bluuebunny/crossref_metadata_2025 huggingface dataset:
Response to “Comment on ‘Collisionless m=1 reconnection in tokamaks’ ” [Phys. Plasmas 3, 2411 (1996)]
Authors: Rogers B. N. , Zakharov L.
Published: July 2002

Our numerical simulation of collisionless m = 1 reconnection in tokamaks do not support the Wang and Bhattacharjee theory of explosive growth of plasma instabilities. We disagree with their assumptions link-ing the poloidal flow to the plasma pressure. (AIP)
Collisionless electron heating in inductively coupled discharges
Authors: Shaing K. C. , Aydemir A. Y.
Published: July 2002

A kinetic theory of collisionless electron heating is developed for inductively coupled discharges with a finite length L. The novel effect associated with the finite-length system is the resonance between the bounce motion of the electrons and the wave frequency, leading to enhanced heating. The theory is in agreement with results of electromagnetic particle simulations.
Turbulization of nonlinear Langmuir oscillations in a cold plasma
Authors: Kovalenko A. V. , Kovalenko V. P.
Published: July 2002

It is shown that the electric field of Langmuir oscillations in a cold plasma contains a component, independent of time, setting ions in motion. Using Lagrange variables, one-dimensional dynamics of plasma in respect to the interaction between electron oscillations and ion movement is investigated. As a consequence of this interaction, the crossing of electron trajectories occurs even at small amplitudes at time tc, i.e., one-dimensional turbulence appears in the system. The expression for tc is derived. In time tc ion displacements as well as ion energy are found to depend only on the electron–ion mass relationship.
Resistive pressure gradient-driven turbulence at stellarator plasma edge
Authors: Garcia L. , Carreras B. A. , Lynch V. E. , Leboeuf J. N. , Newman D. E.
Published: July 2002

High resolution calculations of resistive pressure gradient-driven turbulence for the plasma edge parameters of the Advanced Toroidal Facility (ATF) [J. F. Lyon et al., Fusion Technol. 10, 179 (1986)] electron cyclotron heated discharges give fluctuation levels, consistent with the experimental measurements. This turbulence model is also used to simulate the transition from the low confinement to the high confinement mode. The transition is triggered through the poloidal flow amplification induced by the Reynolds stress. After the transition, the confinement improvement is relatively low (30%–40%), even for unrealistically low poloidal viscosity. In the high confinement mode, the characteristic radial scale length of the poloidal flow in the three-dimensional calculations (separation between the lowest-n resonant surfaces) is different from the single helicity results (radial correlation length of the fluctuations). The simple criterion based on the ratio of shearing rate to the linear growth rate does not quantitatively account for the fluctuation reduction.
Measurement of and hypothesis for particle influx and density peaking in a tokamak plasma
Authors: Chu T. K.
Published: July 2002

The particle influx, density peaking, and a concomitant change of the poloidal magnetic field Bθ, occurring after the particle source rate at the boundary is reduced from an earlier higher rate, are measured in an inductively driven tokamak plasma. A hypothesis is proposed to interpret the measurement: in neoclassical theory the toroidal electric field that drives the coupled transport in the Onsager relation is an inductive field; it is the differential field in a nonuniform resistive toroidal electric field, Eηj(r). The transport is nonlocal and not at the steady state because the boundary and initial conditions of Eηj(r) must be satisfied; neoclassical theory describes the transport due to perturbations on the steady state. That state, determined by the absence of the coupled transport in the Onsager relation, is uniform resistive dissipation: Eηj=const. The source of the perturbation is the particle source just outside the boundary.
Interpretation of particle acceleration in a simulation study of collisionless reconnection
Authors: Litvinenko Yuri E.
Published: July 2002

A recent simulation study [Horiuchi and Sato, Phys. Plasmas 4, 277 (1997)] investigated collisionless magnetic reconnection in a sheared magnetic field. Theoretical models for particle acceleration in current sheets are used to interpret some of the simulation results, which are found to be consistent with analytical expressions for values of the electron energy gain, the acceleration time, and the longitudinal magnetic field giving rise to adiabatic particle motion. The simulation also identified an ion acceleration mechanism that will require additional theoretical study.
Transport theory in the collisionless limit
Authors: Hazeltine R. D.
Published: July 2002

Traditional transport theory provides a closure of fluid equations that is valid in the collisional, short mean-free-path limit. The possibility of extending an analogous closure to long mean-free path is examined here. An appropriate kinetic equation, using a model collision operator, is solved rigorously for arbitrary collisionality but weak, Maxwellian source terms. The corresponding particle and heat flows are then expressed in terms of the density and temperature profiles. The transport matrix is found to be symmetric even at vanishing collision frequency; in the collisionless limit it takes the form of nonlocal operators. The operator corresponding to thermal conductivity agrees with one found previously by other authors. However particle diffusion, which turns out to satisfy a local Fick’s law for any finite collision frequency, becomes singular at vanishing collisionality, where the pressure gradient vanishes. It is concluded that the fluxes can generally be expressed in terms of particle and energy sources, but not always in terms of pressure and temperature profiles.
Theory of wire number scaling in wire-array Z pinches
Authors: Desjarlais M. P. , Marder B. M.
Published: July 2002

