bluuebunny/crossref_metadata_2025 huggingface dataset:
Far-infrared scattering experiment on a bumpy torus
Authors: Casson W. H.
Published: July 2002

A far-infrared scattering experiment was installed on the ELMO bumpy torus experiment at Oak Ridge National Laboratory [Plasma Physics and Controlled Nuclear Fusion Research (IAEA, Vienna, 1975), Vol. II, p. 141]. The design allowed for coupled scanning of spatial and wave vector parameters while recording the frequency spectrum. Coherent waves and incoherent density fluctuations were observed for varying plasma conditions. Also, coherent waves were recorded in conjunction with ion cyclotron heating fast wave heating experiments, which demonstrated fast wave penetration into the plasma and ion-Bernstein wave conversion between harmonic zones.
Experimental and numerical study of a turbulent free square jet
Authors: Quinn W. R. , Militzer J.
Published: July 2002

Results of an experimental and numerical study of a turbulent free jet of air from a sharp-edged square slot are presented. The jet was treated as elliptic in the numerical study that predicted mean streamwise velocity, mean static pressure, and turbulence kinetic energy distributions. The experimental results include the mean velocity, the turbulent normal and shearing stresses obtained with hot-wire anemometry, and the mean static pressure acquired with a pitot-static tube in conjunction with a pressure transducer. The experimental results reveal the existence of pronounced mean streamwise velocity off-center peaks in the very near field, where positive mean static pressures were also found. Furthermore, the square jet is found to spread significantly faster in the near flow field than a jet from a round slot that has the same exit area as the square slot under identical test conditions. The general agreement between experimental results and numerical predictions is relatively good.
Pressure-driven flow of suspensions of liquid drops
Authors: Zhou Hua , Pozrikidis C.
Published: July 2002

The pressure-driven flow of a periodic suspension of two-dimensional viscous drops in a channel that is bounded by two parallel plane walls is studied numerically using the method of interfacial dynamics, which is an improved version of the boundary integral method. The viscosity of the drops is assumed to be equal to that of the suspending fluid. The effects of capillary number, volume fraction, and number of rows are examined for ordered suspensions, where the drops are initially arranged in several rows on a hexagonal lattice. Results of dynamic simulations for random monodisperse suspensions with up to 12 drops per periodic cell are performed, and the salient features of the motion are discussed. It is found that, in all cases, the drops tend to migrate toward the centerline of the channel, forming either a single row or multiple rows. The effect of the instantaneous suspension microstructure on the effective viscosity is illustrated, and some important differences in the behavior of suspensions in pressure-driven and shear-driven flows are identified and discussed. Numerical evidence is presented, suggesting that the behavior of suspensions of high viscosity drops may be significantly different from that of suspensions of drops with small and moderate viscosity.
A comparative study of subgrid scale models in homogeneous isotropic turbulence
Authors: Fureby C. , Tabor G. , Weller H. G. , Gosman A. D.
Published: July 2002

Recently, a number of studies have indicated that Large Eddy Simulation (LES) models are fairly insensitive to the adopted Subgrid Scale (SGS) models. In order to study this and to gain further insight into LES, simulations of forced and decaying homogeneous isotropic turbulence have been performed for Taylor Re numbers between 35 and 248 using various SGS models, representative of the contemporary state of the art. The predictive capability of the LES concept is analyzed by comparison with DNS data and with results obtained from a theoretical model of the energy spectrum. The resolved flow is examined by visualizing the morphology and by analyzing the distribution of resolved enstrophy, rate of strain, stretching, SGS kinetic energy, and viscosity. Furthermore, the correlation between eigenvalues of the resolved rate of strain tensor and the vorticity is investigated. Although the gross features of the flow appear independent of the SGS model, pronounced differences between the models become apparent when the SGS kinetic energy and the interscale energy transfer are investigated.
Effect of the subgrid scales on particle motion
Authors: Armenio Vincenzo , Piomelli Ugo , Fiorotto Virgilio
Published: July 2002

In this study, the effects of small-scale velocity fluctuations on the motion of tracer particles is investigated by releasing particles in a turbulent channel flow at Reτ=175, and following their motion in time. Two types of numerical experiments were carried out: first, the Eulerian velocity field was evaluated by the direct numerical simulation (DNS) and the particles were advanced in time using the resolved and several filtered velocity fields to study the effect of the subgrid-scale velocity fluctuations on particle motion without the influence of modeling errors. In the second stage, the particle-motion study was performed using independent DNS and large-eddy simulations (LES), thus including the effect of interpolation and subgrid-scale stress modeling errors on the dispersion statistics. At this Reynolds number the small scales were found to have a limited effect on the statistics examined (one-particle dispersion, one-particle velocity autocorrelation, Lagrangian integral time scale, turbulent diffusivity, and two-particles rms dispersion). Only when a significant percentage of the energy was removed from the velocity field some differences were observed between filtered and unfiltered data (especially near the wall). It was found that when the dynamic eddy-viscosity model was employed, modeling errors did not affect the results as much as the filtering itself; the use of the Smagorinsky model, on the other hand, gave inaccurate results. Additional computations for finite-inertia particles have shown that these results represent a conservative estimate, in the sense that actual particles with inertia are less sensitive than the tracer particles examined in the first part of the investigation, and that LES provides improved results when particles with inertia are used.
The subgrid-scale estimation model on nonuniform grids
Authors: Loh Kuo-Chieh , Domaradzki J. Andrzej
Published: July 2002

