bluuebunny/crossref_metadata_2025 huggingface dataset:
Electron heat flux constraints in the solar wind
Authors: Gary S. Peter , Skoug Ruth M. , Daughton William
Published: July 2002

Enhanced fluctuations from electromagnetic heat flux instabilities may, through wave-particle scattering, constrain the electron heat flux which flows parallel to the background magnetic field in the solar wind. A corollary of this hypothesis is that instability thresholds should correspond to observable bounds on the heat flux. Here plasma and magnetic field data from February and March 1995 of the Ulysses mission is analyzed in terms of the core/halo electron model to yield scaling relations of dimensionless electron parameters and empirical upper bounds on the dimensionless heat flux as functions of the core β. Use of these scaling relations in linear Vlasov theory for the whistler and Alfvén heat flux instabilities in homogeneous plasmas yields threshold conditions on the dimensionless heat flux which are also functions of the electron core β. The empirical bounds and the theoretical thresholds are similar and are therefore consistent with the hypothesis.
The optimized li advanced tokamak scenario with high bootstrap current fraction
Authors: Lin-Liu Y. R. , Turnbull A. D. , Chu M. S. , Ferron J. R. , Miller R. L. , Taylor T. S.
Published: July 2002

Equilibrium and stability analyses have identified a class of tokamak configurations with conventional safety factor profiles (q0∼qmin≳1) at moderately high li(li∼1.0), and high normalized β(βN∼3.5–4.0), that are stable to the ideal n=1 kink without the requirement of wall stabilization. In contrast to previously identified high li, high βN equilibria, these configurations have high bootstrap current fractions (fBS∼50%–70%); they require only modest central current drive for maintaining steady state and are therefore compatible with advanced tokamak (AT) operation. Strong plasma shaping is crucial for achieving the high β and high bootstrap fraction simultaneously.
Nonadiabatic behavior of fast escaped ions born near the core of a multiple-helicity heliotron
Authors: Smirnova M. S.
Published: July 2002

In the present paper, the direct losses of fast particles born near the core of a current heliotron [K. Uo, J. Phys. Soc. Jpn. 16, 1380 (1961)] with a complicated magnetic field harmonic spectrum are investigated numerically with the help of the Monte Carlo technique. The main purpose of the paper is to verify the degree of agreement between the guiding center motion of fast particles and their approximate adiabatic motion. It is shown that in heliotron configurations with low values of the rotational transform at the axis, the behavior of more than 20% of fast particles is nonadiabatic in nature. For such particles, the second adiabatic invariant of motion cannot be conserved during not only the full drift motion, but even during one bounce-period of the particle oscillation. It is found that typical features of these nonadiabatic particles are anomalously high radial excursions from the initial flux surface. The orbits of these particles are revealed to be stochastic.
Stability studies and the origin of the n=1 mode in the SPHEX spheromak experiment
Authors: Brennan D. , Browning P. K. , Van der Linden R. A. M. , Hood A. W. , Woodruff S.
Published: July 2002

Oscillations with toroidal mode number n=1 are ubiquitous in helicity injected spheromaks and spherical tokamaks, and play a crucial role in current drive. It has been proposed that these arise from a current driven instability of the open flux tube. Stability calculations are presented to confirm this, and they are compared with experimental data from the Spheromak Experiment (SPHEX) [M. Rusbridge et al., Plasma Phys. Control. Fusion 39, 683 (1997)]. The equilibria are modelled as piece-wise constant μ profile force-free plasmas with different values for the μ in the open (μc) and closed (μa) flux regions. A stability map in μc,μa space is then calculated. The SPHEX experimental data is also reduced to the same space both as a culmination of direct single point measurements of μ and as a time history of the reconstructed equilibrium from a particular shot. The results show a favorable comparison of the stability map with experiment, both in magnitude and shape. The effect of inserting a central current-carrying rod on the stability is also discussed.
Electron transport in Tore Supra with fast wave electron heating
Authors: Horton W. , Zhu P. , Hoang G. T. , Aniel T. , Ottaviani M. , Garbet X.
Published: July 2002

The hot electron plasmas (Te>2Ti) in Tore Supra (Equipe Tore Supra (presented by R. Aymar) in Plasma Physics and Controlled Nuclear Fusion Research [Proc. 12th Int. Conf., Nice, 1988 (IAEA, Vienna, 1989), Vol. 1, p. 9]) driven by fast wave electron heating (FWEH) are analyzed for thermal transport. Both neoclassical and anomalous transport processes are taken into account. The dominant power flow is through the electron channel of anomalous thermal diffusivity. The electron and ion temperature gradient driven instabilities are analyzed for a well documented discharge and shown to explain the diffusivities inferred from the steady state power balance analysis. The discharges are maintained in a quasi-steady state for periods up to 100 global energy replacement times. A large Tore Supra database is tested against two models for the turbulent electron thermal conductivity. Good correlation is obtained with an updated version of the collisionless skin depth formula. The electrostatic turbulence-based formula for electron temperature gradient (ETG) mode performs poorly in the core but well in the outer plasma. The electromagnetic turbulence theory based formula for ETG mode is benchmarked with the empirical Taroni–Bohm formula derived from Joint European Torus (JET) data.
Progress in target physics and design for heavy ion fusion
Authors: Callahan-Miller Debra A. , Tabak Max
Published: July 2002

