bluuebunny/crossref_metadata_2025 huggingface dataset:
Computer studies on powerful magnetic energy conversion by the spontaneous fast reconnection mechanism
Authors: Ugai M.
Published: July 2002

On the basis of the spontaneous reconnection model, computer simulations study the physical mechanism by which magnetic energy, initially stored in a current sheet system, is released into plasma energies. For the uniform resistivity model, the Sweet–Parker mechanism is eventually set up with the diffusion region becoming longer with time. It is the Ohmic heating ηJ2 in the diffusion region that plays the dominant role in releasing the magnetic energy. Attached to the diffusion region, a long plasmoid is formed and propagates like a large-amplitude Alfvén pulse, where the generator and motor effects are canceled along the plasmoid boundary. For the anomalous resistivity model, the fast reconnection mechanism is eventually set up with the diffusion region remaining to be localized near an X neutral point. It is the powerful motor effect [u⋅(J×B)≳0] along the slow shock layers that drastically releases the stored magnetic energy. A large-scale plasmoid distinctly swells, so that the ambient magnetic fields are compressed (by the generator effect), and the enhanced magnetic energy is then reduced by the strong motor effect in the backward half of the plasmoid. The slow shocks extend with time from near the X point, leading to a drastic catastrophe for the overall magnetic field system.
Transport, energy balance, and stability of a large field-reversed configuration
Authors: Slough J. T. , Hoffman A. L. , Milroy R. D. , Maqueda R. , Steinhauer L. C.
Published: July 2002

Experiments have been conducted on the Large s Experiment (LSX) [Phys. Rev. Lett. 69, 2212 (1992)] field-reversed theta pinch, where plasmas confined in a field-reversed configuration (FRC) have exhibited record energy, particle, and configuration lifetimes. By careful control of the formation process, it was possible to form symmetric, quiescent FRCs with s values (the number of ion gyroradii from the field null to the separatrix of the FRC) as large as 5. LSX particle confinement showed a strong scaling with s. The inferred particle diffusivity, Ds, at large s approached ∼2 m2/s, which, along with previous experimental results, indicate a favorable Ds∼s−1/2 scaling. At large s, both electron and ion cross-field thermal conduction losses become negligible compared to convective losses, with the inferred χ⊥e∼4 m2/s, which was near classical values. Data from several diagnostics employed on the LSX device were analyzed to seek correlation between distortions in the plasma shape and the confinement properties of the FRCs formed. No clear correlation between the quality of confinement and distortion was observed. Experiments conducted over a large range of s (1<s<8) appeared to be grossly stable to low-order modes, such as the internal tilt.
Induction response of plasma in nonadiabatic magnetic compression heating
Authors: Xie H. X.
Published: July 2002

Fast magnetic compression, where the compression time is shorter than the ion gyroperiod, is illustrated by a simple model. In this model the Vlasov–Ampère equation gives a Bernstein–Greene–Kruskal (BGK) stationary state at the so-called zero-β limit. It is possible to achieve hundreds of keV ion energy by the fast compression heating, because there is very little shielding from the plasma currents in the heating phase. Strong shielding appears when the compression has generated strongly phase-correlated oscillations of the ion orbits. Thresholds of plasma β for the appearance of ion stochasticity and ion trapping are estimated. Parameters in a 500 keV ion energy case are presented.
An improved version of the view factor method for simulating inertial confinement fusion hohlraums
Authors: Basko Mikhail
Published: July 2002

A modified version of the view factor equations is proposed which improves the accuracy of the description of temporal effects in energy redistribution by thermal radiation in cavities driven by power pulses typical for inertial confinement fusion (ICF). The method is applied to analyze the process of radiative symmetrization in the simplest type of closed cylindrical hohlraums heated by two x-ray rings on the sidewall of the hohlraum case. Such hohlraums may be used in certain types of ICF targets driven by ion beams.
Measurements of the hole boring velocity from Doppler shifted harmonic emission from solid targets
Authors: Zepf M. , Castro-Colin M. , Chambers D. , Preston S. G. , Wark J. S. , Zhang J. , Danson C. N. , Neely D. , Norreys P. A. , Dangor A. E. , Dyson A. , Lee P. , Fews A. P. , Gibbon P. , Moustaizis S. , Key M. H.
Published: July 2002

The fast ignitor scheme for inertial confinement fusion requires forward driving of the critical density surface by light pressure (hole boring) to allow energy deposition close to the dense fuel. The recession velocity of the critical density surface has been observed to be v/c=0.015 at an irradiance of 1.0×1019 W cm−2 at a wavelength of 1.05 micron, in quantitative agreement with modeling.
Electron parametric instabilities of ultraintense laser pulses propagating in plasmas of arbitrary density
Authors: Quesnel B. , Mora P. , Adam J. C. , Héron A. , Laval G.
Published: July 2002

The dispersion relation for electron parametric instabilities of a circularly polarized laser wave of arbitrary intensity is established without restrictions on the plasma density. It is obtained in an implicit analytical form and solved numerically. The well-known stimulated Raman scattering, relativistic modulational instability, relativistic filamentation instability, and two-plasmon decay are recovered at low intensity. Their behavior in the ultrarelativistic regime is characterized by a wide extent of the unstable region in the wave vector space, with growth rates equal to a fraction of the laser frequency, and a strong harmonic generation. Particle-in-cell simulations confirm these results and show that the instability leads to a very strong heating of the plasma.
Theory of resonance influence of sawtooth crashes on ions with large orbit width
Authors: Kolesnichenko Ya. I. , Lutsenko V. V. , White R. B. , Yakovenko Yu. V.
Published: July 2002

