bluuebunny/crossref_metadata_2025 huggingface dataset:
E-157: A 1.4-m-long plasma wake field acceleration experiment using a 30 GeV electron beam from the Stanford Linear Accelerator Center Linac
Authors: Hogan M. J. , Assmann R. , Decker F.-J. , Iverson R. , Raimondi P. , Rokni S. , Siemann R. H. , Walz D. , Whittum D. , Blue B. , Clayton C. E. , Dodd E. , Hemker R. , Joshi C. , Marsh K. A. , Mori W. B. , Wang S. , Katsouleas T. , Lee S. , Muggli P. , Catravas P. , Chattopadhyay S. , Esarey E. , Leemans W. P.
Published: July 2002

In the E-157 experiment now being conducted at the Stanford Linear Accelerator Center, a 30 GeV electron beam of 2×1010 electrons in a 0.65-mm-long bunch is propagated through a 1.4-m-long lithium plasma of density up to 2×1014 e−/cm3. The initial beam density is greater than the plasma density, and the head of the bunch expels the plasma electrons leaving behind a uniform ion channel with transverse focusing fields of up to several thousand tesla per meter. The initial transverse beam size with σ=50–100 μm is larger than the matched size of 5 μm resulting in up to three beam envelope oscillations within the plasma. Time integrated optical transition radiation is used to study the transverse beam profile immediately before and after the plasma and to characterize the transverse beam dynamics as a function of plasma density. The head of the bunch deposits energy into plasma wakes, resulting in longitudinal accelerating fields which are witnessed by the tail of the same bunch. A time-resolved Cherenkov imaging system is located in an energy dispersive plane downstream of the plasma. It images the beam onto a streak camera allowing time-resolved measurements of the beam energy spectrum as a function of plasma density. Preliminary experimental data from the first three runs are compared to theory and computer simulations.
Time-resolved ellipsometry measurements of the optical properties of silicon during pulsed excimer laser irradiation
Authors: Jellison G. E. , Lowndes D. H.
Published: July 2002

A technique has been developed for continuously carrying out time-resolved ellipsometric measurements on the nanosecond timescale. Using this technique, the optical properties of silicon have been measured during and immediately after pulsed excimer (KrF, λ=248 nm) laser irradiation. From these data the optical functions of liquid silicon at λ=632.8 nm have been determined to be n=3.8 and k=5.2±0.1, in minor disagreement with the results of Shvarev, Baum, and Gel’d [High Temp. 15, 548 (1977)]. The surface temperature before and after melting was also continuously determined by comparing these results with elevated constant-temperature measurements of the optical functions. The results demonstrate that time-resolved ellipsometry is a powerful technique for examining changes in optical properties on the nanosecond timescale.
Generalized Brooks’ formula and the electron mobility in SixGe1−x alloys
Authors: Krishnamurthy Srinivasan , Sher A. , Chen An-Ban
Published: July 2002

A formula for alloy-scattering-limited electron mobility in semiconductors is obtained for indirect gap systems with multiple band minima. All the input parameters needed are defined explicitly. The drift mobility of SixGe1−x which has a dip at x ∼0.13 and a broader minimum at x ∼0.5 is calculated by adding alloy scattering to other scattering mechanisms and correlates well with the measured Hall mobility.
Growth of GaN single crystal films using electron cyclotron resonance plasma excited metalorganic vapor phase epitaxy
Authors: Zembutsu Sakae , Sasaki Toru
Published: July 2002

A low-temperature growth technique for GaN single crystal films has been developed utilizing electron cyclotron resonance (ECR) plasma excitation. The GaN film has been grown in a low pressure metalorganic vapor phase epitaxy (MOVPE) system using the reaction of trimethylgallium with highly activated nitrogen extracted from the ECR plasma chamber. Growth conditions of GaN single crystal films have been clarified by examining reflection high-energy electron diffraction patterns. The surface morphology of the GaN single crystal film is very smooth and electrical properties are comparable to those of a MOVPE technique at high growth temperatures.
Deep level transient spectroscopy of interfacial traps at ion-implanted ultrahigh p-Si Schottky barriers
Authors: Slowik John H. , Ashok S.
Published: July 2002

Sequential implantation of Ar and low-energy H produces a high (0.83 eV), near-ideal Schottky barrier for Al deposited on p-Si. Deep level transient spectroscopy (DLTS) measurements reveal majority-carrier interfacial traps due to the implantation steps. Without H, Ar implantation alone results in an interfacial trap doublet at 0.48 eV with high emission rates. Such samples display an elevated barrier relative to the implanted control samples, but with serious leakage current. When H implant is added, however, only a single interfacial trap, with a very low emission rate, is present at 0.47 eV. Thus DLTS suggests that H may idealize the barrier by substituting interfacial traps having reduced charge transport rate, so that there is less competition with thermionic emission.
Optimization of the discharge characteristics of a laser device employing a plasma electrode
Authors: Nakamura Kenshi , Yukawa Nobuo , Mochizuki Takehiro , Horiguchi Shiro , Nakaya Toshizo
Published: July 2002

Discharge characteristics have been investigated of a laser device in which the surface-discharge plasma from a dielectric surface is used as a preionizer and an electrode, the plasma electrode. It is demonstrated that a highly homogeneous discharge can be obtained by optimizing the delay time of the main volume discharge with respect to the surface discharge. The output energy from the device used as a N2 laser is also discussed.
Study of dynamic current distribution in logic circuits by Joule displacement microscopy
Authors: Martin Y. , Wickramasinghe H. K.
Published: July 2002

