bluuebunny/crossref_metadata_2025 huggingface dataset:
Thermotunnel refrigerator with vacuum/insulator tunnel barrier: A theoretical analysis
Authors: Tavkhelidze Avto , Svanidze Vasiko , Tsakadze Leri
Published: January 2008

The authors use two insulator layers in thermotunnel refrigerator to modify the shape of the tunneling barrier so that electrons with high kinetic energy pass it with increased probability. Theoretical analysis show that the overall tunneling current between the electrodes contains an increased number of high kinetic energy electrons and a reduced number of low energy ones, leading to high efficiency. The particular case of vacuum gap and solid insulator layer is calculated using digital methods. Efficiency remains high in the wide range of the emitter electric field. The cooling coefficient is found to be as high as 40%−50% in the wide range of the emitter electric field.
Damage-free microwave-excited plasma etching without carrier deactivation of heavily doped Si under thin silicide layer
Authors: Goto Tetsuya , Ikenaga Kazuyuki , Teramoto Akinobu , Hirayama Masaki , Sugawa Shigetoshi , Ohmi Tadahiro
Published: January 2008

Microwave-excited high-density plasma etching equipment with a dual shower-plate structure has been developed to overcome various disadvantageous of current reactive-ion etching equipment. Disadvantages include severe charge-up damage, heavy dependence of etching speed on pattern size, and very limited etching conditions, where the plasma uniformity over the entire wafer surface is only maintained for predetermined gas species, gas working pressure, self-bias voltage, and wafer surface patterns and materials. The authors’ new system has been confirmed to be free from charge-up damage, have pattern-size-dependent etching speed, and maintain the plasma uniformity over the entire wafer surface even if gas species, gas working pressure, self-bias voltage, and wafer surface patterns and materials are changed. To establish damage-free contact-hole etching without degradation of contact resistance of source and drain electrodes of metal-oxide-semiconductor transistors, damage of heavily doped Si induced by ion bombardment through the silicide (TaSi2) is investigated by using this new system. Carrier deactivation and Si lattice damage are found at the heavily doped Si layer even by ion-bombardment through the silicide when the energy of the bombarding ions to the wafer surface is larger than the critical value, which depends on gas species and frequency of rf power applied to the wafer electrode. Highly productive damage-free etching has been established for source and drain contact-hole etching by combining high-speed etching and damage-free etching using this new system, where the self-bias voltage is set at high voltages for high-speed etching and decreased to −300to−500V for damage-free etching at the final stage of contact-hole etching. In this new system, the plasma uniformity is widely maintained even if the self-bias voltage is widely varied during processes.
Physical vapor deposition synthesis of tungsten monocarbide (WC) thin films on different carbon substrates
Authors: Weigert E. C. , Humbert M. P. , Mellinger Z. J. , Ren Q. , Beebe T. P. , Bao L. , Chen J. G.
Published: January 2008

The synthesis of tungsten monocarbide (WC) thin films has been performed by physical vapor deposition on various substrates including glassy carbon, carbon fiber sheet, carbon foam, and carbon cloth. The WC and W2C phase contents of these films have been evaluated with bulk and surface analysis techniques such as x-ray diffraction, x-ray photoelectron spectroscopy, and scanning electron microscopy. These characterization techniques were also used to determine the effects of synthesis by nonreactive and reactive sputtering. The synthesis of WC particles supported on the carbon fiber substrate has also been accomplished using the temperature programmed reaction method. Overall, the results demonstrate that the phase purity of tungsten carbides can be controlled by the deposition environment and annealing temperatures.
Thermal stability and thermo-mechanical properties of magnetron sputtered Cr-Al-Y-N coatings
Authors: Rovere Florian , Mayrhofer Paul H.
Published: January 2008

Cr 1 − x Al x N coatings are promising candidates for advanced machining and high temperature applications due to their good mechanical and thermal properties. Recently the authors have shown that reactive magnetron sputtering using Cr-Al targets with Al/Cr ratios of 1.5 and Y contents of 0, 2, 4, and 8 at % results in the formation of stoichiometric (Cr1−xAlx)1−yYyN films with Al/Cr ratios of ∼1.2 and YN mole fractions of 0%, 2%, 4%, and 8%, respectively. Here, the impact of Y on thermal stability, structural evolution, and thermo-mechanical properties is investigated in detail. Based on in situ stress measurements, thermal analyzing, x-ray diffraction, and transmission electron microscopy studies the authors conclude that Y effectively retards diffusional processes such as recovery, precipitation of hcp-AlN and fcc-YN, grain growth, and decomposition induced N2 release. Hence, the onset temperature of the latter shifts from ∼1010 to 1125 °C and the hardness after annealing at Ta=1100 °C increases from ∼32 to 39 GPa with increasing YN mole fraction from 0% to 8%, respectively.
Fundamental reliability of 1.5-nm-thick silicon oxide gate films grown at 150°C by modified reactive ion beam deposition
Authors: Yamada Hiroshi
Published: January 2008

The reliability of 1.5-nm-thick silicon oxide gate films grown at 150°C by modified reactive ion beam deposition (RIBD) with in situ pyrolytic-gas passivation (PGP) using N2O and NF3 was investigated. RIBD uses low-energy-controlled reactive, ionized species and potentializes low-temperature film growth. Although the oxide films were grown at a low temperature of 150°C, their fundamental indices of reliability, such as the time-dependent dielectric breakdown lifetime and interface state density, were almost equivalent to those of oxide films grown at 850°C using a furnace. This is probably due to localized interfacial N and F atoms. The number density of interfacial N atoms was about seven times larger than that for the furnace-grown oxide films, and this is a key factor for improving the reliability through the compensation of residual inconsistent-state bonding sites.
Stress evolution and defect diffusion in Cu during low energy ion irradiation: Experiments and modeling
Authors: Chan Wai Lun , Chason Eric
Published: January 2008

