bluuebunny/crossref_metadata_2025_split huggingface dataset:
What factors determine where invertebrate‐feeding birds forage in dry agricultural grasslands?
Authors: ATKINSON PHILIP W. , BUCKINGHAM DAVID , MORRIS ANTONY J. 
Published: November 2004

Increases in the intensity of the management of agricultural grasslands over the past 50 years have reduced plant species diversity in swards and increased uniformity in structure through changes in fertilizer regimes, grazing and mowing practices. These factors, as well as increased disturbance and trampling, have reduced the number and diversity of forbs and thus the diversity and abundance of invertebrates, in particular of foliar species. Associated with these changes in management, there has been a large decline in the abundance of many species of farmland birds in pastoral areas and more local extinctions compared with arable areas. To understand the impact of these management changes on bird populations, and design measures to reverse the declines, it is necessary to identify the key factors influencing bird usage of fields. We review results from five studies, which have related fertilizer and grazing management to bird usage of grass fields. Species that fed on soil invertebrates tended to show a positive response to the amount of nitrogen fertilizer added and increased grazing pressure, although there was a high degree of correlation between these two variables. In summer, many species, including corvids, Common Blackbird Turdus merula, Common Starling Sturnus vulgaris, Pied Wagtail Motacilla alba and Hedge Accentor Prunella modularis, showed a negative relationship with sward height, and in winter more species showed a positive relationship with bare ground. Taller sward heights are associated with a greater abundance and diversity of bird invertebrate food resources, and accessibility of food items or a lower risk of predation (actual or perceived) are likely to be the reasons for birds choosing to forage on shorter swards and in areas with more bare ground. Birds feeding on soil invertebrates were found to be generally tolerant of modern management practices that maintain short swards short, as accessibility to the soil has been increased. Species that feed on foliar invertebrates or forb seeds have been affected negatively by modern grassland agricultural practices.
KatG Is the Primary Detoxifier of Hydrogen Peroxide Produced by Aerobic Metabolism in
Bradyrhizobium japonicum
Authors: Panek Heather R. , O'Brian Mark R. 
Published: November 2004

ABSTRACT

Bacteria are exposed to reactive oxygen species from the environment and from those generated by aerobic metabolism. Catalases are heme proteins that detoxify H
2
O
2
, and many bacteria contain more than one catalase enzyme. Also, the nonheme peroxidase alkyl hydroperoxide reductase (Ahp) is the major scavenger of endogenous H
2
O
2
in
Escherichia coli
. Here, we show that aerobically grown
Bradyrhizobium japonicum
cells express a single catalase activity. Four genes encoding putative catalases in the
B. japonicum
genome were identified, including a
katG
homolog encoding a catalase-peroxidase. Deletion of the
katG
gene resulted in loss of catalase activity in cell extracts and of exogenous H
2
O
2
consumption by whole cells. The
katG
strain had a severe aerobic growth phenotype but showed improved growth in the absence of O
2
. By contrast, a
B. japonicum ahpCD
mutant grew well aerobically and consumed H
2
O
2
at wild-type rates. A heme-deficient
hemA
mutant expressed about one-third of the KatG activity as the wild type but grew well aerobically and scavenged low concentrations of exogenous H
2
O
2
. However, cells of the
hemA
strain were deficient in consumption of high concentrations of H
2
O
2
and were very sensitive to killing by short exposure to H
2
O
2
. In addition, KatG activity did not decrease as a result of mutation of the gene encoding the transcriptional activator OxyR. We conclude that aerobic metabolism produces toxic levels of H
2
O
2
in
B. japonicum
, which is detoxified primarily by KatG. Furthermore, the
katG
level sufficient for detoxification does not require OxyR.
Purification and Initial Characterization of the
Salmonella enterica
PduO ATP:Cob(I)alamin Adenosyltransferase
Authors: Johnson Celeste L. V. , Buszko Marian L. , Bobik Thomas A. 
Published: November 2004

ABSTRACT

The PduO enzyme of
Salmonella enterica
is an ATP:cob(I)alamin adenosyltransferase that catalyzes the final step in the conversion of vitamin B
12
to coenzyme B
12
. The primary physiological role of this enzyme is to support coenzyme B
12
-dependent 1,2-propanediol degradation, and bioinformatic analysis has indicated that it has two domains. Here the PduO adenosyltransferase was produced in
Escherichia coli
, solubilized from inclusion bodies, purified to apparent homogeneity, and partially characterized biochemically. The

