bluuebunny/crossref_metadata_2025 huggingface dataset:
Biochemical characterization of the native Kv2.1 potassium channel
Authors: Chung Jean‐Ju , Li Min
Published: July 2005

Functional diversity of potassium channels in both prokaryotic and eukaryotic cells suggests multiple levels of regulation. Posttranslational regulation includes differential subunit assembly of homologous pore‐forming subunits. In addition, a variety of modulatory subunits may interact with the pore complex either statically or dynamically. Kv2.1 is a delayed rectifier potassium channel isolated by expression cloning. The native polypeptide has not been purified, hence composition of the Kv2.1 channel complexes was not well understood. Here we report a biochemical characterization of Kv2.1 channel complexes from both recombinant cell lines and native rat brain. The channel complexes behave as large macromolecular complexes with an apparent oligomeric size of 650 kDa as judged by gel filtration chromatography. The molecular complexes have distinct biochemical populations detectable by a panel of antibodies. This is indicative of functional heterogeneity. Despite mRNA distribution in a variety of tissues, the native Kv2.1 polypeptides are more abundantly found in brain and have predominantly Kv2.1 subunits but not homologous Kv2.2 subunits. The proteins precipitated by anti‐Kv2.1 and their physiological relevance are of interest for further investigation.
Numerical and Experimental Investigations on Flexible Multi-bearing Rotor Dynamics
Authors: Ding Q. , Leung A. Y. T.
Published: July 2005

An experimental test rig is built to verify the dynamics of a multi-bearing rotor. It consists of two flexibly coupled shafts and is connected to a motor at one end via a flexible coupling. Each of the shafts is supported at the ends by two hydrodynamic bearings and is attached with two disks with equal and unequal masses, respectively. The mathematical model of the test rig is developed and is simulated numerically. The non-stationary dynamic responses of the system during speed-up with a constant angular acceleration are shown, respectively, by the non-stationary bifurcation diagrams, the selected time flows, and the spectrum cascades. Experiments are then carried out on the test rig. Generally, the numerical results are verified qualitatively by the experiments. Both results indicate that the non-synchronous whirls of the two shafts influence each other when flexibly coupled together. In particular, a new phenomenon is found for the four-bearing rotor system: the pre-existing non-synchronous whirl/whip resulted from the instability of one shaft can activate the onset of oil instability of another shaft. In the theoretical simulation, this phenomenon represents the rapid increase of the non-synchronous whirl orbit, whereas in the experiment, it represents the simultaneous existence of two whirl/whip frequencies in the spectra.
Analysis of Static Deformation, Vibration and Active Damping of Cylindrical Composite Shells with Piezoelectric Shear Actuators
Authors: Vel Senthil S. , Baillargeon Brian P.
Published: July 2005

An analytical solution is presented for the static deformation and steady-state vibration of simply supported hybrid cylindrical shells consisting of fiber-reinforced layers with embedded piezoelectric shear sensors and actuators. The piezoelectric shear actuator, which is poled in the circumferential direction, will induce transverse shear deformation of the hybrid shell when it is subjected to an electric field in the radial direction. Suitable displacement and electric potential functions that identically satisfy the boundary conditions at the simply supported edges are used to reduce the governing equations of static deformation and steady-state vibrations of the hybrid laminate to a set of coupled ordinary differential equations in the radial coordinate, which are solved by employing the Frobenius method. Natural frequencies, mode shapes, displacements, electric potential, and stresses are presented for four-layer hybrid laminates consisting of a piezoelectric shear sensor and actuator sandwiched between fiber-reinforced composite layers. Active vibration damping is implemented using a positive position feedback controller. Frequency response curves for different controller frequencies, controller damping ratio, and feedback gain demonstrate that the embedded shear actuator can be used for active damping of the fundamental flexural mode. In addition, it is demonstrated that vibration suppression of thickness modes is also feasible using the piezoelectric shear actuator.
HMM-Based Fault Detection and Diagnosis Scheme for Rolling Element Bearings
Authors: Ocak Hasan , Loparo Kenneth A.
Published: July 2005

In this paper, we introduce a new bearing fault detection and diagnosis scheme based on hidden Markov modeling (HMM) of vibration signals. Features extracted from amplitude demodulated vibration signals from both normal and faulty bearings were used to train HMMs to represent various bearing conditions. The features were based on the reflection coefficients of the polynomial transfer function of an autoregressive model of the vibration signals. Faults can be detected online by monitoring the probabilities of the pretrained HMM for the normal case given the features extracted from the vibration signals. The new technique also allows for diagnosis of the type of bearing fault by selecting the HMM with the highest probability. The new scheme was also adapted to diagnose multiple bearing faults. In this adapted scheme, features were based on the selected node energies of a wavelet packet decomposition of the vibration signal. For each fault, a different set of nodes, which correlates with the fault, is chosen. Both schemes were tested with experimental data collected from an accelerometer measuring the vibration from the drive-end ball bearing of an induction motor (Reliance Electric 2 HP IQPreAlert) driven mechanical system and have proven to be very accurate.
Friction-Compensating Command Shaping for Vibration Reduction
Authors: Lawrence Jason , Singhose William , Hekman Keith
Published: July 2005

Fast and accurate point-to-point motion is a common operation for industrial machines, but vibration will frequently corrupt such motion. This paper develops commands that can move machines without vibration, even in the presence of Coulomb friction. Previous studies have shown that input shaping can be used on linear systems to produce point-to-point motion with no residual vibration. This paper extends command-shaping theory to nonlinear systems, specifically systems with Coulomb friction. This idea is applied to a PD-controlled mass with Coulomb friction to ground. The theoretical developments are experimentally verified on a solder cell machine. The results show that the new commands allow the proportional gain to be increased, resulting in reduced rise time, settling time, and steady-state error.
Nonlinear Vibrations of an Inclined Cable
Authors: Berlioz A. , Lamarque C-H.
Published: July 2005

