bluuebunny/crossref_metadata_2025 huggingface dataset:
A dynamic subgrid-scale model for compressible turbulence and scalar transport
Authors: Moin P. , Squires K. , Cabot W. , Lee S.
Published: July 2002

The dynamic subgrid-scale (SGS) model of Germano et al. [Phys. Fluids A 3, 1760 (1991)] is generalized for the large eddy simulation (LES) of compressible flows and transport of a scalar. The model was applied to the LES of decaying isotropic turbulence, and the results are in excellent agreement with experimental data and direct numerical simulations. The expression for the SGS turbulent Prandtl number was evaluated using direct numerical simulation (DNS) data in isotropic turbulence, homogeneous shear flow, and turbulent channel flow. The qualitative behavior of the model for turbulent Prandtl number and its dependence on molecular Prandtl number, direction of scalar gradient, and distance from the wall are in accordance with the total turbulent Prandtl number from the DNS data.
Probability distributions and thermal transport in a turbulent grid flow
Authors: Lane B. R. , Mesquita O. N. , Meyers S. R. , Gollub J. P.
Published: July 2002

Recent theoretical proposals concerning non-Gaussian statistics of passive scalars in random velocity fields are tested experimentally, by measuring the probability distributions of fluctuating temperature in an oscillating grid flow across which a steady temperature gradient is maintained. Pronounced exponential tails occur at sufficiently high Reynolds number R, and predominantly Gaussian statistics at low R. When the extended tails are present for the passive scalar, the corresponding velocity power spectrum shows reasonable scaling, and the velocity distribution is not far from Gaussian. The present paper provides a more complete characterization of the flow field than an earlier brief report [Phys. Rev. Lett. 67, 3507 (1991)], and also contains a description of additional features, such as the skewness of the distributions. Finally, the effective or eddy diffusivity of both heat and a molecular impurity are measured and compared.
Hysteresis in a swirling jet as a model tornado
Authors: Shtern V. , Hussain F.
Published: July 2002

A swirling jet, emerging normal to a plane, serves as a model of a tornado and is characterized by its flow force and outer circulation. This model is examined here using the full Navier–Stokes equations. Three branches of solutions are found which form a hysteresis loop and a cusp catastrophe that means jump transitions between flow regimes. One of the jumps relates to vortex breakdown and the other relates to a new (opposite) effect: abrupt vortex consolidation. These results are compared with those of Long [J. Fluid Mech. 11, 611 (1961)], who considered a near-axis jet in the boundary layer approximation. More detailed analysis made here for high circulation values allows discovery of two new types of asymptotic solutions corresponding to a near-plane fan jet and a two-cell flow. It was also found that the boundary layer approach for the near-axis jet fails to accurately yield the total flow force because the outer flow contributes a share of the momentum flux of comparable magnitude to that of the inner flow. The prediction of the jump transitions between one- and two-cell flow patterns agrees with observations of abrupt changes in tornado patterns in nature.
Nonlinear evolution of stimulated Raman scattering in homogeneous plasmas
Authors: Rozmus W. , Sharma R. P. , Samson J. C. , Tighe W.
Published: July 2002

A model for stimulated Raman scattering (SRS) in a homogeneous plasma has been designed to account for the presence of stimulated Brillouin scattering (SBS) and the nonlinear coupling between Langmuir and ion waves described by Zakharov equations. The nonlinear evolution of electron plasma waves also includes an effective damping resulting from electron diffusion in localized Langmuir fields produced during simultaneous SRS and SBS evolutions. Numerical results based on this model show two distinct SRS behaviors. Close to ncr/4 the Langmuir collapse dominates nonlinear evolution of the instability. At lower densities low level SRS is observed for a relatively long time after which SRS is terminated as a result of ion fluctuations produced by SBS. In addition, the anomalous absorption of backscattered SRS radiation by ion fluctuations produced by the collapse is proposed as a mechanism that may explain some recent experimental observations showing a gap in the SRS spectrum.
Second harmonic emission from an underdense laser-produced plasma and filamentation
Authors: Meyer J. , Zhu Y.
Published: July 2002

It is shown theoretically that filamentation can lead to sizable second harmonic generation. The 2ω0 radiation is emitted into a forward-directed cone, its angle determined by the wavelength of the fundamental radiation in the plasma waveguide. Experimental observations confirm the theoretical predictions. Aside from the forward-directed emission cone, non-negligible 2ω0 power is detected over a broad angular range in the backward direction showing a broadened red-shifted spectrum.
Singular front formation in a model for quasigeostrophic flow
Authors: Constantin Peter , Majda Andrew J. , Tabak Esteban G.
Published: July 2002

A two-dimensional model for quasigeostrophic flow which exhibits an analogy with the three-dimensional incompressible Euler equations is considered. Numerical experiments show that this model develops sharp fronts without the need to explicitly incorporate any ageostrophic effect. Furthermore, these fronts appear to become singular in finite time. The numerical evidence for singular behavior survives the tests of rigorous mathematical criteria.
Oblique shocks and the combined Rayleigh–Taylor, Kelvin–Helmholtz, and Richtmyer–Meshkov instabilities
Authors: Mikaelian Karnig O.
Published: July 2002

