bluuebunny/crossref_metadata_2025 huggingface dataset:
Ion transit pathways and gating in ClC chloride channels
Authors: Yin Jian , Kuang Zhifeng , Mahankali Uma , Beck Thomas L.
Published: June 2004

ClC chloride channels possess a homodimeric structure in which each monomer contains an independent chloride ion pathway. ClC channel gating is regulated by chloride ion concentration, pH and voltage. Based on structural and physiological evidence, it has been proposed that a glutamate residue on the extracellular end of the selectivity filter acts as a fast gate. We utilized a new search algorithm that incorporates electrostatic information to explore the ion transit pathways through wild‐type and mutant bacterial ClC channels. Examination of the chloride ion permeation pathways supports the importance of the glutamate residue in gating. An external chloride binding site previously postulated in physiological experiments is located near a conserved basic residue adjacent to the gate. In addition, access pathways are found for proton migration to the gate, enabling pH control at hyperpolarized membrane potentials. A chloride ion in the selectivity filter is required for the pH‐dependent gating mechanism. Proteins © 2004 Wiley‐Liss, Inc.
Charge‐transfer transitions and optical spectra of titanates
Authors: Zenkov A. V.
Published: June 2004

In the framework of the cluster approach, we consider the peculiarities of charge‐transfer (CT) states and CT transitions O 2p → Ti 3d in the octahedral (TiO6)9− complex. We have computed the reduced matrix elements of the electric‐dipole transition operator on many‐electron wave functions – the initial and final states of a CT transition. Using the local approximation, we have parameterized the results obtained and computed the relative intensities of various allowed CT transitions in the absence of mixing of CT configurations having the same symmetry. Using the Tanabe–Sugano technique, we have taken this mixing into account and obtained the energies of many‐electron CT transitions and their actual intensities as well.

Modelling the optical spectrum of titanium‐based oxides has yielded a complicated CT band consisting of 42 lines with the main maxima at 6–8 eV and satellites in the range of 1.5–4 eV. The total extent of the CT band is about 7 eV. The model spectrum is in satisfactory agreement with experimental data. Thus, the appearance of the spectrum does not at all resemble the oversimplified one‐ or two‐peaked structure that is usually spoken about when analyzing spectra in terms of CT transitions. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Photoluminescence of layered semiconductor GaS doped with Mn
Authors: Shigetomi S. , Sakai K. , Ikari T.
Published: June 2004

Manganese (Mn)‐doped GaS single crystals were grown by the Bridgman technique. Radiative recombination mechanisms have been investigated using photoluminescence (PL) measurement. The PL spectrum (at 77 K) related to the impurity level is dominated by the new emission band at 2.002 eV. The temperature dependences of the PL intensity, peak energy, and full width at half‐maximum are characterized by the recombination mechanism of the configurational coordinate model. It was found that the 2.002 eV emission band is related to the acceptor–vacancy complex center. Moreover, the concentration of the defect is very high in the Mn‐doped GaS. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Level‐spacing distributions of the Gaussian unitary random matrix ensemble
Authors: Grimm Uwe
Published: June 2004

Level‐spacing distributions of the Gaussian Unitary Ensemble (GUE) of random matrix theory are expressed in terms of solutions of coupled differential equations. Series solutions up to order 50 in the level spacing are obtained, thus providing a very good description of the small‐spacing part of the level‐spacing distribution, which can be used to make comparisons with experimental or numerical data. The level‐spacing distributions can be obtained by solving the system of differential equations numerically. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Multiscale simulations of micro‐structure selection in binary alloy solidification
Authors: Emmerich Heike , Jurgk Matthias , Siquieri Ricardo
Published: June 2004

We demonstrate that the competition of dendritic crystals in a solidifying sample gives rise to two qualitatively different micro‐structure solutions depending on the density ρ of crystals in the melt. Here we show for the first time, that there is a non‐steady transition from one to the other. The precise ρ‐dependence of the transition point is determined by the Biot number. Our investigation is based on a scaling analysis for the tip velocity of the dendritic crystals, which we assume to be aligned in an array and to be coupled via the transport of heat. We develop our analytical solutions based upon the asymptotic Kruskal‐Segur reduction to a differential equation in the complex plane. It is supported by numerical simulations of a multiscale model of alloy growth. On the one hand this solution can be used to improve the accuracy of applied solidification simulations. On the other hand it yields additional insight in the universality of diffusion limited crystal growth in the presence of competing micro‐structures. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Conservation laws in disordered electron systems: Thermodynamic limit and configurational averaging
Authors: Janiš V. , Kolorenč J.
Published: June 2004

We discuss conservation of probability in noninteracting disordered electron systems. We argue that although the norm of the electron wave function is conserved in individual realizations of the random potential, we cannot extend this conservation law easily to configurationally averaged systems in the thermodynamic limit. A direct generalization of the norm conservation to averaged functions is hindered by the existence of localized states breaking translational invariance. Such states are elusive to the description with periodic Bloch waves. Mathematically this difficulty manifests itself via the diffusion pole in the electron–hole irreducible vertex. The pole leads to a clash with analyticity of the self‐energy, reflecting causality of the theory, when norm conservation is enforced by a Ward identity. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A Monte Carlo method for propagating multi‐dimensional wave packets
Authors: Schröder Markus , Kleinekathöfer Ulrich
Published: June 2004

