bluuebunny/crossref_metadata_2025 huggingface dataset:
An update on the energy dissipation rate in isotropic turbulence
Authors: Sreenivasan Katepalli R.
Published: July 2002

Direct numerical simulations of homogeneous turbulence in a periodic box are examined here to support the traditional expectation that the dissipation rate at high Reynolds numbers is independent of fluid viscosity, and is a constant of order unity when scaled on the integral scale and root-mean-square velocity. However, the numerical value of the constant appears to depend on details of forcing at low wavenumbers, or, perhaps, the structure of the large scale itself.
Baroclinic circulation generation on shock accelerated slow/fast gas interfaces
Authors: Samtaney Ravi , Ray Jaideep , Zabusky Norman J.
Published: July 2002

Vorticity is deposited baroclinically by shock waves on density inhomogeneities. In two dimensions, for a planar “slow–fast” interface, we present analytical results for σ, the circulation deposited per unit unshocked interface length, within the regular refraction regime. The parameters that describe the interaction are the Mach number (M), the density ratio of the two gases (η, η<1), the local angle between the shock and the interface (α), and the ratio of specific heats of the two gases (γ0,γb). For weak shocks σ scales as σ∝(1−η−1/2)ξ(M)sin α and for strong shocks σ→K(η,α,γ)/(1−ξ(M)). For scaling purposes, the gases are assumed to have the same γ. K(η,α,γ) is a function of the density ratio, the interface angle, and the ratio of specific heats γ [Eq. (4.6)] and ξ(M) is the normalized pressure gradient across the shock. The planar interface approach is used to find formulas to calculate the total circulation deposited on sinusoidal interfaces. To validate the formulas, numerical simulations of the compressible Euler equations were made using a second-order Godunov code. Simulations were done for 1.05⩽M⩽3.0 and η=0.14, 0.33 and 0.65.
Propagation of a topological transition: The Rayleigh instability
Authors: Powers Thomas R. , Zhang Dengfu , Goldstein Raymond E. , Stone Howard A.
Published: July 2002

The Rayleigh capillary instability of a cylindrical interface between two immiscible fluids is one of the most fundamental in fluid dynamics. As Plateau observed from energetic considerations and Rayleigh clarified through hydrodynamics, such an interface is linearly unstable to fission due to surface tension. In traditional descriptions of this instability it occurs everywhere along the cylinder at once, triggered by infinitesimal perturbations. Here we explore in detail a recently conjectured alternate scenario for this instability: front propagation. Using boundary integral techniques for Stokes flow, we provide numerical evidence that the viscous Rayleigh instability can indeed spread behind a front moving at constant velocity, in some cases leading to a periodic sequence of pinching events. These basic results are in quantitative agreement with the marginal stability criterion, yet there are important qualitative differences associated with the discontinuous nature of droplet fission. A number of experiments immediately suggest themselves in light of these results.
Control of streamwise vortices with uniform magnetic fluxes
Authors: Lim Junwoo , Choi Haecheon , Kim John
Published: July 2002

Numerical experiments are conducted to investigate the effect of uniform magnetic fluxes on streamwise vortices in conducting fluids. A simple flow configuration, in which a pair of two-dimensional vortices interact with a wall, is used to study the effect of magnetic forcing on the vortices. Effects of a uniform magnetic flux applied in three directions—streamwise, wall-normal, and spanwise—are investigated. The electromagnetic force induced from either the wall-normal or spanwise magnetic flux inhibits the induced motion by the streamwise vortices and reduces their strength, while the streamwise magnetic flux does not affect the flow in the present flow configuration. It is also shown that, in the case of a closely interacting pair of vortices, the spanwise magnetic flux is more effective than the wall-normal magnetic flux in reducing the strength of the streamwise vortices.
A priori subgrid analysis of temporal mixing layers with evaporating droplets
Authors: Okong’o Nora , Bellan Josette
Published: July 2002

Subgrid analysis of a transitional temporal mixing layer with evaporating droplets has been performed using three sets of results from a direct numerical simulation (DNS) database, with Reynolds numbers (based on initial vorticity thickness) as large as 600 and with droplet mass loadings as large as 0.5. In the DNS, the gas phase is computed using an Eulerian formulation, with Lagrangian droplet tracking. The large eddy simulation (LES) equations corresponding to the DNS are first derived, and key assumptions in deriving them are first confirmed by using the DNS database. Since LES of this flow requires the computation of droplet source terms, it is essential to obtain the unfiltered gas-phase variables at droplet locations from filtered gas-phase variables at the grid points. This paper proposes to model these unfiltered gas-phase variables at the drop locations by assuming the gas-phase variables to be the sum of the filtered variables and a correction based on the filtered standard deviation; this correction is then computed from the subgrid scale (SGS) standard deviation. This model predicts the unfiltered variables at droplet locations considerably better than simply interpolating the filtered variables. Three methods are investigated for modeling the SGS standard deviation: the Smagorinsky approach, the gradient model and the scale-similarity formulation. When the proportionality constant inherent in the SGS models is properly calculated, the gradient and scale-similarity methods give results in excellent agreement with the DNS.
Large amplitude ion-acoustic waves in a plasma with an electron beam
Authors: Nejoh Yasunori , Sanuki Heiji
Published: July 2002

