bluuebunny/crossref_metadata_2025 huggingface dataset:
Estimation of thermal durability and intrinsic critical currents of magnetization switching for spin-transfer based magnetic random access memory
Authors: Yagami K. , Tulapurkar A. A. , Fukushima A. , Suzuki Y.
Published: May 2005

To realize a large capacity magnetic random access memory (MRAM) that uses spin-transfer switching for writing, it is essential to evaluate thermal durability and intrinsic critical currents correctly. Here, we examined the theoretically predicted logarithmic relationship between critical currents of spin-transfer switching and duration of injected pulsed currents using giant magnetoresistive (GMR) samples with different magnetic materials, e.g., Co, Co–Fe25, and CoFeB. This relationship was verified for the samples by giving reasonable thermal-durability coefficients and intrinsic critical currents as fitting parameters. We found that thermal durability was underestimated when an effective magnetic field acted on magnetic memory cells antiparallel to their magnetization. We then experimentally demonstrated that thermal assistance in spin-transfer switching decreased with increasing thermal durability.
Correlation of telegraph noise between parallel and antiparallel states of magnetic tunnel junctions
Authors: Dhagat P. , Jander A. , Nordman C. A.
Published: May 2005

An alternating positive and negative saturating field is applied to near simultaneously observe the resistance of a magnetic tunnel junction in its parallel and antiparallel configuration. The random telegraph noise in the two configurations is found to be correlated in some devices and anticorrelated in others. These measurements provide insight into the noise mechanism and show that the noise cannot accurately be modeled as purely additive.
Fabrication and characterization of Co–Mn–Al Heusler-type thin film
Authors: Kubota H. , Nakata J. , Oogane M. , Ando Y. , Kato H. , Sakuma A. , Miyazaki T.
Published: May 2005

Co–Mn–Al thin films were prepared using ultrahigh-vacuum magnetron sputtering on thermally oxidized silicon substrates at various substrate temperatures. Composition, crystal structure, magnetic property, and surface roughness of the films were investigated. The film prepared at a substrate temperature (Ts) of around 300°C had Co2MnAl B2 structure, revealing partial disorder between Mn and Al sites. Magnetization exhibited a maximum and coercive field exhibited a minimum around Ts=300°C. Surface roughness increased with the substrate temperature. The film prepared at a substrate temperature of 300°C was applied to a bottom electrode of a magnetic tunnel junction, thereby creating a large tunnel magnetoresistance.
Micromagnetic simulations of current-induced microwave excitations
Authors: Montigny B. , Miltat J.
Published: May 2005

Spin-transfer effects on the magnetization motion are investigated in the free layer of a giant magnetoresistance device flooded with spin-polarized electrons, and more specifically microwave excitations in elliptical permalloy elements. The spin torque is found to excite at low current precessional trajectories compatible with the platelet eigenmodes. Then a forced regime is activated that is, characterized by trajectory broadening with increasing current and an almost spatially uniform power density. The effect of temperature on resonance frequencies and linewidth becomes negligible at high current.
Effect of the classical ampere field in micromagnetic computations of spin polarized current-driven magnetization processes
Authors: Carpentieri M. , Finocchio G. , Azzerboni B. , Torres L. , Lopez-Diaz L. , Martinez E.
Published: May 2005

Magnetization reversal by spin polarized current flowing perpendicular to pillar nanostructures with different geometries and materials is studied by means of a micromagnetic model. The spin transfer torque is included as an additional term in the Gilbert equation following previous theoretical calculations by Slonczewski. The ampere field (HAmp) due to the current and the dipolar antiferromagnetic coupling between the ferromagnetic layers are also taken into account. The HAmp plays a crucial role; in fact it can speed, retard or even inhibit the magnetization switching process depending on the kind of structure under test. The studied nanostructures are circular and elliptic nanopillars of Co∕Cu∕Co and permalloy∕Cu∕permalloy.
Pulsed laser deposition grown CoFe2O4∕Fe3O4 bilayers and their tunneling characteristics
Authors: Chapline Michael G. , Wang Shan X.
Published: May 2005

We have investigated the electrical and magnetic properties of thin epitaxial films of CoFe2O4 on Fe3O4 under layers. CoFe2O4 may be a promising barrier for use in spin dependent tunneling devices using half-metallic Fe3O4 as an electrode due to the small lattice mismatch between the two layers. We were able to characterize the electrical properties of the CoFe2O4 layer by measuring the local tunneling current with an atomic force microscope equipped with a conductive tip. The measured barrier height as determined by fitting the current–voltage curves to Simmons' formula was 0.29eV.
Suppression of bias voltage dependence in double-barrier magnetic tunnel junctions comprised of freelayers with an amorphous layer insertion
Authors: Song Min-Sung , Chun Byong Sun , Kim Young Keun , Hwang Injun , Kim Taewan
Published: May 2005

A double-barrier magnetic tunnel junction (DMTJ) comprising an amorphous freelayer was investigated. The typical sample structure consists of Ta42∕CoZrNb9.2∕IrMn15.5∕CoFe3.3∕AlOx2∕freelayer∕AlOx2∕CoFe7.5∕IrMn15.5∕Ru60(nm). The freelayer includes CoFe2.3∕CoZrNb3.4∕CoFe3. A CoFe 5nm single freelayer was also prepared for reference purpose. Although TMR ratio and RA product appear similar, less attenuation in the TMR ratio was observed at 0.4V for the junction with CoZrNb layer. Coercivity and interlayer coupling were reduced while squareness was improved. The top portion of the DMTJ including top barrier became more uniform after amorphous layer insertion.
Spin-transfer-induced magnetic excitation: The role of spin-pumping induced damping
Authors: Sun Jonathan Z. , Özyilmaz Barbaros , Chen Wenyu , Tsoi Maxim , Kent Andrew D.
Published: May 2005

