bluuebunny/crossref_metadata_2025 huggingface dataset:
Deposition of sol-gel derived lead lanthanum zirconate titanate thin films on copper substrates
Authors: Narayanan M. , Kwon D.-K. , Ma B. , Balachandran U.
Published: June 2008

Lead lanthanum zirconate titanate (PLZT) thin films were directly deposited on copper substrates by chemical solution deposition and crystallized at temperatures of ⩾650°C under low pO2 conditions. Although the crystallization conditions used are conducive for copper oxidation, a thin layer (∼115nm) of PLZT was sufficient to protect the underlying copper from oxidation. Films exhibited well saturated hysteresis loops with remanent polarization ∼24μC∕cm2 and dielectric constants ∼730. Indirect evidence suggests that the oxygen vacancies created during the high temperature processing are responsible for the degradation of the electrical properties of these thin films. Techniques for avoiding this problem are proposed.
Refractive indices and elasto-optic coefficients of GaN studied by optical waveguiding
Authors: Pezzagna S. , Brault J. , Leroux M. , Massies J. , de Micheli M.
Published: June 2008

Asymmetric GaN planar waveguides were grown on (0001) sapphire by molecular beam epitaxy or by metal-organic chemical vapor deposition. The GaN chromatic dispersion is measured in these samples by the prism coupling method at several discrete wavelengths over a large spectral domain (458–1550 nm). Two-term Sellmeier equations are adequate to fit the ordinary no and extraordinary ne refractive index curves as a function of wavelength. GaN waveguides were also grown on AlxGa1−xN and AlN cladding layers, and the GaN refractive indices are further measured from these samples. On the other hand, the biaxial stress state of each sample is determined by measuring the A, B, and C free exciton transition energies by low temperature (10 K) reflectivity measurements. The refractive indices versus in-plane stress σ1 reveal linear variations in the studied range and the slopes ∂n/∂σ1 are determined. It is found that these variations are more than seven times larger for the ordinary index than for the extraordinary index depending on the optical wavelength. We report here for the first time the measurement of the elasto-optic coefficients (p11+p12) and p13 of GaN in the visible wavelength range.
Ab initio calculations of structural and energetic properties of defects in gallium nitride
Authors: Xiao H. Y. , Zu X. T. , Gao Fei , Weber W. J.
Published: June 2008

Ab initio total energy calculations have been performed to investigate the properties of intrinsic defects in GaN. It is found that the nitrogen defects are more stable than the Ga defects under nitrogen-rich conditions, and the results are generally consistent with those obtained by recent first-principles calculations. For the four types of nitrogen interstitials investigated, relaxation of all configurations leads to a N–N⟨112¯0⟩ split configuration. The most stable configuration for Ga interstitials is the Ga octahedral interstitial, but the energy difference between the octahedral and tetrahedral configurations is small (<0.35 eV) and depends on the basis set employed. While the ⟨N–N⟩ bond distance in the N–N split interstitial is very close to that of a free N2 molecule, the Mulliken charge analysis indicates that the N atoms are partially charged, which is in contrast with previous theoretical suggestions. Based on the calculated results, the relative stabilities of various defects in GaN are determined.
Formulization of long-time domain switching around the coercive field from imprint measurements on ferroelectric thin films
Authors: Jiang A. Q. , Fei J. W. , Lin Y. Y. , Tang T. A.
Published: June 2008

The time interval for the completion of slow polarization reversal in ferroelectric thin films measured in the order of magnitude of 10−9–100s is broadened by more than two decades as the applied field approaches the coercive field of domain switching. The domain-switching kinetics is conjectured to change from the classical Kolmogorov–Avrami–Ishibashi (KAI) model at high fields to nucleation-limited-switching (NLS) model at low fields. However, the true voltage drop across the film from the real-time measurement of the oscilloscope remains constant at a coercive voltage Vc during polarization reversal irrespective of the applied voltage. Therefore, the above high-field assumption for KAI does not exist. From our measurements, a long-time effect of imprint can occur for any slow processes of physical phenomena, even if the imprint field is very weak. The imprinted Vc can be estimated either from the voltage shift in the curve of switched polarization versus the applied voltage or directly from the height variation in domain-switching current plateau after an imprint voltage Vimp for time timp (1μs<timp<10ms). Vc reduces continually with timp under Vimp>0 to exhibit a linear time dependence in a logarithmic scale above an initial time on the order of 1.0μs, even if under Vimp<Vc, which foretells the possibility of the initial unswitched domains with negative polarizations to switch into positive states with the prolonged imprint time under a positive voltage of Vimp. After formulation of the Vc-timp dependence under Vimp according to imprint principles, we derive the time evolution of slow polarization reversal without evoking KAI and NLS approaches once the Vc distribution is obtained for a genuine thin film. The spectrum derivation is completely comparable to experimental measurements, which suggests the common physics between imprint and long-time domain switching of ferroelectric thin films.
Characterization of ZnO plasma in a radio frequency sputtering system
Authors: Joshy N. V. , Isaac Johney , Jayaraj M. K.
Published: June 2008

