bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of carrier loss through waveguide layer recombination on the internal quantum efficiency in large-optical-cavity laser diodes
Authors: Ryvkin B. S. , Avrutin E. A.
Published: June 2005

An analytical treatment for carrier distribution in optical confinement layers (OCLs) of semiconductor lasers with bimolecular recombination is developed. On the basis of this approach, the effect of OCL recombination on the internal quantum efficiency of a laser is evaluated. It is shown that this effect can lead to a rapid deterioration in efficiency with increased waveguide thickness at high enough currents, and also contributes to the efficiency decrease with current in a given structure. An asymmetric, narrow waveguide structure is shown to avoid this problem while still providing a good-quality beam.
Recombination activity of iron-gallium and iron-indium pairs in silicon
Authors: Schmidt Jan , Macdonald Daniel
Published: June 2005

The recombination activity of iron-gallium (FeGa) and iron-indium (FeIn) pairs in crystalline silicon is studied by means of injection-dependent carrier lifetime measurements on Fe-implanted, Ga- and In-doped p-type silicon wafers of different resistivities (0.3–15Ωcm). Compared to FeB pairs, FeGa and FeIn pairs are found to be much more effective recombination centers in p-type silicon. Using Shockley–Read–Hall statistics we determine the energy level Et of the FeGa-related center to be 0.20eV above the valence-band edge Eν. The strong recombination activity of FeGa is assigned to its large electron-capture cross section σn of 4×10−14cm2. The hole-capture cross section σp is 2×10−14cm2. For the FeIn-related recombination center, our measurements show that Et=Eν+0.15eV, σn=3.5×10−13cm2, and σp=1.5×10−14cm2. Strong illumination with white light is found to dissociate both types of pairs. Storage of the samples in the dark leads to a full repairing of FeGa and FeIn pairs. Lifetime changes measured before and after illumination can be used to determine the interstitial iron concentration in Ga- and In-doped silicon using calibration factors determined from the measured defect parameters.
Helicon plasma production in a torus at very high frequency
Authors: Paul Manash Kr. , Bora D.
Published: June 2005

Helicon breakdown in a toroidal vessel is observed with a right helical antenna (m=+1) at a frequency of 32MHz. A toroidal magnetic field of 1kG (max) is applied at the central axis of a toroidal vessel of aspect ratio equal to 3. During experiments, transition from antenna field sustained to helicon wave sustained discharge is also observed. Nonlinear increase in plasma density with input rf power and with magnetic field is observed. However, the wave magnetic field profiles measured in this experiment are different from the earlier experiments conducted in similar toroidal configurations.
Correlation between morphology and ambipolar transport in organic field-effect transistors
Authors: Singh Th. B. , Günes S. , Marjanović N. , Sariciftci N. S. , Menon R.
Published: June 2005

Attaining ambipolar charge transport in organic field-effect transistors (OFET) is highly desirable from both fundamental understanding and application points of view. We present the results of an approach to obtain ambipolar OFET with an active layer of organic semiconductor blends using semiconducting polymers in composite with fullerene derivatives. Clear features of forming the superposition of both hole and electron-enhanced channels for an applied gate field are observed. The present studies suggest a strong correlation of thin-film nanomorphology and ambipolar transport in field-effect devices.
High-spatial-resolution strain measurements by Auger electron spectroscopy in epitaxial-lateral-overgrowth GaN
Authors: Cai Duanjun , Xu Fuchun , Kang Junyong , Gibart Pierre , Beaumont Bernard
Published: June 2005

A high-spatial-resolution strain measurement by Auger electron spectroscopy was established and applied to analyze the strain distributions in epitaxial-lateral-overgrowth (ELO) GaN. The theoretical N KVV Auger line was set by fitting the experimental data and then the relation between Auger shift and strain was obtained. By this relation the local strain distributions in regions of special interest were measured, which well interpret the mechanism of ELO process. A crucial stage for strain release was found within a distance range above the mask. This evidence confirms the existence of the Auger physical shift.
Observations of improved confinement in field reversed configurations sustained by antisymmetric rotating magnetic fields
Authors: Guo H. Y. , Hoffman A. L. , Steinhauer L. C.
Published: June 2005

Rotating magnetic fields (RMF) have been employed to both form and sustain currents in field reversed configurations (FRC). A major concern about this method has been the fear of opening up magnetic field lines with even small ratios of vacuum RMF Bω to external confinement field Be. A recently proposed innovation was to use an antisymmetric arrangement of RMF, but vacuum calculations with full RMF penetration showed that very low values of Bω∕Be would still be required to provide field-line closure. Recent comparisons of symmetric and antisymmetric RMF drive on the translation, confinement, and sustainment (TCS) facility [A. L. Hoffman, H. Y. Guo, J. T. Slough et al., Fusion Sci. Technol. 41, 92 (2002)] have shown strong improvements in the basic confinement properties of the FRCs when using antisymmetric drive, even with ratios of Bω∕Be as high as 0.3. This is due to normal standard operation with only partial penetration of the RMF beyond the FRC separatrix. The uniform transverse RMF in vacuum is shielded by the conducting plasma, resulting in a mostly azimuthal field near the FRC separatrix with a very small radial component. Simple numerical calculations using analytical solutions for the partially penetrated antisymmetric RMF, superimposed on Grad–Shafranov solutions for the poloidal FRC fields, show good field-line closure for the TCS experimental conditions. The antisymmetric arrangement also leads to more efficient current drive and improved stabilization of rotational modes.
Near-infrared intersubband transitions in InGaAs–AlAs–InAlAs double quantum wells
Authors: Semtsiv M. P. , Ziegler M. , Masselink W. T. , Georgiev N. , Dekorsy T. , Helm M.
Published: June 2005

