bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular Analysis of Carbon Monoxide-Oxidizing Bacteria Associated with Recent Hawaiian Volcanic Deposits
Authors: Dunfield Kari E. , King Gary M. 
Published: July 2004

ABSTRACT

Genomic DNA extracts from four sites at Kilauea Volcano were used as templates for PCR amplification of the large subunit (
coxL
) of aerobic carbon monoxide dehydrogenase. The sites included a 42-year-old tephra deposit, a 108-year-old lava flow, a 212-year-old partially vegetated ash-and-tephra deposit, and an approximately 300-year-old forest. PCR primers amplified
coxL
sequences from the OMP clade of CO oxidizers, which includes isolates such as
Oligotropha carboxidovorans
,
Mycobacterium tuberculosis
, and
Pseudomonas thermocarboxydovorans
. PCR products were used to create clone libraries that provide the first insights into the diversity and phylogenetic affiliations of CO oxidizers in situ. On the basis of phylogenetic and statistical analyses, clone libraries for each site were distinct. Although some clone sequences were similar to
coxL
sequences from known organisms, many sequences appeared to represent phylogenetic lineages not previously known to harbor CO oxidizers. On the basis of average nucleotide diversity and average pairwise difference, a forested site supported the most diverse CO-oxidizing populations, while an 1894 lava flow supported the least diverse populations. Neither parameter correlated with previous estimates of atmospheric CO uptake rates, but both parameters correlated positively with estimates of microbial biomass and respiration. Collectively, the results indicate that the CO oxidizer functional group associated with recent volcanic deposits of the remote Hawaiian Islands contains substantial and previously unsuspected diversity.
Enzymatic Synthesis of High-Molecular-Mass Poly-γ-Glutamate and Regulation of Its Stereochemistry
Authors: Ashiuchi Makoto , Shimanouchi Kazuya , Nakamura Hisaaki , Kamei Tohru , Soda Kenji , Park Chung , Sung Moon-Hee , Misono Haruo 
Published: July 2004

ABSTRACT

For the first time, we succeeded in synthesizing in vitro poly-γ-glutamate (PGA) with high molecular masses (>1,000 kDa) by the use of enzyme-associated cell membranes from
Bacillus subtilis
subsp.
chungkookjang
. The activity for PGA synthesis, however, was readily lost in the presence of critical concentrations of detergents tested in micelles. The optimum pH for the reaction was found to be ∼7.0. We examined the effects of some divalent cations on PGA synthesis and found that Mg
2+
was essential in catalysis and that Zn
2+
additionally boosted the activity. In contrast, Fe
2+
and Ca
2+
acted as inhibitors. Mn
2+
did not apparently influence the in vitro formation of PGA.
dl
-Glutamate (
d
isomer content, 60 to 80%) apparently served as the best substrate;
d
-Glutamate was preferable to the
l
isomer as a substrate. When
d
- and
l
-glutamate were used for the reaction, the elongated chains of PGAs were composed of the
d
- and
l
-isomers, respectively. Our results suggest that the stereochemical properties of enzymatically synthesized PGAs substantially depend on the stereochemistry (
dl
ratio) of glutamate as the substrate. Furthermore, genetic analysis indicated that all the
pgsB
,
-C
, and
-A
gene products, which are responsible for PGA production by
B. subtilis
cells, were also indispensable for enzymatic PGA synthesis.
Identification of Bacterial Populations in Dairy Wastewaters by Use of 16S rRNA Gene Sequences and Other Genetic Markers
Authors: McGarvey Jeffery A. , Miller William G. , Sanchez Susan , Stanker Larry 
Published: July 2004

ABSTRACT

Hydraulic flush waste removal systems coupled to solid/liquid separators and circulated treatment lagoons are commonly utilized to manage the large amounts of animal waste produced on high-intensity dairy farms. Although these systems are common, little is known about the microbial populations that inhabit them or how they change as they traverse the system. Using culture-based and non-culture-based methods, we characterized the microbial community structure of manure, water from the separator pit, and water from the circulated treatment lagoon from a large dairy in the San Joaquin Valley of California. Our results show that both total bacterial numbers and bacterial diversity are highest in manure, followed by the separator pit water and the lagoon water. The most prevalent phylum in all locations was the
Firmicutes
(low-G+C, gram-positive bacteria). The most commonly occurring operational taxonomic unit (OTU) had a 16S rRNA gene (rDNA) sequence 96 to 99% similar to that of
Clostridium lituseburense
and represented approximately 6% of the manure derived sequences, 14% of the separator pit-derived sequences and 20% of the lagoon-derived sequences. Also highly prevalent was an OTU with a 16S rDNA sequence 97 to 100% similar to that of
Eubacterium tenue
, comprising approximately 3% of the manure-derived sequences, 6% of the separator pit-derived sequences and 9% of the lagoon-derived sequences. Taken together, these sequences represent approximately one-third of the total organisms in the lagoon waters, suggesting that they are well adapted to this environment.
Presence of Acylated Homoserine Lactones (AHLs) and AHL-Producing Bacteria in Meat and Potential Role of AHL in Spoilage of Meat
Authors: Bruhn Jesper Bartholin , Christensen Allan Beck , Flodgaard Lars Ravn , Nielsen Kristian Fog , Larsen Thomas Ostenfeld , Givskov Michael , Gram Lone 
Published: July 2004

