bluuebunny/crossref_metadata_2025 huggingface dataset:
The effect of streamwise braid vortices on the particle dispersion in a plane mixing layer. I. Equilibrium points and their stability
Authors: Marcu B. , Meiburg E.
Published: July 2002

The dynamics of small, heavy, spherical particles are investigated in an analytical model of the stretched counterrotating streamwise braid vortices commonly found in three-dimensionally evolving mixing layers. The flow field consists of two superimposed rows of Stuart vortices of opposite sign, with an additional two-dimensional strain field. The particle dynamics are determined by a balance of inertial, gravitational, and viscous drag forces, i.e., the dimensionless Stokes and Froude numbers, St and Fr, as well as by the dimensionless strain rate, and the Stuart vortex family parameter. Equilibrium points for the particles, as well as their stability criteria, are determined analytically, both in the absence and in the presence of gravity, and for different orientations of the gravity vector. In the absence of gravity, accumulation of low St particles can occur at the center of the braid vortices. An analytical expression for the critical particle diameter, below which accumulation is possible, is derived. The presence of gravity can lead to the emergence of multiple equilibrium points, whose stability properties depend on their locations. For a horizontal mixing layer flow and strong gravity effects, unconditional accumulation can occur midway between the streamwise braid vortices in the upwelling regions. Conditionally stable accumulation regions exist a short horizontal distance away from the centers of the braid vortices. If the gravity vector lies within the plane of the mixing layer, accumulation points exist only for moderate strengths of gravity. Under these circumstances, conditional accumulation is possible near the streamwise vortex centers.
Solutions of uniform, open-channel, liquid metal flow in a strong, oblique magnetic field
Authors: Morley Neil B. , Roberts Paul H.
Published: July 2002

The flow of an electrically conducting fluid in an open channel in the presence of a strong magnetic field of oblique incidence to both the channel walls and the force of gravity is explored. This type of flow has possible applications to the protection of high heat flux surfaces in magnetic confinement fusion reactors. The governing equations of fully-developed flow are derived retaining all viscous terms. They are then solved in the strong field limit in an asymptotic, iterative fashion, carrying the first two terms in the expansion with powers of the effective Hartmann number. The asymptotic solutions for the velocity, induced magnetic field and the flow rate are compared with a numerical solution of the complete governing equations. Good agreement is seen between the asymptotic and numerical predictions of velocity and electric current distribution when the core regions are dominated by magnetic forces. One novel feature of open channel flow of this type is the existence, predicted by the asymptotic analysis and confirmed by the numerical integration, of a second-order Hartmann layer on the free surface. Its presence is required to ensure the condition of no shear stress on this boundary. Also seen is the presence of strong discontinuities across free shear layers, which form along the field lines that extend from the free surface/sidewall corner.
Scalar imaging velocimetry measurements of the velocity gradient tensor field in turbulent flows. II. Experimental results
Authors: Su Lester K. , Dahm Werner J. A.
Published: July 2002

Scalar imaging velocimetry is here applied to experimental turbulent flow scalar field data to yield the first fully resolved, non-intrusive laboratory measurements of the spatio-temporal structure and dynamics of the full nine-component velocity gradient tensor field ∇u(x,t), as well as the pressure gradient field ∇p(x,t), in a turbulent flow. Results are from turbulent flows at outer scale Reynolds numbers in the range 3,000≤Reδ≤4,200, with Taylor scale Reynolds numbers Reλ≊45. These give a previously inaccessible level of detailed experimental access to the spatial structure in the velocity gradient tensor field at the small scales of turbulent flows, and through the much longer temporal dimension of these four-dimensional data spaces allow access to the inertial range of scales as well. Sample spatio-temporal data planes and probability distributions spanning more than 75 advection time scales (λν/U) are presented for various dynamical fields of interest, including the three components of the velocity field u(x,t), the nine components of the velocity gradient tensor field ∇u(x,t) through the full vector vorticity field ωi(x,t) and tensor strain rate field εij(x,t), the kinetic energy dissipation rate field Φ(x,t)≡2νε:ε(x,t), the enstrophy field 1/2ω⋅ω(x,t), the enstrophy production rate field ω⋅ε⋅ω(x,t), and the pressure gradient field ∇p(x,t). Continuity tests show agreement with the zero divergence requirement that exceeds the highest values reported from single-point, invasive, multi-probe measurements. Distributions of strain rate eigenvalues as well as alignments of the strain rate eigenvectors with both the vorticity and scalar gradient vectors are in agreement with DNS results, as are distributions of the measured helicity density fields u⋅ω(x,t). Results obtained for the true kinetic energy dissipation rate field show good agreement, up to 14th-order, with previous inertial range structure function exponents measured by Anselmet et al. [J. Fluid Mech. 140, 63 (1984)] at much higher Reynolds numbers. In addition, probability distributions scaled on inner variables show good agreement among buoyant and non-buoyant turbulent flow cases, further suggesting that these results are largely indicative of the high Reynolds number state of the inner scales of fully developed turbulent flows.
Response of the dynamic LES model to heat release induced effects
Authors: Réveillon Julien , Vervisch Luc
Published: July 2002

The response of the dynamic large eddy simulation (LES) subgrid model to heat release effects is investigated. Nonpremixed turbulent flames are considered in the case of large Damköhler number combustion in homogeneous and isotropic flows. The subgrid fluctuations of mixture fraction are accounted for through a presumed probability density function approach. In this work, dynamic LES includes a procedure minimizing, over flow path lines, the error in the determination of the parameters entering the turbulence model [Meneveau, Lund, and Cabot, Proceedings of the 1994 Summer Program (CTR, Stanford, CA, 1994), pp. 271–299]. Both direct numerical simulation (DNS) and LES are performed. It is found that the flux of turbulent kinetic energy toward the subgrid is correctly represented by the dynamic LES model in the presence of heat release.
Counter-gradient diffusion in a confined turbulent premixed flame
Authors: Bailly P. , Champion M. , Garréton D.
Published: July 2002