The subgrid-scale estimation procedure developed previously using one-dimensional top hat filters on uniform grids is generalized to nonuniform grids. The method is evaluated in large eddy simulations of turbulent channel flow performed on a grid which is non-uniform in the wall-normal direction.
Laser ionization and heating of gas targets for long-scale-length instability experiments
Authors: Denavit J. , Phillion D. W.
Published: July 2002

This paper examines the use of gas targets to create low- and mid-Z plasmas ≊3 mm in size at 5% to 10% critical density for green and blue light (ne≊2×1020 to 1021 cm−3) with an electron temperature of several keV. At sufficiently high intensities (≊1014 W/cm2) the gas is ionized and heated by a laser absorption wave propagating faster than the sound speed. For pulses under 2 ns, the bulk of the plasma remains stationary, resulting in efficient heating minimizing density and velocity gradients, which are particularly important for instability thresholds in nonuniform plasmas. The propagation of a laser absorption wave in a preionized plasma is derived analytically. Ionization resulting from multiphoton and electron avalanche processes is studied by numerical methods and dimensional analysis. This establishes the length and time scales over which an absorption wave can be observed. Computer simulations, using the lasnex code, are presented for several implementations of this concept, applicable to the relevant regime for inertial confinement fusion. These examples include a gas jet (≊3×1 mm in cross section), 3 to 4 mm diameter gas balloons, and gas puffs generated by exploding a foil with a low-energy prepulse (≊200 J).
Flow shear induced fluctuation suppression in finite aspect ratio shaped tokamak plasma
Authors: Hahm T. S. , Burrell K. H.
Published: July 2002

The suppression of turbulence by the E×B flow shear and parallel flow shear is studied in an arbitrary shape finite aspect ratio tokamak plasma using the two point nonlinear analysis previously utilized in a high aspect ratio tokamak plasma [Phys. Plasmas 1, 2940 (1994)]. The result shows that only the E×B flow shear is responsible for the suppression of flute-like fluctuations. This suppression occurs regardless of the plasma rotation direction and is, therefore, relevant for the very high (VH) mode plasma core as well as for the high (H) mode plasma edge. Experimentally observed in–out asymmetry of fluctuation reduction behavior can be addressed in the context of flux expansion and magnetic field pitch variation on a given flux surface. The adverse effect of neutral particles on confinement improvement is also discussed in the context of the charge exchange induced parallel momentum damping.
Helical temperature perturbations associated with tearing modes in tokamak plasmas
Authors: Fitzpatrick Richard
Published: July 2002

An investigation is made into the electron temperature perturbations associated with tearing modes in tokamak plasmas. It is found that there is a critical magnetic island width below which the conventional picture where the temperature is flattened inside the separatrix is invalid. This effect comes about because of the stagnation of magnetic field lines in the vicinity of the rational surface and the finite parallel thermal conductivity of the plasma. Islands whose widths lie below the critical value are not destabilized by the perturbed bootstrap current, unlike conventional magnetic islands. This effect may provide an explanation for some puzzling experimental results regarding error field-induced magnetic reconnection. The critical island width is found to be fairly substantial in conventional tokamak plasmas, provided that the long mean-free path nature of parallel heat transport and the anomalous nature of perpendicular heat transport are taken into account in the calculation.
Laser driven electron acceleration in vacuum, gases, and plasmas
Authors: Sprangle Phillip , Esarey Eric , Krall Jonathan
Published: July 2002

In this paper we discuss some of the important issues pertaining to laser acceleration in vacuum, neutral gases, and plasmas. The limitations of laser vacuum acceleration as they relate to electron slippage, laser diffraction, material damage, and electron aperture effects, are discussed. An inverse Cherenkov laser acceleration configuration is presented in which a laser beam is self-guided in a partially ionized gas. Optical self-guiding is the result of a balance between the nonlinear self-focusing properties of neutral gases and the diffraction effects of ionization. The stability of self-guided beams is analyzed and discussed. In addition, aspects of the laser wakefield accelerator are presented and laser-driven accelerator experiments are briefly discussed.
Study of driven magnetic reconnection in a laboratory plasma
Authors: Yamada Masaaki , Ji Hantao , Hsu Scott , Carter Troy , Kulsrud Russell , Bretz Norton , Jobes Forrest , Ono Yasushi , Perkins Francis
Published: July 2002

The magnetic reconnection experiment has been constructed to investigate the fundamental physics of magnetic reconnection in a well-controlled laboratory setting. This device creates an environment satisfying the criteria for a magnetohydrodynamic plasma (S≫1, ρi≪L). The boundary conditions can be controlled externally, and experiments with fully three-dimensional reconnection are now possible. In the initial experiments, the effects of the third vector component of reconnecting fields have been studied. Two distinctively different shapes of neutral sheet current layers, depending on the third component, are identified during driven magnetic reconnection. Without the third component (antiparallel or null–helicity reconnection), a thin double-Y-shaped diffusion region is identified. A neutral sheet current profile is measured accurately to be as narrow as the order of the ion gyroradius. In the presence of an appreciable third component (co-helicity reconnection), an O-shaped diffusion region appears and grows into a spheromak configuration.
On the stabilization of neoclassical magnetohydrodynamic tearing modes using localized current drive or heating
Authors: Hegna C. C. , Callen J. D.
Published: July 2002

