bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysing the Agricultural Costs and Non‐market Benefits of Implementing the Water Framework Directive
Authors: Bateman Ian J. , Brouwer Roy , Davies Helen , Day Brett H. , Deflandre Amelie , Falco Salvatore Di , Georgiou Stavros , Hadley David , Hutchins Michael , Jones Andrew P. , Kay David , Leeks Graham , Lewis Mervyn , Lovett Andrew A. , Neal Colin , Posen Paulette , Rigby Dan , Kerry Turner R. 
Published: June 2006

AbstractImplementation of the Water Framework Directive (WFD) represents a fundamental change in the management of water in Europe with a requirement that member states ensure ‘good ecological status’ for all water bodies by 2015. Agriculture is expected to bear a major share of WFD implementation costs as it is compelled to reduce the emission of diffuse water pollutants. The research outlined here comprises interdisciplinary modelling of agricultural land use, hydrology and consequent water quality effects to consider both agricultural costs and the non‐market recreational use (and potentially non‐use) values that implementation of the Directive may generate. A theme throughout the research is the spatial distribution of the costs and benefits of WFD implementation, which is addressed through the use of GIS techniques in the modelling of agricultural land use, the integration of land use and hydrological models, and the estimation, aggregation and transfer of the economic value of the benefits.
Managing Food Chain Risks: Integrating Technical and Stakeholder Perspectives on Uncertainty
Authors: Shepherd Richard , Barker Gary , French Simon , Hart Andy , Maule John , Cassidy Angela 
Published: June 2006

AbstractWe explore ways for expressing and communicating uncertainties about food risks and the options for including views from different stakeholders, including members of the public, in risk assessment and risk management. Uncertainty is not only a major consideration of technical risk assessments but also needs to be understood within the two‐way interaction with various stakeholders, ranging from specialist risk managers to members of the public. We consider techniques for integration of technical risk assessment methodologies, including measures of the uncertainties, with social science inputs on participation processes, consumer behaviour and effective risk communication. We use case studies representing different types of risk – chemical contamination, and microbial contamination – to focus the discussion. The paper reviews the approach of ongoing interdisciplinary research which is exploring ways of communicating risks and involving members of the public and other stakeholders in defining the interfaces and processes needed.
RELU Special Issue: Editorial Reflections
Authors: Harvey David R. 
Published: June 2006

AbstractThis special issue is special in two major dimensions: the papers range intentionally over a much wider spectrum of social and natural science approaches and disciplines than is normal for the Journal of Agricultural Economics; and, the articles relate to ongoing research rather than completed work. These reflections, perhaps peculiar to a practicing applied economist and policy analyst, concentrate on the lessons to be learned and messages to be heard from the RELU programme, both by those engaged on the programme's research portfolio, and by other researchers.
Dehydroepiandrosterone Alleviates Copulatory Disorder Induced by Social Stress in Male Rats
Authors: Mizuno Tsuyoshi , Yotsuyanagi Satoshi , Nagasaka Yasuhiro , Namiki Mikio 
Published: June 2006

ABSTRACT

Introduction
Social stress induces sexual dysfunction and reduces serum testosterone (T) level in rats. Stressful events exert an influence on a variety of behaviors and physiology through hormonal changes. The mechanism of stress-induced sexual dysfunction is unknown.

Aim
To investigate the role of dehydroepiandrosterone (DHEA) in copulatory behavior induced by social stress in rats.

Methods
Stress-induced male rats were subjected to social stress in which the males lived in a wire-mesh siege located in a colony of male and female rats and were exposed daily to a brief defeat by the colony of males for five consecutive days. After the stress period, copulatory behavior and serum concentrations of DHEA and T were measured.

Main Outcome Measures
The effects of DHEA, T, and NE-100, a selective sigma 1 receptor antagonist, on copulatory behavior following social stress were examined.

Results
The males exhibited a marked suppression of copulatory behavior (elongation of intromission and ejaculation latencies). Serum concentrations of DHEA and T were significantly lower than those in nonstressed control males. Another three groups of social stressed males were injected daily with DHEA, T, or DHEA + NE-100 during the stress period. Injections of DHEA attenuated the stress-induced suppression of copulatory behavior, whereas T had no effect. The combined treatment of NE-100 made DHEA ineffective at restoring copulatory behavior.

