bluuebunny/crossref_metadata_2025 huggingface dataset:
Observations of fast anisotropic ion heating, ion cooling, and ion recycling in large-amplitude drift waves
Authors: Sanders S. J. , Bellan P. M. , Stern R. A.
Published: July 2002

Large-amplitude drift wave fluctuations are observed to cause severe ion temperature oscillations in plasmas of the Caltech Encore tokamak [J. M. McChesney, P. M. Bellan, and R. A. Stern, Phys. Fluids B 3, 3370 (1991)]. Experimental investigations of the complete ion dynamical behavior in these waves are presented. The wave electric field excites stochastic ion orbits in the plane normal (⊥) to B, resulting in rapid ⊥ heating. Ion–ion collisions impart energy along (∥) B, relaxing the ⊥-∥ temperature anisotropy. Hot ions with large orbit radii escape confinement, reaching the chamber wall and cooling the distribution. Cold ions from the plasma edge convect back into the plasma (i.e., recycle), causing further cooling and significantly replenishing the density depleted by orbit losses. The ion–ion collision period τii∼T3/2/n fluctuates strongly with the drift wave phase, due to intense (≈50%) fluctuations in n and T. Evidence for particle recycling is given by observations of bimodal ion velocity distributions near the plasma edge, indicating the presence of cold ions (0.4 eV) superposed atop the hot (4–8 eV) plasma background. These appear periodically, synchronous with the drift wave phase at which ion fluid flow from the wall toward the plasma center peaks. Evidence is presented that such a periodic heat/loss/recycle/cool process is expected in plasmas with strong stochastic heating.
Nonlinear dynamics of electromagnetic turbulence in a nonuniform magnetized plasma
Authors: Shukla P. K. , Mirza Arshad M. , Faria R. T.
Published: July 2002

By using the hydrodynamic electron response with fixed (kinetic) ions along with Poisson’s equation as well as Ampère’s law, a system of nonlinear equations for low-frequency (in comparison with the electron gyrofrequency) long-(short-) wavelength electromagnetic waves in a nonuniform resistive magnetoplasma has been derived. The plasma contains equilibrium density gradient and sheared equilibrium plasma flows. In the linear limit, local dispersion relations are obtained and analyzed. It is found that sheared equilibrium flows can cause instability of Alfvén-like electromagnetic waves even in the absence of a density gradient. Furthermore, it is shown that possible stationary solutions of the nonlinear equations without dissipation can be represented in the form of various types of vortices. On the other hand, the temporal behavior of our nonlinear dissipative systems without the equilibrium density inhomogeneity can be described by the generalized Lorenz equations which admit chaotic trajectories. The density inhomogeneity may lead to even qualitative changes in the chaotic dynamics. The results of our investigation should be useful in understanding the linear and nonlinear properties of nonthermal electromagnetic waves in space and laboratory plasmas.
Analytical stability condition for the ideal m=n=1 kink mode in a toroidal plasma with elliptic cross section
Authors: Wahlberg C.
Published: July 2002

An analytical stability condition for the ideal kink mode with toroidal mode number n=1 and (dominating) poloidal mode number m=1 in a toroidal plasma with elliptic cross section in derived from a large aspect ratio expansion of the ideal magnetohydrodynamic equations. The ellipticity (e) is treated as a small parameter independent of the inverse aspect ratio (ε), and the expansion is performed up to order ε2e in the potential energy δW. It is found that the ellipticity has a strong, destabilizing effect on the kink mode in vertically elongated tokamaks, particularly when Δq=1−q0 is small (q0 is the safety factor at the magnetic axis), whereas an ellipticity of opposite sign (horizontal elongation) is stabilizing. By means of an additional expansion, in Δq, this effect is shown to be due to a Δq-independent term in δW proportional to the ellipticity and to the poloidal beta value (βp) at the q=1 surface. Since the leading order term in δW in the absence of ellipticity is of order Δq [Bussac et al., Phys. Rev. Lett. 35, 1638 (1975)], the ellipticity term dominates δW for sufficiently small values of Δq. The analytical result is in agreement with previous, numerical results [Lütjens et al., Nucl. Fusion 32, 1625 (1992)], and leads, already for rather moderately vertically elongated plasmas, to stability limits in βp much lower than the value 0.3 valid in the limit Δq→0 for a plasma with circular cross section.
About hysteresis phenomena in microwave’s plasmatrons
Authors: Petrin Andrei B.
Published: July 2002

A method for calculating the interaction of a microwave with a plane layer of magnetoactive low-pressure plasma is presented. In this paper, the plasma layer is situated between a plane dielectric layer and a plane metal screen. The calculation model contains the microwave energy balance, particle balance, and electron energy balance. The numerical calculations of the nonlinear interaction of the incident plane microwave and the plane plasma layer show that there are hysteresis phenomena when the external magnetic field and intensity of the incident microwave are changed. The cause of these hysteresis phenomena is considered. As a result of this investigation, the estimations for conditions of the plasma uniformity near the surface being worked in a real microwave plasmatron have been considered.
The energy injection into waves with a zero group velocity
Authors: Dieckmann M. E. , Chapman S. C. , Ynnerman A. , Rowlands G.
Published: July 2002