Intersubband optical transitions at short wavelengths in strain-compensated In0.70Ga0.30As—AlAs double quantum wells are investigated by means of mid-infrared absorption. Trade-offs between achieving a high transition energy and a large oscillator strength of the two highest-energy intersubband transitions using our strain-compensation approach are analyzed as a function of the widths of the two wells. Two design strategies leading to relatively strong intersubband optical transitions at 800 meV, 1.55μm, are described and the corresponding structures grown using gas-source molecular-beam epitaxy on (001)InP are investigated. The strongest intersubband transitions obtained experimentally are generally between 300 and 600 meV, 2–4μm. Significant oscillator strength, however, also extends out to 800 meV, 1.55μm.
Representation of the contextual statistical model by hyperbolic amplitudes
Authors: Khrennikov Andrei
Published: June 2005

We continue the development of a so-called contextual statistical model (here context has the meaning of a complex of physical conditions). It is shown that, besides contexts producing the conventional trigonometric cos-interference, there exist contexts producing the hyperbolic cos-interference. Starting with the corresponding interference formula of total probability we represent such contexts by hyperbolic probabilistic amplitudes or in the abstract formalism by normalized vectors of a hyperbolic analogue of the Hilbert space. There is obtained a hyperbolic Born’s rule. Incompatible observables are represented by noncommutative operators. This paper can be considered as the first step towards hyperbolic quantum probability. We also discuss possibilities of experimental verification of hyperbolic quantum mechanics: in physics of elementary particles, string theory as well as in experiments with nonphysical systems, e.g., in psychology, cognitive sciences, and economy.
Observation of momentum confinement time scalings in a rotating plasma
Authors: Messer S. , Ellis R. , Case A. , Gupta D. , Hassam A. , Lunsford R. , Teodorescu C.
Published: June 2005

The Maryland Centrifugal Experiment (MCX) is designed to explore the use of supersonic rotation and strong perpendicular velocity shear for plasma confinement [R. F. Ellis, A. B. Hassam, S. Messer, and B. R. Osborne, Phys. Plasmas 8, 2057 (2001)]. This paper reports MCX data showing scalings with the strength and geometry of the magnetic field and comparisons to some standard models of confinement, none of which fit the data over the whole range. For midplane fields less than 1200 G and mirror ratios between 3 and 17, the momentum confinement time suggests a combination of Bohm-like diffusion and mirror losses. At mirror ratio 9, τM increases with B, saturates for B≈1kG, and then decreases. The measured confinement times peak in the range of 200μs, which is much longer than a magnetohydrodynamic instability growth time. The data do not exclude the possibility that confinement is strongly affected by charge exchange collisions with neutrals.
Stochastic differential equation models of vortex merging and reconnection
Authors: Kevlahan N. K.-R.
Published: June 2005

We show that the stochastic differential equation (SDE) model for the merger of two identical two-dimensional vortices proposed by Agullo and Verga [“Exact two vortices solution of Navier–Stokes equation,” Phys. Rev. Lett. 78, 2361 (1997)] is a special case of a more general class of SDE models for N interacting vortex filaments. These toy models include vorticity diffusion via a white noise forcing of the inviscid equations, and thus extend inviscid models to include core dynamics and topology change (e.g., merger in two dimensions and vortex reconnection in three dimensions). We demonstrate that although the N=2 two-dimensional model is qualitatively and quantitatively incorrect, it can be dramatically improved by accounting for self-advection. We then extend the two-dimensional SDE model to three dimensions using the semi-inviscid asymptotic approximation of Klein et al. [“Simplified equations for the interactions of nearly parallel vortex filaments,” J. Fluid Mech. 288, 201 (1995)] for nearly parallel vortices. This model is nonsingular and is shown to give qualitatively reasonable results until the approximation of nearly parallel vortices fails. We hope these simple toy models of vortex reconnection will eventually provide an alternative perspective on the essential physical processes involved in vortex merging and reconnection.
Galvanic effects in Si-based microelectromechanical systems: Thick oxide formation and its implications for fatigue reliability
Authors: Pierron O. N. , Macdonald D. D. , Muhlstein C. L.
Published: June 2005

Nanometer-scale reaction layers have a profound impact on the fracture and fatigue resistance of the Si films used in microelectromechanical systems (MEMS). This letter presents experimental evidence that thick (i.e., greater than 10nm) oxides can form at room temperature during manufacturing due to a galvanic effect between n+-type Si and Au. The growth of such oxides in concentrated HF solutions that are usually associated with oxide dissolution can be predicted from the measured current density–voltage (i–V) behavior and geometry of the galvanic couple. These results can account for unexplained findings in the literature and can be used to improve the performance of MEMS.
Nanometer-scale crystallization of thin HfO2 films studied by HF-chemical etching
Authors: Fujii Shinji , Miyata Noriyuki , Migita Shinji , Horikawa Tsuyoshi , Toriumi Akira
Published: June 2005