A method for propagating multi‐dimensional wave packets in time using a product ansatz for the wave function is presented. Other than in the time‐dependent Hartree approach which is based on a variational scheme, the current method is based on the stochastic Ito calculus. The correlations between the different one‐dimensional wave functions are taken into account via stochastic processes such that on average the original Schrödinger equation is reproduced. Numerical tests of the proposed scheme have been performed in two and four dimensions. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Spin singlet excitons of composite fermions
Authors: Kramer B. , Merlo M. , Magnoli N. , Sassetti M.
Published: June 2004

Interacting electrons in two degenerate Landau levels with opposite spins at total filling factor 1 are considered. Using the Chern–Simons gauge transformation, the system is mapped to composite fermions. These are non‐interacting on the average. The fluctuations of the Chern–Simons gauge field can introduce an effective interaction which is attractive for particle–hole pairs. The spin‐singlet ground state of such excitonic pairs is considered. At zero temperature, the pair‐breaking energy is estimated. It is given by the Fermi energy if the original interaction is sufficiently strong. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Few‐electron transfer reactions in donor–acceptor complexes and molecular wires
Authors: May V. , Petrov E. G.
Published: June 2004

A unified description is presented for electron transfer reactions in molecular systems which proceed against the background of fast vibrational relaxation processes. By generalizing earlier treatments a common approach is developed which covers single‐ and two‐electron transfer as well as processes with the participation of even more electrons. Different types of reactions are discussed taking place either in donor–bridge–acceptor complexes or molecular wires attached to nanolectrodes. In particular, it is underlined that measuring the dependence of the transfer rate or of the stationary current on the length of the molecular system may represent an efficient way to uncover the concrete mechanism of charge transfer. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Exponents of the localization length in the 2D Anderson model with off‐diagonal disorder
Authors: Eilmes Andrzej , A. Römer Rudolf
Published: June 2004

We study Anderson localization in two‐dimensional systems with purely off‐diagonal disorder. Localization lengths are computed by the transfer‐matrix method and their finite‐size and scaling properties are investigated. We find various numerically challenging differences to the usual problems with diagonal disorder. In particular, the divergence of the localization lengths close to the band centre is investigated in detail for bipartite and non‐bipartite lattices as well as different distributions of the off‐diagonal disorder. Divergence exponents for the localization lengths are constructed that appear to describe the data well down to at least 10−5. We find only little evidence for a crossover energy scale below which the power law has been argued to fail. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Random‐matrix model of resonant Rayleigh scattering in systems with exciton fine‐structure splitting
Authors: Runge Erich , Zimmermann Roland
Published: June 2004

We extend our recently developed local random‐matrix model of resonant Rayleigh scattering at the exciton transition in semiconductor nanostructure [Phys. Rev. B 69, 155307 (2004)] to systems with finite fine‐structure (exchange) splitting. A much richer phenomenology is found due to the interplay of two small characteristic energies, one being the exchange energy and the other given by the average energetic distance of two exciton state localized in the same spatial region. Three contributions to the Rayleigh signal can be distinguished by their temporal and angular behavior. They correspond to forward scattering, backscattering and a broad isotropic background. The change of their relative weight as function of average exchange energies provides further insight into the intimate connection of level repulsion and enhanced backscattering and the origin of the universal 2:3 ratio predicted in our earlier work. The time‐dependent Rayleigh signal is found to depend strongly on the polarization of excitation and detection. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Fluctuations of the Shannon capacity in a Rayleigh model of wireless communication
Authors: Stäring J. , Eriksson A. , Mehlig B.
Published: June 2004

We consider a Rayleigh model [Foschini and Gans, Wirel. Pers. Commun. 6, 311 (1998)] for the Shannon capacity characterising wireless information transfer in a network of antennae. In this model, the capacity C is a linear statistic of the channel matrix of the network. We use this fact to calculate the variance [C] of the Shannon capacity. We find that the expected value 〈C〉 of the Shannon capacity is typical, that is the coefficient of variation $\sqrt {{\rm var} [C]}/\langle C \rangle$ is small. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Phorbol ester‐induced translocation of PKC epsilon to the nucleus in fibroblasts: identification of nuclear PKC epsilon‐associating proteins
Authors: Xu Tian-Rui , Rumsby Martin G
Published: June 2004

We show that phorbol ester treatment of NIH 3T3 fibroblasts induces rapid translocation of PKCε from a perinuclear site to the nucleus, extending findings in PC12 and NG108‐15 cells and in myocytes. We have immunoprecipitated the PKCε from nuclei isolated from phorbol ester‐treated fibroblasts and identified six proteins which associate with nuclear PKCε. These have been characterised as matrin 3, transferrin, Rac GTPase activating protein 1, vimentin, β‐actin and annexin II by MALDI–TOF–MS. We have confirmed that these proteins associate with PKCε by gel overlay and/or dot blotting assays. The role of these PKCε‐associating proteins in the nucleus and their interaction with PKCε are considered.
Characterization of H2O2‐induced acute apoptosis in cultured neural stem/progenitor cells
Authors: Lin Hsingchi J , Wang Xiantao , Shaffer Kara M , Sasaki Carl Y , Ma Wu
Published: June 2004