K
m

values of PduO for ATP and cob(I)alamin were 19.8 and 4.5 μM, respectively, and the enzyme
V
max
was 243 nmol min
−1
mg of protein
−1
. Further investigations showed that PduO was active with ATP and partially active with deoxy-ATP, but lacked measurable activity with other nucleotides.
31
P nuclear magnetic resonance established that triphosphate was a product of the PduO reaction, and kinetic studies indicated a ternary complex mechanism. A series of truncated versions of the PduO protein were produced in
Escherichia coli
, partially purified, and used to show that adenosyltransferase activity is associated with the N-terminal domain. The N-terminal domain was purified to near homogeneity and shown to have biochemical properties and kinetic constants similar to those of the full-length enzyme. This indicated that the C-terminal domain was not directly involved in catalysis or substrate binding and may have another role.
Positive and Negative Transcriptional Regulators of Glutathione-Dependent Formaldehyde Metabolism
Authors: Hickman Jason W. , Witthuhn Vernon C. , Dominguez Miguel , Donohue Timothy J. 
Published: November 2004

ABSTRACTA glutathione (GSH)-dependent pathway is used for formaldehyde metabolism by a wide variety of prokaryotes and eukaryotes. In this pathway,S-hydroxymethylglutathione, produced by the reaction of formaldehyde with the thiolate moiety of glutathione, is the substrate for a GSH-dependent formaldehyde dehydrogenase (GSH-FDH). While expression of GSH-FDH often increases in the presence of metabolic or exogenous sources of formaldehyde, little is known about the factors that regulate this response. Here, we identify two signal transduction pathways that regulate expression ofadhI, the gene encoding GSH-FDH, inRhodobacter sphaeroides. The loss of the histidine kinase response regulator pair RfdRS or the histidine kinase RfdS increasesadhItranscription in the absence of metabolic sources of formaldehyde. Cells lacking RfdRS further increaseadhIexpression in the presence of metabolic sources of formaldehyde (methanol), suggesting that this negative regulator of GSH-FDH expression does not respond to this compound. In contrast, mutants lacking the histidine kinase response regulator pair AfdRS or the histidine kinase AfdS cannot induceadhIexpression in the presence of either formaldehyde or metabolic sources of this compound. AfdR stimulates activity of theadhIpromoter in vitro, indicating that this protein is a direct activator of GSH-FDH expression. Activation by AfdR is detectable only after incubation of the protein with acetyl phosphate, suggesting that phosphorylation is necessary for transcription activation. Activation ofadhItranscription by acetyl-phosphate-treated AfdR in vitro is inhibited by a truncated RfdR protein, suggesting that this protein is a direct repressor of GSH-FDH expression. Together, the data indicate that AfdRS and RfdRS positively and negatively regulateadhItranscription in response to different signals.
Global Transposon Mutagenesis and Essential Gene Analysis of
Helicobacter pylori
Authors: Salama Nina R. , Shepherd Benjamin , Falkow Stanley 
Published: November 2004

ABSTRACT

We have constructed a genome-saturating mutant library of the human gastric pathogen
Helicobacter pylori
. Microarray tracking of transposon mutants (MATT) allowed us to map the position of 5,363 transposon mutants in our library. While we generally found insertions well distributed throughout the genome, 344 genes had no detectable transposon insertions, and this list is predicted to be highly enriched for essential genes. Comparison to the essential gene set of other bacteria revealed a surprisingly limited overlap with all organisms tested (11%), while 55% were essential in some organisms but not others. We independently verified the essentiality of several gene products, including an HtrA family serine protease, a hypothetical protein with putative phospholipase D activity, and a riboflavin specific deaminase. A limited screen for motility mutants allowed us to estimate that 4.5% of the genome is dedicated to this virulence-associated phenotype.
Systematic Inactivation and Phenotypic Characterization of Two-Component Signal Transduction Systems ofEnterococcus faecalisV583
Authors: Hancock Lynn E. , Perego Marta 
Published: November 2004