Joule displacement microscopy, where the periodic expansion caused by Joule heating in a thin-film track carrying ac current is mapped using a focused probe, has recently been described. In this letter, we demonstrate the application of this technique to the study of current distribution within a bipolar inverting gate.
InGaP/InP waveguides
Authors: Joyner C. H. , Dentai A. G. , Alferness R. C. , Buhl L. L. , Divino M. D. , Dautremont-Smith W. C.
Published: July 2002

We have made InGaP/InP waveguides on InP substrates by atmospheric pressure metalorganic vapor phase epitaxy. The introduction of Ga in the cladding layers causes a large relative index change (Δn=0 to >0.18) that can be varied with the Ga concentration (Δn=0.18 with Ga at 5×1019 cm−3), creating strong, low loss (∼1.25 dB/cm) waveguides. In addition some of these structures were doped with Fe, using ferrocene as the Fe doping source. Typical resistivities of 107 Ω cm have been achieved at Fe concentrations of 5×1017 cm−3, allowing electric fields in excess of 10 000 V/cm to be applied to the waveguides. InGaP/InP Fe-doped waveguides should prove extremely useful in fabricating switches, modulators, couplers, and filters for integrated optics devices.
Effect of crystal structure on superconductivity of Y-Ba-Cu-O system compounds
Authors: Jiang Xiaoping , Yu Huafeng , Zhang Ze , Zhu Naiping , Qi Hongbo , Shu Guoyue , Tian Yunchuan , Pang Dexing , Zeng Xiaobiao , Yang Zhongjin
Published: July 2002

This letter reports the effect of distortion of crystal structure on the superconductivity of Y-Ba-Cu-O compounds. The result shows that the cooling rate is responsible for the superconductivity in the range of LN2 temperature with the same composition and heat treatment temperature. The changes of intensity of three dominant x-ray diffraction peaks caused by structural distortion in the perovskite orthorhombic phase may become an important criterion of superconductivity.
Far infrared spectroscopy with subpicosecond electrical pulses on transmission lines
Authors: Sprik R. , Duling I. N. , Chi C.-C. , Grischkowsky D.
Published: July 2002

Optically generated and detected electrical pulses on transmission lines in the subpicosecond range have frequencies extending up to 1 THz, thereby covering the far infrared region of the spectrum from 0 to 30 cm−1. We have studied the propagation of these short pulses through a section of the transmission line covered with erbium iron garnet which shows distinct absorption lines in the far infrared at low temperatures (2–30 K). The absorption and dispersion of the garnet modify the shape of the pulse, and the absorption spectrum is obtained by Fourier transforming the propagated pulse shape.
Simultaneous oscillation at 0.91, 1.08, and 1.53 μm in a fusion-spliced fiber laser
Authors: Nakazawa Masataka , Kimura Yasuo
Published: July 2002

Multiple wavelength oscillation at 0.91, 1.08, 1.53, and 1.55 μm has been simultaneously obtained in a fusion-spliced silica-based fiber laser consisting of Er3+-doped and Nd3+-doped fibers. The laser mirrors, which are butted against the cleaved fiber ends, have high reflectivities at these wavelengths with a high transmission at a pumping wavelength of 514 nm. The output powers at 0.91, 1.08, and 1.53 μm are 2.0, 1.7, and 0.42 mW, respectively, for absorbed powers of 115 mW in a Nd3+-doped fiber and 185 mW in an Er3+-doped fiber.
Localization of degradation in InP/InGaAsP mushroom stripe lasers
Authors: Jung H. , Marschall P.
Published: July 2002

The rapid degradation observed in InP/InGaAsP mushroom stripe lasers covered with phosphosilicate glass (PSG) was investigated by comparing the light-current characteristics as a function of the preparation technique. We were able to show that the PSG-covering layer is not the reason for the rapid degradation. By inspecting the light-current characteristics before and after degradation and by additional underetching the laser structure after degradation we were able to localize the degraded regions on the open side walls of the InGaAsP active layer.
Temperature dependence of hydrogen vibrational modes in passivated boron-doped silicon
Authors: Stutzmann M. , Herrero C. P.
Published: July 2002

Vibrational spectra of hydrogen and deuterium in the passivated layer of bulk boron doped crystalline silicon are investigated by Raman scattering. The temperature dependence of line positions and widths is measured in the range 5–450 K and for H(D) concentrations between 1×1019 and 1×1020 cm−3. A strong correlation between shift and broadening of the Raman lines is observed for all samples.
High-temperature resistivity of the Ba2YCu3Ox superconductor
Authors: Grader G. Sageev , Gallagher P. K. , Gyorgy E. M.
Published: July 2002

The resistivity of Ba2YCu3Ox was measured in the 450–850 °C range at various oxygen partial pressures. The tetragonal to orthorhombic phase transition is observed as a change in the slope of the resistivity curve. The lack of a discontinuity in the curve is consistent with the phase transition being higher than first order. It was found that decreasing the oxygen content x below 6.2 changed the resistivity of the tetragonal phase from metallic character to semiconducting character. In the metallic region of the tetragonal phase the superconducting transition temperature is depressed below 60 K, while in the semiconducting region, no superconducting onset was observed down to 6 K. In the orthorhombic phase, the resistivity of the material is shown to be governed by the number of oxygens per unit cell, suggesting that the resistivity can serve as a quality control parameter in the production of superconducting devices.
Surface-to-surface segregation during growth of polycrystalline thin films
Authors: Hellman F.
Published: July 2002