We used a HF-chemical etching process to examine crystalline structures in thin HfO2 films grown by metal organic chemical vapor deposition at 350–550°C. Nanometer-scale crystalline HfO2 nuclei were identified from all the HfO2 films. The nucleus density exponentially increased with increasing deposition temperature, but the diameter of the nuclei did not depend on the deposition temperature. We propose that the crystallization of thin HfO2 film during growth proceeds in a patchwork process with the increase of the crystalline HfO2 nuclei.
Epitaxial tilting of GaN grown on vicinal surfaces of sapphire
Authors: Huang X. R. , Bai J. , Dudley M. , Dupuis R. D. , Chowdhury U.
Published: June 2005

The epitaxial tilting effect of GaN films grown on vicinal (0001) surfaces of sapphire and its relationship with the offcut angles and the substrate surface steps have been revealed using synchrotron Laue method and high-resolution x-ray diffraction. This effect is a general consequence of the large out-of-plane lattice mismatch between GaN and sapphire and can be explained by the extended Nagai theory based on the step configurations. The large lattice tilts and their formation mechanism indicate that the substrate surface morphology may be a very important factor that influences the epitaxy process and the crystalline quality of GaN films in vicinal surface epitaxy.
Cobalt–polypyrrole–cobalt nanowire field-effect transistors
Authors: Chung Hyun-Jong , Jung Hun Huy , Cho Yong-Sung , Lee Sungjun , Ha Jeong-Hoon , Choi Je Hyuk , Kuk Young
Published: June 2005

Cobalt–polypyrrole(PPy)–cobalt nanowires were fabricated electrochemically in single-wire form inside anodic aluminum oxide templates. These wires were isolated by dissolving the template with chromic acid. Grown cobalt segments at both ends reveal a polycrystalline structure of a hexagonal-closest-packed structure and their [001] directions are 16° off the wire axis. By patterning a gate on one side of the wire, field-effect transistors (FETs) were produced. The measured output and transfer characteristics are as good as or better than film FETs of PPy. The gain of the wire FET could be controlled with successive electrochemical doping of the PPy segment.
High-gain multipass noncollinear optical parametric chirped pulse amplifier
Authors: Stepanenko Yuriy , Radzewicz Czesław
Published: June 2005

We demonstrate a multipass noncollinear optical parametric chirped pulse amplifier seeded by pulses from a femtosecond Ti:sapphire oscillator and pumped by a commercial Q-switched, frequency doubled Nd:yttrium–aluminum–garnet laser. Amplification higher than 106 and pulse energy exceeding 1.7 mJ are achieved with four passes through a single β-barium borate crystal. Good beam quality and high gain, together with broad amplification bandwidth, make it an attractive alternative to Ti:sapphire chirped pulse amplifier systems.
Electromigration-induced grain rotation in anisotropic conducting beta tin
Authors: Wu Albert T. , Gusak A. M. , Tu K. N. , Kao C. R.
Published: June 2005

Electromigration in beta-Sn has shown a 10% drop of resistance due to the anisotropic properties of the material. The drop was proposed due to reorientation of grains to reduce the resistance. The driving force as well as the atomic mechanism of grain rotation under electromigration has been considered in this letter. We propose that the anisotropic resistivity causes the divergence of the vacancy fluxes at the grain boundaries and induces the vacancy fluxes to/from the free surface along the grain boundary. The vacancy gradients along the grain boundaries correspond to the gradients of stress. The opposite sign of the stress along grain boundaries generates a torque which leads to rotation of the grain by grain boundary diffusion or creep. The rate of rotation estimated on the base of the model seems to agree well with the observed experimental data.
Raman study of electric-field-induced first-order metal-insulator transition in VO2-based devices
Authors: Kim Hyun-Tak , Chae Byung-Gyu , Youn Doo-Hyeb , Kim Gyungock , Kang Kwang-Yong , Lee Seung-Joon , Kim Kwan , Lim Yong-Sik
Published: June 2005

An abrupt first-order metal-insulator transition (MIT) as a current jump has been observed by applying a dc electric field to Mott insulator VO2-based two-terminal devices. The size of the jumps was measured to be asymmetrical depending on the direction of the applied voltage due to heating effects. The structure of VO2 is investigated by micro-Raman scattering experiments. An analysis of the Raman-active Ag modes at 195 and 222cm−1, explained by pairing and tilting of V cations, and 622cm−1, shows that the modes below a low compliance (restricted) current do not change when the MIT occurs, whereas a structural phase transition above the low compliance current is found to occur secondarily, due to heating effects in the device induced by the MIT. The MIT has applications in the development of high-speed and high-gain switching devices.
Band engineering of carbon nanotube field-effect transistors via selected area chemical gating
Authors: Liu Xiaolei , Luo Zhicheng , Han Song , Tang Tao , Zhang Daihua , Zhou Chongwu
Published: June 2005

This letter presents an approach to engineer the band structure of carbon nanotube field-effect transistors via selected area chemical gating. By exposing the center part, or the contacts, of nanotube devices to oxidizing or reducing gases, a good control over the threshold voltage and subthreshold swing has been achieved. Our experiments reveal that NO2 shifts the threshold voltage positively, while NH3 shifts it negatively for both center-exposed and contact-exposed devices. However, modulations to the subthreshold swing are in opposite directions for center-exposed and contact-exposed devices: NO2 lowers the subthreshold swing of the contact-exposed devices, but increases that of the center-exposed devices. In contrast, NH3 reduces the subthreshold swing of the center-exposed devices, but increases that of the contact-exposed devices.
Improved current densities in MgB2 by liquid-assisted sintering
Authors: Chen S. K. , Lockman Z. , Wei M. , Glowacki B. A. , MacManus-Driscoll J. L.
Published: June 2005

