bluuebunny/crossref_metadata_2025 huggingface dataset:
Turbulence measurements and implications for gravity wave dissipation during the MaCWAVE/MIDAS rocket program
Authors: Rapp M. , Strelnikov B. , Müllemann A. , Lübken F.‐J. , Fritts D. C.
Published: October 2004

Three altitude profiles of turbulent energy dissipation rates measured during the MaCWAVE/MIDAS summer rocket program are presented. All measurements show near continuous turbulent layers from ∼72–90 km altitude. Above 82 km altitude measured dissipation rates are comparable to former results. Below 82 km the MaCWAVE/MIDAS measurements provide the first evidence for turbulence in summer at these altitudes ever obtained. This unusual turbulence activity is accompanied by a reduced altitude of the zonal wind maximum, colder temperatures below 85 km, and enhanced gravity wave amplitudes above ∼75 km. The larger gravity wave amplitudes can be explained by the different local thermal structure through the wave amplitude dependence on the buoyancy frequency. These larger wave amplitudes lead to wave breaking, turbulence production, and forcing of the zonal wind at lower altitudes. Our measurements hence imply that the altitude of the zonal wind maximum is a sensitive indicator for the altitude distribution of turbulence in the upper mesosphere.
Observations of extreme temperature and wind gradients near the summer mesopause during the MaCWAVE/MIDAS rocket campaign
Authors: Fritts D. C. , Williams B. P. , She C. Y. , Vance J. D. , Rapp M. , Lübken F.‐J. , Müllemann A. , Schmidlin F. J. , Goldberg R. A.
Published: October 2004

We present measurements of extremely large gradients of temperature and zonal wind near the arctic summer mesopause obtained with sodium lidar and falling spheres during the MaCWAVE/MIDAS rocket and ground‐based measurement campaign performed at the Andøya Rocket Range (ARR) and the ALOMAR observatory (69.3°N, 16.0°E) in July 2002. The gradients appear to result from strong gravity wave forcing of the summer mesopause, vertical scale compression and amplitude increases accompanying increasing stratification and decreasing intrinsic phase speeds, and the turbulent transport accompanying wave instability in the lower thermosphere. Zonal wind gradients are found to exceed 100 m s−1 km−1, while temperature gradients range from super‐adiabatic to ∼40 to 100 K km−1. We also explore the implications of these large gradients for further instability of the gravity wave and mean fields.
Solar cycle variations in solar and interplanetary ions observed with Interplanetary Monitoring Platform 8
Authors: Simunac K. D. C. , Armstrong T. P.
Published: October 2004

Energetic protons (0.39–440 MeV), alpha particles (0.59–52 MeV/nucleon), and medium nuclei (carbon, nitrogen, and oxygen; 0.7–8.8 MeV/nucleon) have been observed with the Charged Particle Measurement Experiment (CPME) aboard the Interplanetary Monitoring Platform 8 (IMP 8) spacecraft from 1973 to the present. We summarize the results obtained for the period October 1973 through November 2000, more than two complete solar cycles. We believe that these observations of solar and interplanetary particles are the longest set from a single instrument yet obtained. Artifacts have been carefully removed from this data set, including background changes due to the failure in 1989 of an electronic anticoincidence shield. We have computed averages over individual solar cycles as well as “grand” averages of everything seen over the 27‐year period. The “grand” average energy spectrum of protons, alphas, and medium nuclei is well described by a power law function in total energy with exponent −2, where E is in units of MeV total energy and flux is particles/(cm2 s sr MeV). Compositional abundance ratios for energetic nuclei at the same speeds are calculated for times of minimum (H/He = 30; He/medium = 95) and maximum (H/He = 61; He/medium = 45) solar activity. We also considered possible relationships between sunspot number and interplanetary particle flux using a variety of averaging intervals and time lags and leads but found no result that could be used to predict particle fluxes from sunspot numbers over short intervals (typically several solar rotations).
Predictability of hydrologic response at the plot and catchment scales: Role of initial conditions
Authors: Zehe Erwin , Blöschl Günter
Published: October 2004

This paper examines the effect of uncertain initial soil moisture on hydrologic response at the plot scale (1 m2) and the catchment scale (3.6 km2) in the presence of threshold transitions between matrix and preferential flow. We adopt the concepts of microstates and macrostates from statistical mechanics. The microstates are the detailed patterns of initial soil moisture that are inherently unknown, while the macrostates are specified by the statistical distributions of initial soil moisture that can be derived from the measurements typically available in field experiments. We use a physically based model and ensure that it closely represents the processes in the Weiherbach catchment, Germany. We then use the model to generate hydrologic response to hypothetical irrigation events and rainfall events for multiple realizations of initial soil moisture microstates that are all consistent with the same macrostate. As the measures of uncertainty at the plot scale we use the coefficient of variation and the scaled range of simulated vertical bromide transport distances between realizations. At the catchment scale we use similar statistics derived from simulated flood peak discharges. The simulations indicate that at both scales the predictability depends on the average initial soil moisture state and is at a minimum around the soil moisture value where the transition from matrix to macropore flow occurs. The predictability increases with rainfall intensity. The predictability increases with scale with maximum absolute errors of 90 and 32% at the plot scale and the catchment scale, respectively. It is argued that even if we assume perfect knowledge on the processes, the level of detail with which one can measure the initial conditions along with the nonlinearity of the system will set limits to the repeatability of experiments and limits to the predictability of models at the plot and catchment scales.
Characterization and identification of aquifer heterogeneity with generalized parameterization and Bayesian estimation
Authors: Tsai Frank T.‐C. , Yeh William W.‐G.
Published: October 2004