Two-dimensional, integrated calculations of a close-coupled version of the distributed radiator, heavy ion target predict gain 130 from 3.3 MJ of beam energy. To achieve these results, the case-to-capsule ratio was decreased by about 25% from the previous heavy ion targets [M. Tabak and D. Callahan-Miller, Phys. Plasmas 5, 1895 (1998)]. These targets are robust to changes in the ion stopping model because changes in the ion stopping model can be accommodated by changes to the target. The capsule is also insensitive to changes in the deuterium–tritium (DT) gas fill in the center of the capsule over the range that is of interest for target fabrication and target injection. Single-mode Rayleigh–Taylor growth rates for this capsule are smaller than those for at least one National Ignition Facility (NIF) [J. A. Paisner et al., Laser Focus World 30, 75 (1994)] design. As a result, stability issues for the heavy ion capsule can be settled on NIF. The close-coupled target also opens up the possibility of a high gain engineering test facility from a 1.5–2 MJ driver; calculations predict that gain 90 is achievable from 1.75 MJ of beam energy. Finally, the choice of hohlraum wall material, which must satisfy constraints from target physics, environment and safety, chamber design, and target fabrication, is discussed.
Ultrahigh relaxation oscillation frequency (up to 30 GHz) of highly p-doped GaAs/GaAlAs multiple quantum well lasers
Authors: Uomi K. , Mishima T. , Chinone N.
Published: July 2002

We have demonstrated a relaxation oscillation frequency (fr) of up to 30 GHz in highly p-doped (Be=1×1019 cm−3) GaAs/GaAlAs multiple quantum well (MQW) lasers grown by molecular beam epitaxy. This is the highest fr achieved at room temperature for III-V semiconductor lasers. The high fr is attained by the large differential gain in the p-doped MQW structure having a low threshold electron density resulted from the excess hole density in addition to the quantum size effect.
1.3 μm electro-optic silicon switch
Authors: Lorenzo J. P. , Soref R. A.
Published: July 2002

Silicon-based optical switches have been fabricated which rely on refractive index change induced by injected minority carriers. Multimode raised-rib 2×2 structures are fabricated using epitaxial silicon and diffused homojunctions. The first evidence of 1.3 μm optical switching is observed.
High T
C superconductors—composite wire fabrication
Authors: Jin S. , Sherwood R. C. , van Dover R. B. , Tiefel T. H. , Johnson D. W.
Published: July 2002

Commercially useful, bulk superconductors typically require stabilization using a normal metal cladding for reasons of electrical, thermal, and mechanical protection and, in general, need to be drawn into fine fibers and wound into a magnet configuration. The recent discovery of high-TC superconductor materials such as Ba2YCu3O7 stimulated worldwide interest in the subject, however, with much concern about fabricability of such brittle ceramic materials into desirable fine wire geometry. In this letter, we report preliminary success in the fabrication of fine-wire, composite superconductors consisting of a high-conductivity normal metal shell such as Ag or Cu/Ni/Au and a superconducting core of Ba2YCu3O7 oxide. The wire is would into a coil, and then heat treated to produce the desired chemistry in a dense structure. The resistivity of the composite wire is measured to be zero at ≊90 K (in zero field) with a zero-field critical density of ≊175 A/cm2. Microscopy and x-ray analysis show that the superconducting core is continuous, and retains phase composition after wire drawing and heat treatment. These results demonstrate the feasibility of producing superconducting ceramic composite wire, although the practical applications must await the resolution of many practical problems and reliability issues.
Novel method for measuring excimer laser ablation thresholds of polymers
Authors: Dyer P. E. , Jenkins S. D. , Sidhu J.
Published: July 2002

Conical features produced on excimer laser ablated polymers are shown to provide a sensitive technique for determining ablation thresholds. This has been applied to polyimide, polyethylene terephthalate, polyethylene, and nylon 66 ablated using the 157 nm vacuum ultraviolet F2 laser.
The amino terminus of the mixed lineage leukemia protein (MLL) promotes cell cycle arrest and monocytic differentiation
Authors: Caslini Corrado , Shilatifard Ali , Yang Liping , Hess Jay L.
Published: July 2002

Several lines of evidence suggest that the mixed lineage leukemia
protein (MLL, ALL-1, HRX) plays a role in regulating myelomonocytic
differentiation. In this study we examined the effect of expression of
MLL-AF9 on differentiation of the monoblastic U937 cell line by using a
tetracycline-inducible expression system. MLL-AF9 arrested growth of
U937 cells and induced these cells to differentiate into macrophages;
induction was accompanied by expression of CD11b and CD14 and
ultimately cell death. Deletion mutants of MLL-AF9 were used to map the
sequences responsible for this effect. The amino-terminal half of MLL
was sufficient for both cell cycle arrest and macrophage
differentiation, whereas the carboxyl terminus of MLL or AF9 was found
to be dispensable for this effect. Further deletions showed that a
35-kDa amino-terminal fragment spanning two AT hook motifs was
sufficient for cell cycle arrest, up-regulation of p21
Cip1
and p27
Kip1
, and partial differentiation toward
macrophages. These findings suggest a possible role for the MLL AT
hook-containing region in regulating myelomonocytic differentiation.
Dynamic chemical devices: Modulation of contraction/extension molecular motion by coupled-ion binding/pH change-induced structural switching
Authors: Barboiu Mihail , Lehn Jean-Marie
Published: July 2002

