bluuebunny/crossref_metadata_2025 huggingface dataset:
Determination of electric field and electron temperature in the positive column of a high-power hydrogen thyratron from nonintrusive measurements
Authors: Erwin D. A. , Kunc J. A. , Gundersen M. A.
Published: July 2002

This work presents a simple method for calculating the conductivity, electron temperature, and electric field in a high-current hydrogen thyratron positive column as functions of the current density and electron density. The method is based on an analysis that takes into account the partially ionized nature of the plasma, and includes the effects of electron-electron and electron-ion collisions. Data are presented for a typical thyratron discharge (hydrogen pressure 0.4 Torr, current density 50–250 A/cm2, electron density 2–8×1014 cm−3). The electron temperature is found to be close to 1 eV, while the electric field ranges between 5 and 15 V/cm.
Radiation effects on phase separation and viscosity in a B2O3-PbO glass
Authors: Biron Isabelle , Barbu Alain
Published: July 2002

Taking into account the temperature rise under the electron beam, phase separation in a supersaturated B2O3-PbO glass is shown to be enhanced by electron irradiation. Coagulation of PbO-rich particles is observed during in situ electron microscopic experiments. This mechanism of coalescence is discussed. Using the Smoluchowski model of coagulation we show that the glass viscosity is drastically lowered: typically eight to nine orders of magnitude at 270 °C and only one order at 420 °C. This effect is shown to disappear almost instantaneously when irradiation is stopped.
Monolithic two-dimensional arrays of high-power GaInAsP/InP surface-emitting diode lasers
Authors: Walpole J. N. , Liau Z. L.
Published: July 2002

Two-dimensional arrays of 16 laser elements have been fabricated using the mass transport process. Good uniformity, low threshold current (typically 11–14 mA per element), and high total cw power (up to 0.27 W at 22 °C) were obtained.
Nonlinear spectroscopy of InGaAs/InAlAs multiple quantum well structures
Authors: Weiner J. S. , Pearson D. B. , Miller D. A. B. , Chemla D. S. , Sivco D. , Cho A. Y.
Published: July 2002

The first investigation of nonlinear absorption in InGaAs/InAlAs multiple quantum wells using picosecond and cw infrared lasers is presented. The nonlinearity is demonstrated to be due to plasma-induced excitonic bleaching. The measured saturation densities agree with those predicted by theory.
Phase-locked arrays of unstable resonator semiconductor lasers
Authors: Salzman J. , Yariv A.
Published: July 2002

A phase-locked array of several unstable resonator semiconductor lasers is demonstrated. Single lateral mode was obtained for currents I<2.5Ith, and partial spatial coherence for I≤5Ith, with an optical output power of 0.95 W.
InP metal-semiconductor field-effect transistors with mercury and cadmium gates
Authors: Meiners L. G. , Clawson A. R. , Nguyen R.
Published: July 2002

Depletion-type InP field-effect transistors have been constructed employing metal-semiconductor junctions between both mercury and InP and cadmium and InP as the blocking electrodes. The barrier height (0.6–0.7 eV) that can be obtained between electroplated Cd and InP is sufficiently large to give negligibly small (J<10−4 A/cm2) gate current densities at reverse bias voltages of 10 V. Although probably not of much technological usefulness, the Hg gate InP metal-semiconductor field-effect transistor is interesting because the large Schottky barrier height between Hg and n-InP (∼0.9 eV) permits the fabrication of devices for the nondestructive profiling of the mobility and carrier concentration in thin epitaxial layers of InP.
Orientational dependence of the electron beam induced order-disorder transition in quasicrystalline Al86Mn14
Authors: Murray E. R. , Ast D. G.
Published: July 2002

The order-disorder transition of quasicrystalline Al86Mn14 under 1 MeV electron irradiation at 135 K was investigated. The dose required to completely amorphize an area was found to depend on the axis aligned with the beam. Analysis showed that, for a given orientation, the transition obeyed the excluded volume theory of disordering. The dose required was not directly proportional to the current density which indicates that some recovery takes place during irradiation.
Nonperiodic power coupling in highly birefringent nonlinear optical fibers
Authors: Vatarescu A.
Published: July 2002

Nonperiodic codirectional power coupling between the polarization eigenmodes of a highly birefringent fiber, possessing propagation constants βx and βy, is possible with the assistance of contradirectionally propagating modes. When the fiber length L is adjusted so that (βx−βy)L=2mπ(m=±1, ±2,...) and the fiber ends are unequally excited, the coupling term gives rise only to a nonreciprocal phase between counterpropagating waves.
New processing technique for forming flexible A-15 superconducting tapes with extremely high critical current densities and magnetic fields
Authors: Clapp Mireille Treuil , Shi Donglu
Published: July 2002

Alloys of Nb73Al12Si14.5B0.5 were rapidly quenched using the melt spinning technique to form fine amorphous ribbons. These were then annealed into A-15 tapes with a variety of grain sizes. The smaller the grain was the more flexible the tape and the higher the critical current density Jc. The best results were obtained for a tape with a grain size of 15 nm; it could be bent to a diameter of 1 mm without breaking and it had a Jc of 3.3×1010 A/m2 at a magnetic field of 20 T.
Response to ‘‘Comment on ‘Mobility of Ni versus Zr in an amorphous Ni-Zr alloy’ ’’ [Appl. Phys. Lett. 4
9, 1311 (1986)]
Authors: Barbour J. C. , Nastasi M. , Mayer J. W.
Published: July 2002

A response to a comment on  mobility of Ni versus Zr in an amorphous Ni−Zr alloy  is given pointing out the need to use a more detailed model of diffusion. (AIP)
Glass forming ability in mechanically alloyed Fe-Zr
Authors: Hellstern E. , Schultz L.
Published: July 2002