A model is proposed for a novel surface-to-surface segregation process which would be observed during growth by vapor deposition of thin polycrystalline films of alloys exhibiting classic surface segregation. The model depends on sufficient surface mobility to allow equilibration between surfaces of different grains and insufficient bulk mobility to allow equilibration between the surface and bulk of each grain before the present surfaces are covered by the next layer of material. This high ratio of surface to bulk mobility is easily found under standard deposition conditions. The model leads to an inhomogeneous film in which the composition of each grain is dependent on its crystallographic orientation.
Electron beam epitaxy of AlxGa1−xP (a new type of solid phase epitaxy produced by a high-energy electron beam)
Authors: Wada Takao , Maeda Yoshinobu
Published: July 2002

Solid phase epitaxial layers of Al0.25Ga0.75P, Al0.5Ga0.5P, and Al0.75Ga0.25P were grown on (111), (100), and (110) GaP substrates, respectively, by using an electron beam epitaxy technique at 50 °C. The surfaces of Al layers deposited by vacuum evaporation on GaP wafers were irradiated with a fluence of (0.1–1.0)×1018 electrons cm−2 at 7 MeV. After the irradiation and removal of the Al layers, evidence of the creation of epilayers that had been formed before annealing was obtained from a secondary-ion mass spectrometer, an x-ray diffractometer, and a reflection high-energy electron diffractometer.
Nonlinear microwave susceptibility measurement of an artificial Kerr medium
Authors: Bobbs Bradley , Shih Robert , Fetterman Harold R. , Ho W. W.
Published: July 2002

A suspension of short graphite fibers was shown to provide an effective medium for nonlinear microwave interactions. Using a 18-GHz pump beam with up to 20 W continuous power, changes in the 94-GHz refractive index were measured by interferometry. The induced birefringence and anisotropic absorption indicate an alignment of the fibers with the electric field of the pump beam. The resulting nonlinear refractive index coefficient of n2=2.6×10−4 cm2/W is of sufficient magnitude to demonstrate microwave bistability.
Surface compositional and topographical changes resulting from excimer laser impacting on YBa2Cu3O7 single phase superconductors
Authors: Auciello O. , Krauss A. R. , Santiago-Aviles J. , Schreiner A. F. , Gruen D. M.
Published: July 2002

Superconducting pressed pellets of YBa2Cu3O7 (Tc=90 K), which were used as ablation targets for laser-induced vapor deposition of high Tc(85 K) superconducting thin films, have been analyzed by secondary electron microscopy, scanning Auger microscopy, energy dispersive x-ray analysis, and x-ray diffractometry. The elemental distribution of Y, Ba, and Cu appears reasonably uniform at depths corresponding to that probed by energy dispersive x-ray analysis (∼1 μm). However, scanning Auger microscopy analysis of the laser-impacted area shows a significant depletion of Cu and spatial redistribution of Y, Ba, Cu, and O on the target surface. X-ray diffractometry of the laser-impacted area shows the appearance of a new broad peak at a diffraction angle 2θ=29.7°, characteristic of BaY2O4 and a poorly defined peak at 2θ=29.3°, that can be attributed to BaCuO2. A possible influence of the laser-induced bulk superconductor compositional changes on the film composition is discussed in relation to recently reported experimental results on laser vapor deposition of high Tc films.
Laser irradiation effects on photoluminescence spectra of undoped GaAs grown by metalorganic vapor phase epitaxy
Authors: Kusano Jun-ichi , Segawa Yusaburo , Iwai Sohachi , Aoyagi Yoshinobu , Namba Susumu
Published: July 2002

Photoluminescence spectra of undoped GaAs grown by metalorganic vapor phase epitaxy with Ar+ laser irradiation were measured at 1.8 K. The enhancement of the incorporation of the carbon acceptor and the increase of the luminescence intensity were recognized as laser irradiation effects. These experimental results suggest that the surface reaction between the radicals involving the Ga atom and the photoinduced carrier at the substrate surface is enhanced by the laser irradiation.
Photon-controlled fabrication of amorphous superlattice structures using ArF (193 nm) excimer laser photolysis
Authors: Lowndes D. H. , Geohegan D. B. , Eres D. , Pennycook S. J. , Mashburn D. N. , Jellison G. E.
Published: July 2002

Pulsed ArF (193 nm) excimer laser photolysis of disilane, germane, and disilane-ammonia mixtures has been used to deposit amorphous superlattices containing silicon, germanium, and silicon nitride layers. Transmission electron microscope cross-section views demonstrate that structures having thin (5–25 nm) layers and sharp interlayer boundaries can be deposited at substrate temperatures below the pyrolytic threshold, entirely under laser photolytic control.
Laser photoionization mass spectroscopy with picosecond resolution
Authors: Danielzik B. , Harten P. , Seeger T. , von der Linde D.
Published: July 2002

We demonstrate a new technique for measuring the desorption products as a function of time during ultrafast laser-induced desorption. Measurements of the evaporation of Ga atoms and desorption of surface oxides from picosecond laser-heated GaAs are presented.
Efficient AlGaAs channeled-substrate-planar distributed feedback laser
Authors: Goldstein B. , Evans G. , Connolly J. , Dinkel N. , Kirk J.
Published: July 2002

A wavelength-locked, AlGaAs channeled-substrate-planar distributed feedback laser has been made that operates to 40 mW pulsed. The Bragg grating is situated at the shoulders of the layers of AlGaAs and GaAs. Overall power efficiencies of 15% have been measured at 40 mW of output power.
Direct test of a model of efficient second-harmonic generation in glass optical fibers
Authors: Mizrahi Victor , Österberg U. , Krautschik C. , Stegeman G. I. , Sipe J. E. , Morse T. F.
Published: July 2002

We report the first direct test of the only viable model of efficient second-harmonic generation in glass optical fibers put forth to date. We conclude that modifications of the model are necessary.
Enhancement of effective electron mobility in the channel of InP metal-insulator-semiconductor field-effect transistors
Authors: Iwase Y. , Arai F. , Sugano T.
Published: July 2002