Conclusions
These results indicate that DHEA, but not its conversion to T, alleviates the suppressive effect of social stress on copulatory behavior via sigma 1 receptors. We suggest that the decreased endogenous DHEA is involved in copulatory disorders induced by social stress in rats.
Seed Dispersal by Geochelone carbonaria and Geochelone denticulata in Northwestern Brazil1
Authors: Strong Joel N. , Fragoso José M. V. 
Published: June 2006

ABSTRACTThe role of red‐footed tortoises (Geochelone carbonaria) and yellow‐footed tortoises (G. denticulata) as seed dispersal agents was investigated in northwestern Brazil from 5 to 26 January 2002 by analyzing fecal samples for frequency and viability of seed species and estimating daily displacement of tortoises from recaptured and thread‐trailed individuals. Fourteen of 19 fecal samples contained a total of 646 seeds represented by 11 plant species. The most abundant species was Ficus sp. (N= 400) with 100 percent of seeds viable, followed by Aechmea sp. (N = 88) with 93 percent of seeds viable, and Genipa americana (N= 59) with 91 percent of seeds viable. Mean minimum retention time of seeds was 1.6 d and mean daily displacement of tortoises based on recaptured (N= 7) and thread‐trailed tortoises (N= 2) was 57 m. Thus, the diversity and proportion of viable seeds consumed by tortoises, combined with the seed retention times and daily movements, suggest they may be effective dispersal agents. These preliminary findings warrant further investigation into the ecological role of these tortoises in Neotropical ecosystems and their contribution to the maintenance of species diversity and forest structure.
GlnR-Mediated Regulation of Nitrogen Metabolism in
Lactococcus lactis
Authors: Larsen Rasmus , Kloosterman Tomas G. , Kok Jan , Kuipers Oscar P. 
Published: June 2006

ABSTRACT

We show that the nitrogen regulatory protein GlnR of
Lactococcus lactis
represses transcription of the
amtB-glnK
,
glnRA
, and
glnPQ
operons. This likely occurs through a conserved DNA motif, 5′-TGTNA-7N-TNACAT-3′, and takes place in response to extracellular glutamine and ammonium. GlnR-independent repression of
amtB-glnK
is mediated by the pleiotropic nitrogen regulator CodY.
Characterization of the Primary Starch Utilization Operon in the Obligate Anaerobe
Bacteroides fragilis
: Regulation by Carbon Source and Oxygen
Authors: Spence Cheryl , Wells W. Greg , Smith C. Jeffrey 
Published: June 2006

ABSTRACT

The opportunistic pathogen
Bacteroides fragilis
is a commensal organism in the large intestine, where it utilizes both dietary and host-derived polysaccharides as a source of carbon and energy. In this study, a four-gene operon required for starch utilization was identified. The operon also was found to be oxygen responsive and thus was designated
osu
for
o
xygen-induced
s
tarch
u
tilization. The first three genes in the operon were predicted to encode outer membrane proteins involved in starch binding, and a fourth gene,
osuD
, encoded an amylase involved in starch hydrolysis. Insertional mutation of the
osuA
gene (Ω
osuA
) resulted in the inability to utilize starch or glycogen and an insertional mutation into the
osuD
gene (Ω
osuD
) was severely impaired for growth on starch media. Transcriptional studies indicated that maltose, maltooligosaccharides, and starch were inducers of
osu
expression and that maltose was the strongest inducer. A transcriptional activator of
osuABCD
, OsuR, was identified and found to mediate maltose induction. The Ω
osuA
and Ω
osuD
mutants were able to grow on maltose but not starch, whereas a mutation in
osuR
abolished growth on both substrates, indicating that additional genes under the control of OsuR are needed for maltose utilization. The
osuABCD
operon also was induced by exposure to oxygen and was shown to be part of the oxidative stress response important for aerotolerance of
B. fragilis
. Transcriptional analyses showed that
osuA
was induced 20-fold by oxygen, but OsuR was not required for this activation. Analysis of
osu
mutants suggested that expression of the operon was important for survival during oxygen exposure but not to hydrogen peroxide stress.
Spx Is a Global Effector Impacting Stress Tolerance and Biofilm Formation inStaphylococcus aureus
Authors: Pamp Sünje Johanna , Frees Dorte , Engelmann Susanne , Hecker Michael , Ingmer Hanne 
Published: June 2006

