bluuebunny/crossref_metadata_2025 huggingface dataset:
Current-injection spiral-shaped microcavity disk laser diodes with unidirectional emission
Authors: Kneissl M. , Teepe M. , Miyashita N. , Johnson N. M. , Chern G. D. , Chang R. K.
Published: April 2004

A spiral-shaped microcavity heterojunction laser diode fabricated with InGaN multiple quantum wells is demonstrated to operate under current injection conditions and emit unidirectionally. Room-temperature laser operation was achieved for microcavity disk radii ranging from 50 to 350 μm and threshold current densities as low as 4.6 kA/cm2. Unidirectional laser emission is clearly revealed in the far-field pattern with the lateral divergence angle ranging from 60° to 75°. Output power of more than 25 mW was obtained for emission wavelengths near 400 nm.
Microsecond time scale lateral-mode dynamics in a narrow stripe InGaN laser
Authors: Eichler Christoph , Hofstetter Daniel , Chow Weng W. , Miller Stephan , Weimar Andreas , Lell Alfred , Härle Volker
Published: April 2004

Time-resolved measurements of the spectrum and the far field of InGaN-based laser diodes show lateral-mode changes and gradual tilting of the far field on a microsecond time scale. Numerical simulations based on a microscopic theory are in good agreement with the measurements. The observed effects are attributed to lateral carrier diffusion in combination with thermal lensing.
Reduction of resistivity in Cu thin films by partial oxidation: Microstructural mechanisms
Authors: Prater Walter L. , Allen Emily L. , Lee Wen-Y. , Toney Michael F. , Daniels Jonathan , Hedstrom Jonathan A.
Published: April 2004

We report on the electrical resistance and microstructure of sputter deposited copper thin films grown in an oxygen containing ion-beam sputtering atmosphere. For films thinner than 5 nm, 6%–10% oxygen causes a minimum in film resistivity, while for thicker films, there is a monotonic increase in resistivity. X-ray reflectivity measurements show significantly smoother films for these oxygen flow rates. X-ray diffraction shows that the oxygen doping causes a refinement of the copper grain size and the formation of cuprous oxide. We suggest that the formation of cuprous oxide limits copper grain growth, which causes smoother interfaces, and thus reduces resistivity by increasing specular scattering of electrons at interfaces.
Optically pumped ultraviolet microdisk laser on a silicon substrate
Authors: Liu X. , Fang W. , Huang Y. , Wu X. H. , Ho S. T. , Cao H. , Chang R. P. H.
Published: April 2004

We have fabricated ultraviolet microdisk lasers on silicon substrates. A thin layer of zinc oxide is grown on top of the silica microdisks and serves as the gain medium. Under optical pumping, lasing occurs in the whispering gallery modes of the hybrid microdisks at room temperature. Above the lasing threshold, a drastic increase of emission intensity is accompanied by a decrease of spectral width of the lasing modes.
Structure and photoluminescence of ZnSe nanoribbons grown by metal organic chemical vapor deposition
Authors: Zhang X. T. , Ip K. M. , Liu Z. , Leung Y. P. , Li Quan , Hark S. K.
Published: April 2004

ZnSe nanoribbons have been synthesized using sputter-coated gold films as catalysts via metalorganic chemical vapor deposition on Si (100) substrates. Both x-ray and selected area electron diffractions determine that they have the zinc-blende structure. High-resolution transmission electron microscopic investigations show that their structure is highly ordered and contains coherent twin lamellae near one edge but is essentially free of dislocations. Photoluminescence studies at 10 K show that sharp excitonic peaks dominate their spectra, reflecting their high purity and nearly perfect stoichiometry. New excitonic peaks are observed in the nanoribbons and their possible origins are discussed.
Self-catalytic synthesis and photoluminescence of ZnO nanostructures on ZnO nanocrystal substrates
Authors: Yu W. D. , Li X. M. , Gao X. D.
Published: April 2004

ZnO tetrapods and ZnO nanorods were synthesized on ZnO nanocrystal substrates by a vapor transport process. The source materials were ZnCO3 powder and ZnO powder, respectively, which were reduced by graphite powder to yield different amounts of the vapor. The catalysts were ZnO nanocrystal layers prepared by successive ionic layer adsorption and reaction method. The effect of the source materials on the structure was investigated. Results showed that for the source of ZnCO3 powder, ZnO tetropds constituted by the four pillarlike ZnO nanorods were obtained, while for the source of ZnO powder a nanorods array was formed. Possible growth mechanism and room-temperature photoluminescence of ZnO nanostructures are discussed.
Magnetic anisotropy control of SrRuO3 films by tunable epitaxial strain
Authors: Jung C. U. , Yamada Hiroyuki , Kawasaki M. , Tokura Y.
Published: April 2004

We have investigated the effect of anisotropic structural modification through epitaxial strain on the magnetic properties in an itinerant ferromagnet SrRuO3. For giving tunable and anisotropic in-plane strain, variable thickness CaHfO3 buffer layer and SrTiO3 (STO) (110) substrate were employed, respectively. The strain could be tuned from compressive to tensile along in-plane STO[001]∥ direction, while keeping slightly compressive and coherent along another in-plane STO[1-10]∥ direction. Magnetic easy axis can always be aligned with elongated lattice direction either parallel or perpendicular to the surface, due to strong spin–orbit coupling.
Fabrication of GaN cantilevers on silicon substrates for microelectromechanical devices
Authors: Davies S. , Huang T. S. , Gass M. H. , Papworth A. J. , Joyce T. B. , Chalker P. R.
Published: April 2004

