bluuebunny/crossref_metadata_2025 huggingface dataset:
Microcavity organic light emitting diodes with double sided light emission of different colors
Authors: Liu X. , Poitras D. , Tao Y. , Py C.
Published: May 2004

An organic light emitting diode was fabricated using a thin semitransparent Mg:Ag metal film (30 nm) and a distributed Bragg reflector with a reflectance of 99.5% as a microcavity. Double-sided electroluminescence was observed: green from the metal side and red from the glass side, both in directions normal to the surface. A maximum luminance of 2523 cd/m2 was obtained from the metal side, where most light was coupled out of the cavity.
Growth of InGaN self-assembled quantum dots and their application to photodiodes
Authors: Ji L. W. , Su Y. K. , Chang S. J. , Tsai S. T. , Hung S. C. , Chuang R. W. , Fang T. H. , Tsai T. Y.
Published: May 2004

Nanometer-scale InGaN self-assembled quantum dots (QDs) have been prepared by growth interruption during metalorganic chemical vapor deposition growth. With a 12 s growth interruption, we successfully formed InGaN QDs with a typical lateral size of 25 nm and an average height of 4.1 nm. The QD density was about 2×1010 cm−2. In contrast, much larger InGaN QDs were obtained without growth interruption. InGaN metal-semiconductor-metal photodiodes with and without QDs were also fabricated. It was found that the QD photodiode with lower dark current could operate in the normal incidence mode, and exhibit a stronger photoresponse.
Amorphous silicon shift registers for display drivers
Authors: Kumar A. , Sambandan S. , Sakariya K. , Servati P. , Nathan A.
Published: May 2004

Hydrogenated amorphous silicon (a-Si:H) based shift registers are presented. The gate-driver switching requirements, for the quarter video graphics array, are discussed. Advantages of the shift-register integration with the pixel array are discussed. The circuit metastability considerations due to the threshold voltage shift in the a-Si:H devices under electrical stress are also presented.
Fabrication of a self-absorbing, self-supported complementary metal-oxide-semiconductor compatible micromachined bolometer
Authors: Ahmed A. H. Z. , Tait R. N.
Published: May 2004

This work describes a fabrication process for the manufacturing of a surface micromachined microbridge-type bolometer for infrared thermal imaging applications, which is compatible with any standard complementary metal-oxide-semiconductor process. The bolometer uses a high resistivity amorphous GexSi1−xOy active layer incorporated in a self-absorbing structure for infrared radiation, requiring no additional absorber layer. The device is surface micromachined for thermal isolation and is self-supported by its contact metal legs, with no additional support structure. The design uses a vertical current flow arrangement suitable for a high resistivity a-GexSi1−xOy sensing layer and both sandwich and sandwich-gap configurations are demonstrated. Optimum polyimide sacrificial layer patterning for subsequent deposition of layers is described and optimum metal thickness for the required sheet resistance is studied. A planar surface for the deposited semiconductor layer is obtained by using a recessed base electrode structure. Finally optimum conditions for plasma releasing of the structure are described.
Monocrystalline CuInSe2 photovoltaic cell of superior performance
Authors: Du H. , Shih I. , Champness C. H.
Published: May 2004

Using a wafer cut from a Bridgman-grown ingot of CuInSe2 as the p-type monocrystalline absorber substrate, a photovoltaic cell has been fabricated with the layer structure Au–CuInSe2 (p)-CdS–ZnO–In. This device has shown superior photovoltaic performance with an apparent initial effective area conversion efficiency of some 12.5% (11.3% total area efficiency), without an antireflection coating, under direct sunlight, where the irradiance corresponded approximately to 90.5 mW/cm2. The effective cell area was 12.6 mm2 (total area 13.8 mm2) and the acceptor concentration in the CuInSe2, estimated from a Mott–Schottky plot, was about 1017 cm−3. However, the photocurrent–capacitance method applied to the cell indicated an electron diffusion length of only about 0.3 μm.
High-k titanium silicate thin films grown by reactive magnetron sputtering for complementary metal–oxide–semiconductor applications
Authors: Brassard D. , Sarkar D. K. , El Khakani M. A. , Ouellet L.
Published: May 2004

Titanium silicate (TiSixOy) thin films have been successfully deposited by means of radio-frequency magnetron sputtering of a TiO2/SiO2 composite target in a reactive gas atmosphere. The deposition of the films was investigated as a function of the [O2]/([Ar]+[O2]) flow ratio in the 0%–30% range. The bonding states and the dielectric properties of the sputter-deposited TiSixOy films were systematically investigated as a function of the O2 flow ratio. For all the O2 flow ratios studied, Fourier-transform infrared and x-ray photoelectron spectroscopy analyses have clearly revealed the presence of Ti–O–Si type of local environments, which are the fingerprint of the titanium silicate phase. Increasing the O2 proportion in the sputtering chamber was found to cause a significant decrease of the deposition rate and a drastic improvement in the dielectric properties of the films. TiSixOy films exhibiting excellent dielectric properties (i.e., a dielectric constant as high as ∼20, a dissipation factor as low as 0.01, and a low leakage current density of 10−3 A/cm2 at 1 MV/cm) were indeed achieved under high O2 flow ratio conditions (⩾20%). In contrast, films deposited under low O2 flow ratio conditions (⩽5%) have exhibited poor dielectric properties. The presence of oxygen vacancies in the films is invoked as a possible explanation for the observed variations of their dielectric properties with the O2 flow ratio.
Metal–insulator–metal capacitors using Y2O3 dielectric grown by pulsed-injection plasma enhanced metalorganic chemical vapor deposition
Authors: Durand C. , Vallée C. , Loup V. , Salicio O. , Dubourdieu C. , Blonkowski S. , Bonvalot M. , Holliger P. , Joubert O.
Published: May 2004