The role of resonances in the sawtooth-crash-induced redistribution of fast ions is investigated. In particular, the conditions of wave-particle resonant interaction in the presence of the equilibrium electric field and the mode rotation are obtained, and effects of sawteeth on the resonant particles with arbitrary width of nonperturbed orbits are studied. It is found that resonances play the dominant role in the transport of ions having sufficiently high energy. It is shown that the resonance regions may overlap, in which case the resonant particles may constitute the main fraction of the fast ion population in the sawtooth mixing region. The behavior of the resonant particles is studied both by constructing a Poincaré map and analytically, by means of the adiabatic invariant derived in this paper and calculation of the characteristic frequencies of the particle motion.
Guiding and stability of short laser pulses in partially stripped ionizing plasmas
Authors: Sprangle P. , Hafizi B.
Published: July 2002

Laser pulse propagation can be strongly influenced by nonlinearity effects (relativistic and/or atomic electrons), ionization processes, and finite pulse length effects. In this paper these processes are included in the analysis of the propagation and stability of intense laser pulses in plasmas. An envelope equation, which includes ionization and nonlinear effects, is derived and the spot size is found to be unstable to an ionization–modulation instability. Introducing a quasiparaxial approximation to the wave equation, a pair of coupled envelope-power equations including finite pulse length effects, as well as nonlinearities, is derived and analyzed. In addition, short laser pulses propagating in plasma channels are found to undergo an envelope modulation that is always damped in the front and initially grows in the back of the pulse. Finite pulse length effects are also shown to modify nonlinear focusing processes. Finally, it is shown that, in a partially stripped plasma, the bound electrons can significantly alter the stability of laser pulses. In the presence of both free and bound electrons, an atomic modulation instability develops that can have a growth rate substantially higher than either the conventional relativistic modulational instability or the forward Raman instability. The filamentation instability is shown to be enhanced by bound electrons while the backward Raman instability is unaffected. An example of laser wakefield acceleration to electron energies greater than 2.5 GeV in a plasma channel is described.
Does flow shear suppress turbulence in nonionized flows?
Authors: Terry P. W.
Published: July 2002

The suppression of turbulence by mean flow shear is shown to apply to nonionized flows as well as plasmas. However, besides the criterion that the shearing rate exceed the turbulent decorrelation rate, there are three additional conditions. These stipulate that the shear flow must be stable, that turbulence must remain in the domain of flow shear for longer than an eddy turnover time, and that the dynamics should be two dimensional (2D). In nonionized flows, these conditions are not typically satisfied, explaining why shear suppression is not a familiar phenomenon in hydrodynamics. The three conditions are discussed in the context of nonionized and plasma flows. Two examples of suppression in nonionized flows are presented. One involves the formation of coherent structures in 2D Navier–Stokes turbulence and the other involves large-scale turbulence in the stratosphere.
Experimental investigation of short scalelength density fluctuations in laser-produced plasmas
Authors: Moody J. D. , MacGowan B. J. , Glenzer S. H. , Kirkwood R. K. , Kruer W. L. , Montgomery D. S. , Schmitt A. J. , Williams E. A. , Stone G. F.
Published: July 2002

The technique of near forward laser scattering is used to infer characteristics of intrinsic and controlled density fluctuations in laser-produced plasmas. Intrinsic fluctuations are studied in long-scalelength plasmas where it is found that the fluctuations exhibit scale sizes related to the intensity variation scales in the plasma forming and interaction beams. Stimulated Brillouin forward scattering and filamentation appear to be the primary mechanism through which these fluctuations originate. The beam spray resulting from these fluctuations is important to understand, since it can affect symmetry in an inertial confinement fusion (ICF) experiment. Controlled fluctuations are studied in foam and exploding foil targets. Forward scattered light from foam targets shows evidence that the initial target inhomogeneities remain after the target is laser heated. Forward scattered light from an exploding foil plasma shows that a regular intensity pattern can be used to produce a spatially correlated density fluctuation pattern. These results provide data which are being used to benchmark numerical models of beam spray.
Analytical axial view factors and thermal radiation distribution inside a cylindrical hohlraum
Authors: Srivastava M. K. , Kumar Vinod , Menon S. V. G.
Published: July 2002

Thermal radiation redistribution inside a cylindrical hohlraum is discussed for uniform disc and two-ring sources. The flux conservation equation, coupled with self-similar scaling relation for the re-emitted flux, is solved to obtain the radiation temperature profile inside a gold capillary hohlraum at various times. The axial view factors required for the calculations are derived analytically in a closed form, which not only exactly reproduce the numerical results [G. D. Tsakiris, Phys. Fluids B 4, 992 (1992)] but also simplifies the overall problem enormously, both in terms of computational time and effort.
Preferential nucleation along SiO2 steps in amorphous Si
Authors: Moniwa M. , Miyao M. , Tsuchiyama R. , Ishizaka A. , Ichikawa M. , Sunami H. , Tokuyama T.
Published: July 2002

Annealing characteristics for amorphous Si film deposited on an SiO2 layer were investigated with the hope that this would throw further light on aspects of solid phase epitaxy. Preferential nucleation, which initiated from the bottom region of deposited Si film, was found along SiO2 steps. The activation energy for the growth speed of the nuclei was evaluated to be 1.7 eV. As this value is significantly smaller than 2.0 eV, the bond breaking energy of Si, stress originating mainly from the thermal expansion difference between SiO2 and Si, is considered to be the driving force.
Nd-Fe-B-Co-Al based permanent magnets with improved magnetic properties and temperature characteristics
Authors: Mizoguchi T. , Sakai I. , Inomata K.
Published: July 2002

