bluuebunny/crossref_metadata_2025 huggingface dataset:
Lattice Boltzmann methods for modeling microscale flow in fibrous porous media
Authors: Spaid Michael A. A. , Phelan Frederick R.
Published: July 2002

A lattice Boltzmann description of fluid flow in heterogeneous porous media is presented which is intended for modeling flow processes which occur in liquid composite molding applications. The lattice Boltzmann method is equivalent to solving a hybrid method of the Stokes and Brinkman equations, with the Brinkman equation being implemented to model flow through porous structures, while the Stokes equation is applied to the open regions outside the porous structures. The Brinkman equation is recovered through a modification of the particle equilibrium distribution function, which reduces the magnitude of momentum at specified lattice sites, while leaving the direction of momentum unchanged. As a test of the new lattice Boltzmann model, steady transverse flow (saturated) through a square array of porous cylinders of elliptical cross section is investigated. Cell permeabilities obtained from the lattice Boltzmann simulations are in excellent agreement with a lubrication model, validating the lattice Boltzmann formulation of the Stokes and Brinkman equations.
Shock induced turbulence in composite materials at moderate Reynolds numbers
Authors: Kotelnikov Alexei D. , Montgomery David C.
Published: July 2002

Numerical simulation is used to study the turbulence generated by the passage of strong shocks (typical Mach number 7.3) through an inhomogeneous fluid at moderate Reynolds numbers. Before passage of the shock, the material consists of mass-density inhomogeneities embedded in a background fluid. The entire system is initially at uniform temperature, pressure, and number density, with the nonuniform mass density resulting from differing mass species in different regions. In the present application, the substances are treated as ideal gases, though in the motivating physical problems they are more complex materials. The shock retains its identity and a sharp front, but leaves behind it a turbulent state whose locally averaged properties only slowly become spatially uniform. The shock acquires a turbulent “thickness” (the linear dimension of the nonuniform region behind the shock front) that seems ultimately damped by viscous and thermally conducting properties that are dependent on transport coefficients and (highly uncertain) Reynolds numbers. Typically, the turbulence is highly compressible, with comparable mean divergences and curls in the velocity field, and fractional rms density fluctuations of the order of 0.25 in the parameter ranges studied. The rms vorticity generated can be estimated reasonably well from dimensional considerations. The effect of the high density inhomogeneities is primarily to create a wide region of compressible turbulence behind the shock. The inhomogeneities create both a succession of reflected shocks and considerable vorticity.
Lorentz self-forces on curved current loops
Authors: Garren David A. , Chen James
Published: July 2002

A derivation is presented for the Lorentz self-force arising from the interaction of a slender current loop of arbitrary shape with its own magnetic field. The self-force on any loop segment depends explicitly on the global shape of the remainder of the loop. Calculations of the self-force are presented for various model loops. For loops having small to moderate noncircularity, it is shown that the self-force on a segment with local major (R) and minor (a) radii is approximately that for an axisymmetric torus having uniform R and a. These properties of the self-force critically influence the equilibrium and dynamics of thin current loops in solar and astrophysical plasmas.
Wave propagation through cyclotron resonance in the presence of large Larmor radius particles
Authors: Cairns R. A. , Holt H. , McDonald D. C. , Taylor M. , Lashmore-Davies C. N.
Published: July 2002

Absorption of waves propagating across an inhomogenous magnetic field is of crucial importance for cyclotron resonance heating. When the Larmor radius of the resonant particles is small compared to the wavelength then the propagation is described by differential equations, a comparatively simple method for obtaining which has recently been given by Cairns et al. [Phys. Fluids B 3, 2953 (1991)]. In a fusion plasma there may, however, be a significant population of ions whose Larmor radius is not small compared to the wavelength. In this case the system is described by integro-differential equations, reflecting the fact that the plasma response at a given position is determined by the wave field over a region of width of the order of the Larmor radius. The simplified method referred to above is adapted to this case and used to obtain various forms of the equations. Methods of simplifying the equations while still retaining information from the non-local response, are discussed and some illustrated numerical results presented.
High-gain reverse guide field free electron lasers
Authors: Tsui K. H.
Published: July 2002

Electron beam trajectories under circularly polarized external wigglers in free electron laser devices with axial guide fields are reconsidered by introducing the self-fields of the electron beam. The competition between the self-fields and the wiggler field plus the action of the guide field are not only responsible for the known positive guide field singularity, but also the new reverse guide field singularity. The physics of the new reverse field singularity relies on the fact that an azimuthal magnetic field uniform in z is able to generate steady-state helical beam orbits just as if it were a transverse wiggler. According to this theory, the handness of the circularly polarized microwave should depend on the guide field configuration. High-gain strong pump equations coupled to these trajectories are used to account for the Massachusetts Institute of Technology reverse guide field results [Phys. Rev. Lett. 67, 3082 (1991)].
Beam-type instabilities of the sheath in a grazing magnetic field
Authors: Cohen Ronald H. , Ryutov Dmitri D.
Published: July 2002

A plasma sheath in a strongly tilted magnetic field is considered. It is shown that, if the incoming plasma flux contains two ion populations with clearly distinguishable energies (e.g., an admixture of cold ions to the main ion distribution), vigorous beam-type instabilities may be excited in the sheath. One should emphasize that these instabilities may be present even if the ion distribution function in the bulk of the plasma does not have beam structure.
A high-efficiency free-electron laser-peniotron hybrid with a longitudinal wiggler magnetic field
Authors: Gong Jianmin
Published: July 2002

