bluuebunny/crossref_metadata_2025 huggingface dataset:
Transient reconnection caused by the impact and switch-off of a transverse shear flow
Authors: Chen T. , Liu Z. X. , Zhang X. X.
Published: July 2002

It is supposed that local and transient reconnection in the plasma boundary layer can be caused by the impact and switch-off of a single directional transverse shear flow. MHD (magnetohydrodynamic) simulation is used to investigate the reconnection processes in the two cases. It is found that if the inflow is homogeneous, it does not cause reconnection; if the inflow is shearing flow, no matter how great the shear of the flow is, it may cause reconnection either during impacting period or after stop impacting. It is pointed out that the sudden stop of external force may be an important triggering mechanism of energy transformation and reconnection in the plasma boundary layer region.
Influence of continuous spectrum on ballooning instabilities in plasmas with shear-flow
Authors: Taylor J. B.
Published: July 2002

The influence of shear-flow on stability of plasma ballooning modes is important for Tokamak experiments. In a static plasma, the growth rate of ballooning modes is readily determined using the “ballooning transformation,” but this is ineffective for plasmas with flow. One then has only the quasi-static approximation. This gives the growth rate in the limit that shear velocity Ω′→0, but no other information on the effect of shear-flow. Furthermore, it is invalid in typical cases because of the intervention of the stable magnetohydrodynamic continuum. In this paper, a simple model is used to investigate the influence of shear-flow on ballooning modes. This shows that the intervention of the continuum leads to a reduction in the growth rate proportional to |Ω′| for small Ω′. This is in accord with some numerical simulations—but contrary to the (Ω′)2 variation expected from a perturbation expansion. In fact, since the effect is nonanalytic in Ω′, it cannot be obtained from a perturbation expansion in Ω′ and an alternative formalism is first developed for dealing with this problem.
Global Alfvén eigenmodes in a stellarator with trapped energetic particles
Authors: Andrushchenko Zh. N. , Cheremnykh O. K. , Edenstrasser J. W.
Published: July 2002

The presence of a super-thermal ion component in tokamak as well as in stellarator plasmas, can give rise to Alfvén-type instabilities. In the present paper an analytical investigation of global Alfvén eigenmodes (GAEs) in a stellarator with planar magnetic axis is performed and analytical expressions for the dominant mode numbers are derived. The effect of trapped highly energetic particles on the GAEs is investigated. The frequencies and corresponding growth rates of the discrete GAE spectrum are found for different distributions of the energetic particles. It is shown that for given background conditions, the slowing-down distributions yield the largest values for the growth rates. The inclusion of the highly energetic particles leads to a change of the conditions for the existence of GAEs and in the dominant mode numbers. A shear dependent threshold for the pressure of the trapped energetic particles has been found, above which GAEs cannot be excited.
Dynamic response of detached recombining plasmas to plasma heat pulse in a divertor simulator
Authors: Ohno N. , Tanaka M. , Ezumi N. , Nishijima D. , Takamura S. , Krasheninnikov S. I. , Pigarov A. Yu. , Park J.
Published: July 2002

The experiments on the plasma heat pulse to the detached recombining helium plasma associated with the volumetric radiative and three-body recombination (EIR) have been performed in a linear divertor plasma simulator. Detailed observations of the time evolution of plasma parameters and helium Balmer series spectra show that the dynamic response of the detached recombining plasma to the heat pulse depends strongly on the heat transport through energetic electrons generated by the heat pulse. For the detached recombining plasma with a relatively low neutral pressure, it was found that the EIR is not sufficient to suppress an increase of ion flux to the target plate during the pulse. Several key characteristic time scales involved in this system are also analyzed.
The radial electric field in a tokamak with reversed magnetic shear
Authors: Zhu P. , Horton W. , Sugama H.
Published: July 2002

Neoclassical theory with the impurity rotational velocity is used to evaluate the radial electric field, Er, in a tokamak. The result of using the complete matrix method for the deuterium–carbon plasma is compared with a reduced analytic formula for determining Er [Ernst et al., Phys. Plasmas 5, 665 (1998)]. The analytic formula is shown to overestimate the Er magnitude and its gradient. Two transport measures of the effect of the Er shear are compared for the reversed shear and enhanced reversed shear discharges in Tokamak Fusion Test Reactor [Mazzucato et al., Phys. Rev. Lett. 77, 3145 (1996)]. It is shown that the combined Er and magnetic shear measure, Υs, from linear stability theory gives a higher correlation with the observed transition between the two discharges than the vorticity measure ωs from Er shear alone.
Experimental study of laser penetration in overdense plasmas at relativistic intensities. II: Explosion of thin foils by laser driven fast electrons
Authors: Fuchs J. , Adam J. C. , Amiranoff F. , Baton S. D. , Blanchot N. , Gallant P. , Gremillet L. , Héron A. , Kieffer J. C. , Laval G. , Malka G. , Miquel J. , Mora P. , Pépin H. , Rousseaux C.
Published: July 2002

Propagation of a high-contrast frequency-doubled subpicosecond (300 fs) relativistic (Iλ2 up to 5×1018 W⋅cm−2⋅μm2) laser pulse through thin and initially solid foils is studied. Transmission values up to 10% are measured through targets with initial near solid densities. The strong intensity threshold observed for the transmitted energy is correlated with clear modifications of the transmitted and reflected spectra, electron generation, and beam imaging. Two-dimensional Cartesian particle-in-cell (PIC) simulations that qualitatively reproduce the experimental results suggest specific rapid heating of the thin targets by fast electrons, plasma expansion, and density decrease to relativistically transmissive conditions during the pulse.
Computation of the diocotron spectrum of a cylindrical non-neutral plasma
Authors: Goswami Priyanka , Bhattacharyya S. N. , Sen A. , Maheshwari K. P.
Published: July 2002

