bluuebunny/crossref_metadata_2025 huggingface dataset:
Experimental characterization of a puff-gas z-pinch plasma prior to implosion
Authors: Smith Richard S. , Doggett Wesley O.
Published: July 2002

An argon annular puff-gas z-pinch has been experimentally investigated during the early phase of the current pulse using a magnetic flux probe and streak interferometry. The current is seen to follow the flared outer edge of the gas jet and to be returned primarily at axial positions z<15 mm by six posts supporting the wire mesh anode. A theoretical estimate of the skin depth agrees with the measured ∼1-cm thickness of the current sheath. The electron to neutral density ratio is determined to be peaked both near the posts and near the cathode.
Nuclear quadrupole resonance detected at 30 MHz with a dc superconducting quantum interference device
Authors: Hilbert Claude , Clarke John , Sleator Tycho , Hahn Erwin L.
Published: July 2002

A dc superconducting quantum interference device is used as a tuned radio frequency amplifier at liquid helium temperatures to detect pulsed nuclear quadrupole resonance at ∼30 MHz. At a bath temperature of 4.2 K, a total system noise temperature of 6±1 K has been achieved, with a quality factor Q of 2500. A novel Q spoiler, consisting of a series array of Josephson tunnel junctions, reduces the ring-down time of the tuned circuit after each pulse. The minimum number of Bohr magnetons observable from a free precession signal after a single pulse is ∼2×1016 in a bandwidth of 10 kHz.
Laser enhanced metalorganic chemical vapor deposition crystal growth in GaAs
Authors: Aoyagi Yoshinobu , Masuda Satoshi , Namba Susumu , Doi Atsutoshi
Published: July 2002

An enhanced crystal growth of GaAs is observed in metalorganic chemical vapor deposition (MOCVD) under laser illumination. It is difficult to understand this enhancement effect only by a pyrolitic effect and we should consider photochemical processes like photoassisted catalytic or surface effect. This laser enhancement makes patterned crystal growth in MOCVD possible.
Response of piezoelectric lead metaniobate to high compressive stresses
Authors: Amin A. , Lukasiewicz S. J.
Published: July 2002

The induced polarization, P3(C/m2), in piezoelectric lead metaniobate was examined as a function of monotonically increasing uniaxial stress parallel to the poling direction. Comparison to the induced polarization as extrapolated from small oscillating force measurements illustrates, as expected, a nonlinear response at high compressive stress levels. The stress level beyond which nonlinearities occur was determined
Reactive ion beam etching of InP with N2 and N2/O2 mixtures
Authors: Katzschner W. , Niggebrügge U. , Löffler R. , Schröter-Janssen H.
Published: July 2002

A reactive ion beam etching process (RIBE) of InP with N2 and N2/O2 mixtures is described. The application of N2 or N2/O2 ion beams to InP results in high quality surfaces with the virtual elimination of cone formation. The influence of the process parameters ion incidence angle, ion energy, ion beam current density, and N2/O2 ratio on etching rates is given for InP, Ni, Ti, Al, Si, and two types of photoresist (AZ4210, MP15). N2 RIBE has been used for the fabrication of grating structures with λ=2400 Å periodicity. The gratings have been overgrown by liquid phase epitaxy without any degradation of the initial shape of the structure.
High efficiency multikilojoule HF chemical lasers using an electron beam initiated low-pressure mixture of H2/F2/NF3 or H2/F2/SF6
Authors: Kannari Fumihiko , Inagaki Hirohito , Obara Minoru
Published: July 2002

High electrical and high chemical efficiencies were simultaneously achieved for the multikilojoule HF chemical laser using a Lambda-type (inclined type) electron beam initiation scheme. The optimum addition of NF3 or SF6 fluorine donor could increase both efficiencies and could reduce the total pressure of the laser gas mixture. The laser output obtained from the low-pressure mixture of H2/F2/O2/NF3=30/208/62.5/70 (Torr) was 4.5 kJ in a 50-ns FWHM pulse width with an electrical laser efficiency of 226% and a chemical efficiency of 18.5%.
Hydrogen radical assisted chemical vapor deposition of ZnSe
Authors: Oda S. , Kawase R. , Sato T. , Shimizu I. , Kokado H.
Published: July 2002

Hydrogen radicals are employed in the growth of ZnSe. They react with starting gases to form long-lifetime precursors for deposition. The major advantages of hydrogen radical assisted chemical vapor deposition over the existing methods include (1) low-temperature growth, (2) plasma-free substrate, (3) selective precursor formation, (4) substrate cleaning effect, (5) rearrangement of atoms on the growing surface, and (6) passivation of grain boundaries or dangling bonds. Highly (111) axis oriented ZnSe films have been prepared on glass substrates at 200 °C. The temperature dependence of the electrical conductivity in the dark and the photoconductive response suggest low density of traps. Epitaxial ZnSe films on GaAs substrates have been obtained at 200 °C.
Overtone pumped superfluorescent HCl laser frequency converter
Authors: Shimoji Y. , Djeu N.
Published: July 2002

Superfluorescent emission from a hollow waveguide filled with HCl has been obtained on the v=2→v=1 band when optically pumped on the v=0→v=2 band. Energy conversion efficiency in excess of 10% has been measured. The beam quality of the emission was three times better than that of the pump radiation under optimal conditions.
Laser beam modulator and pulse former with an adjustable transmission-voltage characteristic provided by persistent spectral hole burning
Authors: Schätz P. , Bogner U. , Maier Max
Published: July 2002