This research proposes a generalized parameterization method (referred to as GP) and Bayesian estimation for parameter heterogeneity characterization and identification in groundwater modeling. GP unifies zonation and interpolation through a set of weighting coefficients and is capable of creating a zonation structure, a continuous distribution, or a mixed structure. GP shows greater flexibility not only in manipulating the highly complex spatial distribution but also in identifying the parameter structure. With GP, parameter structure identification seeks to identify the parameter dimension, parameter pattern, parameter values, as well as the values of the weighting coefficients simultaneously through a set of basis points. Additionally, this study develops an embedded genetic algorithm (GA) for solving the structure identification problem. A Bayesian estimator that estimates the basis point values as well as the values of the weighing coefficients is embedded in the GA, which searches for the best basis point locations. We demonstrate the inverse methodology by a numerical example in which the distributed transmissivity in a two‐dimensional confined aquifer is identified. We calculate the Jacobian matrix by the adjoint state method. With GP we have successfully identified the transmissivity structure with four basis points that results in a good fitting in groundwater heads and captures the nonsmooth characteristic as well as the trend of the true transmissivity field. We compare GP with Voronoi tessellation (zonation) and natural neighbor interpolation. Results show that GP outperforms the other two parameterization methods in that GP identified the transmissivity field with a smaller parameter uncertainty along with a sufficiently small fitting residual and without over‐parameterization.
Three‐phase flow analysis of dense nonaqueous phase liquid infiltration in horizontally layered porous media
Authors: Wipfler E. L. , van Dijke M. I. J. , van der Zee S. E. A. T. M.
Published: October 2004

We considered dense nonaqueous phase liquid (DNAPL) infiltration into a water‐unsaturated porous medium that consists of two horizontal layers, of which the top layer has a lower intrinsic permeability than the bottom layer. DNAPL is the intermediate‐wetting fluid with respect to the wetting water and the nonwetting air. The layer interface forms a barrier to DNAPL flow, which causes the DNAPL to spread out horizontally just above the interface. An analytical approximation has been developed to estimate the DNAPL pressure and saturation and the horizontal extension of the DNAPL above the layer interface at steady state for low water saturations. The analytical approximation shows that the DNAPL infiltration is determined by five dimensionless numbers: the heterogeneity factor γ, the capillary pressure parameter λ, the gravity number Ng, the ratio of the capillary and gravity numbers Nc/Ng, and the critical DNAPL pressure Poc. Its predictions were compared with the results of a numerical three‐phase flow simulator for a number of parameter combinations. For most of these combinations the analytical approximation predicts the DNAPL pressure and saturation profiles at the interface adequately. Using the analytical approximation, we carried out a sensitivity study with respect to the maximum horizontal extension of the plume. The extension of the plumes appears to be highly sensitive to variation of the dimensionless numbers Poc, λ and γ.
The MaCWAVE/MIDAS rocket and ground‐based measurements of polar summer dynamics: Overview and mean state structure
Authors: Goldberg R. A. , Fritts D. C. , Williams B. P. , Lübken F.‐J. , Rapp M. , Singer W. , Latteck R. , Hoffmann P. , Müllemann A. , Baumgarten G. , Schmidlin F. J. , She C.‐Y. , Krueger D. A.
Published: October 2004

The MaCWAVE/MIDAS collaborative rocket and ground‐based measurement programs were performed at the Andøya Rocket Range and the nearby ALOMAR observatory in northern Norway during July 2002. The summer component of the MaCWAVE (Mountain and Convective Waves Ascending Vertically) program was focused on gravity wave propagation, instability, and wave‐wave and wave‐mean flow interaction dynamics contributing to summer mesopause structure and variability. The MIDAS (Middle Atmosphere Dynamics and Structure) program concentrated on small‐scale dynamical and microphysical processes near the summer mesopause. Our merged program yielded a comprehensive data set comprising two ∼12‐hour rocket salvoes, including 25 MET rockets and 5 sounding rockets, ground‐based lidar, radar, and balloon data, and coordinated overpasses of the TIMED satellite. This paper describes the measurement program and rationale, the mean state observed during the rocket salvoes, and evidence that the mean state structure during 2002 differed in important respects from previous years.
High Rossby‐wave activity in austral winter 2002: Modulation of the general circulation of the MLT during the MaCWAVE/MIDAS northern summer program
Authors: Becker E. , Müllemann A. , Lübken F.‐J. , Körnich H. , Hoffmann P. , Rapp M.
Published: October 2004

The seasonally and zonally averaged effects of the anomalously strong Rossby‐wave activity in austral winter 2002 are estimated by a sensitivity experiment using an idealized general circulation model. The approach focuses on the modulation of gravity‐wave saturation via the altered mean winds in the mesosphere and MLT. In the northern summer MLT the effects consist of increased vertical gradients of the mean zonal wind and temperature, as well as downward shifts of the residual circulation and the gravity wave‐induced frictional heating. All these signals agree reasonably with observations obtained during the MaCWAVE/MIDAS program 2002.
Gravity waves in the troposphere and stratosphere during the MaCWAVE/MIDAS summer rocket program
Authors: Schöch A. , Baumgarten G. , Fritts D. C. , Hoffmann P. , Serafimovich A. , Wang L. , Dalin P. , Müllemann A. , Schmidlin F. J.
Published: October 2004

