bluuebunny/crossref_metadata_2025 huggingface dataset:
Galvanomagnetic effect in AlGaAs/GaAs heterostructures grown by organometallic vapor phase epitaxy
Authors: Aina Leye , Mattingly Mike , Pande Krishna
Published: July 2002

A new galvanomagnetic effect in AlGaAs/GaAs heterostructures is described. The Hall coefficient of such structures is shown to decrease with the magnetic field in a low field regime where magnetoresistive effects are negligible. The effect is explained in terms of two-band conduction in the AlGaAs and in the two-dimensional electron gas at the heterojunction where the electrons have different energies and substantially differing mobilities and concentrations. It is shown that the low magnetic field Hall mobilities can be used to estimate the mobility of the two-dimensional electron gas in a heterostructure where there is parallel conduction.
Study of the moving species in ion-induced reactions
Authors: Tao K. , Hewett C. A. , Lau S. S. , Buchal Ch. , Poker D. B.
Published: July 2002

We present evidence in this study that the moving species under ion mixing conditions are affected by the implantation damage distribution in the sample. This observation holds for metal-semiconductor, metal-metal, and semiconductor-semiconductor systems. The direction of thermal annealing atomic transport appears to play a role in ion mixing as well. When these two factors are in the same direction, only one dominant moving species is observed. When these two factors are in opposite directions, both constituents can contribute to the atomic transport in ion mixing.
New technique to detect the GaAs semi-insulating surface property—cw electro-optic probing
Authors: Lo Y. H. , Zhu Z. H. , Pan C. L. , Wang S. Y. , Wang S.
Published: July 2002

The continuous wave electro-optic probing (CWEOP) technique is for the first time used to probe the GaAs Czochralski liquid encapsulated semi-insulating surface property. From the second derivative profile of the signal, the space-charge boundary under different bias is clearly observed. The motion of the detected space-charge boundary with applied bias shows that the substrate surface evolves from a highly compensated semi-insulating surface to a p− surface with thermal annealing. The CWEOP experiment also concludes that there is no other level except EL2 possessing enough concentration to compensate the background shallow acceptor. Since this technique is extremely sensitive to the GaAs surface property, it can be used to directly probe the surface potential, field, and charge distribution in GaAs material and device.
Space-charge-limited current in thin-film diamond
Authors: Ashok S. , Srikanth K. , Badzian A. , Badzian T. , Messier R.
Published: July 2002

The electrical conduction in thin-film diamond synthesized by microwave plasma enhanced chemical vapor deposition has been studied with metal-diamond-silicon metal-insulator-semiconductor structures. Measurements over a wide temperature range provide evidence for space-charge-limited current in the presence of traps. An exponential distribution of traps with a peak value of the order of 3×1020 cm−3 eV−1 has been deduced from the current-voltage-temperature data.
Differential scanning calorimetry study of solid-state amorphization in multilayer thin-film Ni/Zr
Authors: Highmore R. J. , Evetts J. E. , Greer A. L. , Somekh R. E.
Published: July 2002

Differential scanning calorimetry (DSC) has been used to study solid-state amorphization and subsequent crystallization in sputtered multilayer Ni/Zr thin films. Initial results provide quantitative information about the thermodynamics and kinetics of these processes. An analysis of DSC data enables the activation energy and pre-exponential factor for interdiffusion of Ni and Zr in a-NiZr to be found.
Pulsed laser etching of high T
c superconducting films
Authors: Inam Arun , Wu X. D. , Venkatesan T. , Ogale S. B. , Chang C. C. , Dijkkamp D.
Published: July 2002

Etching of Y-Ba-Cu-O superconducting thin films has been accomplished using a pulsed excimer laser (248 nm, 30 ns). Etch depth as a function of the number of laser pulses was linear over a wide range of incident laser energy densities. An etch threshold energy density of 0.11 J/cm2 was observed and etch rate per pulse scaled linearly with the logarithm of the incident energy density. The dependence is adequately explained by a linear absorption model with an inverse absorption length of 2.3×105 cm−1.
High acceptor production rate in electron-irradiated n-type GaAs: Impact on defect models
Authors: Look D. C.
Published: July 2002

Defect production rates have been studied in electron-irradiated GaAs by temperature-dependent Hall-effect (TDH) measurements. The TDH results agree well with deep level transient spectroscopy (DLTS) results for the well-known electron traps E1, E2, and E3, but conclusively demonstrate a much higher production rate (4±1 cm−1) of acceptors below E3 than the total of all other DLTS traps. These findings strongly affect current defect models, and, e.g., are consistent with the existence of Ga sublattice damage, not seen before.
Damage annealing behavior of 3 MeV Si+-implanted silicon
Authors: Rai A. K. , Baker J. , Ingram D. C.
Published: July 2002

Cross-sectional transmission electron microscopy has been used to study the recrystallization behavior of a buried amorphous layer in 3 MeV Si+-implanted (100) silicon at a dose of 5×1015 cm−2. The lower (deeper) amorphous/crystalline (a/c) interface is found to be more abrupt compared to the upper (closer to the surface) a/c interface. During recrystallization similar rates of advancement of the two a/c interfaces are observed. V-shaped dislocations are observed in the completely recrystallized layer. The defect density in the upper recrystallized region is found to be higher than that in the lower recrystallized region. These observations are correlated with the shape of the damage profile. The secondary defects grown at higher temperatures (>750 °C) are found to be very stable and difficult to anneal out. The overall recrystallization behavior of the buried amorphous layer is found to be similar to that of lower energy implants.
Enhanced efficiency in separation of Rb isotopes by light-induced drift with the use of a diode laser with relaxation sidebands
Authors: Streater A. D. , Mooibroek J. , Woerdman J. P.
Published: July 2002