The effectiveness of using localized current drive or heating to suppress the formation and growth of neoclassical magnetohydrodynamic (MHD) tearing modes is addressed. The most efficient way to use an auxiliary current source is to cause current to flow in the same direction as the equilibrium bootstrap current and phase the current relative to the magnetic island such that the current is deposited on the O-point of the island. Theoretical estimates for the amount of required current to suppress the formation of a large magnetic island is of order a few percent of the equilibrium current. If the suppression is successful, the magnetic island will saturate at a width of order the radial localization width of the current source. Localized heating at the O-point of the magnetic island can also produce stabilizing effects relative to magnetic island growth. The effects of the driven current or heating can be illustrated by using a phase diagram of the island growth.
Characteristic analysis of a complex two-dimensional magnetohydrodynamic bow shock flow with steady compound shocks
Authors: De Sterck H. , Low B. C. , Poedts S.
Published: July 2002

A simple, compact, and systematic derivation is given of the characteristic properties of the magnetohydrodynamic (MHD) equations with two independent variables (time-dependent MHD in the xt plane and steady MHD in the xy plane), based on the symmetrizable Galilean invariant form of the equations and using a matrix approach. A numerically obtained stationary planar field-aligned MHD bow shock flow with interacting shocks is then analyzed in terms of hyperbolic and elliptic regions, steady xy characteristics, limiting lines, and allowed shock transitions. With the help of this analysis, a wave structure present in the bow shock flow can be interpreted as a double steady compound shock. This interpretation is based on the complete analogy demonstrated in our analysis, between the xy characteristic structure of this novel steady compound shock and the xt characteristic structure of the well-known time-dependent MHD compound shock.
KNbO3 electro-optic induced optical waveguide/cut-off modulator
Authors: Baumert J.-C. , Walther C. , Buchmann P. , Kaufmann H. , Melchior H. , Günter P.
Published: July 2002

Optical waveguiding and cut-off modulation have been observed in a structure based on KNbO3 single crystals. The refractive index changes induced by the electro-optic coefficient r33=64 pm/V allow waveguiding for a voltage of about 20 V. Guided modes have been measured in the wavelength range 0.5–1.3 μm.
Genetic control of quorum-sensing signal turnover in
Agrobacterium tumefaciens
Authors: Zhang Hai-Bao , Wang Lian-Hui , Zhang Lian-Hui
Published: July 2002

A signal turnover system is an essential component of many genetic regulatory mechanisms. The best-known example is the ubiquitin-dependent protein degradation system that exists in many organisms. We found that
Agrobacterium tumefaciens
adopts a unique signal turnover system to control exiting from a quorum-sensing mode.
A. tumefaciens
regulates Ti plasmid conjugal transfer by a quorum-sensing signal,
N
-3-oxo-octanoyl homoserine lactone (3OC8HSL), also known as
Agrobacterium
autoinducer. By using Tn
5
mutagenesis and a functional cloning approach, we identified two genes that are involved in switching from a conjugal quorum-sensing mode to a nonconjugal mode at the onset of stationary phase. First, we located
attJ,
which codes for an IclR-type suppressor that regulates the second gene
attM.
The latter encodes a homologue of
N-
acylhomoserine lactone (AHL)-lactonase. Mass spectrometry analysis shows that the enzyme encoded by
attM
is an AHL-lactonase that hydrolyzes the lactone ring of 3OC8HSL. In wild-type
A. tumefaciens
,
attM
expression is initially suppressed by AttJ but significantly elevated at the stationary phase accompanied a sharp decline in 3OC8HSL. DNA gel retardation analysis shows that AttJ specifically binds to the promoter that controls AHL-lactonase expression. Mutation of
attJ
resulted in constitutive production of AHL-lactonase that abolishes 3OC8HSL accumulation and Ti plasmid transfer. These data suggest that
A. tumefaciens
has a sophisticated multicomponent quorum-sensing signal turnover system, allowing the cell to sense a change in growth and adjust cellular activities accordingly.
Molecular analysis of mutations in DNA polymerase η in xeroderma pigmentosum-variant patients
Authors: Broughton Bernard C. , Cordonnier Agnes , Kleijer Wim J. , Jaspers Nicolaas G. J. , Fawcett Heather , Raams Anja , Garritsen Victor H. , Stary Anne , Avril Marie-Françoise , Boudsocq François , Masutani Chikahide , Hanaoka Fumio , Fuchs Robert P. , Sarasin Alain , Lehmann Alan R.
Published: July 2002

Xeroderma pigmentosum variant (XP-V) cells are deficient in their ability to synthesize intact daughter DNA strands after UV irradiation. This deficiency results from mutations in the gene encoding DNA polymerase η, which is required for effecting translesion synthesis (TLS) past UV photoproducts. We have developed a simple cellular procedure to identify XP-V cell strains, and have subsequently analyzed the mutations in 21 patients with XP-V. The 16 mutations that we have identified fall into three categories. Many of them result in severe truncations of the protein and are effectively null alleles. However, we have also identified five missense mutations located in the conserved catalytic domain of the protein. Extracts of cells falling into these two categories are defective in the ability to carry out TLS past sites of DNA damage. Three mutations cause truncations at the C terminus such that the catalytic domains are intact, and extracts from these cells are able to carry out TLS. From our previous work, however, we anticipate that protein in these cells will not be localized in the nucleus nor will it be relocalized into replication foci during DNA replication. The spectrum of both missense and truncating mutations is markedly skewed toward the N-terminal half of the protein. Two of the missense mutations are predicted to affect the interaction with DNA, the others are likely to disrupt the three-dimensional structure of the protein. There is a wide variability in clinical features among patients, which is not obviously related to the site or type of mutation.
Establishment of medaka (
Oryzias latipes
) transgenic lines with the expression of green fluorescent protein fluorescence exclusively in germ cells: A useful model to monitor germ cells in a live vertebrate
Authors: Tanaka Minoru , Kinoshita Masato , Kobayashi Daisuke , Nagahama Yoshitaka
Published: July 2002

