bluuebunny/crossref_metadata_2025 huggingface dataset:
Stationary Bianchi type II perfect fluid models
Authors: Nilsson Ulf S. , Uggla Claes
Published: July 2002

Einstein’s field equations for stationary Bianchi type II models with a perfect fluid source are investigated. The field equations are rewritten as a system of autonomous first-order differential equations. Dimensionless variables are subsequently introduced for which the reduced phase space is compact. The system is then studied qualitatively using the theory of dynamical systems. It is shown that the locally rotationally symmetric models are not asymptotically self-similar for small values of the independent variable. A new exact solution is also given.
Quasifinite highest weight modules over the Lie algebra of matrix differential operators on the circle
Authors: Boyallian Carina , Kac Victor G. , Liberati José I. , Yan Catherine H.
Published: July 2002

We give a complete description of the quasifinite highest weight modules over the central extension of the Lie algebra of M×M-matrix differential operators on the circle and obtain them in terms of representation theory of the Lie algebra ĝl(∞,Rm) of infinite matrices with only finitely many nonzero diagonals over the algebra Rm=C[t]/(tm+1). We also classify the unitary ones, and construct them in terms of charged free fermions. This construction provides a large (and conjecturally complete) family of irreducible modules over the associated vertex algebra W1+∞,cM, where c is a positive integer.
Measure-valued solution to the strongly degenerate compressible Heisenberg chain equations
Authors: Ding Shijin , Guo Boling , Su Fengqiu
Published: July 2002

In this paper we are concerned with the existence of solutions to the compressible Heisenberg chain equations. By the vanishing viscosity method we prove that this system admits at least one measure-valued solution.
Vortex dynamics in the presence of free surface waves
Authors: Fish S.
Published: July 2002

Results are presented of flow visualization experiments on vortex pairs launched toward a free surface containing waves. The two-dimensional vortex pair is generated with an initial depth/separation value of 1.0 using a pivoting pair of flaps. Two-dimensional waves are generated with an oscillating-plate-type wavemaker. The resulting flows indicate a strong interaction between the waves and the vortex trajectories. The aspects of vortex/wave interaction examined in this Letter are (1) elimination of the ‘‘rebounding’’ effect on the upstream traveling vortex and (2) an increase in rebound effect on the downstream vortex. These influences of the surface waves on the vortex appear to be related to the near-surface drift current produced by the waves.
Physical interpretation of certain invariants for vortex filament motion under LIA
Authors: Ricca Renzo L.
Published: July 2002

In the context of the localized induction approximation (LIA) for the motion of a thin vortex filament in a perfect fluid, the present work deals with certain conserved quantities that emerge from the Betchov–Da Rios equations. Here, by showing that these invariants belong to a countable family of polynomial invariants for the related nonlinear Schrödinger equation (NLSE), it is demonstrated how to interpret them in terms of kinetic energy, pseudohelicity, and associated Lagrangian. It is also shown that under LIA both linear momentum and angular momentum are conserved quantities and the relation between these quantities and the whole family of polynomial invariants is discussed.
Comment on ‘‘Parametric instabilities near the critical density on steepened density profiles’’ [Phys. Fluids 26, 1888 (1983)]
Authors: Sinha B. K. , Gupta G. P.
Published: July 2002

Theoretical estimates of density scale length as reported by earlier workers have been compared with those of experimental observations in laser-produced plasma experiments and the limitation of the theoretical formulations have been discussed.
Transport of energetic ions by low-n magnetic perturbations
Authors: Mynick H. E.
Published: July 2002

The stochastic transport of MeV ions induced by low-n magnetic perturbations is studied, focusing chiefly on the stochastic mechanism operative for passing particles in low-frequency perturbations. Beginning with a single-harmonic form for the perturbing field, it is first shown numerically and analytically that the stochastic threshold of energetic particles can be substantially lower than that of the magnetic field, contrary to earlier expectations, so that magnetic perturbations could cause appreciable loss of energetic ions without destroying the bulk confinement. The analytic theory is then extended in a number of directions, to clarify the relation of the present stochastic mechanism to instances already found, to allow for more complex perturbations, and to consider the more general relationship between the stochasticity of magnetic fields and that of particles of differing energies (and pitch angles) moving in those fields. It is shown that the stochastic threshold is, in general, a nonmonotonic function of energy, whose form can to some extent be tailored to achieve desired goals (e.g., burn control or ash removal) by a judicious choice of the perturbation. Illustrative perturbations are exhibited that are stochastic for low- but not for high-energy ions, for high- but not for low-energy ions, and for intermediate-energy ions, but not for low or high energy. The second possibility is the behavior needed for burn control; the third provides a possible mechanism for ash removal.
Is Navier–Stokes turbulence chaotic?
Authors: Deissler R. G.
Published: July 2002

Whether turbulent solutions of the Navier–Stokes equations are chaotic is considered. Initially neighboring solutions for a low-Reynolds-number fully developed turbulence are compared. The turbulence is sustained by a nonrandom time-independent external force. The solutions separate exponentially with time, having a positive Liapunov characteristic exponent. Thus the turbulence is characterized as chaotic.
Experimental study of tracer dispersion in sintered glass porous materials of variable compaction
Authors: Charlaix E. , Hulin J. P. , Plona T. J.
Published: July 2002

