bluuebunny/crossref_metadata_2025 huggingface dataset:
Neoclassical electron and ion transport in toroidally rotating plasmas
Authors: Sugama H. , Horton W.
Published: July 2002

Neoclassical transport processes of electrons and ions are investigated in detail for toroidally rotating axisymmetric plasmas with large flow velocities on the order of the ion thermal speed. The Onsager relations for the flow-dependent neoclassical transport coefficients are derived from the symmetry properties of the drift kinetic equation with the self-adjoint collision operator. The complete neoclassical transport matrix with the Onsager symmetry is obtained for the rotating plasma consisting of electrons and single-species ions in the Pfirsch–Schlüter and banana regimes. It is found that the inward banana fluxes of particles and toroidal momentum are driven by the parallel electric field, which are phenomena coupled through the Onsager symmetric off-diagonal coefficients to the parallel currents caused by the radial thermodynamic forces conjugate to the inward fluxes, respectively.
The effects of the density profile on the power absorption and the equilibrium density in helicon plasmas
Authors: Cho Suwon , Kwak Jong-Gu
Published: July 2002

Power absorption profiles are computed using numerical integration for radially non-uniform helicon plasmas with finite axial lengths. As in a uniform plasma, the Trivelpiece–Gould mode dominates the power absorption causing the surface deposition of the rf power. In addition to the surface heating, there is bulk electron heating for non-uniform plasmas, and the portion of this bulk heating increases with the degree of the inhomogeneity. It has been also found that the radial inhomogeneity of the plasma density results in the suppression of the m=−1 mode and reveals the axial resonance condition. Finally, the global power balance is considered to estimate average equilibrium densities, which are found to be in agreement with experimental values.
Formation of edge and internal transport barriers in tokamaks by Alfvén waves
Authors: Tsypin V. S. , Elfimov A. G. , Tendler M. , de Assis A. S. , de Azevedo C. A.
Published: July 2002

It is demonstrated that Alfvén waves may be the convenient trigger for the formation of transport barriers in tokamaks. Kinetic or slow Alfvén waves, which appear in the tokamak plasma as a result of the rf wave’s conversion, have small radial localizations. It is proposed that these waves can be used to create strongly sheared plasma flows at any point of the plasma minor radius, to suppress the plasma turbulence and to obtain the locally reversed magnetic shear configuration. Estimations concerning the absorbed power of Alfvén waves, which are necessary to suppress the plasma turbulence in some tokamaks, are about the level of absorbed power to be used in early fulfilled experiments. This method can assist the achievement of self-organization processes in tokamaks.
The Kelvin–Helmholtz instability in the presence of dust charge fluctuations
Authors: Singh S. V. , Rao N. N. , Bharuthram R.
Published: July 2002

Kelvin–Helmholtz instability is examined by considering the dust charge fluctuations in a dusty plasma. Electrons and ions are assumed to be in Boltzmann equilibria and the dust grains to follow the fluid equations with a full adiabatic equation of state. The transverse shear in the flow parallel to the magnetic field is considered. The instability is found to grow for limiting wave numbers for a particular value of shear velocity. The effect of adiabatic dust plasma pressure is to enhance the growth rate of the instability. For dense plasma, growth of the instability is affected by the presence of dust charge fluctuations.
Electrostatic modes and instabilities in nonideal dusty plasmas with sheared flows and grain charge fluctuations
Authors: Rao N. N.
Published: July 2002

The combined effects of nonideal contributions and grain charge fluctuations on the propagation of low-frequency electrostatic modes, such as the dust-acoustic waves and drift waves, as well as on the excitation of (parallel) Kelvin–Helmholtz instabilities in a dusty inhomogeneous magnetoplasma are investigated. In the low-frequency regime, dust-acoustic waves and drift waves are recovered with modifications due to the nonideal, as well as charge fluctuation contributions. Magnetized dusty plasmas support a dust temperature gradient-driven drift wave, which exists even in the absence of density inhomogeneities. In the dust gyro-frequency regime, the electrostatic dust cyclotron mode is modified by the transverse shear in the field-aligned flow. The other branch of the cyclotron mode becomes unstable when the shear flow exceeds a threshold value, which is determined by the ratio of the parallel to perpendicular component of the wave number. In general, the charge fluctuation leads to an overall decrease in the growth rate of the excited instability. For the Kelvin–Helmholtz configuration, the existence of a temperature gradient-driven instability that occurs when the relative flow speed between adjacent layers exceeds a critical value is shown. The latter is found to be much smaller than the dust-acoustic phase speed which is applicable for the density gradient-driven Kelvin–Helmholtz instability. On the other hand, the effects of the nonideal contributions in the two cases show quantitative behavior which are complementary to each other. For frequencies larger than the charging frequency, there is a net reduction in the growth rate of the instabilities due to the grain charge fluctuations.
Thermal instabilities in the edge transport barrier
Authors: Stacey Weston M.
Published: July 2002

A linear analysis of the edge transport barrier identifies localized, two-dimensional (radial-perpendicular) thermal instabilities driven by both impurity radiation and atomic (ionization/charge-exchange/elastic scattering) cooling and suppressed by conductive and convective heat transport. These instabilities are stabilized by sufficiently large values of the edge temperature gradient. Numerical calculations indicate that such instabilities would be expected for edge conditions (electron, impurity and neutral atom densities, temperatures, gradient scale lengths) typical of current tokamak experiments.
Correlation among geodesic curvature of the magnetic field lines, plasma rotation and improved confinement regimes in present tokamak experiments
Authors: Alladio F. , Crisanti F. , Mancuso A. , Micozzi P. , Tudisco O. , Burrell K. H. , Chu M. S. , Lao L. L. , Osborne T. H. , Giannella R. , Lomas P. , O’Brien D. , Riccardo V. , Schunke B.
Published: July 2002