Plasma generated by the radio frequency (rf) magnetron sputtering of gallium doped zinc oxide (ZnO) has been studied using cylindrical Langmuir probe and optical emission spectroscopy. The electron density and electron temperature were calculated for various rf powers at different spatial positions along the propagation direction of the plume. The electron density was found to increase with argon gas pressure whereas electron temperature decreased. The focusing of the plasma due to the magnetic field of the magnetron was observed at 3cm distance from the target at low rf powers, while shift in the focusing of the plume was observed for high sputtering powers. Plasma potential of the plume was also evaluated at all sputtering conditions and its spatial variations were studied. Optical emission spectra of the plume were recorded at various spatial positions of the plume to get qualitative estimate of species in the plasma at various sputtering conditions. ZnO thin films were deposited on glass substrates placed at 3 and 6cm distances from the target at different sputtering conditions. X-ray diffraction and scanning electron microscopy studies were carried out to investigate the crystallographic properties and the surface morphology of films deposited at these distances in relation to the plasma parameters.
All-optical switching and multistability in photonic structures with liquid crystal defects
Authors: Miroshnichenko Andrey E. , Brasselet Etienne , Kivshar Yuri S.
Published: June 2008

We demonstrate that one-dimensional photonic crystals with pure nematic liquid-crystal defects can operate as all-optical switching devices based on optical orientational nonlinearities of liquid crystals. We show that such a periodic structure is responsible for a modulated threshold of the optical Fréedericksz transition in the spectral domain, and this leads to all-optical switching and light-induced multistability. This effect has no quasistatics electric field analog, and it results from nonlinear coupling between light and a defect mode.
Modeling and characterization of a cantilever-based near-field scanning microwave impedance microscope
Authors: Lai K. , Kundhikanjana W. , Kelly M. , Shen Z. X.
Published: June 2008

This paper presents a detailed modeling and characterization of a microfabricated cantilever-based scanning microwave probe with separated excitation and sensing electrodes. Using finite-element analysis, we model the tip-sample interaction as small impedance changes between the tip electrode and the ground at our working frequencies near 1GHz. The equivalent lumped elements of the cantilever can be determined by transmission line simulation of the matching network, which routes the cantilever signals to 50Ω feed lines. In the microwave electronics, the background common-mode signal is canceled before the amplifier stage so that high sensitivity (below 1aF capacitance changes) is obtained. Experimental characterization of the microwave microscope was performed on ion-implanted Si wafers and patterned semiconductor samples. Pure electrical or topographical signals can be obtained from different reflection modes of the probe.
Parametrically pumped ultrahigh Q electromechanical resonator
Authors: Mahboob I. , Yamaguchi H.
Published: June 2008

The spectral purity of an electromechanical resonance (quality factor Q) can be enhanced by more than one order of magnitude to ∼2.5×106 by parametrically exciting the fundamental mode via double frequency modulations to the spring constant mediated by the piezoelectric effect. We theoretically demonstrate that this Q enhancement is an intrinsic property of the parametric resonator by solving the equation of motion for this system. The Q enhancement demonstrated here results in smaller perturbations in the resonance (∼0.05Hz) becoming visible which enables the charge sensitivity of the electromechanical oscillator to improve by a factor equal to the Q enhancement.
Electron transport through electrically induced nanoconstrictions in HfSiON gate stacks
Authors: Miranda E. , Falbo P. , Nafría M. , Crupi F.
Published: June 2008

A microscopic picture for the progressive leakage current growth in electrically stressed HfxSi1−xON∕SiON gate stacks in metal-oxide-semiconductor transistors based on the physics of mesoscopic conductors is proposed. The breakdown spot is modeled as a nanoconstriction connecting two electron reservoirs. We show that after eliminating the tunneling current component that flows through the nondamaged device area, the postbreakdown conductance exhibits levels of the order of the quantum unit 2e2∕h, where e is the electron charge and h the Planck’s constant, as is expected for atomic-sized contacts. Similarities and differences with previous studied systems are discussed.
Ultraviolet photoluminescence from 6H silicon carbide nanoparticles
Authors: Rossi Andrea M. , Murphy Thomas E. , Reipa Vytas
Published: June 2008

We report stable photoluminescence from 6H silicon carbide nanocrystals dispersed in three different solvents: water, hydrofluoric acid, and toluene. Transmission electron micrograph surveys reveal a size distribution that contains a significant fraction of monocrystal particles with diameters below 3nm—small enough for quantum confinement to play a role in increasing the effective bandgap energy. The ultraviolet photoluminescence band observed at 3.5eV in the colloidal solutions is consistent with quantum confinement estimates based on the effective mass model.
Effect of InGaN quantum dot size on the recombination process in light-emitting diodes
Authors: Park Il-Kyu , Kwon Min-Ki , Cho Chu-Young , Kim Ja-Yeon , Cho Chang-Hee , Park Seong-Ju
Published: June 2008

The effect of InGaN quantum dot (QD) size on the performance of light-emitting diodes (LEDs) was investigated by varying the QD size from 1.32to2.81nm. The electroluminescence peak of the LEDs containing small QDs (1.32nm) was redshifted with increasing input current while that of large QDs (2.81nm) was blueshifted up to 40mA due to the screening effect of the piezoelectric field. The optical output power of LEDs fabricated with small QDs was much higher compared to those with large QDs. These results were attributed to a weaker piezoelectric field and enhanced quantum confinement in small QDs.
High-performance AlGaN∕GaN lateral field-effect rectifiers compatible with high electron mobility transistors
Authors: Chen Wanjun , Wong King-Yuen , Huang Wei , Chen Kevin J.
Published: June 2008

