bluuebunny/crossref_metadata_2025 huggingface dataset:
Synthesis and optical properties of PbS/ZnO composite films
Authors: Wang Xianghua , Shi Jianlin , Yang Yong , You Guanjun , Liu Ye , Mi Jun , Qian Shixiong
Published: April 2004

Pure ZnO films and PbS/ZnO nanocomposite films of optical quality were prepared with a sol–gel method. The particle size, optical absorption, and linear refractive index of the PbS/ZnO films were measured by TEM (transmission electron microscopy), UV-Vis absorption, and ellipsometry techniques, respectively. For high Pb/Zn ratios, PbS particles of size 5–8 nm are observed in TEM, and a large refractive nonlinearity of 10−7 esu with a saturable absorption was measured in picosecond Z-scan experiments.
Microstructural evolution of Co nanostructures in diamond-like carbon by plasma-assisted processing
Authors: Wang F. L. , Jiang J. C. , Meletis E. I.
Published: April 2004

Nanocomposite thin films consisting of Co nanoparticles in a diamond-like carbon (DLC) matrix were synthesized by plasma-assisted magnetron sputtering using a discharge with different Ar/CH4 gas flow ratio and chamber pressure. The evolution of the Co nanostructures was studied by x-ray photoelectron spectroscopy and transmission electron microscopy. It was found that depending on processing parameters, the Co nanostructures develop from slightly elongated nanoparticles to self-assembled nanorods of high aspect ratio. Flow rate and pressure were also found not only to influence the degree of crystallinity of the Co nanostructures, but also the chemical state of C in the DLC matrix. It is suggested that under the prevailing processing conditions the evolution of the Co nanorods is under kinetic control.
Effective mass approximation for two extreme semiconductors: Band gap of PbS and CuBr nanoparticles
Authors: Nanda K. K. , Kruis F. E. , Fissan H. , Behera S. N.
Published: April 2004

An effective mass approximation (EMA) with finite-depth square-well potential is used to investigate the size-dependent band gap (BG) of PbS and CuBr nanoparticles embedded in different matrices. These two materials are interesting from the theoretical point of view as PbS is a low-BG material with smaller effective masses and larger dielectric constants, whereas CuBr is a wide-BG material with larger effective masses and smaller dielectric constants. Comparing the experimental BGs with our theoretical calculations, it is shown that EMA provides a better description of the experimental data, especially for CuBr, when the Coulomb interaction having the size-dependent dielectric constant is included in the calculation. Further, comparing the change in the BG of spherical nanoparticle, nanowire and thin film, it is predicted that the effective dimensionality of semiconductor nanoparticles can be increased by embedding them in another semiconducting matrix.
Perpendicular magnetic recording: Writing process
Authors: Khizroev S. , Litvinov D.
Published: April 2004

In this article, a detailed overview of the methodology to design a write transducer for recording onto perpendicular media at areal densities beyond 1 Tbit/in.2 is presented. The two basic modes of perpendicular recording, single-layer recording media in combination with a ring type head and double-layer recording media with a soft underlayer in combination with a single pole head, are compared with each other theoretically and experimentally. Moreover, perpendicular recording is compared to longitudinal recording from the perspective of the writing process. The system efficiency is redefined for perpendicular recording to take into account the critical role of the soft underlayer. The effects of using “soft” magnetic shields around the trailing pole are analyzed. It is shown that at least a factor of 2 increase in the field can be obtained at areal densities beyond 500 Gbit/in.2 if shields are used. Such an open issue as the skew angle sensitivity in perpendicular recording is analyzed. It is shown that using soft magnetic shields around the trailing pole substantially improves the skew angle sensitivity. Moreover, using shields substantially improves the system efficiency and to some degree fulfills the role of the soft underlayer in perpendicular recording.
Thermal simulation for a two-dimensional near-field optical recording system using a vertical-cavity surface-emitting laser
Authors: Kurihara Kazuma , Nanri Kenzo , Goto Kenya
Published: April 2004

An optical recording method with high throughput is required to create a two-dimensional near-field optical memory system using a vertical-cavity surface-emitting laser (VCSEL). Optical recording is possible with the combination of a near-field probe and patterned medium. A patterned medium consisting of 40 nm periodic dots with phase change medium and silver nanoparticles were used for plasmon resonance induced by an electromagnetic wave. The electric field power density at the silver nanoparticles was increased about 87 000 times over that with a structure without patterned medium. Heat from this structure is effectively used by thermal conduction out of a silver nanoparticle and by concentrating the heat on a particle. When the 1 mW optical intensity from a VCSEL is used, near-field optical recording is achieved. The recorded feature size was estimated at 40 nm. In this letter, a recording method is described using plasmon resonance and thermal conduction effects.
A smart model to estimate effective thermal conductivity and viscosity in the weld pool
Authors: De A. , DebRoy T.
Published: April 2004

Calculations of fluid flow and heat transfer in the weld pool are strongly influenced by the values of effective thermal conductivity and effective viscosity of the liquid metal. The values of these variables are uncertain since the welding conditions and the fluid flow characteristics within the weld pool influence them. Following an inverse modeling approach, the present work develops a smart model that embodies a multivariable optimization scheme within the framework of a phenomenological heat transfer and fluid flow model to estimate the uncertain parameters necessary for weld pool modeling. The optimization scheme considers the sensitivity of the calculated weld geometry with respect to the unknown parameters. To avoid unrealistic optimized solutions, the smart model is internally guided to look for only the physically significant solutions. The model could estimate the effective thermal conductivity and effective viscosity for conduction mode laser welding as a function of nondimensional heat input from six sets of experimental measurements of weld pool depth and width.
Magnetic field-induced stress in the Ni–Mn–Ga magnetic shape memory alloy
Authors: Suorsa I. , Pagounis E.
Published: April 2004