In toroidal magnetic confinement configurations all the charged particles align their magnetic drifts with the flux surfaces if, and only if, the lines of force have zero geodesic curvature (omnigeneous configuration). In this condition, the neoclassical transport is zero; unfortunately, standard tokamak devices are far from meeting such a condition. Nevertheless, a minimization of the geodesic curvature of the lines of force in tokamaks minimizes the neoclassical transport, and could as well reduce any other transport terms depending on the noncoincidence between magnetic and drift surfaces. In particular, the geodesic curvature of the lines of force generates both the neoclassical Pfirsch–Schlüter current density j∥PS, as well as Hirshman factor q̂ [Nucl. Fusion 18, 917 (1978)], which increases the moment of inertia of the magnetic configuration. The improved confinement observed in the VH-mode (very high confinement) and in reversed magnetic shear discharges of the DIII-D tokamak [Plasma Physics Controlled Nuclear Fusion Research 1986 (International Atomic Energy Agency, Vienna, 1987), Vol. I, p. 159] and the high plasma performances of the Joint European Torus (JET) [Plasma Physics Controlled Nuclear Fusion Research 1990 (International Atomic Energy Agency, Vienna, 1991), Vol. I, p. 27] can be correlated with the reduction of geodesic curvature. This reduction influences also the absolute value and the profile of the v∧B part of the radial electric field Er, which are invoked by many authors as main ingredients in reducing the anomalous transport in tokamak plasmas.
Linear gyrokinetic theory for kinetic magnetohydrodynamic eigenmodes in tokamak plasmas
Authors: Qin H. , Tang W. M. , Rewoldt G.
Published: July 2002

A two-dimensional (2D) numerical solution method is developed for the recently derived linear gyrokinetic system which describes arbitrary wavelength electromagnetic perturbations in tokamak plasmas. The system consists of the gyrokinetic equation, the gyrokinetic Poisson equation, and the gyrokinetic moment equation. Since familiar magnetohydrodynamic (MHD) results can be recovered entirely from this gyrokinetic model, and all interesting kinetic effects are intrinsically included, this gyrokinetic system offers an approach for kinetic MHD phenomena which is more rigorous, self-consistent, and comprehensive than the previous hybrid models. Meanwhile, drift type microinstabilities can be also investigated systematically in this theoretical framework. The linear gyrokinetic equation is solved for the distribution function in terms of the perturbed fields by integrating along unperturbed particle orbits. The solution is substituted back into the gyrokinetic moment equation and the gyrokinetic Poisson equation. When the boundary conditions are incorporated, an eigenvalue problem is formed. The resulting numerical code, KIN-2DEM, is applied to kinetic ballooning modes, internal kink modes, and toroidal Alfvén eigenmodes (TAEs). The numerical results are benchmarked against the well-established FULL code [G. Rewoldt, W. M. Tang, and M. S. Chance, Phys. Fluids 25, 480 (1982)], the PEST code [J. Manickam, Nucl. Fusion 24, 595 (1984)], and the NOVA-K code [C. Z. Cheng, Phys. Rep. 211, No. 1 (1992)]. More importantly, kinetic effects on MHD modes can be investigated nonperturbatively. In particular, the kinetic effects of the background plasma on internal kink modes and the hot particle destabilization of TAEs are studied numerically.
Frequency and power response of high-power plasma-filled backward-wave oscillators
Authors: Goebel D. M. , Ponti E. S. , Eisenhart R. L. , Lemke R. W.
Published: July 2002

Backward-wave oscillators (BWO) have long been used as voltage-tunable signal sources, and more recently as high-power microwave (HPM) sources. The frequency at which a BWO oscillates is commonly viewed as being determined by the circuit geometry and the electron beam parameters. However, several techniques used to improve the efficiency and reduce the size of HPM BWOs, such as the Pasotron, cause the frequency to vary in discrete steps with changes in the beam parameters, and a plasma in these device can cause the frequency to chirp (increase significantly) during the pulse. End reflections in low-loss circuit designs and excessive plasma generation in these new source geometries produce nonclassical frequency and power behavior.
Thermodynamics of a neutrino gas in a dense plasma
Authors: Tsintsadze N. L. , Silva L. O. , Tsintsadze L. N. , Mendonça J. T.
Published: July 2002

The thermodynamic properties of a neutrino gas in a background plasma are described, including the contribution of the weak interaction between the neutrinos and the background plasma. The free energy of the neutrino gas is calculated explicitly, thus allowing the derivation of all the relevant thermodynamic quantities. The equation of state of the neutrino gas in the plasma is also derived for different astrophysical conditions.
Interaction of microwave and magnetoactive plasma in microwave’s plasmatrons
Authors: Petrin Andrei B.
Published: July 2002

