bluuebunny/crossref_metadata_2025 huggingface dataset:
Construction of a variable aperture cell for source flux control in a molecular-beam epitaxy environment
Authors: Mattord Terry J. , Oye Michael M. , Gotthold David , Hansing Chad , Holmes Archie L. , Streetman Ben G.
Published: May 2004

A molecular-beam source utilizing instant flux adjustment for growth rate control is presented. The design uses a two-filament pyrolytic boron nitride (pBN) heater constructed with eight heated exit aperture holes, masked by an aperture-mating pBN closed end cylinder. The rotatable pBN mask opens and closes the effusion cell apertures to provide mechanical control of the source flux. This adjustment is provided by a rotational manipulator that translates rotary motion through the vacuum environment to the mounting journal of the pBN mask cylinder. RHEED oscillation changes in GaAs homoepitaxial growth shows an effectively instantaneous change of nearly an order of magnitude in the growth rate.
Analysis of the chemical composition and deposition mechanism of the SiOx–Cly layer on the plasma chamber walls during silicon gate etching
Authors: Kogelschatz Martin , Cunge Gilles , Sadeghi Nader
Published: May 2004

During silicon gate etching in low pressure high density HBr/Cl2/O2 plasma, SiOClx layers are deposited on the reactor walls. These layers are at the origin of process drifts. However their chemical composition, deposition mechanism and their influence on the plasma chemistry remains poorly understood. In this study, the chemical composition of this layer has been investigated by a “plasma etching-sputtering” technique: the silicon oxychloride layer deposited on the reactor walls during the etching of a 200 mm diam silicon wafer has been subsequently submitted to an Ar plasma with the addition of a few % SF6. During the slow etch process of this layer, time-resolved optical emission spectroscopy and mass spectrometry have been used to follow the time evolution of the gas phase concentration of different atoms and radicals, the etch products of the SiOClx layer. The results give insight into the chemical nature of the deposited layer and of its variation as a function of the depth. In particular, it will be shown that these layers are chlorine-rich and not oxidelike. Also, their composition is not homogeneous through their depth. In a second set of experiments, the SiOClx layer has been exposed to an Ar/O2 plasma providing information on the oxidation mechanism of the Si–Cl bonds and thus on the SiOClx film deposition mechanism in HBr/Cl2/O2 plasmas. This oxidation mechanism is acting through the entire volume of the 10 nm thick layers and proceeds by substitution of Cl atoms of SiCl bonds by O atoms, resulting in desorption of a large amount of Cl atoms from the chamber walls during the layer oxidation. Finally, the layer on the chamber walls has been exposed to an Ar/Cl2 plasma, demonstrating that SiOClx layers are not etched significantly by Cl atoms.
Oxygen plasma rapid thermal annealing to improve the electrical properties of Pt–SrBi2Nb2O9–SiO2–Si gate structure
Authors: Kim Ik Soo , Kim Seong-Il , Kim Yong Tae
Published: May 2004

A rapid thermal annealing (RTA) method in oxygen plasma improves the ferroelectric properties of SrBi2Nb2O9 (SBN) film at relatively lower temperature than the conventional furnace annealing in oxygen ambient. The oxygen plasma RTA raises the oxygen content from 44 to 48 at. %, which may improve the oxygen deficiency in the SBN films. The thickness of SiO2 becomes thinner due to the shorter RTA time. As a result, a typical effective memory window of the Pt–SBN–SiO2–Si gate structure is increased from 0.17 to 0.49 V at 3 V of the applied gate bias and the remnant polarization is also increased from 18.03 to 22.6 C/cm2 at ±6 V. The flat band voltage shift of the oxygen plasma RTA samples is quite stable and smaller than that of the furnace annealed ones because charge trapping is relatively smaller at the interface between Si and the oxygen plasma annealed SBN film.
Physical and mechanical properties of sputtered Ta–Si–N films with a high (⩾40 at %) content of Si
Authors: Zeman H. , Musil J. , Zeman P.
Published: May 2004

This article reports on ternary Ta–Si–N films with a high (⩾40 at %) content of Si sputtered from an alloyed TaSi2 target using an unbalanced dc magnetron. The films were deposited under the following conditions: magnetron discharge current Id=1 and 2 A, negative substrate bias Us ranging from Ufl to −500 V, substrate ion current density is=0.5, 0.75, and 1 mA/cm2, substrate temperature Ts ranging from 100 to 750 °C, substrate-to-target distance ds–t=60 mm, partial pressure of nitrogen pN2 ranging from 0 to 0.7 Pa and two values of a total pressure pT=pAr+pN2=0.5 and 0.7 Pa. Main attention is devoted to the investigation of the effect of partial pressure of nitrogen pN2 on mechanical properties of Ta–Si–N films. It was demonstrated that (1) the Ta–Si–N films exhibit an x-ray amorphous structure, (2) all films are electrically conductive but their electrical resistivity increases with increasing Si3N4 content from about 10−5 to about 102 Ω cm, and (3) the hardness H of the Ta–Si–N films is comparable to that of TaN films and achieves relatively high values (H≈30 GPa) and so it is considerably higher than that of a bulk Si3N4 material with HSi3N4=17.2 GPa. The interrelationships between mechanical properties—hardness H, Young’s modulus E, and elastic recovery We—are discussed in detail. Special attention is devoted to the macrostress σ generated in the Ta–Si–N films during their growth and to the thermal stability of these films.
Electron backscattered diffraction study of poly-Si by Ni-mediated crystallization of amorphous silicon using a SiO2 nanocap
Authors: Chang Y. J. , Oh J. H. , Kim K. H. , Jang Jin , Kim D. I. , Oh K. H.
Published: May 2004

