bluuebunny/crossref_metadata_2025 huggingface dataset:
Ion heating and magnetohydrodynamic dynamo fluctuations in the reversed-field pinch
Authors: Scime Earl , Cekic Miodrag , Den Hartog D. J. , Hokin Samuel , Holly D. J. , Watts Christopher
Published: July 2002

Ion temperatures have been measured in the Madison Symmetric Torus (MST) [Dexter et al., Fusion Technol. 19, 131 (1991)] reversed-field pinch (RFP) with a five channel charge exchange analyzer. The characteristic anomalously high ion temperature of RFP discharges has been observed in the MST. The ion heating expected from ion–electron collisions is calculated and shown to be too small to explain the measured ion temperatures. The charge exchange determined ion temperature is also compared to measurements of the thermally broadened Cv 227.1 nm line. The ion temperature, Ti≊250 eV for I=360 kA, increases by more than 100% during discrete dynamo bursts in MST discharges. Magnetic field fluctuations in the range 0.5–5 MHz were also measured during the dynamo bursts. Structure in the fluctuation frequency spectrum at the ion cyclotron frequency suggests that the mechanism of ion heating involves the dissipation of dynamo fluctuations at ion cyclotron frequencies.
Asymmetric vortex merger in two dimensions: Which vortex is ‘‘victorious’’?
Authors: Melander M. V. , Zabusky N. J. , McWilliams J. C.
Published: July 2002

Merger of two like-signed vorticity monopoles is the chief mechanism for the emergence and growth of vortices in 2-D turbulent flows. The merger processes in turbulent flows generally involve vortices of different size and vorticity amplitude. This normally causes one of the vortices to dominate. Results of a numerical survey are presented that determine which vortex is dominant or ‘‘victorious.’’ These results are obtained through the complementary use of a low-order Hamiltonian moment model and a high-resolution pseudospectral algorithm.
A connection between the Camassa–Holm equations and turbulent flows in channels and pipes
Authors: Chen S. , Foias C. , Holm D. D. , Olson E. , Titi E. S. , Wynne S.
Published: July 2002

In this paper we discuss recent progress in using the Camassa–Holm equations to model turbulent flows. The Camassa–Holm equations, given their special geometric and physical properties, appear particularly well suited for studying turbulent flows. We identify the steady solution of the Camassa–Holm equation with the mean flow of the Reynolds equation and compare the results with empirical data for turbulent flows in channels and pipes. The data suggest that the constant α version of the Camassa–Holm equations, derived under the assumptions that the fluctuation statistics are isotropic and homogeneous, holds to order α distance from the boundaries. Near a boundary, these assumptions are no longer valid and the length scale α is seen to depend on the distance to the nearest wall. Thus, a turbulent flow is divided into two regions: the constant α region away from boundaries, and the near wall region. In the near wall region, Reynolds number scaling conditions imply that α decreases as Reynolds number increases. Away from boundaries, these scaling conditions imply α is independent of Reynolds number. Given the agreement with empirical and numerical data, our current work indicates that the Camassa–Holm equations provide a promising theoretical framework from which to understand some turbulent flows.
Direct numerical simulations of three-dimensional bubbly flows
Authors: Bunner Bernard , Tryggvason Grétar
Published: July 2002

Direct numerical simulations of the motion of many buoyant bubbles are presented. The Navier–Stokes equation is solved by a front tracking/finite difference method that allows a fully deformable interface. The evolution of 91 nearly spherical bubbles at a void fraction of 6% is followed as the bubbles rise over 100 bubble diameters. While the individual bubble velocities fluctuate, the average motion reaches a statistical steady state with a rise Reynolds number of about 25.
Application of the separatrix map to study perturbed magnetic field lines near the separatrix
Authors: Abdullaev S. S. , Zaslavsky G. M.
Published: July 2002

In this paper a generalized separatrix map to study perturbed magnetic field lines in a confined magnetic system with the separatrix is discussed. The separatrix map is an iteration transform for the magnetic flux and a toroidal angle at a certain cross section after one period of the unperturbed trajectory. The map can be derived from magnetic field line equations and can be shifted along the toroidal angle, depending on the point of interest. Different asymptotic forms of the shifted separatrix map, with respect to the distance between the cross section of the toroidal angle and the X point, are considered, and their invariant properties are discussed in regard to the renormalization transformation of the perturbation amplitude. A method to find the map’s parameters for any specific magnetic system is proposed. It is shown that the shifted separatrix map can be directly applied to obtain magnetic footprints at the divertor plates, and to study chaotic scattering of field lines.
Dynamic screening effects on antiscreening excitations for ion–ion collisions in dense plasma
Authors: Yoon Jung-Sik , Jung Young-Dae
Published: July 2002

In dense plasmas, dynamic plasma screening effects are investigated on antiscreening channels for excitation of a one-electron ion target by a one-electron ion projectile. The ion–ion interaction potential is considered by the introduction of the longitudinal plasma dielectric function. A semiclassical straight-line trajectory method is applied to the ion projectile path in order to visualize the dynamic plasma screening effects on the transition probabilities in dense plasmas as a function of the impact parameter and the collision energy. The transition probabilities including the dynamic plasma screening effects are found to always be greater than those including the static plasma screening effects. When the projectile velocity is greater than the electron thermal velocity, the interaction potential is almost unshielded. The difference between the dynamic and static plasma screening effects is more significant for low-energy projectiles. It is also found that the quadrupole transitions (dipole-quadrupole and quadrupole–quadrupole) show the double peaks due to the node of the 2s radial wave function.
Dynamic plasma screening effects on semiclassical electron captures from hydrogenic ions by protons in weakly coupled plasmas
Authors: Kim Chang-Geun , Jung Young-Dae
Published: July 2002