ABSTRACTThe ability of enterococci to adapt and respond to different environmental stimuli, including the host environment, led us to investigate the role of two-component signal transduction in the regulation ofEnterococcus faecalisphysiology. Using a bioinformatic approach, we previously identified 17 two-component systems (TCS), consisting of a sensory histidine kinase and the cognate response regulator, as well as an additional orphan response regulator (L. E. Hancock and M. Perego, J. Bacteriol. 184:5819-5825, 2002). In an effort to identify the potential function of each TCS in the biology ofE. faecalisclinical isolate strain V583, we constructed insertion mutations in each of the response regulators. We were able to inactivate 17 of 18 response regulators, the exception being an ortholog of YycF, previously shown to be essential for viability in a variety of gram-positive microorganisms. The biological effects of the remaining mutations were assessed by using a number of assays, including antibiotic resistance, biofilm formation, and environmental stress. We identified TCS related to antibiotic resistance and environmental stress and found one system which controls the initiation of biofilm development byE. faecalis.
Sequence Tolerance of the Phage λ
P
RM
Promoter: Implications for Evolution of Gene Regulatory Circuitry
Authors: Michalowski Christine B. , Short Megan D. , Little John W. 
Published: November 2004

ABSTRACT

Much
of the gene regulatory circuitry of phage λ
centers on a complex region called the
O
R
region. This ∼100-bp region is densely
packed with regulatory sites, including two promoters and three
repressor-binding sites. The dense packing of this region is likely to
impose severe constraints on its ability to change during evolution,
raising the question of how the specific arrangement of sites and their
exact sequences could evolve to their present form. Here we ask whether
the sequence of a
cis
-acting site can be widely varied while
retaining its function; if it can, evolution could proceed by a larger
number of paths. To help address this question, we developed aλ
cloning vector that allowed us to clone fragments spanning
the
O
R
region. By using this vector, we carried out
intensive mutagenesis of the
P
RM
promoter, which
drives expression of CI repressor and is activated by CI itself. We
made a pool of fragments in which 8 of the 12 positions in the−
35 and −10 regions were randomized and cloned this
pool into the vector, making a pool of
P
RM
variant
phage. About 10% of the
P
RM
variants were
able to lysogenize, suggesting that the λ regulatory circuitry
is compatible with a wide range of
P
RM
sequences.
Analysis of several of these phages indicated a range of behaviors in
prophage induction. Several isolates had induction properties
similar to those of the wild type, and their promoters resembled the
wild type in their responses to CI. We term this property of different
sequences allowing roughly equivalent function “sequence
tolerance ” and discuss its role in the evolution of gene
regulatory
circuitry.
Kinetic Analysis of the Oxidative Conversion of the [4Fe-4S]
2+
Cluster of FNR to a [2Fe-2S]
2+
Cluster
Authors: Sutton Victoria R. , Mettert Erin L. , Beinert Helmut , Kiley Patricia J. 
Published: November 2004

ABSTRACT

The ability of FNR to sense and respond to cellular O
2
levels depends on its [4Fe-4S]
2+
cluster. In the presence of O
2
, the [4Fe-4S]
2+
cluster is converted to a [2Fe-2S]
2+
cluster, which inactivates FNR as a transcriptional regulator. In this study, we demonstrate that ∼2 Fe
2+
ions are released from the reaction of O
2
with the [4Fe-4S]
2+
cluster. Fe
2+
release was then used as an assay of reaction progress to investigate the rate of [4Fe-4S]
2+
to [2Fe-2S]
2+
cluster conversion in vitro. We also found that there was no detectable difference in the rate of O
2
-induced cluster conversion for FNR free in solution compared to its DNA-bound form. In addition, the rate of FNR inactivation was monitored in vivo by measuring the rate at which transcriptional regulation by FNR is lost upon the exposure of cells to O
2
; a comparison of the in vitro and in vivo rates of conversion suggests that O
2
-induced cluster conversion is sufficient to explain FNR inactivation in cells. FNR protein levels were also compared for cells grown under aerobic and anaerobic conditions.
Novel Roles for the AIDA Adhesin from DiarrheagenicEscherichia coli: Cell Aggregation and Biofilm Formation
Authors: Sherlock Orla , Schembri Mark A. , Reisner Andreas , Klemm Per 
Published: November 2004

