bluuebunny/crossref_metadata_2025 huggingface dataset:
Direct numerical simulation of particle entrainment in turbulent channel flow
Authors: Soltani Mehdi , Ahmadi Goodarz
Published: July 2002

Particle entrainment process in a turbulent channel flow is studied. The time history of the instantaneous turbulent velocity vector field is generated by the direct numerical simulation of the Navier–Stokes equation with the aid of a pseudospectral code. The equation of motion of submicrometer particles including Stokes drag and Brownian diffusion is used, and typical entrained particle trajectories are evaluated and statistically analyzed. It is shown that the wall coherent structure plays a dominant role on the particle entrainment process. Particles are removed from the wall region by being captured in the high speed streams moving away from the wall, which are formed by the flow structure. Furthermore, single streamwise vortices are shown to be more frequent than pairs of counter-rotating ones at every instance of time. Temporal average of the vorticity field, however, shows roughly periodic sequence of counter-rotating vortices in the wall region.
Mode A secondary instability in wake transition
Authors: Williamson C. H. K.
Published: July 2002

It is now well known that the wake transition regime for a circular cylinder involves two modes of secondary three-dimensional instability (modes ‘‘A’’ and ‘‘B’’), depending on the regime of Reynolds number (Re). However, there exists a surprisingly large scatter in previous measurements of critical Re for the inception of the mode A instability (Re from 140 to 190) and in previous measurements of spanwise length scale. It is deduced in this work that the large variation in previous measurements concerning mode A are due to the presence of vortex dislocations. In the absence of such dislocations, we find an excellent agreement of the critical Re as well as spanwise wavelength of mode A with the linear secondary stability analysis of Henderson and Barkley [Phys. Fluids 8, 1683 (1996)]. We further demonstrate that these large-scale dislocations in wake transition are triggered at the sites of some of the vortex loops for mode A; they are an intrinsic feature of transition, independent of end conditions. These studies lead us to a new clarification of the possible flow states through wake transition, as follows. If one defines a Mode A* as (Mode A+Dislocations), then the route through transition appears to follow the scenario of wake modes: (2D→A→A*→B).
Evolution of a shock-accelerated thin fluid layer
Authors: Rightley P. M. , Vorobieff P. , Benjamin R. F.
Published: July 2002

Multi-exposure flow visualization experiments with laser-sheet illumination provide growth-rate measurement of Richtmyer–Meshkov instability of a thin, perturbed heavy-gas layer embedded in a lower-density gas and accelerated by a planar shock wave. The measurements clearly show the three-stage transition to turbulence of this gas-curtain instability and the single-event coexistence of the three primary flow morphologies discovered previously. The shock-induced circulation for each event is estimated using a simple model based on Richtmyer–Meshkov instability and an infinite linear array of vortex points. These estimates are consistent with simplified flow simulations using a finite-core vortex-blob model.
Stability of stagnation points in rotating flows
Authors: Leblanc Stéphane
Published: July 2002

The Lifschitz and Hameiri theory for short-wave instabilities is used to show that any steady inviscid plane flow subjected (or not) to a Coriolis with perpendicular angular velocity vector is unstable to three-dimensional perturbations if Φ(x0)<0 on a stagnation point located at x0. Φ is the second invariant of the inertial tensor [Leblanc and Cambon, Phys. Fluids 9, 1307 (1997)]. The particular cases of zero absolute W(x0)+2Ω=0 and zero tilting W(x0)+4Ω=0 vorticities are also considered. The criterion is applied to Chaplygin’s non-symmetric dipolar vortex moving along a circular path, which is shown to be unstable.
Pattern study in the 2-D solutal convection above a Bridgman-type solidification front
Authors: Le Marec C. , Guérin R. , Haldenwang P.
Published: July 2002

We numerically investigate the two-dimensional (2-D) convective flow developing in the liquid phase above an alloy growing in the upward Bridgman configuration of directional solidification. Using a time-dependent approach, we are able to describe the various cycles of hysteresis that connect the different branches of stable steady solutions. The main trends of the present results show that the bifurcation diagram, composed of the branches, found in previous works for the partition coefficient k=0.3, remains qualitatively valid for k=1.1: for a small frontal width the leading primary bifurcation is subcritical, while a transcritical bifurcation occurs for larger front. We bring the new complementary feature that the subcritical bifurcation becomes supercritical when the front width tends to zero. Furthermore, for an intermediate frontal width, we address the question of the nature of upper stability limits on various stable steady branches. We show that the limit occurs via either a steady secondary bifurcation or a Hopf bifurcation that initiates an unsteady solution branch which is followed up to chaos. The related route is a subharmonic cascade. When following this chaotic branch, a striking relaminarization process towards a steady secondary branch occurs. Finally we shortly investigate the case of a twice larger frontal width, for which several cycles of hysteresis are equally reported.
Three-point statistics and the anisotropy of a turbulent passive scalar
Authors: Mydlarski L. , Warhaft Z.
Published: July 2002

The mixing of passive scalar (temperature) fluctuations produced by the action of a mean temperature gradient in decaying isotropic grid-generated turbulence is studied experimentally for the range 200<Rλ<500. Previously, the observed anisotropy of the small scale (inertial range) scalar fluctuation statistics has been described in terms of two-point structure functions. Here we map the three-point cross-correlation and structure functions. We show that they exhibit universal characteristics. These are related to the ramp-cliff morphology that is ubiquitous to all flows with mean gradients of a passive scalar.
Vortices in rotating systems: Centrifugal, elliptic and hyperbolic type instabilities
Authors: Sipp D. , Lauga E. , Jacquin L.
Published: July 2002

