bluuebunny/crossref_metadata_2025 huggingface dataset:
Vortex structures and microfronts
Authors: Gerz Thomas , Howell Jim , Mahrt Larry
Published: July 2002

This study addresses the relationship between thermal microfronts and coherent vortex structures in homogeneous turbulence. The turbulence is created by mean shear in a weakly stratified flow. The data set is generated by direct numerical simulation providing highly resolved instantaneous three-dimensional fields of fluctuating velocity and temperature (1603 data points for each field). Vertically inclined large-scale horseshoe vortices develop due to stretching and rotation by the mean shear rate, as would also occur in neutrally stratified flow. In a homogeneous shear flow, the structures on the tilted plane are oriented both upward and downward with equal probability, and are referred to as ‘‘head-up’’ and ‘‘head-down’’ horseshoe eddies. Vorticity structures are sampled in those regions of the flow where the strongest coherent local temperature gradients occur. The sampled fields are composited. It is found that the microfronts are caused by the local outflow between the legs of the horseshoe eddies. A head-up eddy always forms a cold microfront (moving toward warmer fluid) and a head-down eddy forms a warm microfront. In most of the sampled cases, the two vortex structures occur in pairs, such that the head-down vortex always lies above the head-up vortex. Therefore, local shear layers with enhanced cross-stream vorticity form between the outflows of the structures. The strongest temperature gradients also occur at this location. Typical length, width, and thickness of a coherent vortex structure are found to be 1.4l, 1.4l, and 0.72l, respectively, where l is the integral length scale (based on the three-dimensional energy–density spectrum). The typical distance between two vortices forming a pair is about one integral length.
Direct simulation of a self-similar turbulent mixing layer
Authors: Rogers Michael M. , Moser Robert D.
Published: July 2002

Three direct numerical simulations of incompressible turbulent plane mixing layers have been performed. All the simulations were initialized with the same two velocity fields obtained from a direct numerical simulation of a turbulent boundary layer with a momentum thickness Reynolds number of 300 computed by Spalart [J. Fluid Mech. 187, 61 (1988)]. In addition to a baseline case with no additional disturbances, two simulations were begun with two-dimensional disturbances of varying strength in addition to the boundary layer turbulence. After a development stage, the baseline case and the case with weaker additional two-dimensional disturbances evolve self-similarly, reaching visual thickness Reynolds numbers of up to 20 000. This self-similar period is characterized by a lack of large-scale organized pairings, a lack of streamwise vortices in the ‘‘braid’’ regions, and scalar mixing that is characterized by ‘‘marching’’ probability density functions (PDFs). The case begun with strong additional two-dimensional disturbances only becomes approximately self-similar, but exhibits sustained organized large-scale pairings, clearly defined braid regions with streamwise vortices that span them, and scalar PDFs that are ‘‘nonmarching.’’ It is also characterized by much more intense vertical velocity fluctuations than the other two cases. The statistics and structures in several experiments involving turbulent mixing layers are in better agreement with those of the simulations that do not exhibit organized pairings. .
Convective instability mechanisms in thermocapillary liquid bridges
Authors: Wanschura M. , Shevtsova V. M. , Kuhlmann H. C. , Rath H. J.
Published: July 2002

The primary instability of axisymmetric steady thermocapillary flow in a cylindrical liquid bridge with non-deformable free surface is calculated by a mixed Chebychev-finite difference method. For unit aspect ratio the most dangerous mode has an azimuthal wavenumber m=2. The physical instability mechanisms are studied by analyzing the linear energy balance of the neutral mode. If the Prandtl number is small (Pr≪1), the bifurcation is stationary. The associated neutral mode is amplified in the shear layer close to the free surface. For large Prandtl number (Pr=4), the basic state becomes linearly unstable to a pair of hydrothermal waves propagating nearly azimuthally. Both mechanisms are compared with those previously proposed in the literature.
Bulk viscosity as a relaxation parameter: Fact or fiction?
Authors: Meador Willard E. , Miner Gilda A. , Townsend Lawrence W.
Published: July 2002

The interpretation of bulk viscosity as a relaxation parameter for describing nonequilibrium polyatomic gases is challenged both qualitatively and quantitatively. Its presumed proportionality to a relaxation time is an artificial concept restricted to very rapid equilibration of translational and internal modes compared with some characteristic time of the system. Application of a generalized methodology to small-signal sound waves of intermediate and high frequencies demonstrates this artificiality and shows that bulk viscosity can at best be used as a nonphysical adjustable parameter to force fit a single aspect of relaxation. Sound absorption can be force fitted in this way, but not the dispersion of the sound speed. Accordingly, recent applications of bulk viscosity in solving such problems as heat transfer in hypersonic boundary layers may be seriously deficient.
Origin of high kurtosis levels in the viscous sublayer. Direct numerical simulation and experiment
Authors: Xu C. , Zhang Z. , den Toonder J. M. J. , Nieuwstadt F. T. M.
Published: July 2002

