bluuebunny/crossref_metadata_2025 huggingface dataset:
Reduction of transport in stellarators by self-shielding
Authors: Boozer Allen H.
Published: July 2002

In neoclassical transport theory the parallel viscosity causes the plasma pressure orthogonal to the magnetic field to depend on the poloidal and toroidal angles. If the Fourier components of the perpendicular pressure and the field strength are pMN and εMNB0, then one obtains strong shielding of a Fourier component of the field when |pMN|/|εMN|>B20/μ0. Estimates imply shielding becomes important in a stellarator for |εMN| smaller than a few tenths of a percent.
Does high density–low pressure etching depend on the type of plasma source?
Authors: Hershkowitz N. , Ding J. , Breun R. A. , Chen R. T. S. , Meyer J. , Quick A. K.
Published: July 2002

Etching of SiO2 with CF4 in three types of high density–low pressure (5×1011 cm−3, 1–10 mTorr) etch tools: electron cyclotron resonance (ECR), inductively coupled (ICP), and helicon (HRF) is described. Although the physical processes that produce the plasma in the three types of sources are quite different, the etch rate processes are identical when viewed from the wafer sheath boundary. Measurements demonstrate that if sufficient fluorine is present, the etch rate limiting step depends only on the ion energy flux to the wafer, rather than on the details of the chemical species. Etch rate control depends only on the wafer bias power. Experimental results are device independent so the etch rate in high density–low pressure plasma sources does not depend on the plasma source power. Major differences in tool etch rate characteristics are more likely determined by tool wall material (and wall chemistry) and tool geometry rather than the physical process that is used to produce the plasma.
Toroidal ηi-mode global vortices in a rotating plasma
Authors: Pakyari Alireza , Pavlenko Vladimir P.
Published: July 2002

Model equations describing dynamics of a toroidal ηi mode in a rotating plasma are derived. The stationary solution of the model equations is investigated analytically and the condition for global vortex formation is found. The form of the solution is verified numerically and it is shown that the shape of global vortices is affected strongly by the shear of the plasma poloidal rotation. In weak shear, the stationary solution looks like a dipole vortex, while in strong shear, the main part of the plasma cross section is occupied by vortex flow.
A comparison of compressible and incompressible magnetohydrodynamics in toroidal plasmas
Authors: Wahlberg C.
Published: July 2002

A comparison is made of the properties of compressible and incompressible magnetohydrodynamic (MHD) oscillations in toroidal plasmas. In the main part of the paper we deal with the compressible case, and it is shown that the Alfvén wave equation describing toroidal Alfvén eigenmodes (TAE modes) in a low-β tokamak [Berk et al., Phys. Fluids B 4, 1806 (1992)], including the toroidal coupling of the shear Alfvén continuum modes with poloidal mode numbers m and m±1, can be obtained by means of an inverse aspect ratio expansion of the usual set of compressible MHD equations. This method provides an alternative, and more straightforward, approach to the analysis of such modes as compared with previous studies based on reduced MHD, or on different formulations of MHD. In the case of incompressible MHD, it is found that the Alfvén continua are strongly modified by the finite value of the toroidal component of the plasma perturbation. In particular, a large frequency gap where global eigenmodes can be found appears already to lowest order in the inverse aspect ratio in the case of incompressible oscillations.
Magnetohydrodynamic stability of an axisymmetric mirror device with ‘‘massive’’ end-sections
Authors: Lotov K. V.
Published: July 2002

Magnetohydrodynamic (MHD) stability of an axisymmetric mirror device with long end-sections filled with a collisional plasma is studied. It is shown that unstable perturbations in such a system, if they exist, are localized at a distance ∼vA/Γ near the central cell (vA is the Alfvén velocity and Γ is the growth rate). Perturbations of the magnetic field do not penetrate into regions where plasma beta is greater than unity. Therefore, regions of weak magnetic field has a stabilizing effect on MHD-perturbations.
On the resonant particle dynamics in the field of a finite-amplitude circularly polarized wave propagating along the axis of a magnetic trap
Authors: Krasovsky V. L. , Matsumoto H.
Published: July 2002

The motion of electrons in gyroresonance with a quasimonochromatic transverse electromagnetic wave propagating along a weakly nonuniform axially symmetric external magnetic field is analyzed. With allowance made for spatial dependencies of the wave amplitude and wave number, approximate equations of motion are derived via an averaging over the fast Larmor gyration. Wave amplitude finiteness effects and interrelationships between exact and approximate invariants of the motion are discussed.
The dynamics of wire array Z-pinch implosions
Authors: Lebedev S. V. , Aliaga-Rossel R. , Bland S. N. , Chittenden J. P. , Dangor A. E. , Haines M. G. , Mitchell I. H.
Published: July 2002

Wire array Z-pinch dynamics are studied in experiments with 16-mm diameter arrays of between 8 and 64, 15-μm diameter aluminum wires, imploded in 200–260 ns by a 1.4-MA current pulse. Side-on laser probing shows early development of noncorrelated m=0-like instabilities with an axial wavelength ∼0.5 mm in individual wires. End-on interferometry (r-θ plane) shows azimuthal merging of the plasma with a density of 1017 cm−3 in 90–65 ns for 8–64 wires, respectively. At the same time low-density plasma reaches the array axis and forms a precursor pinch by 120–140 ns. At 0.7–0.85 of the implosion time a global m=0 instability with a wavelength of 1.7–2.3 mm was detected in soft x-ray gated images, laser probing, and optical streaks. The time when the instability reaches the observable level corresponds to the number of e-foldings for the growth of the classical Rayleigh–Taylor instability of ∫γ dt∼5.6–7. The scaling of this number with the number of wires is consistent with the instability growth from the seed level determined by the averaging of uncorrelated density perturbations in individual wires. Preliminary results from a 4×4 array permit the simultaneous observation by laser probing of the characteristic bubble and spike structure of the magneto Rayleigh–Taylor instability.
Dust–Coulomb waves in dense dusty plasmas
Authors: Rao N. N.
Published: July 2002