A finite difference method is developed and used to compute the diocotron spectrum (discrete plus continuum) of a non-neutral plasma column with an arbitrary profile of the number density. For step function density profiles the results agree with the analytical dispersion relation. In contrast to earlier results, it is found that for a continuously varying hollow density profile the mode with azimuthal mode number l=2 has a growth rate comparable to that for a step function hollow density profile. The results obtained have been verified using an alternative numerical method in which the density is assumed to be constant over small intervals in the radius.
Nonlinear theory of helix traveling wave tubes in the frequency domain
Authors: Freund H. P.
Published: July 2002

A nonlinear helix traveling wave tube (TWT) analysis in the frequency domain is presented for a sheath helix surrounded by a conducting wall. Dielectric- and vane-loading of the helix are included as is circuit tapering and external focusing by either a solenoid or a field produced by a periodic permanent magnet (PPM) stack. The electromagnetic field is treated as a superposition of waves where the amplitudes and phases vary slowly in z. The field equations are solved in conjunction with the three-dimensional Lorentz force equations for an ensemble of electrons. Beam space-charge waves are included using a superposition of solutions of the Helmholtz equation. The dc (direct current) self-fields of the beam are also included. The simulation is compared with linear theory as well as a time-domain simulation, each of which is applied to an example of a tube built at Northrop-Grumman Corp. The frequency- and time-domain simulations are in substantial agreement. The advantage of the frequency-domain formulation is a shorter run time than for the time-domain simulation. Hence, the frequency-domain simulation can more easily treat beam thermal effects and multiple waves with closely spaced frequencies.
Theory of Langmuir wave generation in the presence of Alfvén wave turbulence in an electron-positron plasma
Authors: Kakati H. , Goswami K. S. , Bujarbarua S.
Published: July 2002

The plasma maser interaction of the test Langmuir wave in the presence of Alfvén wave turbulence is studied theoretically in a magnetized electron–positron (e-p) plasma where the turbulence is produced by a temperature anisotropy. Langmuir waves are found to grow without the necessity of an electron (or positron) beam component. The growth takes place in a direction opposite to that of Alfvén waves.
Drift mode calculations in nonaxisymmetric geometry
Authors: Rewoldt G. , Ku L.-P. , Tang W. M. , Cooper W. A.
Published: July 2002

A fully kinetic assessment of the stability properties of toroidal drift modes has been obtained for nonaxisymmetric (stellarator) geometry, in the electrostatic limit. This calculation is a comprehensive solution of the linearized gyrokinetic equation, using the lowest-order “ballooning representation” for high toroidal mode number instabilities, with a model collision operator. Results for toroidal drift waves destabilized by temperature gradients and/or trapped particle dynamics are presented, using three-dimensional magnetohydrodynamic equilibria generated as part of a design effort for a quasiaxisymmetric stellarator. Comparisons of these results with those obtained for typical tokamak cases indicate that the basic trends are similar.
Kinetic simulations of the formation and stability of the field-reversed configuration
Authors: Omelchenko Yu. A.
Published: July 2002

The Field-Reversed Configuration (FRC) is a high-beta compact toroidal plasma confined primarily by poloidal fields. In the FRC the external field is reversed on axis by the diamagnetic current carried by thermal plasma particles. A three-dimensional, hybrid, particle-in-cell (zero-inertia fluid electrons, and kinetic ions), code FLAME, previously used to study ion rings [Yu. A. Omelchenko and R. N. Sudan, J. Comp. Phys. 133, 146 (1997)], is applied to investigate FRC formation and tilt instability. Axisymmetric FRC equilibria are obtained by simulating the standard experimental reversed theta-pinch technique. These are used to study the nonlinear tilt mode in the “kinetic” and “fluid-like” cases characterized by “small” (∼3) and “large” (∼12) ratios of the characteristic radial plasma size to the mean ion gyro-radius, respectively. The formation simulations have revealed the presence of a substantial toroidal (azimuthal) magnetic field inside the separatrix, generated due to the stretching of the poloidal field by a sheared toroidal electron flow. This is shown to be an important tilt-stabilizing effect in both cases. On the other hand, the tilt mode stabilization by finite Larmor radius effects has been found relatively insignificant for the chosen equilibria.
Wavelength dependence of the lateral photovoltage in amorphous superlattice films of Si and Ti
Authors: Levine B. F. , Willens R. H. , Bethea C. G. , Brasen D.
Published: July 2002

Experiments are reported on the lateral photoeffect in a novel type of amorphous superlattice consisting of 6 Å of Ti and 13 Å of Si grown on Si substrate. The spectral, temperature, bias voltage, and time dependences have been measured for this new position sensitive detector.
Energy relaxation of two-dimensional electrons and the deformation potential constant in selectively doped AlGaAs/GaAs heterojunctions
Authors: Hirakawa K. , Sakaki H.
Published: July 2002