Experimental measurements of tracer dispersion in sintered glass samples of variable compaction are reported. The results are compared to measurements in nonconsolidated packings of the same glass beads used to prepare the sintered material. While normal ‘‘Gaussian’’ dispersion is obtained in nonconsolidated samples (37% porosity), clear-cut anomalies (such as dispersion ‘‘tails’’ at long times) are observed in sintered materials even with a very low degree of compaction (34% porosity). Experimental curves are analyzed with a ‘‘capacitance’’-type model. The effective dispersion coefficient increases by a factor of 60 when the porosity decreases from 37% to 14% at higher degrees of compaction. The characteristic exchange time between the low-velocity regions and the main flow varies linearly with the transit time through the sample. These results are interpreted by the presence of inhomogeneities with a size of several grain diameters.
Equilibrium salt-fingering convection
Authors: Shen Colin Y.
Published: July 2002

The possible existence of equilibrium salt fingering in a deep fingering domain, equivalent to large Rayleigh number fingering convection, is investigated with a numerical model of a continuously heat and salt stratified fluid system. The growth of fingering heat and salt fluxes in this system is shown to be limited by the instability of fingering cells, and an equilibrium state is achieved when the instability has increased the energy dissipation sufficiently to balance the buoyancy forcing generated by double diffusion. The equilibrium fluxes are shown to vary proportional to the mean vertical T and S gradients, in contrast to the inverse relationship that holds for convection across a finite height, or low Rayleigh number, fingering zone. The structure of equilibrium convection is shown to be disorganized and turbulent-like, characterized by incoherently rising and sinking blobs of anomalous density fluid. A model of equilibrium fingering based on the blob structure is presented to interpret the convective processes. Estimates of the finger blob scale and the heat-to-salt flux ratio are also made from the model and are shown to be consistent with those determined from direct numerical simulations. Finally, a critical Rayleigh number is suggested and estimated to delineate the equilibrium fingering regime from the low Rayleigh number fingering regime.
The oscillatory instability of plane variable-density jets
Authors: Raynal L. , Harion J-L. , Favre-Marinet M. , Binder G.
Published: July 2002

The results of an experimental investigation of the instability of variable-density plane jets issuing into ambient air are reported. When the jet to ambient fluid density ratio S(S=ρj/ρ∞) is less than a critical value, an intense oscillating instability is observed. This instability is characterized by sharp peaks in the power spectral density measured in the near field of the jet. The effects of the control parameters S, Re, and H/θ (jet width to exit momentum thickness) on the instability regime are determined. It is shown that Re is a better scaling parameter than H/θ. The Strouhal number of the dominant mode StH increases with S and Re up to a constant value of 0.25, which is in rather good agreement with the theory and the experiments of Yu and Monkewitz [Phys. Fluids A 2, 1175 (1990); J. Fluid Mech. 255, 323 (1993)]. In the present experiments the critical value Sc above which the oscillating regime disappears is an increasing function of Re and Sc seems to reach a limiting value in the neighborhood of 0.7, which does not agree well either with the theory or with the experiments of Yu and Monkewitz [Phys. Fluids A 2, 1175 (1990); J. Fluid Mech. 255, 323 (1993)]. This difference is in qualitative agreement with the results of linear stability computations, also reported in the paper, which take into account differences in shape and relative positions of the density and velocity profiles.
The emergence of jets and vortices in freely evolving, shallow-water turbulence on a sphere
Authors: Cho James Y-K. , Polvani Lorenzo M.
Published: July 2002

Results from a series of simulations of unforced turbulence evolving within a shallow layer of fluid on a rotating sphere are presented. Simulations show that the turbulent evolution in the spherical domain is strongly dependent on numerical and physical conditions. The independent effects of (1) (hyper)dissipation and initial spectrum, (2) rotation rate, and (3) Rossby deformation radius are carefully isolated and studied in detail. In the nondivergent and nonrotating case, an initially turbulent flow evolves into a vorticity quadrupole at long times, a direct consequence of angular momentum conservation. In the presence of sufficiently strong rotation, the nondivergent long-time behavior yields a field dominated by polar vortices—as previously reported by Yoden and Yamada. In contrast, the case with a finite deformation radius (i.e., the full spherical shallow-water system) spontaneously evolves toward a banded configuration, the number of bands increasing with the rotation rate. A direct application of this shallow-water model to the Jovian atmosphere is discussed. Using standard values for the planetary radius and rotation, we show how the initially turbulent flow self-organizes into a potential vorticity field containing zonal structures, where regions of steep potential vorticity gradients (jets) separate relatively homogenized bands. Moreover, Jovian parameter values in our simulations lead to a strong vorticity asymmetry, favoring anticyclonic vortices—in further agreement with observations.
On consistency conditions for rotating turbulent flows
Authors: Speziale C. G. , Younis B. A. , Rubinstein R. , Zhou Y.
Published: July 2002

Consistency conditions for the prediction of turbulent flows in a rotating frame are examined. It is shown that the dissipation rate should vanish along with the eddy viscosity in the limit of rapid rotations. The latter result is also true when the eddy viscosity is anisotropic and formally follows from the explicit algebraic stress approximation as well as from a phenomenological treatment. The former result has been built into the modeled dissipation rate equation of recent turbulence models where the second result has been violated. In fact, some of these models have the eddy viscosity going to infinity while the dissipation rate vanishes, leading to an inconsistency. For consistency, both of these conditions must be satisfied. The implications of these results for turbulence modeling are thoroughly discussed.
Numerical simulation of breakup of a viscous drop in simple shear flow through a volume-of-fluid method
Authors: Li Jie , Renardy Yuriko Y. , Renardy Michael
Published: July 2002