The nonlinear wave structures of large amplitude ion-acoustic waves are studied in a plasma with an electron beam, by the pseudopotential method. The region of the existence of large amplitude ion-acoustic waves is examined, showing that the condition of the existence sensitively depends on the parameters such as the electron beam temperature, the ion temperature, the electrostatic potential, and the concentration of the electron beam density. It turns out that the region of the existence spreads as the beam temperature increases but the effect of the electron beam velocity is relatively small. New findings of large amplitude ion-acoustic waves in a plasma with an electron beam are predicted.
Helicon wave excitation and propagation in a toroidal heliac: Experiment and theory
Authors: Zhang B. C. , Borg G. G. , Blackwell B. D.
Published: July 2002

In this paper a comparison between theoretical calculations and experimental measurements of helicon wave coupling by a partial-turn shielded antenna in a toroidal heliac is presented. Despite the complicated heliac geometry, the wave dispersion, field profiles, and antenna radiation resistance are described well by a cylindrical uniform plasma theory. It also presents a simple formula relating the radiation resistance to the measured wave magnetic field per unit antenna current. Finally, the scaling of these results to the Heliac-1 (H-1) [Fusion Technol. 17, 123 (1990)]; a larger heliac now operating at the Australian National University (ANU), is discussed.
Fast electron transport and lower hybrid absorbed power profiles from hard x-ray imaging in the Princeton Beta Experiment-Modified
Authors: Jones S. E. , Kesner J. , Luckhardt S. , Paoletti F. , von Goeler S. , Bernabei S. , Kaita R. , Giruzzi G. ,   the PBX-M Team
Published: July 2002

Recent hardware improvements on the hard x-ray camera of the Princeton Beta Experiment-Modified (PBX-M) expand the capabilities for observing bremsstrahlung radiation from fast electrons during lower hybrid current drive (LHCD) experiments, thereby allowing accurate fast electron transport studies. Developed methods to directly invert two-dimensional x-ray images reveal radial profiles of the emitted intensity and isotropy. Such profiles extracted from lower hybrid (LH) modulation experiments permit computation of the lower hybrid power absorption profile. Results from application to the LH phase scans demonstrate the ability to control the peak location of the driven current. Incorporating these results into simulations using both a three-dimensional Fokker–Planck code and a simple modulation model provides lower and upper bound estimates for the hot electron diffusion coefficient D*.
A study of picosecond laser–solid interactions up to 1019 W cm−2
Authors: Beg F. N. , Bell A. R. , Dangor A. E. , Danson C. N. , Fews A. P. , Glinsky M. E. , Hammel B. A. , Lee P. , Norreys P. A. , Tatarakis M.
Published: July 2002

The interaction of a 1053 nm picosecond laser pulse with a solid target has been studied for focused intensities of up to 1019 W cm−2. The maximum ion energy cutoff Emax (which is related to the hot electron temperature) is in the range 1.0–12.0 MeV and is shown to scale as Emax≈I1/3. The hot electron temperatures were in the range 70–400 keV for intensities up to 5×1018 W cm−2 with an indication of a high absorption of laser energy. Measurements of x-ray/γ-ray bremsstrahlung emission suggest the existence of at least two electron temperatures. Collimation of the plasma flow has been observed by optical probing techniques.
Toroidal Alfvén eigenmodes in TFTR deuterium–tritium plasmas
Authors: Nazikian R. , Fu G. Y. , Chang Z. , Batha S. H. , Berk H. , Budny R. V. , Chen Y. , Cheng C. Z. , Darrow D. S. , Gorelenkov N. N. , Levinton F. M. , Medley S. , Petrov M. P. , Redi M. , Ruskov E. , Spong D. A. , White R. B. , Zweben S. J.
Published: July 2002

Purely alpha-particle-driven toroidal Alfvén eigenmodes (TAEs) with toroidal mode numbers n=1–6 have been observed in deuterium–tritium (D–T) plasmas on the tokamak fusion test reactor [D. J. Grove and D. M. Meade, Nucl. Fusion 25, 1167 (1985)]. The appearance of mode activity following termination of neutral beam injection in plasmas with q(0)>1 is generally consistent with theoretical predictions of TAE stability [G. Y. Fu et al. Phys. Plasmas 3, 4036 (1996)]. Internal reflectometer measurements of TAE activity is compared with theoretical calculations of the radial mode structure. Core localization of the modes to the region of reduced central magnetic shear is confirmed, however the mode structure can deviate significantly from theoretical estimates. The peak measured TAE amplitude of δn/n∼10−4 at r/a∼0.3−0.4 corresponds to δB/B∼10−5, while δB/B∼10−8 is measured at the plasma edge. Enhanced alpha particle loss associated with TAE activity has not been observed.
Stability of a plasma confined in a dipole field
Authors: Kesner J.
Published: July 2002

Plasma confined in a magnetic dipole field is stabilized by the expansion of the magnetic flux. The stability of low beta electrostatic modes in a magnetic dipole field is examined when the distribution function is Maxwellian to lowest order. It is shown using a Nyquist analysis that for sufficiently gentle density and temperature gradients the configuration would be expected to be stable to both magnetohydrodynamic and collisionless interchange modes. Furthermore, it is shown that when it is stable to the interchange mode it is also stable to ion temperature gradient and collisionless trapped particle modes, as well as modes driven by parallel dynamics such as the “universal” instability.
Particle acceleration in relativistic laser channels
Authors: Pukhov A. , Sheng Z.-M. , Meyer-ter-Vehn J.
Published: July 2002