Measurements of stress generation in Cu during low energy ion irradiation show that the induced stress depends on temperature and ion flux. A steady-state compressive stress is observed during irradiation, which turns into tensile stress after the irradiation is stopped. The results cannot be explained by the incorporation of gas ions alone, and point defects generated by the ions must be considered. In this work, the authors develop a continuum model that includes ion implantation, sputtering, and defect diffusion to explain the experimental data. The authors show that the experimental results can be reproduced primarily by considering a difference in diffusivity between interstitials and vacancies.
Silicon etch in the presence of a fluorocarbon overlayer: The role of fluorocarbon cluster ejection
Authors: Végh Joseph J. , Humbird David , Graves David B.
Published: January 2008

Molecular dynamics (MD) simulations have been carried out to examine the role of large fluorocarbon (FC) cluster ejection during steady state Si plasma etching in the presence of a FC overlayer on the surface. Previous MD studies showed that the thickness of the FC film fluctuates during steady state Si etch, and that these fluctuations are an integral component of the Si etch mechanism. This work focuses on how the ejection of large FC clusters (containing six or more carbon atoms) contribute to FC film thickness fluctuations. Simulations reveal that ∼40%–60% of the carbon removal occurs through these clusters at steady state. Large FC cluster ejection was always observed when FC films form during etching. Product and kinetic energy distributions illustrate the effects of the plasma chemistry (i.e., the FC∕F∕Ar+ ratio impacting the surface) on the cluster ejection process. Further studies have also been carried out to examine the possibility of cluster redeposition on the surface and evaluate the likelihood of these large clusters contributing to FC film growth in typical plasma systems. Several clusters were found to have comparable (or even higher) sticking probability than the original FC deposition precursors. Overall, this work suggests that FC clusters play a key role in the Si etch process in these systems, and can also contribute to FC film growth. The effects of clusters in profile simulations and other plasma processing analyses may be more important than previously thought.
Numerical investigation via three-dimensional Monte Carlo modeling of sputtering and deposition processes in a direct current unbalanced magnetron discharge
Authors: Sobbia R. , Browning P. K. , Bradley J. W.
Published: January 2008

A linked set of Monte Carlo applications has been developed in order to investigate the sputtering, deposition, and ionization processes in a circular direct current unbalanced magnetron discharge. Particles respond to prescribed electric and magnetic fields, the former taken from experimental measurements, and self-consistent plasma behavior resulting in changes in the fields is not accounted for. The motion of energetic electrons emitted from the target surface by ion impacts is followed in the gas phase in order to characterize ionization and excitation collisions and elastic scattering with argon filling gas. The inhomogeneous erosion track profile is computed and compared with experimental measurements. The transport of titanium sputtered neutrals between the target and substrate surfaces is then analyzed using both a rigid sphere collision model and an interatomic potential model to describe collisions between sputtered neutrals and background gas atoms. The radial emission distribution of sputtered atoms is taken from the electron transport model. The mean arrival energy and the angular distribution of titanium neutrals impinging on the substrate surface, and the metal density profile between target and substrate are calculated. Finally, the electron impact ionization of titanium neutrals in a plasma formed by a mixture of titanium (10% of argon density) and argon atoms is simulated, motivated by the promising possibility of controlling the deposition process by influencing the direction of the ion flux.
Tritium migration along the cryopumping section
Authors: Malyshev Oleg B.
Published: January 2008

The transport section of the Karlsruhe Tritium Neutrino experiment (KATRIN) must provide the dramatic reduction of tritium flow and gas density from the end of a 10-m-long windowless gaseous tritium source throughout several stages of a differential pumping system. The final stage of this section, the cryogenic pumping section (CPS) based on pumping of tritium on argon frost at 4.5 K, should provide the flow ratio between inlet and outlet in the range of 107. Cryosorbed tritium may decay, emitting a few keV electrons. These electrons in their turn cause the electron-stimulated desorption of cryosorbed argon and tritium, which is redistributed along the CPS (migration process). This effect was modeled with the use of the method of angular coefficients. The main result is that the tritium migration process does not affect the CPS performance at KATRIN for a given inlet flow. Meanwhile, if the flow chosen is larger, the migration effect could be dominant.
Growth of ordered SrO layers on Si(100) using metal-organic surface reactions
Authors: Willis B. G. , Mathew A.
Published: January 2008

The formation of ordered alkaline earth metal-oxide layers on Si(100) through metal-organic surface reactions has been investigated. Strontium oxide layers were deposited on a thin (1.0±0.2nm) SiO2 layer grown on Si(100) using a saturation coverage of the β-diketonate precursor bis(2,2,6,6-tetramethyl-3,5-heptanedionato)strontium [Sr(thd)2] followed by reaction with H2O. Oxide desorption at high temperatures (>800°C) leads to an ordered strontium layer on the silicon surface. Auger electron spectroscopy, x-ray photoelectron spectroscopy, Rutherford backscattering spectrometry, and low-energy electron diffraction have been used to investigate the progress of the reaction. The data show a Sr∕Si(100) surface with 3× order and a Sr coverage of (0.9±0.1)×1014∕cm2. The observed metal coverage and ordering are explained by the saturation of the adsorbed metal-organic layer due to steric interactions that limit the adsorbed coverage. The results are promising for alternative methods to fabricate epitaxial oxides on silicon substrates.
Growth and characterization of vanadium dioxide thin films prepared by reactive-biased target ion beam deposition
Authors: West Kevin G. , Lu Jiwei , Yu Jiani , Kirkwood David , Chen Wei , Pei Yonghang , Claassen John , Wolf Stuart A.
Published: January 2008