Combining data taken during the MaCWAVE summer rocket campaign at the Andøya Rocket Range (69.3°N, 16.0°E) with a lidar, radiosondes, falling spheres, and VHF radars at Andøya and at the Esrange, the gravity wave content of the troposphere and stratosphere during the campaign nights was analyzed. The lidar yielded vertical wavelengths and periods of gravity waves in the stratosphere. A Stokes parameter analysis was performed for the radiosonde and falling sphere data to estimate propagation directions of the gravity waves. The wave content in the troposphere was inferred by applying wavelet and cross‐spectral methods to the radar data. We found propagation conditions and spectra of the waves to vary with height following the change in the background wind. The waves were excited both at the ground and in the tropopause/lower stratosphere region.
Coordinated investigation of plasma and neutral density fluctuations and particles during the MaCWAVE/MIDAS summer 2002 program
Authors: Croskey Charles L. , Mitchell John D. , Goldberg Richard A. , Blix Tom A. , Rapp Markus , Latteck Ralph , Friedrich Martin , Smiley Byron
Published: October 2004

The MaCWAVE/MIDAS program for investigating high‐latitude mesospheric dynamics has produced an extensive set of charged particle, plasma and neutral density measurements. We report on the results from one rocket salvo involving a MaCWAVE and two MIDAS payloads launched within a one‐hour period. Each payload carried probes for evaluating the plasma and charged particle environment, and additionally, neutral density measurements were obtained by the CONE instrument on the MIDAS payloads. With the combination of particle and electron/ion density measurements, regions with and without charged particles have been clearly identified, and the plasma measurements outside the particle layers have proven useful to characterize the turbulent activity of the neutral gas.
Infrasonic observations of open ocean swells in the Pacific: Deciphering the song of the sea
Authors: Willis M. , Garcés M. , Hetzer C. , Businger S.
Published: October 2004

Microbaroms are infrasonic waves generated by nonlinear interactions of ocean surface waves traveling in nearly opposite directions with similar frequencies. Such interactions commonly occur between ocean waves with ∼10 s periods, which are abundant in the open oceans and correspond to the observed 0.2 Hz infrasonic spectral peak. Microbarom observations from Hawai'i during 2002–2003 show a relationship with storm and ocean wave activity in the Pacific. Seasonal patterns of observed microbarom arrival azimuths are affected by the size and distribution of swells, by the dominant wind directions in the atmosphere, and by topographic shadowing.
Resonant coupling of a traveling air pressure disturbance with the east Adriatic coastal waters
Authors: Vilibić Ivica , Domijan Nenad , Orlić Mirko , Leder Nenad , Pasarić Miroslava
Published: October 2004

Exceptional sea level oscillations and strong current reversals, observed in the east Adriatic on 27 June 2003, are analyzed using available meteorological and tide‐gauge measurements and numerical model results. It is shown that the variability in the atmosphere‐sea system was characterized by high frequencies (0.01–0.1 min−1) and sea level and current amplitudes surpassing 1 m and 1 m s−1, respectively. The event was related to the occurrence of a gravity disturbance in the atmosphere above the Adriatic. The disturbance traveled toward the east‐southeast at a speed of 22 m s−1 and was resonantly coupled with a wave in the sea 50 m deep. The resulting forced wave was further amplified when entering funnel‐shaped bays opened to it. There are indications that the forcing disturbance and its counterpart in the sea excited normal modes of the bays and harbors in the area. Moreover, nonlinear steepening of the forced wave seemingly occurred, resulting in the formation of high‐frequency wave trains. This process, along with the generation of coastal seiches, could explain the observed and modeled differences between the spectra of coastal variability and the spectrum of forcing wave.
Vertical profile and origin of wintertime tropospheric ozone over China during the PEACE‐A period
Authors: Chan C. Y. , Zheng X. D. , Chan L. Y. , Cui H. , Ginn E. W. L. , Leung Y. K. , Lam H. M. , Zheng Y. G. , Qin Y. , Zhao C. S. , Wang T. , Blake D. R. , Li Y. S.
Published: October 2004

During the Pacific Exploration of Asian Continental Emission (PEACE) phase A mission in January 2002, we launched ozonesondes in subtropical southeast China at Hong Kong (114.17°E, 22.31°N), middle latitude northeast China at Beijing (116.47°E, 39.81°N), and northwest China at Xining (101.45°E, 36.43°N) in order to study long‐range ozone (O3) transport from Eurasia, tropospheric O3 sources in China, and O3 outflow to the Pacific. Tropospheric O3 showed a complex vertical distribution with average tropospheric O3 columns of 39 ± 4, 23 ± 3, and 30 ± 6 DU in Hong Kong, Beijing, and Xining, respectively, which accounted for 17 ± 2%, 7 ± 1%, and 10 ± 1% of the total O3 column. The lower tropospheric and boundary layer (BL) O3 over Xining and especially Beijing exhibited low values, suggesting negligible O3 formation in middle latitudes of China during the winter season. The results also revealed frequent propagation of enhanced O3 layers from the lower stratosphere to the upper troposphere over Xining and especially Beijing, suggesting that stratospheric O3 is an important source of O3 in the upper troposphere of northern China. This “natural” O3 is transported downwind by the prevailing westerly wind and acts as a source of O3 to the east Asian coast and northwestern Pacific. We observed elevated O3, with a maximum mixing ratio up to 111 ppbv, at 1.5 km in the upper BL over Hong Kong. The elevated O3 was resulted from transport of pollutants from northwest‐central or southwest China and regional O3 formation and accumulation in south China including the Pearl River Delta and Hong Kong. We also observed enhanced O3 (>95 ppbv) in the middle and upper troposphere over Hong Kong in air masses transported along the subtropical jet from tropical and subtropical East Africa, south Asia, and Southeast Asia. The O3 enhancements were most likely due to intrusion of stratospheric O3 into the troposphere in the Indo‐Burmese region of tropical Southeast Asia, where substantial downward motion had been observed.
Stable isotope fractionation of nitrous oxide during thermal decomposition and reduction processes
Authors: Ogawa Mitsuteru , Yoshida Naohiro
Published: October 2004

