bluuebunny/crossref_metadata_2025 huggingface dataset:
High-Throughput Quantitative Analysis of the Human Intestinal Microbiota with a Phylogenetic Microarray
Authors: Paliy Oleg , Kenche Harshavardhan , Abernathy Frank , Michail Sonia
Published: April 2009

Gut microbiota carry out key functions in health and participate in the pathogenesis of a growing number of diseases. The aim of this study was to develop a custom microarray that is able to identify hundreds of intestinal bacterial species. We used the Entrez nucleotide database to compile a data set of bacterial 16S rRNA gene sequences isolated from human intestinal and fecal samples. Identified sequences were clustered into separate phylospecies groups. Representative sequences from each phylospecies were used to develop a microbiota microarray based on the Affymetrix GeneChip platform. The designed microbiota array contains probes to 775 different bacterial phylospecies. In our validation experiments, the array correctly identified genomic DNA from all 15 bacterial species used. Microbiota array has a detection sensitivity of at least 1 pg of genomic DNA and can detect bacteria present at a 0.00025% level of overall sample. Using the developed microarray, fecal samples from two healthy children and two healthy adults were analyzed for bacterial presence. Between 227 and 232 species were detected in fecal samples from children, whereas 191 to 208 species were found in adult stools. The majority of identified phylospecies belonged to the classes
Clostridia
and
Bacteroidetes
. The microarray revealed putative differences between the gut microbiota of healthy children and adults: fecal samples from adults had more
Clostridia
and less
Bacteroidetes
and
Proteobacteria
than those from children. A number of other putative differences were found at the genus level.
Differential Utilization of Carbon Substrates by Bacteria and Fungi in Tundra Soil
Authors: Rinnan Riikka , Bååth Erland
Published: April 2009

Little is known about the contribution of bacteria and fungi to decomposition of different carbon compounds in arctic soils, which are an important carbon store and possibly vulnerable to climate warming. Soil samples from a subarctic tundra heath were incubated with
13
C-labeled glucose, acetic acid, glycine, starch, and vanillin, and the incorporation of
13
C into different phospholipid fatty acids (PLFA; indicative of growth) and neutral lipid fatty acids (NLFA; indicative of fungal storage) was measured after 1 and 7 days. The use of
13
C-labeled substrates allowed the addition of substrates at concentrations low enough not to affect the total amount of PLFA. The label of glucose and acetic acid was rapidly incorporated into the PLFA in a pattern largely corresponding to the fatty acid concentration profile, while glycine and especially starch were mainly taken up by bacteria and not fungi, showing that different groups of the microbial community were responsible for substrate utilization. The
13
C-incorporation from the complex substrates (starch and vanillin) increased over time. There was significant allocation of
13
C into the fungal NLFA, except for starch. For glucose, acetic acid, and glycine, the allocation decreased over time, indicating use of the storage products, whereas for vanillin incorporation into fungal NLFA increased during the incubation. In addition to providing information on functioning of the microbial communities in an arctic soil, our study showed that the combination of PLFA and NLFA analyses yields additional information on the dynamics of substrate degradation.
Maternally and Naturally Acquired Antibodies to Shiga Toxins in a Cohort of Calves Shedding Shiga-ToxigenicEscherichia coli
Authors: Fröhlich Julia , Baljer Georg , Menge Christian
Published: April 2009