Using a novel growth technique called reactive bias target ion beam deposition, the authors have prepared highly oriented VO2 thin films on Al2O3 (0001) substrates at various growth temperatures ranging from 250to550°C. The influence of the growth parameters on the microstructure and transport properties of VO2 thin films was systematically investigated. A change in electrical conductivity of 103 was measured at 341K associated with the well known metal-insulator transition (MIT). It was observed that the MIT temperature can be tuned to higher temperatures by mixing VO2 and other vanadium oxide phases. In addition, a current/electric-field induced MIT was observed at room temperature with a drop in electrical conductivity by a factor of 8. The current densities required to induce the MIT in VO2 are about 3×104A∕cm2. The switching time of the MIT, as measured by voltage pulsed measurements, was determined to be no more than 10ns.
Synthesis and characteristics of new quaternary Ti–Mo–Si–N coatings by a hybrid coating system
Authors: Jeon Jin Woo , Hong Seung Gyun , Kim Kwang Ryul , Kim Kwang Ho
Published: January 2008

Ternary Ti–Mo–N and new quaternary Ti–Mo–Si–N coatings were synthesized on substrates (AISI D2) and Si wafers by a hybrid coating system of an arc-ion plating technique using a Ti target and a dc magnetron sputtering technique using Mo and Si targets in N2∕Ar gaseous mixture. The ternary Ti–Mo–N coatings were substitutional solid solutions of (Ti,Mo)N and showed maximum hardness of about 30GPa at a Mo content of ∼10at.%. With the addition of Si, the Ti–Mo–Si–N coating transformed into a nanocomposite consisting of fine (Ti,Mo)N crystallites and an amorphous Si3N4 phase. The hardness of the Ti–Mo–Si(8.8at.%)–N coatings significantly increased to ∼48GPa due to the microstructural change to the nanocomposite containing finer (Ti,Mo)N crystallites by the grain-size refinement effect of Si addition. The averaged friction coefficient of the Ti–Mo–Si–N coatings gradually decreased by increasing the Si content in the Ti–Mo–N coating. The microstructures of Ti–Mo–Si–N coatings were investigated with instrumental analyses of x-ray diffraction, x-ray photoelectron, and high-resolution transmission electron microscopy. In this work, the authors also investigated the effects of substrate bias voltage during deposition on the microstructure and mechanical property of Ti–Mo–Si–N coatings.
Synthesis and mechanical properties of CrMoCxN1−x coatings deposited by a hybrid coating system
Authors: Yun Ji Hwan , Heo Su Jeong , Kim Kwang Ryul , Kim Kwang Ho
Published: January 2008

Quaternary CrMoCxN1−x coatings were deposited on steel substrates (AISI D2) and Si wafers by a hybrid coating system combining an arc-ion plating technique and a dc reactive magnetron sputtering technique using Cr and Mo targets in an Ar∕N2∕CH4 gaseous mixture. The carbon content of CrMoCxN1−x coatings was linearly increased with increasing CH4∕(CH4+N2) gas flow rate ratio. The maximum hardness of 44GPa was obtained from the CrMoCxN1−x coatings containing a carbon content of x=0.33 with a residual stress of −4.4GPa. The average friction coefficient of Cr–Mo–N coatings was 0.42, and it is decreased to 0.31 after applying CrMoCxN1−x coatings. This result was caused by the formation of a carbon-rich transfer layer that acted as a solid lubricant to reduce contact between the coating surface and steel ball. The microstructure of the coatings was investigated by x-ray diffraction, scanning electron microscopy, and x-ray photoelectron spectroscopy. In this work, the microstructure and mechanical properties of the CrMoCxN1−x coatings were systematically investigated with the instrumental analyses.
Effects of interfacial layer structures on crystal structural properties of ZnO films
Authors: Park J. S. , Minegishi T. , Lee S. H. , Im I. H. , Park S. H. , Hanada T. , Goto T. , Cho M. W. , Yao T. , Hong S. K. , Chang J. H.
Published: January 2008

Single crystalline ZnO films were grown on Cr compound buffer layers on (0001) Al2O3 substrates by plasma assisted molecular beam epitaxy. In terms of lattice misfit reduction between ZnO and substrate, the CrN and Cr2O3/CrN buffers are investigated. The structural and optical qualities of ZnO films suggest the feasibility of Cr compound buffers for high-quality ZnO films growth on (0001) Al2O3 substrates. Moreover, the effects of interfacial structures on selective growth of different polar ZnO films are investigated. Zn-polar ZnO films are grown on the rocksalt CrN buffer and the formation of rhombohedral Cr2O3 results in the growth of O-polar films. The possible mechanism of polarity conversion is proposed. By employing the simple patterning and regrowth procedures, a periodical polarity converted structure in lateral is fabricated. The periodical change of the polarity is clearly confirmed by the polarity sensitive piezo response microscope images and the opposite hysteretic characteristic of the piezo response curves, which are strict evidences for the validity of the polarity controlling method as well as the successful fabrication of the periodical polarity controlled ZnO structure.
Charge-state distributions of metallic electron cyclotron resonance plasmas
Authors: Kumar P. , Rodrigues G. , Lakshmy P. S. , Kanjilal D. , Kumar R.
Published: January 2008