A high electron mobility transistor (HEMT)-compatible power lateral field-effect rectifier (L-FER) with low turn-on voltage is demonstrated using the same fabrication process as that for normally off AlGaN∕GaN HEMT, providing a low-cost solution for GaN power integrated circuits. The power rectifier features a Schottky-gate-controlled two-dimensional electron gas channel between the cathode and anode. By tying up the Schottky gate and anode together, the forward turn-on voltage of the rectifier is determined by the threshold voltage of the channel instead of the Schottky barrier. The L-FER with a drift length of 10μm features a forward turn-on voltage of 0.63V at a current density of 100A∕cm2. This device also exhibits a reverse breakdown voltage (BV) of 390V at a current level of 1mA∕mm and a specific on resistance (RON,sp) of 1.4mΩcm2, yielding a figure of merit (BV2∕RON,sp) of 108MW∕cm2. The excellent device performance, coupled with the lateral device structure and process compatibility with AlGaN∕GaN HEMT, make the proposed L-FER a promising candidate for GaN power integrated circuits.
A 140GHz prepolarizer for dissolution dynamic nuclear polarization
Authors: Jannin S. , Comment A. , Kurdzesau F. , Konter J. A. , Hautle P. , van den Brandt B. , van der Klink J. J.
Published: June 2008

Apart from their very classical use to build polarized targets for particle physics, the methods of dynamic nuclear polarization (DNP) have more recently found application for sensitivity enhancement in high-resolution NMR, both in the solid and in the liquid state. It is often thought that the possible signal enhancement in such applications deteriorates when the DNP is performed at higher fields. We show that for a dissolution-DNP method that uses conventional (2,2,6,6-tetramethylpiperidine 1-oxyl) radicals as the paramagnetic agent, this is not the case for fields up to 5T.
Formation of nickel-based nanocrystal monolayers for nonvolatile memory applications
Authors: Jang Yoo-Sung , Yoon Jong-Hwan , Elliman Robert G.
Published: June 2008

A simple method for fabricating metal silicide nanocrystal layers with narrow spatial distributions is demonstrated and shown to produce structures suitable for nonvolatile memory applications. The method is based on high-temperature annealing of a sandwich structure comprised of a thin metal (Ni) film sandwiched between two silicon-rich oxide (SiOx) layers and has the feature in which the size of the NCs can be controlled by varying the silicon concentrations in the SiOx layers or the initial nickel film thickness. The typical nanocrystal diameters and densities are 3.6nm and 1.2×1012cm−2, respectively. Capacitance-voltage (C-V) measurements on test structures with these characteristics are shown to have C-V characteristics suitable for nonvolatile memory applications, including a C-V memory window of 11.7V for sweep voltages between −12V and +12.
Highly efficient green phosphorescent organic light-emitting diodes with simplified device geometry
Authors: Haldi A. , Domercq B. , Kippelen B. , Hreha R. D. , Cho J.-Y. , Marder S. R.
Published: June 2008

We report on the performance of green phosphorescent organic light-emitting diodes based on the well-known host 4,4′-di(carbazol-9-yl)-biphenyl and the green phosphor emitter fac tris(2-phenylpyridinato-N,C2′) iridium. Using a spin-coated hole-injection/transport layer of poly(N-vinyl-carbazole) and a hole-blocking/electron-transport layer of 2,9-dimethyl-4,7-diphenyl-1,10-phenanthroline, devices with efficiencies of 21.2% and 72cd∕A at 100cd∕m2 were obtained in a simplified device geometry that requires the deposition of only two organic layers from the vapor phase.
Tunneling-injection of electrons and holes into quantum dots: A tool for high-power lasing
Authors: Han Dae-Seob , Asryan Levon V.
Published: June 2008

We study the optical output power of a semiconductor laser, which exploits tunneling-injection of electrons and holes into quantum dots (QDs) from two separate quantum wells. Even if there is out-tunneling leakage of carriers from QDs, the intensity of parasitic recombination outside QDs remains restricted with increasing injection current. As a result, the light-current characteristic becomes increasingly linear, and the slope efficiency grows closer to unity at high injection currents—a fascinating feature favoring the use of tunneling-injection of both electrons and holes into QDs for high-power lasing.
s- and r-Process Element Abundances in the CMD of 47 Tucanæ Using the Robert Stobie Spectrograph on SALT
Authors: Worley C. C. , Cottrell P. L. , Wylie de Boer E. C.
Published: June 2008

A recent study by Wylie et al. (2006) has revealed that s-process element abundances are enhanced relative to iron in both red giant branch and asymptotic giant branch stars of 47 Tuc. A more detailed investigation into s-process element abundances throughout the colour-magnitude diagram of 47 Tuc is vital in order to determine whether the observed enhancements are intrinsic to the cluster. This paper explores this possibility through observational and theoretical means. The visibility of s- and r-process element lines in synthetic spectra of giant and dwarf stars throughout the colour magnitude diagram of 47 Tuc has been explored. It was determined that a resolving power of 10 000 was sufficient to observe s-process element abundance variations in globular cluster giant-branch stars. These synthetic results were compared with the spectra of eleven 47 Tuc giant branch stars observed during the performance verification of the Robert Stobie Spectrograph on the Southern African Large Telescope. Three s-process elements (Zr, Ba and Nd) and one r-process element (Eu) were investigated. No abundance variations were found such that [X/Fe] = 0.0 ± 0.5 dex. It was concluded that this resolving power, R ∼ 5000, was not sufficient to obtain exact abundances but upper limits on the s-process element abundances could be determined.
The Coherent Radio Emission from the RS CVn Binary HR 1099
Authors: Slee O. B. , Wilson W. , Ramsay G.
Published: June 2008