Spin-transfer-induced magnetic excitation in large magnetic field applied perpendicular to the thin film junction surface reveals both a current threshold Ic and a voltage threshold. The current threshold follows the Slonczewski-type of magnetic field dependence [J. C. Slonczewski, J. Magn. Magn. Mater. 159, L1 (1996)]. The voltage step at Ic is ΔV which appears to scale with the applied field with a prefactor of the order of 2μB∕e, suggesting a threshold to magnetic excitation. Furthermore, experimentally it is observed that ΔV≈IcδR, where δR is the magnetoreistance between the parallel and the antiparallel states. This apparent coincidence can be unified when one includes the effect of spin-pumping-related nonlocal damping. The spin-pump damping relates magnetic instability threshold Ic to δR, producing (dIc∕dH)δR that is about 2μB∕e, explaining the origin of the coincidence.
The switching behaviors of submicron magnetic tunnel junctions with synthetic antiferromagnetic free layers
Authors: Wang Yung-Hung , Chen Wei-Chuan , Chen Young-Shying , Shen Kuei-Hung , Lee Yuan-Jen , Hung Chien-Chung , Chen Chi-Ming , Hsu Hong-Hui , Chen W. S. , Liou Dau-Chi , Kao Ming-Jer , Wang Lien-Chang , Lai Chih-Huang , Lin Wen-Chin , Tang D. D. , Tsai Ming-Jinn
Published: May 2005

The switching behaviors in elliptic shaped (aspect ratio=2) submicron magnetic tunnel junctions using CoFeB single free layer and CoFeB∕Ru∕CoFeB synthetic antiferromagnetic (SAF) free layers are studied. It is found that under considerable stray fields originating from pinned layers, junctions with single free layer show complex switching behaviors with larger Hc variations. In contrast, junctions with SAF free layers exhibit kink-free R-H loops and less Hc variations. The Hc of junctions with SAF free layers is less dependent on the junction size than that with a single free layer. Furthermore, for junctions smaller than a critical size the SAF free layers have a smaller Hc than single free layers.
Low resistance spin-dependent magnetic tunnel junction with high breakdown voltage for current-induced-magnetization-switching devices
Authors: Meng Hao , Wang Jianguo , Diao Zhitao , Wang Jian-Ping
Published: May 2005

Spin-dependent magnetic tunnel junctions (MTJs) with pure AlOx barriers were fabricated by one-step and two-step natural oxidation processes, respectively (500mTorr 20min; 500mTorr 5min and 1Torr 10min). Preoxidized Al barrier thickness varies from 5to7Å. In this work, a multilayer structure with a low resistance of 0.8Ω∕sq and rms of 1.54Å was developed as the bottom electrode. MTJs with the following structure Ta(30Å)∕NiFe (40Å)∕MnIr (80Å)∕CoFe (30Å)∕Al+oxidation∕CoFe (30Å)∕NiFe (40Å)∕Ta (200Å) were magnetically annealed at 230°C for 30min to set the exchange bias field in the MnIr∕CoFe bilayer. Resistance×area (RA) products varying from 0.5to13Ωμm2 were achieved with tunneling magnetoresistance ratios varying from 8% to 18%. Breakdown voltages higher than 450mV were obtained for a sample with RA 0.5Ω×μm2, which allows a current of 9×107A∕cm2 to flow through the MTJ without damaging the barrier. Current-induced magnetization switching based on spin transfer or spin torque effect with a current density of 1.4×107A∕cm2 for a developed MTJ cell was achieved.
Chromophore orientational mobility and index grating rise time in azo-dye-doped photorefractive polymer composites
Authors: McGee D. J. , Fukunaga J. Y. , Zielinski T. , Yang M. , Salter C.
Published: May 2005

The influence of chromophore solubility enhancements on photorefractive grating rise time and device lifetime is investigated. Three azo chromophores differing primarily in compatibility with a polyvinylcarbazole host polymer were synthesized. Aromatic substitutions to the chromophore increased the device lifetime from several days to years although electric-field-induced poling experiments indicated that chromophore orientational mobility is severely hindered, resulting in photorefractive grating rise times approaching several hours. The incorporation of a flexible butyl chain to the aromatic substituted chromophores significantly enhanced the orientational mobility. These chromophores could be loaded as high as 60wt% with no degradation in transparency for one year following fabrication.
Smooth relativistic Hartree–Fock pseudopotentials for H to Ba and Lu to Hg
Authors: Trail J. R. , Needs R. J.
Published: May 2005

We report smooth relativistic Hartree–Fock pseudopotentials (also known as averaged relativistic effective potentials) and spin–orbit operators for the atoms H to Ba and Lu to Hg. We remove the unphysical extremely nonlocal behavior resulting from the exchange interaction in a controlled manner, and represent the resulting pseudopotentials in an analytic form suitable for use within standard quantum chemistry codes. These pseudopotentials are suitable for use within Hartree–Fock and correlated wave function methods, including diffusion quantum Monte Carlo calculations.
Infrared spectra of CO2–H2 complexes
Authors: McKellar A. R. W.
Published: May 2005

