bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular dynamics simulation of discontinuous volume phase transitions in highly-charged crosslinked polyelectrolyte networks with explicit counterions in good solvent
Authors: Yin De-Wei , Yan Qiliang , de Pablo Juan J.
Published: November 2005

The volumetric properties of highly-charged defect-free polyelectrolyte networks with tetrafunctional crosslinks are studied through molecular dynamics simulations in the canonical ensemble. The network backbone monomers, which are monovalent, and the counterions, which are mono-, di-, or trivalent, are modeled explicitly in the simulations, but the solvent is treated implicitly as a dielectric medium of good solvation quality. The osmotic pressure of the network-solvent system is found to depend greatly on the strength of electrostatic interactions. Discontinuous volume phase transitions are observed when the electrostatic interactions are strong, and the onset of these transitions shifts to higher solvent dielectricity as the counterion valency increases. The roles of the various virial contributions to the osmotic pressure are examined. The network elasticity entropy is found to behave nearly classically. As the network contracts and collapses with increasing strength of electrostatic interactions, the loss of counterion entropy leads to increased counterion osmotic pressure contributions via two mechanisms. The reduction in available configurational space increases the counterion translational entropy contribution to the ideal part of the osmotic pressure, and the greater number of counterion-monomer contacts formed due to counterion condensation and confinement increases the counterion excluded-volume entropy contribution to the excess part of the osmotic pressure. These observations contrast the decrease in the single ideal-gas-like counterion translational entropy contribution to the osmotic pressure predicted by the counterion condensation–charge renormalization theory. An accompanying decrease in the total electrostatic energy balances the loss of counterion excluded-volume entropy as the polyelectrolyte networks collapse in low-dielectric solvents. This interplay between the electrostatic energy and the counterion excluded-volume entropy appears to be responsible for the discontinuous volume phase transitions that are observed in polyelectrolyte networks. The structure of the polyelectrolyte network is also found to be affine in the swollen state, with constituent chains nearly fully extended, and nonaffine in the collapsed state, with the chains adopting a Gaussian conformation.
A physical model for the longitudinal polarizabilities of polymer chains
Authors: Berger J. A. , de Boeij P. L. , van Leeuwen R.
Published: November 2005

The aim of this work is to provide a physical model to relate the polarizability per unit cell of oligomers to that of their corresponding infinite polymer chains. For this we propose an extrapolation method for the polarizability per unit cell of oligomers by fitting them to a physical model describing the dielectric properties of polymer chains. This physical model is based on the concept of a dielectric needle in which we assume a polymer chain to be well described by a cylindrically shaped nonconducting rod with a radius much smaller than its length. With this model we study in which way the polarizability per unit cell approaches the limit of the infinite chain. We show that within this model the macroscopic contribution of the induced electric field to the macroscopic electric field vanishes in the limit of an infinite polymer chain, i.e., there is no macroscopic screening. The macroscopic electric field becomes equal to the external electric field in this limit. We show that this identification leads to a relation between the polarizability per unit cell and the electric susceptibility of the infinite polymer chain. We test our dielectric needle model on the polarizability per unit cell of oligomers of the hydrogen chain and polyacetylene obtained earlier using time-dependent current-density-functional theory in the adiabatic local-density approximation and with the Vignale-Kohn functional. We also perform calculations using the same theory on truly infinite polymer chains by employing periodic boundary conditions. We show that by extrapolating the oligomer results according to our dielectric needle model we get good agreement with our results from calculations on the corresponding infinite polymer chains.
Quasi-single helicity state at shallow reversal in TPE-RX reversed-field pinch experiment
Authors: Hirano Y. , Paccagnella R. , Koguchi H. , Frassinetti L. , Sakakita H. , Kiyama S. , Yagi Y.
Published: November 2005

The operating conditions for obtaining a quasi-single helicity (QSH) state with a good reproducibility are found in a reversed-field pinch (RFP) experiment on the large RFP machine, TPE-RX [Y. Yagi et al., Fusion Eng. Des. 45, 421 (1999)]. In these conditions, the reversal of toroidal magnetic field (Bta) is maintained at a very shallow value (∼−0.2mT) after the setting up phase and the following fast current rising phase. After a certain period at this shallow reversal (∼15–25ms), the m∕n=1∕6 mode (m and n being the poloidal and toroidal Fourier mode numbers, respectively) rapidly grows and saturates before the termination of discharge. The growth of this mode dominates the other modes and the QSH state with m∕n=1∕6 is finally achieved. This QSH state can be sustained for a long period (up to ∼45ms) almost until the end of discharge by applying a delayed reversal of Bta with appropriate trigger timing and magnitude. The initial setup of the QSH states shows a reproducibility of almost 100%, but its sustainment for a long period shows a slightly reduced reproducibility (∼85%). The initial rapid growth of the single dominant mode is compared with the numerical results of linear stability and nonlinear three-dimensional (3D) calculations by assuming the experimental magnetic field profile estimated with a standard model. Linear calculations show that the m∕n=1∕6 mode has the maximum growth rate to the ideal magnetohydrodynamic instability and can explain the dominant growth of this mode. The 3D calculations also show a qualitative agreement with the experiment, where under some conditions the m∕n=1∕6 mode becomes dominant after an initial relaxation and continues to the end of the simulation. These results indicate that the present QSH state is the combined result of the linear growth and nonlinear saturation of a particular mode.
Effect of deposition temperature on surface acoustic wave velocity of aluminum nitride films determined by Brillouin spectroscopy
Authors: Assouar M. B. , Riobóo R. J. Jiménez , Vila M. , Alnot P.
Published: November 2005