Amorphous Fe-Zr powders have been prepared by mechanical alloying in a powder mill. The samples are characterized by x-ray diffraction, differential scanning calorimetry, and saturation magnetization measurements. The glass forming range reaches from 30 to 78 at. % Fe being much wider than for melt-spun samples. Eutectic concentrations do not play any role. The results are compared with the glass forming ability predicted by free-enthalpy diagram calculations based on the Miedema model [A. R. Miedema, Philips Tech. Rev. 36, 217 (1976)]. Amorphization by mechanical alloying seems to be a metastable equilibrium process neglecting intermetallic phases. Rather high crystallization temperatures are found in the concentration range which is not accessible by melt spinning.
Nanosecond switching of bistable ZnSe interference filters at room temperature
Authors: Bigot J. Y. , Daunois A. , Leonelli R. , Sence M. , Mathew J. G. H. , Smith S. D. , Walker A. C.
Published: July 2002

UV light pulses of nanosecond and picosecond duration were used to switch bistable nonlinear interference filters from their low to their high transmission level. At room temperature, switching times in the nanosecond range are measured. They are, to the authors’ knowledge, the shortest reported for such devices.
Ge0.6Si0.4 rib waveguide avalanche photodetectors for 1.3 μm operation
Authors: Temkin H. , Antreasyan A. , Olsson N. A. , Pearsall T. P. , Bean J. C.
Published: July 2002

Performance of strained-layer superlattice Ge0.6Si0.4 waveguide avalanche photodetectors is evaluated for optical fiber applications at 1.3 μm. These devices are grown on Si substrates by molecular beam epitaxy. Waveguiding is accomplished by means of a 1.5–1.8-μm-thick Si rib waveguide which provides an effective index step of δn=8×10−3. The detector response bandwidth exceeds 8 GHz at a gain of 6. A receiver sensitivity of ηP̄=−29.4 dBm has been obtained at the data rate of 800 Mb/s with the corresponding error-free transmission over 45 km of single mode fiber.
Measurements of the nonradiative states of optically illuminated semiconductors by a superconducting tunnel junction
Authors: Iguchi I. , Kasai Y.
Published: July 2002

A novel technique which utilizes a superconducting tunnel junction as a phonon detector is introduced to detect nonequilibrium phonons from the nonradiative states in optically illuminated semiconductors such as Si or GaAs. The method proved to have very high sensitivity for phonon detection with a large S/N ratio. The detected phonon signal as a function of wavelength of the light for GaAs exhibited modulated structures below the band-gap energy consistent with the presence of an EL2 level.
Morphological effects during low pressure chemical vapor deposition and annealing of undoped polycrystalline silicon layers
Authors: Brokman A. , Gat R. , Alpern Y.
Published: July 2002

The microstructure of low pressure chemical vapor deposited silicon layers is investigated during and after annealing. The crystallization of deposited amorphous layers is controlled by microtwins, which are generated during the nucleation stage, and yields the final morphology of elongated grains. Recrystallization and growth of the deposited polycrystalline layers involve twin coarsening which causes the final morphology of regular equiaxed grains.
Photoluminescence of Mg-doped GaAs grown by molecular beam epitaxy using Mg3As2 as a Mg source: A comparison with Mg+ ion implantation
Authors: Makita Yunosuke , Takeuchi Yoshinori , Ohnishi Nobukazu , Nomura Toshio , Kudo Kazuhiro , Tanaka Hideki , Lee Hae-Chol , Mori Masahiko , Mitsuhashi Yoshinobu
Published: July 2002

Photoluminescence spectra of Mg-doped GaAs grown by molecular beam epitaxy (MBE) are for the first time reported. Mg was introduced during MBE growth by using a synergic reaction of Mg3As2. Two near-band-edge emissions, g and [g-g], were observed below bound exciton emissions which were originally obtained in Mg+ ion-implanted GaAs. It is explicitly demonstrated that there is no essential difference of photoluminescence spectra between Mg+ ion-implanted GaAs and the present material. These results conclusively indicate that the above two emissions are definitively related with the acceptor levels and exclusively not associated with crystalline defects produced by ion implantation. It is additionally presented that [g-g] is principally established also in Mg-doped GaAs prepared by liquid phase epitaxy, where [g-g] is significantly suppressed due to the unintentional incorporation of Si donor atoms. For moderately Mg-doped GaAs prepared by MBE a new fine emission with a doublet structure, temporarily denoted by AX, is obtained 5 meV below (A0, X) a bound exciton emission at neutral acceptors.
Use of tertiarybutylarsine for GaAs growth
Authors: Chen C. H. , Larsen C. A. , Stringfellow G. B.
Published: July 2002

The use of AsH3 in the organometallic vapor phase epitaxial (OMVPE) growth of GaAs and other As containing III/V semiconductors has a number of disadvantages, including toxicity hazard, purity problems associated with storage cylinders, and low pyrolysis rate at the low temperatures often desirable in OMVPE growth. A new organometallic source, tertiarybutylarsine (TBAs), has recently become available. In this letter we report the results of OMVPE growth of GaAs using trimethylgallium (TMGa) and TBAs in a one atmosphere ambient. The major results of the study are (1) the vapor pressure of TBAs is measured to be 96 Torr at 10 °C, (2) the pyrolysis rate of TBAs appears to be greater than that of AsH3 under similar conditions, (3) as a consequence of (2), excellent morphology GaAs layers can be grown at lower values of V/III ratio (approximately unity) using TBAs than using AsH3 (4) no additional carbon incorporation is produced by the use of the organometallic group V source. These factors make TBAs a promising candidate to replace AsH3 in vapor phase epitaxial growth of GaAs.
Diode lasers with cylindrical mirror facets and reduced beam divergence
Authors: Walpole J. N. , Liau Z. L. , Missaggia L. J. , Yap D.
Published: July 2002