The frequency maxima of electron cyclotron harmonic (ECH) waves provide strong responses to sounding in various plasma regimes in the solar system. The frequency maxima correspond to waves for which the group velocity and thus the energy propagation velocity in the plasma frame of reference is zero. A particle-in-cell (PIC) code is employed to show that the propagation of wave energy at a non-zero velocity, necessary to couple energy from a stationary antenna to the plasma, is accomplished by propagating wave precursors. The undamped waves at the frequency maxima of the ECH branches are nonpropagating hence the waves remain localized. It is demonstrated that the nonpropagating waves, built up by the wave precursors, are standing waves. The standing wave generation is followed from the linear to nonlinear regimes. For nonlinear emission amplitudes the emission causes a plasma density depletion close to the antenna. The depletion is shown to trigger a modulational instability in which the ECH wave collapses. The generated nonlinear standing wave also develops an electromagnetic component which couples the electrostatic ECH waves to the fast extraordinary wave.
The interaction of stationary and moving objects with dusty plasmas
Authors: Thompson C. O. , D’Angelo N. , Merlino R. L.
Published: July 2002

The interaction of an electrically floating metal object with a dusty plasma formed in a dc discharge was investigated experimentally. Three cases were studied in which (a) the object was at rest in the dusty plasma, or was moved through the dusty plasma with a speed that was either (b) on the order of the dust-acoustic speed or (c) much faster than the dust-acoustic speed. When the object was at rest, a dust-free cavity with a boundary with a sharp dust density gradient was formed around the object. The size of the cavity was largely determined by shielding of the object by the plasma ions. A similar (although dynamic) behavior was observed in the moderate speed case (case b). When the object was moved very rapidly (case c) the dust grains did not have time to respond, and the object mechanically removed the grains, leaving behind a narrow channel which quickly filled in.
Anomalous propagation of planar shock wave in weakly ionized gas
Authors: Popovic S. , Vuskovic L.
Published: July 2002

Shock propagation velocity along the centerline of a cylindrical glow discharge has to be much higher in the cathode region than in the positive column in order to account for the measured propagation time. This is an outcome of detailed analysis of planar shock waves propagating along a cylindrical glow discharge [B. N. Ganguly, P. Bletzinger, and A. Garscadden, Phys. Lett. A 230, 218 (1997)]. The analysis was restricted to shock front propagation time to the two well-defined positions at the centerline where the motion can be considered one dimensional. Although there is not yet a comprehensive interpretation of the anomalous propagation velocity, it seems to increase wherever number density of excited states increases. Intensified local ionization due to excessive presence of excited states combined with the excitation of ion acoustic waves could be the mechanism for anomalous shock propagation velocity.
The Coulomb scattering effect on trapped particles bounce-resonance dissipation in magnetized toroidal plasmas
Authors: Nekrasov F. M. , Elfimov A. G. , de Azevedo C. A. , de Assis A. S.
Published: July 2002

The solution of the Vlasov equation with a simplified Fokker–Planck collision operator is presented for axially symmetric tokamak plasmas with a circular cross section of magnetic surfaces. The analytical expression for the parallel component of the dielectric permittivity tensor of trapped particles is obtained. This expression is used for theoretical analyses of the collision effect on the bounce-resonance wave dissipation. Conditions for a collisionless description of radio-frequency (rf) oscillations are found. This dielectric tensor components can be used for computer calculations of the rf field structure and the rf dissipated power related to trapped electrons in tokamak plasmas.
Model for relaxation oscillations in a helicon discharge
Authors: Degeling A. W. , Sheridan T. E. , Boswell R. W.
Published: July 2002

Relaxation oscillations observed in the large-volume, helicon plasma experiment WOMBAT (Waves on Magnetized Beams and Turbulence) [R. W. Boswell and R. K. Porteous, Appl. Phys. Lett. 50, 1130 (1987)] are modeled. These oscillations have a period of several milliseconds and have been identified as transitions between a low-density, inductive discharge and a high-density, helicon-wave discharge. In the model, it is assumed that the mode transitions are triggered by variations in the neutral density in the source region. The neutral density decreases due to ionization augmented by ion pumping and increases due to refilling of the source chamber from the much larger diffusion chamber. The system is modeled using two, coupled, nonlinear, ordinary differential equations that describe the neutral and plasma densities in the source chamber. Ionization by inductively-coupled fields and ionization due to electrons accelerated by helicon waves with phase velocities near the threshold electron velocity for ionization are considered. The model is found to reproduce experimentally measured variations of the plasma density and helicon wave phase velocity with rf power, neutral pressure and magnetic field. The negative impedance needed for the existence of a relaxation oscillation is provided by the helicon-wave coupling mechanism.
Collisionless dissipative nonlinear Alfvén waves: Nonlinear steepening, compressible turbulence, and particle trapping
Authors: Medvedev M. V.
Published: July 2002