Brillouin spectroscopy has been used to study the effect of the deposition temperature on the surface acoustic wave (SAW) propagation velocity of aluminum nitride (AlN) films. The results show a dependence of the SAW propagation velocity on the growth temperature of AlN films. The highest value of acoustic velocity was obtained for the film elaborated without heating. Structural characterization of the AlN films synthesized at various deposition temperatures was carried out by x-ray diffraction. These analyses pointed out that the deposition temperature influences the standard deviation of (002) AlN film preferred orientation. The growth temperature clearly influences the acoustical and crystalline properties of AlN thin films.
Classical nucleation theory applied to molecular orientations in vapor-deposited organic thin films
Authors: Kubono Atsushi , Akiyama Ryuichi
Published: November 2005

Molecular orientational mechanism during physical vapor deposition of various linear long-chain compounds has been interpreted on the basis of a classical nucleation theory modified for the anisotropic nucleus formation. In this model, the anisotropy of the surface energy is considered, and initial small nuclei with two fundamental orientations (normal and lateral) are assumed to be formed and dissociated repeatedly by the thermal energy. The critical energy of nucleus formation for each orientation is calculated as a function of the chemical-potential change of the system. The calculated results are similar to those observed for actual orientational phenomena of long-chain molecules at various chemical-potential changes; i.e., a higher substrate temperature and/or a lower deposition rate result/s in a higher degree of normal orientation.
Ta penetration into template-type porous low-k material during atomic layer deposition of TaN
Authors: Furuya Akira , Ohtsuka Nobuyuki , Misawa Kaori , Shimada Miyoko , Ogawa Shinichi
Published: November 2005

Ta penetration into a planar template-type porous low-k film during atomic layer deposition of TaN has been investigated by evaluating relations between Ta penetration and number of deposition cycles, exposure time of Ta precursor per deposition cycle, substrate temperature, and porosity of the porous low-k. The precursors were pentakisdimethylaminotantalum [PDMAT:Ta(N(CH3)2)5] and NH3. The porous low-k was a methylsiloxane (MSX) whose pore size in the maximum distribution and porosity of the porous low-k were 0–1.9nm and 0%–47%. Depth profile of the Ta penetration was measured by transmission electron microscopy and energy dispersive x-ray spectroscopy. The amount of penetrated and the penetration depth depended on the porosity. It was found that the precursors penetrate into the MSX film dominantly by gas phase diffusion through pores connecting from the surface to the inside. Increased surface area of the MSX film due to the pores results in a depletion of precursor at the wafer edge, and that this depletion causes the penetration characteristics at the edge of wafer differ from those at the center of the wafer. Moreover, the thickness required for the pore sealing by additive liner deposition is discussed.
Calculation of Boozer magnetic coordinates for multiple plasma regions (with either closed or open flux surfaces) connected by magnetic separatrices
Authors: Alladio F. , Mancuso A. , Micozzi P. , Rogier F.
Published: November 2005

Magnetic coordinates (ψT=radial label of flux surfaces, θ=poloidal, and ϕ=toroidal angle) are introduced in toroidal magnetoplasma equilibria in order to straighten the field lines [described by: θ−ι̷(ψT)ϕ=constant on any flux surface, ι̷(ψT) being the rotational transform]. The simplest method for analyzing the ideal magnetohydrodynamic (MHD) stability expands the perturbed plasma displacement ξ⃗ in magnetic coordinates and solves the normal mode equation through one-dimensional (1D) radial finite elements. This paper extends the calculation of (Boozer) magnetic coordinates to simply connected equilibria that embed a magnetic separatrix, with regular X-points (B⃗≠0), and reach the symmetry axis, with singular magnetic X-points (B⃗=0). These configurations include multiple plasma regions, whose outermost one (surrounding plasma) is not composed by toroidal surfaces closed around a single magnetic axis. Two examples are chosen: (i) flux-core-spheromak (FCS) configurations, where the surrounding plasma is a screw pinch, with open flux surfaces; (ii) Chandrasekhar–Kendall–Furth (CKF) configurations, where it is a toroidal shell, carved by multiple toroidal plasma regions. This paper shows that a proper ordering of the radial coordinate ψT, the requirement of continuity for θ and ϕ and an ι̷ matching condition (between neighboring mesh points on opposite sides of the connecting separatrix) resolve the ambiguities in the definition of magnetic coordinates in both CKF and FCS cases. However, a few metric coefficients diverge at the separatrices; therefore, often numerical MHD stability codes do not use magnetic coordinates there, but adopt local two-dimensional (2D) finite elements. This paper instead investigates all the divergences, in order to allow for the asymptotic analysis of ξ⃗ near the separatrices, with the purpose of maintaining the magnetic coordinate method and the 1D radial finite elements in the ideal MHD stability analysis.
The phase-space-resolved two-point correlation function of ion density fluctuations
Authors: Diallo Ahmed , Skiff Frederick
Published: November 2005

Ion density fluctuations are resolved in space, time, and parallel velocity using laser-induced fluorescence and a two-point correlation technique. These measurements reveal two parallel wavelengths of distinct correlation lengths, one of which is explained by fluid theory. The other wavelength (referred to as the kinetic component) is ion velocity dependent. The effect of collisions on the fluctuation spectrum is reported. Ion velocity-dependent measurements of the fluctuation-induced transport rate are also presented.
Highly efficient organic light-emitting diodes with hole injection layer of transition metal oxides
Authors: Kim Soo Young , Baik Jeong Min , Yu Hak Ki , Lee Jong-Lam
Published: November 2005