We investigate the electron heating process in selectively doped AlGaAs/GaAs heterojunctions from magnetotransport measurements at low temperatures. It is shown that the dominant energy-relaxation mechanism of the degenerate two-dimensional (2D) electrons for the electron temperature below 40 K is the emission of acoustic phonons via deformation potential coupling, and that the energy-loss rate is almost independent of 2D electron densities. From a detailed analysis it is derived that the deformation potential constant of the quantized 2D conduction band in GaAs is 11±1 eV.
Conductive, spin-cast carbon films from polyacrylonitrile
Authors: Renschler C. L. , Sylwester A. P.
Published: July 2002

Polyacrylonitrile films have been spin cast and pyrolyzed to produce thin (500–1500 Å) carbon films. These films have higher electrical conductivities than films produced by other methods at similar temperatures. The conductivity can be varied by at least four orders of magnitude by changing the pyrolysis temperature. Ultraviolet, infrared, and Raman spectroscopies were used to investigate the chemical structure of the films during different stages of processing.
Nucleation of GaAs on Si: Experimental evidence for a three-dimensional critical transition
Authors: Hull R. , Fischer-Colbrie A.
Published: July 2002

The initial nucleation and growth stages of ultrathin GaAs films grown by molecular beam epitaxy upon Si(100) substrates are studied by high-resolution transmission electron microscopy. It is found that for a growth temperature of 405 °C, films initially nucleate as islands associated with steps on the substrate surface. In the earliest stages of growth, these islands are strained coherently to the substrate lattice, i.e., are free of misfit dislocations. As the islands grow, they become faulted. The transition from strained to dislocated states is shown to be a function of both the lateral and vertical island dimensions.
Monolayer epitaxy of III-V compounds by low-pressure metalorganic chemical vapor deposition
Authors: Razeghi M. , Maurel Ph. , Omnes F. , Nagle J.
Published: July 2002

We report, in this letter, the successful growth of Ga0.5In0.5As/InP heterostructures by alternating the growth of n(GaAs) and n(InAs) atomic layers. Such structures are designed as (GaAs)n(InAs)n. The influence of parameters such as n or the introduction of a purging time between the InAs-GaAs monolayers has been investigated. Low-temperature photoluminescence experiments showed that (GaAs)n(InAs)n/InP multiquantum wells had a better uniformity in composition and thickness than the conventional Ga0.5In0.5As/InP system.
Overshoot in the response of a photoconductor excited by subpicosecond pulses
Authors: Iverson A. Evan , Wysin G. M. , Smith D. L. , Redondo Antonio
Published: July 2002

Experiments designed to observe velocity overshoot in GaAs photoconductors excited by 2.0 eV photons are discussed. Monte Carlo transient velocity computations are presented which indicate that, for 620 nm (2.0 eV) excitation of GaAs, velocity overshoot will not occur for fields less than 20 kV/cm. Photoconductive device model equations are solved numerically for the case of subpicosecond-pulse excitation. The computed photoconductor response is observed to have an overshoot on the picosecond time scale resulting from charge-separation effects. The overshoot behavior is very similar to that observed in measurements of subpicosecond photoconductor response and previously interpreted in terms of velocity overshoot. We conclude that experimentally observed overshoot response at 620 nm is the result of charge-separation effects and not the result of velocity overshoot.
InGaAs/InAlAs bistable multiple quantum well lasers with large on/off ratio using the resonant tunneling effect
Authors: Kawamura Y. , Wakita K. , Mikami O.
Published: July 2002

Bistable operation with a large on/off ratio of 800:1 is achieved in InGaAs/InAlAs multiple quantum well (MQW) lasers using the resonant tunneling effect at 77 K. Structural dependence of resonant tunneling characteristic in the MQW structures reveals that the threshold current density, at which negative differential resistance appears, increases drastically when the InAlAs barrier width of MQW structures decreases. The increase in the threshold current density has led to an improvement in the bistable characteristics of InGaAs/InAlAs MQW lasers.
Missense mutations but not allelic variants alter the function of ATM by dominant interference in patients with breast cancer
Authors: Scott Shaun P. , Bendix Regina , Chen Philip , Clark Raymond , Dörk Thilo , Lavin Martin F.
Published: July 2002

The human genetic disorder ataxia-telangiectasia (A-T) is characterized by hypersensitivity to ionizing radiation and an elevated risk of malignancy. Epidemiological data support an increased risk for breast and other cancers in A-T heterozygotes. However, screening breast cancer cases for truncating mutations in the
ATM
(A-T mutated) gene has failed largely to reveal an increased incidence in these patients. It has been hypothesized that ATM missense mutations are implicated in breast cancer, and there is some evidence to support this. The presence of a large variety of rare missense variants in addition to common polymorphisms in ATM makes it difficult to establish such a relationship by association studies. To investigate the functional significance of these changes we have introduced missense substitutions, identified in either A-T or breast cancer patients, into ATM cDNA before establishing stable cell lines to determine their effect on ATM function. Pathogenic missense mutations and neutral missense variants were distinguished initially by their capacity to correct the radiosensitive phenotype in A-T cells. Furthermore missense mutations abolished the radiation-induced kinase activity of ATM in normal control cells, caused chromosome instability, and reduced cell viability in irradiated control cells, whereas neutral variants failed to do so. Mutant ATM was expressed at the same level as endogenous protein, and interference with normal ATM function seemed to be by multimerization. This approach represents a means of identifying genuine ATM mutations and addressing the significance of missense changes in the
ATM
gene in a variety of cancers including breast cancer.
Hypothyroidism in transgenic mice expressing IFN-γ in the thyroid
Authors: Caturegli P. , Hejazi M. , Suzuki K. , Dohan O. , Carrasco N. , Kohn L. D. , Rose N. R.
Published: July 2002

