme for computing the free energy of nanoparticles as a function of their crystalline order. The method is applied to small nanoparticles of the biomineral calcium carbonate to determine the preferred structure during early stages of crystal growth. For particles 2nm in diameter, we establish a large energetic preference for amorphous particle morphologies. Particles with partial crystalline order consistent with vaterite are also observed with substantially lower probability. The absence of the stable calcite phase and stability of the amorphous state support recent conjectures that calcite formation starts via the deposition of amorphous calcium carbonate.
Near-ultraviolet photodetector based on hybrid polymer/zinc oxide nanorods by low-temperature solution processes
Authors: Lin Yun-Yue , Chen Chun-Wei , Yen Wei-Che , Su Wei-Fang , Ku Chen-Hao , Wu Jih-Jen
Published: June 2008

In this article, we have proposed a nanostructured near-ultraviolet photodetector (<400nm) based on the ZnO nanorod/polyfluorene hybrid by solution processes at low temperature. The current-voltage characteristic of the hybrid device demonstrates the typical pn-heterojunction diode behavior, consisting of p-type polymer and n-type ZnO nanorods, respectively. The relative quantum efficiencies of the hybrid device exhibit a nearly three order difference while illuminated under UV and visible light, respectively. The responsivity for the device can reach to 0.18A∕W at 300nm by applying a bias of −2V, which provides a route to fabricate a low-cost near-UV photodetector.
Surface chemistry of plasma-assisted atomic layer deposition of Al2O3 studied by infrared spectroscopy
Authors: Langereis E. , Keijmel J. , van de Sanden M. C. M. , Kessels W. M. M.
Published: June 2008

The surface groups created during plasma-assisted atomic layer deposition (ALD) of Al2O3 were studied by infrared spectroscopy. For temperatures in the range of 25–150°C, –CH3 and –OH were unveiled as dominant surface groups after the Al(CH3)3 precursor and O2 plasma half-cycles, respectively. At lower temperatures more –OH and C-related impurities were found to be incorporated in the Al2O3 film, but the impurity level could be reduced by prolonging the plasma exposure. The results demonstrate that –OH surface groups rule the surface chemistry of the Al2O3 process and likely that of plasma-assisted ALD of metal oxides from organometallic precursors in general.
Enhancement of switching speed by laser-induced clustering of nanoparticles in magnetic fluids
Authors: Deng Hai-Dong , Liu Jin , Zhao Wei-Ren , Zhang Wei , Lin Xu-Sheng , Sun Ting , Dai Qiao-Feng , Wu Li-Jun , Lan Sheng , Gopal Achanta Venu
Published: June 2008

The switching speed of magnetic fluids was investigated by using laser light of different power densities as well as incandescent light. It was found that the switching speed exhibited a strong dependence on incident power density and there existed an optimum value at which the fastest switching operation was achieved. In addition, it was revealed that the clustering of magnetic nanoparticles, which became resolved at large power densities, resulted in a rapid agglomeration of nanoparticles when a magnetic field was applied. It is suggested that the optical trapping force of the laser beam is responsible for the formation of clusters.
Photonic bandgap of gradient quasidiamond lattice photonic crystal
Authors: Dong Xian-Zi , Ya Qi , Sheng Xin-Zhi , Li Zhi-Yuan , Zhao Zhen-Sheng , Duan Xuan-Ming
Published: June 2008

A three-dimensional (3D) photonic crystal (PhC) structure consisting of gradient quasidiamond lattices was fabricated using multiphoton photopolymerization nanofabrication technique. The photonic bandgap (PBG) of this 3D PhC was experimentally confirmed by reflection and transmission measurements and simulated with finite-difference time domain calculations. The results indicate that a 3D PhC with gradient lattices could effectively expand the width of the PBG and may be beneficial for developing complete-bandgap PhCs with low refractive index materials for applications in polymer based optoelectronic devices and integrated systems.
Dielectrophoretic trapping of suspended particles by selective pyroelectric effect in lithium niobate crystals
Authors: Grilli Simonetta , Ferraro Pietro
Published: June 2008

