bluuebunny/crossref_metadata_2025 huggingface dataset:
Formation of zonal band structure in forced two-dimensional turbulence on a rotating sphere
Authors: Nozawa Toru , Yoden Shigeo
Published: July 2002

A series of numerical experiments on the forced two-dimensional turbulence on a rotating sphere were done to investigate the formation processes of zonal band structures and their sensitivity to two experimental parameters of the rotation rate and the forcing wave number. A high-resolution barotropic full spherical model of T199 truncation is used with a homogeneous and isotropic formulation of the vorticity forcing function. Three different flow regimes are obtained and one of them is a new regime previously unknown. In the cases of no rotation, a very large flow pattern is obtained as a result of the upward energy cascade to the lowest wave number. The pattern irregularly fluctuates with time. A zonal band structure that consists of alternating easterly and westerly jets becomes dominant with an increase in the rotation rate. The alternating jets, which are robust and persistent, are already formed to be discernible in the very early stage of the time integration. The width of the jets decrease and the number of those increases as the rotation rate increases. The upward cascade of the disturbance energy ceases owing to the effect of rotation around a characteristic wave number nβ at which the “β term” is comparable to the nonlinear Jacobian term. Scale separation between the scale of cascade arrest and the forcing scale allows a systematic alignment of the vortices elongated by the shear in the zonal mean zonal flow, and such an alignment maintains the zonal band structure. When the forcing wave number is small and the rotation rate is large, the band structure is confined in high latitudes yielding a circumpolar vortex with a strong easterly jet, and a wavy structure dominates in middle and low latitudes. This is the new flow regime that is found in this study. Any systematic phase relation is not established in these latitudes because the phases are scrambled by the forcing due to the insufficient scale separation, therefore, the alternating zonal band structure does not emerge.
Detailed simulation of nitrogen dissociation in stagnation regions
Authors: Candler Graham V. , Olejniczak Joseph , Harrold Brent
Published: July 2002

Vibrational relaxation rates from Schwartz–Slawsky–Herzfeld theory and the forced-harmonic oscillator model are used to study the flow of nitrogen in the stagnation region of a blunt body. The mass conservation equations are coupled to the momentum and total energy equations, and solved using an implicit finite-volume computational fluid dynamics method. The effects of single- and multiple-quantum vibration–translation transitions and vibration–vibration transitions are studied. Also, the effect of the mass diffusion of the excited oscillators across the shock layer is investigated. It is found that highly non-Boltzmann vibrational distributions are present in the flow field, and that the forced-harmonic oscillator model predicts that dissociation occurs from the low vibrational levels only.
Similarity law for the streamwise turbulence intensity in zero-pressure-gradient turbulent boundary layers
Authors: Marusic I. , Uddin A. K. M. , Perry A. E.
Published: July 2002

A similarity relationship is proposed to describe the streamwise broadband-turbulence intensity in a zero-pressure-gradient boundary layer. The formulation is applicable to the entire region of the flow beyond the viscous buffer zone and is based on the attached eddy hypothesis, the Reynolds-number-similarity hypothesis and the assumed existence of Kolmogorov eddies with a universal inertial subrange. Experimental data of the authors and those from various published works covering a large Reynolds number range are investigated in light of this formulation.
Energy and velocity of a forming vortex ring
Authors: Shusser Michael , Gharib Morteza
Published: July 2002

It is known that vortex rings formed by large stroke ratios (in a piston/cylinder arrangement) pinch off from their generating jets at a fairly constant universal time scale. In this paper we show that the hypothesis that at the pinch off the translational velocity of the ring equals the jet flow velocity near the ring is equivalent to the recently proposed idea based on a variational principle by Kelvin and Benjamin that the pinch off occurs when the apparatus is no longer able to deliver energy at a rate required for steady vortex ring existence. A formula for the propagation velocity of a thick vortex ring is also proposed and compared with available experimental data and empirical relations.
Passive scalar spectrum in the viscous-convective range in two-dimensional steady turbulence
Authors: Gotoh Toshiyuki , Nagaki Junji , Kaneda Yukio
Published: July 2002

The spectrum of a passive scalar field in the viscous-convective range convected by two-dimensional steady turbulence was studied using the Lagrangian Renormalized Approximation (LRA) and high resolution DNS with a resolution up to 40962. It was found that the scalar spectrum F(k) using the LRA scales as k−1 in the range, and decays Gaussianly in the far diffusive range, and these wavenumber dependencies in both ranges agree with the DNS data. A new Lagrangian closure approximation that is invariant under random Galilean transformation and random uniform rotation is proposed. The approximation makes better quantitative predictions than the LRA and yields F(k)=CVCχ̄(ν/ε̄)1/2k−1 with CVC=5.25 in the viscous-convective range, which is in good agreement with the DNS value CVC=5.11. The importance of molecular diffusion in the far diffusive range when the viscous-convective range exists is also discussed.
Stability of tearing modes in tokamak plasmas
Authors: Hegna C. C. , Callen J. D.
Published: July 2002

The stability properties of m≥2 tearing instabilities in tokamak plasmas are analyzed. A boundary layer theory is used to find asymptotic solutions to the ideal external kink equation, which are used to obtain a simple analytic expression for the tearing instability parameter Δ′. This calculation generalizes previous work on this topic by considering more general toroidal equilibria (however, toroidal coupling effects are ignored.) Constructions of Δ′ are obtained for plasmas with finite beta and for islands that have nonzero width. A simple heuristic estimate is given for the value of the saturated island width when the instability criterion is violated. A connection is made between the calculation of the asymptotic matching parameter in the finite beta and island width case to the nonlinear analog of the Glasser effect [Phys. Fluids 18, 875 (1975)].
The prospects for magnetohydrodynamic stability in advanced tokamak regimes*
Authors: Manickam J. , Chance M. S. , Jardin S. C. , Kessel C. , Monticello D. , Pomphrey N. , Reiman A. , Wang C. , Zakharov L. E.
Published: July 2002