ABSTRACTQuorum-sensing (QS) signals (N-acyl homoserine lactones [AHLs]) were extracted and detected from five commercially produced vacuum-packed meat samples. Ninety-six AHL-producing bacteria were isolated, and 92 were identified asEnterobacteriaceae. Hafnia alveiwas the most commonly identified AHL-producing bacterium. Thin-layer chromatographic profiles of supernatants from sixH. alveiisolates and of extracts from spoiling meat revealed that the major AHL species had anRfvalue and shape similar toN-3-oxo-hexanoyl homoserine lactone (OHHL). Liquid chromatography-mass spectrometry (MS) (high-resolution MS) analysis confirmed the presence of OHHL in pure cultures ofH. alvei. Vacuum-packed meat spoiled at the same rate when inoculated with theH. alveiwild type compared to a corresponding AHL-lacking mutant. Addition of specific QS inhibitors to the AHL-producingH. alveiinoculated in meat or to naturally contaminated meat did not influence the spoilage of vacuum-packed meat. An extracellular protein of approximately 20 kDa produced by theH. alveiwild-type was not produced by the AHL-negative mutant but was restored in the mutant when complemented by OHHL, thus indicating that AHLs do have a regulatory role inH. alvei. Coinoculation ofH. alveiwild-type with an AHL-deficientSerratia proteamaculansB5a, in which protease secretion is QS regulated, caused spoilage of liquid milk. By contrast, coinoculation of AHL-negative strains ofH. alveiandS. proteamaculansB5a did not cause spoilage. In conclusion, AHL and AHL-producing bacteria are present in vacuum-packed meat during storage and spoilage, but AHL does not appear to influence the spoilage of this particular type of conserved meat. Our data indicate that AHL-producingH. alveimay induce food quality-relevant phenotypes in other bacterial species in the same environment.H. alveimay thus influence spoilage of food products in whichEnterobacteriaceaeparticipate in the spoilage process.
Restoration of a Defective
Lactococcus lactis
Xylose Isomerase
Authors: Park Joo-Heon , Batt Carl A. 
Published: July 2004

ABSTRACT

The genes (
xylA
) encoding xylose isomerase (XI) from two
Lactococcus lactis
subsp.
lactis
strains, 210 (Xyl
−
) and IO-1 (Xyl
+
), were cloned, and the activities of their expressed proteins in recombinant strains of
Escherichia coli
were investigated. The nucleotide and amino acid sequence homologies between the
xylA
genes were 98.4 and 98.6%, respectively, and only six amino acid residues differed between the two XIs. The purified IO-1 XI was soluble with
K

m

and
k
cat
being 2.25 mM and 184/s, respectively, while the 210 XI was insoluble and inactive. Site-directed mutagenesis on 210
xylA
showed that a triple mutant possessing R202M/Y218D/V275A mutations regained XI activity and was soluble. The
K

m

and
k
cat
of this mutant were 4.15 mM and 141/s, respectively. One of the IO-1 XI mutants, S388T, was insoluble and showed negligible activity similar to that of 210 XI. The introduction of a K407E mutation to the IO-1 S388T XI mutant restored its activity and solubility. The dissolution of XI activity in
L. lactis
subsp.
lactis
involves a series of mutations that collectively eliminate enzyme activity by reducing the solubility of the enzyme.
Microscale and Molecular Assessment of Impacts of Nickel, Nutrients, and Oxygen Level on Structure and Function of River Biofilm Communities
Authors: Lawrence J. R. , Chenier M. R. , Roy R. , Beaumier D. , Fortin N. , Swerhone G. D. W. , Neu T. R. , Greer C. W. 
Published: July 2004