We report on the advantage of interlayers using transition-metal oxides, such as iridium oxide (IrOx) and ruthenium oxide (RuOx), between indium tin oxide (ITO) anodes and 4′-bis[N-(1-naphtyl)-N-phenyl-amino]biphenyl (α-NPD) hole transport layers on the electrical and optical properties of organic light-emitting diodes (OLEDs). The operation voltage at a current density of 100mA∕cm2 decreased from 17to11V for OLEDs with 3-nm-thick IrOx interlayers and from 17to14V for OLEDs with 2-nm-thick RuOx ones. The maximum luminance value increased about 50% in OLED using IrOx and 108% in OLED using RuOx. Synchrotron radiation photoelectron spectroscopy results revealed that core levels of Ru 3d and Ir 4f shifted to high binding energies and that the valence band was splitting from metallic Fermi level as the surface of the transition metal was treated with O2 plasma. This provides evidence that the transition-metal surface transformed to a transition-metal oxide. The surface of the transition metal became smoother with the O2 plasma treatment. The thickness was calculated to be 0.4nm for IrOx and 0.6nm for RuOx using x-ray reflectivity measurements. Secondary electron emission spectra showed that the work function increased by 0.6eV for IrOx and by 0.4eV for RuOx. Thus, the transition-metal oxides lowered the potential barrier for hole injection from ITO to α-NPD, reducing the turn-on voltage of OLEDs and increasing the quantum efficiency.
Effect of plasma peak density on energetic proton emission in ultrashort high-intensity laser-foil interactions
Authors: Wang Xiaofang , Nemoto Koshichi , Nayuki Takuya , Oishi Yuji , Eidmann Klaus
Published: November 2005

The influence of plasma peak density on energetic proton emission from the rear side of a foil irradiated by a 70-fs intense laser pulse at normal incidence has been studied. When the plasma peak density of the foil is overdense, forward energetic proton emission is dominant and attributed to rear surface acceleration. Along with the plasma peak density changed from overdense to underdense, a transition of proton acceleration from the forward to the radial direction is observed, and in the latter case energetic protons are emitted radially and slightly forward.
The compact microcrystalline Si thin film with structure uniformity in the growth direction by hydrogen dilution profile
Authors: Gu Jinhua , Zhu Meifang , Wang Liujiu , Liu Fengzhen , Zhou Bingqing , Zhou Yuqin , Ding Kun , Li Guohua
Published: November 2005

The hydrogen dilution profiling (HDP) technique has been developed to improve the quality and the crystalline uniformity in the growth direction of μc-Si:H thin films prepared by hot-wire chemical-vapor deposition. The high H dilution in the initial growth stage reduces the amorphous transition layer from 30–50 to less than 10 nm. The uniformity of crystalline content Xc in the growth direction was much improved by the proper design of hydrogen dilution profiling which effectively controls the nonuniform transition region of Xc from 300 to less than 30 nm. Furthermore, the HDP approach restrains the formation of microvoids in μc-Si:H thin films with a high Xc and enhances the compactness of the film. As a result the stability of μc-Si:H thin films by HDP against the oxygen diffusion, as well as the electrical property, is much improved.
Optimal design of microscaled scattering optical elements
Authors: Håkansson Andreas , Sánchez-Dehesa José
Published: November 2005

A method of inverse design is applied to generate an optical device that acts as a wavelength demultiplexer. The ultracompact device, only 2μm thick, is designed to separate two wavelengths 1.55μm and 1.50μm, respectively, and consists of five layers of 0.4μm×0.4μm square-shaped bars etched in gallium arsenide. The expected cross talk is suppressed below −25dB for both wavelengths. The proposed device is an example of a scattering optical element, a name here introduced to define a class of computer-generated optical devices and whose functionalities are based on the multiple scattering by their individual constituents. For realization of the aforementioned devices, two-dimensional photonic plates can be prepared by only a single integrated circuit processing procedure followed by micromanipulation assembling.
Sub-bandgap defect states in polycrystalline hafnium oxide and their suppression by admixture of silicon
Authors: Nguyen N. V. , Davydov Albert V. , Chandler-Horowitz Deane , Frank Martin M.
Published: November 2005

The crystallinity of atomic layer deposition hafnium oxide was found to be thickness dependent, with the thinnest films being amorphous and thick films being at least partially crystalline. Hafnium oxide films fabricated by metalorganic chemical vapor deposition are mostly monoclinic. Formation of hafnium silicate by admixture of 20% Si prevents crystallization. Electronic defects are reflected by an absorption feature 0.2–0.3 eV below the optical bandgap. These defects arise in polycrystalline, but not in amorphous, hafnium-based oxides.
Fluidic photonic integrated circuit for in-line detection
Authors: Lien Victor , Zhao Kai , Lo Yu-Hwa
Published: November 2005

We present a microfabricated fluidic photonic integrated circuit (FPIC) performing the detection function for flow cytometry. This device was entirely made of polymer using micromolding and capillary filling techniques. An array waveguide design was chosen to achieve superb sensitivity and the time-of-flight measurement for each particle flowing by. With multichannel sampling and cross-correlation analysis, the results show significant enhancement of detection sensitivity.
Low-power memory device with NiSi2 nanocrystals embedded in silicon dioxide layer
Authors: Yeh P. H. , Yu C. H. , Chen L. J. , Wu H. H. , Liu P. T. , Chang T. C.
Published: November 2005

