bluuebunny/crossref_metadata_2025_split huggingface dataset:
Preliminary laboratory investigation of disinfection by‐product precursor removal using an advanced oxidation process
Authors: Murray Christine A. , Parsons Simon A. 
Published: February 2006

AbstractNatural organic matter (NOM) is ubiquitous in surface and ground waters throughout the world. During drinking water treatment, the NOM that remains in treated water can react with chlorine to form disinfection by‐products. It has been shown that titanium dioxide photocatalysis can achieve over 96% reduction in ultraviolet (UV)254 absorbing species such as hydrophobic NOM and over 81% reduction in dissolved organic carbon (DOC). However, an additional filtration stage is required to recover the suspended catalyst before it is suitable for municipal drinking water application. To overcome this problem, we have used immobilised catalysts prepared using chemical sol–gels, and their performance has been assessed during bench‐scale experiments. An immobilised catalyst enables in situ regeneration using UV light and subsequent reuse of the catalyst. In this research, titanium dioxide sol–gels have been used to coat substrates at a laboratory scale. Results showed that the various coatings prepared had different removal efficiencies for both DOC and UV254 absorbance. Maximum removals were 1.336 g/m2 and 89%, respectively.
A decision support system for identifying the habitat quality and rehabilitation potential of urban rivers
Authors: Boitsidis A. J. , Gurnell A. M. , Scott M. , Petts G. E. , Armitage P. D. 
Published: February 2006

AbstractFew habitat survey, classification or assessment methodologies have been developed specifically for urban or heavily engineered rivers, and yet these rivers need careful assessment if management options are to be considered and prioritised in an economically and environmentally effective way. This paper presents a refinement of a previously proposed urban river survey (URS), which is a modification of the Environment Agency's River Habitat Survey. It then describes indices and classifications that have been developed from URS data and that provide a link between the type of engineering applied to a stretch of urban river and its habitat characteristics. Finally, some simple decision trees and scenario‐modelling tools are presented that allow (i) newly surveyed urban stretches to be classified and (ii) some simple scenarios of channel management change to be assessed in order to prioritise management options for stretches of urban river across urban catchments.
Monitoring a flood event in a densely instrumented catchment, the Upper Eden, Cumbria, UK
Authors: Mayes W.M. , Walsh C.L. , Bathurst J.C. , Kilsby C.G. , Quinn P.F. , Wilkinson M.E. , Daugherty A.J. , O'Connell P.E. 
Published: February 2006

AbstractMulti‐day rainfall events appear to be an important cause of recent flooding in the UK. Hydrological data from an extensive, nested hydrometric network in the unregulated, predominantly rural Upper Eden catchment in northern England are presented for one such flood event. These highlight antecedent catchment conditions and the propagation of the multi‐day flood event during February 2004. An assessment of flood response is provided over varying scales and land use between the upland Gais Gill catchment (1.1 km2) and the larger Upper Eden catchment (616 km2). Large spatial variations in rainfall totals are identified from a dense raingauge network during the flood event and are principally related to catchment elevation. High cumulative rainfall totals for the 6‐day event, particularly at upland sites appear to be the exceptional feature of the flood event with return periods in the order of 100 years at some upland gauges. Resultant patterns of flood attenuation and translation are quantified in different areas of the catchment, highlighting the flashy response of the headwater catchments and the attenuated downstream response in the lowland environment. The study forms part of the national Catchment Hydrology And Sustainable Management (CHASM) programme.
Pesticides in groundwater: some observations on temporal and spatial trends
Authors: Lapworth D.J. , Gooddy D.C. , Stuart M.E. , Chilton P.J. , Cachandt G. , Knapp M. , Bishop S. 
Published: February 2006

AbstractFollowing a monitoring programme of private shallow boreholes a total of 22 different pesticides were detected in 14 shallow boreholes in the Triassic Sherwood Sandstone aquifer of south Yorkshire, UK between January 2002 and November 2003. Of the 294 positive detections made, 34% were detected in excess of the permitted concentration value (PCV) (drinking water standard) for individual pesticides. Pesticides were detected in 11 (78%) of the boreholes, and in eight (57%) at concentrations exceeding the PCV on at least one occasion. These findings were complemented by data from deeper boreholes in which concentrations exceeding the PCV were also detected. Pesticide occurrence could be related to landuse; mecoprop and isoproturon were frequently detected at several locations reflecting the arable landuse, dicamba at a golf course, and atrazine, propazine and terbutryn near a railway. Temporal variations have emerged at individual sites and across the study area as the result of extended and frequent monitoring.
An examination of the surface characteristics of activated sludge in relation to bulking during the treatment of paper mill wastewater
Authors: Agridiotis V. , Forster C. F. , Balavoine C. , Wolter C. , Carliell‐Marquet C. 
Published: February 2006