Kinetic isotope effects in nitrous oxide thermal decomposition and reduction reactions were investigated in flowing N2O/He and N2O/He/H2 systems. The intramolecular distribution of stable isotopes, isotopomer, was measured and evaluated using an isotope ratio mass spectrometer equipped with a modified collector system. Thermal decomposition and reduction of nitrous oxide were carried out using a flow tube reactor made of quartz glass in the temperature range of 1173–1373 K. Both thermal decomposition and hydrogen reduction of nitrous oxide proceeded by first‐order kinetics. Isotopomer ratios (δ15Nbulk, δ15Nα, δ15Nβ, and δ18O) of residual nitrous oxide were found to follow a Rayleigh model based on batch distillation. Residual nitrous oxide was depleted slightly in 15N during thermal decomposition but slightly enriched in 15N during hydrogen reduction. Regarding the nitrogen isotopomers, results showed that the central nitrogen atom, Nα, was enriched in 15N during both destruction reactions of nitrous oxide. Although the N2O destruction reactions proceeded at high temperature, large isotopic fractionations of nitrogen isotopomers were observed. Enrichment factors for nitrous oxide as a result of thermal decomposition and reduction reactions were evaluated.
Can large wind farms affect local meteorology?
Authors: Baidya Roy S. , Pacala S. W. , Walko R. L.
Published: October 2004

The RAMS model was used to explore the possible impacts of a large wind farm in the Great Plains region on the local meteorology over synoptic timescales under typical summertime conditions. A wind turbine was approximated as a sink of energy and source of turbulence. The wind farm was created by assuming an array of such turbines. Results show that the wind farm significantly slows down the wind at the turbine hub‐height level. Additionally, turbulence generated by rotors create eddies that can enhance vertical mixing of momentum, heat, and scalars, usually leading to a warming and drying of the surface air and reduced surface sensible heat flux. This effect is most intense in the early morning hours when the boundary layer is stably stratified and the hub‐height level wind speed is the strongest due to the nocturnal low‐level jet. The impact on evapotranspiration is small.
High‐altitude clear‐sky direct solar ultraviolet irradiance at Leh and Hanle in the western Himalayas: Observations and model calculations
Authors: Singh Sachchidanand , Singh Risal
Published: October 2004

Here we present a detailed analysis of the observations done from very high altitude remote locations at Hanle (32°47′N, 78°58′E, 4517 m above sea level (asl)) and Leh (34°09′N, 77°34′E, 3441 m asl) in the western Himalayas. The experiments were done using a microprocessor‐controlled total ozone portable spectrometer (MICROTOPS) II Sun photometer and a broadband pyranometer during 4–18 July 2003, but the clear‐sky conditions prevailed only on 8 and 12 July at Leh and 14 and 15 July at Hanle. The measurements were made for direct solar UV irradiances at 305, 312, and 320 nm, total ozone column, and aerosol optical depths at 380 and 500 nm. The observations show typical daytime variation of UV irradiance as a function of time at both locations. These observations are compared with the model calculations done using the tropospheric ultraviolet visible radiation model (TUV) and show a good agreement. The top of the atmosphere irradiances were also retrieved at different wavelengths from the data using Langley analysis and were compared with the model values. The highest CIE‐weighted (Commission Internationale de l'Éclairage) erythemal dose estimated at local noon at Hanle had a value of 375 mW m−1.
Contribution of vegetated littoral zone to winter fluxes of carbon dioxide and methane from boreal lakes
Authors: Larmola Tuula , Alm Jukka , Juutinen Sari , Huttunen Jari T. , Martikainen Pertti J. , Silvola Jouko
Published: October 2004

Littoral zones at the interface of the lake and the catchment are intensive sites for mineralization of organic matter, but the contribution of vegetated littoral zone to winter fluxes of carbon dioxide (CO2) and methane (CH4) from lake ecosystems into the atmosphere is poorly known. We studied littoral carbon gas fluxes and their spatial controls at five boreal lakes of varying trophic state during three consequent winters with contrasting snow conditions and flooding regimes. Lake‐wide estimates including littoral winter release and potential pelagic spring pulse of gases were calculated for three lakes. Large interannual and spatial differences in carbon gas fluxes were controlled by the interaction of climatic factors, ice and snow cover, on‐site hydrology, and apparently substrate supply from biomass production of the previous growing season. Littoral CO2 fluxes ranged from 0.9 to 7.5 mol m−2 winter−1, and the CH4 fluxes ranged from 0.04 to 0.38 mol m−2 winter−1, the latter being highest in eutrophic lakes. The vegetated littoral contributed the most (66–78%) to winter CH4 emissions from two lakes; in the smallest and most productive lake, pelagic accumulation exceeded littoral release. The large variation in littoral CO2 release could contribute to between‐winter differences of 82% in lake‐wide carbon gas emissions. The water level of the preceding summer and precipitation during early winter were found to be useful predictors for littoral carbon gas fluxes in winter. This suggests that the carbon gas exchange of a shallow boreal lake can be highly sensitive to changes in snowfall and subsequent flooding.
Multidecadal variability of rainfall and streamflow: Eastern Australia
Authors: Verdon Danielle C. , Wyatt Adam M. , Kiem Anthony S. , Franks Stewart W.
Published: October 2004

