bluuebunny/crossref_metadata_2025 huggingface dataset:
Simulation of magnetic phenomena driven by parallel ion motion
Authors: Thomas V. A. , Brecht Stephen H.
Published: July 2002

In this paper a one-dimensional Darwin quasineutral hybrid simulation code is used to investigate the large spatial scale (λ∼c/ωpi) low-frequency (ω∼ωci) collisionless evolution of a plasma slug of finite width traveling parallel to an ambient magnetic field in the presence of a uniform background plasma. Such a system may cause excitation of large amplitude magnetosonic waves and mixing of the background and slug ions. Under certain conditions, background ions and slug ions are driven upstream of the interaction region. Particular attention is paid to the width of the plasma slug, thermal effects, the anomalous resistivity, and the relative velocity of the two plasmas.
Resistive effects on the rigid mode ballooning instability
Authors: Kang B. K. , Lichtenberg A. J. , Nevins W. M.
Published: July 2002

From a set of fluid equations, a second-order differential equation, governing the resistive ballooning instability for a mirror confined plasma with a rigid perturbation, is obtained. The resistive effects on the rigid mode ballooning instability are numerically examined for three tandem mirror configurations; those stabilized by walls, by end cusps, and by end quadrupoles. In the model the pressure is taken to be isotropic and constant along the axis except in the cusps and the diverging field regions, and the plasma has a sharp boundary. The theoretical results indicate that the resistivity can play a major role in determining the growth rate for ballooning for lower temperature devices.
Damping of electron cyclotron waves in dense plasmas of a compact ignition tokamak
Authors: Mazzucato E. , Fidone I. , Granata G.
Published: July 2002

The absorption of electron cyclotron waves in hot and dense plasmas is investigated by using the relativistic dispersion relation with finite Larmor radius (FLR) corrections. It is shown that the strong reduction caused by FLR effects on the damping of extraordinary waves propagating perpendicularly to the magnetic field becomes insignificant at large values of the parallel component of the refractive index. An application of these results to the auxiliary heating of dense plasmas of a compact ignition tokamak [Plasma Physics and Controlled Nuclear Fusion 1986 (IAEA, Vienna, 1987), Vol. 3] is given. It is shown that the extraordinary mode with oblique propagation and frequency of 190 GHz can be strongly absorbed by dense plasmas with a toroidal magnetic field of 105 kG and a central electron density of 1×1015 cm−3.
A fluid theory of ion collection by probes in strong magnetic fields with plasma flow
Authors: Hutchinson I. H.
Published: July 2002

A one-dimensional fluid theory of Langmuir probe operation in strong magnetic fields is presented. Cross-field diffusion of ions both into and out of the the collection region is consistently accounted for, in effect taking momentum and particle diffusivity to be equal. The results differ by significant factors from previous analyses, which did not account for outward diffusion but in effect set momentum diffusivity to zero. The differences are especially large when parallel flow of the external plasma is present. It is thus clear that the value assumed for the momentum diffusivity strongly affects the interpretation of recent probe measurements. It is argued that the present results offer a more reliable basis for this interpretation.
Flows over rectangular weirs
Authors: Dias Frédéric , Keller Joseph B. , Vanden-Broeck Jean-Marc
Published: July 2002

Flows over rectangular weirs and the corresponding discharge coefficient Cp are calculated for weirs of various lengths and heights. The fluid is assumed to be incompressible, inviscid, and in irrotational motion in two dimensions with gravity acting. The nonlinear free-surface conditions are treated exactly. The resulting values of Cp are in good qualitative agreement, and in fair quantitative agreement, with experimentally determined values. Flows over thin weirs and over one triangular weir are also calculated, and a method for any polygonal weir is given.
Bubble competition in Rayleigh–Taylor instability
Authors: Zufiria Juan A.
Published: July 2002

The penetration of a front of light fluid into a heavy fluid in a Rayleigh–Taylor unstable flow is studied by using a model that simulates the competition among the bubbles formed in the interface when the density ratio of the two fluids is very large. Several different initial conditions have been considered, and it is found that the front moves with constant acceleration. The values obtained for the acceleration of the front are in very good agreement with experimental results obtained by Read [Physica D 12, 45 (1984)].
Instability of liquid coatings on cylindrical surfaces
Authors: Mashayek F. , Ashgriz N.
Published: July 2002

Capillary instability of long annular viscous liquid layers coating the surface of a cylindrical wire is studied. Effects of Reynolds number, Re, initial disturbance wave numbers, k, and wire radii, s on the growth rate of the instability are considered. The initial disturbance amplitude is chosen as 5% of the initial unperturbed liquid thickness. It is found that the growth rate of the disturbance amplitude is composed of a linear portion, which is well predicted by the linear theory, and a relatively flat portion, which is not predicted by the linear theory and is strongly dependent on the Re, k, and s. A unique feature of this instability is a double pinch-off process (in certain parameter range) which results in the formation of secondary satellite drops.
Stability of capillary–gravity interfacial waves between two bounded fluids
Authors: Christodoulides Paul , Dias Frédéric
Published: July 2002