Calves become infected with Shiga toxin-producingEscherichia coli(STEC) early in life, which frequently results in long-term shedding of the zoonotic pathogen. Little is known about the animals' immunological status at the time of infection. We assessed the quantity and dynamics of maternal and acquired antibodies to Shiga toxins (Stx1 and Stx2), the principal STEC virulence factors, in a cohort of 27 calves. Fecal and serum samples were taken repeatedly from birth until the 24th week of age. Sera, milk, and colostrums of dams were also assessed. STEC shedding was confirmed by detection ofstxin fecal cultures. Stx1- and Stx2-specific antibodies were quantified by Vero cell neutralization assay and further analyzed by immunoblotting. By the eighth week of age, 13 and 15 calves had at least onestx1-type and at least onestx2-type positive culture, respectively. Eleven calves had first positive cultures only past that age. Sera and colostrums of all dams and postcolostral sera of all newborn calves contained Stx1-specific antibodies. Calf serum titers decreased rapidly within the first 6 weeks of age. Only five calves showed Stx1-specific seroconversion. Maternal and acquired Stx1-specific antibodies were mainly directed against the StxA1 subunit. Sparse Stx2-specific titers were detectable in sera and colostrums of three dams and in postcolostral sera of their calves. None of the calves developed Stx2-specific seroconversion. The results indicate that under natural conditions of exposure, first STEC infections frequently coincide with an absence of maternal and acquired Stx-specific antibodies in the animals' sera.
Viability PCR, a Culture-Independent Method for Rapid and Selective Quantification of Viable
Legionella pneumophila
Cells in Environmental Water Samples
Authors: Delgado-Viscogliosi Pilar , Solignac Lydie , Delattre Jean-Marie
Published: April 2009

PCR-based methods have been developed to rapidly screen for
Legionella pneumophila
in water as an alternative to time-consuming culture techniques. However, these methods fail to discriminate between live and dead bacteria. Here, we report a viability assay (viability PCR [v-PCR]) for
L. pneumophila
that combines ethidium monoazide bromide with quantitative real-time PCR (qPCR). The ability of v-PCR to differentiate viable from nonviable
L. pneumophila
cells was confirmed with permeabilizing agents, toluene, or isopropanol. v-PCR suppressed more than 99.9% of the
L. pneumophila
PCR signal in nonviable cultures and was able to discriminate viable cells in mixed samples. A wide range of physiological states, from culturable to dead cells, was observed with 64 domestic hot-water samples after simultaneous quantification of
L. pneumophila
cells by v-PCR, conventional qPCR, and culture methods. v-PCR counts were equal to or higher than those obtained by culture and lower than or equal to conventional qPCR counts. v-PCR was used to successfully monitor in vitro the disinfection efficacy of heating to 70°C and glutaraldehyde and chlorine curative treatments. The v-PCR method appears to be a promising and rapid technique for enumerating
L. pneumophila
bacteria in water and, in comparison with conventional qPCR techniques used to monitor
Legionella
, has the advantage of selectively amplifying only viable cells.
Matrix Metalloproteinases as Drug Targets in Infections Caused by Gram-Negative Bacteria and in Septic Shock
Authors: Vanlaere Ineke , Libert Claude
Published: April 2009

The mammalian immune system is optimized to cope effectively with the constant threat of pathogens. However, when the immune system overreacts, sepsis, severe sepsis, or septic shock can develop. Despite extensive research, these conditions remain the leading cause of death in intensive care units. The matrix metalloproteinases (MMPs) constitute a family of proteases that are expressed in developmental, physiological, and pathological processes and also in response to infections. Studies using MMP inhibitors and MMP knockout mice indicate that MMPs play essential roles in infection and in the host defense against infection. This review provides a brief introduction to some basic concepts of infections caused by gram-negative bacteria and reviews reports describing MMP expression and inhibition, as well as studies with MMP-deficient mice in models of infection caused by gram-negative bacteria and of septic shock. We discuss whether MMPs should be considered novel drug targets in infection and septic shock.
Efflux-Mediated Antifungal Drug Resistance
Authors: Cannon Richard D. , Lamping Erwin , Holmes Ann R. , Niimi Kyoko , Baret Philippe V. , Keniya Mikhail V. , Tanabe Koichi , Niimi Masakazu , Goffeau Andre , Monk Brian C.
Published: April 2009