This Letter considers the evolution of perturbations at an interface between two fluids subjected to an oblique shock. The normal component of the shock generates the Richtmyer–Meshkov (RM) instability, and the parallel component generates the Kelvin–Helmholtz (KH) instability. If a constant normal acceleration is also present it induces the Rayleigh–Taylor (RT) instability or, depending on the sign of gA (g=acceleration, A=Atwood number), it acts to stabilize the KH and RM instabilities. Treating the shock as an instantaneous acceleration, analytic formulas are derived for the evolution of the perturbations. This Letter illustrates with an application to inertial-confinement-fusion capsules.
Bottleneck phenomenon in developed turbulence
Authors: Falkovich Gregory
Published: July 2002

It is shown how viscosity increases turbulence level in the inertial interval by suppressing turbulent transfer.
A study of the fine-scale motions of incompressible time-developing mixing layers
Authors: Soria J. , Sondergaard R. , Cantwell B. J. , Chong M. S. , Perry A. E.
Published: July 2002

The geometry of dissipating motions in direct numerical simulations (DNS) of the incompressible mixing layer is examined. All nine partial derivatives of the velocity field are determined at every grid point in the flow, and various invariants and related quantities are computed from the velocity gradient tensor. Motions characterized by high rates of kinetic energy dissipation and high enstrophy density are of particular interest. Scatter plots of the invariants are mapped out and interesting and unexpected patterns are seen. Depending on initial conditions, each type of shear layer produces its own characteristic scatter plot. In order to provide more detailed information on the distribution of invariants at intermediate and large scales, scatter plots are replaced with more useful number density contour plots. These essentially represent the unnormalized joint probability density function of the two invariants being cross-plotted. Plane mixing layers at the same Reynolds number, but with laminar and turbulent initial conditions, are studied, and comparisons of the rate-of-strain topology of the dissipating motions are made. The results show conclusively that, regardless of initial conditions, the bulk of the total kinetic energy dissipation is contributed by intermediate scale motions, whose local rate-of-strain topology is characterized as unstable-node-saddle–saddle (two positive rate-of-strain eigenvalues, one negative). In addition, it is found that, for these motions, the rate-of-strain invariants tend to approximately follow a straight line relationship, characteristic of a two-dimensional flow with out of plane straining. In contrast, fine-scale motions, which have the highest dissipation, but which only contribute a small fraction of the total dissipation tend toward a fixed ratio of the principal rates of strain.
Meniscus shape experiments in forward roll coating
Authors: Decré M. , Gailly E. , Buchlin J.-M.
Published: July 2002

In the present paper, experiments are reported for the measurement of the complete meniscus profile in asymmetric forward roll coating. A thin laser sheet technique is used to recover accurately the shape and position of the interface for an extensive database of operating conditions. Knowledge of the interface profile and position is then used to measure the total flow rate and its distribution on each cylinder. The results provide for the first time validation of numerical predictions for the extended shape of the meniscus. Comparison with existing theoretical and numerical predictions validates both these approaches, but reveals the need to model the whole flow region, including gravity, instead of restricting to the region downstream of the nip separating the rotating cylinders.
Effects of acceleration on turbulent jets
Authors: Zhang Q. , Johari H.
Published: July 2002

Effects of acceleration on turbulent jets were investigated in a series of flow visualization experiments. Prior to the initiation of acceleration, a steady jet with a Reynolds number of 3000 was established. Three distinct acceleration schemes of linear, quadratic, and exponential were utilized to increase the nozzle exit velocity by an order of magnitude. As the flow accelerated, a discernible ‘‘front’’ was established. The parcels constituting the front were less diluted than the steady jet parcels at the same location. For each acceleration scheme, the temporal evolution of the front position had the same functional form as the nozzle velocity. The front velocity increased linearly with the acceleration rate for the linear and quadratic cases. In comparison with a steady jet, the front’s lateral growth rate was reduced by 16% in the linear case and by 25% in the two nonlinear cases, even though the linear cases had generally larger acceleration rates. A model, based on the scaling of centerline velocity in steady jets, appears to correctly predict the time dependence of the front position.
Large eddy simulations of Rayleigh–Bénard convection using subgrid scale estimation model
Authors: Kimmel Shari J. , Domaradzki J. Andrzej
Published: July 2002

The subgrid scale estimation model, which has been previously studied for large eddy simulations of turbulent channel flow, was extended to convective flows. The estimation procedure involves expanding the temperature and velocities to scales smaller than the grid size using the properties of the top-hat filter, Fourier expansions, and nonlinear interactions among the resolved scales. An expanded field, which contains subgrid scales two times smaller than the grid size, is used to calculate the subgrid scale stresses directly from the definition. In an a priori analysis, the exact quantities computed from the direct numerical simulation data are compared with results from the estimation model and the Smagorinsky model applied without wall functions. The subgrid scale stresses from the estimation model agree well with the exact quantities, but the Smagorinsky model results do not. The same conclusions are reached after both models are implemented in actual large eddy simulations. For both the velocities and temperature, the estimation model produces a more realistic distribution of subgrid scale stresses across the convective layer, does not require wall functions for correct behavior near the boundary, and does not contain any arbitrary constants, in contrast to the Smagorinsky model. Additionally, numerically stable backscatter is inherent in the estimation model.
Filamentation of ultrashort pulse laser beams resulting from their propagation over long distances in air
Authors: La Fontaine B. , Vidal F. , Jiang Z. , Chien C. Y. , Comtois D. , Desparois A. , Johnston T. W. , Kieffer J.-C. , Pépin H. , Mercure H. P.
Published: July 2002

