bluuebunny/crossref_metadata_2025_split huggingface dataset:
VirB Alleviates H-NS Repression of the
icsP
Promoter in
Shigella flexneri
from Sites More Than One Kilobase Upstream of the Transcription Start Site
Authors: Castellanos Maria I. , Harrison Dustin J. , Smith Jennifer M. , Labahn Stephanie K. , Levy Karen M. , Wing Helen J. 
Published: April 2009

ABSTRACT

The
icsP
promoter of
Shigella
spp. is repressed by H-NS and derepressed by VirB. Here, we show that an inverted repeat located between positions −1144 and −1130 relative to the
icsP
transcription start site is necessary for VirB-dependent derepression. The atypical location of this
cis
-acting site is discussed.
Characterization of
Streptococcus gordonii
SecA2 as a Paralogue of SecA
Authors: Bensing Barbara A. , Sullam Paul M. 
Published: April 2009

ABSTRACT

The accessory Sec system of
Streptococcus gordonii
is essential for transport of the glycoprotein GspB to the bacterial cell surface. A key component of this dedicated transport system is SecA2. The SecA2 proteins of streptococci and staphylococci are paralogues of SecA and are presumed to have an analogous role in protein transport, but they may be specifically adapted for the transport of large, serine-rich glycoproteins. We used a combination of genetic and biochemical methods to assess whether the
S. gordonii
SecA2 functions similarly to SecA. Although mutational analyses demonstrated that conserved amino acids are essential for the function of SecA2, replacing such residues in one of two nucleotide binding folds had only minor effects on SecA2 function. SecA2-mediated transport is highly sensitive to azide, as is SecA-mediated transport. Comparison of the
S. gordonii
SecA and SecA2 proteins in vitro revealed that SecA2 can hydrolyze ATP at a rate similar to that of SecA and is comparably sensitive to azide but that the biochemical properties of these enzymes are subtly different. That is, SecA2 has a lower solubility in aqueous solutions and requires higher Mg
2+
concentrations for maximal activity. In spite of the high degree of similarity between the
S. gordonii
paralogues, analysis of SecA-SecA2 chimeras indicates that the domains are not readily interchangeable. This suggests that specific, unique contacts between SecA2 and other components of the accessory Sec system may preclude cross-functioning with the canonical Sec system.
Virulence Gene Regulation by the
agr
System in
Clostridium perfringens
Authors: Ohtani Kaori , Yuan Yonghui , Hassan Sufi , Wang Ruoyu , Wang Yun , Shimizu Tohru 
Published: April 2009

ABSTRACT

A gram-positive anaerobic pathogen,
Clostridium perfringens
, causes clostridial myonecrosis or gas gangrene in humans by producing numerous extracellular toxins and enzymes that act in concert to degrade host tissue. The
agr
system is known to be important for the regulation of virulence genes in a quorum-sensing manner in
Staphylococcus aureus
. A homologue for
S. aureus agrBD
(

agrBD
Sa

) was identified in the
C. perfringens
strain 13 genome, and the role of
C. perfringens agrBD
(

agrBD
Cp

) was examined. The

agrBD
Cp

knockout mutant did not express the theta-toxin gene, and transcription of the alpha- and kappa-toxin genes was also significantly decreased in the mutant strain. The mutant strain showed a recovery of toxin production after the addition of the culture supernatant of the wild-type strain, indicating that the

agrBD
Cp

mutant lacks a signal molecule in the culture supernatant. An
agr-virR
double-knockout mutant was constructed to examine the role of the VirR/VirS two-component regulatory system, a key virulence regulator, in

agrBD
Cp

-mediated regulation of toxin production. The double-mutant strain could not be stimulated for toxin production with the wild-type culture supernatant. These results indicate that the

agrBD
Cp

system plays an important role in virulence regulation and also suggest that VirR/VirS is required for sensing of the extracellular signal and activation of toxin gene transcription in
C. perfringens
.
Identification and Characterization of Hemolysin-Like Proteins Similar to RTX Toxin in
Pasteurella pneumotropica
Authors: Sasaki Hiraku , Kawamoto Eiichi , Tanaka Yoshikazu , Sawada Takuo , Kunita Satoshi , Yagami Ken-ichi 
Published: April 2009