ABSTRACTDiarrhea-causingEscherichia colistrains are responsible for numerous cases of gastrointestinal disease and constitute a serious health problem throughout the world. The ability to recognize and attach to host intestinal surfaces is an essential step in the pathogenesis of such strains. AIDA is a potent bacterial adhesin associated with some diarrheagenicE. colistrains. AIDA mediates bacterial attachment to a broad variety of human and other mammalian cells. It is a surface-displayed autotransporter protein and belongs to the selected group of bacterial glycoproteins; only the glycosylated form binds to mammalian cells. Here, we show that AIDA possesses self-association characteristics and can mediate autoaggregation ofE. colicells. We demonstrate that intercellular AIDA-AIDA interaction is responsible for bacterial autoaggregation. Interestingly, AIDA-expressing cells can interact with antigen 43 (Ag43)-expressing cells, which is indicative of an intercellular AIDA-Ag43 interaction. Additionally, AIDA expression dramatically enhances biofilm formation byE. colion abiotic surfaces in flow chambers.
Structural Similarity of YbeD Protein from
Escherichia coli
to Allosteric Regulatory Domains
Authors: Kozlov Guennadi , Elias Demetra , Semesi Anthony , Yee Adelinda , Cygler Miroslaw , Gehring Kalle 
Published: November 2004

ABSTRACT

Lipoic acid is an essential prosthetic group in several metabolic pathways. The biosynthetic pathway of protein lipoylation in
Escherichia coli
involves gene products of the
lip
operon. YbeD is a conserved bacterial protein located in the
dacA
-
lipB
intergenic region. Here, we report the nuclear magnetic resonance structure of YbeD from
E. coli
. The structure includes a βαββαβ fold with two α-helices on one side of a four-strand antiparallel β-sheet. The β2-β3 loop shows the highest sequence conservation and is likely functionally important. The β-sheet surface contains a patch of conserved hydrophobic residues, suggesting a role in protein-protein interactions. YbeD shows striking structural homology to the regulatory domain from
d
-3-phosphoglycerate dehydrogenase, hinting at a role in the allosteric regulation of lipoic acid biosynthesis or the glycine cleavage system.
COMPLEX MASS FERMIONIC FIELDS
Authors: BARCI D.G. , OXMAN L.E. 
Published: November 2004

We consider a fermionic field obeying a second order equation containing a pair of complex conjugate mass parameters. After obtaining a natural representation for the different degrees of freedom, we are able to construct a unique vacuum as the more symmetric state (zero energy-momentum, charge and spin). This representation, unlike the real mass case, is not holomorphic in the Grassmann variables. The vacuum eigenstate allows the calculation of the field propagator which turns out to be half advanced plus half retarded.
CHAOS IN COOPERATION: CONTINUOUS-VALUED PRISONER’S DILEMMAS IN INFINITE-VALUED LOGIC
Authors: MAR GARY , DENIS PAUL ST. 
Published: November 2004

The Prisoner’s Dilemma (PD) has become a paradigm of the evolution of cooperation. The PD can be generalized to the continuous-valued case in which players are allowed to choose intermediate levels of cooperation. When continuous-valued PDs are played in the spatial context of cellular automata, generous strategies are favored. Continuous-valued PDs are naturally represented in infinite-valued logic. The infinite-valued logic allows us to prove that cooperative interactions between continuous-valued strategies are paradigmatically chaotic. Escape-time diagrams using a given level of mutual cooperation as a threshold produce fractal images. The sensitive dependence of chaotic dynamical systems models a practical unpredictability within the PD (even though only deterministic nonstochastic strategies are involved) that is characteristic of many real life choice situations.
The Si(111) $\sqrt 3 \times \sqrt 3 $ SURFACES FORMED BY THE ADSORPTION OF GROUP-III, IV, AND V METALS
Authors: KONO S. 
Published: November 2004

A compilation of experimental studies is made on the properties of the Si(111) [Formula: see text] surfaces formed by the adsorption of metals of groups-III, IV, and V in the periodic table. The metals treated are Al, Ga, In (group-III), Sn, Pb (group-IV), Sb and Bi (group-V). Experimental studies using scanning tunneling microscopy are included only when they are necessary, since the topics will be covered in the review by J. Nogami in this issue. Theoretical aspects of the studies will be covered in the review by H. Nagayoshi in this issue. The geometric and electronic properties of these Si(111) [Formula: see text] surfaces appeared to be the simplest kinds of surfaces on the Si(111), thus providing prototypic examples of reconstruction on the metal/Si submonolayer interfaces. The simplicity in these surfaces is that there are metal-adatoms over essentially truncated Si(111) 1×1 substrates. The types of "metal building-blocks" are basically two: (i) a single metal adatom on a threefold hollow site (so-called T4 site), (ii) a metal trimer, each of constituent atoms, resides nearly on the ontop site (so-called "milk-stool"). There is large relaxation in the substrate Si due to the presence of metal adatoms.
KIT and Platelet-Derived Growth Factor Receptor Alpha Tyrosine Kinase Gene Mutations and KIT Amplifications in Human Solid Tumors
Authors: Sihto Harri , Sarlomo-Rikala Maarit , Tynninen Olli , Tanner Minna , Andersson Leif C. , Franssila Kaarle , Nupponen Nina N. , Joensuu Heikki 
Published: November 2004