In the literature, a major discrepancy is reported between the value of the kurtosis for the normal velocity fluctuations close to the wall as found from direct numerical simulations and obtained from experiments. The origin of these high kurtosis levels is analyzed with help of a direct numerical simulation of a turbulent channel flow. In addition, a detailed analysis of LDV measurements in the near-wall region of a turbulent pipe flow is made with the results of the DNS as a starting point. In both data sets, i.e. DNS and experiments, similar velocity events were found that contribute to the high kurtosis level. The dynamics of these events can be associated with the regeneration process of streamwise vortices as described by Brooke and Hanratty [Phys. Fluids A 5, 1011 (1993)]. Based on this evidence, we conclude that the high kurtosis is of a truly physical nature. It is caused by very strong events that appear only in the near-wall region and that are rare in time as well as in space. The very rare appearance of these events explains why they are usually missed in experimental data which are mostly obtained from averages over a limited time series. In this respect the DNS results may be considered as more accurate because they are based on surface averages.
Simulations of viscous flows of complex fluids with a Bhatnagar, Gross, and Krook lattice gas
Authors: Rakotomalala N. , Salin D. , Watzky P.
Published: July 2002

We address the question of using a lattice gas method to study flows of complex fluids, such as non-Newtonian or miscible fluids. A Bhatnagar, Gross, and Krook lattice technique provides a tool to simulate the flow of one fluid and the diffusion of a tracer in that fluid. We extend the technique to flows in which the viscosity is space and time dependent. This approach is suitable for non-Newtonian fluids (shear dependent viscosity) and miscible fluids (concentration dependent viscosity). The modified scheme is tested on physical flow situations, analytically tractable for the sake of comparison.
A numerical study of self-similarity in a turbulent plane wake using large-eddy simulation
Authors: Ghosal Sandip , Rogers Michael M.
Published: July 2002

Turbulent wakes are known to develop self-similarly sufficiently far downstream from obstacles that generate them. It has long been assumed that the spreading rate of the wake in the self-similar regime is independent of the details of the body generating the wake, being dependent only on the total drag (or momentum deficit). This assumption seems to be in contradiction with some recent experiments. In this study we attempt to complement these experimental investigations through a numerical study of a time-developing wake. A numerical study has the advantage of eliminating many of the uncontrolled factors present in experiments and allowing precise control of initial conditions. Large-eddy simulations employing the recently developed dynamic localization model are used to extend previous results from direct numerical simulations. The large-eddy simulation results are compared to the direct numerical simulation database, wherever such comparisons are feasible, as a check of the method. Like the experiments, the large-eddy simulations suggest that non-unique self-similar states, characterized by different spreading rates and turbulent statistics, are possible and that they can be maintained for significant time periods. The study also demonstrates the predictive capability of the dynamic localization subgrid model.
Observation of helical traveling-wave convection in a liquid bridge
Authors: Muehlner Kurt A. , Schatz Michael F. , Petrov Valery , McCormick W. D. , Swift J. B. , Swinney Harry L.
Published: July 2002

We use infrared imaging to visualize time-dependent flow in a liquid bridge (Prandtl number 35 and aspect ratio 1) with an imposed vertical temperature gradient. The primary instability leads from an axisymmetric time-independent state to helical traveling waves with an azimuthal wavenumber m=1. A secondary instability introduces an additional traveling wave with m=2. The structure and phase of the modes is determined from the infrared images.
Electrohydrodynamic stability of a liquid column under cross fields: Application to continuous flow electrophoresis
Authors: Limat L. , Stone H. A. , Viovy J. L.
Published: July 2002

An infinite, conductive cylindrical column of electrolyte lying inside another electrolyte flattens when it is submitted to a transverse continuous electric field. This “ribbon” effect can be canceled by a second oscillatory field whose direction is perpendicular to both the column axis and to the first electric field. The linear stability of the equilibrium with respect to elliptic perturbations of the cross section is studied, and it is shown that the stability of the circular shape depends on the sign of a discriminating function of the conductivity and permittivity ratios. Possible applications of the results to continuous flow electrophoresis are discussed: Even for unstable situations the growth rate of disturbances is reduced by the application of a second field so that we expect the efficiency of the separation to be improved.
Spatial instability of planar channel flow with fluid injection through porous walls
Authors: Casalis Grégoire , Avalon Gérard , Pineau Jean-Philippe
Published: July 2002

The present paper deals with the stability properties of a planar channel flow driven by air injection through porous walls. Experimental investigations have been carried out in the so-called VECLA facility and a theoretical linear stability analysis has been performed. The nonparallel effects are studied by using three different stability approaches. They appear to be very significant for this particular flow. This study provides indeed an interesting example of an instability mechanism strongly related to the vertical component (usually negligible) of the mean flow. The obtained results finally agree very well with the measurements with respect to the amplified frequency range and to the streamwise amplification of the instability waves.
Correlations between dispersion and structure in porous media probed by nuclear magnetic resonance
Authors: Manz B. , Alexander P. , Gladden L. F.
Published: July 2002