Using chemical etching and mass transport, we have monolithically integrated cylindrical lenses at one of the ends of buried-heterostructure GaInAsP/InP diode laser cavities. The lenses are designed to provide reflective feedback for low-threshold current (as low as 25 mA), as well as reduction of beam width in the lateral direction (as small as 9.2°).
Interface properties for GaAs/InGaAlP heterojunctions by the capacitance-voltage profiling technique
Authors: Watanabe Miyoko O. , Ohba Yasuo
Published: July 2002

The conduction-band discontinuity ΔEc and interface charge density σ have been studied for GaAs/In0.5(Ga1−xAlx)0.5P heterojunctions, prepared by metalorganic chemical vapor deposition. The dependences of ΔEc and σ on Al composition x were investigated for x from 0 to 1. The In0.5Al0.5P/ In0.5Ga0.5P heterojunction was also examined. The results suggest that the valence-band discontinuity ΔEv for GaAs/In0.5(Ga1−xAlx)0.5P is a linear function of x and is larger than ΔEc, being in reasonable agreement with results on the InAlP/InGaP heterojunction. The σ values for GaAs/InGaAlP were found to be one order of magnitude larger than those for GaAs/AlGaAs and InAlP/InGaP heterojunctions.
Permeation of hydrogen into silicon during low-energy hydrogen ion beam bombardment
Authors: Horn M. W. , Heddleson J. M. , Fonash S. J.
Published: July 2002

In this study we examine the permeating of hydrogen into p-type silicon during low-energy hydrogen ion beam bombardment by monitoring boron doping deactivation. This examination is done for various times and two different exposure temperatures. In addition we explore the effect of temperature during subsequent isochronal anneals on the recovery of silicon exposed to a hydrogen ion beam. As a result of these studies, it is found that there are two distinct permeation regions. Each may be characterized by its own apparent diffusion coefficient, activation energy, and recovery process.
Enhancement of quantum confined Stark effect in a graded gap quantum well
Authors: Nishi K. , Hiroshima T.
Published: July 2002

A graded gap quantum well structure, where the band gap is linearly changing along the growth direction, is proposed for the enhancement of quantum confined Stark effect. Theoretical calculations show that the ground-state exciton peak energy shifts by a larger amount than in a usual square-shaped quantum well under an applied electric field. The wave function modifications in this quantum well result in a smaller decrease of the exciton oscillator strength, according to the electric field applied. These effects reveal the possibility of achieving high-performance optical modulators or other devices which utilize the quantum confined Stark effect.
Optoelectronic transmission and reception of ultrashort electrical pulses
Authors: DeFonzo Alfred P. , Lutz Charles R.
Published: July 2002

We report on the recent advances in using integrated planar antenna technology to photoconductively generate and detect picosecond radiation. Detection of a single pulse of picosecond duration has been achieved using a coplanar antenna structure fabricated on a radiation-damaged silicon-on-sapphire substrate.
Determining height of a leaky Schottky barrier existing in the junction between SnO2 and a highly doped p-type amorphous SiC by using the pulsed laser-induced transient photopotential technique
Authors: Itoh Kiminori , Matsumoto Hidetoshi , Kobata Tsuyoshi , Fujishima Akira , Nakamura Osamu , Fukui Keitaro
Published: July 2002

The junction between SnO2 and a highly doped p-type amorphous SiC [a-SiC(p+)] is very important as a transparent contact to an a-Si alloy based solar cell. An energy-band diagram for this junction has been obtained here for the first time. A thin film of a-SiC(p+) deposited onto a SnO2-coated glass was immersed into a nonaqueous electrolyte solution and was irradiated with N2 laser pulses. The photopotential was monitored against a Ag reference electrode. The photopotential thus obtained showed that a leaky Schottky barrier exists at the SnO2/a-SiC(p+) junction. A band diagram was estimated, using an asymptotic value of the photopotential together with a position of the Fermi level calculated on the basis of the dark conductivity data.
Monte Carlo algorithm for generation-recombination noise in semiconductors
Authors: Reggiani Lino , Lugli Paolo , Mitin Vladimir
Published: July 2002

We present an original Monte Carlo procedure to account for generation-recombination noise through impurity centers in semiconductors. Numerical calculations are specialized to the case of holes in Si at 77 K. Results are found to compare favorably with available experiments.
Variation of the critical layer thickness with In content in strained InxGa1−xAs-GaAs quantum wells grown by molecular beam epitaxy
Authors: Andersson T. G. , Chen Z. G. , Kulakovskii V. D. , Uddin A. , Vallin J. T.
Published: July 2002

The critical width Lc for misfit dislocation generation has been determined for molecular beam epitaxy grown strained InxGa1−xAs (0.1<x≤1) quantum wells in a GaAs matrix by means of photoluminescence measurements. For the full alloy region the dependence Lc(x) is in good agreement with the theoretical expression proposed by J. W. Matthews and A. E. Blakeslee [J. Cryst. Growth 27, 118 (1974)].
Identification of infrared absorption peaks of amorphous silicon-carbon alloy by thermal annealing
Authors: Lin Wei-Liang , Tsai Hsiung-Kuang , Lee Si-Chen , Sah Wen-Jyh , Tzeng Wen-Jer
Published: July 2002