Magnetic properties have been studied with respect to the boron concentration on Nd-Fe-B based magnets. The combined addition of cobalt and aluminum in a Nd-Fe-B magnet is remarkably effective for increasing magnetic hardness in the region of low boron concentration. The following magnetic properties were attained for Nd15Fe62.5B5.5Co16Al1 :Br=13.2 kG, iHc=11.0 kOe, (BH)max=41.0 MGOe, and Tc=500 °C. The reversible temperature coefficient of the remanence of the magnet is −0.071%/deg, approximately one-half of the Nd15Fe77B8 magnet.
Low pressure, light initiated, glow discharge switch for high power applications
Authors: Kirkman George F. , Gundersen Martin A.
Published: July 2002

A low pressure glow discharge switch that has a number of features that are desirable for high power applications is described. The switch has achieved high stand-off voltage and peak current, has potential for very fast current rate of rise, and operates near the glow-to-arc transition in hydrogen or helium. Closure is initiated by light incident on the back of the cathode, and it is observed that surface damage within the area of illumination is less than surrounding areas. Several aspects of the switch are similar to thyratrons and pseudosparks.
cw and pulsed 2.8 μm laser emission from diode-pumped Er3+:LiYF4 at room temperature
Authors: Kintz G. J. , Allen R. , Esterowitz L.
Published: July 2002

Laser emission at 2.8 μm from an Er3+:LiYF4 sample longitudinally pumped with a multiple stripe laser diode array is observed for the first time. The threshold for pulsed laser emission is 33 μJ and for cw laser emission 147 mW. cw laser action in this normally self-terminating laser transition is attributed to a cooperative up-conversion process.
Influence of the beam spot size on ablation rates in pulsed-laser processing
Authors: Eyett M. , Bäuerle D.
Published: July 2002

Ablation rates in pulsed-laser processing depend heavily on the laser beam spot size. This has been observed for the first time for a number of different materials. Detailed investigations on this effect, performed by means of XeCl excimer-laser radiation and the example of LiNbO3, are reported in this letter. With this material, the ablation rate at constant fluence saturates at laser beam spot sizes of 2w≳80 μm and increases by about a factor of 3 when 2w is decreased to 24 μm. The effect is interpreted as being due to changes in the material transport which depend on the size of the region being processed.
Flash-lamp-triggered high-power thyratron-type switch
Authors: Kirkman G. , Hartmann W. , Gundersen M. A.
Published: July 2002

Extremely high cold cathode emission and a plasma current density that is much higher than commercial glow discharge hot cathode switches have been obtained in a flash-triggered hollow cathode thyratron-type switch that operates in a glow mode. The cold cathode emission is higher by several orders of magnitude than emission from thermionic cathodes in high-power hydrogen thyratrons, without arc formation. Peak current >17 kA, dI/dt>3×1011 A/s, and power gain >1400 are observed. The switch has been successfully operated as a thyratron substitute in a commercial XeCl excimer laser. The work demonstrates a new approach to thyratron-type switches, and a wide range of technologically useful physical processes that are poorly understood.
Real-time confocal scanning optical microscope
Authors: Xiao G. Q. , Corle T. R. , Kino G. S.
Published: July 2002

A real-time confocal scanning optical microscope is described. It is capable of generating 640 frames per second with 7000 lines per frame. It achieves this speed by simultaneously illuminating several thousand pinholes arranged in a spiral pattern on a rotating disk. An optical isolator is used to eliminate reflections from the surface of the disk. This type of microscope should have the same range and transverse definitions as a standard, single pinhole, confocal microscope.
Grafts of supplementary thymuses injected with allogeneic pancreatic islets protect nonobese diabetic mice against diabetes
Authors: Salaün J. , Simmenauer N. , Belo P. , Coutinho A. , Le Douarin N. M.
Published: July 2002

In nonobese diabetic (NOD) mice, the autoimmune attack of the β-cells in pancreatic islets is now believed to result from abnormal thymic selection. Accordingly, grafts of thymic epithelium from NOD donors to athymic recipients promote autoimmune islet inflammation in normal strains, and intrathymic islet grafts decrease the incidence of disease in NOD animals. Two competing hypotheses of abnormal thymic selection in diabetic mice have been proposed: deficient negative selection with poor elimination of aggressive organ-specific T cells vs. deficient positive selection of protective T regulatory cells. We have now addressed these alternatives by grafting, into young NOD mice whose own thymus was left intact, newborn NOD thymuses containing allogeneic pancreatic islets. If the NOD defect represented poor negative selection, these animals would develop disease at control rates, as the generation of autoreactive T cells proceeds undisturbed in the autologous thymus. In contrast, if NOD thymuses are defective in the production of T regulatory cells, lower disease incidence is expected in the chimeras, as more protective cells can be produced in the grafted thymus. The results show a reduced incidence of diabetes in the chimeras (24%) as compared with control (72%) NOD mice, throughout adult life. We conclude that amelioration of NOD mice by intrathymic islet grafts is not caused by enhanced negative selection and suggest that autoimmune diabetes in this system is the result of inefficient generation of T regulatory cells in the thymus.
The surface variant antigens of
Plasmodium falciparum
contain cross-reactive epitopes
Authors: Gamain Benoit , Miller Louis H. , Baruch Dror I.
Published: July 2002