A spherical drop, placed in a second liquid of the same density, is subjected to shearing between parallel plates. The subsequent flow is investigated numerically with a volume-of-fluid (VOF) method. The scheme incorporates a semi-implicit Stokes solver to enable computations at low Reynolds number. Our simulations compare well with previous theoretical, numerical, and experimental results. For capillary numbers greater than the critical value, the drop deforms to a dumbbell shape and daughter drops detach via an end-pinching mechanism. The number of daughter drops increases with the capillary number. The breakup can also be initiated by increasing the Reynolds number.
A low-dimensional approach to nonlinear plane-Couette flow of viscoelastic fluids
Authors: Ashrafi Nariman , Khayat Roger E.
Published: July 2002

The nonlinear stability of the one-dimensional plane Couette flow is examined for a Johnson–Segalman fluid. The velocity and stress are represented by symmetric and antisymmetric Chandrasekhar functions in space. The flow field is obtained from the conservation and constitutive equations using the Galerkin projection method. Both inertia and normal stress effects are included. For given Reynolds number and viscosity ratio, two critical Weissenberg numbers are found at which an exchange of stability occurs between the Couette and other steady flows. The critical points coincide with the two extrema of the stress/rate-of-strain curve. At low (high) Reynolds number, the flow decays monotonically (oscillatorily) toward the steady-state solution. The number and stability of the nontrivial branches around the critical points are examined using the method of multiple scales. Comparison between the approximate and the numerical branches leads to excellent agreement in the vicinity of the critical points. The influence of the higher-order modes is assessed, showing low-order convergence and good accuracy when the flow profiles are compared against existing finite-element results.
Nonlinear ω*-stabilization of the m=1 mode in tokamaks
Authors: Rogers B. , Zakharov L.
Published: July 2002

Earlier studies of sawtooth oscillations in Tokamak Fusion Test Reactor (TFTR) supershots [Levinton et al., Phys. Rev. Lett. 72, 2895 (1994); Zakharov et al., ‘‘Onset and stabilization of sawtooth oscillations in tokamaks,’’ in Plasma Physics and Controlled Nuclear Fusion Research, Proceedings of the 15th International Conference, Seville, 1994 (International Atomic Energy Agency, Vienna, in press)] have found an apparent contradiction between conventional linear theory and experiment: even in sawtooth-free discharges, the theory typically predicts instability due to a nearly ideal m=1 mode. Here, the nonlinear evolution of such mode is analyzed using numerical simulations of a two-fluid magnetohydrodynamic (MHD) model. We find the mode saturates nonlinearly at a small amplitude provided the ion and electron drift-frequencies ω*i,e are somewhat above the linear stability threshold of the collisionless m=1 reconnecting mode. The comparison of the simulation results to m=1 mode activity in TFTR suggests additional, stabilizing effects outside the present model are also important.
Absolute measurements of the equations of state of low-Z materials in the multi-Mbar regime using laser-driven shocks
Authors: Cauble R. , Da Silva L. B. , Perry T. S. , Bach D. R. , Budil K. S. , Celliers P. , Collins G. W. , Ng A. , Barbee, Jr. T. W. , Hammel B. A. , Holmes N. C. , Kilkenny J. D. , Wallace R. J. , Chiu G. , Woolsey N. C.
Published: July 2002

Although high intensity lasers offer the opportunity to explore the equations of state (EOSs) of materials under high energy density conditions, experimental difficulties have limited the application of laser-driven shocks to EOS measurements. However, we have recently performed absolute EOS measurements on the principal Hugoniot of liquid deuterium near one Mbar and of polystyrene from 10 to 40 Mbar. The D2 measurements were made with direct drive; the polystyrene experiments were indirectly driven. The data were sufficiently accurate to differentiate between existing EOS models and were surprising, particularly for D2. The results demonstrate that laser driven shocks can be used effectively to investigate high pressure EOSs.
Electrostatic modes in dense dusty plasmas with high fugacity: Numerical results
Authors: Rao N. N.
Published: July 2002

The existence of ultra low-frequency wave modes in dusty plasmas has been investigated over a wide range of dust fugacity [defined by f≡4πnd0λD2R, where nd0 is the dust number density, λD is the plasma Debye length, and R is the grain size (radius)] and the grain charging frequency (ω1) by numerically solving the dispersion relation obtained from the kinetic (Vlasov) theory. A detailed comparison between the numerical and the analytical results applicable for the tenuous (low fugacity, f≪1), the dilute (medium fugacity, f∼1), and the dense (high fugacity, f≫1) regimes has been carried out. In the long wavelength limit and for frequencies ω≪ω1, the dispersion curves obtained from the numerical solutions of the real as well as the complex (kinetic) dispersion relations agree, both qualitatively and quantitatively, with the analytical expressions derived from the fluid and the kinetic theories, and are thus identified with the ultra low-frequency electrostatic dust modes, namely, the dust-acoustic wave (DAW), the dust charge-density wave (DCDW) and the dust-Coulomb wave (DCW) discussed earlier [N. N. Rao, Phys. Plasmas 6, 4414 (1999); 7, 795 (2000)]. In particular, the analytical scaling between the phase speeds of the DCWs and the DAWs predicted from theoretical considerations, namely, (ω/k)DCW=(ω/k)DAW/fδ (where δ is the ratio of the charging frequencies) is in excellent agreement with the numerical results. A simple physical picture of the DCWs has been proposed by defining an effective pressure called “Coulomb pressure” as PC≡nd0qd02/R, where qd0 is the grain surface charge. Accordingly, the DCW dispersion relation is given, in the lowest order, by (ω/k)DCW=PC/ρdδ, where ρd≡nd0md is the dust mass density. Thus, the DCWs which are driven by the Coulomb pressure can be considered as the electrostatic analogue of the hydromagnetic (Alfvén or magnetoacoustic) waves which are driven by the magnetic field pressure. For the frequency regime ω≫ω1, the numerical results confirm the existence of only the DAWs, while the DCWs are absent as predicted by the fluid and the kinetic theories. The wave damping rates due to the charge fluctuations as well as the wave–particle interactions (Landau type) have been numerically computed and compared with the analytical results. For the tenuous as well as the dilute regimes, there is good agreement between the numerical and the analytical results at small wave numbers. However, at larger wave numbers and for the dense regime, the damping rates are underestimated by the theoretical expressions obtained under suitable approximations. Some comments on the sources for these differences have also been presented.
GaInAs/GaAs strained-layer superlattices grown by low pressure metalorganic vapor phase epitaxy
Authors: Roth A. P. , Sacilotti M. , Masut R. A. , D’Arcy P. J. , Watt B. , Sproule G. I. , Mitchell D. F.
Published: July 2002