Two-dimensional periodic capillary–gravity waves at the interface between two bounded fluids of different densities are considered. Based on a variational formulation, the relation between wave frequency and wave amplitude is obtained through a weakly nonlinear analysis. All classes of space-periodic waves are studied: traveling and standing waves as well as a degenerate class of mixed waves. As opposed to water waves, mixed interfacial waves exist even for pure gravity waves. The stability of traveling and standing waves with respect to three-dimensional modulations is then studied. By using the method of multiple scales, Davey–Stewartson-type equations are obtained. A detailed stability analysis is performed in three cases: pure gravity waves, capillary–gravity waves when one layer is infinitely deep, and capillary–gravity waves when both layers are infinitely deep. The main results for oblique (i.e., combined longitudinal and transverse) modulations reveal a mostly stabilizing effect of the density ratio for traveling waves and a destabilizing effect for standing waves.
Velocity fluctuations of a heavy sphere falling through a sedimenting suspension
Authors: Nicolai Hélène , Peysson Yannick , Guazzelli Élisabeth
Published: July 2002

The motion of a test sphere falling through an otherwise monodisperse suspension of different settling velocity has been examined experimentally. Marked test spheres of different sizes and densities were tracked in a monodisperse suspension of unmarked glass spheres, made optically transparent by matching the index of refraction of the suspending fluid to that of the glass spheres. The ratio, Rs, between the Stokes’ velocity of the test particle and that of an isolated sphere of the suspension was varied from 1 to 13 while the particle volume fraction of the suspension was kept constant at 20%. Statistical analyses of the velocities of the test sphere yield the mean settling velocities, the velocity fluctuations and the velocity autocorrelation functions. The long time motion of the test sphere is shown to be diffusive in nature. Correlation times and self-diffusivities are measured as a function of Rs. A change in the behavior of the motion of the test particle is observed for Rs≥5.
The instability of the separated shear layer from a bluff body
Authors: Prasad Anil , Williamson Charles H. K.
Published: July 2002

It has generally been assumed in previous studies that the normalized shear-layer frequency (fSL/fK) versus Reynolds number (Re) varies as Re0.5. There has also been a great deal of scatter in quoted values of the critical Reynolds number (Recrit) for the onset of the shear-layer instability, with values ranging from 350 to 3000. In the present work, we find that Recrit is strongly sensitive to the mode of primary vortex shedding and may vary between 1200–2600 depending on the angle of oblique shedding. In the case of the shear-layer frequency, we have conducted a careful reevaluation of all previous data in the literature, and find the relationship fSL/fK=0.0235×Re0.67. Surprisingly, not one of the previous studies yields a relationship that is close to Re0.5. We suggest an explanation for the variation Re0.67 based on simple physical grounds.
On the three-dimensional instabilities of plane flows subjected to Coriolis force
Authors: Leblanc Stéphane , Cambon Claude
Published: July 2002

Linear stability of two-dimensional flows in a frame rotating with angular velocity vector Ω=Ωez perpendicular to their plane is considered. Sufficient conditions for instability have been derived for simple inviscid flows, namely parallel shear flows (characterized by the “Pedley” or “Bradshaw-Richardson” number), circular vortices (by the “generalized Rayleigh” discriminant) and unbounded flows having a quadratic streamfunction (with elliptical, rectilinear or hyperbolic streamlines). These exact criteria are reviewed and contrasted using stability analysis for both three-dimensional disturbances and oversimplified “pressureless” versions of the linear theory. These suggest that one defines a general inviscid criterion for rotation and curvature, based on the sign of the second invariant of the “inertial tensor,” and stating that, in a Cartesian coordinate frame: a sufficient condition for instability is thatΦ(x,y)=−12S:S+14Wt⋅Wt<0 somewhere in the flow domain. It involves the “tilting vorticity” Wt=W+4Ω [Cambon et al., J. Fluid Mech. 278, 175 (1994)] and the symmetric part S of the velocity gradient of the basic flow.
Molten droplet deposition and solidification at low Weber numbers
Authors: Schiaffino Stefano , Sonin Ain A.
Published: July 2002

Low Weber number deposition of small molten droplets on cold targets is of importance in certain dropwise buildup processes, but at this time, critical elements are absent from our theoretical understanding of the deposition process, and prediction from basic principles is not possible. This paper lays down a framework for understanding low Weber number deposition in terms of similarity laws and experimentation. Based on experiments from the highly viscous limit to the inertia-dominated limit, correlations are given for the spreading velocity, spreading time scales, post-spreading oscillation amplitudes, and oscillation damping time scales. Molten droplets are arrested, and their final solid shape determined, by contact line freezing. In homologous deposition, where the drop and the target are of the same material, the spreading factor is determined principally by the Stefan number, the dimensionless parameter which measures the temperature difference between the fusion point and the target temperature. Some concluding remarks are offered on what needs to be done to accurately compute such deposition processes.
Hysteretic interaction of conical liquid sheets from coaxial atomizers: Influence on the spray characteristics
Authors: Sivakumar D. , Raghunandan B. N.
Published: July 2002

In the context of coaxial swirl injectors used in liquid bipropellant rockets, a detailed experimental study has been made on the mutual interaction between thin coaxial, conical liquid sheets. As the flow rates are increased, the sheets move close to each other and merge at a definite flow condition. The presence of the inner jet influences the behavior of the outer jet, even before merging. The merging and separation processes exhibit hysteresis. This leads to drastic variations in spray characteristics depending on the approach to the hysteresis regime. Many of these features as well as those on the movement of the contact point can be traced to changes occurring in the static pressure in the cavity between the two sheets.
Nonlinear collisional absorption in laser-driven plasmas
Authors: Decker C. D. , Mori W. B. , Dawson J. M. , Katsouleas T.
Published: July 2002