Stability analysis of advanced regime tokamaks is presented. Here advanced regimes are defined to include configurations where the ratio of the bootstrap current, IBS, to the total plasma current, Ip, approaches unity, and the normalized stored energy, βN* = 80π〈p2〉1/2a/IpB0, has a value greater than 4.5. Here, p is the plasma pressure, a the minor radius in meters, Ip is in mega-amps, B0 is the magnetic field in Tesla, and 〈⋅〉 represents a volume average. Specific scenarios are discussed in the context of Toroidal Physics Experiment (TPX) [Proceedings of the 20th European Physical Society Conference on Controlled Fusion and Plasma Physics, Lisbon, 1993, edited by J. A. Costa Cabral, M. E. Manso, F. M. Serra, and F. C. Schuller (European Physical Society, Petit-Lancy, 1993), p. I-80]. The best scenario is one with reversed shear, in the q profile, in the central region of the tokamak. The bootstrap current obtained from the plasma profiles provides 90% of the required current, and is well aligned with the optimal current profile for ideal magnetohydrodynamic stability. This configuration is stable up to βN*≊ 6.8, if the external boundary conditions are relaxed to those corresponding to an ideal structure at a moderate distance of approximately 1.3 times the minor radius.
A novel phase focusing mechanism in multipactor discharge
Authors: Kishek R. A. , Lau Y. Y.
Published: July 2002

In spite of the mutual repulsion among the space charges, a new phase-focusing mechanism is discovered whereby the leading edge of the multipactor discharge in an rf circuit grows at the expense of the trailing edge. This effect arises from the different impact energies, and hence different secondary electron yields, experienced by different portions of the discharge. This phase focusing mechanism may shape the steady-state multipactor discharge in the form of a very tight bunch of electrons.
Experimental constraints on transport from dimensionless parameter scaling studies
Authors: Petty C. C. , Luce T. C. , Baker D. R. , Ballet B. , Carlstrom T. N. , Cordey J. G. , DeBoo J. C. , Gohil P. , Groebner R. J. , Rice B. W. , Thomas D. M. , Wade M. R. , Waltz R. E.
Published: July 2002

The scalings of heat transport with safety factor (q), normalized collisionality (ν), plasma beta (β), and relative gyroradius (ρ*) have been measured on the DIII-D tokamak [Fusion Technol. 8, 441 (1985)]. The measured ρ*, β and ν scalings of heat transport indicate that E×B transport from drift wave turbulence is a plausible basis for anomalous transport. For high confinement (H) mode plasmas where the safety factor was varied at fixed magnetic shear, the effective (or one-fluid) thermal diffusivity was found to scale like χeff∝q2.3±0.64 , with the ion and electron fluids having the same q scaling to within the experimental errors except near the plasma edge. The scaling of the thermal confinement time with safety factor was in good agreement with this local transport dependence, τth∝q−2.42±0.31 ; however, when the magnetic shear was allowed to vary to keep q0 fixed during the (edge) safety factor scan, a weaker global dependence was observed, τth∝q95−1.43±0.23. This weaker dependence was mainly due to the change in the local value of q between the two types of scans. The combined ρ*, β , ν and q scalings of heat transport for H-mode plasmas on DIII-D reproduce the empirical confinement scaling using physical (dimensional) parameters with the exception of weaker power degradation.
Hydrodynamic perturbation growth in start-up phase in laser implosion
Authors: Nishihara K. , Ishizaki R. , Wouchuk J. G. , Fukuda Y. , Shimuta Y.
Published: July 2002

Nonuniform laser ablation caused by nonuniform laser irradiation and initial target roughness induces ripples of shock and ablation surfaces in laser implosion. Hydrodynamic perturbation growth before the shock breakout is investigated by using an analytical model and two-dimensional simulations. The model agrees well with simulation and experimental results. Areal mass density perturbations and growth rate of the Richtmyer–Meshkov instability are estimated for an ignition target. The thermal smoothing in the ablation layer is also studied for perturbations with a wavelength longer than the layer thickness. A large increase of temperature and density perturbations is shown instead of the smoothing for such a wavelength.
Inertial fusion fast ignitor: Igniting pulse parameter window vs the penetration depth of the heating particles and the density of the precompressed fuel
Authors: Atzeni Stefano
Published: July 2002

A key element of the fast ignitor scheme is the pulse of fast particles creating the igniting spark. In this paper, the dependence of the parameters (energy Ep, power Wp, intensity Ip) of such a pulse on the penetration depth ℛ of the fast particles is studied by two-dimensional simulations of the evolution of a deuterium–tritium fuel, precompressed at density ρ, and heated by a beam of particles with assigned ℛ. The ignition windows in the (Ep,Wp,Ip) space are found to depend very little on ℛ over the interval 0.15⩽R⩽1.2 g/cm2. At ρ=300 g/cm3, the minimum ignition energy is about 14 kJ; an optimal set of parameters (with energy and power about the required minimum, and intensity relatively close to the minimum) is Ep≅17 kJ, Wp≅0.85×1015 W, and Ip≅6.5×1019 W/cm2 (achieved at R=0.6 g/cm2). The optimal energy scales with the density as Ep∝ρ−1.85. Scaling laws are also presented for the other pulse parameters and for the limiting energy gain.
The radial and poloidal localization of fast magnetoacoustic eigenmodes in tokamaks
Authors: Fülöp T. , Lisak M. , Kolesnichenko Ya. I. , Anderson D.
Published: July 2002