Strained-layer superlattices (SLS’s) of GaxIn1−xAs/GaAs (x≂0.8–0.9) have been grown by low pressure metalorganic vapor phase epitaxy. The reactants were trimethylgallium, trimethylindium, and arsine. The structures were characterized by Auger profiling and low-temperature photoluminescence. These measurements show that high quality SLS’s with interface widths no larger than 25 Å and very narrow luminescence peaks (6.5 meV) similar to the best structures grown by molecular beam epitaxy, can be easily grown by low pressure metalorganic vapor phase epitaxy.
Room-temperature excitons in Ga0.47In0.53As-InP superlattices grown by low-pressure metalorganic chemical vapor deposition
Authors: Razeghi M. , Nagle J. , Maurel P. , Omnes F. , Pocholle J. P.
Published: July 2002

Very high quality Ga0.47In0.53As-InP heterojunctions, quantum wells, and superlattices have been grown by low-pressure metalorganic chemical vapor deposition. Excitation spectroscopy shows evidence of strong and well-resolved exciton peaks in the luminescence and excitation spectra of GaInAs-InP quantum wells. Optical absorption spectra show room-temperature excitons in GaInAs-InP superlattices.
Stability of 300 K continuous operation of p-n AlxGa1−xAs-GaAs quantum well lasers grown on Si
Authors: Deppe D. G. , Nam D. W. , Holonyak N. , Hsieh K. C. , Matyi R. J. , Shichijo H. , Epler J. E. , Chung H. F.
Published: July 2002

Data are presented on p-n (diode) AlxGa1−xAs-GaAs quantum well lasers grown on Si indicating that continuous 300 K operation is possible for four or more hours. Lower threshold diodes (1.4 kA/cm2) of given dislocation density are not necessarily as stable as higher threshold diodes (1.8 kA/cm2) of lower dislocation density, ∼10 min vs ≳4 h. Stability data on diodes agree with the behavior of photopumped samples of the same crystals with the Si substrates removed.
Effect of fluoride doping on the transition temperature of YBa2Cu3O6.5+δ
Authors: Bansal Narottam P. , Sandkuhl Ann L. , Farrell D. E.
Published: July 2002

The effect of fluoride doping on the superconducting transition temperature, Tc, of YBa2Cu3O6.5+δ has been investigated. Samples of nominal composition YBa2Cu3FxO6.5+δ−0.5x were synthesized where x was varied by two orders of magnitude from 0.0165 to 1.65. Tc systematically increased with x, reached a maximum of 93.4 K (midpoint) for x=0.066 and then dropped for higher concentrations. The sharpest transition, ΔTc(10–90%)=0.7±0.1 K, coincided with a maximum in Tc. From powder x-ray diffraction measurements, samples with x≤0.066 were found to be single phase perovskite whereas those with x≥0.165 also contained BaF2, CuO, and an unknown phase. Although we find no evidence for the very high Tc’s reported by S. R. Ovshinsky, R. T. Young, D. D. Allred, G. DeMaggio, and G. A. Van der Leeden [Phys. Rev. Lett. 58, 2579 (1987)], our results do indicate that the effect of fluorine is qualitatively different from that produced by other dopants.
Plasma emission from laser ablation of the high-temperature superconductor YBa2Cu3O7
Authors: Weimer Wayne A.
Published: July 2002

Emission spectra generated during the excimer laser ablation of the high-temperature superconductor YBa2Cu3O7 at 193 nm are presented. The feasibility of using this emission as a signal source for a thin-film deposition process monitor is discussed. Results indicate the formation of a partially ionized plasma above the target surface.
Snapshot of a key intermediate in enzymatic thiamin catalysis: Crystal structure of the α-carbanion of (α,β-dihydroxyethyl)-thiamin diphosphate in the active site of transketolase from
Saccharomyces cerevisiae
Authors: Fiedler Erik , Thorell Stina , Sandalova Tatyana , Golbik Ralph , König Stephan , Schneider Gunter
Published: July 2002