Effective mobility of electrons in the channel of accumulation type InP metal-insulator-semiconductor field-effect transistors has been enhanced by means of reducing the iron concentration in the InP substrate and by lowering the deposition temperature of the gate insulator. The highest effective electron mobility, which has been obtained in this work, was about 4000 cm2/V s at room temperature. This was achieved by using InP wafers doped with Fe, whose concentration was 1.6×1016 cm−3, as the substrate and by depositing phosphorus nitride film as the gate insulator at 350  °C. The results are attributed to a less density of scattering centers, both in the InP substrates due to the smaller concentration of Fe and at the interface between the phosphorus nitride film and the InP substrate due to the smaller density of defects, induced during the deposition process at a lower temperature.
Liquid phase epitaxial growth of Fe-doped semi-insulating InGaAsP lattice matched to InP over the entire composition range
Authors: Kondo M. , Sugawara M. , Tanahashi T. , Isozumi S. , Nakajima K.
Published: July 2002

Fe-doped semi-insulating In1−x Gax Asy P1−y (0≤y≤1, y=2.2x) epitaxial layers lattice matched to InP with nearly intrinsic carrier concentrations have been successfully grown over the entire composition range by liquid phase epitaxy. Maximum resistivities as high as 8×107 Ω cm for InP, 2×105 Ω cm for InGaAsP (y=0.57), and 2×103 Ω cm for InGaAs (y=1) have been achieved. The critical growth temperature necessary to obtain semi-insulating layers significantly decreased as the composition was varied from y=0 to y=1. The Fe doping characteristics are well defined by the composition dependence of the Fe distribution coefficient.
Photoconductive Hg1−xCdxTe detectors grown by low-temperature metalorganic chemical vapor deposition
Authors: Bethea C. G. , Levine B. F. , Lu P.-Y. , Williams L. M. , Ross M. H.
Published: July 2002

We have fabricated high-sensitivity Hg1−xCdxTe detectors from low-temperature metalorganic vapor deposition samples. Responsivities of R=2000 V/W and detectivities of D*=2×1010 cm  Hz1/2/W have been achieved.
Metal contacts to p-type GaAs with large Schottky barrier heights
Authors: Waldrop J. R.
Published: July 2002

Metal Schottky barrier contacts to p-type (100) GaAs are described in which a large Schottky barrier height φB is attained by using a very thin Si or Ge interface layer to influence the interface Fermi energy EiF. The metals investigated are Au, Cr, Mn, Ni, and Al. Au, Cr, and Mn contacts have φB values from 0.7 to 0.9 eV when ∼15 Å Si and Ge interlayers are made heavily n type. Ni and Al contact φB values were limited to 0.6–0.7 eV. X-ray photoemission spectroscopy was used to obtain the EiF and interface composition during contact formation; the φB for the corresponding thick contacts was measured by current-voltage and capacitance-voltage methods.
Gain characteristics of a 1.5 μm nonlinear split contact laser amplifier
Authors: Marshall I. W. , O’Mahony M. J. , Cooper D. M. , Fiddyment P. J. , Regnault J. C. , Devlin W. J.
Published: July 2002

The gain characteristics of a 1.5 μm split contact nonlinear laser amplifier are reported. With an input power of −51 dBm or greater, a nonlinear transfer function was observed with a maximum gain of 26 dB. The maximum pulse repetition frequency for nonlinear gain was 700 MHz.
Weakly coupled grain model of high-frequency losses in high T
c superconducting thin films
Authors: Hylton T. L. , Kapitulnik A. , Beasley M. R. , Carini John P. , Drabeck L. , Grüner George
Published: July 2002

We propose a model of Josephson coupling between grains to explain the millimeter-wave surface impedance of oriented, polycrystalline thin films of high Tc superconductors. An effective junction IcR product and effective grain size are calculated based on recent measurements of the surface impedance. We suggest a criterion on film quality for the observation of losses intrinsic in the superconductor. The effects of crystalline orientation on surface impedance are considered.
1.3 μm InGaAsP buried crescent lasers with cobalt-doped semi-insulating current blocking layers grown by metalorganic chemical vapor deposition
Authors: Cheng W. H. , Pooladdej J. , Huang S. Y. , Buehring K. D. , Appelbaum A. , Wolf D. , Renner D. , Hess K. L. , Zehr S. W.
Published: July 2002

Cobalt-doped semi-insulating InP layers grown by low-pressure metalorganic chemical vapor deposition (LPMOCVD) have been used for the first time as a current blocking layer for 1.3 μm InGaAsP buried crescent lasers. Lasers with this cobalt-doped InP blocking layer have cw threshold currents as low as 8 mA at room temperature. This is the lowest cw threshold current yet reported for an InGaAsP laser with a semi-insulating current blocking layer. In addition, the lasers exhibit total differential quantum efficiency of 60%, high-temperature operation up to 100 °C, high output power of 30 mW/facet, and a 3-dB modulation bandwidth of 11.6 GHz. These results indicate that the cobalt-doped semi-insulating InP layer grown by LPMOCVD provides effective current blocking for high-performance lasers.
Femtosecond observation of benzyne intermediates in a molecular beam: Bergman rearrangement in the isolated molecule
Authors: Diau Eric W.-G. , Casanova Joseph , Roberts John D. , Zewail Ahmed H.
Published: July 2002