Infrared spectra of weakly bound CO2–H2 complexes have been studied in the region of the CO2 v3 asymmetric stretch, using a tunable diode laser probe and a pulsed supersonic jet expansion. For CO2–paraH2, results were obtained for three isotopic species, C12O216, C13O216, and C12O218. These spectra were analyzed using an asymmetric rotor Hamiltonian, with results that resembled those obtained previously for OCS– and N2O–paraH2, except that half the rotational levels were missing due to the symmetry of CO2 and the spin statistics of the O16 or O18 nuclei. However, for CO2–orthoH2, more complicated spectra were observed which could not be assigned, in contrast with OCS– and N2O–H2 where the paraH2 and orthoH2 spectra were similar, though distinct. The CO2–paraH2 complex has a T-shaped structure with and intermolecular distance of about 3.5 Å, and the CO2 v3 vibration exhibits a small redshift (−0.20cm−1) in the complex.
Symmetry-adapted correlation function for semiclassical quantization
Authors: Hotta Koji , Takatsuka Kazuo
Published: May 2005

We study a very simple method to incorporate quantum-mechanical symmetries, including the permutational symmetry on an equal footing with spatial symmetries, into the semiclassical calculation of correlation functions. This method is applied to the calculation of energy spectra to verify its validity by reproducing quantum energy levels for systems of bosons (symmetrized) and fermions (antisymmetrized). The mechanism of how the phase-space structure of classical dynamics is linked with the relevant quantum symmetry is discussed.
Dependence of microwave emissions from hypervelocity impacts on the target material
Authors: Maki K. , Soma E. , Takano T. , Fujiwara A. , Yamori A.
Published: May 2005

Microwave emissions due to hypervelocity impacts and their dependence on the target material are described. Microwave signals were measured for four kinds of target materials: aluminum, alumina ceramic, red brick, and polyurethane rubber. The signals were composed of two kinds of wave form: intermittent sharp pulses and white noise. The pulse signals were emitted strongly, especially with the aluminum target. The energy emitted from each target was estimated from the signal detected after calibrating the measuring system. The energy of the pulses was greater for conductors than for insulators. We hypothesized that the microwaves were emitted from a discharge along a microcrack in the target. The signals detected in the experiment agreed well with theoretical results.
One-dimensional zigzag gallium nitride nanostructures
Authors: Zhou X. T. , Sham T. K. , Shan Y. Y. , Duan X. F. , Lee S. T. , Rosenberg R. A.
Published: May 2005

Two one-dimensional (1D) single-crystalline gallium nitride (GaN) nanostructures with periodic zigzag (type I) and diameter-modulated (type II) shapes have been synthesized by passing through ammonia over a mixture of gallium and gallium oxide (Ga2O3) powders held at elevated temperature. The process was catalyzed by the dispersion of thio-capped Au nanoparticles on the substrate onto which GaN nanostructures were condensed. The transformation between these two nanostructure morphologies was also observed. A possible growth model for the zigzag-shaped nanostructures is proposed, in which the formation of the zigzag nanostructures results from the construction of two different nanoscale unit cells. This work provides an avenue to a group of 1D nanostructures with a zigzag shape. The possibility to form 1D nanostructures yet to be discovered by changing the stacking direction of the (0001) plane will facilitate the fabrication of nanoscale functional devices as well as our understanding of the growth behavior of nanoscale crystallites.
Passivation of AlGaAsSb∕InGaAsSb∕GaSb photodiodes using aqueous (NH4)2S solution and polyimide encapsulation
Authors: Li Jian V. , Chuang Shun Lien , Sulima Oleg V. , Cox Jeff A.
Published: May 2005

We studied passivation effects of treatment in aqueous (NH4)2S (ammonium sulfide) solution and polyimide encapsulation on AlGaAsSb∕InGaAsSb∕GaSb mesa photodiodes. X-ray photoelectron spectroscopy on InGaAsSb material revealed that (NH4)2S passivation reduces oxide bonds, increases III-V bonds, and produces sulfide bonds. Auger electron spectroscopy depth profiling shows a 1:1 replacement of oxygen by sulfur. The percentage of oxygen replaced by sulfur is about 30% at the surface and decays with the depth. Polyimide encapsulation of the photodiode mesa sidewall not preceded by (NH4)2S passivation reduces the dark current of the photodiodes at −0.5V bias by 3.6 times while additional 9.2 times reduction is obtained when it is preceded by (NH4)2S passivation. The dark current performance of devices did not degrade for 240 days after the combined passivation, indicating a promising long-term stability. The capacitance of devices treated with the combined passivation exhibits a standard deviation three times smaller than those with polyimide encapsulation only.
n
-type conductivity in high-fluence Si-implanted diamond
Authors: Weishart H. , Heera V. , Skorupa W.
Published: May 2005

Epitaxial SiC nanocrystals are fabricated by high-fluence Si implantation into natural diamond at elevated temperatures between 760 and 1100 °C. Fluences under investigation range from 4.5 to 6.2×1017Sicm−2. This implantation scheme yields a buried layer rich of epitaxially aligned SiC nanocrystals within slightly damaged diamond. The generation of a small fraction of graphitic sp2 bonds of up to 15% in the diamond host matrix cannot be avoided. Unintentional coimplantation with nitrogen results in a very high doping level of more than 1021cm−3. Resistivity and Hall measurements in van der Pauw geometry reveal a high, thermally stable n-type conductivity with electron concentrations exceeding 1020cm−3 and mobilities higher than 2cm2∕Vs. It is supposed that both the SiC regions as well as the diamond matrix exhibit n-type conductivity and that the electron transport occurs across the low-resistivity SiC nanograins. In the SiC nanocrystals the electrons originate from nitrogen donors whereas in diamond defects are responsible for the electron conductivity. The formation of disordered graphite, which leads to low electron mobility, is substantially reduced by the SiC formation.
Crystallization in HfO2 gate insulators with in situ annealing studied by valence-band photoemission and x-ray absorption spectroscopy
Authors: Toyoda S. , Okabayashi J. , Kumigashira H. , Oshima M. , Yamashita K. , Niwa M. , Usuda K. , Liu G. L.
Published: May 2005