The goal of this experimental and theoretical study is to highlight the nonlinear dynamic behavior of an inclined cable consisting of a steel wire surrounded by copper wire. Measurements around the first frequency of vibration of the cable in and out of plane and around the second harmonic of this frequency were also carried out. These experimental results are in good agreement with the numerical results obtained via the multiple scale method applied to finite (1- and 2- degree-of-freedom (DOF) models). In order to prepare further investigations related to more complicated behavior, a 4-DOF model is added.
Nonlinear Analysis on Hunting Stability for High-Speed Railway Vehicle Trucks on Curved Tracks
Authors: Lee Sen-Yung , Cheng Yung-Chang
Published: July 2005

Based on the heuristic nonlinear creep model, the nonlinear coupled differential equations of the motion of a ten-degree-of-freedom truck system, considering the lateral displacement, the vertical displacement, the roll and yaw angles of the each wheelset, and the lateral displacement and yaw angle of the truck frame, moving on curved tracks, are derived in completeness. To illustrate the accuracy of the analysis, the limiting cases are examined. The influences of the suspension parameters, including those losing in the six-degree-of-freedom system, on the critical hunting speeds evaluated via the linear and nonlinear creep models, respectively, are studied and compared.
Effect of Material Coupling on Wave Vibration of Composite Timoshenko Beams
Authors: Mei C.
Published: July 2005

This paper presents the effect of coupling between bending and torsional deformations on vibrations of composite Timoshenko beams from the wave standpoint. The dispersion characteristics and the modes of vibrations are in general affected by material coupling, except those of the torsional modes at low frequencies; and higher-frequency modes are normally more sensitive to material coupling. The wave mode transition phenomenon is also investigated. It is found that like their metallic counterparts, composite Timoshenko beams also exhibit wave mode transition. Furthermore, the transition frequency is found to be unaffected by material coupling. Numerical examples for which comparative results are available in the literature are presented.
General Interpolated Fast Fourier Transform: A New Tool for Diagnosing Large Rotating Machinery
Authors: Shi D. F. , Qu L. S. , Gindy N. N.
Published: July 2005

Vibration monitoring and diagnosis of rotating machinery is an important part of a predictive maintenance program to reduce operating and maintenance costs. In order to improve the efficiency and accuracy of diagnosis, the general interpolated fast Fourier transform (GIFFT) is introduced in this paper. In comparison to present interpolated fast Fourier transform, this new approach can deal with any type of window functions and possesses high accuracy and robust performance, especially coping with a small number of sampling points. Then, for the purpose of rotating machinery diagnosis, the harmonic vibration ellipse and orbit is reconstructed based on the GIFFT to extract the features of faults and remove the interference from environmental noise and some irrelevant components. This novel scheme is proving to be very effective and reliable in diagnosing several types of malfunctions in gas turbines and compressors and characterizing of the transient behavior of rotating machinery in the run-up stage.
Effect of Drag-Reducing Air Lubrication on Underwater Noise Radiation From Ship Hulls
Authors: Matveev Konstantin I.
Published: July 2005

As the speed and power of surface ships rise, the reduction of ship acoustic signature and self-noise is becoming an important task of naval engineering. A significant decrease in underwater noise can be achieved by using gaseous layers on the ship hull. Two mechanisms for sound radiation from low-drag air-lubricated hulls are discussed.
Buckling of Long Sandwich Cylindrical Shells Under External Pressure
Authors: Kardomateas G. A. , Simitses G. J.
Published: July 2005

An elasticity solution to the problem of buckling of sandwich long cylindrical shells subjected to external pressure is presented. In this context, the structure is considered a three-dimensional body. All constituent phases of the sandwich structure, i.e., the facings and the core, are assumed to be orthotropic. The loading is a uniform hydrostatic pressure, which means that the loading remains normal to the deflected surface during the buckling process. Results are produced for laminated facings, namely, boron/epoxy, graphite/epoxy and kevlar/epoxy laminates with 0deg orientation with respect to the hoop direction, and for alloy-foam core. Shell theory results are generated with and without accounting for the transverse shear effect. Two transverse shear correction approaches are compared, one based only on the core, and the other based on an effective shear modulus that includes the face sheets. The results show that the shell theory predictions without transverse shear can produce highly non-conservative results on the critical pressure, but the shell theory formulas with transverse shear correction produce reasonable results with the shear correction based on the core only being in general conservative (i.e., critical load below the elasticity value). The results are presented for four mean radius over shell thickness ratios, namely 15, 30, 60, and 120 in order to assess the effect of shell thickness (and hence that of transverse shear). For the same thickness, the differences between elasticity and shell theory predictions become larger as the mean radius over thickness ratio is decreased. A comparison is also provided for the same shell with homogeneous composite construction. It is shown that the sandwich construction shows much larger differences between elasticity and shell theory predictions than the homogeneous composite construction. The solution presented herein provides a means of a benchmark for accurately assessing the limitations of shell theories in predicting stability loss in sandwich shells.
Molecular beam epitaxy growth and characterization of mid-IR type-II “W” diode lasers
Authors: Canedy C. L. , Bewley W. W. , Boishin G. I. , Kim C. S. , Vurgaftman I. , Kim M. , Meyer J. R. , Whitman L. J.
Published: July 2005