The collisional heating rate of a fully ionized plasma driven by a strong electromagnetic pump wave is re-examined both analytically and with two-dimensional particle-in-cell (PIC) simulations. The high frequency conductivity model of Dawson and Oberman [J. Dawson and C. Oberman, Phys. Fluids 5, 517(1962)] is extended for the case in which the quiver velocity vo=eE/mωo is much larger than the thermal velocity vth and its equivalence to the results of Silin [V. P. Silin, Sov. Phys. JETP 20, 1510 (1965)] is shown. The Dawson and Oberman model is reduced to two-dimensions for comparison with the PIC simulations. Excellent agreement between the theory and the simulations for vo/vth≤1 is obtained. However, when vo/vth≫1 and the excursion amplitude xo=eE/mω2o is larger than the Debye length λD, the simulations show enhancements in the collision frequency from the theory. A possible mechanism for this enhancement is provided.
On plasma crystal formation
Authors: Vladimirov Sergey V. , Ishihara Osamu
Published: July 2002

It is shown that charged dust grains in a sheath region with plasma ion flow can attract each other in the wake potential cone of an upstream dust particulate. Because of the periodic nature of the potential, periodic structures of the dust grains can be formed in a base plane of the cone.
Plasma–neutral interaction in tokamak divertor for ‘‘gas box’’ neutral model
Authors: Krasheninnikov S. I. , Soboleva T. K.
Published: July 2002

Plasma flow through the gas cloud in a tokamak divertor for ‘‘gas box’’ divertor geometry and Knudsen regime of neutral transport is investigated. It is shown that similar to the neutral models that have considered previously, (i) plasma parameters near the target is sensitive to the energy flux into the hydrogen recycling region and can change rapidly, resulting in bifurcation-like behavior, which might be interpreted as a transition to detached regime, (ii) plasma flux onto the target starts to decrease at a very low plasma temperature near the target, while a strong pressure drop already occurs. At low plasma temperature near the target the recombination processes can significantly alter the plasma flux onto the target.
Electron-ion collisions in intensely illuminated plasmas
Authors: Shvets G. , Fisch N. J.
Published: July 2002

In the presence of a high-frequency intense uniform electric field, the collisions of electrons with ions can be made more frequent or less frequent, depending on the polarization of the hf field, the direction and magnitude of particle velocity, and the ratio of the plasma Debye length to the size of the electron oscillation in the hf field. The stimulated bremsstrahlung emission is calculated for both circularly and linearly polarized fields.
The effect of nonlinear mode coupling on the stability of toroidal Alfvén eigenmodes
Authors: Lashmore-Davies C. N. , Thyagaraja A. , Cairns R. A.
Published: July 2002

A cylindrical model of a tokamak is used to describe the nonlinear coupling between Alfvén waves and sound waves. The model is applied to the case of a toroidal Alfvén eigenmode (TAE) driven unstable by fusion alpha particles to explore its relevance to the nonlinear saturation of such modes, which can produce a loss of alpha particles in a burning plasma. The mechanism is the modulational instability of a finite-amplitude wave, in this case a TAE mode, in which a density fluctuation and Alfvén sidebands are spontaneously excited when the finite-amplitude wave exceeds a threshold amplitude. In general, such a nonlinear calculation in a bounded inhomogeneous plasma would require a numerical solution. However, in the present case, an approximate analytic solution is derived by making use of the fact that the sound wave is logarithmically singular on a particular magnetic surface. The calculation is therefore carried out on the magnetic surface on which the TAE instability is centered and a nonlinear dispersion relation is derived. The threshold for the modulational instability yields a value for the ratio of the perturbed radial component of the magnetic field to the equilibrium magnetic field, which is comparable to the saturated amplitude of a TAE instability obtained by other workers. In addition, the nonlinear dispersion relation also includes a resonant case for which the threshold can be significantly lower. The present, heuristic calculation suggests that the modulational instability may indeed be relevant to the evolution and eventual saturation of a TAE instability.
The realizable Markovian closure and realizable test-field model. II. Application to anisotropic drift-wave dynamics
Authors: Bowman John C. , Krommes John A.
Published: July 2002

The test-field model is shown to be potentially nonrealizable in the presence of linear waves such as those frequently encountered in models of plasma and geophysical turbulence. A new statistical closure, the realizable test-field model (RTFM), is proposed as a remedy. Both the damping rate and frequency are renormalized to account for nonlinear damping and frequency shifts. Like the realizable Markovian closure (RMC), the RTFM is based on a modified fluctuation-dissipation ansatz. Numerical solutions of the RTFM, RMC, and direct-interaction approximation for the Hasegawa–Mima equation are presented; rough agreement with direct numerical solution is found. The number of retained Fourier modes is dramatically reduced with an anisotropic generalization of a recently developed wave-number partitioning scheme.
Strongly nonlinear magnetosonic waves and ion acceleration
Authors: Rau Bernhard , Tajima Toshi
Published: July 2002

The electromagnetic fields associated with a nonlinear compressional Alfvén wave propagating perpendicular to an arbitrarily strong external magnetic field are derived. While recovering the known properties of nonlinear Alfvén waves in the weakly magnetized regime, new scaling laws are found for the strongly magnetized case. It is shown that the electric field increases only with the first power of the external magnetic field strength for the strongly magnetized and high phase velocity case relevant for ion acceleration to high energies. An experimental setup suitable for the pickup and acceleration of background plasma ions that is not subjected to detrapping of ions due to a v×B acceleration is sketched.
A comparative study of modified Korteweg–de Vries (MKdV) and Korteweg–de Vries (KdV) solitons in plasmas with negative ions under the influence of electrons’ drift motion
Authors: Kalita B. C. , Das R.
Published: July 2002