The fabrication of free-standing GaN cantilevers on Si(111) is demonstrated, and the growth of III-nitride epilayers on silicon (111) using an AlN buffer layer is characterized. Mechanically releasing GaN structures from Si(111) required a combination of two dry inductively coupled plasma etch processes using Cl2/Ar and CF4/Ar/O2 chemistries, and a potassium hydroxide (KOH) aqueous etch. Scanning transmission electron microscopy reveals a columnar growth habit for the nitrides. Electron energy loss spectroscopy imaging of an AlGaN/GaN interface indicates columnar growth may strongly influence the potential piezoelectric properties of III-nitride cantilever microelectromechanical devices.
Giant planar Hall effect in colossal magnetoresistive La0.84Sr0.16MnO3 thin films
Authors: Bason Y. , Klein L. , Yau J.-B. , Hong X. , Ahn C. H.
Published: April 2004

The transverse resistivity in thin films of La0.84Sr0.16MnO3 (LSMO) exhibits sharp field-symmetric jumps below TC. We show that a likely source of this behavior is the giant planar Hall effect combined with biaxial magnetic anisotropy. The effect is comparable in magnitude to that observed recently in the magnetic semiconductor Ga(Mn)As. It can be potentially used in applications such as magnetic sensors and nonvolatile memory devices.
Effect of nucleation layer on the magnetic properties of GaMnN
Authors: Thaler G. , Frazier R. , Gila B. , Stapleton J. , Davidson M. , Abernathy C. R. , Pearton S. J. , Segre Carlos
Published: April 2004

The effects of nucleation layer and growth temperature on the magnetic properties of GaMnN have been investigated. It was found that the largest magnetic moment was measured in films prepared on metalorganic chemical vapor deposition (MOCVD) GaN buffers at a growth temperature of 700 °C. Extended x ray absorption fine structure measurements indicate that the improved magnetic quality of the films grown on MOCVD layers versus gas source molecular beam epitaxy nucleation layers is not due to a change in the lattice position of the Mn and is more likely due to a reduction in defect density. Growth temperature was also found to have a significant impact on the magnetic properties, with the optimal growth temperature found to be 700 °C.
Bulk-surface vacancy exchange on Pt(111)
Authors: Poelsema Bene , Hannon J. B. , Bartelt N. C. , Kellogg G. L.
Published: April 2004

We have used low-energy electron microscopy to study atomic exchange between the bulk and the (111) surface of Pt above 1100 K. We find that the area of two-dimensional surface islands increases when the temperature is raised and decreases when the temperature is lowered, suggesting that thermal bulk vacancies are created at the surface. By measuring the temperature dependence of the change in area of the islands, we determine a Pt bulk vacancy formation energy of 1.54±0.07 eV, consistent with previous measurements and calculations.
Enhancement-mode thin-film field-effect transistor using phosphorus-doped (Zn,Mg)O channel
Authors: Kwon Y. , Li Y. , Heo Y. W. , Jones M. , Holloway P. H. , Norton D. P. , Park Z. V. , Li S.
Published: April 2004

We report on enhancement-mode ZnO-based field-effect transistors that utilize an acceptor-doped channel. In particular, the active channel is polycrystalline ZnO doped with Mg, to increase the band gap, and P, to decrease the electron carrier concentration. Devices are realized that display an on/off ratio of 103 and a channel mobility on the order of 5 cm2/V s. HfO2 serves as the gate dielectric. Capacitance–voltage properties measured across the gate indicate that the ZnO channel is n type. The use of acceptor doping improves the control of the initial channel conductance while having a minimal impact on channel mobility relative to undoped ZnO polycrystalline channels.
Characterization of Si/GexSi1−x structures by micro-Raman imaging
Authors: Nakashima S. , Yamamoto T. , Ogura A. , Uejima K. , Yamamoto T.
Published: April 2004

Ge x Si 1−x are characterized by Raman microspectroscopy. The strain of the 17.5-nm-thick Si layer was examined through deep UV Raman measurements. The depth profile of the GexSi1−x alloy composition and crystallinity was determined by visible Raman image measurement of the sample cross section. These measurements give results consistent with transmission electron microscopy and secondary ion mass spectrometry analyses.
Optical and electrical properties of amorphous GdxGa0.4−xO0.6 films in GdxGa0.4−xO0.6/Ga2O3 gate dielectric stacks on GaAs
Authors: Passlack M. , Medendorp N. , Zollner S. , Gregory R. , Braddock D.
Published: April 2004

Optical and electrical properties of amorphous GdxGa0.4−xO0.6 films have been systematically investigated as a function of Gd mole fraction x (0⩽x⩽0.31). The GdxGa0.4−xO0.6 films are part of GdxGa0.4−xO0.6/Ga2O3 gate dielectric stacks grown onto the GaAs(001) surface by molecular-beam deposition. When the Gd mole percent is raised from 0 to 25 at. % (0⩽x⩽0.25), the refractive index n and the optical band gap increase from 1.908 to 1.987 and from 4.22 to 5.08 eV, respectively. The electrical properties of GdxGa0.4−xO0.6 films improve dramatically with increasing Gd concentration: The leakage current falls from 7.8×10−1 to 9.7×10−10 A/cm2 (measured at an electric field of 1 MV/cm) when the Gd mole percent is raised from 8.8 to 31 at. %, and the dielectric breakdown field exceeds 4 MV/cm for x>0.21.
Near-field three-dimensional coherent imaging: Theory and simulations
Authors: Silverstein Seth D. , Zheng Yibin
Published: April 2004