Dusty plasmas can be considered as tenuous, dilute or dense when the dust fugacity parameter f≡4πnd0λD2R∼NDR/λD satisfies f≪1, ∼1, or ≫1, where nd0, λD and R denote, respectively, the dust number density, the plasma Debye length and the dust grain size (radius), and ND=nd0λD3 is the dust plasma parameter. Dense dusty plasmas are shown to support a new kind of ultra low-frequency electrostatic dust mode which may be called the “Dust–Coulomb Wave” (DCW). In contrast to the dust–acoustic wave (DAW) and the dust–lattice wave (DLW) which exist even for constant grain charge, DCWs are accompanied by dust charge as well as number density perturbations which are proportional to each other. For frequencies much smaller than the grain charging frequency, DCWs propagate as normal modes with the phase speed CDC≡qd0/mdR, where qd0 (md) is the charge (mass) of the dust grains. In the long wavelength limit, the DCW phase speed is much smaller than that of DAW (CDA), and scales as ∼CDA/f. Thus, for a given wave number, the frequency regime for the existence of DCW is much lower than the DAW regime. A comparison between the three types of dust–modes (DCWs, DAWs, and DLWs) has been carried out.
Dust-Coulomb and dust-acoustic wave propagation in dense dusty plasmas with high fugacity
Authors: Rao N. N.
Published: July 2002

A detailed investigation of electrostatic dust wave modes in unmagnetized dusty plasmas consisting of electrons, ions and dust grains has been carried out over a wide range of dust fugacity and wave frequency by using fluid as well as kinetic (Vlasov) theories. The dust fugacity parameter is defined by f≡4πnd0λD2R∼ND R/λD where nd0, λD and R are respectively the dust number density, the plasma Debye length and the grain size (radius), and ND=4πnd0λD3/3 is the dust plasma parameter. Dusty plasmas are considered to be tenuous, dilute or dense according as f≪1,   ∼1,   or   ≫1. In particular, attention is focused on the “dust–acoustic waves” (DAWs) and the “dust–Coulomb waves” (DCWs) which exist in the tenuous (low fugacity) and the dense (high fugacity) regimes, respectively, when the wave frequency is much smaller than the grain charging frequency. Unlike the DAWs, which exist even with constant grain charge, the DCWs [N. N. Rao, Phys. Plasmas 6, 4414 (1999)] are the normal modes associated with grain charge fluctuations, and exist in dense dusty plasmas. In the long wavelength limit, the DCW phase speed scales as ∼CDA/f where CDA is the DAW phase speed. In the dilute (medium fugacity) regime, the two modes merge into a single mode, which may be called the “dust charge–density wave” (DCDW) since the latter involves contributions arising from both the DAW and the DCW. On the other hand, for frequencies much larger than the charging frequency, DAWs are shown to exist also in the dilute regime. The real frequency as well as the damping rate in each case are explicitly calculated from both the fluid as well the kinetic theories, and a comparison between the two has been carried out. In the allowed fugacity regimes (tenuous, dilute or dense), all the three waves are weakly damped and, hence, can propagate as normal modes. The present analysis of wave propagation in dusty plasmas over different fugacity regimes suggests the introduction of a new length scale defined by λR≡dWSdWS/3Rδ, where dWS is the Wigner–Seitz radius and δ is a parameter related to the charging frequencies. This length scale which governs the dispersive properties of the DCW modes is most useful in the dense regime, and plays a role which is very similar to that of the Debye length in the tenuous regime. The ratio of λR to λD is a measure of the dust fugacity, and is given through fδ=λD2/λR2. The very recent experimental observation [S. Nunomura et al., Phys. Rev. Lett. 83, 1970 (1999)] on a self-excited instability associated with grain charge fluctuations may be an indication of DCWs in the strong coupling regime. The possibility of the existence of a dust thermal wave (DTW) in the super-dense regime has been pointed out. A heuristic, but simple, derivation of DCWs based on grain dynamics but supplemented by physical inputs from the plasma response has also been presented.
Theory of vortex crystal formation in two-dimensional turbulence
Authors: Jin Dezhe Z. , Dubin Daniel H. E.
Published: July 2002

Experiments on pure electron plasmas have found that the decay of two-dimensional (2D) turbulence can lead to spontaneous formation of “vortex crystals,” which are symmetric arrays of strong vortices within a background of weaker vorticity. This paper presents a theory of these novel equilibrium states of 2D turbulence. The paper consists of two parts. In the first part, we show that the vortex crystals are well described as “regional” maximum fluid entropy (RMFE) states, which are equilibrium states reached through ergodic mixing of the background by the strong vortices. In the second part, a theory is advanced that allows us to predict from the initial conditions the approximate number of the strong vortices in the final state.
Stimulated emission and laser oscillations in ZnSe-Zn1−xMnxSe multiple quantum wells at ∼453 nm
Authors: Bylsma R. B. , Becker W. M. , Bonsett T. C. , Kolodziejski L. A. , Gunshor R. L. , Yamanishi M. , Datta S.
Published: July 2002