Magnetic Shape Memory (MSM) materials generate stress in a magnetic field, which can change the shape of the material. Up to now, little work has been carried out in modeling and measuring the magnetic field-induced (MFI) stress in MSM materials. In the present study, direct MFI stress measurements in a Ni–Mn–Ga MSM material, giving full 6% MFI strain, were performed at different field strengths. The MFI stress was also calculated from the magnetic anisotropy of the material, based on the magnetization curves along the easy and the hard magnetization directions. Both measurement methods are described in detail. The measurement results demonstrated good agreement with the calculated ones. The dependence of the MFI stress on the MFI strain and the magnetic field strength was also revealed. Potential errors during MFI stress measurements in MSM materials are discussed, and avoided by properly selecting the measurement conditions during the study.
Domain structure in a micron-sized PbZr1−xTixO3 single crystal on a Ti substrate fabricated by hydrothermal synthesis
Authors: You D. J. , Jung W. W. , Choi S. K. , Cho Yasuo
Published: April 2004

Hydrothermal synthesis is an attractive method for the deposition of ferroelectric thin films because it can realize a low processing temperature of 200 °C or less. In this study, micron-sized PbZr1−xTixO3 (PZT) single crystals and thin films were fabricated on a Ti substrate at 160 °C by hydrothermal synthesis. The ferroelectricity of the crystals was investigated using local piezoresponse hysteresis, while their domain structure was investigated using high-resolution transmission electron microscopy (HRTEM) measurement. The isolated PZT single crystal exhibited hysteresis behavior of the piezoresponse, which represents ferroelectricity. From the HRTEM observations of a crystallite in polycrystalline PZT thin film, we found a twinned domain structure in the form of a … c/a/c/a … polydomain pattern. On the basis of the HRTEM observations, we proposed a three-dimensional domain structure for the isolated PZT single crystal; the c/a domain walls form along coherent {101} planes in the tetragonal cell. This structure was experimentally verified by scanning nonlinear dielectric microscopy.
Microwave absorption properties of the ZnO nanowire-polyester composites
Authors: Chen Y. J. , Cao M. S. , Wang T. H. , Wan Q.
Published: April 2004

We report on the microwave response properties of the ZnO nanowire-polyester composites fabricated into a planar plate with the area of 180×180 mm2 and the thickness of about 1 mm. Strong microwave absorption has been observed in X band and the maximum absorption is enhanced as the concentration of the nanowires increases in the composites. Both the low complex permittivity and the low dissipation of the pure nanowires demonstrate the pure nanowires are low-loss materials for microwave absorption in X band. The strong absorption is related to interfacial multipoles at the interface between the polyester and the ZnO nanowires, a high surface-to-volume ratio and a similar shape of the nanowires to antenna.
Current saturation in multiwalled carbon nanotubes by large bias
Authors: Liang Y. X. , Li Q. H. , Wang T. H.
Published: April 2004

Transport properties of a single multiwalled carbon nanotube (MWNT) have been investigated in vacuum at room temperature. The MWNTs show the large current carrying capacity at large bias due to the ballistic transport. The conductance for a single MWNT around zero bias is 0.4G0, and increases almost linearly with the applied voltage until it reaches its acmes. Being the signature of the ballistic transport for MWNTs, the conductance acmes are observed at the bias of ±5.8 V equal to ±2γ0/e, where γ0 is the π bonding energy for carbon nanotubes. Our calculation shows a similar curve to our experimental results, which further indicates the ballistic transport through the single MWNT.
Tuning of the electronic properties of self-assembled InAs/InP(001) quantum dots by rapid thermal annealing
Authors: Girard J. F. , Dion C. , Desjardins P. , Allen C. Nı̀ , Poole P. J. , Raymond S.
Published: April 2004

We have investigated the effect of post-growth rapid thermal annealing on the low-temperature photoluminescence (PL) spectra of self-assembled InAs quantum dots (QDs) grown in InP(001) by chemical-beam epitaxy using both conventional and modified capping procedures. As-grown samples are characterized by a broad emission peak centered near 800–900 meV corresponding to distinct QD families of different sizes with no observable wetting-layer emission. Rapid thermal anneals were performed at 650 to 800 °C for 210 s, resulting in blueshifts of up to 120 meV due to intermixing. While the PL emission energies of the various QD families shift at similar rates upon annealing, the peak widths remain approximately constant. Finally, we show that the growth of a low-temperature InP cap layer containing a large number of point defects significantly enhances interdiffusion and results in PL blueshifts in excess of 300 meV.
Current-controlled group delay using a semiconductor Fabry–Perot amplifier
Authors: Minin Serge , Fisher Matthew Robert , Chuang Shun Lien
Published: April 2004