In the present study, we develop a full second order model and a new flamelet closure relation for the mean chemical source term to describe turbulent reactive flows with premixed reactants. This description ensures that non-gradient and counter-gradient diffusion which can appear in such flames, are taken into account in 2-D or 3-D geometries. 2-D calculations are performed in the case of a confined turbulent premixed flame stabilized by a backward facing step, a configuration which reveals experimentally counter-gradient diffusion and combustion induced production of turbulence. Numerical results are found to be in excellent agreement with measurements of Shepherd et al. [Nineteenth Symposium (International) on Combustion (The Combustion Institute, Pittsburgh, 1982)]. The important influence of counter-gradient diffusion on first order quantities, i.e., mean velocity and length of the recirculation zone is shown.
Effects of lift on the motion of particles in the recessed regions of a slider
Authors: Zhang Shuyu , Bogy David B.
Published: July 2002

Particle contamination in a cavity, or a recessed region, on the slider surface is an important issue in slider designs for magnetic recording. In this paper, a model is developed for the simulation of particle motion in a recessed region, in which various forces such as viscous drag, Saffman lift, Magnus lift, and gravity are considered. It is found that the latter two forces have a very small effect on the vertical motion of the particles compared with the Saffman lift, and they can be neglected in the analysis. It is also found, through the simulation for various cases, that the Saffman lift is not so important for the motion of the smaller particles (d<100 nm) as for the motion of larger particles, and that the magnitude of the velocity of particles relative to the air flow affects the Saffman lift, or vertical motion of the particles, significantly. The air flow velocity is relatively low in a recessed region, and a particle often has a large relative velocity with positive sign when entering it, which causes the Saffman lift force to point to the surface of the slider. Therefore, particle contamination on the slider occurs at the edges of the recessed region. A similar result can also be obtained for the particles entering an air bearing under a taper, which explains why the contamination is concentrated on the surface of tapers.
Three-dimensional direct simulation Monte Carlo method for slider air bearings
Authors: Huang Weidong , Bogy David B. , Garcia Alejandro L.
Published: July 2002

The direct simulation Monte Carlo (DSMC) method is used to solve the three-dimensional nano-scale gas film lubrication problem between a gas bearing slider and a rotating disk, and this solution is compared to the numerical solution of the compressible Reynolds equations with the slip flow correction based on the linearized Boltzmann equation as presented by Fukui and Kaneko [molecular gas film lubrication (MGL) method] [ASME J. Tribol. 110, 253 (1988)]. In the DSMC method, hundreds of thousands of simulated particles are used and their three velocity components and three spatial coordinates are calculated and recorded by using a hard-sphere collision model. Two-dimensional pressure profiles are obtained across the film thickness direction. The results obtained from the two methods agree well with each other for Knudsen numbers as large as 35 which corresponds to a minimum spacing of 2 nm. The result for contact slider is also obtained by the DSMC simulation and presented in this paper.
Rolling droplets
Authors: Mahadevan L. , Pomeau Yves
Published: July 2002

A droplet of nonwetting viscous liquid moves on an inclined plane by rolling along it. We give a scaling law for the uniform speed of such a droplet. We then analyze the flow in the contact region and show that the classical stress singularity at the contact line is alleviated in this case.
Nonlinear dynamical behavior of thermionic low pressure discharges. I. Simulation
Authors: Greiner F. , Klinger T. , Piel A.
Published: July 2002

The discharge modes of a thermionic low pressure discharge (p<1Pa) are investigated with the one-dimensional particle-in-cell simulation codes PDP1 and XPDP1 [C. K. Birdsall, IEEE Trans. Plasma Sci. 19, 65 (1991)]. The simulation results provide a model approach for stable discharge modes, hysteresis, and for nonlinear relaxation-oscillations. During this potential-relaxation instability, nonlinear structures, e.g. electron holes and double layers, are observed. A Pierce–Buneman-mode is suggested as a trigger mechanism for the onset of the instability. The detailed oscillation process can be subdivided into three distinct phases: expansion phase, double layer phase, and relaxation phase. This allows one to explain the parameter dependencies of the oscillation frequency. For a periodically driven discharge, mode-locking in a period-2 state is found and explained by the model. The mode-locking phenomenon is studied systematically. The results of the simulations are well confirmed by experimental observations presented in Part II of this paper [T. Klinger et al., Phys. Plasmas 2, 1822 (1995)].
Kinetic theory in self-similar variables for neutral atoms in plasma
Authors: Helander P. , Krasheninnikov S. I.
Published: July 2002

The kinetics of neutral atoms in a plasma undergoing charge-exchange, ionization, and recombination is considered. It is shown that if the mean-free path divided by the macroscopic scale length is constant, it is possible to introduce self-similar variables in the Boltzmann equation for the neutral particles. This equation is then solved analytically, and the nonlocal transport of heat and particles is calculated. Since the mean-free path increases with increasing energy, a one-sided, high-energy tail is formed in the neutral distribution function. This tail may contribute significantly to the heat and particle fluxes. When this is the case, the fluid approximation of these quantities breaks down at arbitrarily short mean-free paths.
Gyrofluid simulations of turbulence suppression in reversed-shear experiments on the Tokamak Fusion Test Reactor
Authors: Beer M. A. , Hammett G. W. , Rewoldt G. , Synakowski E. J. , Zarnstorff M. C. , Dorland W.
Published: July 2002