A method for calculating the interaction of a microwave with a plane layer of magnetoactive low-pressure plasma under conditions of electron cyclotron resonance is presented. In this paper, the plasma layer is situated between a plane dielectric layer and a plane metal screen. The calculation model contains the microwave energy balance, particle balance and electron energy balance. It is demonstrated that the description of the microwave electromagnetic properties of the magnetoactive plasma by means of the conductivity tensor or the resistivity tensor must only be applied to a uniform plasma. For a nonuniform magnetoactive plasma the equation that expresses the microwave properties has been found. The importance of taking into account the viscosity of the plasma is shown. Numerical calculations of the microwave-plasma interaction for a one-dimensional (1D) formulation of the problem are presented.
Equilibria for intense ion beam transport in low-pressure gas or vacuum
Authors: Ottinger P. F. , Rose D. V. , Oliver B. V.
Published: July 2002

Two fluid equilibrium solutions for intense ion beam transport in low-pressure gas or vacuum are derived. The equilibria that are most relevant to beam transport have neutralizing electrons drifting in the same direction as the beam. These solutions require a small net positive charge within the beam channel to support an equilibrium radial electric field to allow the electrons to E×B drift axially. At the extremes of the domain of allowable solutions this electric field approaches zero and complete charge neutrality is achieved. In this case, two solutions are obtained. The first describes ballistic beam transport with complete neutralization of the beam current by the electrons, and the second describes pinched beam transport with no neutralizing electron current. Equilibria between these two extremes exhibit both a small net positive charge within the beam channel and partial current neutralization.
Particle pinch in collisionless drift-wave turbulence
Authors: Jenko Frank
Published: July 2002

Nonlinear numerical simulations show that the particle flux from collisionless drift-wave turbulence is directed up-gradient for sufficiently high values of ηe=Ln/LTe. This “particle pinch” results from the completely different perpendicular dynamics of slow (resonant) and fast (nonresonant) electrons, making it a genuinely kinetic effect which cannot easily be described by fluid models. Moreover, the linearly stable system self-sustains its turbulent state through a finite-amplitude (nonlinear) instability. Therefore, quasilinear estimates of turbulent transport caused by collisionless drift waves are practically useless and have to be replaced by nonlinear kinetic simulations like the present one.
Chaotic transport in zonal flows in analogous geophysical and plasma systems
Authors: del-Castillo-Negrete Diego
Published: July 2002

Zonal flows occur naturally in geophysical fluids. Important examples include Jupiter’s zonal flows, large scale jets in the earth’s stratosphere, and oceanic jets like the Gulf Stream. These zonal flows create transport barriers that have a crucial influence on mixing and confinement. On the other hand, zonal flows have also been observed in fusion plasmas and their role in the reduction of transport has been widely recognized. Based on the analogy between Rossby waves in quasigeostrophic flows and drift waves in magnetically confined plasmas, recent models and laboratory experiments developed for studying transport in geophysical fluid dynamics are discussed in the context of plasma physics. The flows considered are not turbulent and are dominated by large scale coherent structures which we describe with simple deterministic Hamiltonian models that exhibit chaotic transport. Two transport problems are studied: the role of drift/Rossby waves in the destruction of transport barriers, and the statistics of test particle motion. It is shown that non-monotonic zonal flows close to marginal stability typically exhibit robust transport barriers at the peak velocity where the shear locally vanishes. Also, it is shown that the trapping effect of vortices combined with the zonal flows gives rise to anomalous diffusion and Lévy (non-Gaussian) statistics. The models are compared with fluid laboratory experiment.
Flux generation and sustainment of a field reversed configuration with rotating magnetic field current drive
Authors: Slough J. T. , Miller K. E.
Published: July 2002

A new experimental device has been constructed to study the flux build-up and sustainment of a field reversed configuration (FRC) with a rotating magnetic field (RMF). Even though complete penetration was expected from RMF theory, the RMF field was observed to penetrate only a few centimeters inside the FRC separatrix. Despite the limited penetration, significantly larger toroidal currents (40 kA) were driven than in previous experiments (∼2 kA) with the same RMF field. The high currents and lack of deep penetration allowed the axial field to be the dominant field throughout the FRC. The radially inward pondermotive force arising from axial screening currents at the FRC edge had a significant influence on energy and particle confinement, reducing convective losses to the limit of observability. With only ohmic heating, the measured low ion temperatures (2 eV) left the ions unmagnetized while the electrons (∼40 eV) were well magnetized. No destructive instability was observed for the RMF driven FRC despite the lack of a strong kinetic ion component.
Period doubling and chaos in a directly modulated laser diode
Authors: Lee Chang-Hee , Yoon Tae-Hoon , Shin Sang-Yung
Published: July 2002

It is shown theoretically that the directly modulated laser diode, with the modulation frequency of its injection current comparable to the relaxation oscillation frequency, exhibits period doubling route to chaos as the modulation index of current is increased. The effect of spontaneous emission factor on the chaotic behavior in the laser diode is also studied.
Silicide formation by thermal annealing of Ni and Pd on hydrogenated amorphous silicon films
Authors: Hung L. S. , Kennedy E. F. , Palmstro/m C. J. , Olowolafe J. O. , Mayer J. W. , Rhodes H.
Published: July 2002

Silicide formation with the near-noble metals Ni and Pd on hydrogenated amorphous silicon substrates was studied with Rutherford backscattering spectrometry and forward recoil spectrometry. Upon annealing, Ni2Si (or Pd2Si) grows with the square root of time, and the activation energy is identical to that of the corresponding metal on single-crystal silicon substrates. The growth is slightly faster for hydrogenated amorphous silicon, which is attributed to the amorphous structure. During silicide formation, the hydrogen is released from silicides and presumably outdiffuses into a vacuum without interfacial accumulation. Thus, barrier formation does not occur, and the presence of hydrogen in the substrates has no effect on silicide growth.
Low resistance Pd/Ge/Au and Ge/Pd/Au ohmic contacts to n-type GaAs
Authors: Chen C. L. , Mahoney L. J. , Finn M. C. , Brooks R. C. , Chu A. , Mavroides J. G.
Published: July 2002