Energy spectra of ions and fast electrons accelerated by a channeling laser pulse in near-critical plasma are studied using three-dimensional (3D) Particle-In-Cell simulations. The realistic 3D geometry of the simulations allows us to obtain not only the shape of the spectra, but also the absolute numbers of accelerated particles. It is shown that ions are accelerated by a collisionless radial expansion of the channel and have nonthermal energy spectra. The electron energy spectra instead are Boltzmann-like. The effective temperature Teff scales as I1/2. The form of electron spectra and Teff depends also on the length of the plasma channel. The major mechanism of electron acceleration in relativistic channels is identified. Electrons make transverse betatron oscillations in the self-generated static electric and magnetic fields. When the betatron frequency coincides with the laser frequency as witnessed by the relativistic electron, a resonance occurs, leading to an effective energy exchange between the laser and electron. This is the inverse free-electron laser mechanism. Electrons are accelerated at the betatron resonance when the laser power overcomes significantly the critical power for self-focusing.
Simulations of electron/electron instabilities: Electromagnetic fluctuations
Authors: Gary S. Peter , Kazimura Yoshihiro , Li Hui , Sakai Jun-Ichi
Published: July 2002

Electron/electron instabilities arise in collisionless plasmas when the electron velocity distribution consists of two distinct components with a sufficiently large relative drift speed between them. If the less dense beam component is not too tenuous and sufficiently fast, the electron/electron beam instability is excited over a relatively broad range of frequencies. This instability is often studied in the electrostatic limit, which is appropriate at ωe/|Ωe|≫1, where ωe is the electron plasma frequency and Ωe is the electron cyclotron frequency, but is not necessarily valid at ωe/|Ωe|∼1. Here linear Vlasov dispersion theory has been used and fully electromagnetic particle-in-cell simulations have been run in a spatially homogeneous, magnetized plasma model at βe≪1 and 0.5 ⩽ωe/|Ωe|⩽4.0. Theory and simulations (run to times of order 100ωe−1) of the electron/electron beam instability show the growth of appreciable magnetic fluctuations at ωe/|Ωe|<2; these waves bear right-hand elliptical magnetic polarization. The simulations reproduce the well-known slowing and heating of the beam; at ωe/|Ωe|<1 this heating is predominantly parallel to the background magnetic field, but as ωe/|Ωe| becomes greater than unity the perpendicular heating of the beam increases. The simulations also demonstrate that, for ωe/|Ωe|∼1, electromagnetic fluctuations impart to the more dense electron core component significant heating perpendicular to the background magnetic field.
Electron-acoustic solitons in an electron-beam plasma system
Authors: Berthomier Matthieu , Pottelette Raymond , Malingre Michel , Khotyaintsev Yuri
Published: July 2002

Electron-acoustic solitons exist in a two electron temperature plasma (with “cold” and “hot” electrons) and take the form of negative electrostatic potential pulses. They develop on a spatial scale of a few Debye lengths and propagate at the electron-acoustic velocity which is intermediate between the two electron thermal velocities. They correspond to local enhancement of the cold electron density. It is shown that the introduction of an electron beam in such a plasma allows the existence of new electron-acoustic solitons with velocity related to the beam velocity. Depending on the beam density and temperature and below a critical velocity of the electron beam, they often have a positive potential signature. In such conditions they correspond to electron density holes for the cold electron population. The properties of these solitons are studied in detail. These results suggest that further analysis of recent observations of electron density holes might provide the means to identify these structures in the magnetospheric plasma.
Dorsal anterior cingulate cortex: A role in reward-based decision making
Authors: Bush George , Vogt Brent A. , Holmes Jennifer , Dale Anders M. , Greve Douglas , Jenike Michael A. , Rosen Bruce R.
Published: July 2002

Dorsal anterior cingulate cortex (dACC) is a brain region that
subserves cognition and motor control, but the mechanisms of these
functions remain unknown. Human neuroimaging and monkey
electrophysiology studies have provided valuable insights, but it has
been difficult to link the two literatures. Based on monkey
single-unit recordings, we hypothesized that human dACC is comprised of
a mixture of functionally distinct cells that variously anticipate and
detect targets, indicate novelty, influence motor responses, encode
reward values, and signal errors. As an initial test of this
conceptualization, the current event-related functional MRI study used
a reward-based decision-making task to isolate responses from a
subpopulation of dACC cells sensitive to reward reduction. As
predicted, seven of eight subjects showed significant
(
P
< 10
−4
) dACC activation when
contrasting reduced reward (REDrew) trials to fixation (FIX).
Confirmatory group analyses then corroborated the predicted ordinal
relationships of functional MRI activation expected during each trial
type (REDrew > SWITCH > CONrew ≥ FIX). The data
support a role for dACC in reward-based decision making, and by linking
the human and monkey literatures, provide initial support for the
existence of heterogeneity within dACC. These findings should be of
interest to those studying reward, cognition, emotion, motivation, and
motor control.
∥
The perceptual reality of synesthetic colors
Authors: Palmeri Thomas J. , Blake Randolph , Marois René , Flanery Marci A. , Whetsell William
Published: July 2002

Synesthesia is a remarkable, rare condition where an individual has multimodal perceptual experiences from a unimodal sensory event. We have studied such an individual, an adult male for whom achromatic words and alphanumeric characters are seen in vivid, reliable colors. We used a variety of perceptual tasks to document the perceptual reality of synesthetic colors and to begin to localize the stage of visual processing where this anomalous binding of externally specified form and internally generated color may take place. Synesthetic colors were elicited by forms defined solely by binocular cues or solely by motion cues, which implies a central locus of visual processing for synesthetic binding of form and color. Also included among our measurements was a difficult visual search task on which non-synesthetic subjects required an effortful search through the visual display. Our subject, in contrast to non-synesthetic subjects, accomplished the task with relative ease because the target of the search had a different synesthetic color from the distractors. Thus, synesthetic experiences appear to originate from a binding of color and form that takes place within central stages of visual processing.
Heterogeneous proliferative potential of occult metastatic cells in bone marrow of patients with solid epithelial tumors
Authors: Solakoglu Oender , Maierhofer Christine , Lahr Georgia , Breit Elisabeth , Scheunemann Peter , Heumos Isabella , Pichlmeier Uwe , Schlimok Günter , Oberneder Ralph , Köllermann Manfred W. , Köllermann Jens , Speicher Michael R. , Pantel Klaus
Published: July 2002