This paper is devoted to the effects of rotation on the linear dynamics of two-dimensional vortices. The asymmetric behavior of cyclones and anticyclones, a basic problem with respect to the dynamics of rotating flows, is particularly addressed. This problem is investigated by means of linear stability analyses of flattened Taylor–Green vortices in a rotating system. This flow constitutes an infinite array of contra-rotating one-signed nonaxisymmetric vorticity structures. We address the stability of this flow with respect to three-dimensional short-wave perturbations via both the geometrical optics method and via a classical normal mode analysis, based on a matrix eigenvalue method. From a physical point of view, we show that vortices are affected by elliptic, hyperbolic and centrifugal instabilities. A complete picture of the short-wave stability properties of the flow is given for various levels of the background rotation. For Taylor–Green cells with aspect ratio E=2, we show that anticyclones undergo centrifugal instability if the Rossby number verifies Ro>1, elliptic instability for all values of Ro except 0.75<Ro<1.25 and hyperbolic instability. The Rossby number is here defined as the ratio of the maximum amplitude of vorticity to twice the background rotation. On the other hand, cyclones bear elliptic and hyperbolic instabilities whatever the Rossby number. Besides, depending on the Rossby number, rotation can either strengthen (anticyclonic vortices) or weaken elliptic instability. From a technical point of view, in this article we bring an assessment of the links between the short-wave asymptotics and the normal mode analysis. Normal modes are exhibited which are in complete agreement with the short-wave asymptotics both with respect to the amplification rate and with respect to the structure of the eigenmode. For example, we show centrifugal eigenmodes which are localized in the vicinity of closed streamlines in the anticyclones; elliptical eigenmodes which are concentrated in the center of the cyclones or anticyclones; hyperbolic eigenmodes which are localized in the neighborhood of closed streamlines in cyclones.
Regimes of suprathermal electron transport
Authors: Glinsky Michael E.
Published: July 2002

Regimes of the one-dimensional (1-D) transport of suprathermal electrons into a cold background plasma are delineated. A well ordered temporal progression is found through eras where J⋅E heating, hot electron–cold electron collisional heating, and diffusive heat flow dominate the cold electron energy equation. Scaling relations for how important quantities such as the width and temperature of the heated layer of cold electrons evolve with time are presented. These scaling relations are extracted from a simple 1-D model of the transport which can be written in dimensionless form with one free parameter. The parameter is shown to be the suprathermal electron velocity divided by the drift velocity of cold electrons which balances the suprathermal current. Special attention is paid to the assumptions which allow the reduction from the collisional Vlasov equation, using a Fokker–Planck collision operator, to this simple model. These model equations are numerically solved and compared to both the scaling relations and a more complete multigroup electron diffusion transport. Implications of the scaling relations on fast ion generation, magnetic field generation, and electric field inhibition of electron transport are examined as they apply to laser heated plasmas.
Simultaneous measurement of viscosity and flow velocity in Texas Experimental Tokamak-Upgrade (TEXT-U) edge plasmas by using a Visco-Mach probe
Authors: Chung Kyu-Sun , Bengtson Roger D.
Published: July 2002

Shear viscosity [η≡α×(mass density)×(diffusivity)] and parallel flow velocity [M∞×(Te+Ti)/mi] of tokamak edge plasma were simultaneously measured in the Texas Experimental Tokamak-Upgrade (TEXT-U) tokamak by using a “Visco-Mach” probe with the iteration method (VMPI) [K-S. Chung, Nucl. Fusion 34, 1213 (1994)]. The VMPI was composed of two Mach probes measuring two ratios of ion saturation current densities, with the small Mach probe located within the free presheath generated by the large Mach probe (LMP). Radial variations of the normalized shear viscosity, α, and parallel Mach number, M∞, for typical discharges were deduced from two measured ratios of ion saturation current densities, and plasma density from ion saturation currents by LMP. Here α varied from 0.7 to 1.3 with an estimated error of ±40%, and M∞ from 0 to 0.2 for 0<r−rl<4.5 cm, where rl=27 cm is the limiter radius. Also, α and M∞ increased with the radial direction, while cross-field diffusivity (D⊥) was approximately constant. Here D⊥ is obtained as ∼3DB, where a typical Bohm diffusivity (DB) is ∼1 m2/s.
Electric-drift generated trajectories and particle acceleration in collisionless magnetic reconnection
Authors: Vekstein G. E. , Browning P. K.
Published: July 2002

Adiabatic acceleration of charged particles along magnetic field lines originates from the coupling between the electric drift and longitudinal motion in a nonunidirectional magnetic field. As a result, initially slow particles entering the reconnection site of an X-type magnetic geometry can leave the latter as substantially accelerated jets directed along the magnetic separatrices. The corresponding energy spectrum has a power-law form, with the spectral index depending on the angle between the separatrices.
The formation of large-scale structures in supersonic magnetohydrodynamic flows
Authors: Balsara D. , Pouquet A.
Published: July 2002

In this paper we investigate the existence of an inverse cascade of magnetic helicity for statistically steady compressible magnetohydrodynamic flows with rms Mach numbers that go up to unity. This has been done by performing a set of three-dimensional numerical simulations that were carried out using the RIEMANN code for astrophysical fluid and magnetofluid dynamics [D. S. Balsara, Astrophys. J. Suppl. 116, 133 (1988)]. The random forcing is made up of ABC flows corresponding to helical wave patterns at an intermediate scale. Both time histories of integral quantities and Fourier spectra are shown, illustrating the inverse cascade process. The observed build-up of large-scale magnetic helical structures for a wide range of Mach numbers indicates that, in the context of the generation of the magnetic field of the Galaxy where supersonic flows are common, a dynamo mechanism based on the nonlinear dynamics of magnetic helicity may be at work.
Rayleigh–Taylor instability of magnetized density transition layer
Authors: Tavakoli A. , Hadzievski L. , Tskhakaya D. D.
Published: July 2002