Polycrystalline MgB2 samples with GaN additions were prepared by reaction of Mg, B, and GaN powders. The presence of Ga leads to a low melting eutectic phase which allowed liquid phase sintering and produces platelike grains. For low-level GaN additions (⩽5at.%), the critical transition temperature, Tc, remained unchanged and in 1T magnetic field, the critical current density, Jc was enhanced by a factor of 2 and 10, for temperatures of ∼5K and 20K, respectively. The values obtained are approaching those of hot isostatically pressed samples.
Impact of Ru doping in bilayered manganese oxide La1.2Sr1.8Mn2O7
Authors: Onose Y. , He J. P. , Kaneko Y. , Arima T. , Tokura Y.
Published: June 2005

The Ru doping effect on the bilayered manganese oxide La1.2Sr1.8(Mn1−yRuy)2O7 has been investigated in the range of 0⩽y⩽0.2. The ferromagnetic transition temperature (TC) increases, while the saturated magnetization decreases, with Ru doping. These indicate that in addition to the doping-induced suppression of charge-orbital correlation, the antiferromagnetic coupling between the Ru and the Mn moments is relevant to the enhancement of TC. The axis of easy magnetization changes from within the in plane to along the c axis with Ru doping, owing to the strong magnetic anisotropy of Ru spins.
Effects of the orientation of magnetostrictive nickel strip on torsional wave transduction efficiency of cylindrical waveguides
Authors: Cho Seung Hyun , Park Chan Il , Kim Yoon Young
Published: June 2005

Magnetostrictive transducers are receiving growing attention as an alternative to piezoelectric transducers in generating guided torsional waves in cylindrical waveguides. A recent study shows that torsional wave generation is possible if a set of thin magnetostrictive nickel strips are bonded to the surface of a cylindrical waveguide at an oblique angle and a combination of static and dynamic magnetic fields is applied to the strips. The objective of this work is to experimentally investigate the intriguing effects of the angle on the transduction efficiency and to provide a physical explanation for the observed phenomena. Excitation frequencies used for wave experiments were between 40 and 100 kHz, for which the highest transduction was observed.
Long-lived electron spins in InxGa1−xN multiquantum well
Authors: Nagahara Seiji , Arita Munetaka , Arakawa Yasuhiko
Published: June 2005

We first observed spin relaxation at room temperature in InxGa1−xN multiquantum wells using spin-dependent pump and probe measurements. The spin lifetime increases with In molar fraction x. The observed spin lifetime obeys ∼x3.3, which shows different behavior from typical results for D’yakonov-Perel’ and Elliott-Yafet processes involving the alloy scattering. The increase of In molar fraction induces indium-composition fluctuations, which cause the electron localization. The remarkable increase of the spin lifetime is due to the formation of quantum dots through the phase separation in InxGa1−xN multiquantum-well layers.
The seasonal accrual and loss of benthic algae (Spirogyra) in the Daly River, an oligotrophic river in tropical Australia
Authors: Townsend Simon A. , Padovan Armando V.
Published: June 2005

The hierarchy of factors that control the growth and biomass of Spirogyra sp. was examined for an 18-km reach of the Daly River in the wet/dry tropics of northern Australia. On an annual temporal scale, hydrological disturbances control Spirogyra. Over the wet season (typically December–April), frequent runoff events prevent the colonisation and growth of Spirogyra in the Daly River. This is followed, however, by a lengthy period (typically May–November) without hydrological disturbances and river velocities that favour benthic algal growth. In 2001, Spirogyra became visible in mid-May, then grew to reach a maximum biomass in early August of 28 mg m−2 of chlorophyll a. The standing crop of Spirogyra was primarily determined by the availability of gravel substrate and the velocity and shear stress at the river-bed. Photosynthetically available radiation (200–800 μE m−2 s−1) reaching the river-bed should not have limited algal growth, though self shading within the Spirogyra mats may have been important. Although the growth rate of Spirogyra was probably limited by nutrients, the maximum biomass was constrained by autogenic sloughing. The biomass of Spirogyra steadily declined to half its maximum in early October despite favourable river velocities, most likely a result of nutrient limitation. Spirogyra was then removed from the river by the first major runoff event of the wet season in late October. The hierarchy of factors that control benthic algal biomass in the Daly River are the same as in lower latitudes, though the long period of favourable river velocities when smaller scale, proximate factors (e.g. nutrients, shear stress) control biomass should be noted.
Nutrients in Australian tropical rivers: changes with agricultural development and implications for receiving environments
Authors: Brodie Jon E. , Mitchell Alan W.
Published: June 2005

In tropical Australia, intensive studies of river suspended sediment (SS) and nutrient dynamics have been restricted to streams on the north-east coast between the Fitzroy and Normanby Rivers (Queensland), Magela Creek/East Alligator River (Northern Territory) and the Ord River (Western Australia). Historical conditions in these rivers were probably characterised by low–moderate SS concentrations and low concentrations of dissolved inorganic nitrogen and phosphorus in flow events. Introduction of agriculture has transformed SS and nutrient dynamics. Grazing has led to soil erosion and increased SS and particulate nutrient concentrations and fluxes in event flows. Fertilised cropping has increased nutrient inputs to catchments, where it forms a substantial proportion of the catchment area. Consequently, both particulate and dissolved inorganic nutrient concentrations and fluxes have increased. Australian tropical rivers have episodic flows, with most material transport occurring during large flow events. The restricted period of these highly energetic flows means little trapping of materials in waterways occurs. Loads are transported efficiently downstream and processes such as denitrification and in-channel sedimentation may be of limited importance. Owing to excessive nutrient inputs associated with agriculture, a number of northern freshwater, estuarine and coastal ecosystems are now eutrophic. Continued development, especially fertilised cropping, without adequate management of nutrient losses is likely to exacerbate these problems.
River and wetland food webs in Australia's wet - dry tropics: general principles and implications for management
Authors: Douglas Michael M. , Bunn Stuart E. , Davies Peter M.
Published: June 2005