Fungi cause serious infections in the immunocompromised and debilitated, and the incidence of invasive mycoses has increased significantly over the last 3 decades. Slow diagnosis and the relatively few classes of antifungal drugs result in high attributable mortality for systemic fungal infections. Azole antifungals are commonly used for fungal infections, but azole resistance can be a problem for some patient groups. High-level, clinically significant azole resistance usually involves overexpression of plasma membrane efflux pumps belonging to the ATP-binding cassette (ABC) or the major facilitator superfamily class of transporters. The heterologous expression of efflux pumps in model systems, such Saccharomyces cerevisiae, has enabled the functional analysis of efflux pumps from a variety of fungi. Phylogenetic analysis of the ABC pleiotropic drug resistance family has provided a new view of the evolution of this important class of efflux pumps. There are several ways in which the clinical significance of efflux-mediated antifungal drug resistance can be mitigated. Alternative antifungal drugs, such as the echinocandins, that are not efflux pump substrates provide one option. Potential therapeutic approaches that could overcome azole resistance include targeting efflux pump transcriptional regulators and fungal stress response pathways, blockade of energy supply, and direct inhibition of efflux pumps.
Emergence of the Severe Syndrome and Mortality Associated with Dengue and Dengue-Like Illness: Historical Records (1890 to 1950) and Their Compatibility with Current Hypotheses on the Shift of Disease Manifestation
Authors: Kuno Goro
Published: April 2009

Outbreaks of the severe dengue syndrome, dengue hemorrhagic fever (DHF), emerged beginning in the 1950s, marking a dramatic change in the dengue syndrome. While intense investigations in multiple directions have been conducted for many years to elucidate the intrinsic mechanisms conducive to the development of DHF, no consensus has yet emerged. Meanwhile, relatively little attention has been paid to the occurrence of severe dengue and death prior to the 1950s. This comprehensive review was designed to evaluate outbreak records in the early dengue history to better understand the epidemiologic background and other factors that existed before the emergence of DHF outbreaks. By applying a set of stringent criteria to remove unreliable data as much as possible and by interpreting the results conservatively, a short list of etiologically more reliable outbreaks with high mortality was obtained. The results show that severe dengue syndrome, clinically very much compatible with DHF, occurred far more frequently in multiple locations than it had been assumed before; that the magnitudes of mortality in several outbreaks were not negligible; and that the epidemiologic background features shared among these outbreaks in the early period were, with the exceptions of more limited demographic changes, generally similar to the post-1950 conditions.
Growth at High pH and Sodium and Potassium Tolerance in Media above the Cytoplasmic pH Depend on ENA ATPases in
Ustilago maydis
Authors: Benito Begoña , Garciadeblás Blanca , Pérez-Martín José , Rodríguez-Navarro Alonso
Published: April 2009

Potassium and Na
+
effluxes across the plasma membrane are crucial processes for the ionic homeostasis of cells. In fungal cells, these effluxes are mediated by cation/H
+
antiporters and ENA ATPases. We have cloned and studied the functions of the two ENA ATPases of
Ustilago maydis
,
U. maydis
Ena1 (UmEna1) and UmEna2. UmEna1 is a typical K
+
or Na
+
efflux ATPase whose function is indispensable for growth at pH 9.0 and for even modest Na
+
or K
+
tolerances above pH 8.0. UmEna1 locates to the plasma membrane and has the characteristics of the low-Na
+
/K
+
-discrimination ENA ATPases. However, it still protects
U. maydis
cells in high-Na
+
media because Na
+
showed a low cytoplasmic toxicity. The UmEna2 ATPase is phylogenetically distant from UmEna1 and is located mainly at the endoplasmic reticulum. The function of UmEna2 is not clear, but we found that it shares several similarities with
Neurospora crassa
ENA2, which suggests that endomembrane ENA ATPases may exist in many fungi. The expression of
ena1
and
ena2
transcripts in
U. maydis
was enhanced at high pH and at high K
+
and Na
+
concentrations. We discuss that there are two modes of Na
+
tolerance in fungi: the high-Na
+
-content mode, involving ENA ATPases with low Na
+
/K
+
discrimination, as described here for
U. maydis
, and the low-Na
+
-content mode, involving Na
+
-specific ENA ATPases, as in
Neurospora crassa
.
Formation of Hirano Bodies after Inducible Expression of a Modified Form of an Actin-Cross-Linking Protein
Authors: Reyes Juan F. , Stone Karen , Ramos Jeanie , Maselli Andrew
Published: April 2009