Magnetic Resonance Imaging (MRI) and Pulsed Gradient Stimulated Echo (PGSTE) Nuclear Magnetic Resonance (NMR) experiments have been used to probe structure and dispersion in a model porous system formed from a packed bed of spherical particles. The structure of the pore space is characterized from the MRI images by determining radial distribution functions for the pore space. The PGSTE experiments yield an average displacement propagator from which the variance of the average molecular displacement and dispersion coefficient are determined at a range of times over which the flow develops. Experiments have been performed over a wide range of Péclet number and flow velocity. The behavior of the dispersion is shown to be closely related to the structure of the pore space. Dispersion transverse to the direction of superficial flow is dominated by Taylor dispersion. In the axial direction, non-Fickian effects become important, even for flow within a single pore. The axial dispersion coefficient approaches an asymptotic limit characterized by a scale length that corresponds to the pore-to-packing correlation length in the direction of flow, suggesting that the non-Fickian dispersion reaches a limiting behavior after just one mixing between streams merging from two interconnected pores.
A numerical revisit of backward-facing step flow problem
Authors: Chiang T. P. , Sheu Tony W. H.
Published: July 2002

In the present study we take a fresh look at a laminar flow evolving into a larger channel through a step configured in a backward-facing format. We conduct steady three-dimensional Navier–Stokes flow analysis in the channel using the step geometry and flow conditions reported by Armaly et al. This allows a direct comparison with the results of physical experiments, thus serving to validate the numerical results computed in the range of 100⩽Re⩽1000. Results show that there is generally excellent agreement between the present results and the experimental data for Re=100 and 389. Fair agreement for Re=1000 is also achieved, except in the streamwise range of 15⩽x⩽25. The main difference stems from the fact that the roof eddy is not extended toward the midspan in the channel with a span width 35 times of the height of the upstream channel. In the present study we also reveal that the flow at the plane of symmetry develops into a two-dimensional-like profile only when the channel width is increased up to 100 times of the upstream step height for the case with Re=800. The present computational results allow the topological features of the flow to be identified using critical point theory. The insight thus gained is useful in revealing a mechanism for the development of an end-wall-induced three-dimensional vortical flow with increasing Reynolds number.
Effects of shallowness on the development of free-surface mixing layers
Authors: Uijttewaal W. S. J. , Booij R.
Published: July 2002

The development of two shallow mixing layers with different water depths is analyzed experimentally by means of laser Doppler anemometry. The experiments show that bottom friction plays an important role in the growth of the mixing layer width and in the strength and dimensions of the large quasi two-dimensional turbulence structures therein. It is found in this study that the initial growth rate of both mixing layers is similar to what has been found for deep water plane mixing layers. Further downstream the reduction of the growth rate can be ascribed to the decrease of the velocity difference between the two ambient streams in combination with the suppression of the growth of the large turbulence structures. In the most shallow mixing layer considered, the influence of the bottom friction is dominant, impeding the further growth of the mixing layer width. It is demonstrated that the reduced mixing layer growth is related to a loss of coherence in the large turbulence structures. This loss of coherence also reduces the characteristic length-scale that establishes the lateral mixing of matter and momentum in the mixing layer. Eventually the water depth becomes the dominant length scale that determines the characteristic motion of the turbulence in that case. From the energy density spectra of the turbulence fluctuations and from the phase relation between the two velocity components in the horizontal plane it is concluded that large structures contribute most to the exchange of momentum in the mixing layer and thus to the Reynolds-stresses.
The inviscid impingement of a jet with arbitrary velocity profile
Authors: Phares Denis J. , Smedley Gregory T. , Flagan Richard C.
Published: July 2002

Accurate determination of wall shear stress and heat and mass transfer rates under an impinging jet requires careful analysis of the boundary layer at the impingement surface due to the large pressure gradients near the stagnation point. Modeling the inviscid flow just outside the boundary layer provides the boundary conditions necessary for such an analysis. Previous inviscid models have considered only a small subset of possible jet velocity profiles and with limited spatial resolution. In the present work, analytical solutions to the stream-vorticity equation for two-dimensional and axisymmetric impingement flow with arbitrary velocity profile are found in terms of a surface integral involving the vorticity function, allowing an iterative determination of the stream function throughout the impingement region. Surface pressure distributions and streamline plots are calculated for various impinging jet configurations, including plane, round, and annular jet nozzles. The calculations show excellent agreement with previous experimental and numerical results, while requiring relatively short computation times. Flow predictions are also made for impinging jet configurations for which no previous data or calculations exist.
Simple formulation of magnetoplasmadynamic acceleration
Authors: Sasoh A.
Published: July 2002

A simple formulation of magnetoplasmadynamic acceleration has been made based on energy conservation relations and a generalized Ohm’s law. An exhaust velocity is expressed using three characteristic parameters: (1) a dimensionless characteristic velocity Ũ≡μ0J2D/(ṁuA) (JD is the discharge current, ṁ is the mass flow rate of working fluid, uA is the Alfvén’s critical velocity, and μ0 is the permeability in vacuum); (2) the ratio of an applied to self-induced magnetic fields; and (3) an electron Hall parameter. An exhaust velocity calculated using the formula agrees well with the experimentally measured value.
Collisional and collisionless magnetic reconnection
Authors: Biskamp D.
Published: July 2002