ABSTRACT

Pasteurella pneumotropica
is an opportunistic pathogen that causes lethal pneumonia in immunodeficient rodents. The virulence factors of this bacterium remain unknown. In this study, we identified the genes encoding two RTX toxins, designated as
pnxI
and
pnxII
, from the genomic DNA of
P. pneumotropica
ATCC 35149 and characterized with respect to hemolysis. The
pnxI
operon was organized according to the manner in which the genes encoded the structural RTX toxin (
pnxIA
), the type I secretion systems (
pnxIB
and
pnxID
), and the unknown
orf
. The
pnxII
gene was involved only with the
pnxIIA
that coded for a structural RTX toxin. Both the structural RTX toxins of deduced PnxIA and PnxIIA were involved in seven of the RTX repeat and repeat-like sequences. By quantitative PCR analysis of the structural RTX toxin-encoding genes in
P. pneumotropica
ATCC 35149, the gene expression of
pnxIA
was found to have increased from the early log phase, while that of
pnxIIA
increased from the late log to the early stationary phase. As expressed in
Escherichia coli
, both the recombinant proteins of PnxIA and PnxIIA showed weak hemolytic activity in both sheep and murine erythrocytes. On the basis of the results of the Southern blotting analysis, the
pnxIA
gene was detected in 82% of the isolates, while the
pnxIIA
gene was detected in 39%. These results indicate that the products of both
pnxIA
and
pnxIIA
were putative associations of virulence factors in the rodent pathogen
P. pneumotropica
.
Phosphate-Dependent Behavior of the ArchaeonHalobacterium salinarumStrain R1
Authors: Wende Andy , Furtwängler Katarina , Oesterhelt Dieter 
Published: April 2009

ABSTRACTPhosphate is essential for life on earth, since it is an integral part of important biomolecules. The mechanisms applied by bacteria and eukarya to combat phosphate limitation are fairly well understood. However, it is not known how archaea sense phosphate limitation or which genes are regulated upon limitation. We conducted a microarray analysis to explore the phosphate-dependent gene expression ofHalobacterium salinarumstrain R1. We identified a set of 17 genes whose transcript levels increased up to several hundredfold upon phosphate limitation. Analysis of deletion mutants showed that this set of genes, the PHO stimulon, is very likely independent of signaling via two-component systems. Our experiments further indicate that PHO stimulon induction might be dependent on the intracellular phosphate concentration, which turned out to be subject to substantial changes. Finally, the study revealed thatH. salinarumexhibits a phosphate-directed chemotaxis, which is induced by phosphate starvation.
Tourists’ attitudes towards ban on smoking in air-conditioned hotel lobbies in Thailand
Authors: Viriyachaiyo V , Lim A 
Published: April 2009

Background:Thailand is internationally renowned for its stringent tobacco control measures. In Thailand, a regulation banning smoking in air-conditioned hotel lobbies was issued in late 2006, causing substantial apprehension within the hospitality industry. A survey of tourists’ attitudes toward the ban was conducted.Methods:A cross-sectional survey of 5550 travellers staying in various hotels in Bangkok, Surat Thani, Phuket, Krabi and Songkhla provinces, October 2005 to December 2006. Travellers aged 15 years or older with a check-in duration of at least one day and willing to complete the questionnaire were requested by hotel staff to fill in the 5-minute questionnaire at check-in or later at their convenience.Results:Secondhand cigarette smoke was recognised as harmful to health by 89.7% of respondents. 47.8% of travellers were aware of the Thai regulation banning smoking in air-conditioned restaurants. 80.9% of the respondents agreed with the ban, particularly female non-smokers. 38.6% of survey respondents indicated that they would be more likely to visit Thailand again because of the regulation, 53.4% that the regulation would not affect their decision and 7.9% that they would be less likely to visit Thailand again.Conclusion:Banning smoking in air-conditioned hotel lobbies in Thailand is widely supported by tourists. Enforcement of the regulation is more likely to attract tourists than dissuade them from holidaying in Thailand.
Belowground starch consumption after recurrent severe disturbance in three resprouter species of the genusErica
Authors: Paula Susana , Ojeda Fernando 
Published: April 2009