An AlGaAs diode laser oscillating in a single Fabry–Perot mode with strong relaxation sidebands is observed to separate the two naturally occurring isotopes of rubidium by means of light-induced drift at much lower powers than has been reported with a single-mode ring dye laser. The sideband frequency displacement is approximately equal to the ground-state hyperfine splitting, so that optical hyperfine pumping is largely eliminated.
Observation of a change in the form of polarization reversal in a vinylidene fluoride/trifluoroethylene copolymer
Authors: Guy I. L. , Unsworth J.
Published: July 2002

Polarization reversal in the ferroelectric polymer PVF2 is known to involve chains rotating in 60° steps. In a 75/25 mol % VF2/VF3 copolymer, chains rotate by two different mechanisms involving either 60° or 180° steps. The extent to which the 180° process contributes to the total polarization reversal is increased by poling.
Impurity-stimulated crystallization and diffusion in amorphous silicon
Authors: Nygren E. , Pogany A. P. , Short K. T. , Williams J. S. , Elliman R. G. , Poate J. M.
Published: July 2002

An amorphous-to-polycrystalline silicon transformation and concomitant In redistribution have been observed in In-implanted silicon at temperatures well below those at which solid phase epitaxial growth or random crystallization is observed in undoped films. The process is extremely rapid and exhibits a strong dependence on both In concentration and temperature. It is proposed that the In redistribution and accompanying silicon crystallization are mediated by molten, In-rich precipitates in amorphous silicon.
High quality InP layers grown by organometallic vapor phase epitaxy using tertiarybutylphosphine and phosphine
Authors: Saxena R. R. , Fouquet J. E. , Sardi V. M. , Moon R. L.
Published: July 2002

A systematic study compares the quality of InP epitaxial layers grown by low-pressure organometallic vapor phase epitaxy (OMVPE) using triethylindium, phosphine, and tertiarybutylphosphine (TBP) sources. High quality InP layers are obtained with either phosphorus source for growth at a high V/III ratio. The full widths at half-maximum (FWHM) of the main 4 K photoluminescence peak from InP layers grown with phosphine and TBP sources are 1.1 and 1.3 meV, respectively. This 1.3 meV FWHM is the narrowest reported for InP grown by OMVPE with a nonhydride phosphorus source. High quality InP layers can be grown at a lower V/III ratio with the TBP source than with the phosphine source.
Photovoltaic infrared sensors in heteroepitaxial PbTe on Si
Authors: Maissen C. , Masek J. , Zogg H. , Blunier S.
Published: July 2002

Arrays of photovoltaic infrared sensors for thermal imaging applications have been fabricated in narrow gap PbTe grown heteroepitaxially on Si substrates. PbTe epitaxy was achieved with the aid of intermediate CaF2 /BaF2 buffer layers of only ≊2000 Å thickness. Blocking Pb contacts on about 3-μm-thick p-PbTe layers form the active areas of the sensors. Cutoff wavelengths are 5.6 μm, and resistance-area products are up to R0A=400 Ω cm2 at 85 K with mean value R0A≊150 Ω cm2 for 66 element linear arrays, well above the room-temperature photon field background noise limit. The temperature dependence of R0A indicates a depletion-limited noise current behavior between 250 and 100 K.
Speciation through homoploid hybridization between allotetraploids in peonies (Paeonia)
Authors: Ferguson Diane , Sang Tao
Published: July 2002

Phylogenies ofAdh1andAdh2genes suggest that a widespread Mediterranean peony,Paeonia officinalis, is a homoploid hybrid species between two allotetraploid species,Paeonia peregrinaand a member of thePaeonia arietinaspecies group. Three phylogenetically distinct types ofAdhsequences have been identified from both accessions ofP. officinalis, of which two types are most closely related to the two homoeologousAdhloci of theP. arietinagroup and the remaining type came from one of the twoAdhhomoeologs ofP. peregrina. The otherAdhhomoeolog ofP. peregrinawas apparently lost from the hybrid genome, possibly through backcrossing with theP. arietinagroup. This is a documentation of homoploid hybrid speciation between allotetraploid species in nature. This study suggests that hybrid speciation between allotetraploids can occur without an intermediate stage of genome diploidization or a further doubling of genome size.
Posttranslational modification of the
umuD
-encoded subunit of
Escherichia coli
DNA polymerase V regulates its interactions with the β processivity clamp
Authors: Sutton Mark D. , Narumi Issay , Walker Graham C.
Published: July 2002

The
Escherichia coli umuDC
(pol V) gene products participate in both a DNA damage checkpoint control and translesion DNA synthesis. Interactions of the two
umuD
gene products, the 139-aa UmuD and the 115-aa UmuD′ proteins, with components of the replicative DNA polymerase (pol III), are important for determining which biological role the
umuDC
gene products will play. Here we report our biochemical characterizations of the interactions of UmuD and UmuD′ with the pol III β processivity clamp. These analyses demonstrate that UmuD possesses a higher affinity for β than does UmuD′ because of the N-terminal arm of UmuD (residues 1–39), much of which is missing in UmuD′. Furthermore, we have identified specific amino acid residues of UmuD that crosslink to β with
p
-azidoiodoacetanilide, defining the domain of UmuD important for the interaction. We have recently proposed a model for the solution structure of UmuD
2
in which the N-terminal arm of each protomer makes extensive contacts with the C-terminal globular domain of its intradimer partner, masking part of each surface. Taken together, our findings suggest that UmuD
2
has a higher affinity for the β-clamp than does UmuD′
2
because of the structures of its N-terminal arms. Viewed in this way, posttranslational modification of UmuD, which entails the removal of its N-terminal 24 residues to yield UmuD′, acts in part to attenuate the affinity of the
umuD
gene product for the β-clamp. Implications of these structure–function analyses for the checkpoint and translesion DNA synthesis functions of the
umuDC
gene products are discussed.
Ubc9 interacts with a nuclear localization signal and mediates nuclear localization of the paired-like homeobox protein Vsx-1 independent of SUMO-1 modification
Authors: Kurtzman Aaron L. , Schechter Nisson
Published: July 2002