This work presents a rigorous mathematical derivation of an effective approximate solution to the three-dimensional inverse scattering/imaging problem that is applicable for all imaging zones ranging from the near to the far field. Simulation results for the point spread function illustrate the range and cross-range resolution as a function of the optical f number. The model system operates in a synthetic aperture type mode, where the coherent signals are transmitted, and the scattered signals are subsequently received at individual transmitters and receivers. Potential applications of this technology include: Medical ultrasound, foliage penetrating synthetic aperture radar, ground penetrating radar for land mine detection, and electromagnetic millimeter-wave scanning for concealed weapon detection.
Thermoelectric figure of merit and maximum power factor in III–V semiconductor nanowires
Authors: Mingo N.
Published: April 2004

The relative contributions of electronic and lattice effects to figure of merit enhancement are studied, for nanowires made of InSb, InAs, GaAs, and InP, as a function of nanowire thickness. The main thermoelectric magnitudes are computed in the bulk and nanowire cases by the exact solution of the Boltzmann transport equation. The lattice thermal conductivity is obtained by a full dispersions transmission function approach, using interatomic potentials for the system. An upper limit to the maximum power factor is obtained for narrow thickness. InSb nanowires stand out as the best choice for thermoelectric applications among the four compounds considered, while GaAs and InP are not expected to be suitable for practical applications.
Visible photoluminescence in ZnO tetrapod and multipod structures
Authors: Djurišić Aleksandra B. , Leung Yu Hang , Choy Wallace C. H. , Cheah Kok Wai , Chan Wai Kin
Published: April 2004

The properties of ZnO tetrapod and multipod structures were investigated using scanning electron microscopy, x-ray diffraction, photoluminescence (PL), and electron paramagnetic resonance (EPR) spectroscopy. While there is relationship between g=1.96 EPR and green PL in some of the samples, this is not the case for all the samples. Therefore, the commonly assumed transition between a singly charged oxygen vacancy and photoexcited hole [K. Vanheusden, C. H. Seager, W. L. Warren, D. R. Tallant, and J. A. Voigt, Appl. Phys. Lett. 68, 403 (1996)] does not explain the green emission in all ZnO samples. The green emission likely originates from surface defects.
Acoustic manipulation of electron–hole pairs in GaAs at room temperature
Authors: de Lima M. M. , Hey R. , Stotz J. A. H. , Santos P. V.
Published: April 2004

We demonstrate the optically detected long-range (>100 μm) ambipolar transport of photogenerated electrons and holes at room temperature by surface acoustic waves (SAWs) in (In,Ga)As-based quantum well structures coupled to an optical microcavity. We also show the control of the propagation direction of the carriers by a switch composed of orthogonal SAW beams, which can be used as a basic control gate for information processing based on ambipolar transport.
Tunable multiple plasmon resonance wavelengths response from multicomponent polymer-metal nanocomposite systems
Authors: Biswas A. , Aktas O. C. , Schürmann U. , Saeed U. , Zaporojtchenko V. , Faupel F. , Strunskus T.
Published: April 2004

A method of vapor phase codeposition has been used at elevated target temperature coupled with selective masking technique to produce a multicomponent optical material with seven different ultraviolet-visible optical active planes. Such a system consists of different nanocomposites of Teflon AF/Ag, Teflon AF/Au, and Teflon AF/Cu with sharp interfaces. The fabricated system has regions of single nanocomposite plane together with multilayer structures facilitating tunable multiple particle plasmon resonance wavelength response from a single system. Distinct double and triple plasmon wavelength resonance absorptions could be obtained from such interfaces forming multilayers of either two or three nanocomposite structures.
Enhanced optical properties of the GaAsN/GaAs quantum-well structure by the insertion of InAs monolayers
Authors: Gao Q. , Tan H. H. , Jagadish C. , Sun B. Q. , Gal M. , Ouyang L. , Zou J.
Published: April 2004

Microstructural and optical properties of InAs-inserted and reference single GaAsN/GaAs quantum-well (QW) structures grown by metalorganic chemical vapor deposition were investigated using cross-sectional transmission electron microscopy and photoluminescence (PL). Significant enhancement of PL intensity and a blueshift of PL emission were observed from the InAs-inserted GaAsN/GaAs QW structure, compared with the single GaAsN/GaAs QW structure. Strain compensation and In-induced reduction of N incorporation are suggested to be two major factors affecting the optical properties.
Realization of InAs-based two-dimensional artificial lattice by selective area metalorganic vapor-phase epitaxy
Authors: Mohan Premila , Motohisa Junichi , Fukui Takashi
Published: April 2004

The experimental realization of two-dimensional semiconductor artificial lattice based on InAs quantum wires is reported here. Artificial Kagome lattice fabricated using InAs quantum wires of unit cell size 0.7 μm has been theoretically proved to show ferromagnetism. Fabrication of such a structure with InAs quantum wires was attempted by selective area metalorganic vapor phase epitaxy using GaAs (111)A substrates. Temperature-dependent growth mode change was observed and Volmer-Weber growth mode at high temperature inhibited the formation of uniform structure. Low temperature and low AsH3 partial pressure resulted in the successful fabrication of 0.7 μm period InAs-based Kagome lattice structure.
Enhanced photoluminescence at poly(3-octyl-thiophene)/TiO2 interfaces
Authors: van der Zanden Barbara , van de Krol Roel , Schoonman Joop , Goossens Albert
Published: April 2004