In this communication, we report our femtosecond real-time observation of the dynamics for the three didehydrobenzene molecules (p-,m-, ando-benzyne) generated from 1,4-, 1,3-, and 1,2-dibromobenzene, respectively, in a molecular beam, by using femtosecond time-resolved mass spectrometry. The time required for the first and the second C-Br bond breakage is less than 100 fs; the benzyne molecules are produced within 100 fs and then decay with a lifetime of 400 ps or more. Density functional theory and high-levelab initiocalculations are also reported herein to elucidate the energetics along the reaction path. We discuss the dynamics and possible reaction mechanisms for the disappearance of benzyne intermediates. Our effort focuses on the isolated molecule dynamics of the three isomers on the femtosecond time scale.
Knotting probability of DNA molecules confined in restricted volumes: DNA knotting in phage capsids
Authors: Arsuaga Javier , Vázquez Mariel , Trigueros Sonia , Sumners De Witt , Roca Joaquim
Published: July 2002

When linear double-stranded DNA is packed inside bacteriophage capsids, it becomes highly compacted. However, the phage is believed to be fully effective only if the DNA is not entangled. Nevertheless, when DNA is extracted from a tailless mutant of the P4 phage, DNA is found to be cyclic and knotted (probability of 0.95). The knot spectrum is very complex, and most of the knots have a large number of crossings. We quantified the frequency and crossing numbers of these knots and concluded that, for the P4 tailless mutant, at least half the knotted molecules are formed while the DNA is still inside the viral capsid rather than during extraction. To analyze the origin of the knots formed inside the capsid, we compared our experimental results to Monte Carlo simulations of random knotting of equilateral polygons in confined volumes. These simulations showed that confinement of closed chains to tightly restricted volumes results in high knotting probabilities and the formation of knots with large crossing numbers. We conclude that the formation of the knots inside the viral capsid is driven mainly by the effects of confinement.
A serologically identified tumor antigen encoded by a homeobox gene promotes growth of ovarian epithelial cells
Authors: Naora Honami , Yang YanQin , Montz Fredrick J. , Seidman Jeffrey D. , Kurman Robert J. , Roden Richard B. S.
Published: July 2002

Ovarian carcinomas are thought to arise from cells of the ovarian
surface epithelium by mechanisms that are poorly understood. Molecules
associated with neoplasia are potentially immunogenic, but few ovarian
tumor antigens have been identified. Because ovarian carcinomas can
elicit humoral responses in patients, we searched for novel tumor
antigens by immunoscreening a cDNA expression library with ovarian
cancer patient serum. Seven clones corresponding to the homeobox gene
HOXB7
were isolated. ELISAs using purified recombinant
HOXB7 protein revealed significant serologic reactivity to HOXB7 in 13
of 39 ovarian cancer patients and in only one of 29 healthy women
(
P
< 0.0001). Ovarian carcinomas were found to
express
HOXB7
at markedly higher levels than normal
ovarian surface epithelium, suggesting that immunogenicity of HOXB7 in
patients could be associated with its elevated expression in ovarian
carcinomas. Overexpression of
HOXB7
in immortalized
normal ovarian surface epithelial cells dramatically enhanced cellular
proliferation. Furthermore,
HOXB7
overexpression
increased intracellular accumulation and secretion of basic fibroblast
growth factor, a potent angiogenic and mitogenic factor. These results
reveal HOXB7 as a tumor antigen whose up-regulated expression could
play a significant role in promoting growth and development of ovarian
carcinomas.
Trans-spliced leader addition to mRNAs in a cnidarian
Authors: Stover Nicholas A. , Steele Robert E.
Published: July 2002

A search of databases with the sequence from the 5′ untranslated
region of a
Hydra
cDNA clone encoding a receptor
protein-tyrosine kinase revealed that a number of
Hydra
cDNAs contain one of two different sequences at their 5′ ends. This
finding suggested the possibility that mRNAs in
Hydra
receive leader sequences by trans
-
splicing. This
hypothesis was confirmed by the finding that the leader sequences are
transcribed as parts of small RNAs encoded by genes located in the 5S
rRNA clusters of
Hydra
. The two spliced leader (SL) RNAs
(SL-A and -B) contain splice donor dinucleotides at the predicted
positions, and genes that receive SLs contain splice acceptor
dinucleotides at the predicted positions. Both of the SL RNAs are bound
by antibody against trimethylguanosine, suggesting that they contain a
trimethylguanosine cap. The predicted secondary structures of the
Hydra
SL RNAs show significant differences from the
structures predicted for the SLs of other organisms. Messenger RNAs
have been identified that can receive either SL-A or -B, although the
impact of the two different SLs on the function of the mRNA is unknown.
The presence and features of SL addition in the phylum Cnidaria raise
interesting questions regarding the evolution of this process.
Conformational coupling in the chemotaxis response regulator CheY
Authors: Schuster Martin , Silversmith Ruth E. , Bourret Robert B.
Published: July 2002

CheY, a response regulator protein in bacterial chemotaxis, serves
as a prototype for the analysis of response regulator function in
two-component signal transduction. Phosphorylation of a conserved
aspartate at the active site mediates a conformational change at a
distal signaling surface that modulates interactions with the flagellar
motor component FliM, the sensor kinase CheA, and the phosphatase CheZ.
The objective of this study was to probe the conformational coupling
between the phosphorylation site and the signaling surface of CheY in
the reverse direction by quantifying phosphorylation activity in the
presence and absence of peptides of CheA, CheZ, and FliM that
specifically interact with CheY. Binding of these peptides dramatically
impacted autophosphorylation of CheY by small molecule phosphodonors,
which is indicative of reverse signal propagation in CheY.
Autodephosphorylation and substrate affinity, however, were not
significantly affected. Kinetic characterization of several CheY
mutants suggested that conserved residues Thr-87, Tyr-106, and Lys-109,
implicated in the activation mechanism, are not essential for
conformational coupling. These findings provide structural and
conceptual insights into the mechanism of CheY activation. Our results
are consistent with a multistate thermodynamic model of response
regulator activation.
Total synthesis of cytochrome b562 by native chemical ligation using a removable auxiliary
Authors: Low Donald W. , Hill Michael G. , Carrasco Michael R. , Kent Stephen B. H. , Botti Paolo
Published: July 2002