The authors have developed metallic ion beams in the energy range of a few keV to a few MeV using a low-energy ion-beam facility (LEIBF) consisting of a 10GHz all-permanent-magnet electron cyclotron resonance (ECR) ion source placed on a high-voltage (200kV) platform. The metallic vapors were achieved by plasma sputtering, using a micro-oven and volatile compounds to produce multiply charged ECR plasma. The ions were then extracted from the plasma and their energy and momentum were analyzed using a high-resolution dipole magnet. Charge-state distributions (CSDs) of three metallic ECR plasmas (Cu, Ni, and Sn) produced by different techniques are presented to help in using low-energy metallic ions for implantation. We present the CSD studies of metallic ECR plasma and highlight the physics of the process involved.
Lithium manganese oxide films fabricated by electron beam directed vapor deposition
Authors: Jin S. W. , Wadley H. N. G.
Published: January 2008

Lithium manganese oxide thin films have been grown using a gas jet based, electron beam directed vapor deposition technique. The deposition rate could be controlled by the electron beam power as well as the gas jet density and speed. This enabled films to be grown at deposition rates up to 16nm∕s which is a significantly higher deposition rate than that reported for the growth of this material by sputtering and other vapor deposition techniques. The lithium manganese oxide films grown by this approach were slightly manganese deficient with a composition Li1+xMn2−yO4, where 0.08<x<0.125 and y∼0.2. After annealing in air at 700°C, thin films grown with a low jet speed had a cubic spinel structure and were composed of very small size grains. The small grain size resulted from the vapor phase formation of clusters and resulted in a nanocrystalline random film texture. These films were highly porous with a spongelike interconnected pore network. The use of a higher jet speed and lower growth pressure resulted in less vapor phase clustering. The films contained small, uniformly distributed pores and exhibited a significant ⟨111⟩ texture. These annealed films appeared well suited for use as the cathode layers in thin film Li∕Li-ion batteries.
A Simple Method to Measure the Angular Speed of a Spinning Object
Authors: Misra Raj M.
Published: January 2008

The angular speed of a spinning object is commonly measured using a stroboscope or a mechanically or optically coupled tachometer. We present here an alternate, simple, and instructive method to measure it using a microphone and a computer.
Prevalence and Abundance of Uncultivated
Megasphaera
-Like Bacteria in the Human Vaginal Environment
Authors: Zozaya-Hinchliffe Marcela , Martin David H. , Ferris Michael J.
Published: January 2008

Cultivation-independent analysis of 16S rRNA gene sequences in vaginal samples revealed two previously unrecognized, uncultivated
Megasphaera
-like phylotypes. Phylogenetic analysis and environmental distribution suggest that these
Megasphaera
types may be unique to the vaginal environment. Quantitative PCR suggests that both phylotypes are present in higher concentrations in women with bacterial vaginosis.
The Exotic Legume Tree Species
Acacia holosericea
Alters Microbial Soil Functionalities and the Structure of the Arbuscular Mycorrhizal Community
Authors: Remigi P. , Faye A. , Kane A. , Deruaz M. , Thioulouse J. , Cissoko M. , Prin Y. , Galiana A. , Dreyfus B. , Duponnois R.
Published: January 2008

The response of microbial functional diversity as well as its resistance to stress or disturbances caused by the introduction of an exotic tree species,
Acacia holosericea
, ectomycorrhized or not with
Pisolithus albus
, was examined. The results show that this ectomycorrhizal fungus promotes drastically the growth of this fast-growing tree species in field conditions after 7 years of plantation. Compared to the crop soil surrounding the
A. holosericea
plantation, this exotic tree species, associated or not with the ectomycorrhizal symbiont, induced strong modifications in soil microbial functionalities (assessed by measuring the patterns of in situ catabolic potential of microbial communities) and reduced soil resistance in response to increasing stress or disturbance (salinity, temperature, and freeze-thaw and wet-dry cycles). In addition,
A. holosericea
strongly modified the structure of arbuscular mycorrhizal fungus communities. These results show clearly that exotic plants may be responsible for important changes in soil microbiota affecting the structure and functions of microbial communities.
A Novel Gene, Encoding 6-Hydroxy-3-Succinoylpyridine Hydroxylase, Involved in Nicotine Degradation by
Pseudomonas putida
Strain S16
Authors: Tang Hongzhi , Wang Shuning , Ma Lanying , Meng Xiangzhou , Deng Zixin , Zhang Dake , Ma Cuiqing , Xu Ping
Published: January 2008

Previous research suggested that
Pseudomonas
spp. may attack the pyrrolidine ring of nicotine in a way similar to mammalian metabolism, resulting in the formation of pseudooxynicotine, the direct precursor of a potent tobacco-specific lung carcinogen. In addition, the subsequent intermediates, 6-hydroxy-3-succinoylpyridine (HSP) and 2,5-dihydroxypyridine (DHP) in the
Pseudomonas
nicotine degradation pathway are two important precursors for drug syntheses. However, there is little information on the molecular mechanism for nicotine degradation via the pyrrolidine pathway until now. In this study we cloned and sequenced a 4,879-bp gene cluster involved in nicotine degradation. Intermediates
N
-methylmyosmine, pseudooxynicotine, 3-succinoylpyridine, HSP, and DHP were identified from resting cell reactions of the transformant containing the gene cluster and shown to be identical to those of the pyrrolidine pathway reported in wild-type strain
Pseudomonas putida
S16. The gene for 6-hydroxy-3-succinoylpyridine hydroxylase (HSP hydroxylase) catalyzing HSP directly to DHP was cloned, sequenced, and expressed in
Escherichia coli
, and the purified HSP hydroxylase (38 kDa) is NADH dependent. DNA sequence analysis of this 936-bp fragment reveals that the deduced amino acid shows no similarity with any protein of known function.
Molecular Analysis of Maltotriose Active Transport and Fermentation by
Saccharomyces cerevisiae
Reveals a Determinant Role for the
AGT1
Permease
Authors: Alves Sergio L. , Herberts Ricardo A. , Hollatz Claudia , Trichez Debora , Miletti Luiz C. , de Araujo Pedro S. , Stambuk Boris U.
Published: January 2008