We have fabricated Pd/Ge/Au and Ge/Pd/Au sintered ohmic contacts on n-type GaAs. These contacts have specific resistances similar to those of conventional Ni/Ge/Au alloyed ohmic contacts, but their surfaces are much smoother and their edges are well defined. The fabrication procedure is compatible with GaAs technology, and the sintered contacts are thermally stable. The properties of these low resistance contacts are insensitive to the sintering temperature and to the thickness of the Pd and Ge layers or their order of deposition.
Stability of semiconductor strained-layer superlattices
Authors: Hull R. , Bean J. C. , Cerdeira F. , Fiory A. T. , Gibson J. M.
Published: July 2002

The criteria for strained-layer growth of semiconductor superlattices are discussed. It is shown that to avoid misfit dislocations, careful attention has to be paid to the composition, geometry, and dimensions of the quantum well structure. Two critical thicknesses are found to apply to strained-layer superlattice growth, one relating to the thickness of individual layers and one relating to the overall thickness of the superlattice. We derive the relationship between these two critical values. Experimental studies of the GexSi1−x/Si on Si and GexSi1−x/Ge on Ge systems using electron microscopy, Raman scattering, and ion channeling show that exceeding the critical superlattice thickness results in a network of dislocations between the substrate and first superlattice layer.
Low-loss Te-based chalcogenide glass optical fibers
Authors: Katsuyama Toshio , Matsumura Hiroyoshi
Published: July 2002

Infrared optical fibers composed of Te-based chalcogenide glass have been fabricated by using a high-speed drawing method. Transmission loss at 10.6 μm wavelength is reduced to 1.5 dB/m.
Ordering in GaAs1−xSbx grown by molecular beam epitaxy
Authors: Ihm Yeong-Eon , Otsuka N. , Klem J. , Morkoç H.
Published: July 2002

Ordering in (100) GaAs1–x Sbx epilayers grown by molecular beam epitaxy has been studied by transmission electron microscopy. Diffraction patterns taken from plan-view and cross-sectional samples of epilayers reveal a unique evolution of the ordering with the growth temperature, showing the formation of a short range order at lower temperatures and a long range order at higher temperatures. A distinct anisotropy of the formation of ordered structures between [011] and [01̄1] axes is observed from all epilayers investigated. Based on the analysis of the growth conditions, it is suggested that the anisotropy of the ordering is caused by the surface atomic structure of the growing epilayers.
Effect of size nonuniformity on the absorption spectrum of a semiconductor quantum dot system
Authors: Wu Wei-Yu , Schulman J. N. , Hsu T. Y. , Efron Uzi
Published: July 2002

The interband optical absorption of a nonuniform semiconductor quantum dot system is calculated. The effect of dot size variation on the resolvability of the absorption peaks is estimated. The dots are assumed to be cubic, with a size distribution described by a Gaussian function. It is shown that the total absorption spectrum of such a dot system depends strongly on the dot size distribution described by the parameter ξ, the ratio of the standard deviation of the dot size to the average dot size of the system. The range of ξ values for which the absorption peaks are resolvable is given.
Microwave surface resistance of YBa2Cu3O6.9 superconducting films
Authors: Martens J. S. , Beyer J. B. , Ginley D. S.
Published: July 2002

The microwave surface resistance of an YBa2Cu3O6.9 superconducting thick film was measured over the range 7.0–16.7 GHz at 77 K. This was done by placing a sample in a TE01n wavemeter cavity and observing the change in selectivity of the cavity. The material’s surface resistance is of the same order of magnitude as that of silver at 77 K from 8 to 12 GHz and improves about another order at 4.2 K. The power-law behavior of surface resistance with frequency is probably close to quadratic. This is similar to the behavior of low critical temperature superconductors.
A positivity result in the theory of Macdonald polynomials
Authors: Garsia A. M. , Haglund J.
Published: July 2002

We outline here a proof that a certain rational functionCn(q, t), which has come to be known as the “q,t-Catalan,” is in fact a polynomial with positive integer coefficients. This has been an open problem since 1994. BecauseCn(q, t) evaluates to the Catalan number att=q= 1, it has also been an open problem to find a pair of statisticsa,bon the collection 𝒟nof Dyck paths Π of length 2nyieldingCn(q, t) = ∑πta(Π)qb(Π). Our proof is based on a recursion forCn(q, t) suggested by a pair of statistics recently proposed by J. Haglund. One of the byproducts of our results is a proof of the validity of Haglund's conjecture.
Transferred DNA (T-DNA)-associated proteins of
Agrobacterium tumefaciens
are exported independently of
virB
Authors: Chen Lishan , Li Catherine M. , Nester Eugene W.
Published: July 2002