Pulsed-power-driven Z pinches, produced by imploding cylindrical arrays of many wires, have generated very high x-ray radiation powers (>200 TW) and energies (2 MJ). Experiments have revealed a steady improvement in Z-pinch performance with increasing wire number at fixed total mass and array radius. The dominant mechanism acting to limit the performance of these devices is believed to be the Rayleigh-Taylor instability which broadens the radially imploding plasma sheath and consequently reduces the peak radiation power. A model is presented which describes an amplification over the two-dimensional Rayleigh-Taylor growth rate brought about by kink-like forces on the individual wires. This amplification factor goes to zero as the number of wires approaches infinity. This model gives results which are in good agreement with the experimental data and provides a scaling for wire-array Z pinches.
Magnetohydrodynamic modeling of the global solar corona
Authors: Mikić Zoran , Linker Jon A. , Schnack Dalton D. , Lionello Roberto , Tarditi Alfonso
Published: July 2002

A three-dimensional magnetohydrodynamic model of the global solar corona is described. The model uses observed photospheric magnetic fields as a boundary condition. A version of the model with a polytropic energy equation is used to interpret solar observations, including eclipse images of the corona, Ulysses spacecraft measurements of the interplanetary magnetic field, and coronal hole boundaries from Kitt Peak He 10 830 Å maps and extreme ultraviolet images from the Solar Heliospheric Observatory. Observed magnetic fields are used as a boundary condition to model the evolution of the solar corona during the period February 1997–March 1998. A model with an improved energy equation and Alfvén waves that is better able to model the solar wind is also presented.
Modeling of ultra-short-pulse reflectometry
Authors: Cohen B. I. , Hooper E. B. , Kaiser T. B. , Williams E. A. , Domier C. W.
Published: July 2002

Pulsed reflectometry using both ordinary (O) and extraordinary (X) modes can provide time- and space-resolved measurements of the electron density, the magnitude of the magnetic field, the magnetic shear as a function of radius, and information on density and magnetic fluctuations. Such a diagnostic also yields the current profile from the curl of the magnetic field. This research addresses theoretical issues associated with the use of pulsed reflectometry with particular emphasis on applications in the Sustained Spheromak Physics Experiment (SSPX) at the Lawrence Livermore National Laboratory [E. B. Hooper et al., “Sustained Spheromak Physics Experiment,” in Proceedings of the 17th International Atomic Energy Agency (IAEA) Fusion Energy Conference, Yokohama, Japan, October 19–24, 1998, Lawrence Livermore National Laboratory Report UCRL-JC-132034 (September 29, 1998)]. Simulation results are presented for O- and X-mode mixed-polarization reflectometry and linear mode conversion in two spatial dimensions. The profile reconstruction algorithms depend on Wentzel–Kramers–Brillouin–Jeffreys (WKBJ) formulae for group delays and linear mode conversion, which agree reasonably well with direct numerical solutions of the wave equation. Reconstructions of the electron density and modulus of the magnetic field are relatively robust in the presence of two-dimensional electron density and magnetic perturbations of the plasma.
Physics of compact stellarators
Authors: Hirshman S. P. , Spong D. A. , Whitson J. C. , Nelson B. , Batchelor D. B. , Lyon J. F. , Sanchez R. , Brooks A. , Y.-Fu G. , Goldston R. J. , Ku L-P. , Monticello D. A. , Mynick H. , Neilson G. H. , Pomphrey N. , Redi M. , Reiersen W. , Reiman A. H. , Schmidt J. , White R. , Zarnstorff M. C. , Miner W. H. , Valanju P. M. , Boozer A.
Published: July 2002

Recent progress in the theoretical understanding and design of compact stellarators is described. Hybrid devices, which depart from canonical stellarators by deriving benefits from the bootstrap current which flows at finite beta, comprise a class of low aspect ratio A<4 stellarators. They possess external kink stability (at moderate beta) in the absence of a conducting wall, possible immunity to disruptions through external control of the transform and magnetic shear, and they achieve volume-averaged ballooning beta limits (4%–6%) similar to those in tokamaks. In addition, bootstrap currents can reduce the effects of magnetic islands (self-healing effect) and lead to simpler stellarator coils by reducing the required external transform. Powerful physics and coil optimization codes have been developed and integrated to design experiments aimed at exploring compact stellarators. The physics basis for designing the national compact stellarator will be discussed.
Whistler excitation by short current pulses in a magnetoplasma
Authors: Starodubtsev M. , Krafft C.
Published: July 2002

In the frame of laboratory studies devoted to whistler excitation by a modulated electron beam injected in a magnetoplasma under conditions relevant to space experiments, fast processes have been investigated using the modulated electron beam as a train of short-time current pulses injected in the plasma. Single pulses of duration of the order of τ≃15 ns as well as unmodulated beams with sharp fronts (step functions with rise time of the order of τ≃10 ns) have been injected in the afterglow plasma with an energy of the order of 300 eV. Plasma responses to the fast perturbations are transported by whistler waves in the frequency range ωlh≪1/τ<ωc<ωp. Different types of responses have been evidenced and characterized, depending on the nature of the whistler excitation mechanism involved: Nonresonant transition radiation from the beam injection point and Cherenkov resonant emission. Both emissions could be distinguished one from each other owing to adequate choices of plasma parameters and observation conditions. The formation of wake fields associated with the propagating current pulses has also been observed for the first time in the whistler range. This study should shed light on the physical mechanisms connected with the injection of modulated and pulsed electron beams in space plasmas, as well as on fast processes induced in the whistler frequency range by the presence of suprathermal fluxes of electrons traveling in the ionospheric and magnetospheric plasmas.
Enhancement of electron temperature in a laser-induced plasma using a radio-frequency electric field
Authors: Ohzu Akira , Suzuki Yoji , Maruyama Yoichiro , Arisawa Takashi
Published: July 2002