Bone marrow is a major homing site for circulating epithelial tumor cells. The present study was aimed to assess the proliferative capacity of occult metastatic cells in bone marrow of patients with operable solid tumors especially with regard to their clinical outcome. We obtained bone marrow aspirates from 153 patients with carcinomas of the prostate (
n
= 46), breast (
n
= 45), colon (
n
= 33), and kidney (
n
= 29). Most of the patients (87%) had primary disease with no clinical signs of overt metastases [tumor-node-metastasis (TNM)-stage UICC (Union Internationale Contre le Cancer) I-III]. After bone marrow was cultured for 21–102 days under special cell culture conditions, viable epithelial cells were detected by cytokeratin staining in 124 patients (81%). The cultured epithelial cells harbored Ki-ras2 mutations and numerical chromosomal aberrations. The highest median number of expanded tumor cells was observed in prostate cancer (2,619 per flask). There was a significant positive correlation between the number of expanded tumor cells and the UICC-stage of the patients (
P
= 0.03) or the presence of overt metastases (
P
= 0.04). Moreover, a strong expansion of tumor cells was correlated to an increased rate of cancer-related deaths (
P
= 0.007) and a reduced survival of the patients (
P
= 0.006). In conclusion, the majority of cancer patients have viable tumor cells in their bone marrow at primary tumor diagnosis, and the proliferative potential of these cells determines the clinical outcome.
Augmentation of immune responses to HIV-1 and simian immunodeficiency virus DNA vaccines by IL-2/Ig plasmid administration in rhesus monkeys
Authors: Barouch Dan H. , Craiu Abie , Kuroda Marcelo J. , Schmitz Jörn E. , Zheng Xin Xiao , Santra Sampa , Frost Julie D. , Krivulka Georgia R. , Lifton Michelle A. , Crabbs Carroll L. , Heidecker Gwendolyn , Perry Helen C. , Davies Mary-Ellen , Xie Hong , Nickerson Christine E. , Steenbeke Tavis D. , Lord Carol I. , Montefiori David C. , Strom Terry B. , Shiver John W. , Lewis Mark G. , Letvin Norman L.
Published: July 2002

The potential utility of plasmid DNA as an HIV-1 vaccination modality currently is an area of active investigation. However, recent studies have raised doubts as to whether plasmid DNA alone will elicit immune responses of sufficient magnitude to protect against pathogenic AIDS virus challenges. We therefore investigated whether DNA vaccine-elicited immune responses in rhesus monkeys could be augmented by using either an IL-2/Ig fusion protein or a plasmid expressing IL-2/Ig. Sixteen monkeys, divided into four experimental groups, were immunized with (i) sham plasmid, (ii) HIV-1 Env 89.6P and simian immunodeficiency virus mac239 Gag DNA vaccines alone, (iii) these DNA vaccines and IL-2/Ig protein, or (iv) these DNA vaccines and IL-2/Ig plasmid. The administration of both IL-2/Ig protein and IL-2/Ig plasmid induced a significant and sustainedin vivoactivation of peripheral T cells in the vaccinated monkeys. The monkeys that received IL-2/Ig plasmid generated 30-fold higher Env-specific antibody titers and 5-fold higher Gag-specific, tetramer-positive CD8+ T cell levels than the monkeys receiving the DNA vaccines alone. IL-2/Ig protein also augmented the vaccine-elicited immune responses, but less effectively than IL-2/Ig plasmid. Augmentation of the immune responses by IL-2/Ig was evident after the primary immunization and increased with subsequent boost immunizations. These results demonstrate that the administration of IL-2/Ig plasmid can substantially augment vaccine-elicited humoral and cellular immune responses in higher primates.
13
C NMR isotopomer analysis reveals a connection between pyruvate cycling and glucose-stimulated insulin secretion (GSIS)
Authors: Lu Danhong , Mulder Hindrik , Zhao Piyu , Burgess Shawn C. , Jensen Mette V. , Kamzolova Svetlana , Newgard Christopher B. , Sherry A. Dean
Published: July 2002

Cellular metabolism of glucose is required for stimulation of insulin secretion from pancreatic β cells, but the precise metabolic coupling factors involved in this process are not known. In an effort to better understand mechanisms of fuel-mediated insulin secretion, we have adapted
13
C NMR and isotopomer methods to measure influx of metabolic fuels into the tricarboxylic acid (TCA) cycle in insulinoma cells. Mitochondrial metabolism of [U-
13
C
3
]pyruvate, derived from [U-
13
C
6
]glucose, was compared in four clonal rat insulinoma cell 1-derived cell lines with varying degrees of glucose responsiveness. A
13
C isotopomer analysis of glutamate isolated from these cells showed that the fraction of acetyl-CoA derived from [U-
13
C
6
]glucose was the same in all four cell lines (44 ± 5%, 70 ± 3%, and 84 ± 4% with 3, 6, or 12 mM glucose, respectively). The
13
C NMR spectra also demonstrated the existence of two compartmental pools of pyruvate, one that exchanges with TCA cycle intermediates and a second pool derived from [U-
13
C
6
]glucose that feeds acetyl-CoA into the TCA cycle. The
13
C NMR spectra were consistent with a metabolic model where the two pyruvate pools do not randomly mix. Flux between the mitochondrial intermediates and the first pool of pyruvate (pyruvate cycling) varied in proportion to glucose responsiveness in the four cell lines. Furthermore, stimulation of pyruvate cycling with dimethylmalate or its inhibition with phenylacetic acid led to proportional changes in insulin secretion. These findings indicate that exchange of pyruvate with TCA cycle intermediates, rather than oxidation of pyruvate via acetyl-CoA, correlates with glucose-stimulated insulin secretion.
Glial protein S100B modulates long-term neuronal synaptic plasticity
Authors: Nishiyama Hiroshi , Knöpfel Thomas , Endo Shogo , Itohara Shigeyoshi
Published: July 2002