Stimulated emission from the interaction of a cold, relativistic beam of electrons gyrating in a combined solenoidal and longitudinally polarized periodic wiggler magnetic field is considered as a source of high-efficiency and short-wavelength radiation. The analysis of electron motion in such a combined field shows the motion covers rich Fourier components. The first Fourier component, with the cyclotron frequency of ωc+kwv∥, has relatively large transverse velocity compared with the velocity of the motion. The study of the interaction of this Fourier component with the peniotron electromagnetic mode indicates that a high efficiency of 36% is obtained. Its working mechanism is explained and the influence of the wiggler field on the saturation efficiency is analyzed. The electron bunching in the transverse plane and the evolution of the efficiency with the interaction distance is given.
Stabilization of neoclassical tearing modes by electron cyclotron current drive
Authors: Zohm Hartmut
Published: July 2002

The generalized Rutherford equation for the neoclassical tearing mode is studied. New analytical expressions for the nonlinear stability criterion, the seed island width, and the saturated island width are derived. These are especially useful when the saturated island width is small. A formalism for calculating the current needed to stabilize the mode is established by adding an externally driven current. Inserting the reference parameters of the International Thermonuclear Experimental Reactor (ITER) [ITER-JCT and Home Teams, Plasma Phys. Controlled Fusion 37, A19 (1995)], a value of 160 kA to be driven by Electron Cyclotron Current Drive (ECCD) in order to completely stabilize an m=2 mode is found, well within the capabilities of the ITER ECCD system. If higher currents can be driven, the local βp at the resonant surface can be increased significantly.
Ponderomotive force in an anisotropic temperature plasma
Authors: Ghildyal V. , Kalra G. L.
Published: July 2002

The paper bridges the need for a theoretical formulation for the ponderomotive force, which is necessary for laboratory regimes where plasmas are thermally anisotropic. The calculations are based on a closed set of moment equations obtained from the Vlasov equation, under the assumption of negligible heat flow, for an arbitrary strength of the external magnetic field. The formulation also results in the inclusion of the finite Larmor radius effect, besides pointing out the limitations in the Chew, Goldberger, and Low [Proc. R. Soc. London, Ser. A 236, 112 (1956)] equations which have been frequently used to describe an anisotropic temperature plasma.
Quantum drift waves
Authors: Shokri B. , Rukhadze A. A.
Published: July 2002

The results of theoretical analysis of the oscillation spectrum of a plasma placed in a very strong quantizing magnetic field are presented. It is shown that in ultra-quantum limit, when all particles occupy the first Landau level, in an inhomogeneous quantized two-component plasma, volume quantum drift waves arise. These waves become unstable under some circumstances.
A normal mode theory of capacitive radio frequency discharges between parallel electrodes under diffusion and recombination gas-discharge regimes
Authors: Nonaka S. , Tsuge S.
Published: July 2002

A normal mode theory of standard capacitive rf discharges between parallel electrodes is achieved in terms of electron plasma wave resonances by solving electrostatic fluid equations under so-called linear-diffusion and nonlinear-recombination gas-discharge regimes for a wide gas-pressure range. The rf plasma is produced by the main resonance and also by another new and lowest resonance of the electron plasma wave. With a very thin plasma-thickness, the plasma is produced by this new lowest resonance. Even under an off-resonance condition, the plasma can be produced. Behavior of rf plasma under the recombination regime is quite different from that under the diffusion regime, for example, nonlinear low-density discharges and hysteresis phenomena of up-/down-jumping with gas pressure. Thresholds of applied rf voltage and gas pressure for maintaining the discharge are obtained within a first-order approximation.
Laser action in chromium-doped forsterite
Authors: Petričević V. , Gayen S. K. , Alfano R. R. , Yamagishi Kiyoshi , Anzai H. , Yamaguchi Y.
Published: July 2002

Room-temperature vibronic pulsed laser action in trivalent chromium-activated forsterite (Cr3+:Mg2SiO4) is reported for the first time. The free-running laser emission is centered at 1235 nm of the broad 4T2→4A2 fluorescence band, and has a bandwidth of ∼22 nm.
Measuring tubulin content in
Toxoplasma gondii
: A comparison of laser-scanning confocal and wide-field fluorescence microscopy
Authors: Swedlow Jason R. , Hu Ke , Andrews Paul D. , Roos David S. , Murray John M.
Published: July 2002

Toxoplasma gondii
is an intracellular parasite that proliferates within most nucleated cells, an important human pathogen, and a model for the study of human and veterinary parasitic infections. We used a stable yellow fluorescent protein-α-tubulin transgenic line to determine the structure of the microtubule cytoskeleton in
T. gondii
. Imaging of living yellow fluorescent protein-α-tubulin parasites by laser-scanning confocal microscopy (LSCM) failed to resolve the 22 subpellicular microtubules characteristic of the parasite cytoskeleton. To understand this result, we analyzed sources of noise in the LSCM and identified illumination fluctuations on time scales from microseconds to hours that introduce significant amounts of noise. We confirmed that weakly fluorescent structures could not be imaged in LSCM by using fluorescent bead standards. By contrast, wide-field microscopy (WFM) did visualize weak fluorescent standards and the individual microtubules of the parasite cytoskeleton. We therefore measured the fluorescence per unit length of microtubule by using WFM and used this information to estimate the tubulin content of the conoid (a structure important for
T. gondii
infection) and in the mitotic spindle pole. The conoid contains sufficient tubulin for ≈10 microtubule segments of 0.5-μm length, indicating that tubulin forms the structural core of the organelle. We also show that the
T. gondii
mitotic spindle contains ≈1 microtubule per chromosome. This analysis expands the understanding of structures used for invasion and intracellular proliferation by an important human pathogen and shows the advantage of WFM combined with image deconvolution over LSCM for quantitative studies of weakly fluorescent structures in moderately thin living cells.
Caenorhabditis elegans
DNA mismatch repair gene
msh-2
is required for microsatellite stability and maintenance of genome integrity
Authors: Degtyareva Natasha P. , Greenwell Patricia , Hofmann E. Randal , Hengartner Michael O. , Zhang Lijia , Culotti Joseph G. , Petes Thomas D.
Published: July 2002