The confinement improvement in reversed-shear experiments on the Tokamak Fusion Test Reactor [Plasma Phys. Controlled Fusion 26, 11 (1984)] is investigated using nonlinear gyrofluid simulations including a bounce-averaged trapped electron fluid model. This model includes important kinetic effects for both ions and electrons, and agrees well with linear kinetic theory. Both reversed shear and the Shafranov shift reverse the precession drifts of a large fraction of the trapped electrons, which significantly reduces the growth rate of the trapped electron mode, found to be the dominant instability in the core. Two positive feedback transition mechanisms for the sudden improvement in core confinement are discussed: (1) Shafranov shift suppression of the trapped electron mode, and (2) turbulence suppression by radially sheared E×B flows. While both effects appear to be playing roles in the transition dynamics in most experiments, we show that Shafranov shift stabilization alone can cause a transition.
Diffusive, supersonic x-ray transport in radiatively heated foam cylinders
Authors: Back C. A. , Bauer J. D. , Hammer J. H. , Lasinski B. F. , Turner R. E. , Rambo P. W. , Landen O. L. , Suter L. J. , Rosen M. D. , Hsing W. W.
Published: July 2002

Diffusive supersonic radiation transport, where the ratio of the diffusive radiation front velocity to the material sound speed >2 has been studied in experiments on low density (40 mg/cc to 50 mg/cc) foams. Laser-heated Au hohlraums provided a radiation drive that heated SiO2 and Ta2O5 aerogel foams of varying lengths. Face-on emission measurements at 550 eV provided clean signatures of the radiation breakout. The high quality data provides new detailed information on the importance of both the fill and wall material opacities and heat capacities in determining the radiation front speed and curvature. The Marshak radiation wave transport is studied in a geometry that allows direct comparisons with analytic models and two-dimensional code simulations. Experiments show important effects that will affect even nondiffusive and transonic radiation transport experiments studied by others in the field. This work is of basic science interest with applications to inertial confinement fusion and astrophysics.
High quality Nb/Al-AlOx/Nb Josephson junction
Authors: Morohashi Shin’ichi , Shinoki Fujitoshi , Shoji Akira , Aoyagi Masahiro , Hayakawa Hisao
Published: July 2002

We have improved the quality of Nb/Al-AlOx/Nb Josephson junctions and obtained the most excellent junction characteristics ever obtained for all refractory Josephson junctions. The Vm values (the product of the critical current and the subgap resistance measured at 2 mV) are 88 mV at the critical current density Ij =500 A/cm2 and 72 mV at Ij =1000 A/cm2. The Vm values are larger than 40 mV up to Ij of 2400 A/cm2. The high Vm values are important to obtain the low subgap leakage current and not to reduce the transfer current to the load in Josephson circuit. These characteristics have been achieved by improving the quality of the Nb film and optimizing the Al thickness. We have also confirmed that Ij can be controlled by both the oxidation pressure and time in the range of 40–4600 A/cm2.
Wide-bandwidth guided-wave electro-optic intensity modulator at λ=3.39 μm
Authors: Becker R. A. , Rediker R. H. , Lind T. A.
Published: July 2002

A Ti-indiffused guided-wave interferometric modulator has been demonstrated at λ=3.39 μm with a linear small-signal 3-dB bandwidth of 1.8 GHz. This is the first interferometric modulator operating at λ>1.6 μm. An extinction ratio of 18.9 dB was obtained with Vπ=31 V for TE-polarized radiation. This value of Vπ is consistent with predictions based upon λ=0.85 μm modulator data and simple λ2 scaling rules, indicating little dispersion in the electro-optical coefficients of LiNbO3 over the 0.85–3.39-μm region. Such modulators are important components for the long-distance repeaterless data links which is the goal of the large effort in the development of ultra-low-loss fibers at the longer wavelengths.
Raman, transmission electron microscopy, and conductivity measurements in molecular beam deposited microcrystalline Si and Ge: A comparative study
Authors: Gonzalez-Hernandez J. , Azarbayejani G. H. , Tsu R. , Pollak F. H.
Published: July 2002

The structure of molecular beam deposited microcrystalline silicon and germanium films prepared under different growth conditions has been analyzed by conventional transmission electron microscope (TEM) and Raman scattering (RS) and compared to electrical conductivity experiments. The TEM measurements yield an average grain size L0 ranging from 200 Å to 1.5 μm. On the other hand, the line shape of the RS is determined by a mean free path related to the average separation l between defects (or impurities), where l≤150 Å. We find in a number of cases that the electrical conductivity is determined by l rather than L0. This experiment demonstrates the significance of RS as a structural characterization method when used in conjunction with other techniques such as TEM.
50× optical fiber pulse compression at 1.319 μm
Authors: Tai K. , Tomita A.
Published: July 2002

We report a 50-fold fiber-grating pulse compression in the near-infrared region. 100 ps (FWHM) pulses from a mode-locked neodymium:yttrium aluminum garnet laser operated at 1.319 μm have been compressed into 2 ps pulses by using a 2-km dispersion-shifted fiber and a grating pair separated by 2.41 m in a double-pass configuration. The novel feature of this demonstration is the use of dispersion-shifted fiber (zero-dispersion wavelength at 1.59 μm) for producing a linear chirp over most of the pulse and, thus, almost all the input power appears in the compressed pulse.
Simple laser-driven, metal-photocathode electron source
Authors: Downey S. W. , Builta L. A. , Moir D. C. , Ringler T. J. , Saunders J. D.
Published: July 2002

