bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lepidopteran Soral Crypsis on Caribbean Ferns1
Authors: Barker Michael S. , Shaw Shane W. , Hickey R. James , Rawlins John E. , Fetzner James W. 
Published: May 2005

ABSTRACTInsect‐fern interactions are not as well characterized as insect‐angiosperm interactions. For example, the imitation of unique fern structures by insects has not been observed. On a recent trip to Puerto Rico, we collected ferns that bore small Lepidoptera imitating fern sori. Herbarium specimen searches indicate that these Lepidoptera are restricted to the Caribbean on ferns with highly visible sporangia. A possible selective pressure for the evolution of lepidopteran soral crypsis is wasp parasitism, as evidence of parasitoid wasps was found. However, it is more likely that soral crypsis evolved to avoid visually oriented predators such as birds or lizards.
Population Density and Home Range Size of Red‐Rumped Agoutis (Dasyprocta leporina) Within and Outside a Natural Brazil Nut Stand in Southeastern Amazonia1
Authors: Jorge Malu S. P. , Peres Carlos A. 
Published: May 2005

ABSTRACTThis study examined whether the population density and home range size of red‐rumped agoutis were affected by the spatial distribution of Brazil nut trees, at the Pinkaiti Research Station, in eastern Amazonia. Agouti densities in a Brazil nut grove were two‐fold higher and home ranges were half the size than those outside it. This indicates that the large supply of Brazil nuts results in higher densities and smaller home ranges of agoutis in this seasonally dry Amazonian forest.
The Case for Hydrogen in a Carbon Constrained World
Authors: Berry Gene D. , Aceves Salvador M. 
Published: May 2005

Abstract
Unlike other fuels, hydrogen (H2) can be generated and consumed without generating carbon dioxide (CO2). This creates both significant engineering challenges and unsurpassed ecological advantages for H2 as a fuel, while enabling an inexhaustible (closed) global fuel cycle based on the cleanest, most abundant, natural, and elementary substances: H2, O2, and H2O. If generated using light, heat, and/or electrical energy from solar, wind, fission, or (future) fusion power sources, H2 becomes a versatile, storable, and universal carbonless energy carrier, a necessary element for future global energy system(s) aimed at being free of air and water pollution, CO2, and other greenhouse gases. The case for hydrogen rests fundamentally on the need to eliminate pollution and stabilize Earth’s atmosphere and climate system.
BordetellaAlcS Transporter Functions in Alcaligin Siderophore Export and Is Central to Inducer Sensing in Positive Regulation of Alcaligin System Gene Expression
Authors: Brickman Timothy J. , Armstrong Sandra K. 
Published: May 2005

ABSTRACTBordetella pertussisandBordetella bronchiseptica, which are respiratory mucosal pathogens of mammals, produce and utilize the siderophore alcaligin to acquire iron in response to iron starvation. A predicted permease of the major facilitator superfamily class of membrane efflux pumps, AlcS (synonyms, OrfX and Bcr), was reported to be encoded within the alcaligin gene cluster. In this study,alcSnull mutants were found to be defective in growth under iron starvation conditions, in iron source utilization, and in alcaligin export.transcomplementation using clonedalcSgenes ofB. pertussisorB. bronchisepticarestored the wild-type phenotype to thealcSmutants. Although the levels of extracellular alcaligin measured inalcSstrain culture fluids were severely reduced compared with the wild-type levels,alcSmutants had elevated levels of cell-associated alcaligin, implicating AlcS in alcaligin export. Interestingly, a ΔalcAmutation that eliminated alcaligin production suppressed the growth defects ofalcSmutants. This suppression and the alcaligin production defect were reversed bytranscomplementation of the ΔalcAmutation in the double-mutant strain, confirming that the growth-defective phenotype ofalcSmutants is associated with alcaligin production. In analcA::mini-Tn5 lacZ1operon fusion strain background, analcSnull mutation resulted in enhanced AlcR-dependent transcriptional responsiveness to alcaligin inducer; conversely, AlcS overproduction blunted the transcriptional response to alcaligin. These transcription studies indicate that the alcaligin exporter activity of AlcS is required to maintain appropriate intracellular alcaligin levels for normal inducer sensing and responsiveness necessary for positive regulation of alcaligin system gene expression.
The
Campylobacter jejuni
Response Regulator, CbrR, Modulates Sodium Deoxycholate Resistance and Chicken Colonization
Authors: Raphael Brian H. , Pereira Sonia , Flom Gary A. , Zhang Qijing , Ketley Julian M. , Konkel Michael E. 
Published: May 2005

