bluuebunny/crossref_metadata_2025 huggingface dataset:
OEDIPUS-C observations of electrons accelerated by radio frequency fields at whistler-mode frequencies
Authors: James H. G. , Sotnikov V. I. , Burke W. J. , Huang C. Y.
Published: July 2002

Simultaneous measurements of transmitted 500 kHz electric fields and of electron fluxes nonlinearly energized by those fields were made during the ionospheric flight of the rocket double payload OEDIPUS C. Given the local plasma parameters, 500 kHz corresponded to the whistler mode of cold-plasma propagation. As the separation between each payload end increased from 153 to 537 m, enhanced electron fluxes were detected at energies up to 20 keV, at the receiver end of the tether. Rf (radio frequency) electric fields created by the OEDIPUS-C transmitter have been computed for positions close to the whistler-mode group resonance cone and also for locations very close to the active dipoles. Test-particle trajectory tracings show that linear acceleration can account for the energy increases of electrons with starting energies up to about 100 eV. Neither resonant field-particle interactions of background energetic electrons nor strong turbulence of the background thermal particles explain the creation of sounder-accelerated electrons at 1–10 keV. The calculated magnitudes of the very near potentials, up to 550 V, point to acceleration by intense fields in the rf sheath region.
Ion temperature gradient turbulence simulations and plasma flux surface shape
Authors: Waltz R. E. , Miller R. L.
Published: July 2002

A generalization of the circular ŝ-α local magnetohydrodynamic (MHD) equilibrium model to finite aspect ratio (A), elongation (κ), and triangularity (δ) has been added to a gyrokinetic stability code and our gyrofluid nonlinear ballooning mode code for ion temperature gradient (ITG) turbulence. This allows systematic studies of stability and transport for shaped flux surfaces with the same minor midplane radius label (r), plasma gradients, q, ŝ, and α while varying A, κ, and δ. It is shown that the (linear, nonlinear, and sheared) E×B terms in the equation of motion are unchanged from a circle at radius r with an effective field Bunit=B0ρdρ/rdr, where χ=B0ρ2/2 is the toroidal flux, r is the flux surface label, and B0 is the magnetic axis field. This leads to a “natural gyroBohm diffusivity” χnatural, which at moderate q=2 to 3 is weakly dependent on shape (κ) at fixed Bunit. Since Bunit/B0∝κ and 〈|∇r|2〉≈(1+κ2)/(2κ2), the label independent χITER=χnatural/〈|∇r|2〉 at fixed B0 scales as 2/(1+κ2) with much weaker scaling at high-q and stronger at low-q where increased κ is stabilizing. The generalized critical E×B shear rate to be compared to the maximum linear growth rate is a flux surface quantity (r/q)d/dr(cq/rBunitdφ0/dr)=(r/q)d(Ex0/BpR)/dr.
Higher mode stability in spheromak equilibria
Authors: Shumlak U. , Jarboe T. R.
Published: July 2002

Spheromak equilibria with current profiles varying from peaked to hollow are analyzed for higher mode stability using a linear magnetohydrodynamic (MHD) code. For a cylindrical flux conserver with a radius equal to length the n=2, m=2 mode is found to be marginally unstable for the same hollow current profile as the n=1, m=1 mode. While the growth rate for this n=2 mode is much lower than the n=1 mode, the presence of the n=2 mode may explain experimentally observed relaxation phenomena involving short wavelength turbulence in spheromak equilibria with sufficiently hollow current profiles.
Three-dimensional spontaneous magnetic reconnection in neutral current sheets
Authors: Schumacher Jörg , Kliem Bernhard , Seehafer Norbert
Published: July 2002

Magnetic reconnection in an antiparallel uniform Harris current sheet equilibrium, which is initially perturbed by a region of enhanced resistivity limited in all three dimensions, is investigated through compressible magnetohydrodynamic simulations. Variable resistivity, coupled to the dynamics of the plasma by an electron–ion drift velocity criterion, is used during the evolution. A phase of magnetic reconnection amplifying with time and leading to eruptive energy release is triggered only if the initial perturbation is strongly elongated in the direction of current flow or if the threshold for the onset of anomalous resistivity is significantly lower than in the corresponding two-dimensional case. A Petschek-like configuration is then built up for ∼102 Alfvén times, but remains localized in the third dimension. Subsequently, a change of topology to an O-line at the center of the system (“secondary tearing”) occurs. This leads to enhanced and time-variable reconnection, to a second pair of outflow jets directed along the O-line, and to expansion of the reconnection process into the third dimension. High parallel current density components are created mainly near the region of enhanced resistivity.
Low-frequency dispersion properties of plasmas with variable-charge impurities
Authors: Ostrikov K. N. , Vladimirov S. V. , Yu M. Y. , Morfill G. E.
Published: July 2002

A theory of low-frequency dust-acoustic waves in low-temperature collisional plasmas containing variable-charge impurities is presented. Physical processes such as dust-charge relaxation, ionization-recombination of the electrons and ions, electron and ion elastic collisions with neutrals and dusts, as well as charging collisions with the dusts, are taken into account. Inclusion of these processes allows a balance of the plasma particles and thus a self-consistent determination of the stationary state of the unperturbed plasma. The generalized dispersion relation describing the propagation and damping of the dust acoustic waves is derived and analyzed.
Magnetohydrodynamic treatment of collisional transport in toroidal configurations: Application to elliptic cross sections
Authors: Martin P.
Published: July 2002