An ArF excimer laser was used to produce photoelectrons from common metal surfaces at modest vacuum. The photoelectrons are subsequently accelerated across an anode-cathode gap. Both space-charge and emission-limited flow were examined. The temporal characteristics of the emission-limited electron beam produced by this device are nearly identical to those of the laser pulse used to produce the photoemission. In the space-charge-limited case, a rise time of 3 ns was obtained. Maximum current densities of 70 A/cm2 were achieved.
Quantum shift of the optical absorption edge in ultrathin amorphous hydrogenated germanium
Authors: Yang L. , Abeles B.
Published: July 2002

The optical absorption coefficient in ultrathin (∼10 Å) hydrogenated amorphous germanium (a-Ge:H) layers deposited on hydrogenated amorphous silicon layers was determined by in situ reflectivity measurements. The decrease in the absorption coefficient in the ultrathin a-Ge:H layers, compared to that of thick films, is explained by an upward shift in the conduction band edge due to quantum confinement of electrons with effective mass of 0.4m0.
Pulsed laser processing of ceramics in water
Authors: Morita Noboru , Ishida Shuichi , Fujimori Yasutomo , Ishikawa Ken
Published: July 2002

A new method for defect-free processing of ceramics is presented. This method consists of processing ceramics in water with a Q-switched yttrium aluminum garnet (YAG) laser. In laser machining, a recast layer and cracks are usually formed in the machined part. Using this method, these defects are not formed.
Induced-frequency shift of copropagating ultrafast optical pulses
Authors: Baldeck P. L. , Alfano R. R. , Agrawal Govind P.
Published: July 2002

The combined effects of cross-phase modulation and pulse walk-off on copropagating optical pulses are investigated. It is shown that ultrafast pulses which overlap in a nonlinear dispersive medium undergo a substantial shift of their carrier frequencies. This new coherent phenomenon of induced-frequency shift has been demonstrated using strong infrared picosecond pulses which shift the frequency of weak green picosecond pulses propagating in a 1-m-long single-mode optical fiber.
CCAAT/enhancer binding protein-β is a mediator of keratinocyte survival and skin tumorigenesis involving oncogenic Ras signaling
Authors: Zhu Songyun , Yoon Kyungsil , Sterneck Esta , Johnson Peter F. , Smart Robert C.
Published: July 2002

The basic leucine zipper transcription factor CCAAT/enhancer binding protein-β (C/EBPβ) is expressed in many cell types, including keratinocytes. C/EBPβ activity can be increased by phosphorylation through pathways stimulated by oncogenic Ras, although the biological implications of Ras-C/EBPβ signaling are not currently understood. We report here thatC/EBPβ-nullizygous mice are completely refractory to skin tumor development induced by a variety of carcinogens and carcinogenesis protocols, including 7,12-dimethylbenz[a]anthracene-initiation/12-O-tetradecanoylphorbol 13-acetate promotion, that produce tumors containing oncogenicRasmutations. No significant differences in TPA-induced epidermal keratinocyte proliferation were observed inC/EBPβ-null versus wild-type mice. However, apoptosis was significantly elevated (17-fold) in the epidermal keratinocytes of 7,12-dimethylbenz[a]anthracene-treatedC/EBPβ-null mice compared with wild-type mice. In v-Ha-rastransgenic mice,C/EBPβ deficiency also led to greatly reduced skin tumor multiplicity and size, providing additional evidence for a tumorigenesis pathway linking Ras and C/EBPβ. Oncogenic Ras potently stimulated C/EBPβ to activate a C/EBP-responsive promoter-reporter in keratinocytes and mutating an ERK1/2 phosphorylation site (T188) in C/EBPβ abolished this Ras effect. Finally, we observed that C/EBPβ participates in oncogenic Ras-induced transformation of NIH 3T3 cells. These findings indicate that C/EBPβ has a critical role in Ras-mediated tumorigenesis and cell survival and implicate C/EBPβ as a target for tumor inhibition.
Elimination of fast inactivation in Kv4 A-type potassium channels by an auxiliary subunit domain
Authors: Holmqvist Mats H. , Cao Jie , Hernandez-Pineda Ricardo , Jacobson Michael D. , Carroll Karen I. , Sung M. Amy , Betty Maria , Ge Pei , Gilbride Kevin J. , Brown Melissa E. , Jurman Mark E. , Lawson Deborah , Silos-Santiago Inmaculada , Xie Yu , Covarrubias Manuel , Rhodes Kenneth J. , Distefano Peter S. , An W. Frank
Published: July 2002

The Kv4 A-type potassium currents contribute to controlling the frequency of slow repetitive firing and back-propagation of action potentials in neurons and shape the action potential in heart. Kv4 currents exhibit rapid activation and inactivation and are specifically modulated by K-channel interacting proteins (KChIPs). Here we report the discovery and functional characterization of a modular K-channel inactivation suppressor (KIS) domain located in the first 34 aa of an additional KChIP (KChIP4a). Coexpression of KChIP4a with Kv4 α-subunits abolishes fast inactivation of the Kv4 currents in various cell types, including cerebellar granule neurons. Kinetic analysis shows that the KIS domain delays Kv4.3 opening, but once the channel is open, it disrupts rapid inactivation and slows Kv4.3 closing. Accordingly, KChIP4a increases the open probability of single Kv4.3 channels. The net effects of KChIP4a and KChIP1–3 on Kv4 gating are quite different. When both KChIP4a and KChIP1 are present, the Kv4.3 current shows mixed inactivation profiles dependent on KChIP4a/KChIP1 ratios. The KIS domain effectively converts the A-type Kv4 current to a slowly inactivating delayed rectifier-type potassium current. This conversion is opposite to that mediated by the Kv1-specific “ball” domain of the Kvβ1 subunit. Together, these results demonstrate that specific auxiliary subunits with distinct functions actively modulate gating of potassium channels that govern membrane excitability.
Paranodal junction formation and spermatogenesis require sulfoglycolipids
Authors: Honke Koichi , Hirahara Yukie , Dupree Jeffrey , Suzuki Kinuko , Popko Brian , Fukushima Kikuro , Fukushima Junko , Nagasawa Takashi , Yoshida Nobuaki , Wada Yoshinao , Taniguchi Naoyuki
Published: July 2002