Yttrium oxide-based metal–insulator–metal (MIM) capacitors were investigated. The dielectric films were grown on Si/TiSi2/TiN substrates using a low thermal budget metalorganic chemical vapor deposition process (T⩽350 °C). Low-temperature (450 °C) or high-temperature (700 °C) postdeposition annealings were carried out in different atmospheres (O2 or argon). X-ray diffraction, x-ray photoelectron spectroscopy, and secondary ion mass spectrometry were used to determine the structural and microstructural changes in the films. The films were incorporated into simple MIM test structures. A significant capacitance value of the order of 2.2 fF/μm2, a low leakage current density (∼10−8 A cm−2 at ±10 V) and a high electrical breakdown field of 7–8 MV/cm were measured for capacitors prepared from as-deposited or low temperature (450 °C) annealed films. These results indicate that yttrium oxide is a very promising dielectric to be used in silicon integrated circuits applications.
Phase transition behavior of reactive sputtering deposited Co–N thin films using transmission electron microscopy
Authors: Fang Jau-Shiung , Yang Li-Chung , Hsu Chen-Siang , Chen Gin-Shiang , Lin Yen-Wei , Chen Giin-Shan
Published: May 2004

Cobalt nitride thin films could be prepared by employing a direct current reactive sputtering deposition on (100) silicon substrates in mixtures of fixed Ar (4×10−1 Pa) and N2 at various partial pressures. The CoxN thin films could be tailored by appropriately controlling the partial pressure of the reactive nitrogen. With adequately increasing nitrogen to argon partial pressure, a series of sequence phase formation from α-Co, Co4N, Co3N, Co2N, and CoN could be observed. The phase transition sequence was accompanied by a substantial refinement and improvement of the films’ grain structure. Rapid thermal annealing of cobalt nitride thin films exhibited a stepwise decomposition via the dissociating of Co4N→Co3N+β-Co(N), Co3N→Co2N+β-Co(N), and Co2N→CoN+β-Co(N) with increasing the elevated temperature. Phase formation, thermal decomposition, electrical resistivity, and microstructure of reactive sputtered cobalt nitride films were discussed in this study.
Angular dependence of etch rates in the etching of poly-Si and fluorocarbon polymer using SF6, C4F8, and O2 plasmas
Authors: Min Jae-Ho , Lee Gyeo-Re , Lee Jin-Kwan , Moon Sang Heup , Kim Chang-Koo
Published: May 2004

The dependences of etch rates on the angle of ions incident on the substrate surface in four plasma/substrate systems that constitute the advanced Bosch process were investigated using a Faraday cage designed for the accurate control of the ion-incident angle. The four systems, established by combining discharge gases and substrates, were a SF6/poly-Si, a SF6/fluorocarbon polymer, an O2/fluorocarbon polymer, and a C4F8/Si. In the case of SF6/poly-Si, the normalized etch rates (NERs), defined as the etch rates normalized by the rate on the horizontal surface, were higher at all angles than values predicted from the cosine of the ion-incident angle. This characteristic curve shape was independent of changes in process variables including the source power and bias voltage. Contrary to the earlier case, the NERs for the O2/polymer decreased and eventually reached much lower values than the cosine values at angles between 30° and 70° when the source power was increased and the bias voltage was decreased. On the other hand, the NERs for the SF6/polymer showed a weak dependence on the process variables. In the case of C4F8/Si, which is used in the Bosch process for depositing a fluorocarbon layer on the substrate surface, the deposition rate varied with the ion incident angle, showing an S-shaped curve. These characteristic deposition rate curves, which were highly dependent on the process conditions, could be divided into four distinct regions: a Si sputtering region, an ion-suppressed polymer deposition region, an ion-enhanced polymer deposition region, and an ion-free polymer deposition region. Based on the earlier characteristic angular dependences of the etch (or deposition) rates in the individual systems, ideal process conditions for obtaining an anisotropic etch profile in the advanced Bosch process are proposed.
Outgassing properties of the spallation neutron source ring vacuum chambers coated with titanium nitride
Authors: He P. , Hseuh H. C. , Mapes M. , Todd R. , Weiss D. , Wilson D.
Published: May 2004

The stainless steel vacuum chambers of the 248 m accumulator ring of the Spallation Neutron Source are to be coated with ∼100 nm of titanium nitride (TiN). This is to minimize the secondary electron yield from the chamber wall, and thus avoid the so-called e–p instability caused by electron multipacting as observed in a few high-intensity proton storage rings. Reports in the literature suggest that a TiN coating, by acting as a hydrogen permeation barrier, may also reduce the ultimate outgassing rate. The outgassing rate of TiN coated chambers deposited at various sputtering pressures was measured and compared to uncoated chambers, both with and without 250 °C in situ bake. Some coated chambers were subjected to glow discharge treatment (GDT). It was found that the surface roughness, analyzed with a scanning electron microscope, depends on the deposition pressure and is also influenced by GDT. The outgassing rate varies as a function of the surface roughness of the TiN layer, with rougher coatings more hydroscopic in nature. The in situ postbake outgassing rate was reduced ∼30% for a chamber coated with TiN at low pressure and subsequently subjected to GDT, thus giving evidence that the TiN layer acts as a permeation barrier to hydrogen diffusion. It was also found that a 450 °C vacuum degas reduced the hydrogen outgassing rate one order of magnitude, although the amount of reduction does not agree with the value predicted by standard diffusion equations.
Femtosecond pulsed laser deposition of amorphous, ultrahard boride thin films
Authors: Stock Michael , Molian Pal
Published: May 2004