Amorphous silicon-carbon hydrogen alloy was prepared by radio frequency glow discharge decomposition of a silane-methane mixture. The infrared absorption spectra were measured at various stages of thermal annealing. By observing the change of relative intensities between these peaks the hydrogen bonding responsible for the absorption peaks could be assigned more accurately, for example, the stretching mode of monohydride Si–H is determined by its local environment, which supports H. Wagner’s and W. Beyer’s results [Solid State Commun. 48, 585 (1983)] but is inconsistent with the commonly believed view. It is also found that a significant fraction of carbon atoms are introduced into the film in –CH3 configuration which forms a local void and enhances the formation of polysilane chain and dangling bond defects. Only after high-temperature annealing are the hydrogen atoms driven out, and Si and C start to form a better silicon carbide network.
Large optical nonlinearities in a GaAs/AlGaAs hetero n-i-p-i structure
Authors: Kost A. , Garmire E. , Danner A. , Dapkus P. D.
Published: July 2002

Light-induced changes in the absorption of a multiple quantum well hetero n-i-p-i structure at room temperature have been measured using a pump-probe method. Changes in the absorption coefficient in the quantum wells of more than 2000 cm−1 have been observed with pump intensities as small as 375 mW/cm2. Corresponding changes in the index of refraction of ≊0.02 have been calculated.
CdS photoelectric device: Modulation and optical bistability at 514 nm
Authors: Witt A. , Wegener M. , Klingshirn C. , Gnass D. , Jäger D.
Published: July 2002

We discuss the nonlinear characteristics of hybrid CdS devices at room temperature by using increasing absorption at a wavelength of 514.5 nm. Via the thermo-optical properties, a self-electro-optic effect occurs due to the optically induced dissipation of electrical power. As a special application, the device can be utilized as an electro-optic modulator for Ar+ laser light. In addition, voltage controlled optical bistability is also observed.
Formation of thermally stable high-resistivity AlGaAs by oxygen implantation
Authors: Pearton S. J. , Iannuzzi M. P. , Reynolds C. L. , Peticolas L.
Published: July 2002

Oxygen implantation into n+-AlGaAs, followed by annealing above 600 °C, creates a deep acceptor level that compensates the shallow donors present in the material. Temperature-dependent Hall measurements show that the resistivity of this compensated AlGaAs has a thermal activation energy of 0.49 eV, in contrast to a value of 0.79 eV for compensation caused by ion-induced damage. The latter is stable only to 600 °C, whereas the chemically induced compensation in O-implanted AlGaAs is stable above 950 °C.
Relationship between hole trapping and interface state generation in metal-oxide-silicon structures
Authors: Wang S. J. , Sung J. M. , Lyon S. A.
Published: July 2002

We have discovered a general relationship between the location of trapped holes and the subsequent generation of interface states. Experimentally, we find that a hole can become an interface state, but it must first be trapped between 20 and 70 Å from the Si/SiO2 interface (near-interfacial hole trap) and then transfer to within 18 Å of the interface (interfacial trapped holes). Finally, the hole captures an electron and becomes an interface state. The transfer process between near-interfacial and interfacial trapped holes does not seem to be a simple release-capture process. Rather it appears to involve a complicated migration of the trapped hole defect towards the interface. Radiation-hardened oxides are shown to have a similar number of near-interfacial traps, but these traps are shallower than those in the soft oxides.
Characterization of thin films of Y-Ba-Cu-O on oxidized silicon with a zirconia buffer layer
Authors: Mogro-Campero A. , Turner L. G. , Hall E. L. , Burrell M. C.
Published: July 2002

Thin films of the high-temperature superconductor Y-Ba-Cu-O with zero-resistance transition temperatures up to 83 K have been recently reported by using a zirconia buffer layer on the primary materials of interest for electronics, Si and SiO2. In this letter, various characteristics of these films are discussed. Microstructural analysis using transmission electron microscopy shows the complex morphology of the unoriented polycrystalline films. Elemental depth profiling by x-ray photoelectron spectroscopy shows the effectiveness of the zirconia buffer layer in preventing interdiffusion; fluorine is found throughout the film at an abundance of 4 at. % The critical current density was measured as a function of temperature; its value is 5 kA cm−2 at 4.2 K.
Conserved regulation of the lymphocyte-specific expression oflckin the Fugu and mammals
Authors: Brenner Sydney , Venkatesh Byrappa , Yap Wai Ho , Chou Chih-Fong , Tay Alice , Ponniah Sathivel , Wang Yue , Tan Y. H.
Published: July 2002

Thelckgene encodes a lymphocyte-specific protein-tyrosine kinase that is implicated in T cell maturation and signaling. In mammals, the transcription of thelckgene is regulated by two independent promoters, the proximal promoter, which is active in thymocytes, and the distal promoter, which dominates in mature T cells. In the human and mouselckgene loci, the two promoter elements are separated by at least 40 kb and 10 kb, respectively. In this study, we have cloned and sequenced 60 kb from the pufferfish (Fugu rubripes)lcklocus. The promoter region of the Fugulckspans only 4.2 kb and contains a proximal and a distal promoter in the 2.3-kb region adjacent to the coding sequence. By generating transgenic mice, we have demonstrated that the compact promoter of the Fugulckcontains regulatory elements that direct expression to lymphoid organs of mice. We were able to localize the regulatory elements to a short region of 830 bp without losing specificity to cultured human T cell line. These results show that the basic mechanisms that mediate lymphocyte-specific expression are conserved between teleosts and mammals. The short promoter of the Fugulckisolated by us offers a powerful tool for labeling T cells, targeting expression, and manipulating T cell activity in fishes as well as in mammals.
The interaction of nitric oxide (NO) with the yeast transcription factor Ace1: A model system for NO-protein thiol interactions with implications to metal metabolism
Authors: Shinyashiki Masaru , Chiang Kenneth T. , Switzer Christopher H. , Gralla Edith B. , Valentine Joan S. , Thiele Dennis J. , Fukuto Jon M.
Published: July 2002