The Australia Telescope was used in March–April 2005 to observe the 1.384 and 2.368-GHz emissions from the RS CVn binary HR 1099 in two sessions, each of 9-h duration and 11 days apart. Two intervals of highly polarised emission, each lasting 2–3 h, were recorded. During this coherent emission we employed a recently installed facility to sample the data at 78-ms intervals to measure the fine temporal structure and, in addition, all the data were used to search for fine spectral structure. We present the following observational results: (1) ∼100% left-hand circularly polarised emission was seen at both 1.384 and 2.368 GHz during separate epochs; (2) the intervals of highly polarised emission lasted for 2–3 h on each occasion; (3) three 22-min integrations made at 78-ms time resolution showed that the modulation index of the StokesVparameter increased monotonically as the integration time was decreased and was still increasing at our resolution limit; (4) the extremely fine temporal structure strongly indicates that the highly polarised emission is due to an electron-cyclotron maser operating in the corona of one of the binary components; (5) the first episode of what we believe is ECME (electron-cyclotron maser emission) at 1.384 GHz contained a regular frequency structure of bursts with FWHM ∼48 MHz, which drifted across the spectrum at ∼0.7 MHz min−1. Our second episode of ECME at 2.368 GHz contained wider-band frequency structure, which did not permit us to estimate an accurate bandwidth or direction of drift; (6) the two ECME events reported in this paper agree with six others reported in the literature in occurring in the binary orbital phase range 0.5–0.7; (7) in one event of 8-h duration, two independent maser sources were operating simultaneously at 1.384 and 2.368 GHz.

We discuss two kinds of maser sources that may be responsible for driving the observed events that we believe are powered by ECME. One is based on the widely reported ‘loss-cone anisotropy', the second on an auroral analogue, which is driven by an unstable ‘horseshoe' distribution of fast-electron velocities with respect to the magnetic field direction. Generally, we favour the latter, because of its higher growth rate and the possibility of the escape of radiation which has been emitted at the fundamental electron cyclotron frequency. If the auroral analogue is operating, the magnetic field in the source cavity is ∼500 G at 1.384 GHz and ∼850 G at 2.368 GHz; the source brightness temperatures are of the orderTB∼ 1015K.

We suggest that the ECME source may be an aurora-like phenomenon due to the transfer of plasma from the K2 subgiant to the G5 dwarf in a strong stellar wind, an idea that is based on VLBA maps showing the establishment of an 8.4 GHz source near the G5 dwarf at times of enhanced radio activity in HR 1099.
A Pilot Survey for the H2O Southern Galactic Plane Survey
Authors: Walsh Andrew J. , Lo Nadia , Burton Michael G. , White Graeme L. , Purcell Cormac R. , Longmore Steven N. , Phillips Chris J. , Brooks Kate J.
Published: June 2008

We describe observations with the Mopra radiotelescope designed to assess the feasibility of the H2O Maser Southern Galactic Plane Survey. We mapped two one-square-degree regions along the Galactic plane using the new 12-mm receiver and the UNSW Mopra spectrometer. We covered the entire spectrum between 19.5 and 27.5 GHz using this setup with the main aim of finding out which spectral lines can be detected with a quick mapping survey. We report on detected emission from H2O masers, NH3 inversion transitions (1,1), (2,2) and (3,3), HC3N (3–2), as well as several radio recombination lines.
Comparative molecular modeling ofAnopheles gambiaeCYP6Z1, a mosquito P450 capable of metabolizing DDT
Authors: Chiu Ting-Lan , Wen Zhimou , Rupasinghe Sanjeewa G. , Schuler Mary A.
Published: June 2008

One of the challenges faced in malarial control is the acquisition of insecticide resistance that has developed in mosquitoes that are vectors for this disease.Anopheles gambiae, which has been the major mosquito vector of the malaria parasitePlasmodium falciparumin Africa, has over the years developed resistance to insecticides including dieldrin, 1,1-bis(p-chlorophenyl)-2,2,2-trichloroethane (DDT), and pyrethroids. Previous microarray studies using fragments of 230An. gambiaegenes identified five P450 loci, including CYP4C27, CYP4H15, CYP6Z1, CYP6Z2, and CYP12F1, that showed significantly higher expression in the DDT-resistantZAN/Ustrain compared with the DDT-susceptibleKisumustrain. To predict whether either of the CYP6Z1 and CYP6Z2 proteins might potentially metabolize DDT, we generated and compared molecular models of these two proteins with and without DDT docked in their catalytic sites. This comparison indicated that, although these two CYP6Z proteins share high sequence identity, their metabolic profiles were likely to differ dramatically from the larger catalytic site of CYP6Z1, potentially involved in DDT metabolism, and the more constrained catalytic site of CYP6Z2, not likely to metabolize DDT. Heterologous expressions of these proteins have corroborated these predictions: only CYP6Z1 is capable of metabolizing DDT. Overlays of these models indicate that slight differences in the backbone of SRS1 and variations of side chains in SRS2 and SRS4 account for the significant differences in their catalytic site volumes and DDT-metabolic capacities. These data identify CYP6Z1 as one important target for inhibitor design aimed at inactivating insecticide-metabolizing P450s in natural populations of this malarial mosquito.
Multiphoton fabrication of chemically responsive protein hydrogels for microactuation
Authors: Kaehr Bryan , Shear Jason B.
Published: June 2008