Edge-localized fast magnetoacoustic eigenmodes (FME) may be responsible for the observed superthermal ion cyclotron emission in recent deuterium/deuterium (DD) and deuterium/tritium (DT) experiments. These modes can be driven unstable by resonant interaction with a small population of energetic ions (e.g., fusion alphas), having an anisotropic distribution in velocity space, provided that the mode frequency is close to the ion cyclotron frequency. In the present paper, the radial and poloidal structure of these eigenmodes is analyzed, by solving the two-dimensional (2D) eigenmode equation both numerically and analytically using a variational approach. In particular, the conditions for the mode localization and the dependence of the mode structure on aspect ratio and ellipticity are investigated. The eigenmode is found to be radially localized near the plasma edge. In a tokamak with finite aspect ratio, the mode is localized also poloidally near the outer midplane edge. The existence of localized solutions for both sign of the poloidal mode number is found to be sensitive to the ellipticity, the magnitude of parallel wave number and the plasma density profile.
Enhanced quantum efficiency internal photoemission detectors by grating coupling to surface plasma waves
Authors: Brueck S. R. J. , Diadiuk V. , Jones T. , Lenth W.
Published: July 2002

Enhanced quantum efficiencies have been obtained for Au-InP internal photoemission detectors using grating coupling of incident radiation into surface plasma waves confined to the air-metal interface. Enhancements of over a factor of 30 are observed at the resonance coupling angles. A model calculation of the surface plasma wave coupling is in good qualitative agreement with the experiment. Time-resolved response measurements show that the present detectors are capacitance limited; picosecond response speeds are attainable with lower carrier concentration materials and smaller active areas.
Negative photoconductivity of two-dimensional holes in GaAs/AlGaAs heterojunctions
Authors: Chou M. J. , Tsui D. C. , Weimann G.
Published: July 2002

A negative photoconductivity is observed due to the two-dimensional (2D) holes at GaAs/Al0.5Ga0.5As heterojunctions under illumination by a red light-emitting diode below ∼6 K. The photoconductivity follows a nonexponential decay after the illumination is turned off. Quantum transport measurements are made to demonstrate explicitly that the photoconductivity is due to a decrease in the density and mobility of the 2D holes, and a model is proposed to explain the phenomenon.
New capping technique for zone-melting recrystallization of silicon-on-insulator films
Authors: Chen C. K. , Geis M. W. , Finn M. C. , Tsaur B-Y.
Published: July 2002

A new capping technique employing high-temperature NH3 annealing has been developed to ensure uniform wetting by the molten Si zone during zone-melting recrystallization of Si-on-insulator films. By using this technique, we have reproducibly prepared 0.5-μm-thick films with 〈100〉 crystalline texture that are greatly improved in smoothness, void density, and thickness uniformity. In addition, recrystallized 1-μm-thick films have been obtained with large areas that are free of subboundaries, containing only threading dislocations at densities of less than 2×106 cm−2.
Low-frequency noise in dc superconducting quantum interference devices below 1 K
Authors: Wellstood Frederick C. , Urbina Cristian , Clarke John
Published: July 2002

At temperatures below about 1 K, a series of dc superconducting quantum interference devices (SQUID’s) exhibited an apparent flux noise with a spectral density scaling as 1/f α, where 0.58<α<0.80. Typically, the magnitude of the noise increased as the temperature was lowered below 1 K, tending to flatten out at low temperatures with a value of 7±3 μΦ0Hz−1/2 at 1 Hz that was nearly independent of the parameters and materials of the SQUID’s. Although a large number of hypothetical sources of the noise have been eliminated, the origin remains unidentified.
Submicrosecond electro-optic switching in the liquid-crystal smectic A phase: The soft-mode ferroelectric effect
Authors: Andersson G. , Dahl I. , Keller P. , Kuczyński W. , Lagerwall S. T. , Skarp K. , Stebler B.
Published: July 2002

A new liquid-crystal electro-optic modulating device similar to the surface-stabilized ferroelectric liquid-crystal device is described. It uses the same kind of ferroelectric chiral smectics and the same geometry as that device (thin sample in the ‘‘bookshelf ’’ layer arrangement) but instead of using a tilted smectic phase like the C* phase, it utilizes the above-lying, nonferroelectric A phase, taking advantage of the electroclinic effect. The achievable optical intensity modulation that can be detected through the full range of the A phase is considerably lower than for the surface-stabilized device, but the response is much faster. Furthermore, the response is strictly linear with respect to the applied electric field. The device concept is thus appropriate for modulator rather than for display applications. We describe the underlying physics and present measurements of induced tilt angle, of light modulation depth, and of rise time.
Subboundary-free zone-melt recrystallization of thin-film silicon
Authors: Pfeiffer Loren , Gelman A. E. , Jackson K. A. , West K. W. , Batstone J. L.
Published: July 2002