Glial cells are traditionally regarded as elements for structural support and ionic homeostasis, but have recently attracted attention as putative integral elements of the machinery involved in synaptic transmission and plasticity. Here, we demonstrate that calcium-binding protein S100B, which is synthesized in considerable amounts in astrocytes (a major glial cell subtype), modulates long-term synaptic plasticity. Mutant mice devoid of S100B developed normally and had no detectable abnormalities in the cytoarchitecture of the brain. These mutant mice, however, had strengthened synaptic plasticity as identified by enhanced long-term potentiation (LTP) in the hippocampal CA1 region. Perfusion of hippocampal slices with recombinant S100B proteins reversed the levels of LTP in the mutant slices to those of the wild-type slices, indicating that S100B might act extracellularly. In addition to enhanced LTP, mutant mice had enhanced spatial memory in the Morris water maze test and enhanced fear memory in the contextual fear conditioning. The results indicate that S100B is a glial modulator of neuronal synaptic plasticity and strengthen the notion that glial–neuronal interaction is important for information processing in the brain.
General and variable features of varicosity spacing along unmyelinated axons in the hippocampus and cerebellum
Authors: Shepherd Gordon M. G. , Raastad Morten , Andersen Per
Published: July 2002

Along unmyelinated central axons, synapses occur at focal swellings called axonal varicosities (boutons). The mechanisms regulating how frequently synapses and varicosities occur along axons remain poorly understood. Here, to investigate varicosity distribution patterns and the extent to which they may be conserved across different axons, we analyzed varicosity numbers and positions along fluorescently labeled axon branches in hippocampal area CA1 (CA3-to-CA1 “Schaffer collateral” axons) and five other synaptic regions of rat hippocampus and cerebellum. Varicosity spacing varied by region; e.g., 3.7 ± 0.6 μm (mean ± SD) for CA3-to-CA1 axons and 5.2 ± 1.0 μm for cerebellar parallel fibers. Surprisingly, when 56 axons from these different regions were pooled into a single heterogeneous group, a general relationship emerged: the spacing variability (SD) was a constant fraction of the mean spacing, suggesting that varicosities along different axons are distributed in a fundamentally similar, scaled manner. Varicosity spacing was neither regular nor random but followed a pattern consistent with random synaptic distributions and the occurrence of multiple-synapse boutons. A quantitative model reproduced the salient features of the data and distinguished between two proposed mechanisms relating axonal morphogenesis and synaptogenesis.
Genetic instability favoring transversions associated with ErbB2-induced mammary tumorigenesis
Authors: Liu Shiquan , Liu Wenjing , Jakubczak John L. , Erexson Gregory L. , Tindall Kenneth R. , Chan Richard , Muller William J. , Adhya Sankar , Garges Susan , Merlino Glenn
Published: July 2002

It has been argued that genetic instability is required to generate the myriad mutations that fuel tumor initiation and progression and, in fact, patients with heritable cancer susceptibility syndromes harbor defects in specific genes that normally maintain DNA integrity. However, the vast majority of human cancers arise sporadically, in the absence of deficiencies in known “mutator” genes. We used a
cII
-based mutation detection assay to show that the mean frequency of forward mutations in primary mammary adenocarcinomas arising in mouse mammary tumor virus-c-
erbB2
transgenic mice harboring multiple copies of the λ bacteriophage genome was significantly higher than in aged-matched, wild-type mammary tissue. Analysis of the
cII
mutational spectrum within the mammary tumor genomic DNA demonstrated a >6-fold elevation in transversion mutation frequency, resulting in a highly unusual inversion of the transition/transversion ratio characteristic of normal epithelium; frameshift mutation frequencies were unaltered. Arising oncogenic point mutations within the c-
erbB2
transgene of such tumors were predominantly transversions as well. Data from this model system support the notion that elaboration of a mutator phenotype is a consequential event in breast cancer and suggest that a novel DNA replication/repair gene is a relatively early mutational target in c-
erbB2
-induced mammary tumorigenesis.
Recombination-mediated lengthening of terminal telomeric repeats requires the Sgs1 DNA helicase
Authors: Cohen Haim , Sinclair David A.
Published: July 2002