This study investigates the influence of the El Niño–Southern Oscillation (ENSO) and the Interdecadal Pacific Oscillation (IPO) on rainfall and streamflow regimes of eastern Australia. An analysis of historical rainfall and streamflow data for Queensland (QLD), New South Wales (NSW), and Victoria (VIC) reveals strong relationships between these indices and seasonal rainfall and streamflow totals. Rainfall and streamflow in NSW and QLD are shown to be significantly enhanced during the La Niña phase of ENSO, with La Niña impacts diminishing as one moves south into VIC. In addition, the study shows that on a multidecadal timescale the negative phase of the IPO is associated with “wetter” conditions than the positive phase. Importantly, the already enhanced La Niña rainfall and streamflow is demonstrated to be even further magnified during La Niña events that occur in the IPO negative phase. This result is of particular importance as the influence of ENSO in VIC appears to be weak; however, the results indicate that some useful predictability of ENSO impacts can be achieved during the negative phase of the IPO for VIC.
Global full-wave simulation of the Tore-Supra doppler reflectometer
Authors: Silva F. da , Heuraux S. , Lemoine N. , Honoré C. , Hennequin P. , Manso M. , Sabot R.
Published: October 2004

The Tore-Supra doppler reflectometer (TSDR) aims at measuring the poloidal wave number spectrum (k spectrum) of the density fluctuations. To evaluate the performance and the sensitivity of the TSDR, simulations were made using a global full-wave code. The TSDR modeling with a finite-difference time-domain scheme and the required constraints of the simulation are presented, namely the account of the real size of the system: Distance horn plasma and plasma size. Particular attention is given to the role of the radiation pattern both on the TSDR spatial resolution and the wave number detection.
Effects of relativistic frequency downshift on measurements of electron cyclotron emission in Large Helical Device plasma
Authors: Sato M. , Isayama A. , Inagaki S. , Nagayama Y. , Kawahata K. , Iwama N.
Published: October 2004

The effects of relativistic down shift frequency on the determination of the electron temperature profile from electron cyclotron emission (ECE) in a large helical device(LHD) have been studied by a numerical calculation. since the value of toroidal magnetic field has maximum at the magnetic axis along the sight line in the LHD, the emissivity at the magnetic axis decreases due to the relativistic effect. We found an apparent drop in electron temperature around the magnetic axis due to the relativistic effect. The parametric dependences of the relativistic effect on electron temperature measurement have been studied. When the electron temperature is higher and/or optical thickness is thinner, the gap from the nonrelativistic electron cyclotron frequency is wider. In the case of Te(0)=5 keV and ne=1×1019 m−3, the frequency gap is about 0.5 GHz. Calculation shows that the electron temperature at the central region (ρ<0.1) apparently decreases less than one-half even at 5 keV, in the case of ne=1×1019 m-3 due to the its unique magnetic configuration. Therefore, it is necessary for precise measurement of the electron temperature profile to take into account the relativistic downshift frequency in LHD plasma. To verify the relativistic effect on electron temperature measurement from ECE in the LHD experimentally, the parameter region is evaluated numerically. It is possible to verify the relativistic effect in LHD experimentally.
Two-dimensional full-wave code for reflectometry simulations in TJ-II
Authors: Blanco E. , Heuraux S. , Estrada T. , Sánchez J. , Cupido L.
Published: October 2004

A two-dimensional full-wave code in the extraordinary mode has been developed to simulate reflectometry in TJ-II. The code allows us to study the measurement capabilities of the future correlation reflectometer that is being installed in TJ-II. The code uses the finite-difference-time-domain technique to solve Maxwell’s equations in the presence of density fluctuations. Boundary conditions are implemented by a perfectly matched layer to simulate free propagation. To assure the stability of the code, the current equations are solved by a fourth-order Runge–Kutta method. Density fluctuation parameters such as fluctuation level, wave numbers, and correlation lengths are extrapolated from those measured at the plasma edge using Langmuir probes. In addition, realistic plasma shape, density profile, magnetic configuration, and experimental setup of TJ-II are included to determine the plasma regimes in which accurate information may be obtained.
Least-squares fit analysis program for the evaluation of spatially resolved x-ray spectra from tokamak plasmas
Authors: Mastrovito D. , Bitter M. , Hill K. W. , Gu M. F.
Published: October 2004

A least-squares fit analysis program is being developed for the study of spatially resolved x-ray spectra from tokamak plasmas. The program, written in interactive data language, can handle analysis of spectra from multiple sightlines through the plasma and compare the experimental data with a least-square fit of synthetic spectra, which are constructed from atomic modeling codes. The input parameters such as shot numbers, time groups, spatial range, spectral lines to fit and fitting parameters can be entered interactively through a graphical user interface or automatically via a script. The output consists of graphical presentations of the obtained spectral fits and fit parameter profiles as a function of time, including ion and electron temperature profiles, which are of particular interest. Output can also be sent to any open database connectivity compliant database. The features of the program are demonstrated with the analysis of the spectra of helium-like ArXVII, which were obtained with a new x-ray imaging crystal spectrometer.
Use of fast scopes to enable Thomson scattering measurement in presence of fluctuating plasma light
Authors: McLean H. S. , Moller J. , Hill D. N.
Published: October 2004