Kinetic and spectroscopic data indicated that addition of the donor substrate hydroxypyruvate to the thiamin diphosphate (ThDP)-dependent enzyme transketolase (TK) led to the accumulation of the α-carbanion/enamine of (α,β-dihydroxyethyl) ThDP, the key reaction intermediate in enzymatic thiamin catalysis. The three-dimensional structure of this intermediate trapped in the active site of yeast TK was determined to 1.9-Å resolution by using cryocrystallography. The electron density suggests a planar α-carbanion/enamine intermediate having the
E
-configuration. The reaction intermediate is firmly held in place through direct hydrogen bonds to His-103 and His-481 and an indirect hydrogen bond via a water molecule to His-69. The 4-NH
2
group of the amino-pyrimidine ring of ThDP is within 3 Å distance to the α-hydroxy oxygen atom of the dihydroxyethyl moiety but at an angle unfavorable for a strong hydrogen bond. No structural changes occur in TK on formation of the reaction intermediate, suggesting that the active site is poised for catalysis and conformational changes during the enzyme reaction are not very likely. The intermediate is present with high occupancy in both active sites, arguing against previous proposals of half-of-the-sites reactivity in yeast TK.
A phosphatidylinositol 3-kinase/Akt/mTOR pathway mediates and PTEN antagonizes tumor necrosis factor inhibition of insulin signaling through insulin receptor substrate-1
Authors: Ozes Osman Nidai , Akca Hakan , Mayo Lindsey D. , Gustin Jason A. , Maehama Tomohiko , Dixon Jack E. , Donner David B.
Published: July 2002

Tyrosine phosphorylation of insulin receptor substrate-1 (IRS-1) by
the insulin receptor permits this docking protein to interact with
signaling proteins that promote insulin action. Serine phosphorylation
uncouples IRS-1 from the insulin receptor, thereby inhibiting its
tyrosine phosphorylation and insulin signaling. For this reason, there
is great interest in identifying serine/threonine kinases for which
IRS-1 is a substrate. Tumor necrosis factor (TNF) inhibited
insulin-promoted tyrosine phosphorylation of IRS-1 and activated the
Akt/protein kinase B serine-threonine kinase, a downstream target for
phosphatidylinositol 3-kinase (PI 3-kinase). The effect of TNF on
insulin-promoted tyrosine phosphorylation of IRS-1 was blocked by
inhibition of PI 3-kinase and the PTEN tumor suppessor, which
dephosphorylates the lipids that mediate PI 3-kinase functions, whereas
constitutively active Akt impaired insulin-promoted IRS-1 tyrosine
phosphorylation. Conversely, TNF inhibition of IRS-1 tyrosine
phosphorylation was blocked by kinase dead Akt. Inhibition of IRS-1
tyrosine phosphorylation by TNF was blocked by rapamycin, an inhibitor
of the mammalian target of rapamycin (mTOR), a downstream target of
Akt. mTOR induced the serine phosphorylation of IRS-1 (Ser-636/639),
and such phosphorylation was inhibited by rapamycin. These results
suggest that TNF impairs insulin signaling through IRS-1 by activation
of a PI 3-kinase/Akt/mTOR pathway, which is antagonized by PTEN.
ARF-GEP
100
, a guanine nucleotide-exchange protein for ADP-ribosylation factor 6
Authors: Someya Akimasa , Sata Makoto , Takeda Kazuyo , Pacheco-Rodriguez Gustavo , Ferrans Victor J. , Moss Joel , Vaughan Martha
Published: July 2002

A human cDNA encoding an 841-aa guanine nucleotide-exchange
protein (GEP) for ADP-ribosylation factors (ARFs), named
ARF-GEP
100
, which contains a Sec7 domain, a pleckstrin
homology (PH)-like domain, and an incomplete IQ-motif, was identified.
On Northern blot analysis of human tissues, a ≈8-kb mRNA that
hybridized with an ARF-GEP
100
cDNA was abundant in
peripheral blood leukocytes, brain, and spleen. ARF-GEP
100
accelerated [
35
S]GTPγS binding to ARF1 (class I) and
ARF5 (class II) 2- to 3-fold, and to ARF6 (class III)
ca.
12-fold. The ARF-GEP
100
Sec7 domain
contains Asp
543
and Met
555
, corresponding to
residues associated with sensitivity to the inhibitory effect of the
fungal metabolite brefeldin A (BFA) in yeast Sec7, but also
Phe
535
and Ala
536
, associated with
BFA-insensitivity. The PH-like domain differs greatly from those of
other ARF GEPs in regions involved in phospholipid binding. Consistent
with its structure, ARF-GEP
100
activity was not affected by
BFA or phospholipids. After subcellular fractionation of cultured T98G
human glioblastoma cells, ARF6 was almost entirely in the crude
membrane fraction, whereas ARF-GEP
100
, a 100-kDa protein
detected with antipeptide antibodies, was cytosolic. On
immunofluorescence microscopy, both proteins had a punctate pattern of
distribution throughout the cells, with apparent colocalization only in
peripheral areas. The coarse punctate distribution of EEA-1 in regions
nearer the nucleus appeared to coincide with that of
ARF-GEP
100
in those areas. No similar coincidence of
ARF-GEP
100
with AP-1, AP-2, catenin, LAMP-1, or 58K was
observed. The new human BFA-insensitive GEP may function with ARF6 in
specific endocytic processes.
Preselective gene therapy for Fabry disease
Authors: Qin Gangjian , Takenaka Toshihiro , Telsch Kimberly , Kelley Leslie , Howard Tazuko , Levade Thierry , Deans Robert , Howard Bruce H. , Malech Harry L. , Brady Roscoe O. , Medin Jeffrey A.
Published: July 2002