We report a method for creating stimuli-responsive biomaterials in which scanning nonlinear excitation is used to photocrosslink proteins at submicrometer 3D coordinates. Proteins with differing hydration properties can be combined to achieve tunable volume changes that are rapid and reversible in response to changes in chemical environment. Protein matrices having arbitrary 3D topographies and definable density gradients over micrometer dimensions provide the ability to effect rapid (<1 sec) and precise mechanical manipulations by means of changes in hydrogel size and shape, and applicability of these materials to cell biology is shown through the fabrication of responsive bacterial cages.
Force-generation and dynamic instability of microtubule bundles
Authors: Laan Liedewij , Husson Julien , Munteanu E. Laura , Kerssemakers Jacob W. J. , Dogterom Marileen
Published: June 2008

Individual dynamic microtubules can generate pushing or pulling forces when their growing or shrinking ends are in contact with cellular objects such as the cortex or chromosomes. These microtubules can operate in parallel bundles, for example when interacting with mitotic chromosomes. Here, we investigate the force-generating capabilities of a bundle of growing microtubules and study the effect that force has on the cooperative dynamics of such a bundle. We used an optical tweezers setup to study microtubule bundles growing against a microfabricated rigid barrier
in vitro
. We show that multiple microtubules can generate a pushing force that increases linearly with the number of microtubules present. In addition, the bundle can cooperatively switch to a shrinking state, due to a force-induced coupling of the dynamic instability of single microtubules. In the presence of GMPCPP, bundle catastrophes no longer occur, and high bundle forces are reached more effectively. We reproduce the observed behavior with a simple simulation of microtubule bundle dynamics that takes into account previously measured force effects on single microtubules. Using this simulation, we also show that a constant compressive force on a growing bundle leads to oscillations in bundle length that are of potential relevance for chromosome oscillations observed in living cells.
An autocrine axis in the testis that coordinates spermiation and blood–testis barrier restructuring during spermatogenesis
Authors: Yan Helen H. N. , Mruk Dolores D. , Wong Elissa W. P. , Lee Will M. , Cheng C. Yan
Published: June 2008

The mechanism(s) that regulate and coordinate the events of spermiation and blood–testis barrier (BTB) restructuring in the seminiferous epithelium that occur concurrently at stage VIII of the seminiferous epithelial cycle of spermatogenesis are unknown. In this report, fragments derived from the laminin complex composed of laminin α3, β3, and γ3 chains (laminin-333) at the apical ectoplasmic specialization (apical ES) were shown to modulate BTB dynamics directly and/or indirectly via hemidesmosome. Experiments were performed using cultured Sertoli cells with functional tight junction (TJ) barrier and the ultrastructural features of the BTB but not apical ES. Recombinant protein fragments of laminin β3 and γ3 chains were shown to reduce the protein levels of occludin and β1-integrin dose dependently at the Sertoli–Sertoli and Sertoli–basement membrane interface, respectively, thereby destabilizing the BTB permeability function. These results were corroborated by transient overexpression of laminin fragments in Sertoli cells. To further assess the role of β1-integrin in hemidesmosome, knockdown of β1-integrin in Sertoli cells by RNAi was found to associate with occludin redistribution at the Sertoli–Sertoli cell interface, wherein occludin moved away from the cell surface and became associated with endosomes, thereby destabilizing the BTB. In short, an apical ES-BTB-hemidesmosome autocrine regulatory axis was identified in testes, coordinating the events of spermiation and BTB restructuring that occur at the opposite ends of the seminiferous epithelium during spermatogenesis.
Acetylation in the globular core of histone H3 on lysine-56 promotes chromatin disassembly during transcriptional activation
Authors: Williams Stephanie K. , Truong David , Tyler Jessica K.
Published: June 2008

Promoter chromatin disassembly is a widely used mechanism to regulate eukaryotic transcriptional induction. Delaying histone H3/H4 removal from the yeast
PHO5
promoter also leads to delayed removal of histones H2A/H2B, suggesting a constant equilibrium of assembly and disassembly of H2A/H2B, whereas H3/H4 disassembly is the highly regulated step. Toward understanding how H3/H4 disassembly is regulated, we observe a drastic increase in the levels of histone H3 acetylated on lysine-56 (K56ac) during promoter chromatin disassembly. Indeed, promoter chromatin disassembly is driven by Rtt109 and Asf1-dependent acetylation of H3 K56. Conversely, promoter chromatin reassembly during transcriptional repression is accompanied by decreased levels of histone H3 acetylated on lysine-56, and a mutation that prevents K56 acetylation increases the rate of transcriptional repression. As such, H3 K56 acetylation drives chromatin toward the disassembled state during transcriptional activation, whereas loss of H3 K56 acetylation drives the chromatin toward the assembled state.
Assembly of the cnidarian camera-type eye from vertebrate-like components
Authors: Kozmik Zbynek , Ruzickova Jana , Jonasova Kristyna , Matsumoto Yoshifumi , Vopalensky Pavel , Kozmikova Iryna , Strnad Hynek , Kawamura Shoji , Piatigorsky Joram , Paces Vaclav , Vlcek Cestmir
Published: June 2008