A metal-oxide-semiconductor structure with NiSi2 nanocrystals embedded in the SiO2 layer has been fabricated. A pronounced capacitance-voltage hysteresis was observed with a memory window of 1 V under the 2 V programming voltage. The processing of the structure is compatible with the current manufacturing technology of semiconductor industry.
Fast and simple one-way quantum key distribution
Authors: Stucki Damien , Brunner Nicolas , Gisin Nicolas , Scarani Valerio , Zbinden Hugo
Published: November 2005

We present and demonstrate a new protocol for practical quantum cryptography, tailored for an implementation with weak coherent pulses to obtain a high key generation rate. The key is obtained by a simple time-of-arrival measurement on the dataline; the presence of an eavesdropper is checked by an interferometer on an additional monitoring line. The setup is experimentally simple; moreover, it is tolerant to reduced interference visibility and to photon number splitting attacks, thus featuring a high efficiency in terms of distilled secret bit per qubit.
Single-quantum-well grating-gated terahertz plasmon detectors
Authors: Shaner E. A. , Lee Mark , Wanke M. C. , Grine A. D. , Reno J. L. , Allen S. J.
Published: November 2005

A grating-gated field-effect transistor fabricated from a single-quantum well in a high-mobility GaAs–AlGaAs heterostructure is shown to function as a continuously electrically tunable photodetector of terahertz radiation via excitation of resonant plasmon modes in the well. Different harmonics of the plasmon wave vector are mapped, showing different branches of the dispersion relation. As a function of temperature, the resonant response magnitude peaks at around 30K. Both photovoltaic and photoconductive responses have been observed under different incident power and bias conditions.
Laser-based ultrasonic generation and detection of zero-group velocity Lamb waves in thin plates
Authors: Prada C. , Balogun O. , Murray T. W.
Published: November 2005

A novel laser-based ultrasonic technique for the inspection of thin plates and membranes is presented, in which a modulated continuous-wave laser source is used to excite narrow bandwidth Lamb waves. The dominant feature in the acoustic spectrum is a sharp resonance peak that occurs at the minimum frequency of the first-order symmetric Lamb mode, where the group velocity of the Lamb wave goes to zero while the phase velocity remains finite. Experimental results with the laser source and receiver on epicenter demonstrate that the zero-group velocity resonance generated with a low-power modulated excitation source can be detected using a Michelson interferometer coupled to a lock-in amplifier. This resonance peak is sensitive to the thickness and mechanical properties of plates and may be suitable, for example, for the measurement and mapping of nanoscale thickness variations.
High electron mobility of 0.1cm2V−1s−1 in the highly ordered columnar phase of hexahexylthiotriphenylene
Authors: Iino Hiroaki , Takayashiki Yukiko , Hanna Jun-ichi , Bushby Richard J. , Haarer Dietrich
Published: November 2005

Negative charge carrier transport has been investigated in the columnar mesophases of 2,3,6,7,10,11-hexahexylthiotriphenylene (HHTT), (the best-known conducting discotic liquid crystal because of its high bulk hole mobility) using the time-of-flight method. It was shown that fast electron transport takes place in the highly ordered helical columnar phase. The electron mobility was 0.08cm2V−1s−1 at 45°C, which was the same as the hole mobility reported previously. Electron transport was also observed in the lower-order columnar hexagonal phase, but an additional slow transit appeared in the transient photocurrents, suggesting ionic transport originating from ionized impurities.
In situ energy dispersive x-ray reflectometry measurements on organic solar cells upon working
Authors: Paci B. , Generosi A. , Albertini V. Rossi , Perfetti P. , de Bettignies R. , Firon M. , Leroy J. , Sentein C.
Published: November 2005

The change in the morphology of plastic solar cells was studied by means of time-resolved energy dispersive x-ray reflectivity (XRR). This unconventional application of the XRR technique allowed the follow up of in situ morphological evolution of an organic photovoltaic device upon working. The study consisted of three steps: A preliminary set of XRR measurements on various samples representing the intermediate stages of cell construction, which provided accurate data regarding the electronic densities of the different layers; the verification of the morphological stability of the device under ambient condition; a real-time collection of XRR patterns, both in the dark and during 15h in artificial light conditions which allowed the changes in the system morphology at the electrode-active layer interface to be monitored. In this way, a progressive thickening of this interface, responsible for a reduction in the performances of the device, was observed directly.
An efficient method of ovarian stimulation and in vitro embryo production from prepubertal lambs
Authors: Morton K. M. , Catt S. L. , Maxwell W. M. C. , Evans G.
Published: November 2005