Mismatch repair genes are important in maintaining the fidelity of DNA replication. To determine the function of the
Caenorhabditis elegans
homologue of the
MSH2
mismatch repair gene (
msh-2
), we isolated a strain of
C. elegans
with an insertion of the transposable element Tc1 within
msh-2
. Early-passage
msh-2
mutants were similar to wild-type worms with regard to lifespan and meiotic chromosome segregation but had slightly reduced fertility. The mutant worms had reduced DNA damage-induced germ-line apoptosis after genotoxic stress. The
msh-2
mutants also had elevated levels of microsatellite instability and increased rates of reversion of the dominant
unc-58
(
e665
) mutation. In addition, serially passaged cultures of
msh-2
worms died out much more quickly than those of wild-type worms. These results demonstrate that
msh-2
function in
C. elegans
is important in regulating both short- and long-term genomic stability.
Nerve growth factor control of neuronal expression of angiogenetic and vasoactive factors
Authors: Calzà Laura , Giardino Luciana , Giuliani Alessandro , Aloe Luigi , Levi-Montalcini Rita
Published: July 2002

In postnatal tissues, angiogenesis occurs in nontumoral conditions
on appropriate stimuli. In the nervous tissue, hypoxia, neural graft,
increased neural function, and synaptic activity are associated with
neoangiogenesis. We have investigated the occurrence of neoangiogenesis
in the superior cervical ganglia (scg) of newborn rats treated for
8–21 days with 6-hydroxy-dopamine (6-OHDA), nerve growth factor (NGF),
or 6-OHDA + NGF. The two latter treatments induced a significant
increase in scg size. However, the increase after combined treatment
far exceeded that of NGF alone. Similarly, histological and
histochemical analysis revealed neuronal hypertrophy and endothelial
cell hyperplasia associated with stromal hypertrophy (as described by
laminin immunostaining) and increased vascular bed (as revealed by
platelet/endothelial cell adhesion molecule-1 immunostaining) in
6-OHDA + NGF-treated pups. NGF, either alone or associated with 6-OHDA,
also induced a significant up-regulation of NADPH diaphorase, neuronal
nitric oxide synthase, and vascular endothelial growth factor
expression in scg neurons. The present investigation suggests that the
increase of scg size induced by NGF and 6-OHDA + NGF is associated with
neoangiogenesis, and that the induction of vasoactive and angiogenic
factors in neurons represents a further and previously undisclosed
effect of NGF.
Control of gating mode by a single amino acid residue in transmembrane segment IS3 of the N-type Ca
2+
channel
Authors: Zhong Huijun , Li Bin , Scheuer Todd , Catterall William A.
Published: July 2002

N-type Ca
2+
channels can be inhibited by
neurotransmitter-induced release of G protein βγ subunits. Two
isoforms of Ca
v
2.2 α1 subunits of N-type calcium channels
from rat brain (Ca
v
2.2a and Ca
v
2.2b; initially
termed rbB-I and rbB-II) have different functional properties.
Unmodulated Ca
v
2.2b channels are in an easily activated
“willing” (
W
) state with fast activation kinetics
and no prepulse facilitation. Activating G proteins shifts
Ca
v
2.2b channels to a difficult to activate
“reluctant” (
R
) state with slow activation
kinetics; they can be returned to the
W
state by strong
depolarization resulting in prepulse facilitation. This contrasts with
Ca
v
2.2a channels, which are tonically in the
R
state and exhibit strong prepulse facilitation.
Activating or inhibiting G proteins has no effect. Thus, the
R
state of Ca
v
2.2a and its reversal by
prepulse facilitation are intrinsic to the channel and independent of G
protein modulation. Mutating G177 in segment IS3 of Ca
v
2.2b
to E as in Ca
v
2.2a converts Ca
v
2.2b tonically
to the
R
state, insensitive to further G protein
modulation. The converse substitution in Ca
v
2.2a, E177G,
converts it to the
W
state and restores G protein
modulation. We propose that negatively charged E177 in IS3 interacts
with a positive charge in the IS4 voltage sensor when the channel is
closed and produces the
R
state of Ca
v
2.2a
by a voltage sensor-trapping mechanism. G protein βγ subunits may
produce reluctant channels by a similar molecular mechanism.
A screen for dominant mutations applied to components in the
Drosophila
EGF-R pathway
Authors: Guichard Annabel , Srinivasan Shaila , Zimm Georgianna , Bier Ethan
Published: July 2002