Type II “W” diodes designed for emission at the spectral line of methane (3.31μm) when operated near 80K were grown on a compact 21T RIBER molecular beam epitaxy system. Photoluminescence and cross-sectional scanning tunneling microscopy were used as tools to improve the growth quality of these structures. The diodes exhibited very low lasing thresholds at T=80K (24–40A∕cm2), although further development will be required to enhance the characteristic temperature (T0∼40K) and the maximum operating temperature (∼190K). The lasers had favorable internal losses at all T up to 190K (∼7cm−1), and favorable internal efficiencies at low T (up to 85%). The I–V characteristics of nonlasing test structures were improved substantially by adding n-side “transition” regions that smoothed out abrupt steps in the conduction-band offset.
Midinfrared InAs∕InGaSb “W” diode lasers with digitally grown tensile-strained AlGaAsSb barriers
Authors: Li W. , Héroux J. B. , Shao H. , Wang W. I. , Vurgaftman I. , Meyer J. R.
Published: July 2005

W-shaped InAs∕In0.2Ga0.8Sb∕InAs∕Al0.25Ga0.75As0.08Sb0.92 quantum wells (QWs) have been grown by solid-source molecular beam epitaxy for midinfrared wavelength emission. The tensile strain and the higher As composition in the tensile AlGaAsSb barriers lower the energy level of the heavy holes and increase the hole confinement in the “W” quantum wells, which can improve the temperature properties of the “W” lasers. The tensile-strained Al0.25Ga0.75As0.08Sb0.92 barriers were obtained by growing Al0.25Ga0.75Sb(2ML)∕Al0.25Ga0.75As0.24Sb0.76 (1 ML) digital layers. As evidenced from low-temperature photoluminescence (PL) and x-ray diffraction measurements, the “W” QWs with digitally grown AlGaAsSb barriers show better interface quality and higher PL efficiency than analogous structures with random-alloy AlGaAsSb barriers. Broad-area diode lasers with five-period “W” QWs have been fabricated. A low threshold of 734A∕cm2 at a lasing wavelength of 3.238μm was measured for the 800μm×200μm stripe at 153K. Characteristic temperatures as high as 103K are achieved in the 80–150K range.
Interface roughness characterization by electron mobility of pseudomorphic In0.74Ga0.26As∕In0.52Al0.48As modulation-doped quantum wells grown on (411)A InP substrates by molecular beam epitaxy
Authors: Katoh S. , Sagisaka H. , Yamamoto M. , Watanabe I. , Kitada T. , Shimomura S. , Hiyamizu S.
Published: July 2005

Interface roughness of pseudomorphic In0.74Ga0.26As∕In0.52Al0.48As modulation-doped quantum wells (MD-QWs) grown on the (411)A and (100) InP substrates by molecular beam epitaxy was characterized by sheet electron concentration (Ns) dependence of two-dimensional electron gas (2DEG) mobility by applying gate bias at 15K. The (411)A MD-QW with well width of 4nm (8nm) showed value of 1.8–2.1 (1.5–1.6) times higher 2DEG mobility at 15K comparing to the corresponding (100) sample in the range of Ns (1.2–2.3×1012cm−2), which results from reduced interface roughness scattering due to the super-flat (411)A InGaAs∕InAlAs interfaces. By analyzing Ns dependence of the 2DEG mobility, we deduced wave-number dependence of the Fourier components of the lateral well-width fluctuation (Δq0) arising from the interface roughness in the range of q0=0.55–0.7nm−1. Values of ∣Δq0∣2 of the (411)A InGaAs∕InAlAs interface were about half of those of the (100) interface in the whole range of q0=0.55–0.7nm−1.
Comparative studies of the epireadiness of 4in. InP substrates for molecular-beam epitaxy growth
Authors: Fastenau J. M. , Lubyshev D. , Wu Y. , Doss C. , Liu W. K.
Published: July 2005

Four in. (100mm)-diameter semi-insulating InP substrates from multiple suppliers were evaluated and compared in terms of their epiready crystal quality and surface properties as required for growth in a multiwafer molecular-beam epitaxy system. All epiwafers in this work exhibited excellent crystalline and structural properties. The postgrowth surface morphology and defect density were typically within standard expectations; however, some fallout was observed due to variations in surface finish. Upon investigation of epilayer-substrate interfacial properties, significant differences were observed between the various vendors and also within substrate lots from individual vendors. While some substrates exhibited a clean interface, others had n-type charge accumulations of varying magnitudes. The interface contamination, silicon or sulfur arising from the substrate surface preparation process or from the substrate packaging, resulted in poor device isolation. Buffer leakage currents were proportional to the interface charge concentration and were measured in the range of 10mA∕mmto10nA∕mm. For growths of high electron mobility transistor epiwafers, the Hall transport properties were consistent for all vendors, with room temperature mobilities >10000cm2∕Vs at a channel charge of 3×1012cm−2. Similarly, the dc parameters of double heterojunction bipolar transistors grown on substrates from each vendor were nominally the same.
Uniformly doped InAs∕GaAs quantum-dot infrared photodetector structures
Authors: Pal D. , Towe E.
Published: July 2005

We have studied InAs∕GaAs quantum-dot photodetector devices that are sensitive to normal incidence radiation. Photoluminescence measurements indicate that there are three bound states within the conduction band of the quantum dots. The detector structures were uniformly doped to supply approximately 9 electrons per dot. The peak of the photoresponse spectrum is observed at about 5.12 μm. In general the characteristics of our devices are similar to those where the dopant impurities are placed within the wetting layer or just below the quantum dots.
Single layer and stacked CdSe self-assembled quantum dots with ZnCdMgSe barriers for visible and white light emitters
Authors: Perez-Paz M. Noemi , Zhou Xuecong , Muñoz Martin , Sohel Mohammad , Lu Hong , Fernandez Francisco , Jean-Mary Fleumingue , Akins Daniel L. , Tamargo Maria C.
Published: July 2005