IFN-γ has been implicated with contradictory results in the pathogenetic process of autoimmune (Hashimoto's) thyroiditis, the most common cause of hypothyroidism in adults. To test whether the local production of IFN-γ can lead to thyroid dysfunction, we have generated transgenic mice that express constitutively IFN-γ in the thyroid follicular cells. This expression resulted in severe hypothyroidism, with growth retardation and disruption of the thyroid architecture. The hypothyroidism derived from a profound inhibition of the expression of the sodium iodide symporter gene. Taken together, these results indicate a direct role of IFN-γ in the thyroid dysfunction that occurs in autoimmune thyroiditis.
The protein translocation channel mediates glycopeptide export across the endoplasmic reticulum membrane
Authors: Gillece Pauline , Pilon Marinus , Römisch Karin
Published: July 2002

Peptides and misfolded secretory proteins are transported efficiently from the endoplasmic reticulum (ER) lumen to the cytosol, where the proteins are degraded by proteasomes. Protein export depends on Sec61p, the ribosome-binding core component of the protein translocation channel in the ER membrane. We found that prebinding of ribosomes abolished export of a glycopeptide from yeast microsomes. Deletion of
SSH1,
which encodes a ribosome-binding Sec61p homologue in the ER, had no effect on glycopeptide export. A collection of cold-sensitive
sec61
mutants displayed a variety of phenotypes: two mutants strongly defective in misfolded protein export from the ER,
sec61-32
and
sec61-41
, displayed only minor peptide export defects. Glycopeptide export was severely impaired, however, in several
sec61
mutants that were only marginally defective in misfolded protein export. In addition, a mutation in
SEC63
strongly reduced peptide export from the ER. ER-luminal ATP was required for both misfolded protein and glycopeptide export. We conclude that the protein translocation channel in the ER membrane mediates glycopeptide transport across the ER membrane.
The γ-secretase-generated intracellular domain of β-amyloid precursor protein binds Numb and inhibits Notch signaling
Authors: Roncarati Roberta , Šestan Nenad , Scheinfeld Meir H. , Berechid Bridget E. , Lopez Peter A. , Meucci Olimpia , McGlade Jane C. , Rakic Pasko , D'Adamio Luciano
Published: July 2002

The β-amyloid precursor protein (APP) and the Notch receptor undergo intramembranous proteolysis by the Presenilin-dependent γ-secretase. The cleavage of APP by γ-secretase releases amyloid-β peptides, which have been implicated in the pathogenesis of Alzheimer's disease, and the APP intracellular domain (AID), for which the function is not yet well understood. A similar γ-secretase-mediated cleavage of the Notch receptor liberates the Notch intracellular domain (NICD). NICD translocates to the nucleus and activates the transcription of genes that regulate the generation, differentiation, and survival of neuronal cells. Hence, some of the effects of APP signaling and Alzheimer's disease pathology may be mediated by the interaction of APP and Notch. Here, we show that membrane-tethered APP binds to the cytosolic Notch inhibitors Numb and Numb-like in mouse brain lysates. AID also binds Numb and Numb-like, and represses Notch activity when released by APP. Thus, γ-secretase may have opposing effects on Notch signaling; positive by cleaving Notch and generating NICD, and negative by processing APP and generating AID, which inhibits the function of NICD.
Cell adhesion regulates gene expression at translational checkpoints in human myeloid leukocytes
Authors: Mahoney Tracey S. , Weyrich Andrew S. , Dixon Dan A. , McIntyre Thomas , Prescott Stephen M. , Zimmerman Guy A.
Published: July 2002

Engagement of adhesion molecules on monocytes and other myeloid leukocytes, which are effector cells of the innate immune system, not only tethers the leukocytes in place but also transmits outside-in signals that induce functional changes and alter gene expression. We found that a subset of mRNAs that are induced or amplified by adhesion of human monocytes to P-selectin via its surface ligand, P-selectin glycoprotein 1, have characteristics that suggest specialized translational control. One of these codes for urokinase plasminogen activator receptor (UPAR), a critical surface protease receptor and regulator of cell adhesion and migration. Although UPAR transcripts are induced by adhesion, rapid synthesis of the protein uses constitutive mRNA without a requirement for new transcription and is regulated by mammalian target of rapamycin, demonstrating new biologic roles for the signal-dependent translation pathway controlled by this intracellular kinase. The synthesis of UPAR in monocytic cells is also regulated by eukaryotic translation initiation factor 4E, a second key translational checkpoint, and phosphorylation of eukaryotic translation initiation factor 4E is induced by adhesion of monocytes to P-selectin. Translationally controlled display of UPAR by monocytes confers recognition of the matrix protein, vitronectin. Adhesion-dependent signaling from the plasma membrane to translational checkpoints represents a previously unrecognized mechanism for regulating surface phenotype that may be particularly important for myeloid leukocytes and other cells that are specialized for rapid inflammatory and vascular responses.
Suppressed kindling epileptogenesis in mice with ectopic overexpression of galanin
Authors: Kokaia Merab , Holmberg Kristina , Nanobashvili Avtandil , Xu Zhi-Qing D. , Kokaia Zaal , Lendahl Urban , Hilke Susanne , Theodorsson Elvar , Kahl Ulrika , Bartfai Tamas , Lindvall Olle , Hökfelt Tomas
Published: July 2002