Fabry disease is a lipid storage disorder resulting from
mutations in the gene encoding the enzyme α-galactosidase A (α-gal
A; EC
3.2.1.22
). We previously have demonstrated long-term α-gal A
enzyme correction and lipid reduction mediated by therapeutic
ex
vivo
transduction and transplantation of hematopoietic cells in
a mouse model of Fabry disease. We now report marked improvement in the
efficiency of this gene-therapy approach. For this study we used a
novel bicistronic retroviral vector that engineers expression of both
the therapeutic α-gal A gene and the human IL-2Rα chain (huCD25)
gene as a selectable marker. Coexpression of huCD25 allowed selective
immunoenrichment (preselection) of a variety of transduced human and
murine cells, resulting in enhanced intracellular and secreted α-gal
A enzyme activities. Of particular significance for clinical
applicability, mobilized CD34
+
peripheral blood
hematopoietic stem/progenitor cells from Fabry patients have
low-background huCD25 expression and could be enriched effectively
after
ex vivo
transduction, resulting in increased
α-gal A activity. We evaluated effects of preselection in the mouse
model of Fabry disease. Preselection of transduced Fabry mouse bone
marrow cells elevated the level of multilineage gene-corrected
hematopoietic cells in the circulation of transplanted animals and
improved
in vivo
enzymatic activity levels in plasma and
organs for more than 6 months after both primary and secondary
transplantation. These studies demonstrate the potential of using a
huCD25-based preselection strategy to enhance the clinical utility of
ex vivo
hematopoietic stem/progenitor cell gene
therapy of Fabry disease and other disorders.
The identification of E2F1-specific target genes
Authors: Wells Julie , Graveel Carrie R. , Bartley Stephanie M. , Madore Steven J. , Farnham Peggy J.
Published: July 2002

The E2F family of transcriptional regulators consists of six different members. Analysis of E2F-regulated promoters by using cultured cells suggests that E2Fs may have redundant functions. However, animal studies have shown that loss of individual E2Fs can have distinct biological consequences. Such seemingly conflicting results could be due to a difference in E2F-mediated regulation in cell culture vs. animals. Alternatively, there may be genes that are specifically regulated by an individual E2F which have not yet been identified. To investigate this possibility further, we have analyzed gene expression in E2F1 nullizygous mice. We found that loss of E2F1 did not cause changes in expression of known E2F target genes, suggesting that perhaps E2F1-specific promoters are distinct from known E2F target promoters. Therefore, we used oligonucleotide microarrays to identify mRNAs whose expression is altered on loss of E2F1. We demonstrate by chromatin immunoprecipitation that several of the promoters that drive expression of the deregulated mRNAs selectively recruit E2F1, but not other E2Fs, and this recruitment is via an element distinct from a consensus E2F binding site. To our knowledge, these are as yet undocumented examples of promoters being occupied in asynchronously growing cells by a single E2F family member. Interestingly, the E2F1-specific target genes that we identified encode proteins having functions quite different from the function of known E2F target genes. Thus, whereas E2F1 may share redundant functions in cell growth control with other E2F family members, it may also play an important biological role distinct from the other E2Fs.
Expression of α
1D
subunit mRNA is correlated with L-type Ca
2+
channel activity in single neurons of hippocampal “zipper” slices
Authors: Chen K. C. , Blalock E. M. , Thibault O. , Kaminker P. , Landfield P. W.
Published: July 2002

L-type voltage-sensitive Ca
2+
channels (L-VSCCs) play an important role in developmental and aging processes, as well as during normal function of brain neurons. Here, we tested a prediction of the hypothesis that membrane density of functional L-VSCCs is regulated by the level of gene expression for its α
1D
pore-forming subunit. If so, α
1D
mRNA and L-VSCC activity should be positively correlated within individual neurons. Conventional methods of aspiration and/or acute cell dissociation used in prior single-cell studies have generally yielded variable and incomplete recovery of intracellular mRNA. Thus, quantitative relationships between channel function and expression have been difficult to define. In this study, we used the partially dissociated (“zipper”) hippocampal slice preparation as a method for collecting a single neuron's mRNA complement. This preparation, developed to expose neuronal somata for recording, also enables the extraction of a neuron with major processes largely intact. Thus, single-cell measures of gene/mRNA expression can be based on approximately the cell's full set of mRNA transcripts. In adult and aged rat hippocampal zipper slices, L-VSCC activity was first recorded in CA1 neurons in cell-attached patch mode. The same neurons were then extracted and collected for semiquantitative reverse transcriptase–PCR analysis of α
1D
and calmodulin A (CaM) mRNA content. Across multiple single neurons, a significant, positive correlation was found between the rank orders of L-VSCC activity and of α
1D
, but not CaM, mRNA expression. Thus, these studies support the possibility that the level of α
1D
gene expression regulates the density of functional L-VSCCs.
Staphylococcus aureus
sortase mutants defective in the display of surface proteins and in the pathogenesis of animal infections
Authors: Mazmanian Sarkis K. , Liu Gwen , Jensen Eric R. , Lenoy Eileen , Schneewind Olaf
Published: July 2002

Many Gram-positive bacteria covalently tether their surface adhesins to the cell wall peptidoglycan. We find that surface proteins of
Staphylococcus aureus
are linked to the cell wall by sortase, an enzyme that cleaves polypeptides at a conserved LPXTG motif.
S. aureus
mutants lacking sortase fail to process and display surface proteins and are defective in the establishment of infections. Thus, the cell wall envelope of Gram-positive bacteria represents a surface organelle responsible for interactions with the host environment during the pathogenesis of bacterial infections.
Systemic spread of an RNA insect virus in plants expressing plant viral movement protein genes
Authors: Dasgupta Ranjit , Garcia Bradley H. , Goodman Robert M.
Published: July 2002