The production of embryos from prepubertal lambs is inefficient, partly resulting from the low developmental competence of prepubertal lamb oocytes, and partly because a high proportion of lambs fail to respond to hormone stimulation. The development of a hormone stimulation regimen that all lambs respond to would increase the efficiency of breeding from prepubertal animals. Using a hormone stimulation regimen consisting of oestradiol benzoate (50 µg), a norgestomet implant (1.5 mg), pregnant mare serum gonadotrophin (400 IU) and follicle stimulating hormone (130 mg) all lambs (n = 19) responded to hormone stimulation. Uterine and ovarian weight ranged from 2.8 to 7.2 g (11.8 ± 0.7 g) and from 1.7 to 54.1 (12.5 ± 2.9 g), respectively. The number of ovarian follicles and oocytes recovered ranged from 20.0 to 500.0 (118.2 ± 29.2) and from 13.0 to 455.0 (82.0 ± 24.2), respectively, and oocytes suitable for in vitro production were obtained from all 19 lambs. Uterine weight was related to both bodyweight and growth rate (P < 0.05), although ovarian weight and the number of ovarian follicles were not related to either bodyweight or growth rate. Oocyte cleavage varied between hormone-stimulated lambs (0.0–93.0%; P < 0.05), and 484/775 (62.2%) of the oocytes cultured cleaved. Oocytes from 17 of the 19 lambs (89.5%) developed to the blastocyst stage in vitro, and the proportion of zygotes forming a blastocyst (by Day 7) ranged from 0.0 to 66.7% for individual lambs. Overall, 33.9% of zygotes (n = 164) developed to the blastocyst stage, producing 8.6 ± 2.8 blastocysts per lamb.
Selection of ribozymes that catalyse multiple-turnover Diels–Alder cycloadditions by using in vitro compartmentalization
Authors: Agresti Jeremy J. , Kelly Bernard T. , Jäschke Andres , Griffiths Andrew D.
Published: November 2005

In vitro
compartmentalization (IVC) has previously been used to evolve protein enzymes. Here, we demonstrate how IVC can be applied to select RNA enzymes (ribozymes) for a property that has previously been unselectable: true intermolecular catalysis. Libraries containing 10
11
ribozyme genes are compartmentalized in the aqueous droplets of a water-in-oil emulsion, such that most droplets contain no more than one gene, and transcribed
in situ
. By coencapsulating the gene, RNA, and the substrates/products of the catalyzed reaction, ribozymes can be selected for all enzymatic properties: substrate recognition, product formation, rate acceleration, and turnover. Here we exploit the complementarity of IVC with systematic evolution of ligands by exponential enrichment (SELEX), which allows selection of larger libraries (≥10
15
) and for very small rate accelerations (
k
cat
/
k
uncat
) but only selects for intramolecular single-turnover reactions. We selected ≈10
14
random RNAs for Diels–Alderase activity with five rounds of SELEX, then six to nine rounds with IVC. All selected ribozymes catalyzed the Diels–Alder reaction in a truly bimolecular fashion and with multiple turnover. Nearly all ribozymes selected by using eleven rounds of SELEX alone contain a common catalytic motif. Selecting with SELEX then IVC gave ribozymes with significant sequence variations in this catalytic motif and ribozymes with completely novel motifs. Interestingly, the catalytic properties of all of the selected ribozymes were quite similar. The ribozymes are strongly product inhibited, consistent with the Diels–Alder transition state closely resembling the product. More efficient Diels–Alderases may need to catalyze a second reaction that transforms the product and prevents product inhibition.
Community inertia of Quaternary small mammal assemblages in North America
Authors: McGill Brian J. , Hadly Elizabeth A. , Maurer Brian A.
Published: November 2005

One of the longest running debates in ecology is whether chance or determinism structures biotic communities, and this question is often studied by looking for the presence or absence of community inertia (lack of change) over time or space. Results have been equivocal. We adopted three tactics for a fresh approach: (i) allowing the answer to vary with the geographic, temporal, and taxonomic scale of study, (ii) using appropriate reference points for the amount of inertia in random biological systems, and (iii) using a robust approach for measurement of inertia. We examined fossil assemblages of mammalian communities across almost 1,000,000 years and at sites spanning ≈3,500 km. We showed that in general there is good evidence for inertia but that the results change in a quantifiable fashion with taxonomic, spatial, and temporal scales. By using neutral theory we place a reference point on the degree of inertia and demonstrate that empirical mammalian communities show greater inertia than neutral communities over time scales >3,000 year. Although our results do not specifically reveal mechanism, they emphasize that deterministic forces are at work in structuring communities over millennia.
High-efficiency transformation of
Plasmodium falciparum
by the lepidopteran transposable element
piggyBac
Authors: Balu Bharath , Shoue Douglas A. , Fraser Malcolm J. , Adams John H.
Published: November 2005

Functional analysis of the
Plasmodium falciparum
genome is restricted because of the limited ability to genetically manipulate this important human pathogen. We have developed an efficient transposon-mediated insertional mutagenesis method much needed for high-throughput functional genomics of malaria parasites. A drug-selectable marker,
human dihydrofolate reductase,
added to the lepidopteran transposon
piggyBac
, transformed parasites by integration into the
P. falciparum
genome in the presence of a transposase-expressing helper plasmid. Multiple integrations occurred at the expected TTAA target sites throughout the genome of the parasite. We were able to transform
P. falciparum
with this
piggyBac
element at high frequencies, in the range of 10
-3
, and obtain stable clones of insertional mutants in a few weeks instead of 6–12 months. Our results show that the
piggyBac
transposition system can be used as an efficient, random integration tool needed for large-scale, whole-genome mutagenesis of malaria parasites. The availability of such an adaptable genetic tool opens the way for much needed forward genetic approaches to study this lethal human parasite.
Three genomes differentially contribute to the biosynthesis of benzoxazinones in hexaploid wheat
Authors: Nomura Taiji , Ishihara Atsushi , Yanagita Ryo C. , Endo Takashi R. , Iwamura Hajime
Published: November 2005