Transport in the collisional regime is analyzed here for tokamaks and compact toroid of any shape. Toroidal axisymmetry is assumed. The treatment is performed with an improved system of coordinates, here described. Pfirsch–Schlüter current is determined in a general case. The average velocity around a magnetic surface is found as a function of closed geometrical integrals and separated factors that include the electric and magnetic fields. The contribution of the induced electric field Eφ is analyzed and the similarities with the Ware pinch are shown. The general equations have been applied to families of nested curves with elliptic shapes.
Role of thin multiquantum wells in controlling intrinsic interface quality in molecular beam epitaxially grown heterostructures
Authors: Singh Jasprit , Bajaj K. K.
Published: July 2002

A model based on Monte Carlo simulations and theory of statistical fluctuations is presented for molecular beam epitaxy growth of III-V semiconductors. It is shown that under normally employed growth conditions, cation surface migration controls the surface (interface) quality. The surface of a growing film gets rougher with increasing thickness of the film due to statistical fluctuations in the cation flux and limited cation migration. An important outcome of this theory is that the substrate temperature for high quality semiconductor surfaces and interfaces can be substantially reduced if growth is punctuated by thin layers (5–10 monolayers) of a low melting temperature semiconductor. Potential use of thin layers of InAs and GaAs for low-temperature growth of GaAs and AlGaAs, respectively, is discussed.
Oxygen-rich polycrystalline magnesium oxide—A high quality thin-film dielectric
Authors: Hebard A. F. , Fiory A. T. , Nakahara S. , Eick R. H.
Published: July 2002

Sputtering of a magnesium target with a beam of argon ions in the presence of a partial pressure of reactive oxygen gas has been found to yield smooth MgOx thin-film dielectrics with low electrical loss, good mechanical stability, and excellent reproducibility. The films consist of polycrystalline MgO with a grain size ≲50 Å and an OH-containing component. The thickness dependence of the areal capacitance is discussed in the context of a two-layer model in which this oxygen-rich phase (x≂1.4) overlays a thin (≲40 Å) stoichiometric phase (x≂1.0). Observation of superconducting tunneling characteristics in trilayer Au-MgOx-Pb structures confirms pinhole-free coverage which may have possible application as artificial tunnel barriers.
Active Q switching in a GaAs/AlGaAs multiquantum well laser with an intracavity monolithic loss modulator
Authors: Arakawa Y. , Larsson A. , Paslaski J. , Yariv A.
Published: July 2002

Active Q switching in a GaAs/AlGaAs multiquantum well laser with an intracavity electroabsorption monolithic loss modulator is demonstrated. In this device, an efficient loss modulation is achieved through the quantum confined Stark effect in a modulator section and the enhanced carrier induced band shrinkage effect in an optical amplifier section. It is found that a picosecond pulse as narrow as 18.6 ps full width at half-maximum is generated and a high repetition rate of more than 3 GHz is obtained.
Capless rapid thermal annealing of GaAs using an enhanced overpressure proximity technique
Authors: Armiento C. A. , Prince F. C.
Published: July 2002

A new approach for capless rapid thermal annealing of ion implanted III-V semiconductors, the enhanced overpressure proximity (EOP) technique, has been developed and applied to GaAs implanted with Si+. The EOP method relies on the use of a Sn-coated GaAs wafer to provide a localized arsenic overpressure around the ion implanted wafer during the annealing cycle. The arsenic overpressure resulting from this arrangement is greater than the overpressure obtained with the conventional proximity method, which utilizes an untreated GaAs wafer as an arsenic source. This new annealing technique has yielded higher electrical activation and electron mobilities in GaAs than the conventional proximity method as well as an increased latitude in annealing times and temperatures. The EOP approach can be easily extended for capless rapid thermal annealing of other III-V compounds such as InP and InGaAs.
High power, high intensity CO infrared laser transmission through As2S3 glass fibers
Authors: Sato Shun-ichi , Watanabe Shusuke , Fujioka Tomoo , Saito Mitsunori , Sakuragi Shiro
Published: July 2002

Optical power transmission of 5-μm band CO laser beam through As2S3 glass core Teflon fluorinated ethylene propylene clad fibers is described. The maximum transmitted power is as high as 62 W with a 700-μm core diameter fiber, which corresponds to a power intensity of 16 kW/cm2 at the fiber output end. The influence of fiber bending on the transmission characteristics is also reported.
Electroabsorption in an InGaAs/GaAs strained-layer multiple quantum well structure
Authors: Van Eck T. E. , Chu P. , Chang W. S. C. , Wieder H. H.
Published: July 2002

Electroabsorption in an InGaAs/GaAs strained-layer multiple quantum well structure has been observed. With only ten quantum wells, 6.4% transmission modulation was obtained at 0.950 μm with 2 V reverse bias. A single absorption peak was observed, in contrast to the double peak observed in similar GaAs/AlGaAs structures. The present structure is fabricated on a GaAs substrate which is transparent to light at the exciton absorption wavelength.
Reactively sputtered RuO2 diffusion barriers
Authors: Kolawa E. , So F. C. T. , Pan E. T-S. , Nicolet M-A.
Published: July 2002

The thermal stability of reactively sputtered RuO2 films is investigated from the point of view of their application as diffusion barriers in silicon contact metallizations with an Al overlayer. Backscattering spectra of Si/RuO2/Al samples and electrical measurements on shallow junction diodes with 〈Si〉/TiSi2.3/RuO2/Al contacts both show that RuO2 films are effective diffusion barriers between Al and Si for 30-min annealing at temperatures as high as 600 °C.
Three-dimensional reconstruction of the ion velocity distribution function of plasma with a retarding-grid analyzer
Authors: Iwama Naofumi , Lehner Thierry , Noziri Hisayoshi , Okado Masataka
Published: July 2002