ABSTRACT

Two-component regulatory systems play a major role in the physiological response of bacteria to environmental stimuli. Such systems are composed of a sensor histidine kinase and a response regulator whose ultimate function is to affect the expression of target genes. Response regulator mutants of
Campylobacter jejuni
strain F38011 were screened for sensitivity to sodium deoxycholate. A mutation in Cj0643, which encodes a response regulator with no obvious cognate histidine kinase, resulted in an absence of growth on plates containing a subinhibitory concentration of sodium deoxcholate (1%, wt/vol). In broth cultures containing 0.05% (wt/vol) sodium deoxycholate, growth of the mutant was significantly inhibited compared to growth of the
C. jejuni
F38011 wild-type strain. Complementation of the
C. jejuni cbrR
mutant in
trans
restored growth in both broth and plate cultures supplemented with sodium deoxycholate. Based on the phenotype displayed by its mutation, we designated the gene corresponding to Cj0643 as
cbrR
(
Campylobacter b
ile
r
esistance
r
egulator). While the MICs of a variety of bile salts and other detergents for the
C. jejuni cbrR
mutant were lower, no difference was noted in its sensitivity to antibiotics or osmolarity. Finally, chicken colonization studies demonstrated that the
C. jejuni cbrR
mutant had a reduced ability to colonize compared to the wild-type strain. These data support previous findings that bile resistance contributes to colonization of chickens and establish that the response regulator, CbrR, modulates resistance to bile salts in
C. jejuni
.
Characterization of Two New Aminopeptidases in
Escherichia coli
Authors: Zheng Yu , Roberts Richard J. , Kasif Simon , Guan Chudi 
Published: May 2005

ABSTRACT

Two genes in the
Escherichia coli
genome,
ypdE
and
ypdF
, have been cloned and expressed, and their products have been purified. YpdF is shown to be a metalloenzyme with Xaa-Pro aminopeptidase activity and limited methionine aminopeptidase activity. Genes homologous to
ypdF
are widely distributed in bacterial species. The unique feature in the sequences of the products of these genes is a conserved C-terminal domain and a variable N-terminal domain. Full or partial deletion of the N terminus in YpdF leads to the loss of enzymatic activity. The conserved C-terminal domain is homologous to that of the methionyl aminopeptidase (encoded by
map
) in
E. coli
. However, YpdF and Map differ in their preference for the amino acid next to the initial methionine in the peptide substrates. The implication of this difference is discussed.
ypdE
is the immediate downstream gene of
ypdF
, and its start codon overlaps with the stop codon of
ypdF
by 1 base. YpdE is shown to be a metalloaminopeptidase and has a broad exoaminopeptidase activity.
Levels and Activity of the
Pseudomonas putida
Global Regulatory Protein Crc Vary According to Growth Conditions
Authors: Ruiz-Manzano Ana , Yuste Luis , Rojo Fernando 
Published: May 2005

ABSTRACT

The global regulatory protein Crc is involved in the repression of several catabolic pathways for sugars, hydrocarbons, and nitrogenated and aromatic compounds in
Pseudomonas putida
and
Pseudomonas aeruginosa
when other preferred carbon sources are present in the culture medium (catabolite repression), therefore modulating carbon metabolism. We have analyzed whether the levels or the activity of Crc is regulated. Crc activity was followed by its ability to inhibit the induction by alkanes of the
P. putida
OCT plasmid alkane degradation pathway when cells grow in a complete medium, where the effect of Crc is very strong. The abundance of
crc
transcripts and the amounts of Crc protein were higher under repressing conditions than under nonrepressing conditions. The presence of
crc
on a high-copy-number plasmid considerably increased Crc levels, but this impaired its ability to inhibit the alkane degradation pathway. Crc shows similarity to a family of nucleases that have highly conserved residues at their catalytic sites. Mutation of the corresponding residues in Crc (Asp
220
and His
246
) led to proteins that can inhibit induction of the alkane degradation pathway when present at normal or elevated levels in the cell. Repression by these mutant proteins occurred only under repressing conditions. These results suggest that both the amounts and the activity of Crc are modulated and support previous proposals that Crc may form part of a signal transduction pathway. Furthermore, the activity of the mutant proteins suggests that Crc is not a nuclease.
Iron-Responsive Regulation of theHelicobacter pyloriIron-Cofactored Superoxide Dismutase SodB Is Mediated by Fur
Authors: Ernst Florian D. , Homuth Georg , Stoof Jeroen , Mäder Ulrike , Waidner Barbara , Kuipers Ernst J. , Kist Manfred , Kusters Johannes G. , Bereswill Stefan , van Vliet Arnoud H. M. 
Published: May 2005