Amorphous thin films (300–500 nm) of ultrahard AlMgB10 with oxygen and carbon impurities were grown on Si (100) substrates at 300 K using a solid target of AlMgB14 containing a spinel phase (MgAl2O4) and using a 120 fs pulsed, 800 nm wavelength Ti:sapphire laser. The films were subsequently annealed in argon gas up to 1373 K for 2 h. Scanning electron microscopy (SEM) was used to examine the particulate formation, atomic force microscopy was employed to characterize the film surface topography, x-ray diffraction and transmission electron microscopy were used to determine the microstructure, x-ray photoelectron spectroscopy was performed to examine the film composition, and nanoindentation was employed to study the hardness of thin films. The as-deposited and postannealed films (up to 1273 K) had a stochiometry of AlMgB10 with a significant amount of oxygen and carbon impurities and exhibited amorphous structures for a maximum hardness of 40±3 GPa. However, postannealing at higher temperatures led to crystallization and transformation of the film to SiB6 with a substantial loss in hardness. Results are also compared with our previous study on 23 ns, 248 nm wavelength (KrF excimer) pulsed laser deposition of AlMgB14 reported in this journal [Y. Tian, A. Constant, C. C. H. Lo, J. W. Anderegg, A. M. Russell, J. E. Snyder, and P. A. Molian, J. Vac. Sci. Technol. A 21, 1055 (2003)].
Bedout: A Possible End-Permian Impact Crater Offshore of Northwestern Australia
Authors: Becker L. , Poreda R. J. , Basu A. R. , Pope K. O. , Harrison T. M. , Nicholson C. , Iasky R.
Published: May 2004

The Bedout High, located on the northwestern continental margin of Australia, has emerged as a prime candidate for an end-Permian impact structure. Seismic imaging, gravity data, and the identification of melt rocks and impact breccias from drill cores located on top of Bedout are consistent with the presence of a buried impact crater. The impact breccias contain nearly pure silica glass (SiO
2
), fractured and shock-melted plagioclases, and spherulitic glass. The distribution of glass and shocked minerals over hundreds of meters of core material implies that a melt sheet is present. Available gravity and seismic data suggest that the Bedout High represents the central uplift of a crater similar in size to Chicxulub. A plagioclase separate from the Lagrange-1 exploration well has an Ar/Ar age of 250.1 ± 4.5 million years. The location, size, and age of the Bedout crater can account for reported occurrences of impact debris in Permian-Triassic boundary sediments worldwide.
Atomic Force Microscopy of Cell Growth and Division in
Staphylococcus aureus
Authors: Touhami Ahmed , Jericho Manfred H. , Beveridge Terry J.
Published: May 2004

The growth and division of
Staphylococcus aureus
was monitored by atomic force microscopy (AFM) and thin-section transmission electron microscopy (TEM). A good correlation of the structural events of division was found using the two microscopies, and AFM was able to provide new additional information. AFM was performed under water, ensuring that all structures were in the hydrated condition. Sequential images on the same structure revealed progressive changes to surfaces, suggesting the cells were growing while images were being taken. Using AFM small depressions were seen around the septal annulus at the onset of division that could be attributed to so-called murosomes (Giesbrecht et al., Arch. Microbiol.
141:
315-324, 1985). The new cell wall formed from the cross wall (i.e., completed septum) after cell separation and possessed concentric surface rings and a central depression; these structures could be correlated to a midline of reactive material in the developing septum that was seen by TEM. The older wall, that which was not derived from a newly formed cross wall, was partitioned into two different surface zones, smooth and gel-like zones, with different adhesive properties that could be attributed to cell wall turnover. The new and old wall topographies are equated to possible peptidoglycan arrangements, but no conclusion can be made regarding the planar or scaffolding models.
Secretion of Virulence Proteins from
Campylobacter jejuni
Is Dependent on a Functional Flagellar Export Apparatus
Authors: Konkel Michael E. , Klena John D. , Rivera-Amill Vanessa , Monteville Marshall R. , Biswas Debabrata , Raphael Brian , Mickelson Joey
Published: May 2004

Campylobacter jejuni
, a gram-negative motile bacterium, secretes a set of proteins termed the
Campylobacter
invasion antigens (Cia proteins). The purpose of this study was to determine whether the flagellar apparatus serves as the export apparatus for the Cia proteins. Mutations were generated in five genes encoding three structural components of the flagella, the flagellar basal body (
flgB
and
flgC
), hook (
flgE2
), and filament (
flaA
and
flaB
) genes, as well as in genes whose products are essential for flagellar protein export (
flhB
and
fliI
). While mutations that affected filament assembly were found to be nonmotile (Mot
−
) and did not secrete Cia proteins (S
−
), a
flaA
(

flaB
+

) filament mutant was found to be nonmotile but Cia protein secretion competent (Mot
−
, S
+
). Complementation of a
flaA flaB
double mutant with a shuttle plasmid harboring either the
flaA
or
flaB
gene restored Cia protein secretion, suggesting that Cia export requires at least one of the two filament proteins. Infection of INT 407 human intestinal cells with the
C. jejuni
mutants revealed that maximal invasion of the epithelial cells required motile bacteria that are secretion competent. Collectively, these data suggest that the
C. jejuni
Cia proteins are secreted from the flagellar export apparatus.
Isolation and Characterization of
rpoS
from a Pathogenic Bacterium,
Vibrio vulnificus
: Role of σ
S
in Survival of Exponential-Phase Cells under Oxidative Stress
Authors: Park Kyung-Je , Kang Min-Jin , Kim Songhee H. , Lee Hyun-Jung , Lim Jae-Kyu , Choi Sang Ho , Park Soon-Jung , Lee Kyu-Ho
Published: May 2004