Incomplete and/or sluggish maltotriose fermentation causes both quality and economic problems in the ale-brewing industry. Although it has been proposed previously that the sugar uptake must be responsible for these undesirable phenotypes, there have been conflicting reports on whether all the known α-glucoside transporters in
Saccharomyces cerevisiae
(
MALx1
,
AGT1
, and
MPH2
and
MPH3
transporters) allow efficient maltotriose utilization by yeast cells. We characterized the kinetics of yeast cell growth, sugar consumption, and ethanol production during maltose or maltotriose utilization by several
S. cerevisiae
yeast strains (both
MAL
constitutive and
MAL
inducible) and by their isogenic counterparts with specific deletions of the
AGT1
gene. Our results clearly showed that yeast strains carrying functional permeases encoded by the
MAL21
,
MAL31
, and/or
MAL41
gene in their plasma membranes were unable to utilize maltotriose. While both high- and low-affinity transport activities were responsible for maltose uptake from the medium, in the case of maltotriose, the only low-affinity (

K
m

, 36 ± 2 mM) transport activity was mediated by the
AGT1
permease. In conclusion, the
AGT1
transporter is required for efficient maltotriose fermentation by
S. cerevisiae
yeasts, highlighting the importance of this permease for breeding and/or selection programs aimed at improving sluggish maltotriose fermentations.
Infections Caused byScedosporiumspp
Authors: Cortez Karoll J. , Roilides Emmanuel , Quiroz-Telles Flavio , Meletiadis Joseph , Antachopoulos Charalampos , Knudsen Tena , Buchanan Wendy , Milanovich Jeffrey , Sutton Deanna A. , Fothergill Annette , Rinaldi Michael G. , Shea Yvonne R. , Zaoutis Theoklis , Kottilil Shyam , Walsh Thomas J.
Published: January 2008

Scedosporiumspp. are increasingly recognized as causes of resistant life-threatening infections in immunocompromised patients.Scedosporiumspp. also cause a wide spectrum of conditions, including mycetoma, saprobic involvement and colonization of the airways, sinopulmonary infections, extrapulmonary localized infections, and disseminated infections. Invasive scedosporium infections are also associated with central nervous infection following near-drowning accidents. The most common sites of infection are the lungs, sinuses, bones, joints, eyes, and brain.Scedosporium apiospermumandScedosporium prolificansare the two principal medically important species of this genus.Pseudallescheria boydii, the teleomorph ofS. apiospermum, is recognized by the presence of cleistothecia. Recent advances in molecular taxonomy have advanced the understanding of the genusScedosporiumand have demonstrated a wider range of species than heretofore recognized. Studies of the pathogenesis of and immune response toScedosporiumspp. underscore the importance of innate host defenses in protection against these organisms. Microbiological diagnosis ofScedosporiumspp. currently depends upon culture and morphological characterization. Molecular tools for clinical microbiological detection ofScedosporiumspp. are currently investigational. Infections caused byS. apiospermumandP. boydiiin patients and animals may respond to antifungal triazoles. By comparison, infections caused byS. prolificansseldom respond to medical therapy alone. Surgery and reversal of immunosuppression may be the only effective therapeutic options for infections caused byS. prolificans.
Response ofSchizosaccharomyces pombeto Zinc Deficiency
Authors: Dainty Samantha J. , Kennedy Ciara A. , Watt Stephen , Bähler Jürg , Whitehall Simon K.
Published: January 2008

A component of the cellular response to zinc deficiency operates via control of transcript abundance. Therefore, microarray analysis was employed to identifySchizosaccharomyces pombegenes whose mRNA levels are regulated by intracellular zinc status. A set of 57 genes whose mRNA levels were substantially reduced in response to zinc deficiency was identified, while the mRNA levels of 63 genes were increased by this condition. In order to investigate the mechanisms that control these responses, a genetic screen was employed to identify mutants with defective zinc-responsive gene expression. Two strains (II-1 and V7) that were identified by this screen harbor mutations that are linked tozrt1+, which encodes a putative Zrt/IRT-like protein (ZIP) zinc uptake transporter. Importantly,zrt1+mRNA levels are increased in response to zinc deprivation, and cells lacking functional Zrt1 are highly impaired in their ability to proliferate at limiting zinc concentrations. Furthermore,zrt1null cells were found to have severely reduced zinc contents, indicating that Zrt1 functions as a key regulator of intracellular zinc levels in fission yeast. The deletion offet4+, another zinc-responsive gene encoding a putative metal ion transporter, exacerbated the phenotypes associated with the loss of Zrt1, suggesting that Fet4 also plays a role in zinc uptake under limiting conditions.
Cloning and Genetic Analyses of the Bacteriocin 41 Determinant Encoded on the
Enterococcus faecalis
Pheromone-Responsive Conjugative Plasmid pYI14: a Novel Bacteriocin Complemented by Two Extracellular Components (Lysin and Activator)
Authors: Tomita Haruyoshi , Kamei Elizabeth , Ike Yasuyoshi
Published: January 2008