The neuropeptide galanin has been shown to suppress epileptic seizures. In cortical and hippocampal areas, galanin is normally mainly expressed in noradrenergic afferents. We have generated a mouse overexpressing galanin in neurons under the platelet-derived growth factor B promoter. RIA and HPLC analysis revealed up to 8-fold higher levels of galanin in transgenic as compared with wild-type mice. Ectopic galanin overexpression was detected especially in dentate granule cells and hippocampal and cortical pyramidal neurons. Galanin-overexpressing mice showed retardation of seizure generalization during hippocampal kindling, a model for human complex partial epilepsy. The high levels of galanin in mossy fibers found in the transgenic mice were further increased after seizures. Frequency facilitation of field excitatory postsynaptic potentials, a form of short-term synaptic plasticity assessed in hippocampal slices, was reduced in mossy fiber–CA3 cell synapses of galanin-overexpressing mice, indicating suppressed glutamate release. This effect was reversed by application of the putative galanin receptor antagonist M35. These data provide evidence that ectopically overexpressed galanin can be released and dampen the development of epilepsy by means of receptor-mediated action, at least partly by reducing glutamate release from mossy fibers.
Phase separation in aqueous solutions of lens gamma-crystallins: special role of gamma s.
Authors: Liu C , Asherie N , Lomakin A , Pande J , Ogun O , Benedek G B
Published: July 2002

We have studied liquid-liquid phase separation in aqueous ternary solutions of calf lens gamma-crystallin proteins. Specifically, we have examined two ternary systems containing gamma s--namely, gamma IVa with gamma s in water and gamma II with gamma s in water. For each system, the phase-separation temperatures (Tph (phi)) alpha as a function of the overall protein volume fraction phi at various fixed compositions alpha (the "cloud-point curves") were measured. For the gamma IVa, gamma s, and water ternary solution, a binodal curve composed of pairs of coexisting points, (phi I, alpha 1) and (phi II, alpha II), at a fixed temperature (20 degrees C) was also determined. We observe that on the cloud-point curve the critical point is at a higher volume fraction than the maximum phase-separation temperature point. We also find that typically the difference in composition between the coexisting phases is at least as significant as the difference in volume fraction. We show that the asymmetric shape of the cloud-point curve is a consequence of this significant composition difference. Our observation that the phase-separation temperature of the mixtures in the high volume fraction region is strongly suppressed suggests that gamma s-crystallin may play an important role in maintaining the transparency of the lens.
Genomic structure of the human retinoblastoma-related Rb2/p130 gene.
Authors: Baldi A , Boccia V , Claudio P P , De Luca A , Giordano A
Published: July 2002

The human Rb2/p130 gene shares many structural and functional features with the retinoblastoma gene and the retinoblastoma-related p107 gene. In the present study, we have cloned and partially sequenced the gene coding for the Rb2/p130 protein from human genomic libraries. The complete intron-exon organization of this gene has been elucidated. The gene contains 22 exons spanning over 50 kb of genomic DNA. The length of individual exons ranges from 65 to 1517 bp. The largest intron spans over 9 kb, and the smallest has only 82 bp. The 5' flanking region revealed a structural organization characteristic of promoters of "housekeeping" and growth control-related genes. A typical TATA or CAAT box is not present, but there are several GC boxes and potential binding sites for numerous transcription factors. This study provides the molecular basis for understanding the transcriptional control of the Rb2/p130 gene and for implementing a comprehensive Rb2/p130 mutation screen using genomic DNA as a template.
Hepatocyte nuclear factor 6, a transcription factor that contains a novel type of homeodomain and a single cut domain.
Authors: Lemaigre F P , Durviaux S M , Truong O , Lannoy V J , Hsuan J J , Rousseau G G
Published: July 2002

Tissue-specific transcription is regulated in part by cell type-restricted proteins that bind to defined sequences in target genes. The DNA-binding domain of these proteins is often evolutionarily conserved. On this basis, liver-enriched transcription factors were classified into five families. We describe here the mammalian prototype of a sixth family, which we therefore call hepatocyte nuclear factor 6 (HNF-6). It activates the promoter of a gene involved in the control of glucose metabolism. HNF-6 contains two different DNA-binding domains. One of these corresponds to a novel type of homeodomain. The other is homologous to the Drosophila cut domain. A similar bipartite sequence is coded by the genome of Caenorhabditis elegans.
How the first biopolymers could have evolved.
Authors: Abkevich V I , Gutin A M , Shakhnovich E I
Published: July 2002

In this work, we discuss a possible origin of the first biopolymers with stable unique structures. We suggest that at the prebiotic stage of evolution, long organic polymers had to be compact to avoid hydrolysis and had to be soluble and thus must not be exceedingly hydrophobic. We present an algorithm that generates such sequences for model proteins. The evolved sequences turn out to have a stable unique structure, into which they quickly fold. This result illustrates the idea that the unique three-dimensional native structures of first biopolymers could have evolved as a side effect of nonspecific physicochemical factors acting at the prebiotic stage of evolution.
Transcription factor EGR-1 suppresses the growth and transformation of human HT-1080 fibrosarcoma cells by induction of transforming growth factor beta 1.
Authors: Liu C , Adamson E , Mercola D
Published: July 2002