Flock house virus (FHV), a single-stranded RNA insect virus, has previously been reported to cross the kingdom barrier and replicate in barley protoplasts and in inoculated leaves of several plant species [Selling, B. H., Allison, R. F. & Kaesberg, P. (1990)Proc. Natl. Acad. Sci. USA87, 434–438]. There was no systemic movement of FHV in plants. We tested the ability of movement proteins (MPs) of plant viruses to provide movement functions and cause systemic spread of FHV in plants. We compared the growth of FHV in leaves of nontransgenic and transgenic plants expressing the MP of tobacco mosaic virus or red clover necrotic mosaic virus (RCNMV). Both MPs mobilized cell-to-cell and systemic movement of FHV inNicotiana benthamianaplants. The yield of FHV was more than 100-fold higher in the inoculated leaves of transgenic plants than in the inoculated leaves of nontransgenic plants. In addition, FHV accumulated in the noninoculated upper leaves of both MP-transgenic plants. RCNMV MP was more efficient in mobilizing FHV to noninoculated upper leaves. We also report here that FHV replicates in inoculated leaves of six additional plant species: alfalfa,Arabidopsis,Brassica, cucumber, maize, and rice. Our results demonstrate that plant viral MPs cause cell-to-cell and long-distance movement of an animal virus in plants and offer approaches to the study of the evolution of viruses and mechanisms governing mRNA trafficking in plants as well as to the development of promising vectors for transient expression of foreign genes in plants.
Inhibition of huntingtin fibrillogenesis by specific antibodies and small molecules: Implications for Huntington's disease therapy
Authors: Heiser Volker , Scherzinger Eberhard , Boeddrich Annett , Nordhoff Eckhard , Lurz Rudi , Schugardt Nancy , Lehrach Hans , Wanker Erich E.
Published: July 2002

The accumulation of insoluble protein aggregates in intra and perinuclear inclusions is a hallmark of Huntington's disease (HD) and related glutamine-repeat disorders. A central question is whether protein aggregation plays a direct role in the pathogenesis of these neurodegenerative diseases. Here we show by using a filter retardation assay that the mAb 1C2, which specifically recognizes the elongated polyglutamine (polyQ) stretch in huntingtin, and the chemical compounds Congo red, thioflavine S, chrysamine G, and Direct fast yellow inhibit HD exon 1 protein aggregation in a dose-dependent manner. On the other hand, potential inhibitors of amyloid-β formation such as thioflavine T, gossypol, melatonin, and rifampicin had little or no inhibitory effect on huntingtin aggregation
in vitro
. The results obtained by the filtration assay were confirmed by electron microscopy, SDS/PAGE, and MS. Furthermore, cell culture studies revealed that the Congo red dye at micromolar concentrations reduced the extent of HD exon 1 aggregation in transiently transfected COS cells. Together, these findings contribute to a better understanding of the mechanism of huntingtin fibrillogenesis
in vitro
and provide the basis for the development of new huntingtin aggregation inhibitors that may be effective in treating HD.
Modeling RNA folding paths with pseudoknots: Application to hepatitis delta virus ribozyme
Authors: Isambert Hervé , Siggia Eric D.
Published: July 2002

A quantitative understanding of nucleic acid hybridization is
essential to many aspects of biotechnology, such as DNA microarrays, as
well as to the structure and folding kinetics of RNA. However,
predictions of nucleic acid secondary structures have long been impeded
by the presence of helices interior to loops, so-called pseudoknots,
which impose complex three-dimensional conformational constraints. In
this paper we compute the pseudoknot free energies analytically in
terms of known standard parameters, and we show how the results can be
included in a kinetic Monte Carlo code to follow the succession of
secondary structures during quenched or sequential folding. For the
hepatitis delta virus ribozyme, we predict several nonnative stems on
the folding path, characterize a kinetically trapped state, interpret
several experimentally characterized mutations in terms of the folding
path, and suggest how hybridization with other parts of the genome
inactivates the newly formed ribozyme.
Immune-type receptor genes in zebrafish share genetic and functional properties with genes encoded by the mammalian leukocyte receptor cluster
Authors: Yoder Jeffrey A. , Mueller M. Gail , Wei Sheng , Corliss Brian C. , Prather Donald M. , Willis Toni , Litman Ronda T. , Djeu Julie Y. , Litman Gary W.
Published: July 2002

An extensive, highly diversified multigene family of novel
immune-type receptor (
nitr
) genes has been defined in
Danio rerio
(zebrafish). The genes are predicted to
encode type I transmembrane glycoproteins consisting of extracellular
variable (V) and V-like C2 (V/C2) domains, a transmembrane region and
a cytoplasmic tail. All of the genes examined encode immunoreceptor
tyrosine-based inhibition motifs in the cytoplasmic tail. Radiation
hybrid panel mapping and analysis of a deletion mutant line (b240)
indicate that a minimum of ≈40
nitr
genes are
contiguous in the genome and span ≈0.6 Mb near the top of zebrafish
linkage group 7. One flanking region of the
nitr
gene
complex shares conserved synteny with a region of mouse chromosome 7,
which shares conserved synteny with human 19q13.3-q13.4 that encodes
the leukocyte receptor cluster. Antibody-induced crosslinking of Nitrs
that have been introduced into a human natural killer cell line
inhibits the phosphorylation of mitogen-activated protein kinase that
is triggered by natural killer-sensitive tumor target cells. Nitrs
likely represent intermediates in the evolution of the leukocyte
receptor cluster.
Heart-targeted overexpression of
caspase3
in mice increases infarct size and depresses cardiac function
Authors: Condorelli Gianluigi , Roncarati Roberta , Ross John , Pisani Angela , Stassi Giorgio , Todaro Matilde , Trocha Stephen , Drusco Alessandra , Gu Yusu , Russo Matteo A. , Frati Giacomo , Jones Steven P. , Lefer David J. , Napoli Claudio , Croce Carlo M.
Published: July 2002