ABSTRACTMaintaining iron homeostasis is a necessity for all living organisms, as free iron augments the generation of reactive oxygen species like superoxide anions, at the risk of subsequent lethal cellular damage. The iron-responsive regulator Fur controls iron metabolism in many bacteria, including the important human pathogenHelicobacter pylori, and thus is directly or indirectly involved in regulation of oxidative stress defense. Here we demonstrate that Fur is a direct regulator of theH. pyloriiron-cofactored superoxide dismutase SodB, which is essential for the defense against toxic superoxide radicals. Transcription of thesodBgene was iron induced inH. pyloriwild-type strain 26695, resulting in expression of the SodB protein in iron-replete conditions but an absence of expression in iron-restricted conditions. Mutation of thefurgene resulted in constitutive, iron-independent expression of SodB. RecombinantH. pyloriFur protein bound with low affinity to thesodBpromoter region, but addition of the iron substitute Mn2+abolished binding. The operator sequence of the iron-free form of Fur, as identified by DNase I footprinting, was located directly upstream of thesodBgene at positions −5 to −47 from the transcription start site. The direct role of Fur in regulation of theH. pylori sodBgene contrasts with the small-RNA-mediatedsodBregulation observed inEscherichia coli. In conclusion,H. pyloriFur is a versatile regulator involved in many pathways essential for gastric colonization, including superoxide stress defense.
Characterization of Pathways Dependent on the
uvsE
,
uvrA1
, or
uvrA2
Gene Product for UV Resistance in
Deinococcus radiodurans
Authors: Tanaka Masashi , Narumi Issay , Funayama Tomoo , Kikuchi Masahiro , Watanabe Hiroshi , Matsunaga Tsukasa , Nikaido Osamu , Yamamoto Kazuo 
Published: May 2005

ABSTRACT

The genome of a radiation-resistant bacterium,
Deinococcus radiodurans
, contains one
uvsE
gene and two
uvrA
genes,
uvrA1
and
uvrA2
. Using a series of mutants lacking these genes, we determined the biological significance of these components to UV resistance. The UV damage endonuclease (UvsE)-dependent excision repair (UVER) pathway and UvrA1-dependent pathway show some redundancy in their function to counteract the lethal effects of UV. Loss of these pathways does not cause increased sensitivity to UV mutagenesis, suggesting either that these pathways play no function in inducing mutations or that there are mechanisms to prevent mutation other than these excision repair pathways. UVER efficiently removes both cyclobutane pyrimidine dimers (CPDs) and pyrimidine (6-4) pyrimidone photoproducts (6-4PPs) from genomic DNA. In contrast, the UvrA1 pathway does not significantly contribute to the repair of CPDs but eliminates 6-4PPs. Inactivation of
uvrA2
does not result in a deleterious effect on survival, mutagenesis, or the repair kinetics of CPDs and 6-4PPs, indicating a minor role in resistance to UV. Loss of
uvsE
,
uvrA1
, and
uvrA2
reduces but does not completely abolish the ability to eliminate CPDs and 6-4PPs from genomic DNA. The result indicates the existence of a system that removes UV damage yet to be identified.
Structural Comparison of Ten Serotypes of Staphylocoagulases in
Staphylococcus aureus
Authors: Watanabe S. , Ito T. , Takeuchi F. , Endo M. , Okuno E. , Hiramatsu K. 
Published: May 2005