Plasmodium falciparum
parasites evade the host
immune system by clonal expression of the variant antigen,
P.
falciparum
erythrocyte membrane protein 1 (PfEMP1). Antibodies
to PfEMP1 correlate with development of clinical immunity but are
predominantly variant-specific. To overcome this major limitation for
vaccine development, we set out to identify cross-reactive epitopes on
the surface of parasitized erythrocytes (PEs). We prepared mAbs to the
cysteine-rich interdomain region 1 (CIDR1) of PfEMP1 that is
functionally conserved for binding to CD36. Two mAbs, targeting
different regions of CIDR1, reacted with multiple
P.
falciparum
strains expressing variant PfEMP1s. One of these
mAbs, mAb 6A2-B1, recognized nine of 10 strains tested, failing to
react with only one strain that does not bind CD36. Flow cytometry with
Chinese hamster ovary cells expressing variant CIDR1s demonstrated that
both mAbs recognized the CIDR1 of various CD36-binding PfEMP1s and are
truly cross-reactive. The demonstration of cross-reactive epitopes on
the PE surface provides further credence for development of effective
vaccines against the variant antigen on the surface of
P.
falciparum
-infected erythrocytes.
NMR structure of the calreticulin P-domain
Authors: Ellgaard Lars , Riek Roland , Herrmann Torsten , Güntert Peter , Braun Daniel , Helenius Ari , Wüthrich Kurt
Published: July 2002

The NMR structure of the rat calreticulin P-domain, comprising
residues 189–288, CRT(189–288), shows a hairpin fold that involves
the entire polypeptide chain, has the two chain ends in close spatial
proximity, and does not fold back on itself. This globally extended
structure is stabilized by three antiparallel β-sheets, with the
β-strands comprising the residues 189–192 and 276–279, 206–209 and
262–265, and 223–226 and 248–251, respectively. The hairpin loop of
residues 227–247 and the two connecting regions between the β-sheets
contain a hydrophobic cluster, where each of the three clusters
includes two highly conserved tryptophyl residues, one from each strand
of the hairpin. The three β-sheets and the three hydrophobic clusters
form a repeating pattern of interactions across the hairpin that
reflects the periodicity of the amino acid sequence, which consists of
three 17-residue repeats followed by three 14-residue repeats. Within
the global hairpin fold there are two well-ordered subdomains
comprising the residues 219–258, and 189–209 and 262–284,
respectively. These are separated by a poorly ordered linker region, so
that the relative orientation of the two subdomains cannot be precisely
described. The structure type observed for CRT(189–288) provides an
additional basis for functional studies of the abundant endoplasmic
reticulum chaperone calreticulin.
Learning to see the trees before the forest: Reversible deactivation of the superior colliculus during learning of local and global visual features
Authors: Lomber Stephen G.
Published: July 2002

Previous studies have established that deactivation of the superior colliculus severely retards the normally rapid learning of pattern discriminations in the mature cat. The purpose of this study was to test the hypothesis that the midbrain plays an important role in the learning of simple pattern discriminations and that the contribution of this pathway is to the perception of global, rather than local, features of a figure. To answer this question, pattern discrimination learning was studied in three intact cats and in three experimental cats during bilateral reversible deactivation of the superficial layers of the superior colliculus (SC). The animals concurrently learned to discriminate three pairs of compound visual patterns composed of small (local element) Ts or 7s. Congruent and incongruent stimulus pairs were large (global) Ts vs. 7s comprising the same or different local elements, respectively. The random stimulus pair consisted of randomly scattered local elements (Ts vs. 7s). The animals were trained to respond to the large Ts in the congruent and incongruent pairs and the small Ts in the random pair. In the normal cats, learning of the random pair was much slower than the learning of the congruent and incongruent pairs. This finding demonstrated the theory of global precedence, because the animals learned the global features of the congruent and incongruent pairs much more quickly than the local features of the random pair. In contrast, during bilateral deactivation of the superficial layers of the SC, the learning of the incongruent pair was significantly retarded and took longer to learn than the random pair. Congruent and random pair learning rates were unchanged. The specific deficit in learning the incongruent pair indicates that the learning of global, but not local, elements of the visual pattern is impaired during deactivation of the SC. The unimpaired use of local features permitted the animals to learn the congruent and random pairs at normal rates. Therefore, deactivation of the superficial layers of the SC during pattern discrimination learning reverses the precedence for global visual features that is typical of normal learning.
Adenovirus-mediated suppression of HMGI(Y) protein synthesis as potential therapy of human malignant neoplasias
Authors: Scala Stefania , Portella Giuseppe , Fedele Monica , Chiappetta Gennaro , Fusco Alfredo
Published: July 2002

High mobility group I (HMGI) proteins are overexpressed in several human malignant tumors. We previously demonstrated that inhibition of HMGI synthesis prevents thyroid cell transformation. Here, we report that an adenovirus carrying the HMGI(Y) gene in an antisense orientation (Ad-Yas) induced programmed cell death of two human thyroid anaplastic carcinoma cell lines (ARO and FB-1), but not normal thyroid cells. The Ad-Yas virus led to death of lung, colon, and breast carcinoma cells. A control adenovirus carrying the
lacZ
gene did not inhibit the growth of either normal or neoplastic cells. Ad-Yas treatment of tumors induced in athymic mice by ARO cells caused a drastic reduction in tumor size. Therefore, suppression of HMGI(Y) protein synthesis by an HMGI(Y) antisense adenoviral vector may be a useful treatment strategy in a variety of human malignant neoplasias, in which HMGI(Y) gene overexpression is a general event.
Specific repression of β-globin promoter activity by nuclear ferritin
Authors: Broyles Robert H. , Belegu Visar , DeWitt Christina R. , Shah Sandeep N. , Stewart Charles A. , Pye Quentin N. , Floyd Robert A.
Published: July 2002