The transmission of a polymer film doped with dye molecules is modulated by voltage-induced changes of the population in the center of a persistent spectral hole. It is demonstrated that the transmission versus voltage characteristic of the sample is adjustable to the requirements of the desired application by applying a selected time-dependent voltage during spectral hole burning. Various characteristic curves have been tailor made and used for modulation and pulse forming of laser beams.
X-ray photoemission core level determination of the GaSb/AlSb heterojunction valence-band discontinuity
Authors: Gualtieri G. J. , Schwartz G. P. , Nuzzo R. G. , Sunder W. A.
Published: July 2002

The valence-band discontinuity ΔEv has been determined for the (100) GaSb/AlSb strained-layer heterojunction with a room-temperature lattice mismatch of 0.65%, using x-ray photoemission core level spectroscopy. For 30 Å epitaxial layers of AlSb grown on GaSb, the measured valence-band offset was ΔEv=0.40±0.15 eV. The reverse growth sequence consisting of a thin GaSb layer grown on an AlSb buffer exhibited the same valence-band offset, indicating that for the (100) oriented heterojunction ΔEv is not strongly affected by the growth sequence.
Mesotaxy: Single-crystal growth of buried CoSi2 layers
Authors: White Alice E. , Short K. T. , Dynes R. C. , Garno J. P. , Gibson J. M.
Published: July 2002

Buried single-crystal CoSi2 layers in silicon have been formed by high dose implantation of cobalt followed by annealing. These layers grow in both the (100) and (111) orientations—those in (111) have better crystallinity, but those in (100) are of higher electrical quality. Electrical transport measurements on the layers give values for the resistance ratios and superconducting critical temperatures that are better than the best films grown by conventional techniques and comparable to bulk CoSi2.
Electro-optic sampling measurements of high-speed InP integrated circuits
Authors: Wiesenfeld J. M. , Tucker R. S. , Antreasyan A. , Burrus C. A. , Taylor A. J. , Mattera V. D. , Garbinski P. A.
Published: July 2002

Multigigahertz waveforms in an InGaAs/InP metal-insulator-semiconductor field-effect transistor inverter circuit have been measured noninvasively using the electro-optic sampling technique with pulses from a gain-switched InGaAsP laser. Propagation delays as low as 15 ps in a single inverter stage have been measured.
Epitaxial alignment of arsenic implanted polycrystalline silicon films on 〈100〉 silicon obtained by rapid thermal annealing
Authors: Hoyt J. L. , Crabbé E. , Gibbons J. F. , Pease R. F. W.
Published: July 2002

We have performed a quantitative analysis of epitaxial quality and arsenic diffusion in ion implanted polycrystalline silicon (polysilicon) layers on 〈100〉 Si, and find a clear advantage for the use of high-temperature rapid thermal annealing (RTA) in the 10-s regime to induce intentional, complete epitaxial alignment. The RTA-induced alignment kinetics and associated arsenic diffusion were studied in the 1050–1150 °C temperature range for arsenic doping concentrations between 1×1020 and 1×1021 cm−3, and were characterized by Rutherford backscattering, ion channeling, and cross-sectional transmission electron microscopy. The information about the relationship between arsenic diffusion, arsenic concentration, and epitaxial quality resulting from a given RTA cycle will be useful for optimizing bipolar transistors with realigned polysilicon emitter contacts.
Band discontinuities in GaAs/AlxGa1−xAs heterojunction photodiodes
Authors: Haase M. A. , Emanuel M. A. , Smith S. C. , Coleman J. J. , Stillman G. E.
Published: July 2002

We have developed a technique for determining band discontinuities in GaAs/AlxGa1−xAs heterostructures by measuring the spectral response of specially designed p+N− heterojunction photodiodes. The spectral response exhibits internal photoemission with well defined threshold energies from which band offsets are easily deduced. This technique is applicable for GaAs/AlxGa1−xAs heterojunctions for which x≳0.5.
Metalorganic vapor phase epitaxial growth for buried heterostructure GaAlAs lasers with semi-insulating blocking layers
Authors: Okayasu Masanobu , Kozen Atsuo , Hasumi Yuji , Temmyo Jiro , Uehara Shingo
Published: July 2002

A two-step metalorganic vapor phase epitaxial growth technique for fully planar GaAs/GaAlAs single quantum well buried heterostructure lasers with oxygen-doped semi-insulating blocking layers is described. GaAlAs blocking layer with resistivity above 106 Ω cm is reproducibly obtained by introducing oxygen at a concentration above 0.03 ppm during the growth. The selective growth mode of GaAlAs layers in etched grooves is studied to realize fully planar buried structures. Lasing characteristics with threshold current of 19 mA, external differential quantum efficiency of 50%, and maximum light output power of 100 mW/facet are confirmed.
Experimental determination of hot-carrier scattering processes in AlxGa1−xAs
Authors: Wise F. W. , Walmsley I. A. , Tang C. L.
Published: July 2002

The initial relaxation of hot electrons in Al0.35Ga0.65As has been measured using optical transmission-correlation spectroscopy. In order to determine the contributions of distinct scattering processes, the kinetic energy of the photoexcited carriers was varied by temperature tuning the band gap of the material. We obtain the rates of intervalley scattering, carrier-carrier scattering, and polar phonon emission from the measured decays. When scattering to the satellite (L and X) valleys is energetically possible, this process dominates the relaxation.
Formation and nondestructive characterization of ion implanted silicon-on-insulator layers
Authors: Narayan J. , Kim S. Y. , Vedam K. , Manukonda R.
Published: July 2002