Mammalian sulfoglycolipids comprise two major members, sulfatide (HSO
3
-3-galactosylceramide) and seminolipid (HSO
3
-3-monogalactosylalkylacylglycerol). Sulfatide is a major lipid component of the myelin sheath and serves as the epitope for the well known oligodendrocyte-marker antibody O4. Seminolipid is synthesized in spermatocytes and maintained in the subsequent germ cell stages. Both sulfoglycolipids can be synthesized
in vitro
by using the isolated cerebroside sulfotransferase. To investigate the physiological role of sulfoglycolipids and to determine whether sulfatide and seminolipid are biosynthesized
in vivo
by a single sulfotransferase,
Cst
-null mice were generated by gene targeting.
Cst
−/−
mice lacked sulfatide in brain and seminolipid in testis, proving that a single gene copy is responsible for their biosynthesis.
Cst
−/−
mice were born healthy, but began to display hindlimb weakness by 6 weeks of age and subsequently showed a pronounced tremor and progressive ataxia. Although compact myelin was preserved,
Cst
−/−
mice displayed abnormalities in paranodal junctions. On the other hand,
Cst
−/−
males were sterile because of a block in spermatogenesis before the first meiotic division, whereas females were able to breed. These data show a critical role for sulfoglycolipids in myelin function and spermatogenesis.
Place recognition monitored by location-driven operant responding during passive transport of the rat over a circular trajectory
Authors: Klement D. , Bures J.
Published: July 2002

Spatial memory of animals is usually tested in navigation tasks
that do not allow recognition and recall processes to be separated from
the mechanisms of goal-directed locomotion. In the present study, place
recognition was examined in rats (
n
= 7) confined
in an operant chamber mounted on the periphery of a slowly rotating
disk (diameter 1 m, angular velocity 9°/s). The animals were
passively transported over a circular trajectory and were rewarded for
bar pressing when they passed across a 60°-wide segment of the path.
This segment was recognizable with reference to room landmarks visible
from the operant box. Responding defined in the coordinate system of
the room increased when the chamber entered the 60°-wide approach
zone, culminated at the entrance into the reward sector, was decreased
inside it by eating the available reward, and rapidly declined to zero
at the exit from this zone. When reward was discontinued, the skewed
response distribution changed into a symmetric one with a maximum in
the center of the reward sector. With advancing extinction, the
response peak in the reward sector decreased in most rats
proportionally to the overall decline of bar pressing. The rewarded and
nonrewarded response patterns indicate that passively transported rats
can recognize their position in the environment with an accuracy
comparable to that of actively navigating animals and that
location-driven operant responding can serve as a useful tool in the
analysis of the underlying neural mechanisms.
Impact of the terminal Cretaceous event on plant–insect associations
Authors: Labandeira Conrad C. , Johnson Kirk R. , Wilf Peter
Published: July 2002

Evidence for a major extinction of insect herbivores is provided by presence–absence data for 51 plant–insect associations on 13,441 fossil plant specimens, spanning the Cretaceous/Paleogene boundary in southwestern North Dakota. The most specialized associations, which were diverse and abundant during the latest Cretaceous, almost disappeared at the boundary and failed to recover in younger strata even while generalized associations regained their Cretaceous abundances. These results are consistent with a sudden ecological perturbation that precipitated a diversity bottleneck for insects and plants.
Internal initiation of translation of five dendritically localized neuronal mRNAs
Authors: Pinkstaff Jason K. , Chappell Stephen A. , Mauro Vincent P. , Edelman Gerald M. , Krushel Les A.
Published: July 2002

In neurons, translation of dendritically localized mRNAs is thought
to play a role in affecting synaptic efficacy. Inasmuch as components
of the translation machinery may be limiting in dendrites, we
investigated the mechanisms by which translation of five dendritically
localized mRNAs is initiated. The 5′ leader sequences of mRNAs encoding
the activity-regulated cytoskeletal protein, the α subunit of
calcium–calmodulin-dependent kinase II, dendrin, the
microtubule-associated protein 2, and neurogranin (RC3) were evaluated
for their ability to affect translation in the 5′ untranslated region
of a monocistronic reporter mRNA. In both neural and nonneural cell
lines, the activity-regulated cytoskeletal protein,
microtubule-associated protein 2, and α-CaM Kinase II leader
sequences enhanced translation, whereas the dendrin and RC3 5′
untranslated regions slightly inhibited translation as compared with
controls. When cap-dependent translation of these constructs was
suppressed by overexpression of a protein that binds the cap-binding
protein eIF4E, it was revealed that translation of these mRNAs had both
cap-dependent and cap-independent components. The cap-independent
component was further analyzed by inserting the 5′ leader sequences
into the intercistronic region of dicistronic mRNAs. All five leader
sequences mediated internal initiation via internal ribosome entry
sites (IRESes). The RC3 IRES was most active and was further
characterized after transfection in primary neurons. Although
translation mediated by this IRES occurred throughout the cell, it was
relatively more efficient in dendrites. These data suggest that IRESes
may increase translation efficiency at postsynaptic sites after
synaptic activation.
Mycobacterium tuberculosis
WhiB3 interacts with RpoV to affect host survival but is dispensable for
in vivo
growth
Authors: Steyn Adrie J. C. , Collins Desmond M. , Hondalus Mary K. , Jacobs William R. , Kawakami R. Pamela , Bloom Barry R.
Published: July 2002