Nitric oxide (NO) was found to inhibit the
copper-dependent induction of the yeast
CUP1
gene. This
effect is attributable to an inhibition of the copper-responsive
CUP1
transcriptional activator Ace1. A mechanism is
proposed whereby the metal binding thiols of Ace1 are chemically
modified via NO- and O
2
-dependent chemistry, thereby
diminishing the ability of Ace1 to bind and respond to copper.
Moreover, it is proposed that demetallated Ace1 is proteolytically
degraded in the cell, resulting in a prolonged inhibition of
copper-dependent
CUP1
induction. These findings indicate
that NO may serve as a disrupter of yeast copper metabolism. More
importantly, considering the similarity of Ace1 to other mammalian
metal-binding proteins, this work lends support to the hypothesis that
NO may regulate/disrupt metal homeostasis under both normal
physiological and pathophysiological circumstances.
Surface-exposed positions in the transmembrane helices of the lactose permease of
Escherichia coli
determined by intermolecular thiol cross-linking
Authors: Guan Lan , Murphy Franklin D. , Kaback H. Ronald
Published: July 2002

Intermolecular thiol cross-linking was used to determine surface-exposed positions in 250 lactose permease mutants containing single-Cys replacements in each transmembrane helix. Significant cross-linking of monomers to produce homodimers is observed in nine mutants with a 5-Å-long cross-linking agent containing
bis
-methane thiosulfonate reactive groups [position 78 (helix III); positions 185, 186, and 187 (helix VI); positions 263, 275, and 278 (helix VIII); and positions 308 (helix IX) and 398 (helix XII)]. The results are consistent with a current helix-packing model of the permease. Seven of the nine mutants that exhibit intermolecular cross-linking are located at or near the cytoplasmic ends of transmembrane helices; two are near periplasmic ends. The results suggest that only those Cys replacements accessible from the aqueous phase and not from the hydrophobic core of the membrane are susceptible to cross-linking because of the much higher reactivity of the thiolate anion relative to the thiol. Single-Cys mutants at positions 278 (helix VIII) and 398 (helix XII), which are located in opposite sides of the 12-helix bundle, exhibit similar rates of cross-linking with sigmoid kinetics. Furthermore, cross-linking is markedly decreased at 0°C, suggesting that lateral diffusion of the permease within the plane of the membrane is important for intermolecular cross-linking. The findings confirm previous observations indicating that intermolecular cross-linking is a stochastic process resulting from random collisions and support a number of other lines of evidence that lactose permease is a monomer.
PATE,a gene expressed in prostate cancer, normal prostate, and testis, identified by a functional genomic approach
Authors: Bera Tapan K. , Maitra Rangan , Iavarone Carlo , Salvatore Giuliana , Kumar Vasantha , Vincent James J. , Sathyanarayana B. K. , Duray Paul , Lee B. K. , Pastan Ira
Published: July 2002

To identify target antigens for prostate cancer therapy, we have combined computer-based screening of the human expressed sequence tag database and experimental expression analysis to identify genes that are expressed in normal prostate and prostate cancer but not in essential human tissues. Using this approach, we identified a gene that is expressed specifically in prostate cancer, normal prostate, and testis. The gene has a 1.5-kb transcript that encodes a protein of 14 kDa. We named this genePATE(expressed inprostateandtestis).In situhybridization shows thatPATEmRNA is expressed in the epithelial cells of prostate cancers and in normal prostate. Transfection of the PATE cDNA with a Myc epitope tag into NIH 3T3 cells and subsequent cell fractionation analysis shows that the PATE protein is localized in the membrane fraction of the cell. Analysis of the amino acid sequence of PATE shows that it has structural similarities to a group of proteins known as three-finger toxins, which includes the extracellular domain of the type β transforming growth factor receptor. Restricted expression of PATE makes it a potential candidate for the immunotherapy of prostate cancer.
Selective
in vivo
suppression of T lymphocyte responses in experimental measles virus infection
Authors: Niewiesk Stefan , Götzelmann Michaela , ter Meulen Volker
Published: July 2002

During and after measles virus (MV) infection humans are highly susceptible to opportunistic infections because of a marked immunosuppressive effect of the virus. The mechanisms by which the virus induces this phenomenon is not well understood. In particular, detailed information is missing on the targets of suppression in relation to antigen-specific T and B cell responses. Because such studies require animal experiments, we used the cotton rat model, in which the MV causes a respiratory tract infection. Primary as well as secondary T cell responses were impaired
in vivo
and
ex vivo
by MV infection. The proliferation of T cells was greatly reduced, but their effector functions, such as cytolysis or cytokine secretion, were not. In contrast, primary and secondary B cell responses
in vivo
as measured by the frequency of antigen-specific plasma cells in an enzyme-linked immunospot (ELISPOT) assay were not altered by MV infection. Only the secretion of immunoglobulins was reduced slightly in animals primarily infected with MV after 2 weeks. These data demonstrate that MV-induced immunosuppression acts primarily on the T cell responses
in vivo
.
Paranasal sinus anatomy of
Aegyptopithecus
: Implications for hominoid origins
Authors: Rossie James B. , Simons Elwyn L. , Gauld Suellen C. , Rasmussen D. Tab
Published: July 2002

