bluuebunny/crossref_metadata_2025 huggingface dataset:
Convection at very low Prandtl numbers
Authors: Clever R. M. , Busse F. H.
Published: July 2002

The transition from thermal convection in the form of rolls in a fluid layer heated from below to traveling wave convection occurs at the Rayleigh number RII=1854 in the limit of low Prandtl numbers and in the presence of no-slip boundaries. While the traveling wave convection exhibits similar properties at moderately low and very low Prandtl numbers, the tertiary transition to asymmetric waves experiences a qualitative change at a Prandtl number of about 0.02. Instead of the double frequency asymmetric waves that occur at higher Prandtl numbers the traveling wave convection becomes just asymmetric, but remains stationary with respect to the moving frame of reference. The heat transport carried by the new form of convection is larger than for symmetric traveling wave convection.
Transverse dimension effects in the dielectric wake-field accelerator
Authors: Garate Eusebio , Fisher Amnon
Published: July 2002

The wake-field amplitude and frequency of a dielectric wake-field accelerator is calculated, taking into account the transverse dimensions of the wake-field cavity, including the ratio of inner to outer radii of the dielectric liner S. It is assumed that the accelerator is driven by a linearly ramped current pulse with an infinitely sharp cutoff. The results indicate that the total wake-field amplitude will have a significant contribution from the first two transverse magnetic modes (TM01 and TM02) of the dielectric lined cavity for S≤0.65. Additionally, the wake-field amplitude of the fundamental mode (TM01) decreases as the ratio of inner to outer radii S increases. The theoretical results are shown to be in good agreement, when predicting the wake-field frequencies, with recent results of an experimental test of the dielectric wake-field accelerator concept.
Statistical properties of laser hot spots produced by a random phase plate
Authors: Rose Harvey A. , DuBois D. F.
Published: July 2002

A quantitative theory of laser hot spots, which control plasma instabilities in real laser–plasma interactions, is presented in the case of random phase plate (RPP) optics. It is shown that the probability density of intense hot spots with intensity I, Phot(I), is given by Phot(I)∼(I/I02)exp(−I/I0) where I0 is the average intensity, and that the detailed amplitude and phase variation of the laser field in the vicinity of an intense hot spot is uniquely specified by the optics and is deterministic. These hot spots may be the source of below threshold stimulated Raman scattering (SRS) and its variation with I0 is shown to be super exponential. A brief preview of a quantitative nonlinear theory of hot-spot-induced laser filamentation is presented.
A model for the spectrum of passive scalars in an isotropic turbulence field
Authors: Driscoll Richard J. , Kennedy Lawrence A.
Published: July 2002

A simple model is developed for the wavenumber spectrum of the variance of a passive scalar quantity in an isotropic turbulence field. The model can define the spectral distributions at all wavenumbers as an arbitrary function of a scalar Reynolds number Reθ=R Reλ and the Schmidt number Sc=ν/D (where R=τθ/τe is the scalar/kinetic energy time scale ratio and Reλ=u′λ/ν is the turbulence Reynolds number). The model is compared with one-dimensional spectral data over a range of Reynolds numbers and for Sc=0.7, 7, and 700; model and data are shown to be in reasonable agreement.
Hydrodynamics of exploding foil x-ray lasers
Authors: London Richard A. , Rosen M. D.
Published: July 2002

An accurate simple model for the hydrodynamics of laser heated exploding foils is presented. Particular emphasis is given to applications in the design of soft x-ray lasers. The model predicts the conditions in the foil plasma (e.g., temperature, density, and scale length), given the experimental parameters (e.g., optical laser intensity, laser pulse duration, target thickness, and target composition). The simple model is based on an isothermal, homogeneous expansion similarity solution of the ideal hydrodynamic equations. Both analytical and numerical solutions of the similarity equations are studied. The numerical solutions agree closely with computational hydrodynamic simulations at times of interest—after the laser burns through the foil. Analytic solutions for constant intensity laser irradiation provide useful power-law scaling relations between the input laser and target parameters and the plasma variables. The simple model is a powerful design tool that reproduces the essential results of more expensive and time-consuming simulations over a large and important range of parameter space.
Fluid mixing (stretching) by time periodic sequences for weak flows
Authors: Khakhar D. V. , Ottino J. M.
Published: July 2002

The stretching of material lines in time periodic sequences of ‘‘weak’’ flows (i.e., characterized by a linear stretching for long times) in which streamlines change at the end of each periodic unit is quantified in terms of a mixing efficiency. Two different flows and two different strain distributions give nearly identical results in terms of the mixing efficiency and indicate the existence of an optimal operating condition for maximum stretch. The results are relevant to fluid mixing in chaotic flows.
Transient electrostatic potentials driven by short-pulse electron cyclotron heating
Authors: Lichtenberg A. J. , Lieberman M. A. , Cohen R. H.
Published: July 2002