Vsx-1 is a
paired
-like:CVC homeobox gene whose
expression is linked to bipolar cell differentiation during zebrafish
retinogenesis. We used a yeast two-hybrid screen to identify proteins
interacting with Vsx-1 and isolated Ubc9, an enzyme that conjugates the
small ubiquitin-like modifier SUMO-1. Despite its interaction with
Ubc9, we show that Vsx-1 is not a substrate for SUMO-1 in COS-7 cells
or
in vitro
. When a yeast two-hybrid assay is used,
deletion analysis of the interacting domain on Vsx-1 shows that Ubc9
binds to a nuclear localization signal (NLS) at the NH
2
terminus of the homeodomain. In SW13 cells, Vsx-1 localizes to the
nucleus and is excluded from nucleoli. Deletion of the NLS disrupts
this nuclear localization, resulting in a diffuse cytoplasmic
distribution of Vsx-1. In SW13 AK1 cells that express low levels of
endogenous Ubc9, Vsx-1 accumulates in a perinuclear ring
and colocalizes with an endoplasmic reticulum marker. However,
NLS-tagged STAT1 protein exhibits normal nuclear localization in both
SW13 and SW13 AK1 cells, suggesting that nuclear import is not globally
disrupted. Cotransfection of Vsx-1 with Ubc9 restores Vsx-1 nuclear
localization in SW3 AK1 cells and demonstrates that Ubc9 is required
for the nuclear localization of Vsx-1. Ubc9 continues to restore
nuclear localization even after a C93S active site mutation has
eliminated its SUMO-1-conjugating ability. These results suggest that
Ubc9 mediates the nuclear localization of Vsx-1, and possibly other
proteins, through a nonenzymatic mechanism that is independent of
SUMO-1 conjugation.
Kinetics and mechanism of DNA uptake into the cell nucleus
Authors: Salman H. , Zbaida D. , Rabin Y. , Chatenay D. , Elbaum M.
Published: July 2002

Gene transfer to eukaryotic cells requires the uptake of exogenous DNA into the cell nucleus. Except during mitosis, molecular access to the nuclear interior is limited to passage through the nuclear pores. Here we demonstrate the nuclear uptake of extended linear DNA molecules by a combination of fluorescence microscopy and single-molecule manipulation techniques, using the latter to follow uptake kinetics of individual molecules in real time. The assays were carried out on nuclei reconstituted
in vitro
from extracts of
Xenopus
eggs, which provide both a complete complement of biochemical factors involved in nuclear protein import, and unobstructed access to the nuclear pores. We find that uptake of DNA is independent of ATP or GTP hydrolysis, but is blocked by wheat germ agglutinin. The kinetics are much slower than would be expected from hydrodynamic considerations. A fit of the data to a simple model suggests femto-Newton forces and a large friction relevant to the uptake process.
Deoxysugars in glycopeptide antibiotics: Enzymatic synthesis of TDP-
l
-epivancosamine in chloroeremomycin biosynthesis
Authors: Chen Huawei , Thomas Michael G. , Hubbard Brian K. , Losey Heather C. , Walsh Christopher T. , Burkart Michael D.
Published: July 2002

The 2,3,6-trideoxysugar
l
-epivancosamine is the
terminal sugar added to the aglycone scaffold in chloroeremomycin, a
member of the vancomycin family of glycopeptide antibiotics. Five
proteins from the chloroeremomycin biosynthetic cluster, ORF14 and
ORF23 to ORF26, have been expressed heterologously in
Escherichia coli
and purified to near homogeneity, and
each has been characterized for an enzymatic activity. These five
enzymes reconstitute the complete biosynthesis of
TDP-
l
-epivancosamine from
TDP-4-keto-6-deoxy-
d
-glucose. This process involves C-2
deoxygenation, C-3 amination and methylation, C-5 epimerization, and
C-4 ketoreduction. Intermediates and the final product of this pathway
have been identified by mass spectrometry and NMR. The pathway
established here represents the complete
in vitro
reconstitution of an unusual sugar for an important class of
antibiotics and sets the groundwork for future combinatorial
biosynthesis for new bioactive compounds.
Coexistence of phycoerythrin and a chlorophyll a/b antenna in a marine prokaryote.
Authors: Hess W R , Partensky F , van der Staay G W , Garcia-Fernandez J M , Börner T , Vaulot D
Published: July 2002

Prochlorococcus marinus CCMP 1375, a ubiquitous and ecologically important marine prochlorophyte, was bound to possess functional genes coding for the alpha and beta subunits of a phycobiliprotein. The latter is similar to phycoerythrins (PE) from marine Synechococcus cyanobacteria and bind a phycourobilin-like pigment as the major chromophore. However, differences in the sequences of the alpha and beta chains compared with known PE subunits and the presence of a single bilin attachment site on the alpha subunit designate it as a novel PE type, which we propose naming PE-III. P. marinus is the sole prokaryotic organisms known so far that contains chlorophylls a and b as well as phycobilins. These data strongly suggest that the common ancestor of prochlorophytes and the Synechococcus cyanobacteria contained phycobilins. Flow cytometric data from the tropical Pacific Ocean provide evidence that deep populations of Prochlorococcus possess low amounts of a PE-like pigment, which could serve either in light harvesting or nitrogen storage or both.
An unusual mechanism for the major human apurinic/apyrimidinic (AP) endonuclease involving 5′ cleavage of DNA containing a benzene-derived exocyclic adduct in the absence of an AP site
Authors: Hang B. , Chenna A. , Fraenkel-Conrat H. , Singer B.
Published: July 2002