Low-temperature polycrystalline silicon (poly-Si) is of increasing interest for the display on glass. Among several techniques for the low-temperature poly-Si the Ni-mediated crystallization of amorphous silicon (a-Si) is promising one. We studied the crystalline orientation of the disk-shaped grains in the poly-Si formed by Ni-mediated crystallization of a-Si using a SiO2 nanocap by electron backscattered diffraction measurements. A SiO2 nanocap layer was formed by O2 plasma treatment on a-Si and an ultrathin Ni layer was deposited on the nanocap. It was heated in a UV scan system for crystallization. The Ni atoms in a-Si diffused through the nanocap and formed NiSi2 crystallites. Disk-shaped grains were then grown from these nuclei. The size of disk-shaped grains in poly-Si increases from ∼6 to ∼20 μm when the thickness of nanocap on a-Si changes from 2.4 to 3.2 nm. On the other hand, without the nanocap layer, its size is ∼3.5 μm. The crystalline quality of poly-Si is improved by introducing a nanocap layer, which is due mainly to the increase of the grain size.
Suitability of II–VI semiconductors for photonic applications: Common-anion versus common-cation superlattices
Authors: Tit Nacir
Published: May 2004

Based on the sp3s* tight-binding method, the electronic band structures of both common-anion and common-cation II–VI superlattices (SLs) are investigated. As models, I took for the former one the case of CdTe/ZnTe(001) SLs, where the common anion is confirmed to yield a vanishing or a small valence-band offset (VBO). Here, the biaxial strain contributes in the valence-band splittings and yield type-I SLs in most of the studied cases. Whereas, I took as a second model two different SLs: the ZnS/ZnSe(001) and ZnSe/ZnTe(001) SLs. I have confirmed that the common-cation SLs cannot have a vanishing conduction-band offsets (CBOs), as speculated, but rather the CBO could be as large as the VBO. The biaxial strain, again, can participate here in the formation of the band offsets and yield either type-I SLs, as in the case of the ZnS/ZnSe, or type-II SLs, as in the case of ZnSe/ZnTe. Moreover, my theoretical results are compared to some available photoluminescence data and conclusions have been drawn about the strain morphology and the structural and optical qualities of the experimental samples.
Investigation and modeling of plasma-wall interactions in inductively coupled fluorocarbon plasmas
Authors: Joseph E. A. , Zhou B. , Sant S. P. , Overzet L. J. , Goeckner M. J.
Published: May 2004

Plasma-wall interactions in fluorocarbon based feedgas chemistries, namely CF4, are examined in a standard inductively coupled Gaseous Electronics Conference reference cell using in situ Fourier-transform infrared spectroscopy and microwave interferometry. Measurements show the dissociation of the CF4 feedgas into radical CFx species, as has been observed elsewhere [M. J. Goeckner and R. A. Breun, J. Vac. Sci. Technol. A 11, 3 (1993)], and qualitatively reveal a decrease in plasma-wall interactions as wall temperature is increased. Experimental results such as plasma density, 1011 cm−3, and CF4 density 1013 cm−3, are further compared to results from the hybrid plasma equipment model [R. Kinder and M. J. Kushner, J. Vac. Sci. Technol. A 19, 76 (2001)] to better elucidate the influence of wall temperature on plasma exposed surfaces and sticking coefficients. Last, CF4 vibrational temperatures were also measured, revealing that the line-averaged vibrational temperature remains at a constant 40–60 K above the chamber wall temperature while the vibrational temperature in the center of the discharge is significantly higher. Moreover, the vibrational temperatures are further compared to results from a global thermal model and are in good agreement.
Effects of the insertion of a thick sp2 buffer layer on the adhesion of cBN-rich film
Authors: Wong S. F. , Ong C. W. , Pang G. K. H. , Baba-Kishi K. Z. , Lau W. M.
Published: May 2004

A method was proposed and examined to deposit thick cubic boron nitride (cBN)-rich layer of good adhesion to silicon substrate. The method combined (i) the insertion of a thick sp2 buffer layer, and (ii) the use of an appropriate assist ion beam energy for the growth of the cBN-rich top layer. The sp2-bonded boron nitride buffer layer was deposited under irradiation of ions with energies in the range of 200–360 eV. The buffer layer was found to contain curled graphitic basal planes, and so was supposed to be relatively deformable, and facilitate the relaxation of stresses in the cBN-rich top layer. The ion assist introduced during the growth of the cBN-rich layer was supposed to both create and annihilate defects, and so resulted in the generation and relaxation of internal stresses. Results showed that the insertion of a 492 nm sp2 buffer layer, and the use of a beam energy of 450 eV for assisting the growth of the top layer can produce a 643-nm-thick cBN-rich top layer with satisfactory adhesion, a high cBN content of 87 vol %, a hardness of 57 GPa, and an elastic modulus of 612 GPa.
Phase and structural characterization of vanadium oxide films grown on amorphous SiO2/Si substrates
Authors: Youn Doo-Hyeb , Kim Hyun-Tak , Chae Byung-Gue , Hwang Young-Joo , Lee Ju-Wook , Maeng Sung-Lyul , Kang Kwang-Yong
Published: May 2004

