bluuebunny/crossref_metadata_2025 huggingface dataset:
Elastic Guided Waves in a Layered Plate With a Rectangular Cross Section
Authors: Mukdadi O. M. , Datta S. K. , Dunn M. L.
Published: October 2002

Ultrasonic guided waves in a layered elastic plate of rectangular cross section (finite width and thickness) are studied in this paper. A semi-analytical finite element method in which the deformation of the cross section is modeled by two-dimensional finite elements and analytical representation of propagating waves along the long dimension of the plate is used. The method is applicable to an arbitrary number of layers of anisotropic properties and is similar to that used earlier to study guided waves in layered anisotropic plates of infinite width. Numerical results are presented for acoustic phonon modes of quasi-one-dimensional (QID) wires. For homogeneous wires, these agree well with recently reported results for dispersion of these modes.
Diffusion barrier properties of transition metal thin films grown by plasma-enhanced atomic-layer deposition
Authors: Kim H. , Cabral C. , Lavoie C. , Rossnagel S. M.
Published: October 2002

Ta thin films were grown on Si(001) and polycrystalline Si substrates by plasma-enhanced atomic-layer deposition (PE-ALD) using TaCl5 and atomic hydrogen as precursors. The grown films have resistivity of 150–180 μm cm with a small Cl concentration between 0.5 and 2 at. %. The diffusion barrier properties were investigated using bilayer structures consisting of 200 nm Cu deposited by sputtering on ALD Ta films with various thicknesses. Three in situ analysis techniques consisting of x-ray diffraction, elastic light scattering, and resistance analysis were used to determine the diffusion barrier failure temperature of Ta films. The barriers were annealed at a temperature ramp rate of 3 °C/s from 100 to 1000 °C in forming gas. For this method using x-ray diffraction, the barrier failure temperatures were determined by monitoring the disappearance of the Cu(111) x-ray diffraction peak and appearance of Cu silicide diffraction peaks. At the diffusion barrier failure temperature, elastic light scattering indicated a rapid increase in surface roughness, and concurrent increases in sheet resistance of the blanket Cu/ALD Ta films on polycrystalline Si were monitored using a four-point-probe technique. The same analyses were performed on bilayer structures of Cu/physical-vapor-deposition Ta films with comparable thicknesses. The ALD Ta barrier films show significantly higher failure temperatures compared to PVD Ta; at least 70 °C at comparable thicknesses, which is thought to be due to the uniform, smooth surface and amorphous or nanocrystalline microstructure of ALD Ta.
Structure and photoluminescence features of nanocrystalline Si/SiO2 films produced by plasma chemical vapor deposition and post-treatment
Authors: Wu Xiaochun , Ossadnik Ch. , Eggs Ch. , Veprek S. , Phillipp F.
Published: October 2002

Experimental results of the visible photoluminescence (PL) from nanocrystalline Si (nc-Si) embedded in a SiO2 matrix, prepared by plasma Chemical vapor deposition and a subsequent post-treatment, are reported here. Scanning electron microscopy, transmission electron microscopy, x-ray diffraction, and Fourier transform infrared are used to characterize the morphology, crystallite size, and the composition and structure of nc-Si/SiO2 films. The visible PL can be finely tuned from 1.3 to 1.75 eV by changing annealing time and temperature. The effect of high temperature (870 °C) forming gas (FG) annealing on the visible PL can be divided into three stages. In the first stage, the visible PL blueshifts from 1.3 to 1.55 eV, and the PL intensity increases. In the second stage, the peak energy shows a small shift, and the PL intensity continues increasing. In the last stage, the peak energy blueshifts to ∼1.75 eV, but the PL intensity decreases. The visible PL shows a maximum intensity around 1.5±0.05 eV. For a PL obtained after a high temperature anneal, a subsequent low temperature FG annealing (400 °C) will lead to a redshift of peak energy and an increase in PL intensity. In particular, for a PL around 1.75 eV, a kinetic oscillation of the spectral shift and the PL intensity has been observed upon this annealing. Detailed analysis indicates that the most probable candidates for the visible PL are two oxygen thermal donor-like defect states (TDs) (Si-NL8 and Si-NL10) generated during annealing. The effect of annealing temperature and time on the spectral change and the kinetic oscillation of the spectral change can be explained by the formation and decay kinetics of these two oxygen TDs-like defect states. On the one hand, these experimental results verified the Si–O bond related origin for the visible PL in this system; on the other hand, they also pointed out that apart from the common features of Si–O related visible PL, the detailed configuration and composition of this PL center by different synthesis methods may be different and possess some features of their own.
Improvements of characteristics of fluorinated dielectric films integrated as interlayer dielectrics
Authors: Shieh Jia-Min , Tsai Kou-Chiang , Suen Shich-Chang , Dai Bau-Tong
Published: October 2002

Fluorinated amorphous carbon films (a-C:F) with postnitrogen plasma treatments demonstrate the characteristics of interlayer dielectrics, including high resistance to pyrolysis, copper diffusion, and penetration of corrosive species into intermetals. Nitrogen plasma nitridation was performed to passivate a-C:F films against copper diffusion, and to prevent the fluorine contents from penetrating into copper intermetals. These improvements to a-C:F films are potentially applicable to fluorinated dielectrics, such as SiOF.
Improved GaNxAs1−x quality grown by molecular beam epitaxy with dispersive nitrogen source
Authors: Wang S. Z. , Yoon S. F. , Loke W. K. , Ng T. K. , Fan W. J.
Published: October 2002