Electrons heated in a local resonance zone of a magnetic well created either by a linear mirror or a finite aspect ratio torus are considered. If the heating has sufficient strength to drive a significant nonisotropy in the electron distribution function, an electrostatic potential variation along a field line is developed to maintain charge neutrality. The buildup of this space varying potential for times shorter than ion-transit times is determined analytically, and a limit to the number of electrons within the well that can be heated is found. The subsequent evolution of the potential on ion-transit and collision time scales is also determined. The theory is applied both to large mirror ratio devices characteristic of magnetic mirror confinement and to small mirror ratio devices characteristic of tokamaks. In the former configuration the theory is compared to experimental observations of potential buildup and decay in the multiple-mirror experiment (MMX) device [Phys. Fluids 29, 1208 (1986)] and shown to be consistent with the experiments. In the latter configuration, using the expected parameters of the Microwave Tokamak Experiment (MTX) [Proceedings of the 14th Annual Conference on Plasma Physics (Pergamon, New York, in press)], it is found that ΔΦ∼0.3Te is built up on the hot-electron-transit time scale, dropping to about 0.2Te on the ion-transit time scale, and then decaying further on a collisional time scale. Here Te is the electron temperature before heating. The potential has both poloidal and toroidal variation. Possible consequences include enhanced neoclassical transport and ion heating, and parametric excitation of low-frequency modes.
Nonlinear evolution of longitudinal plasma waves
Authors: Pao Young-ping
Published: July 2002

Long-time nonlinear behavior of single-mode longitudinal plasma waves is studied on the basis of the Vlasov equation with Fokker–Planck collision terms. The resonant layer, trapped island, collisional sublayers, and X-point neighborhoods are analyzed. A nonlinear evolution equation is obtained and the wave-generated current is also evaluated.
A numerical study of pressure fluctuations in three-dimensional, incompressible, homogeneous, isotropic turbulence
Authors: Pumir Alain
Published: July 2002

Pressure fluctuations in incompressible turbulence are studied by direct numerical simulations of the three-dimensional (3-D) Navier–Stokes equations. The pressure probability distribution function (PDF) is shown to have an exponential tail on the negative side, and to be independent of the Reynolds number for Reλ≲60. At higher Reynolds numbers, the low pressure part of the pressure PDF becomes super exponential. The joint PDFs of strain, vorticity, and pressure (considered pairwise) show a strong dissymmetry between positive and negative pressure fluctuations. The results obtained from the numerical solutions of the Navier–Stokes equations are compared with a Gaussian velocity field. The two statistical ensembles are shown to lead to quantitatively different results.
Heat and mass transport in a near supercritical fluid
Authors: Zappoli Bernard , Durand-Daubin Arnaud
Published: July 2002

The analytical solution of the equations describing the propagation of a temperature step at the boundary in a near supercritical van der Waals gas is obtained and discussed. The quantitative properties of the velocity and thermodynamic fields are given on a long-time scale. Quantitative evidence of the speeding up of the heat transport compared to a purely diffusive process is given. The numerical solution obtained by means of the piso algorithm, which is performed and discussed confirms the validity of the obtained analytical solution.
Exponential decay rate of the power spectrum for solutions of the Navier–Stokes equations
Authors: Doering Charles R. , Titi Edriss S.
Published: July 2002

Using a method developed by Foias and Temam [J. Funct. Anal. 87, 359 (1989)], exponential decay of the spatial Fourier power spectrum for solutions of the incompressible Navier–Stokes equations is established and explicit rigorous lower bounds on a small length scale defined by the exponential decay rate are obtained.
Low nonzero Reynolds number drag of a thin disk settling axisymmetrically within a cylindrical outer boundary
Authors: Pulley Joe Wade , Hussey R. G. , Davis A. M. J.
Published: July 2002

Measurements have been made of the drag on a thin disk of diameter d moving broadside through a liquid of viscosity μ and density ρ. The liquid is bounded on the outside by a cylindrical tube, diameter D, which is coaxial with the disk. The geometrical parameter ξ=d/D ranges from 0.0189 to 0.112. The Reynolds number Re=ρUd/μ ranges from 0.0167 to 6.89. When the measured values are extrapolated to Re=0, the results agree with the calculations of Shail and Norton. When extrapolated to ξ=0, the results agree with the matched-asymptotic series solution of Breach for Re<1. A new theoretical result, based upon the Oseen approximation, is obtained for the case in which both inertial effects and boundary effects are included, and the results agree with experiment over the range 4ξ<Re<0.62 as long as ξ<0.05. An empirical scheme is developed to represent our measurements for Re<5 and ξ<0.13. Comparison is made between our results for the drag on a disk and the results of Sutterby for the drag on a sphere.
Development of a Reynolds stress closure for modeling of homogeneous MHD turbulence
Authors: Widlund Ola , Zahrai Said , Bark Fritz H.
Published: July 2002

A Reynolds stress closure is developed for homogeneous shear-free turbulence subjected to a strong magnetic field at low magnetic Reynolds numbers. A scalar dimensionality anisotropy parameter is introduced to carry information about the distribution of energy in spectral space. This information is vital in modeling MHD turbulence, as it determines both magnitude and anisotropy of the Joule dissipation tensor. The Joule dissipation tensor is modeled by a tensor function, which is bilinear in the Reynolds stress anisotropy and the unit direction vector of the magnetic field. The tensor function coefficients are second-order in the scalar dimensionality parameter. A phenomenological transport equation for the dimensionality parameter is proposed. The model is closed using the pressure–strain model of Sarkar, Speziale and Gatski and a magnetic destruction term in the standard dissipation equation. The purely magnetic linear problem contains no undetermined constants, while the complete model contains two constants. Model predictions for the case of decaying turbulence show very good agreement with direct numerical simulations.
Measurements of thermal creep in binary gas mixtures
Authors: Huang C. M. , Tompson R. V. , Ghosh T. K. , Ivchenko I. N. , Loyalka S. K.
Published: July 2002