The major human apurinic/apyrimidinic (AP) endonuclease (class
II) is known to cleave DNA 5′ adjacent to an AP site, which is probably
the most common DNA damage produced hydrolytically or by
glycosylase-mediated removal of modified bases.
p
-Benzoquinone (pBQ), one of the major benzene
metabolites, reacts with DNA to form bulky exocyclic adducts. Herein we
report that the human AP endonuclease directly catalyzes incision in a
defined oligonucleotide containing
3,
N
4
-benzetheno-2′-deoxycytidine (pBQ-dC)
without prior generation of an AP site. The enzyme incises the
oligonucleotide 5′ to the adduct and generates 3′-hydroxyl and
5′-phosphoryl termini but leaves the pBQ-dC on the 5′ terminus of the
cleavage fragment. The AP function of the enzyme is not involved in
this action, as no preexisting AP site is present nor is a DNA
glycosylase activity involved. Nicking of the pBQ-dC adduct also leads
to the same “dangling base” cleavage when two
Escherichia
coli
enzymes, exonuclease III and endonuclease IV, are used.
Our finding of this unusual mode of action used by both human and
bacterial AP endonucleases raises important questions regarding the
requirements for substrate recognition and catalytic active site(s) for
this essential cellular repair enzyme. We believe this to be the first
instance of the presence of a bulky carcinogen adduct leading to this
unusual mode of action.
Close correspondence between the action spectra for the blue light responses of the guard cell and coleoptile chloroplasts, and the spectra for blue light-dependent stomatal opening and coleoptile phototropism.
Authors: Quiñones M A , Lu Z , Zeiger E
Published: July 2002

Fluorescence spectroscopy was used to characterize blue light responses from chloroplasts of adaxial guard cells from Pima cotton (Gossypium barbadense) and coleoptile tips from corn (Zea mays). The chloroplast response to blue light was quantified by measurements of the blue light-induced enhancement of a red light-stimulated quenching of chlorophyll a fluorescence. In adaxial (upper) guard cells, low fluence rates of blue light applied under saturating fluence rates of red light enhanced the red light-stimulated fluorescence quenching by up to 50%. In contrast, added blue light did not alter the red light-stimulated quenching from abaxial (lower) guard cells. This response pattern paralleled the blue light sensitivity of stomatal opening in the two leaf surfaces. An action spectrum for the blue light-induced enhancement of the red light-stimulated quenching showed a major peak at 450 nm and two minor peaks at 420 and 470 nm. This spectrum matched closely an action spectrum for blue light-stimulated stomatal opening. Coleoptile chloroplasts also showed an enhancement by blue light of red light-stimulated quenching. The action spectrum of this response, showing a major peak at 450 nm, a minor peak at 470 nm, and a shoulder at 430 nm, closely matched an action spectrum for blue light-stimulated coleoptile phototropism. Both action spectra match the absorption spectrum of zeaxanthin, a chloroplastic carotenoid recently implicated in blue light photoreception of both guard cells and coleoptiles. The remarkable similarity between the action spectra for the blue light responses of guard cells and coleoptile chloroplasts and the spectra for blue light-stimulated stomatal opening and phototropism, coupled to the recently reported evidence on a role of zeaxanthin in blue light photoreception, indicates that the guard cell and coleoptile chloroplasts specialize in sensory transduction.
A long-range regulatory element of Hoxc8 identified by using the pClasper vector.
Authors: Bradshaw M S , Shashikant C S , Belting H G , Bollekens J A , Ruddle F H
Published: July 2002

Hox genes are located in highly conserved clusters. The significance of this organization is unclear, but one possibility is that regulatory regions for individual genes are dispersed throughout the cluster and shared with other Hox genes. This hypothesis is supported by studies on several Hox genes in which even large genomic regions immediately surrounding the gene fail to direct the complete expression pattern in transgenic mice. In particular, previous studies have identified proximal regulatory regions that are primarily responsible for early phases of mouse Hoxc8 expression. To locate additional regulatory regions governing expression during the later periods of development, a yeast homologous recombination-based strategy utilizing the pClasper vector was employed. Using homologous recombination into pClasper, we cloned a 27-kb region around the Hoxc8 gene from a yeast artificial chromosome. A reporter gene was introduced into the coding region of the isolated gene by homologous recombination in yeast. This large fragment recapitulates critical aspects of Hoxc8 expression in transgenic mice. We show that the regulatory elements that maintain the anterior boundaries of expression in the neural tube and paraxial mesoderm are located between 11 and 19 kb downstream of the gene.
Expression of a protective gene-prolongs survival of T cells in human immunodeficiency virus-infected patients.
Authors: Woffendin C , Ranga U , Yang Z , Xu L , Nabel G J
Published: July 2002