The addition of inexpensive high-speed oscilloscopes has enabled higher Te Thomson scattering measurements on the Sustained Spheromak Physics Experiment. Along with signal correlation techniques, the scopes allow analyses based on the shape of the scattered laser pulse to discriminate against fluctuating background plasma light that often make gated-integrator measurements unreliable. A 1.4 J Nd:YAG laser at 1064 nm is the scattering source. Spatial locations are coupled by viewing optics and fibers to four-wavelength-channel filter polychrometers. Ratios between the channels determine Te while summations of the channels determine density. Typically, the channel that provides a scattered signal at higher Te is contaminated by fluctuating background light. Individual channels are correlated with either a modeled representation of the laser pulse or a noise-free scattered laser light signal to extract channel amplitudes.
Full-wave simulations on ultrashort-pulse reflectometry for helical plasmas
Authors: Hojo H. , Fukuchi A. , Itakura A. , Mase A.
Published: October 2004

The full-wave simulations on ultrashort-pulse reflectometry for helical plasmas are studied based on the FDTD method in two dimensions. The propagation of an ultrashort-pulse electromagnetic wave is computed in helical plasmas modeled for the Large Helical Device magnetic field configuration. The density-profile reconstruction is performed by the Abel inversion method with the time delay data for the reflected waves from plasma, and it is shown that the reconstructed density profile coincides well with the original profile.
Interaction between the GAGA factor and Mod(mdg4) proteins promotes insulator bypass in
Drosophila
Authors: Melnikova Larisa , Juge François , Gruzdeva Natalia , Mazur Aleksandr , Cavalli Giacomo , Georgiev Pavel
Published: October 2004

Chromatin insulators or boundaries are proposed to structure the chromatin fiber into functionally independent domains by promoting the formation of chromatin loops. These elements can block the communication between an enhancer and a gene when placed between them. Interestingly, it has been previously observed that two tandem copies of the
Drosophila
Su(Hw) insulator abolish this enhancer-blocking activity, presumably through pairing. This bypass effect has not been described with other insulators, however. In this report, we show that the insertion of binding sites for the GAGA factor (GAF) between an enhancer and the Su(Hw) insulator allows bypassing of the insulator. This bypass relies on the activity of both the GAF protein and the Mod(mdg4)-67.2 protein, a factor required for Su(Hw) insulator activity. We show that these two proteins interact
in vitro
and
in vivo
, providing molecular evidence of pairing between the GAF sites and the Su(Hw) insulator. Finally, we show that placing the
Mcp
boundary together with the Su(Hw) insulator between an enhancer and a promoter leads to bypass, again in a GAF- and Mod(mdg4)-dependent manner. Our data provide direct evidence that heterologous insulators can be bypassed by distal enhancers and identify the interaction between GAF and Mod(mdg4) as a possible means to regulate insulator activity.
Using fluorescent sensors to detect botulinum neurotoxin activity
in vitro
and in living cells
Authors: Dong Min , Tepp William H. , Johnson Eric A. , Chapman Edwin R.
Published: October 2004

Botulinum neurotoxins (BoNTs) act as zinc-dependent endopeptidases that cleave proteins required for neurotransmitter release. To detect toxin activity, fragments of the toxin substrate proteins, synaptobrevin (Syb) or synaptosome-associated protein of 25 kDa (SNAP-25), were used to link cyan fluorescent protein (CFP) to yellow fluorescent protein (YFP). Cleavage of these fusion proteins by BoNTs abolished fluorescence resonance energy transfer between the CFP and YFP, providing a sensitive means to detect toxin activity in real-time
in vitro
. Furthermore, using full-length SNAP-25 and Syb as the linkers, we report two fluorescent biosensors that can detect toxin activity within living cells. Cleavage of the SNAP-25 fusion protein abolished fluorescence resonance energy transfer between CFP and YFP, and cleavage of Syb resulted in spatial redistribution of YFP fluorescence in cells. This approach provides a means to carry out cell-based screening of toxin inhibitors and to study toxin activity in situ. By using these biosensors, we found that the subcellular localizations of SNAP-25 and Syb are critical for efficient cleavage by BoNT/A and B, respectively.
Conditional mutagenesis using site-specific recombination in
Plasmodium berghei
Authors: Carvalho Teresa Gil , Thiberge Sabine , Sakamoto Hiroshi , Ménard Robert
Published: October 2004

Reverse genetics in
Plasmodium
, the genus of parasites that cause malaria, still faces major limitations. Only red blood cell stages of this haploid parasite can be transfected. Consequently, the function of many essential genes in these and subsequent stages, including those encoding vaccine candidates, cannot be addressed genetically. Here, we establish conditional mutagenesis in
Plasmodium
by using site-specific recombination and the
Flp
/
FRT
system of yeast. Site-specific recombination is induced after cross-fertilization in the mosquito vector of two clones containing either the target sequence flanked by two
FRT
sites or the Flp recombinase. Parasites that have undergone recombination are recognized in the cross progeny through the expression of a fluorescence marker. This approach should permit to dissect the function of any essential gene of
Plasmodium
during the haploid phase of its life, i.e., during infection of salivary glands in the mosquito and infection of both the liver and red blood cells in the mammal.
Sparsely populated folding intermediates of the Fyn SH3 domain: Matching native-centric essential dynamics and experiment
Authors: Ollerenshaw Jason E. , Kaya Hüseyin , Chan Hue Sun , Kay Lewis E.
Published: October 2004