Thermal creep occurs in all nonisothermal gas–mixture systems. The effect is more pronounced in rarefied gases and can play a significant role in, for example, microgravity crystal growth experiments, where natural convection is suppressed. Experimental measurements of the thermal creep in gas mixtures are, however, simply not available. We report experimental measurements of thermal creep in three binary gas mixtures: He:Ar, He:CO2, and Ar:CO2 at different mole ratios (mixture fractions). A stainless steel two-bulb measurement system employing seven capillaries to connect the bulbs is used to measure the steady-state pressure differences that develop between the bulbs for each mixture at a selection of total system pressures. Values of the total system pressure that were used range from 0.12 to 10.00 Torr. For all of the data reported, the two bulbs were held at temperatures of 397 and 297 K for the hot and cold sides, respectively. From the measured pressure differences, experimental values are obtained for a newly identified creep factor from which the thermal creep is extracted. These experimental values agree well with those obtained from some recently reported theoretical expressions, provided that suitable values for the accommodation coefficients of the gases are chosen.
Lattice Boltzmann magnetohydrodynamics
Authors: Martínez Daniel O. , Chen Shiyi , Matthaeus William H.
Published: July 2002

Lattice gas and lattice Boltzmann methods are recently developed numerical schemes for simulating a variety of physical systems. In this paper a new lattice Boltzmann model for modeling two-dimensional (2-D) incompressible magnetohydrodynamics (MHD) is presented. The current model fully utilizes the flexibility of the lattice Boltzmann method in comparison with previous lattice gas and lattice Boltzmann MHD models, reducing the number of moving directions from 36 in other models to 12 only. To increase computational efficiency, a simple single time relaxation rule is used for collisions, which directly controls the transport coefficients. The bidirectional streaming process of the particle distribution function in this paper is similar to the original model [H. Chen and W. H. Matthaeus, Phys. Rev. Lett. 58, 1845 (1987), S. Chen et al., Phys. Rev. Lett. 67, 3776 (1991)], but has been greatly simplified, affording simpler implementation of boundary conditions and increasing the feasibility of extension into a workable three-dimensional (3-D) model. Analytical expressions for the transport coefficients are presented. Also, as example cases, numerical calculation for the Hartmann flow is performed, showing a good agreement between the theoretical prediction and numerical simulation, and a sheet-pinch simulation is performed and compared with the results obtained with a spectral method.
Interaction of two neighboring laser beams taking into account the effects of plasma hydrodynamics
Authors: Hüller S. , Mounaix Ph. , Tikhonchuk V. T. , Pesme D.
Published: July 2002

The interaction between two neighboring laser beams focused in a hot underdense homogeneous plasma is investigated using the non-paraxial wave coupling code KOLIBRI [S. Hüller et al., Phys. Scr. T63, 151 (1996)] in two and three spatial dimensions. Both the plasma hydrodynamic evolution and the stimulated Brillouin scattering (SBS) aspects are studied in the case of strongly damped ion sound waves. The hydrodynamic effects consist in ponderomotively driven density perturbations located between the beams which may, in turn, influence strongly the light propagation through the plasma. The two beams are found to merge whenever the distance between them is smaller than or of the order of their diameter. Concerning the SBS aspect, it is found that due to interference effects between the beams, the spatial amplification of the backscattered light is asymmetric with respect to the laser axis. SBS can also enforce the hydrodynamic effects and the beam merging.
Effect of the speckle self-focusing on the stationary stimulated Brillouin scattering reflectivity from a randomized laser beam in an inhomogeneous plasma
Authors: Tikhonchuk V. T. , Hüller S. , Mounaix Ph.
Published: July 2002

The effect of laser light self-focusing (SF) in speckles on stimulated Brillouin scattering (SBS) in an inhomogeneous plasma is studied. It is found that below but near critical power SF dramatically enhances the SBS reflectivity from an individual speckle, while above the critical power the pump power depletion due to SBS prevents strong SF and limits the maximum laser intensity in a speckle. The parameters that control the SBS/SF interplay are the ratio of plasma inhomogeneity scale length to the speckle length and the product of the plasma density and the speckle cross section. The consequences of the SF effect on the averaged SBS reflectivity of the randomized laser beam are revealed and their manifestations in recent SBS experiments with preformed plasmas are discussed.
Fusion neutrons from the gas–pusher interface in deuterated-shell inertial confinement fusion implosions
Authors: Chrien R. E. , Hoffman N. M. , Colvin J. D. , Keane C. J. , Landen O. L. , Hammel B. A.
Published: July 2002

The first measurements and numerical simulations of fusion neutrons from the gas–pusher interface of indirectly-driven inertial confinement fusion implosions have been performed using hydrogen-filled capsules made with a deuterated inner layer. Nonlinear saturation of the growth of hydrodynamic perturbations in high linear growth factor (≃325) implosions was varied by adjusting the initial surface roughness of the capsule. The neutron yields are in quantitative agreement with the direct simulations of perturbation growth, and also with a linear mode superposition and saturation model including enhanced thermal loss in the mixed region. Neutron spectra from these capsules are broader than expected for the calculated ion temperatures, suggesting the presence of nonthermal broadening from mass motion during the fusion burn.
Nonlinear theory of power transfer between multiple crossed laser beams in a flowing plasma
Authors: Rose Harvey A. , Ghosal Sandip
Published: July 2002