ABSTRACT

Studies were carried out to assess the influence of nutrients, dissolved oxygen (DO) concentration, and nickel (Ni) on river biofilm development, structure, function, and community composition. Biofilms were cultivated in rotating annular reactors with river water at a DO concentration of 0.5 or 7.5 mg liter
−1
, with or without a combination of carbon, nitrogen, and phosphorus (CNP) and with or without Ni at 0.5 mg liter
−1
. The effects of Ni were apparent in the elimination of cyanobacterial populations and reduced photosynthetic biomass in the biofilm. Application of lectin-binding analyses indicated changes in exopolymer abundance and a shift in the glycoconjugate makeup of the biofilms, as well as in the response to all treatments. Application of the fluorescent live-dead staining (BacLight Live-Dead staining kit; Molecular Probes, Eugene, Oreg.) indicated an increase in the ratio of live to dead cells under low-oxygen conditions. Nickel treatments had 50 to 75% fewer ‘live’ cells than their corresponding controls. Nickel at 0.5 mg liter
−1
corresponding to the industrial release rate concentration for nickel resulted in reductions in carbon utilization spectra relative to control and CNP treatments without nickel. In these cases, the presence of nickel eliminated the positive influence of nutrients on the biofilm. Other culture-dependent analyses (plate counts and most probable number) revealed no significant treatment effect on the biofilm communities. In the presence of CNP and at both DO levels, Ni negatively affected denitrification but had no effect on hexadecane mineralization or sulfate reduction. Analysis of total community DNA indicated abundant eubacterial 16S ribosomal DNA (rDNA), whereas
Archaea
were not detected. Amplification of the
alkB
gene indicated a positive effect of CNP and a negative effect of Ni. The
nirS
gene was not detected in samples treated with Ni at 0.5 mg liter
−1
, indicating a negative effect on specific populations of bacteria, such as denitrifiers, resulting in a reduction in diversity. Denaturing gradient gel electrophoresis revealed that CNP had a beneficial impact on biofilm bacterial diversity at high DO concentrations, but none at low DO concentrations, and that the negative effect of Ni on diversity was similar at both DO concentrations. Notably, Ni resulted in the appearance of unique bands in 16S rDNA from Ni, DO, and CNP treatments. Sequencing results confirmed that the bands belonged to bacteria originating from freshwater and marine environments or from agricultural soils and industrial effluents. The observations indicate that significant interactions occur between Ni, oxygen, and nutrients and that Ni at 0.5 mg liter
−1
may have significant impacts on river microbial community diversity and function.
Development of a Multispecies Oral Bacterial Community in a Saliva-Conditioned Flow Cell
Authors: Foster Jamie S. , Kolenbrander Paul E. 
Published: July 2004

ABSTRACT

Microbial communities within the human oral cavity are dynamic associations of more than 500 bacterial species that form biofilms on the soft and hard tissues of the mouth. Understanding the development and spatial organization of oral biofilms has been facilitated by the use of in vitro models. We used a saliva-conditioned flow cell, with saliva as the sole nutritional source, as a model to examine the development of multispecies biofilm communities from an inoculum containing the coaggregation partners
Streptococcus gordonii
,
Actinomyces naeslundii
,
Veillonella atypica
, and
Fusobacterium nucleatum
. Biofilms inoculated with individual species in a sequential order were compared with biofilms inoculated with coaggregates of the four species. Our results indicated that flow cells inoculated sequentially produced biofilms with larger biovolumes compared to those biofilms inoculated with coaggregates. Individual-species biovolumes within the four-species communities also differed between the two modes of inoculation. Fluorescence in situ hybridization with genus- and species-specific probes revealed that the majority of cells in both sequentially and coaggregate-inoculated biofilms were
S. gordonii
, regardless of the inoculation order. However, the representation of
A. naeslundii
and
V. atypica
was significantly higher in biofilms inoculated with coaggregates compared to sequentially inoculated biofilms. Thus, these results indicate that the development of multispecies biofilm communities is influenced by coaggregations preformed in planktonic phase. Coaggregating bacteria such as certain streptococci are especially adapted to primary colonization of saliva-conditioned surfaces independent of the mode of inoculation and order of addition in the multispecies inoculum. Preformed coaggregations favor other bacterial strains and may facilitate symbiotic relationships.
Fur Is Involved in Manganese-Dependent Regulation of
mntA
(
sitA
) Expression in
Sinorhizobium meliloti
Authors: Platero Raúl , Peixoto Lucía , O'Brian Mark R. , Fabiano Elena 
Published: July 2004