Previous work established that the principal sigma factor (RpoV) of virulent
Mycobacterium bovis
, a member of the
Mycobacterium tuberculosis
complex, restores virulence to an attenuated strain containing a point mutation (Arg-515→His) in the 4.2 domain of RpoV. We used the 4.2 domain of RpoV as bait in a yeast two-hybrid screen of an
M. tuberculosis
H37Rv library and identified a putative transcription factor, WhiB3, which selectively interacts with the 4.2 domain of RpoV in virulent strains but not with the mutated (Arg-515→His) allele. Infection of mice and guinea pigs with a
M. tuberculosis
H37Rv
whiB3
deletion mutant strain showed that
whiB3
is not necessary for
in vivo
bacterial replication in either animal model. In contrast, an
M. bovis whiB3
deletion mutant was completely attenuated for growth in guinea pigs. However, we found that immunocompetent mice infected with the
M. tuberculosis
H37Rv
whiB3
mutant strain had significantly longer mean survival times as compared with mice challenged with wild-type
M. tuberculosis
. Remarkably, the bacterial organ burdens of both mutant and wild-type infected mice were identical during the acute and persistent phases of infection. Our results imply that
M. tuberculosis
replication
per se
is not a sufficient condition for virulence
in vivo
. They also indicate a different role for
M. bovis
and
M. tuberculosis whiB3
genes in pathogenesis generated in different animal models. We propose that
M. tuberculosis
WhiB3 functions as a transcription factor regulating genes that influence the immune response of the host.
SQV-7, a protein involved in
Caenorhabditis elegans
epithelial invagination and early embryogenesis, transports UDP-glucuronic acid, UDP-
N
- acetylgalactosamine, and UDP-galactose
Authors: Berninsone Patricia , Hwang Ho-Yon , Zemtseva Irina , Horvitz H. Robert , Hirschberg Carlos B.
Published: July 2002

Caenorhabditis elegans sqv
mutants
are defective in vulval epithelial invagination and have a severe
reduction in hermaphrodite fertility. The gene
sqv-7
encodes a multitransmembrane hydrophobic protein resembling nucleotide
sugar transporters of the Golgi membrane. A Golgi vesicle enriched
fraction of
Saccharomyces cerevisiae
expressing SQV-7
transported UDP-glucuronic acid,
UDP-
N
-acetylgalactosamine, and UDP-galactose (Gal) in a
temperature-dependent and saturable manner. These nucleotide sugars are
competitive, alternate, noncooperative substrates. The two mutant
sqv-7
missense alleles resulted in a severe reduction of
these three transport activities. SQV-7 did not transport CMP-sialic
acid, GDP-fucose, UDP-
N
-acetylglucosamine, UDP-glucose,
or GDP-mannose. SQV-7 is able to transport UDP-Gal
in
vivo
, as shown by its ability to complement the phenotype of
Madin-Darby canine kidney ricin resistant cells, a mammalian cell line
deficient in UDP-Gal transport into the Golgi. These results
demonstrate that unlike most nucleotide sugar transporters, SQV-7 can
transport multiple distinct nucleotide sugars. We propose that SQV-7
translocates multiple nucleotide sugars into the Golgi lumen for
the biosynthesis of glycoconjugates that play a pivotal role
in development.
NMDA receptor function is regulated by the inhibitory scaffolding protein, RACK1
Authors: Yaka Rami , Thornton Claire , Vagts Alicia J. , Phamluong Khanhky , Bonci Antonello , Ron Dorit
Published: July 2002

Phosphorylation regulates the function of ligand-gated ion channels such as the
N-
methyl
d
-aspartate (NMDA) receptor. Here we report a mechanism for modulation of the phosphorylation state and function of the NMDA receptor via an inhibitory scaffolding protein, RACK1. We found that RACK1 binds both the NR2B subunit of the NMDA receptor and the nonreceptor protein tyrosine kinase, Fyn. RACK1 inhibits Fyn phosphorylation of NR2B and decreases NMDA receptor-mediated currents in CA1 hippocampal slices. Peptides that disrupt the interactions between RACK1, NR2B, and Fyn induce phosphorylation and potentiate NMDA receptor-mediated currents. Therefore, RACK1 is a regulator of NMDA receptor function and may play a role in synaptic plasticity, addiction, learning, and memory.
Restoration of spermatogenesis by lentiviral gene transfer: Offspring from infertile mice
Authors: Ikawa Masahito , Tergaonkar Vinay , Ogura Atsuo , Ogonuki Narumi , Inoue Kimiko , Verma Inder M.
Published: July 2002

Disruption of spermatogenesis found in azoospermia and oligozoospermia is thought to be of primarily genetic origin.