In the plasma under consideration, the existence of modified Korteweg–de Vries (MKdV) solitons has been established for different values of electrons’ drift velocities νe′ and of Q′ (=mj/mi, negative to positive ion mass ratio). The amplitudes of the MKdV solitons are found to be much smaller (<1) than those of the corresponding amplitudes (>1) of the KdV solitons for Q′<0.6 when νe′=10. Unlike the existence of both compressive and rarefactive KdV solitons with two unaccountable regions of νe′, there is found to exist only compressive MKdV solitons of small amplitudes in the lower but entire range of νe′ for U=1.09, 1.12, and 1.15 when Q′=0.4. It is noteworthy to mention that, the width of the KdV soliton does not depend on Q′, i.e., on the concentration of negative ions whereas that of the MKdV soliton depends on Q′.
Development of the laser evaporation ion source for lithium beam generation on the Particle Beam Fusion Accelerator (PBFA-II)
Authors: Renk T. J. , Tisone G. C. , Adams R. G. , Johnson D. J. , Ruiz C. L. , Cooper G. W.
Published: July 2002

The Laser Evaporation Ion Source (LEVIS) active lithium ion source has been developed for use on the focusing ion diode operated on the 10 TW Particle Beam Fusion Accelerator-II (PBFA-II) [J. P. VanDevender and D. L. Cook, Science 232, 831 (1986)] at Sandia National Laboratories. The source configuration consists of two laser pulses impinging on a heated (200 °C) thin-film LiAg layer on the anode surface. A short-pulse Nd:YAG laser creates a high-density vapor, which is then ionized by a long-pulse dye laser using the LIBORS (laser ionization based on resonant saturation) ionization method. Small-scale experiments determined that this dual laser-based approach can produce a source plasma of adequate density and confinement for acceleration and transport. Hardware modifications were undertaken to correct problems of premature impedance collapse and lack of beam lithium seen on previous PBFA-II experiments. As much as 85 kJ of Li is measured at the beam focus, but the source may not have been operating in a fully active (i.e., preformed) manner. Focusing performance appears superior to a passive LiF ion source operated on PBFA-II with the same magnetic field topology.
The neoclassical “Electron Root” feature in the Wendelstein-7-AS stellarator
Authors: Maaßberg H. , Beidler C. D. , Gasparino U. , Romé M. ,   W7-AS Team, Dyabilin K. S. , Marushchenko N. B. , Murakami S.
Published: July 2002

The neoclassical prediction of the “electron root,” i.e., a strongly positive radial electric field, Er (being the solution of the ambipolarity condition of the particle fluxes), is analyzed for low-density discharges in Wendelstein-7-AS [G. Grieger, W. Lotz, P. Merkel, et al., Phys. Fluids B 4, 2081 (1992)]. In these electron cyclotron resonance heated (ECRH) discharges with highly localized central power deposition, peaked Te profiles [with Te(0) up to 6 keV and with Ti≪Te] and strongly positive Er in the central region are measured. It is shown that this “electron root” feature at W7-AS is driven by ripple-trapped suprathermal electrons generated by the ECRH. The fraction of ripple-trapped particles in the ECRH launching plane, which can be varied at W7-AS, is found to be the most important. After switching off the heating the “electron root” feature disappears nearly immediately, i.e., two different time scales for the electron temperature decay in the central region are observed. Monte Carlo simulations in five-dimensional phase space are presented, clearly indicating that the additional “convective” electron fluxes driven by the ECRH are of the same order as the ambipolar neoclassical prediction for the “ion root” at much lower Er. For the predicted “electron root,” the ion fluxes calculated based on the traditional neoclassical ordering are much too small; shortcomings of the usual approach are indentified and a new ordering scheme is proposed.
Spanwise homogeneous buoyancy-drag model for Rayleigh–Taylor mixing and experimental evaluation
Authors: Dimonte Guy
Published: July 2002

A buoyancy-drag model for Rayleigh–Taylor (RT) mixing is developed on the premise that the bubble and spike regions behave as distinct and spanwise homogeneous fluids. Then, mass conservation is applied accross the mixing zone to obtain their average mixture densities dynamically. These are used to explicitly calculate the inertia and buoyancy terms in the evolutionary equation. The only unknown parameter in the model is the Newtonian drag constant C∼2.5±0.6, which is determined from turbulent RT experiments over various Atwood numbers A and acceleration histories g(t). The bubble (i=2) and spike (i=1) amplitudes are found to obey the familiar hi=αiAgt2 for a constant g and hi∼tθi for an impulsive g. For bubbles, both α2 and θ2 are insensitive to A. For the spikes, both α1 and θ1 increase as a power law with the density ratio. However, θ1 is not universal because it depends on the initial value of h1/h2.
Temperature dependence of the current-voltage characteristics of metal-semiconductor field-effect transistors in n-type β-SiC grown via chemical vapor deposition
Authors: Kong H. S. , Palmour J. W. , Glass J. T. , Davis R. F.
Published: July 2002