In this letter we report the first observation of stimulated emission and laser oscillations occurring in ZnSe-Zn1−xMnxSe quantum well structures. The results were obtained in superlattices consisting of alternating layers of ZnSe and Zn1−xMnxSe on a ZnSe buffer layer grown by molecular beam epitaxy on GaAs. Gain spectra were measured on these samples and thresholds for stimulated emission determined for various emission wavelengths. Optically pumped lasers were fabricated from one of these quantum well structures and found to operate in the blue portion of the visible spectrum from 451.5 to 455 nm. Lasing was observed up to 80 K.
Epitaxial growth of NiSi2 on ion-implanted silicon at 250–280 °C
Authors: Lu S. W. , Nieh C. W. , Chen L. J.
Published: July 2002

Striking effects of dopant atoms on the formation of Ni silicides were observed. Epitaxial NiSi2 was found to grow on both BF+2- and B+-implanted (001) and (111)Si at 250–280 °C. The formation of Ni2Si was suppressed. It is conjectured that the presence of dopant atoms may lower the activation energy substantially to promote the formation of epitaxial NiSi2 at low temperatures. The effects may be exploited to grow other epitaxial silicides on silicon at low temperatures.
Interface structures in beta-silicon carbide thin films
Authors: Nutt Steven R. , Smith David J. , Kim H. J. , Davis Robert F.
Published: July 2002

Interface structures in monocrystalline beta-silicon carbide thin films grown on (001) silicon substrates have been studied by high-resolution electron microscopy of cross-sectional specimens. Despite a large lattice mismatch, there is a periodic registry of {111} atom planes across the SiC-Si interface. Planar defects on SiC {111} planes are grown-in and arise primarily from lattice and thermal expansion mismatch. Thermal oxidation in wet atmospheres results in preferential attack of the SiC film at sites where planar defects intersect the film surface, whereas oxidation in dry atmospheres does not.
High-voltage, high-power operation of the plasma erosion opening switch
Authors: Neri J. M. , Boller J. R. , Ottinger P. F. , Weber B. V. , Young F. C.
Published: July 2002

A plasma erosion opening switch (PEOS) is used as the opening switch for a vacuum inductive storage system driven by a 1.8-MV, 1.6-TW pulsed power generator. A 135-nH vacuum inductor is current charged to ∼750 kA in 50 ns through the closed PEOS which then opens in <10 ns into an inverse ion diode load. Electrical diagnostics and nuclear activations from ions accelerated in the diode yield a peak load voltage (4.25 MV) and peak load power (2.8 TW) that are 2.4 and 1.8 times greater than ideal matched load values for the same generator values.
2-cyclooctylamino-5-nitropyridine, a new nonlinear optical crystal with orthorhombic symmetry
Authors: Günter P. , Bosshard Ch. , Sutter K. , Arend H. , Chapuis G. , Twieg R. J. , Dobrowolski D.
Published: July 2002

A new nonlinear optical crystal 2-cyclooctylamino-5-nitropyridine (COANP) with point group symmetry mm2 has been grown by a temperature difference solution growth technique. Its linear and nonlinear optical properties have been investigated. The refractive indices na =1.702, nb =1.847, and nc =1.681 (λ=550 nm) and the nonlinear optical susceptibilities d31 and d33 (λω =1.06 μm) have been determined. Type I phase matching for Nd:YAG lasers (λ=1.06 μm) has been demonstrated for the configuration using a combination of d31 and d32 by angle tuning. A peak efficiency η=P2ω/Pω =3.6% has been observed with a 0.90-mm-thick crystal and a fundamental power Pω =560 W.
High-temperature depletion-mode metal-oxide-semiconductor field-effect transistors in beta-SiC thin films
Authors: Palmour J. W. , Kong H. S. , Davis R. F.
Published: July 2002

Depletion-mode n-channel metal-oxide-semiconductor field-effect transistors were fabricated on n-type β-SiC (111) thin films epitaxially grown by chemical vapor deposition on the Si (0001) face of 6H α-SiC single crystals. The gate oxide was thermally grown on the SiC; the source and drain were doped n+ by N+ ion implantation at 823 K. Stable saturation and low subthreshold current were achieved at drain voltages exceeding 25 V. Transconductances as high as 11.9 mS/mm were achieved. Stable transistor action was observed at temperatures as high as 923 K, the highest temperature reported to date for a transistor in any material.
Si-SiO2 interface trap production by low-temperature thermal processing
Authors: Reed Michael L. , Plummer James D.
Published: July 2002

Post-metal annealing of aluminum gate metal-oxide-semiconductor capacitors can produce, as well as anneal, interface traps at the Si-SiO2 interface. The production mechanism is shown to be a thermal decomposition of passivated traps. Mechanisms involving interactions with atomic or molecular hydrogen are inconsistent with the experimental data.
Evidence of a photon effect during the visible laser-assisted deposition of polycrystalline silicon from silane
Authors: Auvert G. , Tonneau D. , Pauleau Y.
Published: July 2002

Silicon dots have been produced by the decomposition of silane on Si layers deposited on quartz plates and irradiated by a cw Ar+ laser beam. The vertical deposition rate of Si dots was investigated as a function of irradiation time, output laser power, and silane pressure. The Si layer on quartz was first irradiated with the laser beam penetrating through the transparent quartz plate (back irradiation). The deposition of Si dots occurred by pyrolytic decomposition of ‘‘cold’’ silane molecules impinging on the laser heated area. When the surface of the Si layer on quartz was directly irradiated with the visible laser beam (front irradiation), the deposition of Si dots was accomplished at lower temperatures and involved an interaction of photons with reactive species. The kinetics of this photon-aided process is surface controlled and characterized by an apparent activation energy of about 38 kcal mol−1.
Observation of subbands in the GaAlAs on two-dimensional electron gas field-effect transistor structures
Authors: Smoliner J. , Hauser M. , Gornik E. , Weimann G.
Published: July 2002