We have grown structures with single layers of self-assembled quantum dots (SAQDs) and stacked layers of SAQDs in the II-VI materials systems CdSe∕ZnCdMgSe. The structures were grown on InP substrates by molecular beam epitaxy. Good control of the quantum dot (QD) size by controlling the CdSe deposition time was obtained, giving structures whose emission can be adjusted to be at any wavelength within the visible spectrum range. Stacked QD structures consisting of three QD layers emitting in the red, green and blue (R-G-B) regions of the spectrum, respectively, were grown. Photoluminescence measurements exhibited bright white emission that could be observed by eye, at 77K or at room temperature, as a result of the mixing of the three lines. These results indicate that this material may be an attractive alternative for optical applications in the R-G-B range and may be useful for the fabrication of white light sources.
Formation of atomic hydrogen during radio frequency nitrogen plasma assisted chemical beam epitaxy of III–V dilute nitrides
Authors: Fotkatzikis A. , Pinault M.-A. , Coaquira J. A. H. , Freundlich A.
Published: July 2005

In this study the interaction of a rf nitrogen plasma source with hydride precursors, during the chemical beam epitaxy of III–V dilute nitrides is investigated. For this purpose the rf nitrogen plasma cavity spectrum is monitored in real time. During the growth of III–V dilute nitrides and upon introduction of hydride precursors, such as AsH3, in the chemical beam epitaxy chamber the cavity plasma spectrum is marked by the appearance of a sharp emission at 656 nm, the energy of which corresponds to the first term of the Balmer series of the hydrogen atom, suggesting the retro diffusion of residual hydrogen in the plasma cavity and the formation of atomic hydrogen species. The evolution of the intensity of this peak as a function of rf plasma source parameters and hydrogen flow is investigated in an attempt to offer practical means of minimizing the possible effects of hydrogen atoms on the fabricated material. Improved optical properties as attested by the sharp photoluminescence (PL) emissions in as-grown samples and minimal thermal annealing induced PL energy shifts are reported for GaAsN epilayers grown under low H2∕N2 partial pressure conditions.
GaNAs(001) surface phases under growing condition
Authors: Mori Takahiro , Morimura Toshiharu , Hanada Takashi , Yao Takafumi
Published: July 2005

GaNAs ∕ GaAs ( 001 ) growth surfaces were investigated by reflectance difference (RD)∕anisotropy spectroscopy. In situ monitoring was carried out in a plasma-assisted molecular-beam epitaxy system during growth. In the growth temperature range of our experiment, the reflection high-energy electron diffraction pattern always showed a (2×4) reconstruction pattern, however, we observed three types of RD spectra. It was suggested that the GaNAs growth surface has three phases because RD spectra properly reflect surface electronic states. It is revealed that the phases are independent from nitrogen concentration, but dependent upon growth temperature and As4∕Ga flux ratio. In this article, we show the results of the RD observation, present a phase diagram, and discuss possible GaNAs growth surfaces.
Electrical characterization for ZnO layers grown on GaN templates by molecular-beam epitaxy
Authors: Oh D. C. , Suzuki T. , Kim J. J. , Makino H. , Hanada T. , Cho M. W. , Yao T. , Song J. S. , Ko H. J.
Published: July 2005

We have extensively studied electrical properties for ZnO layers grown on GaN templates by molecular-beam epitaxy. First, the Schottky characteristics of Au contacts onto ZnO:N layers have been investigated by current-voltage measurements. Barrier heights and ideality factors for Au/ZnO:N Schottky contacts are systematically varied by controlling the growth temperatures and crystal-polar directions of ZnO:N layers. Second, the capacitance-voltage (C-V) characteristics of ZnO/GaN heterostructures has been investigated. Large plateau regions are observed in C-V characteristics, which are ascribed to the confined charges caused by band offset at the ZnO/GaN heterointerface. Finally, electron-trap centers in ZnO layers have been investigated by capacitance-temperature measurements. ZnO layers exhibit two electron-trap centers ET1 and ET2, whose thermal activation energies are estimated to be 33 and 0.15 eV, respectively.
Protecting wafer surface during plasma ignition using an arsenic cap
Authors: Wistey M. A. , Bank S. R. , Yuen H. B. , Goddard L. L. , Gugov T. , Harris J. S.
Published: July 2005

Dilute nitrides such as GaInNAs are often grown by plasma-assisted molecular-beam epitaxy (MBE), and the plasma that provides reactive nitrogen also damages the semiconductor surface. Direct exposure to the plasma has been studied extensively, but here we report damage due to indirect exposure, while the shutter remains closed. The use of a protective arsenic cap on the wafer is found to prevent such indirect damage, resulting in a 2–3x increase in photoluminescence intensity, sharper features in transmission electron microscopy, and a 30% decrease in laser thresholds. This technique requires no changes to the MBE chamber, unlike a gate valve.
Low resistance ohmic contact to p-type GaN using Pd∕Ir∕Au multilayer scheme
Authors: Bae J. W. , Hossain T. , Adesida I. , Bogart K. H. , Koleske D. , Allerman A. A. , Jang J. H.
Published: July 2005