A study of computerized tomography is made for the purpose of reconstructing the ion velocity distribution function of plasma in the three-dimensional velocity space. A conventional type of ion energy analyzer with retarding grids is rotated in a plasma in order to acquire the data to be processed. Experimental results are presented on an argon plasma with a low-energy ion beam, which is generated in a double-plasma machine.
Resonant tunneling and negative differential resistance in a variably spaced superlattice energy filter
Authors: Summers C. J. , Brennan K. F. , Torabi A. , Harris H. M.
Published: July 2002

Resonant tunneling is reported for the first time in a series of variably spaced AlGaAs/GaAs multiple quantum well structures in which the levels in adjacent quantum wells are brought into alignment by an applied bias. Resonant tunneling and negative differential resistance effects are observed for two- and three-well structures designed for electron injection at voltages between 0.1 and 0.2 V.
Impurity-induced layer disordering of high gap Iny(AlxGa1−x)1−yP heterostructures
Authors: Deppe D. G. , Nam D. W. , Holonyak N. , Hsieh K. C. , Baker J. E. , Kuo C. P. , Fletcher R. M. , Osentowski T. D. , Craford M. G.
Published: July 2002

Data are presented showing the impurity-induced layer disordering (IILD), via low-temperature (600–675 °C) Zn diffusion, of In0.5(AlxGa1−x)0.5P quantum well heterostructures and an In0.5Al0.2Ga0.3P-GaAs heterojunction grown using metalorganic chemical vapor deposition. Secondary ion mass spectroscopy, transmission electron microscopy, and photoluminescence are used to confirm IILD, which occurs via atom intermixing on the column III site aided by column-III-atom interstitials. In addition, high-temperature anneals (800–850 °C) are performed on the same crystals to confirm the thermal stability of the heterointerfaces.
Monte Carlo study of electron heating and enhanced thermionic emission by hot phonons in heterolayers
Authors: Kim Kiwook , Hess Karl , Capasso Federico
Published: July 2002

We present a numerical study of the effects of nonthermal phonon distributions on electron transport across heterolayers. For the microscopic analysis of both the electron and phonon dynamics, an ensemble Monte Carlo method has been used which includes a realistic band structure. It is observed that the abrupt energy gain at the heterointerface generates significant perturbations in the phonon distribution through the subsequent relaxation and heats the electron distribution because of the reabsorption of nonequilibrium phonons. The influence of a wide range of operating conditions on hot-phonon effects is also discussed.
Nearly ideal electronic surfaces on naked In0.53Ga0.47As quantum wells
Authors: Yablonovitch E. , Cox H. M. , Gmitter T. J.
Published: July 2002

We have discovered that hydroxide-coated In0.53Ga0.47Ag has the lowest known surface recombination velocity of any III-V semiconductor. To demonstrate the excellent electronic quality of such interfaces, we have measured the quantum shifts in the room-temperature luminescence spectrum of ‘‘naked’’ In0.53Ga0.47As quantum wells (i.e., quantum wells with one face uncovered) in the thickness range 15–50 Å. These nearly ideal electronic surfaces should allow the fabrication of lateral quantum confinement structures that operate at room temperature.
Growth, regeneration, and tumorigenesis of the prostate activates the PSCA promoter
Authors: Watabe Tetsuro , Lin Mark , Ide Hisamitsu , Donjacour Annemarie A. , Cunha Gerald R. , Witte Owen N. , Reiter Robert E.
Published: July 2002

The prostate gland undergoes dramatic changes in growth
status during normal physiologic development, following androgen
administration to castrate animals, and during tumor
development. The prostate stem cell antigen (PSCA, named for its
strong sequence homology to the thymocyte marker stem cell antigen 2)
is a cell surface molecule associated with human and murine prostate
cancer. To help define the regulation of this molecule, we created a
transgenic mouse strain, which uses the human PSCA promoter region to
control the expression of enhanced green fluorescent protein (GFP).
Expression of GFP was detected in mid-gestation following the
appearance of prostatic buds from the urogenital sinus. In adult mice,
GFP expression was restricted to a subset of cells located in the
distal tips of the glands. GFP expression increased during puberty and
regeneration driven by androgen and associated with expansive growth of
the prostate. GFP-positive cells coexpressed markers associated with
both basal and secretory cells in the human prostate. Prostate
carcinogenesis driven by T antigen in the
tr
ansgenic
a
denocarcinoma of the
m
ouse
p
rostate (TRAMP) model results in an increased
percentage and intensity level for PSCA promoter-driven GFP-positive
cells. This transgenic system helps define the range of cellular
changes associated with altered expression of PSCA, shows that
transcriptional control is a major component regulating PSCA levels,
and provides a useful tool to study subpopulations of prostate
epithelial cells and factors that regulate the PSCA promoter.
Combinatorial approaches: A new tool to search for highly structured β-hairpin peptides
Authors: Pastor Maria Teresa , López de la Paz Manuela , Lacroix Emmanuel , Serrano Luis , Pérez-Payá Enrique
Published: July 2002