ABSTRACTInBacillus subtilis, Spx was recently characterized as a novel type of global regulator whose activity is regulated by the redox status of the cells. In the present study, we demonstrate that inactivation of Spx in the important pathogenStaphylococcus aureusrenders the cells hypersensitive to a wide range of stress conditions including high and low temperature, high osmolarity, and hydrogen peroxide. Moreover, growth was restricted under nonstress conditions. Two-dimensional gel electrophoresis revealed that the proteome of thespxmutant differs substantially from the proteome of wild-type cells, supporting the finding that Spx is also a global regulator inS. aureus. More specifically, we demonstrated that Spx is required for transcription oftrxB, encoding thioredoxin reductase, under all growth conditions examined. AstrxBis essential inS. aureus, we speculate that the severely reducedtrxBtranscription could account for some of the growth defects of thespxmutant. Inactivation ofspxalso enhanced biofilm formation.S. aureusbiofilm formation is associated with the production of the polysaccharide intercellular adhesin encoded by theicaoperon. Interestingly, our data indicate that the augmented capacity of thespxmutant to form biofilms is due to Spx modulating the expression oficaR, encoding a repressor of the structuralicagenes (icaABCD). In summary, we conclude that Spx fulfills an important role for growth, general stress protection, and biofilm formation inS. aureus.
Phosphorylation of the Group A Streptococcal CovR Response Regulator Causes Dimerization and Promoter-Specific Recruitment by RNA Polymerase
Authors: Gusa Asiya A. , Gao Jinxin , Stringer Virginia , Churchward Gordon , Scott June R. 
Published: June 2006

ABSTRACT

The group A streptococcus (GAS),
Streptococcus pyogenes
, is an important human pathogen that causes infections ranging in severity from self-limiting pharyngitis to severe invasive diseases that are associated with significant morbidity and mortality. The pathogenic effects of GAS are mediated by the expression of virulence factors, one of which is the hyaluronic acid capsule (encoded by genes in the
has
operon). The expression of these virulence factors is controlled by the CovR/S (CsrR/S) two-component regulatory system of GAS which regulates, directly or indirectly, the expression of about 15% of the genome. CovR is a member of the OmpR/PhoB family of transcriptional regulators. Here we show that phosphorylation by acetyl phosphate results in dimerization of CovR. Dimerization was not observed using a D53A mutant of CovR, indicating that D53 is the site of phosphorylation in CovR. Phosphorylation stimulated binding of CovR to a DNA fragment containing the promoter of the
has
operon (P
has
) approximately twofold. Binding of CovR D53A mutant protein to P
has
was indistinguishable from the binding of wild-type unphosphorylated CovR. In vitro transcription, using purified GAS RNA polymerase, showed that wild-type CovR repressed transcription, and repression was stimulated more than sixfold by phosphorylation. In the presence of RNA polymerase, binding at P
ha
s of phosphorylated, but not unphosphorylated, CovR was stimulated about fourfold, which accounts for the difference in the effect of phosphorylation on repression versus DNA binding. Thus, regulation of P
has
by CovR is direct, and the degree of repression of P
has
is controlled by the phosphorylation of CovR.
Transcriptional Regulation of the
Borrelia burgdorferi
Antigenically Variable VlsE Surface Protein
Authors: Bykowski Tomasz , Babb Kelly , von Lackum Kate , Riley Sean P. , Norris Steven J. , Stevenson Brian 
Published: June 2006

ABSTRACT

The Lyme disease agent
Borrelia burgdorferi
can persistently infect humans and other animals despite host active immune responses. This is facilitated, in part, by the
vls
locus, a complex system consisting of the
vlsE
expression site and an adjacent set of 11 to 15 silent
vls
cassettes. Segments of nonexpressed cassettes recombine with the
vlsE
region during infection of mammalian hosts, resulting in combinatorial antigenic variation of the VlsE outer surface protein. We now demonstrate that synthesis of VlsE is regulated during the natural mammal-tick infectious cycle, being activated in mammals but repressed during tick colonization. Examination of cultured
B. burgdorferi
cells indicated that the spirochete controls
vlsE
transcription levels in response to environmental cues. Analysis of P
vlsE
::
gfp
fusions in
B. burgdorferi
indicated that VlsE production is controlled at the level of transcriptional initiation, and regions of 5′ DNA involved in the regulation were identified. Electrophoretic mobility shift assays detected qualitative and quantitative changes in patterns of protein-DNA complexes formed between the
vlsE
promoter and cytoplasmic proteins, suggesting the involvement of DNA-binding proteins in the regulation of
vlsE
, with at least one protein acting as a transcriptional activator.
Distinctive Repertoire of Contingency Genes Conferring Mutation- Based Phase Variation and Combinatorial Expression of Surface Lipoproteins in
Mycoplasma capricolum
subsp.
capricolum
of the
Mycoplasma mycoides
Phylogenetic Cluster
Authors: Wise Kim S. , Foecking Mark F. , Röske Kerstin , Lee Young Jin , Lee Young Moo , Madan Anup , Calcutt Michael J. 
Published: June 2006