We have generated transgenic medaka (teleost,
Oryzias
latipes
), which allow us to monitor germ cells by green
fluorescent protein (GFP) fluorescence in live specimens. Two medaka
strains, himedaka (orange–red variety) and inbred QurtE, were used.
The transgenic lines were achieved by microinjection of a construct
containing the putative promoter region and 3′ region of the medaka
vasa
gene (
olvas
). The intensity of GFP
fluorescence increases dramatically in primordial germ cells (PGCs)
located in the ventrolateral region of the posterior intestine around
stage 25 (the onset of blood circulation). Whole-mount
in
situ
hybridization and monitoring of ectopically located cells
by GFP fluorescence suggested that (
i
) the increase in
zygotic
olvas
expression occurs after PGC specification
and (
ii
) PGCs can maintain their cell characteristics
ectopically after stages 20–25. Around the day of hatching, the QurtE
strain clearly exhibits sexual dimorphisms in the number of GFP
fluorescent germ cells, a finding consistent with the appearance of
leucophores, a sex-specific marker of QurtE. The GFP expression
persists throughout the later stages in the mature ovary and testis.
Thus, these transgenic medaka represent a live vertebrate model to
investigate how germ cells migrate to form sexually dimorphic gonads,
as well as a potential assay system for environmental substances that
may affect gonad development. The use of a transgenic construct as a
selective marker to efficiently isolate germ-line-transmitting founders
during embryogenesis is also discussed.
Activation and targeting of extracellular signal-regulated kinases by β-arrestin scaffolds
Authors: Luttrell Louis M. , Roudabush Francine L. , Choy Eric W. , Miller William E. , Field Michael E. , Pierce Kristen L. , Lefkowitz Robert J.
Published: July 2002

Using both confocal immunofluorescence microscopy and
biochemical approaches, we have examined the role of β-arrestins
in the activation and targeting of extracellular signal-regulated
kinase 2 (ERK2) following stimulation of angiotensin II type 1a
receptors (AT1aR). In HEK-293 cells expressing hemagglutinin-tagged
AT1aR, angiotensin stimulation triggered β-arrestin-2 binding to the
receptor and internalization of AT1aR-β-arrestin complexes. Using red
fluorescent protein-tagged ERK2 to track the subcellular distribution
of ERK2, we found that angiotensin treatment caused the redistribution
of activated ERK2 into endosomal vesicles that also contained
AT1aR-β-arrestin complexes. This targeting of ERK2 reflects the
formation of multiprotein complexes containing AT1aR, β-arrestin-2,
and the component kinases of the ERK cascade, cRaf-1, MEK1, and ERK2.
Myc-tagged cRaf-1, MEK1, and green fluorescent protein-tagged ERK2
coprecipitated with Flag-tagged β-arrestin-2 from transfected COS-7
cells. Coprecipitation of cRaf-1 with β-arrestin-2 was independent of
MEK1 and ERK2, whereas the coprecipitation of MEK1 and ERK2 with
β-arrestin-2 was significantly enhanced in the presence of
overexpressed cRaf-1, suggesting that binding of cRaf-1 to β-arrestin
facilitates the assembly of a cRaf-1, MEK1, ERK2 complex. The
phosphorylation of ERK2 in β-arrestin complexes was markedly enhanced
by coexpression of cRaf-1, and this effect is blocked by expression of
a catalytically inactive dominant inhibitory mutant of MEK1.
Stimulation with angiotensin increased the binding of both cRaf-1 and
ERK2 to β-arrestin-2, and the association of β-arrestin-2, cRaf-1,
and ERK2 with AT1aR. These data suggest that β-arrestins function
both as scaffolds to enhance cRaf-1 and MEK-dependent activation of
ERK2, and as targeting proteins that direct activated ERK to specific
subcellular locations.
Neurotoxin-induced degeneration of dopamine neurons in
Caenorhabditis elegans
Authors: Nass Richard , Hall David H. , Miller David M. , Blakely Randy D.
Published: July 2002

Parkinson's disease is a complex neurodegenerative disorder characterized by the death of brain dopamine neurons. In mammals, dopamine neuronal degeneration can be triggered through exposure to neurotoxins accumulated by the presynaptic dopamine transporter (DAT), including 6-hydroxydopamine (6-OHDA) and 1-methyl-4-phenylpyridinium. We have established a system for the pharmacological and genetic evaluation of neurotoxin-induced dopamine neuronal death in
Caenorhabditis elegans
. Brief (1 h) exposure of green fluorescent protein-tagged, living worms to 6-OHDA causes selective degeneration of dopamine neurons. We demonstrate that agents that interfere with DAT function protect against 6-OHDA toxicity. 6-OHDA-triggered neural degeneration does not require the CED-3/CED-4 cell death pathway, but is abolished by the genetic disruption of the
C. elegans
DAT.
Processive movement of single 22S dynein molecules occurs only at low ATP concentrations
Authors: Hirakawa Emi , Higuchi Hideo , Toyoshima Yoko Y.
Published: July 2002