We present a demonstration of a current-controlled group delay using a semiconductor waveguide Fabry–Perot optical amplifier operated in reflection. Current injection allows us to tune the resonant wavelength as well as provide the gain required for all-pass reflection, which leads to group delay tunability with relatively small power variation. We show very good agreement between our experimental data and theoretical results, which are analogous to waveguide-coupled active ring resonators.
High detectivity InAs quantum dot infrared photodetectors
Authors: Kim Eui-Tae , Madhukar Anupam , Ye Zhengmao , Campbell Joe C.
Published: April 2004

We report a high detectivity of 3×1011 cm Hz1/2/W at 78 K for normal-incidence quantum dot infrared photodetectors with ten layers of undoped InAs/InGaAs/GaAs quantum dot active regions. The high detectivity seen at 1.4 V corresponds to photoresponse peaks at 9.3 and 8.7 μm for positive and negative bias, respectively.
Continuous-wave laser operation at 1.3 μm in Nd3+-doped Zn:LiNbO3 channel waveguides
Authors: Domenech M. , Lifante G.
Published: April 2004

This work reports continuous laser action around 1.3 μm at room temperature in LiNbO3:Nd3+ channel waveguides, fabricated by the two-steps Zn diffusion technique. A threshold of 64 mW and a slope efficiency of around 0.5% were obtained in an 8 μm wide channel guide. These results have been compared with laser oscillation around 1.08 μm in LiNbO3:Nd3+ waveguides in terms of the launched pump powers, taking into account the emission cross section values of the F3/24→4I13/2 and F3/24→4I11/2 transitions.
Electrical characteristics and interface structure of magnetic tunnel junctions with aluminum oxyfluoride barrier
Authors: Kim D. S. , Yu Y. Y. , Ham J. H. , Char K.
Published: April 2004

The effects of fluorine inclusion in the aluminum oxide tunnel barrier on the electrical characteristics and the interface structure of magnetic tunnel junctions were studied. Compared with conventional junctions without fluorine, the fluorine-containing junctions exhibit larger and nearly constant tunneling magnetoresistance (TMR) values over a wide range of oxidation times and exhibit a smaller bias dependence for TMR. X-ray photoelectron spectroscopy indicates that the fluorine forms an aluminum oxyfluoride barrier together with an oxygen and that the fluorine-rich oxyfluoride layer at the barrier top surface plays an important role in the formation of the highly insulating barrier, resulting in nearly ideal barrier/electrode interfaces without a detrimental magnetically dead layer.
Zinc oxide thin-film random lasers on silicon substrate
Authors: Yu S. F. , Yuen Clement , Lau S. P. , Lee H. W.
Published: April 2004

Room-temperature ultraviolet lasing is demonstrated in mirrorless zinc oxide thin-film waveguides on (100) silicon substrate. Laser cavities, due to closed-loop optical scattering from the lateral facets of the irregular zinc oxide grains, are generated through the post-growth annealing of high-crystal-quality zinc oxide thin films obtained from the filtered cathodic vacuum arc technique. It is found that the lasing wavelength and linewidth of the zinc oxide random lasers under 355 nm optical excitation are around 390 nm and less than 0.4 nm, respectively. In addition, the lasing threshold characteristics are in good agreement with the random laser theory.
Small-size sonic crystals with strong attenuation bands in the audible frequency range
Authors: Hirsekorn Martin
Published: April 2004

Recent experiments have proved that sonic crystals containing locally resonant structures exhibit strong sound attenuation bands at frequencies about two orders of magnitude smaller than predicted by Bragg’s theory. The effect is well reproduced here by means of two-dimensional numerical simulations of the elastic wave propagation in a 13 cm slab of locally resonant sonic crystals. Three strong attenuation bands are found in the frequency range from 0.3 to 6.0 kHz. A heuristic model is proposed, which allows one to predict the resonance frequencies in good agreement with the numerical simulations.
Narrow fluence window and giant isotope effect in low-energy hydrogen ion blistering of silicon
Authors: Moutanabbir O. , Giguère A. , Terreault B.
Published: April 2004

We have found that blisters due to low-keV H-ion implantation and annealing of Si appear at low fluence (e.g., 2×1016 H cm−2) but disappear at slightly higher fluence (3.5×1016 H cm−2); this fluence “window” widens at higher ion energy. For D-ion blistering the window is shifted upwards by a surprising factor of 2–3. Thermal desorption spectrometry suggests that D is somehow more stable than H in Si. Hypotheses to explain blistering disappearance and the giant isotope effect are discussed. This phenomenon has an impact for the ion-cut process at the sub 100 nm scale.
Periodic array of uniform ZnO nanorods by second-order self-assembly
Authors: Chik H. , Liang J. , Cloutier S. G. , Kouklin N. , Xu J. M.
Published: April 2004

A nonlithographic second-order self-assembly process for synthesizing uniform and ordered arrays of nanorods and nanodots is presented and applied to the fabrication of ZnO nanorod arrays. Nucleation sites were defined by patterning Au nanodot catalysts with a self-organized array of nanopores formed in anodized aluminum oxide (AAO). The self-assembled vertically aligned ZnO nanorods grown on GaN exhibit hexagonal facets, and have a uniform diameter of 60 nm and a mean length of 400 nm. The growth technique is simple, robust, and offers a direct control over array and single nanorod configurations. The growth temperature is significantly lower than normal, and yet, the resultant defect level is much lower than normal.
Room-temperature direct current operation of 290 nm light-emitting diodes with milliwatt power levels
Authors: Fischer A. J. , Allerman A. A. , Crawford M. H. , Bogart K. H. A. , Lee S. R. , Kaplar R. J. , Chow W. W. , Kurtz S. R. , Fullmer K. W. , Figiel J. J.
Published: April 2004