AbstractThe addition of mineral talc, Aquatal®(Toulouse, France), to activated sludge treating paper mill effluents and its effect on settlement characteristics has been investigated. One laboratory study and a full‐scale investigation on a large waste water treatment plant (WWTP) with a capacity of 500.000 population equivalent (p.e.) have been carried out using this mineral. The sludge in the full‐scale plant was filamentous and had specific sludge volume index (SSVI) values in excess of 250. The talc dosing which was adapted to sludge settleability reduced SSVI values by 38%, improved the total suspended solids' concentrations by 86% and reduced the specific sludge load by 34%. In the laboratory‐scale plant, the sludge had SSVI values of 200–260 before treatment and was hydrophilic. The use of Aquatal® at a dose of 0.7 g/g mixed liquor suspended solids (MLSS) took 2 weeks to reduce the SSVI to 78. It also increased the hydrophobicity to a balanced 50%. The use of mineral converted the somewhat diffuse flocs into a compact structure.
JFLOW: a multiscale two‐dimensional dynamic flood model
Authors: Bradbrook Kate 
Published: February 2006

AbstractA multiscale two‐dimensional (2D) dynamic flood model, known as JFLOW, has been developed by JBA Consulting for simulation of overland flooding. This paper first describes the background to the model development before explaining its technical basis. The model is based on a 2D diffusion wave equation and the computational engine has been linked with a geographic information system interface to provide a stand‐alone product. It has been applied on a variety of different scales which are illustrated in a number of example applications.
Biodegradation of domestic wastewater under the simulated conditions of Thailand
Authors: Giri R. R. , Takeuchi J. , Ozaki H. 
Published: February 2006

AbstractSerious concerns have been raised about the sustainability of conventional mechanized linear wastewater treatment systems in the developing world. Bangkok in Thailand is no exception to these concerns, and merits closer examination. This paper is aimed at unveiling the fundamental facts and characteristics relating to the organic degradation potentials of domestic wastewater in Bangkok. It is supported by evidence from simple laboratory experiments in which existing local conditions were simulated. The results showed that greywater‐like qualities of domestic wastewater do predominate in Bangkok, most probably as a result of three main factors: (1) continued use of leaching septic tanks, (2) the tradition of using water after defecation, instead of toilet paper, and (3) high organic degradation potentials under tropical monsoon conditions. Considering the small organic content, coupled with high organic degradation rates of the freshly collected greywater‐based sewage in Bangkok, low‐cost and decentralized natural treatment systems could be far more suitable for environmental sustainability in such tropical monsoon areas than the implementation of large‐scale sewage works.
Trapping of a Spiral-Like Intermediate of the Bacterial Cytokinetic Protein FtsZ
Authors: Michie Katherine A. , Monahan Leigh G. , Beech Peter L. , Harry Elizabeth J. 
Published: February 2006

ABSTRACT

The earliest stage in bacterial cell division is the formation of a ring, composed of the tubulin-like protein FtsZ, at the division site. Tight spatial and temporal regulation of Z-ring formation is required to ensure that division occurs precisely at midcell between two replicated chromosomes. However, the mechanism of Z-ring formation and its regulation in vivo remain unresolved. Here we identify the defect of an interesting temperature-sensitive
ftsZ
mutant (
ts1
) of
Bacillus subtilis
. At the nonpermissive temperature, the mutant protein, FtsZ(Ts1), assembles into spiral-like structures between chromosomes. When shifted back down to the permissive temperature, functional Z rings form and division resumes. Our observations support a model in which Z-ring formation at the division site arises from reorganization of a long cytoskeletal spiral form of FtsZ and suggest that the FtsZ(Ts1) protein is captured as a shorter spiral-forming intermediate that is unable to complete this reorganization step. The
ts1
mutant is likely to be very valuable in revealing how FtsZ assembles into a ring and how this occurs precisely at the division site.
Differential Localization of Mre Proteins with PBP2 in
Rhodobacter sphaeroides
Authors: Slovak Peter M. , Porter Steven L. , Armitage Judith P. 
Published: February 2006