Electron capture processes by protons from hydrogenic ions in dense plasmas, including dynamic screening effects, are investigated using the semiclassical version of the Bohr and Lindhard model with the straight-line trajectory method. The dynamic interaction potential and screened electron radius are obtained by considering the longitudinal component of the plasma dielectric function. The scaled semiclassical electron capture probability is obtained as a function of the impact parameter, Debye length, and projectile velocity. The plasma screening effects on the target system is known to be quite small, so that the plasma screening effects on the capture probability is mainly determined by the screened capture radius. The dynamic screening effect on the scaled semiclassical capture probability is found to be more significant for low projectile velocities. When the projectile velocity is smaller than the electron thermal velocity, the dynamic screening effect is weaker than the static screening effect. However, when the projectile velocity is greater than the electron thermal velocity, the dynamic screening effect leads to the static screening effect. The maximum position of the scaled capture probability approaches to the target nucleus as an increase of the projectile energy.
Observation of shock wave elimination by a plasma in a Mach-2.5 flow
Authors: Kuo S. P. , Kalkhoran Iraj M. , Bivolaru Daniel , Orlick Lester
Published: July 2002

An experimental study on the influence of a plasma on the structure of an attached conical shock front appearing at the front end of a missile-shaped model has been carried out in a Mach-2.5 flow. The tip and the body of the model are designed as the cathode and anode for gaseous discharge, which produces a spraylike plasma moving around the tip. It is observed that the plasma has caused the shock front to separate from the model. The shock wave moves upstream in the form of a detached bow shock a sensible distance away from the model tip. The detached shock front appears to be highly dispersed in its new location as seen in the shadow video graphs of the flow. As the discharge current increases, experimental evidence shown in the video further reveals a distinct state of the flow without the presence of any shock wave.
Dust acoustic waves in thin dusty layers
Authors: Stenflo L. , Shukla P. K.
Published: July 2002

The propagation of dust acoustic waves (DAWs) in a lattice of thin dusty plasma layers is investigated. A new dispersion relation for the DAWs is found.
Growth of rare-earth single crystals by molecular beam epitaxy: The epitaxial relationship between hcp rare earth and bcc niobium
Authors: Kwo J. , Hong M. , Nakahara S.
Published: July 2002

High-quality rare-earth (RE) single-crystal films of yttrium (Y) and gadolinium (Gd) were successfully grown with the metal molecular beam epitaxy technique on a bcc Nb single-crystal film which serves as a buffer layer to the sapphire substrates. With reflection high-energy electron diffraction, the hcp RE (0001) was found to grow epitaxially on the (110) Nb in the Nishiyama–Wasserman orientation. The regrowth of Nb on this RE (0001) surface yielded the (110) orientation with 120° in-plane domains. These epitaxial relationships suggest the possibility of fabricating an ultrathin, coherent crystalline superlattice in the Nb (110)/ RE (0001) system.
Preparation of Y-Ba-Cu-O thin films on MgO by dc magnetron sputtering from a stoichiometric Y1Ba2Cu3O7−δ target
Authors: Lee S. J. , Rippert E. D. , Jin B. Y. , Song S. N. , Hwu S. J. , Poeppelmeier K. , Ketterson J. B.
Published: July 2002

Y-Ba-Cu-O thin films have been deposited on MgO substrates by dc magnetron sputtering from a stoichiometric YBa2Cu3O7−δ target, after which they are subjected to a short heat treatment. Zero resistance is routinely achieved near 60 K, and one film shows zero resistance at 68.0 K.
Enhanced Cu-Teflon adhesion by presputtering treatment: Effect of surface morphology changes
Authors: Chang Chin-An
Published: July 2002

The recently observed enhancement in adhesion between Cu and Teflon due to a presputtering treatment of Teflon prior to the Cu deposition is analyzed. The sputtering treatment resulted in a morphology change of the Teflon, with the deposited Cu showing similar textures, and changes in chemical bondings between the two. A simple geometric model is used to analyze the contribution from the morphology changes to the observed peel strength. It is shown that, for a finite chemical bonding, an appreciable contribution to the peel strength is possible from the morphology changes observed.
Versatile new metalorganic process for preparing superconducting thin films
Authors: Gross M. E. , Hong M. , Liou S. H. , Gallagher P. K. , Kwo J.
Published: July 2002

A new technique for producing thin films of the high-temperature perovskite superconductors, LnBa2Cu3O7−x, where Ln represents a rare-earth element, using spin-on metalorganic precursors is described. Pyrolysis of the spin-coated films, consisting of mixed metal (2-ethyl hexanoates), leads to black films up to several microns thick whose degree of orientation is a function of the processing temperature and duration. Representative films of YBa2Cu3O7−x on MgO begin to exhibit orientation with the c axis perpendicular to the film plane at heat treatments above 900 °C. The superconducting behavior of a highly oriented film produced at 990 °C is characterized by Tc(onset)=89 K, Tc(R=0)=77 K, and Jc=103 A cm−2 at 65 K.
Picosecond reflection high-energy electron diffraction
Authors: Elsayed-Ali H. E. , Mourou G. A.
Published: July 2002

Reflection high-energy electron diffraction with picosecond time resolution is demonstrated. The surface diffraction patterns are obtained using a laser driven picosecond electron gun. Due to the synchronization of the photogenerated electron pulses with the laser source, such a technique provides a picosecond time-resolved surface structural probe sensitive to the first few monolayers.
Low-temperature preparation of high T
c superconducting thin films
Authors: Wu X. D. , Inam A. , Venkatesan T. , Chang C. C. , Chase E. W. , Barboux P. , Tarascon J. M. , Wilkens B.
Published: July 2002