The photoluminescence (PL) of poly(3-octyl-thiophene) (P3OT) thin films applied on TiO2 substrates is compared to the PL of P3OT films applied on quartz. Quenching of excitons occurs at the P3OT/TiO2 interface and not at the P3OT/quartz interface. Yet, in the former case the PL intensity is stronger than in the latter. In particular, P3OT films less than 5 nm thick lumines much more when applied on TiO2, which is in striking contrast to what one expects. For films thicker than 10 nm, the increase of the PL as function of the film thickness is the same for TiO2 and for quartz, which indicates that the PL enhancement originates at the interface. The dissociation of excitons at the P3OT/TiO2 interface yields positive polarons in P3OT, which is not the case at the P3OT/quartz interface. We postulate that interaction between positive polarons and excitons explain the observed enhancement of the PL at the P3OT/TiO2 interface.
Origin of luminescence from Si−-implanted (11¯02) Al2O3
Authors: Park C. J. , Kwon Y. H. , Lee Y. H. , Kang T. W. , Cho H. Y. , Kim Sung , Choi Suk-Ho , Elliman R. G.
Published: April 2004

Cathodoluminescence (CL), photoluminescence, and transmission electron microscopy have been used to study the light-emitting and structural properties of (11¯02) sapphire implanted with 30-keV Si ions and subsequently annealed at temperatures up to 1100 °C. This procedure creates oriented Si crystallites with diameters in the range 4–5 nm together with extended defects parallel to the (0001) planes of (11¯02) Al2O3. Several CL bands found in Si−-implanted Al2O3(Al2O3:Si−) before and/or after annealing are compared with those from O−- and Al−-implanted samples. These and related experiments, including annealing temperature and implant dose dependence, suggest that a yellow CL band (2.16 eV/574 nm) from annealed Al2O3:Si− is nanocrystal related, while others are defect related.
Relaxation of nanopatterns on Nb-doped SrTiO3 surface
Authors: Li Run-Wei , Kanki Teruo , Hirooka Motoyuki , Takagi Akihiko , Matsumoto Takuya , Tanaka Hidekazu , Kawai Tomoji
Published: April 2004

By atomic force microscopy (AFM), we have realized nanolithography and changed the physical properties within a desired nanosized region on Nb-doped SrTiO3 single-crystal substrate. Importantly, a considerable relaxation of these written patterns was observed directly, which evidently indicates that a significant chemical transport occurs during and after the AFM lithography. Furthermore, we found that defects introduced by Ar bombardment can stabilize these patterns, which is quite effective for the application of AFM lithography in perovskite oxides.
Manganite-based heterojunction and its photovoltaic effects
Authors: Sun J. R. , Xiong C. M. , Shen B. G. , Wang P. Y. , Weng Y. X.
Published: April 2004

A heterojunction is fabricated by growing a La0.29Pr0.38Ca0.33MnO3 (LPCM) film on the 0.5 wt % Nb-doped SrTiO3 (STON) substrate, and its properties have been experimentally studied. In addition to fairly good rectifying behavior, the heterojunction exhibits a significant photovoltaic effect. The photovoltage on the two electrodes LPCM and STON increases almost linearly with the power of the laser beam (λ=532 nm) at a rate of ∼0.19 V/W, and no tendency to saturation is observed up to the light power of 100 mW. The lifetime of the extra carriers is between 7 and 9 ms (slightly pulse laser energy dependent), obtained from the decay of photovoltage after shutting down light illumination. The present work shows a great potential of the manganite-based heterojunction as photoelectric devices.
Dependence of the sputter-etching characteristics of strontium–titanate–oxide thin films on their structural properties
Authors: Stafford L. , Gaidi M. , Chaker M. , Langlois O. , Margot J. , Schiettekatte F. , Wei P.
Published: April 2004

Sputter-etching characteristics of polycrystalline strontium–titanate–oxide (STO) thin films are investigated using a high-density argon plasma. STO thin films were grown by means of a reactive pulsed-laser deposition technique in which the buffer oxygen pressure was varied to change the structural properties of the films. The sputter-etch rate of the rf-biased films is found to linearly increase with the oxygen deposition pressure. This result is shown to be related to the corresponding decrease of the film density. This dependence of the etch rate on the structural properties of the films has very important consequences on etching studies and on the optimization of etching processes.
Modified transmission line model and its application to aluminum ohmic contacts with n-type GaN
Authors: Chen N. C. , Chang P. H. , Chiu A. P. , Wang M. C. , Feng W. S. , Wu G. M. , Shih C. F. , Liu K. S.
Published: April 2004

A modified transmission line model (MTLM) of ohmic contact measurement is presented. This model preserves the simplicity of the circular transmission line model but eliminates the shortcoming of the possibility of obtaining misleading results. This model was applied to n-type GaN ohmic contacts and results similar to those obtained by Hall measurement were obtained. The ohmic contact pattern used in MTLM method occasionally exists during the fabrication of several devices. In such cases, the method can be used to determine the device processing quality without the need for any other test pattern.
Observation of coherent interfacial optical phonons in GaInP/GaAs/GaInP single quantum wells
Authors: Chang Y.-M. , Lin H. H. , Chia C. T. , Chen Y. F.
Published: April 2004

Coherent phonon spectroscopy of GaInP/GaAs/GaInP single quantum wells is demonstrated with time-resolved second-harmonic generation. Coherent longitudinal optical phonons are impulsively launched via transient pump-induced field screening and stimulated Raman scattering in the well and barrier regions. A phonon mode at 9.4 THz is identified as interfacial phonon localized in the GaAs/GaInP hetero-interface. The free induced dephasing of this coherent interfacial phonon is analyzed with window-gated Fourier transform. Its dephasing time is used to characterize the interface quality of semiconductor heterostructures.
Cyclic Analogues of the Hendrickson ‘POP’ Reagent
Authors: Elson Kathryn E. , Jenkins Ian D. , Loughlin Wendy A.
Published: April 2004