Animal eyes are morphologically diverse. Their assembly, however, always relies on the same basic principle, i.e., photoreceptors located in the vicinity of dark shielding pigment. Cnidaria as the likely sister group to the Bilateria are the earliest branching phylum with a well developed visual system. Here, we show that camera-type eyes of the cubozoan jellyfish,
Tripedalia cystophora
, use genetic building blocks typical of vertebrate eyes, namely, a ciliary phototransduction cascade and melanogenic pathway. Our findings indicative of parallelism provide an insight into eye evolution. Combined, the available data favor the possibility that vertebrate and cubozoan eyes arose by independent recruitment of orthologous genes during evolution.
Chromosomal transposition of
PiggyBac
in mouse embryonic stem cells
Authors: Wang Wei , Lin Chengyi , Lu Dong , Ning Zeming , Cox Tony , Melvin David , Wang Xiaozhong , Bradley Allan , Liu Pentao
Published: June 2008

Transposon systems are widely used for generating mutations in various model organisms.
PiggyBac
(
PB
) has recently been shown to transpose efficiently in the mouse germ line and other mammalian cell lines. To facilitate
PB
's application in mammalian genetics, we characterized the properties of the
PB
transposon in mouse embryonic stem (ES) cells. We first measured the transposition efficiencies of
PB
transposon in mouse embryonic stem cells. We next constructed a
PB
/
SB
hybrid transposon to compare
PB
and
Sleeping Beauty
(
SB
) transposon systems and demonstrated that
PB
transposition was inhibited by DNA methylation. The excision and reintegration rates of a single
PB
from two independent genomic loci were measured and its ability to mutate genes with gene trap cassettes was tested. We examined
PB
's integration site distribution in the mouse genome and found that
PB
transposition exhibited local hopping. The comprehensive information from this study should facilitate further exploration of the potential of
PB
and
SB
DNA transposons in mammalian genetics.
IL-6 blockade inhibits the induction of myelin antigen-specific Th17 cells and Th1 cells in experimental autoimmune encephalomyelitis
Authors: Serada Satoshi , Fujimoto Minoru , Mihara Masahiko , Koike Nobuo , Ohsugi Yoshiyuki , Nomura Shintaro , Yoshida Hiroto , Nishikawa Teppei , Terabe Fumitaka , Ohkawara Tomoharu , Takahashi Tsuyoshi , Ripley Barry , Kimura Akihiro , Kishimoto Tadamitsu , Naka Tetsuji
Published: June 2008

The development of Th17 cells is a key event in the pathogenesis of experimental autoimmune encephalomyelitis (EAE), a murine model of human multiple sclerosis (MS). Previous studies have demonstrated that an IL-6-dependent pathway is involved in the differentiation of Th17 cells from naïve CD4-positive T cellsin vitro. However, the role of IL-6in vivoin the development of Th17 cells in EAE has remained unclear. In the present study, we found that IL-6 blockade by treatment with an anti-IL-6 receptor monoclonal antibody (anti-IL-6R mAb) inhibited the development of EAE and inhibited the induction of myelin oligodendrocyte glycoprotein (MOG) peptide-specific CD4-positive, CD8-positive, and Th17 T cells, in inguinal lymph nodes. Thus, the protective effect of IL-6 blockade in EAE is likely to be mediated via the inhibition of the development of MOG-peptide-specific Th17 cells and Th1 cells, which in turn leads to reduced infiltration of T cells into the CNS. These findings indicate that anti-IL-6R mAb treatment might represent a novel therapy for human MS.
The stochastic nature of larval connectivity among nearshore marine populations
Authors: Siegel D. A. , Mitarai S. , Costello C. J. , Gaines S. D. , Kendall B. E. , Warner R. R. , Winters K. B.
Published: June 2008

Many nearshore fish and invertebrate populations are overexploited even when apparently coherent management structures are in place. One potential cause of mismanagement may be a poor understanding and accounting of stochasticity, particularly for stock recruitment. Many of the fishes and invertebrates that comprise nearshore fisheries are relatively sedentary as adults but have an obligate larval pelagic stage that is dispersed by ocean currents. Here, we demonstrate that larval connectivity is inherently an intermittent and heterogeneous process on annual time scales. This stochasticity arises from the advection of pelagic larvae by chaotic coastal circulations. This result departs from typical assumptions where larvae simply diffuse from one site to another or where complex connectivity patterns are created by transport within spatially complicated environments. We derive a statistical model for the expected variability in larval settlement patterns and demonstrate how larval connectivity varies as a function of different biological and physical processes. The stochastic nature of larval connectivity creates an unavoidable uncertainty in the assessment of fish recruitment and the resulting forecasts of sustainable yields.
Central projections of photoreceptor axons originating from ectopic eyes in
Drosophila
Authors: Clements Jason , Lu Zhiyuan , Gehring Walter J. , Meinertzhagen Ian A. , Callaerts Patrick
Published: June 2008