Hexaploid wheat (
Triticum aestivum
) accumulates benzoxazinones (Bxs) as defensive compounds. Previously, we found that five Bx biosynthetic genes,
TaBx1
-
TaBx5
, are located on each of the three genomes (A, B, and D) of hexaploid wheat. In this study, we isolated three homoeologous cDNAs of each
TaBx
gene to estimate the contribution of individual homoeologous
TaBx
genes to the biosynthesis of Bxs in hexaploid wheat. We analyzed their transcript levels by homoeolog- or genome-specific quantitative RT-PCR and the catalytic properties of their translation products by kinetic analyses using recombinant TaBX enzymes. The three homoeologs were transcribed differentially, and the ratio of the individual homoeologous transcripts to total homoeologous transcripts also varied with the tissue, i.e., shoots or roots, as well as with the developmental stage. Moreover, the translation products of the three homoeologs had different catalytic properties. Some
TaBx
homoeologs were efficiently transcribed, but the translation products showed only weak enzymatic activities, which inferred their weak contribution to Bx biosynthesis. Considering the transcript levels and the catalytic properties collectively, we concluded that the homoeologs on the B genome generally contributed the most to the Bx biosynthesis in hexaploid wheat, especially in shoots. In tetraploid wheat and the three diploid progenitors of hexaploid wheat, the respective transcript levels of the
TaBx
homoeologs were similar in ratio to those observed in hexaploid wheat. This result indicates that the genomic bias in the transcription of the
TaBx
genes in hexaploid wheat originated in the diploid progenitors and has been retained through the polyploidization.
Structural basis of the resistance of an insect carboxypeptidase to plant protease inhibitors
Authors: Bayés Alex , Comellas-Bigler Mireia , de la Vega Monica Rodríguez , Maskos Klaus , Bode Wolfram , Aviles Francesc X. , Jongsma Maarten A. , Beekwilder Jules , Vendrell Josep
Published: November 2005

Corn earworm (Helicoverpa zea), also called tomato fruitworm, is a common pest of many Solanaceous plants. This insect is known to adapt to the ingestion of plant serine protease inhibitors by using digestive proteases that are insensitive to inhibition. We have now identified a B-type carboxypeptidase ofH. zea(CPBHz) insensitive to potato carboxypeptidase inhibitor (PCI) in corn earworm. To elucidate the structural features leading to the adaptation of the insect enzyme, the crystal structure of the recombinant CPBHz protein was determined by x-ray diffraction. CPBHz is a member of the A/B subfamily of metallocarboxypeptidases, which displays the characteristic metallocarboxypeptidase α/β-hydrolase fold, and does not differ essentially from the previously describedHelicoverpa armigeraCPA, which is very sensitive to PCI. The data provide structural insight into several functional properties of CPBHz. The high selectivity shown by CPBHz for C-terminal lysine residues is due to residue changes in the S1′ substrate specificity pocket that render it unable to accommodate the side chain of an arginine. The insensitivity of CPBHz to plant inhibitors is explained by the exceptional positioning of two of the main regions that stabilize other carboxypeptidase–PCI complexes, the β8-α9 loop, and α7 together with the α7-α8 loop. The rearrangement of these two regions leads to a displacement of the active-site entrance that impairs the proper interaction with PCI. This report explains a crystal structure of an insect protease and its adaptation to defensive plant protease inhibitors.
Semantic congruity affects numerical judgments similarly in monkeys and humans
Authors: Cantlon Jessica F. , Brannon Elizabeth M.
Published: November 2005

Monkeys (
Macaca mulatta
) were trained to order visual arrays based on their number of elements and to conditionally choose the array with the larger or smaller number of elements dependent on a color cue. When the screen background was red, monkeys were reinforced for choosing the smaller numerical value first. When the screen background was blue, monkeys were reinforced for choosing the larger numerical value first. Monkeys showed a semantic congruity effect analogous to that reported for human comparison judgments. Specifically, decision time was systematically influenced by the semantic congruity between the cue (“choose smaller” or “choose larger”) and the magnitude of the choice stimuli (small or large numbers of dots). This finding demonstrates a semantic congruity effect in a nonlinguistic animal and provides strong evidence for an evolutionarily primitive magnitude-comparison algorithm common to humans and monkeys.
Structural basis for the recognition between HIV-1 integrase and transcriptional coactivator p75
Authors: Cherepanov Peter , Ambrosio Andre L. B. , Rahman Shaila , Ellenberger Tom , Engelman Alan
Published: November 2005

Integrase (IN) is an essential retroviral enzyme, and human transcriptional coactivator p75, which is also referred to as lens epithelium-derived growth factor (LEDGF), is the dominant cellular binding partner of HIV-1 IN. Here, we report the crystal structure of the dimeric catalytic core domain of HIV-1 IN complexed to the IN-binding domain of LEDGF. Previously identified LEDGF hotspot residues anchor the protein to both monomers at the IN dimer interface. The principal structural features of IN that are recognized by the host factor are the backbone conformation of residues 168–171 from one monomer and a hydrophobic patch that is primarily comprised of α-helices 1 and 3 of the second IN monomer. Inspection of diverse retroviral primary and secondary sequence elements helps to explain the apparent lentiviral tropism of the LEDGF-IN interaction. Because the lethal phenotypes of HIV-1 mutant viruses unable to interact with LEDGF indicate that IN function is highly sensitive to perturbations of the structure around the LEDGF-binding site, we propose that small molecule inhibitors of the protein–protein interaction might similarly disrupt HIV-1 replication.
Studies on the regulation of ornithine decarboxylase in yeast: Effect of deletion in the MEU1 gene
Authors: Chattopadhyay Manas K. , Tabor Celia White , Tabor Herbert
Published: November 2005