The propagation of high-power short-pulse laser beams over considerable distances in air is studied both experimentally and via numerical simulations. Filaments are formed after 5–10 m and their propagation over distances in excess of 200 m is reported for the first time. The lateral dimensions of the filaments are found to range from about 100 μm to a few millimeters in diameter. The early values of plasma electron density have been inferred to be a few times 1016 cm−3 using longitudinal spectral interferometry. For 500 fs pulses and a wavelength of 1053 nm, the energy in the filament can be quite high initially (∼8 mJ) and is found to stabilize at about 1.5–2 mJ, after about 35 m. A simple model based on the nonlinear Schrödinger equation coupled to a multiphoton ionization law appears to describe several experimental results quite well.
Third harmonic generation as a structural diagnostic of ion-implanted amorphous and crystalline silicon
Authors: Moss D. J. , van Driel H. M. , Sipe J. E.
Published: July 2002

We demonstrate the use of third harmonic generation as a probe of the bulk symmetry properties of semiconductors. Using 20 ns, 1.06 μm laser pulses we have applied this probe to structural diagnostics of (100) annealed and unannealed Si wafers implanted with boron and arsenic ions at dosages above and below the threshold for amorphization. The presence of free carriers with densities up to 1021 cm−3 is found to increase the intensity but not alter the symmetry characteristics of the third harmonic light; the enhancement in the light level is attributed to a change in the reflectivity.
Role of Hg in junction formation in ion-implanted HgCdTe
Authors: Bubulac L. O. , Tennant W. E.
Published: July 2002

The present work clarifies the role of Hg diffusion in forming ion-implanted junctions in HgCdTe. Two experiments indicate that displaced Hg acts as a limited diffusion source. The first experiment contrasts n/p junction electrical profiles in two HgCdTe wafers, one p doped primarily by cation vacancies and the other primarily by the addition of As in the liquid phase epitaxy melt. The second experiment compares the carrier concentration near the junction with the residual net background doping of the sample. The results indicate that Hg released from the implant region operates as a limited diffusion source in the post-implant anneal process. Adjusting these material and process parameters allows n-on-p junctions to be formed with a controllable electrical profile.
Chemical defense against predation in an insect egg
Authors: Eisner Thomas , Eisner Maria , Rossini Carmen , Iyengar Vikram K. , Roach Braden L. , Benedikt Eva , Meinwald Jerrold
Published: July 2002

The larva of the green lacewing (
Ceraeochrysa cubana
) (Neuroptera, Chrysopidae) is a natural predator of eggs of
Utetheisa ornatrix
(Lepidoptera, Arctiidae), a moth that sequesters pyrrolizidine alkaloids from its larval foodplant (Fabaceae,
Crotalaria
spp.).
Utetheisa
eggs are ordinarily endowed with the alkaloid. Alkaloid-free
Utetheisa
eggs, produced experimentally, are pierced by the larva with its sharp tubular jaws and sucked out. Alkaloid-laden eggs, in contrast, are rejected. When attacking an
Utetheisa
egg cluster (numbering on average 20 eggs), the larva subjects it to an inspection process. It prods and/or pierces a small number of eggs (on average two to three) and, if these contain alkaloid, it passes “negative judgement” on the remainder of the cluster and turns away. Such generalization on the part of the larva makes sense, because the eggs within clusters differ little in alkaloid content. There is, however, considerable between-cluster variation in egg alkaloid content, so clusters in nature can be expected to range widely in palatability. To check each cluster for acceptability must therefore be adaptive for the larva, just as it must be adaptive for
Utetheisa
to lay its eggs in large clusters and to apportion alkaloid evenly among eggs of a cluster.
A library of bacteriophage-displayed antibody fragments directed against proteins of the inner ear
Authors: Cyr Janet L. , Hudspeth A. J.
Published: July 2002

Bacteriophage display of antibodies provides a method for the generation of immunological reagents against rare and uncharacterized antigens. To ascertain the usefulness of this approach for the characterization of inner-ear proteins, we produced a bacteriophage-displayed antibody-fragment library directed against proteins from the bullfrog's sacculus. This library was probed for bacteriophage that bound to proteins present in a lysate of hair cells, the sensory receptors of the inner ear. The predominant bacteriophage clone after selection expressed an antibody fragment that recognized a single protein in the inner ear. This antigen occurred in both the nonsensory and sensory epithelia of the sacculus. The specificity of the antibody fragment indicates that our bacteriophage-displayed library provides a useful source of immunological tools that should facilitate the identification and biochemical characterization of novel proteins in the inner ear.
Molecular mobility in the cytoplasm: An approach to describe and predict lifespan of dry germplasm
Authors: Buitink Julia , Leprince Olivier , Hemminga Marcus A. , Hoekstra Folkert A.
Published: July 2002

Molecular mobility is increasingly considered a key factor influencing storage stability of biomolecular substances, because it is thought to control the rate of detrimental reactions responsible for reducing the shelf life of, for instance, pharmaceuticals, food, and germplasm. We investigated the relationship between aging rates of germplasm and the rotational motion of a polar spin probe in the cytoplasm under different storage conditions using saturation transfer electron paramagnetic resonance spectroscopy. Rotational motion of the spin probe in the cytoplasm of seed and pollen of various plant species changed as a function of moisture content and temperature in a manner similar to aging rates or longevity. A linear relationship was established between the logarithms of rotational motion and aging rates or longevity. This linearity suggests that detrimental aging rates are associated with molecular mobility in the cytoplasm. By measuring the rotational correlation times at low temperatures at which experimental determination of longevity is practically impossible, this linearity enabled us to predict vigor loss or longevity. At subzero temperatures, moisture contents for maximum life span were predicted to be higher than those hitherto used in genebanks, urging for a reexamination of seed storage protocols.
Extraterrestrial amino acids in Orgueil and Ivuna: Tracing the parent body of CI type carbonaceous chondrites
Authors: Ehrenfreund Pascale , Glavin Daniel P. , Botta Oliver , Cooper George , Bada Jeffrey L.
Published: July 2002