A complete description of how a protein folds requires the characterization of intermediate conformations traversed during the folding transition. We have calculated dynamics trajectories of a simplified model of the Fyn SH3 domain with a native-centric potential energy function. Analysis of the resulting site-resolved energy trajectory identifies an ensemble of intermediate conformations for folding and another for unfolding. The model's folding intermediate is structured in the three β-strands that make up the protein's core and is strikingly similar to intermediates detected in a recent NMR study of Fyn SH3 folding and to folding transition states elucidated in mutagenesis studies of SH3 domains. The unfolding intermediate is formed by dissociation of the folded protein's two terminal β-strands from its core. The presence of such an intermediate is consistent with the results of a protein-engineering study on the src SH3 domain showing that these strands separate before the rate-limiting step of unfolding. Despite the presence of these conformations intermediate between the native and fully unfolded states, the computed heat capacity vs. temperature profile of the model protein indicates that its thermodynamics satisfies the usual calorimetric criterion for two-state folding. This observation highlights the fact that, if not properly interpreted, methods such as calorimetry that do not probe multiple sites in a molecule can lead to an oversimplified view of folding. The close agreement between results from this simplified model and experimental work underscores the important contributions that computational methods can make in providing insights into protein folding.
Aqueous urea solution destabilizes Aβ16–22oligomers
Authors: Klimov D. K. , Straub John E. , Thirumalai D.
Published: October 2004

We use long multiple trajectories generated by molecular dynamics simulations to probe the stability of oligomers of Aβ16–22(KLVFFAE) peptides in aqueous urea solution. High concentration of urea promotes the formation of β-strand structures in Aβ16–22monomers, whereas in water they adopt largely compact random coil structures. The tripeptide system, which forms stable antiparallel β-sheet structure in water, is destabilized in urea solution. The enhancement of β-strand content in the monomers and the disruption of oligomeric structure occur largely by direct interaction of urea with the peptide backbone. Our simulations suggest that the oligomer unbinding dynamics is determined by two opposing effects, namely, by the increased propensity of monomers to form β-strands and the rapid disruption of the oligomers. The qualitative conclusions are affirmed by using two urea models. Because the proposed destabilization mechanism depends largely on hydrogen bond formation between urea and the peptide backbone, we predict that high urea concentration will destabilize oligomers of other amyloidogenic peptides as well.
Phosphatidylinositol (4,5) bisphosphate regulates HIV-1 Gag targeting to the plasma membrane
Authors: Ono Akira , Ablan Sherimay D. , Lockett Stephen J. , Nagashima Kunio , Freed Eric O.
Published: October 2004

A critical early event in the HIV type 1 (HIV-1) particle assembly pathway is the targeting of the Gag protein to the site of virus assembly. In many cell types, assembly takes place predominantly at the plasma membrane. Cellular factors that regulate Gag targeting remain undefined. The phosphoinositide phosphatidylinositol (4,5) bisphosphate [PI(4,5)P
2
] controls the plasma membrane localization of a number of cellular proteins. To explore the possibility that this lipid may be involved in Gag targeting and virus particle production, we overexpressed phosphoinositide 5-phosphatase IV, an enzyme that depletes cellular PI(4,5)P
2
, or overexpressed a constitutively active form of Arf6 (Arf6/Q67L), which induces the formation of PI(4,5)P
2
-enriched endosomal structures. Both approaches severely reduced virus production. Upon 5-phosphatase IV overexpression, Gag was no longer localized on the plasma membrane but instead was retargeted to late endosomes. Strikingly, in cells expressing Arf6/Q67L, Gag was redirected to the PI(4,5)P
2
-enriched vesicles and HIV-1 virions budded into these vesicles. These results demonstrate that PI(4,5)P
2
plays a key role in Gag targeting to the plasma membrane and thus serves as a cellular determinant of HIV-1 particle production.
Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterflyAstraptes fulgerator
Authors: Hebert Paul D. N. , Penton Erin H. , Burns John M. , Janzen Daniel H. , Hallwachs Winnie
Published: October 2004

Astraptes fulgerator, first described in 1775, is a common and widely distributed neotropical skipper butterfly (Lepidoptera: Hesperiidae). We combine 25 years of natural history observations in northwestern Costa Rica with morphological study and DNA barcoding of museum specimens to show thatA. fulgeratoris a complex of at least 10 species in this region. Largely sympatric, these taxa have mostly different caterpillar food plants, mostly distinctive caterpillars, and somewhat different ecosystem preferences but only subtly differing adults with no genitalic divergence. Our results add to the evidence that cryptic species are prevalent in tropical regions, a critical issue in efforts to document global species richness. They also illustrate the value of DNA barcoding, especially when coupled with traditional taxonomic tools, in disclosing hidden diversity.
Activation of naïve CD4 T cells by anti-CD3 reveals an important role for Fyn in Lck-mediated signaling
Authors: Sugie Katsuji , Jeon Myung-Shin , Grey Howard M.
Published: October 2004