Ohmic contacts on p-type GaN utilizing Pd∕Ir∕Au metallization were fabricated and characterized. Metallized samples that were rapid thermally annealed at 400°C for 1min exhibited linear current-voltage characteristics. Specific ohmic contact resistivities as low as 2×10−5Ωcm2 were achieved. Auger electron spectroscopy and x-ray photoelectron spectroscopy depth profiles of annealed Pd∕Ir∕Au contact revealed the formation of Pd- and Ir-related alloys at the metal–semiconductor junction with the creation of Ga vacancies below the contact. The excellent contact resistance obtained is attributed to the formation of these Ga vacancies which resulted in the reduction of the depletion region width at the junction.
High quality AlSb bulk material on Si substrates using a monolithic self-assembled quantum dot nucleation layer
Authors: Balakrishnan G. , Huang S. , Khoshakhlagh A. , Dawson L. R. , Xin Y.-C. , Conlin P. , Huffaker D. L.
Published: July 2005

We report and characterize the growth of defect-free AlSb bulk material on Si (001) substrates using a monolithic self-assembled AlSb quantum dot (QD) nucleation layer. During the first few monolayers of AlSb growth on Si, highly crystalline QDs form. With continued deposition, the islands coalesce into a planar material with no detectable defects. The QD nucleation layer facilitates a completely relaxed AlSb within ∼100 ML of deposition according to x-ray diffraction. We attribute the success of AlSb growth on Si to both the large AlSb∕Si lattice mismatch (Δa0∕a0=13.5%) in combination with the strong AlSb atomic bond. We also demonstrate room temperature photoluminescence from an InGaSb QW grown on the AlSb bulk layer.
Strain analysis in silicon substrates under uniaxial and biaxial stress by convergent beam electron diffraction
Authors: Toh Suey Li , Loh K. P. , Boothroyd C. B. , Li K. , Ang C. H. , Chan L.
Published: July 2005

A detailed description of the application of the convergent beam electron diffraction (CBED) technique for studying strain propagation in the Si1−xGex∕Si blanket wafers as well as silicon-based metal–oxide–semiconductor field-effect transistors is presented. Specifically, a simple and robust experimental procedure and analysis for silicon lattice strain measurement using the CBED technique is detailed in this article. The use of focused ion beam milling allows for better control of the thickness and site-specific analysis, especially for nanoscaled devices. A pictorial representation of the analytical conditions for the higher order Laue zone lines in CBED patterns is also reported in this work. Based on the Si lattice strain measurement results, we determined that a thin buffer layer of SiOxNy incorporated below the Si3N4 overlay film could render the uniaxial channel strain less compressive. Stress studied on Si1−xGex∕Si blanket wafers reveals that a steeper SiGe compositional gradient would induce larger biaxial strain in the underlying Si substrate and hence a smaller amount of misfit dislocations.
Topography simulations for contact formation involving reactive ion etching, sputtering and chemical vapor deposition
Authors: Takagi S. , Onoue S. , Iyanagi K. , Nishitani K. , Shinmura T.
Published: July 2005

With the shrinking design rule of semiconductor devices, the aspect ratios of contact holes that connect transistor electrodes to wirings have exceeded 10 at a design rule less than 0.15μm. The contact is formed through sequential processes of reactive ion etching (RIE), TiN sputtering, and tungsten chemical vapor deposition (W–CVD). In such a formation process, a contact hole with a large bottom diameter is required to reduce contact resistance. We developed a contact simulation method for optimizing contact formation. This contact simulation involves sequential simulations of RIE, TiN sputtering, and W–CVD processes, which adopt a particle model based on the Monte Carlo method. These topography simulations were calibrated using experimental results, and each simulation was combined in order to calculate these sequential simulations. We calculated the dependences of etching and W–CVD filling profiles on contact hole depth. The simulation profiles of etching and W–CVD filling were in agreement with the experimental results. The sequential simulations showed that W disconnection occurs at over 2.5μm contact depth with a aspect ratio of 19.2 and the contact resistance increases markedly.
Iron-Dependent Cytochrome
c
1
Expression Is Mediated by the Status of Heme in
Bradyrhizobium japonicum
Authors: Gao Tao , O'Brian Mark R.
Published: July 2005

The heme prosthetic group of heme proteins contains iron, which can be a limiting nutrient. Here, we show that cytochrome
c
1
protein from
Bradyrhizobium japonicum
was strongly affected by the iron status, with low expression in cells grown under iron limitation. This control was not affected in mutants encoding the iron regulator Irr or Fur. Furthermore, cytochrome
c
1
mRNA was not influenced by the iron status, suggesting control at a posttranscriptional step. Cytochrome
c
1
protein levels were very low in mutants defective in the genes encoding δ-aminolevulinic acid (ALA) synthase and ferrochelatase, enzymes that catalyze the first and final steps of the heme biosynthetic pathway, respectively. Iron-dependent cytochrome
c
1
expression was restored in the ALA synthase mutant by supplementation of the medium with the heme precursor ALA. Supplementation with heme resulted in high levels of cytochrome
c
1
protein in the wild type and in both mutants, but expression was no longer iron dependent. Cytochrome
c
1
is synthesized as a protein precursor fused with cytochrome
b
. A plasmid-borne construct encoding only cytochrome
c
1
was expressed in an iron- and heme-dependent manner similar to that of the wild-type gene, indicating that control by those effectors is not linked to posttranslational processing of the fusion protein. Mutation of the cytochrome
c
1
cysteines involved in covalent binding to heme nearly abolished immunodetectable protein. Thus, defects in heme synthesis or heme binding abrogate cytochrome
c
1
accumulation, apparently due to protein degradation. We suggest that iron-dependent cytochrome
c
1
expression is mediated by heme availability for heme protein formation
Carboxyl-Terminal Extensions beyond the Conserved Pentapeptide Reduce Rates of Chemoreceptor Adaptational Modification
Authors: Lai Wing-Cheung , Hazelbauer Gerald L.
Published: July 2005