ABSTRACT

Staphylocoagulase detection is the hallmark of a
Staphylococcus aureus
infection. Ten different serotypes of staphylocoagulases have been reported to date. We determined the nucleotide sequences of seven staphylocoagulase genes (
coa
) and their surrounding regions to compare structures of all 10 staphylocoagulase serotypes, and we inferred their derivations. We found that all staphylocoagulases are comprised of six regions: signal sequence, D1 region, D2 region, central region, repeat region, and C-terminal sequence. Amino acids at both ends, 33 amino acids in the N terminal (the signal sequences and the seven N-terminal amino acids in the D1 region) and 5 amino acids in the C terminal, were exactly identical among the 10 serotypes. The central regions were conserved with identities between 80.6 and 94.1% and similarities between 82.8 and 94.6%. Repeat regions comprising tandem repeats of 27 amino acids with a 92% identity on average were polymorphic in the number of repeats. On the other hand, D1 regions other than the seven N-terminal amino acids and D2 regions were less homologous, with diverged identities from 41.5 to 84.5% and 47.0 to 88.9%, respectively, and similarities from 53.5 to 88.7% and 56.8 to 91.9%, respectively, although the predicted prothrombin-binding sites were conserved among them. In contrast, flanking regions of
coa
were highly homologous, with nucleotide identities of more than 97.1%. Phylogenetic relations among
coa
did not correlate with those among the flanking regions or housekeeping genes used for multilocus sequence typing. These data indicate that
coa
could be transmitted to
S. aureus
, while the less homologous regions in
coa
presumed to be responsible for different antigenicities might have evolved independently.
Expression and Site-Directed Mutagenesis of the Lactococcal Abortive Phage Infection Protein AbiK
Authors: Fortier Louis-Charles , Bouchard Julie D. , Moineau Sylvain 
Published: May 2005

ABSTRACTAbortive infection mechanisms ofLactococcus lactisform a heterogeneous group of phage resistance systems that act after early phage gene expression. One of these systems, AbiK, aborts infection of the three most prevalent lactococcal phage groups of the dairy industry. In this study, it is demonstrated that the antiphage activity depends on the level of expression of theabiKgene and on the presence of a reverse transcriptase (RT) motif in AbiK. TheabiKgene was shown to be part of an operon that includes two additional open reading frames, with one of these encoding a phage-related transcriptional repressor named Orf4. Expression of AbiK is driven by two promoters, PabiKand Porf3, the latter being repressed by Orf4 in vivo. Binding of the purified Orf4 to the Porf3promoter was demonstrated in vitro by gel retardation assays. The N-terminal half of the deduced AbiK protein possesses an RT motif that was modified by site-directed mutagenesis. Conservative mutations in key positions resulted in the complete loss of the resistance phenotype. These data suggest that an RT activity might be involved in the phage resistance activity of AbiK. A model for the mode of action of AbiK is proposed.
Purification and Characterization of Allophanate Hydrolase (AtzF) from
Pseudomonas
sp. Strain ADP
Authors: Shapir Nir , Sadowsky Michael J. , Wackett Lawrence P. 
Published: May 2005

ABSTRACT

AtzF, allophanate hydrolase, is a recently discovered member of the amidase signature family that catalyzes the terminal reaction during metabolism of
s
-triazine ring compounds by bacteria. In the present study, the
atzF
gene from
Pseudomonas
sp. strain ADP was cloned and expressed as a His-tagged protein, and the protein was purified and characterized. AtzF had a deduced subunit molecular mass of 66,223, based on the gene sequence, and an estimated holoenzyme molecular mass of 260,000. The active protein did not contain detectable metals or organic cofactors. Purified AtzF hydrolyzed allophanate with a
k
cat
/

K
m

of 1.1 × 10
4
s
−1
M
−1
, and 2 mol of ammonia was released per mol allophanate. The substrate range of AtzF was very narrow. Urea, biuret, hydroxyurea, methylcarbamate, and other structurally analogous compounds were not substrates for AtzF. Only malonamate, which strongly inhibited allophanate hydrolysis, was an alternative substrate, with a greatly reduced
k
cat
/