The transfer of T-DNA from
Agrobacterium
to plant cells is mediated by a system which involves the
virB
operon of the Ti plasmid. We report that VirE2 and VirD2, two T-DNA-associated proteins, as well as VirF, a protein known to be secreted into plant cells, are present in the periplasm and supernatant fractions of growing cells of
Agrobacterium
as are VirJ and ChvE, two known periplasmic proteins. Two cytoplasmic proteins, Ros and chloramphenicol acetyl transferase, and a VirE2∷green fluorescent protein construct were not detected in the above fraction. Export of VirE2 into the culture supernatant did not require any Ti plasmid genes, except for VirE1, a specific chaperone for VirE2. The levels of the VirE2 and VirD2 proteins in the supernatant increased significantly when cells were grown at 19°C as compared with 28°C. When
Agrobacterium
expressed the oncogenic suppressive activity protein (Osa), VirE2 and VirF proteins could not be detected in the supernatant or the periplasm and the level of VirD2 was greatly reduced. However, oncogenic suppressive activity protein did not block the accumulation of VirJ and ChvE in the periplasm. Our data suggest that VirD2, VirE2, and VirF are transported across the cytoplasmic membrane by a specific pathway, independent of
virB
. Thus, transfer of the T-complex of
Agrobacterium
may take place in two steps, the first mediated by an unidentified pathway and the second by the
virB
system.
Computer-modeling origin of a simple genetic apparatus
Authors: Kuhn Christoph
Published: July 2002

This computer simulation is based on a model of the origin of life proposed by H. Kuhn and J. Waser, where the evolution of short molecular strands is assumed to take place in a distinct spatiotemporal structured environment. In their model, the prebiotic situation is strongly simplified to grasp essential features of the evolution of the genetic apparatus without attempts to trace the historic path. With the tool of computer implementation confining to principle aspects and focused on critical features of the model, a deeper understanding of the model's premises is achieved. Each generation consists of three steps: (i) construction of devices (entities exposed to selection) presently available; (ii) selection; and (iii) multiplication of the isolated strands (R oligomers) by complementary copying with occasional variation by copying mismatch. In the beginning, the devices are single strands with random sequences; later, increasingly complex aggregates of strands form devices such as a hairpin-assembler device which develop in favorable cases. A monomers interlink by binding to the hairpin-assembler device, and a translation machinery, called the hairpin-assembler-enzyme device, emerges, which translates the sequence of R1and R2monomers in the assembler strand to the sequence of A1and A2monomers in the A oligomer, working as an enzyme.
Local uncaging of caged Ca
2+
reveals distribution of Ca
2+
-activated Cl
−
channels in pancreatic acinar cells
Authors: Park Myoung Kyu , Lomax Richard B. , Tepikin Alexei V. , Petersen Ole H.
Published: July 2002

In exocrine acinar cells, Ca
2+
-activated Cl
−
channels in the apical membrane are essential for fluid secretion, but it is unclear whether such channels are important for Cl
−
uptake at the base. Whole-cell current recording, combined with local uncaging of caged Ca
2+
, was used to reveal the Cl
−
channel distribution in mouse pancreatic acinar cells, where ≈90% of the current activated by Ca
2+
in response to acetylcholine was carried by Cl
−
. When caged Ca
2+
in the cytosol was uncaged locally in the apical pole, the Cl
−
current was activated, whereas local Ca
2+
uncaging in the basal or lateral areas of the cell had no effect. Even when Ca
2+
was uncaged along the whole inner surface of the basolateral membrane, no Cl
−
current was elicited. There was little current deactivation at a high cytosolic Ca
2+
concentration ([Ca
2+
]
c
), but at a low [Ca
2+
]
c
there was clear voltage-dependent deactivation, which increased with hyperpolarization. Functional Ca
2+
-activated Cl
−
channels are expressed exclusively in the apical membrane and channel opening is strictly regulated by [Ca
2+
]
c
and membrane potential. Ca
2+
-activated Cl
−
channels do not mediate Cl
−
uptake at the base, but acetylcholine-elicited local [Ca
2+
]
c
spiking in the apical pole can regulate fluid secretion by controlling the opening of these channels in the apical membrane.
A role for IL-1α in inducing pathologic inflammation during bacterial infection
Authors: Dube Peter H. , Revell Paula A. , Chaplin David D. , Lorenz Robin G. , Miller Virginia L.
Published: July 2002

Infection with pathogenic microbes often results in a significant inflammatory response. A cascade of proinflammatory cytokines including tumor necrosis factor α (TNF-α) and IL-1 initiates this response. Although there is a clear role for IL-1 during infection, little is known to distinguish the role of IL-1α from that of IL-1β during this process. With the use ofYersinia enterocoliticaas a model enteric pathogen, we have identified a specific role for IL-1α in inducing pathologic inflammation during bacterial infection. Depletion of IL-1α in mice infected with wild-typeY. enterocoliticaresults in significantly decreased intestinal inflammation. Furthermore, a bacterial mutant that does not induce IL-1α expression but induces normal levels of IL-1β, TNF-α, and IFN-γ, causes greatly reduced intestinal inflammation and is attenuated by LD50analysis in the C57BL/6 mouse model. These results demonstrate a distinct and unrecognized role for IL-1α in inducing intestinal inflammation that cannot be compensated for by the endogenous levels of IL-1β, TNF-α, or IFN-γ that are produced in response toY. enterocolitica. Additionally, these results suggest that IL-1α-induced inflammation is a major contributor to the pathology of yersiniosis.
Quantification of intrinsic residual viral replication in treated HIV-infected patients
Authors: Fraser Christophe , Ferguson Neil M. , Anderson Roy M.
Published: July 2002