We have analyzed the movement of single 22S dynein molecules from
Tetrahymena
cilia by using a nanometer measuring system
equipped with optical tweezers. Statistical analysis proved that a
single molecule of 22S dynein can move processively and develop force
at low concentrations of ATP (<20 μM). The maximum force was ≈4.7
pN, and the force-velocity curve was convex down. During force
development, dynein molecules showed stepwise displacement of ≈8 nm
and frequently exhibited backward steps of ≈8 nm. At higher
concentrations of ATP (≧20 μM) single molecules of 22S dynein were
not observed to move processively. Twenty-two S dynein seems to switch
over from a processive mode to a nonprocessive mode, sensing a subtle
change of ATP concentrations. These observations indicate that the
processivity, maximum force, and step size of dynein are similar to
those of kinesin, but the ATP concentration-dependence, force-velocity
relationship, and backward steps are clearly distinct from kinesin.
Oxygen isotope ratios of PO
4
: An inorganic indicator of enzymatic activity and P metabolism and a new biomarker in the search for life
Authors: Blake Ruth E. , Alt Jeffrey C. , Martini Anna M.
Published: July 2002

The distinctive relations between biological activity and isotopic
effect recorded in biomarkers (e.g., carbon and sulfur isotope ratios)
have allowed scientists to suggest that life originated on this planet
nearly 3.8 billion years ago. The existence of life on other planets
may be similarly identified by geochemical biomarkers, including the
oxygen isotope ratio of phosphate (δ
18
O
p
)
presented here. At low near-surface temperatures, the exchange of
oxygen isotopes between phosphate and water requires enzymatic
catalysis. Because enzymes are indicative of cellular activity, the
demonstration of enzyme-catalyzed PO
4
–H
2
O
exchange is indicative of the presence of life. Results of laboratory
experiments are presented that clearly show that
δ
18
O
P
values of inorganic phosphate can be
used to detect enzymatic activity and microbial metabolism of
phosphate. Applications of δ
18
O
p
as a
biomarker are presented for two Earth environments relevant to the
search for extraterrestrial life: a shallow groundwater reservoir and a
marine hydrothermal vent system. With the development of
in
situ
analytical techniques and future planned sample return
strategies, δ
18
O
p
may provide an important
biosignature of the presence of life in extraterrestrial systems such
as that on Mars.
Indirect recognition of allopeptides promotes the development of cardiac allograft vasculopathy
Authors: Lee Richard S. , Yamada Kazuhiko , Houser Stuart L. , Womer Karl L. , Maloney Michaella E. , Rose Harris S. , Sayegh Mohamed H. , Madsen Joren C.
Published: July 2002

Graft loss from chronic rejection has become the major
obstacle to the long-term success of whole organ transplantation. In
cardiac allografts, chronic rejection is manifested as a diffuse and
accelerated form of arteriosclerosis, termed cardiac allograft
vasculopathy. It has been suggested that T-cell recognition of
processed alloantigens (allopeptides) presented by recipient
antigen-presenting cells through the indirect pathway of
allorecognition plays a critical role in the development and
progression of chronic rejection. However, definitive preclinical
evidence to support this hypothesis is lacking. To examine the role of
indirect allorecognition in a clinically relevant large animal model of
cardiac allograft vasculopathy, we immunized MHC inbred miniature swine
with synthetic polymorphic peptides spanning the α
1
domain of an allogeneic donor-derived swine leukocyte antigen class I
gene. Pigs immunized with swine leukocyte antigen class I allopeptides
showed
in vitro
proliferative responses and
in
vivo
delayed-type hypersensitivity responses to the allogeneic
peptides. Donor MHC class I disparate hearts transplanted into
peptide-immunized cyclosporine-treated pigs not only rejected faster
than unimmunized cyclosporine-treated controls (mean survival time
= 5.5 +/−1.7 vs. 54.7 +/−3.8 days,
P
<
0.001), but they also developed obstructive fibroproliferative coronary
artery lesions much earlier than unimmunized controls (<9 vs. >30
days). These results definitively link indirect allorecognition and
cardiac allograft vasculopathy.
Somatic mosaicism in Fanconi anemia: Evidence of genotypic reversion in lymphohematopoietic stem cells
Authors: Gregory John J. , Wagner John E. , Verlander Peter C. , Levran Orna , Batish Sat Dev , Eide Cindy R. , Steffenhagen Amy , Hirsch Betsy , Auerbach Arleen D.
Published: July 2002

Somatic mosaicism has been observed previously in the
lymphocyte population of patients with Fanconi anemia (FA). To identify
the cellular origin of the genotypic reversion, we examined each
lymphohematopoietic and stromal cell lineage in an FA patient with a
2815–2816ins19 mutation in
FANCA
and known lymphocyte
somatic mosaicism. DNA extracted from individually plucked peripheral
blood T cell colonies and marrow colony-forming unit
granulocyte–macrophage and burst-forming unit erythroid cells revealed
absence of the maternal
FANCA
exon 29 mutation in
74.0%, 80.3%, and 86.2% of colonies, respectively. These data,
together with the absence of the
FANCA
exon 29 mutation
in Epstein–Barr virus-transformed B cells and its presence in
fibroblasts, indicate that genotypic reversion, most likely because of
back mutation, originated in a lymphohematopoietic stem cell and not
solely in a lymphocyte population. Contrary to a predicted increase in
marrow cellularity resulting from reversion in a hematopoietic stem
cell, pancytopenia was progressive. Additional evaluations revealed a
partial deletion of 11q in 3 of 20 bone marrow metaphase cells. By
using interphase fluorescence
in situ
hybridization with
an MLL gene probe mapped to band 11q23 to identify colony-forming unit
granulocyte–macrophage and burst-forming unit erythroid cells with the
11q deletion, the abnormal clone was exclusive to colonies with the
FANCA
exon 29 mutation. Thus, we demonstrate the
spontaneous genotypic reversion in a lymphohematopoietic stem cell. The
subsequent development of a clonal cytogenetic abnormality in
nonrevertant cells suggests that
ex vivo
correction of
hematopoietic stem cells by gene transfer may not be sufficient for
providing life-long stable hematopoiesis in patients with FA.
A single nucleotide polymorphism in the
RAD51
gene modifies cancer risk in
BRCA2
but not
BRCA1
carriers
Authors: Levy-Lahad E. , Lahad A. , Eisenberg S. , Dagan E. , Paperna T. , Kasinetz L. , Catane R. , Kaufman B. , Beller U. , Renbaum P. , Gershoni-Baruch R.
Published: July 2002