Amino acid analyses using HPLC of pristine interior pieces of the CI carbonaceous chondrites Orgueil and Ivuna have found that β-alanine, glycine, and γ-amino-n-butyric acid (ABA) are the most abundant amino acids in these two meteorites, with concentrations ranging from ≈600 to 2,000 parts per billion (ppb). Other α-amino acids such as alanine, α-ABA, α-aminoisobutyric acid (AIB), and isovaline are present only in trace amounts (<200 ppb). Carbon isotopic measurements of β-alanine and glycine and the presence of racemic (D/L ≈ 1) alanine and β-ABA in Orgueil suggest that these amino acids are extraterrestrial in origin. In comparison to the CM carbonaceous chondrites Murchison and Murray, the amino acid composition of the CIs is strikingly distinct, suggesting that these meteorites came from a different type of parent body, possibly an extinct comet, than did the CM carbonaceous chondrites.
Increased mitochondrial oxidative stress in the Sod2 (+/−) mouse results in the age-related decline of mitochondrial function culminating in increased apoptosis
Authors: Kokoszka Jason E. , Coskun Pinar , Esposito Luke A. , Wallace Douglas C.
Published: July 2002

To determine the importance of mitochondrial reactive oxygen
species toxicity in aging and senescence, we analyzed changes in
mitochondrial function with age in mice with partial or complete
deficiencies in the mitochondrial antioxidant enzyme manganese
superoxide dismutase (MnSOD). Liver mitochondria from homozygous mutant
mice, with a complete deficiency in MnSOD, exhibited substantial
respiration inhibition and marked sensitization of the mitochondrial
permeability transition pore. Mitochondria from heterozygous mice, with
a partial deficiency in MnSOD, showed evidence of increased proton
leak, inhibition of respiration, and early and rapid accumulation of
mitochondrial oxidative damage. Furthermore, chronic oxidative stress
in the heterozygous mice resulted in an increased sensitization of the
mitochondrial permeability transition pore and the premature induction
of apoptosis, which presumably eliminates the cells with
damaged mitochondria. Mice with normal MnSOD levels show the same
age-related mitochondrial decline as the heterozygotes but occurring
later in life. The premature decline in mitochondrial function in the
heterozygote was associated with the compensatory up-regulation of
oxidative phosphorylation enzyme activity. Thus mitochondrial reactive
oxygen species production, oxidative stress, functional decline, and
the initiation of apoptosis appear to be central components of
the aging process.
Inorganic polyphosphate is needed for swimming, swarming, and twitching motilities of
Pseudomonas aeruginosa
Authors: Rashid M. Harunur , Kornberg Arthur
Published: July 2002

Polyphosphate kinase (PPK), encoded by the
ppk
gene,
is the principal enzyme in many bacteria for the synthesis of inorganic
polyphosphate (poly P) from ATP. A knockout mutant in the
ppk
gene of
Pseudomonas aeruginosa
PAO1
is impaired in flagellar swimming motility on semisolid agar plates.
The mutant is deficient in type IV pili-mediated twitching motility and
in a “swarming motility” previously unobserved in
P.
aeruginosa
. In swarming cultures, the polar monotrichous
bacteria have differentiated into elongated and polar multitrichous
cells that navigate the surface of solid media. All of the motility
defects in the
ppk
mutant could be complemented by a
plasmid harboring the
ppk
gene. Because bacterial
motility is often crucial for their survival in a natural environment
and for systemic infection inside a host, the dependence for motility
on PPK reveals important roles for poly P in diverse processes such as
biofilm formation, symbiosis, and virulence.
Multiscale assessment of patterns of avian species richness
Authors: Rahbek Carsten , Graves Gary R.
Published: July 2002

The search for a common cause of species richness gradients has spawned more than 100 explanatory hypotheses in just the past two decades. Despite recent conceptual advances, further refinement of the most plausible models has been stifled by the difficulty of compiling high-resolution databases at continental scales. We used a database of the geographic ranges of 2,869 species of birds breeding in South America (nearly a third of the world's living avian species) to explore the influence of climate, quadrat area, ecosystem diversity, and topography on species richness gradients at 10 spatial scales (quadrat area, ≈12,300 to ≈1,225,000 km2). Topography, precipitation, topography × latitude, ecosystem diversity, and cloud cover emerged as the most important predictors of regional variability of species richness in regression models incorporating 16 independent variables, although ranking of variables depended on spatial scale. Direct measures of ambient energy such as mean and maximum temperature were of ancillary importance. Species richness values for 1° × 1° latitude-longitude quadrats in the Andes (peaking at 845 species) were ≈30–250% greater than those recorded at equivalent latitudes in the central Amazon basin. These findings reflect the extraordinary abundance of species associated with humid montane regions at equatorial latitudes and the importance of orography in avian speciation. In a broader context, our data reinforce the hypothesis that terrestrial species richness from the equator to the poles is ultimately governed by a synergism between climate and coarse-scale topographic heterogeneity.
Genetic evidence for different male and female roles during cultural transitions in the British Isles
Authors: Wilson James F. , Weiss Deborah A. , Richards Martin , Thomas Mark G. , Bradman Neil , Goldstein David B.
Published: July 2002