The East African Early Miocene apes, or proconsulids, have often been considered to be among the earliest members of the Hominoidea, as defined by the divergence of the Cercopithecoidea, but this hypothesis is only weakly supported by available fossil evidence. The ethmofrontal sinus is one of a few morphological features that may link proconsulids with later hominoids. Here we present direct evidence of an ethmofrontal sinus in an early Oligocene stem catarrhine,
Aegyptopithecus zeuxis
. The presence of this sinus in
Aegyptopithecus
suggests that its presence in proconsulids is most likely to be a retained primitive condition. The morphological evidence bearing on proconsulids' purported hominoid affinities is further weakened by this conclusion, and alternative phylogenetic possibilities, such as the placement of proconsulids as stem catarrhines are considered more likely.
Large carbon isotope fractionation associated with oxidation of methyl halides by methylotrophic bacteria
Authors: Miller L. G. , Kalin R. M. , McCauley S. E. , Hamilton J. T. G. , Harper D. B. , Millet D. B. , Oremland R. S. , Goldstein A. H.
Published: July 2002

The largest biological fractionations of stable carbon isotopes
observed in nature occur during production of methane by methanogenic
archaea. These fractionations result in substantial (as much as
≈70‰) shifts in δ
13
C relative to the initial
substrate. We now report that a stable carbon isotopic fractionation of
comparable magnitude (up to 70‰) occurs during oxidation of methyl
halides by methylotrophic bacteria. We have demonstrated biological
fractionation with whole cells of three methylotrophs (strain IMB-1,
strain CC495, and strain MB2) and, to a lesser extent, with the
purified cobalamin-dependent methyltransferase enzyme obtained from
strain CC495. Thus, the genetic similarities recently reported between
methylotrophs, and methanogens with respect to their pathways for
C
1
-unit metabolism are also reflected in the carbon
isotopic fractionations achieved by these organisms. We found that only
part of the observed fractionation of carbon isotopes could be
accounted for by the activity of the corrinoid methyltransferase
enzyme, suggesting fractionation by enzymes further along the
degradation pathway. These observations are of potential biogeochemical
significance in the application of stable carbon isotope ratios to
constrain the tropospheric budgets for the ozone-depleting
halocarbons, methyl bromide and methyl chloride.
Structure of 2C-methyl-
d
-erythritol 2,4- cyclodiphosphate synthase: An essential enzyme for isoprenoid biosynthesis and target for antimicrobial drug development
Authors: Kemp Lauris E. , Bond Charles S. , Hunter William N.
Published: July 2002

The crystal structure of the zinc enzyme
Escherichia coli
2C-methyl-
d
-erythritol 2,4-cyclodiphosphate synthase in complex with cytidine 5′-diphosphate and Mn
2+
has been determined to 1.8-Å resolution. This enzyme is essential in
E. coli
and participates in the nonmevalonate pathway of isoprenoid biosynthesis, a critical pathway present in some bacterial and apicomplexans but distinct from that used by mammals. Our analysis reveals a homotrimer, built around a β prism, carrying three active sites, each of which is formed in a cleft between pairs of subunits. Residues from two subunits recognize and bind the nucleotide in an active site that contains a Zn
2+
with tetrahedral coordination. A Mn
2+
, with octahedral geometry, is positioned between the α and β phosphates acting in concert with the Zn
2+
to align and polarize the substrate for catalysis. A high degree of sequence conservation for the enzymes from
E. coli
,
Plasmodium falciparum
, and
Mycobacterium tuberculosis
suggests similarities in secondary structure, subunit fold, quaternary structure, and active sites. Our model will therefore serve as a template to facilitate the structure-based design of potential antimicrobial agents targeting two of the most serious human diseases, tuberculosis and malaria.
How does a β-hairpin fold/unfold? Competition between topology and heterogeneity in a solvable model
Authors: Guo Chinlin , Levine Herbert , Kessler David A.
Published: July 2002

We study the competition between topological effects and sequence
inhomogeneities in determining the thermodynamics and the un/folding
kinetics of a β-hairpin. Our work utilizes a new exactly solvable
model that allows for arbitrary configurations of native contacts. In
general, the competition between heterogeneity and topology results in
a crossover of the dominant transition state. Interestingly, near this
crossover, the single reaction coordinate picture can be seriously
misleading. Our results also suggest that inferring the folding pathway
from unfolding simulations is not always justified.
1998 SM
165
: A large Kuiper belt object with an irregular shape
Authors: Romanishin W. , Tegler S. C. , Rettig T. W. , Consolmagno G. , Botthof B.
Published: July 2002

The recent discovery of an ancient reservoir of icy bodies at and beyond the orbit of Neptune—the Kuiper belt—has opened a new frontier in astronomy. Measurements of the physical and chemical nature of Kuiper belt objects (KBOs) can constrain our ideas of the processes of planet formation and evolution. Our 1.8-m Vatican Advanced Technology Telescope and charge-coupled device camera observations of the KBO 1998 SM
165
indicate its brightness periodically varies by 0.56 magnitudes over a 4-h interval. If we assume a uniform albedo of 0.04, which is typical of values found in the literature for a handful of KBOs, and an “equator-on” aspect, we find 1998 SM
165
has axes of length 600 × 360 km. If our assumptions are correct, such dimensions put 1998 SM
165
among the largest elongated objects known in our solar system. Perhaps long ago, two nearly spherical KBOs of comparable size coalesced to form a compound object, or perhaps 1998 SM
165
is the residual core of a catastrophic fragmentation of a larger precursor.
Long-term expression of γ-globin mRNA in mouse erythrocytes from retrovirus vectors containing the human γ-globin gene fused to the ankyrin-1 promoter
Authors: Sabatino Denise E. , Seidel Nancy E. , Aviles-Mendoza Guillermo J. , Cline Amanda P. , Anderson Stacie M. , Gallagher Patrick G. , Bodine David M.
Published: July 2002