In the present study, we characterized hydrogen peroxide (H2O2)‐induced cell apoptosis and related cell signaling pathways in cultured embryonic neural stem/progenitor cells (NS/PCs). Our data indicated that H2O2 induced acute cell apoptosis in NS/PC in concentration‐ and time‐dependent manners and selectively, it transiently increased PI3K‐Akt and Mek‐Erk1/2 in a dose‐dependent manner. Inhibition of PI3K‐Akt with wortmannin, a PI3‐K inhibitor, was found to significantly increase H2O2‐induced acute apoptosis and dramatically decrease basal pGSK3β levels. The level of pGSK3β remained unchanged with H2O2 exposure. We conclude that the transient activation of PI3K‐Akt signaling delays the H2O2‐induced acute apoptosis in cultured NS/PCs in part through maintaining the basal pGSK3β level and activating other downstream effectors.
Control of superoxide production in mitochondria from maize mesocotyls
Authors: Camacho Adriana , Moreno-Sanchez Rafael , Bernal-Lugo Irma
Published: June 2004

To understand the biochemical events that control the generation of superoxide, the effect of inhibiting the respiratory complexes III and IV (C‐III and C‐IV) and alternative oxidase (AOX) on the rate of superoxide production was analyzed in mitochondria from maize seedlings. To increase superoxide production, it was required to inhibit C‐III or C‐IV by at least 30% or 50%, respectively. Below this inhibition threshold, AOX exerted the highest degree of control on superoxide production, whereas above it, the highest degree of control was exerted by C‐IV. The contribution of C‐III to control superoxide production became significant when AOX activity was modulated.
Investigations on the binding and antioxidant properties of the plant flavonoid fisetin in model biomembranes
Authors: Sengupta Bidisa , Banerjee Anwesha , Sengupta Pradeep K
Published: June 2004

Plant flavonoids are emerging as potent therapeutic drugs for free radical mediated diseases, for which cell membranes generally serve as targets for lipid peroxidation and related deleterious effects. Screening and characterization of these ubiquitous, therapeutically potent polyphenolic compounds, require a clear understanding regarding their incorporation and possible location in membranes, as well as quantitative estimates of their antioxidative and radical scavenging capacities. Here, we demonstrate the novel use of the intrinsic fluorescence characteristics of the plant flavonoid fisetin (3,3′,4′,7‐OH flavone) to explore its binding and site(s) of solubilisation in egg lecithin liposomal membranes. Spectrophotometric assays have been used to obtain quantitative estimates of its antioxidative capacity. Furthermore, our quantum mechanical semi‐empirical calculations provide a quantitative measure for the free radical scavenging activity of fisetin from the OH (at 3, 3′, 4′, 7 positions of the molecule)‐bond dissociation enthalpies. Implications of these findings are discussed.
Erythrocyte osmotic fragility test for screening of alpha‐thalassemia‐1 and beta‐thalassemia trait in pregnancy
Authors: Sirichotiyakul S. , Tantipalakorn C. , Sanguansermsri T. , Wanapirak C. , Tongsong T.
Published: June 2004

Objectives: To evaluate the sensitivity and specificity of osmotic fragility test (OFT) as a screening test in predicting the severe thalassemia trait (α‐thalassemia‐1 & β‐thalassemia). Methods: A descriptive analysis and diagnostic test of non‐anemic pregnant women attending antenatal care clinic, Maharaj Nakorn Chiang Mai, during April, and July 2002 was made. Blood samples were collected from 446 singleton pregnancies with no obvious medical complication such as iron deficiency anemia. OFT was performed in the same day, using 0.45% glycerin saline solution and the cut‐off value of less than 60% was used for an abnormal test. Quantitative HbA2 test and PCR (SEA type) were done as a gold standard to confirm the diagnosis of β‐thalassemia trait and α‐thalassemia‐1 trait, respectively. Results: The main outcome measures were sensitivity, specificity, positive and negative predictive value of OFT. If the OFT cut‐off value of less than 60% was considered positive, the test had a sensitivity, specificity, positive and negative predictive value of 97.6%, 72.9%, 33.6%, and 99.5%, respectively. Conclusion: OFT has high sensitivity in detection of α‐thalassemia‐1 trait or β‐thalassemia trait and due to its simplicity with very low cost it may, therefore, be considered as a screening test in a wide population.
Gadolinium Enhanced Mr Assessment of Proximal Fragment Vascularity in Nonunions after Scaphoid Fracture: Does It Predict the Outcome of Reconstructive Surgery?
Authors: SINGH A.K. , DAVIS T.R.C. , DAWSON J.S. , ONI J.A. , DOWNING N.D.
Published: June 2004

This study investigated whether the outcome of bone graft and internal fixation surgery for nonunion of scaphoid fractures could be predicted by gadolinium-enhanced MR assessments of proximal fragment vascularity. Sixteen established scaphoid fracture nonunions underwent gadolinium-enhanced MR scanning before surgical treatment with bone grafting and internal fixation. No relationship was found between MR enhancement and the outcome of surgery. Union was achieved in eight of the 12 nonunions with more than 50% enhancement, and three of the four with less than 50% enhancement, of the proximal pole. Furthermore, union was achieved in both of the nonunions which had less than 25% enhancement of the proximal pole. We conclude that enhanced MR assessments of the vascularity of the proximal fragment of a scaphoid fracture nonunion do not accurately predict the outcome of reconstructive surgery.
Properties of the two neuromuscular compartments in a split bipennate muscle
Authors: Pereira Barry P. , Kumar V. Prem , Lim Aymeric Y. T. , Tan Jessie A. C. , Tan Bee‐Leng
Published: June 2004