High-temperature oxygen ion implantation has been used to form buried oxide layers in silicon single crystals. The ion implantation and substrate variables, particularly the substrate temperature, were optimized to obtain silicon layers with controlled microstructures near the surface. The as-implanted specimens were subsequently annealed at high temperatures to form a buried SiO2 layer with sharp interfaces and to minimize dislocation densities in the top silicon layers. The specimens were characterized by cross-section transmission electron microscopy and these results were compared with those obtained using spectroscopic ellipsometry. We discuss the application of the nondestructive scanning ellipsometry technique in the characterization of silicon-on-insulator materials.
Time-resolved direct observation of Auger recombination in semiconductor-doped glasses
Authors: Roussignol P. , Kull M. , Ricard D. , de Rougemont F. , Frey R. , Flytzanis C.
Published: July 2002

Using time-resolved techniques, absorption recovery, and degenerate four-wave mixing, we directly observe the nonexponential intensity-dependent recombination of free carriers photoexcited in semiconductor-doped glasses. We assign this behavior to Auger recombination.
Identification of residual donors in high-purity epitaxial GaAs by magnetophotoluminescence
Authors: Bose S. S. , Lee B. , Kim M. H. , Stillman G. E.
Published: July 2002

The magnetophotoluminescence peaks in the ‘‘two-electron’’ satellites of the donor bound exciton transitions corresponding to the shallow donors S, Si, Ge, Sn, and Te have been identified by correlation of photoluminescence measurements with photothermal ionization measurements on the same high-purity epitaxial GaAs samples. The magnetophotoluminescence measurements were made at 1.7 K and a magnetic field of 9.0 T. These results permit the use of magnetophotoluminescence measurements for the identification of residual donor impurity species in high-purity GaAs.
Low-temperature epitaxial growth of silicon by low-pressure chemical vapor deposition
Authors: Meakin D. , Stobbs M. , Stoemenos J. , Economou N. A.
Published: July 2002

Low-pressure chemical deposition of silicon by the pyrolysis of pure silane at relatively low temperatures and pressures below 100 mTorr can lead to structurally well-defined films. Below 10 mTorr the films exhibit evidence of local epitaxial growth, which can be particularly well defined on Si(100) wafers chemically treated prior to deposition outside the deposition chamber. Even so, the interface was found to be highly strained, and high-resolution electron microscopy observations were used to analyze the defect structures in the epitaxial layer as initiated at the interface.
Surface structure change during solid phase epitaxial growth of an amorphous Si film deposited on Si (111)
Authors: Shigeta Y.
Published: July 2002

Some surface structure change of an amorphous Si film deposited on Si (111) during the solid phase epitaxy was observed by low-energy electron diffraction (LEED). The LEED intensity profile shows the formation of 7×7 structure whenever a crystallized surface is constructed. The intensity increases with an increase of the annealing temperature Ta, where the increasing rate with Ta becomes small for 590<Ta<700 °C, and for 780<Ta<850 °C. It is discussed that there exists some process inhibiting the growth of the 7×7 structure regions in these two temperature ranges.
Organometallic vapor phase epitaxial growth of a new semiconductor alloy: GaP1−xSbx
Authors: Jou M. J. , Cherng Y. T. , Jen H. R. , Stringfellow G. B.
Published: July 2002

The III/V semiconductor alloy GaP1−xSbx has been grown for the first time. This alloy, which has a large miscibility gap at the growth temperatures of 530–600 °C, has been grown by organometallic vapor phase epitaxy at atmospheric pressure. In spite of the miscibility gap, which is calculated to extend from x=0.01 to 0.99 at 530 °C, layers with excellent surface morphologies could be grown throughout the entire composition range. The 10 K energy band gap has been determined as a function of composition by using photoluminescence, x-ray diffraction, and electron microprobe analysis, yielding bowing parameters of 3.8 and 2.7 eV for the Γ and X conduction band minima, respectively.
High-frequency characterization of thin-film Y-Ba-Cu oxide superconducting transmission lines
Authors: Dykaar Douglas R. , Sobolewski Roman , Chwalek James M. , Whitaker John F. , Hsiang Thomas Y. , Mourou Gerard A. , Lathrop Daniel K. , Russek Stephen E. , Buhrman Robert A.
Published: July 2002

We report the first measurements of picosecond pulse propagation on transmission lines patterned from YBa2Cu3O7−x films. Distortion-free propagation of high current density transients is demonstrated. The high-frequency properties were analyzed by careful study of the relative phase delays of the electrical transients as the temperature of the sample was varied from 1.8 K to Tc. Simulations using Mattis–Bardeen complex conductivities showed good agreement with the measured results. High-frequency critical current densities in excess of 105 A/cm2 were measured.
Hydrogen plasma induced defects in silicon
Authors: Jeng S. J. , Oehrlein G. S. , Scilla G. J.
Published: July 2002

The nature of extended defects in silicon introduced by hydrogen containing plasmas has been studied by transmission electron microscopy for a variety of technological processes. Depending on the doping level of the substrate, the substrate temperature and the presence/absence of simultaneous energetic ion bombardment, {111} planar defects, gas bubbles, and a heavily damaged near-surface region have been observed.
Effects of peroxisome proliferator-activated receptor δ on placentation, adiposity, and colorectal cancer
Authors: Barak Yaacov , Liao Debbie , He Weimin , Ong Estelita S. , Nelson Michael C. , Olefsky Jerrold M. , Boland Richard , Evans Ronald M.
Published: July 2002