We have completed the total chemical synthesis of cytochrome b562
and an axial ligand analogue, [SeMet
7
]cyt b562, by
thioester-mediated chemical ligation of unprotected peptide segments. A
novel auxiliary-mediated native chemical ligation that enables peptide
ligation to be applied to protein sequences lacking cysteine was used.
A cleavable thiol-containing auxiliary group, 1-phenyl-2-mercaptoethyl,
was added to the α-amino group of one peptide segment to facilitate
amide bond-forming ligation. The amine-linked 1-phenyl-2-mercaptoethyl
auxiliary was stable to anhydrous hydrogen fluoride used to cleave and
deprotect peptides after solid-phase peptide synthesis. Following
native chemical ligation with a thioester-containing segment, the
auxiliary group was cleanly removed from the newly formed amide bond by
treatment with anhydrous hydrogen fluoride, yielding a full-length
unmodified polypeptide product. The resulting polypeptide was
reconstituted with heme and folded to form the functional protein
molecule. Synthetic wild-type cyt b562 exhibited spectroscopic and
electrochemical properties identical to the recombinant protein,
whereas the engineered [SeMet
7
]cyt b562 analogue protein
was spectroscopically and functionally distinct, with a reduction
potential shifted by ≈45 mV. The use of the 1-phenyl-2-mercaptoethyl
removable auxiliary reported here will greatly expand the applicability
of total protein synthesis by native chemical ligation of unprotected
peptide segments.
In vitro
characterization of DNA gyrase inhibition by microcin B17 analogs with altered bisheterocyclic sites
Authors: Zamble Deborah B. , Miller Deborah A. , Heddle Jonathan G. , Maxwell Anthony , Walsh Christopher T. , Hollfelder Florian
Published: July 2002

Microcin B17 (MccB17) is a 3.1-kDa
Escherichia coli
antibiotic that contains thiazole and oxazole heterocycles in a peptide backbone. MccB17 inhibits its cellular target, DNA gyrase, by trapping the enzyme in a complex that is covalently bound to double-strand cleaved DNA, in a manner similar to the well-known quinolone drugs. The identification of gyrase as the target of MccB17 provides an opportunity to analyze the relationship between the structure of this unusual antibiotic and its activity. In this report, steady-state parameters are used to describe the induction of the cleavable complex by MccB17 analogs containing modified bisheterocyclic sites. The relative potency of these analogs corresponds to the capacity of the compounds to prevent growth of sensitive cells. In contrast to previously reported experiments, inhibition of DNA gyrase supercoiling activity by wild-type MccB17 also was observed. These results suggest that DNA gyrase is the main intracellular target of MccB17. This study probes the structure-function relationship of a new class of gyrase inhibitors and demonstrates that these techniques could be used to analyze compounds in the search for clinically useful antibiotics that block DNA gyrase.
Genome sequence of the hyperthermophilic crenarchaeon
Pyrobaculum aerophilum
Authors: Fitz-Gibbon Sorel T. , Ladner Heidi , Kim Ung-Jin , Stetter Karl O. , Simon Melvin I. , Miller Jeffrey H.
Published: July 2002

We determined and annotated the complete 2.2-megabase genome sequence of
Pyrobaculum aerophilum
, a facultatively aerobic nitrate-reducing hyperthermophilic (
T
opt
= 100°C) crenarchaeon. Clues were found suggesting explanations of the organism's surprising intolerance to sulfur, which may aid in the development of methods for genetic studies of the organism. Many interesting features worthy of further genetic studies were revealed. Whole genome computational analysis confirmed experiments showing that
P. aerophilum
(and perhaps all crenarchaea) lack 5′ untranslated regions in their mRNAs and thus appear not to use a ribosome-binding site (Shine–Dalgarno)-based mechanism for translation initiation at the 5′ end of transcripts. Inspection of the lengths and distribution of mononucleotide repeat-tracts revealed some interesting features. For instance, it was seen that mononucleotide repeat-tracts of Gs (or Cs) are highly unstable, a pattern expected for an organism deficient in mismatch repair. This result, together with an independent study on mutation rates, suggests a “mutator” phenotype.
Platelet-derived growth factor activates protein kinase C epsilon through redundant and independent signaling pathways involving phospholipase C gamma or phosphatidylinositol 3-kinase.
Authors: Moriya S , Kazlauskas A , Akimoto K , Hirai S , Mizuno K , Takenawa T , Fukui Y , Watanabe Y , Ozaki S , Ohno S
Published: July 2002