Hirano bodies are cytoplasmic inclusions composed mainly of actin and actin-associated proteins. The formation of Hirano bodies during various neurodegenerative disorders, including Alzheimer's disease and amyotrophic lateral sclerosis, has been reported. Although the underlying molecular mechanisms that lead to the formation of these inclusions in the brain are not known, expression of the C-terminal fragment (CT) (amino acids 124 to 295) from the endogenous 34-kDa actin-binding protein of
Dictyostelium discoideum
leads to the formation of actin inclusions in vivo. In the current study, we report the development of an inducible expression system to study the early phases of Hirano body formation using an inducible promoter system (
rnrB
). By fusing the CT to a green fluorescent protein (CT-GFP), we monitored protein expression and localization by fluorescence microscopy, flow cytometry, and Western blot analysis. We observed an increase in the number and size of inclusions formed following induction of the CT-GFP vector system. Time-lapse microscopy studies revealed that the CT-GFP foci associated with the cell cortex and fused to form a single large aggregate. Transmission electron microscopy further demonstrates that these inclusions have a highly ordered ultrastructure, a pathological hallmark of Hirano bodies observed in postmortem brain samples from patients with various neurodegenerative disorders. Collectively, this system provides a method to visualize and characterize the events that surround early actin inclusion formation in a eukaryotic model.
Matrix Metalloproteinase 9 Plays a Key Role in Lyme Arthritis but Not in Dissemination ofBorrelia burgdorferi
Authors: Heilpern Andrew J. , Wertheim Warren , He Jia , Perides George , Bronson Roderick T. , Hu Linden T.
Published: April 2009

Borrelia burgdorferi, the causative agent of Lyme arthritis, does not produce any exported proteases capable of degrading extracellular matrix despite the fact that it is able to disseminate from a skin insertion site to infect multiple organs. Prior studies have shown thatB. burgdorferiinduces the host protease, matrix metalloproteinase 9 (MMP-9), and suggested that the induction of MMP-9 may allow the organism to disseminate and produce local tissue destruction. We examined the role of MMP-9 in dissemination ofB. burgdorferiand pathogenesis of Lyme arthritis. In a MMP-9−/−mouse model, MMP-9 was not required for the dissemination of the spirochete to distant sites. However, MMP-9−/−exhibited significantly decreased arthritis compared to wild-type mice. The decrease in arthritis was not due to an inability to control infection since the spirochete numbers in the joints were identical. Levels of inflammatory chemokines and cytokines were also similar in MMP-9−/−and wild-type mice. We examined whether decreased inflammation in MMP-9−/−mice may be the result of decreased production of neoattractants by MMP-9-dependent cleavage of collagen. MMP-9 cleavage of type I collagen results in increased monocyte chemoattraction. MMP-9 plays an important role in regulating inflammation in Lyme arthritis, potentially through the cleavage of type I collagen.
Simultaneous Inactivation of Sigma Factors B and D Interferes with Light Acclimation of the Cyanobacterium
Synechocystis
sp. Strain PCC 6803
Authors: Pollari Maija , Ruotsalainen Virpi , Rantamäki Susanne , Tyystjärvi Esa , Tyystjärvi Taina
Published: April 2009