The
Drosophila
epidermal growth factor receptor (EGF-R) controls many critical cell fate choices throughout development. Several proteins collaborate to promote localized EGF-R activation, such as Star and Rhomboid (Rho), which act sequentially to ensure the maturation and processing of inactive membrane-bound EGF ligands. To gain insights into the mechanisms underlying Rho and Star function, we developed a mutagenesis scheme to isolate novel overexpression activity (NOVA) alleles. In the case of
rho
, we isolated a dominant neomorphic allele, which interferes with
Notch
signaling, as well as a dominant-negative allele, which produces RNA interference-like flip-back transcripts that reduce endogenous
rho
expression. We also obtained dominant-negative and neomorphic
Star
mutations, which have phenotypes similar to those of
rho
NOVA alleles, as well as dominant-negative
Egf-r
alleles. The isolation of dominant alleles in several different genes suggests that NOVA mutagenesis should be widely applicable and emerge as an effective tool for generating dominant mutations in genes of unknown function.
The cholesterol-regulated StarD4 gene encodes a StAR-related lipid transfer protein with two closely related homologues, StarD5 and StarD6
Authors: Soccio Raymond E. , Adams Rachel M. , Romanowski Michael J. , Sehayek Ephraim , Burley Stephen K. , Breslow Jan L.
Published: July 2002

Using cDNA microarrays, we identified StarD4 as a gene whose expression decreased more than 2-fold in the livers of mice fed a high-cholesterol diet. StarD4 expression in cultured 3T3 cells was also sterol-regulated, and known sterol regulatory element binding protein (SREBP)-target genes showed coordinate regulation. The closest homologues to StarD4 were two other StAR-related lipid transfer (START) proteins named StarD5 and StarD6. StarD4, StarD5, and StarD6 are 205- to 233-aa proteins consisting almost entirely of START domains. These three constitute a subfamily among START proteins, sharing ≈30% amino acid identity with one another, ≈20% identity with the cholesterol-binding START domains of StAR and MLN64, and less than 15% identity with phosphatidylcholine transfer protein (PCTP) and other START domains. StarD4 and StarD5 were expressed in most tissues, with highest levels in liver and kidney, whereas StarD6 was expressed exclusively in the testis. In contrast to StarD4, expression of StarD5 and MLN64 was not sterol-regulated. StarD4, StarD5, and StarD6 may be involved in the intracellular transport of sterols or other lipids.
Effect of nicotine on brain activation during performance of a working memory task
Authors: Ernst Monique , Matochik John A. , Heishman Stephen J. , Van Horn John D. , Jons Peter H. , Henningfield Jack E. , London Edythe D.
Published: July 2002

Nicotine influences cognition and behavior, but the
mechanisms by which these effects occur are unclear. By using positron
emission tomography, we measured cognitive activation (increases in
relative regional cerebral blood flow) during a working memory task
[2-back task (2BT)] in 11 abstinent smokers and 11 ex-smokers. Assays
were performed both after administration of placebo gum and 4-mg
nicotine gum. Performance on the 2BT did not differ between groups in
either condition, and the pattern of brain activation by the 2BT was
consistent with reports in the literature. However, in the placebo
condition, activation in ex-smokers predominated in the left
hemisphere, whereas in smokers, it occurred in the right hemisphere.
When nicotine was administered, activation was reduced in smokers but
enhanced in ex-smokers. The lateralization of activation as a function
of nicotine dependence suggests that chronic exposure to nicotine or
withdrawal from nicotine affects cognitive strategies used to perform
the memory task. Furthermore, the lack of enhancement of activation
after nicotine administration in smokers likely reflects tolerance.
Cells exposed to antifolates show increased cellular levels of proteins fused to dihydrofolate reductase: A method to modulate gene expression
Authors: Mayer-Kuckuk Philipp , Banerjee Debabrata , Malhotra Sundeep , Doubrovin Mikhail , Iwamoto Marian , Akhurst Tim , Balatoni Julius , Bornmann William , Finn Ronald , Larson Steven , Fong Yuman , Gelovani Tjuvajev Juri , Blasberg Ronald , Bertino Joseph R.
Published: July 2002

Human cells exposed to antifolates show a rapid increase in the levels of the enzyme dihydrofolate reductase (DHFR). We hypothesized that this adaptive response mechanism can be used to elevate cellular levels of proteins fused to DHFR. In this study, mouse cells transfected to express a green fluorescent protein-DHFR fusion protein and subsequently exposed to the antifolate trimetrexate (TMTX) showed a specific and time-dependent increase in cellular levels of the fusion protein. Next, human HCT-8 and HCT-116 colon cancer cells retrovirally transduced to express a DHFR-herpes simplex virus 1 thymidine kinase (HSV1 TK) fusion protein and treated with the DHFR inhibitor TMTX exhibited increased levels of the DHFR-HSV1 TK fusion protein and an increase in ganciclovir sensitivity by 250-fold. The level of fusion protein in antifolate-treated human tumor cells was increased in response to a 24-h exposure of methotrexate, trimetrexate, as well as dihydrofolate. This effect depended on the antifolate concentration and was independent of the fusion-protein mRNA levels, consistent with this increase occurring at a translational level. In a xenograft model, nude rats bearing DHFR-HSV1 TK-transduced HCT-8 tumors and treated with TMTX showed, after 24 h, a 2- to 4-fold increase of fusion-protein levels in tumor tissue from treated animals compared with controls, as determined by Western blotting. The fusion-protein increase was imaged with positron-emission tomography, where a substantially enhanced signal of the transduced tumor was detected in animals after antifolate administration. Drug-mediated elevation of cellular DHFR-fused proteins is a very useful method to modulate gene expression
in vivo
for imaging as well as therapeutic purposes.
Endogenous tumor necrosis factor protects the adult cardiac myocyte against ischemic-induced apoptosis in a murine model of acute myocardial infarction
Authors: Kurrelmeyer Karla M. , Michael Lloyd H. , Baumgarten Georg , Taffet George E. , Peschon Jacques J. , Sivasubramanian Natarajan , Entman Mark L. , Mann Douglas L.
Published: July 2002