Protein kinase C (PKC), a major cellular receptor for tumor-promoting phorbol esters and diacylglycerols (DGs), appears to be involved in a variety of cellular functions, although its activation mechanism in vivo is not yet fully understood. To evaluate the signaling pathways involved in the activation of PKC epsilon upon stimulation by platelet-derived growth factor (PDGF) receptor (PDGFR), we used a series of PDGFR "add-back" mutants. Activation of a PDGFR mutant (Y40/51) that binds and activates phosphatidylinositol 3-kinase (PI 3-kinase) caused translocation of PKC epsilon from the cytosol to the membrane in response to PDGF. A PDGFR mutant (Y1021) that binds and activates phospholipase C gamma (PLC gamma), but not PI 3-kinase, also caused the PDGF-dependent translocation of PKC epsilon. The translocation of PKC epsilon upon stimulation of PDGFR (Y40/51) was inhibited by wortmannin, an inhibitor of PI 3-kinase. Activation of PKC epsilon was further confirmed in terms of PKC epsilon-dependent expression of a phorbol 12-tetradecanoate 13-acetate response element (TRE)-luciferase reporter. Further, purified PKC epsilon was activated in vitro by either DG or synthetic phosphatidylinositol 3,4,5-trisphosphate. These results clearly demonstrate that PKC epsilon is activated through redundant and independent signaling pathways which most likely involve PLC gamma or PI 3-kinase in vivo and that PKC epsilon is one of the downstream mediators of PI 3-kinase whose downstream targets remain to be identified.
Expression cloning and functional characterization of the kidney cortex high-affinity proton-coupled peptide transporter.
Authors: Boll M , Herget M , Wagener M , Weber W M , Markovich D , Biber J , Clauss W , Murer H , Daniel H
Published: July 2002

The presence of a proton-coupled electrogenic high-affinity peptide transporter in the apical membrane of tubular cells has been demonstrated by microperfusion studies and by use of brush border membrane vesicles. The transporter mediates tubular uptake of filtered di- and tripeptides and aminocephalosporin antibiotics. We have used expression cloning in Xenopus laevis oocytes for identification and characterization of the renal high-affinity peptide transporter. Injection of poly(A)+ RNA isolated from rabbit kidney cortex into oocytes resulted in expression of a pH-dependent transport activity for the aminocephalosporin antibiotic cefadroxil. After size fractionation of poly(A)+ RNA the transport activity was identified in the 3.0- to 5.0-kb fractions, which were used for construction of a cDNA library. The library was screened for expression of cefadroxil transport after injection of complementary RNA synthesized in vitro from different pools of clones. A single clone (rPepT2) was isolated that stimulated cefadroxil uptake into oocytes approximately 70-fold at a pH of 6.0. Kinetic analysis of cefadroxil uptake expressed by the transporter's complementary RNA showed a single saturable high-affinity transport system shared by dipeptides, tripeptides, and selected amino-beta-lactam antibiotics. Electrophysiological studies established that the transport activity is electrogenic and affected by membrane potential. Sequencing of the cDNA predicts a protein of 729 amino acids with 12 membrane-spanning domains. Although there is a significant amino acid sequence identity (47%) to the recently cloned peptide transporters from rabbit and human small intestine, the renal transporter shows distinct structural and functional differences.
Effect of deletion of 5'HS3 or 5'HS2 of the human beta-globin locus control region on the developmental regulation of globin gene expression in beta-globin locus yeast artificial chromosome transgenic mice.
Authors: Peterson K R , Clegg C H , Navas P A , Norton E J , Kimbrough T G , Stamatoyannopoulos G
Published: July 2002

To analyze the function of the 5' DNase I hypersensitive sites (HSs) of the locus control region (LCR) on beta-like globin gene expression, a 2.3-kb deletion of 5'HS3 or a 1.9-kb deletion of 5'HS2 was recombined into a beta-globin locus yeast artificial chromosome, and transgenic mice were produced. Deletion of 5'HS3 resulted in a significant decrease of epsilon-globin gene expression and an increase of gamma-globin gene expression in embryonic cells. Deletion of 5'HS2 resulted in only a small decrease in expression of epsilon-, gamma-, and beta-globin mRNA at all stages of development. Neither deletion affected the temporal pattern of globin gene switching. These results suggest that the LCR contains functionally redundant elements and that LCR complex formation does not require the presence of all DNase I hypersensitive sites. The phenotype of the 5'HS3 deletion suggests that individual HSs may influence the interaction of the LCR with specific globin gene promoters during the course of ontogeny.
Toxoplasma invasion: the parasitophorous vacuole is formed from host cell plasma membrane and pinches off via a fission pore.
Authors: Suss-Toby E , Zimmerberg J , Ward G E
Published: July 2002

Most intracellular pathogens avoid lysing their host cells during invasion by wrapping themselves in a vacuolar membrane. This parasitophorous vacuole membrane (PVM) is often retained, serving as a critical transport interface between the parasite and the host cell cytoplasm. To test whether the PVM formed by the parasite Toxoplasma gondii is derived from host cell membrane or from lipids secreted by the parasite, we used time-resolved capacitance measurements and video microscopy to assay host cell surface area during invasion. We observed no significant change in host cell surface area during PVM formation, demonstrating that the PVM consists primarily of invaginated host cell membrane. Pinching off of the PVM from the host cell membrane occurred after an unexpected delay (34-305 sec) and was seen as a 0.219 +/- 0.006 pF drop in capacitance, which corresponds well to the predicted surface area of the entire PVM (30-33 microns2). The formation and closure of a fission pore connecting the extracellular medium and the vacuolar space was detected as the PVM pinched off. This final stage of parasite entry was accomplished without any breach in cell membrane integrity.
Residue 225 determines the Na(+)-induced allosteric regulation of catalytic activity in serine proteases.
Authors: Dang Q D , Di Cera E
Published: July 2002