An experimental study of the enhancement of the electron temperature of a laser-induced plasma by use of radio-frequency dielectric heating has been carried out. A radio-frequency electric field of 140 MHz is used to heat the plasma produced by multistep resonant photoinization. It is clearly observed that the electron temperature increases from 0.3 to 1.0 eV when a radio-frequency input power of 1.0 W is applied. Also, applying heating induces a plasma oscillation. This is due to the generation of ion waves in the plasma, and therefore, means that the enhanced electron temperature is higher than the ion temperature. It is expected that this method will improve the efficiency for extracting ions rapidly from a laser-induced plasma in atomic vapor laser isotope separation.
Stimulated scattering of radiation off quasi-modes in an electron–positron plasma
Authors: Shukla P. K. , Stenflo L.
Published: July 2002

Stimulated electron Compton scattering (SECS) as well as kinetic modulational instabilities of a large amplitude electromagnetic wave in an unmagnetized electron–positron plasma are considered when the radiation is scattered off a quasi-mode whose phase velocity equals the electron or positron thermal velocity. The growth rates of the instabilities are presented.
Kinetic theory of solitary waves on coasting beams in synchrotrons
Authors: Schamel Hans , Fedele Renato
Published: July 2002

A generalization of the Vlasov–Poisson system describing the collective dynamics of stored, high-energy hadron beams under the influence of a complex wall impedance is derived in the highly relativistic beam limit γ≫1. A coherent electric field structure Ez(r,z) is found to affect the beam dynamics in O(γ−2), giving rise to an updated feedback between line density (respectively, beam current) and self-fields. Propagating solitary wave solutions as special solutions of this system are obtained by the potential method known from plasma physics. Various parameter regimes are investigated and wave structures are found which are characterized by notches (respectively, humps) in the resonant part of the distribution function. These coherent waves typically travel with thermal velocities and below (kinetic solitary waves) but also structures moving with larger phase velocities (hydrodynamic solitons) are found. Dory’s conjecture about mass conjugation is approved a posteriori in the purely reactive case but is found to be substantially altered in the strongly resistive case. Hydrodynamic Korteweg–de Vries solitons are shown to exist in the purely reactive case and for beams above transition energy and for weak space charge effects only.
Superconductivity in YBa2−xSrxCu3O7−δ
Authors: Veal B. W. , Kwok W. K. , Umezawa A. , Crabtree G. W. , Jorgensen J. D. , Downey J. W. , Nowicki L. J. , Mitchell A. W. , Paulikas A. P. , Sowers C. H.
Published: July 2002

We report structure, resistivity, and Meissner effect measurements on YBa2−xSrxCu3O7−δ for 0<x<2.0. We find a region of solid solubility extending at least to x=1.0 and a monotonic depression of Tc with x. Using arguments based on structural changes with Sr doping, we speculate that the depression of Tc is due to the local distortion of the lattice in the neighborhood of the Sr site and the introduction of additional oxygen vacancies.
Study of thermally oxidized yttrium films on silicon
Authors: Gurvitch M. , Manchanda L. , Gibson J. M.
Published: July 2002

Electrical and structural characteristics of thin thermally oxidized yttrium layers on Si and on Si covered with 40 Å of SiO2 have been investigated. The factor of ∼ four advantage in the dielectric constant of Y2O3 over SiO2, coupled with extremely low leakage current density of better than 10−10 A/cm2 in a field of 1.9 MV/cm, sufficiently high breakdown strength, and well-behaved capacitance-voltage characteristics makes Y2O3 a viable candidate for Si very large scale integration applications, at least in passive devices. High-resolution transmission electron microscopy reveals the structure of the composite dielectric and provides good agreement between calculated and experimental capacitance.
Fabrication of diode arrays for photovoltaic characterization of silicon substrates
Authors: Sopori B. L.
Published: July 2002

A simple process sequence for the fabrication of passivated mesa diode arrays for photovoltaic characterization of single/polycrystalline silicon substrates is described. These diodes are used to measure a variety of substrate and cell parameters including resistivity, minority-carrier diffusion length, Voc, Jsc, fill factor, and current-voltage characteristics for analysis of the electronic transport properties. Evaluation techniques which use these diodes for determining spatial variations in the material/device charateristics are described. These devices are also suitable for characterizing various cell fabrication processes and for analysis of crystal defects on the solar cell characteristics.
Hysteretic levitation forces in superconducting ceramics
Authors: Moon F. C. , Yanoviak M. M. , Ware R.
Published: July 2002

Magnetization forces between small permanent magnets and bulk high Tc superconducting ceramic materials have been measured and show marked hysteretic behavior as a function of the distance between the magnet and superconductor. Magnetic forces of up to 2500 dyn, both normal and tangential to the superconductor surface, have been made. Near-reversible forces are obtained for small motions of the magnet, however, which are believed to be related to flux pinning.
Superconducting properties of Nb3Al multifilamentary wire
Authors: Inoue K. , Iijima Y. , Takeuchi T.
Published: July 2002