Purpose Mutated KIT and platelet-derived growth factor receptor alpha (PDGFRα) tyrosine kinases are the principal targets for imatinib mesylate in the treatment of gastrointestinal stromal tumors (GISTs). The frequency of activating KIT and PDGFRA gene mutations in most other histologic types of human cancer is not known. Materials and Methods KIT exons 9, 11, 13, and 17 and PDGFRA exons 11 and 17 of 334 human cancers were screened for mutations using sensitive denaturing high-performance liquid chromatography (DHPLC). In addition, all KIT exons from 9 to 21 of 115 tumors were screened. Thirty-two histologic tumor types were examined. Samples with abnormal findings in DHLPC were sequenced. Immunostaining for the KIT protein (CD117) was performed in 322 (96.4%) of the 334 cases. Results Of the 3,039 exons screened, only 17 had mutation. All 17 cases with either mutated KIT (n = 15) or PDGFRA (n = 2) were histologically GIST tumors, whereas none of the other histologic types of cancer (n = 316) harbored KIT or PDGFRA mutation. KIT immunostaining was rarely positive except in GISTs (18 of 18), small-cell lung cancer (10 of 30; 33%), and testicular teratocarcinoma (four of 17; 24%). Wild-type KIT gene amplification or chromosome 4 aneuploidy was common (seven of 12) in non-GIST tumors with strong KIT protein expression when studied with fluorescence in situ hybridization. Conclusion Despite frequent KIT protein expression in some tumor types, KIT and PDGFRA gene mutations are uncommon in most human cancers. Cancer KIT expression is frequently associated with multiple copies of the wild-type KIT gene.
Incommensurate modulations made visible by the Maximum Entropy Method in superspace
Authors: Palatinus Lukás , van Smaalen Sander 
Published: November 2004

Abstract
This paper presents the application of the Maximum Entropy Method (MEM) to structure solution of incommensurately modulated structures within the superspace formalism. The basic principles of the MEM are outlined, and its generalization toward superspace is discussed. Possible problems in MEM reconstructions and their solutions are summarized. They include series-termination errors in the reconstructed electron density, the effect of insufficient constraints, and the effect of missing data. The use of the MEM in superspace is illustrated by three examples: the structure of the misfit-layer compound (LaS)1.14NbS2, the structure of the high-pressure phase III of bismuth, and the modulated structure of ammonium tetrafluoroberyllate. It is shown that the MEM is able to extract more information about the modulation functions than can be obtained by structure refinements. The MEM can also be used for the study of accurate charge densities of modulated structures. An illustration is given by the charge density of ammonium tetrafluoroberyllate.
Genetic Variation for Total Fitness in Drosophila melanogaster
Authors: Gardner Michael P , Fowler Kevin , Barton Nicholas H , Partridge Linda 
Published: November 2004

Abstract
The extent of genetic variation in fitness is a crucial issue in evolutionary biology and yet remains largely unresolved. In Drosophila melanogaster, we have devised a method that allows the net effects on fitness of heterozygous wild-type chromosomes to be measured, by competing them against two different “balancer” chromosomes. We have applied the method to a large sample of 40 wild-type third chromosomes and have measured fitnesses of nonlethal chromosomes as well as chromosomes bearing recessive lethals. The measurements were made in the environment to which the population was adapted and did not involve inbreeding. The results show an extraordinary similarity in the behavior of replicates of the same chromosome, indicating consistent genetic effects on total fitness. Some invading chromosomes increased rapidly and some slowly, and some rose to appreciable frequency after several months, but then declined again: in every case, the same pattern was seen in each replicate. We estimated relative fitnesses, rates of change of fitness, and relative viabilities, for each chromosome. There were significant fluctuations around the fitted model, which were also highly replicable. Wild-type chromosomes varied substantially in their effects on heterozygous fitness, and these effects vary through time, most likely as a result of genotype × environment interactions.