ABSTRACT

Fur is a transcriptional regulator involved in iron-dependent control of gene expression in many bacteria. In this work we analyzed the phenotype of a
fur
mutant in
Sinorhizobium meliloti
, an α-proteobacterium that fixes N
2
in association with host plants. We demonstrated that some functions involved in high-affinity iron transport, siderophore production, and iron-regulated outer membrane protein expression respond to iron in a Fur-independent manner. However, manganese-dependent expression of the MntABCD manganese transport system was lost in a
fur
strain as discerned by constitutive expression of a
mntA::gfp
fusion reporter gene in the mutant. Thus, Fur directly or indirectly regulates a manganese-dependent function. The data indicate a novel function for a bacterial Fur protein in mediating manganese-dependent regulation of gene expression.
Liquid Serial Dilution Is Inferior to Solid Media for Isolation of Cultures Representative of the Phylum-Level Diversity of Soil Bacteria
Authors: Schoenborn Liesbeth , Yates Penelope S. , Grinton Bronwyn E. , Hugenholtz Philip , Janssen Peter H. 
Published: July 2004

ABSTRACT

Representatives of only four well-characterized bacterial phyla were isolated from a pasture soil by using liquid serial dilution culture. In contrast, members of
Acidobacteria
,
Verrucomicrobia
, and
Gemmatimonadetes
and of other poorly represented bacterial lineages were isolated in earlier experiments with solidified versions of the same media. We conclude that, contrary to expectation, liquid serial dilution culture is inferior to culturing on solid media for isolating representatives of many bacterial phyla from soil.
Comparison of Shiga-Toxigenic
Escherichia coli
Prevalences among Dairy, Feedlot, and Cow-Calf Herds in Washington State
Authors: Cobbold Rowland N. , Rice Daniel H. , Szymanski Maryanne , Call Douglas R. , Hancock Dale D. 
Published: July 2004

ABSTRACT

Shiga-toxigenic
Escherichia coli
(STEC) strains were isolated from 7.4% of 1,440 fecal and farm environmental samples. Shiga toxin gene and STEC prevalences were significantly associated with animal production type and season. A range of serogroups were identified. Nine percent of isolates possessed all three principal virulence markers:
stx
2
,
eae
, and
ehx
.
Validation of a PCR-Based Method for Detection of Food-Borne Thermotolerant Campylobacters in a Multicenter Collaborative Trial
Authors: Josefsen M. H. , Cook N. , D'Agostino M. , Hansen F. , Wagner M. , Demnerova K. , Heuvelink A. E. , Tassios P. T. , Lindmark H. , Kmet V. , Barbanera M. , Fach P. , Loncarevic S. , Hoorfar J. 
Published: July 2004

ABSTRACT
A PCR-based method for rapid detection of food-borne thermotolerant campylobacters was evaluated through a collaborative trial with 12 laboratories testing spiked carcass rinse samples. The method showed an interlaboratory diagnostic sensitivity of 96.7% and a diagnostic specificity of 100% for chicken samples, while these values were 94.2 and 83.3%, respectively, for pig samples.
Degradation and Turnover of Extracellular DNA in Marine Sediments: Ecological and Methodological Considerations
Authors: Dell'Anno Antonio , Corinaldesi Cinzia 
Published: July 2004

ABSTRACT
Degradation rates of extracellular DNA determined in marine sediments were much higher than those in the water column. However, due to the high sediment DNA content, turnover times were much shorter in seawater. Results reported here provide new insights into the role of extracellular DNA in P cycling in marine ecosystems.
Isolates of
Piscirickettsia salmonis
from Scotland and Ireland Show Evidence of Clonal Diversity
Authors: Reid H. I. , Griffen A. A. , Birkbeck T. H. 
Published: July 2004

ABSTRACT

Salmonid rickettsial septicemia, caused by
Piscirickettsia salmonis
, causes major mortalities in Chilean salmonid aquaculture and is an increasing problem in Atlantic salmon in Ireland and Scotland. Analysis of 16S-to-23S internal transcribed sequences and 16S ribosomal DNA (rDNA) shows that Irish isolates of
P. salmonis
form two new groups of the organism while Scottish isolates cluster together with Norwegian and Canadian isolates from Atlantic salmon.
Influence of Biosurfactants from Probiotic Bacteria on Formation of Biofilms on Voice Prostheses
Authors: Rodrigues Lígia , van der Mei Henny C. , Teixeira José , Oliveira Rosário 
Published: July 2004

ABSTRACT

Biofilms were grown on preconditioned voice prostheses with biosurfactants obtained from probiotic bacteria
Lactococcus lactis
53 and
Streptococcus thermophilus
A in an artificial throat model. Both biosurfactants greatly reduced microbial numbers on prostheses and also induced a decrease in the airflow resistance that occurs on voice prostheses after biofilm formation. This study presents a promising strategy for prolonging the lifespan of voice prostheses.
Use of Oligonucleotide Microarrays for Rapid Detection and Serotyping of Acute Respiratory Disease-Associated Adenoviruses
Authors: Lin Baochuan , Vora Gary J. , Thach Dzung , Walter Elizabeth , Metzgar David , Tibbetts Clark , Stenger David A. 
Published: July 2004