Sensory adaptation in bacterial chemotaxis is mediated by covalent modification of chemoreceptors. Specific glutamyl residues are methylated and demethylated in reactions catalyzed by methyltransferase CheR and methylesterase CheB. In the well-characterized chemosensory systems of
Escherichia coli
and
Salmonella
spp., efficient modification by either enzyme is dependent on a conserved pentapeptide sequence, NWETF or NWESF, present at the extreme carboxyl terminus of high-abundance chemoreceptors. To what extent is position at the extreme carboxyl terminus important for pentapeptide-mediated enhancement of adaptational modification? Is this position equally important for enhancement of both enzyme activities? To address these questions, we created forms of high-abundance receptor Tsr or Tar carrying one, six, or eight additional amino acids extending beyond the pentapeptide at their carboxyl termini and assayed methylation, demethylation, deamidation, and ability to mediate chemotaxis. In vitro and in vivo, all three carboxyl-terminal extensions reduced pentapeptide-mediated enhancement of rates of adaptational modification. CheB-catalyzed reactions were more affected than CheR-catalyzed reactions. Effects were less severe for the complete sensory system in vivo than for the minimal system of receptor and modification enzymes in vitro. Notably, extended receptors mediated chemotaxis as efficiently as wild-type receptors, providing a striking example of robustness in chemotactic systems. This could reflect compensatory reductions of rates for both modification reactions, mitigation of effects of slower reactions by the intertwined circuitry of signaling and adaptation, or tolerance of a range of reactions rates for adaptational modification. No matter what the mechanism, the observations provide a challenging test for mathematical models of chemotaxis.
Contribution of ExsFA and ExsFB Proteins to the Localization of BclA on the Spore Surface and to the Stability of the
Bacillus anthracis
Exosporium
Authors: Sylvestre Patricia , Couture-Tosi Evelyne , Mock Michèle
Published: July 2005

Spores of
Bacillus anthracis
, the etiological agent of anthrax, and the closely related species
Bacillus cereus
and
Bacillus thuringiensis
, possess an exosporium, which is the outermost structure surrounding the mature spore. It consists of a paracrystalline basal layer and a hair-like outer layer. To date, the structural contribution of only one exosporium component, the collagen-like glycoprotein BclA, has been described. It is the structural component of the hair-like filaments. Here, we describe two other proteins, ExsFA and ExsFB, which are probably organized in multimeric complexes with other exosporium components, including BclA. Single and double
exsF
deletion mutants were constructed and analyzed. We found that inactivation of
exsF
genes affects the BclA content of spores. BclA is produced by all mutants. However, it is partially and totally released after mother cell lysis of the Δ
exsFA
and Δ
exsFA
Δ
exsFB
mutant strains, respectively. Electron microscopy revealed that the
exsF
mutant spores have defective exosporia. The Δ
exsFA
and Δ
exsFA
Δ
exsFB
spore surfaces are partially and totally devoid of filaments, respectively. Moreover, for all mutants, the crystalline basal layer appeared unstable. This instability revealed the presence of two distinct crystalline arrays that are sloughed off from the spore surface. These results indicate that ExsF proteins are required for the proper localization of BclA on the spore surface and for the stability of the exosporium crystalline layers.
Novel Intracellular 3-Hydroxybutyrate-Oligomer Hydrolase in
Wautersia eutropha
H16
Authors: Kobayashi Teruyuki , Uchino Keiichi , Abe Tomoko , Yamazaki Yuya , Saito Terumi
Published: July 2005

Wautersia eutropha
H16 (formerly
Ralstonia eutropha
) mobilizes intracellularly accumulated poly(3-hydroxybutyrate) (PHB) with intracellular poly(3-hydroxybutyrate) depolymerases. In this study, a novel intracellular 3-hydroxybutyrate-oligomer hydrolase (PhaZc) gene was cloned and overexpressed in
Escherichia coli
. Then PhaZc was purified and characterized. Immunoblot analysis with polyclonal antiserum against PhaZc revealed that most PhaZc is present in the cytosolic fraction and a small amount is present in the poly(3-hydroxybutyrate) inclusion bodies of
W. eutropha
. PhaZc degraded various 3-hydroxybutyrate oligomers at a high specific activity and artificial amorphous poly(3-hydroxybutyrate) at a lower specific activity. Native PHB granules and semicrystalline PHB were not degraded by PhaZc. A PhaZ deletion mutation enhanced the deposition of PHB in the logarithmic phase in nutrient-rich medium. PhaZc differs from the hydrolases of
W. eutropha
previously reported and is a novel type of intracellular 3-hydroxybutyrate-oligomer hydrolase, and it participates in the mobilization of PHB along with other hydrolases.
CitI, a Transcription Factor Involved in Regulation of Citrate Metabolism in Lactic Acid Bacteria
Authors: Martin Mauricio G. , Magni Christian , de Mendoza Diego , López Paloma
Published: July 2005