Bipennate muscles may be split along their distal aponeurosis, dividing each into two compartments. These sub‐muscle units may be used in tendon transfers. This paper presents the contractile properties of the two sub‐units of the flexor carpi ulnaris in a macaca fascicularis, after it was split by up to 80% of its length. The sub‐muscle units were electrically stimulated and found to have independent isometric contraction, with minimal contraction recorded from the non‐stimulated sub‐unit. Also, the sum of the forces measured from each unit when stimulated individually, was found to be greater than the force of the whole muscle, given the same isometric conditions. The distal aponeurosis which is common allows force transmission between the compartments. Splitting the muscle along this distal aponeurosis alters this function and the force capacity of the muscle, providing a new potential for using the sub‐units as grafts for tendon transfers. © 2004 Orthopaedic Research Society. Published y Elsevier Ltd. All rights reserved.
Temperature dependence of magnetic hysteresis
Authors: Yu Yongjae , Tauxe Lisa , Moskowitz Bruce M.
Published: June 2004

Hysteresis measurements have become a routine procedure in characterizing the magnetic remanence carriers of rocks. In this study we have investigated the temperature dependence of magnetic hysteresis in order to better recognize the dominant anisotropy and changes of domain state at various temperatures. Hysteresis properties have been measured at a series of temperatures between 20 K and 873 K for synthetic magnetites and natural (titano)magnetite‐bearing samples. For synthetic samples and gabbros, shape anisotropy dominates most temperature ranges, while magnetocrystalline anisotropy controls hysteresis properties below 120 K. Titanomagnetite‐bearing oceanic basalts show quite different behavior with much higher coercivity, resulting from prominent magnetostrictive anisotropy. While many factors such as composition, field treatment, grain shape and size, and stress affect hysteresis properties at various temperature ranges, a dominant anisotropy was better recognized when remanence ratio was plotted against coercivity.
Influence of coronal mass ejection interaction on propagation of interplanetary shocks
Authors: Manoharan P. K. , Gopalswamy N. , Yashiro S. , Lara A. , Michalek G. , Howard R. A.
Published: June 2004

We studied 91 interplanetary (IP) shocks associated with coronal mass ejections (CMEs) originating within about ±30° in longitude and latitude from the center of the Sun during 1997–2002. These CMEs cover a wide range of initial speeds of about 120 to 2400 kms−1 and they also include a special population of 25 interacting CMEs. This study provides the characteristics of propagation effects of more number of high‐speed CMEs (VCME > 1500 kms−1) than the data used in earlier studies. It enables to extend the shock‐arrival prediction model to high‐speed CMEs. The results on comparison of IP shock speed and transit time at 1 AU suggest that the shock transit time is not controlled by its final speed but is primarily determined by the initial speed of the CME and effects encountered by it during the propagation. It is found that the CME interaction tends to slow the shock and associated CME. The deviations of shock arrival times from the empirical model are considerably large for slow (VCME < 300 kms−1) and fast (VCME > 800 kms−1) CMEs. Results show that the slow and fast CMEs experience stronger effective acceleration.
Stress transfer and strain rate variations during the seismic cycle
Authors: Perfettini H. , Avouac J.‐P.
Published: June 2004

The balance of forces implies stress transfers during the seismic cycle between the elastobrittle upper crust and the viscoelastic lower crust. This could induce observable time variations of crustal straining in the interseismic period. We simulate these variations using a one‐dimensional system of springs, sliders, and dashpot loaded by a constant force. The seismogenic zone and the zone of afterslip below are modeled from rate‐and‐state friction. The ductile deeper fault zone is modeled from a viscous slider with Newtonian viscosity ν. The force per unit length, F, must exceed a critical value Fc to overcome friction resistance of the fault system. This simple system produces periodic earthquakes. The recurrence period, Tcycle, and the duration of the postseismic relaxation phase, which is driven dominantly by afterslip, then both scale linearly with ν. Between two earthquakes, interseismic strain buildup across the whole system is nonstationary with the convergence rates Vi, just after each earthquake, being systematically higher than the value Vf at the end of the interseismic period. We show that Vi/Vf is an exponential function of α = Tcycle/TM ∝ Δτ/(F − Fc) ∝ Δτ/(νV0), where Δτ is the coseismic stress drop and V0 is the long‐term fault slip rate. It follows that departure from stationary strain buildup is higher if the contribution of viscous forces to the force balance is small compared to the coseismic stress drop (due to a low viscosity or low convergence rate, for example). This simple model is meant to show that the far‐field deformation rate in the interseismic period, which can be determined from geodetic measurements, might not necessarily be uniform and equal to the long‐term geologic rate.
On the fate of the Antarctic Slope Front and the origin of the Weddell Front
Authors: Heywood Karen J. , Naveira Garabato Alberto C. , Stevens David P. , Muench Robin D.
Published: June 2004