Metal-semiconductor field-effect transistors (MESFET’s) have been fabricated in an unintentionally doped, n-type β-SiC thin film grown by chemical vapor deposition (CVD). This n-type layer was deposited on a monocrystalline p-type β-SiC (100) CVD layer previously grown on a p-type Si (100) substrate. The buried p layer allowed the devices to be fabricated several microns away from the SiC/Si interface region which contained numerous defects formed as a result of the poor lattice match and different coefficients of thermal expansion between SiC and Si. Thermally evaporated Au was utilized for the gate contact. Sputtered TaSi2 was employed for the source and drain contacts. The gate lengths and channel depths of these MESFET’s were 3.5 and 0.60 μm, respectively. Saturation of the drain currents was achieved at room temperature. Furthermore, the current-voltage characteristics, measured from 298 to 623 K for the first time, indicated that these MESFET’s performed reasonably well throughout this temperature range. The maximum transconductance obtained was 1.6 mS/mm; the value of this parameter decreased with temperature.
Projecting the future of the U.S. carbon sink
Authors: Hurtt G. C. , Pacala S. W. , Moorcroft P. R. , Caspersen J. , Shevliakova E. , Houghton R. A. , Moore B.
Published: July 2002

Atmospheric and ground-based methods agree on the presence of a carbon sink in the coterminous United States (the United States minus Alaska and Hawaii), and the primary causes for the sink recently have been identified. Projecting the future behavior of the sink is necessary for projecting future net emissions. Here we use two models, the Ecosystem Demography model and a second simpler empirically based model (Miami Land Use History), to estimate the spatio-temporal patterns of ecosystem carbon stocks and fluxes resulting from land-use changes and fire suppression from 1700 to 2100. Our results are compared with other historical reconstructions of ecosystem carbon fluxes and to a detailed carbon budget for the 1980s. Our projections indicate that the ecosystem recovery processes that are primarily responsible for the contemporary U.S. carbon sink will slow over the next century, resulting in a significant reduction of the sink. The projected rate of decrease depends strongly on scenarios of future land use and the long-term effectiveness of fire suppression.
A significant portion of mitochondrial proton leak in intact thymocytes depends on expression of UCP2
Authors: Krauss Stefan , Zhang Chen-Yu , Lowell Bradford B.
Published: July 2002

The uncoupling protein homologue UCP2 is expressed in a
variety of mammalian cells. It is thought to be an uncoupler of
oxidative phosphorylation. Uncoupling proteins previously have been
shown to be capable of translocating protons across phospholipid
bilayers in proteoliposome systems. Furthermore, studies in
mitochondria from yeast overexpressing the proteins have led to
suggestions that they may act as uncouplers in cells. However, this
issue is controversial, and to date, definitive experimental evidence
is lacking as to whether UCP2 mediates part or all of the basal
mitochondrial proton leak in mammalian cells
in situ
. In
the present study, by using thymocytes isolated from UCP2-deficient and
wild-type (WT) mice, we addressed the question whether UCP2 is directly
involved in catalyzing proton leak in intact cells. Over a range of
mitochondrial membrane potentials (ΔΨ
m
), proton leak
activity was lower in thymocytes from UCP2-deficient mice compared with
WT mice. At physiological levels of ΔΨ
m
, a significant
portion (50%) of basal proton leak in resting cells depended on UCP2.
Of note, proton leak in whole cells from WT mice, but not
UCP2-deficient mice, responded to stimulation by
4-[(E)-2-(5,6,7,8-tetrahydro-5,5,8,8-tetramethyl-2-napthalenyl)-1-propenyl]benzoic
acid (TTNPB), a known activator of UCP2 activity. Consistent with the
observed changes in proton leak, ΔΨ
m
and ATP levels
were increased in untreated thymocytes from UCP2-deficient mice.
Interestingly, resting respiration was unaltered, suggesting that UCP2
function in resting cells may be concerned with the control of ATP
production rather than substrate oxidation. This study
establishes that UCP2, expressed at endogenous levels,
mediates proton leak in intact cells.
Dysadherin, a cancer-associated cell membrane glycoprotein, down-regulates E-cadherin and promotes metastasis
Authors: Ino Yoshinori , Gotoh Masahiro , Sakamoto Michiie , Tsukagoshi Kiyomi , Hirohashi Setsuo
Published: July 2002

We report the cloning and characterization of a cancer-associated
cell membrane glycoprotein recognized by mAb NCC-3G10. The
antibody showed strong reactivity to a wide variety of cancer cells,
but only to a limited number of normal cells including lymphocytes,
endothelial cells, and basal cells of stratified squamous epithelium.
The cDNA for the antigen encodes 178 aa, which includes a putative
signal sequence, a potential O-glycosylated extracellular domain, a
single transmembrane domain, and a short cytoplasmic tail. Transfection
of the cDNA into PLC/PRF/5 liver cancer cells resulted in reduced
cell–cell adhesiveness, based on both morphology and results of
Ca
2+
-dependent cell aggregation assay. In transfected
cells, E-cadherin was markedly decreased at the protein level in
inverse proportion to the expression level of the antigen recognized by
NCC-3G10, but not at the mRNA level. Aggregation of the antigen by
NCC-3G10-coated beads triggered accumulation of actin, suggesting some
interplay between this antigen and E-cadherin through actin. When
metastatic ability was examined in severe combined immunodeficient mice
by injecting PLC/PRF/5 cells into the spleen, the transfectants
formed a markedly higher number of metastatic nodules in comparison
with controls. We have named this cell membrane glycoprotein, which
down-regulates E-cadherin and promotes metastasis, dysadherin.
A mutation in the peroxisome proliferator-activated receptor γ-binding site in the gene for the cytosolic form of phosphoenolpyruvate carboxykinase reduces adipose tissue size and fat content in mice
Authors: Olswang Yael , Cohen Hannah , Papo Orit , Cassuto Hanoch , Croniger Colleen M. , Hakimi Parvin , Tilghman Shirley M. , Hanson Richard W. , Reshef Lea
Published: July 2002

