bluuebunny/crossref_metadata_2025_split huggingface dataset:
Managing the UK Grey Partridge Perdix perdix recovery: population change, reproduction, habitat and shooting
Authors: AEBISCHER NICHOLAS J. , EWALD JULIE A. 
Published: November 2004

In 1995, the UK Government designated the Grey Partridge Perdix perdix as a priority species under its Biodiversity Action Plan (BAP). The Game Conservancy Trust (GCT), nominated as lead partner for the species, launched a programme to help Grey Partridge recovery by (1) raising awareness among the shooting and farming communities, (2) encouraging land managers and local BAP groups to conserve Partridges by setting numerical targets and offering feedback from counts on how to increase numbers, and (3) motivating by example by setting up a site demonstrating management techniques and the increase in Partridge abundance that ensues. Building on past research, we quantify the amount of habitat management required to achieve the BAP targets of halting the decline and achieving population recovery. Using three major GCT databases, (1) the National Gamebag Census, which collates data on shooting bags and gamebird releasing in the UK, (2) the Partridge Count Scheme, which monitors national Partridge density and reproduction, and (3) the Sussex Study, which monitors local Partridge population dynamics over 37 years, we emphasize the importance of good breeding success for increasing densities, review the evidence that management can be successful and evaluate the impact of shooting on Grey Partridge conservation.
The breeding ecology of Reed Buntings Emberiza schoeniclus in farmland and wetland habitats in lowland England
Authors: BRICKLE NICK W. , PEACH WILL J. 
Published: November 2004

We studied the nesting and feeding ecology of Reed Buntings Emberiza schoeniclus breeding on farmland and wetland habitats along the Trent Valley in Nottinghamshire, England. Rank and emergent vegetation accounted for most nests and most foraging by provisioning adults. Caterpillars and spiders accounted for 70% of chick invertebrate prey and all broods were fed cereal grain or other vegetable matter. Variation in the abundance of key invertebrate prey across habitats accounted for the foraging preferences of adult buntings. Depredation was the main cause of nest failure, and survival of nests at the egg stage was positively related to the extent of nest concealment. A measure of total brood biomass was positively related to the abundance of key invertebrate prey within 100 m of nests. Rank and emergent vegetation provided Reed Buntings with greater nest concealment and a richer source of invertebrate prey than agricultural habitats such as set‐aside, cereals and oilseed rape. The provision of rank and emergent vegetation on farmland is likely to increase the nesting opportunities and productivity of Reed Buntings in agricultural landscapes.
Sustainable Arable Farming For an Improved Environment (SAFFIE): managing winter wheat sward structure for Skylarks Alauda arvensis
Authors: MORRIS ANTONY J. , HOLLAND JOHN M. , SMITH BARBARA , JONES NAOMI E. 
Published: November 2004

Research has shown a close correlation between the decline of the UK Skylark Alauda arvensis population and the replacement of spring‐sown cereals with winter‐sown varieties, in which advanced sward development prevents successful multiple nesting attempts and reduces access for foraging. Widescale reversal of sowing times is unlikely for commercial reasons, so research has recently focused on ways of manipulating the sward structure of winter wheat to prolong access to nest‐sites and food. An RSPB pilot study investigated leaving small ‘undrilled patches’ in otherwise conventionally managed winter wheat crops. This option was later incorporated into a fully replicated experimental design, as part of the Sustainable Arable Farming For an Improved Environment (SAFFIE) project. This large consortium‐led project aims to test solutions for improving biodiversity within winter‐cereal‐dominated rotations. The experiment described here ran over 2002–3, with three field‐scale ‘treatments’ on 15 sites in the first year. The treatments compare (1) conventional winter wheat, (2) winter wheat sown in double‐normal width (25 cm) wide‐spaced rows (WSR) and (3) winter wheat with two 4‐m by 4‐m undrilled patches per hectare (UP). Results from the 2002 breeding season showed that undrilled patch treatments supported more breeding Skylarks for longer, most likely by aiding accessibility of food. WSR rows were little used by Skylarks and did not improve the abundance of favoured seed and invertebrate food items over conventional crops. Nesting performance and foraging patterns are discussed with reference to invertebrate food abundance and its accessibility, as determined by sward structure.
Bullfinch Pyrrhula pyrrhula breeding ecology in lowland farmland and woodland: comparisons across time and habitat
Authors: PROFFITT FIONA M. , NEWTON IAN , WILSON JEREMY D. , SIRIWARDENA GAVIN M. 
Published: November 2004