The
Saccharomyces cerevisiae SGS1
gene encodes a
RecQ-like DNA helicase, human homologues of which are implicated in the
genetic instability disorders, Bloom syndrome (BS), Rothmund-Thomson
syndrome (RTS), and Werner syndrome (WS). Telomerase-negative yeast
cells can recover from senescence via two recombinational telomere
elongation pathways. The “type I” pathway generates telomeres
with large blocks of telomeric and subtelomeric sequences and short
terminal repeat tracts. The “type II” pathway generates telomeres
with extremely long heterogeneous terminal repeat tracts, reminiscent
of the long telomeres observed in telomerase-deficient human tumors and
tumor-derived cell lines. Here, we report that telomerase-negative
(
est2
) yeast cells lacking
SGS1
senesced
more rapidly, experienced a higher rate of telomere erosion, and were
delayed in the generation of survivors. The
est2 sgs1
survivors that were generated grew poorly, arrested in
G
2
/M and possessed exclusively type I telomeres, implying
that
SGS1
is critical for the type II pathway. The mouse
WS gene suppressed the slow growth and G
2
/M arrest
phenotype of
est2 sgs1
survivors, arguing that the
telomeric function of
SGS1
is conserved. Reintroduction
of
SGS1
into
est2 sgs1
survivors restored
growth rate and extended terminal tracts by ≈300 bp. Both phenotypes
were absolutely dependent on Sgs1 helicase activity. Introduction of an
sgs1
carboxyl-terminal truncation allele with helicase
activity restored growth rate without extending telomeres in most
cases, demonstrating that type II telomeres are not necessary for
normal growth in the absence of telomerase.
The plant-specific function of 2-Cys peroxiredoxin-mediated detoxification of peroxides in the redox-hierarchy of photosynthetic electron flux
Authors: König Janine , Baier Margarete , Horling Frank , Kahmann Uwe , Harris Gary , Schürmann Peter , Dietz Karl-Josef
Published: July 2002

The 2-cysteine peroxiredoxins (2-Cys Prx) constitute an ancient family of peroxide detoxifying enzymes and have acquired a plant-specific function in the oxygenic environment of the chloroplast. Immunocytochemical analysis and work with isolated intact chloroplasts revealed a reversible binding of the oligomeric form of 2-Cys Prx to the thylakoid membrane. The oligomeric form of the enzyme was enhanced under stress. The 2-Cys Prx has a broad substrate specificity with activity toward hydrogen peroxides and complex alkyl hydroperoxides. During the peroxide reduction reaction, 2-Cys Prx is alternatively oxidized and reduced as it catalyzes an electron flow from an electron donor to peroxide.
Escherichia coli
thioredoxin, but also spinach thioredoxin f and m were able to reduce oxidized 2-Cys Prx. The midpoint redox potential of −315 mV places 2-Cys Prx reduction after Calvin cycle activation and before switching the malate valve for export of excess reduction equivalents to the cytosol. Thus the 2-Cys Prx has a defined and preferential place in the hierarchy of photosynthetic electron transport. The activity of 2-Cys Prx also is linked to chloroplastic NAD(P)H metabolism as indicated by the presence of the reduced form of the enzyme after feeding dihydroxyacetone phosphate to intact chloroplasts. The function of the 2-Cys Prx is therefore not confined to its role in the water–water cycle pathway for energy dissipation in photosynthesis but also mediates peroxide detoxification in the plastids during the dark phase.
A phage integrase directs efficient site-specific integration in human cells
Authors: Groth Amy C. , Olivares Eric C. , Thyagarajan Bhaskar , Calos Michele P.
Published: July 2002

The integrase from the
Streptomyces
phage φC31 carries out efficient recombination between the
attP
site in the phage genome and the
attB
site in the host bacterial chromosome. In this paper, we show that the enzyme also functions in human cells. A plasmid assay system was constructed that measured intramolecular integration of
attP
into
attB
. This assay was used to demonstrate that in the presence of the φC31 integrase, precise unidirectional integration occurs with an efficiency of 100% in
Escherichia coli
and >50% in human cells. This assay system was also used to define the minimal sizes of
attB
and
attP
at 34 bp and 39 bp, respectively. Furthermore, precise and efficient intermolecular integration of an incoming plasmid bearing
attP
into an established Epstein–Barr virus plasmid bearing
attB
was documented in human cells. This work is a demonstration of efficient, site-specific, unidirectional integration in mammalian cells. These observations form the basis for site-specific integration strategies potentially useful in a broad range of genetic engineering applications.
The silencing protein SIR2 and its homologs are NAD-dependent protein deacetylases
Authors: Landry Joseph , Sutton Ann , Tafrov Stefan T. , Heller Ryan C. , Stebbins John , Pillus Lorraine , Sternglanz Rolf
Published: July 2002

Homologs of the chromatin-bound yeast silent information regulator 2 (SIR2) protein are found in organisms from all biological kingdoms.
SIR2
itself was originally discovered to influence mating-type control in haploid cells by locus-specific transcriptional silencing. Since then, SIR2 and its homologs have been suggested to play additional roles in suppression of recombination, chromosomal stability, metabolic regulation, meiosis, and aging. Considering the far-ranging nature of these functions, a major experimental goal has been to understand the molecular mechanism(s) by which this family of proteins acts. We report here that members of the SIR2 family catalyze an NAD–nicotinamide exchange reaction that requires the presence of acetylated lysines such as those found in the N termini of histones. Significantly, these enzymes also catalyze histone deacetylation in a reaction that absolutely requires NAD, thereby distinguishing them from previously characterized deacetylases. The enzymes are active on histone substrates that have been acetylated by both chromatin assembly-linked and transcription-related acetyltransferases. Contrary to a recent report, we find no evidence that these proteins ADP-ribosylate histones. Discovery of an intrinsic deacetylation activity for the conserved SIR2 family provides a mechanism for modifying histones and other proteins to regulate transcription and diverse biological processes.
The synaptic activity of HsDmc1, a human recombination protein specific to meiosis
Authors: Gupta R. C. , Golub E. , Bi B. , Radding C. M.
Published: July 2002