A modified mode for GaAsN growth using solid-source molecular beam epitaxy in conjunction with dispersive nitrogen to avoid the bombardment effect of energetic nitrogen ions is reported. High-quality GaAsN epilayers and good GaAsN/GaAs interfaces were achieved using this growth mode. The results suggest that the surface of samples grown using dispersive nitrogen has fewer defects than those grown using the direct nitrogen beam. The optical quality of GaAsN samples grown using the dispersive nitrogen technique was found to improve, due to the lower nitrogen ion bombardment effect. This growth technique is expected to be advantageous for growing high-quality GaAsN materials for optoelectronic applications.
Characterization for strontium titinate/Fe3O4 and TiN/Fe3O4 interfaces
Authors: Lussier A. , Idzerda Y. U. , Stadler S. , Ogale S. B. , Shinde S. R. , Venkatesan V.
Published: October 2002

The interface formation between different thicknesses of strontium titanate (SrTiO3) or titanium nitride (TiN) with a 2000 Å Fe3O4 film is studied using x-ray absorption spectroscopy (XAS) and x-ray magnetic circular dichroism (XMCD). Our results show that the deposition of 10–50 Å of TiN results in an immediate and substantial removal of oxygen from the near interface region, resulting in the formation of spin-randomizing FeO interlayers. For the deposition of SrTiO3 on Fe3O4, our measurements show only a small deviation from the Fe3O4 characteristic XAS signature, suggesting the limited formation of perhaps only one monolayer of another Fe oxide at the interface. The persistent XMCD signal, however, confirms the preservation of Fe3O4 in its ferromagnetic state.
Determination of the erosion rate in the transient region of an ultralow energy secondary ion mass spectrometry profile using medium energy ion scattering
Authors: McConville C. F. , Al-Harthi S. H. , Dowsett M. G. , Gard F. S. , Ormsby T. J. , Guzman B. , Noakes T. C. Q. , Bailey P.
Published: October 2002

A method which allows the erosion rate to be established from the earliest stages of an ultralow energy secondary ion mass spectrometry (ule-SIMS) profile is described. Using the technique of medium energy ion scattering (MEIS), this method provides data which enables an accurate depth scale to be established from a depth of a few nanometers onwards. The method is applicable for a thin amorphous layer at the surface or a heavy element marker in the near-surface region, and enables the erosion rate as a function of SIMS ion dose to be established for particular bombardment conditions. The erosion rate obtained is used to calibrate the depth and intensity scales of implant profile measured using ule-SIMS and to interpret the near-surface distribution. In this article we demonstrate this methodology using a Ge preamorphized Si(001) surface with a 1 keV boron implant. The altered layer formed by the primary SIMS O2+ incorporation and the redistribution of Ge in the samples used, are also described. Based on the Ge redistribution results, the possibility of adapting this method for determining erosion rates in crystalline silicon and silicon surface recession measurements, is also discussed.
Enhancement of implantation efficiency by grid biasing in radio-frequency inductively coupled plasma direct-current plasma immersion ion implantation
Authors: Tong Honghui , Fu Ricky K. Y. , Zeng Xuchu , Kwok Dixon T. K. , Chu Paul K.
Published: October 2002

Direct-current plasma immersion ion implantation (dc-PIII) is an emerging method for the treatment of planar samples and particularly attractive as an efficient and economical technique to fabricate silicon-on-insulator. In this article, we report the use of grid biasing to enhance the implantation efficiency such as implantation current density. Experiments in argon plasma show that the implantation current density varies with the biased voltage (Vg), is higher at Vg⩾+30 V or Vg⩽−40 V than at Vg=0, and is saturated at Vg⩾+50 V or Vg⩽−50 V at a pressure of 0.2 mTorr. The implantation current density is always higher at Vg=+50 V than at Vg=0 at different pressure and radio-frequency (rf) power. Moreover, the implantation current density increases with the rf power and pressure at both 0 and +50 V biasing. The results of our particle-in-cell simulation and global model show that the observed phenomenon is partly due to the variation of the plasma density with the bias, and the variation in the shape of emitted plasma surface with the bias is clearly illustrated by our experimental results. Similar results are observed for hydrogen plasma.
Operator methods in classical mechanics
Authors: Fernández Francisco M.
Published: October 2002

By taking into account that the equations of motion of classical mechanics can be expressed in terms of differential operators in phase space, we develop a simple method for obtaining exact solutions for several models in one and more dimensions. We also propose a simple procedure for the systematic construction of exactly solvable models in one dimension.
Resonances and quantum scattering for the Morse potential as a barrier
Authors: Rawitscher G. , Merow Cory , Nguyen Matthew , Simbotin Ionel
Published: October 2002

Quantum scattering in the presence of a potential valley followed by a barrier is examined for a Morse potential, for which exact analytical solutions are known. For our application the sign of the potential is reversed, and the wave function is required to vanish at the origin. This condition requires a special combination of hypergeometric functions, and can lead to resonances for incident energies below the top of the barrier. Numerical values for the analytical phase shifts are presented in and outside the resonant regions, and the corresponding properties of the scattering S matrix are examined in the complex momentum plane. The validity of the Breit–Wigner approximation to the resonant part of the phase shifts is tested, and a new method for finding the location of narrow resonances is described. The time decay of a resonant wave packet slowly leaking out of the valley region (on a time scale proportional to the inverse of the width of the resonance) is compared with theoretical predictions, and complete agreement is not found.
Multibeam volume acoustic backscatter imagery and reverberation measurements in the northeastern Gulf of Mexico
Authors: Gallaudet Timothy C. , de Moustier Christian P.
Published: October 2002