This paper gives an overview of the basic mechanisms of magnetic reconnection. Resistive reconnection is rather well understood. In most hot plasmas of interest, however, collisionless processes are more effective, in particular whistler-mediated reconnection for β∼1 and kinetic Alfvén wave-mediated reconnection for β≪1, which have mainly been studied in the framework of two-fluid theory. Results from kinetic modeling by particle simulation are also briefly discussed.
Argon density measurements from charge–exchange spectroscopy
Authors: Whyte D. G. , Isler R. C. , Wade M. R. , Schultz D. R. , Krstic P. S. , Hung C. C. , West W. P.
Published: July 2002

Charge–exchange spectroscopy is widely used to determine the profiles of fully stripped low-Z ions (carbon, oxygen, neon) in fusion plasmas. Continuing interest in the use of heavier impurities for radiative cooling in boundaries and divertors of fusion plasmas has encouraged the expansion of this technique for elements such as argon which are not completely burned out in present machines. As a first step, it has been necessary to predict the wavelengths of transitions from Ar XVI to Ar XVIII from theoretical calculations. Several of these have been detected in the DIII-D tokamak [Plasma Physics Controlled Nuclear Fusion Research, 1986 (International Atomic Energy Agency, Vienna, 1987), Vol. I, p. 159] subsequent to argon puffing into neutral-beam injected plasmas, and the experimentally determined wavelengths are in good agreement with the predicted values. Argon ion densities have been determined using recent Classical Trajectory Monte Carlo (CTMC) computations of the charge–exchange cross sections, and some radial profiles for specific ionization stages have been measured.
Collisionless reconnection using Alfvén wave radiation resistance
Authors: Bellan P. M.
Published: July 2002

Patchy magnetic reconnection involves transient field-aligned current filaments. The spatial localization, transient time-dependence, and orientation of these current filaments means they must radiate torsional Alfvén waves. Radiation of wave energy does not come for free—it must load the current which acts as the radiative source. This loading (radiation resistance) is proposed as the energy sink required for collisionless magnetic reconnection to proceed. Radiation resistance for both inertial and kinetic Alfvén waves is calculated and, for highly collisionless plasmas, is shown to exceed by a substantial factor both Spitzer resistivity and the effective resistance due to the direct acceleration of electrons (inertial loading). The radiation resistivity is shown to provide the magnetic field diffusivity required for magnetic fields to diffuse across the assumed width of the current filament on the time scale of the reconnection. It is also shown that Landau damping of the radiated waves results in the generation of energetic, field-aligned particles: in the β≪me/mi regime the energetic particles are electrons while in the me/mi≪β≪1 regime, the energetic particles are ions.
Landau damping and transit-time damping of localized plasma waves in general geometries
Authors: Short R. W. , Simon A.
Published: July 2002

Landau’s original derivation of the collisionless damping of small-amplitude Langmuir waves in an infinite homogeneous plasma relied on the introduction of complex velocities and was therefore somewhat difficult to interpret physically. This has inspired many subsequent derivations of Landau damping that involve only real physical quantities throughout. These “physical” derivations, however, have required the calculation of quantities to second order in the wave field, whereas Landau’s approach involved only first-order quantities. More recent generalizations of Landau damping to localized fields, often called “transit-time damping,” have followed the physical approach, and thus also required second-order calculations, which can be quite lengthy. In this paper it is shown that when the equilibrium distribution function depends solely on the energy, invoking the time-reversal invariance of the Vlasov equation allows transit-time damping to be analyzed using only first-order physical quantities. This greatly simplifies the calculation of the damping of localized plasma waves and, in the limit of an infinite plasma, provides a derivation of Landau damping that is both physical and linear in the wave field. This paper investigates the transit-time damping of plasma waves confined in slabs, cylinders, and spheres, analyzing the dependence on size, radius, and mode number, and demonstrating the approach to Landau damping as the systems become large. It is also shown that the same approach can be extended to more general geometries. A companion paper analyzes transit-time damping in a cylinder in more detail, with applications to the problem of stimulated Raman scattering in self-focused light filaments in laser-produced plasmas.
On plasma heating by reconnective magnetic relaxation
Authors: Vekstein Grigory , Jain Rekha
Published: July 2002

A self-consistent derivation of magnetic energy dissipation provided by ongoing external driving and internal current sheet reconnection in a force-free magnetic field is reported. The resulting plasma heating rate shows characteristic relaxation-type dependence on the driving frequency, being most efficient when the time scales of the driving and reconnection are comparable.
Laboratory studies of magnetic vortices. III. Collisions of electron magnetohydrodynamic vortices
Authors: Urrutia J. M. , Stenzel R. L. , Griskey M. C.
Published: July 2002

Magnetic vortices in the parameter regime of electron magnetohydrodynamics are studied in a large laboratory plasma. The vortices consist of magnetic field perturbations, which propagate in the whistler mode along a uniform dc magnetic field. The magnetic self-helicity of the spheromak-like field perturbations depends on the direction of propagation. Vortices with opposite toroidal or poloidal fields are launched from two antennas and propagated through each other. The vortices collide and propagate through one another without an exchange of momentum, energy, and helicity. The absence of nonlinear interactions is explained by the force-free fields of electron magnetohydrodynamic (EMHD) vortices.
Calorimetric and acoustic study of ultraviolet laser ablation of polymers
Authors: Gorodetsky G. , Kazyaka T. G. , Melcher R. L. , Srinivasan R.
Published: July 2002