The intrinsic rate of viral replication in HIV-infected patients treated with antiretroviral combination therapy is estimated by using a mathematical model of viral dynamics. This intrinsic replication is found to be episodic, varying considerably in quantity between patients (even among those achieving long-term undetectable levels of viremia) and is always reduced by increasing the potency of the antiviral drug regimen. The analysis reveals that even in conditions of perfect patient adherence and drug penetration a substantial level of residual viral replication is expected. The rate of evolution in the viral quasispecies, and thus also the probability of new drug-resistant viral strains being created, is proportional to the total amount of residual viral replication. Under most circumstances, the viral population continues to turn over rapidly during therapy, albeit at a much reduced level.
Targeting of proteins to granule subsets is determined by timing and not by sorting: The specific granule protein NGAL is localized to azurophil granules when expressed in HL-60 cells.
Authors: Le Cabec V , Cowland J B , Calafat J , Borregaard N
Published: July 2002

The mechanism of protein targeting to individual granules in cells that contain different subsets of storage granules is poorly understood. The neutrophil contains two highly distinct major types of granules, the peroxidase positive (azurophil) granules and the peroxidase negative (specific and gelatinase) granules. We hypothesized that targeting of proteins to individual granule subsets may be determined by the stage of maturation of the cell, at which the granule proteins are synthesized, rather than by individual sorting information present in the proteins. This was tested by transfecting the cDNA of the specific granule protein, NGAL, which is normally synthesized in metamyelocytes, into the promyelocytic cell line HL-60, which is developmentally arrested at the stage of formation of azurophil granules, and thus does not contain specific and gelatinase granules. Controlled by a cytomegalovirus promoter, NGAL was constitutively expressed in transfected HL-60 cells. This resulted in the targeting of NGAL to azurophil granules as demonstrated by colocalization of NGAL with myeloperoxidase, visualized by immunoelectron microscopy. This shows that targeting of proteins into distinct granule subsets may be determined solely by the time of their biosynthesis and does not depend on individual sorting information present in the proteins.
Complementation of an Escherichia coli adhE mutant by the Entamoeba histolytica EhADH2 gene provides a method for the identification of new antiamebic drugs.
Authors: Yong T S , Li E , Clark D , Stanley S L
Published: July 2002

The pathogenic protozoan parasite Entamoeba histolytica, the cause of amebic dysentery and amebic liver abscess, is an obligate anaerobe, and derives energy from the fermentation of glucose to ethanol with pyruvate and acetyl coenzyme A as intermediates. We have isolated EhADH2, a key enzyme in this pathway, that is a NAD+- and Fe2+-dependent bifunctional enzyme with acetaldehyde dehydrogenase and alcohol dehydrogenase activities. EhADH2 is the only known eukaryotic member of a newly defined family of prokaryotic multifunctional enzymes, which includes the Escherichia coli AdhE enzyme, an enzyme required for anaerobic growth of E. coli. Because of the critical role of EhADH2 in the amebic fermentation pathway and the lack of known eukaryotic homologues of the EhADH2 enzyme, EhADH2 represents a potential target for antiamebic chemotherapy. However, screening of compounds for antiamebic activity is hampered by the cost of large scale growth of Ent. histolytica, and difficulties in quantitating drug efficacy in vitro. To approach this problem, we expressed the EhADH2 gene in a mutant strain of E. coli carrying a deletion of the adhE gene. Expression of EhADH2 restored the ability of the mutant E. coli strain to grow under anaerobic conditions. By screening compounds for the ability to inhibit the anaerobic growth of the E. coli/EhADH2 strain, we have developed a rapid assay for identifying compounds with anti-EhADH2 activity. Using bacteria to bypass the need for parasite culture in the initial screening process for anti-parasitic agents could greatly simplify and reduce the cost of identifying new therapeutic agents effective against parasitic diseases.
Reduction of two functional gamma-globin genes to one: an evolutionary trend in New World monkeys (infraorder Platyrrhini).
Authors: Chiu C H , Schneider H , Schneider M P , Sampaio I , Meireles C , Slightom J L , Gumucio D L , Goodman M
Published: July 2002

Nucleotide sequences were determined for the gamma1- and gamma2-globin loci from representatives of the seven anciently separated clades in the three extant platyrrhine families (Atelidae, Pitheciidae, and Cebidae). These sequences revealed an evolutionary trend in New World monkeys either to inactivate the gamma1 gene or to fuse it with the gamma2 gene, i.e. to have only one functional fetally expressed gamma gene. This trend is clearly evident in six of the seven clades: (i) it occurred in atelids by deletion of most of the gamma1 gene in the basal ancestor of this clade; (ii-iv) in pitheciid titi, saki, and cebid capuchin monkeys by potentially debilitating nucleotide substitutions in the proximal CCAAT box of the gamma1 promoters and (v and vi) in cebid owl and squirrel monkeys by crossovers that fused 5' sequence from gamma1 with 3' sequence from gamma2. In the five clades with gamma1 and gamma2 loci separated by intergenic sequences (the fifth clade being the cebid marmosets), the gamma2 genes retained an unaltered proximal CCAAT motif and their gamma2 promoters accumulated fewer nucleotide substitutions than did the gamma1 promoters. Thus, phylogenetic considerations indicate that the stem platyrrhines, ancestral to all New World monkeys, had gamma2 as the primary fetally expressed gamma gene. A further inference is that when the earlier stem anthropoid gamma gene duplicated, gamma2 (at its greater downstream distance from epsilon) could evade embryonic activation by the locus control region but could be fetally activated once released by regulatory mutations from fetal repressors.
Poly (alpha 2,8-deaminoneuraminic acid) is expressed in lung on a single 150-kDa glycoprotein and is an oncodevelopmental antigen.
Authors: Qu B , Ziak M , Zuber C , Roth J
Published: July 2002