Human Dmc1 protein, a meiosis-specific homolog of
Escherichia coli
RecA protein, has previously been shown to promote DNA homologous pairing and strand-exchange reactions that are qualitatively similar to those of RecA protein and Rad51. Human and yeast Rad51 proteins each form a nucleoprotein filament that is very similar to the filament formed by RecA protein. However, recent studies failed to find a similar filament made by Dmc1 but showed instead that this protein forms octameric rings and stacks of rings. These observations stimulated further efforts to elucidate the mechanism by which Dmc1 promotes the recognition of homology. Dmc1, purified to a state in which nuclease and helicase activities were undetectable, promoted homologous pairing and strand exchange as measured by fluorescence resonance energy transfer (FRET). Observations on the intermediates and products, which can be distinguished by FRET assays, provided direct evidence of a three-stranded synaptic intermediate. The effects of helix stability and mismatched base pairs on the recognition of homology revealed further that human Dmc1, like human Rad51, requires the preferential breathing of A⋅T base pairs for recognition of homology. We conclude that Dmc1, like human Rad51 and
E. coli
RecA protein, promotes homologous pairing and strand exchange by a “synaptic pathway” involving a three-stranded nucleoprotein intermediate, rather than by a “helicase pathway” involving the separation and reannealing of DNA strands.
The identification of secreted carbonic anhydrase VI as a constitutive glycoprotein of human and rat milk
Authors: Karhumaa Pepe , Leinonen Jukka , Parkkila Seppo , Kaunisto Kari , Tapanainen Juha , Rajaniemi Hannu
Published: July 2002

In addition to essential nutrients, human milk contains
several classes of bioactive factors such as enzymes, hormones, and
growth factors, many of which are implicated in infantile growth and
development. Secretory carbonic anhydrase isoenzyme VI (CA VI) has been
identified earlier as an essential component of mammalian saliva, and
we demonstrate here by using biochemical and immunohistochemical
techniques that it is also an elementary component of milk. The 42-kDa
glycopolypeptide purified from human milk in CA inhibitor affinity
chromatography shared 100% homology with salivary CA VI in the protein
sequence analysis (40% coverage), and its digestion with PNGase F
resulted in a polypeptide backbone similar in size to salivary CA VI.
Quantification of CA VI in milk by using a time-resolved
immunofluorometric assay revealed an approximately eight-times-higher
concentration in human colostrum than in mature milk, the latter
corresponding to the levels previously detected in human saliva. The
high concentration in the colostrum, in particular its functional and
structural stability in an acidic milieu, and its growth-supporting
role in the taste buds suggest that milk CA VI is an essential factor
in normal growth and development of the infant alimentary tract.
Endogenous cannabinoids mediate long-term synaptic depression in the nucleus accumbens
Authors: Robbe David , Kopf Manfred , Remaury Anne , Bockaert Joel , Manzoni Olivier J.
Published: July 2002

Do endocannabinoids (eCBs) participate in long-term synaptic plasticity in the brain? Using pharmacological approaches and genetically altered mice, we show that stimulation of prelimbic cortex afferents at naturally occurring frequencies causes a long-term depression of nucleus accumbens glutamatergic synapses mediated by eCB release and presynaptic CB1 receptors. Translation of glutamate synaptic transmission into eCB retrograde signaling involved metabotropic glutamate receptors and postsynaptic intracellular Ca
2+
stores. These findings unveil the role of the eCB system in activity-dependent long-term synaptic plasticity and identify a mechanism by which marijuana can alter synaptic functions in the endogenous brain reward system.
Dynamic spike threshold reveals a mechanism for synaptic coincidence detection in cortical neurons
in vivo
Authors: Azouz Rony , Gray Charles M.
Published: July 2002

Cortical neurons are sensitive to the timing of their synaptic inputs. They can synchronize their firing on a millisecond time scale and follow rapid stimulus fluctuations with high temporal precision. These findings suggest that cortical neurons have an enhanced sensitivity to synchronous synaptic inputs that lead to rapid rates of depolarization. The voltage-gated currents underlying action potential generation may provide one mechanism to amplify rapid depolarizations. We have tested this hypothesis by analyzing the relations between membrane potential fluctuations and spike threshold in cat visual cortical neurons recorded intracellularly
in vivo
. We find that visual stimuli evoke broad variations in spike threshold that are caused in large part by an inverse relation between spike threshold and the rate of membrane depolarization preceding a spike. We also find that spike threshold is inversely related to the rate of rise of the action potential upstroke, suggesting that increases in spike threshold result from a decrease in the availability of Na
+
channels. By using a simple neuronal model, we show that voltage-gated Na
+
and K
+
conductances endow cortical neurons with an enhanced sensitivity to rapid depolarizations that arise from synchronous excitatory synaptic inputs. Thus, the basic mechanism responsible for action potential generation also enhances the sensitivity of cortical neurons to coincident synaptic inputs.
Dual control of LIF expression and LIF receptor function regulate Stat3 activation at the onset of uterine receptivity and embryo implantation
Authors: Cheng Jr-Gang , Chen Jim Ray , Hernandez Lidia , Alvord W. Greg , Stewart Colin L.
Published: July 2002