The VO2 multiphases such as V2O5, VO2, and V2O3 are confirmed and the correlations between structural characteristics and growth conditions was investigated using the scanning electron microscopy (SEM), transmission electron microscopy (TEM), x-ray diffraction (XRD), and x-ray photoelectron spectroscopy (XPS). Also, the electrical characteristics of VO2-based three terminal devices, attributed to structural and phase changes, are discussed. The spectra of VO2 have three peaks composed of VO2 at binding energy (BE)=516.2 eV, V2O3 at BE=515.6 eV, and V2O5 at BE=517.0 eV. With increase in the growth temperature, crystal quality of VO2 films improves and approaches single phase of VO2, then the peak position shifts to the spectra of oxygen-poor phase (V2O3). With increase in the O2 flow, the peak position shifts to the spectra of oxygen-rich phase (V2O5). VO2 films grown at optimal growth conditions have a change in resistivity of the order of 102 near a critical temperature, Tc=340 K.
Optical characteristics and color of TiN/SiN1.3 nanocomposite coatings
Authors: Jedrzejowski P. , Baloukas B. , Klemberg-Sapieha J. E. , Martinu L.
Published: May 2004

Decorative and protective coatings deposited by dry methods are very attractive due to the environmental restrictions on traditional wet chemical techniques. In this context, nanocomposite hard coatings were fabricated by plasma enhanced chemical vapor deposition from TiCl4/SiH4/N2/H2/Ar gas mixtures at substrate temperatures of 300 and 500 °C. Their optical characteristics such as refractive index, extinction coefficient, luminosity, and colors were quantitatively determined by spectroscopic ellipsometry and spectrophotometry. Pure TiN exhibited a metal-like behavior, and its optical properties were modeled by the Drude (free carrier) approach. Nanocomposite films consisting of about 5–10 nm size TiN grains incorporated in an amorphous SiN1.3 matrix were modeled by a sum of Drude and Lorentz (interband) transitions. Optical properties of the films were explained by their morphology and chemical structure, investigated by a multitechnique approach using scanning electron microscopy, transmission electron microscopy, elastic recoil detection in the time-of-flight regime, Auger electron spectroscopy, x-ray photoelectron spectroscopy, and Raman spectroscopy. Subsequent addition of Si to TiN caused a complex transformation from a polycrystalline to nanocomposite microstructure, which adopted a predominantly amorphous character. This was accompanied by a transition from a metallic to a dielectric behavior in terms of the optical response and electronic properties.
Thioethanol on Cu(111) at room temperature: A near edge x-ray absorption fine structure and x-ray photoelectron spectroscopy study
Authors: Syed J. A. , Sardar S. A. , Yagi S. , Tanaka K.
Published: May 2004

Orientation and charge transfer upon adsorption of thioethanol on copper surface at room temperature has been studied by near edge x-ray absorption fine structure (NEXAFS) and x-ray photoelectron spectroscopy (XPS) techniques. It is found that thioethanol adsorbs dissociatively on the Cu(111) surface. Polarization dependent S K-edge NEXAFS indicates that the S–C bond is tilted 47±7° from the surface. Above 400 K, the S–C bond breaks and creates atomic sulfur. An amount of charge transfer (one electron) from copper to thioethanol molecules was measured using S 1s XPS.
Increasing Ozone over the Atlantic Ocean
Authors: Lelieveld J. , van Aardenne J. , Fischer H. , de Reus M. , Williams J. , Winkler P.
Published: May 2004

Ship-borne ozone (O3) measurements over the Atlantic Ocean during the period from 1977 to 2002 show that O3trends in the northern mid-latitudes are small. In contrast, remarkably large O3trends occur at low latitudes and in the Southern Hemisphere, where near-surface O3has increased by up to a factor of 2. The likely cause is the substantial increase of anthropogenic emissions of nitrogen oxides (NOx) associated with energy use in Africa, which has added to NOxfrom biomass burning and natural sources.
Regeneration of Male Germline Stem Cells by Spermatogonial Dedifferentiation in Vivo
Authors: Brawley Crista , Matunis Erika
Published: May 2004

Although the ability of engrafted stem cells to regenerate tissue has received much attention, the molecular mechanisms controlling regeneration are poorly understood. In the
Drosophila
male germline, local activation of the Janus kinase–signal transducer and activator of transcription (Jak-STAT) pathway maintains stem cells; germline stem cells lacking Jak-STAT signaling differentiate into spermatogonia without self-renewal. By conditionally manipulating Jak-STAT signaling, we find that spermatogonia that have initiated differentiation and are undergoing limited mitotic (transit-amplifying) divisions can repopulate the niche and revert to stem cell identity. Thus, in the appropriate microenvironment, transit-amplifying cells dedifferentiate, becoming functional stem cells during tissue regeneration.
Differential Gene Expression in Response to Hydrogen Peroxide and the Putative PerR Regulon ofSynechocystissp. Strain PCC 6803
Authors: Li Hong , Singh Abhay K. , McIntyre Lauren M. , Sherman Louis A.
Published: May 2004

We utilized a full genome cDNA microarray to identify the genes that comprise the peroxide stimulon in the cyanobacteriumSynechocystissp. strain PCC 6803. We determined that a gene (slr1738) encoding a protein similar to PerR inBacillus subtiliswas induced by peroxide. We constructed a PerR knockout strain and used it to help identify components of the PerR regulon, and we found that the regulatory properties were consistent with the hypothesis that PerR functions as a repressor. This effort was guided by finding putative PerR boxes in positions upstream of specific genes and by careful statistical analysis. PerR and sll1621 (ahpC), which codes for a peroxiredoxin, share a divergent promoter that is regulated by PerR. We found thatisiA, encoding a Chl protein that is induced under low-iron conditions, was strongly induced by a short-term peroxide stress. Other genes that were strongly induced by peroxide includedsigD,sigB, and genes encoding peroxiredoxins and Dsb-like proteins that have not been studied yet in this strain. A gene (slr1894) that encoded a protein similar to MrgA inB. subtiliswas upregulated by peroxide, and a strain containing anmrgAknockout mutation was highly sensitive to peroxide. A number of genes were downregulated, including key genes in the chlorophyll biosynthesis pathway and numerous regulatory genes, including those encoding histidine kinases. We used PerR mutants and a thioredoxin mutant (TrxA1) to study differential expression in response to peroxide and determined that neither PerR nor TrxA1 is essential for the peroxide protective response.
Interactions between the Nitrogen Signal Transduction Protein PII and
N
-Acetyl Glutamate Kinase in Organisms That Perform Oxygenic Photosynthesis
Authors: Burillo Sergio , Luque Ignacio , Fuentes Inmaculada , Contreras Asunción
Published: May 2004