Gene therapy for patients with hemoglobin disorders has been
hampered by the inability of retrovirus vectors to transfer globin
genes and their cis-acting regulatory sequences into hematopoietic stem
cells without rearrangement. In addition, the expression from intact
globin gene vectors has been variable in red blood cells due to
position effects and retrovirus silencing. We hypothesized that by
substituting the globin gene promoter for the promoter of another gene
expressed in red blood cells, we could generate stable retrovirus
vectors that would express globin at sufficient levels to treat
hemoglobinopathies. Recently, we have shown that the human ankyrin
(Ank) gene promoter directs position-independent, copy number-dependent
expression of a linked γ-globin gene in transgenic mice. We inserted
the Ank/
A
γ-globin gene into retrovirus vectors that
could transfer one or two copies of the Ank/
A
γ-globin
gene to target cells. Both vectors were stable, transferring only
intact proviral sequences into primary mouse hematopoietic stem cells.
Expression of Ank/
A
γ-globin mRNA in mature red blood
cells was 3% (single copy) and 8% (double copy) of the level of mouse
α-globin mRNA. We conclude that these novel retrovirus vectors may be
valuable for treating a variety of red cell disorders by gene
replacement therapy including severe β-thalassemia if the level of
expression can be further increased.
The primary structures of the Archaeon Halobacterium salinarium blue light receptor sensory rhodopsin II and its transducer, a methyl-accepting protein.
Authors: Zhang W , Brooun A , Mueller M M , Alam M
Published: July 2002

Recently, a large family of transducer proteins in the Archaeon Halobacterium salinarium was identified. On the basis of the comparison of the predicted structural domains of these transducers, three distinct subfamilies of transducers were proposed. Here we report isolation, complete gene sequences, and analysis of the encoded primary structures of transducer gene htrII, a member of family B, and its blue light receptor gene (sopII) of sensory rhodopsin II (SRII). The start codon ATG of the 714-bp sopII gene is one nucleotide beyond the termination codon TGA of the 2298-bp htrII gene. The deduced protein sequence of HtrII predicts a eubacterial chemotaxis transducer type with two hydrophobic membrane-spanning segments connecting sizable domains in the periplasm and cytoplasm. HtrII has a common feature with HtrI, the sensory rhodopsin I transducer; like HtrI, HtrII possesses a hydrophilic loop structure just after the second transmembrane segment. The C-terminal 299 residues (765 amino acid residues total) of HtrII show strong homology to the signaling and methylation domain of eubacterial transducer Tsr. The hydropathy plot of the primary structure of SRII indicates seven membrane-spanning alpha-helical segments, a characteristic feature of retinylidene proteins ("rhodopsins") from a widespread family of photoactive pigments. SRII shows high identity with SRI (42%), bacteriorhodopsin (BR) (32%), and halorhodopsin (24%). The crucial positions for retinal binding sites in these proteins are nearly identical, with the exception of Met-118 (numbering according to the mature BR sequence), which is replaced by Val in SRII. In BR, residues Asp-85 and Asp-96 are crucial in proton pumping. In SRII, the position corresponding to Asp-85 in BR is conserved, but the corresponding position of Asp-96 is replaced by an aromatic Tyr. Coexpression of the htrII and sopII genes restores SRII phototaxis to a mutant (Pho81) that contains a deletion in the htrI/sopI and insertion in htrII/sopII regions. This paper describes the first example that both HtrI and HtrII exist in the same halobacterial cell, confirming that different sensory rhodopsins SRI and SRII in the same organism have their own distinct transducers.
In vitro characterization of mutant yeast RNA polymerase II with reduced binding for elongation factor TFIIS.
Authors: Wu J , Awrey D E , Edwards A M , Archambault J , Friesen J D
Published: July 2002

We have reported previously the isolation and genetic characterization of mutations in the gene encoding the largest subunit of yeast RNA polymerase II (RNAPII), which lead to 6-azauracil (6AU)-sensitive growth. It was suggested that these mutations affect the functional interaction between RNAPII and transcription-elongation factor TFIIS because the 6AU-sensitive phenotype of the mutant strains was similar to that of a strain defective in the production of TFIIS and can be suppressed by increasing the dosage of the yeast TFIIS-encoding gene, PPR2, RNAPIIs were purified and characterized from two independent 6AU-sensitive yeast mutants and from wild-type (wt) cells. In vitro, in the absence of TFIIS, the purified wt polymerase and the two mutant polymerases showed similar specific activity in polymerization, readthrough at intrinsic transcriptional arrest sites and nascent RNA cleavage. In contrast to the wt polymerase, both mutant polymerases were not stimulated by the addition of a 3-fold molar excess of TFIIS in assays of promoter-independent transcription, readthrough or cleavage. However, stimulation of the ability of the mutant RNAPIIs to cleave nascent RNA and to read through intrinsic arrest sites was observed at TFIIS:RNAPII molar ratios greater than 600:1. Consistent with these findings, the binding affinity of the mutant polymerases for TFIIS was found to be reduced by more than 50-fold compared with that of the wt enzyme. These studies demonstrate that TFIIS has an important role in the regulation of transcription by yeast RNAPII and identify a possible binding site for TFIIS on RNAPII.
Olfactory neuroblastoma is a peripheral primitive neuroectodermal tumor related to Ewing sarcoma.
Authors: Sorensen P H , Wu J K , Berean K W , Lim J F , Donn W , Frierson H F , Reynolds C P , López-Terrada D , Triche T J
Published: July 2002