Methylthioadenosine is formed during the biosynthesis of spermidine and of spermine and is metabolized by methylthioadenosine phosphorylase, an enzyme missing in several tumor cell lines. In
Saccharomyces cerevisiae
, this enzyme is coded by the
MEU1
gene. We have now studied the effect of the
meu1
deletion on polyamine metabolism in yeast. We found that the effects of the
meu1
Δ mutation mostly depend on the stage of cell growth. As the cell density increases, there is a marked fall in the level of ornithine decarboxylase (ODC) in the
MEU1
+
cells, which we show is caused by an antizyme-requiring degradation system. In contrast, there is only a small decrease in the ODC level in the
meu1
Δ cells. The
meu1
Δ cells have a higher putrescine and a lower spermidine level than
MEU1
+
cells, suggesting that the decreased spermidine level in the
meu1
Δ cultures is responsible for the greater apparent stability of ODC in the
meu1
Δ cells. The lower spermidine level in the
meu1
Δ cells probably results from an inhibition of spermidine synthase by the methylthioadenosine that presumably accumulates in these mutants. In both
MEU1
+
and the
meu1
Δ cultures, the ODC levels were markedly decreased by the addition of spermidine to the media, and thus our results contradict the postulation of Subhi
et al
. [Subhi, A. L.,
et al
. (2003)
J. Biol. Chem.
278, 49868–49873] of a novel regulatory pathway in
meu1
Δ cells in which ODC is not responsive to spermidine.
Detection of functional single-nucleotide polymorphisms that affect apoptosis
Authors: Harris Sandra L. , Gil German , Robins Harlan , Hu Wenwei , Hirshfield Kim , Bond Elisabeth , Bond Gareth , Levine Arnold J.
Published: November 2005

Human EBV-transformed B lymphocyte cell lines (LCLs) were used to measure the apoptotic response of individuals to γ radiation. The responses form a normal distribution around a median of 35.5% apoptosis with a range of 12-58%. This heterogeneous response has a genetic basis. LCLs from Caucasian donors and African American donors form distinct distributions of apoptotic response; all of the 11 LCLs comprising the lowest responding group (exhibiting between 12-20% apoptosis) are from Caucasian donors. The assay is capable of detecting significant effects of SNPs in two genes,
MDM2
and
AKT1
, whose products are involved in controlling the p53 pathway and cellular response to DNA damage, suggesting that these data and this assay can be used to identify novel SNPs in other genes whose products impact the cellular response to radiation. Finally, the LCLs in the lowest apoptotic response group have the highest concentration of AKT1 protein and all harbor a haplotype in
AKT1
that is present in Caucasians but absent in African Americans.
A cAMP-response element binding protein-induced microRNA regulates neuronal morphogenesis
Authors: Vo Ngan , Klein Matthew E. , Varlamova Olga , Keller David M. , Yamamoto Tadashi , Goodman Richard H. , Impey Soren
Published: November 2005

MicroRNAs (miRNAs) regulate cellular fate by controlling the stability or translation of mRNA transcripts. Although the spatial and temporal patterning of miRNA expression is tightly controlled, little is known about signals that induce their expression nor mechanisms of their transcriptional regulation. Furthermore, few miRNA targets have been validated experimentally. The miRNA, miR132, was identified through a genome-wide screen as a target of the transcription factor, cAMP-response element binding protein (CREB). miR132 is enriched in neurons and, like many neuronal CREB targets, is highly induced by neurotrophins. Expression of miR132 in cortical neurons induced neurite outgrowth. Conversely, inhibition of miR132 function attenuated neuronal outgrowth. We provide evidence that miR132 regulates neuronal morphogenesis by decreasing levels of the GTPase-activating protein, p250GAP. These data reveal that a CREB-regulated miRNA regulates neuronal morphogenesis by responding to extrinsic trophic cues.
Methylprednisolone neutralizes the beneficial effects of erythropoietin in experimental spinal cord injury
Authors: Gorio Alfredo , Madaschi Laura , Di Stefano Barbara , Carelli Stephana , Di Giulio Anna Maria , De Biasi Silvia , Coleman Thomas , Cerami Anthony , Brines Michael
Published: November 2005

Inflammation plays a major pathological role in spinal cord injury (SCI). Although antiinflammatory treatment using the glucocorticoid methyprednisolone sodium succinate (MPSS) improved outcomes in several multicenter clinical trials, additional clinical experience suggests that MPSS is only modestly beneficial in SCI and poses a risk for serious complications. Recent work has shown that erythropoietin (EPO) moderates CNS tissue injury, in part by reducing inflammation, limiting neuronal apoptosis, and restoring vascular autoregulation. We determined whether EPO and MPSS act synergistically in SCI. Using a rat model of contusive SCI, we compared the effects of EPO [500-5,000 units/kg of body weight (kg-bw)] with MPSS (30 mg/kg-bw) for proinflammatory cytokine production, histological damage, and motor function at 1 month after a compression injury. Although high-dose EPO and MPSS suppressed proinflammatory cytokines within the injured spinal cord, only EPO was associated with reduced microglial infiltration, attenuated scar formation, and sustained neurological improvement. Unexpectedly, coadministration of MPSS antagonized the protective effects of EPO, even though the EPO receptor was up-regulated normally after injury. These data illustrate that the suppression of proinflammatory cytokines alone does not necessarily prevent secondary injury and suggest that glucocorticoids should not be coadministered in clinical trials evaluating the use of EPO for treatment of SCI.
Epidermal growth factor receptor signaling is required for normal ovarian steroidogenesis and oocyte maturation
Authors: Jamnongjit Michelle , Gill Arvind , Hammes Stephen R.
Published: November 2005