The early growth response 1 (EGR-1) gene product is a transcription factor with role in differentiation and growth. We have previously shown that expression of exogenous EGR-1 in various human tumor cells unexpectedly and markedly reduces growth and tumorigenicity and, conversely, that suppression of endogenous Egr-1 expression by antisense RNA eliminates protein expression, enhances growth, and promotes phenotypic transformation. However, the mechanism of these effects remained unknown. The promoter of human transforming growth factor beta 1 (TGF-beta 1) contains two GC-rich EGR-1 binding sites. We show that expression of EGR-1 in human HT-1080 fibrosarcoma cells uses increased secretion of biologically active TGF-beta 1 in direct proportion (rPearson = 0.96) to the amount of EGR-1 expressed and addition of recombinant human TGF-beta 1 is strongly growth-suppressive for these cells. Addition of monoclonal anti-TGF-beta 1 antibodies to EGR-1-expressing HT-1080 cells completely reverses the growth inhibitory effects of EGR-1. Reporter constructs bearing the EGR-1 binding segment of the TGF-beta 1 promoter was activated 4- to 6-fold relative to a control reporter in either HT-1080 cells that stably expressed or parental cells cotransfected with an EGR-1 expression vector. Expression of delta EGR-1, a mutant that cannot interact with the corepressors, nerve growth factor-activated factor binding proteins NAB1 and NAB2, due to deletion of the repressor domain, exhibited enhanced transactivation of 2- to 3.5-fold over that of wild-type EGR-1 showing that the reporter construct reflected the appropriate in vivo regulatory context. The EGR-1-stimulated transactivation was inhibited by expression of the Wilms tumor suppressor, a known specific DNA-binding competitor. These results indicate that EGR-1 suppresses growth of human HT-1080 fibrosarcoma cells by induction of TGF-beta 1.
Metal binding properties and secondary structure of the zinc-binding domain of Nup475
Authors: Worthington Mark T. , Amann Barbara T. , Nathans Daniel , Berg Jeremy M.
Published: July 2002

Nup475 is a nuclear zinc-binding protein of unknown function that
is induced in mammalian cells by growth factor mitogens. Nup475
contains two tandemly repeated sequences
YKTELCX
8
CX
5
CX
3
H
(Cys
3
His repeats) that are thought to be zinc-binding
domains. Similar sequences have been found in a number of proteins from
various species of eukaryotes. To determine the metal binding
properties and secondary structure of the putative zinc-binding domains
of Nup475, we have used synthetic or recombinant peptides that contain
one or two domain sequences. The peptide with a single domain bound
1.0 ± 0.1 equivalents of Co
2+
, and the peptide with
two domains bound 1.7 ± 0.4 equivalents of Co
2+
. Both
peptides bound Co
2+
and Zn
2+
with affinities
similar to those of classical zinc finger peptides. In each case, the
Co
2+
complex exhibited strong d-d transitions
characteristic of tetrahedral coordination. For structural studies by
nuclear magnetic resonance spectroscopy, we used a more soluble
two-domain peptide that had a single amino acid substitution in a
nonconserved amino acid residue in the second Cys
3
His
repeat. The mutant peptide unexpectedly showed loss of one of its metal
binding sites and displayed ordered structure for only the first
Cys
3
His sequence. On the basis of the nuclear magnetic
resonance data, we propose a structure for the Nup475 metal-binding
domain in which the zinc ion is coordinated by the conserved cysteines
and histidine, and the conserved YKTEL motif forms a parallel
sheet-like structure with the C terminus of this domain. This structure
is unlike that of any previously described class of metal binding
domain.
A possible mitochondrial gene in the early-branching amitochondriate protist
Trichomonas vaginalis
Authors: Roger Andrew J. , Clark C. Graham , Doolittle W. Ford
Published: July 2002

Trichomonads are anaerobic flagellated protists that, based on
analyses of ribosomal RNA sequences, represent one of the earliest
branching lineages among the eukaryotes. The absence of mitochondria in
these organisms coupled with their deep phylogenetic position has
prompted several authors to suggest that trichomonads, along with other
deeply-branching amitochondriate protist groups, diverged from the main
eukaryotic lineage prior to the endosymbiotic origin of mitochondria.
In this report we describe the presence of a gene in
Trichomonas
vaginalis
specifically related to mitochondrial chaperonin 60
(cpn60). A recent study indicates that a protein immunologically
related to cpn60 is located in trichomonad hydrogenosomes. Together,
these data provide evidence that ancestors of trichomonads perhaps
harbored the endosymbiotic progenitors of mitochondria, but that these
evolved into hydrogenosomes early in trichomonad evolution.
Inositol 1,4,5-trisphosphate receptor subtype 3 in pancreatic islet cell secretory granules revisited.
Authors: Ravazzola M , Halban P A , Orci L
Published: July 2002

It has been reported that the inositol 1,4,5-trisphosphate receptor subtype 3 is expressed in islet cells and is localized to both insulin and somatostatin granules [Blondel, O., Moody, M. M., Depaoli, A. M., Sharp, A. H., Ross, C. A., Swift, H. & Bell, G. I. (1994) Proc. Natl. Acad. Sci. USA 91, 7777-7781]. This subcellular localization was based on electron microscope immunocytochemistry using antibodies (affinity-purified polyclonal antiserum AB3) directed to a 15-residue peptide of rat inositol trisphosphate receptor subtype 3. We now show that these antibodies cross-react with rat, but not human, insulin. Accordingly, the anti-inositol trisphosphate receptor subtype 3 (AB3) antibodies label electron dense cores of mature (insulin-rich) granules of rat pancreatic beta cells, and rat granule labeling was blocked by preabsorption of the AB3 antibodies with rat insulin. The immunostaining of immature, Golgi-associated proinsulin-rich granules with AB3 antibodies was very weak, indicating that cross-reactivity is limited to the hormone and not its precursor. Also, the AB3 antibodies labeled pure rat insulin crystals grown in vitro but failed to stain crystals grown from pure human insulin. By immunoprecipitation, the antibodies similarly displayed a higher affinity for rat than for human insulin. We could not confirm the labeling of somatostatin granules using AB3 antibodies.
Calmodulin regulation of light adaptation and store-operated dark current in
Drosophila
photoreceptors
Authors: Arnon Assaf , Cook Boaz , Gillo Boaz , Montell Craig , Selinger Zvi , Minke Baruch
Published: July 2002