Data from the Deep Ocean Ventilation Through Antarctic Intermediate Layers (DOVETAIL) and Antarctic Large‐Scale Box Analysis and the Role of the Scotia Sea (ALBATROSS) projects are combined in the region of the Antarctic Peninsula and the South Scotia Ridge to determine the paths and transports associated with the Antarctic Coastal Current, the Antarctic Slope Front, and the Weddell Front. The Antarctic Coastal Current flows over the Antarctic continental shelf and is not tied to a particular isobath. It transports ∼1 Sv westward to the Bransfield Strait. Its subsequent course is uncertain, but we speculate that it may continue southwest along the western side of the Antarctic Peninsula, close to the coast. The Antarctic Slope Front, present almost all the way around Antarctica tied to the continental slope, has not previously been mapped after it reaches the tip of the Antarctic Peninsula. We show that the frontal jet splits into two branches in the northwest Powell Basin where the isobaths diverge. The shoreward portion of the water associated with the front (lying above isobaths shallower than 1500 m) is able to cross the South Scotia Ridge and head northwestward and retains many of the properties of the Antarctic Slope Front. It is associated with a transport of ∼7 Sv. The portion of the front constrained to lie above isobaths deeper than 1500 m becomes the Weddell Front. This takes a path around the northern Powell Basin and south of the South Orkney Islands. Of the ∼13 Sv that circulates around the southern flank of the South Orkney Plateau, ∼8 Sv of Weddell Sea Deep Water and Warm Deep Water leaves the front to continue west. The remaining shallow and intermediate water retroflects and returns south associated with the Weddell Front through the Orkney Passage. Approximately 5–7 Sv is transported eastward associated with the Weddell Front, tied closely to the southern flanks of the Bruce and Discovery Banks above the 2000–2500 m isobaths, and forming the southern boundary of the Weddell Scotia Confluence.
Response of the Indo‐Pacific warm pool to interannual variations in net atmospheric freshwater
Authors: Huang Boyin , Mehta Vikram M.
Published: June 2004

We used the ocean general circulation model (OGCM) developed in the Massachusetts Institute of Technology to study the response of the Indo‐Pacific warm pool (IPWP) to net atmospheric freshwater flux (NAFW, equal to evaporation minus precipitation) at interannual timescales. The OGCM is forced by observed, monthly NAFW from 1988 to 2000. Our simulations show that the magnitude of interannual anomalies of salinity and temperature reaches about 0.7 practical salinity unit and 0.4°C, respectively. The typical timescale of these interannual variabilities is about 3–5 years. Averaged over 1988–2000, a decrease (increase) of temperature is accompanied with a decrease (increase) of salinity in the western Pacific and South Indian Ocean. A decrease of temperature, however, is accompanied with an increase of salinity in the surface layer (0–50 m) of the North Indian Ocean. The diagnosed budgets of salinity and temperature (heat) are analyzed to estimate the role of advection and vertical mixing in response to the surface NAFW forcing. The analyses indicate that the salinity anomaly in the IPWP is largely due to vertical mixing, especially in the surface layer. The vertical mixing of salinity, in turn, is associated with the surface NAFW anomaly. In contrast, the temperature anomaly above 300 m is primarily due to changes in advection forced by the NAFW, which is associated with basin‐wide changes in major ocean currents. Because of the strong effect of advection on the interannual variability of temperature, the temperature anomaly in the surface layer lags the salinity anomaly about 14–15 months. The results of our simulations are consistent with previous studies about the nearly immediate response of the tropical upper ocean to NAFW forcing due to vertical mixing. The slower response due to changes in basin‐scale heat advection suggests the possibility that ocean variability at interannual and longer timescales can be generated by large‐scale NAFW forcing at seasonal and longer timescales.
Carbonyl sulfide and dimethyl sulfide exchange between lawn and the atmosphere
Authors: Geng Chunmei , Mu Yujing
Published: June 2004

The exchange of carbonyl sulfide (COS) between lawn and the atmosphere was investigated by using a static enclosure under natural field conditions. The results indicated that the lawn acted as a sink for atmospheric COS and a source of dimethyl sulfide (DMS). The exchange fluxes of COS and DMS ranged between −3.24 pmol m−2 s−1 and −94.52 pmol m−2 s−1, and between 0 and 3.14 pmol m−2 s−1, respectively. The lawn was capable of continuously absorbing COS in nighttime as well as in daytime. The COS fluxes depended strongly on the ambient COS mixing ratios. The dependency of DMS emission fluxes on temperature was observed in November 2002. Soil also acted as a sink for COS during our study. However, the COS exchange fluxes of the lawn were much higher than that of the soil. The average COS and DMS fluxes were much higher in spring than in autumn and in summer. The daytime vertical profiles of COS also indicated that the lawn acted as a net sink for COS.
Forecasting methods for occurrence and magnitude of proton storms with solar hard X rays
Authors: Garcia H. A.
Published: June 2004

A hard X‐ray spectrometer (HXRS) was developed jointly by the National Oceanic and Atmospheric Administration (NOAA) Space Environment Center and the Astronomical Institute of the Czech Republic to determine if proton storms could be forecast with greater accuracies than presently available by the existing methods. The HXRS experiment was conceived as a means of proof testing previously discovered empirical relationships between anomalous hard X‐ray spectra of hard X‐ray flares and solar energetic proton events (SEPs) for space weather forecasting applications. SEPs are showers of highly energetic electrons and ions, mostly protons, that can reach Earth's vicinity within minutes to hours following a moderate to large flare and have the potential of affecting the performance of civilian, military and research satellites as well as certain surface assets. The primary SEP predictor criterion educed during the present study is the requirement that the spectral index, γ, must decline (harden) to at least ≤4 for at least 3 min. Flares meeting this criterion have a high association with SEPs. Flares that fail this criterion do not. Other SEP correlative phenomena such as depressed hard X‐ray flux and anomalous low temperatures were studied to determine their utility for forecasting purposes. During the study period, March 2000 through December 2002, 107 hard X‐ray flares were spectrally analyzed including 16 SEP‐associated flares. Fourteen SEP flares were correctly identified, two SEPs were missed, and three false alarms (untrue predictions) were incurred.
Novel artificial optical annular structures in the high latitude ionosphere over EISCAT
Authors: Kosch M. J. , Rietveld M. T. , Senior A. , McCrea I. W. , Kavanagh A. J. , Isham B. , Honary F.
Published: June 2004