Ectopic expression of the retinal determination gene
eyeless
(
ey
) induces the formation of supernumerary eyes on antennae, legs, wings, and halteres. These ectopic eyes form ommatidia that contain photoreceptors and accessory cells and respond to light. Here, we demonstrate that ectopic eyes on antennae and legs extend axonal projections to the central nervous system. Furthermore, electroretinograms and morphological evidence indicate that the photoreceptor axons of at least the antennal ectopic eyes can form completely constituted ectopic synapses with foreign postsynaptic elements and suggest that transmission at these sites may be functional. However, the ectopic axons do not connect to their correct optic lobe targets and do not project deeply into the neuropile, but rather form synapses at superficial positions in the neuropils. By means of confocal and electron microscopy we show that these ectopic synapses resemble normal synapses, albeit with some distinct morphological differences. Our data strongly suggest that the developmental programs controlling photoreceptor synaptogenesis and visual map formation depend to a considerable extent on presynaptic and thus photoreceptor-autonomous steps. Our data also suggest that photoreceptor axon projections and the establishment of the highly stereotypical neural circuitry in the optic lobe, the normal target neuropil, may depend on target-specific cues that appear to be absent from the antennal lobe and thoracic ganglion.
cis
-Diammine(pyridine)chloroplatinum(II), a monofunctional platinum(II) antitumor agent: Uptake, structure, function, and prospects
Authors: Lovejoy Katherine S. , Todd Ryan C. , Zhang Shuzhong , McCormick Michael S. , D'Aquino J. Alejandro , Reardon Joyce T. , Sancar Aziz , Giacomini Kathleen M. , Lippard Stephen J.
Published: June 2008

We have identified unique chemical and biological properties of a cationic monofunctional platinum(II) complex,
cis
-diammine(pyridine)chloroplatinum(II),
cis
-[Pt(NH
3
)
2
(py)Cl]
+
or cDPCP, a coordination compound previously identified to have significant anticancer activity in a mouse tumor model. This compound is an excellent substrate for organic cation transporters 1 and 2, also designated SLC22A1 and SLC22A2, respectively. These transporters are abundantly expressed in human colorectal cancers, where they mediate uptake of oxaliplatin,
cis
-[Pt(DACH)(oxalate)] (DACH =
trans-R
,
R
-1,2-diaminocyclohexane), an FDA-approved first-line therapy for colorectal cancer. Unlike oxaliplatin, however, cDPCP binds DNA monofunctionally, as revealed by an x-ray crystal structure of
cis
-{Pt(NH
3
)
2
(py)}
2+
bound to the N7 atom of a single guanosine residue in a DNA dodecamer duplex. Although the quaternary structure resembles that of B-form DNA, there is a base-pair step to the 5′ side of the Pt adduct with abnormally large shift and slide values, features characteristic of cisplatin intrastrand cross-links. cDPCP effectively blocks transcription from DNA templates carrying adducts of the complex, unlike DNA lesions of other monofunctional platinum(II) compounds like {Pt(dien)}
2+
. cDPCP–DNA adducts are removed by the nucleotide excision repair apparatus, albeit much less efficiently than bifunctional platinum–DNA intrastrand cross-links. These exceptional characteristics indicate that cDPCP and related complexes merit consideration as therapeutic options for treating colorectal and other cancers bearing appropriate cation transporters.
Gender Differences in Mesenteric Vasoconstrictor Reactivity following Chronic Hypoxia
Authors: GONZALES RAYNA J. , BRYANT JESSICA M. , NAIK JAY S. , RESTA THOMAS C. , WALKER BENJIMEN R.
Published: June 2008

Male rats demonstrate persistent endothelium‐dependent attenuation of vasoconstrictor reactivity following chronic hypoxia (CH). Since estrogen may interfere with hypoxia‐induced gene expression, we hypothesized that gender differences exist in this response to CH. However, in conscious, instrumented rats, we found that CH resulted in a similar persistent reduction of pressor/total peripheral resistance responses to phenylephrine (PE) in rats of both genders. In contrast, although previous studies show mesenteric vascular responses to PE are reduced in CH males, we found that mesenteric reactivity was maintained in CH females. Since normoxic females demonstrate greater nitric oxide (NO) production, we hypothesized that the failure of CH to further diminish mesenteric reactivity in females was due to the inhibition of NO‐dependent vasodilation. To test this hypothesis, constrictor reactivity of mesenteric arteries from male and female rats was examined. NO synthase (NOS) inhibition augmented constrictor responses to PE in arteries from both normoxic and CH males and normoxic females. In contrast, NOS inhibition had no effect in CH female vessels. Endothelial NOS (eNOS) levels were not different in arteries from control and CH females. Endothelial [Ca2 +]iwas greater in arterioles from CH females. Thus, CH reduces NO‐dependent mesenteric dilation in females; this effect is not due to altered eNOS levels or diminished endothelial [Ca2 +]i.
Fluid Shear Attenuates Endothelial Pseudopodia Formation into the Capillary Lumen
Authors: HUECK ISGARD S. , ROSSITER KATHARINE , ARTMANN GERHARD M. , SCHMID‐SCHÖNBEIN GEERT W.
Published: June 2008

Objective: Endothelial cells have the ability to undergo morphological shape changes, including projection of cytoplasmic pseudopodia into the capillary lumen. These cytoplasmic projections significantly influence the hemodynamic resistance to blood flow. To examine mechanotransduction mechanisms, we investigated in vivo the hemodynamic conditions in capillaries that control endothelial pseudopod formation.

Materials and Methods: Capillaries in rat skeletal muscle were fixed under carefully controlled perfusion conditions. The formation of endothelial pseudopodia were observed in cross‐sections with electron microscopy and quantified with differential interference contrast microscopy under physiological, stasis, and reperfusion flow conditions.

Results: Application of physiological levels of fluid flow prevents capillary endothelium to project pseudopodia into the capillary lumen. Reduction of fluid flow to near zero promotes the incidence of pseudopod projection from 5% to 55% of capillaries. After capillary pseudopodia have formed under static conditions, about one‐half retract upon restoration of fluid flow. The presence of red blood cells in the capillary lumen prevents pseudopod formation.