Developmental hemoglobin switching involves sequential globin gene activations and repressions that are incompletely understood. Earlier observations, described herein, led us to hypothesize that nuclear ferritin is a repressor of the adult β-globin gene in embryonic erythroid cells. Our data show that a ferritin-family protein in K562 cell nuclear extracts binds specifically to a highly conserved CAGTGC motif in the β-globin promoter at −153 to −148 bp from the cap site, and mutation of the CAGTGC motif reduces binding 20-fold in competition gel-shift assays. Purified human ferritin that is enriched in ferritin-H chains also binds the CAGTGC promoter segment. Expression clones of ferritin-H markedly repress β-globin promoter-driven reporter gene expression in cotransfected CV-1 cells in which the β-promoter has been stimulated with the transcription activator erythroid Krüppel-like factor (EKLF). We have constructed chloramphenicol acetyltransferase reporter plasmids containing either a wild-type or mutant β-globin promoter for the −150 CAGTGC motif and have compared the constructs for susceptibility to repression by ferritin-H in cotransfection assays. We find that stimulation by cotransfected EKLF is retained with the mutant promoter, whereas repression by ferritin-H is lost. Thus, mutation of the −150 CAGTGC motif not only markedly reduces
in vitro
binding of nuclear ferritin but also abrogates the ability of expressed ferritin-H to repress this promoter in our cell transfection assay, providing a strong link between DNA binding and function, and strong support for our proposal that nuclear ferritin-H is a repressor of the human β-globin gene. Such a repressor could be helpful in treating sickle cell and other genetic diseases.
The
E23
early gene of
Drosophila
encodes an ecdysone-inducible ATP-binding cassette transporter capable of repressing ecdysone-mediated gene activation
Authors: Hock Tommy , Cottrill Tracy , Keegan John , Garza Dan
Published: July 2002

At the onset of
Drosophila
metamorphosis, the steroid hormone 20-OH ecdysone directly induces a small number of early puffs in the polytene chromosomes of the larval salivary gland. Proteins encoded by the early genes corresponding to these transcriptional puffs then regulate the activity of both the early puffs themselves and a much larger set of late puffs. Three of these early genes encode transcription factors that play critical regulatory roles during metamorphosis. Here we report the cloning, DNA sequence, genomic structure, ecdysone inducibility, and temporal expression of an early gene residing in the 23E early puff and denoted
E23
(Early gene at 23). In contrast to other early genes,
E23
encodes a protein with similarity to ATP-binding cassette transporters. Using heat shock-inducible transgenes, we found that
E23
overexpression not only produces phenotypic abnormalities and lethality, but also interferes with ecdysone-mediated gene activation, demonstrating that
E23
is capable of modulating the ecdysone response. Our results suggest the existence of a previously unrecognized regulatory mechanism for modulating steroid hormone signaling in
Drosophila
.
A DNA–porphyrin minor-groove complex at atomic resolution: The structural consequences of porphyrin ruffling
Authors: Bennett Matthew , Krah Alexander , Wien Frank , Garman Elspeth , Mckenna Robert , Sanderson Mark , Neidle Stephen
Published: July 2002

The crystal structure of a B-type DNA hexanucleotide duplex complexed with the porphyrin molecule nickel-[tetra-
N
-methyl-pyridyl] porphyrin has been solved by multiwavelength anomalous diffraction phasing and refined to an
R
factor of 11.5% at a resolution of 0.9 Å. The structure has been solved and refined as two crystallographically independent duplexes, stacked end to end. Contrary to expectation, the porphyrin molecule is not intercalated into the duplex but is stacked onto the ends of the two-duplex stack. The porphyrin molecule is highly buckled as a consequence of the nickel coordination, which produces large changes in local DNA structure. A second mode of porphyrin binding is apparent as a consequence of crystal packing, which places the ligand in the minor groove of an adjacent duplex. This structure thus provides, to our knowledge, the first atomic visualization of minor-groove binding for a porphyrin molecule. The geometry of groove binding provides a ready explanation for porphyrin-induced DNA strand cleavage at deoxyribose residues.
Redundant control of rereplication in fission yeast
Authors: Gopalakrishnan Vidya , Simancek Pamela , Houchens Christopher , Snaith Hilary A. , Frattini Mark G. , Sazer Shelley , Kelly Thomas J.
Published: July 2002