Multibeam volume acoustic backscatter imagery and reverberation measurements are derived from data collected in 200-m-deep waters in the northeastern Gulf of Mexico, with the Toroidal Volume Search Sonar (TVSS), a 68-kHz cylindrical sonar operated by the U.S. Navy’s Coastal System Station. The TVSS’s 360-degree vertical imaging plane allows simultaneous identification of multiple volume scattering sources and their discrimination from backscatter at the sea surface or the seafloor. This imaging capability is used to construct a three-dimensional representation of a pelagic fish school near the bottom. Scattering layers imaged in the mixed layer and upper thermocline are attributed to assemblages of epipelagic zooplankton. The fine scale patchiness of these scatterers is assessed with the two-dimensional variance spectra of vertical volume scattering strength images in the upper and middle water column. Mean volume reverberation levels exhibit a vertical directionality which is attributed to the volume scattering layers. Boundary echo sidelobe interference and reverberation is shown to be the major limitation in obtaining bioacoustic data with the TVSS. Because net tow and trawl samples were not collected with the acoustic data, the analysis presented is based upon comparison to previous biologic surveys in the northeastern Gulf of Mexico and reference to the bioacoustic literature.
Broadband sound generation by confined turbulent jets
Authors: Zhang Zhaoyan , Mongeau Luc , Frankel Steven H.
Published: October 2002

Sound generation by confined stationary jets is of interest to the study of voice and speech production, among other applications. The generation of sound by low Mach number, confined, stationary circular jets was investigated. Experiments were performed using a quiet flow supply, muffler-terminated rigid uniform tubes, and acrylic orifice plates. A spectral decomposition method based on a linear source-filter model was used to decompose radiated nondimensional sound pressure spectra measured for various gas mixtures and mean flow velocities into the product of (1) a source spectral distribution function; (2) a function accounting for near field effects and radiation efficiency; and (3) an acoustic frequency response function. The acoustic frequency response function agreed, as expected, with the transfer function between the radiated acoustic pressure at one fixed location and the strength of an equivalent velocity source located at the orifice. The radiation efficiency function indicated a radiation efficiency of the order (kD)2 over the planar wave frequency range and (kD)4 at higher frequencies, where k is the wavenumber and D is the tube cross sectional dimension. This is consistent with theoretical predictions for the planar wave radiation efficiency of quadrupole sources in uniform rigid anechoic tubes. The effects of the Reynolds number, Re, on the source spectral distribution function were found to be insignificant over the range 2000<Re<20 000. The source spectral distribution function approximately obeyed a St−3 power law for Strouhal number values St<0.9, and a St−5 power law for St>2.5. The influence of a reflective open tube termination on the source function spectral distribution was found to be insignificant, confirming the absence of a feedback mechanism.
Leaky helical flexural wave backscattering contributions from tilted cylindrical shells in water: Observations and modeling
Authors: Blonigen Florian J. , Marston Philip L.
Published: October 2002

For tilt angles smaller than the meridional ray coupling condition previously investigated [S. F. Morse et al., J. Acoust. Soc. Am. 103, 785–794 (1998)], flexural helical waves on cylindrical shells can significantly enhance the backscattering. These contributions are compared and modeled here for an empty cylinder. Experiments using tone bursts were performed on a tilted stainless steel shell to investigate the contributions caused by flexural leaky Lamb waves above the coincidence frequency of the shell. In some of the measurements the tone bursts were of sufficient duration to superpose helical wave contributions of successive circumnavigations, along with the meridional contribution near the critical tilt, to arrive at a quasi-steady-state backscattering amplitude for the cylinder. These measurements are compared with an approximate numerical partial-wave series solution and a ray theory as a function of the tilt angle. The data for ka=20 follow the basic shape of the ray theory and the relevant features of the partial-wave model. They illustrate the importance of the interference of successive helical wave contributions. Measurements (also as a function of the tilt angle) using tone bursts that were sufficiently short to separate the earliest helical wave contribution from later contributions also support the ray theory.
Identification of
Bphs
, an Autoimmune Disease Locus, as Histamine Receptor H
1
Authors: Ma Runlin Z. , Gao Jianfeng , Meeker Nathan D. , Fillmore Parley D. , Tung Kenneth S. K. , Watanabe Takeshi , Zachary James F. , Offner Halina , Blankenhorn Elizabeth P. , Teuscher Cory
Published: October 2002

Bphs controls
Bordetella pertussis
toxin (PTX)–induced vasoactive amine sensitization elicited by histamine (VAASH) and has an established role in autoimmunity. We report that congenic mapping links
Bphs
to the histamine H
1
receptor gene (
Hrh1
/H1R) and that H1R differs at three amino acid residues in VAASH-susceptible and -resistant mice.

Hrh1
-/-

mice are protected from VAASH, which can be restored by genetic complementation with a susceptible
Bphs/Hrh1
allele, and experimental allergic encephalomyelitis and autoimmune orchitis due to immune deviation. Thus, natural alleles of
Hrh1
control both the autoimmune T cell and vascular responses regulated by histamine after PTX sensitization.
Gold from Green Paths
Authors: Pearce David
Published: October 2002

The New Economy of Nature
The Quest to Make Conservation Profitable. Gretchen C. Daily and Katherine Ellison. Shearwater (Island Press), Washington, DC, 2002. 270 pp. $25. ISBN 1-55963-945-8.