Calorimetric and acoustic studies of the mechanism of pulsed laser ablation of a polymer at the wavelengths of 193, 248, and 308 nm are reported. The results are mutually consistent and provide insight into the ablation mechanism.
Optical emission at 1.32 μm from sulfur-doped crystalline silicon
Authors: Brown T. G. , Hall D. G.
Published: July 2002

We report the observation of efficient photoluminescence from a new sulfur-related impurity in crystalline silicon. We tentatively identify this emission as bound-exciton luminescence from sulfur-related isoelectronic impurities. We present the results of measurements of the lifetime, temperature dependence, and external efficiency of the 1.32 μm band.
Photoelectronic and electronic properties of Ti/Si amorphous superlattices
Authors: Willens R. H.
Published: July 2002

Amorphous Ti/Si superlattices have been prepared by electron beam evaporation. These superlattices exhibit electronic and photoelectronic properties which can be used in a variety of different types of devices. The photovoltaic output from this structure is greatly enhanced by deposition on Si substrates with electrical contacts made only to the superlattice film. The mechanism for the photovoltaic signals and illustrations of different types of devices are discussed.
Evidence for oxygen bubbles in subsurface Al2O3 layers formed in aluminum by oxygen implantation
Authors: Musket R. G. , Brown D. W. , Pinizzotto R. F.
Published: July 2002

In an earlier paper [R. G. Musket, D. W. Brown, and H. C. Hayden, Nucl. Instrum. Methods B 7/8, 31 (1985)] we showed that high-dose oxygen ion implantation into bulk aluminum results in the formation of subsurface layers of Al2O3. However, for oxygen doses exceeding that required for oxidation of all the locally available aluminum atoms, the implanted layer contained excess oxygen with the ratio O/Al reaching 3.2. At that time we proposed that excess oxygen was trapped physically at point defects and/or microviods (i.e., bubbles). We have now examined these implanted layers using cross-sectional transmission electron microscopy and cross-sectional scanning electron microscopy. Both of these techniques have provided clear evidence for the existence of 20–100 nm oxygen bubbles. Combining these results with those from Rutherford backscattering and conventional transmission electron microscopy has led to a more complete understanding of the formation process.
Formation of aluminum silicide between two layers of amorphous silicon
Authors: Hentzell H. T. G. , Robertsson A. , Hultman L. , Shaofang G. , Hörnström S.-E. , Psaras P. A.
Published: July 2002

Thin-film structures of amorphous Si/Al/amorphous Si were deposited consecutively without breaking the vacuum. During annealing to 440 K, Al reacts with Si to form a homogeneous compound layer between the two a-Si layers. This compound has a unique and well-defined structure, different from both Al and Si although some similarities exist. The Al silicide observed is stable up to 575 K, at which temperature it dissociates when a-Si crystallizes.
Method for making low-resistivity contacts to high T
c superconductors
Authors: Ekin J. W. , Panson A. J. , Blankenship B. A.
Published: July 2002

A method for making low-resistivity contacts to high Tc superconductors has been developed, which has achieved contact surface resistivities less than 10 μΩ cm2 at 76 K and does not require sample heating above ∼150 °C. This is an upper limit for the contact resistivity obtained at high current densities up to 102–103 A/cm2 across the contact interface. At lower measuring current densities the contact resistivities were lower and the voltage-current curve was nonlinear, having a superconducting transition character. On cooling from 295 to 76 K, the contact resistivity decreased several times, in contrast to indium solder contacts where the resistivity increased on cooling. The contacts showed consistently low resistivity and little degradation when exposed to dry air over a four-month period and when repeatedly cycled between room temperature and 76 K. The contacts are formed by sputter depositing a layer of a noble metal−silver and gold were used−on a clean superconductor surface to protect the surface and serve as a contact pad. External connections to the contact pads have been made using both solder and wire-bonding techniques.
Observation of two distinct components during pulsed laser deposition of high T
c superconducting films
Authors: Venkatesan T. , Wu X. D. , Inam A. , Wachtman J. B.
Published: July 2002

Using Rutherford backscattering technique, we have measured the angular distribution of the composition and thickness of the Y-Ba-Cu oxide film deposited by firing excimer laser (30 ns, 248 nm) pulses at a stoichiometric Y1Ba2Cu3O7−x pellet. The angular distribution consisted of two distinct components: one a cos θ component, a result of evaporation, and the other a highly forward directed component, a result of a secondary ejection process. The evaporated component is nonstoichiometric, as one would expect, whereas the forward-directed component has a composition close to that of the pellet. Further, the forward-directed stoichiometric component increases with the laser energy density in comparison with the evaporated component. These observations are discussed in the context of current models of laser-induced material ejection at surfaces.The laser energy dependence of the deposition is of critical importance in controlling the film stoichiometry.
Evolution of IESs and scrambling in the actin I gene in hypotrichous ciliates
Authors: Hogan Daniel J. , Hewitt Elizabeth A. , Orr Kindra E. , Prescott David M. , Müller Kirsten M.
Published: July 2002