Sl/Sl
d

mutant mice offer a model system in which lack of transmembrane type c-
kit
ligand (KL2) expression on the somatic Sertoli cell surface results in disruption of spermatogenesis. We investigated the ability of adeno-, adeno-associated-, retro-, and lentiviral vectors to transduce Sertoli cells and found that transduction with either adeno- or lentiviral vectors led to reporter gene expression for more than 2 mo after testicular tubule injection. Because adenoviral vectors showed toxicity, lentiviral vectors were used to express the c-
kit
ligand in

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Sertoli cells. Restoration of spermatogenesis was observed in all recipient testes. Furthermore, the sperm collected from recipient testes were able to generate normal pups after intracytoplasmic sperm injection. None of the offspring carried the transgene, suggesting the inability of lentiviral vectors to infect spermatogenic cells
in vivo
. We propose that lentiviral vectors can be used for gene therapy of male infertility without the risk of germ-line transmission.
A self-recombining bacterial artificial chromosome and its application for analysis of herpesvirus pathogenesis
Authors: Smith Gregory A. , Enquist Lynn W.
Published: July 2002

A self-recombining bacterial artificial chromosome (BAC) containing the 142-kb pseudorabies virus genome was constructed such that the viral genome is rapidly excised from the BAC vector backbone on delivery into mammalian cells. The recombination is mediated by
loxP
sites in the plasmid and Cre recombinase encoded within the BAC vector. A synthetic intron inserted in the middle of the
cre
ORF completely inhibits recombination in
Escherichia coli
, but is spliced out after delivery of the plasmid into mammalian cells. Recombination is efficient, and pure virus lacking the BAC vector backbone is immediately isolated from transfected mammalian cells without the need of serial passage or plaque purification.
A postgermination developmental arrest checkpoint is mediated by abscisic acid and requires the ABI5 transcription factor in
Arabidopsis
Authors: Lopez-Molina Luis , Mongrand Sébastien , Chua Nam-Hai
Published: July 2002

Seed dormancy is a trait of considerable adaptive significance
because it maximizes seedling survival by preventing premature
germination under unfavorable conditions. Understanding how seeds break
dormancy and initiate growth is also of great agricultural and
biotechnological interest. Abscisic acid (ABA) plays primary regulatory
roles in the initiation and maintenance of seed dormancy. Here we
report that the basic leucine zipper transcription factor ABI5 confers
an enhanced response to exogenous ABA during germination, and seedling
establishment, as well as subsequent vegetative growth. These responses
correlate with total ABI5 levels. We show that ABI5 expression defines
a narrow developmental window following germination, during which
plants monitor the environmental osmotic status before initiating
vegetative growth. ABI5 is necessary to maintain germinated embryos in
a quiescent state thereby protecting plants from drought. As expected
for a key player in ABA-triggered processes, ABI5 protein accumulation,
phosphorylation, stability, and activity are highly regulated by ABA
during germination and early seedling growth.
Sodium channel Na
v
1.6 is localized at nodes of Ranvier, dendrites, and synapses
Authors: Caldwell John H. , Schaller Kristin L. , Lasher Robert S. , Peles Elior , Levinson S. Rock
Published: July 2002

Voltage-gated sodium channels perform critical roles for electrical signaling in the nervous system by generating action potentials in axons and in dendrites. At least 10 genes encode sodium channels in mammals, but specific physiological roles that distinguish each of these isoforms are not known. One possibility is that each isoform is expressed in a restricted set of cell types or is targeted to a specific domain of a neuron or muscle cell. Using affinity-purified isoform-specific antibodies, we find that Na
v
1.6 is highly concentrated at nodes of Ranvier of both sensory and motor axons in the peripheral nervous system and at nodes in the central nervous system. The specificity of this antibody was also demonstrated with the Na
v
1.6-deficient mouse mutant strain
med
, whose nodes were negative for Na
v
1.6 immunostaining. Both the intensity of labeling and the failure of other isoform-specific antibodies to label nodes suggest that Na
v
1.6 is the predominant channel type in this structure. In the central nervous system, Na
v
1.6 is localized in unmyelinated axons in the retina and cerebellum and is strongly expressed in dendrites of cortical pyramidal cells and cerebellar Purkinje cells. Ultrastructural studies indicate that labeling in dendrites is both intracellular and on dendritic shaft membranes. Remarkably, Na
v
1.6 labeling was observed at both presynaptic and postsynaptic membranes in the cortex and cerebellum. Thus, a single sodium channel isoform is targeted to different neuronal domains and can influence both axonal conduction and synaptic responses.
The biotic crisis and the future of evolution
Authors: Myers Norman , Knoll Andrew H.
Published: July 2002

The biotic crisis overtaking our planet is likely to precipitate a major extinction of species. That much is well known. Not so well known but probably more significant in the long term is that the crisis will surely disrupt and deplete certain basic processes of evolution, with consequences likely to persist for millions of years. Distinctive features of future evolution could include a homogenization of biotas, a proliferation of opportunistic species, a pest-and-weed ecology, an outburst of speciation among taxa that prosper in human-dominated ecosystems, a decline of biodisparity, an end to the speciation of large vertebrates, the depletion of “evolutionary powerhouses” in the tropics, and unpredictable emergent novelties. Despite this likelihood, we have only a rudimentary understanding of how we are altering the evolutionary future. As a result of our ignorance, conservation policies fail to reflect long-term evolutionary aspects of biodiversity loss.
A neuronal β subunit (KCNMB4) makes the large conductance, voltage- and Ca
2+
-activated K
+
channel resistant to charybdotoxin and iberiotoxin
Authors: Meera Pratap , Wallner Martin , Toro Ligia
Published: July 2002