In cyanobacteria, gene expression is regulated mainly at the level of transcription initiation, which is mediated by the RNA polymerase holoenzyme. The RNA polymerase core is catalytically active, while the σ factor recognizes promoter sequences. Group 2 σ factors are similar to the principal σ factor but are nonessential. Group 2 σ factors SigB and SigD are structurally the most similar σ factors in
Synechocystis
sp. strain PCC 6803. Under standard growth conditions, simultaneous inactivation of
sigB
and
sigD
genes did not affect the growth, but the photosynthesis and growth of the Δ
sigBD
strain were slower than in the control strain at double light intensity. Light-saturated electron transfer rates and the fluorescence and thermoluminescence measurements showed that photosynthetic light reactions are fully functional in the Δ
sigBD
strain, but absorption and 77 K emission spectra measurements suggest that the light-harvesting system of the Δ
sigBD
strain does not acclimate normally to higher light intensity. Furthermore, the Δ
sigBD
strain is more sensitive to photoinhibition under bright light because impaired upregulation of
psbA
genes leads to insufficient PSII repair.
GerO, a Putative Na
+
/H
+
-K
+
Antiporter, Is Essential for Normal Germination of Spores of the Pathogenic Bacterium
Clostridium perfringens
Authors: Paredes-Sabja Daniel , Setlow Peter , Sarker Mahfuzur R.
Published: April 2009

The genome of the pathogen
Clostridium perfringens
encodes two proteins, GerO and GerQ, homologous to monovalent cation transporters suggested to have roles in the germination of spores of some
Bacillus
species. GerO and GerQ were able to transport monovalent cations (K
+
and/or Na
+
) in
Escherichia coli
, and
gerO
and
gerQ
were expressed only in the mother cell compartment during
C. perfringens
sporulation.
C. perfringens
spores lacking GerO were defective in germination with a rich medium, KCl,
l
-asparagine, and a 1:1 chelate of Ca
2+
and dipicolinic acid (DPA), but not with dodecylamine, and the defect was prior to DPA release in germination. All defects in
gerO
spores were complemented by ectopic expression of wild-type
gerO
. Loss of GerQ had much smaller effects on spore germination, and these effects were most evident in spores also lacking GerO. A modeled structure of GerO was similar to that of the
E. coli
Na
+
/H
+
antiporter NhaA, and GerO, but not GerQ contained two adjacent Asp residues thought to be important in the function of this group of cation transporters. Replacement of these adjacent Asp residues in GerO with Asn reduced the protein's ability to complement the germination defect in
gerO
spores but not the ability to restore cation transport to
E. coli
cells defective in K
+
uptake. Together, these data suggest that monovalent cation transporters play some role in
C. perfringens
spore germination. However, it is not clear whether this role is directly in germination or perhaps in spore formation.
Inhibition of Selenium Metabolism in the Oral Pathogen
Treponema denticola
Authors: Jackson-Rosario Sarah , Self William T.
Published: April 2009

In this report we provide evidence that the antimicrobial action of stannous salts and a gold drug, auranofin, against
Treponema denticola
is mediated through inhibition of the metabolism of selenium for synthesis of selenoproteins.
RemA (YlzA) and RemB (YaaB) Regulate Extracellular Matrix Operon Expression and Biofilm Formation inBacillus subtilis
Authors: Winkelman Jared T. , Blair Kris M. , Kearns Daniel B.
Published: April 2009

Biofilms are multicellular aggregates stabilized by an extracellular matrix. InBacillus subtilis, the biofilm matrix is composed of an extracellular polysaccharide and the secreted protein TasA. Expression of both of the matrix components is repressed by the DNA-binding master regulator, SinR. Here we identify two small protein regulators of the extracellular matrix: RemA (formerly YlzA) and RemB (formerly YaaB). Mutation of RemA or RemB impairs pellicle formation, complex colony architecture, and motility inhibition in asinRmutant background. Both proteins are required for the activation of the matrix biosynthesis operons and appear to act in parallel to SinR and two other known biofilm regulators, AbrB and DegU.
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

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

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

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

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

Phosphate 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.
Chromosome evolution in wild oat grasses (Aveneae) revealed by molecular phylogeny
Authors: Winterfeld Grit , Döring Elke , Röser Martin
Published: April 2009