Thin superconducting films of Y-Ba-Cu-O were prepared at 650 °C using the pulsed laser deposition technique. The as-deposited films were fully superconducting at low temperature (30 K). After annealing in oxygen at 450 °C for 3 h, the films exhibited superconductivity with zero resistance at temperatures as high as 83 K. Film-substrate interface reaction was minimal as revealed by Rutherford backscattering and Auger electron spectrometry. These films processed at such low temperatures are also found to have excellent planar surface morphology and high critical current density.
Neuropeptide Y (NPY) potentiates phenylephrine-induced mitogen-activated protein kinase activation in primary cardiomyocytes via NPY Y5 receptors
Authors: Pellieux Corinne , Sauthier Thérèse , Domenighetti Andrea , Marsh Donald J. , Palmiter Richard D. , Brunner Hans-R. , Pedrazzini Thierry
Published: July 2002

Neuropeptide Y (NPY) has been shown to participate in the cardiovascular response mediated by the sympathetic system. In this report, we investigate the growth factor properties of NPY on cardiac myocytes. Mitogen-activated protein kinases (MAPK) are key signaling molecules in the transduction of trophic signals. Therefore, the role of NPY in inducing MAPK activation was studied in mouse neonatal cardiomyocytes. Exposure of neonatal cardiomyocytes to either NPY, phenylephrine, or angiotensin II induces a rapid phosphorylation of the extracellular responsive kinase, the c-jun N-terminal kinase, and the p38 kinase as well as an activation of protein kinase C (PKC). Moreover, NPY potentiates phenylephrine-induced MAPK and PKC stimulation. In contrast, NPY has no synergistic effect on angiotensin II-stimulated MAPK phosphorylation or PKC activity. NPY effects are pertussis toxin-sensitive and calcium-independent and are mediated by NPY Y5 receptors. Taken together, these results suggest that NPY, via G
i
protein-coupled NPY Y5 receptors, could participate in the development of cardiac hypertrophy during chronic sympathetic stimulation by potentiating α-adrenergic signals.
Oral administration of a dual analog of two myasthenogenic T cell epitopes down-regulates experimental autoimmune myasthenia gravis in mice
Authors: Paas-Rozner Miri , Dayan Molly , Paas Yoav , Changeux Jean-Pierre , Wirguin Itzhak , Sela Michael , Mozes Edna
Published: July 2002

Myasthenia gravis (MG) and experimental autoimmune MG (EAMG) are T cell-regulated, antibody-mediated autoimmune diseases. The major autoantigen in MG is the nicotinic acetylcholine receptor (AChR). Two peptides, representing sequences of the human AChR α-subunit, p195–212 and p259–271, were previously shown to be immunodominant T cell epitopes in MG patients as well as, respectively, in SJL and BALB/c mice. A dual analog (termed Lys-262–Ala-207) composed of the tandemly arranged two single amino acid analogs of p195–212 and p259–271 was shown to inhibit,in vitroandin vivo, MG-associated autoimmune responses. Furthermore, the dual analog could down-regulate myasthenogenic manifestations in mice with EAMG that was induced by inoculation of a pathogenic T cell line. In the present study, the ability of the dual analog to treat EAMG induced in susceptible C57BL/6 mice by nativeTorpedoAChR was evaluated. Mice that were diagnosed to have clinical symptoms of EAMG were treated with the dual analog by oral administration, 500 μg per mouse three times a week for 5–8 weeks. Treatment with the dual analog down-regulated the clinical manifestations of the ongoing disease as assessed by the clinical score, grip strength (measured by a grip strength meter), and electromyography. The effects on the clinical EAMG correlated with a reduced production of anti-AChR antibody as well as a decrease in the secretion of interleukin-2 and, more dramatically, interferon-γ, in response to AChR triggering. Thus, the dual analog is an efficient immunomodulator of EAMG in mice and might be of specific therapeutic potential for MG.
Effects of nitric oxide-releasing aspirin versus aspirin on restenosis in hypercholesterolemic mice
Authors: Napoli Claudio , Cirino Giuseppe , Del Soldato Piero , Sorrentino Raffaella , Sica Vincenzo , Condorelli Mario , Pinto Aldo , Ignarro Louis J.
Published: July 2002

Restenosis is due to neointimal hyperplasia, which occurs in the
coronary artery after percutaneous transluminal coronary angioplasty
(PTCA). During restenosis, an impairment of nitric oxide (NO)-dependent
pathways may occur. Concomitant hypercholesterolemia may exacerbate
restenosis in patients undergoing PTCA. Here, we show that a
NO-releasing aspirin derivative (NCX-4016) reduces the degree of
restenosis after balloon angioplasty in low-density lipoprotein
receptor-deficient mice and this effect is associated with reduced
vascular smooth muscle cell (VSMC) proliferation and macrophage
deposition at the site of injury. Drugs were administered following
both therapeutic or preventive protocols. We demonstrate that NCX-4016
is effective both in prevention and treatment of restenosis in the
presence of hypercholesterolemia. These data indicate that impairment
of NO-dependent mechanisms may be involved in the development of
restenosis in hypercholesterolemic mice. Although experimental models
of restenosis may not reflect restenosis in humans in all details, we
suggest that a NO-releasing aspirin derivative could be an
effective drug in reducing restenosis following PTCA, especially
in the presence of hypercholesterolemia and/or gastrointestinal
damage.
Allosteric modulation of Ca
2+
channels by G proteins, voltage-dependent facilitation, protein kinase C, and Ca
v
β subunits
Authors: Herlitze Stefan , Zhong Huijun , Scheuer Todd , Catterall William A.
Published: July 2002