Ultraviolet light-emitting diodes (LEDs) have been grown by metalorganic vapor phase epitaxy using AlN nucleation layers and thick n-type Al0.48Ga0.52N current spreading layers. The active region is composed of three Al0.36Ga0.64N quantum wells with Al0.48Ga0.52N barriers for emission at 290 nm. Devices were designed as bottom emitters and flip-chip bonded to thermally conductive submounts using an interdigitated contact geometry. The ratio of quantum well emission to 330 nm sub-band gap emission is as high as 125:1 for these LEDs. Output power as high as 1.34 mW at 300 mA under direct current operation has been demonstrated with a forward voltage of 9.4 V. A peak external quantum efficiency of 0.18% has been measured at an operating current of 55 mA.
InAs/InP quantum-dot pillar microcavities using SiO2/Ta2O5 Bragg reflectors with emission around 1.55 μm
Authors: Dalacu Dan , Poitras Daniel , Lefebvre Jacques , Poole Philip J. , Aers Geof C. , Williams Robin L.
Published: April 2004

We present optical characterization measurements from three-dimensional pillar microcavities comprising an InP spacer layer sandwiched between two SiO2/Ta2O5 Bragg reflectors. InAs quantum dots placed at the center of the InP spacer are used as broadband emitters. Emission into the lowest-order mode is observed at an energy of 820 meV in the wide-pillar limit, with shifts of approximately 30 meV in the ground state and more than 80 meV in higher-order modes for pillars of 2 μm diameter. Excellent agreement is found between the experimentally observed cavity mode energies as a function of pillar diameter and the predictions of guided-mode theory. Cavity quality factors in excess of 2200 are obtained for large diameter pillars, with a decrease to approximately 500 for pillars of 2 μm diameter.
Scalable approach for lensless imaging at x-ray wavelengths
Authors: Eisebitt S. , Lörgen M. , Eberhardt W. , Lüning J. , Andrews S. , Stöhr J.
Published: April 2004

We demonstrate a versatile approach to perform lensless imaging at x-ray wavelength. A special design of a sample holder allows recovery of the low spatial frequency information of the sample from the Patterson map of the measured diffraction. As a result, the phase can be reconstructed from an oversampled x-ray diffraction pattern alone, eliminating the need to resort to a low-resolution image of the sample. As the sample holder provides this functionality due to a suitable reference hole, the technique is applicable to a wide variety of samples and can be easily scaled to investigate large arrays of samples. The method is especially well suited for single-shot experiments as envisioned with x-ray free-electron lasers.
Temperature-dependent fatigue behaviors of ferroelectric ABO3-type and layered perovskite oxide thin films
Authors: Yuan G. L. , Liu J.-M. , Wang Y. P. , Wu D. , Zhang S. T. , Shao Q. Y. , Liu Z. G.
Published: April 2004

The temperature-dependent dielectric and ferroelectric fatigue behaviors of ABO3-type perovskite thin films Pb(Zr0.52Ti0.48)O3 (PZT) and Pb0.75La0.25TiO3 (PLT) and layered Aurivillius thin films SrBi2Ta2O9 (SBT) and Bi3.25La0.75Ti3O12 (BLT) with Pt electrodes are studied. The improved fatigue resistance of PZT and PLT at a low temperature can be explained by the defect-induced suppression of domain switch/nucleation near the film/electrode interface, which requires a long-range diffusion of defects and charges. It is argued that the fatigue effect of SBT and BLT is attributed to the competition between domain-wall pinning and depinning. The perovskitelike slabs and/or (Bi2O2)2+ layers act as barriers for long-range diffusion of defects and charges, resulting in localization of the defects and charges. Thus, the fatigued SBT and BLT can be easily rejuvenated by a high electric field over a wide temperature range.
Interfacial free volumes and segregation effects in nanocrystalline Pd85Zr15 studied by positron annihilation
Authors: Weigand H. , Sprengel W. , Röwer R. , Schaefer H.-E. , Wejrzanowski T. , Kelsch M.
Published: April 2004

Positron annihilation spectroscopy on nanocrystalline Pd85Zr15 shows the segregation of Zr at the interfaces and a decrease of the fraction of nanovoids the size of 10 to 15 missing atoms upon isochronal annealing up to Ta=1100 K by which the grain size increases up to d=185 nm. In this state, the positron trapping at interfacial free volumes reversibly changes contingent upon the temperature whereas the interfacial composition is unchanged when the measuring temperature varies.
Low-noise magnetic-flux sensors based on the extraordinary magnetoresistance effect
Authors: Möller C. H. , Kronenwerth O. , Heyn Ch. , Grundler D.
Published: April 2004

We report noise measurements on Au–InAs hybrid structures involving a high-mobility two-dimensional electron system. Such structures show the extraordinary magnetoresistance (EMR) effect. We find excellent noise performance at room temperature close to the Johnson noise, which is in particular important for a technical application. At 4.2 K and in a magnetic field of about 1 T the nonoptimized EMR device is found to exhibit a low magnetic flux noise, offering the perspective of sensor applications also in a high magnetic field and at cryogenic temperature.
Spectral properties, gas exchange, and water potential of leaves of glandular and non-glandular trichome types in Datura wrightii (Solanaceae)
Authors: II James L. Smith , Hare J. Daniel
Published: April 2004