The conjugative plasmid pYI14 (61 kbp) was isolated from
Enterococcus faecalis
YI714, a clinical isolate. pYI14 conferred a pheromone response on its host and encoded bacteriocin 41 (
bac41
). Bacteriocin 41 (Bac41) only showed activity against
E. faecalis
. Physical mapping of pYI14 showed that it consisted of EcoRI fragments A to P. The clone pHT1100, containing EcoRI fragments A (12.6 kbp) and H (3.5 kbp), conferred the bacteriocin activity on
E. faecalis
strains. Genetic analysis showed that the determinant was located in a 6.6-kbp region within the EcoRI AH fragments. Six open reading frames (ORFs) were identified in this region and designated ORF7 (

bacL
1

) ORF8 (

bacL
2

), ORF9, ORF10, ORF11 (
bacA
), and ORF12 (
bacI
). They were aligned in this order and oriented in the same direction. ORFs

bacL
1

,

bacL
2

,
bacA
, and
bacI
were essential for expression of the bacteriocin in
E. faecalis
. Extracellular complementation of bacteriocin expression was possible for

bacL
1

and -

L
2

and
bacA
mutants.

bacL
1

and -

L
2

and
bacA
encoded bacteriocin component L and activator component A, respectively. The products of these genes are secreted into the culture medium and extracellularly complement bacteriocin expression.
bacI
encoded immunity, providing the host with resistance to its own bacteriocin activity. The

bacL
1

-encoded protein had significant homology with lytic enzymes that attack the gram-positive bacterial cell wall. Sequence data for the deduced

bacL
1

-encoded protein suggested that it has a domain structure consisting of an N-terminal signal peptide, a second domain with the enzymatic activity, and a third domain with a three-repeat structure directing the proenzyme to its cell surface receptor.
Evolution of the Mycobacterial SigK Regulon
Authors: Veyrier Frédéric , Saïd-Salim Battouli , Behr Marcel A.
Published: January 2008

Previous studies have established that members of the
Mycobacterium tuberculosis
complex exhibit variable production of the antigenic proteins MPT70 and MPT83 due to mutations in their positive regulator, SigK (sigma factor K), and their negative regulator, RskA (regulator of sigma K). To further understand this highly specific SigK-controlled regulon, we have undertaken evolutionary studies to determine the presence of homologues of SigK-regulated genes in other organisms and to predict its transcriptional network. Evolutionary analysis indicates that the positive and negative regulators are conserved across many organisms, but that the genes under their control are variable. Moreover, the addition, loss, and movement of various genes in the
mpt70/83
locus suggest that these genes are unlikely to be cotranscribed. To test predictions from sequence analysis, we have used promoter luciferase fusions and Northern blots to show that the majority of genes in this locus have their own promoters, of which a subset are SigK regulated (
mpt83
,
dipZ
,
mpt70
, and Rv0449c). Next, we have shown that the intracellular inducibility of
mpt70
and
mpt83
is a conserved property, shared between
M. tuberculosis
and
Mycobacterium marinum
. In addition, we have shown that SigK and RskA from an environmental mycobacterium isolate (
M. gilvum
PYR-GCK) complemented the regulatory activity of
M. tuberculosis
Δ
sigK rskA
. Together, our data indicate that the regulatory system SigK/RskA is conserved across the
Mycobacterium
genus, whereas the regulon under its control varies considerably across species.
Three-Dimensional Imaging of the Highly Bent Architecture of
Bdellovibrio bacteriovorus
by Using Cryo-Electron Tomography
Authors: Borgnia Mario J. , Subramaniam Sriram , Milne Jacqueline L. S.
Published: January 2008

Bdellovibrio bacteriovorus
cells are small deltaproteobacterial cells that feed on other gram-negative bacteria, including human pathogens. Using cryo-electron tomography, we demonstrated that
B. bacteriovorus
cells are capable of substantial flexibility and local deformation of the outer and inner membranes without loss of cell integrity. These shape changes can occur in less than 2 min, and analysis of the internal architecture of highly bent cells showed that the overall distribution of molecular machines and the nucleoid is similar to that in moderately bent cells.
B. bacteriovorus
cells appear to contain an extensive internal network of short and long filamentous structures. We propose that rearrangements of these structures, in combination with the unique properties of the cell envelope, may underlie the remarkable ability of
B. bacteriovorus
cells to find and enter bacterial prey.
Role of the Nfo and ExoA Apurinic/Apyrimidinic Endonucleases in Repair of DNA Damage during Outgrowth of
Bacillus subtilis
Spores
Authors: Ibarra Juan R. , Orozco Alma D. , Rojas Juan A. , López Karina , Setlow Peter , Yasbin Ronald E. , Pedraza-Reyes Mario
Published: January 2008