BRCA1
and
BRCA2
carriers are at increased
risk for both breast and ovarian cancer, but estimates of lifetime risk
vary widely, suggesting their penetrance is modified by other genetic
and/or environmental factors. The BRCA1 and BRCA2 proteins function
in DNA repair in conjunction with RAD51. A preliminary report suggested
that a single nucleotide polymorphism in the 5′ untranslated region of
RAD51
(135C/G) increases breast cancer risk in
BRCA1
and
BRCA2
carriers. To investigate
this effect we studied 257 female Ashkenazi Jewish carriers of one of
the common
BRCA1
(
185delAG
,
5382insC
) or
BRCA2
(
6174delT
)
mutations. Of this group, 164 were affected with breast and/or
ovarian cancer and 93 were unaffected.
RAD51
genotyping
was performed on all subjects. Among
BRCA1
carriers,
RAD51
-
135C
frequency was similar in
healthy and affected women [6.1% (3 of 49) and 9.9% (12 of 121),
respectively], and RAD-135C did not influence age of cancer diagnosis
[Hazard ratio (HR) = 1.18 for disease in
RAD51
-
135C
heterozygotes, not
significant]. However, in
BRCA2
carriers,
RAD51
-
135C
heterozygote frequency in
affected women was 17.4% (8 of 46) compared with 4.9% (2 of 41) in
unaffected women (
P
= 0.07). Survival analysis in
BRCA2
carriers showed
RAD51
-
135C
increased risk of breast
and/or ovarian cancer with an HR of 4.0 [95% confidence interval
1.6–9.8,
P
= 0.003]. This effect was largely due
to increased breast cancer risk with an HR of 3.46 (95% confidence
interval 1.3–9.2,
P
= 0.01) for breast cancer in
BRCA2
carriers who were
RAD51
-
135C
heterozygotes.
RAD51
status did not affect ovarian cancer risk. These
results show
RAD51
-
135C
is a clinically
significant modifier of
BRCA2
penetrance, specifically
in raising breast cancer risk at younger ages.
Abnormal B lymphocyte development and autoimmunity in hypoxia-inducible factor 1α-deficient chimeric mice
Authors: Kojima Hidefumi , Gu Hua , Nomura Saeko , Caldwell Charles C. , Kobata Tetsuji , Carmeliet Peter , Semenza Gregg L. , Sitkovsky Michail V.
Published: July 2002

Immune cells are exposed to low oxygen tensions as they develop and migrate between blood and different tissues, but the mechanisms by which lymphocytes adapt to hypoxia are poorly understood. Studies reported here of hypoxia-inducible factor 1α (HIF-1α) in lymphocyte development and functions suggest that it has a critical role in regulation of these processes. HIF-1α deficiency in
Hif1α
−/−
→
Rag2
−/−
chimeric mice results in dramatic and cell lineage-specific defects, which include appearance of abnormal peritoneal B-1-like lymphocytes, with high expression of B220 (CD45) receptor-associated protein tyrosine phosphatase and autoimmunity (accumulation of anti-dsDNA antibodies and rheumatoid factor in serum, deposits of IgG and IgM in kidney and proteinuria) as well as distortions of maturation of B-2 lymphocytes in bone marrow.
Ammonium/methylammonium transport (Amt) proteins facilitate diffusion of NH
3
bidirectionally
Authors: Soupene Eric , Lee Haidy , Kustu Sydney
Published: July 2002

The ammonium/methylammonium transport (Amt) proteins of enteric bacteria and their homologues, the methylammonium/ammonium permeases of
Saccharomyces cerevisiae
, are required for fast growth at very low concentrations of the uncharged species NH
3
. For example, they are essential at low ammonium (NH
4
+
+ NH
3
) concentrations under acidic conditions. Based on growth studies in batch culture, the Amt protein of
Salmonella
typhimurium
(AmtB) cannot concentrate either NH
3
or NH
4
+
and this organism appears to have no means of doing so. We now show that
S. typhimurium
releases ammonium into the medium when grown on the alternative nitrogen source arginine and that outward diffusion of ammonium is enhanced by the activity of AmtB. The latter result indicates that AmtB acts bidirectionally. We also confirm a prediction that the AmtB protein would be required at pH 7.0 in ammonium-limited continuous culture, i.e., when the concentration of NH
3
is ≤50 nM. Together with our previous studies, current results are in accord with the view that Amt and methylammonium/ammonium permease proteins increase the rate of diffusion of the uncharged species NH
3
across the cytoplasmic membrane. These proteins are examples of protein facilitators for a gas.
Negative regulation of Lck by Cbl ubiquitin ligase
Authors: Rao Navin , Miyake Sachiko , Reddi Alagarsamy Lakku , Douillard Patrice , Ghosh Amiya K. , Dodge Ingrid L. , Zhou Pengcheng , Fernandes Norvin D. , Band Hamid
Published: July 2002