Targeting of the nuclear prostaglandin receptor peroxisome
proliferator-activated receptor δ (PPAR
δ
) by
homologous recombination results in placental defects and frequent
(>90%) midgestation lethality. Surviving
PPARδ
−/−
mice exhibit a striking
reduction in adiposity relative to wild-type levels. This effect is not
reproduced in mice harboring an adipose tissue-specific deletion of
PPAR
δ
, and thus likely reflects peripheral PPARδ
functions in systemic lipid metabolism. Finally, we observe that
PPAR
δ
is dispensable for polyp formation in the
intestine and colon of
APC
min
mice,
inconsistent with its recently proposed role in the establishment of
colorectal tumors. Together, these observations reveal specific roles
for PPAR
δ
in embryo development and adipocyte
physiology, but not cancer.
Brain activity in ventromedial prefrontal cortex correlates with individual differences in negative affect
Authors: Zald David H. , Mattson Dorothy L. , Pardo José V.
Published: July 2002

Individuals differ in the extent to which they experience negative mood states over time. To explore the relationship between individual differences in negative affect (NA) and brain activity, we asked healthy subjects participating in positron-emission tomography scans to rate the extent to which they had experienced NA terms during the month before scanning. In two independent samples of subjects, resting regional cerebral blood flow within the ventromedial prefrontal cortex (VMPFC) correlated with ratings of NA. The finding converges with recent evidence implicating the VMPFC in emotional and autonomic processing. Moreover, it demonstrates that variability in basal VMPFC activity across subjects is related to individual differences in subjective emotional experience.
Selective ablation of retinoid X receptor α in hepatocytes impairs their lifespan and regenerative capacity
Authors: Imai Takeshi , Jiang Ming , Kastner Philippe , Chambon Pierre , Metzger Daniel
Published: July 2002

Retinoid X receptors (RXRs) are involved in a number of signaling pathways as heterodimeric partners of numerous nuclear receptors. Hepatocytes express high levels of the RXRα isotype, as well as several of its putative heterodimeric partners. Germ-line disruption (knockout) of RXRα has been shown to be lethalin utero, thus precluding analysis of its function at later life stages. Hepatocyte-specific disruption of RXRα during liver organogenesis has recently revealed that the presence of hepatocytes is not mandatory for the mouse, at least under normal mouse facility conditions, even though a number of metabolic events are impaired [Wan, Y.-J.,et al.(2000)Mol. Cell. Biol. 20, 4436–4444]. However, it is unknown whether RXRα plays a role in the control of hepatocyte proliferation and lifespan. Here, we report a detailed analysis of the liver of mice in which RXRα was selectively ablated in adult hepatocytes by using the tamoxifen-inducible chimeric Cre recombinase system. Our results show that the lifespan of adult hepatocytes lacking RXRα is shorter than that of their wild-type counterparts, whereas proliferative hepatocytes of regenerating liver exhibit an even shorter lifespan. These lifespan shortenings are accompanied by increased polyploidy and multinuclearity. We conclude that RXRα plays important cell-autonomous function(s) in the mechanism(s) involved in the lifespan of hepatocytes and liver regeneration.
Selective immobilization of proteins to self-assembled monolayers presenting active site-directed capture ligands
Authors: Hodneland Christian D. , Lee Young-Sam , Min Dal-Hee , Mrksich Milan
Published: July 2002

This paper describes a method for the selective and covalent immobilization of proteins to surfaces with control over the density and orientation of the protein. The strategy is based on binding of the serine esterase cutinase to a self-assembled monolayer presenting a phosphonate ligand and the subsequent displacement reaction that covalently binds the ligand to the enzyme active site. Surface plasmon resonance (SPR) spectroscopy showed that cutinase binds irreversibly to a monolayer presenting the capture ligand at a density of 1% mixed among tri(ethylene glycol) groups. The covalent immobilization is specific for cutinase, and the glycol-terminated monolayer effectively prevents unwanted nonspecific adsorption of proteins. To demonstrate that the method could be used to immobilize proteins of interest, a cutinase-calmodulin fusion protein was constructed and immobilized to the monolayer. SPR showed that calcineurin selectively associated with the immobilized calmodulin. This capture ligand immobilization method combines the advantages that the immobilization reaction is highly selective for the intended protein, the tether is covalent and, hence, stable, and the method avoids the need for synthetic modification and rigorous purification of proteins before immobilization. These characteristics make the method well suited to a range of applications and, in particular, for constructing protein microarrays.
The generation, migration, and differentiation of olfactory neurons in the adult primate brain
Authors: Kornack David R. , Rakic Pasko
Published: July 2002

In adult rodents, neural progenitor cells in the subependymal (SZ)
zone of the lateral cerebral ventricle generate neuroblasts that
migrate in chains via the rostral migratory stream (RMS) into the
olfactory bulb (OB), where they differentiate into interneurons.
However, the existence of this neurogenic migratory system in other
mammals has remained unknown. Here, we report the presence of a
homologue of the rodent SZ/RMS in the adult macaque monkey, a
nonhuman Old World primate with a relatively smaller OB. Our
results—obtained by using combined immunohistochemical detection of a
marker for DNA replication (5-bromodeoxyuridine) and several cell
type-specific markers—indicate that dividing cells in the adult monkey
SZ generate neuroblasts that undergo restricted chain migration over an
extended distance of more than 2 cm to the OB and differentiate into
granule interneurons. These findings in a nonhuman primate extend and
support the use of the SZ/RMS as a model system for studying neural
regenerative mechanisms in the human brain.
Identification of genes expressed with temporal-spatial restriction to developing cerebellar neuron precursors by a functional genomic approach
Authors: Zhao Qing , Kho Alvin , Kenney Anna Marie , Yuk Dong-in , Kohane Isaac , Rowitch David H.
Published: July 2002