In presence of a uniform magnetic field for a smoothly varying density profile in a limit of small Atwood numbers, an analytic solution is obtained. The spectrum of unstable modes is defined. It is shown that this spectrum is two-side-bounded. The external magnetic field stabilizes some or all modes of the spectrum. It was shown that a finite width transition layer undergoes stratification. The magnetic field makes the stratification smoother. A velocity shear between the newly formed sublayers takes place.
High field electron transport in n-InP/GaInAs two-dimensional electron gas
Authors: Tsubaki Kotaro , Fukui Takashi , Saito Hisao
Published: July 2002

High field electron transport in n-InP/GaInAs two-dimensional electron gas (2DEG) is studied at liquid helium temperature. In this experiment two kinds of samples are used: the first has a thick enough GaInAs layer to contain a three-dimensional gas; the other has a thin GaInAs layer containing only a 2DEG on the GaInAs side of the heterojunction. In the sample with the thick GaInAs layer, Gunn oscillations are observed above 2.2 kV/cm. In the sample with the thin GaInAs layer, Gunn oscillations do not occur and an irreversible decrease of the sheet concentration of 2DEG is obtained after applying a high electric field. The highest measured drift velocity of this sample is 4.4×107 cm/s at 3.8 kV/cm.
Amorphous SiN:H dielectrics with low density of defects
Authors: Hasegawa S. , Matuura M. , Kurata Y.
Published: July 2002

Amorphous SiNx:H films were prepared by rf glow discharge (GD) of SiH4-N2-H2 mixtures at 300 °C using a new decomposition technique. The optical gap Eg increases slowly with the ratio N2/SiH4 up to a critical gap Egc of 2.5–3.0 eV, and then rapidly increases up to 5.3 eV. The spin density Ns from electron spin resonance of Si dangling bonds increases with N2/SiH4 until Eg reaches Egc. Above Egc, Ns rapidly decreases in contrast with that of conventional GD films, but in similarity to pyrolytic films. The slope B in Tauc equation for optical absorption corresponds well with Ns.
Characterization of protein kinase C β isoform's action on retinoblastoma protein phosphorylation, vascular endothelial growth factor-induced endothelial cell proliferation, and retinal neovascularization
Authors: Suzuma Kiyoshi , Takahara Noriko , Suzuma Izumi , Isshiki Keiji , Ueki Kohjiro , Leitges Michael , Aiello Lloyd Paul , King George L.
Published: July 2002

Retinal neovascularization is a major cause of blindness and requires the activities of several signaling pathways and multiple cytokines. Activation of protein kinase C (PKC) enhances the angiogenic process and is involved in the signaling of vascular endothelial growth factor (VEGF). We have demonstrated a dramatic increase in the angiogenic response to oxygen-induced retinal ischemia in transgenic mice overexpressing PKCβ2 isoform and a significant decrease in retinal neovascularization in PKCβ isoform null mice. The mitogenic action of VEGF, a potent hypoxia-induced angiogenic factor, was increased by 2-fold in retinal endothelial cells by the overexpression of PKCβ1 or β2 isoforms and inhibited significantly by the overexpression of a dominant-negative PKCβ2 isoform but not by the expression of PKC α, δ, and ζ isoforms. Association of PKCβ2 isoform with retinoblastoma protein was discovered in retinal endothelial cells, and PKCβ2 isoform increased retinoblastoma phosphorylation under basal and VEGF-stimulated conditions. The potential functional consequences of PKCβ-induced retinoblastoma phosphorylation could include enhanced E2 promoter binding factor transcriptional activity and increased VEGF-induced endothelial cell proliferation.
Osteopontin deficiency protects joints against destruction in anti-type II collagen antibody-induced arthritis in mice
Authors: Yumoto Kenji , Ishijima Muneaki , Rittling Susan R. , Tsuji Kunikazu , Tsuchiya Yoko , Kon Shigeyuki , Nifuji Akira , Uede Toshimitsu , Denhardt David T. , Noda Masaki
Published: July 2002

Rheumatoid arthritis is one of the most critical diseases that impair the quality of life of patients, but its pathogenesis has not yet been fully understood. Osteopontin (OPN) is an extracellular matrix protein containing Arg-Gly-Asp (RGD) sequence, which interacts with αvβ3 integrins, promotes cell attachment, and cell migration and is expressed in both synovial cells and chondrocytes in rheumatoid arthritis; however, its functional relationship to arthritis has not been known. Therefore, we investigated the roles of OPN in the pathogenesis of inflammatory process in a rheumatoid arthritis model induced by a mixture of anti-type II collagen mAbs and lipopolysaccharide (mAbs/LPS). mAbs/LPS injection induced OPN expression in synovia as well as cartilage, and this expression was associated with joint swelling, destruction of the surface structures of the joint based on scanning electron microscopy, and loss of toluidine blue-positive proteoglycan content in the articular cartilage in wild-type mice. In contrast, OPN deficiency prevented the mice from such surface destruction, loss of proteoglycan in the articular joint cartilage, and swelling of the joints even when the mice were subjected to mAbs/LPS injection. Furthermore, mAbs/LPS injection in wild-type mice enhanced the levels of CD31-positive vessels in synovia and terminal deoxynucleotidyltransferase-mediated UTP end labeling-positive chondrocytes in the articular cartilage, whereas such angiogenesis as well as chondrocyte apoptosis was suppressed significantly in OPN-deficient mice. These results indicated that OPN plays a critical role in the destruction of joint cartilage in the rheumatoid arthritis model in mice via promotion of angiogenesis and induction of chondrocyte apoptosis.
Human tumor suppressor
EXT
gene family members
EXTL1
and
EXTL3
encode α1,4-
N
-acetylglucosaminyltransferases that likely are involved in heparan sulfate/ heparin biosynthesis
Authors: Kim Byung-Taek , Kitagawa Hiroshi , Tamura Jun-ichi , Saito Toshiyuki , Kusche-Gullberg Marion , Lindahl Ulf , Sugahara Kazuyuki
Published: July 2002