Analytic results are obtained for power transfer among crossing, equal frequency, laser beams, each smoothed by a random phase plate, in a flowing homogeneous plasma. For beams with well-separated directions, interbeam coupling transfers power, while intrabeam coupling causes beam deflection. For any pair of such beams, the beam with the largest positive projection on the flow direction will drain power from the other.
J
*
optimization of small aspect ratio stellarator/tokamak hybrid devices
Authors: Spong D. A. , Hirshman S. P. , Whitson J. C. , Batchelor D. B. , Carreras B. A. , Lynch V. E. , Rome J. A.
Published: July 2002

A new class of low aspect ratio toroidal hybrid stellarators is found using a more general plasma confinement optimization criterion than quasisymmetrization. The plasma current profile and shape of the outer magnetic flux surface are used as control variables to achieve near constancy of the longitudinal invariant J* on internal flux surfaces (quasiomnigeneity), in addition to a number of other desirable physics target properties. A range of compact (small aspect ratio A), low plasma current devices have been found with significantly improved confinement, both for thermal as well as energetic (collisionless) particle components. With reasonable increases in magnetic field and geometric size, such devices can also be scaled to confine 3.5 MeV alpha particle orbits.
Bifurcated neoclassical particle transport
Authors: Helander P.
Published: July 2002

The theory of neoclassical transport in an impure, toroidal plasma is extended to allow for steeper pressure and temperature gradients than are usually considered. It is found that the ion particle flux is a nonmonotonic function of these gradients for plasma parameters typical of the tokamak edge. A sudden transition between states of low and high confinement is therefore possible.
The Hurst exponent and long-time correlation
Authors: Wang Guiding , Antar G. , Devynck P.
Published: July 2002

The rescaled range statistics (R/S) method is applied to the ion saturation current fluctuations measured by the Langmuir probe at the edge of Tore Supra [Equipe Tore Supra, in Proceedings of the 13th International Conference on Plasma Physics and Controlled Nuclear Fusion, Washington, 1990 (International Atomic Energy Agency, Vienna, 1991), Vol. 1, p. 549] to evaluate the Hurst exponent. Data block randomization is carried out to the data sets in order to investigate the relationship between the Hurst exponent and long-time correlation. It is observed that H is well above 0.5 in the long-time self-similar range. However, it is found that the information which leads to H>0.5 is totally contained in the short-time correlation and no link to long times is found.
Microhollow cathode discharge excimer lamps
Authors: Schoenbach Karl H. , El-Habachi Ahmed , Moselhy Mohamed M. , Shi Wenhui , Stark Robert H.
Published: July 2002

Microhollow cathode discharges are high-pressure, nonequilibrium gas discharges between a hollow cathode and a planar or hollow anode with electrode dimensions in the 100 μm range. The large concentration of high-energy electrons, in combination with the high-gas density favors excimer formation. Excimer emission was observed in xenon and argon, at wavelengths of 128 and 172 nm, respectively, and in argon fluoride and xenon chloride, at 193 and 308 nm. The radiant emittance of the excimer radiation was found to increase monotonically with pressure. However, due to the decrease in source size with pressure, the efficiency (ratio of excimer radiant power to input electrical power), has for xenon and argon fluoride a maximum at ∼400 Torr. The maximum efficiency is between 6% and 9% for xenon, and ∼2% for argon fluoride.
Periodic domain walls and ferroelastic bubbles in neodymium pentaphosphate
Authors: Meeks S. W. , Auld B. A.
Published: July 2002

The first observation of accurately periodic ferroelastic domains in neodymium pentaphosphate (NPP) is reported. A description is given of the nucleation process of these periodic domains in terms of a newly discovered phenomena of ferroelastic bubbles. These periodic arrays have been shown to be tunable from 70 to less than 0.5 μm. Device applications of these arrays as tunable active optical Bragg gratings and acoustic filters are discussed.
Zeeman effect polarimetry of Ti XVII 3834 Å line in the Texas Experimental Tokamak
Authors: Wróblewski D. , Moos H. W. , Rowan W. L.
Published: July 2002

We present the first measurement of a tokamak plasma internal magnetic field based on the analysis of polarization of Zeeman components of a magnetic dipole transition in heavy impurity ion. The circular polarization of the Ti XVII 3834 Å line is studied. The values of the component of the toroidal magnetic field in the direction of observation are measured for several observation angles and good agreement with expected values is found. The result indicates that the method may be useful for measuring the local magnetic field and in particular, the poloidal component of the field, in a tokamak.
GaAs structures with electron mobility of 5×106 cm2/V s
Authors: English J. H. , Gossard A. C. , Störmer H. L. , Baldwin K. W.
Published: July 2002

Modulation-doped GaAs heterostructures with low-temperature electron mobilities of 5.0×106 cm2/V s at a two-dimensional electron areal density of 1.6×1011 cm−2 have been made. The mobilities are the highest ever observed in a semiconductor. Multiple quantum wells of GaAs prepared by similar methods showed electron mobilities up to 0.54×106 cm2/V s at an areal density of 5.3×1011 cm−2 per layer, which also exceeds any mobility value previously reported for multiple well structures. The structures were grown by molecular beam epitaxy with an atomic-plane sheet-doping technique.
Detection of individual 0.4–28 μm wavelength photons via impurity-impact ionization in a solid-state photomultiplier
Authors: Petroff M. D. , Stapelbroek M. G. , Kleinhans W. A.
Published: July 2002