A gene homologous to
rpoS
was cloned from a fatal human pathogen,
Vibrio vulnificus
. The functional role of
rpoS
in
V. vulnificus
was accessed by using an
rpoS
knockout mutant strain. This mutant was impaired in terms of the ability to survive under oxidative stress, nutrient starvation, UV irradiation, or acidic conditions. The increased susceptibility of the
V. vulnificus
mutant in the exponential phase to H
2
O
2
was attributed to the reduced activity of hydroperoxidase I (HPI). Although σ
S
synthesis was induced and HPI activity reached the maximal level in the stationary phase, the mutant in the stationary phase showed the same susceptibility to H
2
O
2
as the wild-type strain in the stationary phase. In addition, HPII activity, which is known to be controlled by σ
S
in
Escherichia coli
, was not detectable in
V. vulnificus
strains under the conditions tested. The mutant in the exponential phase complemented with multiple copies of either the
rpoS
or
katG
gene of
V. vulnificus
recovered both resistance to H
2
O
2
and HPI activity compared with the control strain. Expression of the
katG
gene encoding HPI in
V. vulnificus
was monitored by using a
katG
::
luxAB
transcriptional fusion. The expression of this gene was significantly reduced by deletion of σ
S
in both the early exponential and late stationary phases. Thus, σ
S
is necessary for increased synthesis and activity of HPI, and σ
S
is required for exponentially growing
V. vulnificus
to develop the ability to survive in the presence of H
2
O
2
.
An Accessory Protein Is Required for Relaxosome Formation by Small Staphylococcal Plasmids
Authors: Smith Matthew C. A. , Thomas Christopher D.
Published: May 2004

Mobilization of the staphylococcal plasmid pC221 requires at least one plasmid-encoded protein, MobA, in order to form a relaxosome. pC221 and closely related plasmids also possess an overlapping reading frame encoding a protein of 15 kDa, termed MobC. By completing the nucleotide sequence of plasmid pC223, we have found a further example of this small protein, and gene knockouts have shown that MobC is essential for relaxosome formation and plasmid mobilization in both pC221 and pC223. Primer extension analysis has been used to identify the
nic
site in both of these plasmids, located upstream of the
mobC
gene in the sense strand. Although the sequence surrounding the
nic
site is highly conserved between pC221 and pC223, exchange of the
oriT
sequence between plasmids significantly reduces the extent of relaxation complex formation, suggesting that the Mob proteins are selective for their cognate plasmids in vivo.
CcpA-Dependent Regulation of
Bacillus subtilis
Glutamate Dehydrogenase Gene Expression
Authors: Belitsky Boris R. , Kim Hyun-Jin , Sonenshein Abraham L.
Published: May 2004

The
Bacillus subtilis rocG
gene, encoding catabolic glutamate dehydrogenase, was found to be subject to direct CcpA-dependent glucose repression. The effect of CcpA required the presence of both the HPr and Crh proteins. The primary CcpA binding site was identified by mutational analysis and DNase I footprinting. In the absence of inducers of the Roc pathway,
rocG
was still expressed at a low level due to readthrough transcription. CcpA-dependent repression of
rocG
readthrough transcription proved to contribute to the slow growth rate of
B. subtilis
cells in glucose-glutamate medium. Increased readthrough expression of
rocG
was shown to be partially responsible for the growth defect of
ccpA
strains in glucose-ammonium medium.
The
davDT
Operon of
Pseudomonas putida
, Involved in Lysine Catabolism, Is Induced in Response to the Pathway Intermediate δ-Aminovaleric Acid
Authors: Revelles Olga , Espinosa-Urgel Manuel , Molin Soeren , Ramos Juan L.
Published: May 2004

Pseudomonas putida
KT2440 is a soil microorganism that attaches to seeds and efficiently colonizes the plant's rhizosphere. Lysine is one of the major compounds in root exudates, and
P. putida
KT2440 uses this amino acid as a source of carbon, nitrogen, and energy. Lysine is channeled to δ-aminovaleric acid and then further degraded to glutaric acid via the action of the
davDT
gene products. We show that the
davDT
genes form an operon transcribed from a single σ
70
-dependent promoter. The relatively high level of basal expression from the
davD
promoter increased about fourfold in response to the addition of exogenous lysine to the culture medium. However, the true inducer of this operon seems to be δ-aminovaleric acid because in a mutant unable to metabolize lysine to δ-aminovaleric acid, this compound, but not lysine, acted as an effector. Effective induction of the
P. putida
P

davD

promoter by exogenously added lysine requires efficient uptake of this amino acid, which seems to proceed by at least two uptake systems for basic amino acids that belong to the superfamily of ABC transporters. Mutants in these ABC uptake systems retained basal expression from the
davD
promoter but exhibited lower induction levels in response to exogenous lysine than the wild-type strain.
nsd, a Locus That Affects theMyxococcus xanthusCellular Response to Nutrient Concentration
Authors: Brenner Margaret , Garza Anthony G. , Singer Mitchell
Published: May 2004