PII, one of the most conserved signal transduction proteins, is believed to be a key player in the coordination of nitrogen assimilation and carbon metabolism in bacteria, archaea, and plants. However, the identity of PII receptors remains elusive, particularly in photosynthetic organisms. Here we used yeast two-hybrid approaches to identify new PII receptors and to explore the extent of conservation of PII signaling mechanisms between eubacteria and photosynthetic eukaryotes. Screening of
Synechococcus
sp. strain PCC 7942 libraries with PII as bait resulted in identification of
N
-acetyl glutamate kinase (NAGK), a key enzyme in the biosynthesis of arginine. The integrity of Ser49, a residue conserved in PII proteins from organisms that perform oxygenic photosynthesis, appears to be essential for NAGK binding. The effect of
glnB
mutations on NAGK activity is consistent with positive regulation of NAGK by PII. Phylogenetic and yeast two-hybrid analyses strongly suggest that there was conservation of the NAGK-PII regulatory interaction in the evolution of cyanobacteria and chloroplasts, providing insight into the function of eukaryotic PII-like proteins.
The RNA-Binding Protein Hfq ofListeria monocytogenes: Role in Stress Tolerance and Virulence
Authors: Christiansen Janne K. , Larsen Marianne H. , Ingmer Hanne , Søgaard-Andersen Lotte , Kallipolitis Birgitte H.
Published: May 2004

In gram-negative bacteria, the RNA-binding protein Hfq has emerged as an important regulatory factor in a variety of physiological processes, including stress resistance and virulence. InEscherichia coli, Hfq modulates the stability or the translation of mRNAs and interacts with numerous small regulatory RNAs. Here, we studied the role of Hfq in the stress tolerance and virulence of the gram-positive food-borne human pathogenListeria monocytogenes. We present evidence that Hfq is involved in the ability ofL. monocytogenesto tolerate osmotic and ethanol stress and contributes to long-term survival under amino acid-limiting conditions. However, Hfq is not required for resistance to acid and oxidative stress. Transcription ofhfqis induced under various stress conditions, including osmotic and ethanol stress and at the entry into the stationary growth phase, thus supporting the view that Hfq is important for the growth and survival ofL. monocytogenesin harsh environments. The stress-inducible transcription ofhfqdepends on the alternative sigma factor σB, which controls the expression of numerous stress- and virulence-associated genes inL. monocytogenes.Infection studies showed that Hfq contributes to pathogenesis in mice, yet plays no role in the infection of cultured cell lines. This study provides, for the first time, information on the role of Hfq in the stress tolerance and virulence of a gram-positive pathogen.
Stress Response Gene Regulation in
Chlamydia
Is Dependent on HrcA-CIRCE Interactions
Authors: Wilson Adam C. , Tan Ming
Published: May 2004

HrcA is a transcriptional repressor that regulates stress response genes in many bacteria by binding to the CIRCE operator. We have previously shown that HrcA regulates the promoter for the
dnaK
heat shock operon in
Chlamydia
. Here we demonstrate that HrcA represses a second heat shock promoter that controls the expression of
groES
and
groEL
, two other major chlamydial heat shock genes. The CIRCE element of
C. trachomatis groEL
is the most divergent of known bacterial CIRCE elements, and HrcA had a decreased ability to bind to this nonconsensus operator and repress transcription. We demonstrate that the CIRCE element is necessary and sufficient for transcriptional regulation by chlamydial HrcA and that the inverted repeats of CIRCE are the binding sites for HrcA. Addition of a CIRCE element upstream of a non-heat-shock promoter allowed this promoter to be repressed by HrcA, showing in principle that a chlamydial promoter can be genetically modified to be inducible. These results demonstrate that HrcA is the regulator of the major chlamydial heat shock operons, and we infer that the mechanism of the heat shock response in
Chlamydia
is derepression. However, derepression is likely to involve more than a direct effect of increased temperature as we found that HrcA binding to CIRCE and HrcA-mediated repression were not altered at temperatures that induce the heat shock response.
A Cambialistic Superoxide Dismutase in the Thermophilic Photosynthetic Bacterium
Chloroflexus aurantiacus
Authors: Lancaster Vanessa L. , LoBrutto Russell , Selvaraj Fabiyola M. , Blankenship Robert E.
Published: May 2004

Superoxide dismutase from the thermophilic anoxygenic photosynthetic bacterium
Chloroflexus aurantiacus
was cloned, purified, and characterized. This protein is in the manganese- and iron-containing family of superoxide dismutases and is able to use both manganese and iron catalytically. This appears to be the only soluble superoxide dismutase in
C. aurantiacus
. Iron and manganese cofactors were identified by using electron paramagnetic resonance spectroscopy and were quantified by atomic absorption spectroscopy. By metal enrichment of growth media and by performing metal fidelity studies, the enzyme was found to be most efficient with manganese incorporated, yet up to 30% of the activity was retained with iron. Assimilation of iron or manganese ions into superoxide dismutase was also found to be affected by the growth conditions. This enzyme was also found to be remarkably thermostable and was resistant to H
2
O
2
at concentrations up to 80 mM. Reactive oxygen defense mechanisms have not been previously characterized in the organisms belonging to the phylum
Chloroflexi
. These systems are of interest in
C. aurantiacus
since this bacterium lives in a hyperoxic environment and is subject to high UV radiation fluxes.
Mechanism of Intrinsic Resistance to Vancomycin in
Clostridium innocuum
NCIB 10674
Authors: David Véronique , Bozdogan Bülent , Mainardi Jean-Luc , Legrand Raymond , Gutmann Laurent , Leclercq Roland
Published: May 2004