Plant trichomes commonly serve a role in mechanical and chemical defence against herbivores, but may also have the potential to alter physiology by reducing the amount of light absorbed by leaves, lowering temperatures, and reducing water loss. Populations of Datura wrightii Regel in southern California produce 'sticky' plants with glandular trichomes and 'velvety' plants bearing non-glandular trichomes. Because stickiness is inherited as a dominant Mendelian trait, and the proportions of sticky plants vary among populations with the moisture availability of their environment, there may be some ecophysiological differences between trichome types that contribute to their ability to survive in a particular geographic location. To examine the possible physiological significance of trichome variation, we measured the spectral properties, midday gas-exchange rates, and water potentials of D. wrightii leaves from sticky and velvety plants growing in a field experiment. The differences in leaf reflectance (0.9%) and absorptance (1.3%) of photosynthetically active radiation (PAR) between trichome types are too small to have any direct physiologically significant effect. Simulations of leaf temperatures based on the difference in leaf absorptances reveal that leaf temperature would be no more than 1°C lower in velvety compared to sticky plants. Gas-exchange measurements revealed no significant difference between types in their transpiration rates or stomatal conductances. In this case, trichome variation may be more important to plant defenses than to physiology.
Eucalyptus grandis has at least two functional SOC1-like floral activator genes
Authors: Watson John M. , Brill Elizabeth M.
Published: April 2004

In a search for Eucalyptus grandis Hill ex Maiden MADS-box genes involved in floral initiation and development, we isolated two cDNAs (EgrMADS 3 and EgrMADS 4), which are functional orthologues of the Arabidopsis thaliana (L.) Heynh. floral activator gene SOC1. These two E. grandis genes are equally and most-actively expressed in vegetative tissues such as apical shoots and young leaves. The two genes are less actively, but differentially expressed in roots and unopened flowers. Ectopic expression of EgrMADS 3 or EgrMADS 4 in the late-flowering A. thaliana Ler soc1 (agl20) derivative complemented the phenotype of this mutant, and some of these transgenic lines flowered significantly earlier than the wild-type Ler ecotype. Overexpression of EgrMADS 3 or EgrMADS 4 in A. thaliana ecotype Columbia accelerated flowering time under short-day conditions. However, under the same conditions the flowering time of A. thaliana ecotype C24 was altered by the ectopic expression of EgrMADS 3, but not that of EgrMADS 4.The nucleotide sequence data reported will appear in the EMBL and GenBank Nucleotide Databases under the accession numbers AY263807 (EgrMADS 3) and AY263808 (EgrMADS 4).
FLAG UPNESS and its application for mapping seasonally wet to waterlogged soils
Authors: Summerell G. K. , Dowling T. I. , Wild J. A. , Beale G.
Published: April 2004

The UPNESS index derived from the Fuzzy Landscape Analysis Geographic information system (FLAG) model was calculated for the Wagga Wagga and Kyeamba Creek Catchments in NSW, Australia. The model uses digital elevation data only to derive UPNESS and several other indices of relative height in the landscape. UPNESS is an index of surface and subsurface water accumulation calculated as the set of cells above any given point in a raster grid that are connected by a continuous monotonic uphill path. Accumulation of groundwater causes increased secondary weathering, solubilisation of rock and soil minerals, and soil pedogenic development. In this paper the UPNESS index is compared with depth to a shallow water table and groundwater electrical conductivity (EC). Reasonable relationships with r2 = 0.71 and 0.74 were found between the UPNESS index and depth to watertable and groundwater EC, respectively, in the Wagga Wagga study area.UPNESS was then used to predict spatial extents of waterlogged to seasonally waterlogged, saline, and sodic soil landscapes within the Kyeamba Catchment, a larger catchment, with soil landscape mapping at a scale of 1:100 000. Most differences between UPNESS and soil landscape mapping occurred in broad valleys where deeply incised channels have caused UPNESS calculations to be more restricted to the stream lines than mapped boundaries. In valley-filled areas with little incision, the UPNESS index derived similar areas but with substantially more detail than the soil landscape mapping. The UPNESS index provides an efficient method to help differentiate seasonally and fully waterlogged, saline, or sodic soils from the drier soils in a catchment. This may aid in objectively establishing initial soil landscape boundaries with detail that would otherwise be too costly to obtain.
Soil phosphorus enhancement below stormwater outlets in urban bushland: spatial and temporal changes and the relationship with invasive plants
Authors: Leishman Michelle R. , Hughes Miah T. , Gore Damian B.
Published: April 2004