Human history is punctuated by periods of rapid cultural change.
Although archeologists have developed a range of models to describe
cultural transitions, in most real examples we do not know whether the
processes involved the movement of people or the movement of culture
only. With a series of relatively well defined cultural transitions,
the British Isles present an ideal opportunity to assess the
demographic context of cultural change. Important transitions after the
first Paleolithic settlements include the Neolithic, the development of
Iron Age cultures, and various historical invasions from continental
Europe. Here we show that patterns of Y-chromosome variation indicate
that the Neolithic and Iron Age transitions in the British Isles
occurred without large-scale male movements. The more recent invasions
from Scandinavia, on the other hand, appear to have left a significant
paternal genetic legacy. In contrast, patterns of mtDNA and
X-chromosome variation indicate that one or more of these
pre-Anglo-Saxon cultural revolutions had a major effect on the maternal
genetic heritage of the British Isles.
Functional disorders of the sympathetic nervous system in mice lacking the α
1B
subunit (Ca
v
2.2) of N-type calcium channels
Authors: Ino Mitsuhiro , Yoshinaga Takashi , Wakamori Minoru , Miyamoto Norimasa , Takahashi Eiki , Sonoda Jiro , Kagaya Takaki , Oki Tohru , Nagasu Takeshi , Nishizawa Yukio , Tanaka Isao , Imoto Keiji , Aizawa Shinichi , Koch Sheryl , Schwartz Arnold , Niidome Tetsuhiro , Sawada Kohei , Mori Yasuo
Published: July 2002

N-type voltage-dependent Ca
2+
channels (VDCCs),
predominantly localized in the nervous system, have been considered to
play an essential role in a variety of neuronal functions, including
neurotransmitter release at sympathetic nerve terminals. As a direct
approach to elucidating the physiological significance of N-type VDCCs,
we have generated mice genetically deficient in the α
1B
subunit (Ca
v
2.2). The α
1B
-deficient null
mice, surprisingly, have a normal life span and are free from apparent
behavioral defects. A complete and selective elimination of N-type
currents, sensitive to ω-conotoxin GVIA, was observed without
significant changes in the activity of other VDCC types in neuronal
preparations of mutant mice. The baroreflex response, mediated by the
sympathetic nervous system, was markedly reduced after bilateral
carotid occlusion. In isolated left atria prepared from
N-type-deficient mice, the positive inotropic responses to electrical
sympathetic neuronal stimulation were dramatically decreased compared
with those of normal mice. In contrast, parasympathetic nervous
activity in the mutant mice was nearly identical to that of wild-type
mice. Interestingly, the mutant mice showed sustained elevation of
heart rate and blood pressure. These results provide direct evidence
that N-type VDCCs are indispensable for the function of the sympathetic
nervous system in circulatory regulation and indicate that N-type
VDCC-deficient mice will be a useful model for studying disorders
attributable to sympathetic nerve dysfunction.
A ligand-reversible dimerization system for controlling protein–protein interactions
Authors: Rollins Carl T. , Rivera Victor M. , Woolfson Derek N. , Keenan Terence , Hatada Marcos , Adams Susan E. , Andrade Lawrence J. , Yaeger David , van Schravendijk Marie Rose , Holt Dennis A. , Gilman Michael , Clackson Tim
Published: July 2002

Chemically induced dimerization provides a general way to gain control over intracellular processes. Typically, FK506-binding protein (FKBP) domains are fused to a signaling domain of interest, allowing crosslinking to be initiated by addition of a bivalent FKBP ligand. In the course of protein engineering studies on human FKBP, we discovered that a single point mutation in the ligand-binding site (Phe-36 → Met) converts the normally monomeric protein into a ligand-reversible dimer. Two-hybrid, gel filtration, analytical ultracentrifugation, and x-ray crystallographic studies show that the mutant (F
M
) forms discrete homodimers with micromolar affinity that can be completely dissociated within minutes by addition of monomeric synthetic ligands. These unexpected properties form the basis for a “reverse dimerization” regulatory system involving F
M
fusion proteins, in which association is the ground state and addition of ligand abolishes interactions. We have used this strategy to rapidly and reversibly aggregate fusion proteins in different cellular compartments, and to provide an off switch for transcription. Reiterated F
M
domains should be generally useful as conditional aggregation domains (CADs) to control intracellular events where rapid, reversible dissolution of interactions is required. Our results also suggest that dimerization is a latent property of the FKBP fold: the crystal structure reveals a remarkably complementary interaction between the monomer binding sites, with only subtle changes in side-chain disposition accounting for the dramatic change in quaternary structure.
Physical stress and diversity-productivity relationships: The role of positive interactions
Authors: Mulder C. P. H. , Uliassi D. D. , Doak D. F.
Published: July 2002

If environmental stress provides conditions under which positive
relationships between plant species richness and productivity become
apparent, then species that seem functionally redundant under constant
conditions may add to community functioning under variable conditions.
Using naturally co-occurring mosses and liverworts, we constructed
bryophyte communities to test relationships between species diversity
(1, 2, 4, 8, 16, 24, or 32 species) and productivity under constant
conditions and when exposed to experimental drought. We found no
relationship between species richness and biomass under constant
conditions. However, when communities were exposed to experimental
drought, biomass increased with species richness. Responses of
individual species demonstrated that facilitative interactions rather
than sampling effects or niche complementarity best explained
results—survivorship increased for almost all species, and those
species least resistant to drought in monoculture had the greatest
increase in biomass. Positive interactions may be an important but
previously underemphasized mechanism linking high diversity to high
productivity under stressful environmental conditions.
CD147 facilitates HIV-1 infection by interacting with virus-associated cyclophilin A
Authors: Pushkarsky Tatiana , Zybarth Gabriele , Dubrovsky Larisa , Yurchenko Vyacheslav , Tang Hao , Guo Huiming , Toole Bryan , Sherry Barbara , Bukrinsky Michael
Published: July 2002