We have studied the basis for intrinsic resistance to low levels of vancomycin in
Clostridium innocuum
NCIB 10674 (MIC = 8 μg/ml). Analysis by high-pressure liquid chromatography (HPLC) and mass spectrometry of peptidoglycan nucleotide precursors pools revealed the presence of two types of UDP-MurNac-pentapeptide precursors constitutively produced, an UDP-MurNAc-pentapeptide with a serine at the C terminus which represented 93% of the pool and an UDP-MurNAc-pentapeptide with an alanine at the C terminus which represented the rest of the pool.
C. innocuum
cell wall muropeptides containing pentapeptide[Ser], either dialanine substituted on the epsilon amino group of lysine or not, were identified and represented about 10% of the monomers while only 1% of pentapeptide[
d
-Ala] monomers were found. The sequence of a 2,465-bp chromosomal fragment from
C. innocuum
was determined and revealed the presence of

ddl
c. innocuum

and
C. innocuum
racemase genes putatively encoding homologues of
d
-Ala:
d
-X ligases and amino acid racemases, respectively. Analysis of the pool of precursors of
Enterococcus faecalis
JH2-2, containing cloned

ddl
c. innocuum

and
C. innocuum
racemase genes showed in addition to the UDP-MurNAc-pentapeptide[
d
-Ala], the presence of an UDP-MurNAc-pentapeptide[
d
-Ser] precursor. However, the expression of low-level resistance to vancomycin was observed only when both genes were cloned in
E. faecalis
JH2-2 together with the

vanXY
c

gene from
Enterococcus gallinarum
BM4174 which encodes a
d
,
d
-peptidase which eliminates preferentially the high affinity vancomycin UDP-MurNAc-pentapeptide [
d
-Ala] precursors produced by the host. We conclude that resistance to vancomycin in
C. innocuum
NCIB 10674 was related to the presence of the two chromosomal

ddl
c. innocuum

and
C. innocuum
racemase genes allowing the synthesis of a peptidoglycan precursor terminating in serine with low affinity for vancomycin.
Cloning and Functional Analysis by Gene Disruption of a Gene Encoding a γ-Butyrolactone Autoregulator Receptor fromKitasatospora setae
Authors: Choi Sun-Uk , Lee Chang-Kwon , Hwang Yong-Il , Kinoshita Hiroshi , Nihira Takuya
Published: May 2004

γ-Butyrolactone autoregulator receptors of the genusStreptomyceshave a common activity as DNA-binding transcriptional repressors, controlling secondary metabolism and/or morphological differentiation. A gene encoding a γ-butyrolactone autoregulator receptor was cloned from a bafilomycin B1producer,Kitasatospora setae, for the first time from a non-Streptomycesgenus of actinomycetes, and its function was evaluated by in vitro and in vivo analyses. The gene fragment was initially cloned by PCR with primers designed from two highly conserved regions ofStreptomycesautoregulator receptors (BarA, FarA, ScbR, and ArpA), followed by genomic Southern hybridization yielding a 7-kb BamHI fragment on which a 654-bp receptor gene (ksbA) was identified. The recombinant KsbA protein demonstrated clear binding activity toward3H-labeled autoregulators, especially toward [3H]SCB1, confirming thatksbAencodes a real autoregulator receptor ofK. setae. To clarify the in vivo function ofksbA, aksbA-disrupted strain was constructed by means of homologous recombination after introducing aksbAdisruption construct via transconjugation fromEscherichia coli. No difference in morphology was found between the wild-type strain and theksbAdisruptants. However, theksbAdisruptants started producing bafilomycin 18 h earlier than the wild-type strain and showed a 2.4-fold-higher accumulation of bafilomycin. The phenotype was restored to the original wild-type phenotype by complementation with intactksbA, indicating that the autoregulator receptor protein ofK. setaeacts as a primary negative regulator of the biosynthesis of bafilomycin but plays no role in cytodifferentiation ofK. setae. This indicates that, unlike the A-factor receptor ofStreptomyces griseus, the autoregulator receptor (ksbA) ofK. setaebelongs to a family of autoregulator receptors which control secondary metabolism but play no role in morphological differentiation.
Characterization of a Eukaryotic-Like Tyrosine Protein Kinase Expressed by the Shiga Toxin-Encoding Bacteriophage 933W
Authors: Tyler Jessica S. , Friedman David I.
Published: May 2004

The Shiga toxin (Stx)-encoding bacteriophage 933W contains an open reading frame,stk, with amino acid sequence similarity to the catalytic domain of eukaryotic serine/threonine (Ser/Thr) protein kinases (PKs). Eukaryotic PKs are related by a common catalytic domain, consisting of invariant and nearly invariant residues necessary for ATP binding and phosphotransfer. We demonstrate that rather than a Ser/Thr kinase,stkencodes a eukaryotic-like tyrosine (Tyr) kinase. An affinity-purified recombinant Stk (rStk) autophosphorylates and catalyzes the phosphorylation of an artificial substrate on Tyr residues and not on Ser or Thr residues. A change of an invariant lysine within the putative catalytic domain abolishes this kinase activity, indicating that Stk uses a phosphotransfer mechanism similar to the mechanism used by eukaryotic PKs. We provide evidence suggesting thatstkis cotranscribed withcI from the phage promoter responsible for maintaining CI expression during lysogeny. Thestkgene was identified in prophages obtained from independently isolated Stx-producingEscherichia coliclinical isolates, suggesting that selective pressure has maintained thestkgene in these pathogenic bacteria.
Transcriptome Analysis of Crp-Dependent Catabolite Control of Gene Expression in
Escherichia coli
Authors: Gosset Guillermo , Zhang Zhongge , Nayyar Samir , Cuevas William A. , Saier Milton H.
Published: May 2004