Regulation of the turnover of triglycerides in adipose tissue requires the continuous provision of 3-glycerophosphate, which may be supplied by the metabolism of glucose or by glyceroneogenesis, the
de novo
synthesis of 3-glycerophosphate from sources other than hexoses or glycerol. The importance of glyceroneogenesis in adipose tissue was assessed in mice by specifically eliminating the expression of the cytosolic form of phosphoenolpyruvate carboxykinase (PEPCK-C), an enzyme that plays a pivotal role in the pathway. To accomplish this, we mutated the binding site for the peroxisome proliferator-activated receptor γ (PPARγ) called the peroxisome proliferator-activated receptor element (PPARE), in the 5′ flanking region of the PEPCK-C gene in the mouse by homologous recombination. The mutation abolished expression of the gene in white adipose tissue and considerably reduced its expression in brown adipose tissue, whereas the level of PEPCK-C mRNA in liver and kidney remained normal. Epididymal white adipose tissue from these mice had a reduced triglyceride deposition, with 25% of the animals displaying lipodystrophy. There was also a greatly reduced level of lipid accumulation in brown adipose tissue. A strong correlation between the hepatic content of triglycerides and the size of the epididymal fat pad in PPARE
−/−
mice suggests that hepatic triglyceride synthesis predominantly utilizes free fatty acids derived from the adipose tissue. Unlike other models, PPARE
−/−
mice with lipodystrophy did not exhibit the lipodystrophy-associated features of diabetes and displayed only moderate hyperglycemia. These studies establish the importance of the PPARE site for PEPCK-C gene expression in adipose tissue and the role of PEPCK-C in the regulation of glyceroneogenesis, a pathway critical for maintaining the deposition of triglycerides in adipose tissue.
Defective localization of the NADPH phagocyte oxidase toSalmonella-containing phagosomes in tumor necrosis factor p55 receptor-deficient macrophages
Authors: Vázquez-Torres Andrés , Fantuzzi Giamila , Edwards Carl K. , Dinarello Charles A. , Fang Ferric C.
Published: July 2002

Tumor necrosis factor receptor (TNFR) p55-knockout (KO) mice are susceptible profoundly toSalmonellainfection. One day after peritoneal inoculation, TNFR-KO mice harbor 1,000-fold more bacteria in liver and spleen than wild-type mice despite the formation of well organized granulomas. Macrophages from TNFR-KO mice produce abundant quantities of reactive oxygen and nitrogen species in response toSalmonellabut nevertheless exhibit poor bactericidal activity. Treatment with IFN-γ enhances killing by wild-type macrophages but does not restore the killing defect of TNFR-KO cells. Bactericidal activity of macrophages can be abrogated by a deletion in the gene encoding TNFα but not by saturating concentrations of TNF-soluble receptor, suggesting that intracellular TNFα can regulate killing ofSalmonellaby macrophages. Peritoneal macrophages from TNFR-KO mice fail to localize NADPH oxidase-containing vesicles toSalmonella-containing vacuoles. A TNFR-KO mutation substantially restores virulence to an attenuated mutant bacterial strain lacking the type III secretory system encoded bySalmonellapathogenicity island 2 (SPI2), suggesting that TNFα and SPI2 have opposing actions on a common pathway of vesicular trafficking. TNFα–TNFRp55 signaling plays a critical role in the immediate innate immune response to an intracellular pathogen by optimizing the delivery of toxic reactive oxygen species to the phagosome.
Pattern formation by a cell surface-associated morphogen in
Myxococcus xanthus
Authors: Jelsbak Lars , Søgaard-Andersen Lotte
Published: July 2002

In response to starvation, an unstructured population of identical
Myxococcus xanthus
cells rearranges into an asymmetric, stable pattern of multicellular fruiting bodies. Central to this pattern formation process are changes in organized cell movements from swarming to aggregation. Aggregation is induced by the cell surface-associated C-signal. To understand how aggregation is accomplished, we have analyzed how C-signal modulates cell behavior. We show that C-signal induces a motility response that includes increases in transient gliding speeds and in the duration of gliding intervals and decreases in stop and reversal frequencies. This response results in a switch in cell behavior from an oscillatory to a unidirectional type of behavior in which the net-distance traveled by a cell per minute is increased. We propose that the C-signal-dependent regulation of the reversal frequency is essential for aggregation and that the remaining C-signal-dependent changes in motility parameters contribute to aggregation by increasing the net-distance traveled by starving cells per minute. In our model for symmetry-breaking and aggregation, C-signal transmission is a local event involving direct contacts between cells that results in a global organization of cells. This pattern formation mechanism does not require a diffusible substance or other actions at a distance. Rather it depends on contact-induced changes in motility behavior to direct cells appropriately
Mutations in
Drosophila
heat shock cognate 4 are enhancers of
Polycomb
Authors: Mollaaghababa Ramin , Sipos László , Tiong Stanley Y. K. , Papoulas Ophelia , Armstrong Jennifer A. , Tamkun John W. , Bender Welcome
Published: July 2002