A solid-state device capable of continuous detection of individual photons in the wavelength range from 0.4 to 28 μm is described. Operated with a dc applied bias, its response to the absorption of incident photons consists of submicrosecond rise time pulses with amplitudes well above the electronic readout noise level. A counting quantum efficiency of over 30% has been demonstrated at a wavelength of 20 μm, and over 50% was observed in the visible-light region. Optimum photon-counting performance occurs for temperatures between 6 and 10 K and for count rates less than 1010 counts/s per cm2 of detector area. The operating principle of the device is outlined and its performance characteristics as a photon detector are presented.
Subpicosecond gain dynamics in GaAlAs laser diodes
Authors: Kesler Morris P. , Ippen Erich P.
Published: July 2002

Ultrafast gain dynamics in GaAlAs diode amplifiers have been studied using 100 fs optical pulses. Pulse propagation through the amplifier resulted in temporal broadening and pulse shaping due to both gain saturation and material dispersion. Pump-probe experiments indicate the presence of two processes contributing to the gain dynamics but give no evidence of spectral hole burning. A dynamic carrier heating model is presented to explain all of the observed gain nonlinearities, and the implications of our results on the dynamic response of laser diodes are discussed.
Growth of low-density two-dimensional electron system with very high mobility by molecular beam epitaxy
Authors: Shayegan M. , Goldman V. J. , Jiang C. , Sajoto T. , Santos M.
Published: July 2002

We report on the growth of modulation-doped GaAs/Alx Ga1−xAs heterostructures with mobilities (μ) on the order of 1×106 cm2 /V s (at 4.2 K) and areal densities (ns ) below 8×1010 cm−2 . In growing these structures we employ the atomic plane doping technique and ultrathick (>1000 Å) spacer layers. The mobilities of these structures are the highest ever reported for low densities. Measurements of μ vs ns as a function of illumination or gate voltage indicate μ∼nαs behavior with α≂0.6 and, even for ns ≂1.4×1010 cm−2 , μ has a value in excess of 0.3×106 cm2 /V s.
Galactose-extended glycans of antibodies produced by transgenic plants
Authors: Bakker Hans , Bardor Muriel , Molthoff Jos W. , Gomord Véronique , Elbers Ingrid , Stevens Lucas H. , Jordi Wilco , Lommen Arjen , Faye Loïc , Lerouge Patrice , Bosch Dirk
Published: July 2002

Plant-specificN-glycosylation can represent an important limitation for the use of recombinant glycoproteins of mammalian origin produced by transgenic plants. Comparison of plant and mammalianN-glycan biosynthesis indicates that β1,4-galactosyltransferase is the most important enzyme that is missing for conversion of typical plantN-glycans into mammalian-likeN-glycans. Here, the stable expression of human β1,4-galactosyltransferase in tobacco plants is described. Proteins isolated from transgenic tobacco plants expressing the mammalian enzyme bearN-glycans, of which about 15% exhibit terminal β1,4-galactose residues in addition to the specific plantN-glycan epitopes. The results indicate that the human enzyme is fully functional and localizes correctly in the Golgi apparatus. Despite the fact that through the modified glycosylation machinery numerous proteins have acquired unusualN-glycans with terminal β1,4-galactose residues, no obvious changes in the physiology of the transgenic plants are observed, and the feature is inheritable. The crossing of a tobacco plant expressing human β1,4-galactosyltransferase with a plant expressing the heavy and light chains of a mouse antibody results in the expression of a plantibody that exhibits partially galactosylatedN-glycans (30%), which is approximately as abundant as when the same antibody is produced by hybridoma cells. These results are a major step in thein plantaengineering of theN-glycosylation of recombinant antibodies.
Binding ofEscherichia coliadhesin AfaE to CD55 triggers cell-surface expression of the MHC class I-related molecule MICA
Authors: Tieng Vannary , Le Bouguénec Chantal , du Merle Laurence , Bertheau Philippe , Desreumaux Pierre , Janin Anne , Charron Dominique , Toubert Antoine
Published: July 2002

MICA are distant homologs of MHC class I molecules expressed in the normal intestinal epithelium. They are ligands of the NKG2D activating receptor expressed on most γδ T cells, CD8+ αβ T cells, and natural killer cells and therefore play a critical role in innate immune responses. We investigated MICA cell-surface expression on infection of epithelial cell lines by enteric bacteria and show here that MICA expression can be markedly increased by bacteria of the diffusely adherentEscherichia colidiarrheagenic group. This effect is mediated by the specific interaction between bacterial adhesin AfaE and its cellular receptor, CD55, or decay-accelerating factor. It is extremely rapid after AfaE binding, consistent with a stress-induced signal. MICA induction on epithelial cells triggered IFN-γ release by the NKG2D expressing natural killer cell line NKL. This host–bacteria interaction pathway could play a role in the pathogenesis of inflammatory bowel disease, a condition that implicates a bacterial trigger in genetically susceptible individuals. This was supported by the increased MICA expression at the surface of epithelial cells in colonic biopsies from Crohn's disease-affected patients compared with controls.
A sensitized genetic system for the analysis of murine B lymphocyte signal transduction pathways dependent on Bruton's tyrosine kinase
Authors: Satterthwaite Anne B. , Willis Fiona , Kanchanastit Prim , Fruman David , Cantley Lewis C. , Helgason Cheryl D. , Humphries R. Keith , Lowell Clifford A. , Simon Melvin , Leitges Michael , Tarakhovsky Alexander , Tedder Thomas F. , Lesche Ralf , Wu Hong , Witte Owen N.
Published: July 2002