Large conductance voltage and Ca
2+
-activated K
+
(MaxiK) channels couple intracellular Ca
2+
with cellular excitability. They are composed of a pore-forming α subunit and modulatory β subunits. The pore blockers charybdotoxin (CTx) and iberiotoxin (IbTx), at nanomolar concentrations, have been invaluable in unraveling MaxiK channel physiological role in vertebrates. However in mammalian brain, CTx-insensitive MaxiK channels have been described [Reinhart, P. H., Chung, S. & Levitan, I. B. (1989)
Neuron
2, 1031–1041], but their molecular basis is unknown. Here we report a human MaxiK channel β-subunit (β4), highly expressed in brain, which renders the MaxiK channel α-subunit resistant to nanomolar concentrations of CTx and IbTx. The resistance of MaxiK channel to toxin block, a phenotype conferred by the β4 extracellular loop, results from a dramatic (≈1,000 fold) slowdown of the toxin association. However once bound, the toxin block is apparently irreversible. Thus, unusually high toxin concentrations and long exposure times are necessary to determine the role of “CTx/IbTx-insensitive” MaxiK channels formed by α + β4 subunits.
Requirement of the nicotinic acetylcholine receptor β2 subunit for the anatomical and functional development of the visual system
Authors: Rossi Francesco Mattia , Pizzorusso Tommaso , Porciatti Vittorio , Marubio Lisa M. , Maffei Lamberto , Changeux Jean-Pierre
Published: July 2002

In the mammalian visual system the formation of eye-specific
layers at the thalamic level depends on retinal waves of spontaneous
activity, which rely on nicotinic acetylcholine receptor activation. We
found that in mutant mice lacking the β2 subunit of the neuronal
nicotinic receptor, but not in mice lacking the α4 subunit,
retinofugal projections do not segregate into eye-specific areas, both
in the dorso-lateral geniculate nucleus and in the superior colliculus.
Moreover, β2−/− mice show an expansion of the binocular subfield
of the primary visual cortex and a decrease in visual acuity at the
cortical level but not in the retina. We conclude that the β2 subunit
of the nicotinic acetylcholine receptor is necessary for the anatomical
and functional development of the visual system.
Mutant G protein α subunit activated by Gβγ: A model for receptor activation?
Authors: Rondard Philippe , Iiri Taroh , Srinivasan Supriya , Meng Elaine , Fujita Toshiro , Bourne Henry R.
Published: July 2002

How receptors catalyze exchange of GTP for GDP bound to the Gα
subunit of trimeric G proteins is not known. One proposal is that the
receptor uses the G protein's βγ heterodimer as a lever, tilting
it to pull open the guanine nucleotide binding pocket of Gα. To test
this possibility, we designed a mutant Gα that would bind to βγ
in the tilted conformation. To do so, we excised a helical turn (four
residues) from the N-terminal region of α
s
, the α
subunit of G
S
, the stimulatory regulator of adenylyl
cyclase. In the presence, but not in the absence, of transiently
expressed β
1
and γ
2
, this mutant
(α
s
Δ), markedly stimulated cAMP accumulation. This
effect depended on the ability of the coexpressed β protein to
interact normally with the lip of the nucleotide binding pocket of
α
s
Δ. We substituted alanine for an aspartate in
β
1
that binds to a lysine (K206) in the lip of the α
subunit's nucleotide binding pocket. Coexpressed with
α
s
Δ and γ
2
, this mutant,
β
1
-D228A, elevated cAMP much less than did
β
1
-wild type; it did bind to α
s
Δ
normally, however, as indicated by its unimpaired ability to target
α
s
Δ to the plasma membrane. We conclude that βγ can
activate α
s
and that this effect probably involves both a
tilt of βγ relative to α
s
and interaction of β with
the lip of the nucleotide binding pocket. We speculate that receptors
use a similar mechanism to activate trimeric G proteins.
The phytoestrogen genistein induces thymic and immune changes: A human health concern?
Authors: Yellayi Srikanth , Naaz Afia , Szewczykowski Melissa A. , Sato Tomomi , Woods Jeffrey A. , Chang Jongsoo , Segre Mariangela , Allred Clint D. , Helferich William G. , Cooke Paul S.
Published: July 2002

Use of soy-based infant formulas and soy/isoflavone supplements has aroused concern because of potential estrogenic effects of the soy isoflavones genistein and daidzein. Here we show that s.c. genistein injections in ovariectomized adult mice produced dose-responsive decreases in thymic weight of up to 80%. Genistein's thymic effects occurred through both estrogen receptor (ER) and non-ER-mediated mechanisms, as the genistein effects on thymus were only partially blocked by the ER antagonist ICI 182,780. Genistein decreased thymocyte numbers up to 86% and doubled apoptosis, indicating that the mechanism of the genistein effect on loss of thymocytes is caused in part by increased apoptosis. Genistein injection caused decreases in relative percentages of thymic CD4+CD8−and double-positive CD4+CD8+thymocytes, providing evidence that genistein may affect early thymocyte maturation and the maturation of the CD4+CD8−helper T cell lineage. Decreases in the relative percentages of CD4+CD8−thymocytes were accompanied by decreases in relative percentages of splenic CD4+CD8−cells and a systemic lymphocytopenia. In addition, genistein produced suppression of humoral immunity. Genistein injected at 8 mg/kg per day produced serum genistein levels comparable to those reported in soy-fed human infants, and this dose caused significant thymic and immune changes in mice. Critically, dietary genistein at concentrations that produced serum genistein levels substantially less than those in soy-fed infants produced marked thymic atrophy. These results raise the possibility that serum genistein concentrations found in soy-fed infants may be capable of producing thymic and immune abnormalities, as suggested by previous reports of immune impairments in soy-fed human infants.