The homeotic genes controlling segment identity in
Drosophila
are repressed by the
Polycomb
group of genes (PcG) and are activated by genes of the
trithorax
group (trxG). An F
1
screen for
dominant enhancers of
Polycomb
yielded a point mutation
in the heat shock cognate gene,
hsc4,
along with
mutations corresponding to several known PcG loci. The new mutation is
a more potent enhancer of
Polycomb
phenotypes than an
apparent null allele of
hsc4
is, although even the null
allele occasionally displays homeotic phenotypes associated with the
PcG. Previous biochemical results had suggested that HSC4 might
interact with BRAHMA, a trxG member. Further analyses now show that
there is no physical or genetic interaction between HSC4 and the Brahma
complex. HSC4 might be needed for the proper folding of a component of
the
Polycomb
repression complex, or it may be a
functional member of that complex.
The Gcd10p/Gcd14p complex is the essential two-subunit tRNA(1-methyladenosine) methyltransferase of
Saccharomyces cerevisiae
Authors: Anderson James , Phan Lon , Hinnebusch Alan G.
Published: July 2002

The modified nucleoside 1-methyladenosine (m
1
A) is
found at position 58 in the TΨC loop of many eukaryotic tRNAs. The
absence of m
1
A from all tRNAs in
Saccharomyces
cerevisiae
mutants lacking Gcd10p elicits severe defects in
processing and stability of initiator methionine tRNA
(tRNA
i
Met
). Gcd10p is found in a complex with Gcd14p,
which contains conserved motifs for binding
S
-adenosylmethionine (AdoMet). These facts, plus our
demonstration that
gcd14Δ
cells lacked
m
1
A, strongly suggested that Gcd10p/Gcd14p complex is the
yeast tRNA(m
1
A)methyltransferase
[(m
1
A)MTase]. Supporting this prediction,
affinity-purified Gcd10p/Gcd14p complexes used AdoMet as a methyl
donor to synthesize m
1
A in either total tRNA or purified
tRNA
i
Met
lacking only this modification. Kinetic
analysis of the purified complex revealed
K
M
values for AdoMet or tRNA
i
Met
of 5.0 μM and 2.5 nM,
respectively. Mutations in the predicted AdoMet-binding domain
destroyed
GCD14
function
in vivo
and
(m
1
A)MTase activity
in vitro
. Purified
Flag-tagged Gcd14p alone had no enzymatic activity and was severely
impaired for tRNA-binding compared with the wild-type complex,
suggesting that Gcd10p is required for tight binding of the tRNA
substrate. Our results provide a demonstration of a two-component tRNA
MTase and suggest that binding of AdoMet and tRNA substrates depends on
different subunits of the complex.
Oligo(dT) primer generates a high frequency of truncated cDNAs through internal poly(A) priming during reverse transcription
Authors: Nam Douglas Kyung , Lee Sanggyu , Zhou Guolin , Cao Xiaohong , Wang Clarence , Clark Terry , Chen Jianjun , Rowley Janet D. , Wang San Ming
Published: July 2002

We have analyzed a systematic flaw in the current system of gene identification: the oligo(dT) primer widely used for cDNA synthesis generates a high frequency of truncated cDNAs through internal poly(A) priming. Such truncated cDNAs may contribute to 12% of the expressed sequence tags in the current dbEST database. By using a synthetic transcript and real mRNA templates as models, we characterized the patterns of internal poly(A) priming by oligo(dT) primer. We further demonstrated that the internal poly(A) priming can be effectively diminished by replacing the oligo(dT) primer with a set of anchored oligo(dT) primers for reverse transcription. Our study indicates that cDNAs designed for genomewide gene identification should be synthesized by use of the anchored oligo(dT) primers, rather than the oligo(dT) primers, to diminish the generation of truncated cDNAs caused by internal poly(A) priming.
Cell surface expression of the HIV-1 envelope glycoproteins is directed from intracellular CTLA-4-containing regulated secretory granules
Authors: Miranda Luis R. , Schaefer Brian C. , Kupfer Abraham , Hu Zixin , Franzusoff Alex
Published: July 2002

The envelope glycoprotein (Env) of HIV-1 is incorporated into virions that bud from the cell surface of infected T cells. With immunofluorescence microscopy and subcellular membrane fractionation techniques, the intracellular fate of Env in the secretory pathway of HIV-1-infected T cells was evaluated. Rather than trafficking constitutively from the Golgi to the cell surface, Env is directed to intracellular CTLA-4-containing granules, whose recruitment to the cell surface is regulated. The use of the regulated pathway for intracellular Env storage before virion assembly holds implications for the staging of Env exposure at the cell surface of infected cells and of coordinating HIV virion assembly.
RecA protein promotes the regression of stalled replication forks
in vitro
Authors: Robu Mara E. , Inman Ross B. , Cox Michael M.
Published: July 2002