Here we present a combinatorial approach to evolve a stable β-hairpin fold in a linear peptide. Starting with ade novo-designed linear peptide that shows a β-hairpin structure population of around 30%, we selected four positions to build up a combinatorial library of 204sequences. Deconvolution of the library using circular dichroism reduced such a sequence complexity to 36 defined sequences. Circular dichroism and NMR of these peptides resulted in the identification of two linear 14-aa-long peptides that in plain buffered solutions showed a percentage of β-hairpin structure higher than 70%. Our results show how combinatorial approaches can be used to obtain highly structured peptide sequences that could be used as templates in which functionality can be introduced.
The missing organic molecules on Mars
Authors: Benner Steven A. , Devine Kevin G. , Matveeva Lidia N. , Powell David H.
Published: July 2002

GC-MS on the Viking 1976 Mars missions did not detect organic
molecules on the Martian surface, even those expected from meteorite
bombardment. This result suggested that the Martian regolith might hold
a potent oxidant that converts all organic molecules to carbon dioxide
rapidly relative to the rate at which they arrive. This conclusion is
influencing the design of Mars missions. We reexamine this conclusion
in light of what is known about the oxidation of organic compounds
generally and the nature of organics likely to come to Mars via
meteorite. We conclude that nonvolatile salts of benzenecarboxylic
acids, and perhaps oxalic and acetic acid, should be metastable
intermediates of meteoritic organics under oxidizing conditions. Salts
of these organic acids would have been largely invisible to GC-MS.
Experiments show that one of these, benzenehexacarboxylic acid
(mellitic acid), is generated by oxidation of organic matter known to
come to Mars, is rather stable to further oxidation, and would not have
been easily detected by the Viking experiments. Approximately 2 kg of
meteorite-derived mellitic acid may have been generated per
m
2
of Martian surface over 3 billion years. How much
remains depends on decomposition rates under Martian conditions. As
available data do not require that the surface of Mars be very strongly
oxidizing, some organic molecules might be found near the surface of
Mars, perhaps in amounts sufficient to be a resource. Missions should
seek these and recognize that these complicate the search for organics
from entirely hypothetical Martian life.
Membrane hyperpolarization removes inactivation of Ca
2+
channels, leading to Ca
2+
influx and subsequent initiation of sperm motility in the common carp
Authors: Krasznai Zoltán , Márián Teréz , Izumi Hiroko , Damjanovich Sándor , Balkay László , Trón Lajos , Morisawa Masaaki
Published: July 2002

Change of osmolality surrounding spawned sperm from isotonic to hypotonic causes the initiation of sperm motility in the common carp. Here we show that membrane-permeable cAMP does not initiate motility of carp sperm that is quiescent in isotonic solution, and that motility of the demembranated sperm can be reactivated without cAMP. Furthermore, the cAMP level does not change during the initiation of sperm motility, and inhibitors of protein kinase do not affect sperm motility, suggesting that no cAMP-dependent system is necessary for the regulation of sperm motility. Sperm motility could not be initiated in Ca
2+
-free hypoosmotic solutions, and significant increase in the intracellular Ca
2+
level was observed by a Ca-sensitive fluorescence dye during hypoosmolality-induced active motion period. The demembranated sperm cells were fully reactivated in the solutions containing 10
−7
to 10
−5
M Ca
2+
. Ca
2+
channel blockers such as verapamil and ω-conotoxin reversibly inhibited the initiation of sperm motility, suggesting that Ca
2+
influx is the prerequisite for the initiation of carp sperm motility. Motility of intact sperm was completely blocked; however, that of the demembranated sperm was not inhibited by the calmodulin inhibitor W7, suggesting that the calmodulin bound close to the plasma membrane participated in the initiation of sperm motility. Flow cytometric membrane potential measurements and spectrophotometric measurements by using fluorescence dyes showed transient membrane hyperpolarization on hypoosmolality-induced motility. This article discusses the role of membrane hyperpolarization on removal of inactivation of Ca
2+
channels, leading to Ca
2+
influx at the initiation of carp sperm motility.
Patterned deposition of cells and proteins onto surfaces by using three-dimensional microfluidic systems
Authors: Chiu Daniel T. , Jeon Noo Li , Huang Sui , Kane Ravi S. , Wargo Christopher J. , Choi Insung S. , Ingber Donald E. , Whitesides George M.
Published: July 2002

Three-dimensional microfluidic systems were fabricated and used to
pattern proteins and mammalian cells on a planar substrate. The
three-dimensional topology of the microfluidic network in the stamp
makes this technique a versatile one with which to pattern multiple
types of proteins and cells in complex, discontinuous structures on a
surface. The channel structure, formed by the stamp when it is in
contact with the surface of the substrate, limits migration and growth
of cells in the channels. With the channel structure in contact with
the surface, the cells stop dividing once they form a confluent layer.
Removal of the stamp permits the cells to spread and divide.
Environment-dependent residue contact energies for proteins
Authors: Zhang Chao , Kim Sung-Hou
Published: July 2002

We examine the interactions between amino acid residues in the
context of their secondary structural environments (helix, strand, and
coil) in proteins. Effective contact energies for an expanded
60-residue alphabet (20 aa × three secondary structural states)
are estimated from the residue–residue contacts observed in known
protein structures. Similar to the prototypical contact energies for 20
aa, the newly derived energy parameters reflect mainly the hydrophobic
interactions; however, the relative strength of such interactions shows
a strong dependence on the secondary structural environment, with
nonlocal interactions in β-sheet structures and α-helical
structures dominating the energy table. Environment-dependent residue
contact energies outperform existing residue pair potentials in both
threading and three-dimensional contact prediction tests and should be
generally applicable to protein structure prediction.
Role of the F-box protein Skp2 in lymphomagenesis
Authors: Latres Esther , Chiarle Roberto , Schulman Brenda A. , Pavletich Nikola P. , Pellicer Angel , Inghirami Giorgio , Pagano Michele
Published: July 2002