The resistance of acquired immunodeficiency syndrome (AIDS) to traditional drug therapy has prompted a search for alternative treatments for this disease. One potential approach is to provide genetic resistance to viral replication to prolong latency. This strategy requires the definition of effective antiviral genes that extend the survival of T cells in human immunodeficiency virus (HIV)-infected individuals. We report the results of a human study designed to determine whether a genetic intervention can prolong the survival of T cells in HIV-infected individuals. Gene transfer was performed in enriched CD4+ cells with plasmid expression vectors encoding an inhibitory Rev protein, Rev M10, or a deletion mutant control, deltaRev M10, delivered by gold microparticles. Autologous cells separately transfected with each of the vectors were returned to each patient, and toxicity, gene expression, and survival of genetically modified cells were assessed. Cells that expressed Rev M10 were more resistant to HIV infection than those with deltaRev M10 in vitro. In HIV-infected subjects, Rev M10-transduced cells showed preferential survival compared to deltaRev M10 controls. Rev M10 can therefore act as a specific intracellular inhibitor that can prolong T-cell survival in HIV-1-infected individuals and potentially serve as a molecular genetic intervention which can contribute to the treatment of AIDS.
Cross-modulation by transforming growth factor beta in human tuberculosis: suppression of antigen-driven blastogenesis and interferon gamma production.
Authors: Hirsch C S , Hussain R , Toossi Z , Dawood G , Shahid F , Ellner J J
Published: July 2002

In tuberculosis, Mycobacterium tuberculosis (MTB)-stimulated T-cell responses are depressed transiently, whereas antibody levels are increased. Lymphoproliferative responses of peripheral blood mononuclear cells (PBMCs) from Pakistani tuberculosis (TB) patients to both mycobacterial and candidal antigens were suppressed by approximately 50% when compared to healthy purified protein derivative (PPD)-positive household contacts. Production of interferon gamma (IFN-gamma) in response to PPD also was depressed by 78%. Stimulation with PPD and the 30-kDa alpha antigen of MTB (30-kDa antigen) induced greater secretion of transforming growth factor beta (TGF-beta), but not interleukin 10 (IL-10) or tumor necrosis factor alpha (TNF-alpha), by PBMCs from TB patients compared to healthy contacts. The degree of suppression correlated with the duration of treatment; patients treated for <1 month had significantly lower T-cell blastogenesis and IFN-gamma production and higher levels of TGF-beta than did patients treated for >1 month. Neutralizing antibody to TGF-beta normalized lymphocyte proliferation in response to PPD, partially restored blastogenesis to candidal antigen, and significantly increased PPD-stimulated production of IFN-gamma in TB patients but not in contacts. Neutralizing antibody to IL-10 augmented, but did not normalize, T-cell responses to both PPD and candida in TB patients and candidal antigen in contacts. TGF-beta, produced in response to MTB antigens, therefore plays a prominent role in down-regulating potentially protective host effector mechanisms and looms as an important mediator of immunosuppression in TB.
Rock friction and its implications for earthquake prediction examined via models of Parkfield earthquakes.
Authors: Tullis T E
Published: July 2002

The friction of rocks in the laboratory is a function of time, velocity of sliding, and displacement. Although the processes responsible for these dependencies are unknown, constitutive equations have been developed that do a reasonable job of describing the laboratory behavior. These constitutive laws have been used to create a model of earthquakes at Parkfield, CA, by using boundary conditions appropriate for the section of the fault that slips in magnitude 6 earthquakes every 20-30 years. The behavior of this model prior to the earthquakes is investigated to determine whether or not the model earthquakes could be predicted in the real world by using realistic instruments and instrument locations. Premonitory slip does occur in the model, but it is relatively restricted in time and space and detecting it from the surface may be difficult. The magnitude of the strain rate at the earth's surface due to this accelerating slip seems lower than the detectability limit of instruments in the presence of earth noise. Although not specifically modeled, microseismicity related to the accelerating creep and to creep events in the model should be detectable. In fact the logarithm of the moment rate on the hypocentral cell of the fault due to slip increases linearly with minus the logarithm of the time to the earthquake. This could conceivably be used to determine when the earthquake was going to occur. An unresolved question is whether this pattern of accelerating slip could be recognized from the microseismicity, given the discrete nature of seismic events. Nevertheless, the model results suggest that the most likely solution to earthquake prediction is to look for a pattern of acceleration in microseismicity and thereby identify the microearthquakes as foreshocks.
In vivo
NMR and MRI using injection delivery of laser-polarized xenon
Authors: Goodson B. M. , Song Y.-Q. , Taylor R. E. , Schepkin V. D. , Brennan K. M. , Chingas G. C. , Budinger T. F. , Navon G. , Pines A.
Published: July 2002

Because xenon NMR is highly sensitive to the local environment, laser-polarized xenon could be a unique probe of living tissues. Realization of clinical and medical science applications beyond lung airspace imaging requires methods of efficient delivery of laser-polarized xenon to tissues, because of the short spin-lattice relaxation times and relatively low concentrations of xenon attainable in the body. Preliminary results from the application of a polarized xenon injection technique for
in vivo
129
Xe NMR/MRI are extrapolated along with a simple model of xenon transit to show that the peak local concentration of polarized xenon delivered to tissues by injection may exceed that delivered by respiration by severalfold.
Reconstitution of stretch-activated cation channels by expression of the α-subunit of the epithelial sodium channel cloned from osteoblasts
Authors: Kizer Neil , Guo Xiao-Li , Hruska Keith
Published: July 2002