Hedgehog pathway activation is required for proliferation of cerebellar granule cell neuron precursors during development and is etiologic in certain cerebellar tumors. To identify genes expressed specifically in granule cell neuron precursors, we used oligonucleotide microarrays to analyze regulation of 13,179 genes/expressed sequence tags in heterogeneous primary cultures of neonatal mouse cerebellum that respond to the mitogen Sonic hedgehog. In conjunction, we applied experiment-specific noise models to render a gene-by-gene robust indication of up-regulation in Sonic hedgehog-treated cultures. Twelve genes so identified were tested, and 10 (83%) showed appropriate expression in the external granular layer (EGL) of the postnatal day (PN) 7 cerebellum and down-regulation by PN 15, as verified by
in situ
hybridization. Whole-organ profiling of the developing cerebellum was carried out from PN 1 to 30 to generate a database of temporal gene regulation profiles (TRPs). From the database an algorithm was developed to capture the TRP typical of EGL-specific genes. The “TRP-EGL” accurately predicted expression
in vivo
of an additional 18 genes/expressed sequence tags with a sensitivity of 80% and a specificity of 88%. We then compared the positive predictive value of our analytical procedure with other widely used methods, as verified by the TRP-EGL
in silico
. These findings suggest that replicate experiments and incorporation of noise models increase analytical specificity. They further show that genome-wide methods are an effective means to identify stage-specific gene expression in the developing granule cell lineage.
Individual differences versus social dynamics in the formation of animal dominance hierarchies
Authors: Chase Ivan D. , Tovey Craig , Spangler-Martin Debra , Manfredonia Michael
Published: July 2002

Linear hierarchies, the classical pecking-order structures, are formed readily in both nature and the laboratory in a great range of species including humans. However, the probability of getting linear structures by chance alone is quite low. In this paper we investigate the two hypotheses that are proposed most often to explain linear hierarchies: they are predetermined by differences in the attributes of animals, or they are produced by the dynamics of social interaction, i.e., they are self-organizing. We evaluate these hypotheses using cichlid fish as model animals, and although differences in attributes play a significant part, we find that social interaction is necessary for high proportions of groups with linear hierarchies. Our results suggest that dominance hierarchy formation is a much richer and more complex phenomenon than previously thought, and we explore the implications of these results for evolutionary biology, the social sciences, and the use of animal models in understanding human social organization.
An autologous oral DNA vaccine protects against murine melanoma
Authors: Xiang Rong , Lode Holger N. , Chao Ta-Hsiang , Ruehlmann J. Michael , Dolman Carrie S. , Rodriguez Fernando , Whitton J. Lindsay , Overwijk Willem W. , Restifo Nicholas P. , Reisfeld Ralph A.
Published: July 2002

We demonstrated that peripheral T cell tolerance toward murine melanoma self-antigens gp100 and TRP-2 can be broken by an autologous oral DNA vaccine containing the murine ubiquitin gene fused to minigenes encoding peptide epitopes gp10025–33and TRP-2181–188. These epitopes contain dominant anchor residues for MHC class I antigen alleles H-2Dband H-2Kb, respectively. The DNA vaccine was delivered by oral gavage by using an attenuated strain ofSalmonella typhimuriumas carrier. Tumor-protective immunity was mediated by MHC class I antigen-restricted CD8+T cells that secreted TH1 cytokine IFN-γ and induced tumor rejection and growth suppression after a lethal challenge with B16G3.26 murine melanoma cells. Importantly, the protective immunity induced by this autologous DNA vaccine against murine melanoma cells was at least equal to that achieved through xenoimmunization with the human gp10025–33peptide, which differs in its three NH2-terminal amino acid residues from its murine counterpart and was previously reported to be clearly superior to an autologous vaccine in inducing protective immunity. The presence of ubiquitin upstream of the minigene proved to be essential for achieving this tumor-protective immunity, suggesting that effective antigen processing and presentation may make it possible to break peripheral T cell tolerance to a self-antigen. This vaccine design might prove useful for future rational designs of other recombinant DNA vaccines targeting tissue differentiation antigens expressed by tumors.
BRS1, a serine carboxypeptidase, regulates BRI1 signaling in
Arabidopsis thaliana
Authors: Li Jia , Lease Kevin A. , Tax Frans E. , Walker John C.
Published: July 2002

Brassinosteroid-insensitive 1
(
BRI1
)
of
Arabidopsis thaliana
encodes a cell surface receptor
for brassinosteroids. Mutations in BRI1 severely affect plant growth
and development. Activation tagging of a weak
bri1
allele (
bri1
-
5
) resulted in the
identification of a new locus,
brs1
-
1D.
BRS1
is predicted to encode a secreted carboxypeptidase.
Whereas a
brs1
loss-of-function allele has no obvious
mutant phenotype, overexpression of
BRS1
can suppress
bri1
extracellular domain mutants. Genetic analyses
showed that brassinosteroids and a functional BRI1 protein kinase
domain are required for suppression. In addition, overexpressed
BRS1
missense mutants, predicted to abolish BRS1
protease activity, failed to suppress
bri1
-
5
. Finally, the effects of BRS1 are
selective: overexpression in either wild-type or two other receptor
kinase mutants resulted in no phenotypic alterations. These results
strongly suggest that BRS1 processes a protein involved in an early
event in the BRI1 signaling.
Presenilin 1 is linked with γ-secretase activity in the detergent solubilized state
Authors: Li Yue-Ming , Lai Ming-Tain , Xu Min , Huang Qian , DiMuzio-Mower Jillian , Sardana Mohinder K. , Shi Xiao-Ping , Yin Kuo-Chang , Shafer Jules A. , Gardell Stephen J.
Published: July 2002