Residue 225 in serine proteases is typically Pro or Tyr and specifies an important and unanticipated functional aspect of this class of enzymes. Proteases with Y225, like thrombin, are involved in highly specialized functions like blood coagulation and complement that are exclusively found in vertebrates. In these proteases, the catalytic activity is enhanced allosterically by Na+ binding. Proteases with P225, like trypsin, are typically involved in digestive functions and are also found in organisms as primitive as eubacteria. These proteases have no requirement for Na+ or other monovalent cations. The molecular origin of this physiologically important difference is remarkably simple and is revealed by a comparison of the Na+ binding loop of thrombin with the homologous region of trypsin. The carbonyl O atom of residue 224 makes a key contribution to the coordination shell of the bound Na+ in thrombin, but is oriented in a manner incompatible with Na+ binding in trypsin because of constraints imposed by P225 on the protein backbone. Pro at position 225 is therefore incompatible with Na+ binding and is a direct predictor of the lack of allosteric regulation in serine proteases. To directly test this hypothesis, we have engineered the thrombin mutant Y225P. This mutant has lost the ability to bind Na+ and behaves like the allosteric slow (Na(+)-free) form. The Na(+)-induced allosteric regulation also bears on the molecular evolution of serine proteases. A strong correlation exists between residue 225 and the codon used for the active site S195. Proteases with P225 typically use a TCN codon for S195, whereas proteases with Y225 use an AGY codon. It is proposed that serine proteases evolved from two main lineages: (i) TCN/P225 with a trypsin-like ancestor and (ii) AGY/Y225 with a thrombin-like ancestor. We predict that the Na(+)-induced allosteric regulation of catalytic activity can be introduced in the TCN/P225 lineage using the P225Y replacement.
Structure and function in rhodopsin: expression of functional mammalian opsin in Saccharomyces cerevisiae.
Authors: Mollaaghababa R , Davidson F F , Kaiser C , Khorana H G
Published: July 2002

The yeast Saccharomyces cerevisiae has been investigated for expression of mammalian opsin as an alternative to the currently used expression in COS-1 mammalian cells. The synthetic opsin gene was placed under the control of the inducible promoter GAL1 in the multicopy yeast/ Escherichia coli shuttle vector YEpRF1. Transformation of a GAL+ S. cerevisiae strain with the vector and growth of galactose-induced cultures to saturation showed the production of 2.0 +/- 0.5 mg of opsin from about 10(10) cells by ELISA. The addition of 11-cis-retinal to either cell spheroplasts or lysed cells showed that a fraction (2-4%) of the total expressed opsin reconstituted to rhodopsin. This fraction was purified to homogeneity and was shown to be fully functional and indistinguishable from bovine rhodopsin by the following criteria: (i) UV-visible absorption spectra, (ii) the formation of metarhodopsin II and its rate of decay, and (iii) initial rate of transducin activation as measured by the formation of a complex between transducin (alpha subunit) and guanosine 5'-[gamma-[35S]thio]triphosphate. The purified fraction was homogeneously glycosylated. However, glycosylation was distinct from that of bovine rhodopsin as judged by mobility on SDS/PAGE and endoglycosidase H sensitivity.
Regulation of striatal D1A dopamine receptor gene transcription by Brn-4.
Authors: Okazawa H , Imafuku I , Minowa M T , Kanazawa I , Hamada H , Mouradian M M
Published: July 2002

Brn-4 is a member of the POU transcription factor family and is expressed in the central nervous system. In this study, we addressed whether Brn-4 regulates expression of the D1A dopamine receptor gene. We found a functional Brn-4 responsive element in the intron of this gene by means of cotransfection chloramphenical acetyltransferase assays. This region contains two consensus sequences for binding of POU factors. Gel mobility-shift assays using glutathione S-transferase-Brn-4 fusion protein indicated that Brn-4 binds to these sequences. Both these sites are essential for transactivation by Brn-4 because deletion of either significantly reduced this enhancer activity. In situ hybridization revealed colocalization of Brn-4 and D1A mRNAs at the level of a single neuron in the rat striatum where this dopamine receptor is most abundantly expressed. Gel mobility-supershift assay using rat striatal nuclear extract and Brn-4 antibody confirmed the presence of Brn-4 in this brain region and its ability to bind to its consensus sequences in the D1A gene. These data suggest a functional role for Brn-4 in the expression of the D1A dopamine receptor gene both in vitro and in vivo.
Viral RNA trafficking is inhibited in replicase-mediated resistant transgenic tobacco plants.
Authors: Nguyen L , Lucas W J , Ding B , Zaitlin M
Published: July 2002

Transgenic tobacco (Nicotiana tabacum cv. Turkish Samsun NN) plants expressing a truncated replicase gene sequence from RNA-2 of strain Fny of cucumber mosaic virus (CMV) are resistant to systemic CMV disease. This is due to suppression of virus replication and cell-to-cell movement in the inoculated leaves of these plants. In this study, microinjection protocols were used to directly examine cell-to-cell trafficking of CMV viral RNA in these resistant plants. CMV RNA fluorescently labeled with the nucleotide-specific TOTO-1 iodide dye, when coinjected with unlabeled CMV 3a movement protein (MP), moved rapidly into the surrounding mesophyll cells in mature tobacco leaves of vector control and untransformed plants. Such trafficking required the presence of functional CMV 3a MP. In contrast, coinjection of CMV 3a MP and CMV TOTO-RNA failed to move in transgenic resistant plants expressing the CMV truncated replicase gene. Furthermore, coinjection of 9.4-kDa fluorescein-conjugated dextran (F-dextran) along with unlabeled CMV 3a MP resulted in cell-to-cell movement of the F-dextran in control plants, but not in the transgenic plants. Similar results were obtained with viral RNA when the 30-kDa MP of tobacco mosaic virus (TMV) was coinjected with TMV TOTO-RNA into replicase-resistant transgenic tobacco expressing the 54-kDa gene sequence of TMV. However, in these transgenic plants, the TMV-MP was still capable of mediating cell-to-cell movement of itself and the 9.4-kDa F-dextran. These results indicate that an inhibition of cell-to-cell viral RNA trafficking is correlated with replicase-mediated resistance. This raises the possibility that the RNA-2 product is potentially involved in the regulation of cell-to-cell movement of viral infectious material during CMV replication.