ABSTRACTThe cessation of the adenovirus vaccination program for military trainees has resulted in several recent acute respiratory disease (ARD) outbreaks. In the absence of vaccination, rapid detection methods are necessary for the timely implementation of measures to prevent adenovirus transmission within military training facilities. To this end, we have combined a fluorogenic real-time multiplex PCR assay with four sets of degenerate PCR primers that target theE1A,fiber, andhexongenes with a long oligonucleotide microarray capable of identifying the most common adenovirus serotypes associated with adult respiratory tract infections (serotypes 3, 4, 7, 16, and 21) and a representative member of adenovirus subgroup C (serotype 6) that is a common cause of childhood ARD and that often persists into adulthood. Analyses with prototype strains demonstrated unique hybridization patterns for representative members of adenovirus subgroups B1, B2, C, and E, thus allowing serotype determination. Microarray-based sensitivity assessments revealed lower detection limits (between 1 and 100 genomic copies) for adenovirus serotype 4 (Ad4) and Ad7 cell culture lysates, clinical nasal washes, and throat swabs and purified DNA from clinical samples. When adenovirus was detected from coded clinical samples, the results obtained by this approach demonstrated an excellent concordance with those obtained by the more established method of adenovirus identification as well as by cell culture with fluorescent-antibody staining. Finally, the utility of this method was further supported by its ability to detect adenoviral coinfections, contamination, and, potentially, recombination events. Taken together, the results demonstrate the usefulness of the simple and rapid diagnostic method developed for the unequivocal identification of ARD-associated adenoviral serotypes from laboratory or clinical samples that can be completed in 1.5 to 4.0 h.
Septic Arthritis of the Knee Due to
Fusobacterium necrophorum
Authors: Sonsale Paresh D , Philipson Mark R. , Bowskill Jilean 
Published: July 2004

ABSTRACT

Gram-negative, anaerobic bacilli are unusual organisms to be isolated in cases of acute septic arthritis. We report the isolation of
Fusobacterium necrophorum
from joint aspirate in a case of acute septic arthritis, which presented 3 weeks after the drainage of a dental abscess.
QUANTUM ELECTRODYNAMICS OF RELATIVISTIC BOUND STATES WITH CUTOFFS
Authors: BARBAROUX JEAN-MARIE , DIMASSI MOUEZ , GUILLOT JEAN-CLAUDE 
Published: July 2004

We consider a Hamiltonian with ultraviolet and infrared cutoffs, describing the interaction of relativistic electrons and positrons in the Coulomb potential with photons in Coulomb gauge. The interaction includes both interaction of the current density with transversal photons and the Coulomb interaction of charge density with itself.We prove that the Hamiltonian is self-adjoint and has a ground state for sufficiently small coupling constants.
STRONGLY HYPERBOLIC SYSTEMS IN GENERAL RELATIVITY
Authors: REULA OSCAR A. 
Published: July 2004

We discuss several topics related to the notion of strong hyperbolicity which are of interest in general relativity. After introducing the concept and showing its relevance we provide some covariant definitions of strong hyperbolicity. We then prove that if a system is strongly hyperbolic with respect to a given hypersurface, then it is also strongly hyperbolic with respect to any nearby surface. We then study for how much these hypersurfaces can be deformed and discuss then causality, namely what the maximal propagation speed in any given direction is. In contrast with the symmetric hyperbolic case, for which the proof of causality is geometrical and direct, relaying in energy estimates, the proof for general strongly hyperbolic systems is indirect for it is based in Holmgren's theorem. To show that the concept is needed in the area of general relativity we discuss two results for which the theory of symmetric hyperbolic systems shows to be insufficient. The first deals with the hyperbolicity analysis of systems which are second order in space derivatives; they include certain versions of the ADM and the BSSN families of equations. This analysis is considerably simplified by introducing pseudo-differential first-order evolution equations. Well-posedness for some members of the latter family systems is established by showing they satisfy the strong hyperbolicity property. Furthermore it is shown that many other systems of such families are only weakly hyperbolic, implying they should not be used for numerical modeling. The second result deals with systems having constraints. The question posed is which hyperbolicity properties, if any, are inherited from the original evolution system by the subsidiary system satisfied by the constraint quantities. The answer is that, subject to some condition on the constraints, if the evolution system is strongly hyperbolic then the subsidiary system is also strongly hyperbolic and the causality properties of both are identical.