The EISCAT low‐gain HF facility has been used repeatedly to produce artificially stimulated optical emissions in the F‐layer ionosphere over northern Scandinavia. On 12 November 2001, the high‐gain HF facility was used for the first time. The pump beam zenith angle was moved in 3° steps along the north‐south meridian from 3°N to 15°S, with one pump cycle per position. Only when pumping in the 9°S position were annular optical structures produced quite unexpectedly. The annuli were approximately centred on the pump beam but outside the −3 dB locus. The optical signature appears to form a cylinder, which was magnetic field‐aligned, rising above the pump wave reflection altitude. The annulus always collapsed into the well‐known optical blobs after ∼60 s, whilst descending many km in altitude. All other pump beam directions produced optical blobs only. The EISCAT UHF radar, which was scanning from 3° to 15°S zenith angle, shows that enhanced ion‐line backscatter persisted throughout the pump on period and followed the morphology of the optical signature. These observations provide the first experimental evidence that Langmuir turbulence can accelerate electrons sufficiently to produce the optical emissions at high latitudes. Why the optical annulus forms, and for only one zenith angle, remains unexplained.
Fractal dimension of non‐network space of a catchment basin
Authors: Sagar B. S. Daya , Chockalingam L.
Published: June 2004

Topographically convex regions within a catchment basin represent varied degrees of hill‐slopes. The non‐network space (M), the characterization of which we address in this letter, is akin to the space that is achieved by subtracting channelized portions contributed due to concave regions from the watershed space (X). This non‐network space is similar to non‐channelized convex region within a catchment basin. We propose an alternative shape‐dependent quantity like fractal dimension to characterize this non‐network space. Towards this goal, we decompose the non‐network space in two‐dimensional discrete space into simple non‐overlapping disks (NODs) of various sizes by employing mathematical morphological transformations and certain logical operations. Furthermore, we plot the number of NODs of less than threshold radius against the radius, and compute the shape‐dependent fractal dimension of non‐network space.
Estimating the depth and shape of subglacial Lake Vostok's water cavity from aerogravity data
Authors: Studinger Michael , Bell Robin E. , Tikku Anahita A.
Published: June 2004

We use aerogravity data to estimate the water depth of subglacial Lake Vostok in East Antarctica. The inversion produces the first bathymetry map covering the entire lake. Lake Vostok consists of two sub‐basins separated by a ridge with very shallow water depths. The deeper southern sub‐basin is approximately double the spatial area of the smaller northern sub‐basin. The close correlation between the pattern of basal melting and freezing and the bathymetric structure has important ramifications for the water circulation and the sediment deposition. We estimate the lake volume to be 5400 ± 1600 km3.
Ionospheric electron concentration imaging using GPS over the USA during the storm of July 2000
Authors: Yin P. , Mitchell C. N. , Spencer P. S. J. , Foster J. C.
Published: June 2004

A new technique for ionospheric imaging is demonstrated during a severe geomagnetic storm of 15th July 2000. The three‐dimensional time‐dependent imaging algorithm is applied to multi‐directional ground‐based GPS data and yields spatial maps of electron concentration. This technique is demonstrated by showing a series of images of the mid‐latitude ionosphere over the USA during the storm of July 2000. A strong uplift in the height of the F‐layer is observed after 20 UT on 15th July, followed by a severe latitudinal electron concentration gradient. Independent verification of the images is provided by the ionosondes and incoherent scatter radar data. The GPS images reveal the large‐scale dynamics of the ionosphere during the disturbed conditions and show the potential of geophysical imaging for storm‐time ionospheric studies.
Inflation rate of the Colli Albani volcanic complex retrieved by the permanent scatterers SAR interferometry technique
Authors: Salvi S. , Atzori S. , Tolomei C. , Allievi J. , Ferretti A. , Rocca F. , Prati C. , Stramondo S. , Feuillet N.
Published: June 2004

We analyzed 99 ERS SAR images of the Colli Albani volcano using the Permanent Scatterers technique. We retrieved the average surface displacement velocities for over 100,000 scatterers for the period 1993–2000, showing that present deformation is concentrated in the area of most recent volcanic activity, with rates up to 2.6 mm/yr in the satellite line of sight. We inverted the observed deformation using several analytical solutions for volcanic sources in an elastic half space. The best fit is obtained with two Mogi sources aligned in a N‐S direction at 5 and 7 km depth beneath the western flank of the volcano.
Coherent waveforms in the auroral upward current region
Authors: Matsukiyo S. , Treumann R. A. , Scholer M.
Published: June 2004

With the help of one‐dimensional particle‐in‐cell simulations we show that observations of high‐frequency electric wave spectra in the auroral upward current region can be reproduced. Using distribution functions suggested by the measurements, we find that in the nonlinear state, ion acoustic waves and electron two‐stream (Langmuir) waves dominate the spectrum. In the absence of cold electrons, electron acoustic waves are not excited initially but appear only at a late time. They are the result of the formation of a two‐temperature electron plasma by nonlinear interactions when all other instabilities have saturated. However, owing to the weakness of these electron acoustic waves, they are less important for the formation of electron holes and affect the particle dynamics much less than the two‐stream instability.
Biosynthesis of UDP-GlcA, a key metabolite for capsular polysaccharide synthesis in the pathogenic fungus Cryptococcus neoformans
Authors: BAR-PELED Maor , GRIFFITH Cara L. , ORY Jeramia J. , DOERING Tamara L.
Published: June 2004