The Cbl-family ubiquitin ligases function as negative regulators of activated receptor tyrosine kinases by facilitating their ubiquitination and subsequent targeting to lysosomes. Cbl associates with the lymphoid-restricted nonreceptor tyrosine kinase Lck, but the functional relevance of this interaction remains unknown. Here, we demonstrate that T cell receptor and CD4 coligation on human T cells results in enhanced association between Cbl and Lck, together with Lck ubiquitination and degradation. A Cbl
−/−
T cell line showed a marked deficiency in Lck ubiquitination and increased levels of kinase-active Lck. Coexpression in 293T cells demonstrated that Lck kinase activity and Cbl ubiquitin ligase activity were essential for Lck ubiquitination and negative regulation of Lck-dependent serum response element-luciferase reporter activity. The Lck SH3 domain was pivotal for Cbl-Lck association and Cbl-mediated Lck degradation, with a smaller role for interactions mediated by the Cbl tyrosine kinase-binding domain. Finally, analysis of a ZAP-70-deficient T cell line revealed that Cbl inhibited Lck-dependent mitogen-activated protein kinase activation, and an intact Cbl RING finger domain was required for this functional effect. Our results demonstrate a direct, ubiquitination-dependent, negative regulatory role of Cbl for Lck in T cells, independent of Cbl-mediated regulation of ZAP-70.
Integration of emotion and cognition in the lateral prefrontal cortex
Authors: Gray Jeremy R. , Braver Todd S. , Raichle Marcus E.
Published: July 2002

We used functional MRI to test the hypothesis that emotional states can selectively influence cognition-related neural activity in lateral prefrontal cortex (PFC), as evidence for an integration of emotion and cognition. Participants (
n
= 14) watched short videos intended to induce emotional states (pleasant/approach related, unpleasant/withdrawal related, or neutral). After each video, the participants were scanned while performing a 3-back working memory task having either words or faces as stimuli. Task-related neural activity in bilateral PFC showed a predicted pattern: an Emotion × Stimulus crossover interaction, with no main effects, with activity predicting task performance. This highly specific result indicates that emotion and higher cognition can be truly integrated, i.e., at some point of processing, functional specialization is lost, and emotion and cognition conjointly and equally contribute to the control of thought and behavior. Other regions in lateral PFC showed hemispheric specialization for emotion and for stimuli separately, consistent with a hierarchical and hemisphere-based mechanism of integration.
Navigation-related structural change in the hippocampi of taxi drivers
Authors: Maguire Eleanor A. , Gadian David G. , Johnsrude Ingrid S. , Good Catriona D. , Ashburner John , Frackowiak Richard S. J. , Frith Christopher D.
Published: July 2002

Structural MRIs of the brains of humans with extensive navigation experience, licensed London taxi drivers, were analyzed and compared with those of control subjects who did not drive taxis. The posterior hippocampi of taxi drivers were significantly larger relative to those of control subjects. A more anterior hippocampal region was larger in control subjects than in taxi drivers. Hippocampal volume correlated with the amount of time spent as a taxi driver (positively in the posterior and negatively in the anterior hippocampus). These data are in accordance with the idea that the posterior hippocampus stores a spatial representation of the environment and can expand regionally to accommodate elaboration of this representation in people with a high dependence on navigational skills. It seems that there is a capacity for local plastic change in the structure of the healthy adult human brain in response to environmental demands.
Visual constraints in foraging bumblebees: Flower size and color affect search time and flight behavior
Authors: Spaethe J. , Tautz J. , Chittka L.
Published: July 2002

In optimal foraging theory, search time is a key variable defining
the value of a prey type. But the sensory-perceptual processes that
constrain the search for food have rarely been considered. Here we
evaluate the flight behavior of bumblebees (
Bombus
terrestris
) searching for artificial flowers of various sizes
and colors. When flowers were large, search times correlated well with
the color contrast of the targets with their green foliage-type
background, as predicted by a model of color opponent coding using
inputs from the bees' UV, blue, and green receptors. Targets that made
poor color contrast with their backdrop, such as white, UV-reflecting
ones, or red flowers, took longest to detect, even though brightness
contrast with the background was pronounced. When searching for small
targets, bees changed their strategy in several ways. They flew
significantly slower and closer to the ground, so increasing the
minimum detectable area subtended by an object on the ground. In
addition, they used a different neuronal channel for flower detection.
Instead of color contrast, they used only the green receptor signal for
detection. We relate these findings to temporal and spatial limitations
of different neuronal channels involved in stimulus detection and
recognition. Thus, foraging speed may not be limited only by factors
such as prey density, flight energetics, and scramble competition. Our
results show that understanding the behavioral ecology of foraging can
substantially gain from knowledge about mechanisms of visual
information processing.
Filamentous phage as vector-mediated antibody delivery to the brain
Authors: Frenkel Dan , Solomon Beka
Published: July 2002

Early diagnosis of Alzheimer's disease is prevented by lack of means to visualize and target β amyloid plaques in the brains of affected people. There are many methods of detecting amyloid plaques by staining postmortem brain tissue, but none are available for monitoring in living patients. We propose anti-β amyloid antibodies as a highly specific probe to monitor amyloid plaque formation in living patients. Intranasal administration of filamentous phage as delivery vector of anti-β amyloid antibody fragment into Alzheimer's APP transgenic mice enables
in vivo
targeting of β amyloid plaques. The plaques were covisualized both by thioflavin-S and fluorescent-labeled antiphage antibodies in the olfactory bulb and the hippocampus region. The genetically engineered filamentous bacteriophage proved to be an efficient and nontoxic viral delivery vector to the brain, offering an obvious advantage over other mammalian vectors. The ability to image Aβ deposits
in vivo
would arguably provide the most useful diagnostic and monitoring test for early diagnosis of Alzheimer's disease.
Crystal structure of native chicken fibrinogen at 5.5-Å resolution
Authors: Yang Zhe , Mochalkin Igor , Veerapandian Leela , Riley Marcia , Doolittle Russell F.
Published: July 2002