We have developed a dielectrophoretic approach for trapping suspended dielectric particles. The electric forces were produced by using the pyroelectric effect in periodically poled lithium niobate substrates. Complex electric field distributions can be built up through an appropriate control of the temperature and the particles can be distributed according to the geometry of the reversed ferroelectric domain structure. The electrode-less configuration makes the technique easier to accomplish compared to conventional dielectrophoretic devices, with interesting possibilities of applications in the field of biology and biomedicine.
Identification of quantitative trait loci (QTLs) influencing early vigour, height, flowering date, and seed size and their implications for breeding of narrow-leafed lupin (Lupinus angustifolius L.)
Authors: Boersma Jeffrey G. , Li Chengdao , Leśniewska Karolina , Sivasithamparam Krishnapillai , Yang Huaan
Published: June 2008

We report the first quantitative trait loci (QTL) mapped in an F8 recombinant inbred line (RIL) population of Lupinus angustifolius. Traits mapped were early vigour, days to flowering, height at maturity, and seed size. Twenty-two QTLs were found, located on 13 linkage groups, with alleles beneficial to the crop contributed by both parents. Early vigour was controlled by 8 QTLs on 7 linkage groups. Time to flowering was controlled by 10 QTLs and the height at maturity was found to be under the control of 4 QTLs. Seed size was linked to 2 QTLs. A region linked to the Ku gene that promotes early flowering by removal of the vernalisation requirement appeared to play a role in all 4 traits. The gene mollis controlling soft-seededness appeared to also be linked to early vigour, and iucundis controlling alkaloid production was linked to seed size. Five pairs of QTLs were found to be involved in epistasis, 2 of these having an effect on early vigour and another 3 influencing the time to opening of the first florets. Variation explained for each trait ranged from 28% for seed size, to 88% for days to flowering. We showed that it was possible to use these data to predict genotypes of superior progeny for these traits under Mediterranean conditions. QTL regions were compared on a second published linkage map and regions of conserved synteny with the model legume Medicago truncatula highlighted.
Role of the lens in physical dormancy in seeds of Sophora alopecuroides L. (Fabaceae) from north-west China
Authors: Hu X. W. , Wang Y. R. , Wu Y. P. , Nan Z. B. , Baskin C. C.
Published: June 2008

Abstract Although many studies have been done on seeds with physical dormancy, i.e. water-impermeable seed or fruit coat, the primary site of water entry into seeds after dormancy-breaking treatments is still controversial. In this work, the role of the lens in physical dormancy breaking was examined. The present study investigated the primary site of water entry and changes in seed-surface features for seeds of Sophora alopecuroides L. following various periods of scarification with sulfuric acid, hot-water treatments, and exposure to field conditions. Most seed coats first cracked in the hilum when pre-treated with sulfuric acid and after field exposure, but they cracked in both the hilum and extrahilar regions when treated with hot water. After pre-treatment, seeds first became slowly permeable in the hilum or extrahilar region and not in the lens. Acid scarification for 35 or 50 min caused the lens to crack, thus causing seeds to enter a fast imbibition stage. Seeds exposed to field conditions had further damage to the hilum, causing them to enter a fast imbibition stage. Imbibition time is a key point that determines the primary site of water entry into seed, and at least in part explains various results and interpretations about the role of the lens in physical dormancy in previous research.
Seed dormancy in barley: identifying superior genotypes through incorporating epistatic interactions
Authors: Bonnardeaux Y. , Li C. , Lance R. , Zhang X. Q. , Sivasithamparam K. , Appels R.
Published: June 2008