Osteoblasts respond to repetitive strain by activating stretch-activated, nonselective cation channels (SA-CAT) and increasing matrix protein production. SA-CAT channels are thought to be responsible for mechano-transduction in osteoblasts, although the molecular identity of the SA-CAT channel has previously been unknown. We have demonstrated that both the UMR-106 osteoblast-like cell line and human osteoblasts in primary culture express the α-subunit of the epithelial sodium channel (α-ENaC). The ENaC gene product is closely related to a class of proteins that confer touch sensitivity to
Caenorhabditis elegans
and are referred to as degenerins. A cDNA clone was obtained of the entire coding region of rat α-ENaC (α-rENaC). Sequence analysis indicated that the osteoblast clone’s sequence was identical to that originally cloned from rat colon. The α-rENaC cDNA was cloned into an expression plasmid and transfected into LM(TK
−
) cells, a null cell for SA-CAT activity. Stable transfectants expressed mRNA and the expected 74-kDa protein corresponding to α-rENaC. Reconstitution of α-rENaC resulted in the expression of a 24.2 ± 1.0 psec SA-CAT channel (P
Na
:P
K
= 1.1 ± 0.1). The channel is calcium permeable (P
Na
:P
Ca
= 1.4 ± 0.1) and highly selective for cations over anions (P
Na
:P
Cl
≫ 20). The channel is only active after negative pressure is applied to cell attached patches, cell swelling, or patch excision. These results represent the first heterologous expression of an SA-CAT channel in a mammalian cell system and provide evidence that the ENaC/degenerin family of proteins are capable of mediating both transepithelial sodium transport and are involved in signal transduction by mechano-sensitive cells such as osteoblasts.
Crystal structure of Lyme disease antigen outer surface protein A complexed with an Fab
Authors: Li Hong , Dunn John J. , Luft Benjamin J. , Lawson Catherine L.
Published: July 2002

OspA (outer surface protein A) is an abundant immunogenic lipoprotein of the Lyme disease spirocheteBorrelia burgdorferi. The crystal structure of a soluble recombinant form of OspA was solved in a complex with the Fab fragment of mouse monoclonal antibody 184.1 and refined to a resolution of 1.9 Å. OspA has a repetitive antiparallel β topology with an unusual nonglobular region of “freestanding” sheet connecting globular N- and C-terminal domains. Arrays of residues with alternating charges are a predominant feature of the folding pattern in the nonglobular region. The 184.1 epitope overlaps with a well conserved surface in the N-terminal domain, and a hydrophobic cavity buried in a positively charged cleft in the C-terminal domain is a potential binding site for an unknown ligand. An exposed variable region on the C-terminal domain of OspA is predicted to be an important factor in the worldwide effectiveness of OspA-based vaccines.
Photodynamic therapy results in induction of WAF1/CIP1/P21 leading to cell cycle arrest and apoptosis
Authors: Ahmad Nihal , Feyes Denise K. , Agarwal Rajesh , Mukhtar Hasan
Published: July 2002

Photodynamic therapy (PDT) is a promising new modality that utilizes a combination of a photosensitizing chemical and visible light for the management of a variety of solid malignancies. The mechanism of PDT-mediated cell killing is not well defined. We investigated the involvement of cell cycle regulatory events during silicon phthalocyanine (Pc4)-PDT-mediated apoptosis in human epidermoid carcinoma cells A431. PDT resulted in apoptosis, inhibition of cell growth, and G
0
-G
1
phase arrest of the cell cycle, in a time-dependent fashion. Western blot analysis revealed that PDT results in an induction of the cyclin kinase inhibitor WAF1/CIP1/p21, and a down-regulation of cyclin D1 and cyclin E, and their catalytic subunits cyclin-dependent kinase (cdk) 2 and cdk6. The treatment also resulted in a decrease in kinase activities associated with all the cdks and cyclins examined. PDT also resulted in (
i
) an increase in the binding of cyclin D1 and cdk6 toward WAF1/CIP1/p21, and (
ii
) a decrease in the binding of cyclin D1 toward cdk2 and cdk6. The binding of cyclin E and cdk2 toward WAF1/CIP1/p21, and of cyclin E toward cdk2 did not change by the treatment. These data suggest that PDT-mediated induction of WAF1/CIP1/p21 results in an imposition of artificial checkpoint at G
1
 → S transition thereby resulting in an arrest of cells in G
0
-G
1
phase of the cell cycle through inhibition in the cdk2, cdk6, cyclin D1, and cyclin E. We suggest that this arrest is an irreversible process and the cells, unable to repair the damages, ultimately undergo apoptosis.
Localization of tumor suppressor activity important in nonsmall cell lung carcinoma on chromosome 11q
Authors: Murakami Yoshinori , Nobukuni Takahiro , Tamura Kenji , Maruyama Tomoko , Sekiya Takao , Arai Yasuhito , Gomyou Hiroki , Tanigami Akira , Ohki Misao , Cabin Deborah , Frischmeyer Pam , Hunt Piper , Reeves Roger H.
Published: July 2002

Loss of heterozygosity on chromosome 11q23 is observed at high frequency in human nonsmall cell lung carcinomas (NSCLCs), suggesting the presence of a tumor suppressor gene. Previous analysis of DNA from 79 patients identified a commonly deleted segment of 5 centimorgans. Complementation analysis was used to further localize a putative tumor suppressor gene. Three yeast artificial chromosome (YAC) clones spanning the minimal loss of heterozygosity region were modified, and spheroplast fusion was used to transfer them into human A549 NSCLC or murine Lewis lung carcinoma (LLC) cell lines. The resulting yeast × human hybrid cell lines containing an intact copy of a 1.6-Mb YAC, 939b12, showed reduced growth
in vitro
. Injection of parental A549 cells into athymic (
nu/nu
) mice resulted in tumor formation at 27 of 28 injection sites. In contrast, two independent 939b12-containing cell lines formed tumors at only 3 of 20 injection sites. 939b12 also suppressed tumor formation by LLC NSCLC cells in nude mice, but YACs 785e12 and 911f2, which flank 939b12, had no suppressor activity. Further localization of tumor suppression activity on 939b12 was accomplished by introduction of defined fragmentation derivatives into A549 cells and by analysis of YACs that were broken on transfer into LLC cells. This complementation approach localized tumor suppression activity to the central 700 kb of 939b12 and provides a functional assay for positional cloning of this tumor suppressor gene.
Branch migration during Rad51-promoted strand exchange proceeds in either direction
Authors: Namsaraev Eugeni A. , Berg Paul
Published: July 2002