The authors use a series of case stories to discuss efforts at protecting natural systems through market systems.
Structures of Glycoprotein Ibα and Its Complex with von Willebrand Factor A1 Domain
Authors: Huizinga Eric G. , Tsuji Shizuko , Romijn Roland A. P. , Schiphorst Marion E. , de Groot Philip G. , Sixma Jan J. , Gros Piet
Published: October 2002

Transient interactions of platelet-receptor glycoprotein Ibα (GpIbα) and the plasma protein von Willebrand factor (VWF) reduce platelet velocity at sites of vascular damage and play a role in haemostasis and thrombosis. Here we present structures of the GpIbα amino-terminal domain and its complex with the VWF domain A1. In the complex, GpIbα wraps around one side of A1, providing two contact areas bridged by an area of solvated charge interaction. The structures explain the effects of gain-of-function mutations related to bleeding disorders and provide a model for shear-induced activation. These detailed insights into the initial interactions in platelet adhesion are relevant to the development of antithrombotic drugs.
Unexpected Consequences of Connections
Authors: Foster Ian
Published: October 2002

Linked
The New Science of Networks. Albert-László Barabási. Perseus, Cambridge, MA, 2002. 288 pp. $26, C$39.50. ISBN 0-7382-0667-9

Nexus
Small Worlds and the Groundbreaking Science of Networks. Mark Buchanan. Norton, New York, 2002. 235 pp. $25.95, C$37.99. ISBN 0-393-04153-0

Small World
Uncovering Nature's Hidden Networks. Weidenfeld and Nicholson, London, 2002. 235 pp. £18.99. ISBN 0-297-60742-1

These two popular accounts discus im-plications of the structure of networks for our understanding of science, business, and everyday life.
Tracing Black Hole Mergers Through Radio Lobe Morphology
Authors: Merritt David , Ekers R. D.
Published: October 2002

Binary supermassive black holes are produced by galactic mergers as the black holes from the two galaxies fall to the center of the merged system and form a bound pair. The two black holes will eventually coalesce in an enormous burst of gravitational radiation. Here we show that the orientation of a black hole's spin axis would change dramatically even in a minor merger, leading to a sudden flip in the direction of any associated jet. We identify the winged or X-type radio sources with galaxies in which this has occurred. The inferred coalescence rate is similar to the overall galaxy merger rate, implying that of the order of one merger event per year could be detected by gravitational wave interferometers.
Green Chemistry: Science and Politics of Change
Authors: Poliakoff Martyn , Fitzpatrick J. Michael , Farren Trevor R. , Anastas Paul T.
Published: October 2002

The chemical industry plays a key role in sustaining the world economy and underpinning future technologies, yet is under unprecedented pressure from the effects of globalization and change in many of its traditional markets. Against this background, what will be needed for the industry to embrace efforts to make it “greener”? We explore some of the issues raised by the development of “green chemistry” techniques and identify potential barriers to their implementation by industry.
Evaluation of Antibiotic Susceptibilities of Three Rickettsial Species Including
Rickettsia felis
by a Quantitative PCR DNA Assay
Authors: Rolain Jean-Marc , Stuhl Laetitia , Maurin Max , Raoult Didier
Published: October 2002

Rickettsiae grow only intracellularly, and the antibiotic susceptibilities of these bacteria have been assessed by either plaque, dye uptake, or immunofluorescence assays, which are time-consuming. We used a quantitative PCR (with the LightCycler instrument) to assess the levels of inhibition of
Rickettisa felis
,
R. conorii
, and
R. typhi
DNA synthesis in the presence of various antibiotics. We established the kinetics of rickettsial DNA during growth and showed that
R. conorii
grows more quickly than
R. typhi
in cell culture, with maximum replication occurring after 5 and 7 days, respectively. The MICs of the antibiotics tested for
R. conorii
and
R. typhi
by the quantitative PCR assay were similar to those previously obtained by plaque and dye uptake assays. We found that
R. felis
is susceptible to doxycycline, rifampin, thiamphenicol, and fluoroquinolones but not to gentamicin, erythromycin, amoxicillin, or trimethoprim-sulfamethoxazole. The resistance of this new species to erythromycin is consistent with its current taxonomic position within the spotted fever group. We believe that quantitative PCR could be used in the future to simplify and shorten antibiotic susceptibility assays of other rickettsiae and other strict intracellular pathogens.
Effects of Neutrophils on Cefazolin Activity and Penicillin-Binding Proteins in
Staphylococcus aureus
Abscesses
Authors: Bamberger David M. , Herndon Betty L. , Fitch Jeffrey , Florkowski Aaron , Parkhurst Vera
Published: October 2002