Expression of the previously reported Tn5lacΩ4469 insertion inMyxococcus xanthuscells is regulated by the starvation response. Interested in learning more about the starvation response, we cloned and sequenced the region containing the insertion. Our analysis shows that the gene fusion is located in an open reading frame that we have designatednsd(nutrient sensing/utilizing defective) and that its expression is driven by a σ70-like promoter. Sequence analysis of thensdgene product provides no information on the potential structure or function of the encoded protein. In a further effort to learn about the role ofnsdin the starvation response, we closely examined the phenotype of cells carrying thensd::Tn5lacΩ4469 mutation. Our analysis showed that these cells initiate development on medium that contains nutrients sufficient to sustain vegetative growth of wild-type cells. Furthermore, in liquid media these same nutrient concentrations elicit a severe impairment of growth ofnsdcells. The data suggest that thensdcells launch a starvation response when there are enough nutrients to prevent one. In support of this hypothesis, we found that, when grown in these nutrient concentrations,nsdcells accumulate guanosine tetraphosphate, the cellular starvation signal. Therefore, we propose thatnsdis used by cells to respond to available nutrient levels.
Bacteriophage Tuc2009 Encodes a Tail-Associated Cell Wall-Degrading Activity
Authors: Kenny John G. , McGrath Stephen , Fitzgerald Gerald F. , van Sinderen Douwe
Published: May 2004

Tuc2009 is a P335-type member of the tailed-phage supergroup
Siphoviridae
and was originally identified as a resident prophage of the gram-positive bacterium
Lactococcus lactis
UC509. A Tuc2009 gene designated

tal
2009

which is located within the morphogenic module was shown to specify a lytic activity within the 3′ portion of its coding region. Comparative sequence analysis indicated that the cell wall-degrading part of Tal
2009
is a member of the M37 protein family and that Tal
2009
lacks a cell-binding domain, a finding supported by binding studies. Tal
2009
appears to undergo self-mediated posttranslational processing in both
L. lactis
and
Escherichia coli
. Antibodies directed against a purified C-terminal portion of Tal
2009
were used for immunoelectron microscopy, which showed that Tal
2009
is located at the tail tip of Tuc2009. Antibody neutralization studies demonstrated that Tal
2009
-directed antibodies inhibited the ability of phage to mediate host lysis by more than 100-fold. These data indicate that

tal
2009

encodes a tail-associated lysin involved in localized cell wall degradation, thus allowing the Tuc2009 DNA injection machinery access to the membrane of its bacterial host.
Transcription by an Archaeal RNA Polymerase Is Slowed but Not Blocked by an Archaeal Nucleosome
Authors: Xie Yunwei , Reeve John N.
Published: May 2004

Archaeal RNA polymerases (RNAPs) are closely related to eukaryotic RNAPs, and in
Euryarchaea
, genomic DNA is wrapped and compacted by histones into archaeal nucleosomes. In eukaryotes, transcription of DNA bound into nucleosomes is facilitated by histone tail modifications and chromatin remodeling complexes, but archaeal histones do not have histone tails and archaeal genome sequences provide no evidence for archaeal homologs of eukaryotic chromatin remodeling complexes. We have therefore investigated the ability of an archaeal RNAP, purified from
Methanothermobacter thermautotrophicus
, to transcribe DNA bound into an archaeal nucleosome by HMtA2, an archaeal histone from
M. thermautotrophicus
. To do so, we constructed a template that allows transcript elongation to be separated from transcription initiation, on which archaeal nucleosome assembly is positioned downstream from the site of transcription initiation. At 58°C, in the absence of an archaeal nucleosome,
M. thermautotrophicus
RNAP transcribed this template DNA at a rate of ∼20 nucleotides per second. With an archaeal nucleosome present, transcript elongation was slowed but not blocked, with transcription pausing at sites before and within the archaeal nucleosome. With additional HMtA2 binding, complexes were obtained that also incorporated the upstream regulatory region. This inhibited transcription presumably by preventing archaeal TATA-box binding protein, general transcription factor TFB, and RNAP access and thus inhibiting transcription initiation.
Purification and Characterization of the AAA+ Domain ofSinorhizobium melilotiDctD, a σ54-Dependent Transcriptional Activator
Authors: Xu Hao , Gu Baohua , Nixon B. Tracy , Hoover Timothy R.
Published: May 2004

Activators of σ54-RNA polymerase holoenzyme couple ATP hydrolysis to formation of an open complex between the promoter and RNA polymerase. These activators are modular, consisting of an N-terminal regulatory domain, a C-terminal DNA-binding domain, and a central activation domain belonging to the AAA+ superfamily of ATPases. The AAA+ domain ofSinorhizobium melilotiC4-dicarboxylic acid transport protein D (DctD) is sufficient to activate transcription. Deletion analysis of the 3′ end ofdctDidentified the minimal functional C-terminal boundary of the AAA+ domain of DctD as being located between Gly-381 and Ala-384. Histidine-tagged versions of the DctD AAA+ domain were purified and characterized. The DctD AAA+ domain was significantly more soluble than DctD(Δ1-142), a truncated DctD protein consisting of the AAA+ and DNA-binding domains. In addition, the DctD AAA+ domain was more homogeneous than DctD(Δ1-142)when analyzed by native gel electrophoresis, migrating predominantly as a single high-molecular-weight species, while DctD(Δ1-142)displayed multiple species. The DctD AAA+ domain, but not DctD(Δ1-142), formed a stable complex with σ54in the presence of the ATP transition state analogue ADP-aluminum fluoride. The DctD AAA+ domain activated transcription in vitro, but many of the transcripts appeared to terminate prematurely, suggesting that the DctD AAA+ domain interfered with transcription elongation. Thus, the DNA-binding domain of DctD appears to have roles in controlling the oligomerization of the AAA+ domain and modulating interactions with σ54in addition to its role in recognition of upstream activation sequences.
Evidence for an Arginine Exporter Encoded by
yggA
(
argO
) That Is Regulated by the LysR-Type Transcriptional Regulator ArgP in
Escherichia coli
Authors: Nandineni Madhusudan R. , Gowrishankar J.
Published: May 2004