γ-Secretase is a membrane-associated protease that cleaves within the transmembrane region of amyloid precursor protein to generate the C termini of the two Aβ peptide isoforms, Aβ40 and Aβ42. Here we report the detergent solubilization and partial characterization of γ-secretase. The activity of solubilized γ-secretase was measured with a recombinant substrate, C100Flag, consisting largely of the C-terminal fragment of amyloid precursor protein downstream of the β-secretase cleavage site. Cleavage of C100Flag by γ-secretase was detected by electrochemiluminescence using antibodies that specifically recognize the Aβ40 or Aβ42 termini. Incubation of C100Flag with HeLa cell membranes or detergent-solubilized HeLa cell membranes generates both the Aβ40 and Aβ42 termini. Recovery of catalytically competent, soluble γ-secretase critically depends on the choice of detergent; CHAPSO (3-[(3-cholamidopropyl)dimethylammonio]-2-hydroxy-1-propanesulfonate) but not Triton X-100 is suitable. Solubilized γ-secretase activity is inhibited by pepstatin and more potently by a novel aspartyl protease transition-state analog inhibitor that blocks formation of Aβ40 and Aβ42 in mammalian cells. Upon gel exclusion chromatography, solubilized γ-secretase activity coelutes with presenilin 1 (PS1) at an apparent relative molecular weight of approximately 2.0 × 10
6
. Anti-PS1 antibody immunoprecipitates γ-secretase activity from the solubilized γ-secretase preparation. These data suggest that γ-secretase activity is catalyzed by a PS1-containing macromolecular complex.
A brain-enriched polypyrimidine tract-binding protein antagonizes the ability of Nova to regulate neuron-specific alternative splicing
Authors: Polydorides Alexandros D. , Okano Hirotaka J. , Yang Yolanda Y. L. , Stefani Giovanni , Darnell Robert B.
Published: July 2002

The Nova paraneoplastic antigens are neuron-specific RNA binding proteins that participate in the control of alternative splicing. We have used the yeast two-hybrid system to isolate Nova interacting proteins and identify an RNA binding protein that is closely related to the polypyrimidine tract-binding protein (PTB). The expression of this protein, brPTB, is enriched in the brain, where it is expressed in glia and neurons. brPTB interacts with Nova proteins in cell lines and colocalizes with Nova within neuronal nuclei. We previously found that Nova binds to a pyrimidine-rich RNA element present upstream of an alternatively spliced exon, E3A, in glycine receptor α2 (GlyRα2) pre-mRNA, and this binding is implicated in Nova-dependent regulation of splicing. Cotransfection assays with a GlyRα2 minigene demonstrate that brPTB antagonizes the action of Nova to increase utilization of GlyRα2 E3A. brPTB binds to a 90-nt GlyRα2 RNA adjacent to the Nova binding site, but with an affinity that is more than 10-fold lower than Nova. When a putative binding site for brPTB on the GlyRα2 RNA is mutated, binding is abolished and the inhibitory effect on Nova-dependent exon selection disappears. These results suggest that brPTB is a tissue-restricted RNA binding protein that interacts with and inhibits the ability of Nova to activate exon selection in neurons.
A type IB topoisomerase with DNA repair activities
Authors: Belova Galina I. , Prasad Rajendra , Kozyavkin Sergei A. , Lake James A. , Wilson Samuel H. , Slesarev Alexei I.
Published: July 2002

Previously we have characterized type IB DNA topoisomerase V (topo
V) in the hyperthermophile
Methanopyrus kandleri
. The
enzyme has a powerful topoisomerase activity and is abundant in
M. kandleri
. Here we report two characterizations of
topo V. First, we found that its N-terminal domain has sequence
homology with both eukaryotic type IB topoisomerases and the integrase
family of tyrosine recombinases. The C-terminal part of the sequence
includes 12 repeats, each repeat consisting of two similar but distinct
helix-hairpin-helix motifs; the same arrangement is seen in
recombination protein RuvA and mammalian DNA polymerase β. Second, on
the basis of sequence homology between topo V and polymerase β, we
predict and demonstrate that topo V possesses apurinic/apyrimidinic
(AP) site-processing activities that are important in base excision DNA
repair: (
i
) it incises the phosphodiester backbone at
the AP site, and (
ii
) at the AP endonuclease cleaved AP
site, it removes the 5′ 2-deoxyribose 5-phosphate moiety so that a
single-nucleotide gap with a 3′-hydroxyl and 5′-phosphate can be filled
by a DNA polymerase. Topo V is thus the prototype for a new subfamily
of type IB topoisomerases and is the first example of a topoisomerase
with associated DNA repair activities.
The metallochaperone Atox1 plays a critical role in perinatal copper homeostasis
Authors: Hamza Iqbal , Faisst Anja , Prohaska Joseph , Chen Joseph , Gruss Peter , Gitlin Jonathan D.
Published: July 2002

Copper plays a fundamental role in the biochemistry of all aerobic
organisms. The delivery of this metal to specific intracellular targets
is mediated by metallochaperones. To elucidate the role of the
metallochaperone Atox1, we analyzed mice with a disruption of
the
Atox1
locus.
Atox1
−/−
mice failed to thrive immediately after birth, with 45% of pups dying
before weaning. Surviving animals exhibited growth failure, skin
laxity, hypopigmentation, and seizures because of perinatal copper
deficiency. Maternal Atox1 deficiency markedly increased the severity
of
Atox1
−/−
phenotype, resulting in
increased perinatal mortality as well as severe growth retardation and
congenital malformations among surviving
Atox1
−/−
progeny. Furthermore,
Atox1-deficient cells accumulated high levels of intracellular copper,
and metabolic studies indicated that this defect was because of
impaired cellular copper efflux. Taken together, these data reveal a
direct role for Atox1 in trafficking of intracellular copper to the
secretory pathway of mammalian cells and demonstrate that this
metallochaperone plays a critical role in perinatal copper
homeostasis.
Unsaturated fatty acids inhibit transcription of the sterol regulatory element-binding protein-1c (SREBP-1c) gene by antagonizing ligand-dependent activation of the LXR
Authors: Ou Jiafu , Tu Hua , Shan Bei , Luk Alvin , DeBose-Boyd Russell A. , Bashmakov Yuriy , Goldstein Joseph L. , Brown Michael S.
Published: July 2002