The tumor suppressors
EXT1
and
EXT2
are associated with hereditary multiple exostoses and encode bifunctional glycosyltransferases essential for chain polymerization of heparan sulfate (HS) and its analog, heparin (Hep). Three highly homologous
EXT
-like genes,
EXTL1–EXTL3
, have been cloned, and EXTL2 is an α1,4-GlcNAc transferase I, the key enzyme that initiates the HS/Hep synthesis. In the present study, truncated forms of EXTL1 and EXTL3, lacking the putative NH
2
-terminal transmembrane and cytoplasmic domains, were transiently expressed in COS-1 cells and found to harbor α-GlcNAc transferase activity. EXTL3 used not only
N
-acetylheparosan oligosaccharides that represent growing HS chains but also GlcAβ1–3Galβ1-
O
-C
2
H
4
NH-benzyloxycarbonyl (Cbz), a synthetic substrate for α-GlcNAc transferase I that determines and initiates HS/Hep synthesis. In contrast, EXTL1 used only the former acceptor. Neither EXTL1 nor EXTL3 showed any glucuronyltransferase activity as examined with
N
-acetylheparosan oligosaccharides. Heparitinase I digestion of each transferase-reaction product showed that GlcNAc had been transferred exclusively through an α1,4-configuration. Hence, EXTL3 most likely is involved in both chain initiation and elongation, whereas EXTL1 possibly is involved only in the chain elongation of HS and, maybe, Hep as well. Thus, their acceptor specificities of the five family members are overlapping but distinct from each other, except for EXT1 and EXT2 with the same specificity. It now has been clarified that all of the five cloned human
EXT
gene family proteins harbor glycosyltransferase activities, which probably contribute to the synthesis of HS and Hep.
The GABA
B
receptor interacts directly with the related transcription factors CREB2 and ATFx
Authors: White Julia H. , McIllhinney R. A. Jeffrey , Wise Alan , Ciruela Francisco , Chan Wai-Yee , Emson Piers C. , Billinton Andrew , Marshall Fiona H.
Published: July 2002

γ-Aminobutyric acid type B (GABA
B
) receptors mediate
the metabotropic actions of the inhibitory neurotransmitter GABA. These
seven-transmembrane receptors are known to signal primarily through
activation of G proteins to modulate the action of ion channels or
second messengers. The functional GABA
B
receptor is made up
of a heterodimer consisting of two subunits, GABA
B
-R1 and
GABA
B
-R2, which interact via coiled-coil domains in their
C-terminal tails. By using a yeast two-hybrid approach, we have
identified direct interactions between the C-terminal tails of
GABA
B
-R1 and GABA
B
-R2 with two related
transcription factors, CREB2 (ATF4) and ATFx. In primary neuronal
cultures as well in recombinant Chinese hamster ovary cells expressing
GABA
B
receptors, CREB2 is localized within the cytoplasm as
well as the nucleus. Activation of the GABA
B
receptor by
the specific agonist baclofen leads to a marked translocation and
accumulation of CREB2 from the cytoplasm into the nucleus. We
demonstrate that receptor stimulation results in activation of
transcription from a CREB2 responsive reporter gene. Such a signaling
mechanism is unique among Family C G protein-coupled receptors and, in
the case of the GABA
B
receptor and CREB2, may play a role
in long-term changes in the nervous system.
Enzyme interactions in heparan sulfate biosynthesis: Uronosyl 5-epimerase and 2-
O
-sulfotransferase interact
in vivo
Authors: Pinhal Maria A. S. , Smith Brian , Olson Sara , Aikawa Jun-ichi , Kimata Koji , Esko Jeffrey D.
Published: July 2002

The formation of heparan sulfate occurs within the lumen of the endoplasmic reticulum–Golgi complex–trans-Golgi network by the concerted action of several glycosyltransferases, an epimerase, and multiple sulfotransferases. In this report, we have examined the location and interaction of tagged forms of five of the biosynthetic enzymes: galactosyltransferase I and glucuronosyltransferase I, required for the formation of the linkage region, and GlcNAc
N-
deacetylase/
N
-sulfotransferase 1, uronosyl 5-epimerase, and uronosyl 2-
O
-sulfotransferase, the first three enzymes involved in the modification of the chains. All of the enzymes colocalized with the medial-Golgi marker α-mannosidase II. To study whether any of these enzymes interacted with each other, they were relocated to the endoplasmic reticulum (ER) by replacing their cytoplasmic N-terminal tails with an ER retention signal derived from the cytoplasmic domain of human invariant chain (p33). Relocating either galactosyltransferase I or glucuronosyltransferase I had no effect on the other's location or activity. However, relocating the epimerase to the ER caused a parallel redistribution of the 2-
O
-sulfotransferase. Transfected epimerase was also located in the ER in a cell mutant lacking the 2-
O
-sulfotransferase, but moved to the Golgi when the cells were transfected with 2-
O
-sulfotransferase cDNA. Epimerase activity was depressed in the mutant, but increased upon restoration of 2-
O
-sulfotransferase, suggesting that their physical association was required for both epimerase stability and translocation to the Golgi. These findings provide
in vivo
evidence for the formation of complexes among enzymes involved in heparan sulfate biosynthesis. The functional significance of these complexes may relate to the rapidity of heparan sulfate formation.
Targeting endothelium and its dynamic caveolae for tissue-specific transcytosisin vivo: A pathway to overcome cell barriers to drug and gene delivery
Authors: McIntosh Deirdre P. , Tan Xiang-Yang , Oh Phil , Schnitzer Jan E.
Published: July 2002