Scanned zone-melt recrystallization (ZMR) of amorphous Si 1-μm films on SiO2 results in subboundary-free material provided the thermal gradient along the scan is reduced to 4 K/mm or less. Below this value the usual ZMR subboundaries consisting of networks of in-plane edge dislocations are replaced by rows of threading dislocations. We account for the two kinds of crystallization by extending the faceted solidification model that we developed previously. We consider profiles of the solidification front at the intersections of {111} facet pairs where subboundaries are known to form, and postulate that the profiles are aligned approximately normal to the scan in the high gradient case, but become tilted toward the plane of the SiO2 cap layer for the low gradient case. The tilting accounts in a natural way for subboundary removal and the transition from in-plane to threading dislocations.
Thermal desorption of oxides on InP
Authors: Lau W. M. , Sodhi R. N. S. , Ingrey S.
Published: July 2002

The thermal desorption of thin oxide films on n- and p-type InP has been studied by using x-ray photoelectron spectroscopy. It was found that oxides formed on InP could be completely desorbed at 458 °C without causing surface decomposition. The phosphorus and indium oxides desorbed together within 5°. However, heating the oxidized surface to about 453 °C, while not changing the chemical structure of the phosphorus oxides, did remove a significant amount of indium oxides. Heating at this lower temperature also induced changes of the position of the surface Fermi level. On n-InP, it changes from 0.1 eV below the conduction-band minimum to 0.3 eV, and on p-InP, from 0.6 to 0.4 eV. Upon complete desorption of all surface oxides at 458 °C, the Fermi level on n-InP was then pinned at 0.3 eV, whereas that of p-InP moved down to 0.9 eV. This suggests a reduction of donor defects. Heating the surface of 458 °C for more than a few minutes or heating at a slightly higher temperature caused a loss of phosphorus. On such a decomposed surface, the Fermi level of n-InP was pinned at 0.5 eV and p-InP at 0.7 eV, which indicates the formation of more donor and acceptor defects.
An efficient system for conditional gene expression in embryonic stem cells and in their
in vitro
and
in vivo
differentiated derivatives
Authors: Vallier Ludovic , Mancip Jimmy , Markossian Suzy , Lukaszewicz Agnès , Dehay Colette , Metzger Daniel , Chambon Pierre , Samarut Jacques , Savatier Pierre
Published: July 2002

We have developed a universally applicable system for conditional
gene expression in embryonic stem (ES) cells that relies on
tamoxifen-dependent Cre recombinase-loxP site-mediated recombination
and bicistronic gene-trap expression vectors that allow transgene
expression from endogenous cellular promoters. Two vectors
were introduced into the genome of recipient ES cells, successively:
(
i
) a bicistronic gene-trap vector encoding the
β-galactosidase/neo
R
fusion protein and the
Cre-ER
T2
(Cre recombinase fused to a mutated ligand-binding
domain of the human estrogen receptor) and (
ii
) a
bicistronic gene-trap vector encoding the hygro
R
protein
and the human alkaline phosphatase (hAP), the expression of which is
prevented by tandemly repeated stop-of-transcription sequences flanked
by loxP sites. In selected clones, hAP expression was shown to be
regulated accurately by 4′hydroxy-tamoxifen. Strict hormone-dependent
expression of hAP was achieved (
i
)
in
vitro
in undifferentiated ES cells and embryoid bodies,
(
ii
)
in vivo
in virtually all the tissues
of the 10-day-old chimeric fetus (after injection of
4′hydroxy-tamoxifen to foster mothers), and (
iii
)
ex vivo
in primary embryonic fibroblasts isolated from
chimeric fetuses. Therefore, this approach can be applied to drive
conditional expression of virtually any transgene in a large variety of
cell types, both
in vitro
and
in vivo
.
Using three-dimensional microfluidic networks for solving computationally hard problems
Authors: Chiu Daniel T. , Pezzoli Elena , Wu Hongkai , Stroock Abraham D. , Whitesides George M.
Published: July 2002

This paper describes the design of a parallel algorithm that uses
moving fluids in a three-dimensional microfluidic system to solve a
nondeterministically polynomial complete problem (the maximal clique
problem) in polynomial time. This algorithm relies on
(
i
) parallel fabrication of the microfluidic system,
(
ii
) parallel searching of all potential solutions by
using fluid flow, and (
iii
) parallel optical readout of
all solutions. This algorithm was implemented to solve the maximal
clique problem for a simple graph with six vertices. The successful
implementation of this algorithm to compute solutions for small-size
graphs with fluids in microchannels is not useful,
per
se
, but does suggest broader application for microfluidics
in computation and control.
Evolution of the RNA polymerase II C-terminal domain
Authors: Stiller John W. , Hall Benjamin D.
Published: July 2002

In recent years a great deal of biochemical and genetic research has focused on the C-terminal domain (CTD) of the largest subunit (RPB1) of DNA-dependent RNA polymerase II. This strongly conserved domain of tandemly repeated heptapeptides has been linked functionally to important steps in the initiation and processing of mRNA transcripts in both animals and fungi. Although they are absolutely required for viability in these organisms, C-terminal tandem repeats do not occur in RPB1 sequences from diverse eukaryotic taxa. Here we present phylogenetic analyses of
RPB
1 sequences showing that canonical CTD heptads are strongly conserved in only a subset of eukaryotic groups, all apparently descended from a single common ancestor. Moreover, eukaryotic groups in which the most complex patterns of ontogenetic development occur are descended from this CTD-containing ancestor. Consistent with the results of genetic and biochemical investigations of CTD function, these analyses suggest that the enhanced control over RNA polymerase II transcription conveyed by acquired CTD/protein interactions was an important step in the evolution of intricate patterns of gene expression that are a hallmark of large, developmentally complex eukaryotic organisms.
Essential role of
Drosophila Hdac1
in homeotic gene silencing
Authors: Chang Yuh-Long , Peng Yu-Huei , Pan I-Ching , Sun Der-Shan , King Balas , Huang Der-Hwa
Published: July 2002