Germ-line (micronuclear) genes in hypotrichous ciliates are
interrupted by numerous, short, noncoding, AT-rich segments called
internal eliminated segments, or IESs. IESs divide a gene into
macronuclear destined segments, or MDSs. IESs are excised from
micronuclear genes, and the MDSs are spliced when a micronuclear genome
is processed into a macronuclear genome after cell mating. In the
micronuclear version of the actin I gene intramolecular recombination
between IESs during evolution has put MDSs into a scrambled disorder in
some but not all hypotrichs. Studies using rDNA sequences to define
phylogenetic relationships among eight hypotrichs suggests that
evolution of the micronuclear actin I gene proceeds by successive
addition of IESs in earlier diverging species, without MDS scrambling.
Continued addition of IESs and recombination among IESs in later
diverging species produced actin I genes with scrambled MDSs.
Subsequent to MDS scrambling, additional IESs were inserted into the
more recently evolved species. Thus, IES insertions and gene scrambling
occur in a progressive manner during species evolution to produce
micronuclear actin I genes of increasing structural complexity.
A novel precursor recognition element facilitates posttranslational binding to the signal recognition particle in chloroplasts
Authors: DeLille Justin , Peterson Eric C. , Johnson Tracey , Moore Misty , Kight Alicia , Henry Ralph
Published: July 2002

Signal recognition particles (SRPs) in the cytosols of prokaryotes and eukaryotes are used to target proteins to cytoplasmic membranes and the endoplasmic reticulum, respectively. The mechanism of targeting relies on cotranslational SRP binding to hydrophobic signal sequences. An organellar SRP identified in chloroplasts (cpSRP) is unusual in that it functions posttranslationally to localize a subset of nuclear-encoded thylakoid proteins. In assays that reconstitute thylakoid integration of the light harvesting chlorophyll-binding protein (LHCP), stromal cpSRP binds LHCP posttranslationally to form a cpSRP/LHCP transit complex, which is believed to represent the LHCP form targeted to thylakoids. In this investigation, we have identified an 18-aa sequence motif in LHCP (L18) that, along with a hydrophobic domain, is required for transit complex formation. Fusion of L18 to the amino terminus of an endoplasmic reticulum-targeted protein, preprolactin, led to transit complex formation whereas wild-type preprolactin exhibited no ability to form a transit complex. In addition, a synthetic L18 peptide, which competed with LHCP for transit complex formation, caused a parallel inhibition of LHCP integration. Translocation of proteins by the thylakoid Sec and Delta pH transport systems was unaffected by the highest concentration of L18 peptide examined. Our data indicate that a motif contained in L18 functions in precursor recruitment to the posttranslational SRP pathway, one of at least four different thylakoid sorting pathways used by chloroplasts.
Host factor Hfq of
Escherichia coli
stimulates elongation of poly(A) tails by poly(A) polymerase I
Authors: Hajnsdorf Eliane , Régnier Philippe
Published: July 2002

Current evidence suggests that the length of poly(A) tails of bacterial mRNAs result from a competition between poly(A) polymerase and exoribonucleases that attack the 3′ ends of RNAs. Here, we show that host factor Hfq is also involved in poly(A) tail metabolism. Inactivation of the
hfq
gene reduces the length of poly(A) tails synthesized at the 3′ end of the
rpsO
mRNA by poly(A) polymerase I
in vivo
.
In vitro
, Hfq stimulates synthesis of long tails by poly(A) polymerase I. The strong binding of Hfq to oligoadenylated RNA probably explains why it stimulates elongation of primers that already harbor tails of 20–35 A. Polyadenylation becomes processive in the presence of Hfq. The similar properties of Hfq and the PABPII poly(A) binding protein, which stimulates poly(A) tail elongation in mammals, indicates that similar mechanisms control poly(A) tail synthesis in prokaryotes and eukaryotes.
Chronic elevation of plasma thioredoxin: Inhibition of chemotaxis and curtailment of life expectancy in AIDS
Authors: Nakamura Hajime , De Rosa Stephen C. , Yodoi Junji , Holmgren Arne , Ghezzi Pietro , Herzenberg Leonard A. , Herzenberg Leonore A.
Published: July 2002

Thioredoxin (Trx) is an intracellular redox protein with extracellular cytokine-like and chemokine-like activities. We show here that, although plasma Trx levels are unrelated to survival of HIV-infected individuals with CD4 cell counts above 200/μl blood, survival is significantly impaired (P= 0.003) when plasma Trx is chronically elevated in HIV-infected subjects with CD4 T cell counts below this level (i.e., with Centers for Disease Control (CDC)-defined AIDS). Relevant to the mechanism potentially underlying this finding, we also present data from experimental studies in mice showing that elevated plasma Trx efficiently blocks lipopolysaccharide (LPS)-induced chemotaxis, an innate immune mechanism that is particularly crucial when adaptive immunity is compromised. Thus, we propose that elevated plasma Trx in HIV-infected individuals with low CD4 T cell counts directly impairs survival by blocking pathogen-induced chemotaxis, effectively eliminating the last (innate) barrier against establishment of opportunistic and other infections in these immunodeficient individuals.
Spatiotemporal dynamics of guanosine 3′,5′-cyclic monophosphate revealed by a genetically encoded, fluorescent indicator
Authors: Honda Akira , Adams Stephen R. , Sawyer Carolyn L. , Lev-Ram Varda , Tsien Roger Y. , Dostmann Wolfgang R. G.
Published: July 2002