The F-box protein Skp2 (S-phase kinase-associated protein 2) positively regulates the G1-S transition by controlling the stability of several G1regulators, such as the cell cycle inhibitor p27. We show here that Skp2 expression correlates directly with grade of malignancy and inversely with p27 levels in human lymphomas. To directly evaluate the potential of Skp2 to deregulate growthin vivo, we generated transgenic mice expressing Skp2 targeted to the T-lymphoid lineage as well as double transgenic mice coexpressing Skp2 and activated N-Ras. A strong cooperative effect between these two transgenes induced T cell lymphomas with shorter latency and higher penetrance, leading to significantly decreased survival when compared with control and single transgenic animals. Furthermore, lymphomas ofNrassingle transgenic animals often expressed higher levels of endogenous Skp2 than tumors of double transgenic mice. This study provides evidence of a role for an F-box protein in oncogenesis and establishesSKP2as a protooncogene causally involved in the pathogenesis of lymphomas.
Proteome-scale purification of human proteins from bacteria
Authors: Braun Pascal , Hu Yanhui , Shen Binghua , Halleck Allison , Koundinya Malvika , Harlow Ed , LaBaer Joshua
Published: July 2002

The completion of the human genome project and the development of high-throughput approaches herald a dramatic acceleration in the pace of biological research. One of the most compelling next steps will be learning the functional roles of all proteins. Achievement of this goal depends in part on the rapid expression and isolation of proteins at large scale. We exploited recombinational cloning to facilitate the development of methods for the high-throughput purification of human proteins. cDNAs were introduced into a master vector from which they could be rapidly transferred into a variety of protein expression vectors for further analysis. A test set of 32 sequence-verified human cDNAs of various sizes and activities was moved into four different expression vectors encoding different affinity-purification tags. By means of an automatable 2-hr protein purification procedure, all 128 proteins were purified and subsequently characterized for yield, purity, and steps at which losses occurred. Under denaturing conditions when the His
6
tag was used, 84% of samples were purified. Under nondenaturing conditions, both the glutathione
S
-transferase and maltose-binding protein tags were successful in 81% of samples. The developed methods were applied to a larger set of 336 randomly selected cDNAs. Sixty percent of these proteins were successfully purified under denaturing conditions and 82% of these under nondenaturing conditions. A relational database, FLEXProt, was built to compare properties of proteins that were successfully purified and proteins that were not. We observed that some domains in the Pfam database were found almost exclusively in proteins that were successfully purified and thus may have predictive character.
Expression and function of wingless and frizzled homologs in rheumatoid arthritis
Authors: Sen Malini , Lauterbach Kevin , El-Gabalawy Hani , Firestein Gary S. , Corr Maripat , Carson Dennis A.
Published: July 2002

Rheumatoid arthritis (RA) is accompanied by synovial inflammation, proliferation, and cartilage destruction. The reasons the activation of synovial fibroblasts often persists despite antiinflammatory therapy are not known. One possibility is that the synovial membrane becomes gradually repopulated with immature mesenchymal and bone marrow cells with altered properties. To explore this hypothesis, we have investigated the expression in RA synovial tissues of various embryonic growth factors from the wingless (wnt) and frizzled (fz) families, which have been implicated in cell-fate determination in both bone marrow progenitors and limb-bud mesenchyme. Reverse transcriptase–PCR analysis revealed expression of fivewnt(wnt1,5a,10b,11, and13) and threefz(fz2,5, and7) isoforms in RA synovial tissues. Osteoarthritis synovial tissues expressed much lesswnt5aandfz5. Northern blotting confirmed the overexpression ofwnt5aandfz5in RA synovial tissues, in comparison to a panel of normal adult tissues. Compared with normal synovial fibroblasts, cultured RA fibroblast-like synoviocytes expressed higher levels of IL-6, IL-8, and IL-15. Transfection of normal fibroblasts with awnt5aexpression vector reproduced this pattern of cytokine expression and stimulated IL-15 secretion. These results suggest that the unusual phenotypic properties of RA fibroblasts may be attributable partly to their replacement with primitive fibroblast-like synoviocytes with characteristics of immature bone marrow and mesenchymal cells. Clear delineation of the signaling pathway(s) initiated by thewnt5a/fz5ligand–receptor pair in the RA synovium may yield new targets for therapeutic intervention.
The vitelliform macular dystrophy protein defines a new family of chloride channels
Authors: Sun Hui , Tsunenari Takashi , Yau King-Wai , Nathans Jeremy
Published: July 2002

Vitelliform macular dystrophy (VMD/Best disease; MIM*153700) is an early-onset autosomal dominant disorder in which accumulation of lipofuscin-like material within and beneath the retinal pigment epithelium is associated with a progressive loss of central vision. Bestrophin, the protein product of the VMD gene, has four predicted transmembrane domains. There are multiple bestrophin homologues in the human,
Drosophila
, and
Caenorhabditis elegans
genomes, but no function has previously been ascribed to these proteins, and they show no detectable homology to other proteins of known function. Using heterologous expression, we show here that human,
Drosophila
, and
C. elegans
bestrophins form oligomeric chloride channels, and that human bestrophin is sensitive to intracellular calcium. Each of 15 missense mutations asscociated with VMD greatly reduces or abolishes the membrane current. Four of these mutant bestrophins were coexpressed with the wild type and each dominantly inhibited the wild-type membrane current, consistent with the dominant nature of the disease. These experiments establish the existence of a new chloride channel family and VMD as a channelopathy.
The peroxisome proliferator-activated receptor δ, an integrator of transcriptional repression and nuclear receptor signaling
Authors: Shi Yanhong , Hon Michelle , Evans Ronald M.
Published: July 2002