Nb3Al multifilamentary wire has been fabricated by a newly developed process, in which a composite consisting of a niobium matrix and a large number of Al-Mg alloy cores is cold drawn into a wire with ultrafine Al-Mg alloy filaments (about 0.1 μm), and then heat treated to form Nb3Al filaments by the diffusion reaction between the Al-Mg alloy cores and the Nb matrix. The wire shows excellent high-field superconducting properties comparable to those of the practical Nb3Sn multifilamentary wire.
Observation of enhanced properties in samples of silver oxide doped YBa2Cu3Ox
Authors: Peters P. N. , Sisk R. C. , Urban E. W. , Huang C. Y. , Wu M. K.
Published: July 2002

Samples of YBa2 Cu3Ox doped with silver oxide (Tc ∼93 K) have exhibited attractive forces in gradient magnetic fields, both normal and tangential to the surfaces, which are more than twice the sample weight. This allows sample suspension below a rare earth magnet. Critical current density was increased by ∼102 at 77 K. Persistent fields, flux pinning, magnetization, and modeling are described.
Complementary whole-genome technologies reveal the cellular response to proteasome inhibition by PS-341
Authors: Fleming James A. , Lightcap Eric S. , Sadis Seth , Thoroddsen Vala , Bulawa Christine E. , Blackman Ronald K.
Published: July 2002

Although the biochemical targets of most drugs are known, the biological consequences of their actions are typically less well understood. In this study, we have used two whole-genome technologies in
Saccharomyces cerevisiae
to determine the cellular impact of the proteasome inhibitor PS-341. By combining population genomics, the screening of a comprehensive panel of bar-coded mutant strains, and transcript profiling, we have identified the genes and pathways most affected by proteasome inhibition. Many of these function in regulated protein degradation or a subset of mitotic activities. In addition, we identified Rpn4p as the transcription factor most responsible for the cell's ability to compensate for proteasome inhibition. Used together, these complementary technologies provide a general and powerful means to elucidate the cellular ramifications of drug treatment.
The cranium of
Parapithecus grangeri
, an Egyptian Oligocene anthropoidean primate
Authors: Simons Elwyn L.
Published: July 2002

A nearly complete skull of
Parapithecus grangeri
from the early Oligocene of Egypt is described. The specimen is relatively undistorted and is undoubtedly the most complete higher primate skull yet found in the African Oligocene, which also makes it the most complete Oligocene primate cranium worldwide. Belonging in superfamily Parapithecoidea, a group regarded by some as the sister group to all other Anthropoidea, this skull reveals important information about the radiation of stem anthropoideans. This cranium is about 15% larger than size estimates based on a fragmentary cranium of its contemporary and close relative
Apidium phiomense.
It is about the same size as that of the gray gentle lemur,
Hapalemur griseus
, or of platyrrhines such as the owl monkey,
Aotus trivirgatus
, or the titi monkey,
Callicebus torquatus.
Comparatively small orbits and size differences in jaws and teeth show it was both diurnal and dimorphic. This is the only specimen of the species that shows (from sockets) that there were four small upper incisors. Several mandibular specimens of the species establish that there were no permanent lower incisors and that the symphysis was fused. Like other early anthropoideans this species possessed a lower encephalization quotient and less-developed orbital frontality than later anthropoideans. There is full postorbital closure and fusion of the metopic suture, and the ectotympanic forms a rim to the auditory aperture. A probable frontal/alisphenoid contact is a potentially derived resemblance to Catarrhini. A proposed separate genus for the species
P. grangeri
is not sustained.
Cadherin interaction probed by atomic force microscopy
Authors: Baumgartner W. , Hinterdorfer P. , Ness W. , Raab A. , Vestweber D. , Schindler H. , Drenckhahn D.
Published: July 2002

Single molecule atomic force microscopy was used to characterize structure, binding strength (unbinding force), and binding kinetics of a classical cadherin, vascular endothelial (VE)-cadherin, secreted by transfected Chinese hamster ovary cells as cis-dimerized full-length external domain fused to Fc-portion of human IgG. In physiological buffer, the external domain of VE-cadherin dimers is a ≈20-nm-long rod-shaped molecule that collapses and dissociates into monomers (V-shaped structures) in the absence of Ca
2+
. Trans-interaction of dimers is a low-affinity reaction (
K
D
= 10
−3
–10
−5
M,
k
off
= 1.8 s
−1
,
k
on
= 10
3
–10
5
M
−1
·s
−1
) with relatively low unbinding force (35–55 pN at retrace velocities of 200–4,000 nm·s
−1
). Higher order unbinding forces, that increase with interaction time, indicate association of cadherins into complexes with cumulative binding strength. These observations favor a model by which the inherently weak unit binding strength and affinity of cadherin trans-interaction requires clustering and cytoskeletal immobilization for amplification. Binding is regulated by low-affinity Ca
2+
binding sites (
K
D
= 1.15 mM) with high cooperativity (Hill coefficient of 5.04). Local changes of free extracellular Ca
2+
in the narrow intercellular space may be of physiological importance to facilitate rapid remodeling of intercellular adhesion and communication.
Nephrogenic diabetes insipidus in mice lacking aquaporin-3 water channels
Authors: Ma Tonghui , Song Yuanlin , Yang Baoxue , Gillespie Annemarie , Carlson Elaine J. , Epstein Charles J. , Verkman A. S.
Published: July 2002