Dynamic chemical devices involve morphological or constitutional modifications in molecular or supramolecular systems, induced by internal or external physical or chemical triggers. Reversible changes in shape result in molecular motions and define motional dynamic devices presenting mechanical-like actions of various types. Suitably designed polyheterocyclic strands such as compounds 1–5 wrap into helical conformations. The binding of lead(II) ions to the coordination subunits contained in the strand leads to complete uncoiling and yields a polymetallic complex presenting a fully extended shape. The addition of a cryptand complexing agent that strongly binds lead(II) ions and releases them under protonation allows a reversible pH-modulation of lead(II) levels in the medium, which in turn induces coiling/uncoiling of the molecular strand. This system thus represents a motional dynamic device which performs a mechano-chemical process, realizing alternating extension/contraction motions triggered by ion binding. It achieves a linear motor-type of action of very large stroke amplitude fueled by ionic processes.
Stat1-independent regulation of gene expression in response to IFN-γ
Authors: Ramana Chilakamarti V. , Gil M. Pilar , Han Yulong , Ransohoff Richard M. , Schreiber Robert D. , Stark George R.
Published: July 2002

Although Stat1 is essential for cells to respond fully to IFN-γ, there is substantial evidence that, in the absence of Stat1, IFN-γ can still regulate the expression of some genes, induce an antiviral state and affect cell growth. We have now identified many genes that are regulated by IFN-γ in serum-starved Stat1-null mouse fibroblasts. The proteins induced by IFN-γ in Stat1-null cells can account for the substantial biological responses that remain. Some genes are induced in both wild-type and Stat1-null cells and thus are truly Stat1-independent. Others are subject to more complex regulation in response to IFN-γ, repressed by Stat1 in wild-type cells and activated in Stat1-null cells. Many genes induced by IFN-γ in Stat1-null fibroblasts also are induced by platelet-derived growth factor in wild-type cells and thus are likely to be involved in cell proliferation. In mouse cells expressing the docking site mutant Y440F of human IFN-γ receptor subunit 1, the mouse Stat1 is not phosphorylated in response to human IFN-γ, butc-mycandc-junare still induced, showing that the Stat1 docking site is not required for Stat1-independent signaling.
Redox-dependent activation of CO dehydrogenase from
Rhodospirillum rubrum
Authors: Heo Jongyun , Halbleib Cale M. , Ludden Paul W.
Published: July 2002

Studies of initial activities of carbon monoxide dehydrogenase (CODH) from
Rhodospirillum rubrum
show that CODH is mostly inactive at redox potentials higher than −300 mV. Initial activities measured at a wide range of redox potentials (0–500 mV) fit a function corresponding to the Nernst equation with a midpoint potential of −316 mV. Previously, extensive EPR studies of CODH have suggested that CODH has three distinct redox states: (
i
) a spin-coupled state at −60 to −300 mV that gives rise to an EPR signal termed C
red1
; (
ii
) uncoupled states at <−320 mV in the absence of CO
2
referred to as C
unc
; and (
iii
) another spin-coupled state at <−320 mV in the presence of CO
2
that gives rise to an EPR signal termed C
red2B
. Because there is no initial CODH activity at potentials that give rise to C
red1
, the state (C
red1
) is not involved in the catalytic mechanism of this enzyme. At potentials more positive than −380 mV, CODH recovers its full activity over time when incubated with CO. This reductant-dependent conversion of CODH from an inactive to an active form is referred to hereafter as “autocatalysis.” Analyses of the autocatalytic activation process of CODH suggest that the autocatalysis is initiated by a small fraction of activated CODH; the small fraction of active CODH catalyzes CO oxidation and consequently lowers the redox potential of the assay system. This process is accelerated with time because of accumulation of the active enzyme.
CIKS, a connection to IκB kinase and stress-activated protein kinase
Authors: Leonardi Antonio , Chariot Alain , Claudio Estefania , Cunningham Kirk , Siebenlist Ulrich
Published: July 2002

Pathogens, inflammatory signals, and stress cause acute transcriptional responses in cells. The induced expression of genes in response to these signals invariably involves transcription factors of the NF-κB and AP-1/ATF families. Activation of NF-κB factors is thought to be mediated primarily via IκB kinases (IKK), whereas that of AP-1/ATF can be mediated by stress-activated protein kinases (SAPKs; also named Jun kinases or JNKs). IKKα and IKKβ are two catalytic subunits of a core IKK complex that also contains the regulatory subunit NEMO (NF-κB essential modulator)/IKKγ. The latter protein is essential for activation of the IKKs, but its mechanism of action is not known. Here we describe the molecular cloning of CIKS (connection to IKK and SAPK/JNK), a previously unknown protein that directly interacts with NEMO/IKKγ in cells. When ectopically expressed, CIKS stimulates IKK and SAPK/JNK kinases and it transactivates an NF-κB-dependent reporter. Activation of NF-κB is prevented in the presence of kinase-deficient, interfering mutants of the IKKs. CIKS may help to connect upstream signaling events to IKK and SAPK/JNK modules. CIKS could coordinate the activation of two stress-induced signaling pathways, functions reminiscent of those noted for tumor necrosis factor receptor-associated factor adaptor proteins.
A thermodynamic framework for Mg
2+
binding to RNA
Authors: Misra Vinod K. , Draper David E.
Published: July 2002