The anonymous open reading frame
yggA
of
Escherichia coli
was identified in this study as a gene that is under the transcriptional control of
argP
(previously called
iciA
), which encodes a LysR-type transcriptional regulator protein. Strains with null mutations in either
yggA
or
argP
were supersensitive to the arginine analog canavanine, and
yggA-lac
expression in vivo exhibited

argP
+

-dependent induction by arginine. Lysine supplementation phenocopied the
argP
null mutation in that it virtually abolished
yggA
expression, even in the

argP
+

strain. The dipeptides arginylalanine and lysylalanine behaved much like arginine and lysine, respectively, to induce and to turn off
yggA
transcription. Dominant missense mutations in
argP
(

argP
d

) that conferred canavanine resistance and rendered
yggA-lac
expression constitutive were obtained. The protein deduced to be encoded by
yggA
shares similarity with a basic amino acid exporter (LysE) of
Corynebacterium glutamicum
, and we obtained evidence for increased arginine efflux from
E. coli
strains with either the

argP
d

mutation or multicopy

yggA
+

. The null
yggA
mutation abolished the increased arginine efflux from the

argP
d

strain. Our results suggest that
yggA
encodes an ArgP-regulated arginine exporter, and we have accordingly renamed it
argO
(for “arginine outward transport”). We propose that the physiological function of
argO
may be either to prevent the accumulation to toxic levels of canavanine (which is a plant-derived antimetabolite) or arginine or to maintain an appropriate balance between the intracellular lysine and arginine concentrations.
The ETT2 Gene Cluster, Encoding a Second Type III Secretion System from
Escherichia coli
, Is Present in the Majority of Strains but Has Undergone Widespread Mutational Attrition
Authors: Ren Chuan-Peng , Chaudhuri Roy R. , Fivian Amanda , Bailey Christopher M. , Antonio Martin , Barnes Wayne M. , Pallen Mark J.
Published: May 2004

ETT2 is a second cryptic type III secretion system in
Escherichia coli
which was first discovered through the analysis of genome sequences of enterohemorrhagic
E. coli
O157:H7. Comparative analyses of
Escherichia
and
Shigella
genome sequences revealed that the ETT2 gene cluster is larger than was previously thought, encompassing homologues of genes from the Spi-1, Spi-2, and Spi-3
Salmonella
pathogenicity islands. ETT2-associated genes, including regulators and chaperones, were found at the same chromosomal location in the majority of genome-sequenced strains, including the laboratory strain K-12. Using a PCR-based approach, we constructed a complete tiling path through the ETT2 gene cluster for 79 strains, including the well-characterized
E. coli
reference collection supplemented with additional pathotypes. The ETT2 gene cluster was found to be present in whole or in part in the majority of
E. coli
strains, whether pathogenic or commensal, with patterns of distribution and deletion mirroring the known phylogenetic structure of the species. In almost all strains, including enterohemorrhagic
E. coli
O157:H7, ETT2 has been subjected to varying degrees of mutational attrition that render it unable to encode a functioning secretion system. A second type III secretion system-associated locus that likely encodes the ETT2 translocation apparatus was found in some
E. coli
strains. Intact versions of both ETT2-related clusters are apparently present in enteroaggregative
E. coli
strain O42.
Novel Genes That Influence Development inStreptomyces coelicolor
Authors: Gehring Amy M. , Wang Stephanie T. , Kearns Daniel B. , Storer Narie Yoo , Losick Richard
Published: May 2004

Filamentous soil bacteria of the genusStreptomycescarry out complex developmental cycles that result in sporulation and production of numerous secondary metabolites with pharmaceutically important activities. To further characterize the molecular basis of these developmental events, we screened for mutants ofStreptomyces coelicolorthat exhibit aberrant morphological differentiation and/or secondary metabolite production. On the basis of this screening analysis and the subsequent complementation analysis of the mutants obtained we assigned developmental roles to a gene involved in methionine biosynthesis (metH) and two previously uncharacterized genes (SCO6938andSCO2525) and we reidentified two previously described developmental genes (bldAandbldM). In contrast to most previously studied genes involved in development, the genes newly identified in the present study all appear to encode biosynthetic enzymes instead of regulatory proteins. The MetH methionine synthase appears to be required for conversion of aerial hyphae into chains of spores, SCO6938 is a probable acyl coenzyme A dehydrogenase that contributes to the proper timing of aerial mycelium formation and antibiotic production, and SCO2525 is a putative methyltransferase that influences various aspects of colony growth and development.
Recognition of Ferric Catecholates by FepA
Authors: Annamalai Rajasekaran , Jin Bo , Cao Zhenghua , Newton Salete M. C. , Klebba Phillip E.
Published: May 2004