Site-directed pharmacodelivery is a desirable but elusive goal. Endothelium and epithelium create formidable barriers to endogenous molecules as well as targeted therapiesin vivo. Caveolae provide a possible, yet unproven, transcellular pathway to overcome such barriers. By using an antibody- and subfractionation-based strategy, we generated a monoclonal antibody specific for lung caveolae (TX3.833) that targets rat lungs after i.v. injection (up to 89% of dose in 30 min). Unlike control antibodies (nonbinding or to lipid rafts), TX3.833 targets lung caveolae that bud to form free vesicles for selective and quantal transendothelial transport to underlying tissue cellsin vivo. Rapid sequential transcytosis can occur to the alveolar air space via epithelial caveolae. Conjugation to TX3.833 increases drug delivery to the lung up to 172-fold and achieves rapid, localized bioefficacy. We conclude that: (i) molecular heterogeneity of the endothelium and its caveolae permits vascular targeting to achieve theoretical expectations of tissue-specific delivery and bioefficacy; (ii) caveolae can mediate selective transcytosisin vivo; and (iii) targeting caveolae may provide a tissue-specific pathway for overcoming key cell barriers to many drug and gene therapiesin vivo.
Evidence for a
NOD2
-independent susceptibility locus for inflammatory bowel disease on chromosome 16p
Authors: Hampe Jochen , Frenzel Henning , Mirza Muddassar M. , Croucher Peter J. P. , Cuthbert Andrew , Mascheretti Silvia , Huse Klaus , Platzer Matthias , Bridger Stephen , Meyer Birgit , Nürnberg Peter , Stokkers Pieter , Krawczak Michael , Mathew Christopher G. , Curran Mark , Schreiber Stefan
Published: July 2002

Heritable predisposition to inflammatory bowel disease (IBD) has
been demonstrated by epidemiological and genetic analysis.
Linkage of IBD to broad regions of chromosome 16 has been
established by analysis of multiple populations.
NOD2
,
located on proximal 16q, was recently identified as an IBD gene. As the
linkage regions on chromosome 16 are large, we have investigated the
possibility that
NOD2
is not the only IBD gene located
on this chromosome. A high-density experiment using 39 microsatellite
markers was performed to identify additional regions of
association, and to indicate areas of interest for further
investigation. A triple-peaked configuration of the linkage curve with
peak logarithm of odds (lod) scores of 2.7, 3.2, and 3.1 was observed
on proximal 16p, proximal 16q, and central 16q, respectively. The
cohort was stratified by coding individuals carrying the NOD2 single
nucleotide polymorphism (SNP)8 and SNP13 “unknown.” Significance
at the central peak, corresponding to the genomic location of
NOD2
, then decreased from 3.2 to 1.2. The maximal lod
scores on the proximal p-arm (lod = 2.1) and central q-arm
(lod = 2.6) changed only moderately. An exploratory association
analysis (TRANSMIT) yielded a strong lead at D16S3068
(
P
= 0.00028). The region around this marker was
further investigated by using anonymous SNPs. An associated haplotype
containing three SNPs was identified (peak significance
P
= 0.00027, IBD phenotype). On stratification
based on
NOD2
genotype, this significance increased to
P
= 0.0001. These results confirm the importance of
NOD2
and provide evidence for a second IBD gene
located on chromosome 16p.
Leukotriene A4 hydrolase: protection from mechanism-based inactivation by mutation of tyrosine-378.
Authors: Mueller M J , Blomster M , Oppermann U C , Jörnvall H , Samuelsson B , Haeggström J Z
Published: July 2002

Leukotriene A4 (LTA4) hydrolase [(7E,9E,11Z,14Z)-(5S,6S)-5,6-epoxyicosa-7, 9,11,14-tetraenoate hydrolase; EC 3.3.2.6] is a bifunctional zinc metalloenzyme that catalyzes the final step in the biosynthesis of the potent chemotactic agent leukotriene B4 (LTB4). LTA4 hydrolase/aminopeptidase is suicide inactivated during catalysis via an apparently mechanism-based irreversible binding of LTA4 to the protein in a 1:1 stoichiometry. Previously, we have identified a henicosapeptide, encompassing residues Leu-365 to Lys-385 in human LTA4 hydrolase, which contains a site involved in the covalent binding of LTA4 to the native enzyme. To investigate the role of Tyr-378, a potential candidate for this binding site, we exchanged Tyr for Phe or Gln in two separate mutants. In addition, each of two adjacent and potentially reactive residues, Ser-379 and Ser-380, were exchanged for Ala. The mutated enzymes were expressed as (His)6-tagged fusion proteins in Escherichia coli, purified to apparent homogeneity, and characterized. Enzyme activity determinations and differential peptide mapping, before and after repeated exposure to LTA4, revealed that wild-type enzyme and the mutants [S379A] and [S380A]LTA4hydrolase were equally susceptible to suicide inactivation whereas the mutants in position 378 were no longer inactivated or covalently modified by LTA4. Furthermore, in [Y378F]LTA4 hydrolase, the value of kcat for epoxide hydrolysis was increased 2.5-fold over that of the wild-type enzyme. Thus, by a single-point mutation in LTA4 hydrolase, catalysis and covalent modification/inactivation have been dissociated, yielding an enzyme with increased turnover and resistance to mechanism-based inactivation.
Human cyclin-dependent kinase-activating kinase exists in three distinct complexes.
Authors: Drapkin R , Le Roy G , Cho H , Akoulitchev S , Reinberg D
Published: July 2002