Aquaporin-3 (AQP3) is a water channel expressed at the basolateral plasma membrane of kidney collecting-duct epithelial cells. The mouse AQP3 cDNA was isolated and encodes a 292-amino acid water/glycerol-transporting glycoprotein expressed in kidney, large airways, eye, urinary bladder, skin, and gastrointestinal tract. The mouse AQP3 gene was analyzed, and AQP3 null mice were generated by targeted gene disruption. The growth and phenotype of AQP3 null mice were grossly normal except for polyuria. AQP3 deletion had little effect on AQP1 or AQP4 protein expression but decreased AQP2 protein expression particularly in renal cortex. Fluid consumption in AQP3 null mice was more than 10-fold greater than that in wild-type litter mates, and urine osmolality (<275 milliosmol) was much lower than in wild-type mice (>1,200 milliosmol). After 1-desamino-8-
d
-arginine-vasopressin administration or water deprivation, the AQP3 null mice were able to concentrate their urine partially to ≈30% of that in wild-type mice. Osmotic water permeability of cortical collecting-duct basolateral membrane, measured by a spatial filtering optics method, was >3-fold reduced by AQP3 deletion. To test the hypothesis that the residual concentrating ability of AQP3 null mice was due to the inner medullary collecting-duct water channel AQP4, AQP3/AQP4 double-knockout mice were generated. The double-knockout mice had greater impairment of urinary-concentrating ability than did the AQP3 single-knockout mice. Our findings establish a form of nephrogenic diabetes insipidus produced by impaired water permeability in collecting-duct basolateral membrane. Basolateral membrane aquaporins may thus provide blood-accessible targets for drug discovery of aquaretic inhibitors.
A Kaposi's sarcoma-associated herpesviral protein inhibits virus-mediated induction of type I interferon by blocking IRF-7 phosphorylation and nuclear accumulation
Authors: Zhu Fan Xiu , King Sonya M. , Smith Eric J. , Levy David E. , Yuan Yan
Published: July 2002

Interferons constitute the earliest immune response against viral infection. They elicit antiviral effects as well as multiple biological responses involved in cell growth regulation and immune activation. Because the interferon-induced cellular antiviral response is the primary defense mechanism against viral infection, many viruses have evolved strategies to antagonize the inhibitory effects of interferon. Here, we demonstrate a strategy that Kaposi's sarcoma-associated herpesvirus uses to block virus-mediated induction of type I interferon. We found that a viral immediate-early protein, namely ORF45, interacts with cellular interferon-regulatory factor 7 (IRF-7). In consequence, IRF-7 phosphorylation is inhibited and the accumulation of IRF-7 in the nucleus in response to viral infection is blocked. IRF-7 is a transcription regulator that is responsible for virus-mediated activation of type I interferon genes. By blocking the phosphorylation and nuclear translocation of IRF-7, ORF45 efficiently inhibits the activation of interferon α and β genes during viral infection. Inhibition of interferon gene expression through a viral protein blocking the activation and nuclear translocation of a crucial transcription factor is a novel mechanism for viral immune evasion.
Cooperative anion binding and electrochemical sensing by modular podands
Authors: Abouderbala Lagili O. , Belcher Warwick J. , Boutelle Martyn G. , Cragg Peter J. , Steed Jonathan W. , Turner David R. , Wallace Karl J.
Published: July 2002

A series of podands based on two or three hydrogen bonding “arms” situated in mutuallyortho,meta, orpararelationships about an aryl core have been prepared, and their affinities for simple inorganic anions were measured. Of the two-arm hosts themetacompound and to a lesser extent theorthohost exhibit a cooperative anion binding effect. The two arms function essentially independently in theparaderivative. The mutuallymetathree-arm host shows dramatically enhanced cooperative binding. Conformational changes within themetatwo-arm host result in significantly enhanced electrochemical anion sensing compared with the more conformationally rigid three-arm host.
Catalysis of
S
-nitrosothiols formation by serum albumin: The mechanism and implication in vascular control
Authors: Rafikova Olga , Rafikov Ruslan , Nudler Evgeny
Published: July 2002

Nitric oxide (NO
⋅
) is a short-lived physiological messenger. Its various biological activities can be preserved in a more stable form of
S
-nitrosothiols (RS-NO). Here we demonstrate that at physiological NO
⋅
concentrations, plasma albumin becomes saturated with NO
⋅
and accelerates formation of low-molecular-weight (LMW) RS-NO
in vitro
and
in vivo
. The mechanism involves micellar catalysis of NO
⋅
oxidation in the albumin hydrophobic core and specific transfer of NO
+
to LMW thiols. Albumin-mediated
S
-nitrosylation and its vasodilatory effect directly depend on the concentration of circulating LMW thiols. Results suggest that the hydrophobic phase formed by albumin serves as a major reservoir of NO
⋅
and its reactive oxides and controls the dynamics of NO
⋅
-dependant processes in the vasculature.
Copy-choice recombination by reverse transcriptases: Reshuffling of genetic markers mediated by RNA chaperones
Authors: Negroni Matteo , Buc Henri
Published: July 2002