The tropical rivers of northern Australia have received international and national recognition for their high ecological and cultural values. Unlike many tropical systems elsewhere in the world and their temperate Australian counterparts, they have largely unmodified flow regimes and are comparatively free from the impacts associated with intensive land use. However, there is growing demand for agricultural development and existing pressures, such as invasive plants and feral animals, threaten their ecological integrity. Using the international literature to provide a conceptual framework and drawing on limited published and unpublished data on rivers in northern Australia, we have derived five general principles about food webs and related ecosystem processes that both characterise tropical rivers of northern Australia and have important implications for their management. These are: (1) the seasonal hydrology is a strong driver of ecosystem processes and food-web structure; (2) hydrological connectivity is largely intact and underpins important terrestrial–aquatic food-web subsidies; (3) river and wetland food webs are strongly dependent on algal production; (4) a few common macroconsumer species have a strong influence on benthic food webs; and (5) omnivory is widespread and food chains are short. The implications of these ecosystem attributes for the management and protection of tropical rivers and wetlands of northern Australian are discussed in relation to known threats. These principles provide a framework for the formation of testable hypotheses in future research programmes.
Neuroglobin, nitric oxide, and oxygen: Functional pathways and conformational changes
Authors: Brunori Maurizio , Giuffrè Alessandro , Nienhaus Karin , Nienhaus G. Ulrich , Scandurra Francesca Maria , Vallone Beatrice
Published: June 2005

Neuroglobin (Ngb) is a globin expressed in the nervous system of humans and other organisms that is involved in the protection of the brain from ischemic damage. Despite considerable interest, however, the
in vivo
function of Ngb is still a conundrum. In this paper we report a number of kinetic experiments with O
2
and NO that we have interpreted on the basis of the 3D structure of Ngb, now available for human and murine metNgb and murine NgbCO. The reaction of reduced deoxyNgb with O
2
and NO is slow (
t
1/2
≈ 2 s) and ligand concentration-independent, because exogenous ligand binding can only occur upon dissociation of the distal His-64, which is coordinated to the ferrous heme iron. By contrast, NgbO
2
reacts very rapidly with NO, yielding metNgb and

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by means of a heme-bound peroxynitrite intermediate. Steady-state amperometric experiments show that Ngb is devoid of O
2
reductase and NO reductase activities. To achieve this result, we have set up a protocol for efficient reduction of metNgb using a mixture of FMN and NADH under bright illumination. The results are discussed with reference to a global scheme inspired by the 3D structures of metNgb and NgbCO. Based on the ligand-linked conformational changes discovered by crystallography, the pathways of the reactions with O
2
and NO provide a framework that may account for the involvement of Ngb in controlling the activation of a protective signaling mechanism.
Myocardial regeneration by activation of multipotent cardiac stem cells in ischemic heart failure
Authors: Urbanek Konrad , Torella Daniele , Sheikh Farooq , De Angelis Antonella , Nurzynska Daria , Silvestri Furio , Beltrami C. Alberto , Bussani Rossana , Beltrami Antonio P. , Quaini Federico , Bolli Roberto , Leri Annarosa , Kajstura Jan , Anversa Piero
Published: June 2005

In this study, we tested whether the human heart possesses a cardiac stem cell (CSC) pool that promotes regeneration after infarction. For this purpose, CSC growth and senescence were measured in 20 hearts with acute infarcts, 20 hearts with end-stage postinfarction cardiomyopathy, and 12 control hearts. CSC number increased markedly in acute and, to a lesser extent, in chronic infarcts. CSC growth correlated with the increase in telomerase-competent dividing CSCs from 1.5% in controls to 28% in acute infarcts and 14% in chronic infarcts. The CSC mitotic index increased 29-fold in acute and 14-fold in chronic infarcts. CSCs committed to the myocyte, smooth muscle, and endothelial cell lineages increased ≈85-fold in acute infarcts and ≈25-fold in chronic infarcts. However, p16
INK4a
-p53-positive senescent CSCs also increased and were 10%, 18%, and 40% in controls, acute infarcts, and chronic infarcts, respectively. Old CSCs had short telomeres and apoptosis involved 0.3%, 3.8%, and 9.6% of CSCs in controls, acute infarcts, and chronic infarcts, respectively. These variables reduced the number of functionally competent CSCs from ≈26,000/cm
3
of viable myocardium in acute to ≈7,000/cm
3
in chronic infarcts, respectively. In seven acute infarcts, foci of spontaneous myocardial regeneration that did not involve cell fusion were identified. In conclusion, the human heart possesses a CSC compartment, and CSC activation occurs in response to ischemic injury. The loss of functionally competent CSCs in chronic ischemic cardiomyopathy may underlie the progressive functional deterioration and the onset of terminal failure.
Uterine Wnt/β-catenin signaling is required for implantation
Authors: Mohamed Othman A. , Jonnaert Maud , Labelle-Dumais Cassandre , Kuroda Kazuki , Clarke Hugh J. , Dufort Daniel
Published: June 2005