We have investigated the valence-band and conduction-band electronic structures of HfO2 gate insulators on Si substrates and their dependence on the annealing temperature in ultrahigh vacuum and the Hf-metal predeposition at the interface by photoemission spectroscopy and x-ray absorption spectroscopy. In the case with the Hf-metal predeposition before the HfO2 deposition, the valence-band spectra were split into double-peak structures and the line shapes of O K-edge x-ray absorption spectra became sharp due to the annealing at 800 and 900 °C. On the other hand, without the Hf-metal predeposition, annealing-temperature dependence in these spectra was not observed. Cross-sectional transmission electron microscopy images reveal that the changes in both valence-band and O K-edge absorption spectra are related to the crystallization of the HfO2 layer, although it is difficult to distinguish the crystallization in Hf 4f core-level spectra. It suggests that the valence-band photoemission and x-ray absorption spectra can be utilized to investigate the crystallization features in ultrathin gate insulators.
Vortices set and the applied magnetic field for superconductivity in dimension three
Authors: Liu Zuhan
Published: May 2005

In this paper, the structure of vortices set of the Ginzburg–Landau system of the superconductivity in dimension three was studied when applied magnetic field ∣hex∣=O(∣lnε∣). This singularities set is one-dimensional rectifiable. Its generalized mean curvature was given.
A molecular dynamics simulation of the electrical conductivity behaviors of highly concentrated liquid ammoniates NaI∙αNH3: Comparison with experimental measurements
Authors: Picaud S. , Hoang P. N. M. , Herlem G.
Published: May 2005

In this paper, we present a molecular dynamics simulation study devoted to the calculation of the electrical conductivities of highly concentrated liquid electrolytes as a function of their dilution. As an illustration, we give the first such study of the ammoniate NaI∙αNH3. The theoretical results are presented together with experimental data obtained at 293K, and show that the calculated conductivities are in agreement with the experimental values in the whole salt dilution range provided that correlations between the species in the solution are taken into account. Indeed, the usual Nernst–Einstein relation is a crude approximation to calculate accurately the conductivities in such high concentrated electrolytes.
Leakage currents of SiO2 films grown on CoSi2 lines and disks
Authors: Herner S. B. , Petti C. J.
Published: May 2005

Silicon dioxide films were grown by low-temperature anneal in O2 on substrates of CoSi2 lines or disks. The leakage current through SiO2 films grown on CoSi2 lines have a strong dependence on the O2 anneal temperature, while those grown on CoSi2 disks have a weak dependence on anneal temperature. This difference is due to the shape of the oxide grown on the CoSi2. Oxide films were found to grow in a convex shape on CoSi2 disks, being much thicker in the middle of the disk than on the edge. Oxide films grown on CoSi2 lines had relatively uniform thickness across the width of the line.
Nature of room-temperature photoluminescence in ZnO
Authors: Shan W. , Walukiewicz W. , Ager J. W. , Yu K. M. , Yuan H. B. , Xin H. P. , Cantwell G. , Song J. J.
Published: May 2005

The temperature dependence of the photoluminescence (PL) transitions associated with various excitons and their phonon replicas in high-purity bulk ZnO has been studied at temperatures from 12K to above room temperature (320K). Several strong PL emission lines associated with longitudinal optical (LO) phonon replicas of free and bound excitons are clearly observed. The room-temperature PL spectrum is dominated by the phonon replicas of the free exciton transition with the maximum at the first LO phonon replica. The results explain the discrepancy between the transition energy of free exciton determined by reflection measurement and the peak position obtained by the PL measurement.
Diffraction element assisted lithography: Pattern control for photonic crystal fabrication
Authors: Lu Cheng , Hu X. K. , Mitchell I. V. , Lipson R. H.
Published: May 2005

Near-field diffraction element assisted lithography or DEAL has been used to fabricate two-dimensional lattice patterns in a photoresist. Specifically, a diffraction element was used to prepattern the coherent output of a laser prior to its capture in a photoresist. The pattern symmetry and spacing can be readily modified with the same experimental arrangement since the near-field diffraction pattern strongly depends on the nature of the diffractive element and the distance between the element and the photoresist. The patterns that are formed can serve as masks for patterning high index materials to create photonic band gap crystals. Alternatively, they have the potential to behave as two-dimensional photonic band gap arrays provided the polymer used exhibits a large enough index contrast.
Suppression of ionization instability in a magnetohydrodynamic plasma by coupling with a radio-frequency electromagnetic field
Authors: Murakami Tomoyuki , Okuno Yoshihiro , Yamasaki Hiroyuki
Published: May 2005

We describe the suppression of ionization instability and the control of a magnetohydrodynamic electrical power-generating plasma by coupling with a radio-frequency (rf) electromagnetic field. The rf heating stabilizes the unstable plasma behavior and homogenizes the nonuniform plasma structure, whereby the power-generating performance is significantly improved.
Rural Transit Systems Benefits in Tennessee: Methodology and an Empirical Study
Authors: Southworth Frank , Vogt David P , Curlee T Randall
Published: May 2005