We present a model describing how Mg
2+
binds and stabilizes specific RNA structures. In this model, RNA stabilization arises from two energetically distinct modes of Mg
2+
binding: diffuse- and site-binding. Diffusely bound Mg
2+
are electrostatically attracted to the strong anionic field around the RNA and are accurately described by the Poisson–Boltzmann equation as an ensemble distributed according to the electrostatic potentials around the nucleic acid. Site-bound Mg
2+
are strongly attracted to specifically arranged electronegative ligands that desolvate the ion and the RNA binding site. Thus, site-binding is a competition between the strong coulombic attraction and the large cost of desolvating the ion and its binding pocket. By using this framework, we analyze three systems where a single site-bound Mg
2+
may be important for stability: the P5 helix and the P5b stem loop from the P4-P6 domain of the
Tetrahymena thermophila
group I intron and a 58-nt fragment of the
Escherichia coli
23S ribosomal RNA. Diffusely bound Mg
2+
play a dominant role in stabilizing these RNA structures. These ions stabilize the folded structures, in part, by accumulating in regions of high negative electrostatic potential. These regions of Mg
2+
localization correspond to ions that are observed in the x-ray crystallographic and NMR structures of the RNA. In contrast, the contribution of site-binding to RNA stability is often quite small because of the large desolvation penalty. However, in special cases, site-binding of partially dehydrated Mg
2+
to locations with extraordinarily high electrostatic potential can also help stabilize folded RNA structures.
Structured antiretroviral treatment interruptions in chronically HIV-1-infected subjects
Authors: Ortiz Gabriel M. , Wellons Melissa , Brancato Jason , Vo Ha T. T. , Zinn Rebekah L. , Clarkson Daniel E. , Van Loon Katherine , Bonhoeffer Sebastian , Miralles G. Diego , Montefiori David , Bartlett John A. , Nixon Douglas F.
Published: July 2002

The risks and benefits of structured treatment interruption (STI) in HIV-1-infected subjects are not fully understood. A pilot study was performed to compare STI with continuous highly active antiretroviral therapy (HAART) in chronic HIV-1-infected subjects with HIV-1 plasma RNA levels (VL) <400 copies per ml and CD4
+
T cells >400 per μl. CD4
+
T cells, VL, HIV-1-specific neutralizing antibodies, and IFN-γ-producing HIV-1-specific CD8
+
and CD4
+
T cells were measured in all subjects. STIs of 1-month duration separated by 1 month of HAART, before a final 3-month STI, resulted in augmented CD8
+
T cell responses in all eight STI subjects (
P
= 0.003), maintained while on HAART up to 22 weeks after STI, and augmented neutralization titers to autologous HIV-1 isolate in one of eight subjects. However, significant decline of CD4
+
T cell count from pre-STI level, and VL rebound to pre-HAART baseline, occurred during STI (
P
= 0.001 and 0.34, respectively). CD4
+
T cell counts were regained on return to HAART. Control subjects (
n
= 4) maintained VL <400 copies per ml and stable CD4
+
T cell counts, and showed no enhancement of antiviral CD8
+
T cell responses. Despite increases in antiviral immunity, no control of VL was observed. Future studies of STI should proceed with caution.
Structural and mutational studies of the recognition of the arginine tRNA-specific major identity element, A20, by arginyl-tRNA synthetase
Authors: Shimada Atsushi , Nureki Osamu , Goto Mie , Takahashi Seizo , Yokoyama Shigeyuki
Published: July 2002

Arginyl-tRNA synthetase (ArgRS) recognizes two major identity elements of tRNA
Arg
: A20, located at the outside corner of the L-shaped tRNA, and C35, the second letter of the anticodon. Only a few exceptional organisms, such as the yeast
Saccharomyces cerevisiae
, lack A20 in tRNA
Arg
. In the present study, we solved the crystal structure of a typical A20-recognizing ArgRS from
Thermus thermophilus
at 2.3 Å resolution. The structure of the
T. thermophilus
ArgRS was found to be similar to that of the previously reported
S. cerevisiae
ArgRS, except for short insertions and a concomitant conformational change in the N-terminal domain. The structure of the yeast ArgRS⋅tRNA
Arg
complex suggested that two residues in the unique N-terminal domain, Tyr
77
and Asn
79
, which are phylogenetically invariant in the ArgRSs from all organisms with A20 in tRNA
Arg
s, are involved in A20 recognition. However, in a docking model constructed based on the yeast ArgRS⋅tRNA
Arg
and
T. thermophilus
ArgRS structures, Tyr
77
and Asn
79
are not close enough to make direct contact with A20, because of the conformational change in the N-terminal domain. Nevertheless, the replacement of Tyr
77
or Asn
79
by Ala severely reduced the arginylation efficiency. Therefore, some conformational change around A20 is necessary for the recognition. Surprisingly, the N79D mutant equally recognized A20 and G20, with only a slight reduction in the arginylation efficiency as compared with the wild-type enzyme. Other mutants of Asn
79
also exhibited broader specificity for the nucleotide at position 20 of tRNA
Arg
. We propose a model of A20 recognition by the ArgRS that is consistent with the present results of the mutational analyses.
Lifetime correction of genetic deficiency in mice with a single injection of helper-dependent adenoviral vector
Authors: Kim In-Hoo , Józkowicz Alicja , Piedra Pedro A. , Oka Kazuhiro , Chan Lawrence
Published: July 2002

Ideally, somatic gene therapy should result in lifetime reversal of genetic deficiencies. However, to date, phenotypic correction of monogenic hyperlipidemia in mouse models by
in vivo
gene therapy has been short-lived and associated with substantial toxicity. We have developed a helper-dependent adenoviral vector (HD-Ad) containing the apolipoprotein (apo) E gene. A single i.v. injection of this vector completely and stably corrected the hypercholesterolemia in apoE-deficient mice, an effect that lasted the natural lifespan of the mice. At 2.5 years, control aorta was covered 100% by atherosclerotic lesion, whereas aorta of treated mice was essentially lesion-free. There was negligible toxicity associated with the treatment. We also developed a method for repeated HD-Ad vector administration that could be applied to organisms, e.g., humans, with life spans longer than 2–3 years. These studies indicate that HD-Ad is a promising system for liver-directed gene therapy of metabolic diseases.
High-level HIV-1 viremia suppresses viral antigen-specific CD4+T cell proliferation
Authors: McNeil Andrew C. , Shupert W. Lesley , Iyasere Christiana A. , Hallahan Claire W. , Mican JoAnn , Davey Richard T. , Connors Mark
Published: July 2002