The midcycle luteinizing hormone (LH) surge triggers several tightly linked ovarian processes, including steroidogenesis, oocyte maturation, and ovulation. We designed studies to determine whether epidermal growth factor receptor (EGFR)-mediated signaling might serve as a common regulator of these activities. Our results showed that EGF promoted steroidogenesis in two different
in vitro
models of oocyte-granulosa cell complexes. Inhibition of the EGFR kinase prevented EGF-induced steroidogenesis in these
in vitro
systems and blocked LH-induced steroidogenesis in intact follicles primed with pregnant mare serum gonadotropin. Similarly, inhibition of the EGFR kinase attenuated LH-induced steroidogenesis in MA-10 Leydig cells. Together, these results indicate that EGFR signaling is critical for normal gonadotropin-induced steroidogenesis in both male and female gonads. Interestingly, inhibition of metalloproteinase-mediated cleavage of membrane-bound EGF moieties abrogated LH-induced steroidogenesis in ovarian follicles but not MA-10 cells, suggesting that LH receptor signaling activates the EGFR by different mechanisms in these two models. Finally, steroids promoted oocyte maturation in several ovarian follicle models, doing so by signaling through classical steroid receptors. We present a model whereby steroid production may serve as one of many integrated signals triggered by EGFR signaling to promote oocyte maturation in gonadotropin-stimulated follicles.
Traffic of Kv4 K+ channels mediated by KChIP1 is via a novel post-ER vesicular pathway
Authors: Hasdemir Burcu , Fitzgerald Daniel J. , Prior Ian A. , Tepikin Alexei V. , Burgoyne Robert D.
Published: November 2005

The traffic of Kv4 K+ channels is regulated by the potassium channel interacting proteins (KChIPs). Kv4.2 expressed alone was not retained within the ER, but reached the Golgi complex. Coexpression of KChIP1 resulted in traffic of the channel to the plasma membrane, and traffic was abolished when mutations were introduced into the EF-hands with channel captured on vesicular structures that colocalized with KChIP1(2–4)-EYFP. The EF-hand mutant had no effect on general exocytic traffic. Traffic of Kv4.2 was coat protein complex I (COPI)–dependent, but KChIP1-containing vesicles were not COPII-coated, and expression of a GTP-loaded Sar1 mutant to block COPII function more effectively inhibited traffic of vesicular stomatitis virus glycoprotein (VSVG) than did KChIP1/Kv4.2 through the secretory pathway. Therefore, KChIP1seems to be targeted to post-ER transport vesicles, different from COPII-coated vesicles and those involved in traffic of VSVG. When expressed in hippocampal neurons, KChIP1 co-distributed with dendritic Golgi outposts; therefore, the KChIP1 pathway could play an important role in local vesicular traffic in neurons.
Excess of Gβe over Gqαe in vivo prevents dark, spontaneous activity of Drosophila photoreceptors
Authors: Elia Natalie , Frechter Shahar , Gedi Yinon , Minke Baruch , Selinger Zvi
Published: November 2005

Drosophila melanogaster photoreceptor cells are capable of detecting single photons. This utmost sensitivity is critically dependent on the maintenance of an exceedingly low, dark, spontaneous activity of photoreceptor cells. However, the underlying mechanisms of this hallmark of phototransduction are not fully understood. An analysis of the Drosophila visual heterotrimeric (αβγ) Gq protein revealed that wild-type Drosophila flies have about a twofold excess of Gβ over Gα subunits of the visual Gq protein. Studies of Gβe mutants in which the excess of Gβ was genetically eliminated showed dramatic dark, spontaneous activity of the photoreceptor cells, whereas concurrent genetic reduction of the Gα subunit, which restored the excess of Gβ, abolished this effect. These results indicate that an excess of Gβ over Gα is a strategy used in vivo for the suppression of spontaneous activity, thereby yielding a high signal to noise ratio, which is characteristic of the photoreceptor light response. This mechanism could be relevant to the regulation of G protein signaling in general.
A role for dual viral hits in causation of subacute sclerosing panencephalitis
Authors: Oldstone Michael B.A. , Dales Samuel , Tishon Antoinette , Lewicki Hanna , Martin Lee
Published: November 2005

Subacute sclerosing panencephalitis (SSPE) is a progressive fatal neurodegenerative disease associated with persistent infection of the central nervous system (CNS) by measles virus (MV), biased hypermutations of the viral genome affecting primarily the matrix (M) gene with the conversion of U to C and A to G bases, high titers of antibodies to MV, and infiltration of B cells and T cells into the CNS. Neither the precipitating event nor biology underlying the MV infection is understood, nor is their any satisfactory treatment. We report the creation of a transgenic mouse model that mimics the cardinal features of SSPE. This was achieved by initially infecting mice expressing the MV receptor with lymphocytic choriomeningitis virus Cl 13, a virus that transiently suppressed their immune system. Infection by MV 10 days later resulted in persistent MV infection of neurons. Analysis of brains from infected mice showed the biased U to C hypermutations in the MV M gene and T and B lymphocyte infiltration. These sera contained high titers of antibodies to MV. Thus, a small animal model is now available to both molecularly probe the pathogenesis of SSPE and to test a variety of therapies to treat the disease.