Deacetylation of the N-terminal tails of core histones plays a
crucial role in gene silencing.
Rpd3
and
Hda1
represent two major types of genes encoding
trichostatin A-sensitive histone deacetylases. Although they have been
widely found, their cellular and developmental roles remain to be
elucidated in metazoa. We show that
Drosophila Hdac1
, an
Rpd3
-type gene, interacts cooperatively with Polycomb
group repressors in silencing the homeotic genes that are essential for
axial patterning of body segments. The biochemical copurification and
cytological colocalization of HDAC1 and Polycomb group repressors
strongly suggest that HDAC1 is a component of the silencing complex for
chromatin modification on specific regulatory regions of homeotic
genes.
Unbinding process of adsorbed proteins under external stress studied by atomic force microscopy spectroscopy
Authors: Gergely C. , Voegel J.-C. , Schaaf P. , Senger B. , Maaloum M. , Hörber J. K. H. , Hemmerlé J.
Published: July 2002

We report the study of the dynamics of the unbinding process under
a force load
f
of adsorbed proteins (fibrinogen) on a
solid surface (hydrophilic silica) by means of atomic force microscopy
spectroscopy. By varying the loading rate

r
f

, defined by
f
=

r
f

t, t being the time, we find that, as for
specific interactions, the mean rupture force increases with

r
f

. This unbinding process is analyzed in
the framework of the widely used Bell model. The typical dissociation
rate at zero force entering in the model lies between 0.02 and 0.6
s
−1
. Each measured rupture is characterized by a
force
f
0
, which appears to be quantized
in integer multiples of 180–200 pN.
Alternative splicing of the rat sodium/bile acid transporter changes its cellular localization and transport properties
Authors: Lazaridis Konstantinos N. , Tietz Pam , Wu Ting , Kip Sertac , Dawson Paul A. , LaRusso Nicholas F.
Published: July 2002

Bile secretion involves the structural and functional interplay of
hepatocytes and cholangiocytes, the cells lining the intrahepatic bile
ducts. Hepatocytes actively secrete bile acids into the canalicular
space and cholangiocytes then transport bile acids in a vectorial
manner across their apical and basolateral plasma membranes. The
initial step in the transepithelial transport of bile acids across rat
cholangiocytes is apical uptake by a Na
+
-dependent bile
acid transporter (ASBT). To date, the molecular basis of the obligate
efflux mechanism for extrusion of bile acids across the cholangiocyte
basolateral membrane remains unknown. We have identified an exon-2
skipped, alternatively spliced form of ASBT, designated t-ASBT,
expressed in rat cholangiocytes, ileum, and
kidney
.
Alternative splicing causes a frameshift that
produces a 154-aa protein
.
Antipeptide antibodies
detected the ≈19 kDa t-ASBT polypeptide in rat cholangiocytes,
ileum, and kidney. The t-ASBT was specifically localized to the
basolateral domain of cholangiocytes. Transport studies in
Xenopus
oocytes revealed that t-ASBT can function as a
bile acid efflux protein. Thus, alternative splicing changes the
cellular targeting of ASBT, alters its functional properties, and
provides a mechanism for rat cholangiocytes and other bile
acid-transporting epithelia to extrude bile acids. Our work represents
an example in which a single gene appears to encode via alternative
splicing both uptake and obligate efflux carriers in a bile
acid-transporting epithelial cell.
Fossilized high pressure from the Earth's deep interior: The coesite-in-diamond barometer
Authors: Sobolev Nikolai V. , Fursenko Boris A. , Goryainov Sergei V. , Shu Jinfu , Hemley Russell J. , Mao Ho-kwang , Boyd Francis R.
Published: July 2002

Mineral inclusions in diamonds provide an important source of information about the composition of the continental lithosphere at depths exceeding 120–150 km, i.e., within the diamond stability field. Fossilized high pressures in coesite inclusions from a Venezuela diamond have been identified and measured by using laser Raman and synchrotron x-ray microanalytical techniques. Micro-Raman measurements on an intact inclusion of remnant vibrational band shifts give a high confining pressure of 3.62 (±0.18) GPa. Synchrotron single-crystal diffraction measurements of the volume compression are in accord with the Raman results and also revealed direct structural information on the state of the inclusion. In contrast to olivine and garnet inclusions, the thermoelasticity of coesite favors accurate identification of pressure preservation. Owing to the unique combination of physical properties of coesite and diamond, this “coesite-in-diamond” geobarometer is virtually independent of temperature, allowing an estimation of the initial pressure of Venezuela diamond formation of 5.5 (±0.5) GPa.
Identification of multiple CDH1 homologues in vertebrates conferring different substrate specificities
Authors: Wan Yong , Kirschner Marc W.
Published: July 2002

CDC20/CDH1 activates the anaphase-promoting complex (APC) and targets various substrates for degradation, thereby allowing the ordered progression through mitosis and G
1
. We have found multiple functional CDH1 homologues in the chick. The transcripts of these novel genes are differentially localized to proliferating, differentiated, and postmitotic tissues. All four proteins bind and form a complex with APC
in vitro
and in cultural cells and have quantitatively different activities in mediating ubiquitination of various APC substrates. Our results suggest that multiple CDH1s may temporally and spatially regulate APC activity both within and outside of the cell cycle.
Surface structure of the COPII-coated vesicle
Authors: Matsuoka Ken , Schekman Randy , Orci Lelio , Heuser John E.
Published: July 2002