Bullfinch Pyrrhula pyrrhula populations decreased by 33% in Britain over the years 1977–82, the period of steepest decline. The timing of this decline and its greater severity on farmland (−65%) than in woodland (−28%) point to agricultural intensification as a likely environmental cause, but previous analyses of survival rate and breeding success data have not been able to identify a clear demographic mechanism. As part of an investigation into the causes of the decline of Bullfinch populations, we conducted an intensive study of breeding phenology and success in farmland and woodland habitats of Oxfordshire and neighbouring counties in 1999–2001, using a combination of nest monitoring and autumn mist‐netting. Breeding success data were supplemented with nest record and mist‐net capture data collected in the same geographical area during the 1960s and 1990s to compare pre‐ and post‐decline productivity. We found a change in the distribution of first‐egg dates, with median first‐egg dates 17–18 days later in the 1990s. This reflected a change in the centre of gravity of the breeding season rather than the timing of its start and end, with proportionally fewer birds laying in May and early June, and proportionally more between then and the end of July. We found no significant difference in any aspect of productivity per breeding attempt between the two periods, although there was a trend towards higher egg period failure rates in the 1990s. October age ratios indicated higher annual productivity in the 1990s. We found no significant differences between farmland and woodland in Bullfinch breeding success or timing of breeding. The cause of the decline of Bullfinch populations in both woodland and farmland, and the greater severity of the decline in farmland, seems more likely to be found in: (a) the impacts of habitat deterioration on breeding densities, (b) constraints on survival probability outside the breeding season and/or (c) the impacts of increasing populations of Sparrowhawks Accipiter nisus on the ability of Bullfinches to exploit resources in some habitats. Further investigation of the breeding ecology and phenology of Bullfinches would best be focused on understanding the causes and possible demographic consequences of the shift in first‐egg date distribution in favour of later‐summer nesting attempts.
Effects of habitat on the use of supplementary food by farmland birds in winter
Authors: SIRIWARDENA GAVIN M. , STEVENS DANAË K. 
Published: November 2004

Providing supplementary food for seed‐eating birds in winter is likely to be a key strategy, in some form, in future efforts to conserve farmland biodiversity. We present interim analyses of data on the bird use of artificial feeding sites under the RSPB‐led BirdAid project and the BTO‐led Winter Food for Birds (WFFB) project, investigating the influence of the habitat context at the local and landscape scales on the use of supplementary food by Yellowhammer Emberiza citrinella, Corn Bunting Miliaria calandra, Tree Sparrow Passer montanus, House Sparrow Passer domesticus, Chaffinch, Fringilla coelebs, Greenfinch Carduelis chloris, Goldfinch C. carduelis and Reed Bunting Emberiza schoeniclus. Our results reveal species‐specificity, rather than general patterns, in relationships between habitat variables and counts. The responses of the only species for which both BirdAid and WFFB provided data, the Yellowhammer, differed between the projects, suggesting that the results were not geographically general. The results fail to indicate justifiable firm habitat prescriptions for site locations that would suit a number of species. Clearer patterns were apparent in results with respect to areas of major habitats in the landscapes surrounding feeding sites, which suggested that local abundance could have an important effect on the use of supplementary food. Future analyses of data from these projects will attempt to separate the competing probable habitat influences on local bird abundance and alternative resource availability.
ARCHAEOMETRIC ANALYSES ON ‘CORINTHIAN B’ TRANSPORT AMPHORAE FOUND AT GELA (SICILY, ITALY)*
Authors: BARONE G. , CRUPI V. , GALLI S. , LONGO F. , MAJOLINO D. , MAZZOLENI P. , SPAGNOLO G. 
Published: November 2004

The aim of this work is to throw light on the archaic production of ‘Corinthian B’ amphorae, which are widely diffused in the Western Mediterranean basin and are also present in Greece, but whose geographical provenance is still under discussion. We analysed a group of 37 samples belonging to different ceramic classes dated to the sixth and fifth centuries bc. In particular, there were 19 sherds of trade amphorae of the so‐called archaic ‘Corinthian B’ type, from archaeological excavations in Gela (Sicily, Italy). As a comparison, we also investigated 18 samples of tiles and local coarse pottery from Sibari (Calabria, Italy). The samples were analysed using different techniques, such as optical analysis with a polarized‐light microscope (OM), X‐ray diffraction (XRD), Fourier transform–infrared absorption (FT–IR) and inductively coupled plasma–optical emission spectroscopy (ICP–OES). The combination of these complementary analytical methods allowed us to characterize the samples, determine their firing temperatures and identify the probable provenance. The study of thin sections of sherds by OM allowed us to divide the investigated amphorae into two main groups: the first was characterized by a composition that suggested a Western provenance, in particular from the Calabrian–Peloritan region; the second one was very similar to the ‘Corinthian B’ amphorae that come from Corinth and have been classified as ‘fabric class 1’ by