ABSTRACT

In
Rhodobacter sphaeroides
, MreB, MreC, MreD, PBP2, and RodA are encoded at the same locus. The localizations of PBP2, MreB, and MreC, which have all been implicated in the synthesis of the peptidoglycan layer, were investigated under different growth conditions to gain insight into the relationships between these proteins. Immunofluorescence microscopy showed that PBP2 localized to specific sites at the midcell of elongating cells under both aerobic and photoheterotrophic conditions. Visualizing PBP2 at different stages of the cell cycle showed that in elongating cells, PBP2 was found predominately at the midcell, with asymmetric foci and bands across the cell. PBP2 remained at midcell until the start of septation, after which it moved to midcell of the daughter cells. Deconvolution and three-dimensional reconstructions suggested that PBP2 forms a partial ring at the midcell of newly divided cells and elongated cells, while in septating cells, partial PBP2 rings were present at one-quarter and three-quarter positions. Due to the diffraction limits of light microscopy, these partial rings could represent unresolved helices. Colocalization studies showed that MreC always colocalized with PBP2, while MreB colocalized with PBP2 only during elongation; during septation, MreB remained at the septation site, whereas PBP2 relocalized to the one-quarter and three-quarter positions. These results suggest that PBP2 and MreC are involved in peptidoglycan synthesis during elongation and that this occurs at specific sites close to midcell in
R. sphaeroides
.
Integration into the Phage Attachment Site,
attB
, Impairs Multicellular Differentiation in
Stigmatella aurantiaca
Authors: Müller Susanne , Shen Hui , Hofmann Diana , Schairer Hans Ulrich , Kirby John R. 
Published: February 2006

ABSTRACT

Stigmatella aurantiaca
displays a complex developmental life cycle in response to starvation conditions that results in the formation of tree-like fruiting bodies capable of producing spores. The phage Mx8, first isolated from the close relative
Myxococcus xanthus
, is unable to infect
S. aurantiaca
cells and integrate into the genome. However, plasmids containing Mx8 fragments encoding the integrase and
attP
are able to integrate at the
attB
locus in the
S. aurantiaca
genome by site-specific recombination. After recombination between
attP
and
attB
, the
S. aurantiaca
cells were incapable of building normal fruiting bodies but formed clumps and fungus-like structures characteristic of intermediate stages of development displayed by the wild type. We identified two tRNA genes,
trnD
and
trnV
, encoding tRNA
Asp
and tRNA
Val
, respectively, composing an operon at the
attB
locus of
S. aurantiaca
. Integration of
attP
-containing plasmids resulted in the incorporation of the t
Mx8
terminator sequence, in addition to a short sequence of Mx8 DNA downstream of
trnD
. The integrant was unable to process the
trnD
transcript at the normal 3′ processing site and displayed a lower level of expression of the
trnVD
operon. In addition, several developmentally regulated proteins were no longer produced in mutants following insertion at the
attB
locus. We hypothesize that the integration of the t
Mx8
terminator sequence results in reduced levels of mature tRNA
Asp
and tRNA
Val
and that altered protein production during development is thereby responsible for the observed phenotype. The
trnVD
locus thus defines a new developmental checkpoint for
Stigmatella aurantiaca
.
Nla18, a Key Regulatory Protein Required for Normal Growth and Development ofMyxococcus xanthus
Authors: Diodati Michelle E. , Ossa Faisury , Caberoy Nora B. , Jose Ivy R. , Hiraiwa Wataru , Igo Michele M. , Singer Mitchell , Garza Anthony G. 
Published: February 2006