Bacteria survive within abscesses despite antimicrobial therapy, usually necessitating drainage. Our previous work showed that bacterial killing is diminished within the neutrophils of animals with abscesses. To further assess the role of neutrophils in
Staphylococcus aureus
survival and the poor activities of β-lactams in abscesses, tissue cage abscess-bearing rats were given polymorphonuclear leukocyte (PMN)-depleting antibody prior to and several times following inoculation of the tissue cages with
S. aureus.
Cefazolin (300 mg/kg of body weight/day) was administered to all animals in appropriately divided doses. After 7 days of antimicrobial therapy, the 17 animals that received anti-PMN serum had significantly fewer abscess neutrophils than the 18 controls and fewer abscess bacteria (5.55 versus 3.79 log
10
CFU/ml [
P
= 0.04]) than the 18 controls. The data were consistent with the premise that cefazolin is more effective in abscesses depleted of neutrophils. To investigate further,
S. aureus
was incubated with rat peritoneal neutrophils; and bacterial cell membrane proteins were isolated, labeled with biotinylated ampicillin, separated by electrophoresis, blotted onto nitrocellulose, and stained for biotin reactivity. PBP 2 expression was consistently and significantly decreased after a brief, nonkilling PMN exposure. These experiments showed that PMN depletion enhanced the activity of cefazolin in the abscess milieu. Furthermore, altered bacterial cell wall cefazolin targets may be the mechanism by which the PMN diminishes antimicrobial activity, suggesting the importance of the staphylococcus-PMN interaction in the outcome of established infections.
Antistreptococcal Activity of Telithromycin Compared with Seven Other Drugs in Relation to Macrolide Resistance Mechanisms in Russia
Authors: Kozlov Roman S. , Bogdanovitch Tatiana M. , Appelbaum Peter C. , Ednie Lois , Stratchounski Leonid S. , Jacobs Michael R. , Bozdogan Bülent
Published: October 2002

The susceptibilities of 468 recent Russian clinical
Streptococcus pneumoniae
isolates and 600
Streptococcus pyogenes
isolates, from 14 centers in Russia, to telithromycin, erythromycin, azithromycin, clarithromycin, clindamycin, levofloxacin, quinupristin-dalfopristin, and penicillin G were tested. Penicillin-nonsusceptible
S. pneumoniae
strains were rare except in Siberia, where their prevalence rate was 13.5%: most were penicillin intermediate, but for three strains (two from Smolensk and one from Novosibirsk) the MICs of penicillin G were 4 or 8 μg/ml. Overall, 2.5% of
S. pneumoniae
isolates were resistant to erythromycin. Efflux was the prevalent resistance mechanism (five strains; 41.7%), followed by ribosomal methylation encoded by constitutive
erm
(B), which was found in four isolates. Ribosomal mutation was the mechanism of macrolide resistance in three isolates; one erythromycin-resistant
S. pneumoniae
isolate had an A2059G mutation in 23S rRNA, and two isolates had substitution of GTG by TPS at positions 69 to 71 in ribosomal protein L4. All
S. pyogenes
isolates were susceptible to penicillin, and 11% were erythromycin resistant. Ribosomal methylation was the most common resistance mechanism for
S. pyogenes
(89.4%). These methylases were encoded by
erm
(A) [subclass
erm
(TR)] genes, and their expression was inducible in 96.6% of isolates. The rest of the erythromycin-resistant Russian
S. pyogenes
isolates (7.6%) had an efflux resistance mechanism. Telithromycin was active against 100% of pneumococci and 99.2% of
S. pyogenes
, and levofloxacin and quinupristin-dalfopristin were active against all isolates of both species.
Phenylpropenamide Derivatives AT-61 and AT-130 Inhibit Replication of Wild-Type and Lamivudine-Resistant Strains of Hepatitis B Virus In Vitro
Authors: Delaney William E. , Edwards Ros , Colledge Danni , Shaw Tim , Furman Phil , Painter George , Locarnini Stephen
Published: October 2002

The phenylpropenamide derivatives AT-61 and AT-130 are nonnucleoside analogue inhibitors of hepatitis B virus (HBV) replication. They inhibited the replication of wild-type HBV with 50% inhibitory concentrations of 21.2 ± 9.5 and 2.40 ± 0.92 μM, respectively, compared to 0.064 ± 0.020 μM lamivudine. There were no significant differences in sensitivity between wild-type and nucleoside analogue-resistant (rtL180M, rtM204I, and rtL180M + rtM204V) HBV.
Cloning and Expression of the Haloalkane Dehalogenase GenedhmAfromMycobacterium aviumN85 and Preliminary Characterization of DhmA
Authors: Jesenská Andrea , Bartoš Milan , Czerneková Vladimíra , Rychlík Ivan , Pavlík Ivo , Damborský Jiří
Published: October 2002

Haloalkane dehalogenases are microbial enzymes that catalyze cleavage of the carbon-halogen bond by a hydrolytic mechanism. Until recently, these enzymes have been isolated only from bacteria living in contaminated environments. In this report we describe cloning of the dehalogenase genedhmAfromMycobacterium aviumsubsp.aviumN85 isolated from swine mesenteric lymph nodes. ThedhmAgene has a G+C content of 68.21% and codes for a polypeptide that is 301 amino acids long and has a calculated molecular mass of 34.7 kDa. The molecular masses of DhmA determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and by gel permeation chromatography are 34.0 and 35.4 kDa, respectively. Many residues essential for the dehalogenation reaction are conserved in DhmA; the putative catalytic triad consists of Asp123, His279, and Asp250, and the putative oxyanion hole consists of Glu55 and Trp124. Trp124 should be involved in substrate binding and product (halide) stabilization, while the second halide-stabilizing residue cannot be identified from a comparison of the DhmA sequence with the sequences of three dehalogenases with known tertiary structures. The haloalkane dehalogenase DhmA shows broad substrate specificity and good activity with the priority pollutant 1,2-dichloroethane. DhmA is significantly less stable than other currently known haloalkane dehalogenases. This study confirms that a hydrolytic dehalogenase is present in the facultative pathogenM. avium. The presence of dehalogenase-like genes in the genomes of other mycobacteria, including the obligate pathogensMycobacterium tuberculosisandMycobacterium bovis, as well as in other bacterial species, includingMesorhizobium loti, Xylella fastidiosa, Photobacterium profundum, andCaulobacter crescentus, led us to speculate that haloalkane dehalogenases have some other function besides catalysis of hydrolytic dehalogenation of halogenated substances.
Enhanced Production of
Trichoderma reesei
Endoglucanases and Use of the New Cellulase Preparations in Producing the Stonewashed Effect on Denim Fabric
Authors: Miettinen-Oinonen Arja , Suominen Pirkko
Published: October 2002