In chronic viral infections of humans and experimental animals, virus-specific CD4+T cell function is believed to be critical for induction and maintenance of host immunity that mediates effective restriction of viral replication. Becausein vitroproliferation of HIV-specific memory CD4+T cells is only rarely demonstrable in HIV-infected individuals, it is presumed that HIV-specific CD4+T cells are killed upon encountering the virus, and maintenance of CD4+T cell responses in some patients causes the restriction of virus replication. In this study, proliferative responses were absent in patients with poorly restricted virus replication although HIV-specific CD4+T cells capable of producing IFN-γ were detected. In a separate cohort, interruption of antiretroviral therapy resulted in the rapid and complete abrogation of virus-specific proliferation although HIV-1-specific CD4+T cells were present. HIV-specific proliferation returned when therapy was resumed and virus replication was controlled. Further, HIV-specific CD4+T cells of viremic patients could be induced to proliferate in response to HIV antigens when costimulation was provided by anti-CD28 antibodyin vitro. Thus, HIV-1-specific CD4+T cells persist but remain poorly responsive (produce IFN-γ but do not proliferate) in viremic patients. Unrestricted virus replication causes diminished proliferation of virus-specific CD4+T cells. Suppression of proliferation of HIV-specific CD4+T cells in the context of high levels of antigen may be a mechanism by which HIV or other persistently replicating viruses limit the precursor frequency of virus-specific CD4+T cells and disrupt the development of effective virus-specific immune responses.
An O(N log N) algorithm for shape modeling.
Authors: Malladi R , Sethian J A
Published: July 2002

We present a shape-recovery technique in two dimensions and three dimensions with specific applications in modeling anatomical shapes from medical images. This algorithm models extremely corrugated structures like the brain, is topologically adaptable, and runs in O(N log N) time, where N is the total number of points in the domain. Our technique is based on a level set shape-recovery scheme recently introduced by the authors and the fast marching method for computing solutions to static Hamilton-Jacobi equations.
Integration of multiple repeats of geminiviral DNA into the nuclear genome of tobacco during evolution.
Authors: Bejarano E R , Khashoggi A , Witty M , Lichtenstein C
Published: July 2002

Integration of viral DNA into the host nuclear genome, although not unusual in bacterial and animal systems, has surprisingly not been reported for plants. We have discovered geminvirus-related DNA (GRD) sequences, in the form of distinct sets of multiple direct repeats comprising three related repeat classes, situated in a unique locus in the Nicotiana tabacum (tobacco) nuclear genome. The organization of these sequences is similar or identical in eight different tobacco cultivars we have examined. DNA sequence analysis reveals that each repeat has sequences most resembling those of the New World geminiviral DNA replication origin plus the adjacent AL1 gene, encoding the viral replication protein. We believe these GRD sequences originated quite recently in Nicotiana evolution through integration of geminiviral DNA by some combination of the processes of illegitimate recombination, amplification, deletions, and rearrangements. These events must have occurred in plant tissue that was subsequently able to contribute to meristematic tissue yielding gametes. GRD may have been retained in tobacco by selection or by random fixation in a small evolving population. Although we cannot detect transcription of these sequences, this does not exclude the possibility that they may originally have been expressed.
Chronic morphine induces visible changes in the morphology of mesolimbic dopamine neurons.
Authors: Sklair-Tavron L , Shi W X , Lane S B , Harris H W , Bunney B S , Nestler E J
Published: July 2002

The mesolimbic dopamine system, which arises in the ventral tegmental area (VTA), is an important neural substrate for opiate reinforcement and addiction. Chronic exposure to opiates is known to produce biochemical adaptations in this brain region. We now show that these adaptations are associated with structural changes in VTA dopamine neurons. Individual VTA neurons in paraformaldehyde-fixed brain sections from control or morphine-treated rats were injected with the fluorescent dye Lucifer yellow. The identity of the injected cells as dopaminergic or nondopaminergic was determined by immunohistochemical labeling of the sections for tyrosine hydroxylase. Chronic morphine treatment resulted in a mean approximately 25% reduction in the area and perimeter of VTA dopamine neurons. This reduction in cell size was prevented by concomitant treatment of rats with naltrexone, an opioid receptor antagonist, as well as by intra-VTA infusion of brain-derived neurotrophic factor. In contrast, chronic morphine treatment did not alter the size of nondopaminergic neurons in the VTA, nor did it affect the total number of dopaminergic neurons in this brain region. The results of these studies provide direct evidence for structural alterations in VTA dopamine neurons as a consequence of chronic opiate exposure, which could contribute to changes in mesolimbic dopamine function associated with addiction.
Recognition of diverse sequences by class I zinc fingers: asymmetries and indirect effects on specificity in the interaction between CF2II and A+T-rich elements.
Authors: Gogos J A , Jin J , Wan H , Kokkinidis M , Kafatos F C
Published: July 2002