N-type and P/Q-type Ca
2+
channels are inhibited by
neurotransmitters acting through G protein-coupled receptors in a
membrane-delimited pathway involving Gβγ subunits. Inhibition is
caused by a shift from an easily activated “willing”
(
W
) state to a more-difficult-to-activate
“reluctant” (
R
) state. This inhibition can be
reversed by strong depolarization, resulting in prepulse facilitation,
or by protein kinase C (PKC) phosphorylation. Comparison of regulation
of N-type Ca
2+
channels containing Cav2.2a α
1
subunits and P/Q-type Ca
2+
channels containing
Ca
v
2.1 α
1
subunits revealed substantial
differences. In the absence of G protein modulation, Ca
v
2.1
channels containing Ca
v
β subunits were tonically in the
W
state, whereas Ca
v
2.1 channels without β
subunits and Ca
v
2.2a channels with β subunits were
tonically in the
R
state. Both Ca
v
2.1 and
Ca
v
2.2a channels could be shifted back toward the
W
state by strong depolarization or PKC phosphorylation.
Our results show that the
R
state and its modulation by
prepulse facilitation, PKC phosphorylation, and Ca
v
β
subunits are intrinsic properties of the Ca
2+
channel
itself in the absence of G protein modulation. A common allosteric
model of G protein modulation of Ca
2+
-channel activity
incorporating an intrinsic equilibrium between the
W
and
R
states of the α
1
subunits and modulation
of that equilibrium by G proteins, Ca
v
β subunits,
membrane depolarization, and phosphorylation by PKC accommodates our
findings. Such regulation will modulate transmission at synapses that
use N-type and P/Q-type Ca
2+
channels to initiate
neurotransmitter release.
In vitro
assembly of phytochrome B apoprotein with synthetic analogs of the phytochrome chromophore
Authors: Hanzawa Hiroko , Inomata Katsuhiko , Kinoshita Hideki , Kakiuchi Takashi , Jayasundera Krishanthi Padmarani , Sawamoto Daisuke , Ohta Atsuko , Uchida Kenko , Wada Keishiro , Furuya Masaki
Published: July 2002

Phytochrome B (PhyB), one of the major photosensory chromoproteins
in plants, mediates a variety of light-responsive developmental
processes in a photoreversible manner. To analyze the structural
requirements of the chromophore for the spectral properties of PhyB, we
have designed and chemically synthesized 20 analogs of the linear
tetrapyrrole (bilin) chromophore and reconstituted them with PhyB
apoprotein (PHYB). The A-ring acts mainly as the anchor for ligation to
PHYB, because the modification of the side chains at the C2 and C3
positions did not significantly influence the formation or difference
spectra of adducts. In contrast, the side chains of the B- and C-rings
are crucial to position the chromophore properly in the chromophore
pocket of PHYB and for photoreversible spectral changes. The side-chain
structure of the D-ring is required for the photoreversible spectral
change of the adducts. When methyl and ethyl groups at the C17 and C18
positions are replaced with an
n
-propyl,
n
-pentyl, or
n
-octyl group, respectively,
the photoreversible spectral change of the adducts depends on the
length of the side chains. From these studies, we conclude that each
pyrrole ring of the linear tetrapyrrole chromophore plays a different
role in chromophore assembly and the photochromic properties of PhyB.
Predicting crossover generation in DNA shuffling
Authors: Moore Gregory L. , Maranas Costas D. , Lutz Stefan , Benkovic Stephen J.
Published: July 2002

We introduce a quantitative framework for assessing the generation
of crossovers in DNA shuffling experiments. The approach uses free
energy calculations and complete sequence information to model the
annealing process. Statistics obtained for the annealing events then
are combined with a reassembly algorithm to infer crossover allocation
in the reassembled sequences. The fraction of reassembled sequences
containing zero, one, two, or more crossovers and the probability that
a given nucleotide position in a reassembled sequence is the site of a
crossover event are estimated. Comparisons of the predictions against
experimental data for five example systems demonstrate good agreement
despite the fact that no adjustable parameters are used. An
in
silico
case study of a set of 12 subtilases examines the effect
of fragmentation length, annealing temperature, sequence identity and
number of shuffled sequences on the number, type, and distribution of
crossovers. A computational verification of crossover aggregation in
regions of near-perfect sequence identity and the presence of
synergistic reassembly in family DNA shuffling is obtained.
Deletion of cytosolic phospholipase A
2
suppresses Apc
Min
-induced tumorigenesis
Authors: Hong Karen H. , Bonventre Joanna C. , O'Leary Eileen , Bonventre Joseph V. , Lander Eric S.
Published: July 2002

Although nonsteroidal antiinflammatory drugs (NSAIDs) show great
promise as therapies for colon cancer, a dispute remains regarding
their mechanism of action. NSAIDs are known to inhibit cyclooxygenase
(COX) enzymes, which convert arachidonic acid (AA) to prostaglandins
(PGs). Therefore, NSAIDs may suppress tumorigenesis by inhibiting PG
synthesis. However, various experimental studies have suggested the
possibility of PG-independent mechanisms. Notably, disruption of the
mouse group IIA secretory phospholipase A
2
locus
(
Pla2g2a
), a potential source of AA for COX-2, increases
tumor number despite the fact that the mutation has been predicted to
decrease PG production. Some authors have attempted to reconcile the
results by suggesting that the level of the precursor (AA), not the
products (PGs), is the critical factor. To clarify the role of AA in
tumorigenesis, we have examined the effect of deleting the group IV
cytosolic phospholipase A
2
(cPLA
2
) locus
(Pla2g4). We report that Apc
Min/+
,
cPLA
2
−/−
mice show an 83% reduction in tumor
number in the small intestine compared with littermates with genotypes
Apc
Min/+
, cPLA
2
+/−
and
Apc
Min/+
, cPLA
2
+/+
. This tumor
phenotype parallels that of COX-2 knockout mice, suggesting that
cPLA
2
is the predominant source of AA for COX-2 in the
intestine. The protective effect of cPLA
2
deletion is thus
most likely attributed to a decrease in the AA supply to COX-2 and a
resultant decrease in PG synthesis. The tumorigenic effect of
sPLA
2
mutations is likely to be through a completely
different pathway.
Live attenuated HIV vaccines: Predicting the tradeoff between efficacy and safety
Authors: Blower S. M. , Koelle K. , Kirschner D. E. , Mills J.
Published: July 2002