ABSTRACT

The generation of surface variation among many divergent species of
Mollicutes
(mycoplasmas) occurs through stochastic expression patterns of diverse lipoprotein genes. The size and wide distribution of such variable gene sets in minimal (∼0.6- to 1.4-Mb) mycoplasmal genomes suggest their key role in the adaptation and survival of these wall-less monoderms. Diversity through variable genes is less clearly established among phylogenetically similar mycoplasmas, such as the
Mycoplasma mycoides
cluster of ruminant pathogens, which vary widely in host range and pathobiology. Using (i) genome sequences from two members of this clade,
Mycoplasma capricolum
subsp.
capricolum
and
M. mycoides
subsp.
mycoides
small colony biotype (SC), (ii) antibodies to specific peptide determinants of predicted
M. capricolum
subsp.
capricolum
gene products, and (iii) analysis of the membrane-associated proteome of
M. capricolum
subsp.
capricolum
, a novel set of six genes (
vmcA
to
vmcF
) expressing distinct Vmc (variable
M. capricolum
subsp.
capricolum
) lipoproteins is demonstrated. These occur at two separate loci in the
M. capricolum
subsp.
capricolum
genome, which shares striking overall similarity and gene synteny with the
M. mycoides
subsp.
mycoides
SC genome. Collectively, Vmc expression is noncoordinate and combinatorial, subject to a single-unit insertion/deletion in a 5′ flanking dinucleotide repeat that governs expression of each
vmc
gene. All
vmc
genes share modular regions affecting expression and membrane translocation. In contrast,
vmcA
to
vmcD
genes at one locus express surface proteins with highly structured size-variable repeating domains, whereas
vmcE
to
vmcF
genes express products with short repeats devoid of predicted structure. These genes confer a distinctive, dynamic surface architecture that may represent adaptive differences within this important group of pathogens as well as exploitable diagnostic targets.
Regulation of Type IV Fimbrial Biogenesis in
Dichelobacter nodosus
Authors: Parker Dane , Kennan Ruth M. , Myers Garry S. , Paulsen Ian T. , Songer J. Glenn , Rood Julian I. 
Published: June 2006

ABSTRACT

Type IV fimbriae are expressed by several bacterial pathogens and are essential for virulence in
Dichelobacter nodosus
, which causes ovine footrot. We have identified a two-component signal transduction system (PilR/S) and an alternative sigma factor (σ
54
) that were shown by insertional inactivation to be required for the regulation of fimbrial biogenesis in
D. nodosus
. Western blots showed that in both
pilR
and
rpoN
mutants, fimbrial subunit production was significantly reduced by a process that was shown to occur at a PilR- and σ
54
-dependent promoter. The mutants lacked surface fimbriae, which were shown to be required for the adherence of
D. nodosus
cells to tissue culture monolayers. The reduction in fimbrial subunit production in these mutants also resulted in a concomitant loss of the ability to secrete extracellular proteases. A maltose binding protein-PilR fusion protein was purified and was shown to bind specifically to a region located 234 to 594 bp upstream of the
fimA
transcriptional start point. To determine additional targets of PilR and σ
54
, genome-wide transcriptional profiling was performed using a whole-genome oligonucleotide microarray. The results indicated that PilR and σ
54
regulated genes other than
fimA
; these genes appear to encode surface-exposed proteins whose role in virulence is unknown. In conclusion, this study represents a significant advancement in our understanding of how the ability of
D. nodosus
to cause ovine footrot is regulated, as we have shown that the biogenesis of type IV fimbriae in
D. nodosus
is regulated by a σ
54
-dependent PilR/S system that also indirectly controls protease secretion.
Role of CheB and CheR in the Complex Chemotactic and Aerotactic Pathway of
Azospirillum brasilense
Authors: Stephens Bonnie B. , Loar Star N. , Alexandre Gladys 
Published: June 2006