The
Saccharomyces cerevisiae
Rad51 protein is important for genetic recombination and repair of DNA double-strand breaks
in vivo
and can promote strand exchange between linear double-stranded DNA and circular single-stranded DNA
in vitro
. However, unlike
Escherichia coli
RecA, Rad51 requires an overhanging complementary 3′ or 5′ end to initiate strand exchange; given that fact, we previously surmised that the fully exchanged molecules resulted from branch migration in either direction depending on which type of end initiated the joint molecule. Our present experiments confirm that branch migration proceeds in either direction, the polarity depending on whether a 3′ or 5′ end initiates the joint molecules. Furthermore, heteroduplex DNA is formed rapidly, first at the overhanging end of the linear double-stranded DNA’s complementary strand and then more slowly by progressive lengthening of the heteroduplex region until strand exchange is complete. Although joint molecule formation occurs equally efficiently when initiated with a 3′ or 5′ overhanging end, branch migration proceeds more rapidly when it is initiated by an overhanging 3′ end, i.e., in the 5′ to 3′ direction with respect to the single-stranded DNA.
PAGE-1
, an X chromosome-linked
GAGE-
like gene that is expressed in normal and neoplastic prostate, testis, and uterus
Authors: Brinkmann Ulrich , Vasmatzis George , Lee Byungkook , Yerushalmi Noga , Essand Magnus , Pastan Ira
Published: July 2002

We have used a combination of computerized database mining and experimental expression analyses to identify a gene that is preferentially expressed in normal male and female reproductive tissues, prostate, testis, fallopian tube, uterus, and placenta, as well as in prostate cancer, testicular cancer, and uterine cancer. This gene is located on the human X chromosome, and it is homologous to a family of genes encoding GAGE-like proteins. GAGE proteins are expressed in a variety of tumors and in testis. We designate the novel gene
PAGE-1
because the expression pattern in the Cancer Genome Anatomy Project libraries indicates that it is predominantly expressed in normal and neoplastic prostate. Further database analysis indicates the presence of other genes with high homology to
PAGE-1
, which were found in cDNA libraries derived from testis, pooled libraries (with testis), and in a germ cell tumor library. The expression of
PAGE-1
in normal and malignant prostate, testicular, and uterine tissues makes it a possible target for the diagnosis and possibly for the vaccine-based therapy of neoplasms of prostate, testis, and uterus.
Characterization of covalent Adriamycin-DNA adducts
Authors: Zeman Steven M. , Phillips Don R. , Crothers Donald M.
Published: July 2002

Adriamycin is a popular antineoplastic agent whose ability to form covalent adducts with DNA has been correlated to cellular apoptosis (programmed cell death) in tumor models. We have isolated and purified this adduct formed under oxido-reductive (Fenton) conditions in Tris buffer. We show by homo- and heteronuclear NMR spectroscopy that the covalent Adriamycin-DNA adduct is structurally equivalent to that resulting from direct reaction with formaldehyde. Covalent linkage of the drug to one of the DNA strands confers remarkable stability to the duplex, indicated by a 162-fold reduction in the rate of strand displacement compared with the complex with noncovalently bound drug. Glyceraldehyde also engenders covalent Adriamycin-DNA complexes, providing a possible relevant biological context for
in vivo
adduct formation.
Inhibition of dipeptidyl peptidase IV by fluoroolefin-containingN-peptidyl-O-hydroxylamine peptidomimetics
Authors: Lin Jian , Toscano Paul J. , Welch John T.
Published: July 2002

Dipeptidyl peptidase IV (EC3.4.14.5; DPP IV), also known as the leukocyte differentiation antigen CD26 when found as an extracellular membrane-bound proline specific serine protease, cleaves a dipeptide from the N terminus of a polypeptide chain containing a proline residue in the penultimate position. Here we report that known(Z)-Ala-ψ[CF=C]-Pro dipeptide isosteres 1 and 2, which containO-acylhydroxylamines, were isolated as diastereomeric pairsu-1,l-1, andl-2. The effect of each diastereomeric pair as an inhibitor of human placental dipeptidyl peptidase DPP IV has been examined. The inhibition of DPP IV by these compounds is rapid and efficient. The diastereomeric pairu-1 exhibits very potent inhibitory activity with aKiof 188 nM. Fluoroolefin containingN-peptidyl-O-hydroxylamine peptidomimetics, by virtue of their inhibitory potency and stability, are superior toN-peptidyl-O-hydroxylamine inhibitors derived from an Ala-Pro dipeptide.
The antibody catalysis route to the total synthesis of epothilones
Authors: Sinha Subhash C. , Barbas Carlos F. , Lerner Richard A.
Published: July 2002

An efficient monoclonal aldolase antibody that proceeds by an enamine mechanism was generated by reactive immunization. Here, this catalyst has been used in the total synthesis of epothilones A (1) and C (3). The starting materials for the synthesis of these molecules have been obtained by using antibody-catalyzed aldol and retro-aldol reactions. These precursors were then converted to epothilones A (1) and C (3) to complete the total synthesis.
Human erythropoietin dimers with markedly enhancedin vivo activity
Authors: Sytkowski Arthur J. , Lunn Elizabeth Dotimas , Davis Kerry Lynn , Feldman Laurie , Siekman Suvia
Published: July 2002