The Drosophila CF2II protein, which contains zinc fingers of the Cys2His2 type and recognizes an A+T-rich sequence, behaves in cell culture as an activator of a reporter chloramphenicol acetyltransferase gene. This activity depends on C-terminal but not N-terminal zinc fingers, as does in vitro DNA binding. By site-specific mutagenesis and binding site selection, we define the critical amino acid-base interactions. Mutations of single amino acid residues at the leading edge of the recognition helix are rarely neutral: many result in a slight change in affinity for the ideal DNA target site; some cause major loss of affinity; and others change specificity for as many as two bases in the target site. Compared to zinc fingers that recognize G+C-rich DNA, CF2II fingers appear to bind to A+T-rich DNA in a generally similar manner, but with additional flexibility and amino acid-base interactions. The results illustrate how zinc fingers may be evolving to recognize an unusually diverse set of DNA sequences.
Tumor dormancy and cell signaling: anti-mu-induced apoptosis in human B-lymphoma cells is not caused by an APO-1-APO-1 ligand interaction.
Authors: Racila E , Hsueh R , Marches R , Tucker T F , Krammer P H , Scheuermann R H , Uhr J W
Published: July 2002

Signal transduction initiated by crosslinking of antigen-specific receptors on T- and B-lymphoma cells induces apoptosis. In T-lymphoma cells, such crosslinking results in upregulation of the APO-1 ligand, which then interacts with induced or constitutively expressed APO-1, thereby triggering apoptosis. Here we show that crosslinking the membrane immunoglobulin on human lymphoma cells (Daudi) (that constitutively express APO-1) does not induce synthesis of APO-1 ligand. Further, a noncytotoxic fragment of anti-APO-1 antibody that blocks T-cell-receptor-mediated apoptosis in T-lymphoma cells does not block anti-mu-induced apoptosis. Hence, in B-lymphoma cells, apoptosis induced by signaling via membrane IgM is not mediated by the APO-1 ligand.
Keratinocyte expression of the type 2 interleukin 1 receptor mediates local and specific inhibition of interleukin 1-mediated inflammation
Authors: Rauschmayr Tamara , Groves Richard W. , Kupper Thomas S.
Published: July 2002

Epidermal keratinocytes can express two types of interleukin 1 (IL-1) receptors: IL-1R1, which is active in signal transduction, and the less well characterized IL-1R2, which is incapable of transducing a signal and can be shed from cells. The binding of IL-1 in solution by IL-1R2 has been demonstrated, and it has been proposed to inhibit IL-1-mediated responses through this mechanism. We and others have reported that keratinocytes can be induced to express IL-1R2 bothin vitroandin vivo, often under conditions that also favor IL-1 gene expression. We hypothesized that production of IL-1R2 by keratinocytes would be an efficient means to achieve local inhibition of IL-1-mediated responses without systemic consequences. To test this hypothesis, we have generated transgenic mice that constitutively express IL-1R2 on basal keratinocytes. Keratinocytes cultured from these animals shed the soluble form of the receptor into culture supernatants, and IL-1-inducible production of granulocyte/macrophage colony-stimulating factor was markedly inhibited.In vivo, acute cutaneous vascular leakage, as well as chronic inflammation induced by a well characterized IL-1-dependent stimulus, was significantly inhibited in IL-1R2 transgenic animals. In contrast, contact hypersensitivity was unaffected, suggesting that overexpression of IL-1R2 did not inhibit all types of inflammation globally. Finally, systemic injection of IL-1 induced equivalent levels of plasma IL-6 in IL-1R2 transgenic and nontransgenic mice, suggesting that the activity of the transgenic IL-1R2 remained predominantly local and did not influence systemic IL-1 responses. We conclude that tissue-specific production of IL-1R2 can mediate IL-1 antagonism in tissue microenvironments without systemic consequences. Our transgenic mice may be a useful tool for determining the degree to which different types of cutaneous inflammation depend on the IL-1 system.
Thymocyte development is normal in CTLA-4-deficient mice
Authors: Chambers Cynthia A. , Cado Dragana , Truong Thien , Allison James P.
Published: July 2002

Recent studies indicate that CTLA-4 interaction with B7 ligands transduces an inhibitory signal to T lymphocytes. Mice homozygous for a null mutation in CTLA-4 have provided the most dramatic example of the functional importance of CTLA-4in vivo. These animals develop a fatal lymphoproliferative disorder and were reported to have an increase in CD4+and CD8+thymocytes and CD4−CD8−thymocytes, and a decrease in CD4+CD8+thymocytes. Based on these observations, it was proposed that CTLA-4 is necessary for normal thymocyte development. In this study, CTLA-4-deficient mice carrying an insertional mutation into exon 3 of thectla-4gene were generated. Although these mice display a lymphoproliferative disorder similar to previous reports, there was no alteration in the thymocyte profiles when the parathymic lymph nodes were excluded from the thymi. Further, thymocyte development was normal throughout ontogeny and in neonates, and there was no increase in thymocyte production. Finally, T cell antigen receptor signaling, as assessed by proximal and distal events, was not altered in thymocytes from CTLA-4−/−animals. Collectively, these results clearly demonstrate that the abnormal T cell expansion in the CTLA-4-deficient mice is not due to altered thymocyte development and suggest that the apparent altered thymic phenotype previously described was due to the inclusion of parathymic lymph nodes and, in visibly ill animals, to the infiltration of the thymus by activated peripheral T cells. Thus it appears that CTLA-4 is primarily involved in the regulation of peripheral T cell activation.
A possible role for kinase-associated protein phosphatase in the
Arabidopsis
CLAVATA1 signaling pathway
Authors: Williams Robert W. , Wilson Jeanne M. , Meyerowitz Elliot M.
Published: July 2002