ABSTRACT

It has previously been reported that the alpha-proteobacterium
Azospirillum brasilense
undergoes methylation-independent chemotaxis; however, a recent study revealed
cheB
and
cheR
genes in this organism. We have constructed
cheB
,
cheR
, and
cheBR
mutants of
A. brasilense
and determined that the CheB and CheR proteins under study significantly influence chemotaxis and aerotaxis but are not essential for these behaviors to occur. First, we found that although cells lacking CheB, CheR, or both were no longer capable of responding to the addition of most chemoattractants in a temporal gradient assay, they did show a chemotactic response (albeit reduced) in a spatial gradient assay. Second, in comparison to the wild type,
cheB
and
cheR
mutants under steady-state conditions exhibited an altered swimming bias, whereas the
cheBR
mutant and the
che
operon mutant did not. Third,
cheB
and
cheR
mutants were null for aerotaxis, whereas the
cheBR
mutant showed reduced aerotaxis. In contrast to the swimming bias for the model organism
Escherichia coli
, the swimming bias in
A. brasilense
cells was dependent on the carbon source present and cells released methanol upon addition of some attractants and upon removal of other attractants. In comparison to the wild type, the
cheB
,
cheR
, and
cheBR
mutants showed various altered patterns of methanol release upon exposure to attractants. This study reveals a significant difference between the chemotaxis adaptation system of
A. brasilense
and that of the model organism
E. coli
and suggests that multiple chemotaxis systems are present and contribute to chemotaxis and aerotaxis in
A. brasilense
.
Functional Identification of Conjugation and Replication Regions of the Tetracycline Resistance Plasmid pCW3 fromClostridium perfringens
Authors: Bannam Trudi L. , Teng Wee Lin , Bulach Dieter , Lyras Dena , Rood Julian I. 
Published: June 2006

ABSTRACTClostridium perfringenscauses fatal human infections, such as gas gangrene, as well as gastrointestinal diseases in both humans and animals. Detailed molecular analysis of the tetracycline resistance plasmid pCW3 fromC. perfringenshas shown that it represents the prototype of a unique family of conjugative antibiotic resistance and virulence plasmids. We have identified the pCW3 replication region by deletion and transposon mutagenesis and showed that the essentialrepgene encoded a basic protein with no similarity to any known plasmid replication proteins. An 11-gene conjugation locus containing 5 genes that encoded putative proteins with similarity to proteins from the conjugative transposon Tn916was identified, although the genes’ genetic arrangements were different. Functional genetic studies demonstrated that two of the genes in this transfer clostridial plasmid (tcp) locus,tcpFandtcpH, were essential for the conjugative transfer of pCW3, and comparative analysis confirmed that thetcplocus was not confined to pCW3. The conjugation region was present on all known conjugative plasmids fromC. perfringens, including an enterotoxin plasmid and other toxin plasmids. These results have significant implications for plasmid evolution, as they provide evidence that a nonreplicating Tn916-like element can evolve to become the conjugation locus of replicating plasmids that carry major virulence genes or antibiotic resistance determinants.
Staphylococcus aureus
Helicase but Not
Escherichia coli
Helicase Stimulates
S. aureus
Primase Activity and Maintains Initiation Specificity
Authors: Koepsell Scott A. , Larson Marilynn A. , Griep Mark A. , Hinrichs Steven H. 
Published: June 2006

ABSTRACT

Bacterial primases are essential for DNA replication due to their role in polymerizing the formation of short RNA primers repeatedly on the lagging-strand template and at least once on the leading-strand template. The ability of recombinant
Staphylococcus aureus
DnaG primase to utilize different single-stranded DNA templates was tested using oligonucleotides of the sequence 5′-CAGA (CA)
5
XYZ (CA)
3
-3′, where XYZ represented the variable trinucleotide. These experiments demonstrated that
S. aureus
primase synthesized RNA primers predominately on templates containing 5′-d(CTA)-3′ or TTA and to a much lesser degree on GTA-containing templates, in contrast to results seen with the
Escherichia coli
DnaG primase recognition sequence 5′-d(CTG)-3′. Primer synthesis was initiated complementarily to the middle nucleotide of the recognition sequence, while the third nucleotide, an adenosine, was required to support primer synthesis but was not copied into the RNA primer. The replicative helicases from both
S. aureus
and
E. coli
were tested for their ability to stimulate either
S. aureus
or
E. coli
primase. Results showed that each bacterial helicase could only stimulate the cognate bacterial primase. In addition,
S. aureus
helicase stimulated the production of full-length primers, whereas
E. coli
helicase increased the synthesis of only short RNA polymers. These studies identified important differences between
E. coli
and
S. aureus
related to DNA replication and suggest that each bacterial primase and helicase may have adapted unique properties optimized for replication.