Cyclophilin A (CyPA) is specifically incorporated into the virions
of HIV-1 and has been shown to enhance significantly an early step of
cellular HIV-1 infection. Our preliminary studies implicated CD147 as a
receptor for extracellular CyPA. Here, we demonstrate a role for
CyPA–CD147 interaction during the early steps of HIV-1 infection.
Expression of human CD147 increased infection by HIV-1 under one-cycle
conditions. However, susceptibility to infection by viruses lacking
CyPA (simian immunodeficiency virus or HIV-1 produced in the presence
of cyclosporin A) was unaffected by CD147. Virus-associated CyPA
coimmunoprecipitated with CD147 from infected cells. Antibody to CD147
inhibited HIV-1 entry as evidenced by the delay in translocation of the
HIV-1 core proteins from the membrane and inhibition of viral reverse
transcription. Viruses whose replication did not require CyPA (SIV or
mutant HIV-1) were resistant to the inhibitory effect of anti-CD147
antibody. These results suggest that HIV-1 entry depends on an
interaction between virus-associated CyPA and CD147 on a target cell.
Cloning and functional analysis of two gibberellin 3β-hydroxylase genes that are differently expressed during the growth of rice
Authors: Itoh Hironori , Ueguchi-Tanaka Miyako , Sentoku Naoki , Kitano Hidemi , Matsuoka Makoto , Kobayashi Masatomo
Published: July 2002

We have cloned two gibberellin (GA) 3β-hydroxylase genes,
OsGA3ox1
and
OsGA3ox2
, from rice by screening a genomic library with a DNA fragment obtained by PCR using degenerate primers. We have used full-scan GC-MS and Kovats retention indices to show function for the two encoded recombinant fusion proteins. Both proteins show 3β-hydroxylase activity for the steps GA
20
to GA
1
, GA
5
to GA
3
, GA
44
to GA
38
, and GA
9
to GA
4
. In addition, indirect evidence suggests that the OsGA3ox1 protein also has 2,3-desaturase activity, which catalyzes the steps GA
9
to 2,3-dehydro-GA
9
and GA
20
to GA
5
(2,3-dehydro GA
20
), and 2β-hydroxylase activity, which catalyzes the steps GA
1
to GA
8
and GA
4
to GA
34
. Molecular and linkage analysis maps the
OsGA3ox1
gene to the distal end of the short arm of chromosome 5; the
OsGA3ox2
gene maps to the distal end of the short arm of chromosome 1 that corresponds to the
D18
locus. The association of the
OsGA3ox2
gene with the
d18
locus is confirmed by sequence and complementation analysis of three
d18
alleles. Complementation of the
d18-AD
allele with the
OxGA3ox2
gene results in transgenic plants with a normal phenotype. Although both genes show transient expression, the highest level for
OsGA3ox1
is from unopened flower. The highest level for
OsGA3ox2
is from elongating leaves.
Peptide methionine sulfoxide reductase fromEscherichia coliandMycobacterium tuberculosisprotects bacteria against oxidative damage from reactive nitrogen intermediates
Authors: John Gregory St. , Brot Nathan , Ruan Jia , Erdjument-Bromage Hediye , Tempst Paul , Weissbach Herbert , Nathan Carl
Published: July 2002

Inducible nitric oxide synthase (iNOS) plays an important role in host defense. Macrophages expressing iNOS release the reactive nitrogen intermediates (RNI) nitrite and S-nitrosoglutathione (GSNO), which are bactericidalin vitroat a pH characteristic of the phagosome of activated macrophages. We sought to characterize the active intrabacterial forms of these RNI and their molecular targets. Peptide methionine sulfoxide reductase (MsrA; EC1.8.4.6) catalyzes the reduction of methionine sulfoxide (Met-O) in proteins to methionine (Met).E. colilacking MsrA were hypersensitive to killing not only by hydrogen peroxide, but also by nitrite and GSNO. The wild-type phenotype was restored by transformation with plasmids encodingmsrAfromE. coliorM. tuberculosis, but not by an enzymatically inactive mutantmsrA, indicating that Met oxidation was involved in the death of these cells. It seemed paradoxical that nitrite and GSNO kill bacteria by oxidizing Met residues when these RNI cannot themselves oxidize Met. However, under anaerobic conditions, neither nitrite nor GSNO was bactericidal. Nitrite and GSNO can both give rise to NO, which may react with superoxide produced by bacteria during aerobic metabolism, forming peroxynitrite, a known oxidant of Met to Met-O. Thus, the findings are consistent with the hypotheses that nitrite and GSNO killE. coliby intracellular conversion to peroxynitrite, that intracellular Met residues in proteins constitute a critical target for peroxynitrite, and that MsrA can be essential for the repair of peroxynitrite-mediated intracellular damage.
Redox state is a central modulator of the balance between self-renewal and differentiation in a dividing glial precursor cell
Authors: Smith Joel , Ladi Ena , Mayer-Pröschel Margot , Noble Mark
Published: July 2002