The Hendrickson reagent, triphenylphosphonium anhydride trifluoromethanesulfonate, ‘POP’ 1, is a powerful dehydrating agent. Five-, six-, and seven-membered cyclic analogues of the ‘POP’ reagent 2–4 have been prepared and their use for ester and amide synthesis investigated. A kinetic comparison of the cyclic analogues 2–4 revealed that a considerable increase in the rate of esterification could be achieved when the five-membered ring analogue 2 was used, presumably due to the ease of formation of the putative phosphorane intermediate. The rate of ester formation from a primary alcohol using the Hendrickson reagent 1 was shown to be significantly faster when non-polar solvents were employed.
Chiral Conjoined Cavitands
Authors: Irwin Jacob L. , Sinclair David J. , Edwards Alison J. , Sherburn Michael S.
Published: April 2004

Tetrabromocavitand bowls are converted into rim-connected hexabromodimers in one step in 17–22% yields by oxidative coupling of higher order arylcuprates. 1H NMR and single crystal X-ray analyses of the rim-connected dimers reveal a conformationally restricted structure in which the rims of the two cavitand bowls describe planes angled at 78.8° to one another. Each of the two bowl cavities are occupied by a guest, in addition to being partially occluded by a portion of the complementary bowl rim. These new host compounds exhibit a very unusual form of enantioisomerism.
Groundwater-induced accumulation of iron oxides and phosphorus retention in severely leached soils
Authors: Qiu Song , McComb Arthur
Published: April 2004

Many sandy soils of the Swan Coastal Plain, Western Australia, are poor in Fe and P retention. A novel concept proposes to relocate Fe from groundwater to surface soils via watering, which should consequently improve P retention. To test the viability of this concept we examined several soils in Perth suburbs that had been watered for 3–27 years with groundwater containing high Fe. Energy dispersive X-ray microanalysis indicated that ‘Fe-watered’ soils had significantly higher Fe materials on the surface of soil particles. Oxalate-extractable Fe (Feo) increased by 52 times and citrate/dithionite-extractable Fe (Fed) increased by 6.6 times. Unusually high Feo/d ratios (average Feo/d = 0.71) in ‘Fe-watered’ soils strongly suggest that the accumulated Fe materials are predominantly amorphous and secondary Fe oxides, probably ferrihydrite. There was a substantial increase in P retention in top-soils, to a magnitude of 45–128 times, demonstrating that increasing Fe oxides in severely leached soils, caused by groundwater irrigation, increases P retention. This approach could be applied to other areas with similar physical characteristics and the present study demonstrates that watering with Fe rich groundwater might have strategic significance not only in the control of water pollution, but also in the rational use of water resources and the amelioration of soil salinisation associated with rising watertables.
Differential tolerance to ultraviolet-B light and photoenzymatic repair in cladocerans from a Chilean lake
Authors: Ramos-Jiliberto Rodrigo , Dauelsberg Patricia , Zúñiga Luis R.
Published: April 2004

In the present study, the sensitivity of four coexisting cladoceran species to ultraviolet (UV)-B radiation was evaluated. First, the LD50 under conditions inhibiting the action of photoenzymatic repair was calculated by exposing cladocerans to different doses of UV-B light only. Animals in another treatment group were exposed to both UV-B and visible light, which allows for photoenzymatic repair. Photoenzymatic repair contributed significantly towards the degree of total tolerance to UV-B light in all groups of cladocerans, although the magnitude of the contribution varied among species. When no photoenzymatic repair was allowed, the most tolerant species was Moina micrura, followed by Daphnia ambigua and Ceriodaphnia dubia, with Diaphanosoma chilense being the most sensitive species. Under conditions permitting the action of photorepair, M. micrura was again the most tolerant species to UV-B light. Ceriodaphnia dubia showed an intermediate tolerance value, whereas D. chilense and D. ambigua were the least tolerant species, with no significant differences between them. Adults and juveniles of C. dubia differed in their sensitivity to UV-B light under conditions with and without photorepair.
Identifying the influence of channel morphology on physical habitat availability for native fish: application to the two-spined blackfish (Gadopsis bispinosus) in the Cotter River, Australia
Authors: Maddock Ian , Thoms Martin , Jonson Katarina , Dyer Fiona , Lintermans Mark
Published: April 2004

The impact of channel morphology and flow on physical habitat availability for the two-spined blackfish (Gadopsis bispinosus) was assessed in the Cotter River, ACT, Australia. Physical habitat requirements for three life stages were identified based on previous field sampling in the Cotter River. Two sites were selected with contrasting channel morphology: Spur Hole, with a moderate gradient and runs and glides, and Vanity’s Crossing, with a steeper gradient, rapids, and fast-flowing pools. Physical Habitat Simulation System (PHABSIM) was used to simulate the flow v. physical habitat availability relationship for each life stage at both sites. Clear differences were apparent between sites, with Spur Hole characterised by increasing habitat with increasing flow and Vanity’s Crossing showing the opposite relationship. The nature of the channel morphology determined this difference, with Spur Hole characterised by marginal zones becoming inundated at higher flows and providing additional suitable physical habitat as discharge increases. Vanity’s Crossing does not contain similar marginal zones. Further analysis demonstrated that high water velocity was the most important factor limiting physical habitat availability at both sites. This approach demonstrates the importance of channel morphology in determining physical habitat availability and an alternative use of PHABSIM to highlight limiting factors for target species.
Deep phylogenetic structure has conservation implications for ornate rainbowfish (Melanotaeniidae:Rhadinocentrus ornatus) in Queensland, eastern Australia
Authors: Page Timothy J. , Sharma Suman , Hughes Jane M.
Published: April 2004