A large variety of lactic acid bacteria (LAB) can utilize citrate under fermentative conditions. Although much information concerning the metabolic pathways leading to citrate utilization by LAB has been gathered, the mechanisms regulating these pathways are obscure. In
Weissella paramesenteroides
(formerly called
Leuconostoc paramesenteroides
), transcription of the
citMDEFCGRP
citrate operon and the upstream divergent gene
citI
is induced by the presence of citrate in the medium. Although genetic experiments have suggested that CitI is a transcriptional activator whose activity can be modulated in response to citrate availability, specific details of the interaction between CitI and DNA remained unknown. In this study, we show that CitI recognizes two A+T-rich operator sites located between
citI
and
citM
and that the DNA-binding affinity of CitI is increased by citrate. Subsequently, this citrate signal propagation leads to the activation of the
cit
operon through an enhanced recruitment of RNA polymerase to its promoters. Our results indicate that the control of CitI by the cellular pools of citrate provides a mechanism for sensing the availability of citrate and adjusting the expression of the
cit
operon accordingly. In addition, this is the first reported example of a transcription factor directly functioning as a citrate-activated switch allowing the cell to optimize the generation of metabolic energy.
ywfEinBacillus subtilisCodes for a Novel Enzyme,l-Amino Acid Ligase
Authors: Tabata Kazuhiko , Ikeda Hajime , Hashimoto Shin-ichi
Published: July 2005

The ATP-dependent carboxylate-amine/thiol ligase superfamily is known to contain enzymes catalyzing the formation of various types of peptide, such asd-alanyl-d-alanine, polyglutamate, and γ-peptide, but, curiously, no enzyme synthesizing α-dipeptides ofl-amino acids is known. We attempted to find such an enzyme. By in silico screening based on the consensus sequence of the superfamily followed by an in vitro assay with purified enzyme to avoid the degradation of the peptide(s) synthesized,ywfEofBacillus subtiliswas found to code for the activity formingl-alanyl-l-glutamine froml-alanine andl-glutamine with hydrolysis of ATP to ADP. No AMP was formed, supporting the idea that the enzyme belongs to the superfamily. Surprisingly, the enzyme accepted a wide variety ofl-amino acids. Among 231 combinations ofl-amino acids tested, reaction products were obtained for 111 combinations and 44 kinds of α-dipeptides were confirmed by high-performance liquid chromatography analyses, while no tripeptide or longer peptide was detected and thed-amino acids were inert. From these results, we propose thatywfEencodes a new member of the superfamily,l-amino acid ligase.
A DNA Polymerase V Homologue Encoded by TOL Plasmid pWW0 Confers Evolutionary Fitness on
Pseudomonas putida
under Conditions of Environmental Stress
Authors: Tark Mariliis , Tover Andres , Tarassova Kairi , Tegova Radi , Kivi Gaily , Hõrak Rita , Kivisaar Maia
Published: July 2005

Plasmids in conjunction with other mobile elements such as transposons are major players in the genetic adaptation of bacteria in response to changes in environment. Here we show that a large catabolic TOL plasmid, pWW0, from
Pseudomonas putida
carries genes (
rulAB
genes) encoding an error-prone DNA polymerase Pol V homologue which increase the survival of bacteria under conditions of accumulation of DNA damage. A study of population dynamics in stationary phase revealed that the presence of pWW0-derived
rulAB
genes in the bacterial genome allows the expression of a strong growth advantage in stationary phase (GASP) phenotype of
P. putida
. When
rulAB
-carrying cells from an 8-day-old culture were mixed with Pol V-negative cells from a 1-day-old culture, cells derived from the aged culture out-competed cells from the nonaged culture and overtook the whole culture. At the same time, bacteria from an aged culture lacking the
rulAB
genes were only partially able to out-compete cells from a fresh overnight culture of the parental
P. putida
strain. Thus, in addition to conferring resistance to DNA damage, the plasmid-encoded Pol V genes significantly increase the evolutionary fitness of bacteria during prolonged nutritional starvation of a
P. putida
population. The results of our study indicate that RecA is involved in the control of expression of the pWW0-encoded Pol V.
Anagr-Like Two-Component Regulatory System inLactobacillus plantarumIs Involved in Production of a Novel Cyclic Peptide and Regulation of Adherence
Authors: Sturme Mark H. J. , Nakayama Jiro , Molenaar Douwe , Murakami Yoshiko , Kunugi Ryoko , Fujii Toshio , Vaughan Elaine E. , Kleerebezem Michiel , de Vos Willem M.
Published: July 2005

We have analyzed a locus on the annotatedLactobacillus plantarumWCFS1 genome that showed homology to the staphylococcalagrquorum-sensing system and designated itlamforLactobacillus agr-like module. Production of thelamBDCAtranscript was shown to be growth phase dependent. Analysis of a response regulator-defective mutant (ΔlamA) in an adherence assay showed thatlamregulates adherence ofL. plantarumto a glass surface. Global transcription analysis of the wild-type and ΔlamAstrains in early, mid-, and late log phase of growth was performed using a clone-based microarray. Remarkably, only a small set of genes showed significant differences in transcription profiles between the wild-type andlamAmutant strains. The microarray analysis confirmed thatlamBDCAis autoregulatory and showed thatlamAis involved in regulation of expression of genes encoding surface polysaccharides, cell membrane proteins, and sugar utilization proteins. ThelamBDgenes encoding the putative autoinducing peptide precursor (LamD) and its processing protein (LamB) were overexpressed using the nisin-controlled expression system, and culture supernatants were analyzed by liquid chromatography/mass spectrometry (LC/MS) to identify overproduced LamD-derived peptides. In this way, a cyclic thiolactone pentapeptide that possesses a ring structure similar to those of autoinducing peptides of the staphylococcalagrsystem was identified. The peptide was designated LamD558, and its sequence (CVGIW) matched the annotated precursor peptide sequence. Time course analysis of wild-type culture supernatants by LC/MS indicated that LamD558 production was increased markedly from mid-log to late log growth phase. This is the first example of anagr-like system in nonpathogenic bacteria that encodes a cyclic thiolactone autoinducing peptide and is involved in regulation of adherence.
Characterization of a Small Heat Shock Protein, Mx Hsp16.6, ofMyxococcus xanthus
Authors: Otani Mieko , Ueki Toshiyuki , Kozuka Satoshi , Segawa Miki , Sano Keiji , Inouye Sumiko
Published: July 2005