We have discovered that intracellular redox state appears to be a necessary and sufficient modulator of the balance between self-renewal and differentiation in dividing oligodendrocyte-type-2 astrocyte progenitor cells. The intracellular redox state of freshly isolated progenitors allows prospective isolation of cells with different self-renewal characteristics. Redox state is itself modulated by cell-extrinsic signaling molecules that alter the balance between self-renewal and differentiation: growth factors that promote self-renewal cause progenitors to become more reduced, while signaling molecules that promote differentiation cause progenitors to become more oxidized. Moreover, pharmacological antagonists of the redox effects of these cell-extrinsic signaling molecules antagonize their effects on self-renewal and differentiation, indicating that cell-extrinsic signaling molecules that modulate this balance converge on redox modulation as a critical component of their effector mechanism.
Quantitative, chemically specific imaging of selenium transformation in plants
Authors: Pickering Ingrid J. , Prince Roger C. , Salt David E. , George Graham N.
Published: July 2002

Quantitative, chemically specific images of biological systems
would be invaluable in unraveling the bioinorganic chemistry of
biological tissues. Here we report the spatial distribution and
chemical forms of selenium in
Astragalus bisulcatus
(two-grooved poison or milk vetch)
,
a plant capable of
accumulating up to 0.65% of its shoot dry biomass as Se in its natural
habitat. By selectively tuning incident x-ray energies close to the Se
K-absorption edge, we have collected quantitative, 100-μm-resolution
images of the spatial distribution, concentration, and chemical form of
Se in intact root and shoot tissues. To our knowledge, this is the
first report of quantitative concentration-imaging of specific chemical
forms. Plants exposed to 5 μM selenate for 28 days contained
predominantly selenate in the mature leaf tissue at a concentration of
0.3–0.6 mM, whereas the young leaves and the roots contained
organoselenium almost exclusively, indicating that the ability to
biotransform selenate is either inducible or developmentally specific.
While the concentration of organoselenium in the majority of the root
tissue was much lower than that of the youngest leaves (0.2–0.3
compared with 3–4 mM), isolated areas on the extremities of the roots
contained concentrations of organoselenium an order of magnitude
greater than the rest of the root. These imaging results were
corroborated by spatially resolved x-ray absorption near-edge spectra
collected from selected 100 × 100 μm
2
regions of
the same tissues.
Association of yeast DNA topoisomerase III and Sgs1 DNA helicase: Studies of fusion proteins
Authors: Bennett Richard J. , Wang James C.
Published: July 2002

The Sgs1 protein of the budding yeast
Saccharomyces
cerevisiae
is a member of the RecQ DNA helicase family that
includes the human Bloom, Werner, and Rothmund–Thompson syndrome
proteins. The N-terminal region outside the central DNA helicase core
of Sgs1, particularly the part containing the first 100 amino acid
resiudes of the 1,447-residue protein, is known to be functionally
important and has been implicated in Sgs1–DNA topoisomerase III (Top3)
interaction. We show in this work that the functionality of a truncated
Sgs1 lacking its N-terminal 106 residues can be restored by replacing
the truncated region with Top3. Fusion of Top3 to a mutant Sgs1 with a
Val-29 to Glu substitution, which interferes with Sgs1–Top3
interaction, similarly restores the functionality of the mutant
Sgs1(V29E) protein. The Top3-Sgs1(Δ1–106) and Top3-Sgs1(V29E) fusion
proteins behave like wild-type Sgs1 in complementing several aspects of
the
sgs1
phenotype, including the hypersensitivity of
sgs1
cells to methyl methanesulfonate and hydroxyurea.
Complementation by the fusion proteins required both the topoisomerase
activity of Top3 and the helicase activity of the Sgs1 polypeptide.
These results suggest that the sole function of the N-terminal 106
amino acid residues of Sgs1 is for Top3 binding, and that the
coordinated actions of Sgs1 and Top3 are important in cellular
processes such as the processing of DNA after exposure of cells to
DNA-damaging agents.
Plant defense in the absence of jasmonic acid: The role of cyclopentenones
Authors: Stintzi Annick , Weber Hans , Reymond Philippe , Browse John , Farmer Edward E.
Published: July 2002

The
Arabidopsis opr3
mutant is defective in the isoform of 12-oxo-phytodienoate (OPDA) reductase required for jasmonic acid (JA) biosynthesis. Oxylipin signatures of wounded
opr3
leaves revealed the absence of detectable 3R,7S-JA as well as altered levels of its cyclopentenone precursors OPDA and dinor OPDA. In contrast to JA-insensitive
coi1
plants and to the
fad3 fad7 fad8
mutant lacking the fatty acid precursors of JA synthesis,
opr3
plants exhibited strong resistance to the dipteran
Bradysia impatiens
and the fungus
Alternaria brassicicola
. Analysis of transcript profiles in
opr3
showed the wound induction of genes previously known to be JA-dependent, suggesting that cyclopentenones could fulfill some JA roles
in vivo
. Treating
opr3
plants with exogenous OPDA powerfully up-regulated several genes and disclosed two distinct downstream signal pathways, one through COI1, the other via an electrophile effect of the cyclopentenones. We conclude that the jasmonate family cyclopentenone OPDA (most likely together with dinor OPDA) regulates gene expression in concert with JA to fine-tune the expression of defense genes. More generally, resistance to insect and fungal attack can be observed in the absence of JA.
Glycopeptide antibiotic biosynthesis: Enzymatic assembly of the dedicated amino acid monomer (
S
)-3,5-dihydroxyphenylglycine
Authors: Chen Huawei , Tseng Claire C. , Hubbard Brian K. , Walsh Christopher T.
Published: July 2002