Continuous growth and development in plants are accomplished by meristems, groups of undifferentiated cells that persist as stem cells and initiate organs. While the structures of the apical and floral meristems in dicotyledonous plants have been well described, little is known about the underlying molecular mechanisms controlling cell proliferation and differentiation in these structures. We have shown previously that the
CLAVATA1
(
CLV1
) gene in
Arabidopsis
encodes a receptor kinase-like protein that controls the size of the apical and floral meristems. Here, we show that
KAPP
, a gene encoding a kinase-associated protein phosphatase, is expressed in apical and young floral meristems, along with
CLV1
. Overexpression of
KAPP
mimics the
clv1
mutant phenotype. Furthermore, CLV1 has kinase activity: it phosphorylates both itself and KAPP. Finally, KAPP binds and dephosphorylates CLV1. We present a model where KAPP functions as a negative regulator of the CLAVATA1 signal transduction pathway.
ApoNifH functions in iron–molybdenum cofactor synthesis and apodinitrogenase maturation
Authors: Rangaraj Priya , Shah Vinod K. , Ludden Paul W.
Published: July 2002

NifH (dinitrogenase reductase) has three important roles in the nitrogenase enzyme system. In addition to its role as the obligate electron donor to dinitrogenase, NifH is required for the iron–molybdenum cofactor (FeMo-co) synthesis and apodinitrogenase maturation. We have investigated the requirement of the Fe–S cluster of NifH for these processes by preparing apoNifH. The 4Fe–4S cluster of NifH was removed by chelation of the cluster with α, α′-bipyridyl. The resulting apoNifH was tested in
in vitro
FeMo-co synthesis and apodinitrogenase maturation reactions and was found to function in both these processes. Thus, the presence of a redox active 4Fe–4S cluster in NifH is not required for its function in FeMo-co synthesis and in apodinitrogenase maturation. This, in turn, implies that the role of NifH in these processes is not one of electron transfer or of iron or sulfur donation.
Identification of active sites in amidase: Evolutionary relationship between amide bond- and peptide bond-cleaving enzymes
Authors: Kobayashi Michihiko , Fujiwara Yoshie , Goda Masahiko , Komeda Hidenobu , Shimizu Sakayu
Published: July 2002

Mainly based on various inhibitor studies previously performed, amidases came to be regarded as sulfhydryl enzymes. Not completely satisfied with this generally accepted interpretation, we performed a series of site-directed mutagenesis studies on one particular amidase of
Rhodococcus rhodochrous
J1 that was involved in its nitrile metabolism. For these experiments, the recombinant amidase was produced as the inclusion body in
Escherichia coli
to greatly facilitate its recovery and subsequent purification. With regard to the presumptive active site residue Cys203, a Cys203 → Ala mutant enzyme still retained 11.5% of the original specific activity. In sharp contrast, substitutions in certain other positions in the neighborhood of Cys203 had a far more dramatic effect on the amidase. Glutamic acid substitution of Asp191 reduced the specific activity of the mutant enzyme to 1.33% of the wild-type activity. Furthermore, Asp191 → Asn substitution as well as Ser195 → Ala substitution completely abolished the specific activity. It would thus appear that, among various conserved residues residing within the so-called signature sequence common to all amidases, the real active site residues are Asp191 and Ser195 rather than Cys203. Inasmuch as an amide bond (CO-NH
2
) in the amide substrate is not too far structurally removed from a peptide bond (CO-NH-), the signature sequences of various amidases were compared with the active site sequences of various types of proteases. It was found that aspartic acid and serine residues corresponding to Asp191 and Ser195 of the
Rhodococcus
amidase are present within the active site sequences of aspartic proteinases, thus suggesting the evolutionary relationship between the two.
Squid Pax-6 and eye development
Authors: Tomarev Stanislav I. , Callaerts Patrick , Kos Lidia , Zinovieva Rina , Halder Georg , Gehring Walter , Piatigorsky Joram
Published: July 2002

Pax-6in vertebrates and its homologeyelessinDrosophilaare known to be essential for eye development. Here we investigate the role ofPax-6in eye development in another major systematic group, molluscs. We demonstrate that alternatively spliced RNAs derived from a singlePax-6gene in the squid (Loligo opalescens) are expressed in the embryonic eye, olfactory organ, brain, and arms. Despite significant sequence differences between squid Pax-6 andDrosophilaeyeless in the region outside the paired- and homeodomains, squid Pax-6 is able to induce the formation of ectopic eyes inDrosophila. Our results support the idea thatPax-6related genes are necessary for eye and olfactory system formation throughout the animal kingdom.
Modification of protein surface hydrophobicity and methionine oxidation by oxidative systems
Authors: Chao Chien-Chung , Ma Yan-Shan , Stadtman Earl R.
Published: July 2002

Aging and some pathological conditions are associated with the accumulation of altered (inactive or less active) forms of enzymes. It was suggested that these age-related alterations reflect spontaneous changes in protein conformation and/or posttranslational modifications (e.g., oxidation). Because changes in protein conformations are often associated with changes in surface hydrophobicity, we have examined the effects of aging and oxygen radical-dependent oxidation on the hydrophobicity of rat liver proteins. As a measure of hydrophobicity, the increase in fluorescence associated with the binding of 8-anilino-1-naphthalene-sulfonic acid to hydrophobic regions on the proteins was used. By this criterion, the hydrophobicity of liver proteins of 24-month-old rats was 15% greater than that of 2-month-old animals. Exposure of liver proteins to a metal-catalyzed oxidation system (ascorbate/Fe(II)/H
2
O
2
) or a peroxyl radical generating system, 2,2′-azobis(2-amidino-propane) dihydrochloride (AAPH) led to increases of 2% or 30% in surface hydrophobicity, respectively. Treatment of liver proteins with the metal-catalyzed oxidation system led to a significant increase in reactive carbonyl content and to conversion of methionine residues to methionine sulfoxide residues. Treatment with AAPH led also to oxidation of methionine, tyrosine, and tryptophan residues and to the precipitation of some proteins. Dityrosine was detected in AAPH-treated protein, both the precipitate and supernatant fraction. The oxidation-dependent increase of hydrophobicity was correlated with an increase in the levels of methionine sulfoxide and dityrosine. These results suggest that oxidative modification of proteins may be responsible for the age-related increase of protein surface hydrophobicity
in vivo
, and that the oxidation of methionine by an oxidative system may be an important event for the change of protein conformation.
rax
, a novel paired-type homeobox gene, shows expression in the anterior neural fold and developing retina
Authors: Furukawa Takahisa , Kozak Christine A. , Cepko Constance L.
Published: July 2002