Sterol regulatory element-binding protein-1c (SREBP-1c) enhances
transcription of genes encoding enzymes of unsaturated fatty acid
biosynthesis in liver. SREBP-1c mRNA is known to increase when cells
are treated with agonists of liver X receptor (LXR), a nuclear hormone
receptor, and to decrease when cells are treated with unsaturated fatty
acids, the end products of SREBP-1c action. Here we show that
unsaturated fatty acids lower SREBP-1c mRNA levels in part by
antagonizing the actions of LXR. In cultured rat hepatoma cells,
arachidonic acid and other fatty acids competitively inhibited
activation of the endogenous SREBP-1c gene by an LXR
ligand. Arachidonate also blocked the activation of a synthetic
LXR-dependent promoter in transfected human embryonic kidney-293 cells.
In vitro
, arachidonate and other unsaturated fatty acids
competitively blocked activation of LXR, as reflected by a fluorescence
polarization assay that measures ligand-dependent binding of LXR to a
peptide derived from a coactivator. These data offer a potential
mechanism that partially explains the long-known ability of dietary
unsaturated fatty acids to decrease the synthesis and secretion of
fatty acids and triglycerides in livers of humans and other animals.
Arg-302 facilitates deprotonation of Glu-325 in the transport mechanism of the lactose permease from
Escherichia coli
Authors: Sahin-Tóth Miklós , Kaback H. Ronald
Published: July 2002

A mechanistic model for lactose/H
+
symport via the
lactose permease of
Escherichia coli
proposed recently
indicates that the permease must be protonated to bind ligand with high
affinity. Moreover, in the ground state, the symported H
+
is shared between His-322 (helix X) and Glu-269 (helix VIII), whereas
Glu-325 (helix X) is charge-paired with Arg-302 (helix IX). Substrate
binding at the outer surface induces a conformational change that leads
to transfer of the H
+
to Glu-325 and reorientation of the
binding site to the inner surface. After release of the substrate,
Glu-325 is deprotonated on the inside because of rejuxtapositioning
with Arg-302. To test the role of Arg-302 in the mechanism, the
catalytic properties of mutants Arg-302→Ala and Arg-302→Ser were
studied. Both mutants are severely defective in active lactose
transport, as well as in efflux or influx down a concentration
gradient, translocation modes that involve net H
+
movement.
In marked contrast, the mutants catalyze equilibrium exchange of
lactose and bind ligand with high affinity. These characteristics are
remarkably analogous to those of permease mutants with neutral
replacements for Glu-325, a residue that plays a direct role in
H
+
translocation. These observations lend strong support
for the argument that Arg-302 interacts with Glu-325 to facilitate
deprotonation of the carboxylic acid during turnover.
Assessment of mitochondrial energy coupling
in vivo
by
13
C/
31
P NMR
Authors: Jucker Beat M. , Dufour Sylvie , Ren Jianming , Cao Xueying , Previs Stephen F. , Underhill Brian , Cadman Kevin S. , Shulman Gerald I.
Published: July 2002

The recently cloned uncoupling protein homolog UCP3 is expressed primarily in muscle and therefore may play a significant role in the regulation of energy expenditure and body weight. However, investigation into the regulation of uncoupling protein has been hampered by the inability to assess its activity
in vivo
. In this report, we demonstrate the use of a noninvasive NMR technique to assess mitochondrial energy uncoupling in skeletal muscle of awake rats by combining
13
C NMR to measure rates of mitochondrial substrate oxidation with
31
P NMR to assess unidirectional ATP synthesis flux. These combined
31
P/
13
C NMR measurements were performed in control, 10-day triiodo-
l
-thyronine (T
3
)-treated (model of increased UCP3 expression), and acute 2,4-dinitrophenol (DNP)-treated (protonophore and mitochondrial uncoupler) rats. UCP3 mRNA and protein levels increased 8.1-fold (± 1.1) and 2.8-fold (± 0.8), respectively, in the T
3
-treated vs. control rat gastrocnemius muscle.
13
C NMR measurements of tricarboxylic acid cycle flux as an index of mitochondrial substrate oxidation were 61 ± 21, 148 ± 25, and 310 ± 48 nmol/g per min in the control, T
3
, and DNP groups, respectively.
31
P NMR saturation transfer measurements of unidirectional ATP synthesis flux were 83 ± 14, 84 ± 14, and 73 ± 7 nmol/g per s in the control, T
3
, and DNP groups, respectively. Together, these flux measurements, when normalized to the control group, suggest that acute administration of DNP (mitochondrial uncoupler) and chronic administration of T
3
decrease energy coupling by ≈80% and ≈60%, respectively, and that the latter treatment correlates with an increase in UCP3 mRNA and protein expression. This NMR approach could prove useful for exploring the regulation of uncoupling protein activity
in vivo
and elucidating its role in energy metabolism and obesity.
Regulation of theMycobacterium tuberculosishypoxic response gene encoding α-crystallin
Authors: Sherman David R. , Voskuil Martin , Schnappinger Dirk , Liao Reiling , Harrell Maria I. , Schoolnik Gary K.
Published: July 2002