The initiation of DNA replication at replication origins in eukaryotic cells is tightly controlled to ensure that the genome is duplicated only once each cell cycle. We present evidence that in fission yeast, independent regulation of two essential components of the initiation complex, Cdc18 and Cdt1, contributes to the prevention of reinitiation of DNA replication. Cdc18 is negatively controlled by cyclin-dependent kinase (CDK) phosphorylation, but low level expression of a mutant form of Cdc18 lacking CDK phosphorylation sites (Cdc18
CDK
) is not sufficient to induce rereplication. Similar to Cdc18, Cdt1 is expressed periodically in the cell cycle, accumulating in the nucleus in G
1
and declining in G
2
. When Cdt1 is expressed constitutively from an ectopic promoter, it accumulates in the nucleus throughout the cell cycle but does not promote reinitiation. However, constitutive expression of Cdt1, together with Cdc18
CDK
, is sufficient to induce extra rounds of DNA replication in the absence of mitosis. Significantly greater levels of rereplication can be induced by coexpression of Cdc18
CDK
and a Cdt1 mutant lacking a conserved C-terminal motif. In contrast, uncontrolled DNA replication does not occur when either mutant protein is expressed in the absence of the other. Constitutive expression of wild-type or mutant Cdt1 also leads to an increase in the levels of Cdc18
CDK
, possibly as a result of increased protein stability. Our data are consistent with the hypothesis that control of rereplication depends on a redundant mechanism in which negative regulation of Cdt1 functions in parallel with the negative regulation of Cdc18.
Differential display of intestinal mRNAs regulated by dietary zinc.
Authors: Blanchard R K , Cousins R J
Published: July 2002

Regulation of gene expression by zinc is well established, especially through the metal response elements of the metallothionein genes; however, most other aspects of the functions of zinc in gene expression remain unknown. We have looked for intestinal mRNAs that are regulated by dietary zinc status. Using the reverse transcriptase-PCR method of mRNA differential display, we compared intestinal mRNA from rats that were maintained for 18 days in one of three dietary groups: zinc-deficient, zinc-adequate, and pair-fed zinc-adequate. At the end of this period, total RNA was prepared from the intestine and analyzed by mRNA differential display. Under these conditions, only differentially displayed cDNA bands that varied in the zinc-deficient group, relative to the zinc-adequate groups, were selected. Utilizing two anchored oligo-dT3' PCR primers and a total of 27 arbitrary decamers as 5' PCR primers, our results yielded 47 differentially displayed cDNA bands from intestinal RNA. Thirty were increased in zinc deficiency, and 17 were decreased. Nineteen bands were subcloned and sequenced. Eleven of these were detectable on Northern blots, of which four were confirmed as regulated. Three of these have homology to known genes: cholecystokinin, uroguanylin, and ubiquinone oxidoreductase. The fourth is a novel sequence as it has no significant homology in GenBank. The remainder of those cloned included novel sequences, as well as matches to reported expressed sequence tags, and functionally identified genes. Further characterization of the regulated sequences identified here will show whether they are primary or secondary effects of zinc deficiency.
A designed beta-hairpin peptide in crystals.
Authors: Karle I L , Awasthi S K , Balaram P
Published: July 2002

Beta-hairpin structures have been crystallographically characterized only in very short acyclic peptides, in contrast to helices. The structure of the designed beta-hairpin, t-butoxycarbonyl-Leu-Val-Val-D-Pro-Gly-Leu-Val-Val-OMe in crystals is described. The two independent molecules of the octapeptide fold into almost ideal beta-hairpin conformations with the central D-Pro-Gly segment adopting a Type II' beta-turn conformation. The definitive characterization of a beta-hairpin has implications for de novo peptide and protein design, particularly for the development of three- and four-stranded beta-sheets.
Reactivation of denatured proteins by 23S ribosomal RNA: role of domain V.
Authors: Chattopadhyay S , Das B , Dasgupta C
Published: July 2002

Escherichia coli ribosome, its 50S subunit, or simply the 23S rRNA can reactivate denatured proteins in vitro. Here we show that protein synthesis inhibitors chloramphenicol and erythromycin, which bind to domain V of 23S rRNA of E. coli, can inhibit reactivation of denatured pig muscle lactate dehydrogenase and fungal glucose-6-phosphate dehydrogenase by 23S rRNA completely. Oligodeoxynucleotides complementary to two regions within domain V (which cover sites of chloramphenicol resistant mutations and the putative A site of the incoming aminoacyl tRNA), but not to a region outside of domain V, also can inhibit the activity. Domain V of 23S rRNA, therefore, appears to play a crucial role in reactivation of denatured proteins.
The chicken beta 2-microglobulin gene is located on a non-major histocompatibility complex microchromosome: a small, G+C-rich gene with X and Y boxes in the promoter.
Authors: Riegert P , Andersen R , Bumstead N , Döhring C , Dominguez-Steglich M , Engberg J , Salomonsen J , Schmid M , Schwager J , Skjødt K , Kaufman J
Published: July 2002

beta 2-Microglobulin is an essential subunit of major histocompatibility complex (Mhc) class I molecules, which present antigenic peptides to T lymphocytes. We sequenced a number of cDNAs and two genomic clones corresponding to chicken beta 2-microglobulin. The chicken beta 2-microglobulin gene has a similar genomic organization but smaller introns and higher G+C content than mammalian beta 2-microglobulin genes. The promoter region is particularly G+C-rich and contains, in addition to interferon regulatory elements, potential S/W, X, and Y boxes that were originally described for mammalian class II but not class I alpha or beta 2-microglobulin genes. There is a single chicken beta 2-microglobulin gene that has little polymorphism in the coding region. Restriction fragment length polymorphisms from Mhc homozygous lines, Mhc congenic lines, and backcross families, as well as in situ hybridization, show that the beta 2-microglobulin gene is located on a microchromosome different from the one that contains the chicken Mhc. We propose that the structural similarities between the beta 2-microglobulin and Mhc genes in the chicken are due to their presence on microchromosomes and suggest that these features and the microchromosomes appeared by deletion of DNA in the lineage leading to the birds.
Unexpected beta2-microglobulin sequence diversity in individual rainbow trout.
Authors: Shum B P , Azumi K , Zhang S , Kehrer S R , Raison R L , Detrich H W , Parham P
Published: July 2002