This paper describes the application of a detailed benefits assessment framework and sensitivity analysis of the operation of rural public transit services in the state of Tennessee. The paper describes the major components of this benefits framework and its application to the demand-responsive services operated within the state during the 1998/99 fiscal year. An empirical analysis yields a benefit/cost ratio greater than 1.0, with benefits dominated by accessibility gains to current transit patrons through the provision of mobility-enhancing vanpool services. Without these services, the costs of providing an equivalent level of access to health care, job training, and other important household activities would be much higher. Improved and expanded transit rider-based data collection efforts are recommended.
Health, Responsibility, and Choice: Contrasting Negotiations of Air Pollution and Immunisation Information
Authors: Petts Judith
Published: May 2005

This paper presents an empirical study of public conceptions of responsibility and choice in relation to health protection, and the influence of these upon responses to official information. Two contrasting case studies are used, air pollution and childhood immunisation (specifically the MMR vaccination). The results confirm social networks and everyday experiences, and social normalisation of behaviour as important influences upon learning, responses to information, and the taking of personal action. People require information to support the freedom to make personal choices. However, the two cases illustrate that notions of collective responsibility are weaker, in the case of MMR overridden by personal responsibility, in the case of air pollution being transferred to other institutions. Conclusions are developed relating to information provision in an age promoting individualisation and retraction of government, specifically the need for explicit engagement with the benefits (personal and collective) of health protection measures.
p130
Rb2
and p27
kip1
cooperate to control mobilization of angiogenic progenitors from the bone marrow
Authors: Vidal Anxo , Zacharoulis Stergios , Guo Wenjun , Shaffer David , Giancotti Filippo , Bramley Anna H. , de la Hoz Carmen , Jensen Kristian K. , Kato Daniel , MacDonald Daniel D. , Knowles Joseph , Yeh Nancy , Frohman Lawrence A. , Rafii Shahin , Lyden David , Koff Andrew
Published: May 2005

Neoangiogenesis involves both bone marrow-derived myelomonocytic and endothelial progenitor cells as well as endothelial cells coopted from surrounding vessels. Cytokines induce these cells to proliferate, migrate, and exit the cell cycle to establish the vasculature; however, which cell cycle regulators play a role in these processes is largely unknown. Here, we report that mice lacking the cell cycle inhibitors p130 and p27 show defects in tumor neoangiogenesis, both in xenografts and spontaneously arising tumors. This defect is associated with impaired mobilization of endothelial and myelomonocytic angiogenic progenitors from the bone marrow. This article documents the role of these molecules in angiogenesis and further suggests that cell expansion and mobilization from the bone marrow of angiogenic precursors are separable events.
Engineering of protease variants exhibiting high catalytic activity and exquisite substrate selectivity
Authors: Varadarajan Navin , Gam Jongsik , Olsen Mark J. , Georgiou George , Iverson Brent L.
Published: May 2005

The exquisite selectivity and catalytic activity of enzymes have been shaped by the effects of positive and negative selection pressure during the course of evolution. In contrast, enzyme variants engineered by using
in vitro
screening techniques to accept novel substrates typically display a higher degree of catalytic promiscuity and lower total turnover in comparison with their natural counterparts. Using bacterial display and multiparameter flow cytometry, we have developed a novel methodology for emulating positive and negative selective pressure
in vitro
for the isolation of enzyme variants with reactivity for desired novel substrates, while simultaneously excluding those with reactivity toward undesired substrates. Screening of a large library of random mutants of the
Escherichia coli
endopeptidase OmpT led to the isolation of an enzyme variant, 1.3.19, that cleaved an Ala–Arg peptide bond instead of the Arg–Arg bond preferred by the WT enzyme. Variant 1.3.19 exhibited greater than three million-fold selectivity (-Ala–Arg-/-Arg–Arg-) and a catalytic efficiency for Ala–Arg cleavage that is the same as that displayed by the parent for the preferred substrate, Arg–Arg. A single amino acid Ser223Arg substitution was shown to recapitulate completely the unique catalytic properties of the 1.3.19 variant. These results can be explained by proposing that this mutation acts to “swap” the P
1
Arg side chain normally found in WT substrate peptides with the 223Arg side chain in the S
1
subsite of OmpT.
Calix[6]tren and copper(II): A third generation of funnel complexes on the way to redox calix-zymes
Authors: Izzet Guillaume , Douziech Bénédicte , Prangé Thierry , Tomas Alain , Jabin Ivan , Le Mest Yves , Reinaud Olivia
Published: May 2005

Mono-copper enzymes play an important role in biology and their functionality is based on Cu(II)/Cu(I) redox processes. Modeling a mono-nuclear site remains a challenge for a better understanding of its intrinsic reactivity. The first member of a third generation of calixarene-based mono-copper “funnel” complexes is described. The ligand is a calix[6]arene capped by a tren unit, hence presenting a
N
4
coordination site confined in a cavity. Its Cu(II) complexes were characterized by electronic and EPR spectroscopies. The x-ray structure of one of them shows a five-coordinated metal ion in a slightly distorted trigonal bipyramidal geometry thanks to its coordination to a guest ligand L (ethanol). The latter sits in the heart of the hydrophobic calixarene cone that mimics the active site chamber and the hydrophobic access channel of enzymes. Competitive binding experiments showed a preference order dimethylformamide > ethanol > MeCN for L binding at the single exchangeable metal site. Cyclic voltammetry studies showed irreversible redox processes in CH
2
Cl
2
when L is an oxygen donor caused by the redox-driven ejection of the guest at the Cu(I) level. In the presence of MeCN, a pseudoreversible process was obtained, owing to a fast equilibrium between a fourand a five-coordinate Cu(I) species. Finally, a redox-driven ligand interchange of dimethylformamide for MeCN at the Cu(I) state allowed the trapping of the thermodynamically less stable Cu(II)-MeCN adduct. Hence, this work represents an important step toward the elaboration of a functional supramolecular model for redox mono-copper enzymes, named redox calix-zymes.
Evidencein vivothat the DEAD-box RNA helicase RhlB facilitates the degradation of ribosome-free mRNA by RNase E
Authors: Khemici Vanessa , Poljak Leonora , Toesca Isabelle , Carpousis Agamemnon J.
Published: May 2005