Invasion by exotic plant species is a significant problem in urban bushland remnants and is often associated with nutrient enrichment of soils. A major source of nutrient enrichment in urban areas is stormwater runoff, which is transferred from impervious surfaces in urban catchments and discharged at outlets on the residential/bushland interface. We measured the spatial extent of soil total phosphorus (P) enhancement below stormwater outlets on Hawkesbury Sandstone-derived soils in northern Sydney and examined whether total P concentration has increased with time since urban development and extended laterally beyond the stormwater flow path. The average area of soil P enhancement below outlets was 0.24 ± 0.05 ha and was widest 30–50 m downslope from the outlet, where it extended an average 40 m across slope. Catchment area was not significantly related to average soil total P concentration. There was a significant decline in total P across slope from the centre of the flow path and a significant positive relationship between soil total P and proportion of exotic plant cover, with soil P accounting for 77.5% of variation. We found evidence for a build-up in soil total P concentration over time within the run-on zone below outlets, with the rate of enhancement being ~68 mg/kg per decade over a 40-year period. Evidence for lateral transfer of soil P out of the run-on area was more equivocal. There was a significant decline in soil total P across slope from the boundary of the run-on zone, with higher concentrations at distances 0.5 m and 1 m from the boundary compared with >1.5 m. However, this could be due to error in locating the boundary between run-on and non run-on areas. There was no significant relationship between soil P in the non run-on zone and age of development, which would be expected if P was being transferred by biological activity beyond the run-on zone over time. It is clear that the primary areas of concern for management must be the run-on areas below outlets.
The membrane organization of leukotriene synthesis
Authors: Mandal Asim K. , Skoch Jesse , Bacskai Brian J. , Hyman Bradley T. , Christmas Peter , Miller Douglas , Yamin Ting-ting D. , Xu Shihua , Wisniewski Douglas , Evans Jilly F. , Soberman Roy J.
Published: April 2004

Cell signaling leading to the formation of leukotriene (LT)C
4
requires the localization of the four key biosynthetic enzymes on the outer nuclear membrane and endoplasmic reticulum. Whether any macromolecular organization of these proteins exists is unknown. By using fluorescence lifetime imaging microscopy and biochemical analysis, we demonstrate the presence of two distinct multimeric complexes that regulate the formation of LTs in RBL-2H3 cells. One complex consists of multimers of LTC
4
synthase and the 5-lipoxygenase activating protein (FLAP). The second complex consists of multimers of FLAP. Surprisingly, all LTC
4
synthase was found to be in association with FLAP. The results indicate that the formation of LTC
4
and LTB
4
may be determined by the compartmentalization of biosynthetic enzymes in discrete molecular complexes.
Freezing immunoglobulins to see them move
Authors: Bongini L. , Fanelli D. , Piazza F. , De Los Rios P. , Sandin S. , Skoglund U.
Published: April 2004

The issue of protein dynamics and its implications in the biological function of proteins are arousing greater and greater interest in different fields of molecular biology. In cryo-electron tomography experiments one may take several snapshots of a given biological macromolecule. In principle, a large enough collection of snapshots of the molecule may then be used to calculate its equilibrium configuration in terms of the experimentally accessible degrees of freedom and, hence, to estimate its potential energy. This information would be crucial in order to analyze the biological functions of biomolecules by directly accessing the relevant dynamical indicators. In this article, we analyze the results of cryo-electron tomography experiments performed on monoclonal murine IgG2a antibodies. We measure the equilibrium distribution of the molecule in terms of the relevant angular coordinates and build a mechanical model of the antibody dynamics. This approach enables us to derive an explicit expression of the IgG potential energy. Furthermore, we discuss the configuration space at equilibrium in relation to results from other techniques, and we set our discussion in the context of the current debate regarding conformation and flexibility of antibodies.
Modulation of mammalian cell growth and death by prokaryotic and eukaryotic cytochrome
c
Authors: Hiraoka Yoshinori , Yamada Tohru , Goto Masatoshi , Das Gupta Tapas K. , Chakrabarty Ananda M.
Published: April 2004

Cytochrome
c
551
, an 8,685-Da haem-containing protein, is known to be involved in electron transfer during dissimilative denitrification by
Pseudomonas aeruginosa
. Both cytochrome
c
551
and copper-containing redox protein azurin have been used
in vitro
as partners in electron transfer. Azurin has been reported to induce apoptosis in macrophages and cancer cells. We now report that, unlike azurin, cytochrome
c
551
, termed Cyt
c
551
, has very little ability to induce apoptosis in J774 cell line-derived macrophages but demonstrates significant inhibition of cell cycle progression in such cells. A mutant form of Cyt
c
551
, V23DI59E, has significantly reduced ability to inhibit cell cycle progression but demonstrates a higher level of apoptosis-inducing activity in macrophages, compared with WT Cyt
c
551
. Interestingly, the WT Cyt
c
551
, but not the mutant form, significantly enhances the level of tumor suppressor protein p16
Ink4a
, a known inhibitor of cell cycle progression whereas the mutant form seems to form a complex with tumor suppressor protein p53, thereby enhancing its intracellular level to some extent. Eukaryotic cytochromes such as horse and bovine cytochrome
c
have also been shown to induce apoptosis but not inhibition of cell cycle progression in J774 cells, thus signifying a role of this redox protein in entry to, and in the induction of, cell death in mammalian cells.
Estimating metazoan divergence times with a molecular clock
Authors: Peterson Kevin J. , Lyons Jessica B. , Nowak Kristin S. , Takacs Carter M. , Wargo Matthew J. , McPeek Mark A.
Published: April 2004