Leukemia inhibitory factor (LIF) expression in the uterus is essential for embryo implantation in mice. Here we describe the spatial and temporal regulation of LIF signalingin vivoby using tissues isolated from uteri on different days over the implantation period. During this time, LIF receptors are expressed predominantly in the luminal epithelium (LE) of the uterus. Isolated epithelium responds to LIF by phosphorylation and nuclear translocation of signal transducer and activator of transcription (Stat) 3, but not by an increase in mitogen-activated protein kinase levels. The related cytokines Il-6, ciliary neurotrophic factor, as well as epidermal growth factor, do not activate Stat3, although epidermal growth factor stimulates mitogen-activated protein kinase.In vivoStat3 activation is induced by LIF alone, resulting in the localization of Stat3 specifically to the nuclei of the LE coinciding with the onset of uterine receptivity. The responsiveness of the LE to LIF is regulated temporally, with Stat activation being restricted to day 4 of pregnancy despite the presence of constant levels of LIF receptor throughout the preimplantation period. Uterine receptivity is therefore under dual control and is regulated by both the onset of LIF expression in the endometrial glands and the release from inhibition of receptor function in the LE.
Ubiquitination and degradation of Syk and ZAP-70 protein tyrosine kinases in human NK cells upon CD16 engagement
Authors: Paolini Rossella , Molfetta Rosa , Piccoli Mario , Frati Luigi , Santoni Angela
Published: July 2002

Syk and ZAP-70 nonreceptor protein tyrosine kinases (PTKs) are essential elements in several cascades coupling immune receptors to intracellular responses. The critical role of these kinases in promoting the propagation of intracellular signaling requires a tight regulation of their activity, thus the existence of a negative feedback loop regulating their expression can be hypothesized. Herein, we have investigated whether ubiquitin-dependent proteolysis could be a mechanism responsible for controlling the fate of Syk and ZAP-70 after their immunoreceptor-induced activation. We found that both Syk and ZAP-70 become ubiquitinated in response to aggregation of the low affinity Fc receptor for IgG (CD16) on human natural killer cells. We confirmed the identity of the majorin vivoubiquitinated kinase species by performing anin vitroubiquitination assay. In addition, we found that after CD16 stimulation, ubiquitinated forms of Syk and ZAP-70 associate with the receptor complex. After CD16 engagement, we also observed a decrease in the stability of Syk and ZAP-70 PTKs that is counteracted by pretreatment with either proteasome or lysosomal inhibitors. Moreover, in the presence of the proteasome inhibitor, epoxomicin, we observed an accumulation of ubiquitinated forms of both kinases. Our findings provide evidence of ligand-induced ubiquitination of nonreceptor PTKs belonging to the Syk family and propose the ubiquitin-dependent proteasome-mediated degradation pathway as a mechanism for attenuating the propagation of intracellular signaling initiated by immune receptor engagement.
Inhibition of prostate carcinogenesis in TRAMP mice by oral infusion of green tea polyphenols
Authors: Gupta Sanjay , Hastak Kedar , Ahmad Nihal , Lewin Jonathan S. , Mukhtar Hasan
Published: July 2002

Development of effective chemopreventive agents against prostate cancer (CaP) for humans requires conclusive evidence of their efficacy in animal models that closely emulates human disease. The autochthonous
tr
ansgenic
a
denocarcinoma of the
m
ouse
p
rostate (TRAMP) model, which spontaneously develops metastatic CaP, is one such model that mimics progressive forms of human disease. Employing male TRAMP mice, we show that oral infusion of a polyphenolic fraction isolated from green tea (GTP) at a human achievable dose (equivalent to six cups of green tea per day) significantly inhibits CaP development and increases survival in these mice. In two separate experiments, the cumulative incidence of palpable tumors at 32 weeks of age in 20 untreated mice was 100% (20 of 20). In these mice, 95% (19 of 20), 65% (13 of 20), 40% (8 of 20), and 25% (5 of 20) of the animals exhibited distant site metastases to lymph nodes, lungs, liver, and bone, respectively. However, 0.1% GTP (wt/vol) provided as the sole source of drinking fluid to TRAMP mice from 8 to 32 weeks of age resulted in (
i
) significant delay in primary tumor incidence and tumor burden as assessed sequentially by MRI, (
ii
) significant decrease in prostate (64%) and genitourinary (GU) (72%) weight, (
iii
) significant inhibition in serum insulin-like growth factor-I and restoration of insulin-like growth factor binding protein-3 levels, and (
iv
) marked reduction in the protein expression of proliferating cell nuclear antigen (PCNA) in the prostate compared with water-fed TRAMP mice. The striking observation of this study was that GTP infusion resulted in almost complete inhibition of distant site metastases. Furthermore, GTP consumption caused significant apoptosis of CaP cells, which possibly resulted in reduced dissemination of cancer cells, thereby causing inhibition of prostate cancer development, progression, and metastasis of CaP to distant organ sites.
Modifications of cellulose synthase confer resistance to isoxaben and thiazolidinone herbicides in
Arabidopsis Ixr1
mutants
Authors: Scheible Wolf-Rüdiger , Eshed Ravit , Richmond Todd , Delmer Deborah , Somerville Chris
Published: July 2002

In many higher plants, cellulose synthesis is inhibited by isoxaben and thiazolidinone herbicides such as 5-tert-butyl-carbamoyloxy-3-(3-trifluromethyl) phenyl-4-thiazolidinone. Semidominant mutations at the
IXR1
and
IXR2
loci of
Arabidopsis
confer isoxaben and thiazolidinone resistance. Isolation of the
IXR1
gene by map-based cloning revealed that it encodes the
AtCESA3
isoform of cellulose synthase. The two known mutant alleles contain point mutations that replace glycine 998 with aspartic acid, and threonine 942 with isoleucine, respectively. The mutations occur in a highly conserved region of the enzyme near the carboxyl terminus that is well separated from the proposed active site. Although the
IXR1
gene is expressed in the same cells as the structurally related
RSW1
(
AtCESA1
) cellulose synthase gene, these two
CESA
genes are not functionally redundant.