It is generally assumed that belowground starch reserves are consumed partially and gradually after successive resprouting events in resprouter woody plants. We have explored the aboveground (biomass) and belowground (root starch) response of three species of Erica, Erica australis L., Erica scoparia L., and Erica arborea L., after different histories of disturbance intensity to test the existence of a gradual decrease in (i) the final biomass of the aboveground regrowth and (ii) the relative amount of root starch across increasing levels of disturbance frequency. Increasing clipping frequency produced a progressive reduction in the final regrowth in the three species. By contrast, root starch levels dropped markedly in plants of all clipping treatments when compared with root starch of unclipped plants, but significant differences were not detected among clipping frequencies. This pattern was consistent across the three species of Erica. This study highlights a crucial role of belowground (root) starch reserves for postdisturbance regrowth in resprouter species of Erica. It also shows a consistent pattern of rapid, not conservative, consumption of starch reserves after the complete removal of the aboveground part, nearly irrespective of the previous history of disturbance frequency.
Effects of presurgical exercise training on systemic inflammatory markers among patients with malignant lung lesions
Authors: Jones Lee W. , Eves Neil D. , Peddle Carolyn J. , Courneya Kerry S. , Haykowsky Mark , Kumar Vikaash , Winton Timothy W. , Reiman Tony 
Published: April 2009

Systemic inflammation plays an important role in the initiation, promotion, and progression of lung carcinogenesis. The effects of interventions to lower inflammation have not been explored. Accordingly, we conducted a pilot study to explore the effects of exercise training on changes in biomarkers of systemic inflammation among patients with malignant lung lesions. Using a single-group design, 12 patients with suspected operable lung cancer were provided with structured exercise training until surgical resection. Participants underwent cardiopulmonary exercise testing, 6 min walk testing, pulmonary function testing, and blood collection at baseline and immediately prior to surgical resection. Systemic inflammatory markers included intracellular adhesion molecule (ICAM)-1, macrophage inflammatory protein-1α, interleukin (IL)-6, IL-8, monocyte chemotactic protein-1, C-reactive protein, and tumor necrosis factor-α. The overall exercise adherence rate was 78%, with patients completing a mean of 30 ± 25 sessions. Mean peak oxygen consumption increased 2.9 mL·kg–1·min–1 from baseline to presurgery (p = 0.016). Results indicate that exercise training resulted in a significant reduction in ICAM-1 (p = 0.041). Changes in other inflammatory markers did not reach statistical significance. Change in cardiorespiratory fitness was not associated with change in systemic inflammatory markers. This exploratory study provides an initial step for future studies to elucidate the potential role of exercise, as well as identify the underlying mechanisms of action, as a means of modulating the relationship between inflammation and cancer pathogenesis.
Influence of polyphenols on low-loaded synthetic winery wastewater constructed wetland treatment with different plant speciesA paper submitted to the Journal of Environmental Engineering and Science.
Authors: Mena J. , Gómez R. , Villaseñor J. , de Lucas A. 
Published: April 2009

Synthetic wastewaters simulating physically pre-treated low-loaded winery effluents were treated for four months with five pilot-scale horizontal subsurface flow constructed wetlands (HSSF-CWs) using different plants. Species under study were Phragmites australis (HSSF-CW2), Lythrum salicaria (HSSF-CW3), Cladium mariscus (HSSF-CW4), and Iris pseudacorus (HSSF-CW5). The designation HSSF-CW1 was not planted, and was used as a control. The mean dissolved oxygen and oxidation–reduction potential values in all HSSF-CWs indicated anaerobic conditions in the bulk liquid. High pollutant-removal efficiencies were obtained. Apparently, the species with higher growth (Phragmites, Lythrum, and particularly Iris) improved total nitrogen (TN) and nitrogen as ammonium (N-NH4+) removals, but adversely affected sulphate (SO42–) anaerobic reduction. Chemical oxygen demand (COD) removal efficiencies were high, although there were no clear indications how the kinds of plants might have influenced this parameter. A statistical analysis of variance indicated that only N-NH4+ removal efficiencies were statistically different owing to the influence of the different plants. In a second 6 month experimental period, polyphenols (13 mg L–1) were added to the synthetic wastewater to study possible inhibition effects. The addition of polyphenols did not seem to cause inhibition effects on COD, TN, and N-NH4+ removals, but clearly negatively affected SO42– removal. A new two-way analysis of variance confirmed that only SO42– removal was negatively affected by polyphenols, while the effects of the different plants were only significant for N-NH4+ removal. Polyphenols were nearly completely removed. First order rate constants obtained for COD, TN, SO42–, and polyphenol removals were similar to those reported by other authors.
Utilization of zeolite industrial wastewater for removal of copper and zinc from copper-brass pipe industrial wastewaterA paper submitted to the Journal of Environmental Engineering and Science.
Authors: Sreesai Siranee , Sthiannopkao Suthipong 
Published: April 2009