The utility of live attenuated vaccines for controlling HIV
epidemics is being debated. Live attenuated HIV vaccines (LAHVs) could
be extremely effective in protecting against infection with wild-type
strains, but may not be completely safe as the attenuated strain could
cause AIDS in some vaccinated individuals. We present a theoretical
framework for evaluating the consequences of the tradeoff between
vaccine efficacy (in terms of preventing new infections with wild-type
strains) and safety (in terms of vaccine-induced AIDS deaths). We use
our framework to predict, for Zimbabwe and Thailand, the
epidemiological impact of 1,000 different (specified by efficacy and
safety characteristics) LAHVs. We predict that paradoxically:
(
i
) in Zimbabwe (where transmission is high) LAHVs would
significantly decrease the AIDS death rate, but (
ii
) in
Thailand (where transmission is low) exactly the same vaccines (in
terms of efficacy and safety characteristics) would increase the AIDS
death rate. Our results imply that a threshold transmission rate exists
that determines whether any given LAHV has a beneficial or a
detrimental impact. We also determine the vaccine perversity point,
which is defined in terms of the fraction of vaccinated individuals who
progress to AIDS as a result of the vaccine strain. Vaccination with
any LAHV that causes more than 5% of vaccinated individuals to
progress to AIDS in 25 years would, even 50 years later, lead to
perversity (i.e., increase the annual AIDS death rate) in Thailand;
these same vaccines would lead to decreases in the annual AIDS death
rate in Zimbabwe.
Electronic structure of multiquantum giant vortex states in mesoscopic superconducting disks
Authors: Tanaka Kaori , Robel István , Jankó Boldizsár
Published: July 2002

We report self-consistent calculations of the microscopic electronic structure of the so-called giant vortex states. These multiquantum vortex states, detected by recent magnetization measurements on submicron disks, are qualitatively different from the Abrikosov vortices in the bulk. We find that, in addition to multiple branches of bound states in the core region, the local tunneling density of states exhibits Tomasch oscillations caused by the single-particle interference arising from quantum confinement. These features should be directly observable by scanning tunneling spectroscopy.
Impact of a Permo-Carboniferous high O
2
event on the terrestrial carbon cycle
Authors: Beerling D. J. , Berner R. A.
Published: July 2002

Independent models predicting the Phanerozoic (past 600 million
years) history of atmospheric O
2
partial pressure
(
p
O
2
) indicate a marked rise to
approximately 35% in the Permo-Carboniferous, around 300 million years
before present, with the strong potential for altering the
biogeochemical cycling of carbon by terrestrial ecosystems. This
potential, however, would have been modified by the prevailing
atmospheric
p
CO
2
value. Herein, we use a
process-based terrestrial carbon cycle model forced with a late
Carboniferous paleoclimate simulation to evaluate the effects of a rise
from 21 to 35%
p
O
2
on terrestrial biosphere
productivity and assess how this response is modified by current
uncertainties in the prevailing
p
CO
2
value.
Our results indicate that a rise in
p
O
2
from
21 to 35% during the Carboniferous reduced global terrestrial primary
productivity by 20% and led to a 216-Gt (1 Gt = 10
12
kg) C reduction in the vegetation and soil carbon storage, in an
atmosphere with
p
CO
2
= 0.03%. However,
in an atmosphere with
p
CO
2
= 0.06%,
the CO
2
fertilization effect is larger than the cost of
photorespiration, and ecosystem productivity increases leading to the
net sequestration of 117 Gt C into the vegetation and soil carbon
reservoirs. In both cases, the effects result from the strong
interaction between
p
O
2
,
p
CO
2
, and climate in the tropics. From this
analysis, we deduce that a Permo-Carboniferous rise in
p
O
2
was unlikely to have exerted
catastrophic effects on ecosystem productivity (with
p
CO
2
= 0.03%), and if pCO
2
levels at this time were >0.04%, the water-use efficiency of land
plants may even have improved.
Remarkable statistical behavior for truncated Burgers–Hopf dynamics
Authors: Majda Andrew J. , Timofeyev Ilya
Published: July 2002

A simplified one-dimensional model system is introduced and studied
here that exhibits intrinsic chaos with many degrees of freedom as well
as increased predictability and slower decay of correlations for the
large-scale features of the system. These are important features in
common with vastly more complex problems involving climate modeling or
molecular biological systems. This model is a suitable approximation of
the Burgers–Hopf equation involving Galerkin projection on Fourier
modes. The model has a detailed mathematical structure that leads to a
well-defined equilibrium statistical theory as well as a simple scaling
theory for correlations. The numerical evidence presented here strongly
supports the behavior predicted from these statistical theories. Unlike
the celebrated dissipative and dispersive approximations of the
Burgers–Hopf equation, which exhibit exactly solvable and/or
completely integrable behavior, these model approximations have strong
intrinsic chaos with ergodic behavior.
Chimeras ofDictyosteliummyosin II head and neck domains withAcanthamoebaor chicken smooth muscle myosin II tail domain have greatly increased and unregulated actin-dependent MgATPase activity
Authors: Liu Xiong , Shu Shi , Yamashita Roxanne A. , Xu Yuhui , Korn Edward D.
Published: July 2002