Transcription factor IIH (TFIIH) is a multisubunit complex required for transcription and for DNA nucleotide excision repair. TFIIH possesses three enzymatic activities: (i) an ATP-dependent DNA helicase, (ii) a DNA-dependent ATPase, and (iii) a kinase with specificity for the carboxyl-terminal domain of RNA polymerase II. The kinase activity was recently identified as the cdk (cyclin-dependent kinase) activating kinase, CAK, composed of cdk7, cyclin H, and MAT-1. Here we report the isolation and characterization of three distinct CAK-containing complexes from HeLa nuclear extracts: CAK, a novel CAK-ERCC2 complex, and TFIIH. CAK-ERCC2 can efficiently associate with core-TFIIH to reconstitute holo-TFIIH transcription activity. We present evidence proposing a critical role for ERCC2 in mediating the association of CAK with core TFIIH subunits.
bcl-2 overexpression reduces apoptotic photoreceptor cell death in three different retinal degenerations.
Authors: Chen J , Flannery J G , LaVail M M , Steinberg R H , Xu J , Simon M I
Published: July 2002

Apoptosis of photoreceptors occurs infrequently in adult retina but can be triggered in inherited and environmentally induced retinal degenerations. The protooncogene bcl-2 is known to be a potent regulator of cell survival in neurons. We created lines of transgenic mice overexpressing bcl-2 to test for its ability to increase photoreceptor survival. Bcl-2 increased photoreceptor survival in mice with retinal degeneration caused by a defective opsin or cGMP phosphodiesterase. Overexpression of Bcl-2 in normal photoreceptors also decreased the damaging effects of constant light exposure. Apoptosis was induced in normal photoreceptors by very high levels of bcl-2. We conclude that bcl-2 is an important regulator of photoreceptor cell death in retinal degenerations.
Retrotransposons of rice involved in mutations induced by tissue culture.
Authors: Hirochika H , Sugimoto K , Otsuki Y , Tsugawa H , Kanda M
Published: July 2002

Five retrotransposon families of rice (Tos1-Tos5) have been reported previously. Here we report 15 new retrotransposon families of rice (Tos6-Tos20). In contrast to yeast and Drosophila retrotransposons, all of the rice retrotransposons examined appear inactive (or almost inactive) under normal growth conditions. Three of the rice retrotransposons (Tos10, Tos17, and Tos19) are activated under tissue culture conditions. The most active one, Tos17, was studied in detail. The copy number of Tos17 increased with prolonged culture period. In all of the plants regenerated from tissue cultures, including transgenic plants, 5 to 30 transposed Tos17 copies were detected. The transcript of Tos17 was only detected under tissue culture conditions, indicating that the transposition of Tos17 is mainly regulated at the transcriptional level. To examine the target-site specificity of Tos17 transposition, sequences flanking transposed Tos17 copies were analyzed. At least four out of eight target sites examined are coding regions. Other target sites may also be in genes because two out of four were transcribed. The regenerated plants with Tos17-insertions in the phytochrome A gene and the S-receptor kinase-related gene were identified. These results indicate that activation of Tos17 is an important cause of tissue culture-induced mutations. Tissue culture-induced activation of Tos17 may be a useful tool for insertional mutagenesis and functional analysis of genes.
An experimental system for analyzing response to a morphogen gradient.
Authors: Gurdon J B , Mitchell A , Ryan K
Published: July 2002

A recently described experimental system for analyzing the mode of action of a morphogen gradient involves the in situ hybridization of sectioned tissue constructs. In these constructs, a source of activin signaling induces the transcription of several mesodermal genes in blastula animal caps, according to the position of cells in a concentration gradient. New experiments show that activin-loaded beads emit a signal for only 2 hr and that the same cell can be induced to express different genes. We determine the position in the gradient and the time after the start of activin signaling at which early genes, including Mix1, Xpo, Xwnt8, Xchd, and Xlim1, are activated, relative to the previously tested genes Xbra and Xgsc.
Nitric oxide production in SJL mice bearing the RcsX lymphoma: a model for in vivo toxicological evaluation of NO.
Authors: Gal A , Tamir S , Tannenbaum S R , Wogan G N
Published: July 2002

SJL mice spontaneously develop pre-B-cell lymphoma that we hypothesized might stimulate macrophages to produce nitric oxide (NO.). Transplantation of an aggressive lymphoma (RcsX) was used to induce tumor formation. Urinary nitrate excretion was measured as an index of NO. production and was found to increase 50-fold by 13 days after tumor injection. NO. production was prevented by the addition of a nitric oxide synthase (NOS) inhibitor. The expression of inducible NOS (iNOS) in various tissues was estimated by Western blot analysis and localized by immunohistochemistry. The synthase was detected in the spleen, lymph nodes, and liver of treated but not control mice. To assess whether the iNOS-staining cells were macrophages, spleen sections from ResX-bearing animals were costained with anti-iNOS antibody and the anti-macrophage antibody moma-2. Expression of iNOS was found to be limited to a subset of the macrophage population. The concentration of gamma-interferon, a cytokine known to induce NO. production by macrophages, in the serum of tumor-bearing mice, was measured and found to be elevated 25-fold above untreated mice. The ability of ResX-activated macrophages to inhibit splenocyte growth in primary culture was estimated and macrophage-derived NO. was found to inhibit cell division 10-fold. Our findings demonstrate that ResX cells stimulate NO. production by macrophages in the spleen and lymph nodes of SJL mice, and we believe this experimental model will prove useful for study of the toxicological effects of NO. under physiological conditions.
Evidence for a transcriptional activation function of BRCA1 C-terminal region
Authors: Monteiro Alvaro N. A. , August Avery , Hanafusa Hidesaburo
Published: July 2002