To investigate the dynamics of guanosine 3′,5′-cyclic monophosphate
(cGMP) in single living cells, we constructed genetically encoded,
fluorescent cGMP indicators by bracketing cGMP-dependent protein kinase
(cGPK), minus residues 1–77, between cyan and yellow mutants of green
fluorescent protein. cGMP decreased fluorescence resonance energy
transfer (FRET) and increased the ratio of cyan to yellow emissions by
up to 1.5-fold with apparent dissociation constants of ≈2 μM and
>100:1 selectivity for cGMP over cAMP. To eliminate constitutive
kinase activity, Thr
516
of cGPK was mutated to Ala.
Emission ratio imaging of the indicators transfected into rat fetal
lung fibroblast (RFL)-6 showed cGMP transients resulting from
activation of soluble and particulate guanylyl cyclase, respectively,
by nitric oxide (NO) and C-type natriuretic peptide (CNP). Whereas all
naive cells tested responded to CNP, only 68% responded to NO. Both
sets of signals showed large and variable (0.5–4 min) latencies. The
phosphodiesterase (PDE) inhibitor 3-isobutyl-1-methylxanthine (IBMX)
did not elevate cGMP on its own but consistently amplified responses to
NO or CNP, suggesting that basal activity of guanylate cyclase is very
low and emphasizing the importance of PDEs in cGMP recycling. A
fraction of RFL cells showed slowly propagating tides of cGMP spreading
across the cell in response to delocalized application of NO.
Biolistically transfected Purkinje neurons showed cGMP responses to
parallel fiber activity and NO donors, confirming that single-cell
increases in cGMP occur under conditions appropriate to cause synaptic
plasticity.
Direct external imaging of nascent cancer, tumor progression, angiogenesis, and metastasis on internal organs in the fluorescent orthotopic model
Authors: Yang Meng , Baranov Eugene , Wang Jin-Wei , Jiang Ping , Wang Xiaoen , Sun Fang-Xian , Bouvet Michael , Moossa A. R. , Penman Sheldon , Hoffman Robert M.
Published: July 2002

Mouse tumor models have undergone profound improvements in the fidelity of emulating human disease. Replacing ectopic s.c. implantation with organ-specific orthotopic implantation reproduces human tumor growth and metastasis. Strong fluorescent labeling with green fluorescent protein along with inexpensive video detectors, positioned externally to the mouse, allows the monitoring of details of tumor growth, angiogenesis, and metastatic spread. However, the sensitivity of external imaging is limited by light scattering in intervening tissue, most especially in skin. Opening a reversible skin-flap in the light path markedly reduces signal attenuation, increasing detection sensitivity many-fold. The observable depth of tissue is thereby greatly increased and many tumors that were previously hidden are now clearly observable. This report presents tumor images and related quantitative growth data previously impossible to obtain. Single tumor cells, expressing green fluorescent protein, were seeded on the brain image through a scalp skin-flap. Lung tumor microfoci representing a few cells are viewed through a skin-flap over the chest wall, while contralateral micrometastases were imaged through the corresponding skin-flap. Pancreatic tumors and their angiogenic microvessels were imaged by means of a peritoneal wall skin-flap. A skin-flap over the liver allowed imaging of physiologically relevant micrometastases originating in an orthotopically implanted tumor. Single tumor cells on the liver arising from intraportal injection also were detectable. Possible future technical developments are suggested by the image, through a lower-abdominal skin-flap, of an invasive prostate tumor expressing both red and green fluorescent proteins in separate colonies.
A nonspecific fatty acid within the bumblebee mating plug prevents females from remating
Authors: Baer Boris , Morgan E. David , Schmid-Hempel Paul
Published: July 2002

The best mating strategy for males differs from that of females,
because females gain from mating with several males (polyandry), but
males gain from monopolizing the females. As a consequence, males have
evolved a variety of methods, such as the transfer of inhibitory
substances from their accessory glands, to ensure exclusive paternity
of the female's offspring, generally with detrimental effects on
female fitness. Inhibitory substances have been identified as peptides
or other specific molecules. Unfortunately, in social insects
male-mating traits are investigated only poorly, although male social
insects might have the same fundamental influence on female-mating
behavior as found in other species. A recently developed technique for
the artificial insemination of bumblebee queens allowed us to
investigate which chemical compound in the mating plug of male
bumblebees,
Bombus terrestris
L., prevents females
(queens) from further mating. Surprisingly, we found that the active
substance is linoleic acid, a ubiquitous and rather unspecific fatty
acid. Contrary to mating plugs in other insect species, the bumblebee
mating plug is highly efficient and allows the males to determine
queen-mating frequencies.
Ex vivo
propagation of infectious sheep scrapie agent in heterologous epithelial cells expressing ovine prion protein
Authors: Vilette D. , Andreoletti O. , Archer F. , Madelaine M. F. , Vilotte J. L. , Lehmann S. , Laude H.
Published: July 2002