We report here the transcriptome analyses of highly expressed genes that are subject to catabolite repression or activation mediated by the cyclic AMP receptor protein (Crp). The results reveal that many operons encoding enzymes of central carbon metabolic pathways (e.g., Krebs cycle enzymes), as well as transporters and enzymes that initiate carbon metabolism, are subject to direct Crp-mediated catabolite repression. By contrast, few enzyme-encoding genes (direct regulation) but many ribosomal protein- and tRNA-encoding genes (indirect regulation) are subject to Crp-dependent glucose activation. Additionally, Crp mediates strong indirect catabolite repression of many cytoplasmic stress response proteins, including the major chaperone proteins, five ATP-dependent protease complexes, and several cold and heat shock proteins. These results were confirmed by (i) phenotypic analyses, (ii) real-time PCR studies, (iii) reporter gene fusion assays, and (iv) previously published reports about representative genes. The results serve to define and extend our appreciation of the Crp regulon.
Structure of the DNA-SspC Complex: Implications for DNA Packaging, Protection, and Repair in Bacterial Spores
Authors: Frenkiel-Krispin Daphna , Sack Rinat , Englander Joseph , Shimoni Eyal , Eisenstein Miriam , Bullitt Esther , Horowitz-Scherer Rachel , Hayes Christopher S. , Setlow Peter , Minsky Abraham , Wolf Sharon Grayer
Published: May 2004

Bacterial spores have long been recognized as the sturdiest known life forms on earth, revealing extraordinary resistance to a broad range of environmental assaults. A family of highly conserved spore-specific DNA-binding proteins, termed α/β-type small, acid-soluble spore proteins (SASP), plays a major role in mediating spore resistance. The mechanism by which these proteins exert their protective activity remains poorly understood, in part due to the lack of structural data on the DNA-SASP complex. By using cryoelectron microscopy, we have determined the structure of the helical complex formed between DNA and SspC, a characteristic member of the α/β-type SASP family. The protein is found to fully coat the DNA, forming distinct protruding domains, and to modify DNA structure such that it adopts a 3.2-nm pitch. The protruding SspC motifs allow for interdigitation of adjacent DNA-SspC filaments into a tightly packed assembly of nucleoprotein helices. By effectively sequestering DNA molecules, this dense assembly of filaments is proposed to enhance and complement DNA protection obtained by DNA saturation with the α/β-type SASP.
The Essential Nature of the Ubiquitous 26-Kilobase Circular Replicon ofBorrelia burgdorferi
Authors: Byram Rebecca , Stewart Philip E. , Rosa Patricia
Published: May 2004

The genome of the type strain (B31) ofBorrelia burgdorferi, the causative agent of Lyme disease, is composed of 12 linear and 9 circular plasmids and a linear chromosome. Plasmid content can vary among strains, but one 26-kb circular plasmid (cp26) is always present. The ubiquitous nature of cp26 suggests that it provides functions required for bacterial viability. We tested this hypothesis by attempting to selectively displace cp26 with an incompatible but replication-proficient vector, pBSV26. While pBSV26 transformants contained this incompatible vector, the vector coexisted with cp26, which is consistent with the hypothesis that cp26 carries essential genes. Several cp26 genes with ascribed or predicted functions may be essential. These include the BBB29 gene, which has sequence homology to a gene encoding a glucose-specific phosphotransferase system component, and theresTgene, which encodes a telomere resolvase involved in resolution of the replicated telomeres of the linear chromosome and plasmids. The BBB29 gene was successfully inactivated by allelic exchange, but attempted inactivation ofresTresulted in merodiploid transformants, suggesting thatresTis required forB. burgdorferigrowth. To determine ifresTis the only cp26 gene essential for growth, we introducedresTintoB. burgdorferion pBSV26. This did not result in displacement of cp26, suggesting that additional cp26 genes encode vital functions. We concluded thatB. burgdorferiplasmid cp26 encodes functions critical for survival and thus shares some features with the chromosome.
Methionine Sulfoxide Reductase A (MsrA) Deficiency Affects the Survival ofMycobacterium smegmatiswithin Macrophages
Authors: Douglas T. , Daniel D. S. , Parida B. K. , Jagannath C. , Dhandayuthapani S.
Published: May 2004

Methionine sulfoxide reductase A (MsrA) is an antioxidant repair enzyme which reduces oxidized methionine to methionine. Since oxidation of methionine in proteins impairs their function, an absence of MsrA leads to abnormalities in different organisms, including alterations in the adherence patterns and in vivo survival of certain pathogenic bacteria. To understand the role of MsrA in intracellular survival of bacteria, we disrupted the gene encoding MsrA inMycobacterium smegmatisthrough homologous recombination. ThemsrAmutant strain ofM. smegmatisexhibited significantly reduced intracellular survival in murine J774A.1 macrophages compared to the survival of its wild-type counterpart. Furthermore, immunofluorescence and immnunoblotting of phagosomes containingM. smegmatisstrains revealed that the phagosomes with themsrAmutant strain acquired both p67phoxof phagocyte NADPH oxidase and inducible nitric oxide synthase much earlier than the phagosomes with the wild-type strain. In addition, themsrAmutant strain ofM. smegmatiswas observed to be more sensitive to hydroperoxides than the wild-type strain was in vitro. These results suggest that MsrA plays an important role in both extracellular and intracellular survival ofM. smegmatis.
DNA Binding Regions of Q Proteins of Phages λ and φ80
Authors: Guo Jingshu , Roberts Jeffrey W.
Published: May 2004