The spatial arrangement of COPII coat protein subunits was analyzed by crosslinking to an artificial membrane surface and by electron microscopy of coat proteins and coated vesicle surfaces. The efficiency of COPII subunit crosslinking to phospholipids declined in order of protein recruitment to the coat: Sar1p > Sec23/24p ≫ Sec13/31p. Deep-etch rotary shadowing and electron microscopy were used to explore the COPII subunit structure with isolated proteins and coated vesicles. Sec23/24 resembles a bow tie, and Sec13/31p contains terminal bilobed globular structures bordering a central rod. The surface structure of COPII vesicles revealed a coat built with polygonal units. The length of the side of the hexagonal/pentagonal units is close to the dimension of the central rod-like segment of Sec13/31. Partially uncoated profiles revealed strands of Sec13/31p stripped from the vesicle surface. We conclude that the coat subunits form layers displaced from the membrane surface in reverse order of addition to the coat.
Targeted chromatin binding and histone acetylation
in vivo
by thyroid hormone receptor during amphibian development
Authors: Sachs Laurent M. , Shi Yun-Bo
Published: July 2002

Amphibian metamorphosis is marked by dramatic, thyroid hormone
(TH)-induced changes involving gene regulation by TH receptor (TR). It
has been postulated that TR-mediated gene regulation involves chromatin
remodeling. In the absence of ligand, TR can repress gene expression by
recruiting a histone deacetylase complex, whereas liganded TR recruits
a histone acetylase complex for gene activation. Earlier studies have
led us to propose a dual function model for TR during development. In
premetamorphic tadpoles, unliganded TR represses transcription
involving histone deacetylation. During metamorphosis,
endogenous TH allows TR to activate gene expression through
histone acetylation. Here using chromatin immunoprecipitation assay, we
directly demonstrate TR binding to TH response genes constitutively
in vivo
in premetamorphic tadpoles. We further show that
TH treatment leads to histone deacetylase release from TH response gene
promoters. Interestingly, in whole animals, changes in histone
acetylation show little correlation with the expression of TH response
genes. On the other hand, in the intestine and tail, where TH response
genes are known to be up-regulated more dramatically by TH than in most
other organs, we demonstrate that TH treatment induces gene activation
and histone H4 acetylation. These data argue for a role of histone
acetylation in transcriptional regulation by TRs during amphibian
development in some tissues, whereas in others changes in histone
acetylation levels may play no or only a minor role, supporting the
existence of important alternative mechanisms in gene regulation by TR.
Location of a potential transport binding site in a sigma class glutathione transferase by x-ray crystallography.
Authors: Ji X , von Rosenvinge E C , Johnson W W , Armstrong R N , Gilliland G L
Published: July 2002

The crystal structure of the sigma class glutathione transferase from squid digestive gland in complex with S-(3-iodobenzyl)glutathione reveals a third binding site for the glutathione conjugate besides the two in the active sites of the dimer. The additional binding site is near the crystallographic two-fold axis between the two alpha 4-turn-alpha 5 motifs. The principal binding interactions with the conjugate include specific electrostatic interactions between the peptide and the two subunits and a hydrophobic cavity found across the two-fold axis that accommodates the 3-iodobenzyl group. Thus, two identical, symmetry-related but mutually exclusive binding modes for the third conjugate are observed. The hydrophobic pocket is about 14 A from the hydroxyl group of Tyr-7 in the active site. This site is a potential transport binding site for hydrophobic molecules or their glutathione conjugates.
CP-154,526: a potent and selective nonpeptide antagonist of corticotropin releasing factor receptors.
Authors: Schulz D W , Mansbach R S , Sprouse J , Braselton J P , Collins J , Corman M , Dunaiskis A , Faraci S , Schmidt A W , Seeger T , Seymour P , Tingley F D , Winston E N , Chen Y L , Heym J
Published: July 2002

Here we describe the properties of CP-154,526, a potent and selective nonpeptide antagonist of corticotropin (ACTH) releasing factor (CRF) receptors. CP-154,526 binds with high affinity to CRF receptors (Ki < 10 nM) and blocks CRF-stimulated adenylate cyclase activity in membranes prepared from rat cortex and pituitary. Systemically administered CP-154,526 antagonizes the stimulatory effects of exogenous CRF on plasma ACTH, locus coeruleus neuronal firing and startle response amplitude. Potential anxiolytic activity of CP-154,526 was revealed in a fearpotentiated startle paradigm. These data are presented in the context of clinical findings, which suggest that CRF is hypersecreted in certain pathological states. We propose that a CRF antagonist such as CP-154,526 could affirm the role of CRF in certain psychiatric diseases and may be of significant value in the treatment of these disorders.
An X chromosome-linked gene encoding a protein with characteristics of a rhoGAP predominantly expressed in hematopoietic cells.
Authors: Tribioli C , Droetto S , Bione S , Cesareni G , Torrisi M R , Lotti L V , Lanfrancone L , Toniolo D , Pelicci P
Published: July 2002

An increasingly large number of proteins involved in signal transduction have been identified in recent years and shown to control different steps of cell survival, proliferation, and differentiation. Among the genes recently identified at the tip of the long arm of the human X chromosome, a novel gene, C1, encodes a protein that appears to represent a newly discovered member of the group of signaling proteins involved in regulation of the small GTP binding proteins of the ras superfamily. The protein encoded by C1, p115, is synthesized predominantly in cells of hematopoietic origin. It is characterized by two regions of similarity to motifs present in known proteins: GAP and SH3 homologous regions. Its localization in a narrow cytoplasmic region just below the plasma membrane and its inhibitory effect on stress fiber organization indicate that p115 may down regulate rho-like GTPases in hematopoietic cells.
Cloning of human acetyl-CoA carboxylase-beta and its unique features.
Authors: Ha J , Lee J K , Kim K S , Witters L A , Kim K H
Published: July 2002