Unlike many pathogens that are overtly toxic to their hosts, the primary virulence determinant ofMycobacterium tuberculosisappears to be its ability to persist for years or decades within humans in a clinically latent state. Since early in the 20th century latency has been linked to hypoxic conditions within the host, but the response ofM. tuberculosisto a hypoxic signal remains poorly characterized. TheM. tuberculosisα-crystallin (acr) gene is powerfully and rapidly induced at reduced oxygen tensions, providing us with a means to identify regulators of the hypoxic response. Using a whole genome microarray, we identified >100 genes whose expression is rapidly altered by defined hypoxic conditions. Numerous genes involved in biosynthesis and aerobic metabolism are repressed, whereas a high proportion of the induced genes have no known function. Among the induced genes is an apparent operon that includes the putative two-component response regulator pair Rv3133c/Rv3132c. When we interrupted expression of this operon by targeted disruption of the upstream gene Rv3134c, the hypoxic regulation ofacrwas eliminated. These results suggest a possible role for Rv3132c/3133c/3134c in mycobacterial latency.
Modular organization of intrinsic connections associated with spectral tuning in cat auditory cortex
Authors: Read Heather L. , Winer Jeffery A. , Schreiner Christoph E.
Published: July 2002

Many response properties in primary auditory cortex (AI) are segregated spatially and organized topographically as those in primary visual cortex. Intensive study has not revealed an intrinsic, anatomical organizing principle related to an AI functional topography. We used retrograde anatomic tracing and topographic physiologic mapping of acoustic response properties to reveal long-range (≥1.5 mm) convergent intrinsic horizontal connections between AI subregions with similar bandwidth and characteristic frequency selectivity. This suggests a modular organization for processing spectral bandwidth in AI.
Kaposi's sarcoma-associated herpesvirus encodes two proteins that block cell surface display of MHC class I chains by enhancing their endocytosis
Authors: Coscoy Laurent , Ganem Don
Published: July 2002

Down-regulation of the cell surface display of class I MHC proteins is an important mechanism of immune evasion by human and animal viruses. Herpesviruses in particular encode a variety of proteins that function to lower MHC I display by several mechanisms. These include binding and retention of MHC I chains in the endoplasmic reticulum, dislocation of class I chains from the ER, inhibition of the peptide transporter (TAP) involved in antigen presentation, and shunting of newly assembled chains to lysosomes. Kaposi's sarcoma (KS)-associated herpesvirus (KSHV) is a human herpesvirus strongly linked to the development of KS and to certain AIDS-associated lymphoproliferative disorders. Here we show that KSHV encodes two distinctive gene products that function to dramatically reduce cell surface MHC I expression. These viral proteins are localized predominantly to the ER. However, unlike previously described MHC I inhibitors, they do not interfere with the synthesis, translocation, or assembly of class I chains, nor do they retain them in the ER. Rather, they act to enhance endocytosis of MHC I from the cell surface; internalized class I chains are delivered to endolysosomal vesicles, where they undergo degradation. These KSHV proteins define a mechanism of class I down-regulation distinct from the mechanisms of other herpesviruses and are likely to contribute importantly to immune evasion during viral infection.
A mutation in
Rab27a
causes the vesicle transport defects observed in
ashen
mice
Authors: Wilson Scott M. , Yip Richard , Swing Deborah A. , O'Sullivan T. Norene , Zhang Yuke , Novak Edward K. , Swank Richard T. , Russell Liane B. , Copeland Neal G. , Jenkins Nancy A.
Published: July 2002

The
dilute
(
d
),
leaden
(
ln
), and
ashen
(
ash
) mutations provide a unique model system for studying vesicle transport in mammals. All three mutations produce a lightened coat color because of defects in pigment granule transport. In addition, all three mutations are suppressed by the semidominant
dilute-suppressor
(
dsu
), providing genetic evidence that these mutations function in the same or overlapping transport pathways. Previous studies showed that
d
encodes a major vesicle transport motor, myosin-VA, which is mutated in Griscelli syndrome patients. Here, using positional cloning and bacterial artificial chromosome rescue, we show that
ash
encodes
Rab27a
. Rab GTPases represent the largest branch of the p21 Ras superfamily and are recognized as key players in vesicular transport and organelle dynamics in eukaryotic cells. We also show that
ash
mice have platelet defects resulting in increased bleeding times and a reduction in the number of platelet dense granules. These defects have not been reported for
d
and
ln
mice. Collectively, our studies identify
Rab27a
as a critical gene for organelle-specific protein trafficking in melanocytes and platelets and suggest that
Rab27a
functions in both MyoVa dependent and independent pathways.
A relationship between behavior, neurotrophin expression, and new neuron survival
Authors: Li Xiao-Ching , Jarvis Erich D. , Alvarez-Borda Benjamin , Lim Daniel A. , Nottebohm Fernando
Published: July 2002

The high vocal center (HVC) controls song production in songbirds and sends a projection to the robust nucleus of the archistriatum (RA) of the descending vocal pathway. HVC receives new neurons in adulthood. Most of the new neurons project to RA and replace other neurons of the same kind. We show here that singing enhances mRNA and protein expression of brain-derived neurotrophic factor (BDNF) in the HVC of adult male canaries,
Serinus canaria
. The increased BDNF expression is proportional to the number of songs produced per unit time. Singing-induced BDNF expression in HVC occurs mainly in the RA-projecting neurons. Neuronal survival was compared among birds that did or did not sing during days 31–38 after BrdUrd injection. Survival of new HVC neurons is greater in the singing birds than in the nonsinging birds. A positive causal link between pathway use, neurotrophin expression, and new neuron survival may be common among systems that recruit new neurons in adulthood.