The freshwater fish, Rhadinocentrus ornatus Regan, 1914, has a patchy distribution through coastal drainages of Queensland and New South Wales, eastern Australia. Isolated populations of R. ornatus are found on several islands, as well as in a disjunct northern population 350 km from its nearest conspecific population. Deoxyribonucleic acid was extracted and sequenced for the mitochondrial ATPase gene to describe the geographic and genetic subdivision within the species. Four major clades were identified. These clades diverged between two and seven million years ago and so represent long-term divisions and possible units of conservation. There are conservation implications in that the narrow and localised distribution of R. ornatus overlaps with an area of large-scale land clearing, high human population and threats from introduced exotic fish. A particularly high centre of Rhadinocentrus diversity in the Tin Can Bay area of Queensland presents some interesting questions about the evolution of the genus Rhadinocentrus.
Developmental changes in foregut functioning of packhorse lobster, Jasus (Sagmariasus) verreauxi (Decapoda:Palinuridae), phyllosoma larvae
Authors: Cox Serena L. , Johnston Danielle J.
Published: April 2004

The development of foregut structure and digestive function was examined in Jasus (Sagmariasus) verreauxi phyllosomas (instars 1–13) using resin histology and video analysis. Early instar (1–3) phyllosoma had very simple anterior foreguts with little differentiation into ventral and dorsal chambers, no filter press and small lateral comb-row setae. By mid instars (4–7), the filter press had developed and ventral and dorsal chambers of the foregut were distinct. The number and robustness of lateral setae had increased and a dense mat of anterior floor setae had formed. The filter press became increasingly complex in later-instar (8–13) larvae and dense robust lateral comb-row setae, main brushes and a thick mat of anterior floor setae forming longitudinal channels had developed by this stage. The mechanism of food digestion remained similar between instars but changes in foregut structures suggest that the degree of internal mastication, filtration and capacity to sort and mix particles improved with age. This research has implications for artificial diet development in crustacean culture and understanding dietary shifts during larval development.
Dimer destabilization in superoxide dismutase may result in disease-causing properties: Structures of motor neuron disease mutants
Authors: Hough Michael A. , Grossmann J. Günter , Antonyuk Svetlana V. , Strange Richard W. , Doucette Peter A. , Rodriguez Jorge A. , Whitson Lisa J. , Hart P. John , Hayward Lawrence J. , Valentine Joan Selverstone , Hasnain S. Samar
Published: April 2004

More than 90 point mutations in human CuZn superoxide dismutase lead to the development of familial amyotrophic lateral sclerosis, known also as motor neuron disease. A growing body of evidence suggests that a subset of mutations located close to the dimeric interface can lead to a major destabilization of the mutant enzymes. We have determined the crystal structures of the Ala4Val (A4V) and Ile113Thr (I113T) mutants to 1.9 and 1.6 Å, respectively. In the A4V structure, small changes at the dimer interface result in a substantial reorientation of the two monomers. This effect is also seen in the case of the I113T crystal structure, but to a smaller extent. X-ray solution scattering data show that in the solution state, both of the mutants undergo a more pronounced conformational change compared with wild-type superoxide dismutase (SOD) than that observed in the A4V crystal structure. Shape reconstructions from the x-ray scattering data illustrate the nature of this destabilization. Comparison of these scattering data with those for bovine CuZn SOD measured at different temperatures shows that an analogous change in the scattering profile occurs for the bovine enzyme in the temperature range of 70–80°C. These results demonstrate that the A4V and I113T mutants are substantially destabilized in comparison with wild-type SOD1, and it is possible that the pathogenic properties of this subset of familial amyotrophic lateral sclerosis mutants are at least in part due to this destabilization.
Myosin V processivity: Multiple kinetic pathways for head-to-head coordination
Authors: Baker Josh E. , Krementsova Elena B. , Kennedy Guy G. , Armstrong Amy , Trybus Kathleen M. , Warshaw David M.
Published: April 2004

Myosin V, a double-headed molecular motor, transports organelles within cells by walking processively along actin, a process that requires coordination between the heads. To understand the mechanism underlying this coordination, processive runs of single myosin V molecules were perturbed by varying nucleotide content. Contrary to current views, our results show that the two heads of a myosin V molecule communicate, not through any one mechanism but through an elaborate system of cooperative mechanisms involving multiple kinetic pathways. These mechanisms introduce redundancy and safeguards that ensure robust processivity under differing physiologic demands.
Mo-catalyzed asymmetric olefin metathesis in target-oriented synthesis: Enantioselective synthesis of (+)-africanol
Authors: Weatherhead Gabriel S. , Cortez G. A. , Schrock Richard R. , Hoveyda Amir H.
Published: April 2004