Acetyl-CoA carboxylase, which has a molecular mass of 265 kDa (ACC-alpha), catalyzes the rate-limiting step in the biosynthesis of long-chain fatty acids. In this study we report the complete amino acid sequence and unique features of an isoform of ACC with a molecular mass of 275 kDa (ACC-beta), which is primarily expressed in heart and skeletal muscles. In these tissues, ACC-beta may be involved in the regulation of fatty acid oxidation, rather than fatty acid biosynthesis. ACC-beta contains an amino acid sequence at the N terminus which is about 200 amino acids long and may be uniquely related to the role of ACC-beta in controlling carnitine palmitoyltransferase I activity and fatty acid oxidation by mitochondria. If we exclude this unique sequence at the N terminus the two forms of ACC show about 75% amino acid identity. All of the known functional domains of ACC are found in the homologous regions. Human ACC-beta cDNA has an open reading frame of 7,343 bases, encoding a protein of 2,458 amino acids, with a calculated molecular mass of 276,638 Da. The mRNA size of human ACC-beta is approximately 10 kb and is primarily expressed in heart and skeletal muscle tissues, whereas ACC-alpha mRNA is detected in all tissues tested. A fragment of ACC-beta cDNA was expressed in Escherichia coli and antibodies against the peptide were generated to establish that the cDNA sequence that we cloned is that for ACC-beta.
Depletion of intracellular polyamines relieves inward rectification of potassium channels.
Authors: Shyng S L , Sha Q , Ferrigni T , Lopatin A N , Nichols C G
Published: July 2002

Two different approaches were used to examine the in vivo role of polyamines in causing inward rectification of potassium channels. In two-microelectrode voltage-clamp experiments, 24-hr incubation of Xenopus oocytes injected with 50 nl of difluoromethylornithine (5 mM) and methylglyoxal bis(guanylhydrazone) (1 mM) caused an approximate doubling of expressed Kir2.1 currents and relieved rectification by causing an approximately +10-mV shift of the voltage at which currents are half-maximally inhibited. Second, a putrescine auxotrophic, ornithine decarboxylase-deficient Chinese hamster ovary (O-CHO) cell line was stably transfected with the cDNA encoding Kir2.3. Withdrawal of putrescine from the medium led to rapid (1-day) loss of the instantaneous phase of Kir2.3 channel activation, consistent with a decline of intracellular putrescine levels. Four days after putrescine withdrawal, macroscopic conductance, assessed using an 86Rb+ flux assay, was approximately doubled, and this corresponded to a +30-mV shift of V1/2 of rectification. With increasing time after putrescine withdrawal, there was an increase in the slowest phase of current activation, corresponding to an increase in the spermine-to-spermidine ratio over time. These results provide direct evidence for a role of each polyamine in induction of rectification, and they further demonstrate that in vivo modulation of rectification is possible by manipulation of polyamine levels using genetic and pharmacological approaches.
The leucine zipper may induce electrophoretic mobility anomalies without DNA bending
Authors: McCormick Richard J. , Badalian Tina , Fisher David E.
Published: July 2002

Numerous proteins bend DNA upon binding, a phenomenon of potential
significance for regulation of gene expression and chromatin. DNA
bending is commonly predicted from the presence of electrophoretic
mobility anomalies in protein–DNA complexes. However, as compared with
electrophoretic methods, several DNA binding oncoprotein families do
not display comparable evidence of DNA bends in x-ray structural
studies. Herein, circularization kinetics and affinity measurements
with prebent DNA templates were employed to assess bending and DNA
structural preferences for Max and other basic
helix–loop–helix/leucine zipper proteins. In this way, proteins in
the Myc/Max basic helix–loop–helix/leucine zipper family were
found not to bend DNA in solution but to actually stabilize DNA in an
unbent configuration that resists circularization. The mobility anomaly
was found to be induced by the leucine zipper protein motif, rather
than structural distortions of DNA. Thus rigid protein domain
structures may induce anomalous electrophoretic mobility. Moreover, the
energetic preference of non-DNA bending proteins for unbent templates
suggests mechanisms whereby chromatin structure may regulate
transcription.
A heterotrimeric G protein complex couples the muscarinic m1 receptor to phospholipase C-beta.
Authors: Dippel E , Kalkbrenner F , Wittig B , Schultz G
Published: July 2002