Conclusions: The results suggest that there is a mechanism that serves to control cytoplasmic projections in capillary endothelium that is under the control of hemodynamic fluid stress. Investigation of pseudopodia growth on endothelial cells may be significant in understanding capillary obstruction in cardiovascular diseases.
Direct Regulation of BK Channels by Phosphatidylinositol 4,5-Bisphosphate as a Novel Signaling Pathway
Authors: Vaithianathan Thirumalini , Bukiya Anna , Liu Jianxi , Liu Penchong , Asuncion-Chin Maria , Fan Zheng , Dopico Alejandro
Published: June 2008

Large conductance, calcium- and voltage-gated potassium (BK) channels are ubiquitous and critical for neuronal function, immunity, and smooth muscle contractility. BK channels are thought to be regulated by phosphatidylinositol 4,5-bisphosphate (PIP2) only through phospholipase C (PLC)–generated PIP2 metabolites that target Ca2+ stores and protein kinase C and, eventually, the BK channel. Here, we report that PIP2 activates BK channels independently of PIP2 metabolites. PIP2 enhances Ca2+-driven gating and alters both open and closed channel distributions without affecting voltage gating and unitary conductance. Recovery from activation was strongly dependent on PIP2 acyl chain length, with channels exposed to water-soluble diC4 and diC8 showing much faster recovery than those exposed to PIP2 (diC16). The PIP2–channel interaction requires negative charge and the inositol moiety in the phospholipid headgroup, and the sequence RKK in the S6–S7 cytosolic linker of the BK channel-forming (cbv1) subunit. PIP2-induced activation is drastically potentiated by accessory β1 (but not β4) channel subunits. Moreover, PIP2 robustly activates BK channels in vascular myocytes, where β1 subunits are abundantly expressed, but not in skeletal myocytes, where these subunits are barely detectable. These data demonstrate that the final PIP2 effect is determined by channel accessory subunits, and such mechanism is subunit specific. In HEK293 cells, cotransfection of cbv1+β1 and PI4-kinaseIIα robustly activates BK channels, suggesting a role for endogenous PIP2 in modulating channel activity. Indeed, in membrane patches excised from vascular myocytes, BK channel activity runs down and Mg-ATP recovers it, this recovery being abolished by PIP2 antibodies applied to the cytosolic membrane surface. Moreover, in intact arterial myocytes under physiological conditions, PLC inhibition on top of blockade of downstream signaling leads to drastic BK channel activation. Finally, pharmacological treatment that raises PIP2 levels and activates BK channels dilates de-endothelized arteries that regulate cerebral blood flow. These data indicate that endogenous PIP2 directly activates vascular myocyte BK channels to control vascular tone.
Activation of Rac1 by the Guanine Nucleotide Exchange Factor Dck1 Is Required for Invasive Filamentous Growth in the PathogenCandida albicans
Authors: Hope Hannah , Bogliolo Stéphanie , Arkowitz Robert A. , Bassilana Martine
Published: June 2008

Rho G proteins and their regulators are critical for cytoskeleton organization and cell morphology in all eukaryotes. In the opportunistic pathogen Candida albicans, the Rho G proteins Cdc42 and Rac1 are required for the switch from budding to filamentous growth in response to different stimuli. We show that Dck1, a protein with homology to the Ced-5, Dock180, myoblast city family of guanine nucleotide exchange factors, is necessary for filamentous growth in solid media, similar to Rac1. Our results indicate that Dck1 and Rac1 do not function in the same pathway as the transcription factor Czf1, which is also required for embedded filamentous growth. The conserved catalytic region of Dck1 is required for such filamentous growth, and in vitro this region directly binds a Rac1 mutant, which mimics the nucleotide-free state. In vivo overexpression of a constitutively active Rac1 mutant, but not wild-type Rac1, in a dck1 deletion mutant restores filamentous growth. These results indicate that the Dock180 guanine nucleotide exchange factor homologue, Dck1 activates Rac1 during invasive filamentous growth. We conclude that specific exchange factors, together with the G proteins they activate, are required for morphological changes in response to different stimuli.
iFoldRNA: three-dimensional RNA structure prediction and folding
Authors: Sharma Shantanu , Ding Feng , Dokholyan Nikolay V.
Published: June 2008

Summary: Three-dimensional RNA structure prediction and folding is of significant interest in the biological research community. Here, we present iFoldRNA, a novel web-based methodology for RNA structure prediction with near atomic resolution accuracy and analysis of RNA folding thermodynamics. iFoldRNA rapidly explores RNA conformations using discrete molecular dynamics simulations of input RNA sequences. Starting from simplified linear-chain conformations, RNA molecules (<50 nt) fold to native-like structures within half an hour of simulation, facilitating rapid RNA structure prediction. All-atom reconstruction of energetically stable conformations generates iFoldRNA predicted RNA structures. The predicted RNA structures are within 2–5 Å root mean squre deviations (RMSDs) from corresponding experimentally derived structures. RNA folding parameters including specific heat, contact maps, simulation trajectories, gyration radii, RMSDs from native state, fraction of native-like contacts are accessible from iFoldRNA. We expect iFoldRNA will serve as a useful resource for RNA structure prediction and folding thermodynamic analyses.

Availability:  http://iFoldRNA.dokhlab.org.

Contact:  dokh@med.unc.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.