Catalytic asymmetric ring-opening metathesis (AROM) provides an efficient method for the synthesis of a variety of optically enriched small organic molecules that cannot be easily prepared by alternative methods. The development of Mo-catalyzed AROM transformations that occur in tandem with ring-closing metathesis are described. The utility of the Mo-catalyzed AROM/ring-closing metathesis is demonstrated through an enantioselective approach to the synthesis of (+)-africanol.
High-Throughput Gene Discovery in the Rat
Authors: Scheetz Todd E. , Laffin Jennifer J. , Berger Brian , Holte Sara , Baumes Susan A. , Brown Robert , Chang Shereen , Coco Justin , Conklin Jim , Crouch Keith , Donohue Micca , Doonan Greg , Estes Chris , Eyestone Mari , Fishler Katrina , Gardiner Jack , Guo Lankai , Johnson Brad , Keppel Catherine , Kreger Rikki , Lebeck Mark , Marcelino Rudy , Miljkovich Vladan , Perdue Mindee , Qui Ling , Rehmann Joshua , Reiter Rebecca S. , Rhoads Bridgette , Schaefer Kelly , Smith Christina , Sunjevaric Ivana , Trout Kurtis , Wu Ning , Birkett Clayton L. , Bischof Jared , Gackle Barry , Gavin Allen , Grundstad A. Jason , Mokrzycki Brian , Moressi Chris , O'Leary Brian , Pedretti Kevin , Roberts Chad , Robinson Natalie L. , Smith Michael , Tack Dylan , Trivedi Nishank , Kucaba Tamara , Freeman Tom , Lin Jim J.-C. , Bonaldo Maria F. , Casavant Thomas L. , Sheffield Val C. , Soares M. Bento
Published: April 2004

The rat is an important animal model for human diseases and is widely used in physiology. In this article we present a new strategy for gene discovery based on the production of ESTs from serially subtracted and normalized cDNA libraries, and we describe its application for the development of a comprehensive nonredundant collection of rat ESTs. Our new strategy appears to yield substantially more EST clusters per ESTs sequenced than do previous approaches that did not use serial subtraction. However, multiple rounds of library subtraction resulted in high frequencies of otherwise rare internally primed cDNAs, defining the limits of this powerful approach. To date, we have generated >200,000 3′ ESTs from >100 cDNA libraries representing a wide range of tissues and developmental stages of the laboratory rat. Most importantly, we have contributed to ∼50,000 rat UniGene clusters. We have identified, arrayed, and derived 5′ ESTs from >30,000 unique rat cDNA clones. Complete information, including radiation hybrid mapping data, is also maintained locally at http://genome.uiowa.edu/clcg.html. All of the sequences described in this article have been submitted to the dbEST division of the NCBI.
Recent Segmental Duplications in the Working Draft Assembly of the Brown Norway Rat
Authors: Tuzun Eray , Bailey Jeffrey A. , Eichler Evan E.
Published: April 2004

We assessed the content, structure, and distribution of segmental duplications (≥90% sequence identity, ≥5 kb length) within the published version of the Rattus norvegicus genome assembly (v.3.1). The overall fraction of duplicated sequence within the rat assembly (2.92%) is greater than that of the mouse (1%–1.2%) but significantly less than that of human (∼5%). Duplications were nonuniformly distributed, occurring predominantly as tandem and tightly clustered intrachromosomal duplications. Regions containing extensive interchromosomal duplications were observed, particularly within subtelomeric and pericentromeric regions. We identified 41 discrete genomic regions greater than 1 Mb in size, termed “duplication blocks.” These appear to have been the target of extensive duplication over millions of years of evolution. Gene content within duplicated regions (∼1%) was lower than expected based on the genome representation. Interestingly, sequence contigs lacking chromosome assignment (“the unplaced chromosome”) showed a marked enrichment for segmental duplication (45% of 75.2 Mb), indicating that segmental duplications have been problematic for sequence and assembly of the rat genome. Further targeted efforts are required to resolve the organization and complexity of these regions.
Identification of Candidate Disease Genes by EST Alignments, Synteny, and Expression and Verification of Ensembl Genes on Rat Chromosome 1q43-54
Authors: Vitt Ursula , Gietzen Darryl , Stevens Kristian , Wingrove Jim , Becha Shanya , Bulloch Sean , Burrill John , Chawla Narinder , Chien Jennifer , Crawford Matthew , Ison Craig , Kearney Liam , Kwong Mary , Park Joe , Policky Jennifer , Weiler Mark , White Renee , Xu Yuming , Daniels Sue , Jacob Howard , Jensen-Seaman Michael I. , Lazar Jozef , Stuve Laura , Schmidt Jeanette
Published: April 2004

We aligned Incyte ESTs and publicly available sequences to the rat genome and analyzed rat chromosome 1q43-54, a region in which several quantitative trait loci (QTLs) have been identified, including renal disease, diabetes, hypertension, body weight, and encephalomyelitis. Within this region, which contains 255 Ensembl gene predictions, the aligned sequences clustered into 568 Incyte genes and gene fragments. Of the Incyte genes, 261 (46%) overlapped 184 (72%) of the Ensembl gene predictions, whereas 307 were unique to Incyte. The rat-to-human syntenic map displays rearrangement of this region on rat chr. 1 onto human chromosomes 9 and 10. The mapping of corresponding human disease phenotypes to either one of these chromosomes has allowed us to focus in on genes associated with disease phenotypes. As an example, we have used the syntenic information for the rat Rf-1 disease region and the orthologous human ESRD disease region to reduce the size of the original rat QTL to only 11.5 Mb. Using the syntenic information in combination with expression data from ESTs and microarrays, we have selected a set of 66 candidate disease genes for Rf-1. The combination of the results from these different analyses represents a powerful approach for narrowing the number of genes that could play a role in the development of complex diseases.
Aligning Multiple Genomic Sequences With the Threaded Blockset Aligner
Authors: Blanchette Mathieu , Kent W. James , Riemer Cathy , Elnitski Laura , Smit Arian F.A. , Roskin Krishna M. , Baertsch Robert , Rosenbloom Kate , Clawson Hiram , Green Eric D. , Haussler David , Miller Webb
Published: April 2004