We have measured the current-voltage characteristics and its derivatives on GaAs-GaAlAs field-effect transistor samples having a semitransparent Au-Schottky gate contact, varying the band structure by illumination. In these samples electrons tunnel from the two-dimensional electron gas through the GaAlAs into a Schottky gate. Sharp peaks are observed in dI/dV after illumination at liquid-helium temperature. Using a self-consistent model, we are able to explain these peaks by resonant tunneling via subband states in the GaAlAs.
Dependence of the vacuum sublimation rate of CdTe upon crystallographic orientation
Authors: Dubowski J. J. , Wrobel J. M. , Williams D. F.
Published: July 2002

A study of the crystallographic orientation dependence of the vacuum sublimation rate of undoped (111) and (100) CdTe crystals was carried out in the temperature range 310–390 °C. A rate of sublimation as high as 580 Å/min was observed at 380 °C for the (111)Te face which was about 4 and 12 times higher than that of (111)Cd and (100) faces, respectively. The corresponding activation energies for sublimation of these faces were determined as 2.21, 1.79, and 1.54 eV. The differences and magnitudes of the sublimation rates decrease with decreasing temperature and at t≤310 °C the sublimation rate is less than 3 Å/min, independent of the crystallographic orientation. The surface morphology of sublimated samples reveals thermal etch pits which are specific for each studied face. In the case of (111)Cd and (100) faces, etch pit densities up to about 107 cm−2 were observed, which probably corresponds to the concentration of dislocations and other defects present in the studied samples.
Surface-field-induced tunnel junctions on InAs
Authors: Kunze U. , Kowalsky W.
Published: July 2002

We report on tunneling between the two-dimensional electron inversion layer on a degenerate p-InAs substrate and the three-dimensional bulk valence states in Yb/oxide/InAs tunnel junctions. The current-voltage characteristics show negative differential conductance with current peak-to-valley ratio up to 2.7 (17) at T=300 K (77 K). The inversion layer is induced by the high electric surface field that arises from the low work function of the Yb electrode. Tunneling across the oxide provides a low-resistive contact of the metal to the electron layer.
Genomic structure and functional control of the
Dlx3
-
7
bigene cluster
Authors: Sumiyama Kenta , Irvine Steven Q. , Stock David W. , Weiss Kenneth M. , Kawasaki Kazuhiko , Shimizu Nobuyoshi , Shashikant Cooduvalli S. , Miller Webb , Ruddle Frank H.
Published: July 2002

The
Dlx
genes are involved in early vertebrate morphogenesis, notably of the head. The six
Dlx
genes of mammals are arranged in three convergently transcribed bigene clusters. In this study, we examine the regulation of the
Dlx3-7
cluster of the mouse. We obtained and sequenced human and mouse P1 clones covering the entire
Dlx3-7
cluster. Comparative analysis of the human and mouse sequences revealed several highly conserved noncoding regions within 30 kb of the
Dlx3-7
-coding regions. These conserved elements were located both 5′ of the coding exons of each gene and in the intergenic region 3′ of the exons, suggesting that some enhancers might be shared between genes. We also found that the protein sequence of
Dlx7
is evolving more rapidly than that of
Dlx3
. We conducted a functional study of the 79-kb mouse genomic clone to locate cis-element activity able to reproduce the endogenous expression pattern by using transgenic mice. We inserted a
lacZ
reporter gene into the first exon of the
Dlx3
gene by using homologous recombination in yeast. Strong
lacZ
expression in embryonic (E) stage E9.5 and E10.5 mouse embryos was found in the limb buds and first and second visceral arches, consistent with the endogenous
Dlx3
expression pattern. This result shows that the 79-kb region contains the major cis-elements required to direct the endogenous expression of
Dlx3
at stage E10.5. To test for enhancer location, we divided the construct in the mid-intergenic region and injected the
Dlx3
gene portion. This shortened fragment lacking
Dlx7
-flanking sequences is able to drive expression in the limb buds but not in the visceral arches. This observation is consistent with a cis-regulatory enhancer-sharing model within the
Dlx
bigene cluster.
Actin cable dynamics in budding yeast
Authors: Yang Hyeong-Cheol , Pon Liza A.
Published: July 2002

Actin cables, bundles of actin filaments that align along the long axis of budding yeast, are crucial for establishment of cell polarity. We fused green fluorescent protein (GFP) to actin binding protein 140 (Abp140p) and visualized actin cable dynamics in living yeast. We detected two populations of actin cables: (
i
) bud-associated cables, which extend from the bud along the mother-bud axis, and (
ii
) randomly oriented cables, which are relatively short. Time-lapse imaging of Abp140p–GFP revealed an apparent increase in the length of bud-associated actin cables. Analysis of movement of Abp140p–GFP fiduciary marks on bud-associated cables and fluorescence loss in photobleaching experiments revealed that this apparent elongation occurs by assembly of new material at the end of the cable within the bud and movement of the opposite end of the cable toward the tip of the mother cell distal to the bud. The rate of extension of the tip of an elongating actin cable is 0.29 ± 0.08 μm/s. Latrunculin A (Lat-A) treatment completely blocked this process. We also observed movement of randomly oriented cables around the cortex of cells at a rate of 0.59 ± 0.14 μm/s. Mild treatment with Lat-A did not affect the velocity of movement of randomly oriented cables. However, Lat-A treatment did increase the number of randomly oriented, motile cables per cell. Our observations suggest that establishment of bud-associated actin cables during the cell cycle is accomplished not by realignment of existing cables but by assembly of new cables within the bud or bud neck, followed by elongation.
tRNA elements mediate the assembly of an icosahedral RNA virus
Authors: Choi Yoon Gi , Dreher Theo W. , Rao A. L. N.
Published: July 2002