Modifier screens have been powerful genetic tools to define signaling pathways in lower organisms. The identification of modifier loci in mice has begun to allow a similar dissection of mammalian signaling pathways. Transgenic mice (Btklo) expressing 25% of endogenous levels of Bruton's tyrosine kinase (Btk) have B cell functional responses between those of wild-type and Btk−/−mice. We asked whether reduced dosage or complete deficiency of genes previously implicated as Btk regulators would modify the Btklophenotype. We used two independent assays of Btk-dependent B cell function. Proliferative response to B cell antigen receptor cross-linkingin vitrowas chosen as an example of a relatively simple, well-defined signaling system.In vivoresponse to type II T-independent antigens (TI-II) measures complex interactions among multiple cell types over time and may identify additional Btk pathways. All modifiers identified differentially affected these two assays, indicating that Btk mediates these processes via distinct mechanisms. Loss of Lyn, PTEN (phosphatase and tensin homolog), or SH2-containing inositol phosphatase suppressed the Btklophenotypein vitrobut notin vivo, whereas CD19 and the p85α form of phosphoinositide 3-kinase behaved as Btkloenhancersin vivobut notin vitro. Effects of Lyn, PTEN, or p85α haploinsufficiency were observed. Haploinsufficiency or complete deficiency of protein kinase C β, Fyn, CD22, Gαq, or Gα11 had no detectable effect on the function of BtkloB cells. A transgenic system creating a reduction in dosage of Btk can therefore be used to identify modifier loci that affect B cell responses and quantitatively rank their contribution to Btk-mediated processes.
The origin of 15
R
-prostaglandins in the Caribbean coral
Plexaura homomalla
: Molecular cloning and expression of a novel cyclooxygenase
Authors: Valmsen Karin , Järving Ivar , Boeglin William E. , Varvas Külliki , Koljak Reet , Pehk Tõnis , Brash Alan R. , Samel Nigulas
Published: July 2002

The highest concentrations of prostaglandins in nature are found in the Caribbean gorgonian
Plexaura homomalla
. Depending on its geographical location, this coral contains prostaglandins with typical mammalian stereochemistry (15
S
-hydroxy) or the unusual 15
R
-prostaglandins. Their metabolic origin has remained the subject of mechanistic speculations for three decades. Here, we report the structure of a type of cyclooxygenase (COX) that catalyzes transformation of arachidonic acid into 15
R
-prostaglandins. Using a homology-based reverse transcriptase–PCR strategy, we cloned a cDNA corresponding to a COX protein from the
R
variety of
P. homomalla
. The deduced peptide sequence shows 80% identity with the 15
S
-specific coral COX from the Arctic soft coral
Gersemia fruticosa
and ≈50% identity to mammalian COX-1 and COX-2. The predicted tertiary structure shows high homology with mammalian COX isozymes having all of the characteristic structural units and the amino acid residues important in catalysis. Some structural differences are apparent around the peroxidase active site, in the membrane-binding domain, and in the pattern of glycosylation. When expressed in Sf9 cells, the
P. homomalla
enzyme forms a 15
R-
prostaglandin endoperoxide together with 11
R
-hydroxyeicosatetraenoic acid and 15
R
-hydroxyeicosatetraenoic acid as by-products. The endoperoxide gives rise to 15
R
-prostaglandins and 12
R
-hydroxyheptadecatrienoic acid, identified by comparison to authentic standards. Evaluation of the structural differences of this 15
R
-COX isozyme should provide new insights into the substrate binding and stereospecificity of the dioxygenation reaction of arachidonic acid in the cyclooxygenase active site.
Repression of TFII-I-dependent transcription by nuclear exclusion
Authors: Tussié-Luna María Isabel , Bayarsaihan Dashzeveg , Ruddle Frank H. , Roy Ananda L.
Published: July 2002

TFII-I is an unusual transcription factor possessing both basal and signal-induced transcriptional functions. Here we report the characterization of a TFII-I-related factor (MusTRD1/BEN) that regulates transcriptional functions of TFII-I by controlling its nuclear residency. MusTRD1/BEN has five or six direct repeats, each containing helix–loop–helix motifs, and, thus, belongs to the TFII-I family of transcription factors. TFII-I and MusTRD1/BEN, when expressed individually, show predominant nuclear localization. However, when the two proteins are coexpressed ectopically, MusTRD1/BEN locates almost exclusively to the nucleus, whereas TFII-I is largely excluded from the nucleus, resulting in a loss of TFII-I-dependent transcriptional activation of the c-
fos
promoter. Mutation of a consensus nuclear localization signal in MusTRD1/BEN results in a reversal of nuclear residency of the two proteins and a concomitant gain of c-
fos
promoter activity. These data suggest a means of transcriptional repression by competition at the level of nuclear occupancy.
Repeat expansion by homologous recombination in the mouse germ line at palindromic sequences
Authors: Zhou Zhi-Hong , Akgün Ercan , Jasin Maria
Published: July 2002