Phosphorylation of the regulatory light chain ofDictyosteliummyosin II increasesVmaxof its actin-dependent MgATPase activity about 5-fold under normal assay conditions. Under these assay conditions, unphosphorylated chimeric myosins in which the tail domain of theDictyosteliummyosin II heavy chain is replaced by either the tail domain of chicken gizzard smooth muscle orAcanthamoebamyosin II are 20 times more active because of a 10- to 15-fold increase inVmaxand a 2- to 7-fold decrease in apparentKATPaseand are only slightly activated by regulatory light chain phosphorylation. Actin-dependent MgATPase activity of theDictyostelium/Acanthamoebachimera is not affected by phosphorylation of serine residues in the tail whose phosphorylation completely inactivates wild-typeAcanthamoebamyosin II. These results indicate that the actin-dependent MgATPase activity of these myosins involves specific, tightly coupled, interactions between head and tail domains.
DNA tightens the dimeric DNA-binding domain of human papillomavirus E2 protein without changes in volume
Authors: Lima Luís Mauricio T. R. , Foguel Débora , Silva Jerson L.
Published: July 2002

The recognition of palindromic specific DNA sequences by the
human papillomavirus (HPV) E2 proteins is responsible for regulation of
virus transcription. The dimeric E2 DNA-binding domain of HPV-16 (E2c)
dissociates into a partially folded state under high hydrostatic
pressure. We show here that pressure-induced monomers of E2c are highly
structured, as evidenced by NMR hydrogen–deuterium exchange
measurements. On binding to both specific and nonspecific DNA, E2c
becomes stable against pressure. Competitive binding studies using
fluorescence polarization of fluorescein-labeled DNA demonstrate the
reversibility of the specific binding. To assess the thermodynamic
parameters for the linkage between protein dissociation and DNA
binding, urea denaturation curves were obtained at different pressures
in the presence of specific and nonspecific DNA sequences. The change
in free energy on denaturation fell linearly with increase in pressure
for both protein–DNA complexes, and the measured volume change was
similar to that obtained for E2c alone. The data show that the free
energy of dissociation increases when E2c binds to a nonspecific DNA
sequence but increases even more when the protein binds to the specific
DNA sequence. Thus, specific complexes are tighter but do not entail
variation in the volume change. The thermodynamic data indicate that
DNA-bound E2c dissociates into monomers bound to DNA. The existence of
monomeric units of E2c bound to DNA may have implications for the
formation of DNA loops, as an additional target for viral and host
factors binding to the loosely associated dimer of the N-terminal
module of the E2 protein.
The N-terminal domain of Escherichia coli enzyme I of the phosphoenolpyruvate/glycose phosphotransferase system: molecular cloning and characterization.
Authors: Chauvin F , Fomenkov A , Johnson C R , Roseman S
Published: July 2002

The bacterial phosphoenolpyruvate/glycose phosphotransferase system (PTS) comprises a group of proteins that catalyze the transfer of the phosphoryl group from phosphoenolpyruvate (PEP) to sugars concomitant with their translocation. The first two steps of the phosphotransfer sequence are PEP <--> Enzyme I (EI) <--> HPr (the histidine-containing phosphocarrier protein). We have proposed that many functions of the PTS are regulated by EI, which undergoes a monomer/dimer transition. EI monomer (63.5 kDa) comprises two major domains: a flexible C-terminal domain (EI-C) and a protease-resistant, structurally stable N-terminal domain (EI-N) containing the active site His. Trypsin treatment of Salmonella typhimurium EI yielded EI-N, designated EI-N(t). Homogeneous recombinant Escherichia coli EI-N [i.e., EI-N(r)], has now been prepared in quantity, shows the expected thermodynamic unfolding properties and, similarly to EI-N(t), is phosphorylated by phospho-HPr, but not by PEP. In addition, binding of EI-N(r) to HPr was studied by isothermal titration calorimetry: K/a = 1.4 x 10(5) M(-1) and delta H = +8.8 kcal x mol(-1). Both values are comparable to those for HPr binding to intact EI. Fluorescence anisotropy [dansyl-EI-N(r)] and gel filtration of EI-N(r) show that it does not dimerize. These results emphasize the role of EI-C in dimerization and the regulation of intact EI.
Up-regulation of pressure-activated Ca(2+)-permeable cation channel in intact vascular endothelium of hypertensive rats.
Authors: Hoyer J , Köhler R , Haase W , Distler A
Published: July 2002

In endothelial cells, stretch-activated cation channels have been proposed to act as mechanosensors for changes in hemodynamic forces. We have identified a novel mechanosensitive pressure-activated channel in intact endothelium from rat aorta and mesenteric artery. The 18-pS cation channel responded with a multifold increase in channel activity when positive pressure was applied to the luminal cell surface with the patch pipette and inactivated at negative pipette pressure. Channel permeability ratio for K+, Na+, and Ca2+ ions was 1:0.98:0.23. Ca2+ influx through the channel was sufficient to activate a neighboring Ca2(+)-dependent K+ channel. Hemodynamic forces are chronically disturbed in arterial hypertension. Endothelial cell dysfunction has been implicated in the pathogenesis of arterial hypertension. In two comparative studies, density of the pressure-activated channel was found to be significantly higher in spontaneously hypertensive rats and renovascular hypertensive rats compared with their respective normotensive controls. Channel activity presumably leads to mechanosensitive Ca2+ influx and induces cell hyperpolarization by K+ channel activity. Both Ca2+ influx and hyperpolarization are known to induce a vasodilatory endothelial response by stimulating endothelial nitric oxide (NO) production. Up-regulation of channel density in hypertension could, therefore, represent a counterregulatory mechanism of vascular endothelium.
Differential suppression by protease inhibitors and cytokines of apoptosis induced by wild-type p53 and cytotoxic agents.
Authors: Lotem J , Sachs L
Published: July 2002