For mammals beta2-microglobulin (beta2m), the light chain of major histocompatibility complex (MHC) class I molecules, is invariant (or highly conserved) and is encoded by a single gene unlinked to the MHC. We find that beta2m of a salmonid fish, the rainbow trout (Oncorhynchus mykiss), does not conform to the mammalian paradigm. Ten of 12 randomly selected beta2m cDNA clones from an individual fish have different nucleotide sequences. A complex restriction fragment length polymorphism pattern is observed with rainbow trout, suggesting multiple beta2m genes in the genome, in excess of the two genes expected from the ancestral salmonid tetraploidy. Additional duplication and diversification of the beta2m genes might have occurred subsequently. Variation in the beta2m cDNA sequences is mainly at sites that do not perturb the structure of the mature beta2m protein, showing that the observed diversity of the trout beta2m genes is not primarily a result of pathogen selection.
Were bowerbirds part of the New Zealand fauna?
Authors: Christidis L , Leeton P R , Westerman M
Published: July 2002

Bowerbirds (Ptilonorhynchidae) have previously been considered to be confined to the Australo-Papuan continental plate. We provide molecular evidence that the extinct New Zealand Piopio Turnagra capensis is, in fact, a bowerbird. Such a finding is surprising on biogeographical grounds. However, recent molecular evidence on the relationships of the New Zealand moas and kiwis with the Australo-Papuan flightless birds suggests the need for a reassessment of current views on the origins of New Zealand's fauna.
SC35-mediated reconstitution of splicing in U2AF-depleted nuclear extract
Authors: MacMillan Andrew M. , McCaw Patrick S. , Crispino John D. , Sharp Phillip A.
Published: July 2002

Assembly of the mammalian spliceosome is known to proceed in an ordered fashion through several discrete complexes, but the mechanism of this assembly process may not be universal. In an early step, pre-mRNAs are committed to the splicing pathway through association with U1 small nuclear ribonucleoprotein (snRNP) and non-snRNP splicing factors, including U2AF and members of the SR protein family. As a means of studying the steps of spliceosome assembly, we have prepared HeLa nuclear extracts specifically depleted of the splicing factor U2AF. Surprisingly, the SR protein SC35 can functionally substitute for U2AF
65
in the reconstitution of pre-mRNA splicing in U2AF-depleted extracts. This reconstitution is substrate-specific and is reminiscent of the SC35-mediated reconstitution of splicing in extracts depleted of U1 snRNP. However, SC35 reconstitution of splicing in U2AF-depleted extracts is dependent on the presence of functional U1 snRNP. These observations suggest that there are at least three distinguishable mechanisms for the binding of U2 snRNP to the pre-mRNA, including U2AF-dependent and -independent pathways.
Signal changes in the spinal cord of the rat after injection of formalin into the hindpaw: Characterization using functional magnetic resonance imaging
Authors: Pórszász Róbert , Beckmann Nicolau , Bruttel Konrad , Urban Laszlo , Rudin Markus
Published: July 2002

Changes in metabolism and local circulation occur in the spinal cord during peripheral noxious stimulation. Evidence is presented that this stimulation also causes signal intensity alterations in functional magnetic resonance images of the spinal cord during formalin-induced pain. These results indicate the potential of functional magnetic resonance imaging in assessing noninvasively the extent and intensity of spinal cord excitation in this well characterized pain model. Therefore, the aim of this study was to establish functional magnetic resonance imaging as a noninvasive method to characterize temporal changes in the spinal cord after a single injection of 50 μl of formalin subcutaneously into the hindpaw of the anesthetized rat. This challenge produced a biphasic licking activity in the freely moving conscious animal. Images of the spinal cord were acquired within 2 min, enabling monitoring of the site and the temporal evolution of the signal changes during the development of formalin-induced hyperalgesia without the need of any surgical procedure. The time course of changes in the spinal cord functional image in the isoflurane-anesthetized animal was similar to that obtained from behavioral experiments. Also, comparable physiological data, control experiments, and the inhibition of a response through application of the local anesthetic agent lidocaine indicate that the signal changes observed after formalin injection were specifically related to excitability changes in the relevant segments of the lumbar spinal cord. This approach could be useful to characterize different models of pain and hyperalgesia and, more importantly, to evaluate effects of analgesic drugs.
Alternative splicing of the human diacylglycerol kinase ζ gene in muscle
Authors: Ding Li , Bunting Michaeline , Topham Matthew K. , McIntyre Thomas M. , Zimmerman Guy A. , Prescott Stephen M.
Published: July 2002

Diacylglycerol can function as a second messenger, and one mechanism for the attenuation of this signal is its conversion to phosphatidic acid, which is catalyzed by diacylglycerol kinase (DGK). We screened a cDNA library from human skeletal muscle and isolated two DGKζ cDNAs that differed from the 3.5-kb clone originally identified in endothelial cells. One transcript, which was 3.4 kb long, was shown to be nonfunctional; it had a 77-bp deletion that included the translation initiation site. The other was 4.1 kb long with a unique 5′ sequence of 853 bp. We also isolated a genomic clone of DGKζ and determined its organization and location; it contains 32 exons, spans approximately 50 kb of genomic sequence, and maps to chromosome 11p11.2. The protein encoded by the 4.1-kb transcript contains two cysteine-rich regions, a catalytic domain, and ankyrin repeats like the endothelial form of DGKζ, as well as a unique N-terminal domain. The coding sequence was shown to be derived from alternative splicing of the DGKζ gene. In cells transfected with the 4.1-kb clone, we detected a 130-kDa protein with an antibody to DGKζ and demonstrated that it was localized predominantly in the nucleus. We conclude that alternative splicing generates tissue-specific variants of DGKζ that share some properties but may have unique ones as well.
HLA class I and II antigens are partially co-clustered in the plasma membrane of human lymphoblastoid cells
Authors: Jenei Attila , Varga Sándor , Bene László , Mátyus László , Bodnár Andrea , Bacsó Zsolt , Pieri Carlo , Gáspár Rezső , Farkas Tibor , Damjanovich Sándor
Published: July 2002