We addressed the question as to which subtypes of G protein subunits mediate the activation of phospholipase C-beta by the muscarinic m1 receptor. We used the rat basophilic leukemia cell line RBL-2H3-hm1 stably transfected with the human muscarinic m1 receptor cDNA. We microinjected antisense oligonucleotides into the nuclei of the cells to inhibit selectively the expression of G protein subunits; 48 hr later muscarinic receptors were activated by carbachol, and the increase in free cytosolic calcium concentration ([Ca2+]i) was measured. Antisense oligonucleotides directed against the mRNA coding for alpha(q) and alpha11 subunits both suppressed the carbachol-induced increase in [Ca2+]i. In cells injected with antisense oligonucleotides directed against alpha(o1) and alpha14 subunits, the carbachol effect was unchanged. A corresponding reduction of Galpha(q), and Galpha11 proteins by 70-80% compared to uninjected cells was immunochemically detected 2 days after injection of a mixture of alpha(q) and alpha11 antisense oligonucleotides. Expression of Galpha(q) and Galpha11 completely recovered after 4 days. Cells injected with antisense oligonucleotides directed against the mRNAs encoding for beta1, beta4, and gamma4 subunits showed a suppression of the carbachol-induced increase in [Ca2+]i compared to uninjected cells measured at the same time from the same coverslip, whereas in cells injected with antisense oligonucleotides directed against the beta2, beta3, gamma1, gamma2, gamma3, gamma5, and gamma7 subunits, no suppression of carbachol effect was observed. In summary, the results from RBL-2H3-hm1 cells indicate that the m1 receptor utilizes a G protein complex composed of the subunits alpha(q), alpha11, beta1, beta4, and gamma4 to activate phospholipase C.
Arrest of endotoxin-induced hypotension by transforming growth factor beta1.
Authors: Perrella M A , Hsieh C M , Lee W S , Shieh S , Tsai J C , Patterson C , Lowenstein C J , Long N C , Haber E , Shore S , Lee M E
Published: July 2002

Septic shock is a cytokine-mediated process typically caused by a severe underlying infection. Toxins generated by the infecting organism trigger a cascade of events leading to hypotension, to multiple organ system failure, and frequently to death. Beyond supportive care, no effective therapy is available for the treatment of septic shock. Nitric oxide (NO) is a potent vasodilator generated late in the sepsis pathway leading to hypotension; therefore, NO represents a potential target for therapy. We have previously demonstrated that transforming growth factor (TGF) beta1 inhibits inducible NO synthase (iNOS) mRNA and NO production in vascular smooth muscle cells after its induction by cytokines critical in the sepsis cascade. Thus, we hypothesized that TGF-beta1 may inhibit iNOS gene expression in vivo and be beneficial in the treatment of septic shock. In a conscious rat model of septic shock produced by Salmonella typhosa lipopolysaccharide (LPS), TGF-beta1 markedly reduced iNOS mRNA and protein levels in several organs. In contrast, TGF-beta1 did not decrease endothelium-derived constitutive NOS mRNA in organs of rats receiving LPS. We also performed studies in anesthetized rats to evaluate the effect of TGF-beta1 on the hemodynamic compromise of septic shock; after an initial 25% decrease in mean arterial pressure, TGF-beta1 arrested LPS-induced hypotension and decreased mortality. A decrease in iNOS mRNA and protein levels in vascular smooth muscle cells was demonstrated by in situ hybridization and NADPH diaphorase staining in rats treated with TGF-beta1. Thus these studies suggest that TGF-beta1 inhibits iNOS in vivo and that TGF-beta1 may be of future benefit in the therapy of septic shock.
Association of the Est1 protein with telomerase activity in yeast.
Authors: Steiner B R , Hidaka K , Futcher B
Published: July 2002

The est1 mutant was previously identified because it is defective in telomere maintenance and displays a senescent phenotype. To see if Est1 might be a component of yeast telomerase, we examined immunoprecipitated Est1. The yeast telomerase RNA Tlc1 specifically coprecipitated with Est1. Furthermore, the Est1 immunoprecipitates contained a telomerase-like activity. As expected for yeast telomerase, the activity elongated telomeric primers, it required dGTP and dTTP but not dATP or dCTP, and it was sensitive to RNase A. Further evidence suggesting that the activity was telomerase was obtained from experiments using a TLC1-1 mutant strain, which has a mutant telomerase template containing dG residues. The activity immunoprecipitated from TLC1-1 mutant strains incorporated 32P-labeled dCTP, while activity from TLC1 strains did not. Use of different telomeric primer substrates revealed two distinguishable telomerase-like activities: one was dependent on TLC1, and one was not. The TLC1-independent activity may be due to a second yeast telomerase RNA, or it may be some other kind of activity.
Isolation of 10 differentially expressed cDNAs in p53-induced apoptosis: activation of the vertebrate homologue of the drosophila seven in absentia gene.
Authors: Amson R B , Nemani M , Roperch J P , Israeli D , Bougueleret L , Le Gall I , Medhioub M , Linares-Cruz G , Lethrosne F , Pasturaud P , Piouffre L , Prieur S , Susini L , Alvaro V , Millasseau P , Guidicelli C , Bui H , Massart C , Cazes L , Dufour F , Bruzzoni-Giovanelli H , Owadi H , Hennion C , Charpak G , Telerman A
Published: July 2002

We report the isolation of 10 differentially expressed cDNAs in the process of apoptosis induced by the p53 tamor suppressor. As a global analytical method, we performed a differential display of mRNA between mouse M1 myeloid leukemia cells and derived clone LTR6 cells, which contain a stably transfected temperature-sensitive mutant of p53. At 32 degrees C wild-type p53 function is activated in LTR6 cells, resulting in programmed cell death. Eight genes are activated (TSAP; tumor suppressor activated pathway), and two are inhibited (TSIP, tumor suppressor inhibited pathway) in their expression. None of the 10 sequences has hitherto been recognized as part of the p53 signaling pathway. Three TSAPs are homologous to known genes. TSAP1 corresponds to phospholipase C beta 4. TSAP2 has a conserved domain homologous to a multiple endocrine neoplasia I (ZFM1) candidate gene. TSAP3 is the mouse homologue of the Drosophila seven in absentia gene. These data provide novel molecules involved in the pathway of wild-type p53 activation. They establish a functional link between a homologue of a conserved developmental Drosophila gene and signal transduction in tumor suppression leading to programmed cell death.