A number of heat shock proteins inMyxococcus xanthuswere previously identified by two-dimensional (2D) gel electrophoresis. One of these protein was termed Mx Hsp16.6, and the gene encoding Mx Hsp16.6 was isolated. Mx Hsp16.6 consists of 147 amino acid residues and has an estimated molecular weight of 16,642, in accordance with the apparent molecular mass in the 2D gel. An α-crystallin domain, typically conserved in small heat shock proteins, was found in Mx Hsp16.6. Mx Hsp16.6 was not detected during normal vegetative growth but was immediately induced after heat shock. Expression of thehsp16.6gene was not induced by other stresses, such as starvation, oxidation, and high osmolarity. Mx Hsp16.6 was mostly localized in particles formed after heat shock and precipitated by low-speed centrifugation. Furthermore, Mx Hsp16.6 was detected in highly electron-dense particles in heat-shocked cells by immunoelectron microscopy, suggesting that it forms large complexes with heat-denatured proteins. An insertion mutation in thehsp16.6gene resulted in lower viability during heat shock and lower acquired thermotolerance. Therefore, it is likely that Mx Hsp16.6 plays critical roles in the heat shock response inM. xanthus.
Identification of an
Escherichia coli
Operon Required for Formation of the O-Antigen Capsule
Authors: Peleg Adi , Shifrin Yulia , Ilan Ophir , Nadler-Yona Chen , Nov Shani , Koby Simi , Baruch Kobi , Altuvia Shoshy , Elgrably-Weiss Maya , Abe Cecilia M. , Knutton Stuart , Saper Mark A. , Rosenshine Ilan
Published: July 2005

Escherichia coli
produces polysaccharide capsules that, based on their mechanisms of synthesis and assembly, have been classified into four groups. The group 4 capsule (G4C) polysaccharide is frequently identical to that of the cognate lipopolysaccharide O side chain and has, therefore, also been termed the O-antigen capsule. The genes involved in the assembly of the group 1, 2, and 3 capsules have been described, but those required for G4C assembly remained obscure. We found that enteropathogenic
E. coli
(EPEC) produces G4C, and we identified an operon containing seven genes,
ymcD
,
ymcC
,
ymcB
,
ymcA
,
yccZ
,
etp
, and
etk
, which are required for formation of the capsule. The encoded proteins appear to constitute a polysaccharide secretion system. The G4C operon is absent from the genomes of enteroaggregative
E. coli
and uropathogenic
E. coli. E. coli
K-12 contains the G4C operon but does not express it, because of the presence of IS
1
at its promoter region. In contrast, EPEC, enterohemorrhagic
E. coli
, and
Shigella
species possess an intact G4C operon.
Cystic Fibrosis Sputum Supports Growth and Cues Key Aspects of
Pseudomonas aeruginosa
Physiology
Authors: Palmer Kelli L. , Mashburn Lauren M. , Singh Pradeep K. , Whiteley Marvin
Published: July 2005

The opportunistic human pathogen
Pseudomonas aeruginosa
causes persistent airway infections in patients with cystic fibrosis (CF). To establish these chronic infections,
P. aeruginosa
must grow and proliferate within the highly viscous sputum in the lungs of CF patients. In this study, we used Affymetrix GeneChip microarrays to investigate the physiology of
P. aeruginosa
grown using CF sputum as the sole source of carbon and energy. Our results indicate that CF sputum readily supports high-density
P. aeruginosa
growth. Furthermore, multiple signals, which reduce swimming motility and prematurely activate the
Pseudomonas
quinolone signal cell-to-cell signaling cascade in
P. aeruginosa
, are present in CF sputum.
P. aeruginosa
factors critical for lysis of the common CF lung inhabitant
Staphylococcus aureus
were also induced in CF sputum and increased the competitiveness of
P. aeruginosa
during polymicrobial growth in CF sputum.
Use of Suppression-Subtractive Hybridization To Identify Genes in the
Burkholderia cepacia
Complex That Are Unique to
Burkholderia cenocepacia
Authors: Bernier Steve P. , Sokol Pamela A.
Published: July 2005

We have previously shown differences in virulence between species of the
Burkholderia cepacia
complex using the alfalfa infection model and the rat agar bead chronic infection model.
Burkholderia cenocepacia
strains were more virulent in these two infection models than
Burkholderia multivorans
and
Burkholderia stabilis
strains. In order to identify genes that may account for the increased virulence of
B. cenocepacia
, suppression-subtractive hybridization was performed between
B. cenocepacia
K56-2 and
B. multivorans
C5393 and between
B. cenocepacia
K56-2 and
B. stabilis
LMG14294. Genes identified included DNA modification/phage-related/insertion sequences and genes involved in cell membrane/surface structures, resistance, transport, metabolism, regulation, secretion systems, as well as genes of unknown function. Several of these genes were present in the ET12 lineage of
B. cenocepacia
but not in other members of the
B. cepacia
complex. Virulence studies in a chronic lung infection model determined that the hypothetical YfjI protein, which is unique to the ET12 clone, contributes to lung pathology. Other genes specific to
B. cenocepacia
and/or the ET12 lineage were shown to play a role in biofilm formation and swarming or swimming motility.