The magnetic energy of nonlinear Alfvén waves in compressible plasmas may be ponderomotively coupled only to ion-acoustic quasi-modes, which modulate the wave phase velocity and cause wave-front steepening. In the collisionless plasma with β≠0, the dynamics of nonlinear Alfvén wave is also affected by the resonant particle–wave interactions. Upon relatively rapid evolution (compared to the particle bounce time), the quasi-stationary wave structures, identical to the so-called (Alfvénic) Rotational Discontinuities, form, the emergence and dynamics of which has not been previously understood. Collisionless (Landau) dissipation of nonlinear Alfvén waves is also a plausible and natural mechanism of the solar wind heating. Considering a strong, compressible, Alfvénic turbulence as an ensemble of randomly interacting Alfvénic discontinuities and nonlinear waves, it is shown that there exist two distinct phases of turbulence. What phase realizes depends on whether this collisionless damping is strong enough to provide adequate energy sink at all scales and, thus, to support a steady-state cascade of the wave energy. In long-time asymptotics, however, the particle distribution function is affected by the wave magnetic fields. In this regime of nonlinear Landau damping, resonant particles are trapped in the quasi-stationary Alfvénic discontinuities, giving rise to a formation of a plateau on the distribution function and quenching collisionless damping. Using the virial theorem for trapped particles, it is analytically demonstrated that their effect on the nonlinear dynamics of such discontinuities is nontrivial and forces a significant departure of the theory from the conventional paradigm.
Investigation of the turbulent equipartition establishment in tokamaks
Authors: Ivonin Igor A. , Pavlenko Vladimir P. , Persson Hans
Published: July 2002

For a moderate level of turbulence, the self-consistent nonuniform profiles of the turbulent equipartition (TEP) of the density and temperature distribution of magnetized electrons in a tokamak were found analytically and numerically. Only conservation of the adiabatic invariants of the electrons is needed for the solution of this problem. For passing electrons, the profile of the density is determined mainly by the flat radial dependence of the helicity (AB)(r), in contrast to the pinched profile ∼1/q of the trapped electrons determined by the safety factor q(r). The numerically obtained, combined profile of the electron density n∼1/q0.58 was found to be similar to a particular experimental scaling. Also, it was ascertained that the high pinching of the temperature profile is mainly determined by the heating of passing electrons in the potential energy well of the poloidal magnetic field, and depends on the βφ (ratio of the thermal energy to the magnetic one) value. Large values of βφ give small temperature pinching. The TEP distribution also gives one the possibility to obtain self-consistently the profile and the level of the turbulent fluctuations due to the development of quick kinetic instabilities associated with the TEP distribution. The estimation of the time of turbulent mixing of the electrons in the tokamak volume gives a realistic value of the order of 10 ms in the central part of tokamak and 0.1 s in the region near the separatrix.
A potential mechanism for the creation of reversed-magnetic-shear transport barriers in tokamaks
Authors: Throumoulopoulos G. N. , Pfirsch D.
Published: July 2002

The impact of reversed magnetic shear (s<0) along with a radial electric field Er on negative-energy perturbations (NEP’s) is investigated for the case of cylindrical tokamak-like equilibria. NEP’s can imply instabilities leading to anomalous transport [G. N. Throumoulopoulos and D. Pfirsch, Phys. Rev. E 56, 5979 (1997) and references therein]. For equilibria with Er corresponding to |eνφ|≪βTν and ην<4/3 (φ is the electrostatic potential, β≡8πP/B2, ην≡∂lnTν/∂lnNν and ν denotes the particle species) s<0 results in a reduction of the fraction of particles associated with NEP’s (active particles) as compared with equilibria with s>0, by making the pressure profile steeper. The reduction is stronger the closer the minimum of the safety factor (qmin) to the plasma center and the lower the negative value of s. For equilibria with |eνφ|≪βTν and ην>4/3 the fraction of active particles decreases as the magnetic tension Bθ2/r becomes larger. For Er<0 corresponding to |eνφ|≈βTν the electric field leads to a reduction of the fraction of active ions for ηi<4/3 and of the fraction of active electrons for ηe>4/3 in addition to that caused by s<0 and Bθ2/r, respectively. For Tν⩾|eνφ|≫βTν, which corresponds to experimental observations, the reduction of active particles caused by Er<0 is insensitive to the sign and the value of s, the position of qmin, and the value of Bθ2/r. In addition, it is shown that the experimentally evidenced facts that (a) s<0 is associated with a steepness of the pressure profile and (b) the position of qmin is displaced towards the plasma edge as the toroidal current is increased are consistent with equilibrium considerations. It is emphasized that these results cannot yet give a complete picture, since the present paper still neglects toroidal effects.
Improved operation of microsecond plasma opening switch by plasma source modification
Authors: Lisitsyn Igor V. , Kohno Susumu , Teramoto Yusuke , Katsuki Sunao , Akiyama Hidenori
Published: July 2002

The characteristics of a microsecond plasma opening switch have been improved by the modification of the plasma source. Conventional cable plasma guns have been used in the experiments, producing different directions of the plasma flow by changing the guns’ nozzles. The nozzles were arranged to provide the plasma flow, which is not exactly radial, but has an angle to the gun axis. The experiments with the modified plasma guns were carried out with the upstream, downstream, and azimuthally slanted plasma flow directions. The results are compared to a conventional radial flow plasma source. The plasma flow slanted in an angle of 30° downstream resulted in 50% improvement of the load current rise time and switch impedance. The obtained dependencies are explained in the frame of the snowplow model. Radial component of the plasma velocity at the end of the conduction phase is higher for downstream plasma flow. This results in a faster opening of the switch and is in good agreement with experimental data.
On the magnetohydrodynamics of a conducting fluid between two flat plates
Authors: Barnes G. , MacGregor K. B.
Published: July 2002