Trichoderma reesei
strains were constructed for production of elevated amounts of endoglucanase II (EGII) with or without cellobiohydrolase I (CBHI). The endoglucanase activity produced by the EGII transformants correlated with the copy number of the
egl2
expression cassette. One copy of the
egl2
expression cassette in which the
egl2
was under the
cbh1
promoter increased production of endoglucanase activity 2.3-fold, and two copies increased production about 3-fold above that of the parent strain. When the enzyme with elevated EGII content was used, an improved stonewashing effect on denim fabric was achieved. A
T. reesei
strain producing high amounts of EGI and -II activities without CBHI and -II was constructed by replacing the
cbh2
locus with the coding region of the
egl2
gene in the EGI-overproducing CBHI-negative strain. Production of endoglucanase activity by the EG-transformant strain was increased fourfold above that of the host strain. The filter paper-degrading activity of the endoglucanase-overproducing strain was lowered to below detection, presumably because of the lack of cellobiohydrolases.
Exploration of Inorganic C and N Assimilation by Soil Microbes with Time-of-Flight Secondary Ion Mass Spectrometry
Authors: Cliff John B. , Gaspar Daniel J. , Bottomley Peter J. , Myrold David D.
Published: October 2002

Stable C and N isotopes have long been used to examine properties of various C and N cycling processes in soils. Unfortunately, relatively large sample sizes are needed for accurate gas phase isotope ratio mass spectrometric analysis. This limitation has prevented researchers from addressing C and N cycling issues on microbially meaningful scales. Here we explored the use of time-of-flight secondary ion mass spectrometry (TOF-SIMS) to detect
13
C and
15
N assimilation by individual bacterial cells and to quantify N isotope ratios in bacterial samples and individual fungal hyphae. This was accomplished by measuring the relative abundances of mass 26 (
12
C
14
N
−
) and mass 27 (
13
C
14
N
−
and
12
C
15
N
−
) ions sputtered with a Ga
+
probe from cells adhered to an Si contact slide. TOF-SIMS was successfully used to locate and quantify the relative
15
N contents of individual hyphae that grew onto Si contact slides in intimate contact with a model organomineral porous matrix composed of kaolin, straw fragments, and freshly deposited manure that was supplemented with
15
NO
3
−
. We observed that the
15
N content of fungal hyphae grown on the slides was significantly lower in regions where the hyphae were influenced by N-rich manure than in regions influenced by N-deficient straw. This effect occurred over distances of tens to hundreds of microns. Our data illustrate that TOF-SIMS has the potential to locate N-assimilating microorganisms in soil and to quantify the
15
N content of cells that have assimilated
15
N-labeled mineral N and shows promise as a tool with which to explore the factors controlling microsite heterogeneities in soil.
Detection of Anatoxin-a(s) in Environmental Samples of Cyanobacteria by Using a Biosensor with Engineered Acetylcholinesterases
Authors: Devic Eric , Li Dunhai , Dauta Alain , Henriksen Peter , Codd Geoffrey A. , Marty Jean-Louis , Fournier Didier
Published: October 2002

Bioassays are little used to detect individual toxins in the environment because, compared to analytical methods, these assays are still limited by several problems, such as the sensitivity and specificity of detection. We tentatively solved these two drawbacks for detection of anatoxin-a(s) by engineering an acetylcholinesterase to increase its sensitivity and by using a combination of mutants to obtain increased analyte specificity. Anatoxin-a(s), a neurotoxin produced by some freshwater cyanobacteria, was detected by measuring the inhibition of acetylcholinesterase activity. By using mutated enzyme, the sensitivity of detection was brought to below the nanomole-per-liter level. However, anatoxin-a(s) is an organophosphorous compound, as are several synthetic molecules which are widely used as insecticides. The mode of action of these compounds is via inhibition of acetylcholinesterase, which makes the biotest nonspecific. The use of a four-mutant set of acetylcholinesterase variants, two mutants that are sensitive to anatoxin-a(s) and two mutants that are sensitive to the insecticides, allows specific detection of the cyanobacterial neurotoxin.
Enhancement of Protective Efficacy following Intranasal Immunization with Vaccine Plus a Nontoxic LTK63 Mutant Delivered with Nanoparticles
Authors: Baudner B. C. , Balland O. , Giuliani M. M. , Von Hoegen P. , Rappuoli R. , Betbeder D. , Del Giudice G.
Published: October 2002