Copy-choice recombination efficiently reshuffles genetic markers in retroviruses.
In vivo
, the folding of the genomic RNA is controlled by the nucleocapsid protein (NC). We show that binding of NC onto the acceptor RNA molecule is sufficient to enhance recombination, providing evidence for a mechanism where the structure of the acceptor template determines the template switch. NC as well as another RNA chaperone (StpA) converts recombination into a widespread process no longer restricted to rare hot spots, an effect maximized when both the NC and the reverse transcriptase come from HIV-1. These data suggest that RNA chaperones confer a higher genetic flexibility to retroviruses.
Portosystemic shunting and persistent fetal vascular structures in aryl hydrocarbon receptor-deficient mice
Authors: Lahvis Garet P. , Lindell Susanne L. , Thomas Russell S. , McCuskey Robert S. , Murphy Christopher , Glover Edward , Bentz Michael , Southard James , Bradfield Christopher A.
Published: July 2002

A physiological examination of mice harboring a null allele at the aryl hydrocarbon (
Ah
) locus revealed that the encoded aryl hydrocarbon receptor plays a role in the resolution of fetal vascular structures during development. Although the aryl hydrocarbon receptor is more commonly studied for its role in regulating xenobiotic metabolism and dioxin toxicity, a developmental role of this protein is supported by the observation that
Ah
null mice display smaller livers, reduced fecundity, and decreased body weights. Upon investigating the liver phenotype, we found that the decrease in liver size is directly related to a reduction in hepatocyte size. We also found that smaller hepatocyte size is the result of massive portosystemic shunting in null animals. Colloidal carbon uptake and microsphere perfusion studies indicated that 56% of portal blood flow bypasses the liver sinusoids. Latex corrosion casts and angiography demonstrated that shunting is consistent with the existence of a patent ductus venosus in adult animals. Importantly, fetal vascular structures were also observed at other sites. Intravital microscopy demonstrated an immature sinusoidal architecture in the liver and persistent hyaloid arteries in the eyes of adult
Ah
null mice, whereas corrosion casting experiments described aberrations in kidney vascular patterns.
Regulation of melastatin, a TRP-related protein, through interaction with a cytoplasmic isoform
Authors: Xu X.-Z. Shawn , Moebius Fabian , Gill Donald L. , Montell Craig
Published: July 2002

The TRP (transient receptor potential) superfamily includes a group of subfamilies of channel-like proteins mediating a multitude of physiological signaling processes. The TRP-melastatin (TRPM) subfamily includes the putative tumor suppressor melastatin (MLSN) and is a poorly characterized group of TRP-related proteins. Here, we describe the identification and characterization of an additional TRPM protein TRPM4. We reveal that TRPM4 and MLSN each mediate Ca
2+
entry when expressed in HEK293 cells. Furthermore, we demonstrate that a short form of MLSN (MLSN-S) interacts directly with and suppresses the activity of full-length MLSN (MLSN-L). This suppression seems to result from the inhibition of translocation of MLSN-L to the plasma membrane. We propose that control of translocation through interaction between MLSN-S and MLSN-L represents a mode for regulating ion channel activity.
Translational regulation of mammalian and Drosophila citric acid cycle enzymes via iron-responsive elements.
Authors: Gray N K , Pantopoulos K , Dandekar T , Ackrell B A , Hentze M W
Published: July 2002

The posttranscriptional control of iron uptake, storage, and utilization by iron-responsive elements (IREs) and iron regulatory proteins (IRPs) provides a molecular framework for the regulation of iron homeostasis in many animals. We have identified and characterized IREs in the mRNAs for two different mitochondrial citric acid cycle enzymes. Drosophila melanogaster IRP binds to an IRE in the 5' untranslated region of the mRNA encoding the iron-sulfur protein (Ip) subunit of succinate dehydrogenase (SDH). This interaction is developmentally regulated during Drosophila embryogenesis. In a cell-free translation system, recombinant IRP-1 imposes highly specific translational repression on a reporter mRNA bearing the SDH IRE, and the translation of SDH-Ip mRNA is iron regulated in D. melanogaster Schneider cells. In mammals, an IRE was identified in the 5' untranslated regions of mitochondrial aconitase mRNAs from two species. Recombinant IRP-1 represses aconitase synthesis with similar efficiency as ferritin IRE-controlled translation. The interaction between mammalian IRPs and the aconitase IRE is regulated by iron, nitric oxide, and oxidative stress (H2O2), indicating that these three signals can control the expression of mitochondrial aconitase mRNA. Our results identify a regulatory link between energy and iron metabolism in vertebrates and invertebrates, and suggest biological functions for the IRE/IRP regulatory system in addition to the maintenance of iron homeostasis.
Application of capillary electrophoresis-electrospray ionization mass spectometry in the determination of molecular diversity.
Authors: Dunayevskiy Y M , Vouros P , Wintner E A , Shipps G W , Carell T , Rebek J
Published: July 2002

By means of capillary electrophoresis coupled online to electrospray ionization MS, a library of theoretically 171 disubstituted xanthene derivatives was analyzed. The method allowed the purity and makeup of the library to be determined: 160 of the expected compounds were found to be present, and 12 side-products were also detected in the mixture. Due to the ability of capillary electrophoresis to separate analytes on the basis of charge, most of the xanthene derivatives could be resolved by simple capillary electrophoresis-MS procedures even though 124 of the 171 theoretical compounds were isobaric with at least one other molecule in the mixture. Any remaining unresolved peaks were resolved by MS/MS experiments. The method shows promise for the analysis of small combinatorial libraries with fewer than 1000 components.
Muc1, a mucin-like protein that is regulated by Mss10, is critical for pseudohyphal differentiation in yeast.
Authors: Lambrechts M G , Bauer F F , Marmur J , Pretorius I S
Published: July 2002