Previous studies have shown that proinflammatory cytokines, such as tumor necrosis factor (TNF), are expressed after acute hemodynamic overloading and myocardial ischemia/infarction. To define the role of TNF in the setting of ischemia/infarction, we performed a series of acute coronary artery occlusions in mice lacking one or both TNF receptors. Left ventricular infarct size was assessed at 24 h after acute coronary occlusion by triphenyltetrazolium chloride (TTC) staining in wild-type (both TNF receptors present) and mice lacking either the type 1 (TNFR1), type 2 (TNFR2), or both TNF receptors (TNFR1/TNFR2). Left ventricular infarct size as assessed by TTC staining was significantly greater (P< 0.005) in the TNFR1/TNFR2-deficient mice (77.2% ± 15.3%) when compared with either wild-type mice (46.8% ± 19.4%) or TNFR1-deficient (47.9% ± 10.6%) or TNFR2-deficient (41.6% ± 16.5%) mice. Examination of the extent of necrosis in wild-type and TNFR1/TNFR2-deficient mice by anti-myosin Ab staining demonstrated no significant difference between groups; however, the peak frequency and extent of apoptosis were accelerated in the TNFR1/TNFR2-deficient mice when compared with the wild-type mice. The increase in apoptosis in the TNFR1/TNFR2-deficient mice did not appear to be secondary to a selective up-regulation of the Fas ligand/receptor system in these mice. These data suggest that TNF signaling gives rise to one or more cytoprotective signals that prevent and/or delay the development of cardiac myocyte apoptosis after acute ischemic injury.
Antioxidant-induced changes in oxidized DNA
Authors: Malins Donald C. , Hellström Karl Erik , Anderson Katie M. , Johnson Paul M. , Vinson Mark A.
Published: July 2002

N
-acetylcysteine (NAC), a strong antioxidant, has antigenotoxic and anticarcinogenic properties currently being investigated in clinical trials. NAC detoxifies free radicals (e.g., the hydroxyl radical, ·OH) that cause DNA changes implicated in disease (e.g., cancer). The ·OH reacts with purines to form mutagenic 8-hydroxypurine (8-OH) and putatively nonmutagenic formamidopyrimidine (Fapy) lesions. Fapy lesions inhibit DNA synthesis likely modulating the mutagenic potential of the 8-OH lesions, which would suggest that the ratio of these oxidized bases is biologically important. However, little is known about how NAC modifies oxidized DNA structure or how such modifications may affect cellular processes, such as replication and transcription. By using gas chromatography-mass spectrometry and Fourier transform-infrared spectroscopy, we found that dietary NAC (5% in the diet for 14 days) affected ·OH-induced structural changes in DNA of the hind leg of the BALB/c mouse. For example, mutagenic 8-hydroxyguanine (8-OH-Gua) was reduced ≈50% (
P
= 0.02) in mice fed NAC compared with controls. NAC reduced the log
10
(8-OH-Gua/FapyGua) ratio from 0.58 ± 0.15 to essentially zero, a virtually neutral redox status. DNA from control mice had a remarkably high variance compared with mice fed NAC. Moreover, the DNA from treated and control mice was distinct with respect to base structure and vertical base-stacking interactions. The findings showing that NAC lowered the concentration of 8-OH-Gua, the log ratio, and the variance (previously associated with neoplastic changes) suggest that NAC reduces the mutagenic potential of oxidized DNA. These benefits could be offset by the other structural changes found after NAC exposure, which may affect the fidelity of DNA synthesis.
The tomato ethylene receptors NR and LeETR4 are negative regulators of ethylene response and exhibit functional compensation within a multigene family
Authors: Tieman Denise M. , Taylor Mark G. , Ciardi Joseph A. , Klee Harry J.
Published: July 2002

The plant hormone ethylene is involved in many developmental processes, including fruit ripening, abscission, senescence, and leaf epinasty. Tomato contains a family of ethylene receptors, designated LeETR1, LeETR2, NR, LeETR4, and LeETR5, with homology to theArabidopsisETR1 ethylene receptor. Transgenic plants with reducedLeETR4gene expression display multiple symptoms of extreme ethylene sensitivity, including severe epinasty, enhanced flower senescence, and accelerated fruit ripening. Therefore, LeETR4 is a negative regulator of ethylene responses. Reduced expression of this single gene affects multiple developmental processes in tomato, whereas inArabidopsismultiple ethylene receptors must be inactivated to increase ethylene response. Transgenic lines with reducedNRmRNA levels exhibit normal ethylene sensitivity but elevated levels ofLeETR4mRNA, indicating a functional compensation ofLeETR4for reducedNRexpression. Overexpression ofNRin lines with loweredLeETR4gene expression eliminates the ethylene-sensitive phenotype, indicating that despite marked differences in structure these ethylene receptors are functionally redundant.
Selective binding of perfringolysin O derivative to cholesterol-rich membrane microdomains (rafts)
Authors: Waheed A. A. , Shimada Yukiko , Heijnen Harry F. G. , Nakamura Megumi , Inomata Mitsushi , Hayashi Masami , Iwashita Shintaro , Slot Jan W. , Ohno-Iwashita Yoshiko
Published: July 2002