Whitbread (1995

). The XRD and FT–IR results permitted us to determine the mineral composition of the findings and to estimate their firing temperature. The ICP–OES technique was particularly useful in identifying the production centres. In fact, in the studied pottery, this analysis revealed Ni and Cr values that were noticeably different between Greek and southern Italian production.
Genetic Characterization of the Bile Salt Response in
Lactobacillus plantarum
and Analysis of Responsive Promoters In Vitro and In Situ in the Gastrointestinal Tract
Authors: Bron Peter A. , Marco Maria , Hoffer Sally M. , Van Mullekom Esther , de Vos Willem M. , Kleerebezem Michiel 
Published: November 2004

ABSTRACT

In this paper we describe the growth, morphological, and genetic responses of
Lactobacillus plantarum
WCFS1 to bile. Growth experiments revealed that a stepwise increase in the porcine bile concentration led to a gradual decrease in the maximal growth rate. Moreover, the final density reached by an
L. plantarum
culture growing in MRS containing 0.1% bile was approximately threefold lower than that in MRS lacking bile. The morphology of the cells grown in MRS containing 0.1% bile was investigated by scanning electron microscopy, which revealed that cells clumped together and had rough surfaces and that some of the cells had a shrunken and empty appearance, which clearly contrasted with the characteristic rod-shaped, smooth-surface morphology of
L. plantarum
cells grown in MRS without bile. An
alr
complementation-based genome-wide promoter screening analysis was performed with
L. plantarum
, which led to identification of 31 genes whose expression was potentially induced by 0.1% porcine bile. Remarkably, 11 membrane- and cell wall-associated functions appeared to be induced by bile, as were five functions involved in redox reactions and five regulatory factors. Moreover, the lp_0237 and lp_0775 genes, identified here as genes that are inducible by bile in vitro, were previously identified in our laboratory as important for
L. plantarum
in vivo during passage in the mouse gastrointestinal tract (P. A. Bron, C. Grangette, A. Mercenier, W. M. de Vos, and M. Kleerebezem, J. Bacteriol.
186:
5721-5729, 2004). A quantitative reverse transcription-PCR approach focusing on these two genes confirmed that the expression level of lp_0237 and lp_0775 was significantly higher in cells grown in the presence of bile and cells isolated from the mouse duodenum than in cells grown on laboratory medium without bile.
Transcriptional Activation of
sclA
by Mga Requires a Distal Binding Site in
Streptococcus pyogenes
Authors: Almengor Audry C. , McIver Kevin S. 
Published: November 2004

ABSTRACT

Streptococcus pyogenes
(the group A streptococcus [GAS]) is a medically significant pathogen of humans, causing a range of diseases from pharyngitis to necrotizing fasciitis. Several important GAS virulence genes are under the control of a pleiotropic regulator called Mga, or the multiple gene regulator of GAS, including the gene encoding the streptococcal collagen-like protein, or
sclA
. Analysis of the genome sequence upstream of
sclA
revealed two potential Mga-binding sites with homology to the published Mga-binding element, which were called P
sclA
-I (distal) and P
sclA
-II (proximal) based on their location relative to a predicted start of transcription. Primer extension was used to confirm that the Mga-dependent transcriptional start site for
sclA
was located adjacent to the proximal P
sclA
-II binding site. By using overlapping P
sclA
promoter probes and purified Mga-His fusion protein, it was shown by electrophoretic mobility shift assays that, unlike other Mga-regulated promoters, Mga binds only to a distal DNA-binding site (P
sclA
-I). Binding of Mga to P
sclA
-I could be competed with cold probes corresponding to known Mga-regulated promoters (P
emm
, P
scpA
, and P
mga
) but not with a nonspecific probe or the proximal P
sclA
-II fragment. With the use of a plasmid-based green fluorescent protein transcriptional reporter system, the full-length P
sclA
was not sufficient to reproduce normal Mga-regulated activation. However, studies using a single-copy
gusA
transcriptional reporter system integrated at the native
sclA
chromosomal locus clearly demonstrated that the distal P
sclA
-I binding site is required for Mga regulation. Therefore, P
sclA
represents a new class of Mga-regulated promoters that requires a single distal binding site for activation.
Physiological and Gene Expression Analysis of Inhibition of
Desulfovibrio vulgaris
Hildenborough by Nitrite
Authors: Haveman Shelley A. , Greene E. Anne , Stilwell Claire P. , Voordouw Johanna K. , Voordouw Gerrit 
Published: November 2004