ABSTRACTNtrC-like activators regulate the transcription of a wide variety of adaptive genes in bacteria. Previously, we demonstrated that a mutation in thentrC-like activator genenla18causes defects in fruiting body development inMyxococcus xanthus. In this report, we describe the effect thatnla18inactivation has on gene expression patterns during development and vegetative growth. Gene expression innla18mutant cells is altered in the early stages of fruiting body development. Furthermore,nla18mutant cells are defective for two of the earliest events in development, production of the intracellular starvation signal ppGpp and production of A-signal. Taken together, these results indicate that the developmental program innla18mutant cells goes awry very early. Inactivation ofnla18also causes a dramatic decrease in the vegetative growth rate ofM. xanthuscells. DNA microarray analysis revealed that the vegetative expression patterns of more than 700 genes are altered innla18mutant cells. Genes coding for putative membrane and membrane-associated proteins are among the largest classes of genes whose expression is altered bynla18inactivation. This result is supported by our findings that the profiles of membrane proteins isolated from vegetativenla18mutant and wild-type cells are noticeably different. In addition to genes that code for putative membrane proteins,nla18inactivation affects the expression of many genes that are likely to be important for protein synthesis and gene regulation. Our data are consistent with a model in which Nla18 controls vegetative growth and development by activating the expression of genes involved in gene regulation, translation, and membrane structure.
A Hydrophobic Patch in the Competence-Stimulating Peptide, a Pneumococcal Competence Pheromone, Is Essential for Specificity and Biological Activity
Authors: Johnsborg Ola , Kristiansen Per Eugen , Blomqvist Trinelise , Håvarstein Leiv Sigve 
Published: February 2006

ABSTRACT

Induction of competence for natural genetic transformation in
Streptococcus pneumoniae
depends on pheromone-mediated cell-cell communication and a signaling pathway consisting of the competence-stimulating peptide (CSP), its membrane-embedded histidine kinase receptor ComD, and the cognate response regulator ComE. Extensive screening of pneumococcal isolates has revealed that two major CSP variants, CSP1 and CSP2, are found in members of this species. Even though the primary structures of CSP1 and CSP2 are about 50% identical, they are highly specific for their respective receptors, ComD1 and ComD2. In the present work, we have investigated the structural basis of this specificity by determining the three-dimensional structure of CSP1 from nuclear magnetic resonance data and comparing the agonist activity of a number of CSP1/CSP2 hybrid peptides toward the ComD1 and ComD2 receptors. Our results show that upon exposure to membrane-mimicking environments, the 17-amino-acid CSP1 pheromone adopts an amphiphilic α-helical configuration stretching from residue 6 to residue 12. Furthermore, the pattern of agonist activity displayed by the various hybrid peptides revealed that hydrophobic amino acids, some of which are situated on the nonpolar side of the α-helix, strongly contribute to CSP specificity. Together, these data indicate that the identified α-helix is an important structural feature of CSP1 which is essential for effective receptor recognition under natural conditions.
Role of the
Pseudomonas aeruginosa
PlcH Tat Signal Peptide in Protein Secretion, Transcription, and Cross-Species Tat Secretion System Compatibility
Authors: Snyder Aleksandra , Vasil Adriana I. , Zajdowicz Sheryl L. , Wilson Zachary R. , Vasil Michael L. 
Published: February 2006

ABSTRACT

The secretion of PlcH and its homolog PlcN of
Pseudomonas aeruginosa
through the inner membrane depends upon a functional twin arginine translocase (Tat) system and a Tat signal sequence. Conserved twin arginine (Arg) residues within the Tat signal sequence consensus motif (S/TRRxFLK) are considered essential for the secretion of Tat substrates, but some exceptions (e.g., Lys and Arg) to the twin Arg residues in this motif have been noted. The roles of all three Arg residues within the PlcH RRRTFLK consensus motif were examined. Data are presented which indicate that Arg-9 and Arg-10 are essential for PlcH secretion across the inner membrane, but the mutation of Arg-8 (e.g., to Ala or Ser) had no observable effect on the localization of PlcH. In the signal sequence of PlcH and in all of its homologs in other bacteria, there are basic amino acid residues (Arg, Lys, and Gln) immediately adjacent to the signal peptidase cleavage site (Ala-X-Ala) that are not seen in Sec-dependent signal sequences. The mutation of these basic residues to Ala caused slightly decreased levels of extracellular PlcH, but normal localization was still observed. Deletion of the entire Tat signal sequence of PlcH not only resulted in the absence of detectable extracellular PlcH activity and protein but also caused a substantial decrease in the detectable level of
plcH
mRNA. Finally, data are presented which indicate that
P. aeruginosa
PlcH exhibits cross-species compatibility with the
Escherichia coli
Tat secretion machinery, but only when the
E. coli
Tat machinery is expressed in a
P. aeruginosa
host.
Species- and Strain-Specific Control of a Complex, Flexible Regulon by
Bordetella
BvgAS
Authors: Cummings C. A. , Bootsma H. J. , Relman D. A. , Miller J. F. 
Published: February 2006