UDP-glucose dehydrogenase catalyses the conversion of UDP-glucose into UDP-GlcA, a critical precursor for glycan synthesis across evolution. We have cloned the gene encoding this important enzyme from the opportunistic pathogen Cryptococcus neoformans. In this fungus, UDP-GlcA is required for the synthesis of capsule polysaccharides, which in turn are essential for virulence. The gene was expressed in Escherichia coli and the 51.3-kDa recombinant protein from wild-type and five mutants was purified for analysis. The cryptococcal enzyme is strongly inhibited by UDP-xylose and NADH, has highest activity at pH 7.5 and demonstrates Km (app) values of 0.1 and 1.5 mM for NAD+ and UDP-glucose respectively. Its activity was significantly decreased by mutations in the putative sites of NAD+ and UDP-glucose binding. Unlike previously reported eukaryotic UDP-glucose dehydrogenases, which are hexamers, the cryptococcal enzyme is a dimer.
Biochemical analysis of the processive mechanism for epimerization of alginate by mannuronan C-5 epimerase AlgE4
Authors: CAMPA Cristiana , HOLTAN Synnøve , NILSEN Nadra , BJERKAN Tonje M. , STOKKE Bjørn T. , SKJÅK-BRÆK Gudmund
Published: June 2004

The enzymes mannuronan C-5 epimerases catalyse the in-chain epimerisation of β-D-mannuronic acid to α-L-guluronic acid in the last step of alginate biosynthesis. The recombinant C-5 epimerase AlgE4, encoded by the soil bacteria Azotobacter vinelandii and expressed in Escherichia coli, exhibits a non-random mode of action when acting on mannuronan and alginates of various monomeric compositions. The observed residue sequence has been suggested previously to be due to either a preferred attack or a processive mode of action. Based on methodologies involving specific degrading enzymes, NMR, electrospray ionisation mass spectrometry and capillary electrophoresis we show here that on average 10 residues are epimerised for each enzyme–substrate encounter. A subsite model for the enzyme is analysed by the same methodology using native and 13C-labelled mannuronan oligomers as substrate for the AlgE4 epimerase. A hexameric oligomer is the minimum size to accommodate activity. For hexa-, hepta- and octameric substrates the third M residue from the non-reducing end is epimerised first.
Transglutaminase 5 is regulated by guanine–adenine nucleotides
Authors: CANDI Eleonora , PARADISI Andrea , TERRINONI Alessandro , PIETRONI Valentina , ODDI Sergio , CADOT Bruno , JOGINI Vishwanath , MEIYAPPAN Muthuraman , CLARDY Jon , FINAZZI-AGRO Alessandro , MELINO Gerry
Published: June 2004

Transglutaminases (TGases) are Ca2+-dependent enzymes capable of catalysing transamidation of glutamine residues to form intermolecular isopeptide bonds. Nine distinct TGases have been described in mammals, and two of them (types 2 and 3) are regulated by GTP/ATP. TGase2 hydrolyses GTP and is therefore a bifunctional enzyme. In the present study, we report that TGase5 is also regulated by nucleotides. We have identified the putative TGase5 GTP-binding pocket by comparative amino acid sequence alignment and homology-derived three-dimensional modelling. GTP and ATP inhibit TGase5 cross-linking activity in vitro, and Ca2+ is capable of completely reversing this inhibition. In addition, TGase5 mRNA is not restricted to epidermal tissue, but is also present in different adult and foetal tissues, suggesting a role for TGase5 outside the epidermis. These results reveal the reciprocal actions of Ca2+ and nucleotides with respect to TGase5 activity. Taken together, these results indicate that TGases are a complex family of enzymes regulated by calcium, with at least three of them, namely TGase2, TGase3 and TGase5, also being regulated by ATP and GTP.
Enzymic and structural characterization of nepenthesin, a unique member of a novel subfamily of aspartic proteinases
Authors: ATHAUDA Senarath B. P. , MATSUMOTO Koji , RAJAPAKSHE Sanath , KURIBAYASHI Masayuki , KOJIMA Masaki , KUBOMURA-YOSHIDA Nobuko , IWAMATSU Akihiro , SHIBATA Chiaki , INOUE Hideshi , TAKAHASHI Kenji
Published: June 2004

Carnivorous plants are known to secrete acid proteinases to digest prey, mainly insects, for nitrogen uptake. In the present study, we have purified, for the first time, to homogeneity two acid proteinases (nepenthesins I and II) from the pitcher fluid of Nepenthes distillatoria (a pitcher-plant known locally as badura) and investigated their enzymic and structural characteristics. Both enzymes were optimally active at pH approx. 2.6 towards acid-denatured haemoglobin; the specificity of nepenthesin I towards oxidized insulin B chain appears to be similar, but slightly wider than those of other APs (aspartic proteinases). Among the enzymic properties, however, the most notable is their unusual stability: both enzymes were remarkably stable at or below 50 °C, especially nepenthesin I was extremely stable over a wide range of pH from 3 to 10 for over 30 days. This suggests an evolutionary adaptation of the enzymes to their specific habitat. We have also cloned the cDNAs and deduced the complete amino acid sequences of the precursors of nepenthesins I and II (437 and 438 residues respectively) from the pitcher tissue of N. gracilis. Although the corresponding mature enzymes (each 359 residues) are homologous with ordinary pepsin-type APs, both enzymes had a high content of cysteine residues (12 residues/molecule), which are assumed to form six unique disulphide bonds as suggested by computer modelling and are supposed to contribute towards the remarkable stability of nepenthesins. Moreover, the amino acid sequence identity of nepenthesins with ordinary APs, including plant vacuolar APs, is remarkably low (approx. 20%), and phylogenetic comparison shows that nepenthesins are distantly related to them to form a novel subfamily of APs with a high content of cysteine residues and a characteristic insertion, named ‘the nepenthesin-type AP-specific insertion’, that includes a large number of novel, orthologous plant APs emerging in the gene/protein databases.
Characterization of the ATP-hydrolysing activity of α-sarcoglycan
Authors: SANDONÀ Dorianna , GASTALDELLO Stefano , MARTINELLO Tiziana , BETTO Romeo
Published: June 2004