The RNA degradosome ofEscherichia coliis a ribonucleolytic multienzyme complex containing RNase E, polynucleotide phosphorylase, RhlB, and enolase. Previousin vitroandin vivowork has shown that RhlB facilitates the exonucleolytic degradation of structured mRNA decay intermediates by polynucleotide phosphorylase in an ATPase-dependent reaction. Here, we show that deleting the gene encoding RhlB stabilizes alacZmRNA transcribed by bacteriophage T7 RNA polymerase. Deleting the gene encoding enolase has little if any effect. Other messages transcribed by T7 polymerase are also stabilized by ΔrhlB. The effect of point mutations inactivating RhlB is comparable with the effect of deleting the gene. Primer extension analysis of thelacZmessage indicates that RhlB facilitates endoribonucleolytic cleavage by RNase E, demonstrating a functional interaction between the RNA helicase and the endoribonuclease. The possible physiological role of an RhlB-RNase E pathway and the mechanisms by which RhlB could facilitate RNase E cleavage are discussed.
Targeting c-Myc-activated genes with a correlation method: Detection of global changes in large gene expression network dynamics
Authors: Remondini D. , O'Connell B. , Intrator N. , Sedivy J. M. , Neretti N. , Castellani G. C. , Cooper L. N.
Published: May 2005

This work studies the dynamics of a gene expression time series network. The network, which is obtained from the correlation of gene expressions, exhibits global dynamic properties that emerge after a cell state perturbation. The main features of this network appear to be more robust when compared with those obtained with a network obtained from a linear Markov model. In particular, the network properties strongly depend on the exact time sequence relationships between genes and are destroyed by random temporal data shuffling. We discuss in detail the problem of finding targets of the c-mycprotooncogene, which encodes a transcriptional regulator whose inappropriate expression has been correlated with a wide array of malignancies. The data used for network construction are a time series of gene expression, collected by microarray analysis of a rat fibroblast cell line expressing a conditional Myc-estrogen receptor oncoprotein. We show that the correlation-based model can establish a clear relationship between network structure and the cascade of c-myc-activated genes.
Disruption of theJnk2 (Mapk9)gene reduces destructive insulitis and diabetes in a mouse model of type I diabetes
Authors: Jaeschke Anja , Rincón Mercedes , Doran Beth , Reilly Judith , Neuberg Donna , Greiner Dale L. , Shultz Leonard D. , Rossini Aldo A. , Flavell Richard A. , Davis Roger J.
Published: May 2005

The c-Jun NH2-terminal kinase isoform (JNK) 1 is implicated in type 2 diabetes. However, a potential role for the JNK2 protein kinase in diabetes has not been established. Here, we demonstrate that JNK2 may play an important role in type 1 (insulin-dependent) diabetes that is caused by autoimmune destruction of β cells. Studies of nonobese diabetic mice demonstrated that disruption of theMapk9gene (which encodes the JNK2 protein kinase) decreased destructive insulitis and reduced disease progression to diabetes. CD4+T cells from JNK2-deficient nonobese diabetic mice produced less IFN-γ but significantly increased amounts of IL-4 and IL-5, indicating polarization toward the Th2 phenotype. This role of JNK2 to control the Th1/Th2 balance of the immune response represents a mechanism of protection against autoimmune diabetes. We conclude that JNK protein kinases may have important roles in diabetes, including functions of JNK1 in type 2 diabetes and JNK2 in type 1 diabetes.
Fine-mapping milk production quantitative trait loci on BTA6: Analysis of the bovine osteopontin gene
Authors: Schnabel Robert D. , Kim Jong-Joo , Ashwell Melissa S. , Sonstegard Tad S. , Van Tassell Curtis P. , Connor Erin E. , Taylor Jeremy F.
Published: May 2005

Bovine chromosome six (BTA6) harbors up to six quantitative trait loci (QTL) influencing the milk production of dairy cattle. In stark contrast to human, there is long-range linkage disequilibrium in dairy cattle, which has previously made it difficult to identify the mutations underlying these QTL. Using 38 microsatellite markers in a pedigree of 3,147 Holstein bulls, we fine mapped regions of BTA6 that had previously been shown to harbor QTL. Next, we sequenced a 12.3-kb region harboring Osteopontin, a positional candidate for the statistically most significant of the identified QTL. Nine mutations were identified, and only genotypes for the
OPN3907
indel were concordant with the QTL genotypes of eight bulls that were established by segregation analysis. Four of these mutations were genotyped, and a joint linkage/linkage disequilibrium mapping analysis was used to demonstrate the existence of only two functionally distinct clusters of haplotypes within the QTL region, which were uniquely defined by
OPN3907
alleles. We estimate a probability of 0.40 that no other mutation within this region is concordant with the QTL genotypes of these eight bulls. Finally, we demonstrate that the motif harboring
OPN3907
, which is upstream of the promoter and within a region known to harbor tissue-specific osteopontin regulatory elements, is moderately conserved among mammals. The motif was not retrieved from database queries and may be a novel regulatory element.
Enterococcus faecalis divIVA: an essential gene involved in cell division, cell growth and chromosome segregation
Authors: Ramirez-Arcos Sandra , Liao Mingmin , Marthaler Susan , Rigden Marc , Dillon Jo-Anne R.
Published: May 2005