Phototransduction in
Drosophila
occurs through inositol lipid signaling that results in Ca
2+
mobilization. In this system, we investigate the hitherto unknown physiological roles of calmodulin (CaM) in light adaptation and in regulation of the inward current that is brought about by depletion of cellular Ca
2+
stores. To see the effects of a decreased Ca–CaM content in photoreceptor cells, we used several methods. Transgenic
Drosophila
P[
ninaC
Δ

B

] flies, which have CaM-deficient photoreceptors, were studied. The peptide inhibitor M5, which binds to Ca–CaM and prevents its action, was applied. A Ca
2+
-free medium, which prevents Ca
2+
influx and thereby diminishes the generation of Ca–CaM, was used. The decrease in the Ca–CaM level caused the following effects. (
i
) Fluorescence of Ca
2+
indicator revealed an enhanced light-induced Ca
2+
release from internal stores. (
ii
) Measurements of the light-induced current in P[
ninaC
Δ

B

] cells showed a reduced light adaptation. (
iii
) Internal dialysis of M5 initially enhanced excitation and subsequently disrupted the light-induced current. (
iv
) An inward dark current appeared after depletion of the Ca
2+
stores with ryanodine and caffeine. Importantly, application of Ca–CaM into the photoreceptor cells prevented all of the above effects. We propose that negative feedback of Ca–CaM on Ca
2+
release from ryanodine-sensitive stores mediates light adaptation, is essential for light excitation, and keeps the store-operated inward current under a tight control.
A point mutation in the γ
2
subunit of γ-aminobutyric acid type A receptors results in altered benzodiazepine binding site specificity
Authors: Buhr Andreas , Sigel Erwin
Published: July 2002

Benzodiazepines allosterically modulate γ-aminobutyric acid (GABA) evoked chloride currents of γ-aminobutyric acid type A (GABA
A
) receptors. Coexpression of either rat γ
2
or γ
3
, in combination with α
1
and β
2
subunits, results both in receptors displaying high [
3
H]Ro 15-1788 affinity. However, receptors containing a γ
3
subunit display a 178-fold reduced affinity to zolpidem as compared with γ
2
-containing receptors. Eight chimeras between γ
2
and γ
3
were constructed followed by nine different point mutations in γ
2
, each to the homologous amino acid residue found in γ
3
. Chimeric or mutant γ subunits were coexpressed with α
1
and β
2
in human embryonic kidney 293 cells to localize amino acid residues responsible for the reduced zolpidem affinity. Substitution of a methionine-to-leucine at position 130 of γ
2
(γ
2
M130L) resulted in a 51-fold reduction in zolpidem affinity whereas the affinity to [
3
H]Ro 15-1788 remained unchanged. The affinity for diazepam was only decreased by about 2-fold. The same mutation resulted in a 9-fold increase in Cl 218872 affinity. A second mutation (γ
2
M57I) was found to reduce zolpidem affinity by about 4-fold. Wild-type and γ
2
M130L-containing receptors were functionally expressed in
Xenopus
oocytes. Upon mutation allosteric coupling between agonist and modulatory sites is preserved. Dose–response curves for zolpidem and for diazepam showed that the zolpidem but not the diazepam apparent affinity is drastically reduced. The apparent GABA affinity is not significantly affected by the γ
2
M130L mutation. The identified amino acid residues may define part of the benzodiazepine binding pocket of GABA
A
receptors. As the modulatory site in the GABA
A
receptor is homologous to the GABA site, and to all agonist sites of related receptors, γ
2
M130 may either point to a homologous region important for agonist binding in all receptors or define a new region not underlying this principle.
Changes of telomere length cause reciprocal changes in the lifespan of mother cells in
Saccharomyces cerevisiae
Authors: Austriaco Nicanor R. , Guarente Leonard P.
Published: July 2002

Budding yeast cells divide asymmetrically, giving rise to a mother and its daughter. Mother cells have a limited division potential, called their lifespan, which ends in proliferation-arrest and lysis. In this report we mutate telomerase in
Saccharomyces cerevisiae
to shorten telomeres and show that, rather than shortening lifespan, this leads to a significant extension in lifespan. This extension requires the product of the
SIR3
gene, an essential component of the silencing machinery which binds to telomeres. In contrast, longer telomeres in a genotypically wild-type strain lead to a decrease in lifespan. These findings suggest that the length of telomeres dictates the lifespan by regulating the amount of the silencing machinery available to nontelomeric locations in the yeast genome.
Wheat cytosolic acetyl-CoA carboxylase complements an
ACC1
null mutation in yeast
Authors: Joachimiak M. , Tevzadze G. , Podkowinski J. , Haselkorn R. , Gornicki P.
Published: July 2002