Most vaccines are still given parenterally. Mucosal vaccination would offer different advantages over parenteral immunization, including blocking of the pathogens at the portal of entry. In this paper, nontoxic
Escherichia coli
heat-labile enterotoxin (LT) mutants and Supramolecular Biovector systems (SMBV) were evaluated in mice as mucosal adjuvants and delivery systems, respectively, for intranasal immunization with the conjugated group C meningococcal vaccine. The conjugated vaccine formulated together with the LT mutants and the SMBV induced very high titers of serum and mucosal antibodies specific for the group C meningococcal polysaccharide. This vaccination strategy also induced high titers of antibodies with bactericidal activity, which is known to correlate with efficacy. Importantly, the mucosal vaccination, but not the conventional parenteral vaccination, induced bactericidal antibodies at the mucosal level. These data strongly support the feasibility of development of intranasal vaccines with an enhanced protective efficacy against meningococci and possibly against other encapsulated bacteria.
Analysis of Serum Cross-Reactivity and Cross-Protection Elicited by Immunization with DNA Vaccines against
Streptococcus pneumoniae
Expressing PspA Fragments from Different Clades
Authors: Miyaji Eliane N. , Ferreira Daniela M. , Lopes Alexandre P. Y. , Brandileone M. Cristina C. , Dias Waldely O. , Leite Luciana C. C.
Published: October 2002

Streptococcus pneumoniae
is a major cause of disease, especially in developing countries, and cost-effective alternatives to the currently licensed vaccines are needed. We constructed DNA vaccines based on pneumococcal surface protein A (PspA), an antigen shown to induce protection against pneumococcal bacteremia. PspA fragments can be divided into three families, which can be subdivided into six clades, on the basis of PspA amino acid sequence divergence (S. K. Hollingshead, R. Becker, and D. E. Briles, Infect. Immun.
68:
5889-5900, 2000). Since most clinical isolates belong to family 1 or family 2, PspA fragments from members of both of these families were analyzed. Vectors encoding the complete N-terminal regions of PspAs elicited significant humoral responses, and cross-reactivity was mainly restricted to the same family. DNA vaccines encoding fusions between PspA fragments from family 1 and family 2 were also constructed and were able to broaden the cross-reactivity, with induction of antibodies that showed reactions with members of both families. At least for the pneumococcal strains tested, the cross-reactivity of antibodies was not reflected in cross-protection. Animals immunized with DNA vaccines expressing the complete N-terminal regions of PspA fragments were protected only against intraperitoneal challenge with a strain expressing PspA from the same clade.
Lack of Strand Bias in UV-Induced Mutagenesis inEscherichia coli
Authors: Gawel Damian , Maliszewska-Tkaczyk Magdalena , Jonczyk Piotr , Schaaper Roel M. , Fijalkowska Iwona J.
Published: October 2002

We have investigated whether UV-induced mutations are created with equal efficiency on the leading and lagging strands of DNA replication. We employed an assay system that permits measurement of mutagenesis in thelacZgene in pairs of near-identical strains. Within each pair, the strains differ only in the orientation of thelacZgene with respect to the origin of DNA replication. Depending on this orientation, anylacZtarget sequence will be replicated in one orientation as a leading strand and as a lagging strand in the other orientation. In contrast to previous results obtained for mutations resulting from spontaneous replication errors or mutations resulting from the spontaneous SOS mutator effect, measurements of UV-induced mutagenesis inuvrAstrains fail to show significant differences between the two target orientations. These data suggest that SOS-mediated mutagenic translesion synthesis on theEscherichia colichromosome may occur with equal or similar probability on leading and lagging strands.
The Superantigen GeneypmIs Located in an Unstable Chromosomal Locus ofYersinia pseudotuberculosis
Authors: Carnoy Christophe , Floquet Stephanie , Marceau Michael , Sebbane Florent , Haentjens-Herwegh Stephanie , Devalckenaere Annie , Simonet Michel
Published: October 2002

Yersinia pseudotuberculosisproduces YPM (Y. pseudotuberculosis-derived mitogen), a superantigenic toxin that exacerbates the virulence of the bacterium in vivo. To date, three alleles of the superantigen gene (ypmA,ypmB, andypmC) have been described. These genes are not found in allY. pseudotuberculosisstrains and have a low GC content, suggesting their location on mobile genetic elements. To elucidate this question, the genetic environment of the superantigen-encoding genes was characterized and 11 open reading frames (ORFs) were defined. Sequence analysis revealed that theypmgenes were not associated with plasmids, phages, transposons, or pathogenicity islands and that the superantigen genes were always located in the chromosome between ORF3 and ORF4. Nonsuperantigenic strains exhibited the same genetic organization of the locus but lacked theypmgene between ORF3 and ORF4. A new insertion sequence, designated IS1398, which displays features of the Tn3family, was characterized downstream of theypmAandypmCgenes. A 13.3-kb region containing theypmgenes was not found in the genome ofY. pestis(CO92 and KIM 5 strains). We experimentally induced deletion of theypmgene from a superantigen-expressingY. pseudotuberculosis: using the association ofaph(3′)-IIIaandsacBgenes, we demonstrated that when these reporter genes were present in theypmlocus, deletion of these genes was about 250 times more frequent than when they were located in another region of theY. pseudotuberculosischromosome. These results indicate that unlike other superantigenic toxin genes, theYersinia ypmgenes are not associated with mobile genetic elements but are inserted in an unstable locus of the genome.
The Phage Proteomic Tree: a Genome-Based Taxonomy for Phage
Authors: Rohwer Forest , Edwards Rob
Published: October 2002