A genetic linkage map of barley with 128 molecular markers was constructed using a doubled haploid (DH) mapping population derived from a cross between barley (Hordeum vulgare) cvv. Stirling and Harrington. Quantitative trait loci controlling seed dormancy were characterised in the population. A major quantitative trait locus (QTL) controlling seed dormancy and accounting for over half the phenotypic variation (52.17%) was identified on the distal end of the long arm of chromosome 5H. Minor QTLs were also detected near the centromeric region of 5H and on chromosomes 1H and 3H. These minor QTLs with additive effects accounted for 7.52% of the phenotypic variance measured. Examination of epistatic interactions further detected additional minor QTLs near the centromere of 2H and on the long arm and short arms of 4H. Combinations of parental alleles at the QTL locations in predictive analyses indicated dramatic differences in germination. These results emphasise the potential differences in dormancy that can be achieved through the use of specific gene combinations and highlights the importance of minor genes and the epistatic interactions that occur between them. This study found that the combination of Stirling alleles at the two QTL locations on the 5H chromosome and Harrington alleles at the 1H and 3H QTL locations significantly produced the greatest dormancy. Uncovering gene complexes controlling the trait may enable breeders to produce superior genotypes with the desirable allele combinations necessary for manipulating seed dormancy in barley.
Molecular genetic diversity and linked resistance to ascochyta blight in Australian chickpea breeding materials and their wild relatives
Authors: Imtiaz M. , Materne M. , Hobson K. , van Ginkel M. , Malhotra R. S.
Published: June 2008

Simple sequence-repeat (SSR) and sequence characterised amplified regions (SCARs) have been used to characterise the genetic diversity of chickpea germplasm. A set of 48 genotypes comprising cultigen, landraces, and wild relatives important for breeding purposes was used to determine the genetic similarity between genotypes and to assess the association between ascochyta blight (AB) and SCAR phenotypes. The 21 SSR markers amplified a total of 370 alleles, with an average of ~17 alleles per SSR locus among the 48 genotypes. Polymorphic information content (PIC) values ranged from 0.37 for the XGA13 locus to 0.93 for the XGA106. Principal coordinate analysis (PCO) of genetic similarity (GS) estimates revealed a clear differentiation of the chickpea genotypes into 5 groups, which were generally consistent with available pedigree information. Comparison of SCAR and AB phenotypes enabled us to tag the common source(s) of AB resistance in the breeding collection. Based on the SCAR phenotypes, it was evident that the studied chickpea genotypes, including worldwide-known AB-resistant lines (ICC12004, ILC72, ILC3279), carry at least one common source of resistance to AB. Since SSR markers are polymerase chain reaction (PCR)-based markers, highly polymorphic, and amenable to high-throughput technologies, they are therefore well suited for studies of genetic diversity and cultivar identification in chickpea. The broad level of genetic diversity detected in the chickpea germplasm should be useful for selective breeding for specific traits such as AB, backcrossing, and in enhancing the genetic base of breeding programs.
The effect of endophyte on the performance of irrigated perennial ryegrasses in subtropical Australia
Authors: Lowe K. F. , Bowdler T. M. , Hume D. E. , Casey N. D. , Tapper B. A.
Published: June 2008

The effect of fungal endophyte (Neotyphodium lolii) infection on the performance of perennial ryegrass (Lolium perenne) growing under irrigation in a subtropical environment was investigated. Seed of 4 cultivars, infected with standard (common toxic or wild-type) endophyte or the novel endophyte AR1, or free of endophyte (Nil), was sown in pure swards, which were fertilised with 50 kg N/ha.month. Seasonal and total yield, persistence, and rust susceptibility were assessed over 3 years, along with details of the presence of endophyte and alkaloids in plant shoots.
Endophyte occurrence in tillers in both the standard and AR1 treatments was above 95% for Bronsyn and Impact throughout and rose to that level in Samson by the end of the second year. Meridian AR1 only reached 93% while, in the standard treatment, the endophyte had mostly died before sowing. Nil endophyte treatments carried an average of ~0.6% infection throughout.
Infection of the standard endophyte was associated with increased dry matter (DM) yields in all 3 years compared with no endophyte. AR1 also significantly increased yields in the second and third years. Over the full 3 years, standard and AR1 increased yields by 18% and 11%, respectively. Infection with both endophytes was associated with increased yields in all 4 seasons, the effects increasing in intensity over time. There was 27% better persistence in standard infected plants compared with Nil at the end of the first year, increasing to 198% by the end of the experiment, while for AR1 the improvements were 20 and 134%, respectively. The effect of endophyte on crown rust (Puccinia coronata) infection was inconsistent, with endophyte increasing rust damage on one occasion and reducing it on another. Cultivar differences in rust infection were greater than endophyte effects.
Plants infected with the AR1 endophyte had no detectable ergovaline or lolitrem B in leaf, pseudostem, or dead tissue. In standard infected plants, ergovaline and lolitrem B were highest in pseudostem and considerably lower in leaf. Dead tissue had very low or no detectable ergovaline but high lolitrem B concentrations. Peramine concentration was high and at similar levels in leaf and pseudostem, but not detectable in dead material. Concentration was similar in both AR1 and standard infected plants.
Endophyte presence appeared to have a similar effect in the subtropics as has been demonstrated in temperate areas, in terms of improving yields and persistence and increasing tolerance of plants to stress factors.
Preferential subfunctionalization of slow-evolving genes after allopolyploidization inXenopus laevis
Authors: Sémon Marie , Wolfe Kenneth H.
Published: June 2008