Genetic instability can be induced by unusual DNA structures and sequence repeats. We have previously demonstrated that a large palindrome in the mouse germ line derived from transgene integration is extremely unstable and undergoes stabilizing rearrangements at high frequency, often through deletions that produce asymmetry. We have now characterized other palindrome rearrangements that arise from complex homologous recombination events. The structure of the recombinants is consistent with homologous recombination occurring by a noncrossover gene conversion mechanism in which a break induced in the palindrome promotes homologous strand invasion and repair synthesis, similar to mitotic break repair events reported in mammalian cells. Some of the homologous recombination events led to expansion in the size of the palindromic locus, which in the extreme case more than doubled the number of repeats. These results may have implications for instability observed at naturally occurring palindromic or quasipalindromic sequences.
Modulation of intestinal gene expression by dietary zinc status: Effectiveness of cDNA arrays for expression profiling of a single nutrient deficiency
Authors: Blanchard Raymond K. , Moore J. Bernadette , Green Calvert L. , Cousins Robert J.
Published: July 2002

Mammalian nutritional status affects the homeostatic balance of multiple physiological processes and their associated gene expression. Although DNA array analysis can monitor large numbers of genes, there are no reports of expression profiling of a micronutrient deficiency in an intact animal system. In this report, we have tested the feasibility of using cDNA arrays to compare the global changes in expression of genes of known function that occur in the early stages of rodent zinc deficiency. The gene-modulating effects of this deficiency were demonstrated by real-time quantitative PCR measurements of altered mRNA levels for metallothionein 1, zinc transporter 2, and uroguanylin, all of which have been previously documented as zinc-regulated genes. As a result of the low level of inherent noise within this model system and application of a recently reported statistical tool for statistical analysis of microarrays [Tusher, V.G., Tibshirani, R. & Chu, G. (2001)
Proc. Natl. Acad. Sci. USA
98, 5116–5121], we demonstrate the ability to reproducibly identify the modest changes in mRNA abundance produced by this single micronutrient deficiency. Among the genes identified by this array profile are intestinal genes that influence signaling pathways, growth, transcription, redox, and energy utilization. Additionally, the influence of dietary zinc supply on the expression of some of these genes was confirmed by real-time quantitative PCR. Overall, these data support the effectiveness of cDNA array expression profiling to investigate the pleiotropic effects of specific nutrients and may provide an approach to establishing markers for assessment of nutritional status.
Embryonic stem cells express multiple Eph-subfamily receptor tyrosine kinases.
Authors: Lickliter J D , Smith F M , Olsson J E , Mackwell K L , Boyd A W
Published: July 2002

Eph and its homologues form the largest subfamily of receptor tyrosine kinases. Normal expression patterns of this subfamily indicate roles in differentiation and development, whereas their overexpression has been linked to oncogenesis. This study investigated the potential role of Eph-related molecules during very early embryonic development by examining their expression in embryonic stem (ES) cells and embryoid bodies differentiated from ES cells in vitro. By use of a strategy based on reverse transcriptase-mediated PCR, nine clones containing Eph-subfamily sequence were isolated from ES cells. Of these, eight were almost identical to one of four previously identified molecules (Sek, Nuk, Eck, and Mek4). However, one clone contained sequence from a novel Eph-subfamily member, which was termed embryonic stem-cell kinase or Esk. Northern analysis showed expression of Esk in ES cells, embryoid bodies, day 12 mouse embryos, and some tissues of the adult animal. Levels of expression were similar in ES cells and embryoid bodies. By comparison, Mek4 showed no significant transcription in the ES cell cultures by Northern analysis, whereas Eck displayed stronger signals in ES cells than in the embryoid bodies. These results suggest that Eph-subfamily molecules may play roles during the earliest phases of embryogenesis. Furthermore, the relative importance of different members of this subfamily appears to change as development proceeds.
Internal cleavage of the inhibitory 7B2 carboxyl-terminal peptide by PC2: a potential mechanism for its inactivation.
Authors: Zhu X , Rouille Y , Lamango N S , Steiner D F , Lindberg I
Published: July 2002

The neuroendocrine protein 7B2 contains two domains, a 21-kDa protein required for prohormone convertase 2 (PC2) maturation and a carboxyl-terminal (CT) peptide that inhibits PC2 at nanomolar concentrations. To determine how the inhibition of PC2 is terminated, we studied the metabolic fate of the 7B2 CT peptide in RinPE-7B2, AtT-20/PC2-7B2, and alphaTC1-6 cells. Extracts obtained from cells labeled for 6 h with [3H]valine were subjected to immunoprecipitation using an antibody raised against the extreme carboxyl terminus of r7B2, and immunoprecipitated peptides were separated by gel filtration. All three cell lines yielded two distinct peaks at about 3.5 kDa and 1.5 kDa, corresponding to the CT peptide and a smaller fragment consistent with cleavage at an interior Lys-Lys site. These results were corroborated using a newly developed RIA against the carboxyl terminus of the CT peptide which showed that the intact CT peptide represented only about half of the stored CT peptide immunoreactivity, with the remainder present as the 1.5-kDa peptide. Both peptides could be released upon phorbol 12-myristate 13-acetate stimulation. We investigated the possibility that PC2 itself could be responsible for this cleavage by performing in vitro experiments. When 125I-labeled CT peptide was incubated with purified recombinant PC2, a smaller peptide was generated. Analysis of CT peptide derivatives for their inhibitory potency revealed that CT peptide 1-18 (containing Lys-Lys at the carboxyl terminus) represented a potent inhibitor, but that peptide 1-16 was inactive. Inclusion of carboxypeptidase E (CPE) in the reaction greatly diminished the inhibitory potency of the CT peptide against PC2, in line with the notion that the CT peptide cleavage product is not inhibitory after the removal of terminal lysines by CPE. In summary, our data support the idea that PC2 cleaves the 7B2 CT peptide at its internal Lys-Lys site within secretory granules; deactivation of the cleavage product is then accomplished by CPE, thus providing an efficient mechanism for intracellular inactivation of the CT peptide.
A common evolutionary origin for mitochondria and hydrogenosomes.
Authors: Bui E T , Bradley P J , Johnson P J
Published: July 2002