K
m

of 21 s
−1
M
−1
. Data suggested that the AtzF catalytic cycle proceeds through a covalent substrate-enzyme intermediate. AtzF reacts with malonamate and hydroxylamine to generate malonohydroxamate, potentially derived from hydroxylamine capture of an enzyme-tethered acyl group. Three putative catalytically important residues, one lysine and two serines, were altered by site-directed mutagenesis, each with complete loss of enzyme activity. The identity of a putative serine nucleophile was probed using phenyl phosphorodiamidate that was shown to be a time-dependent inhibitor of AtzF. Inhibition was due to phosphoroamidation of Ser189 as shown by liquid chromatography/matrix-assisted laser desorption ionization mass spectrometry. The modified residue corresponds in sequence alignments to the nucleophilic serine previously identified in other members of the amidase signature family. Thus, AtzF affects the cleavage of three carbon-to-nitrogen bonds via a mechanism similar to that of enzymes catalyzing single-amide-bond cleavage reactions. AtzF orthologs appear to be widespread among bacteria.
Novel Molecular Features of the Fibrolytic Intestinal Bacterium
Fibrobacter intestinalis
Not Shared with
Fibrobacter succinogenes
as Determined by Suppressive Subtractive Hybridization
Authors: Qi Meng , Nelson Karen E. , Daugherty Sean C. , Nelson William C. , Hance Ioana R. , Morrison Mark , Forsberg Cecil W. 
Published: May 2005

ABSTRACT

Suppressive subtractive hybridization was conducted to identify unique genes coding for plant cell wall hydrolytic enzymes and other properties of the gastrointestinal bacterium
Fibrobacter intestinalis
DR7 not shared by
Fibrobacter succinogenes
S85. Subtractive clones from
F. intestinalis
were sequenced and assembled to form 712 nonredundant contigs with an average length of 525 bp. Of these, 55 sequences were unique to
F. intestinalis.
The remaining contigs contained 764 genes with BLASTX similarities to other proteins; of these, 80% had the highest similarities to proteins in
F. succinogenes
, including 30 that coded for carbohydrate active enzymes. The expression of 17 of these genes was verified by Northern dot blot analysis. Of genes not exhibiting BLASTX similarity to
F. succinogenes
, 30 encoded putative transposases, 6 encoded restriction modification genes, and 45% had highest similarities to proteins in other species of gastrointestinal bacteria, a finding suggestive of either horizontal gene transfer to
F. intestinalis
or gene loss from
F. succinogenes
. Analysis of contigs containing segments of two or more adjacent genes revealed that only 35% exhibited BLASTX similarity and were in the same orientation as those of
F. succinogenes
, indicating extensive chromosomal rearrangement. The expression of eight transposases, and three restriction-modification genes was confirmed by Northern dot blot analysis. These data clearly document the maintenance of carbohydrate active enzymes in
F. intestinalis
necessitated by the preponderance of polysaccharide substrates available in the ruminal environment. It also documents substantive changes in the genome from that of
F. succinogenes
, which may be related to the introduction of the array of transposase and restriction-modification genes.
Role of π Dimers in Coupling (“Handcuffing”) of Plasmid R6K's γ
ori
Iterons
Authors: Kunnimalaiyaan Selvi , Inman Ross B. , Rakowski Sheryl A. , Filutowicz Marcin 
Published: May 2005

ABSTRACT

One proposed mechanism of replication inhibition in iteron-containing plasmids (ICPs) is “handcuffing,” in which the coupling of origins via iteron-bound replication initiator (Rep) protein turns off origin function. In minimal R6K replicons, copy number control requires the interaction of plasmid-encoded π protein with the seven 22-bp iterons of the γ origin of replication. Like other related Rep proteins, π exists as both monomers and dimers. However, the ability of π dimers to bind iterons distinguishes R6K from most other ICPs, where only monomers have been observed to bind iterons. Here, we describe experiments to determine if monomers or dimers of π protein are involved in the formation of handcuffed complexes. Standard ligation enhancement assays were done using π variants with different propensities to bind iterons as monomers or dimers. Consistent with observations from several ICPs, a hyperreplicative variant (π·P106L
∧
F107S) exhibits deficiencies in handcuffing. Additionally, a novel dimer-biased variant of π protein (π·M36A
∧
M38A), which lacks initiator function, handcuffs iteron-containing DNA more efficiently than does wild-type π. The data suggest that π dimers mediate handcuffing, supporting our previously proposed model of handcuffing in the γ
ori
system. Thus, dimers of π appear to possess three distinct inhibitory functions with respect to R6K replication: transcriptional autorepression of π expression, in
cis
competition (for origin binding) with monomeric activator π, and handcuffing-mediated inhibition of replication in
trans
.