The three PPAR (peroxisome proliferator-activated receptor) isoforms are critical regulators of lipid homeostasis by controlling the balance between the burning and storage of long chain fatty acids. Whereas PPARα and PPARγ have been studied extensively, the function of PPARδ remains the most elusive. Intriguingly, in cotransfection experiments, PPARδ is a potent inhibitor of ligand-induced transcriptional activity of PPARα and PPARγ. This inhibition is achieved, in part, by binding of PPARδ to a peroxisome proliferator response element and the association of nonliganded PPARδ with corepressors SMRT (silencing mediator for retinoid and thyroid hormone receptors), SHARP (SMRT and histone deacetylase-associated repressor protein), and class I histone deacetylases. Stable expression of PPARδ inhibits the expression of endogenous PPARα target gene expression in 3T3-PPARα cells, whereas a PPARδ mutant that does not interact with the corepressor SMRT loses its ability to repress the induction of PPARα target gene. Similarly, stable expression of PPARδ in 3T3-PPARγ cells leads to inhibition of PPARγ target gene expression and PPARγ-mediated adipogenesis. Given the widespread expression of PPARδ and the restricted pattern for PPARα and PPARγ, these results suggest a role for PPARδ as a gateway receptor whose relative levels of expression can be used to modulate PPARα and PPARγ activity.
BRCA1 transcriptionally regulates genes involved in breast tumorigenesis
Authors: Welcsh Piri L. , Lee Ming K. , Gonzalez-Hernandez Rachel M. , Black Daniel J. , Mahadevappa Mamatha , Swisher Elizabeth M. , Warrington Janet A. , King Mary-Claire
Published: July 2002

Loss of function of
BRCA1
caused by inherited mutation and tissue-specific somatic mutation leads to breast and ovarian cancer. Nearly all
BRCA1
germ-line mutations involve truncation or loss of the C-terminal BRCT transcriptional activation domain, suggesting that transcriptional regulation is a critical function of the wild-type gene. The purpose of this project was to determine whether there is a link between the role of BRCA1 in transcriptional regulation and its role in tumor suppression. We developed a cell line (in which BRCA1 can be induced) and used microarray analysis to compare transcription profiles of epithelial cells with low endogenous levels of BRCA1 vs. transcription profiles of cells with 2–4-fold higher induced levels of expression of BRCA1. At these levels of expression, BRCA1 did not induce apoptosis. Undirected cluster analysis of six paired experiments revealed 373 genes, the expression of which was altered significantly and consistently by BRCA1 induction. Expression of 62 genes was altered more than 2-fold. BRCA1-regulated genes associated with breast tumorigenesis included the estrogen-responsive genes
MYC
and cyclin D1, which are overexpressed in many breast tumors;
STAT1
and
JAK1
, key components of the cytokine signal transduction pathway; the extracellular matrix protein laminin 3A;
ID4
, an inhibitor of DNA-binding transcriptional activators, which in turn negatively regulates
BRCA1
expression; and the prohormone stanniocalcin, expression of which is lost in breast tumor cells. Coordinated expression of BRCA1 with ID4 and with stanniocalcin was confirmed in primary breast and ovarian tumors.
Polymerization of a single protein of the pathogen
Yersinia enterocolitica
into needles punctures eukaryotic cells
Authors: Hoiczyk Egbert , Blobel Günter
Published: July 2002

A number of pathogenic, Gram-negative bacteria are able to secrete
specific proteins across three membranes: the inner and outer bacterial
membrane and the eukaryotic plasma membrane. In the pathogen
Yersinia enterocolitica
, the primary structure of the
secreted proteins as well as of the components of the secretion
machinery, both plasmid-encoded, is known. However, the mechanism of
protein translocation is largely unknown. Here we show that
Y.
enterocolitica
polymerizes a 6-kDa protein of the secretion
machinery into needles that are able to puncture the eukaryotic plasma
membrane. These needles form a conduit for the transport of specific
proteins from the bacterial to the eukaryotic cytoplasm, where they
exert their cytotoxic activity. In negatively stained electron
micrographs, the isolated needles were 60–80 nm long and 6–7 nm wide
and contained a hollow center of about 2 nm. Our data indicate that it
is the polymerization of the 6-kDa protein into these needles that
provides the force to perforate the eukaryotic plasma membrane.
Control of HIV-1 viremia and protection from AIDS are associated with HLA-Bw4 homozygosity
Authors: Flores-Villanueva Pedro O. , Yunis Edmond J. , Delgado Julio C. , Vittinghoff Eric , Buchbinder Susan , Leung Jessica Y. , Uglialoro Adele M. , Clavijo Olga P. , Rosenberg Eric S. , Kalams Spyros A. , Braun James D. , Boswell Stephen L. , Walker Bruce D. , Goldfeld Anne E.
Published: July 2002