Accurately dating when the first bilaterally symmetrical animals arose is crucial to our understanding of early animal evolution. The earliest unequivocally bilaterian fossils are ≈555 million years old. In contrast, molecular-clock analyses calibrated by using the fossil record of vertebrates estimate that vertebrates split from dipterans (
Drosophila
) ≈900 million years ago (Ma). Nonetheless, comparative genomic analyses suggest that a significant rate difference exists between vertebrates and dipterans, because the percentage difference between the genomes of mosquito and fly is greater than between fish and mouse, even though the vertebrate divergence is almost twice that of the dipteran. Here we show that the dipteran rate of molecular evolution is similar to other invertebrate taxa (echinoderms and bivalve molluscs) but not to vertebrates, which significantly decreased their rate of molecular evolution with respect to invertebrates. Using a data set consisting of the concatenation of seven different amino acid sequences from 23 ingroup taxa (giving a total of 11 different invertebrate calibration points scattered throughout the bilaterian tree and across the Phanerozoic), we estimate that the last common ancestor of bilaterians arose somewhere between 573 and 656 Ma, depending on the value assigned to the parameter scaling molecular substitution rate heterogeneity. These results are in accord with the known fossil record and support the view that the Cambrian explosion reflects, in part, the diversification of bilaterian phyla.
Recent developments in solid–state magic–angle spinning, nuclear magnetic resonance of fully and significantly isotopically labelled peptides and proteins
Authors: Straus Suzana K.
Published: April 2004

In recent years, a large number of solid–state nuclear magnetic resonance (NMR) techniques have been developed and applied to the study of fully or significantly isotopically labelled (
13
C,
15
N or
13
C/
15
N) biomolecules. In the past few years, the first structures of
13
C/
15
N–labelled peptides, Gly–Ile and Met–Leu–Phe, and a protein, Src–homology 3 domain, were solved using magic–angle spinning NMR, without recourse to any structural information obtained from other methods. This progress has been made possible by the development of NMR experiments to assign solid–state spectra and experiments to extract distance and orientational information. Another key aspect to the success of solid–state NMR is the advances made in sample preparation. These improvements will be reviewed in this contribution. Future prospects for the application of solid–state NMR to interesting biological questions will also briefly be discussed.
Wound healing and inflammation: embryos reveal the way to perfect repair
Authors: Redd Michael J. , Cooper Lisa , Wood Will , Stramer Brian , Martin Paul
Published: April 2004

Tissue repair in embryos is rapid, efficient and perfect and does not leave a scar, an ability that is lost as development proceeds. Wheras adult wound keratinocytes crawl forwards over the exposed substratum to close the gap, a wound in the embryonic epidermis is closed by contraction of a rapidly assembled actin purse string. Blocking assembly of this cable in chick and mouse embryos, by drugs or by inactivation of the small GTPase Rho, severely hinders the re–epithelialization process. Live studies of epithelial repair in GFP–actin–expressingDrosophilaembryos reveal actin–rich filopodia associated with the cable, and although these protrusions from leading edge cells appear to play little role in epithelial migration, they are essential for final zippering of the wound edges together—inactivation of Cdc42 prevents their assembly and blocks the final adhesion step. This wound re–epithelialization machinery appears to recapitulate that used during naturally occurring morphogenetic episodes as typified byDrosophiladorsal closure. One key difference between embryonic and adult repair, which may explain why one heals perfectly and the other scars, is the presence of an inflammatory response at sites of adult repair where there is none in the embryo. Our studies of repair in the PU.1 null mouse, which is genetically incapable of raising an inflammatory response, show that inflammation may indeed be partly responsible for scarring, and our genetic studies of inflammation in zebrafish (Danio rerio) larvae suggest routes to identifying gene targets for therapeutically modulating the recruitment of inflammatory cells and thus improving adult healing.
The Arabidopsis Cyclophilin Gene Family
Authors: Romano Patrick G.N. , Horton Peter , Gray Julie E.
Published: April 2004

Database searching has allowed the identification of a number of previously unreported single and multidomain isoform members of the Arabidopsis cyclophilin gene family. In addition to the cyclophilin-like peptidyl-prolyl cis-trans isomerase domain, the latter contain a variety of other domains with characterized functions. Transcriptional analysis showed they are expressed throughout the plant, and different isoforms are present in all parts of the cell including the cytosol, nucleus, mitochondria, secretory pathway, and chloroplast. The abundance and diversity of cyclophilin isoforms suggests that, like their animal counterparts, plant cyclophilins are likely to be important proteins involved in a wide variety of cellular processes. As well as fulfilling the basic role of protein folding, they may also play important roles in mRNA processing, protein degradation, and signal transduction and thus may be crucial during both development and stress responsiveness.
Heterosis of Biomass Production in Arabidopsis. Establishment during Early Development
Authors: Meyer Rhonda C. , Törjék Ottó , Becher Martina , Altmann Thomas
Published: April 2004