Bacteriophage λ gene
Q
protein and the related proteins of other lambdoid phages are transcription antiterminators that interact both with DNA in the late gene promoter segment and with RNA polymerase subunits. Using hybrids between Q of λ and the related Q of phage 80, we characterized elements of both Q and DNA that contribute to the DNA binding function. In particular, we found a C-terminal segment of the protein that is responsible for binding specificity and an ∼15 residue segment on a predicted alpha helix within this segment at which alanine substitutions decrease DNA binding. We identified a six-nucleotide segment located between the −35 and −10 promoter elements that confers binding specificity and is the site of point mutants that impair binding, and we isolated suppressors in λ Q that restore binding function by increasing the overall binding affinity. We also identified putative zinc finger structures in both proteins.
TheSinorhizobium meliloti furGene Regulates, with Dependence on Mn(II), Transcription of thesitABCDOperon, Encoding a Metal-Type Transporter
Authors: Chao Tzu-Chiao , Becker Anke , Buhrmester Jens , Pühler Alfred , Weidner Stefan
Published: May 2004

Sinorhizobium melilotiis an alpha-proteobacterium able to induce nitrogen-fixing nodules on roots of specific legumes. In order to propagate in the soil and for successful symbiotic interaction the bacterium needs to sequester metals like iron and manganese from its environment. The metal uptake has to be in turn tightly regulated to avoid toxic effects. In this report we describe the characterization of a chromosomal region ofS. melilotiencoding thesitABCDoperon and the putative regulatoryfurgene. It is generally assumed that thesitABCDoperon encodes a metal-type transporter and that thefurgene is involved in iron ion uptake regulation. A constructedS. meliloti sitAdeletion mutant was found to be growth dependent on Mn(II) and to a lesser degree on Fe(II). ThesitApromoter was strongly repressed by Mn(II), with dependence on Fur, and moderately by Fe(II). Applying a genome-wideS. melilotimicroarray it was shown that in thefurdeletion mutant 23 genes were up-regulated and 10 genes were down-regulated when compared to the wild-type strain. Among the up-regulated genes only thesitABCDoperon could be associated with metal uptake. On the other hand, the completerhbABCDEFoperon, which is involved in siderophore synthesis, was identified among the down-regulated genes. Thus, inS. melilotiFur is not a global repressor of iron uptake. Under symbiotic conditions thesitApromoter was strongly expressed and theS. meliloti sitAmutant exhibited an attenuated nitrogen fixation activity resulting in a decreased fresh weight of the host plantMedicago sativa.
A Cytochrome P450 Involved in the Metabolism of Abietane Diterpenoids byPseudomonas abietaniphilaBKME-9
Authors: Smith Daryl J. , Martin Vincent J. J. , Mohn William W.
Published: May 2004

Diterpenoids are naturally occurring plant compounds which have pharmaceutical properties. We have sequenced a 10.4-kbp extension of theditcluster inPseudomonas abietaniphilaBKME-9, containing genes involved in abietane diterpenoid biodegradation. TheditQgene was found to encode a cytochrome P450 monooxygenase, P450dit, and to be homologous to thetdtDgene ofPseudomonas diterpeniphilaA19-6a. Knocking outditQhad little effect on growth of BKME-9 on abietic acid but severely impaired growth on dehydroabietic acid (DhA) and palustric acid (PaA), increasing doubling times from 3.8 to 15 h on DhA and from 5.6 to 18.5 h on PaA. AxylEtranscriptional fusion showed that transcription ofditQwas induced by a range of diterpenoids. Substrate binding assays of P450ditexpressed inEscherichia colirevealed that DhA binds to the enzyme and yields a type I binding spectrum with aKdof 0.4 μM. These results indicate that P450ditis involved in the metabolism of DhA and PaA and are consistent with its putative role in converting DhA to 7-hydroxy-DhA. Finally, an amino acid sequence identity of greater than 72% and conserved gene arrangement support the hypothesis that theditgene cluster ofP. abietaniphilaBKME-9 and thetdtcluster ofP. diterpeniphilaA19-6a contain functional homologues.
Dimethylselenide Demethylation Is an Adaptive Response to Selenium Deprivation in the Archaeon
Methanococcus voltae
Authors: Niess Ulf M. , Klein Albrecht
Published: May 2004

The archaeon
Methanococcus voltae
needs selenium for optimal growth. A gene group most likely involved in the demethylation of dimethylselenide was discovered, the expression of which is induced upon selenium deprivation. The operon comprises open reading frames for a corrinoid protein and two putative methyltransferases. It is shown that the addition of dimethylselenide to selenium-depleted growth medium relieves the lack of selenium, as indicated by the repression of a promoter of a transcription unit encoding selenium-free hydrogenases which is normally active only upon selenium deprivation. Knockout mutants of the corrinoid protein or one of the two methyltransferase genes did not show repression of the hydrogenase promoter in the presence of dimethylselenide. The mutation of the other methyltransferase gene had no effect. Growth rates of the two effective mutants were reduced compared to wild-type cells in selenium-limited medium in the presence of dimethylselenide.
Escherichia coli mazEF
-Mediated Cell Death Is Triggered by Various Stressful Conditions
Authors: Hazan Ronen , Sat Boaz , Engelberg-Kulka Hanna
Published: May 2004

mazEF
is an
Escherichia coli
suicide module specific for a stable toxin and a labile antitoxin. Inhibiting
mazEF
expression appeared to activate the module to cause cell death. Here we show that several stressful conditions, including high temperatures, DNA damage, and oxidative stress, also induce
mazEF
-mediated cell death. We also show that this process takes place only during logarithmic growth and requires an intact
relA
gene.
Dust concentrations and respiratory risks in coalminers: key risk estimates from the British Pneumoconiosis Field Research
Authors: Soutar C A , Hurley J F , Miller B G , Cowie H A , Buchanan D
Published: May 2004