Karyotype structures revealed by in situ hybridization with ribosomal and satellite DNAs and fluorochrome staining of AT- or GC-rich regions are reported for 23 diploid to tetraploid taxa of Aveneae genera Arrhenatherum , Avena , Helictotrichon , and Pseudarrhenatherum . Chromosomal features are compared with a molecular phylogeny generated on nuclear ribosomal (ITS, 5S) and chloroplast (matK) DNA sequences. Ancestral chromosomal character states are (1) two satellite chromosomes per set of x = 7, (2) 5S rDNA localized in nonsatellite chromosomes, (3) large chromosomes with (4) rather equal lengths of their respective chromosome arms, (5) sets with strong variance of chromosome lengths, (6) absence or small amounts of heterochromatin, and (7) absence or no detectable amplification of the satellite DNAs tested. Overall, most karyotype characteristics are species specific, but common patterns were found for the species of two large subgenera of Helictotrichon. Pseudarrhenatherum, although nested in the molecular phylogeny within Helictotrichon subgenus Helictotrichon, deviates strongly in karyotype characters such as Arrhenatherum as sister of Avena. The karyotype of Helictotrichon jahandiezii , sister to the clade of Helictotrichon subgenera Helictotrichon, Avena, and Arrhenatherum, strongly resembles that of Avena macrostachya . Karyotype features suggest that perennial A. macrostachya and H. jahandiezii are close to the C-genome species of annual Avena, whereas the Avena A genome resembles that of Arrhenatherum.
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.
A fuzzy logic model for biogas generation in bioreactor landfillsA paper submitted to the Journal of Environmental Engineering and Science.
Authors: Abdallah Mohamed , Fernandes Leta , Warith Mostafa , Rendra Septa
Published: April 2009

A fuzzy logic model was developed to simulate the effect of leachate recirculation and sludge addition on the biogas generation in anaerobic bioreactor landfills. The model was designed using a fuzzy logic system (FLS) which incorporated 3 input variables (time, leachate recirculation, and sludge addition) and a single manipulated output (biogas generation rate). The biogas production rate was measured during the experiment and was increasing proportionally with the rate of both leachate recirculation and sludge addition. The experimental work involved the operation of six simulated laboratory-scale bioreactors for over a year under different operating schemes. The experimental results were employed in formulating the fuzzy rule base, calibrating the model, and verifying its predictions. Then, the model was validated against other measured data that was compiled from published studies. The FLS model simulations demonstrated high correlation with the experimental observations.
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.
Amiodarone induces stress responses and calcium flux mediated by the cell wall inSaccharomyces cerevisiae
Authors: Courchesne William E. , Tunc Meral , Liao Sha
Published: April 2009

We used a proteomic approach to study effects of amiodarone on cells of the yeast Saccharomyces cerevisiae. Amiodarone has been shown to have antifungal activity in vitro and causes a massive increase in cytoplasmic calcium levels ([Ca2+]cyt). Proteomic analysis of cells exposed to amiodarone show that this drug elicits stress responses and points to involvement of proteins associated with the cell wall. We tested several of those proteins for involvement in the Ca2+flux. In particular, the amiodarone-induced Ca2+flux was decreased in bgl2Δ cells, which have altered levels of β-glucan and chitin. The involvement of the cell wall in the Ca2+flux induced by amiodarone treatment was tested by addition of yeast cell-wall components. While mannan inhibited the rise in [Ca2+]cyt, β-glucan potentiated the Ca2+flux by 4.5-fold, providing evidence that the cell wall is directly involved in controlling this Ca2+flux. This conclusion is corroborated by the inhibition of the Ca2+flux by calcofluor, which is known to bind to cell-wall chitin and inhibit cell growth. Zymolyase treatment altered the kinetics of amiodarone-induced calcium flux and uncoupled the inhibitory effect of calcofluor. These effects demonstrate that the cell-wall β-glucan regulates calcium flux elicited by amiodarone.