The crystal structure of native chicken fibrinogen has been determined at a resolution of 5.5 Å. The full-length molecule is 460 Å in length and sigmoidally shaped. The structure includes the full sweep of the coiled coils that connect the central and terminal domains; the chain paths of the central domain confirm a predicted scheme of planar disulfide rings in apposition with each other. Electron density maps have revealed the outlines of disordered αC domains nestled within the confines of the sinuous coiled coils. The amino-terminal segments of the α- and β-chains, including the fibrinopeptides A and B, are also disordered.
Low cholesterol stimulates the nonamyloidogenic pathway by its effect on the α-secretase ADAM 10
Authors: Kojro Elzbieta , Gimpl Gerald , Lammich Sven , März Winfried , Fahrenholz Falk
Published: July 2002

Biochemical, epidemiological, and genetic findings demonstrate a
link between cholesterol levels, processing of the amyloid precursor
protein (APP), and Alzheimer's disease. In the present report, we
identify the α-secretase ADAM 10 (
a d
isintegrin
a
nd
m
etalloprotease) as a major target
of the cholesterol effects on APP metabolism. Treatment of various
peripheral and neural cell lines with either the cholesterol-extracting
agent methyl-β-cyclodextrin or the hydroxymethyl glutaryl-CoA
reductase inhibitor lovastatin resulted in a drastic increase of
secreted α-secretase cleaved soluble APP. This strong stimulatory
effect was in the range obtained with phorbol esters and was further
increased in cells overexpressing ADAM 10. In cells overexpressing APP,
the increase of α-secretase activity resulted in a decreased
secretion of Aβ peptides. Several mechanisms were elucidated as being
the basis of enhanced α-secretase activity: increased membrane
fluidity and impaired internalization of APP were responsible for the
effect observed with methyl-β-cyclodextrin; treatment with lovastatin
resulted in higher expression of the α-secretase ADAM 10. Our results
demonstrate that cholesterol reduction promotes the nonamyloidogenic
α-secretase pathway and the formation of neuroprotective
α-secretase cleaved soluble APP by several mechanisms and suggest
approaches to prevention of or therapy for Alzheimer's disease.
Comprehensive human genome amplification using multiple displacement amplification
Authors: Dean Frank B. , Hosono Seiyu , Fang Linhua , Wu Xiaohong , Faruqi A. Fawad , Bray-Ward Patricia , Sun Zhenyu , Zong Qiuling , Du Yuefen , Du Jing , Driscoll Mark , Song Wanmin , Kingsmore Stephen F. , Egholm Michael , Lasken Roger S.
Published: July 2002

Fundamental to most genetic analysis is availability of genomic DNA of adequate quality and quantity. Because DNA yield from human samples is frequently limiting, much effort has been invested in developing methods for whole genome amplification (WGA) by random or degenerate oligonucleotide-primed PCR. However, existing WGA methods like degenerate oligonucleotide-primed PCR suffer from incomplete coverage and inadequate average DNA size. We describe a method, termed multiple displacement amplification (MDA), which provides a highly uniform representation across the genome. Amplification bias among eight chromosomal loci was less than 3-fold in contrast to 4–6 orders of magnitude for PCR-based WGA methods. Average product length was >10 kb. MDA is an isothermal, strand-displacing amplification yielding about 20–30 μg product from as few as 1–10 copies of human genomic DNA. Amplification can be carried out directly from biological samples including crude whole blood and tissue culture cells. MDA-amplified human DNA is useful for several common methods of genetic analysis, including genotyping of single nucleotide polymorphisms, chromosome painting, Southern blotting and restriction fragment length polymorphism analysis, subcloning, and DNA sequencing. MDA-based WGA is a simple and reliable method that could have significant implications for genetic studies, forensics, diagnostics, and long-term sample storage.
Mechanism of plasmid-mediated quinolone resistance
Authors: Tran John H. , Jacoby George A.
Published: July 2002

Quinolones are potent antibacterial agents that specifically target bacterial DNA gyrase and topoisomerase IV. Widespread use of these agents has contributed to the rise of bacterial quinolone resistance. Previous studies have shown that quinolone resistance arises by mutations in chromosomal genes. Recently, a multiresistance plasmid was discovered that encodes transferable resistance to quinolones. We have cloned the plasmid-quinolone resistance gene, termed
qnr,
and found it in an integron-like environment upstream from
qacE
Δ
1
and
sulI
. The gene product Qnr was a 218-aa protein belonging to the pentapeptide repeat family and shared sequence homology with the immunity protein McbG, which is thought to protect DNA gyrase from the action of microcin B17. Qnr had pentapeptide repeat domains of 11 and 28 tandem copies, separated by a single glycine with a consensus sequence of A/C D/N L/F X X. Because the primary target of quinolones is DNA gyrase in Gram-negative strains, we tested the ability of Qnr to reverse the inhibition of gyrase activity by quinolones. Purified Qnr-His
6
protected
Escherichia coli
DNA gyrase from inhibition by ciprofloxacin. Gyrase protection was proportional to the concentration of Qnr-His
6
and inversely proportional to the concentration of ciprofloxacin. The protective activity of Qnr-His
6
was lost by boiling the protein and involved neither quinolone inactivation nor independent gyrase activity. Protection of topoisomerase IV, a secondary target of quinolone action in
E. coli
, was not evident. How Qnr protects DNA gyrase and the prevalence of this resistance mechanism in clinical isolates remains to be determined.