Escherichia coliFepA transports certain catecholate ferric siderophores, but not others, nor any noncatecholate compounds. Direct binding and competition experiments demonstrated that this selectivity originates during the adsorption stage. The synthetic tricatecholate Fe-TRENCAM bound to FepA with 50- to 100-fold-lower affinity than Fe-enterobactin (FeEnt), despite an identical metal center, and Fe-corynebactin only bound at much higher concentrations. Neither Fe-agrobactin nor ferrichrome bound at all, even at concentrations 106-fold above theKd. Thus, FepA only adsorbs catecholate iron complexes, and it selects FeEnt among even its close homologs. We used alanine scanning mutagenesis to study the contributions of surface aromatic residues to FeEnt recognition. Although not apparent from crystallography, aromatic residues in L3, L5, L7, L8, and L10 affected FepA's interaction with FeEnt. Among 10 substitutions that eliminated aromatic residues,Kdincreased as much as 20-fold (Y481A and Y638A) andKmincreased as much as 400-fold (Y478), showing the importance of aromaticity around the pore entrance. Although many mutations equally reduced binding and transport, others caused greater deficiencies in the latter. Y638A and Y478A increasedKm10- and 200-fold more, respectively, thanKd. N-domain loop deletions created the same phenotype: Δ60-67 (in NL1) and Δ98-105 (in NL2) increasedKd10- to 20-fold but raisedKm500- to 700-fold. W101A (in NL2) had little effect onKdbut increasedKm1,000-fold. These data suggested that the primary role of the N terminus is in ligand uptake. Fluorescence and radioisotopic experiments showed biphasic release of FeEnt from FepA. In spectroscopic determinations,koff1was 0.03/s andkoff2was 0.003/s. However, FepAY272AF329A did not manifest the rapid dissociation phase, corroborating the role of aromatic residues in the initial binding of FeEnt. Thus, the β-barrel loops contain the principal ligand recognition determinants, and the N-domain loops perform a role in ligand transport.
The
Pseudomonas syringae
HopPtoV Protein Is Secreted in Culture and Translocated into Plant Cells via the Type III Protein Secretion System in a Manner Dependent on the ShcV Type III Chaperone
Authors: Wehling Misty D. , Guo Ming , Fu Zheng Qing , Alfano James R.
Published: May 2004

The bacterial plant pathogen
Pseudomonas syringae
depends on a type III protein secretion system and the effector proteins that it translocates into plant cells to cause disease and to elicit the defense-associated hypersensitive response on resistant plants. The availability of the
P. syringae
pv. tomato DC3000 genome sequence has resulted in the identification of many novel effectors. We identified the
hopPtoV
effector gene on the basis of its location next to a candidate type III chaperone (TTC) gene,
shcV
, and within a pathogenicity island in the DC3000 chromosome. A DC3000 mutant lacking ShcV was unable to secrete detectable amounts of HopPtoV into culture supernatants or translocate HopPtoV into plant cells, based on an assay that tested whether HopPtoV-AvrRpt2 fusions were delivered into plant cells. Coimmunoprecipitation and
Saccharomyces cerevisiae
two-hybrid experiments showed that ShcV and HopPtoV interact directly with each other. The ShcV binding site was delimited to an N-terminal region of HopPtoV between amino acids 76 and 125 of the 391-residue full-length protein. Our results demonstrate that ShcV is a TTC for the HopPtoV effector. DC3000 overexpressing ShcV and HopPtoV and DC3000 mutants lacking either HopPtoV or both ShcV and HopPtoV were not significantly impaired in disease symptoms or bacterial multiplication in planta, suggesting that HopPtoV plays a subtle role in pathogenesis or that other effectors effectively mask the contribution of HopPtoV in plant pathogenesis.
The
Butyrivibrio fibrisolvens tet
(W) Gene Is Carried on the Novel Conjugative Transposon Tn
B1230
, Which Contains Duplicated Nitroreductase Coding Sequences
Authors: Melville Claire M. , Brunel Romain , Flint Harry J. , Scott Karen P.
Published: May 2004

The
Butyrivibrio fibrisolvens tet
(W) gene is located on the conjugative transposon Tn
B1230
. Tn
B1230
encodes transfer proteins with 48 to 67% identity to some of those encoded by Tn
1549. tet
(W) is flanked by directly repeated sequences with significant homology to oxygen-insensitive nitroreductases. The 340 nucleotides upstream of
tet
(W) are strongly conserved and are required for tetracycline resistance.
An epidemiological study of the magnitude and consequences of work related violence: the Minnesota Nurses’ Study
Authors: Gerberich S G , Church T R , McGovern P M , Hansen H E , Nachreiner N M , Geisser M S , Ryan A D , Mongin S J , Watt G D
Published: May 2004

Aims:To identify the magnitude of and potential risk factors for violence within a major occupational population.

Methods:Comprehensive surveys were sent to 6300 Minnesota licensed registered (RNs) and practical (LPNs) nurses to collect data on physical and non-physical violence for the prior 12 months. Re-weighting enabled adjustment for potential biases associated with non-response, accounting for unknown eligibility.

Results:From the 78% responding, combined with non-response rate information, respective adjusted rates per 100 persons per year (95% CI) for physical and non-physical violence were 13.2 (12.2 to 14.3) and 38.8 (37.4 to 40.4); assault rates were increased, respectively, for LPNs versus RNs (16.4 and 12.0) and males versus females (19.4 and 12.9). Perpetrators of physical and non-physical events were patients/clients (97% and 67%, respectively). Consequences appeared greater for non-physical than physical violence. Multivariate modelling identified increased rates for both physical and non-physical violence for working: in a nursing home/long term care facility; in intensive care, psychiatric/behavioural or emergency departments; and with geriatric patients.

Conclusions:Results show that non-fatal physical assault and non-physical forms of violence, and relevant consequences, are frequent among both RNs and LPNs; such violence is mostly perpetrated by patients or clients; and certain environmental factors appear to affect the risk of violence. This serves as the basis for further analytical studies that can enable the development of appropriate prevention and control efforts.
Indices of asthma among atopic and non-atopic woodworkers
Authors: Schlünssen V , Schaumburg I , Heederik D , Taudorf E , Sigsgaard T
Published: May 2004

Aims:To investigate the relation between wood dust exposure and different indices of asthma among woodworkers and non-exposed subjects.

Methods:A total of 302 woodworkers and 71 non-exposed subjects answered a respiratory health questionnaire, underwent a non-specific bronchial provocation test using the Yan method, and received a skin prick test with 12 common inhalant allergens. Subgroups performed repeated peak flow monitoring and underwent a reversibility test. A total of 347 dust measurements among 234 woodworkers were performed with passive dust monitors.