Four proteins, DpgA–D, required for the biosynthesis by
actinomycetes of the nonproteinogenic amino acid monomer
(
S
)-3,5-dihydroxyphenylglycine (Dpg), that is a
crosslinking site in the maturation of vancomycin and teicoplanin
antibiotic scaffolds, were expressed in
Escherichia
coli
, purified in soluble form, and assayed for enzymatic
activity. DpgA is a type III polyketide synthase, converting
four molecules of malonyl-CoA to 3,5-dihydroxyphenylacetyl-CoA
(DPA-CoA) and three free coenzyme A (CoASH) products. Almost no
turnover was observed for DpgA until DpgB was added, producing a net
k
cat
of 1–2 min
−1
at a 3:1
ratio of DpgB:DpgA. Addition of DpgD gave a further 2-fold rate
increase. DpgC had the unusual catalytic capacity to convert DPA-CoA to
3,5-dihydroxyphenylglyoxylate, which is a transamination away from Dpg.
DpgC performed a net CH
2
to C⩵O four-electron oxidation
on the Cα of DPA-CoA and hydrolyzed the thioester linkage with a
k
cat
of 10 min
−1
.
Phenylacetyl-CoA was also processed, to phenylglyoxylate, but with
about 500-fold lower
k
cat
/
K
M
. DpgC
showed no activity in anaerobic incubations, suggesting an oxygenase
function, but had no detectable bound organic cofactors or metals. A
weak enoyl-CoA hydratase activity was detected for both DpgB and DpgD.
Drosophila
MyD88 is an adapter in the Toll signaling pathway
Authors: Horng Tiffany , Medzhitov Ruslan
Published: July 2002

Toll-like receptors comprise a family of cell surface receptors that play a crucial role in the innate immune recognition of both
Drosophila
and mammals. Previous studies have shown that
Drosophila
Toll-1 mediates the induction of antifungal peptides during fungal infection of adult flies. Through genetic studies, Tube, Pelle, Cactus, and Dif have been identified as downstream components of the Toll-1 signaling pathway. Here we report characterization of a
Drosophila
homologue of human MyD88, dMyD88. We show that dMyD88 is an adapter in the Toll signaling pathway that associates with both the Toll receptor and the downstream kinase Pelle. Expression of dMyD88 in S2 cells strongly induced activity of a Drosomycin reporter gene, whereas a dominant-negative version of dMyD88 potently inhibited Toll-mediated signaling. We also show that dMyD88 associates with the death domain-containing adapter
Drosophila
Fas-associated death domain-containing protein (dFADD), which in turn interacts with the apical caspase Dredd. This pathway links a cell surface receptor to an apical caspase in invertebrate cells and therefore suggests that the Toll-mediated pathway of caspase activation may be the evolutionary ancestor of the death receptor-mediated pathway for apoptosis induction in mammals.
Chemical defense: Bestowal of a nuptial alkaloidal garment by a male moth on its mate
Authors: Conner William E. , Boada Ruth , Schroeder Frank C. , González Andrés , Meinwald Jerrold , Eisner Thomas
Published: July 2002

Males of the moth
Cosmosoma myrodora
(Arctiidae) acquire pyrrolizidine alkaloid by feeding on the excrescent
fluids of certain plants (for instance,
Eupatorium
capillifolium
). They incorporate the alkaloid systemically and
as a result are protected against spiders. The males have a pair of
abdominal pouches, densely packed with fine cuticular filaments, which
in alkaloid-fed males are alkaloid laden. The males discharge the
filaments on the female in bursts during courtship, embellishing her
with alkaloid as a result. The topical investiture protects the female
against spiders
.
Alkaloid-free filaments, from
alkaloid-deprived males, convey no such protection. The males also
transmit alkaloid to the female by seminal infusion. The systemic
alkaloid thus received, which itself may contribute to the female's
defense against spiders, is bestowed in part by the female on the eggs.
Although paternal contribution to egg defense had previously been
demonstrated for several arctiid moths, protective nuptial festooning
of a female by its mate, such as is practiced by
C.
myrodora
, appears to be without parallel among insects.
The precursor of PsaD assembles into the photosystem I complex in two steps.
Authors: Minai L , Cohen Y , Chitnis P R , Nechushtai R
Published: July 2002

The present study addresses the assembly in the chloroplast thylakoid membranes of PsaD, a peripheral membrane protein of the photosystem I complex. Located on the stromal side of the thylakoids, PsaD was found to assemble in vitro into the membranes in its precursor (pre-PsaD) and also in its mature (PsaD) form. Newly assembled unprocessed pre-PsaD was resistant to NaBr and alkaline wash. Yet it was sensitive to proteolytic digestion. In contradistinction, when the assembled precursor was processed, the resulting mature PsaD was resistant to proteases to the same extent as endogenous [correction of endogeneous] PsaD. The accumulation of protease-resistant PsaD in the thylakoids correlated with the increase of mature-PsaD in the membranes. This protection of mature PsaD from proteolysis could not be observed when PsaD was in a soluble form-i.e. not assembled within the thylakoids. The data suggest that pre-PsaD assembles to the membranes and only in a second step processing takes place. The observation that the assembly of pre-PsaD is affected by salts to a much lesser extent than that of mature-PsaD supports a two-step assembly of pre-PsaD.