Trichomonads are among the earliest eukaryotes to diverge from the main line of eukaryotic descent. Keeping with their ancient nature, these facultative anaerobic protists lack two "hallmark" organelles found in most eukaryotes: mitochondria and peroxisomes. Trichomonads do, however, contain an unusual organelle involved in carbohydrate metabolism called the hydrogenosome. Like mitochondria, hydrogenosomes are double-membrane bounded organelles that produce ATP using pyruvate as the primary substrate. Hydrogenosomes are, however, markedly different from mitochondria as they lack DNA, cytochromes and the citric acid cycle. Instead, they contain enzymes typically found in anaerobic bacteria and are capable of producing molecular hydrogen. We show here that hydrogenosomes contain heat shock proteins, Hsp70, Hsp60, and Hsp10, with signature sequences that are conserved only in mitochondrial and alpha-Gram-negative purple bacterial Hsps. Biochemical analysis of hydrogenosomal Hsp60 shows that the mature protein isolated from the organelle lacks a short, N-terminal sequence, similar to that observed for most nuclear-encoded mitochondrial matrix proteins. Moreover, phylogenetic analyses of hydrogenosomal Hsp70, Hsp60, and Hsp10 show that these proteins branch within a monophyletic group composed exclusively of mitochondrial homologues. These data establish that mitochondria and hydrogenosomes have a common eubacterial ancestor and imply that the earliest-branching eukaryotes contained the endosymbiont that gave rise to mitochondria in higher eukaryotes.
Large-scale isolation of candidate virulence genes of Pseudomonas aeruginosa by in vivo selection.
Authors: Wang J , Mushegian A , Lory S , Jin S
Published: July 2002

Pseudomonas aeruginosa, an opportunistic human pathogen, is a major causative agent of mortality and morbidity in immunocompromised patients and those with cystic fibrosis genetic disease. To identify new virulence genes of P. aeruginosa, a selection system was developed based on the in vivo expression technology (IVET) that was first reported in Salmonella system. An adenine-requiring auxotrophic mutant strain of P. aeruginosa was isolated and found avirulent on neutropenic mice. A DNA fragment that can complement the mutant strain, containing purEK operon that is required for de novo biosynthesis of purine, was sequenced and used in the IVET vector construction. By applying the IVET selection system to a neutropenic mouse infection model, genetic loci that are specifically induced in vivo were identified. Twenty-two such loci were partially sequenced and analyzed. One of them was a well-studied virulence factor, pyochelin receptor (FptA), that is involved in iron acquisition. Fifteen showed significant homology to reported sequences in GenBank, while the remaining six did not. One locus, designated np20, encodes an open reading frame that shares amino acid sequence homology to transcriptional regulators, especially to the ferric uptake regulator (Fur) proteins of other bacteria. An insertional np20 null mutant strain of P. aeruginosa did not show a growth defect on laboratory media; however, its virulence on neutropenic mice was significantly reduced compared with that of a wild-type parent strain, demonstrating the importance of the np20 locus in the bacterial virulence. The successful isolation of genetic loci that affect bacterial virulence demonstrates the utility of the IVET system in identification of new virulence genes of P. aeruginosa.
Identification of the coding region for a second poly(A) polymerase in Escherichia coli.
Authors: Cao G J , Pogliano J , Sarkar N
Published: July 2002

We had earlier identified the pcnB locus as the gene for the major Escherichia coli poly(A) polymerase (PAP I). In this report, we describe the disruption and identification of a candidate gene for a second poly(A) polymerase (PAP II) by an experimental strategy which was based on the assumption that the viability of E. coli depends on the presence of either PAP I or PAP II. The coding region thus identified is the open reading frame f310, located at about 87 min on the E. coli chromosome. The following lines of evidence support f310 as the gene for PAP II: (i) the deduced peptide encoded by f310 has a molecular weight of 36,300, similar to the molecular weight of 35,000 estimated by gel filtration of PAP II; (ii) the deduced f310 product is a relatively hydrophobic polypeptide with a pI of 9.4, consistent with the properties of partially purified PAP II; (iii) overexpression of f310 leads to the formation of inclusion bodies whose solubilization and renaturation yields poly(A) polymerase activity that corresponds to a 35-kDa protein as shown by enzyme blotting; and (iv) expression of a f310 fusion construct with hexahistidine at the N-terminus of the coding region allowed purification of a poly(A) polymerase fraction whose major component is a 36-kDa protein. E. coli PAP II has no significant sequence homology either to PAP I or to the viral and eukaryotic poly(A) polymerases, suggesting that the bacterial poly(A) polymerases have evolved independently. An interesting feature of the PAP II sequence is the presence of sets of two paired cysteine and histidine residues that resemble the RNA binding motifs seen in some other proteins.