α-Sarcoglycan is a glycoprotein associated with the dystrophin complex at sarcolemma of skeletal and cardiac muscles. Gene defects in α-sarcoglycan lead to a severe muscular dystrophy whose molecular mechanisms are not yet clear. A first insight into the function of α-sarcoglycan was obtained by finding that it is an ATP-binding protein and that it probably confers ability to hydrolyse ATP to the purified dystrophin complex [Betto, Senter, Ceoldo, Tarricone, Biral and Salviati (1999) J. Biol. Chem. 274, 7907–7912]. In the present study, we present definitive evidence showing that α-sarcoglycan is an ATP-hydrolysing enzyme. The appearance of α-sarcoglycan protein expression was correlated with the increase in ecto-nucleotidase activity during differentiation of C2C12 cells. Approx. 25% of ecto-nucleotidase activity displayed by the C2C12 myotubes was inhibited by preincubating cells with an antibody specific for the ATP-binding motif of α-sarcoglycan. This demonstrates that α-sarcoglycan substantially contributes to total ecto-nucleotidase activity of C2C12 myotubes. To characterize further this activity, human embryonic kidney 293 cells were transfected with expression plasmids containing α-sarcoglycan cDNA. Transfected cells exhibited a significant increase in the ATP-hydrolysing activity that was abolished by the anti-α-sarcoglycan antibody. The enzyme had a substrate specificity for ATP and ADP, did not hydrolyse other triphosphonucleosides, and the affinity for ATP was in the low mM range. The ATPase activity strictly required the presence of both Mg2+ and Ca2+ and was completely inhibited by suramin and reactive blue-2. These results show that α-sarcoglycan is a Ca2+, Mg2+-ecto-ATPDase. The possible consequences of the absence of α-sarcoglycan activity in the pathogenesis of muscular dystrophy are discussed.
Binding of the DNA-dependent protein kinase catalytic subunit to Holliday junctions
Authors: DIP Ramiro , NAEGELI Hanspeter
Published: June 2004

DNA-PK (DNA-dependent protein kinase) is a double-strand break sensor involved in DNA repair and signal transduction. In the present study, we constructed site-directed cross-linking probes to explore the range of DNA discontinuities that are recognized by DNA-PKCS (DNA-PK catalytic subunit). A comparison between different substrate architectures showed that DNA-PKCS associates preferentially with the crossover region of synthetic Holliday junctions. This interaction with four-way junctions was preserved when biotin–streptavidin complexes were assembled at the termini to exclude the binding of Ku proteins. The association of DNA-PKCS with Holliday junctions was salt-labile even in the presence of Ku proteins, but this interaction could be stabilized when the DNA probes were incubated with the endogenous enzyme in nuclear extracts of human cells. Cross-linking of the endogenous enzyme in cellular extracts also demonstrated that DNA-PKCS binds to DNA ends and four-way junctions with similar affinities in the context of a nuclear protein environment. Kinase assays using p53 proteins as a substrate showed that, in association with four-way structures, DNA-PKCS adopts an active conformation different from that in the complex with linear DNA. Our results are consistent with a structure-specific, but Ku- and DNA end-independent, recruitment of DNA-PKCS to Holliday junction intermediates. This observation suggests an unexpected functional link between the two main pathways that are responsible for the repair of DNA double-strand breaks in mammalian cells.
Signalling of the M3-muscarinic receptor to the anti-apoptotic pathway
Authors: BUDD David C. , SPRAGG Elizabeth J. , RIDD Katie , TOBIN Andrew B.
Published: June 2004

The process of programmed cell death (or apoptosis) occurs widely in tissue maintenance and embryonic development, and is under tight regulatory control. It is now clear that one of the important regulators of apoptosis are G-protein-coupled receptors. In the present study, we investigate the regulatory mechanism employed by the Gq/11-coupled M3-muscarinic receptor in mediating an anti-apoptotic response. Using a CHO (Chinese-hamster ovary) cell model, we demonstrate that the M3-muscarinic receptor anti-apoptotic response is independent of calcium/phospholipase C signalling. This response can, however, be inhibited by the transcriptional inhibitor actinomycin D at a concentration that inhibits the rapid increase in gene transcription mediated by M3-muscarinic receptor stimulation. Furthermore, apoptosis in CHO cells induced by the DNA-damaging agent, etoposide, is associated with a fall in the levels of the anti-apoptotic Bcl-2 protein. This fall in Bcl-2 protein concentration can be attenuated by M3-muscarinic receptor stimulation. We conclude, therefore, that the M3-muscarinic receptor signals to the anti-apoptotic pathway via a mechanism that is independent of calcium/phospholipase C signalling, but in a manner that involves both gene transcription and the up-regulation of Bcl-2 protein.