tRNAs, the adapter molecules in protein synthesis, also serve as metabolic cofactors and as primers for viral RNA-directed DNA synthesis. The genomic and subgenomic RNAs of some plant viruses have a 3′-terminal tRNA-like structure (TLS) that can accept a specific amino acid and serve as a site for initiation of replication and as a simple telomere. We report a previously undescribed role for the TLS of brome mosaic virus (BMV), and potentially for cellular tRNA, in mediating the assembly of its icosahedral virions. BMV genomic RNAs and subgenomic RNA lacking the TLS failed to assemble into virions when incubated with purified BMV coat protein. Assembly was restored by addition of a 201-nt RNA containing the BMV TLS. TLSs from two other plant viruses as well as tRNAs from wheat germ and yeast were similarly active in the BMV virion assembly reaction, but ribosomal RNA and polyadenylate did not facilitate assembly. Surprisingly, virions assembled from TLS-less BMV RNA in the presence of tRNAs or TLS-containing short RNA did not incorporate the latter molecules. Consistent with a critical role for the BMV TLS in virion assembly, mutations in the BMV genomic RNAs that were designed to disrupt the folding of the TLS also abolished virion assembly. We discuss the likely roles of the TLS in early stages of virion assembly.
Circulating relaxin acts on subfornical organ neurons to stimulate water drinking in the rat
Authors: Sunn N. , Egli M. , Burazin T. C. D. , Burns P. , Colvill L. , Davern P. , Denton D. A. , Oldfield B. J. , Weisinger R. S. , Rauch M. , Schmid H. A. , McKinley M. J.
Published: July 2002

Relaxin, a peptide hormone secreted by the corpus luteum during pregnancy, exerts actions on reproductive tissues such as the pubic symphysis, uterus, and cervix. It may also influence body fluid balance by actions on the brain to stimulate thirst and vasopressin secretion. We mapped the sites in the brain that are activated by i.v. infusion of a dipsogenic dose of relaxin (25 μg/h) by immunohistochemically detecting Fos expression. Relaxin administration resulted in increased Fos expression in the subfornical organ (SFO), organum vasculosum of the lamina terminalis (OVLT), median preoptic nucleus, and magnocellular neurons in the supraoptic and paraventricular nuclei. Ablation of the SFO abolished relaxin-induced water drinking, but did not prevent increased Fos expression in the OVLT, supraoptic or paraventricular nuclei. Although ablation of the OVLT did not inhibit relaxin-induced drinking, it did cause a large reduction in Fos expression in the supraoptic nucleus and posterior magnocellular subdivision of the paraventricular nucleus.
In vitro
single-unit recording of electrical activity of neurons in isolated slices of the SFO showed that relaxin (10
−7
M) added to the perfusion medium caused marked and prolonged increase in neuronal activity. Most of these neurons also responded to 10
−7
M angiotensin II. The data indicate that blood-borne relaxin can directly stimulate neurons in the SFO to initiate water drinking. It is likely that circulating relaxin also stimulates neurons in the OVLT that influence vasopressin secretion. These two circumventricular organs that lack a blood–brain barrier may have regulatory influences on fluid balance during pregnancy in rats.
The production of recombinant proteins in transgenic barley grains
Authors: Horvath Henriette , Huang Jintai , Wong Oi , Kohl Elizabeth , Okita Thomas , Kannangara C. Gamini , von Wettstein Diter
Published: July 2002

The grain of the self-pollinating diploid barley species offers two modes of producing recombinant enzymes or other proteins. One uses the promoters of genes with aleurone-specific expression during germination and the signal peptide code for export of the protein into the endosperm. The other uses promoters of the structural genes for storage proteins deposited in the developing endosperm. Production of a protein-engineered thermotolerant (1, 3–1, 4)-β-glucanase with the D hordein gene (
Hor3–1)
promoter during endosperm development was analyzed in transgenic plants with four different constructs. High expression of the enzyme and its activity in the endosperm of the mature grain required codon optimization to a C+G content of 63% and synthesis as a precursor with a signal peptide for transport through the endoplasmic reticulum and targeting into the storage vacuoles. Synthesis of the recombinant enzyme in the aleurone of germinating transgenic grain with an α-amylase promoter and the code for the export signal peptide yielded ≈1 μg⋅mg
−1
soluble protein, whereas 54 μg⋅mg
−1
soluble protein was produced on average in the maturing grain of 10 transgenic lines with the vector containing the gene for the (1, 3–1, 4)-β-glucanase under the control of the
Hor3–1
promoter.
Use of spacecraft data to derive regions on Mars where liquid water would be stable
Authors: Lobitz Brad , Wood Byron L. , Averner Maurice M. , McKay Christopher P.
Published: July 2002

Combining Viking pressure and temperature data with Mars Orbital Laser Altimeter topography data, we have computed the fraction of the martian year during which pressure and temperature allow for liquid water to be stable on the martian surface. We find that liquid water would be stable within the Hellas and Argyre basin and over the northern lowlands equatorward of about 40°. The location with the maximum period of stable conditions for liquid water is in the southeastern portion of Utopia Planitia, where 34% of the year liquid water would be stable if it were present. Locations of stability appear to correlate with the distribution of valley networks.
Phosphatidylinositol-dependent actin filament binding by the SWI/SNF-like BAF chromatin remodeling complex
Authors: Rando Oliver J. , Zhao Keji , Janmey Paul , Crabtree Gerald R.
Published: July 2002