There are ∼1031phage in the biosphere, making them the most abundant biological entities on the planet. Despite their great numbers and ubiquitous presence, very little is known about phage biodiversity, biogeography, or phylogeny. Information is limited, in part, because the current ICTV taxonomical system is based on culturing phage and measuring physical parameters of the free virion. No sequence-based taxonomic systems have previously been established for phage. We present here the “Phage Proteomic Tree,” which is based on the overall similarity of 105 completely sequenced phage genomes. The Phage Proteomic Tree places phage relative to both their near neighbors and all other phage included in the analysis. This method groups phage into taxa that predicts several aspects of phage biology and highlights genetic markers that can be used for monitoring phage biodiversity. We propose that the Phage Proteomic Tree be used as the basis of a genome-based taxonomical system for phage.
Growth Phase-Dependent Regulation of Target Gene Promoters for Binding of the Essential Orphan Response Regulator HP1043 of
Helicobacter pylori
Authors: Delany Isabel , Spohn Gunther , Rappuoli Rino , Scarlato Vincenzo
Published: October 2002

Helicobacter pylori
encodes three two-component systems and two orphan response regulators (RRs) that are predicted to be involved in transcriptional regulation. The HP1043 gene encodes an essential OmpR-like RR, 1043RR, for which no histidine kinase has been identified. Gel filtration and cross-linking experiments on the purified 1043RR protein reveals that this protein is a dimer and in vivo dimerization assays localize the dimerization to the N-terminal regulatory domain. DNA-binding studies have revealed two targets for specific binding of the 1043RR protein and moreover, phosphorylation of the protein was not needed for the activation of binding. Footprinting analysis demonstrated that the 1043RR protein binds to its own promoter, P
1043
, overlapping the −35 promoter element from positions −17 to −45, suggesting that this protein is autoregulatory. In addition, it binds at a similar location, spanning nucleotides from positions −22 to −51 at the promoter of the methyl-accepting chemotaxis
tlpB
gene, P

tlpB

. A possible inverted repeat was identified in the binding sites of both promoters. In an attempt to overexpress 1043RR in
H. pylori
, the 10-fold induction in transcription of a second copy of HP1043 with use of an inducible promoter failed to increase cellular levels of the RR protein, suggesting that 1043RR is tightly regulated at a posttranscriptional level. The P
1043
and P

tlpB

promoters were demonstrated to be coordinately regulated in response to growth phase in
H. pylori
. The essential role of HP1043 in encoding a cell cycle regulator is discussed.
SpiC Is Required for Translocation ofSalmonellaPathogenicity Island 2 Effectors and Secretion of Translocon Proteins SseB and SseC
Authors: Freeman Jeremy A. , Rappl Catherine , Kuhle Volker , Hensel Michael , Miller Samuel I.
Published: October 2002

TheSalmonellapathogenicity island 2 (SPI2) type III secretion system (TTSS) promotesSalmonella entericaserovar Typhimurium virulence for mice and increased survival and replication within eukaryotic cells. After phagocytosis,Salmonellaserovar Typhimurium assembles the SPI2 TTSS to translocate over a dozen effector proteins across the phagosome membrane. SpiC has been previously shown to be a translocated effector with a large contribution to virulence (K. Uchiya, M. A. Barbieri, K. Funato, A. H. Shah, P. D. Stahl, and E. A. Groisman, EMBO J. 18:3924-3933, 1999). This report demonstrates by competitive index that the virulence phenotype of aspiCmutant is equivalent to that of a secretion component mutant. In addition, translocation of SPI2 effector proteins was shown to require SpiC. Thus, the severe virulence phenotype resulting from deletion ofspiCis likely due to the inability to translocate all SPI2 effectors. SpiC was also required to secrete translocon proteins SseB and SseC but not translocated effector SseJ, indicating that lack of assembly of the translocon explains thespiCmutant phenotype.
The MexJK Efflux Pump of
Pseudomonas aeruginosa
Requires OprM for Antibiotic Efflux but Not for Efflux of Triclosan
Authors: Chuanchuen Rungtip , Narasaki Craig T. , Schweizer Herbert P.
Published: October 2002

Using the biocide triclosan as a selective agent, several triclosan-resistant mutants of a susceptible
Pseudomonas aeruginosa
strain were isolated. Cloning and characterization of a DNA fragment conferring triclosan resistance from one of these mutants revealed a hitherto uncharacterized efflux system of the resistance nodulation cell division (RND) family, which was named MexJK and which is encoded by the
mexJK
operon. Expression of this operon is negatively regulated by the product of
mexL
, a gene located upstream of and transcribed divergently from
mexJK
. The triclosan-resistant mutant contained a single nucleotide change in
mexL
, which caused an amino acid change in the putative helix-turn-helix domain of MexL. The MexL protein belongs to the TetR family of repressor proteins. The MexJK system effluxed tetracycline and erythromycin but only in the presence of the outer membrane protein channel OprM; OprJ and OprN did not function with MexJK. Triclosan efflux required neither of the outer membrane protein channels tested but necessitated the MexJ membrane fusion protein and the MexK inner membrane RND transporter. The results presented in this study suggest that MexJK may function as a two-component RND pump for triclosan efflux but must associate with OprM to form a tripartite antibiotic efflux system. Furthermore, the results confirm that triclosan is an excellent tool for the study of RND multidrug efflux systems and that this popular biocide therefore readily selects mutants which are cross-resistant with antibiotics.