ABSTRACT

A
Desulfovibrio vulgaris
Hildenborough mutant lacking the
nrfA
gene for the catalytic subunit of periplasmic cytochrome
c
nitrite reductase (NrfHA) was constructed. In mid-log phase, growth of the wild type in medium containing lactate and sulfate was inhibited by 10 mM nitrite, whereas 0.6 mM nitrite inhibited the
nrfA
mutant. Lower concentrations (0.04 mM) inhibited the growth of both mutant and wild-type cells on plates. Macroarray hybridization indicated that nitrite upregulates the
nrfHA
genes and downregulates genes for sulfate reduction enzymes catalyzing steps preceding the reduction of sulfite to sulfide by dissimilatory sulfite reductase (DsrAB), for two membrane-bound electron transport complexes (
qmoABC
and
dsrMKJOP
) and for ATP synthase (
atp
). DsrAB is known to bind and slowly reduce nitrite. The data support a model in which nitrite inhibits DsrAB (apparent dissociation constant

K
m

for nitrite = 0.03 mM), and in which NrfHA (

K
m

for nitrite = 1.4 mM) limits nitrite entry by reducing it to ammonia when nitrite concentrations are at millimolar levels. The gene expression data and consideration of relative gene locations suggest that QmoABC and DsrMKJOP donate electrons to adenosine phosphosulfate reductase and DsrAB, respectively. Downregulation of
atp
genes, as well as the recorded cell death following addition of inhibitory nitrite concentrations, suggests that the proton gradient collapses when electrons are diverted from cytoplasmic sulfate to periplasmic nitrite reduction.
Two Outer Membrane Proteins Are Required for Maximal Type I Secretion of the
Caulobacter crescentus
S-Layer Protein
Authors: Toporowski Michael C. , Nomellini John F. , Awram Peter , Smit John 
Published: November 2004

ABSTRACT

Transport of RsaA, the crystalline S-layer subunit protein of
Caulobacter crescentus
, is mediated by a type I secretion mechanism. Two proteins have been identified that play the role of the outer membrane protein (OMP) component in the RsaA secretion machinery. The genes
rsaF
a
and
rsaF
b
were identified by similarity to the
Escherichia coli
hemolysin secretion OMP TolC by using the
C. crescentus
genome sequence. The
rsaF
a
gene is located several kilobases downstream of the other transporter genes, while
rsaF
b
is completely unlinked. An
rsaF
a
knockout had ∼56% secretion compared to wild-type levels, while the
rsaF
b
knockout reduced secretion levels to ∼79%. When expression of both proteins was eliminated, there was no RsaA secretion, but a residual level of ∼9% remained inside the cell, suggesting posttranslational autoregulation. Complementation with either of the individual
rsaF
genes by use of a multicopy vector, which resulted in 8- to 10-fold overexpression of the proteins, did not restore RsaA secretion to wild-type levels, indicating that both
rsaF
genes were required for full-level secretion. However, overexpression of

rsaF
a

(with normal
rsaF
b
levels) in concert with overexpression of
rsaA
resulted in a 28% increase in RsaA secretion, indicating a potential for significantly increasing expression levels of an already highly expressing type I secretion system. This is the only known example of type I secretion requiring two OMPs to assemble a fully functional system.
Phenylphosphate Synthase: a New Phosphotransferase Catalyzing the First Step in Anaerobic Phenol Metabolism in
Thauera aromatica
Authors: Schmeling Sirko , Narmandakh Ariun , Schmitt Oliver , Gad'on Nasser , Schühle Karola , Fuchs Georg 
Published: November 2004