Recently, several chromatin remodeling complexes in yeast,
Drosophila
, and mammals have been shown to contain actin and actin-related proteins (arps). However, the function of actin in these complexes is unclear. Here, we show that the mammalian SWI/SNF-like BAF complex binds to phosphatidylinositol 4,5-bisphosphate (PIP
2
) micelles and PIP
2
-containing mixed lipid vesicles, and that PIP
2
binding allows the complex to associate with actin pointed ends and branch points. Actin binds to at least two distinct domains in the C terminus of the Brg1 protein, and interaction with only one of these domains is sensitive to PIP
2
. Based on these findings, we propose a model for PIP
2
activation of actin binding by relief of intramolecular capping of actin by Brg1.
The role of cavities in protein dynamics: Crystal structure of a photolytic intermediate of a mutant myoglobin
Authors: Brunori Maurizio , Vallone Beatrice , Cutruzzolà Francesca , Travaglini-Allocatelli Carlo , Berendzen Joel , Chu Kelvin , Sweet Robert M. , Schlichting Ilme
Published: July 2002

We determined the structure of the photolytic intermediate of a sperm whale myoglobin (Mb) mutant called Mb-YQR [Leu-(B10)→Tyr; His(E7)→Gln; Thr(E10)→Arg] to 1.4-Å resolution by ultra-low temperature (20 K) x-ray diffraction. Starting with the CO complex, illumination leads to photolysis of the Fe–CO bond, and migration of the photolyzed carbon monoxide (CO*) to a niche in the protein 8.1 Å from the heme iron; this cavity corresponds to that hosting an atom of Xe when the crystal is equilibrated with xenon gas at 7 atmospheres [Tilton, R. F., Jr., Kuntz, I. D. & Petsko, G. A. (1984)
Biochemistry
23, 2849–2857]. The site occupied by CO* corresponds to that predicted by molecular dynamics simulations previously carried out to account for the NO geminate rebinding of Mb-YQR observed in laser photolysis experiments at room temperature. This secondary docking site differs from the primary docking site identified by previous crystallographic studies on the photolyzed intermediate of wild-type sperm whale Mb performed at cryogenic temperatures [Teng
et al.
(1994)
Nat. Struct. Biol
. 1, 701–705] and room temperature [Šrajer
et al.
(1996)
Science
274, 1726–1729]. Our experiment shows that the pathway of a small molecule in its trajectory through a protein may be modified by site-directed mutagenesis, and that migration within the protein matrix to the active site involves a limited number of pre-existing cavities identified in the interior space of the protein.
Erythroid Krüppel-like factor is recruited to the CACCC box in the β-globin promoter but not to the CACCC box in the γ-globin promoter: The role of the neighboring promoter elements
Authors: Lee Jong-Soo , Ngo Hailong , Kim David , Chung Jay H.
Published: July 2002

The programmed expression of the five β-like globin genes (ɛ,
A
γ,
G
γ, δ, and β) is characterized by a
series of switches that are developmentally regulated. The
A
γ- and
G
γ- (fetus) to β-globin (adult)
switch depends on transcription factor erythroid Krüppel-like
factor (EKLF), which, like Sp1, binds to CACCC boxes. EKLF is essential
for the expression of the β-globin but not the γ-globin gene.
Because both γ-globin and β-globin promoters contain the CACCC box,
and their promoter elements are similar, it is not known why the two
promoters behave so differently. In this report, we searched for the
functional differences between the two promoters by studying their
ability to recruit EKLF. We used the
in vivo
PIN*POINT
assay to show that EKLF is recruited to the β-globin promoter but not
to the γ-globin promoter. We show that this selectivity is a result
of differences in surrounding promoter elements and not CACCC box
alone. One of the differences between the two promoters with a
functional consequence is the CCTTG repeat that is present in the
γ-globin promoter but not in the β-globin promoter. The repeat,
when inserted in the β-globin promoter, decreases EKLF recruitment to
and activity of the β-globin promoter, suggesting that the repeat
functions as a suppressor element. The CCTTG repeat can also suppress
the SV40 promoter in cis, and the suppressor factor binding to the
repeat can be squelched with a plasmid containing a high copy number of
the repeat. These findings may have implications in designing drug
targets for treatment of β-globin disorders.
Protein folding and unfolding on a complex energy landscape
Authors: Leeson Daan Thorn , Gai Feng , Rodriguez Hector M. , Gregoret Lydia M. , Dyer R. Brian
Published: July 2002

Recent theories of protein folding suggest that individual proteins
within a large ensemble may follow different routes in conformation
space from the unfolded state toward the native state and vice versa.
Herein, we introduce a new type of kinetics experiment that shows how
different unfolding pathways can be selected by varying the initial
reaction conditions. The relaxation kinetics of the major cold shock
protein of
Escherichia coli
(CspA) in response to a
laser-induced temperature jump are exponential for small temperature
jumps, indicative of folding through a two-state mechanism. However,
for larger jumps, the kinetics become strongly nonexponential, implying
the existence of multiple unfolding pathways. We provide evidence that
both unfolding across an energy barrier and diffusive downhill
unfolding can occur simultaneously in the same ensemble and provide the
experimental requirements for these to be observed.
Solvent effects on the energy landscapes and folding kinetics of polyalanine
Authors: Levy Yaakov , Jortner Joshua , Becker Oren M.
Published: July 2002

The effect of a solvation on the thermodynamics and kinetics
of polyalanine (Ala
12
) is explored on the basis of its
energy landscapes in vacuum and in an aqueous solution. Both energy
landscapes are characterized by two basins, one associated with
α-helical structures and the other with coil and β-structures of
the peptide. In both environments, the basin that corresponds to the
α-helical structure is considerably narrower than the basin
corresponding to the β-state, reflecting their different
contributions to the entropy of the peptide. In vacuum, the α-helical
state of Ala
12
constitutes the native state, in agreement
with common helical propensity scales, whereas in the aqueous medium,
the α-helical state is destabilized, and the β-state becomes the
native state. Thus solvation has a dramatic effect on the energy
landscape of this peptide, resulting in an inverted stability of the
two states. Different folding and unfolding time scales for
Ala
12
in hydrophilic and hydrophobic chemical environments
are caused by the higher entropy of the native state in water relative
to vacuum. The concept of a helical propensity has to be extended to
incorporate environmental solvent effects.
α-Helical stabilization by side chain shielding of backbone hydrogen bonds
Authors: García Angel E. , Sanbonmatsu Kevin Y.
Published: July 2002