Certain HLA-B antigens have been associated with lack of progression to AIDS. HLA-B alleles can be divided into two mutually exclusive groups based on the expression of the molecular epitopes HLA-Bw4 and HLA-Bw6. Notably, in addition to its role in presenting viral peptides for immune recognition, the HLA-Bw4, but not HLA-Bw6, motif functions as a ligand for a natural killer cell inhibitory receptor (KIR). Here, we show that profound suppression of HIV-1 viremia is significantly associated with homozygosity for HLA-B alleles that share the HLA-Bw4 epitope. Furthermore, homozygosity for HLA-Bw4 alleles was also significantly associated with the ability to remain AIDS free and to maintain a normal CD4 T cell count in a second cohort of HIV-1-infected individuals with well defined dates of seroconversion. This association was independent of the presence of a mutation in CC chemokine receptor 5 (CCR5) associated with resistance to HIV-1 infection, and it was independent of the presence of HLA alleles that could potentially confound the results. We conclude that homozygosity for HLA-Bw4-bearing B alleles is associated with a significant advantage and that the HLA-Bw4 motif is important in AIDS pathogenesis.
Outer mitochondrial membrane permeability can regulate coupled respiration and cell survival
Authors: Vander Heiden Matthew G. , Chandel Navdeep S. , Li Xiao Xian , Schumacker Paul T. , Colombini Marco , Thompson Craig B.
Published: July 2002

Coupled cellular respiration requires that ATP and ADP be efficiently exchanged between the cytosol and the mitochondrial matrix. When growth factors are withdrawn from dependent cells, metabolism is disrupted by a defect in ATP/ADP exchange across the mitochondrial membranes. Unexpectedly, we find that this defect results from loss of outer mitochondrial membrane permeability to metabolic anions. This decrease in anion permeability correlates with the changes in conductance properties that accompany closure of the voltage-dependent anion channel (also known as mitochondrial porin). Loss of outer membrane permeability (
i
) results in the accumulation of stored metabolic energy within the intermembrane space in the form of creatine phosphate, (
ii
) is prevented by the outer mitochondrial membrane proteins Bcl-x
L
and Bcl-2, and (
iii
) can be reversed by growth factor readdition. If outer membrane impermeability persists, the disruption of mitochondrial homeostasis culminates in loss of outer mitochondrial membrane integrity, cytochrome
c
redistribution, and apoptosis. The recognition that outer membrane permeability is regulated under physiological conditions has important implications for the understanding of bioenergetics and cell survival.
Characterization of PDZ-binding kinase, a mitotic kinase
Authors: Gaudet Suzanne , Branton Daniel , Lue Robert A.
Published: July 2002

hDlg, the human homologue of the
Drosophila D
iscs-
l
ar
g
e (Dlg) tumor suppressor protein, is known to interact with the tumor suppressor protein APC and the human papillomavirus E6 transforming protein. In a two-hybrid screen, we identified a 322-aa serine/threonine kinase that binds to the PDZ2 domain of hDlg. The mRNA for this PDZ-binding kinase, or PBK, is most abundant in placenta and absent from adult brain tissue. The protein sequence of PBK has all the characteristic protein kinase subdomains and a C-terminal PDZ-binding T/SXV motif.
In vitro
, PBK binds specifically to PDZ2 of hDlg through its C-terminal T/SXV motif. PBK and hDlg are phosphorylated at mitosis in HeLa cells, and the mitotic phosphorylation of PBK is required for its kinase activity.
In vitro
, cdc2/cyclin B phosphorylates PBK. This evidence shows how PBK could link hDlg or other PDZ-containing proteins to signal transduction pathways regulating the cell cycle or cellular proliferation.
A Nedd8 conjugation pathway is essential for proteolytic targeting of p27
Kip1
by ubiquitination
Authors: Podust Vladimir N. , Brownell James E. , Gladysheva Tatiana B. , Luo Rong-Shu , Wang Chunhua , Coggins Michael B. , Pierce Jacqueline W. , Lightcap Eric S. , Chau Vincent
Published: July 2002

Temporal control of p27
Kip1
(p27) degradation imposes periodicity in its activity during cell cycle progression and its accumulation during cell cycle exit. Degradation of p27 is initiated by phosphorylation of p27 at Thr-187, which marks the protein for ubiquitination by SCF
Skp2
and subsequent proteolysis by the 26S proteasome. Here we show that the p27 ubiquitination activity in cell extracts depends on the presence of the ubiquitin-like protein Nedd8 and enzymes that catalyze Nedd8 conjugation to proteins. Moreover, we show that reconstitution of the p27 ubiquitination activity of recombinant SCF
Skp2
also requires Nedd8 conjugation pathway components. Inactivation of the Nedd8 conjugation pathway by a dominant negative mutant of the Nedd8-conjugating enzyme Nce1/Ubc12 blocks the ubiquitination and degradation of p27 in cell extracts. Consistent with a role in cell-cycle progression, Nedd8 is expressed in proliferating cells and is itself down-regulated upon cellular differentiation. These results suggest that the Nedd8 conjugation pathway may regulate the turnover of p27
Kip1
, independently of p27 phosphorylation, and further establishes the identity of protein components involved in p27 ubiquitination. Finally, these findings provide a direct demonstration of a function for Nedd8 in a biological process.
Rescue of a pathogenic Marek's disease virus with overlapping cosmid DNAs: Use of a pp38 mutant to validate the technology for the study of gene function
Authors: Reddy Sanjay M. , Lupiani Blanca , Gimeno Isabel M. , Silva Robert F. , Lee Lucy F. , Witter Richard L.
Published: July 2002