Human erythropoietin, a widely used and important therapeutic glycoprotein, has a relatively short plasma half-life due to clearance by glomerular filtration as well as by other mechanisms. We hypothesized that an erythropoietin species with a larger molecular size would exhibit an increased plasma half-life and, potentially, an enhanced biological activity. We now report the production of biologically active erythropoietin dimers and trimers by chemical crosslinking of the conventional monomeric form. We imparted free sulfhydryl residues to a pool of erythropoietin monomer by chemical modification. A second pool was reacted with another modifying reagent to yield monomer with maleimido groups. Upon mixing these two pools, covalently linked dimers and trimers were formed that were biologically activein vitro. The plasma half-life of erythropoietin dimers in rabbits was >24 h compared with 4 h for the monomers. Importantly, erythropoietin dimers were biologically activein vivoas shown by their ability to increase the hematocrits of mice when injected subcutaneously. In addition, the dimers exhibited >26-fold higher activityin vivothan did the monomers and were very effective after only one dose. Dimeric and other oligomeric forms of Epo may have an important role in therapy.
Brome mosaic virus RNA replication protein 1a dramatically increases
in vivo
stability but not translation of viral genomic RNA3
Authors: Janda Michael , Ahlquist Paul
Published: July 2002

Brome mosaic virus (BMV), a positive-strand RNA virus in the alphavirus-like superfamily, encodes two RNA replication proteins: 1a, which contains a helicase-like domain and a domain implicated in RNA capping, and 2a, which contains a polymerase-like domain. To further explore their functions, we expressed 1a and 2a individually and together in yeast also expressing replicatable transcripts of BMV genomic RNA3. Complementing prior results that 1a and 2a are required jointly for positive-strand RNA synthesis, both also were required for negative-strand RNA synthesis. Nevertheless, in the absence of 2a, 1a expression increased the accumulation of DNA-derived RNA3 transcripts 8-fold. Increased accumulation was specific for RNA3: none of a diverse set of yeast mRNAs tested showed increased accumulation in the presence of 1a. Increased RNA3 accumulation was not due to increased DNA transcription, but to a 20- to 40-fold increase in the
in vivo
half-life of RNA3 from 5–10 min in the absence of 1a to more than 3 hr in the presence of 1a. Although (1a+2a)-dependent RNA replication selectively amplified the natural viral 5′ end from among multiple transcription starts of DNA-derived RNA3 transcripts, 1a-induced stabilization affected all RNA3 transcripts, without specificity for the precise viral 5′ end. Increased RNA3 accumulation did not increase expression of a directly translatable, 5′-proximal gene in RNA3, implying that 1a-induced stabilization blocked rather than facilitated RNA3 translation. These and other results suggest that the striking, 1a-induced stabilization of RNA3 may reflect an interaction involved in recruiting viral RNA templates into RNA replication while diverting them from the competing processes of translation and degradation.
High- and low-affinity single-peptide/MHC ligands have distinct effects on the development of mucosal CD8αα and CD8αβ T lymphocytes
Authors: Levelt Christiaan N. , de Jong Ype P. , Mizoguchi Emiko , O’Farrelly Cliona , Bhan Atul K. , Tonegawa Susumu , Terhorst Cox , Simpson Stephen J.
Published: July 2002

In this study, we compared the influence of two peptides on the selection of CD8αα and CD8αβ intraepithelial lymphocytes (IELs) of the intestine, which develop by a unique and partially thymus-independent process. Mice were used in which all T cells carried one transgenic T cell antigen receptor (TCR) (F5), and in which only well defined transgenic peptides were presented by H-2Db. The first peptide, for which the F5 TCR has a high affinity, derives from the influenza virus nucleoprotein (NP68). The second peptide, NP34, is an antagonistic variant of NP68 and is recognized by the F5 TCR with low affinity. To avoid presentation of endogenous peptides or production of T cells carrying alternative TCRs, F5 TCR transgenic mice were generated that were deficient for Tap-1 and Rag-1. In these mice, no CD3+CD8+cells were found in lymph nodes, spleen, or intestine. Introduction of transgenes encoding either NP34 or NP68 along with an endoplasmic reticulum signal sequence enabled Tap-1-independent expression of each peptide in these mice. Positive selection of F5TCR+CD8+thymocytes was not rescued by these transgenic peptides. However, the high-affinity NP68 peptide induced maturation of CD8αα IEL, whereas the low-affinity NP34 peptide stimulated development of both CD8αβ and CD8αα IEL, but in smaller numbers. When both peptides were present, CD8αβ T cells failed to develop and the number of CD8αα IELs was lower than in mice carrying the NP68 transgene alone. These data demonstrate that single ligands with a high or low affinity for TCR are capable of inducing or inhibiting the maturation of alternative subsets of IELs.
RecA polymerization on double-stranded DNA by using single-molecule manipulation: The role of ATP hydrolysis
Authors: Shivashankar G. V. , Feingold M. , Krichevsky O. , Libchaber A.
Published: July 2002

The polymerization of RecA on individual double-stranded DNA molecules is studied. A linear DNA (λ DNA, 48.5 Kb), anchored at one end to a cover glass and at the other end to an optically trapped 3-μm diameter polystyrene bead, serves as a template. The elongation caused by RecA assembly is measured in the presence of ATP and ATP[γS]. By using force extension and hydrodynamic recoil, a value of the persistence length of the RecA–DNA complex is obtained. In the presence of ATP, the polymer length is unstable, first growing to saturation and then decreasing. This suggests a transient dynamics of association and dissociation for RecA on a double-stranded DNA, the process being controlled by ATP hydrolysis. Part of this dynamics is suppressed in the presence of ATP[γS], leading to a stabilized RecA–DNA complex. A one-dimensional nucleation and growth model is presented that may account for the protein assembly.