We define a “threaded blockset,” which is a novel generalization of the classic notion of a multiple alignment. A new computer program called TBA (for “threaded blockset aligner”) builds a threaded blockset under the assumption that all matching segments occur in the same order and orientation in the given sequences; inversions and duplications are not addressed. TBA is designed to be appropriate for aligning many, but by no means all, megabase-sized regions of multiple mammalian genomes. The output of TBA can be projected onto any genome chosen as a reference, thus guaranteeing that different projections present consistent predictions of which genomic positions are orthologous. This capability is illustrated using a new visualization tool to view TBA-generated alignments of vertebrateHoxclusters from both the mammalian and fish perspectives. Experimental evaluation of alignment quality, using a program that simulates evolutionary change in genomic sequences, indicates that TBA is more accurate than earlier programs. To perform the dynamic-programming alignment step, TBA runs a stand-alone program called MULTIZ, which can be used to align highly rearranged or incompletely sequenced genomes. We describe our use of MULTIZ to produce the whole-genome multiple alignments at the Santa Cruz Genome Browser.
Identification of Rat Genes by TWINSCAN Gene Prediction, RT–PCR, and Direct Sequencing
Authors: Wu Jia Qian , Shteynberg David , Arumugam Manimozhiyan , Gibbs Richard A. , Brent Michael R.
Published: April 2004

The publication of a draft sequence of a third mammalian genome—that of the rat—suggests a need to rethink genome annotation. New mammalian sequences will not receive the kind of labor-intensive annotation efforts that are currently being devoted to human. In this paper, we demonstrate an alternative approach: reverse transcription-polymerase chain reaction (RT–PCR) and direct sequencing based on dual-genome de novo predictions from TWINSCAN. We tested 444 TWINSCAN-predicted rat genes that showed significant homology to known human genes implicated in disease but that were partially or completely missed by methods based on protein-to-genome mapping. Using primers in exons flanking a single predicted intron, we were able to verify the existence of 59% of these predicted genes. We then attempted to amplify the complete predicted open reading frames of 136 genes that were verified in the single-intron experiment. Spliced sequences were amplified in 46 cases (34%). We conclude that this procedure for elucidating gene structures with native cDNA sequences is cost-effective and will become even more so as it is further optimized.
MAVID: Constrained Ancestral Alignment of Multiple Sequences
Authors: Bray Nicolas , Pachter Lior
Published: April 2004

We describe a new global multiple-alignment program capable of aligning a large number of genomic regions. Our progressive-alignment approach incorporates the following ideas: maximum-likelihood inference of ancestral sequences, automatic guide-tree construction, protein-based anchoring of ab-initio gene predictions, and constraints derived from a global homology map of the sequences. We have implemented these ideas in the MAVID program, which is able to accurately align multiple genomic regions up to megabases long. MAVID is able to effectively align divergent sequences, as well as incomplete unfinished sequences. We demonstrate the capabilities of the program on the benchmark CFTR region, which consists of 1.8 Mb of human sequence and 20 orthologous regions in marsupials, birds, fish, and mammals. Finally, we describe two large MAVID alignments, an alignment of all the available HIV genomes and a multiple alignment of the entire human, mouse, and rat genomes.
Pash: Efficient Genome-Scale Sequence Anchoring by Positional Hashing
Authors: Kalafus Ken J. , Jackson Andrew R. , Milosavljevic Aleksandar
Published: April 2004

Pash is a computer program for efficient, parallel, all-against-all comparison of very long DNA sequences. Pash implements Positional Hashing, a novel parallelizable method for sequence comparison based on k-mer representation of sequences. The Positional Hashing method breaks the comparison problem in a unique way that avoids the quadratic penalty encountered with other sensitive methods and confers inherent low-level parallelism. Furthermore, Positional Hashing allows one to readily and predictably trade between sensitivity and speed. In a simulated comparison task, anchoring computationally mutated reads onto a genome, the sensitivity of Pash was equal to or greater than that of BLAST and BLAT, with Pash outperforming these programs as the reads became shorter and less similar to the genome. Using modest computing resources, we employed Pash for two large-scale sequence comparison tasks: comparison of three mammalian genomes, and anchoring millions of chimpanzee whole-genome shotgun sequencing reads onto the human genome. The results of these comparisons by Pash agree with those computed by other methods that use more than an order of magnitude more computing resources. These results confirm the sensitivity of Positional Hashing.
Identification of Evolutionary Hotspots in the Rodent Genomes
Authors: Yap Von Bing , Pachter Lior
Published: April 2004

We describe a whole-genome comparative analysis of the human, mouse, and rat genomes to describe the average substitution patterns of four genomic regions: ancient repeats, rodent-specific DNA, exons, and conserved (coding and noncoding) regions, and to identify rodent evolutionary hotspots. In all types of regions, except the rodent-specific DNA, the rat branch is slightly longer than the mouse branch. Moreover, the mouse–rat distance is longer in the rodent-specific DNA than in the ancient repeats. Analysis of individual conserved regions with different substitution models yielded the conclusion that the Jukes–Cantor model is inadequate, and the Hasegawa–Kishino–Yano model is almost as good as the REV model. Using human as an outgroup, we identified 5055 evolutionary hotspots, which are highly conserved subalignment blocks (each consisting of at least 100 aligned sites and a small fraction of gaps) with a large and statistically significant difference in the branch lengths of the rodent species. The cutoffs used to identify the hotspots are partially based on estimates of the average rates of substitution. The fractions of hotspots overlapping with the rodent RefSeq genes, RefSeq exons, and ESTs are all higher than expected. Still, more than half of the hotspots lie in noncoding regions of the mouse genome. We believe that the hotspots represent biologically interesting regions in the rodent genomes.