Enterococcus faecalis divIVA (divIVA
Ef) is an essential gene implicated in cell division and chromosome segregation. This gene was disrupted by insertional inactivation creating E. faecalis JHSR1, which was viable only when a wild-type copy of divIVA
Ef was expressed in trans, confirming the essentiality of the gene. The absence of DivIVAEf in E. faecalis JHSR1 inhibited proper cell division, which resulted in abnormal cell clusters possessing enlarged cells of altered shape instead of the characteristic diplococcal morphology of enterococci. The lower viability of the divIVA
Ef mutant is caused by improper nucleoid segregation and impaired septation within the numerous cells generated in each cluster. Overexpression of DivIVAEf in Escherichia coli KJB24 resulted in enlarged cells with disrupted cell division, suggesting that this round E. coli mutant strain could be used as an indicator for functionality of DivIVAEf. A Bacillus subtilis divIVA mutant was not complemented by DivIVAEf, indicating that this protein does not recognize DivIVA-specific target sites in B. subtilis, or that it does not interact with other proteins of the cell division machinery of this micro-organism. DivIVAEf also failed to complement a Streptococcus pneumoniae divIVA mutant, supporting the phylogenetic distance between Enterococcus and Streptococcus. Our results indicate that DivIVA is a species-specific multifunctional protein implicated in cell division and chromosome segregation in E. faecalis.
The dynamic behaviour of microtubules and their contributions to hyphal tip growth in Aspergillus nidulans
Authors: Sampson Karina , Heath I. Brent
Published: May 2005

Creating and maintaining cell polarity are complex processes that are not fully understood. Fungal hyphal tip growth is a highly polarized and dynamic process involving both F-actin and microtubules (MTs), but the behaviour and roles of the latter are unclear. To address this issue, MT dynamics and subunit distribution were analysed in a strain ofAspergillus nidulansexpressing GFP–α-tubulin. Apical MTs are the most dynamic, the bulk of which move tipwards from multiple subapical spindle pole bodies, the only clear region of microtubule nucleation detected. MTs populate the apex predominantly by elongation at rates about three times faster than tip extension. This polymerization was facilitated by the tipward migration of MT subunits, which generated a tip-high gradient. Subapical regions of apical cells showed variable tubulin subunit distributions, without tipward flow, while subapical cells showed even tubulin subunit distribution and low MT dynamics. Short MTs, of a similar size to those reported in axons, also occasionally slid into the apex. During mitosis in apical cells, MT populations at the tip varied. Cells with less distance between the tip and the first nucleus were more likely to loose normal MT populations and dynamics. Reduced MTs in the tip, during mitosis or after exposure to the MT inhibitor carbendazim (MBC), generally correlated with reduced, but continuing growth and near-normal tip morphology. In contrast, the actin-disrupting agent latrunculin B reduced growth rates much more severely and dramatically distorted tip morphology. These results suggest substantial independence between MTs and hyphal tip growth and a more essential role for F-actin. Among MT-dependent processes possibly contributing to tip growth is the transportation of vesicles. However, preliminary ultrastructural data indicated a lack of direct MT–organelle interactions. It is suggested that the population of dynamic apical MTs enhance migration of the ‘cytomatrix’, thus ensuring that organelles and proteins maintain proximity to the constantly elongating tip.
Analysis of the Candida albicans Als2p and Als4p adhesins suggests the potential for compensatory function within the Als family
Authors: Zhao X. , Oh S.-H. , Yeater K. M. , Hoyer L. L.
Published: May 2005

The ALS (agglutinin-likesequence) gene family encodes eight large cell-surface glycoproteins. The work presented here focuses on Als2p and Als4p, and is part of a larger effort to deduce the function of each Als protein. BothALS4alleles were deleted from theCandida albicansgenome and the phenotype of the mutant strain (als4Δ/als4Δ; named 2034) studied. Loss of Als4p slowed germ tube formation of cells grown in RPMI 1640 medium and resulted in decreased adhesion ofC. albicansto vascular endothelial cells. Loss of Als4p did not affect adhesion to buccal epithelial cells, biofilm formation in a catheter model, or adhesion to or destruction of oral reconstituted human epithelium (RHE). Although deletion of oneALS2allele was achieved readily, a strain lacking the second allele was not identified despite screening thousands of transformants. The remainingALS2allele was placed under control of theC. albicans MAL2promoter to create anals2Δ/PMAL2-ALS2strain (named 2342). Real-time RT-PCR analysis of strain 2342 grown in glucose-containing medium (non-inducing conditions) showed that althoughALS2transcript levels were greatly reduced compared to wild-type cells, someALS2transcript remained. The decreasedALS2expression levels were sufficient to slow germ tube formation in RPMI 1640 and Lee medium, reduce adhesion to vascular endothelial cells and to RHE, decrease RHE destruction, and impair biofilm formation. Growth of strain 2342 in maltose-containing medium (inducing conditions) restored the wild-type phenotype in all assays. Real-time RT-PCR analysis demonstrated that in maltose-containing medium, strain 2342 overexpressedALS2compared to wild-type cells; however no overexpression phenotype was apparent. Microarray analysis revealed little transcriptional response toALS4deletion, but showed twofold up-regulation of orf19.4765 in the glucose-medium-grownals2Δ/PMAL2-ALS2strain. orf19.4765 encodes a protein with features of a glycosylated cell wall protein with similarity toSaccharomyces cerevisiaeCcw12p, although initial analysis suggested functional differences between the two proteins. Real-time RT-PCR measurement ofALS2andALS4transcript copy number showed a 2·8-fold increase inALS2expression in theals4Δ/als4Δ strain and a 3·2-fold increase inALS4expression in theals2Δ/PMAL2-ALS2strain, suggesting the potential for compensatory function between these related proteins.
Role of RpoS and MutS in phase variation of Pseudomonas sp. PCL1171
Authors: van den Broek Daan , Chin-A-Woeng Thomas F. C. , Bloemberg Guido V. , Lugtenberg Ben J. J.
Published: May 2005