ABSTRACT

The anaerobic metabolism of phenol in the beta-proteobacterium
Thauera aromatica
proceeds via
para
-carboxylation of phenol (biological Kolbe-Schmitt carboxylation). In the first step, phenol is converted to phenylphosphate which is then carboxylated to 4-hydroxybenzoate in the second step. Phenylphosphate formation is catalyzed by the novel enzyme phenylphosphate synthase, which was studied. Phenylphosphate synthase consists of three proteins whose genes are located adjacent to each other on the phenol operon and were overproduced in
Escherichia coli
. The promoter region and operon structure of the phenol gene cluster were investigated. Protein 1 (70 kDa) resembles the central part of classical phosphoenolpyruvate synthase which contains a conserved histidine residue. It catalyzes the exchange of free [
14
C]phenol and the phenol moiety of phenylphosphate but not the phosphorylation of phenol. Phosphorylation of phenol requires protein 1, MgATP, and another protein, protein 2 (40 kDa), which resembles the N-terminal part of phosphoenol pyruvate synthase. Proteins 1 and 2 catalyze the following reaction: phenol + MgATP + H
2
O→phenylphosphate + MgAMP + orthophosphate. The phosphoryl group in phenylphosphate is derived from the β-phosphate group of ATP. The free energy of ATP hydrolysis obviously favors the trapping of phenol (

K
m

, 0.04 mM), even at a low ambient substrate concentration. The reaction is stimulated severalfold by another protein, protein 3 (24 kDa), which contains two cystathionine-β-synthase domains of unknown function but does not show significant overall similarity to known proteins. The molecular and catalytic features of phenylphosphate synthase resemble those of phosphoenolpyruvate synthase, albeit with interesting modifications.
Bacteriophage and Phenotypic Variation in
Pseudomonas aeruginosa
Biofilm Development
Authors: Webb Jeremy S. , Lau Mathew , Kjelleberg Staffan 
Published: November 2004

ABSTRACT

A current question in biofilm research is whether biofilm-specific genetic processes can lead to differentiation in physiology and function among biofilm cells. In
Pseudomonas aeruginosa
, phenotypic variants which exhibit a small-colony phenotype on agar media and a markedly accelerated pattern of biofilm development compared to that of the parental strain are often isolated from biofilms. We grew
P. aeruginosa
biofilms in glass flow cell reactors and observed that the emergence of small-colony variants (SCVs) in the effluent runoff from the biofilms correlated with the emergence of plaque-forming Pf1-like filamentous phage (designated Pf4) from the biofilm. Because several recent studies have shown that bacteriophage genes are among the most highly upregulated groups of genes during biofilm development, we investigated whether Pf4 plays a role in SCV formation during
P. aeruginosa
biofilm development. We carried out immunoelectron microscopy using anti-Pf4 antibodies and observed that SCV cells, but not parental-type cells, exhibited high densities of Pf4 filaments on the cell surface and that these filaments were often tightly interwoven into complex latticeworks surrounding the cells. Moreover, infection of
P. aeruginosa
planktonic cultures with Pf4 caused the emergence of SCVs within the culture. These SCVs exhibited enhanced attachment, accelerated biofilm development, and large regions of dead and lysed cells inside microcolonies in a manner identical to that of SCVs obtained from biofilms. We concluded that Pf4 can mediate phenotypic variation in
P. aeruginosa
biofilms. We also performed partial sequencing and analysis of the Pf4 replicative form and identified a number of open reading frames not previously recognized in the genome of
P. aeruginosa
, including a putative postsegregational killing operon.
Crystal Structure of the PdxY Protein from
Escherichia coli
Authors: Safo Martin K. , Musayev Faik N. , Hunt Sharyn , di Salvo Martino L. , Scarsdale Neel , Schirch Verne 
Published: November 2004

ABSTRACT

The crystal structure of
Escherichia coli
PdxY, the protein product of the
pdxY
gene, has been determined to a 2.2-Å resolution. PdxY is a member of the ribokinase superfamily of enzymes and has sequence homology with pyridoxal kinases that phosphorylate pyridoxal at the C-5′ hydroxyl. The protein is a homodimer with an active site on each monomer composed of residues that come exclusively from each respective subunit. The active site is filled with a density that fits that of pyridoxal. In monomer A, the ligand appears to be covalently attached to Cys122 as a thiohemiacetal, while in monomer B it is not covalently attached but appears to be partially present as pyridoxal 5′-phosphate. The presence of pyridoxal phosphate and pyridoxal as ligands was confirmed by the activation of aposerine hydroxymethyltransferase after release of the ligand by the denaturation of PdxY. The ligand, which appears to be covalently attached to Cys122, does not dissociate after denaturation of the protein. A detailed comparison (of functional properties, sequence homology, active site and ATP-binding-site residues, and active site flap types) of PdxY with other pyridoxal kinases as well as the ribokinase superfamily in general suggested that PdxY is a member of a new subclass of the ribokinase superfamily. The structure of PdxY also permitted an interpretation of work that was previously published about this enzyme.