Germination and outgrowth are critical steps for returning
Bacillus subtilis
spores to life. However, oxidative stress due to full hydration of the spore core during germination and activation of metabolism in spore outgrowth may generate oxidative DNA damage that in many species is processed by apurinic/apyrimidinic (AP) endonucleases.
B. subtilis
spores possess two AP endonucleases, Nfo and ExoA; the outgrowth of spores lacking both of these enzymes was slowed, and the spores had an elevated mutation frequency, suggesting that these enzymes repair DNA lesions induced by oxidative stress during spore germination and outgrowth. Addition of H
2
O
2
also slowed the outgrowth of
nfo exoA
spores and increased the mutation frequency, and
nfo
and
exoA
mutations slowed the outgrowth of spores deficient in either RecA, nucleotide excision repair (NER), or the DNA-protective α/β-type small acid-soluble spore proteins (SASP). These results suggest that α/β-type SASP protect DNA of germinating spores against damage that can be repaired by Nfo and ExoA, which is generated either spontaneously or promoted by addition of H
2
O
2
. The contribution of RecA and Nfo/ExoA was similar to but greater than that of NER in repair of DNA damage generated during spore germination and outgrowth. However,
nfo
and
exoA
mutations increased the spontaneous mutation frequencies of outgrown spores lacking
uvrA
or
recA
to about the same extent, suggesting that DNA lesions generated during spore germination and outgrowth are processed by Nfo/ExoA in combination with NER and/or RecA. These results suggest that Nfo/ExoA, RecA, the NER system, and α/β-type SASP all contribute to the repair of and/or protection against oxidative damage of DNA in germinating and outgrowing spores.
Cel9D, an Atypical 1,4-β-
d
-Glucan Glucohydrolase from
Fibrobacter succinogenes
: Characteristics, Catalytic Residues, and Synergistic Interactions with Other Cellulases
Authors: Qi Meng , Jun Hyun-Sik , Forsberg Cecil W.
Published: January 2008

The increasing demands of renewable energy have led to the critical emphasis on novel enzymes to enhance cellulose biodegradation for biomass conversion. To identify new cellulases in the ruminal bacterium
Fibrobacter succinogenes
, a cell extract of cellulose-grown cells was separated by ion-exchange chromatography and cellulases were located by zymogram analysis and identified by peptide mass fingerprinting. An atypical family 9 glycoside hydrolase (GH9), Cel9D, with less than 20% identity to typical GH9 cellulases, was identified. Purified recombinant Cel9D enhanced the production of reducing sugar from acid swollen cellulose (ASC) and Avicel by 1.5- to 4-fold when mixed separately with each of four other glucanases, although it had low activity on these substrates. Cel9D degraded ASC and cellodextrins with a degree of polymerization higher than 2 to glucose with no apparent endoglucanase activity, and its activity was restricted to β-1→4-linked glucose residues. It catalyzed the hydrolysis of cellulose by an inverting mode of reaction, releasing glucose from the nonreducing end. Unlike many GH9 cellulases, calcium ions were not required for its function. Cel9D had increased
k
cat
/K

m

values for cello-oligosaccharides with higher degrees of polymerization. The
k
cat
/K

m

value for cellohexaose was 2,300 times higher than that on cellobiose. This result indicates that Cel9D is a 1,4-β-
d
-glucan glucohydrolase (EC 3.2.1.74) in the GH9 family. Site-directed mutagenesis of Cel9D identified Asp166 and Glu612 as the candidate catalytic residues, while Ser168, which is not present in typical GH9 cellulases, has a crucial structural role. This enzyme has an important role in crystalline cellulose digestion by releasing glucose from accessible cello-oligosaccharides.
Variation in the Group BStreptococcusCsrRS Regulon and Effects on Pathogenicity
Authors: Jiang Sheng-Mei , Ishmael Nadeeza , Hotopp Julie Dunning , Puliti Manuela , Tissi Luciana , Kumar Nikhil , Cieslewicz Michael J. , Tettelin Hervé , Wessels Michael R.
Published: January 2008

CsrRS (or CovRS) is a two-component regulatory system that controls expression of multiple virulence factors in the important human pathogen group BStreptococcus(GBS). We now report global gene expression studies in GBS strains 2603V/R and 515 and their isogeniccsrRandcsrSmutants. Together with data reported previously for strain NEM316, the results reveal a conserved 39-gene CsrRS regulon. In vitro phosphorylation-dependent binding of recombinant CsrR to promoter regions of both positively and negatively regulated genes suggests that direct binding of CsrR can mediate activation as well as repression of target gene expression. Distinct patterns of gene regulation incsrRversuscsrSmutants in strain 2603V/R compared to 515 were associated with different hierarchies of relative virulence of wild-type,csrR, andcsrSmutants in murine models of systemic infection and septic arthritis. We conclude that CsrRS regulates a core group of genes including important virulence factors in diverse strains of GBS but also displays marked variability in the repertoire of regulated genes and in the relative effects of CsrS signaling on CsrR-mediated gene regulation. Such variation is likely to play an important role in strain-specific adaptation of GBS to particular host environments and pathogenic potential in susceptible hosts.
Induction and Loss of Ti Plasmid Conjugative Competence in Response to the Acyl-Homoserine Lactone Quorum-Sensing Signal
Authors: Su Shengchang , Khan Sharik R. , Farrand Stephen K.
Published: January 2008

Conjugative transfer of the Ti plasmids ofAgrobacterium tumefaciensis controlled by a quorum-sensing system composed of TraR and its signalN-(3-oxo-octanoyl)-l-homoserine lactone. This system is, in turn, controlled by the conjugative opines produced by crown gall tumors induced on plants by the bacteria. Using nonpolartraImutants, we examined the kinetics of induction of conjugative transfer in response to exogenous acyl-homoserine lactone. In the absence of the antiactivator TraM, onset of induction of transfer requires about 30 min, 15 to 20 min of which is needed for expression and construction of the conjugative apparatus. TraM delays the onset of conjugation by 30 min. While the rate of development of conjugative competence was not significantly affected by levels of TraR, maximum efficiencies of transfer were correlated with amounts of the activator in the donors. Donors harboring Ti plasmids lacking TraM were fully induced by the quormone at concentrations as low as 100 pM. TraM raised the concentration of signal required for maximum activity to 1 nM. Donors grown in batch culture retained conjugative competence following signal removal, even when in stationary phase. However, donors kept in balanced growth rapidly lost transfer ability following signal removal. Loss of transfer was mirrored by a decrease in levels of active TraR. Decreases in TraR activity and conjugative competence could be accounted for by dilution associated with cell division, suggesting that while induction of Ti plasmid conjugation is an active process, the cells lack a mechanism for disassembling the conjugative apparatus when signals become limiting.
The UP Element Is Necessary but Not Sufficient for Growth Rate-Dependent Control of the
Escherichia coli guaB
Promoter
Authors: Husnain Seyyed I. , Thomas Mark S.
Published: January 2008