As paleopolyploid genomes evolve, the expression profiles of retained gene pairs are expected to diverge. To examine this divergence process on a large scale in a vertebrate system, we compareXenopus laevis, which has retained ≈40% of loci in duplicate after a recent whole-genome duplication (WGD), with its unduplicated relativeSilurana (Xenopus)tropicalis. This comparison of ingroup pairs to an outgroup allows the direction of change in expression profiles to be inferred for a set of 1,300X. laevispairs, relative to their single orthologs inS. tropicalis, across 11 tissues. We identify 68 pairs in whichX. laevisis inferred to have undergone a significant reduction of expression in at least two tissues since WGD. Of these pairs, one-third show evidence of subfunctionalization, with decreases in the expression levels of different gene copies in two different tissues. Surprisingly, we find that genes with slow rates of evolution are particularly prone to subfunctionalization, even when the tendency for highly expressed genes to evolve slowly is controlled for. We interpret this result to be an effect of allopolyploidization. We then compare the outcomes of this WGD with an independent one that happened in the teleost fish lineage. We find that if a gene pair was retained in duplicate inX. laevis, the orthologous pair is more likely to have been retained in duplicate in zebrafish, suggesting that similar factors, among them subfunctionalization, determined which gene pairs survived in duplicate after the two WGDs.
In vivo
diffusion of lactoferrin in brain extracellular space is regulated by interactions with heparan sulfate
Authors: Thorne Robert G. , Lakkaraju Aparna , Rodriguez-Boulan Enrique , Nicholson Charles
Published: June 2008

The intercellular spaces between neurons and glia contain an amorphous, negatively charged extracellular matrix (ECM) with the potential to shape and regulate the distribution of many diffusing ions, proteins and drugs. However, little evidence exists for direct regulation of extracellular diffusion by the ECM in living tissue. Here, we demonstrate macromolecule sequestration by an ECM component
in vivo
, using quantitative diffusion measurements from integrative optical imaging. Diffusion measurements in free solution, supported by confocal imaging and binding assays with cultured cells, were used to characterize the properties of a fluorescently labeled protein, lactoferrin (Lf), and its association with heparin and heparan sulfate
in vitro. In vivo
diffusion measurements were then performed through an open cranial window over rat somatosensory cortex to measure effective diffusion coefficients (
D
*) under different conditions, revealing that
D
* for Lf was reduced ≈60% by binding to heparan sulfate proteoglycans, a prominent component of the ECM and cell surfaces in brain. Finally, we describe a method for quantifying heparan sulfate binding site density from data for Lf and the structurally similar protein transferrin, allowing us to predict a low micromolar concentration of these binding sites in neocortex, the first estimate in living tissue. Our results have significance for many tissues, because heparan sulfate is synthesized by almost every type of cell in the body. Quantifying ECM effects on diffusion will also aid in the modeling and design of drug delivery strategies for growth factors and viral vectors, some of which are likely to interact with heparan sulfate.
Heterogeneities in granular dynamics
Authors: Mehta A. , Barker G. C. , Luck J. M.
Published: June 2008