Pseudohyphal differentiation in Saccharomyces cerevisiae was first described as a response of diploid cells to nitrogen limitation. Here we report that haploid and diploid starch-degrading S. cerevisiae strains were able to switch from a yeast form to a filamentous pseudohyphal form in response to carbon limitation in the presence of an ample supply of nitrogen. Two genes, MSS10 and MUC1, were cloned and shown to be involved in pseudohyphal differentiation and invasive growth. The deletion of MSS10 resulted in extremely reduced amounts of pseudohyphal differentiation and invasive growth, whereas the deletion of MUC1 abolished pseudohyphal differentiation and invasive growth completely. Mss10 appears to be a transcriptional activator that responds to nutrient limitation and coregulates the expression of MUC1 and the STA1-3 glucoamylase genes, which are involved in starch degradation. MUC1 encodes a 1367-amino acid protein, containing several serine/threonine-rich repeats. Muc1 is a putative integral membrane-bound protein, similar to mammalian mucin-like membrane proteins that have been implicated to play a role in the ability of cancer cells to invade other tissues.
Cross talk between cell death and cell cycle progression: BCL-2 regulates NFAT-mediated activation.
Authors: Linette G P , Li Y , Roth K , Korsmeyer S J
Published: July 2002

BCL-2-deficient T cells demonstrate accelerated cell cycle progression and increased apoptosis following activation. Increasing the levels of BCL-2 retarded the G0-->S transition, sustained the levels of cyclin-dependent kinase inhibitor p27Kip1, and repressed postactivation death. Proximal signal transduction events and immediate early gene transcription were unaffected. However, the transcription and synthesis of interleukin 2 and other delayed early cytokines were markedly attenuated by BCL-2. In contrast, a cysteine protease inhibitor that also blocks apoptosis had no substantial affect upon cytokine production. InterleUkin 2 expression requires several transcription factors of which nuclear translocation of NFAT (nuclear factor of activated T cells) and NFAT-mediated transactivation were impaired by BCL-2. Thus, select genetic aberrations in the apoptotic pathway reveal a cell autonomous coregulation of activation.
Stress signaling in plants: a mitogen-activated protein kinase pathway is activated by cold and drought.
Authors: Jonak C , Kiegerl S , Ligterink W , Barker P J , Huskisson N S , Hirt H
Published: July 2002

Yeast and animals use mitogen-activated protein (MAP) kinase cascades to mediate stress and extracellular signals. We have tested whether MAP kinases are involved in mediating environmental stress responses in plants. Using specific peptide antibodies that were raised against different alfalfa MAP kinases, we found exclusive activation of p44MMK4 kinase in drought- and cold-treated plants. p44MMK4 kinase was transiently activated by these treatments and was correlated with a shift in the electrophoretic mobility of the p44MMK4 protein. Although transcript levels of the MMK4 gene accumulated after drought and cold treatment, no changes in p44MMK4 steady state protein levels were observed, indicating a posttranslational activation mechanism. Extreme temperatures, drought, and salt stress are considered to be different forms of osmotic stress. However, high salt concentrations or heat shock did not induce activation of p44MMK4, indicating the existence of distinct mechanisms to mediate different stresses in alfalfa. Stress adaptation in plants is mediated by abscisic acid (ABA)-dependent and ABA-independent processes. Although ABA rapidly induced the transcription of an ABA-inducible marker gene, MMK4 transcript levels did not increase and p44MMK4 kinase was not activated. These data indicate that the MMK4 kinase pathway mediates drought and cold signaling independently of ABA.
A natural experiment on plant acclimation: lifetime stomatal frequency response of an individual tree to annual atmospheric CO2 increase.
Authors: Wagner F , Below R , Klerk P D , Dilcher D L , Joosten H , Kürschner W M , Visscher H
Published: July 2002

Carbon dioxide (CO2) has been increasing in atmospheric concentration since the Industrial Revolution. A decreasing number of stomata on leaves of land plants still provides the only morphological evidence that this man-made increase has already affected the biosphere. The current rate of CO2 responsiveness in individual long-lived species cannot be accurately determined from field studies or by controlled-environment experiments. However, the required long-term data sets can be obtained from continuous records of buried leaves from living trees in wetland ecosystems. Fine-resolution analysis of the lifetime leaf record of an individual birch (Betula pendula) indicates a gradual reduction of stomatal frequency as a phenotypic acclimation to CO2 increase. During the past four decades, CO2 increments of 1 part per million by volume resulted in a stomatal density decline of approximately 0.6%. It may be hypothesized that this plastic stomatal frequency response of deciduous tree species has evolved in conjunction with the overall Cenozoic reduction of atmospheric CO2 concentrations.
Isolation of a superfamily of candidate disease-resistance genes in soybean based on a conserved nucleotide-binding site.
Authors: Yu Y G , Buss G R , Maroof M A
Published: July 2002