We study atomic models of the thermodynamics of the structural transition of peptides that form α-helices. The effect of sequence variation on α-helix formation for alanine-rich peptides, Ac-Ala
21
- methyl amide (A21) and Ac-A
5
(AAARA)
3
A-methyl amide (Fs peptide), is investigated by atomic simulation studies of the thermodynamics of the helix-coil transition in explicit water. The simulations show that the guanidinium group in the Arg side chains in the Fs peptide interacts with the carbonyl group four amino acids upstream in the chain and desolvates backbone hydrogen bonds. This desolvation can be directly correlated with a higher probability of hydrogen bond formation. We find that Fs has higher helical content than A21 at all temperatures. A small modification in the
amber
force field reproduces the experimental helical content and helix-coil transition temperatures for the Fs peptide.
Telomerase inhibitors based on quadruplex ligands selected by a fluorescence assay
Authors: Mergny Jean-Louis , Lacroix Laurent , Teulade-Fichou Marie-Paule , Hounsou Candide , Guittat Lionel , Hoarau Magali , Arimondo Paola B. , Vigneron Jean-Pierre , Lehn Jean-Marie , Riou Jean-François , Garestier Thérèse , Hélène Claude
Published: July 2002

The reactivation of telomerase activity in most cancer cells
supports the concept that telomerase is a relevant target in oncology,
and telomerase inhibitors have been proposed as new potential
anticancer agents. The telomeric G-rich single-stranded DNA can adopt
in vitro
an intramolecular quadruplex structure, which
has been shown to inhibit telomerase activity. We used a fluorescence
assay to identify molecules that stabilize G-quadruplexes.
Intramolecular folding of an oligonucleotide with four repeats of the
human telomeric sequence into a G-quadruplex structure led to
fluorescence excitation energy transfer between a donor (fluorescein)
and an acceptor (tetramethylrhodamine) covalently attached to the 5′
and 3′ ends of the oligonucleotide, respectively. The melting of
the G-quadruplex was monitored in the presence of putative
G-quadruplex-binding molecules by measuring the fluorescence emission
of the donor. A series of compounds (pentacyclic crescent-shaped
dibenzophenanthroline derivatives) was shown to increase the melting
temperature of the G-quadruplex by 2–20°C at 1 μM dye
concentration. This increase in
T
m
value was
well correlated with an increase in the efficiency of telomerase
inhibition
in vitro
. The best telomerase inhibitor
showed an IC
50
value of 28 nM in a standard telomerase
repeat amplification protocol assay. Fluorescence energy transfer can
thus be used to reveal the formation of four-stranded DNA structures,
and its stabilization by quadruplex-binding agents, in an effort to
discover new potent telomerase inhibitors.
Most central nervous system D2 dopamine receptors are coupled to their effectors by Go
Authors: Jiang Meisheng , Spicher Karsten , Boulay Guylain , Wang Ying , Birnbaumer Lutz
Published: July 2002

We reported previously that Go-deficient mice develop severe neurological defects that include hyperalgesia, a generalized tremor, lack of coordination, and a turning syndrome somewhat reminiscent of unilateral lesions of the dopaminergic nigro-striatal pathway. By using frozen coronal sections of serially sectioned brains of normal and Go-deficient mice, we studied the ability of several G protein coupled receptors to promote binding of GTPγS to G proteins and the ability of GTP to promote a shift in the affinity of D2 dopamine receptor for its physiologic agonist dopamine. We found a generalized, but not abolished reduction in agonist-stimulated binding of GTPγS to frozen brain sections, with no significant left–right differences. Unexpectedly, the ability of GTP to regulate the binding affinity of dopamine to D2 receptors (as seen inin situ[35S]sulpiride displacement curves) that was robust in control mice, was absent in Go-deficient mice. The data suggest that most of the effects of the Gi/Go-coupled D2 receptors in the central nervous system are mediated by Go instead of Gi1, Gi2, or Gi3. In agreement with this, the effect of GTP on dopamine binding to D2 receptors in double Gi1 plus Gi2- and Gi1 plus Gi3-deficient mice was essentially unaffected.
Binding of rainbow trout sperm to egg is mediated by strong carbohydrate-to-carbohydrate interaction between (KDN)GM3 (deaminated neuraminyl ganglioside) and Gg3-like epitope
Authors: Yu Song , Kojima Naoya , Hakomori Sen-itiroh , Kudo Shigeharu , Inoue Sadako , Inoue Yasuo
Published: July 2002