The absence of Brownian motion in granular media is a source of much complexity, including the prevalence of heterogeneity, whether static or dynamic, within a given system. Such strong heterogeneities can exist as a function of depth in a box of grains; this is the system we study here. First, we present results from three-dimensional, cooperative and stochastic Monte Carlo shaking simulations of spheres on heterogeneous density fluctuations. Next, we juxtapose these with results obtained from a theoretical model of a column of grains under gravity; frustration via competing local fields is included in our model, whereas the effect of gravity is to slow down the dynamics of successively deeper layers. The combined conclusions suggest that the dynamics of a real granular column can be divided into different phases—ballistic, logarithmic, activated, and glassy—as a function of depth. The nature of the ground states and their retrieval (under zero-temperature dynamics) is analyzed; the glassy phase shows clear evidence of its intrinsic (“crystalline”) states, which lie below a band of approximately degenerate ground states. In the other three phases, by contrast, the system jams into a state chosen randomly from this upper band of metastable states.
GDNF is a fast-acting potent inhibitor of alcohol consumption and relapse
Authors: Carnicella Sebastien , Kharazia Viktor , Jeanblanc Jerome , Janak Patricia H. , Ron Dorit
Published: June 2008

Previously, we demonstrated that the action of the natural alkaloid, ibogaine, to reduce alcohol (ethanol) consumption is mediated by the glial cell line-derived neurotrophic factor (GDNF) in the ventral tegmental area (VTA). Here we set out to test the actions of GDNF in the VTA on ethanol-drinking behaviors. We found that GDNF infusion very rapidly and dose-dependently reduced rat ethanol, but not sucrose, operant self-administration. A GDNF-mediated decrease in ethanol consumption was also observed in rats with a history of high voluntary ethanol intake. We found that the action of GDNF on ethanol consumption was specific to the VTA as infusion of the growth factor into the neighboring substantia nigra did not affect operant responses for ethanol. We further show that intra-VTA GDNF administration rapidly activated the MAPK signaling pathway in the VTA and that inhibition of the MAPK pathway in the VTA blocked the reduction of ethanol self-administration by GDNF. Importantly, we demonstrate that GDNF infused into the VTA alters rats' responses in a model of relapse. Specifically, GDNF application blocked reacquisition of ethanol self-administration after extinction. Together, these results suggest that GDNF, via activation of the MAPK pathway, is a fast-acting selective agent to reduce the motivation to consume and seek alcohol.
Variation in
MAPT
is associated with cerebrospinal fluid tau levels in the presence of amyloid-beta deposition
Authors: Kauwe John S. K. , Cruchaga Carlos , Mayo Kevin , Fenoglio Chiara , Bertelsen Sarah , Nowotny Petra , Galimberti Daniela , Scarpini Elio , Morris John C. , Fagan Anne M. , Holtzman David M. , Goate Alison M.
Published: June 2008

There is substantial evidence that cerebrospinal fluid (CSF) levels of both Aβ42 and tau/ptau are promising biomarkers for Alzheimer's disease (AD). We show that both Aβ and tau exhibit more than 10-fold interindividual variation in CSF levels suggesting that these biomarkers may also be effectively used as endophenotypes for genetic studies of AD. To test the role of common variation in the gene encoding microtubule associated protein tau (
MAPT
) in influencing CSF tau/ptau levels, we genotyped 21
MAPT
single nucleotide polymorphisms (SNPs) in 313 individuals and tested for association with CSF tau/ptau levels. We identified alleles of several SNPs that show association with increased CSF tau/ptau levels. When CSF Aβ42 levels were used to stratify the sample into those with and without likely Aβ deposition in the brain the association was only observed in individuals with evidence of Aβ deposition. This association was replicated in an independent CSF series. When these SNPs were evaluated in a late-onset AD case control series the alleles associated with higher CSF tau/ptau were associated with an earlier age at onset but had no effect on risk for AD.
In vivo
gene expression studies show that these alleles are associated with increased
MAPT
mRNA levels in individuals with evidence of brain Aβ deposition. This endophenotype-based approach provides evidence for a gene (
MAPT
SNPs)–physiological environment (Aβ deposition) interaction that places changes in CSF tau after Aβ deposition and suggest that this interaction predisposes for the development of tauopathy and accelerated disease progression.
Protein kinase C epsilon mediation of CRF- and ethanol-induced GABA release in central amygdala
Authors: Bajo Michal , Cruz Maureen T. , Siggins George R. , Messing Robert , Roberto Marisa
Published: June 2008