The time-dependent flow of a viscous, electrically conducting fluid contained within the space between two parallel, semi-infinite, perfectly conducting plates is considered. A uniform magnetic field directed perpendicular to the plate surfaces is assumed to pervade the fluid. Oscillatory motion of one of the plates in its own plane is induced through the application of a prescribed acceleration, the magnitude and direction of which vary sinusoidally in time. For a system forced in this manner, the resulting flow and transverse field component are solved for, as well as for the motion of the plate as a function of time. The magnetic and viscous stresses exerted on the boundary plate by the contiguous field and fluid are explicitly incorporated into the treatment of its motion. The physical properties and behavior of this system are investigated by examining analytic and numerical solutions obtained for a range of forcing periods, Reynolds numbers, and plate mass column densities. The relevance of these results to the interpretation of a model for Alfvénic torsional oscillations in the solar interior are discussed.
Spatio-temporal response of stochastic resonance in an excitable discharge plasma
Authors: Dinklage A. , Wilke C. , Klinger T.
Published: July 2002

Stochastic resonance is experimentally studied in a discharge plasma which is operated close to the threshold of ionization instability. It is shown that ionization wave-trains are excited by noise superimposed on the discharge current. There is a maximum signal-to-noise ratio at an optimum level of noise, indicating stochastic resonance. The corresponding spatio-temporal dynamics is investigated and it is shown that noise drives the stable discharge stochastically into the convectively unstable regime. This also reveals similarities to other physical system, for instance chemical waves.
Nonlinear thermal instability in two dimensions
Authors: Steele C. D. C. , Ibáñez S. M. H.
Published: July 2002

Nonlinear thermal disturbances are analyzed for a two-dimensional structure taking into account thermal conduction parallel to and perpendicular to the magnetic field, as well as heating and cooling effects. In general, small structures are linearly stable while larger ones are unstable. Heat conduction perpendicular to the field has a stabilizing effect and increases the maximum stable size of a structure. In many cases, the second-order growth rate is positive (enhancing heating but preventing cooling) for very large structures and is negative (opposite effect) otherwise. The perpendicular conduction causes a negative correction other than for the largest structures. This perpendicular conduction is particularly important for structures in the marginal linear state; strong cooling occurs in the absence of perpendicular conduction but if such conduction is included and is strong enough, catastrophic heating may occur. Perpendicular heat conduction is found to be most significant in long, thin, cool structures.
Mechanisms and control of beam halo formation in intense microwave sources and accelerators
Authors: Chen C. , Pakter R.
Published: July 2002

Halo formation and control in space-charge-dominated electron and ion beams are investigated in parameter regimes relevant to the development of high-power microwave (HPM) sources and high-intensity electron and ion linear accelerators. In particular, a mechanism for electron beam halo formation is identified in high-power periodic permanent magnet (PPM) focusing klystron amplifiers. It is found in self-consistent simulations that large-amplitude current oscillations induce mismatched beam envelope oscillations and electron beam halo formation. Qualitative agreement is found between simulations and the 50 MW 11.4 GHz PPM focusing klystron experiment at Stanford Linear Accelerator Center (SLAC) (D. Sprehn, G. Caryotakis, E. Jongewaard, and R. M. Phillips, “Periodic permanent magnetic development for linear collider X-band klystrons,” Proceedings of the XIXth International Linac Conference, Argonne National Laboratory Report ANL-98/28, 1998, p. 689). Moreover, a new class of cold-fluid corkscrewing elliptic beam equilibria is discovered for ultrahigh-brightness, space-charge dominated electron or ion beam propagation through a linear focusing channel consisting of uniform solenoidal magnetic focusing fields, periodic solenoidal magnetic focusing fields, and/or alternating-gradient quadrupole magnetic focusing fields in an arbitrary arrangement including field tapering. As an important application of such new cold-fluid corkscrewing elliptic beam equilibria, a technique is developed and demonstrated for controlling of halo formation and beam hollowing in a rms-matched ultrahigh-brightness ion beam as it is injected from an axisymmetric Pierce diode into an alternating-gradient magnetic quadrupole focusing channel.
Layer-by-layer sublimation observed by reflection high-energy electron diffraction intensity oscillation in a molecular beam epitaxy system
Authors: Kojima Takeshi , Kawai Naoyuki J. , Nakagawa Tadashi , Ohta Kimihiro , Sakamoto Tsunenori , Kawashima Mitsuo
Published: July 2002

Reflection high-energy electron diffraction (RHEED) intensity oscillation during sublimation of GaAs is observed at high substrate temperatures above 690 °C. This post-growth RHEED intensity oscillation suggests that the sublimation occurs layer by layer. One period of this oscillation precisely corresponds to sublimation of one monolayer. Aluminum arsenide acts as a sublimation stopper. The sublimation rate was measured accurately as a function of substrate temperature.
Interdiffusion in Si/Ge amorphous multilayer films
Authors: Prokes S. M. , Spaepen F.
Published: July 2002

Multilayered or compositionally modulated amorphous Si/amorphous Ge films with a repeat length of 5.83 nm have been fabricated using ion beam sputtering. The interdiffusion coefficient Dλ was determined by measuring the intensity of the x-ray satellite arising from the modulation as a function of annealing time. The interdiffusion was found to be relatively rapid, in that it could be measured easily without crystallization occurring. The temperature dependence in the range 550–630 K is described by Dλ=1.07 × 10−10 exp (−1.6 eV/kT) m2s−1.
Phase matching in symmetrical single-mode magneto-optic waveguides by application of stress
Authors: Dammann H. , Pross E. , Rabe G. , Tolksdorf W. , Zinke M.
Published: July 2002