Development of the vertebrate eye has been found to require the activity of several genes encoding homeodomain proteins (Freund, C., Horsford, D. J. & McInnes, R. R. (1996)
Hum. Mol. Genet.
5, 1471–1488). Some of these genes, or portions thereof, are highly conserved across phyla. In this paper, we report the identification of a novel homeobox gene,
rax
(
r
etina and
a
nterior neural fold homeobo
x
), whose expression pattern suggests an important role in eye development. The predicted amino acid sequence of Rax comprises a protein with a paired-type homeobox, as well as the octapeptide that is found in many paired-type homeobox genes. In addition, in the C terminus of Rax, we found a 15-aa domain that we have named the OAR domain. This domain is also found in several other homeobox genes. In the early mouse embryo,
rax
is expressed in the anterior neural fold, including areas that will give rise to the ventral forebrain and optic vesicles. Once the optic vesicles form,
rax
expression is restricted to the ventral diencephalon and the optic vesicles. At later stages,
rax
expression is found only in the developing retina. After birth, the expression of
rax
is restricted to the zone of proliferating cells within the retina, and expression gradually decreases as proliferation declines. These findings suggest that
rax
is one of the molecules that define the eye field during early development and that it has a role in the proliferation and/or differentiation of retinal cells.
A double-stranded RNA-activated protein kinase-dependent pathway mediating stress-induced apoptosis
Authors: Der Sandy D. , Yang Yi-Li , Weissmann Charles , Williams Bryan R. G.
Published: July 2002

Apoptosis occurs in response to different cellular stresses, including viral infection, inflammatory cytokines, growth factor deprivation, and UV light, but it is unclear whether these inducers share a common mechanism of induction. The interferon-induced, double-stranded RNA-activated protein kinase (PKR) has been implicated in processes that rely on apoptosis as control mechanismsin vivo, including antiviral activities, cell growth regulation, and tumorigenesis. Here we report that mouse embryo fibroblasts from mutant mice containing homozygous deletions in the PKR gene (Pkro/omice) were resistant to apoptotic cell death in response to double-stranded RNA, tumor necrosis factor-α, or lipopolysaccharide. The mechanism underlying the suppression of apoptosis in thePkro/ocells could be attributed to defects in the activation of DNA-binding activity for the transcription factor interferon regulatory factor-1 and in Fas mRNA induction. Thus, these results provide genetic evidence implicating a requirement for PKR in mediating different forms of stress-related apoptosis.
Identification of novel susceptibility loci for inflammatory bowel disease on chromosomes 1p, 3q, and 4q: Evidence for epistasis between 1p and
IBD1
Authors: Cho Judy H. , Nicolae Dan L. , Gold Leslee H. , Fields Carter T. , LaBuda Michele C. , Rohal Patrick M. , Pickles Michael R. , Qin Li , Fu Yifan , Mann Jasdeep S. , Kirschner Barbara S. , Jabs Ethylin Wang , Weber James , Hanauer Stephen B. , Bayless Theodore M. , Brant Steven R.
Published: July 2002

The idiopathic inflammatory bowel diseases, Crohn’s disease (CD) and ulcerative colitis (UC), are chronic, frequently disabling diseases of the intestines. Segregation analyses, twin concordance, and ethnic differences in familial risks have established that CD and UC are complex, non-Mendelian, related genetic disorders. We performed a genome-wide screen using 377 autosomal markers, on 297 CD, UC, or mixed relative pairs from 174 families, 37% Ashkenazim. We observed evidence for linkage at 3q for all families (multipoint logarithm of the odds score (MLod) = 2.29,
P
= 5.7 × 10
−4
), with greatest significance for non-Ashkenazim Caucasians (MLod = 3.39,
P
= 3.92 × 10
−5
), and at chromosome 1p (MLod = 2.65,
P
= 2.4 × 10
−4
) for all families. In a limited subset of mixed families (containing one member with CD and another with UC), evidence for linkage was observed on chromosome 4q (MLod = 2.76,
P
= 1.9 × 10
−4
), especially among Ashkenazim. There was confirmatory evidence for a CD locus, overlapping
IBD1
, in the pericentromeric region of chromosome 16 (MLod = 1.69,
P
= 2.6 × 10
−3
), particularly among Ashkenazim (MLod = 1.51,
P
= 7.8 × 10
−3
); however, positive MLod scores were observed over a very broad region of chromosome 16. Furthermore, evidence for epistasis between
IBD1
and chromosome 1p was observed. Thirteen additional loci demonstrated nominal (MLod > 1.0,
P
< 0.016) evidence for linkage. This screen provides strong evidence that there are several major susceptibility loci contributing to the genetic risk for CD and UC.