In the central amygdala (CeA), ethanol acts via corticotrophin-releasing factor (CRF) type 1 receptors to enhance GABA release. Amygdala CRF mediates anxiety associated with stress and drug dependence, and it regulates ethanol intake. Because mutant mice that lack PKCε exhibit reduced anxiety-like behavior and alcohol consumption, we investigated whether PKCε lies downstream of CRF
1
receptors in the CeA. Compared with PKCε
+/+
CeA neurons, PKCε
−/−
neurons showed increased GABAergic tone due to enhanced GABA release. CRF and ethanol stimulated GABA release in the PKCε
+/+
CeA, but not in the PKCε
−/−
CeA. A PKCε-specific inhibitor blocked both CRF- and ethanol-induced GABA release in the PKCε
+/+
CeA, confirming findings in the PKCε
−/−
CeA. These results identify a PKCε signaling pathway in the CeA that is activated by CRF
1
receptor stimulation, mediates GABA release at nerve terminals, and regulates anxiety and alcohol consumption.
Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes
Authors: Gilbert M. Thomas P. , Drautz Daniela I. , Lesk Arthur M. , Ho Simon Y. W. , Qi Ji , Ratan Aakrosh , Hsu Chih-Hao , Sher Andrei , Dalén Love , Götherström Anders , Tomsho Lynn P. , Rendulic Snjezana , Packard Michael , Campos Paula F. , Kuznetsova Tatyana V. , Shidlovskiy Fyodor , Tikhonov Alexei , Willerslev Eske , Iacumin Paola , Buigues Bernard , Ericson Per G. P. , Germonpré Mietje , Kosintsev Pavel , Nikolaev Vladimir , Nowak-Kemp Malgosia , Knight James R. , Irzyk Gerard P. , Perbost Clotilde S. , Fredrikson Karin M. , Harkins Timothy T. , Sheridan Sharon , Miller Webb , Schuster Stephan C.
Published: June 2008

We report five new complete mitochondrial DNA (mtDNA) genomes of Siberian woolly mammoth (
Mammuthus primigenius
), sequenced with up to 73-fold coverage from DNA extracted from hair shaft material. Three of the sequences present the first complete mtDNA genomes of mammoth clade II. Analysis of these and 13 recently published mtDNA genomes demonstrates the existence of two apparently sympatric mtDNA clades that exhibit high interclade divergence. The analytical power afforded by the analysis of the complete mtDNA genomes reveals a surprisingly ancient coalescence age of the two clades, ≈1–2 million years, depending on the calibration technique. Furthermore, statistical analysis of the temporal distribution of the
14
C ages of these and previously identified members of the two mammoth clades suggests that clade II went extinct before clade I. Modeling of protein structures failed to indicate any important functional difference between genomes belonging to the two clades, suggesting that the loss of clade II more likely is due to genetic drift than a selective sweep.
Regulation of neural progenitor cell state by ephrin-B
Authors: Qiu Runxiang , Wang Xiuyun , Davy Alice , Wu Chen , Murai Kiyohito , Zhang Heying , Flanagan John G. , Soriano Philippe , Lu Qiang
Published: June 2008

Maintaining a balance between self-renewal and differentiation in neural progenitor cells during development is important to ensure that correct numbers of neural cells are generated. We report that the ephrin-B–PDZ-RGS3 signaling pathway functions to regulate this balance in the developing mammalian cerebral cortex. During cortical neurogenesis, expression of ephrin-B1 and PDZ-RGS3 is specifically seen in progenitor cells and is turned off at the onset of neuronal differentiation. Persistent expression of ephrin-B1 and PDZ-RGS3 prevents differentiation of neural progenitor cells. Blocking RGS-mediated ephrin-B1 signaling in progenitor cells through RNA interference or expression of dominant-negative mutants results in differentiation. Genetic knockout of ephrin-B1 causes early cell cycle exit and leads to a concomitant loss of neural progenitor cells. Our results indicate that ephrin-B function is critical for the maintenance of the neural progenitor cell state and that this role of ephrin-B is mediated by PDZ-RGS3, likely via interacting with the noncanonical G protein signaling pathway, which is essential in neural progenitor asymmetrical cell division.