KDNα2→3Galβ4Glcβ1Cer [(KDN)GM3] is a major (≈90%) component of total gangliosides found in sperm of rainbow trout (
Oncorhynchus mykiss
) and was shown to be present prominently at the sperm head by immunochemical staining with its specific mAb kdn3G. Liposomes containing (KDN)GM3 adhere specifically to GalNAcβ4Galβ4Glcβ1Cer (Gg3Cer)-coated plastic plates. Interaction between (KDN)GM3 and Gg3Cer was much stronger than that previously observed between Neu5Acα2→3Galβ4Glcβ1Cer and Gg3Cer. (KDN)GM3–Gg3Cer interaction did not require the presence of Ca
2+
and Mg
2+
, but was enhanced in the presence of Mn
2+
. Fresh trout sperm adhered specifically to Gg3Cer-coated plates under physiological conditions, and the binding was inhibited by pretreatment of sperm with mAb kdn3G. The presence of Gg3 or Gg3-related epitope structure in the specific area surrounding the micropyle, through which sperm enter the egg, was confirmed by immunogold labeling under electron microscopy. These findings suggest that initial sperm-egg adhesion during the process of fertilization occurs when sperm adhere to the area surrounding the micropyle through specific interaction between (KDN)GM3 on the sperm head and Gg3 epitope (GalNAcβ4Galβ1→) expressed at a defined region of the egg surface membrane.
How the folding rate constant of simple, single-domain proteins depends on the number of native contacts
Authors: Makarov Dmitrii E. , Keller Craig A. , Plaxco Kevin W. , Metiu Horia
Published: July 2002

Experiments have shown that the folding rate constants of two dozen structurally unrelated, small, single-domain proteins can be expressed in terms of one quantity (the contact order) that depends exclusively on the topology of the folded state. Such dependence is unique in chemical kinetics. Here we investigate its physical origin and derive the approximate formula ln(
k
) = ln(
N
) +
a
+
bN
, were
N
is the number of contacts in the folded state, and
a
and
b
are constants whose physical meaning is understood. This formula fits well the experimentally determined folding rate constants of the 24 proteins, with single values for
a
and
b
.
Identification of a germ-line pro-B cell subset that distinguishes the fetal/neonatal from the adult B cell development pathway
Authors: Lu Li-Sheng , Tung James , Baumgarth Nicole , Herman Ometa , Gleimer Michael , Herzenberg Leonard A. , Herzenberg Leonore A.
Published: July 2002

Studies presented here show that the expression of CD4, MHC class II (Ia,) and B220 cleanly resolves a major and a minor subset within the earliest pro-B cell population (germ-line pro-B) in adult bone marrow (BM). The major subset expresses intermediate B220 and low CD4 levels. The minor subset, which constitutes roughly 20% of the adult germ-line pro-B, expresses very low B220 levels and does not express CD4. Ia is clearly detectable at low levels on the major germ-line pro-B subset, both in wild-type adult mice and in gene-targeted mice (RAG2−/−and μMT), in which B cell development terminates before the pre-B cell stage. A small proportion of cells in the more mature pro-B cell subsets (Hardy Fractions B and C) also express Ia at this level. In contrast, Ia levels on the minor subset are barely above (or equal to) background. Surprisingly, the major germ-line pro-B cell subset found in adults is missing in fetal and neonatal animals. All of the germ-line pro-B in these immature animals express a phenotype (very low B220, no CD4, or Ia) similar to that of the minor pro-B cell subset in adult BM. Because B cell development in fetal/neonatal animals principally results in B-1 cells, these findings demonstrate that the B-1 development pathway does not include the major germ-line pro-B subset found in adult BM and hence identify a very early difference between the B-1 and -2 development pathways.
Solution structure of a Bcl-2 homolog from Kaposi sarcoma virus
Authors: Huang Qiulong , Petros Andrew M. , Virgin Herbert W. , Fesik Stephen W. , Olejniczak Edward T.
Published: July 2002

Kaposi sarcoma-associated herpes virus (KSHV) contains a gene that has functional and sequence homology to the apoptotic Bcl-2 family of proteins [Sarid, R., Sato, T., Bohenzky, R. A., Russo, J. J. & Chang, Y. (1997)
Nat. Med.
3, 293–298]. The viral Bcl-2 protein promotes survival of infected cells and may contribute to the development of Kaposi sarcoma tumors [Boshoff, C. & Chang, Y. (2001)
Annu. Rev. Med.
52, 453–470]. Here we describe the solution structure of the viral Bcl-2 homolog from KSHV. Comparison of the KSHV Bcl-2 structure to that of Bcl-2 and Bcl-x
L
shows that although the overall fold is the same, there are key differences in the lengths of the helices and loops. Binding studies on peptides derived from the Bcl-2 homology region 3 of proapoptotic family members indicate that the specificity of the viral protein is very different from what was previously observed for Bcl-x
L
and Bcl-2, suggesting that the viral protein has evolved to have a different mechanism of action than the host proteins.
The thermodynamic origin of the stability of a thermophilic ribozyme
Authors: Fang X.-W. , Golden B. L. , Littrell K. , Shelton V. , Thiyagarajan P. , Pan T. , Sosnick T. R.
Published: July 2002

Understanding the mechanism of thermodynamic stability of an RNA
structure has significant implications for the function and design of
RNA. We investigated the equilibrium folding of a thermophilic ribozyme
and its mesophilic homologue by using hydroxyl radical protection,
small-angle x-ray scattering, and circular dichroism. Both RNAs require
Mg
2+
to fold to their native structures that are very
similar. The stability is measured as a function of Mg
2+
and urea concentrations at different temperatures. The enhanced
stability of the thermophilic ribozyme primarily is derived from a
tremendous increase in the amount of structure formed in the ultimate
folding transition. This increase in structure formation and
cooperativity arises because the penultimate and the ultimate folding
transitions in the mesophilic ribozyme become linked into a single
transition in the folding of the thermophilic ribozyme. Therefore, the
starting point, or reference state, for the transition to the native,
functional thermophilic ribozyme is significantly less structured. The
shift in the reference state, and the resulting increase in folding
cooperativity, is likely due to the stabilization of selected native
interactions that only form in the ultimate transition. This mechanism
of using a less structured intermediate and increased cooperativity to
achieve higher functional stability for tertiary RNAs is fundamentally
different from that commonly proposed to explain the increased
stability of thermophilic proteins.