There is increasing evidence that sphingolipid- and
cholesterol-rich microdomains (rafts) exist in the plasma membrane.
Specific proteins assemble in these membrane domains and play a role in
signal transduction and many other cellular events. Cholesterol
depletion causes disassembly of the raft-associated proteins,
suggesting an essential role of cholesterol in the structural
maintenance and function of rafts. However, no tool has been available
for the detection and monitoring of raft cholesterol in living cells.
Here we show that a protease-nicked and biotinylated derivative
(BCθ) of perfringolysin O (θ-toxin) binds selectively to
cholesterol-rich microdomains of intact cells, the domains that fulfill
the criteria of rafts. We fractionated the homogenates of nontreated
and Triton X-100-treated platelets after incubation with BCθ on a
sucrose gradient. BC
θ
was predominantly localized in
the floating low-density fractions (FLDF) where cholesterol,
sphingomyelin, and Src family kinases are enriched. Immunoelectron
microscopy demonstrated that BC
θ
binds to a
subpopulation of vesicles in FLDF. Depletion of 35% cholesterol from
platelets with cyclodextrin, which accompanied 76% reduction in
cholesterol from FLDF, almost completely abolished BCθ binding to
FLDF. The staining patterns of BCθ and filipin in human epidermoid
carcinoma A431 cells with and without cholesterol depletion suggest
that BCθ binds to specific membrane domains on the cell surface,
whereas filipin binding is indiscriminate to cell cholesterol.
Furthermore, BCθ binding does not cause any damage to cell membranes,
indicating that BCθ is a useful probe for the detection of membrane
rafts in living cells.
Deficits in memory and motor performance in synaptotagmin IV mutant mice
Authors: Ferguson Gregory D. , Anagnostaras Stephan G. , Silva Alcino J. , Herschman Harvey R.
Published: July 2002

Synaptotagmin (Syt) IV is a synaptic vesicle protein. Syt IV expression is induced in the rat hippocampus after systemic kainic acid treatment. To examine the functional role of this protein
in vivo
, we derived Syt IV null [Syt IV(−/−)] mutant mice. Studies with the rotorod revealed that the Syt IV mutants have impaired motor coordination, a result consistent with constitutive Syt IV expression in the cerebellum. Because Syt IV is thought to modulate synaptic function, we also have examined Syt IV mutant mice in learning and memory tests. Our studies show that the Syt IV mutation disrupts contextual fear conditioning, a learning task sensitive to hippocampal and amygdala lesions. In contrast, cued fear conditioning is normal in the Syt IV mutants, suggesting that this mutation did not disrupt amygdala function. Conditioned taste aversion, which also depends on the amygdala, is normal in the Syt IV mutants. Consistent with the idea that the Syt IV mutation preferentially affects hippocampal function, Syt IV mutant mice also display impaired social transmission of food preference. These studies demonstrate that Syt IV is critical for brain function and suggest that the Syt IV mutation affects hippocampal-dependent learning and memory, as well as motor coordination.
Femtosecond linear dichroism of DNA-intercalating chromophores: Solvation and charge separation dynamics of [Ru(phen)2dppz]2+systems
Authors: Önfelt Björn , Lincoln Per , Nordén Bengt , Baskin J. Spencer , Zewail Ahmed H.
Published: July 2002

The DNA-intercalating chromophore [Ru(phen)2dppz]2+has unique photophysical properties, the most striking of which is the “light-switch” characteristic when binding to DNA. As a dimer, it acts as a molecular staple for DNA, exhibiting a remarkable double-intercalating topology. Herein, we report femtosecond dynamics of the monomeric and the covalently linked dimeric chromophores, both free in aqueous solution and complexed with DNA. Transient absorption and linear dichroism show the electronic relaxation to the lowest metal-to-ligand charge-transfer (CT) state, and subpicosecond kinetics have been observed for this chromophore for what is, to our knowledge, the first time. We observe two distinct relaxation processes in aqueous solution with time constants of 700 fs and 4 ps. Interestingly, these two time constants are very similar to those observed for the reorientational modes of bulk water. The 700-fs process involves a major dichroism change. We relate these observations to the change in charge distribution and to the time scales involved in solvation of the CT state. Slower processes, with lifetimes of ≈7 and 37 ps, were observed for both monomer and dimer when bound to DNA. Such a difference can be ascribed to the change of the structural and electronic relaxation experienced in the DNA intercalation pocket. Finally, the recombination lifetime of the final metal-to-ligand CT state to the ground state, which is a key in the light-switch process, is found in aqueous solution to be sensitive to structural modification, ranging from 260 ps for [Ru(phen)2dppz]2+and 360 ps for the monomer chromophore derivative to 2.0 ns for the dimer. This large change reflects the direct role of solvation in the light-switch process.
Fluid shear stress inhibits TNF-α activation of JNK but not ERK1/2 or p38 in human umbilical vein endothelial cells: Inhibitory crosstalk among MAPK family members
Authors: Surapisitchat James , Hoefen Ryan J. , Pi Xinchun , Yoshizumi Masanori , Yan Chen , Berk Bradford C.
Published: July 2002