Mutations inBRCA1account for 45% of families with high incidence of breast cancer and for 80–90% of families with both breast and ovarian cancer. BRCA1 protein includes an amino-terminal zinc finger motif as well as an excess of negatively charged amino acids near the C terminus. In addition, BRCA1 contains two nuclear localization signals and localizes to the nucleus of normal cells. While these features suggest a role in transcriptional regulation, no function has been assigned to BRCA1. Here, we show that the C-terminal region, comprising exons 16–24 (aa 1560–1863) of BRCA1 fused to GAL4 DNA binding domain can activate transcription both in yeast and mammalian cells. Furthermore, we define the region comprising exons 21–24 (aa 1760–1863) as the minimal transactivation domain. Any one of four germ-line mutations in the C-terminal region found in patients with breast or ovarian cancer (Ala-1708 → Glu, Gln-1756 C+, Met-1775 → Arg, Tyr-1853 → Stop), had markedly impaired transcription activity. Together these data underscore the notion that one of the functions of BRCA1 may be the regulation of transcription.
Zinc folds the N-terminal domain of HIV-1 integrase, promotes multimerization, and enhances catalytic activity
Authors: Zheng Ronglan , Jenkins Timothy M. , Craigie Robert
Published: July 2002

The N-terminal domain of HIV-1 integrase contains a pair of His and
Cys residues (the HHCC motif) that are conserved among retroviral
integrases. Although His and Cys residues are often involved in binding
zinc, the HHCC motif does not correspond to any recognized class of
zinc binding domain. We have investigated the binding of zinc to HIV-1
integrase protein and find that it binds zinc with a stoichiometry of
one zinc per integrase monomer. Analysis of zinc binding to deletion
derivatives of integrase locates the binding site to the N-terminal
domain. Integrase with a mutation in the HHCC motif does not bind zinc,
consistent with coordination of zinc by these residues. The isolated
N-terminal domain is disordered in the absence of zinc but, in the
presence of zinc, it adopts a secondary structure with a high alpha
helical content. Integrase bound by zinc tetramerizes more readily than
the apoenzyme and is also more active than the apoenzyme in
in
vitro
integration assays. We conclude that binding of zinc to
the HHCC motif stabilizes the folded state of the N-terminal domain of
integrase and bound zinc is required for optimal enzymatic activity.
Fidelity of RNA polymerase II transcription controlled by elongation factor TFIIS
Authors: Jeon ChoonJu , Agarwal Kan
Published: July 2002

Fidelity of DNA and protein synthesis is regulated by a
proofreading mechanism but function of a similar mechanism during RNA
synthesis has not been demonstrated. Analysis of transcriptional
fidelity and its control has been hampered by the necessity to employ
complex DNA templates requiring either a promoter and initiation
factors or 3′-extended templates. To circumvent this difficulty, we
have created an RNA–DNA dumbbell template that can be recognized as a
template-primer and extended by RNA polymerase II. By employing this
system, we demonstrate that RNA polymerase II can misincorporate a
nucleotide and carry out template-dependent elongation at the mispaired
end. The transcripts containing misincorporated residues can be cleaved
by the very slow 3′ → 5′ ribonuclease activity of the RNA polymerase
II, but enhancement of this activity by the elongation factor TFIIS
generates RNA with a high degree of fidelity. This enhanced
preferential cleavage of misincorporated transcripts suggests an
important role for TFIIS in maintaining transcriptional fidelity.
Prevention of cardiovascular and renal pathology of aging by the advanced glycation inhibitor aminoguanidine.
Authors: Li Y M , Steffes M , Donnelly T , Liu C , Fuh H , Basgen J , Bucala R , Vlassara H
Published: July 2002

Human aging is impacted severely by cardiovascular disease and significantly but less overtly by renal dysfunction. Advanced glycation endproducts (AGEs) have been linked to tissue damage in diabetes and aging, and the AGE inhibitor aminoguanidine (AG) has been shown to inhibit renal and vascular pathology in diabetic animals. In the present study, the effects of AG on aging-related renal and vascular changes and AGE accumulation were studied in nondiabetic female Sprague-Dawley (S-D) and Fischer 344 (F344) rats treated with AG (0.1% in drinking water) for 18 mo. Significant increases in the AGE content in aged cardiac (P < 0.05), aortic (P < 0.005), and renal (P < 0.05) tissues were prevented by AG treatment (P < 0.05 for each tissue). A marked age-linked vasodilatory impairment in response to acetylcholine and nitroglycerine was prevented by AG treatment (P < 0.005), as was an age-related cardiac hypertrophy evident in both strains (P < 0.05). While creatinine clearance was unaffected by aging in these studies, the AGE/ creatinine clearance ratio declined 3-fold in old rats vs. young rats (S-D, P < 0.05; F344, P < 0.01), while it declined significantly less in AG-treated old rats (P < 0.05). In S-D but not in F344 rats, a significant (P < 0.05) age-linked 24% nephron loss was completely prevented by AG treatment, and glomerular sclerosis was markedly suppressed (P < 0.01). Age-related albuminuria and proteinuria were markedly inhibited by AG in both strains (S-D, P < 0.01; F344, P < 0.01). These data suggest that early interference with AGE accumulation by AG treatment may impart significant protection against the progressive cardiovascular and renal decline afflicting the last decades of life.
Assembly and positioning of microtubule asters in microfabricated chambers
Authors: Holy Timothy E. , Dogterom Marileen , Yurke Bernard , Leibler Stanislas
Published: July 2002