Tuning of the propagation constant difference Δβ=βTM−βTE in single-mode symmetrical yttrium iron garnet (YIG) film waveguides over a range of 250°/cm by means of external stress is demonstrated. An a posteriori, precise setting of phase match Δβ→0, which is a precondition for nonreciprocal mode coupling type components, can be achieved by this method.
Work function reduction of a tungsten surface due to cesium ion bombardment
Authors: Tompa G. S. , Carr W. E. , Seidl M.
Published: July 2002

The reduction of the work function of a polycrystalline W surface due to Cs+ bombardment has been investigated in the incident energy range below 500 eV. Upon exposure of the surface to a Cs+ beam, the work function decreases until a steady state is reached with a total Cs+ dose of less than 1×1016 ions/cm2. A minimum steady state work function surface is produced at an incident energy of ≊40 eV and the steady state work function rapidly increases with bombarding energy. Coverages are significantly lower than that produced on Mo for the same bombarding energies. Auger electron spectroscopy is used to confirm surface coverages. The cesium surface concentration is determined by reflection, sputtering, and implantation.
Infrared spectroscopic evidence of silicon related hydrogen complexes in hydrogenated n-type GaAs doped with silicon
Authors: Jalil A. , Chevallier J. , Pesant J. C. , Mostefaoui R. , Pajot B. , Murawala P. , Azoulay R.
Published: July 2002

Infrared absorption spectroscopy has been performed on hydrogenated and deuterated n-type silicon-doped GaAs. It reveals the presence of a sharp vibrational mode at 890 cm−1 in hydrogenated samples and at 637 cm−1 in deuterated ones. These bands are absent in undoped GaAs. Analysis of the isotopic shift frequency reveals that the band is associated with a hydrogen–arsenic bond where arsenic is supposed to sit as a first nearest neighbor of the silicon donor atom giving rise to (SiAs3)As-H complexes. Isochronal annealing experiments show the direct correlation between the absorption line intensity and the amount of neutralized donors, confirming the view that the extra electrons of the silicon donors are involved in the hydrogen–arsenic bonds.
Plastic flow of borosilicate glass under bombardment with heavy ions
Authors: Klaumünzer S. , Li Changlin , Schumacher G.
Published: July 2002

Irradiation of borosilicate glass at temperatures between 80 and 150 K with a beam of 129Xe ions of 360 MeV produces macroscopically visible plastic flow without any cracks. With respect to this effect the brittle borosilicate glass behaves in the same way as ductile metallic glasses. Even the quantitative details are surprisingly comparable. It is suggested that ion-beam-induced plastic flow will occur virtually in every amorphous material.
Long-range order in InxGa1−xAs
Authors: Kuan T. S. , Wang W. I. , Wilkie E. L.
Published: July 2002

We have found by electron diffraction that In0.5Ga0.5As thin crystals, grown on InP substrates by molecular beam epitaxy along the 〈110〉 direction, exhibit a long-range order identical to those observed previously in the AlxGa1−xAs alloy system. In the ordered In0.5Ga0.5As structure, the 0, 0, 0 and 1/2, 1/2, 0 sites in each unit cell are preferentially occupied by Ga atoms, and the 1/2, 0, 1/2 and 0, 1/2, 1/2 sites are occupied by In atoms. Our diffraction results also indicate the presence of a high density of antiphase boundaries in the ordered In0.5Ga0.5As phase.
Realization of a quasi-three-dimensional modulation-doped semiconductor structure
Authors: Shayegan M. , Sajoto T. , Santos M. , Silvestre C.
Published: July 2002

We report the realization of a modulation-doped quasi-three-dimensional electron system. The structure consists of a 2000-Å-wide undoped AlxGa1−xAs well bounded by undoped (spacer) and doped layers of AlyGa1−yAs (y>x) on both sides. The alloy composition in the well (x) is varied quadratically so that the combined potentials due to the AlxGa1−xAs and the electric charge in the well produce a square potential well with a nearly uniform carrier density. Magnetotransport data reveal that the system contains ≂2.5×1011 cm−2 electrons, which occupy four electric subbands and have a low-temperature mobility in excess of 1×105 cm2/V s indicating the high quality of the structure.
Polygyny, mate-guarding, and posthumous fertilization as alternative male mating strategies
Authors: Zamudio Kelly R. , Sinervo Barry
Published: July 2002

Alternative male mating strategies within populations are thought
to be evolutionarily stable because different behaviors allow each male
type to successfully gain access to females. Although alternative male
strategies are widespread among animals, quantitative evidence for the
success of discrete male strategies is available for only a few
systems. We use nuclear microsatellites to estimate the paternity rates
of three male lizard strategies previously modeled as a
rock-paper-scissors game. Each strategy has strengths that allow it to
outcompete one morph, and weaknesses that leave it vulnerable to the
strategy of another. Blue-throated males mate-guard their females and
avoid cuckoldry by yellow-throated “sneaker” males, but
mate-guarding is ineffective against aggressive orange-throated
neighbors. The ultradominant orange-throated males are highly
polygynous and maintain large territories; they overpower blue-throated
neighbors and cosire offspring with their females, but are often
cuckolded by yellow-throated males. Finally, yellow-throated sneaker
males sire offspring via secretive copulations and often share
paternity of offspring within a female's clutch. Sneaker males sire
more offspring posthumously, indicating that sperm competition may be
an important component of their strategy.
Formation of transitory intrachain and interchain disulfide bonds accompanies the folding and oligomerization of simian virus 40 Vp1 in the cytoplasm
Authors: Li Peggy P. , Nakanishi Akira , Clark Sean W. , Kasamatsu Harumi
Published: July 2002