Atherosclerosis preferentially occurs in areas of turbulent flow and low fluid shear stress, whereas laminar flow and high shear stress are atheroprotective. Inflammatory cytokines, such as tumor necrosis factor-α (TNF-α) and IL-1 stimulate expression of endothelial cell (EC) genes that may promote atherosclerosis. TNF-α and IL-1 regulate gene expression in ECs, in part, by stimulating mitogen-activated protein kinases (MAPK), which phosphorylate transcription factors. We hypothesized that steady laminar flow inhibits cytokine-mediated activation of MAPK in EC. To test this hypothesis, we determined the effects of flow (shear stress = 12 dynes/cm2) on TNF-α and IL-1-stimulated activity of three MAPK in human umbilical vein ECs (HUVEC): extracellular signal-regulated kinase (ERK1/2), p38, and c-Jun N-terminal kinase (JNK). Flow alone stimulated ERK1/2 and p38 activity but decreased JNK activity compared with static controls. TNF-α or IL-1 alone activated ERK1/2, p38, and JNK maximally at 15 min in HUVEC. Preexposing HUVEC for 10 min to flow inhibited TNF-α and IL-1 activation of JNK by 46% and 49%, respectively, but had no significant effect on ERK1/2 or p38 activation. Incubation of HUVEC with PD98059, which inhibits flow-mediated ERK1/2 activation, prevented flow from inhibiting cytokine activation of JNK. Phorbol 12-myristate 13-acetate, which strongly activates ERK1/2, also inhibited TNF-α activation of JNK. These findings indicate that fluid shear stress inhibits TNF-α-mediated signaling events in HUVEC via the activation of the ERK1/2 signaling pathway. Inhibition of TNF-α signal transduction represents a mechanism by which steady laminar flow may exert atheroprotective effects on the endothelium.
Cerebellar role in fear-conditioning consolidation
Authors: Sacchetti Benedetto , Baldi Elisabetta , Lorenzini Carlo Ambrogi , Bucherelli Corrado
Published: July 2002

Some cerebellar structures are known to be involved in the memorization of several conditioned responses. The role of the interpositus nucleus (IN) and the vermis (VE) in fear-conditioning consolidation was investigated by means of a combined behavioral and neurophysiological technique. The IN and VE were subjected to fully reversible tetrodotoxin (TTX) inactivation during consolidation in adult male Wistar rats that underwent acoustic conditioned stimulus (CS) and context fear training. TTX was injected in different groups of rats at increasing intervals after the acquisition session. Memory was assessed as conditioned freezing duration measured during retention testing, always performed 72 and 96 h after the stereotaxic TTX administration. This schedule ensures that there is no interference with normal cerebellar function during either the acquisition or the retrieval phase so that any amnesic effect may be due only to consolidation disruption. Our results show that IN functional integrity is necessary for acoustic CS fear response memory formation up to the 96-h after-acquisition delay. VE functional integrity was shown to be necessary for memory formation of both context (up to the 96-h after-acquisition delay) and acoustic CS (up to the 192-h after-acquisition delay) fear responses. The present findings help to elucidate the role of the cerebellum in memory consolidation and better define the neural circuits involved in fear memories.
Interlocked feedback loops contribute to the robustness of the
Neurospora
circadian clock
Authors: Cheng Ping , Yang Yuhong , Liu Yi
Published: July 2002

Interlocked feedback loops may represent a common feature among the regulatory systems controlling circadian rhythms. The
Neurospora
circadian feedback loops involve
white collar-1
(
wc-1
),
wc-2
, and
frequency
(
frq
) genes. We show that WC-1 and WC-2 proteins activate the transcription of
frq
gene, whereas FRQ protein plays dual roles: repressing its own transcription, probably by interacting with the WC-1/WC-2 complex, and activating the expression of both WC proteins. Thus, they form two interlocked feedback loops: one negative and one positive. We establish the physiological significance of the interlocked positive feedback loops by showing that the levels of WC-1 and WC-2 determine the robustness and stability of the clock. Our data demonstrate that with WC-1 being the limiting factor in the WC-1/WC-2 complex, the greater the levels of WC-1 and WC-2, the higher the level of the FRQ oscillation and the more robust the overt rhythms. Our data also show that, despite considerable changes in the levels of WC-1, WC-2, and FRQ, the period of the clock has been limited to a small range, suggesting that the interlocked circadian feedback loops are also important for determining the circadian period length of the clock.
A new form of cerebellar long-term potentiation is postsynaptic and depends on nitric oxide but not cAMP
Authors: Lev-Ram Varda , Wong Scott T. , Storm Daniel R. , Tsien Roger Y.
Published: July 2002

Long-term depression (LTD) at cerebellar parallel fiber (PF)-Purkinje cell synapses must be balanced by long-term potentiation (LTP) to prevent saturation and allow reversal of motor learning. The only previously analyzed form of cerebellar LTP is induced by 4–8 Hz PF stimulation and requires cAMP but not nitric oxide. It is a poor candidate to reverse LTD because it is presynaptically expressed whereas LTD is postsynaptic. We now characterize a new form of LTP induced by 1 Hz PF stimulation for at least 300 s. This LTP is postsynaptically expressed, enhanced by chelating postsynaptic Ca
2+
, and depends on nitric oxide but not cAMP or cGMP, making it a plausible anti-Hebbian counterpart to Hebbian LTD.
Tuning the membrane surface potential for efficient toxin import
Authors: Zakharov Stanislav D. , Rokitskaya Tatyana I. , Shapovalov Vladimir L. , Antonenko Yuri N. , Cramer William A.
Published: July 2002