The
Escherichia coli guaB
promoter (P

guaB

) regulates the transcription of two genes,
guaB
and
guaA
, that are required for de novo synthesis of GMP, a precursor for the synthesis of guanine nucleoside triphosphates. The activity of P

guaB

is subject to growth rate-dependent control (GRDC). Here we show that the A+T-rich sequence located between positions −59 and −38 relative to the
guaB
transcription start site stimulates transcription from P

guaB

∼8- to 10-fold and, in common with other UP elements, requires the C-terminal domain of the RNA polymerase α subunit for activity. Like the
rrnB
P1 UP element, the P

guaB

UP element contains two independently acting subsites located at positions −59 to −47 and −46 to −38 and can stimulate transcription when placed upstream of the
lacP1
promoter. We reveal a novel role for the P

guaB

UP element by demonstrating that it is required for GRDC. The involvement of the UP element in GRDC also requires the participation of sequences located at least 100 bp upstream of the
guaB
transcription start site. These sequences are required for down-regulation of P

guaB

activity at lower growth rates.
Widespread Distribution in Pathogenic Bacteria of Di-Iron Proteins That Repair Oxidative and Nitrosative Damage to Iron-Sulfur Centers
Authors: Overton Tim W. , Justino Marta C. , Li Ying , Baptista Joana M. , Melo Ana M. P. , Cole Jeffrey A. , Saraiva Lígia M.
Published: January 2008

Expression of two genes of unknown function,
Staphylococcus aureus scdA
and
Neisseria gonorrhoeae dnrN
, is induced by exposure to oxidative or nitrosative stress. We show that DnrN and ScdA are di-iron proteins that protect their hosts from damage caused by exposure to nitric oxide and to hydrogen peroxide. Loss of FNR-dependent activation of
aniA
expression and NsrR-dependent repression of
norB
and
dnrN
expression on exposure to NO was restored in the gonococcal parent strain but not in a
dnrN
mutant, suggesting that DnrN is necessary for the repair of NO damage to the gonococcal transcription factors, FNR and NsrR. Restoration of aconitase activity destroyed by exposure of
S. aureus
to NO or H
2
O
2
required a functional
scdA
gene. Electron paramagnetic resonance spectra of recombinant ScdA purified from
Escherichia coli
confirmed the presence of a di-iron center. The recombinant
scdA
plasmid, but not recombinant plasmids encoding the complete
Escherichia coli sufABCDSE
or
iscRSUAhscBAfdx
operons, complemented repair defects of an
E. coli ytfE
mutant. Analysis of the protein sequence database revealed the importance of the two proteins based on the widespread distribution of highly conserved homologues in both gram-positive and gram-negative bacteria that are human pathogens. We provide in vivo and in vitro evidence that Fe-S clusters damaged by exposure to NO and H
2
O
2
can be repaired by this new protein family, for which we propose the name
r
epair of
i
ron
c
enters, or RIC, proteins.
Functional Analysis of Predicted Coiled-Coil Regions in the
Escherichia coli
K-12 O-Antigen Polysaccharide Chain Length Determinant Wzz
Authors: Marolda Cristina L. , Haggerty Emily R. , Lung Michael , Valvano Miguel A.
Published: January 2008

Wzz is a membrane protein that determines the chain length distribution of the O-antigen lipopolysaccharide by an unknown mechanism. Wzz proteins consist of two transmembrane helices separated by a large periplasmic loop. The periplasmic loop of
Escherichia coli
K-12 Wzz (244 amino acids from K65 to A308) was purified and found to be a monomer with an extended conformation, as determined by gel filtration chromatography and analytical ultracentrifugation. Circular dichroism showed that the loop has a 60% helical content. The Wzz periplasmic loop also contains three regions with predicted coiled coils. To probe the function of the predicted coiled coils, we constructed amino acid replacement mutants of the
E. coli
K-12 Wzz protein, which were designed so that the coiled coils could be separate without compromising the helicity of the individual molecules. Mutations in one of the regions, spanning amino acids 108 to 130 (region I), were associated with a partial defect in O-antigen chain length distribution, while mutants with mutations in the region spanning amino acids 209 to 223 (region III) did not have an apparent functional defect. In contrast, mutations in the region spanning amino acids 153 to 173 (region II) eliminated the Wzz function. This phenotype was associated with protein instability, most likely due to conformational changes caused by the amino acid replacements, which was confirmed by limited trypsin proteolysis. Additional mutagenesis based on a three-dimensional model of region I demonstrated that the amino acids implicated in function are all located at the same face of a predicted α-helix, suggesting that a coiled coil actually does not exist in this region. Together, our results suggest that the regions predicted to be coiled coils are important for Wzz function because they maintain the native conformation of the protein, although the existence of coiled coils could not be demonstrated experimentally.