Major histocompatibility complex (MHC) class II molecules displayed clustered patterns at the surfaces of T (HUT-102B2) and B (JY) lymphoma cells characterized by interreceptor distances in the micrometer range as detected by scanning force microscopy of immunogold-labeled antigens. Electron microscopy revealed that a fraction of the MHC class II molecules was also heteroclustered with MHC class I antigens at the same hierarchical level as described by the scanning force microscopy data, after specifically and sequentially labeling the antigens with 30- and 15-nm immunogold beads. On JY cells the estimated fraction of co-clustered HLA II was 0.61, whereas that of the HLA I was 0.24. Clusterization of the antigens was detected by the deviation of their spatial distribution from the Poissonian distribution representing the random case. Fluorescence resonance energy transfer measurements also confirmed partial co-clustering of the HLA class I and II molecules at another hierarchical level characterized by the 2- to 10-nm Förster distance range and providing fine details of the molecular organization of receptors. The larger-scale topological organization of the MHC class I and II antigens may reflect underlying membrane lipid domains and may fulfill significant functions in cell-to-cell contacts and signal transduction.
Gestational exposure to ethanol suppresses msx2 expression in developing mouse embryos
Authors: Rifas Leonard , Towler Dwight A. , Avioli Louis V.
Published: July 2002

Ethanol acts as a teratogen in developing fetuses causing abnormalities of the brain, heart, craniofacial bones, and limb skeletal elements. To assess whether some teratogenic actions of ethanol might occur via dysregulation of
msx2
expression, we examined
msx2
expression in developing mouse embryos exposed to ethanol on embryonic day (E) 8 of gestation and subjected to whole mount
in situ
hybridization on E11–11.5 using a riboprobe for mouse
msx2
. Control mice exhibited expression of
msx2
in developing brain, the developing limb buds and apical ectodermal ridge, the lateral and nasal processes, olfactory pit, palatal shelf of the maxilla, the eye, the lens of the eye, otic vesicle, prevertebral bodies (notochord), and endocardial cushion. Embryos exposed to ethanol
in utero
were significantly smaller than their normal counterparts and did not exhibit expression of
msx2
in any structures. Similarly,
msx2
expression, as determined by reverse transcription–PCR and Northern blot hybridization, was reduced ≈40–50% in fetal mouse calvarial osteoblastic cells exposed to 1% ethanol for 48 hr while alkaline phosphatase was increased by 2-fold and bone morphogenetic protein showed essentially no change. Transcriptional activity of the
msx2
promoter was specifically suppressed by alcohol in MC3T3-E1 osteoblasts. Taken together, these data demonstrate that fetal alcohol exposure decreases
msx2
expression, a known regulator of osteoblast and myoblast differentiation, and suggest that one of the “putative” mechanisms for fetal alcohol syndrome is the inhibition of
msx2
expression during key developmental periods leading to developmental retardation, altered craniofacial morphogenesis, and cardiac defects.
A single peripheral CD8+T cell can give rise to progeny expressing type 1 and/or type 2 cytokine genes and can retain its multipotentiality through many cell divisions
Authors: Kelso Anne , Groves Penny
Published: July 2002

The lineage relationships between murine CD8+T cells with different cytokine profiles were investigated by paired-daughter analysis in the presence and absence of the type 2 cytokine-inducing stimulus, interleukin 4 (IL-4). Single CD8+CD44lowlymph node T cells were activated to divide at high frequency with IL-2 and immobilized antibodies to CD3, CD8, and LFA-1. When these parent cells were subcloned by transferring their daughter or granddaughter cells into secondary cultures with or without IL-4, the subclones expressed diverse combinations of the mRNAs for the type 1 cytokines, interferon γ (IFN-γ), and IL-2, and the type 2 cytokines, IL-4, IL-5, IL-6, and IL-10. Frequencies of subclones that expressed IL-4, IL-6, and, to a lesser extent, IL-2, IL-5, and IL-10 were higher among those grown with IL-4, but a significant proportion of those grown without exogenous IL-4 also expressed one or more type 2 cytokines. Subclones within 89% of families displayed different cytokine profiles, indicating that their parent cells were multipotential for this function. Because 98% of parent cells yielded subclones that produced type 1 cytokines and 77% yielded type 2 cytokine producers, we conclude that type 1 and type 2 cytokine-producing CD8+T cells can be derived from a common precursor. Similar analyses performed by subcloning after ≥7 or ≥13 cell divisions without IL-4 showed that many CD8+T cells retained the potential to shift toward a type 2 cytokine profile in response to IL-4, even after prolonged expansion under conditions that favored type 1 cytokine expression. CD8+T cells that express type 1 and/or type 2 cytokines therefore are derived from the same peripheral T cell lineage whose multipotentiality can persist through many cell divisions.