Homopolymers of alpha 2,8-linked N-acetylneuraminic acid [poly(alpha 2,8-Neu5Ac)] of the neural cell adhesion molecule NCAM have been shown to be temporally expressed during lung development and represent a marker for small cell lung carcinoma. We report the presence of a further polysialic acid in lung that consists of oligo/polymers of alpha 2,8-linked deaminoneuraminic acid residues [poly (alpha 2,8-KDN)], as detected with a monoclonal antibody in conjunction with a specific sialidase. Although the various cell types forming the bronchi, alveolar septs, and blood vessels were positive for poly (alpha 2,8-KDN) by immunohistochemistry, this polysialic acid was found on a single 150-kDa glycoprotein by immunoblot analysis. The poly(alpha 2,8-KDN)-bearing glycoprotein was not related to an NCAM protein based on immunochemical criteria. The expression of the poly (alpha 2,8-KDN) was developmentally regulated as evidenced by its gradual disappearance in the rat lung parenchyma commencing 1 week after birth. In adult lung the blood vessel endothelia and the smooth muscle fibers of both blood vessels and bronchi were positive but not the bronchial and alveolar epithelium. The poly (alpha 2,8-KDN)-bearing 150-kDa glycoprotein became reexpressed in various histological types of lung carcinomas and cell lines derived from them and represents a new oncodevelopmental antigen in lung.
Retention of replication fidelity by a DNA polymerase functioning in a distantly related environment
Authors: Dressman Holly Kloos , Wang Chien-Chia , Karam Jim D. , Drake John W.
Published: July 2002

The primary structures of the replicative DNA polymerases (gp43s) of bacteriophage T4 and its distant phylogenetic relative RB69 are diverged, retaining only 61% identity and 74% similarity. Nevertheless, RB69 gp43 substitutes effectively for T4 gp43 in T4 DNA replication
in vivo
. We show here that RB69 gp43 replicates T4 genomes
in vivo
with a fidelity similar to that achieved by T4 gp43. Furthermore, replication by RB69 gp43 in the distantly related environment does not enhance the mutator activities of mutations in T4 genes that encode other components of the multienzyme DNA replicase. We also show that the fidelities of RB69 gp43 and T4 gp43 are both high
in vitro
and that they are similarly and sharply reduced
in vivo
by mutations that eliminate the 3′-exonucleolytic proofreading function. We conclude that gp43 interactions with the other replication proteins are probably nonessential for polymerase fidelity.
East Gondwana ancestry of the sunflower alliance of families
Authors: Bremer Kåre , Gustafsson Mats H. G.
Published: July 2002

The sunflower alliance of families comprises nearly 10% of all flowering plant species and includes the largest of all plant families, the sunflower family Asteraceae, which has 23,000 species, and the bellflower family Campanulaceae. Both are worldwide in distribution, but the majority of their species occur in the northern hemisphere. Recently it has been shown that a number of small, woody families from the Australian–Southwest Pacific area also belong in this relationship. Here we add yet another such family and present phylogenetic, biogeographic, and chronological analyses elucidating the origin of this large group of plants. We show that the ancestral lineages are confined to Malesia, Australia, New Guinea, and New Zealand and that the sunflower and bellflower families represent phylogenetically derived lineages within a larger group with a Cretaceous and southern-hemisphere, presumably East Gondwana, ancestry. Their highly derived position in the flowering plant phylogeny makes this significant for understanding the evolution of flowering plants in general.
Complementation of sporulation and motility defects in a prokaryote by a eukaryotic GTPase
Authors: Hartzell Patricia L.
Published: July 2002

The complex prokaryote,
Myxococcus xanthus
, undergoes a program of multicellular development when starved for nutrients, culminating in sporulation.
M. xanthus
makes MglA, a 22-kDa, soluble protein that is required for both multicellular development and gliding motility. MglA is similar in sequence to the
Saccharomyces cerevisiae SAR1
protein, a member of the Ras/Rab/Rho superfamily of small eukaryotic GTPases. The
SAR1
gene, when integrated into the
M. xanthus
genome, complements the sporulation defect of a Δ
mglA
strain. A forward, second-site mutation on the
M. xanthus
chromosome,
rpm
, in combination with
SAR1
, restores fruiting body morphogenesis and gliding motility to a Δ
mglA
strain. The result that the
rpm
mutation suppresses the substitution of
SAR1
for
mglA
suggests that Sar1p interacts with other
M. xanthus
proteins to control the motility-dependent aggregation of cells during development.
Control of time-dependent biological processes by temporally patterned input
Authors: Brezina Vladimir , Orekhova Irina V. , Weiss Klaudiusz R.
Published: July 2002

Temporal patterning of biological variables, in the form of oscillations and rhythms on many time scales, is ubiquitous. Altering the temporal pattern of an input variable greatly affects the output of many biological processes. We develop here a conceptual framework for a quantitative understanding of such pattern dependence, focusing particularly on nonlinear, saturable, time-dependent processes that abound in biophysics, biochemistry, and physiology. We show theoretically that pattern dependence is governed by the nonlinearity of the input–output transformation as well as its time constant. As a result, only patterns on certain time scales permit the expression of pattern dependence, and processes with different time constants can respond preferentially to different patterns. This has implications for temporal coding and decoding, and allows differential control of processes through pattern. We show how pattern dependence can be quantitatively predicted using only information from steady, unpatterned input. To apply our ideas, we analyze, in an experimental example, how muscle contraction depends on the pattern of motorneuron firing.
Subunit rotation in
Escherichia coli
F
o
F
1
–ATP synthase during oxidative phosphorylation
Authors: Zhou Yuantai , Duncan Thomas M. , Cross Richard L.
Published: July 2002