Pentamer formation by Vp1, the major capsid protein of simian virus 40, requires an interdigitation of structural elements from the Vp1 monomers [Liddington, R. C., Yan, Y., Moulai, J., Sahli, R., Benjamin, T. L. & Harrison, S. C. (1991)
Nature (London)
354, 278–284]. Our analyses reveal that disulfide-linked Vp1 homooligomers are present in the simian virus 40-infected cytoplasm and that they are derived from a 41-kDa monomeric intermediate containing an intrachain disulfide bond(s). The 41-kDa species, emerging within 5 min of pulse labeling with [
35
S]methionine, is converted into a 45-kDa, disulfide-free Vp1 monomer and disulfide-bonded dimers through pentamers. The covalent oligomer formation is blocked in the presence of a sulfhydryl-modifying reagent. We propose that there are two stages in this Vp1 disulfide bonding. First, the newly synthesized Vp1 monomers acquire intrachain bonds as they fold and begin to interact. Next, these bonds are replaced with intermolecular bonds as the monomers assemble into pentamers. This sequential appearance of transitory disulfide bonds is consistent with a role for sulfhydryl–disulfide redox reactions in the coordinate folding of Vp1 chains into pentamers. The cytoplasmic Vp1 does not colocalize with marker proteins of the endoplasmic reticulum. This paper demonstrates
in vivo
disulfide formations and exchanges coupled to the folding and oligomerization of a mammalian protein in the cytoplasm, outside the secretory pathway. Such disulfide dynamics may be a general phenomenon for other cysteine-bearing mammalian proteins that fold in the cytoplasm.
Synergistic contributions of cyclin-dependant kinase 5/p35 and Reelin/Dab1 to the positioning of cortical neurons in the developing mouse brain
Authors: Ohshima Toshio , Ogawa Masaharu , Veeranna  , Hirasawa Motoyuki , Longenecker Glenn , Ishiguro Koichi , Pant Harish C. , Brady Roscoe O. , Kulkarni Ashok B. , Mikoshiba Katsuhiko
Published: July 2002

Cyclin-dependent kinase (Cdk) 5 is a unique member of the Cdk
family, because Cdk5 kinase activity is detected only in the nervous
tissue. Two neuron-specific activating subunits of Cdk5, p35 and p39,
have been identified. Overlapping expression pattern of these isoforms
in the embryonic mouse brain and the significant residual Cdk5 kinase
activity in brain homogenate of the p35−/− mice indicate the
redundant functions of the Cdk5 activators
in vivo
.
Severe neuronal migration defects in p35−/−Cdk5 +/− mice further
support the idea that the redundant expression of the Cdk5 activators
may cause a milder phenotype in p35−/− mice compared with
Cdk5−/− mice. Mutant mice lacking either Cdk5 or p35 exhibit
certain similarities with Reelin/Dab1-mutant mice in the
disorganization of cortical laminar structure in the brain. To
elucidate the relationship between Cdk5/p35 and Reelin/Dab1
signaling, we generated mouse lines that have combined defects of these
genes. The addition of heterozygosity of either Dab1 or Reelin mutation
to p35−/− causes the extensive migration defects of cortical
neurons in the cerebellum. In the double-null mice of p35 and either
Dab1 or Reelin, additional migration defects occur in the Purkinje
cells in the cerebellum and in the pyramidal neurons in the
hippocampus. These additional defects in neuronal migration in mice
lacking both Cdk5/p35 and Reelin/Dab1 indicate that Cdk5/p35 may
contribute synergistically to the positioning of the cortical neurons
in the developing mouse brain.
Biomechanical activation of vascular endothelium as a determinant of its functional phenotype
Authors: García-Cardeña Guillermo , Comander Jason , Anderson Keith R. , Blackman Brett R. , Gimbrone Michael A.
Published: July 2002

One of the striking features of vascular endothelium, the
single-cell-thick lining of the cardiovascular system, is its
phenotypic plasticity. Various pathophysiologic factors, such as
cytokines, growth factors, hormones, and metabolic products, can
modulate its functional phenotype in health and disease. In addition to
these humoral stimuli, endothelial cells respond to their biomechanical
environment, although the functional implications of this biomechanical
paradigm of activation have not been fully explored. Here we describe a
high-throughput genomic analysis of modulation of gene expression
observed in cultured human endothelial cells exposed to two well
defined biomechanical stimuli—a steady laminar shear stress and a
turbulent shear stress of equivalent spatial and temporal average
intensity. Comparison of the transcriptional activity of 11,397 unique
genes revealed distinctive patterns of up- and down-regulation
associated with each type of stimulus. Cluster analyses of
transcriptional profiling data were coupled with other molecular and
cell biological techniques to examine whether these global patterns of
biomechanical activation are translated into distinct functional
phenotypes. Confocal immunofluorescence microscopy of structural and
contractile proteins revealed the formation of a complex apical
cytoskeleton in response to laminar shear stress. Cell cycle analysis
documented different effects of laminar and turbulent shear stresses on
cell proliferation. Thus, endothelial cells have the capacity to
discriminate among specific biomechanical forces and to translate these
input stimuli into distinctive phenotypes. The demonstration that
hemodynamically derived stimuli can be strong modulators of
endothelial gene expression has important implications for our
understanding of the mechanisms of vascular homeostasis and
atherogenesis.
Thymocyte-targeted overexpression of
xiap
transgene disrupts T lymphoid apoptosis and maturation
Authors: Conte Damiano , Liston Peter , Wong James W. , Wright Kathryn E. , Korneluk Robert G.
Published: July 2002