Apoptosis induced in myeloid leukemic cells by wild-type p53 was suppressed by different cleavage-site directed protease inhibitors, which inhibit interleukin-1 beta-converting enzyme-like, granzyme B and cathepsins B and L proteases. Apoptosis was also suppressed by the serine and cysteine protease inhibitor N-tosyl-L-phenylalanine chloromethylketone (TPCK) [corrected], but not by other serine or cysteine protease inhibitors including N alpha-p-tosyl-L-lysine chloromethylketone (TLCK), E64, pepstatin A, or chymostatin. Protease inhibitors suppressed induction of apoptosis by gamma-irradiation and cycloheximide but not by doxorubicin, vincristine, or withdrawal of interleukin 3 from interleukin 3-dependent 32D non-malignant myeloid cells. Induction of apoptosis in normal thymocytes by gamma-irradiation or dexamethasone was also suppressed by the cleavage-site directed protease inhibitors, but in contrast to the myeloid leukemic cells apoptosis in thymocytes was suppressed by TLCK but not by TPCK. The results indicate that (i) inhibitors of interleukin-1 beta-converting enzyme-like proteases and some other protease inhibitors suppressed induction of apoptosis by wild-type p53 and certain p53-independent pathways of apoptosis; (ii) the protease inhibitors together with the cytokines interleukin 6 and interferon-gamma or the antioxidant butylated hydroxyanisole gave a cooperative protection against apoptosis; (iii) these protease inhibitors did not suppress induction of apoptosis by some cytotoxic agents or by viability-factor withdrawal from 32D cells, whereas these pathways of apoptosis were suppressed by cytokines; (iv) there are cell type differences in the proteases involved in apoptosis; and (v) there are multiple pathways leading to apoptosis that can be selectively induced and suppressed by different agents.
Regulation of phosducin phosphorylation in retinal rods by Ca2+/calmodulin-dependent adenylyl cyclase.
Authors: Willardson B M , Wilkins J F , Yoshida T , Bitensky M W
Published: July 2002

The phosphoprotein phosducin (Pd) regulates many guanine nucleotide binding protein (G protein)-linked signaling pathways. In visual signal transduction, unphosphorylated Pd blocks the interaction of light-activated rhodopsin with its G protein (Gt) by binding to the beta gamma subunits of Gt and preventing their association with the Gt alpha subunit. When Pd is phosphorylated by cAMP-dependent protein kinase, it no longer inhibits Gt subunit interactions. Thus, factors that determine the phosphorylation state of Pd in rod outer segments are important in controlling the number of Gts available for activation by rhodopsin. The cyclic nucleotide dependencies of the rate of Pd phosphorylation by endogenous cAMP-dependent protein kinase suggest that cAMP, and not cGMP, controls Pd phosphorylation. The synthesis of cAMP by adenylyl cyclase in rod outer segment preparations was found to be dependent on Ca2+ and calmodulin. The Ca2+ dependence was within the physiological range of Ca2+ concentrations in rods (K1/2 = 230 +/- 9 nM) and was highly cooperative (n app = 3.6 +/- 0.5). Through its effect on adenylyl cyclase and cAMP-dependent protein kinase, physiologically high Ca2+ (1100 nM) was found to increase the rate of Pd phosphorylation 3-fold compared to the rate of phosphorylation at physiologically low Ca2+ (8 nM). No evidence for Pd phosphorylation by other (Ca2+)-dependent kinases was found. These results suggest that Ca2+ can regulate the light response at the level of Gt activation through its effect on the phosphorylation state of Pd.
Early divergence of magnocellular and parvocellular functional subsystems in the embryonic primate visual system
Authors: Meissirel Claire , Wikler Kenneth C. , Chalupa Leo M. , Rakic Pasko
Published: July 2002

In both human and Old World primates visual information is conveyed by two parallel pathways: the magnocellular (M) and parvocellular (P) streams that project to separate layers of the lateral geniculate nucleus and are involved primarily in motion and color/form discrimination. The present study provides evidence that retinal ganglion cells in the macaque monkey embryo diverge into M and P subtypes soon after their last mitotic division and that optic axons project directly and selectively to either the M or P moieties of the developing lateral geniculate nucleus. Thus, initial M projections from the eyes overlap only in prospective layers 1 and 2, whereas initial P projections overlap within prospective layers 3–6. We suggest that the divergence of the M and P pathways requires developmental mechanisms different from those underlying competition-driven segregation of initially intermixed eye-specific domains in the primate visual system.
An endogenous calcium oscillator may control early embryonic division
Authors: Swanson Craig A. , Arkin Adam P. , Ross John
Published: July 2002