We report evidence for proton-driven subunit rotation in membrane-bound F
o
F
1
–ATP synthase during oxidative phosphorylation. A βD380C/γC87 crosslinked hybrid F
1
having epitope-tagged βD380C subunits (β
flag
) exclusively in the two noncrosslinked positions was bound to F
o
in F
1
-depleted membranes. After reduction of the β–γ crosslink, a brief exposure to conditions for ATP synthesis followed by reoxidation resulted in a significant amount of β
flag
appearing in the β–γ crosslinked product. Such a reorientation of γC87 relative to the three β subunits can only occur through subunit rotation. Rotation was inhibited when proton transport through F
o
was blocked or when ADP and P
i
were omitted. These results establish F
o
F
1
as the second example in nature where proton transport is coupled to subunit rotation.
Novel mechanism for carbamoyl-phosphate synthetase: A nucleotide switch for functionally equivalent domains
Authors: Kothe Michael , Eroglu Binnur , Mazza Holly , Samudera Henry , Powers-Lee Susan
Published: July 2002

Carbamoyl-phosphate synthetases (CPSs) utilize two molecules of ATP at two internally duplicated domains, B and C. Domains B and C have recently been shown to be structurally [Thoden, J. B., Holden, H. M., Wesenberg, G., Raushel, F. M. & Rayment, I. (1997)
Biochemistry
36, 6305–6316] and functionally [Guy, H. I. & Evans, D. R. (1996)
J. Biol. Chem.
271, 13762–13769] equivalent. We have carried out a site-directed mutagenic analysis that is consistent with ATP binding to a palmate motif rather than to a Walker A/B motif in domains B and C. To accommodate our present findings, as well as the other recent findings of structural and functional equivalence, we are proposing a novel mechanism for CPS. In this mechanism utilization of ATP bound to domain C is coupled to carbamoyl-phosphate synthesis at domain B via a nucleotide switch, with the energy of ATP hydrolysis at domain C allowing domain B to cycle between two alternative conformations.
Graft-versus-host-disease-associated lymphoid hypoplasia and B cell dysfunction is dependent upon donor T cell-mediated Fas-ligand function, but not perforin function
Authors: Baker Matthew B. , Riley Richard L. , Podack Eckhard R. , Levy Robert B.
Published: July 2002

Allogeneic bone marrow transplant recipients often exhibit a graft-versus-host-disease (GVHD)-associated immune deficiency that can be prolonged and lead to life-threatening infections. We have examined the role of donor T cell-mediated cytotoxic function in the development of GVHD-associated immune deficiency. A major histocompatibility complex-matched model of allogeneic bone marrow transplantation was employed in which lethally irradiated C3H.SW mice received a nonlethal dose of T cells from either perforin-deficient (B6-perforin 0/0), Fas-ligand (FasL)-defective (B6-gld), or normal (B6) allogeneic donor mice. T cell-depleted marrow from B6-Ly-5.1 congenic donor mice was transplanted along with the donor T cell populations to determine the effects of donor T cell-mediated cytotoxicity on engraftment. Our results demonstrate that recipients of perforin-deficient or normal allogeneic T cells exhibit profound lymphoid hypoplasia and severely reduced splenic proliferative responses to lipopolysaccharidein vitro. In contrast, GVHD-associated lymphoid hypoplasia is dramatically reduced andin vitroB cell function is intact in recipients of FasL-defective allogeneic T cells. Engraftment of myeloid and erythroid lineage cells occurs irrespective of donor T cell cytotoxic function. Although recipients of perforin-deficient or normal allogeneic T cells exhibited hematopoietic engraftment exclusively of donor origin, recipients of FasL-defective donor T cells exhibited significant mixed chimerism (Ly-5.1/Ly-5.2). Because only marrow of donor origin was transplanted, this finding suggests that Fas-mediated antirecipient cytotoxicity is required for clearance of residual hematopoietic stem cells of host origin that persist following lethal irradiation.
S
-Sulfohemoglobin and disulfide exchange: The mechanisms of sulfide binding by
Riftia pachyptila
hemoglobins
Authors: Zal Franck , Leize Emmanuelle , Lallier François H. , Toulmond André , Van Dorsselaer Alain , Childress James J.
Published: July 2002

The deep sea hydrothermal tube worm
Riftia pachyptila
possesses a multihemoglobin system with three different extracellular hemoglobins (Hbs; V1, V2, and C1): two dissolved in the vascular blood, V1 and V2, and one in the coelomic fluid, C1. V1 consists of four heme-containing chains and four linker chains. The globin chains making up V2 and C1 are, with one exception, common to V1. Remarkably these Hbs are able to bind oxygen and sulfide simultaneously and reversibly at two different sites. Two of the globin chains found in these three
Riftia
Hbs possess one free Cys residue and for at least one of the globins, the
b
-Cys
75
is conserved among vestimentifera (
Lamellibrachia
sp.) and pogonophora (
Oligobrachia mashikoi
). By selectively blocking the free Cys with
N-
ethylmaleimide and using electrospray ionization mass spectrometry experiments, we show that these Cys residues are involved in sulfide binding by
Riftia
Hbs. Moreover, we also demonstrate that the larger V1 Hb can form persulfide groups on its linker chains, a mechanism that can account for the higher sulfide-binding potential of this Hb.