The X-linked inhibitor of apoptosis (XIAP) and other
members of the inhibitor of apoptosis (IAP) family can suppress
apoptosis induced by a diverse variety of triggers. Functional
studies done to date have focused on tissue culture models and
adenovirus overexpression of XIAP and other IAP proteins. Here we
report the phenotype of an engineered transgenic mouse overexpressing a
human IAP, as well as assessing the long-term consequence of IAP
overexpression. We document the relative protein expression levels of
the endogenous mouse homologue to XIAP, mouse inhibitor of
apoptosis (MIAP 3), within thymocyte and T cell subpopulations.
The consequence of lymphoid-targeted overexpression of XIAP in
transgenic mice suggests a physiological role for the
endogenous protein, MIAP3.
Xiap
-transgenic
mice accumulated thymocytes and/or T cells in primary and secondary
lymphoid tissue, T cell maturation was perturbed, and transgenic
thymocytes resisted a variety of apoptotic triggers both
in vitro
and
in vivo
. These observations
imply a possible key function for the intrinsic cellular inhibitor XIAP
in maintaining the homeostasis of the immune system.
brakeless
is required for photoreceptor growth-cone targeting in
Drosophila
Authors: Rao Yong , Pang Peng , Ruan Wenjing , Gunning Dorian , Zipursky S. Lawrence
Published: July 2002

The R1-R6 subclass of photoreceptor neurons (R cells) in the
Drosophila
compound eye form specific connections with targets in the optic ganglia. In this paper, we report the identification of a gene,
brakeless
(
bks
), that is essential for R1-R6 growth cone targeting. In
brakeless
mutants, R1-R6 growth cones frequently fail to terminate migration in their normal target, the lamina, and instead project through it and terminate in the second optic ganglion, the medulla. Genetic mosaic analysis and transgene rescue experiments indicate that
bks
functions in R cells and not within the lamina target region.
bks
encodes a nuclear protein. We propose that it participates in a gene expression pathway regulating one or more growth cone components controlling R1-R6 targeting.
A role of transcriptional activators as antirepressors for the autoinhibitory activity of TATA box binding of transcription factor IID
Authors: Kotani Tomohiro , Banno Ken-ichi , Ikura Mitsuhiko , Hinnebusch Alan G. , Nakatani Yoshihiro , Kawaichi Masashi , Kokubo Tetsuro
Published: July 2002

The TATA box-binding activity of transcription factor IID (TFIID) is autoinhibited by the N-terminal domain of the
Drosophila
TATA box-binding protein- (TBP) associated factor 230/yeast TBP-associated factor 145 subunit, which binds to the TATA box-binding domain of TBP by mimicking the TATA box structure. Here, we propose a mechanism of transcriptional activation that involves antirepression of this autoinhibitory activity by transcriptional activators. Like the autoinhibitory domain of TFIID, various acidic activators interact with the TATA box-binding domain of TBP. Moreover, the autoinhibitory domain of TFIID, which is known to interact with only the TATA box-binding domain of TBP, acts as an activation domain when fused to the GAL4 DNA-binding domain, indicating that interaction with the TATA-binding domain of TBP is crucial for activation of transcription. In a reciprocal fashion, the acidic activation domains can function as the autoinhibitory domain when the latter is replaced by the former within TFIID. These results indicate that activation domains and the autoinhibitory domain of TFIID are interchangeable, supporting a role for transcriptional activators as antirepressors of the autoinhibitory activity of the TATA box binding of TFIID.
The molecular basis of vancomycin resistance in clinically relevant
Enterococci:
Crystal structure of
d
-alanyl-
d
-lactate ligase (VanA)
Authors: Roper David I. , Huyton Trevor , Vagin Alexei , Dodson Guy
Published: July 2002

d
-alanine-
d
-lactate ligase from
Enterococcus faecium
BM4147 is directly responsible for the biosynthesis of alternate cell-wall precursors in bacteria, which are resistant to the glycopeptide antibiotic vancomycin. The crystal structure has been determined with data extending to 2.5-Å resolution. This structure shows that the active site has unexpected interactions and is distinct from previous models for
d
-alanyl-
d
-lactate ligase mechanistic studies. It appears that the preference of the enzyme for lactate as a ligand over
d
-alanine could be mediated by electrostatic effects and/or a hydrogen-bonding network, which principally involve His-244. The structure of
d
-alanyl-
d
-lactate ligase provides a revised interpretation of the molecular events that lead to vancomycin resistance.
Inhibition of IL-2-induced Jak-STAT signaling by glucocorticoids
Authors: Bianchi Marina , Meng Charis , Ivashkiv Lionel B.
Published: July 2002