ABSTRACT

The
Bordetella
master virulence regulatory system, BvgAS, controls a spectrum of gene expression states, including the virulent Bvg
+
phase, the avirulent Bvg
−
phase, and at least one Bvg-intermediate (Bvg
i
) phase. We set out to define the species- and strain-specific features of this regulon based on global gene expression profiling. Rather than functioning as a switch, Bvg controls a remarkable continuum of gene expression states, with hundreds of genes maximally expressed in intermediate phases between the Bvg
+
and Bvg
−
poles. Comparative analysis of Bvg regulation in
B. pertussis
and
B. bronchiseptica
revealed a relatively conserved Bvg
+
phase transcriptional program and identified previously uncharacterized candidate virulence factors. In contrast, control of Bvg
−
- and Bvg
i
-phase genes diverged substantially between species; regulation of metabolic, transporter, and motility loci indicated an increased capacity in
B. bronchiseptica
, compared to
B. pertussis
, for ex vivo adaptation. Strain comparisons also demonstrated variation in gene expression patterns within species. Among the genes with the greatest variability in patterns of expression, predicted promoter sequences were nearly identical. Our data suggest that the complement of transcriptional regulators is largely responsible for transcriptional diversity. In support of this hypothesis, many putative transcriptional regulators that were Bvg regulated in
B. bronchiseptica
were deleted, inactivated, or unregulated by BvgAS in
B. pertussis
. We propose the concept of a “flexible regulon.” This flexible regulon may prove to be important for pathogen evolution and the diversification of host range specificity.
Chromosomal Integration Mechanism of Infecting Mu Virion DNA
Authors: Au T. K. , Agrawal Pushpa , Harshey Rasika M. 
Published: February 2006

ABSTRACT
DNA transposition is central to the propagation of temperate phage Mu. A long-standing problem in Mu biology has been the mechanism by which the linear genome of an infecting phage, which is linked at both ends to DNA acquired from a previous host, integrates into the new host chromosome. If Mu were to use its well-established cointegrate mechanism for integration (single-strand nicks at Mu ends, joined to a staggered double-strand break in the target), the flanking host sequences would remain linked to Mu; target-primed replication of the linear integrant would subsequently break the chromosome. The absence of evidence for chromosome breaks has led to speculation that infecting Mu might use a cut-and-paste mechanism, whereby Mu DNA is cut away from the flanking sequences prior to integration. In this study we have followed the fate of the flanking DNA during the time course of Mu infection. We have found that these sequences are still attached to Mu upon integration and that they disappear soon after. The data rule out a cut-and-paste mechanism and suggest that infecting Mu integrates to generate simple insertions by a variation of its established cointegrate mechanism in which, instead of a “nick, join, and replicate” pathway, it follows a “nick, join, and process” pathway. The results show similarities with human immunodeficiency virus integration and provide a unifying mechanism for development of Mu along either the lysogenic or lytic pathway.
A
Caulobacter crescentus
Extracytoplasmic Function Sigma Factor Mediating the Response to Oxidative Stress in Stationary Phase
Authors: Alvarez-Martinez Cristina E. , Baldini Regina L. , Gomes Suely L. 
Published: February 2006

ABSTRACT

Alternative sigma factors of the extracytoplasmic function (ECF) subfamily are important regulators of stress responses in bacteria and have been implicated in the control of homeostasis of the extracytoplasmic compartment of the cell. This work describes the characterization of
sigF
, encoding 1 of the 13 members of this subfamily identified in
Caulobacter crescentus
. A
sigF
-null strain was obtained and shown to be severely impaired in resistance to oxidative stress, caused by hydrogen peroxide treatment, exclusively during the stationary phase. Although
sigF
mRNA levels decrease in stationary-phase cells, the amount of σ
F
protein is greatly increased at this stage, indicating a posttranscriptional control. Data obtained indicate that the FtsH protease is either directly or indirectly involved in the control of σ
F
levels, as cells lacking this enzyme present larger amounts of the sigma factor. Increased stability of σ
F
protein in stationary-phase cells of the parental strain and in exponential-phase cells of the
ftsH
-null strain is also demonstrated. Transcriptome analysis of the
sigF
-null strain led to the identification of eight genes regulated by σ
F
during the stationary phase, including
sodA
and
msrA
, which are known to be involved in oxidative stress response.