Utilization of zeolite industrial wastewater as a sorbent and (or) precipitant to remove Cu and Zn from copper-brass pipe industrial wastewater was conducted. These wastewaters were sampled and values for pH, temperature, biochemical oxygen demand (BOD5), chemical oxygen demand (COD), total solids (TS), total dissolved solids (TDS), total suspended solids (TSS), and heavy metals were determined. In addition, the sorption isotherms of Cu and Zn in copper-brass pipe industrial wastewater onto solids of zeolite industrial wastewater at various dilutions of copper-brass pipe industrial wastewater were explored. The relationship between Cu and Zn concentrations and their removal efficiencies under different conditions of wastewater pH, contact times, and ratios between copper-brass pipe industrial wastewater and zeolite industrial wastewater was examined. Zeolite industrial wastewater contained various carbonate compounds that contributed to high pH and TDS values, and low heavy metals contamination whereas copper-brass pipe industrial wastewater had a low pH value and was contaminated with heavy metals, especially Cu and Zn. Application of zeolite industrial wastewater significantly increased the pH of copper-brass pipe industrial wastewater and consequently removed Cu and Zn. The increase in pH of the wastewater mixture significantly enhanced the heavy metals removal. The Langmuir equation described sorption isotherms of Cu and Zn onto solids of zeolite industrial wastewater at neutral pH (6–7) while the Freundlich equation fitted well at pH > 12. The maximum Cu (97%–98%) and Zn (92%–96%) removal efficiencies occurred at the original pH 12.8 of zeolite industrial wastewater, at the ratio of copper-brass pipe industrial wastewater to zeolite industrial wastewater 3:1 (vol.:vol.) and at 30 min contact time.
Durability and structural performance of carbon fibre reinforced polymer – reinforced concrete parking garage slabs
Authors: El-Gamal S. , Benmokrane B. , El-Salakawy E. , Cousin P. , Wiseman A. 
Published: April 2009

This paper presents a laboratory investigation on the durability and structural performance of carbon fibre reinforced polymer (CFRP) – reinforced concrete (RC) slab specimens extracted from the Laurier-Taché Parking Garage (in the National Capital Region, Canada) after being subjected to service field conditions for about 8 years (1997–2005). The laboratory investigation comprised two phases. The first phase evaluated the durability of the CFRP bars, the concrete, and the interface between the two materials by conducting microstructural and chemical analyses on core samples extracted from the slabs. As part of this phase, five CFRP bar samples were extracted and tested in tension to investigate if the CFRP bars experienced any degradation in strength or stiffness. The second phase investigated the structural behaviour of the slabs by testing four slab segments (3.0 m long × 1.0 m wide × 0.2 m deep) in flexure. Test results showed that neither the CFRP bars nor the CFRP–RC slabs have been adversely affected after being in service for 8 years.
Structural modeling identified the tRNA-binding domain of Utp8p, an essential nucleolar component of the nuclear tRNA export machinery of Saccharomyces cerevisiae
Authors: McGuire Andrew T. , Keates Robert A.B. , Cook Stephanie , Mangroo Dev 
Published: April 2009