Results:The overall geometric mean (geometric standard deviation) exposure to inhalable dust was 0.96 (2.02) mg/m3. There was a tendency to increased risk of asthma among atopic woodworkers compared to atopic non-exposed subjects, with ORs between 3.0 (0.8–11.9) (symptomatic BHR) and 1.3 (0.5–4.2) (work related symptoms). In woodworkers, asthma was associated with atopy, with ORs between 7.4 (2.8–19.7) (symptomatic BHR) and 4.2 (2.4–7.7) (asthma symptoms). Asthma was related to dust level, most pronounced for symptomatic BHR among atopics, with OR 22.9 (1.0–523.6) for the highest compared to the lowest dust level. For work related asthma symptoms the association with dust level was seen only for non-atopics.

Conclusions:Wood dust exposure was associated with asthma, despite a low dust level compared to other studies. Atopy was an important effect modifier in the association between asthma and wood dust exposure.
A descriptive study of work aggravated asthma
Authors: Goe S K , Henneberger P K , Reilly M J , Rosenman K D , Schill D P , Valiante D , Flattery J , Harrison R , Reinisch F , Tumpowsky C , Filios M S
Published: May 2004

Background and Aims:Work related asthma (WRA) is one of the most frequently reported occupational lung diseases in a number of industrialised countries. A better understanding of work aggravated asthma (WAA), as well as work related new onset asthma (NOA), is needed to aid in prevention efforts.

Methods:WAA and NOA in the United States were compared using cases reported to the National Institute for Occupational Safety and Health (NIOSH) from four state Sentinel Event Notification Systems for Occupational Risks (SENSOR) surveillance programmes for 1993–95.

Results:A total of 210 WAA cases and 891 NOA cases were reported. WAA cases reported mineral and inorganic dusts as the most common exposure agent, as opposed to NOA cases, in which diisocyanates were reported most frequently. A similar percentage of WAA and NOA cases still experienced breathing problems at the time of the interview or had visited a hospital or emergency room for work related breathing problems. NOA cases were twice as likely to have applied for workers’ compensation compared with WAA cases. However, among those who had applied for worker compensation, approximately three-fourths of both WAA and NOA cases had received awards. The services and manufacturing industrial categories together accounted for the majority of both WAA (62%) and NOA (75%) cases. The risk of WAA, measured by average annual rate, was clearly the highest in the public administration (14.2 cases/105) industrial category, while the risk of NOA was increased in both the manufacturing (3.2 cases/105) and public administration (2.9 cases/105) categories.

Conclusions:WAA cases reported many of the same adverse consequences as NOA cases. Certain industries were identified as potential targets for prevention efforts based on either the number of cases or the risk of WAA and NOA.
Mortality and cancer incidence among Lithuanian cement producing workers
Authors: Smailyte G , Kurtinaitis J , Andersen A
Published: May 2004

Aims:To investigate mortality and cancer incidence of cement producing workers.

Methods:A total of 2498 cement workers who have been employed at Portland cement producing departments for at least one year from 1956 to 2000 were followed up from 1 January 1978 to 31 December 2000. The cohort contributed 43 490 person-years to the study. Standardised incidence ratios (SIR) and standardised mortality ratios (SMR) were calculated as ratios between observed and expected numbers of cancers and deaths. The expected numbers were based on sex specific incidence and mortality rates for the total Lithuanian population.

Results:Significantly increased SMRs were found for all malignant neoplasms (SMR 1.3, 95% CI 1.0 to 1.5) and for lung cancer (SMR 1.4, 95% CI 1.0 to 1.9) among male cement workers. SIR for all cancer sites was 1.2 (95% CI 1.0 to 1.4). Excess risk was found for cancer of the lung (SIR 1.5, 95% CI 1.1 to 2.1). The SIR for urinary bladder cancer was also increased (SIR 1.8, 95% CI 0.9 to 3.5). The overall cancer incidence was not increased among females (SIR 0.8, 95% CI 0.6 to 1.1). With increasing cumulated exposure to cement dust, there were indications of an increasing risk of lung and stomach cancers among males.

Conclusions:This study supported the hypothesis that exposure to cement dust may increase the lung and bladder cancer risk. A dose related risk was found for stomach cancer, but no support was found for an increased risk of colorectal cancer.
Expanding the traditional physiology class with asynchronous online discussions and collaborative projects
Authors: Taradi Sunčana Kukolja , Taradi Milan
Published: May 2004

Discussion and writing are very powerful ways to support learning. This article describes the use of a free, asynchronous online forum to expand student-teacher discussions beyond the time/place constraints of the physical physiology classroom. The main participants were medical students enrolled in physiology class at the University of Zagreb Medical School and their teachers. The assessment data were collected by the electronic administration of the software, by anonymous paper questionnaires, and by the results of the final examination in physiology. During one academic year, 25% ( n = 55) of 220 students enrolled in a traditional physiology course participated in online discussions. Physiology teachers and other faculty also joined the forum. All forum members ( n = 99) posted 395 messages. Nine documents were published by six students who participated in two online collaborative projects. The difference in the mean grade of the final examination in physiology between student members and nonmembers was statistically significant ( P = 0.0328, t = 2.1526). Students who participated in Web discussions were self-selected. Likely, they are the most motivated students, who would perform better on the final examination with or without this resource. Nevertheless, using an online forum could be very successful in teaching critical thinking in physiology because the Internet removes traditional time/place barriers. However, new barriers related to technology and behavioral changes are created. For most teachers and students, the main obstacles to information technology implementation are lack of motivation and lack of professional incentives. To overcome these barriers, institutional support is needed for both students and teachers.