To help inform the setting of dust control standards in coalmines, this brief review summarises the most recent and reliable exposure-response relations, for damaging respiratory effects, derived from the Pneumoconiosis Field Research (PFR). Collecting data over 38 years in the British coal industry, this was a programme of prospective research on the respiratory health of coal miners, characterised by regular health surveys and detailed measurements of dust and silica concentrations in the workplace. Exposure-response relations are presented for coal workers’ simple pneumoconiosis category II, progressive massive fibrosis, defined deficits of lung function (FEV1), and category II silicosis. This simplified overview provides a guide to the most recent and most reliable estimates from the PFR of dust-related risks of substantial pulmonary disease, and to the magnitude of the effects. Control of dust sufficient to prevent category II simple pneumoconiosis should prevent most cases of progressive massive fibrosis and most dust related large lung function deficits. Where the dust contains high proportions of silica, control to low levels is essential, and even quite brief excursions of silica to high levels must be avoided.
Professional and medical outcomes for French train drivers after “person under train” accidents: three year follow up study
Authors: Cothereau C , de Beaurepaire C , Payan C , Cambou J P , Rouillon F , Conso F
Published: May 2004

Aims:To investigate psychiatric disorders, somatic health, and professional effects in French train drivers having experienced a “person under train” accident, and somatic health and professional effects.

Methods:A total of 202 train drivers were evaluated several times: immediately after the event, three months later, and one, two, and three years later. These drivers were compared with 186 train drivers not exposed to that psychotraumatic shock. The evaluations relied primarily on the GHQ-28 and MINI questionnaires.

Results:In the exposed group, at the first evaluation, the prevalence of post-traumatic stress was 4%; scores ⩾5 on the GHQ-28 were significantly higher than in the non-exposed group (32% versus 6%), for both the overall result and three sub-scores (somatic symptoms, anxiety and sleep, and psychosocial functioning). All these differences disappeared within a year. Vulnerability factors concerned prior traumas, acute and lasting life events, and the particular occupational situation where the driver is not accompanied but drives the train away alone in the aftermath of the accident. Over 95% of subjects had no short, medium, or long term impairment of their occupational fitness.

Conclusions:Most of the psycho-behavioural disorders were observed in the immediate aftermath of the accident and disappeared within a year. The driver’s occupational future does not seem to be affected by the “person under train” accident. Consideration of a traumatic accident as a job related risk and close psychological support of drivers after an accident probably increase the subject’s ability to recover from the event.
Enhanced oxidative stress in workers with a standing occupation: Table 1
Authors: Flore R , Gerardino L , Santoliquido A , Pola R , Flex A , Di Campli C , Pola P , Tondi P
Published: May 2004

Background:Several epidemiological studies have shown a statistically significant association between standing work and chronic venous insufficiency of lower limbs. This condition has been associated with an enhanced oxidative stress that, according to the literature, could represent a risk factor for cardiovascular and other systemic diseases.

Aims and Methods:To evaluate venous pressure of the lower limbs and reactive oxygen species (ROS) before and after work in 62 workers with a standing occupation (surgery room nurses) and 65 outpatient department nurses who can walk during their working time.

Results:After work, a statistically significant increase of venous pressure of the lower limbs levels was observed in both the study group and controls. Standing workers showed significantly higher mean levels of ROS after work.
Mortality and cancer incidence in New Zealand meat workers
Authors: McLean D , Cheng S , ’t Mannetje A , Woodward A , Pearce N
Published: May 2004

Aims:To ascertain whether there is an increased risk of cancers of the lung and lymphohaematopoietic tissue in workers employed in the New Zealand meat processing industry, and to identify exposures associated with any increased risks.

Methods:A cohort of 6647 individuals assembled from personnel records from three plants was followed from 1988 until 2000. The observed number of deaths and cancer registrations was compared with expected numbers using five year age and gender specific rates for the New Zealand population. Subgroup analyses evaluated the effect of duration of exposure to selected agents, based on job titles and departments.

Results:Vital status was determined for 84% of the cohort, and 92% of the total possible person-years. Mortality from all causes and all cancers was increased, and there was a significant excess of lung cancer. There were significant trends of increasing risk of lung and lymphohaematopoietic cancer with increasing duration of exposure to biological material.

Conclusions:Excess risks were observed for mortality from all causes, all cancers, and lung cancer. Although the increased risk of lung cancer may be partly due to confounding by smoking, it is unlikely to be entirely due to this cause. Furthermore, the dose-response relation observed for lung cancer suggests the effect is related to exposure to biological material contained in animal urine, faeces, and blood. Although numbers were small, the risk of lymphohaematopoietic cancer was also associated with increasing duration and level of exposure to biological material.
The polymerase chain reaction
Authors: Powledge Tabitha M.
Published: May 2004

This essay on the polymerase chain reaction is one of a series developed as part of FASEB’S efforts to educate the general public, and the legislators whom it elects, about the benefits of fundamental biomedical research—particularly how investment in such research leads to scientific progress, improved health, and economic well-being. 1