The tobacco N and Arabidopsis RPS2 genes, among several recently cloned disease-resistance genes, share highly conserved structure, a nucleotide-binding site (NBS). Using degenerate oligonucleotide primers for the NBS region of N and RPS2, we have amplified and cloned the NBS sequences from soybean. Each of these PCR-derived NBS clones detected low-or moderate-copy soybean DNA sequences and belongs to 1 of 11 different classes. Sequence analysis showed that all PCR clones encode three motifs (P-loop, kinase-2, and kinase-3a) of NBS nearly identical to those in N and RPS2. The intervening region between P-loop and kinase-3a of the 11 classes has high (26% average) amino acid sequence similarity to the N gene although not as high (19% average) to RPS2. These 11 classes represent a superfamily of NBS-containing soybean genes that are homologous to N and RPS2. Each class or subfamily was assessed for its positional association with known soybean disease-resistance genes through near-isogenic line assays, followed by linkage analysis in F2 populations using restriction fragment length polymorphisms. Five of the 11 subfamilies have thus far been mapped to the vicinity of known soybean genes for resistance to potyviruses (Rsv1 and Rpv), Phytophthora root rot (Rps1, Rps2, and Rps3), and powdery mildew (rmd). The conserved N- or RPS2-homologous NBS sequences and their positional associations with mapped soybean-resistance genes suggest that a number of the soybean disease-resistance genes may belong to this superfamily. The candidate subfamilies of NBS-containing genes identified by genetic mapping should greatly facilitate the molecular cloning of disease-resistance genes.
No ·NO from NO synthase
Authors: Schmidt Harald H. H. W. , Hofmann Heinrich , Schindler Ursula , Shutenko Zhanna S. , Cunningham David D. , Feelisch Martin
Published: July 2002

The nitric-oxide synthase (NOS; EC
1.14.13.39
) reaction is
formulated as a partially tetrahydrobiopterin
(H
4
Bip)-dependent 5-electron oxidation of a terminal
guanidino nitrogen of
l
-arginine (Arg) associated with
stoichiometric consumption of dioxygen (O
2
) and 1.5 mol of
NADPH to form
l
-citrulline (Cit) and nitric oxide
(·NO). Analysis of NOS activity has relied largely on indirect
methods such as quantification of nitrite/nitrate or the coproduct
Cit; we therefore sought to directly quantify ·NO formation from
purified NOS. However, by two independent methods, NOS did not yield
detectable ·NO unless superoxide dismutase (SOD; EC
1.15.1.1
) was
present. In the presence of H
4
Bip, internal ·NO
standards were only partially recovered and the dismutation of
superoxide (O
2⨪
), which otherwise scavenges ·NO to yield
ONOO
−
, was a plausible mechanism of action of SOD. Under
these conditions, a reaction between NADPH and ONOO
−
resulted in considerable overestimation of enzymatic NADPH consumption.
SOD lowered the NADPH:Cit stoichiometry to 0.8–1.1, suggesting either
that additional reducing equivalents besides NADPH are required to
explain Arg oxidation to ·NO or that ·NO was not primarily
formed. The latter was supported by an additional set of experiments in
the absence of H
4
Bip. Here, recovery of internal ·NO
standards was unaffected. Thus, a second activity of SOD, the
conversion of nitroxyl (NO
−
) to ·NO, was a more
likely mechanism of action of SOD. Detection of NOS-derived nitrous
oxide (N
2
O) and hydroxylamine (NH
2
OH), which
cannot arise from ·NO decomposition, was consistent with formation
of an ·NO precursor molecule such as NO
−
. When, in
the presence of SOD, glutathione was added,
S
-nitrosoglutathione was detected. Our results indicate
that ·NO is not the primary reaction product of NOS-catalyzed Arg
turnover and an alternative reaction mechanism and stoichiometry have
to be taken into account.
Inhibition of the association of RNA polymerase II with the preinitiation complex by a viral transcriptional repressor.
Authors: Lee G , Wu J , Luu P , Ghazal P , Flores O
Published: July 2002

Transcriptional repression is an important component of regulatory networks that govern gene expression. In this report, we have characterized the mechanisms by which the immediate early protein 2 (IE2 or IE86), a master transcriptional regulator of human cytomegalovirus, down-regulates its own expression. In vitro transcription and DNA binding experiments demonstrate that IE2 blocks specifically the association of RNA polymerase II with the preinitiation complex. Although, to our knowledge, this is the first report to describe a eukaryotic transcriptional repressor that selectively impedes RNA polymerase II recruitment, we present data that suggest that this type of repression might be widely used in the control of transcription by RNA polymerase II.
A serum-resistant cytofectin for cellular delivery of antisense oligodeoxynucleotides and plasmid DNA.
Authors: Lewis J G , Lin K Y , Kothavale A , Flanagan W M , Matteucci M D , DePrince R B , Mook R A , Hendren R W , Wagner R W
Published: July 2002

Development of antisense technology has focused in part on creating improved methods for delivering oligodeoxynucleotides (ODNs) to cells. In this report, we describe a cationic lipid that, when formulated with the fusogenic lipid dioleoylphosphatidyliethanolamine, greatly improves the cellular uptake properties of antisense ODNs, as well as plasmid DNA. This lipid formulation, termed GS 2888 cytofectin, (i) efficiently transfects ODNs and plasmids into many cell types in the presence or absence of 10% serum in the medium, (ii) uses a 4- to 10-fold lower concentration of the agent as compared to the commercially available Lipofectin liposome, and (iii) is > or = 20-fold more effective at eliciting antisense effects in the presence of serum when compared to Lipofectin. Here we show antisense effects using GS 2888 cytofectin together with C-5 propynyl pyrimidine phosphorothioate ODNs in which we achieve inhibition of gene expression using low nanomolar concentrations of ODN. This agent expands the utility of antisense ODNs for their use in understanding gene function and offers the potential for its use in DNA delivery applications in vivo.