Intracellular organization depends on a variety of molecular assembly processes; while some of these have been studied in simplified cell-free systems, others depend on the confined geometry of cells and cannot be reconstructed using bulk techniques. To study the latter processes
in vitro
, we fabricated microscopic chambers that simulate the closed environment of cells. We used these chambers to study the positioning of microtubule asters. Microtubule assembly alone, without the action of molecular motors, is sufficient to position asters. Asters with short microtubules move toward the position expected from symmetry; however, once the microtubules become long enough to buckle, symmetry is broken. Calculations and experiments show that the bending-energy landscape has multiple minima. Microtubule dynamic instability modifies the landscape over time and allows asters to explore otherwise inaccessible configurations.
Integration of local pattern elements into a global shape in human vision
Authors: Saarinen Jukka , Levi Dennis M. , Shen Bridgitte
Published: July 2002

The spatial extent of the cortical filters selective for different spatial frequencies and orientations is limited. We studied psychophysically how information from the local filters is integrated into global pattern shapes, i.e., whether performance in the identification of a global pattern consisting of small, locally oriented Gabor elements depends on the orientations of those elements. The observer was presented with an E-like stimulus pattern shape comprised of oriented Gabor patches on a blank background, and the performance measure was the threshold contrast for identifying the orientation of the E pattern (four possible rotated orientations). The results showed that contrast thresholds were significantly lower when the local elements all shared the same orientation (e.g., all horizontal) compared with the condition in which the elements had mixed orientations (both horizontal and vertical). The enhancement effect due to uniform local orientations can be explained by two factors: One is local facilitatory interactions between the orientation selective filters, and the other is second-order information integration across the filters.
Modulation of cognition-specific cortical activity by gonadal steroids: A positron-emission tomography study in women
Authors: Berman Karen Faith , Schmidt Peter J. , Rubinow David R. , Danaceau Merry A. , Van Horn John D. , Esposito Giuseppe , Ostrem Jill L. , Weinberger Daniel R.
Published: July 2002

There is considerable evidence from animal studies that gonadal steroid hormones modulate neuronal activity and affect behavior. To study this in humans directly, we used H
2
15
O positron-emission tomography to measure regional cerebral blood flow (rCBF) in young women during three pharmacologically controlled hormonal conditions spanning 4–5 months: ovarian suppression induced by the gonadotropin-releasing hormone agonist leuprolide acetate (Lupron), Lupron plus estradiol replacement, and Lupron plus progesterone replacement. Estradiol and progesterone were administered in a double-blind cross-over design. On each occasion positron-emission tomography scans were performed during (
i
) the Wisconsin Card Sorting Test, a neuropsychological test that physiologically activates prefrontal cortex (PFC) and an associated cortical network including inferior parietal lobule and posterior inferolateral temporal gyrus, and (
ii
) a no-delay matching-to-sample sensorimotor control task. During treatment with Lupron alone (i.e., with virtual absence of gonadal steroid hormones), there was marked attenuation of the typical Wisconsin Card Sorting Test activation pattern even though task performance did not change. Most strikingly, there was no rCBF increase in PFC. When either progesterone or estrogen was added to the Lupron regimen, there was normalization of the rCBF activation pattern with augmentation of the parietal and temporal foci and return of the dorsolateral PFC activation. These data directly demonstrate that the hormonal milieu modulates cognition-related neural activity in humans.
DNA bending and the initiation of transcription at σ
54
-dependent bacterial promoters
Authors: Carmona Manuel , Claverie-Martin Felix , Magasanik Boris
Published: July 2002

We have examined the effects on transcription initiation of promoter and enhancer strength and of the curvature of the DNA separating these entities on wild-type and mutated enhancer–promoter regions at the
Escherichia coli
σ
54
-dependent promoters
glnAp2
and
glnHp2
on supercoiled and linear DNA. Our results, together with previously reported observations by other investigators, show that the initiation of transcription on linear DNA requires a single intrinsic or induced bend in the DNA, as well as a promoter with high affinity for σ
54
-RNA polymerase, but on supercoiled DNA requires either such a bend or a high affinity promoter but not both. The examination of the DNA sequence of all
nif
gene activator- or nitrogen regulator I-σ
54
promoters reveals that those lacking a binding site for the integration host factor have an intrinsic single bend in the DNA separating enhancer from promoter.
Molecular keys to speciation: DNA polymorphism and the control of genetic exchange in enterobacteria
Authors: Vulić Marin , Dionisio Francisco , Taddei François , Radman Miroslav
Published: July 2002

Speciation involves the establishment of genetic barriers between closely related organisms. The extent of genetic recombination is a key determinant and a measure of genetic isolation. The results reported here reveal that genetic barriers can be established, eliminated, or modified by manipulating two systems which control genetic recombination, SOS and mismatch repair. The extent of genetic isolation between enterobacteria is a simple mathematical function of DNA sequence divergence. The function does not depend on hybrid DNA stability, but rather on the number of blocks of sequences identical in the two mating partners and sufficiently large to allow the initiation of recombination. Further, there is no obvious discontinuity in the function that could be used to define a level of divergence for distinguishing species.