Up-regulation of proapoptotic genes has been reported in
heart failure and myocardial infarction. To determine whether caspase
genes can affect cardiac function, a transgenic mouse was generated.
Cardiac tissue-specific overexpression of the proapoptotic gene
Caspase3
was induced by using the rat promoter of
α-myosin heavy chain, a model that may represent a unique tool for
investigating new molecules and antiapoptotic therapeutic
strategies. Cardiac-specific
Caspase3
expression induced
transient depression of cardiac function and abnormal nuclear and
myofibrillar ultrastructural damage. When subjected to myocardial
ischemia–reperfusion injury,
Caspase3
transgenic mice
showed increased infarct size and a pronounced susceptibility to die.
In this report, we document an unexpected property of the
proapoptotic gene caspase3 on cardiac contractility. Despite
inducing ultrastructural damage,
Caspase3
does not
trigger a full apoptotic response in the cardiomyocyte. We also
implicate
Caspase3
in determining myocardial infarct
size after ischemia–reperfusion injury, because its
cardiomyocyte-specific overexpression increases infarct size.
Molecular phylogenetic analyses of the mitochondrial ADP-ATP carriers: The Plantae/Fungi/Metazoa trichotomy revisited
Authors: Löytynoja Ari , Milinkovitch Michel C.
Published: July 2002

We investigated the basal phylogeny of eukaryotes through analyses of sequences from the ADP–ATP mitochondrial carrier, a transmembrane protein that is stable in function across eukaryote kingdoms. The ADP–ATP data strongly suggest the grouping of Plantae and Fungi to the exclusion of Metazoa. We implemented several procedures to avoid pervasive analytical artifacts such as erroneous alignment, random rooting, long branch attraction, and misidentification of noisy characters. The quest of an eukaryote tree that would be largely consistent across multiple loci might be essentially illusory because of differential lineage sorting, horizontal gene transfer, and the chimeric nature of early eukaryotes. Better understanding of these evolutionary parameters, requiring separate phylogenetic analyses of multiple independent loci, is fundamental for resolution of the modes of emergence and evolution of the major eukaryote lineages.
Basolateral membrane expression of a K
+
channel, Kir 2.3, is directed by a cytoplasmic COOH-terminal domain
Authors: Le Maout Sophie , Welling Paul A. , Brejon Manuel , Olsen Olav , Merot Jean
Published: July 2002

The inwardly rectifying potassium channel Kir 2.3 is specifically targeted and expressed on the basolateral membrane of certain renal epithelial cells. In the present study, the structural basis for polarized targeting was elucidated. Deletion of a unique COOH-terminal domain produced channels that were mistargeted to the apical membrane, consistent with the removal of a basolateral membrane-sorting signal. By characterizing a series of progressively smaller truncation mutants, an essential targeting signal was defined (residues 431–442) within a domain that juxtaposes or overlaps with a type I PDZ binding motif (442). Fusion of the COOH-terminal structure onto CD4 was sufficient to change a random membrane-trafficking and expression pattern into a basolateral membrane one. Using metabolic labeling and pulse–chase and surface immunoprecipitation, we found that CD4-Kir2.3 COOH-terminal chimeras were rapidly and directly targeted to the basolateral membrane, consistent with a sorting signal that is processed in the biosynthetic pathway. Collectively, the data indicate that the basolateral sorting determinant in Kir 2.3 is composed of a unique arrangement of trafficking motifs, containing tandem, conceivably overlapping, biosynthetic targeting and PDZ-based signals. The previously unrecognized domain corresponds to a highly degenerate structure within the Kir channel family, raising the possibility that the extreme COOH terminus of Kir channels may differentially coordinate membrane targeting of different channel isoforms.
Disordered to ordered folding in the regulation of diphtheria toxin repressor activity
Authors: Twigg P. D. , Parthasarathy G. , Guerrero L. , Logan T. M. , Caspar D. L. D.
Published: July 2002

Understanding how metal binding regulates the activity of the
diphtheria toxin repressor protein (DtxR) requires information about
the structure in solution. We have prepared a DtxR mutant construct
with three additional N-terminal residues, Gly-Ser-His-DtxR(Cys-102 →
Asp), that retains metal-binding capabilities, but remains monomeric in
solution and does not bind DNA under conditions that effect
dimerization and DNA binding in the functional DtxR(Cys-102 → Asp)
construct. Although the interaction properties of this inactive mutant
in solution are very different from that of active repressors,
crystallization imposes the same dimeric structure as observed in all
crystal forms of the active repressor with and without bound metal. Our
solution NMR analyses of active and inactive metal-free diphtheria
toxin repressors demonstrate that whereas the C-terminal one-third of
the protein is well ordered, the N-terminal two-thirds exhibits
conformational flexibility and exists as an ensemble of structural
substates with undefined tertiary structure. Fluorescence binding
assays with 1-anilino naphthalene-8-sulfonic acid (ANS) confirm that
the highly α-helical N-terminal two-thirds of the apoprotein is
molten globule-like in solution. Binding of divalent metal cations
induces a substantial conformational reorganization to a more ordered
state, as evidenced by changes in the NMR spectra and ANS binding. The
evident disorder to order transition upon binding of metal in solution
is in contrast to the minor conformational changes seen comparing apo-
and holo-DtxR crystal structures. Disordered to ordered folding appears
to be a general mechanism for regulating specific recognition in
protein action and this mechanism provides a plausible explanation for
how metal binding controls the DtxR repressor activity.