Heterosis has been widely used in agriculture to increase yield and to broaden adaptability of hybrid varieties and is applied to an increasing number of crop species. We performed a systematic survey of the extent and degree of heterosis for dry biomass in 63 Arabidopsis accessions crossed to three reference lines (Col-0, C24, and Nd). We detected a high heritability (69%) for biomass production in Arabidopsis. Among the 169 crosses analyzed, 29 exhibited significant mid-parent-heterosis for shoot biomass. Furthermore, we analyzed two divergent accessions, C24 and Col-0, the F1 hybrids of which were shown to exhibit hybrid vigor, in more detail. In the combination Col-0/C24, heterosis for biomass was enhanced at higher light intensities; we found 51% to 66% mid-parent-heterosis at low and intermediate light intensities (60 and 120 μmol m−2 s−1), and 161% at high light intensity (240 μmol m−2 s−1). While at the low and intermediate light intensities relative growth rates of the hybrids were higher only in the early developmental phase (0–15 d after sowing [DAS]), at high light intensity the hybrids showed increased relative growth rates over the entire vegetative phase (until 25 DAS). An important finding was the early onset of heterosis for biomass; in the cross Col-0/C24, differences between parental and hybrid lines in leaf size and dry shoot mass could be detected as early as 10 DAS. The widespread occurrence of heterosis in the model plant Arabidopsis opens the possibility to investigate the genetic basis of this phenomenon using the tools of genetical genomics.
When Defense Pathways Collide. The Response of Arabidopsis to a Combination of Drought and Heat Stress
Authors: Rizhsky Ludmila , Liang Hongjian , Shuman Joel , Shulaev Vladimir , Davletova Sholpan , Mittler Ron
Published: April 2004

Within their natural habitat, plants are subjected to a combination of abiotic conditions that include stresses such as drought and heat. Drought and heat stress have been extensively studied; however, little is known about how their combination impacts plants. The response of Arabidopsis plants to a combination of drought and heat stress was found to be distinct from that of plants subjected to drought or heat stress. Transcriptome analysis of Arabidopsis plants subjected to a combination of drought and heat stress revealed a new pattern of defense response in plants that includes a partial combination of two multigene defense pathways (i.e. drought and heat stress), as well as 454 transcripts that are specifically expressed in plants during a combination of drought and heat stress. Metabolic profiling of plants subjected to drought, heat stress, or a combination of drought and heat stress revealed that plants subject to a combination of drought and heat stress accumulated sucrose and other sugars such as maltose and gulose. In contrast, Pro that accumulated in plants subjected to drought did not accumulate in plants during a combination of drought and heat stress. Heat stress was found to ameliorate the toxicity of Pro to cells, suggesting that during a combination of drought and heat stress sucrose replaces Pro in plants as the major osmoprotectant. Our results highlight the plasticity of the plant genome and demonstrate its ability to respond to complex environmental conditions that occur in the field.
An Overview of Gibberellin Metabolism Enzyme Genes and Their Related Mutants in Rice
Authors: Sakamoto Tomoaki , Miura Koutarou , Itoh Hironori , Tatsumi Tomoko , Ueguchi-Tanaka Miyako , Ishiyama Kanako , Kobayashi Masatomo , Agrawal Ganesh K. , Takeda Shin , Abe Kiyomi , Miyao Akio , Hirochika Hirohiko , Kitano Hidemi , Ashikari Motoyuki , Matsuoka Makoto
Published: April 2004

To enhance our understanding of GA metabolism in rice (Oryza sativa), we intensively screened and identified 29 candidate genes encoding the following GA metabolic enzymes using all available rice DNA databases: ent-copalyl diphosphate synthase (CPS), ent-kaurene synthase (KS), ent-kaurene oxidase (KO), ent-kaurenoic acid oxidase (KAO), GA 20-oxidase (GA20ox), GA 3-oxidase (GA3ox), and GA 2-oxidase (GA2ox). In contrast to the Arabidopsis genome, multiple CPS-like, KS-like, and KO-like genes were identified in the rice genome, most of which are contiguously arranged. We also identified 18 GA-deficient rice mutants at six different loci from rice mutant collections. Based on the mutant and expression analyses, we demonstrated that the enzymes catalyzing the early steps in the GA biosynthetic pathway (i.e. CPS, KS, KO, and KAO) are mainly encoded by single genes, while those for later steps (i.e. GA20ox, GA3ox, and GA2ox) are encoded by gene families. The remaining CPS-like, KS-like, and KO-like genes were likely to be involved in the biosynthesis of diterpene phytoalexins rather than GAs because the expression of two CPS-like and three KS-like genes (OsCPS2, OsCPS4, OsKS4, OsKS7, and OsKS8) were increased by UV irradiation, and four of these genes (OsCPS2, OsCPS4, OsKS4, and OsKS7) were also induced by an elicitor treatment.
Ethylene Insensitivity Does Not Increase Leaf Area or Relative Growth Rate in Arabidopsis,Nicotiana tabacum,andPetunia x hybrida
Authors: Tholen Danny , Voesenek Laurentius A.C.J. , Poorter Hendrik
Published: April 2004

The plant hormone ethylene plays a role in various growth related processes. In this detailed study of the vegetative growth of Arabidopsis, Nicotiana tabacum, and Petunia x hybrida plants, we show that ethylene insensitivity does not result in an increased total leaf area or relative growth rate (RGR) under optimal growth conditions. When grown in semiclosed containers, leaf area of ethylene-insensitive plants was larger compared to the wild type. This effect was caused by a buildup of ethylene inside these containers, which inhibited the growth of wild-type plants. Ethylene-insensitive Arabidopsis and N. tabacum plants had a lower biomass, which was mainly the result of a smaller seed mass. RGR of vegetative plants was not affected by ethylene insensitivity, but the underlying components of RGR differed; specific leaf area (leaf area per unit leaf mass) was higher, and unit leaf rate (growth rate per unit leaf area) was lower. The latter was a result of a slower rate of photosynthesis per unit leaf area in the ethylene-insensitive plants.