Pseudomonas sp. strain PCL1171 undergoes reversible colony phase variation between opaque phase I and translucent phase II colonies, which is dependent on spontaneous mutations in the regulatory genes gacA and gacS. Mutation of the mutS gene and constitutive expression of rpoS increases the frequency at which gac mutants appear 1000- and 10-fold, respectively. Experiments were designed to study the relationship between gacS, rpoS and mutS. These studies showed that (i) a functional gac system is required for the expression of rpoS, (ii) RpoS suppresses the expression of mutS and therefore increases the frequency of gac mutants, and (iii) upon mutation of rpoS and gacS, the expression of mutS is increased. Mutation of gacS abolishes suppression of mutS expression in stationary growth, suggesting that additional gac-dependent factors are involved in this suppression. In conclusion, inefficient mutation repair via MutS, of which the expression is influenced by gacA/S itself and by rpoS in combination with other factors, contributes to the high frequency of mutations accumulating in gacA/S. The role of RpoS in the growth advantage of a gac mutant was analysed, and mutation of rpoS only reduced the length of the lag phase, but did not affect the growth rate, suggesting a role for both RpoS and a reduction of metabolic load in the growth advantage of a gac mutant.
The Ess1 prolyl isomerase is dispensable for growth but required for virulence in Cryptococcus neoformans
Authors: Ren Ping , Rossettini Anne , Chaturvedi Vishnu , Hanes Steven D.
Published: May 2005

Cryptococcus neoformansis an important human fungal pathogen that also serves as a model for studies of fungal pathogenesis.C. neoformanscontains several genes encoding peptidyl-prolylcis/transisomerases (PPIases), enzymes that catalyse changes in the folding and conformation of target proteins. Three distinct classes of PPIases have been identified: cyclophilins, FK506-binding proteins (FKBPs) and parvulins. This paper reports the cloning and characterization ofESS1, which is believed to be the first (and probably only) parvulin-class PPIase inC. neoformans. It is shown thatESS1fromC. neoformansis structurally and functionally homologous toESS1fromSaccharomyces cerevisiae, which encodes an essential PPIase that interacts with RNA polymerase II and plays a role in transcription. InC. neoformans,ESS1was found to be dispensable for growth, haploid fruiting and capsule formation. However,ESS1was required for virulence in a murine model of cryptococcosis. Loss of virulence might have been due to the defects in melanin and urease production observed iness1mutants, or to defects in transcription of as-yet-unidentified virulence genes. The fact that Ess1 is not essential inC. neoformanssuggests that, in this organism, some of its functions might be subsumed by other prolyl isomerases, in particular, cyclophilins Cpa1 or Cpa2. This is supported by the finding thatess1mutants were hypersensitive to cyclosporin A.C. neoformansmight therefore be a useful organism in which to investigate crosstalk among different families of prolyl isomerases.
Direct molecular mass determination of trehalose monomycolate from 11 species of mycobacteria by MALDI-TOF mass spectrometry
Authors: Fujita Yukiko , Naka Takashi , Doi Takeshi , Yano Ikuya
Published: May 2005

Direct estimation of the molecular mass of single molecular species of trehalose 6-monomycolate (TMM), a ubiquitous cell-wall component of mycobacteria, was performed by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. When less than 1 μg TMM was analysed by MALDI-TOF mass spectrometry, quasimolecular ions [M+Na]+of each molecular species were demonstrated and the numbers of carbons and double bonds (or cyclopropane rings) were determined. Since the introduction of oxygen atoms such as carbonyl, methoxy and ester groups yielded the appropriate shift of mass ions, the major subclasses of mycolic acid (α, methoxy, keto and wax ester) were identified without resorting to hydrolytic procedures. The results showed a marked difference in the molecular species composition of TMM among mycobacterial species. Unexpectedly, differing from other mycoloyl glycolipids, TMM fromMycobacterium tuberculosisshowed a distinctive mass pattern, with abundant odd-carbon-numbered monocyclopropanoic (or monoenoic)α-mycolates besides dicyclopropanoic mycolate, ranging from C75to C85, odd- and even-carbon-numbered methoxymycolates ranging from C83to C94and even- and odd-carbon-numbered ketomycolates ranging from C83to C90. In contrast, TMM fromMycobacterium bovis(wild strain and BCG substrains) possessed even-carbon-numbered dicyclopropanoicα-mycolates. BCG Connaught strain lacked methoxymycolates almost completely. These results were confirmed by MALDI-TOF mass analysis of mycolic acid methyl esters liberated by alkaline hydrolysis and methylation of the original TMM. Wax ester-mycoloyl TMM molecular species were demonstrated for the first time as an intact form in theMycobacterium avium–intracellularegroup,M. phleiandM. flavescens. TheM. avium–intracellularegroup possessed predominantly C85and C87wax ester-mycoloyl TMM, whileM. phleiand the rapid growers tested contained C80, C81, C82and C83wax ester-mycoloyl TMM. This technique has marked advantages in the rapid analysis of not only intact glycolipid TMM, but also the mycolic acid composition of each mycobacterial species, since it does not require any degradation process.