Successful implantation relies on precisely orchestrated and reciprocal signaling between the implanting blastocyst and the receptive uterus. We have examined the role of the Wnt/β-catenin signaling pathway during the process of implantation and demonstrate that this pathway is activated during two distinct stages. Wnt/β-catenin signaling is first transiently activated in circular smooth muscle forming a banding pattern of activity within the uterus on early day 4. Subsequently, activation is restricted to the luminal epithelium at the prospective site of implantation. Activation at both sites requires the presence of the blastocyst. Furthermore, inhibition of Wnt/β-catenin signaling interferes with the process of implantation. Our results demonstrate that the Wnt/β-catenin signaling pathway plays a central role in coordinating uterus–embryo interactions required for implantation.
Intermittent pollen-tube growth in pistils of alders (Alnus)
Authors: Sogo Akiko , Tobe Hiroshi
Published: June 2005

In alders, where fertilization occurs ≈8 weeks after pollination, the pollen tube (male gametophyte) grows intermittently in four steps in close association with the development of the ovary and its ovules. Pollen tubes stop growing in the style, at the ovarian locule, and at the chalaza (ovule), before reaching an embryo sac for fertilization. At the stage when the ovary develops an ovule primordium in each of the two locules, many pollen tubes germinate on the stigma, and a few of them reach the style, where they remain for ≈7 weeks. Thereafter, a single tube resumes growing; with a short stop in the upper space of the ovarian locule, it reaches the older of the two ovules when it has developed a two-nucleate embryo sac. Except in the last step, where the tube grows from the chalaza to an embryo sac (female gametophyte), an eight-nucleate mature embryo sac is not necessary for pollen-tube guidance in the pistil. Although the intermittent pollen-tube growth appears to play an important role in the selection of a single pollen tube from many and one ovule from two, its detection provides insight into the study of the mechanism of pollen-tube guidance.
Polyglutamine-expanded spinocerebellar ataxia-7 protein disrupts normal SAGA and SLIK histone acetyltransferase activity
Authors: McMahon Stacey J. , Pray-Grant Marilyn G. , Schieltz David , Yates John R. , Grant Patrick A.
Published: June 2005

Histone acetyltransferases have been shown to participate in many essential cellular processes, particularly those associated with activation of transcription. SAGA (Spt-Ada-Gcn5 acetyltransferase) and SLIK (SAGA-like) are two highly homologous multisubunit histone acetyltransferase complexes that were originally identified in the yeastSaccharomyces cerevisiae. Here, we identify the protein Sgf73/Sca7 as a component of SAGA and SLIK, and a homologue of the human SCA7-encoded protein ataxin-7, which, in its polyglutamine expanded pathological form, is responsible for the neurodegenerative disease spinocerebellar ataxia 7 (SCA7). Our findings indicate that yeast Sca7 is necessary for the integrity and function of both SAGA and SLIK, and that the human ataxin-7 is able to compliment the loss of Sca7 in yeast. A polyglutamine-expanded version of ataxin-7 assembles a SAGA complex that is depleted of critical proteins that regulate the ability of SAGA to acetylate nucleosomes. These observations have significant implications for the function of the human Sca7 protein in disease pathogenesis.
Polyglutamine-expanded ataxin-7 inhibits STAGA histone acetyltransferase activity to produce retinal degeneration
Authors: Palhan Vikas B. , Chen Shiming , Peng Guang-Hua , Tjernberg Agneta , Gamper Armin M. , Fan Yuxin , Chait Brian T. , La Spada Albert R. , Roeder Robert G.
Published: June 2005

Spinocerebellar ataxia type 7 (SCA7) is characterized by cone-rod dystrophy retinal degeneration and is caused by a polyglutamine [poly(Q)] expansion within ataxin-7, a protein of previously unknown function. Here, we report that ataxin-7 is an integral component of the mammalian STAGA (SPT3-TAF9-ADA-GCN5 acetyltransferase) transcription coactivator complex, interacts directly with the GCN5 histone acetyltransferase component of STAGA, and mediates a direct interaction of STAGA with the CRX (cone-rod homeobox) transactivator of photoreceptor genes. Consistent with these results, chromatin immunoprecipitation assays document retinal-specific association of CRX, GCN5, and acetylated histone H3 with CRX target genes. RNA interference studies also implicate ataxin-7 and GCN5 in CRX-dependent gene activation, and histone deacetylase inhibitors restore the compromised expression of a CRX target gene in an ataxin-7-deficient background. Significantly, in relation to SCA7, poly(Q)-expanded ataxin-7 gets incorporated into STAGA and, in a dominant-negative manner, inhibits the nucleosomal histone acetylation function of STAGA GCN5 both
in vitro
and, based on chromatin immunoprecipitation assays, in SCA7 transgenic mice. These results suggest that the normal function of a poly(Q) disease protein may intersect with its pathogenic mechanism, an observation with significant implications for the molecular basis of all poly(Q) disorders and ultimately for their treatment.
Structural basis of the Sir1–origin recognition complex interaction in transcriptional silencing
Authors: Hou Zhonggang , Bernstein Douglas A. , Fox Catherine A. , Keck James L.
Published: June 2005