Membrane surface electrostatic interactions impose structural constraints on imported proteins. An unprecedented sensitive dependence on these constraints was seen in the voltage-gated import and channel formation by the C-terminal pore-forming domain of the bacteriocin, colicin E1. At physiological ionic strengths, significant channel current was observed only in a narrow interval of anionic lipid content ([L
−
]), with the maximum current (
I
max
) at 25–30 mol% (dioleoyl)-phosphatidylglycerol ([L
−
]
max
) corresponding to a surface potential of the lipid bilayer in the absence of protein, ψ

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= −60 ± 5 mV. Higher ionic strength shifted [L
−
]
max
to larger values, but ψ

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remained approximately constant. It is proposed that the channel current (
i
) increases and (
ii
) decreases at |ψ
o
| values <55 mV and >65 mV, because of (
i
) electrostatic interactions needed for effective insertion of the channel polypeptide and (
ii
) constraints due to electrostatic forces on the flexibility needed for cooperative insertion into the membrane. The loss of flexibility for |ψ
o
| ≫ 65 mV was demonstrated by the absence of thermally induced intraprotein distance changes of the bound polypeptide. The anionic lipid content, 25–30 mol%, corresponding to the channel current maxima, is similar to that of the target
Escherichia coli
cytoplasmic membrane and membranes of mesophilic microorganisms. This suggests that one reason the membrane surface potential is tuned
in vivo
is to facilitate protein import.
Dissociating the role of the medial and lateral anterior prefrontal cortex in human planning
Authors: Koechlin Etienne , Corrado Gregory , Pietrini Pietro , Grafman Jordan
Published: July 2002

The anterior prefrontal cortex is known to subserve higher cognitive functions such as task management and planning. Less is known, however, about the functional specialization of this cortical region in humans. Using functional MRI, we report a double dissociation: the medial anterior prefrontal cortex, in association with the ventral striatum, was engaged preferentially when subjects executed tasks in sequences that were expected, whereas the polar prefrontal cortex, in association with the dorsolateral striatum, was involved preferentially when subjects performed tasks in sequences that were contingent on unpredictable events. These results parallel the functional segregation previously described between the medial and lateral premotor cortex underlying planned and contingent motor control and extend this division to the anterior prefrontal cortex, when task management and planning are required. Thus, our findings support the assumption that common frontal organizational principles underlie motor and higher executive functions in humans.
Light-induced phase-delay of the chicken pineal circadian clock is associated with the induction of
cE4bp4
, a potential transcriptional repressor of
cPer2
gene
Authors: Doi Masao , Nakajima Yoshito , Okano Toshiyuki , Fukada Yoshitaka
Published: July 2002

The chicken pineal gland contains the autonomous circadian oscillator together with the photic-input pathway. We searched for chicken pineal genes that are induced by light in a time-of-day-dependent manner, and isolated chicken homolog of bZIP transcription factor
E4bp4
(
cE4bp4
) showing high similarity to
vrille
, one of the
Drosophila
clock genes.
cE4bp4
was expressed rhythmically in the pineal gland with a peak at very early (subjective) night under both 12-h light/12-h dark cycle and constant dark conditions, and the phase was nearly opposite to the expression rhythm of
cPer2
, a chicken pineal clock gene. Luciferase reporter gene assays showed that cE4BP4 represses
cPer2
promoter through a E4BP4-recognition sequence present in the 5′-flanking region, indicating that cE4BP4 can down-regulate the chick pineal
cPer2
expression.
In vivo
light-perturbation studies showed that the prolongation of the light period to early subjective night maintained the high level expression of the pineal
cE4bp4
, and presumably as a consequence delayed the onset of the induction of the pineal
cPer2
expression in the next morning. These light-dependent changes in the mRNA levels of the pineal
cE4bp4
and
cPer2
were followed by a phase-delay of the subsequent cycles of
cE4bp4
/
cPer2
expression, suggesting that cE4BP4 plays an important role in the phase-delaying process as a light-dependent suppressor of
cPer2
gene.
DNA replication meets genetic exchange: Chromosomal damage and its repair by homologous recombination
Authors: Kuzminov Andrei
Published: July 2002

Proceedings of the National Academy of Sciences Colloquium on the roles of homologous recombination in DNA replication are summarized. Current findings in experimental systems ranging from bacteriophages to mammalian cell lines substantiate the idea that homologous recombination is a system supporting DNA replication when either the template DNA is damaged or the replication machinery malfunctions. There are several lines of supporting evidence: (
i
) DNA replication aggravates preexisting DNA damage, which then blocks subsequent replication; (
ii
) replication forks abandoned by malfunctioning replisomes become prone to breakage; (
iii
) mutants with malfunctioning replisomes or with elevated levels of DNA damage depend on homologous recombination; and (
iv
) homologous recombination primes DNA replication
in vivo
and can restore replication fork structures
in vitro
. The mechanisms of recombinational repair in bacteriophage T4,
Escherichia coli
, and
Saccharomyces cerevisiae
are compared.
In vitro
properties of the eukaryotic recombinases suggest a bigger role for single-strand annealing in the eukaryotic recombinational repair.