Transient elevations in the concentration of free cytosolic calcium ion ([Ca
2+
]
i
) promote cell phase transitions in early embryonic division and persist even if these transitions are blocked. These observations suggest that a [Ca
2+
]
i
oscillator is an essential timing element of the early embryonic “master clock.” We explore this possibility by coupling a [Ca
2+
]
i
oscillator model to an early embryonic cell cycle model based on the protein interactions that govern the activity of the M-phase-promoting factor (MPF). We hypothesize three dynamical states of the MPF system and choose parameter sets to represent each. We then investigate how [Ca
2+
]
i
dynamics may control early embryonic division in both sea urchin and
Xenopus
embryos. To investigate both systems, distinct [Ca
2+
]
i
profiles matching those observed in sea urchin embryos (in which [Ca
2+
]
i
exhibits sharp transients) and
Xenopus
embryos (in which [Ca
2+
]
i
is elevated and oscillates sinusoidally) are imposed on each of the hypothesized dynamical states of MPF. In the first hypothesis, [Ca
2+
]
i
oscillations entrain the autonomous MPF oscillator. In the second and third hypotheses, where the MPF system rests in excitatory and bistable states, respectively, [Ca
2+
]
i
oscillations drive MPF activation cycles. Simulation results show that hypotheses two and three, in which a [Ca
2+
]
i
oscillator is a fundamental timing element of the master clock, best account for key experimental observations and the questions that they raise. Finally, we propose experiments to elucidate further [Ca
2+
]
i
regulation and the fundamental components of the early embryonic master clock.
Infrared spectral models demonstrate that exposure to environmental chemicals leads to new forms of DNA
Authors: Malins Donald C. , Polissar Nayak L. , Gunselman Sandra J.
Published: July 2002

Environmental chemicals are known to induce a high degree of hydroxyl radical-mediated damage in DNA. Accordingly, we tested the hypothesis that this exposure leads to new forms of DNA using principal components analysis of Fourier transform infrared spectra. The hepatic DNA of English sole (controls) from an essentially clean environment was compared with that of sole inhabiting a chemically contaminated environment. All livers studied were cancer-free; however, a high incidence of liver cancer has been found in the exposed population. The exposed sole were sampled twice, 2 years apart, while the sediments in which they live were under remediation. After obtaining infrared spectra, the first three principal components (PC1, PC2, and PC3) were calculated and found to represent 97% of the total spectral variance. When the principal component scores were plotted in 3-dimensional space, clusters of points were obtained that represented the DNA from the control and exposed groups. Each of the points was derived from ≈10
6
wavenumber–absorbance correlations. The spatial location of a point was a highly discriminating measure of DNA structure. The clusters of points were completely separated, demonstrating that the three groups could be 100% correctly classified. The points from the control group were tightly clustered whereas those from the exposed groups were highly diverse. The findings demonstrate that exposure to environmental chemicals results in new, structurally diverse forms of DNA that likely play an important role in carcinogenesis.
Antiatherogenic effects of the antioxidant BO-653 in three different animal models
Authors: Cynshi Osamu , Kawabe Yoshiki , Suzuki Tsukasa , Takashima Yoshiaki , Kaise Hiroshi , Nakamura Minako , Ohba Yasuhiro , Kato Yoshiaki , Tamura Kunio , Hayasaka Akira , Higashida Atsuko , Sakaguchi Hisashi , Takeya Motohiro , Takahashi Kiyoshi , Inoue Kenji , Noguchi Noriko , Niki Etsuo , Kodama Tatsuhiko
Published: July 2002

Antioxidants have been proposed to have antiatherogenic potential by their inhibition of low density lipoprotein (LDL) oxidation. Here, we report an antioxidant, BO-653 (2,3-dihydro-5-hydroxy-2,2-dipentyl-4,6-di-
tert-
butylbenzofuran), designed to exhibit antioxidative potency comparable to that of α-tocopherol, but yet possess a high degree of lipophilicity comparable to that of probucol. BO-653 exhibits a high affinity for LDL and is well distributed in aortic vessels
in vivo
. In atherosclerosis models of rabbits and mice, BO-653 has been shown to be able to suppress the formation of atherosclerotic lesions without untoward side effects. Specifically, there was no reduction of high density lipoprotein levels. This antioxidant provides additional evidence in support of the oxidized-LDL hypothesis, and itself is a promising candidate antioxidant for clinical use.
Quantitative assessment of enzyme specificity
in vivo
: P
2
recognition by Kex2 protease defined in a genetic system
Authors: Bevan Alison , Brenner Charles , Fuller Robert S.
Published: July 2002

The specificity of the yeast proprotein-processing Kex2 protease was examined
in vivo
by using a sensitive, quantitative assay. A truncated prepro-α-factor gene encoding an α-factor precursor with a single α-factor repeat was constructed with restriction sites for cassette mutagenesis flanking the single Kex2 cleavage site (-SLDKR↓EAEA-). All of the 19 substitutions for the Lys (P
2
) residue in the cleavage site were made. The wild-type and mutant precursors were expressed in a yeast strain lacking the chromosomal genes encoding Kex2 and prepro-α-factor. Cleavage of the 20 sites by Kex2, expressed at the wild-type level, was assessed by using a quantitative-mating assay with an effective range greater than six orders of magnitude. All substitutions for Lys at P
2
decreased mating, from 2-fold for Arg to >10
6
-fold for Trp. Eviction of the Kex2-encoding plasmid indicated that cleavage of mutant sites by other cellular proteases was not a complicating factor. Mating efficiencies of strains expressing the mutant precursors correlated well with the specificity (
k
cat
/
K
M
) of purified Kex2 for comparable model peptide substrates, validating the
in vivo
approach as a quantitative method. The results support the conclusion that
K
M
, which is heavily influenced by the nature of the P
2
residue, is a major determinant of cleavage efficiency
in vivo
. P
2
preference followed the rank order: Lys > Arg > Thr > Pro > Glu > Ile > Ser > Ala > Asn > Val > Cys > As
P
> Gln > Gly > His > Met > Leu > Tyr > Phe > Trp.