Replication forks are halted by many types of DNA damage. At the site of a leading-strand DNA lesion, forks may stall and leave the lesion in a single-strand gap. Fork regression is the first step in several proposed pathways that permit repair without generating a double-strand break. Using model DNA substrates designed to mimic one of the known structures of a fork stalled at a leading-strand lesion, we show here that RecA protein of
Escherichia coli
will promote a fork regression reaction
in vitro
. The regression process exhibits an absolute requirement for ATP hydrolysis and is enhanced when dATP replaces ATP. The reaction is not affected by the inclusion of the RecO and R proteins. We present this reaction as one of several potential RecA protein roles in the repair of stalled and/or collapsed replication forks in bacteria.
DT40 cells lacking the Ca
2+
-binding protein annexin 5 are resistant to Ca
2+
-dependent apoptosis
Authors: Hawkins Timothy E. , Das Debipriya , Young Barry , Moss Stephen E.
Published: July 2002

Annexins are widely expressed Ca
2+
-dependent phospholipid-binding proteins with poorly understood physiological roles. Proposed functions include Ca
2+
channel activity and vesicle trafficking, but neither have been proven
in vivo
. Here we used targeted gene disruption to generate B-lymphocytes lacking annexin 5 (Anx5) expression and show that this results in reduced susceptibility to a range of apoptotic stimuli. By comparison B-lymphocytes lacking annexin 2 (Anx2) showed no such resistance, providing evidence that this effect is specific to loss of Anx5. The defect in the
ANX5
−/−
cells occurs early in the apoptotic program before nuclear condensation, caspase 3 activation, and cell shrinkage, but downstream of an initial Ca
2+
influx. Only UVA/B irradiation induced similar levels of apoptosis in wild-type and
ANX5
−/−
cells. Unexpectedly,
ANX5
−/−
cells permeabilized
in vitro
also failed to release mitochondrial cytochrome C, suggesting a possible mechanism for their resistance to apoptosis. These findings demonstrate a role for Anx5 in determining the susceptibility of B-lymphocytes to apoptosis.
Substrate conformational transitions in the active site of chorismate mutase: Their role in the catalytic mechanism
Authors: Guo Hong , Cui Qiang , Lipscomb William N. , Karplus Martin
Published: July 2002

Chorismate mutase acts at the first branch-point of aromatic amino acid biosynthesis and catalyzes the conversion of chorismate to prephenate. The results of molecular dynamics simulations of the substrate in solution and in the active site of chorismate mutase are reported. Two nonreactive conformers of chorismate are found to be more stable than the reactive pseudodiaxial chair conformer in solution. It is shown by QM/MM molecular dynamics simulations, which take into account the motions of the enzyme, that when these inactive conformers are bound to the active site, they are rapidly converted to the reactive chair conformer. This result suggests that one contribution of the enzyme is to bind the more prevalent nonreactive conformers and transform them into the active form in a step before the chemical reaction. The motion of the reactive chair conformer in the active site calculated by using the QM/MM potential generates transient structures that are closer to the transition state than is the stable CHAIR conformer.
Contact interactions between epitheliocytes and fibroblasts: Formation of heterotypic cadherin-containing adhesion sites is accompanied by local cytoskeletal reorganization
Authors: Omelchenko T. , Fetisova E. , Ivanova O. , Bonder E. M. , Feder H. , Vasiliev J. M. , Gelfand I. M.
Published: July 2002

Contact interactions between different cell types play a number of important roles in development, for example in cell sorting, tissue organization, and ordered migration of cells. The nature of such heterocellular interactions, in contrast to interactions between cells of the same type, remains largely unknown. In this report, we present experimental data examining the dynamics of heterocellular interactions between epitheliocytes and fibroblasts, which express different cadherin cell adhesion molecules and possess different actin cytoskeletal organizations. Our analysis revealed two striking features of heterocellular contact. First, the active free edge of an epitheliocyte reorganizes its actin cytoskeleton after making contact with a fibroblast. Upon contact with the leading edge of a fibroblast, epitheliocytes disassemble their marginal bundle of actin filaments and reassemble actin filaments into a geometric organization more typical of a fibroblast lamella. Second, epitheliocytes and fibroblasts form cell–cell adhesion structures that have an irregular organization and are associated with components of cell adhesion complexes. The structural organization of these adhesions is more closely related to the type of contacts formed between fibroblasts rather than to those between epitheliocytes. Heterotypic epithelio-fibroblastic contacts, like homotypic contacts between fibroblasts, are transient and do not lead to formation of stable contact interactions. We suggest that heterocellular contact interactions in culture may be regarded as models of how tissue systems consisting of epithelia and mesenchyme interact and become organized
in vivo
.
Inactivation of wild-type p53 tumor suppressor by electrophilic prostaglandins
Authors: Moos P. J. , Edes K. , Fitzpatrick F. A.
Published: July 2002

The electrophilic eicosanoids prostaglandins A
1
or A
2
impaired p53-dependent transcription of endogenous genes and exogenous p53-luciferase reporter plasmids in RKO and HCT 116 colon cancer cells. Cellular accumulation of genetically wild-type, but transcriptionally silent p53 varied as a function of exposure time and concentration of prostaglandins A
1
and A
2
. Prostaglandins A
1
and A
2
induced a conformational change in wild-type p53 that corresponded with its inactivation and its aberrant redistribution from the cytosol to the nucleus. Derangement of its transcriptional activity manifested as inhibition of p53-mediated apoptosis by etoposide, a representative antineoplastic agent. We conclude that electrophilic eicosanoids impair the role of wild-type p53 as a guardian of genomic integrity by a process distinct from somatic mutation or viral oncoprotein binding. This process may pertain to malignant and premalignant conditions, such as colon carcinoma and adenoma, which often harbor a genetically wild-type, but inactive form of p53 tumor suppressor.