Spores harboring an
ACC1
deletion derived from a diploid
Saccharomyces cerevisiae
strain, in which one copy of the entire
ACC1
gene is replaced with a
LEU2
cassette, fail to grow. A chimeric gene consisting of the yeast
GAL10
promoter, yeast
ACC1
leader, wheat cytosolic acetyl-CoA carboxylase (ACCase) cDNA, and yeast
ACC1
3′ tail was used to complement a yeast
ACC1
mutation. The complementation demonstrates that active wheat ACCase can be produced in yeast. At low concentrations of galactose, the activity of the “wheat gene” driven by the
GAL10
promoter is low and ACCase becomes limiting for growth, a condition expected to enhance transgenic yeast sensitivity to wheat ACCase-specific inhibitors. An aryloxyphenoxypropionate and two cyclohexanediones do not inhibit growth of haploid yeast strains containing the yeast
ACC1
gene, but one cyclohexanedione inhibits growth of the gene-replacement strains at concentrations below 0.2 mM.
In vitro
, the activity of wheat cytosolic ACCase produced by the gene-replacement yeast strain is inhibited by haloxyfop and cethoxydim at concentrations above 0.02 mM. The activity of yeast ACCase is less affected. The wheat plastid ACCase in wheat germ extract is inhibited by all three herbicides at concentrations below 0.02 mM. Yeast gene-replacement strains will provide a convenient system for the study of plant ACCases.
Severe genital herpes infections in HIV-infected individuals with impaired herpes simplex virus-specific CD8+cytotoxic T lymphocyte responses
Authors: Posavad Christine M. , Koelle David M. , Shaughnessy Mary F. , Corey Lawrence
Published: July 2002

The specific mechanisms underlying the varied susceptibility of HIV-infected (HIV+) individuals to opportunistic infections (OI) are still incompletely understood. One hypothesis is that quantitative differences in specific T cell responses to a colonizing organism determine the development of an AIDS-defining OI. We evaluated this hypothesis for herpes simplex virus (HSV) infection, a common OI in HIV+ patients. Using limiting dilution analyses, the frequency of HSV-specific CD8+cytotoxic T lymphocyte precursors (pCTL) and proliferative precursors were quantitated in peripheral blood mononuclear cells from 20 patients coinfected with HIV and HSV-2. The frequency of HSV-specific CD8+pCTL in HSV+HIV+ individuals was significantly lower than in HSV+HIV− individuals (1 in 77,000 vs. 1 in 6,000,P= .0005) and was not different than in HSV-HIV− individuals (1 in 100,000,P= .24). HIV+ patients who suffered more severe genital herpes recurrences had significantly lower HSV-specific CD8+pCTL frequencies than those patients with mild recurrences (1 in 170,000 vs. 1 in 26,000,P= .03). In contrast, no significant difference was seen in proliferative precursor frequencies between those patients with mild vs. severe genital herpes (1 in 3,800 vs. 1 in 6,600,P> .5). Quantitative differences in pCTL frequency to HSV appear to be the most important host factor influencing the frequency and severity of HSV reactivation in HIV+ patients. Studies to reconstitute such immunity, especially in people with acyclovir-resistant HSV, appear warranted.
Formation of stable adducts and absence of depurinating DNA adducts in cells and DNA treated with the potent carcinogen dibenzo[
a,l
]pyrene or its diol epoxides
Authors: Melendez-Colon Victor J. , Smith Charles Allen , Seidel Albrecht , Luch Andreas , Platt Karl L. , Baird William M.
Published: July 2002

Polycyclic aromatic hydrocarbons (PAH) are widespread environmental contaminants, and some are potent carcinogens in rodents. Carcinogenic PAH are activated in cells to metabolites that react with DNA to form stable covalent DNA adducts. It has been proposed [Cavalieri, E. L. & Roger, E. G. (1995)
Xenobiotica
25, 677–688] that unstable DNA adducts are also formed and that apurinic sites in the DNA resulting from unstable PAH adducts play a key role in the initiation of cancer. The potent carcinogen dibenzo[
a,l
]pyrene (DB[
a,l
]P) is activated in cells to (+)-
syn
- and (−)-
anti
-DB[
a,l
]P-11,12-diol-13,14-epoxide (DB[
a,l
]PDE), which have been shown to form stable adducts with DNA. To evaluate the importance of unstable PAH adducts, we compared stable adduct formation to apurinic site formation. Stable DB[
a,l
]PDE adducts were determined by
33
P-postlabeling and HPLC. To measure apurinic sites they were converted to strand breaks, and these were monitored by examining the integrity of a particular restriction fragment of the dihydrofolate reductase gene. The method easily detected apurinic sites resulting from methylation by treatment of cells or DNA with dimethyl sulfate or from reaction of DNA with DB[
a,l
]P in the presence of horseradish peroxidase. We estimate the method could detect 0.1 apurinic site in the 14-kb fragment examined. However, apurinic sites were below our limit of detection in DNA treated directly with (+)-
syn
- or (−)-
anti
-DB[
a,l
]PDE or in DNA from Chinese hamster ovary B11 cells so treated, although in these samples the frequency of stable adducts ranged from 3 to 10 per 14 kb. We also treated the human mammary carcinoma cell line MCF-7 with DB[
a,l
]P and again could not detect significant amounts of unstable adducts. These results indicate that the proportion of stable adducts formed by DB[
a,l
]P activated in cells and its diol epoxides is greater than 99% and suggest a predominant role for stable DNA adducts in the carcinogenic activity of DB[
a,l
]P.