The Sir1 protein plays a key role in establishing a silent chromatin structure at the cryptic mating-type loci
HMR
and
HML
in
Saccharomyces cerevisiae
by interacting with the bromo-adjacent homology (BAH) domain of the Orc1p subunit of the origin recognition complex (ORC). Here, we present the high-resolution crystal structures of the ORC interaction region (OIR) of Sir1p and that of the complex formed between the OIR and BAH domains. Amino acids within the OIR previously shown to be required for a Sir1p/ORC interaction are presented on a conserved, convex surface that forms a complementary interface with a concave region of the Orc1 BAH domain that is critical for transcriptional silencing. The OIR/BAH interaction surface comprises a network of hydrophobic and polar/ionic interactions between discrete structural modules in each protein and involves several residues that were not implicated in previous studies. These data provide important structural insights into a protein–protein interaction critical for the formation of a specialized chromatin domain within eukaryotic chromosomes.
Nef from pathogenic simian immunodeficiency virus is a negative factor for vaccinia virus
Authors: Chan Kenneth S. , Verardi Paulo H. , Legrand Fatema A. , Yilma Tilahun D.
Published: June 2005

The
nef
gene of human and simian immunodeficiency viruses (HIV and SIV) is important for pathogenicity and maintenance of high virus loads. We previously reported that recombinant vaccinia viruses (rVVs) expressing
nef
from attenuated SIVmac1A11 (vNef1A11) produced typical plaques on thymidine kinase-deficient 143B cells, whereas rVVs expressing
nef
derived from the pathogenic SIVmac239 (vNef157) formed plaques with altered morphology. Here, we show that vNef157 is attenuated in normal and nude mice, whereas the pathogenicity of vNef1A11 is similar to that of a control virus. Thus, Nef157 is an attenuating factor in the vaccinia virus (VV) system, contrasting sharply with its function in lentiviruses. We also show that Nef157 inhibits VV cell-to-cell spread, causing formation of atypical plaques regardless of thymidine kinase deficiency, neoplasticity, and species of the infected cell line. We hypothesized that Nef157 interferes with VV spread by association with actin, but no direct colocalization of Nef and the cytoskeletal actin network was detected. Instead, higher levels of Nef157 protein were observed, although mRNAs for both
nef
genes were produced at comparable levels. Thus, the mechanism behind such Nef157 protein accumulation and Nef157-mediated VV attenuation could be related to the process that causes an opposite effect in its native SIV system, making SIVmac239 more pathogenic than SIVmac1A11.
Functional Role of Syndecan-1 Cytoplasmic V Region in Lamellipodial Spreading, Actin Bundling, and Cell Migration
Authors: Chakravarti Ritu , Sapountzi Vasileia , Adams Josephine C.
Published: June 2005

Cell protrusions contribute to cell motility and migration by mediating the outward extension and initial adhesion of cell edges. In many cells, these extensions are supported by actin bundles assembled by the actin cross-linking protein, fascin. Multiple extracellular cues regulate fascin and here we focus on the mechanism by which the transmembrane proteoglycan, syndecan-1, specifically activates lamellipodial cell spreading and fascin-and-actin bundling when clustered either by thrombospondin-1, laminin, or antibody to the syndecan-1 extracellular domain. There is almost no knowledge of the signaling mechanisms of syndecan-1 cytoplasmic domain and we have tested the hypothesis that the unique V region of syndecan-1 cytoplasmic domain has a crucial role in these processes. By four criteria—the activities of N-cadherin/V region chimeras, syndecan-1 deletion mutants, or syndecan-1 point mutants, and specific inhibition by a membrane-permeable TAT-V peptide—we demonstrate that the V region is necessary and sufficient for these cell behaviors and map the molecular basis for its activity to multiple residues located across the V region. These activities correlate with a V-region-dependent incorporation of cell-surface syndecan-1 into a detergent-insoluble form. We also demonstrate functional roles of syndecan-1 V region in laminin-dependent C2C12 cell adhesion and three-dimensional cell migration. These data identify for the first time specific cell behaviors that depend on signaling through the V region of syndecan-1.
MLN64 Is Involved in Actin-mediated Dynamics of Late Endocytic Organelles
Authors: Hölttä-Vuori Maarit , Alpy Fabien , Tanhuanpää Kimmo , Jokitalo Eija , Mutka Aino-Liisa , Ikonen Elina
Published: June 2005

MLN64 is a late endosomal cholesterol-binding membrane protein of an unknown function. Here, we show that MLN64 depletion results in the dispersion of late endocytic organelles to the cell periphery similarly as upon pharmacological actin disruption. The dispersed organelles in MLN64 knockdown cells exhibited decreased association with actin and the Arp2/3 complex subunit p34-Arc. MLN64 depletion was accompanied by impaired fusion of late endocytic organelles and delayed cargo degradation. MLN64 overexpression increased the number of actin and p34-Arc-positive patches on late endosomes, enhanced the fusion of late endocytic organelles in an actin-dependent manner, and stimulated the deposition of sterol in late endosomes harboring the protein. Overexpression of wild-type MLN64 was capable of rescuing the endosome dispersion in MLN64-depleted cells, whereas mutants of MLN64 defective in cholesterol binding were not, suggesting a functional connection between MLN64-mediated sterol transfer and actin-dependent late endosome dynamics. We propose that local sterol enrichment by MLN64 in the late endosomal membranes facilitates their association with actin, thereby governing actin-dependent fusion and degradative activity of late endocytic organelles.
Vasopressin-dependent Myogenic Cell Differentiation Is Mediated by Both Ca2+/Calmodulin-dependent Kinase and Calcineurin Pathways
Authors: Scicchitano Bianca Maria , Spath Lucia , Musarò Antonio , Molinaro Mario , Rosenthal Nadia , Nervi Clara , Adamo Sergio
Published: June 2005