Marek's disease virus (MDV) genetics has lagged behind that of other herpesviruses because of the lack of tools for the introduction of site-specific mutations into the genome of highly cell-associated oncogenic strains. Overlapping cosmid clones have been successfully used for the introduction of mutations in other highly cell-associated herpesviruses. Here we describe the development of overlapping cosmid DNA clones from a very virulent oncogenic strain of MDV. Transfection of these cosmid clones into MDV-susceptible cells resulted in the generation of a recombinant MDV (rMd5) with biological properties similar to the parental strain. To demonstrate the applicability of this technology for elucidation of gene function of MDV, we have generated a mutant virus lacking an MDV unique phosphoprotein, pp38, which has previously been associated with the maintenance of transformation in MDV-induced tumor cell lines. Inoculation of Marek's disease-susceptible birds with the pp38 deletion mutant virus (rMd5Δpp38) revealed that pp38 is involved in early cytolytic infection in lymphocytes but not in the induction of tumors. This powerful technology will speed the characterization of MDV gene function, leading to a better understanding of the molecular mechanisms of MDV pathogenesis. In addition, because Marek's disease is a major oncogenic system, the knowledge obtained from these studies may shed light on the oncogenic mechanisms of other herpesviruses.
Molecular dissection of hippocampal theta-burst pairing potentiation
Authors: Hoffman D. A. , Sprengel R. , Sakmann B.
Published: July 2002

Long-term potentiation (LTP) of synaptic efficacy in the hippocampus is frequently induced by tetanic stimulation of presynaptic afferents or by pairing low frequency stimulation with postsynaptic depolarization. Adult (P42) GluR-A
−/−
mice largely lack these forms of LTP. LTP in wt mice can also be induced by coincident pre- and postsynaptic action potentials, where an initial rapid component is expressed but a substantial fraction of the potentiation develops with a delayed time course. We report here that this stimulation protocol, delivered at theta frequency (5 Hz), induces LTP in GluR-A
−/−
mice in which the initial component is substantially reduced. The remaining GluR-A independent component differs from the initial component in that its expression develops over time after induction and its induction is differentially dependent on postsynaptic intracellular Ca
2+
buffering. Thus, in adult mice, theta-burst pairing evokes two forms of synaptic potentiation that are induced simultaneously but whose expression levels vary inversely with time. The two components of synaptic potentiation could be relevant for different forms of information storage that are dependent on hippocampal synaptic transmission such as spatial reference and working memory.
The Bloom's syndrome gene product promotes branch migration of Holliday junctions
Authors: Karow Julia K. , Constantinou Angelos , Li Ji-Liang , West Stephen C. , Hickson Ian D.
Published: July 2002

Bloom's syndrome (BS) is an autosomal recessive disorder associated with dwarfism, immunodeficiency, reduced fertility, and elevated levels of many types of cancer. BS cells show marked genomic instability; in particular, hyperrecombination between sister chromatids and homologous chromosomes. This instability is thought to result from defective processing of DNA replication intermediates. The gene mutated in BS,
BLM
, encodes a member of the RecQ family of DExH box DNA helicases, which also includes the Werner's syndrome gene product. We have investigated the mechanism by which BLM suppresses hyperrecombination. Here, we show that BLM selectively binds Holliday junctions
in vitro
and acts on recombination intermediates containing a Holliday junction to promote ATP-dependent branch migration. We present a model in which BLM disrupts potentially recombinogenic molecules that arise at sites of stalled replication forks. Our results have implications for the role of BLM as an anti-recombinase in the suppression of tumorigenesis.
Hybrid vigor, fetal overgrowth, and viability of mice derived by nuclear cloning and tetraploid embryo complementation
Authors: Eggan Kevin , Akutsu Hidenori , Loring Janet , Jackson-Grusby Laurie , Klemm Martina , Rideout William M. , Yanagimachi Ryuzo , Jaenisch Rudolf
Published: July 2002

To assess whether heterozygosity of the donor cell genome was a
general parameter crucial for long-term survival of cloned animals, we
tested the ability of embryonic stem (ES) cells with either an inbred
or F
1
genetic background to generate cloned mice by nuclear
transfer. Most clones derived from five F
1
ES cell lines
survived to adulthood. In contrast, clones from three inbred ES cell
lines invariably died shortly after birth due to respiratory failure.
Comparison of mice derived from nuclear cloning, in which a complete
blastocyst is derived from a single ES cell, and tetraploid blastocyst
complementation, in which only the inner cell mass is formed from a few
injected ES cells, allows us to determine which phenotypes depend on
the technique or on the characteristics of the ES cell line. Neonatal
lethality also has been reported in mice entirely derived from inbred
ES cells that had been injected into tetraploid blastocysts (ES
cell-tetraploids). Like inbred clones, ES cell-tetraploid pups derived
from inbred ES cell lines died shortly after delivery with signs of
respiratory distress. In contrast, most ES cell-tetraploid neonates,
derived from six F
1
ES cell lines, developed into fertile
adults. Cloned pups obtained from both inbred and F
1
ES
cell nuclei frequently displayed increased placental and birth weights
whereas ES cell-tetraploid pups were of normal weight. The potency of
F
1
ES cells to generate live, fertile adults was not lost
after either long-term
in vitro
culture or serial gene
targeting events. We conclude that genetic heterozygosity is a crucial
parameter for postnatal survival of mice that are entirely derived from
ES cells by either nuclear cloning or tetraploid embryo
complementation. In addition, our results demonstrate that tetraploid
embryo complementation using F
1
ES cells represents a
simple, efficient procedure for deriving animals with complex genetic
alterations without the need for a chimeric intermediate.