Utp8p is an essential 80 kDa intranuclear tRNA chaperone that transports tRNAs from the nucleolus to the nuclear tRNA export receptors in Saccharomyces cerevisiae . To help understand the mechanism of Utp8p function, predictive tools were used to derive a partial model of the tertiary structure of Utp8p. Secondary structure prediction, supported by circular dichroism measurements, indicated that Utp8p is divided into 2 domains: the N-terminal beta sheet and the C-terminal alpha helical domain. Tertiary structure prediction was more challenging, because the amino acid sequence of Utp8p is not directly homologous to any known protein structure. The tertiary structures predicted by threading and fold recognition had generally modest scores, but for the C-terminal domain, threading and fold recognition consistently pointed to an alpha–alpha superhelix. Because of the sequence diversity of this fold type, no single structural template was an ideal fit to the Utp8p sequence. Instead, a composite template was constructed from 3 different alpha–alpha superhelix structures that gave the best matches to different portions of the C-terminal domain sequence. In the resulting model, the most conserved sequences grouped in a tight cluster of positive charges on a protein that is otherwise predominantly negative, suggesting that the positive-charge cleft may be the tRNA-binding site. Mutations of conserved positive residues in the proposed binding site resulted in a reduction in the affinity of Utp8p for tRNA both in vivo and in vitro. Models were also derived for the 10 fungal homologues of Utp8p, and the localization of the positive charges on the conserved surface was found in all cases. Taken together, these data suggest that the positive-charge cleft of the C-terminal domain of Utp8p is involved in tRNA-binding.
Experimental and numerical studies of the hydromechanical behaviour of a natural unsaturated swelling soil
Authors: Nowamooz H. , Mrad M. , Abdallah A. , Masrouri F. 
Published: April 2009

This paper presents experimental studies performed on a natural swelling soil. Initially, the soil fabric was studied by a mercury porosimetry test, revealing a clear bimodal pore distribution that corresponds to micro- and macrostructural levels. The water-retention curve of the soil was then determined using two suction-imposition techniques: the osmotic and the vapour equilibrium methods. During the main testing program, three successive wetting and drying cycles were applied in a suction range between 0 and 2 MPa under different values of constant vertical net stress using osmotic oedometers. The test samples showed cumulative swelling strains during the cycles. The volumetric strains reached an equilibrium stage, indicating an elastic behaviour of the samples at the end of the suction cycles. Based on these results, the parameters of an elastoplastic model for swelling unsaturated soils (BExM) were derived. This model, implemented in a finite element code (Code_Bright), was applied to a practical problem of a shallow foundation based on a swelling soil. This application studies the effects of hydraulic solicitations on settlements of this foundation. The results show the capacity of the model to solve complex hydromechanically coupled problems.
Nitrifier and denitrifier molecular operational taxonomic unit compositions from sites of a freshwater estuary of Chesapeake Bay
Authors: Fortunato Caroline S. , Carlini David B. , Ewers Evan , Bushaw-Newton Karen L. 
Published: April 2009

Temporal and spatial changes in the molecular operational taxonomic unit (OTU) compositions of bacteria harboring genes for nitrification and denitrification were assessed using denaturing gradient gel electrophoresis (DGGE), clone-based DNA sequencing of selected PCR products, and analyses of ammonium and organic matter concentrations. Sediment, overlying water, and pore-water samples were taken from different vegetated sites of Jug Bay National Estuarine Research Reserve, Maryland, during spring, summer, and fall 2006. OTU richness and the diversities of nitrifiers and denitrifiers were assessed by the presence of bands on DGGE gels, both ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) were seasonally dependent. AOB OTU richness was highest in the summer when NOB richness was decreased, whereas NOB richness was highest in the spring when AOB richness was decreased. The OTU diversities of nitrifiers did not correlate with ammonium concentrations, organic matter concentrations, or the presence of vegetation. The OTU diversities of denitrifiers possessing either the nirK or nosZ genes were not seasonally dependent but were positively correlated with organic matter content (p = 0.0015, r2 = 0.27; p < 0.0001, r2 = 0.39, respectively). Additionally, the presence of vegetation significantly enhanced nosZ species richness (Wilcoxon/Kruskal–Wallis test, p < 0.008), but this trend was not seen for nirK OTU richness. Banding patterns for nirK OTUs were more similar within sites for each season compared with any of the other genes. Over all seasons, nirK OTU richness was highest and AOB and nosZ OTU richness were lowest (Wilcoxon/Kruskal–Wallis test, p < 0.0001). High levels of sequence divergence among cloned nirK PCR products indicate a broad diversity of nirK homologs in this freshwater estuary.