Olfactory neuroblastoma (ONB) is a malignant tumor of the nasal mucosa whose histogenesis is unclear. A relationship to neuroblastoma (NB), a pediatric tumor of the sympathetic nervous system, is based on morphologic similarities and the expression of similar neural antigens. However, the clinical presentation of ONB differs from that of NB, and MYCN amplification characteristic of NB is not observed. We have therefore examined the relationship of this malignancy to other classes of neural tumors. In previous studies, two ONB cell lines demonstrated cytogenetic features and patterns of protooncogene expression suggestive of a relationship to the Ewing sarcoma family of childhood peripheral primitive neuroectodermal tumors (pPNETs). The pPNETs show t(11;22)(q24;q12) or t(21;22)(q22;q12) chromosomal translocations fusing the EWS gene from 22q12 with either the FL11 gene on 11q24 or the ERG gene on 21q22. We therefore analyzed ONBs for the presence of pPNET-associated gene fusions. Both cell lines showed rearrangement of the EWS gene, and fluorescence in situ hybridization (FISH) of each case demonstrated fusion of EWS and FL11 genomic sequences. Moreover, both lines expressed EWS/FL11 fusion transcripts with in-frame junctions between exon 7 of EWS and exon 6 of FL11 as described for pPNETs. We identified similar gene fusions in four of six primary ONB cases. None of the cases expressed tyrosine hydroxylase, a catecholamine biosynthetic enzyme widely expressed in NB. Our studies indicate that ONB is not a NB but is a member of the pPNET family.
The invariant system of coordinates of antibody molecules: prediction of the "standard" C alpha framework of VL and VH domains.
Authors: Gelfand I M , Kister A E , Leshchiner D
Published: July 2002

A new approach of comparing protein structures that does not involve the procedure of superposition is suggested. An invariant system of coordinates for immunoglobulin molecules that is based on the geometrical symmetry inherent to the variable domain light-chain (VL)-heavy-chain (VH) complex is described. The coordinates of the Calpha atoms in 22 immunoglobulin structures are calculated in the invariant system of coordinates. We found that 76 identical positions in this Calpha framework are symmetrical about the twofold axis. Comparison of the identical positions in these molecules allows us to select 96 positions in the light chains and 87 positions in the heavy chains whose Calpha atom coordinates are approximately the same. To check whether the average coordinates of Calpha atoms in these positions complies with the stereochemical requirements, we calculated Calpha-Calpha distances. Seventy-three positions of the light chains and 72 positions of the heavy chains satisfy the Calpha-Calpha distance criterion. The Calpha atoms in these positions are used for constructing the "standard" Calpha framework of VL and VH complexes. The average coordinates of Calpha atoms are presented.
Drosophila
TAF
II
230 and the transcriptional activator VP16 bind competitively to the TATA box-binding domain of the TATA box-binding protein
Authors: Nishikawa Jun-ichi , Kokubo Tetsuro , Horikoshi Masami , Roeder Robert G. , Nakatani Yoshihiro
Published: July 2002

The transcription initiation factor TFIID, consisting of the TATA
box-binding protein (TBP) and many TBP-associated factors (TAFs), plays
a central role in both basal and activated transcription. An intriguing
finding is that the 80-residue N-terminal region of
Drosophila
TAF
II
230
[dTAF
II
230-(2–81)] can bind directly to TBP and inhibit
its function. Here, studies with mutated forms of TBP demonstrate that
dTAF
II
230-(2–81) binds to the concave surface of TBP,
which is important for TATA box binding. Previously, it was reported
that a point mutation (L114K) on this concave surface destroys the
ability of TBP to bind VP16 and to mediate VP16-dependent activation
in vitro
, but has no effect on basal transcription.
Importantly, the same TBP mutation eliminates TBP binding to
dTAF
II
230-(2–81). Consistent with these effects of the
L114K mutation, dTAF
II
230-(2–81) and the VP16 activation
domain compete for binding to wild-type TBP. These results indicate
that transcriptional regulation may involve, in part, competitive
interactions between transcriptional activators and TAFs on the TBP
surface.
Both an N-terminal 65-kDa domain and a C-terminal 30-kDa domain of SecA cycle into the membrane at SecYEG during translocation
Authors: Eichler Jerry , Wickner William
Published: July 2002

SecA, a 102-kDa hydrophilic protein, couples the energy of ATP binding to the translocation of preprotein across the bacterial inner membrane. SecA function and topology were studied with metabolically labeled [
35
S]SecA and with inner membrane vesicles from cells that overexpressed SecYEGDFyajC, the integral domain of preprotein translocase. During translocation in the presence of ATP and preprotein, a 65-kDa N-terminal domain of SecA is protected from proteolytic digestion through insertion into the membrane, as previously reported for a 30-kDa C-terminal domain [Economou, A. & Wickner, W. (1994)
Cell
78, 835–843]. Insertion of both domains occurs at saturable SecYEGDFyajC sites and is rapidly followed by deinsertion. SecA also associates nonsaturably and unproductively with lipid. In the presence of ATP, yet without involvement of preprotein or SecYEG, lipid-bound SecA forms domains that are protease-resistant and that remain so even upon subsequent membrane disruption. Unlike the [
35
S]SecA that inserts into the membrane at SecYEGDFyajC as it promotes preprotein translocation, lipid-associated [
35
S]SecA does not chase from its protease-resistant state upon the addition of excess SecA. The finding that two domains of SecA (which together represent most regions of the polypeptide chain) cycle into the membrane during preprotein translocation, as well as the distinction between the membrane association of SecA at translocation sites of SecYEGDFyajC and at nonproductive lipid sites, are fundamental to the study of the role of SecA in preprotein movement.