Transmissible spongiform encephalopathies, or prion diseases, are
fatal degenerative disorders of the central nervous system that affect
humans and animals. Prions are nonconventional infectious agents whose
replication depends on the host prion protein (PrP). Transmission of
prions to cultured cells has proved to be a particularly difficult
task, and with a few exceptions, their experimental propagation relies
on inoculation to laboratory animals. Here, we report on the
development of a permanent cell line supporting propagation of natural
sheep scrapie. This model was obtained by stable expression of a
tetracycline-regulatable ovine PrP gene in a rabbit epithelial cell
line. After exposure to scrapie agent, cultures were repeatedly found
to accumulate high levels of abnormal PrP (PrPres). Cell extracts
induced a scrapie-like disease in transgenic mice overexpressing ovine
PrP. These cultures remained healthy and stably infected upon
subpassaging. Such data show that (
i
) cultivated cells
from a nonneuronal origin can efficiently replicate prions; and
(
ii
) species barrier can be crossed
ex
vivo
through the expression of a relevant PrP gene. This
approach led to the
ex vivo
propagation of a natural
transmissible spongiform encephalopathy agent (i.e., without previous
experimental adaptation to rodents) and might be applied to human or
bovine prions.
Etoposide induces heritable chromosomal aberrations and aneuploidy during male meiosis in the mouse
Authors: Marchetti Francesco , Bishop Jack B. , Lowe Xiu , Generoso Walderico M. , Hozier John , Wyrobek Andrew J.
Published: July 2002

Etoposide, a topoisomerase II inhibitor widely used in cancer
therapy, is suspected of inducing secondary tumors and affecting the
genetic constitution of germ cells. A better understanding of the
potential heritable risk of etoposide is needed to provide sound
genetic counseling to cancer patients treated with this drug in their
reproductive years. We used a mouse model to investigate the effects
of clinical doses of etoposide on the induction of chromosomal
abnormalities in spermatocytes and their transmission to zygotes by
using a combination of chromosome painting and
4′,6-diamidino-2-phenylindole staining. High frequencies of
chromosomal aberrations were detected in spermatocytes within 64 h
after treatment when over 30% of the metaphases analyzed had
structural aberrations (
P
< 0.01). Significant
increases in the percentages of zygotic metaphases with structural
aberrations were found only for matings that sampled treated pachytene
(28-fold,
P
< 0.0001) and preleptotene
spermatocytes (13-fold,
P
< 0.001). Etoposide
induced mostly acentric fragments and deletions, types of aberrations
expected to result in embryonic lethality, because they represent loss
of genetic material. Chromosomal exchanges were rare. Etoposide
treatment of pachytene cells induced aneuploidy in both spermatocytes
(18-fold,
P
< 0.01) and zygotes (8-fold,
P
< 0.05). We know of no other report of an agent
for which paternal exposure leads to an increased incidence of
aneuploidy in the offspring. Thus, we found that therapeutic doses of
etoposide affect primarily meiotic germ cells, producing unstable
structural aberrations and aneuploidy, effects that are transmitted to
the progeny. This finding suggests that individuals who undergo
chemotherapy with etoposide may be at a higher risk for abnormal
reproductive outcomes especially within the 2 months after
chemotherapy.
Predicting protein function from structure: Unique structural features of proteases
Authors: Stawiski Eric W. , Baucom Albion E. , Lohr Scott C. , Gregoret Lydia M.
Published: July 2002

We have noted consistent structural similarities among unrelated proteases. In comparison with other proteins of similar size, proteases have smaller than average surface areas, smaller radii of gyration, and higher C
α
densities. These findings imply that proteases are, as a group, more tightly packed than other proteins. There are also notable differences in secondary structure content between these two groups of proteins: proteases have fewer helices and more loops. We speculate that both high packing density and low α-helical content coevolved in proteases to avoid autolysis. By using the structural parameters that seem to show some separation between proteases and nonproteases, a neural network has been trained to predict protease function with over 86% accuracy. Moreover, it is possible to identify proteases whose folds were not represented during training. Similar structural analyses may be useful for identifying other classes of proteins and may be of great utility for categorizing the flood of structures soon to flow from structural genomics initiatives.
Origin of a complex key innovation in an obligate insect–plant mutualism
Authors: Pellmyr Olle , Krenn Harald W.
Published: July 2002

Evolutionary key innovations give organisms access to new ecological resources and cause rapid, sometimes spectacular adaptive radiation. The well known obligate pollination mutualism between yuccas and yucca moths is a major model system for studies of coevolution, and it relies on the key innovation in the moths of complex tentacles used for pollen collecting and active pollination. These structures lack apparent homology in other insects, making them a rare example of a novel limb. We performed anatomical and behavioral studies to determine their origin and found evidence of a remarkably simple mechanism. Morphological analyses of the tentacles and adjacent mouthparts in pollinators and closely related taxa showed that the tentacle appears abruptly in female pollinating yucca moths. Several morphological synapomorphies between the galeae, which constitute the characteristic lepidopteran proboscis, and the tentacle suggest that the tentacle evolved quickly through expression of the genetic template for the galea at an apical growth bud on the first segment of the maxillary palp. Behavioral data indicate that tentacle and proboscis movements are controlled by a shared hydraulic extension mechanism, thus no new mechanism was needed for tentacle function. Known developmental paths from other insects can explain the origin of this sex-specific key innovation in a few steps.