Arg8-vasopressin (AVP) promotes the differentiation of myogenic cell lines and mouse primary satellite cells by mechanisms involving the transcriptional activation of myogenic bHLH regulatory factors and myocyte enhancer factor 2 (MEF2). We here report that AVP treatment of L6 cells results in the activation of calcineurin-dependent differentiation, increased expression of MEF2 and GATA2, and nuclear translocation of the calcineurin target NFATc1. Interaction of these three factors occurs at MEF2 sites of muscle specific genes. The different kinetics of AVP-dependent expression of early (myogenin) and late (MCK) muscle-specific genes correlate with different acetylation levels of histones at their MEF2 sites. The cooperative role of calcineurin and Ca2+/calmodulin-dependent kinase (CaMK) in AVP-dependent differentiation is demonstrated by the effect of inhibitors of the two pathways. We show here, for the first time, that AVP, a “novel” myogenesis promoting factor, activates both the calcineurin and the CaMK pathways, whose combined activation leads to the formation of multifactor complexes and is required for the full expression of the differentiated phenotype. Although MEF2–NFATc1 complexes appear to regulate the expression of an early muscle-specific gene product (myogenin), the activation of late muscle-specific gene expression (MCK) involves the formation of complexes including GATA2.
Importance of eIF2α Phosphorylation and Stress Granule Assembly in Alphavirus Translation Regulation
Authors: McInerney Gerald M. , Kedersha Nancy L. , Kaufman Randal J. , Anderson Paul , Liljeström Peter
Published: June 2005

Alphavirus infection results in the shutoff of host protein synthesis in favor of viral translation. Here, we show that during Semliki Forest virus (SFV) infection, the translation inhibition is largely due to the activation of the cellular stress response via phosphorylation of eukaryotic translation initiation factor 2α subunit (eIF2α). Infection of mouse embryo fibroblasts (MEFs) expressing a nonphosphorylatable mutant of eIF2α does not result in efficient shutoff, despite efficient viral protein production. Furthermore, we show that the SFV translation enhancer element counteracts the translation inhibition imposed by eIF2α phosphorylation. In wild-type MEFs, viral infection induces the transient formation of stress granules (SGs) containing the cellular TIA-1/R proteins. These SGs are disassembled in the vicinity of viral RNA replication, synchronously with the switch from cellular to viral gene expression. We propose that phosphorylation of eIF2α and the consequent SG assembly is important for shutoff to occur and that the localized SG disassembly and the presence of the enhancer aid the SFV mRNAs to elude general translational arrest.
ER-Golgi Transport Defects Are Associated with Mutations in the Sed5p-binding Domain of the COPII Coat Subunit, Sec24p
Authors: Miller Elizabeth A. , Liu Yiting , Barlowe Charles , Schekman Randy
Published: June 2005

Selective cargo capture into ER-derived vesicles is driven by the Sec24p subunit of the COPII coat, which contains at least three independent cargo-binding sites. One of these, the “A-site,” interacts with a NPF motif found on the SNARE, Sed5p. We have characterized the Sec24p-Sed5p interaction through mutation of the putative ER export motifs of Sed5p and the cargo-binding A-site of Sec24p. Mutational analysis of Sed5p suggests that the NPF motif is the dominant ER export signal. Mutation of the NPF binding pocket on Sec24p led to a dramatic reduction in the capture of Sed5p into COPII vesicles, whereas packaging of other ER-Golgi SNAREs was normal. Of all the cargoes tested, only Sed5p was depleted in vesicles made with Sec24p A-site mutants. Surprisingly, vesicles generated with the mutant Sec24p were unable to fuse with the Golgi apparatus. This inability to fuse was not the result of the lack of Sed5p, because vesicles specifically depleted of Sed5p generated by antibody inhibition targeted and fused normally. We propose that the A-site of Sec24p is a multipurpose cargo-binding site that must recognize additional unidentified cargo proteins, at least one of which is essential at a late stage of vesicle fusion.
Tension-dependent Regulation of Microtubule Dynamics at Kinetochores Can Explain Metaphase Congression in Yeast
Authors: Gardner Melissa K. , Pearson Chad G. , Sprague Brian L. , Zarzar Ted R. , Bloom Kerry , Salmon E. D. , Odde David J.
Published: June 2005

During metaphase in budding yeast mitosis, sister kinetochores are tethered to opposite poles and separated, stretching their intervening chromatin, by singly attached kinetochore microtubules (kMTs). Kinetochore movements are coupled to single microtubule plus-end polymerization/depolymerization at kinetochore attachment sites. Here, we use computer modeling to test possible mechanisms controlling chromosome alignment during yeast metaphase by simulating experiments that determine the 1) mean positions of kinetochore Cse4-GFP, 2) extent of oscillation of kinetochores during metaphase as measured by fluorescence recovery after photobleaching (FRAP) of kinetochore Cse4-GFP, 3) dynamics of kMTs as measured by FRAP of GFP-tubulin, and 4) mean positions of unreplicated chromosome kinetochores that lack pulling forces from a sister kinetochore. We rule out a number of possible models and find the best fit between theory and experiment when it is assumed that kinetochores sense both a spatial gradient that suppresses kMT catastrophe near the poles and attachment site tension that promotes kMT rescue at higher amounts of chromatin stretch.