Although there was no impairment in IL-2 secretion and proliferation of Fyn-deficient naïve CD4 cells after stimulation with antigen and antigen-presenting cells, stimulation of these cells with anti-CD3 and anti-CD28 revealed profound defects. Crosslinking of purified wild-type naïve CD4 cells with anti-CD3 activated Lck and initiated the signaling cascade downstream of Lck, including phosphorylation of ZAP-70, LAT, and PLC-γ1; calcium flux; and dephosphorylation and nuclear translocation of the nuclear factor of activated T cells (NFAT)p. All of these signaling events were diminished severely in Fyn-deficient naïve cells activated by CD3 crosslinking. Coaggregation of CD3 and CD4 reconstituted this Lck-dependent signaling pathway in Fyn-/-T cells. These results suggest that when signaling of naïve T cells is restricted to the T cell antigen receptor, Fyn plays an essential role by positive regulation of Lck activity.
Paracellular Cl
-
permeability is regulated by WNK4 kinase: Insight into normal physiology and hypertension
Authors: Kahle Kristopher T. , MacGregor Gordon G. , Wilson Frederick H. , Van Hoek Alfred N. , Brown Dennis , Ardito Thomas , Kashgarian Michael , Giebisch Gerhard , Hebert Steven C. , Boulpaep Emile L. , Lifton Richard P.
Published: October 2004

Paracellular ion flux across epithelia occurs through selective and regulated pores in tight junctions; this process is poorly understood. Mutations in the kinase WNK4 cause pseudohypoaldosteronism type II (PHAII), a disease featuring hypertension and hyperkalemia. Whereas WNK4 is known to regulate several transcellular transporters and channels involved in NaCl and K
+
homeostasis, its localization to tight junctions suggests it might also regulate paracellular flux. We performed electrophysiology on mammalian kidney epithelia with inducible expression of various WNK4 constructs. Induction of wild-type WNK4 reduced transepithelial resistance by increasing absolute chloride permeability. PHAII-mutant WNK4 produced markedly larger effects, whereas kinase-mutant WNK4 had no effect. The electrochemical and pharmacologic properties of these effects indicate they are attributable to the paracellular pathway. The effects of WNK4 persist when induction is delayed until after tight-junction formation, demonstrating a dynamic effect. WNK4 did not alter the flux of uncharged solutes, or the expression or localization of selected tight-junction proteins. Transmission and freeze-fracture electron microscopy showed no effect of WNK4 on tight-junction structure. These findings implicate WNK signaling in the coordination of transcellular and paracellular flux to achieve NaCl and K
+
homeostasis, explain PHAII pathophysiology, and suggest that modifiers of WNK signaling may be potent antihypertensive agents.
Reverse transcriptase and endonuclease activities encoded by
Penelope
-like retroelements
Authors: Pyatkov Konstantin I. , Arkhipova Irina R. , Malkova Natalia V. , Finnegan David J. , Evgen'ev Michael B.
Published: October 2004

Penelope
-like elements are a class of retroelement that have now been identified in >50 species belonging to at least 10 animal phyla. The
Penelope
element isolated from
Drosophila virilis
is the only transpositionally active representative of this class isolated so far. The single ORF of
Penelope
and its relatives contains regions homologous to a reverse transcriptase of atypical structure and to the GIY-YIG, or Uri, an endonuclease (EN) domain not previously found in retroelements. We have expressed the single ORF of
Penelope
in a baculovirus expression system and have shown that it encodes a polyprotein with reverse transcriptase activity that requires divalent cations (Mn
2+
and Mg
2+
). We have also expressed and purified the EN domain in
Escherichia coli
and have demonstrated that it has EN activity
in vitro
. Mutations in the conserved residues of the EN catalytic module abolish its nicking activity, whereas the DNA-binding properties of the mutant proteins remain unaffected. Only one strand of the target sequence is cleaved, and there is a certain degree of cleavage specificity. We propose that the
Penelope
EN cleaves the target DNA during transposition, generating a primer for reverse transcription. Our results show that an active Uri EN has been adopted by a retrotransposon.
Double-knockout mice for α- and β-synucleins: Effect on synaptic functions
Authors: Chandra Sreeganga , Fornai Francesco , Kwon Hyung-Bae , Yazdani Umar , Atasoy Deniz , Liu Xinran , Hammer Robert E. , Battaglia Giuseppe , German Dwight C. , Castillo Pablo E. , Südhof Thomas C.
Published: October 2004

An abundant presynaptic protein, α-synuclein, is centrally involved in the pathogenesis of Parkinson's disease. However, conflicting data exist about the normal function of α-synuclein, possibly because α-synuclein is redundant with the very similar β-synuclein. To investigate the functions of synucleins systematically, we have now generated single- and double-knockout (KO) mice that lack α- and/or β-synuclein. We find that deletion of synucleins in mice does not impair basic brain functions or survival. We detected no significant changes in the ultrastructure of synuclein-deficient synapses, in short- or long-term synaptic plasticity, or in the pool size or replenishment of recycling synaptic vesicles. However, protein quantitations revealed that KO of synucleins caused selective changes in two small synaptic signaling proteins, complexins and 14-3-3 proteins. Moreover, we found that dopamine levels in the brains of double-KO but not single-KO mice were decreased by ≈20%. In contrast, serotonin levels were unchanged, and dopamine uptake and release from isolated nerve terminals were normal. These results show that synucleins are not essential components of the basic machinery for neurotransmitter release but may contribute to the long-term regulation and/or maintenance of presynaptic function.