Glucocorticoids (GCs) are potent anti-inflammatory agents that block cytokine production. We investigated whether GCs also block cytokine signaling via the Janus kinase (Jak)-signal transducer and activator of transcription (STAT) pathway. Dexamethasone inhibited IL-2-induced DNA binding, tyrosine phosphorylation, and nuclear translocation of Stat5 in primary T cells. Inhibition of Stat5 correlated with inhibition of expression of IL-2-inducible genes and T cell proliferation. The mechanism of inhibition involved suppression of IL-2 receptor and Jak3 expression. Signaling by IL-4, IL-7, and IL-15, which use IL-2 receptor components, also was inhibited, indicating a block in T cell responses similar to that seen in immunodeficient patients lacking the IL-2 receptor gamma chain or Jak3. IL-2 signaling also was blocked in patients after treatment with GCs, suggesting that inhibition of cytokine signaling contributes to the clinical efficacy of these agents. These results identify inhibition of Jak-STAT signaling by IL-2 and related cytokines as a novel mechanism of GC action and suggest that inhibition of both cytokine production and signaling contribute to their therapeutic potency.
Furin inhibition results in absent or decreased invasiveness and tumorigenicity of human cancer cells
Authors: Bassi Daniel E. , Lopez De Cicco Ricardo , Mahloogi Haleh , Zucker Stanley , Thomas Gary , Klein-Szanto Andres J. P.
Published: July 2002

Pro-protein convertases such as furin are expressed in many human tumor lines and primary tumors. Furin processes stromelysin-3, membrane type 1 matrix metalloproteinase (MMPs) involved in tumor cell invasiveness, as well as growth factors such as transforming growth factor β1. Evaluation of furin expression in head and neck squamous cell carcinoma (HNSCC) cells exhibiting different invasive ability showed that furin overexpression correlated with their respective invasiveness. The use of a selective furin inhibitor, alpha 1-PDX (PDX) was studied in three furin-expressing invasive HNSCC cell lines. The effects of PDX transfection were evaluated
in vivo
and
in vitro
to determine changes in the malignant phenotype. Transfection of HNSCC cell lines with PDX resulted in significant decrease or absence of tumorigenicity after s.c. inoculation into severe combined immunodeficient mice. Likewise,
in vitro
invasiveness was reduced ≈50%. The
in vivo
invasion assay using tracheal xenotransplants showed even more drastic reductions of the invasive ability of PDX-transfected cells (up to an 80% decrease). PDX-transfected cells did not invade or penetrated less into the tracheal wall tissues than their vector alone-transfected counterparts. In addition, the former cells showed a remarkable decrease in MMP-2 processing and activity. After PDX transfection the cells were less efficient in processing the tumor progression-associated furin substrates transforming growth factor β1 and pro-membrane type 1-MMP. These findings indicate that furin inhibition is a feasible approach to attenuate and even abolish certain critical attributes of the advanced malignant phenotype. Thus, furin should be considered as a promising target for cancer therapy.
Structure of the interferon-receptor complex determined by distance constraints from double-mutant cycles and flexible docking
Authors: Roisman Laila C. , Piehler Jacob , Trosset Jean-Yves , Scheraga Harold A. , Schreiber Gideon
Published: July 2002

The pleiotropic activity of type I interferons has been attributed to the specific interaction of IFN with the cell-surface receptor components ifnar1 and ifnar2. To date, the structure of IFN has been solved, but not that of the receptor or the complex. In this study, the structure of the IFN-α2–ifnar2 complex was generated with a docking procedure, using nuclear Overhauser effect-like distance constraints obtained from double-mutant cycle experiments. The interaction free energy between 13 residues of the ligand and 11 of the receptor was measured by double-mutant cycles. Of the 100 pairwise interactions probed, five pairs of residues were found to interact. These five interactions were incorporated as distance constraints into the flexible docking programprodockby using fixed and movable energy-gradient grids attached to the receptor and ligand, respectively. Multistart minimization and Monte Carlo minimization docking of IFN-α2 onto ifnar2 converged to a well-defined average structure, with the five distance constraints being satisfied. Furthermore, no structural artifacts or intraloop energy strain were observed. The mutual binding sites on IFN-α2 and ifnar2 predicted from the model showed an almost complete superposition with the ones determined from mutagenesis studies. Based on this structure, differences in IFN-α2 versus IFN-β binding are discussed.
Engineering salt-tolerantBrassicaplants: Characterization of yield and seed oil quality in transgenic plants with increased vacuolar sodium accumulation
Authors: Zhang Hong-Xia , Hodson Joanna N. , Williams John P. , Blumwald Eduardo
Published: July 2002

TransgenicBrassica napusplants overexpressingAtNHX1,a vacuolar Na+/H+antiport fromArabidopsis thaliana,were able to grow, flower, and produce seeds in the presence of 200 mM sodium chloride. Although the transgenic plants grown in high salinity accumulated sodium up to 6% of their dry weight, growth of the these plants was only marginally affected by the high salt concentration. Moreover, seed yields and the seed oil quality were not affected by the high salinity of the soil. Our results demonstrate the potential use of these transgenic plants for agricultural use in saline soils. Our findings, showing that the modification of a single trait significantly improved the salinity tolerance of this crop plant, suggest that with a combination of breeding and transgenic plants it could be possible to produce salt-tolerant crops with far fewer target traits than had been anticipated.