bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization ofFerroplasmaIsolates andFerroplasma acidarmanussp. nov., Extreme Acidophiles from Acid Mine Drainage and Industrial Bioleaching Environments
Authors: Dopson Mark , Baker-Austin Craig , Hind Andrew , Bowman John P. , Bond Philip L. 
Published: April 2004

ABSTRACTThree recently isolated extremely acidophilic archaeal strains have been shown to be phylogenetically similar toFerroplasma acidiphilumYTby 16S rRNA gene sequencing. All fourFerroplasmaisolates were capable of growing chemoorganotrophically on yeast extract or a range of sugars and chemomixotrophically on ferrous iron and yeast extract or sugars, and isolate “Ferroplasma acidarmanus” Fer1Trequired much higher levels of organic carbon. All four isolates were facultative anaerobes, coupling chemoorganotrophic growth on yeast extract to the reduction of ferric iron. The temperature optima for the four isolates were between 35 and 42°C and the pH optima were 1.0 to 1.7, and “F. acidarmanus” Fer1Twas capable of growing at pH 0. The optimum yeast extract concentration for “F. acidarmanus” Fer1Twas higher than that for the other three isolates. Phenotypic results suggested that isolate “F. acidarmanus” Fer1Tis of a different species than the other three strains, and 16S rRNA sequence data, DNA-DNA similarity values, and two-dimensional polyacrylamide gel electrophoresis protein profiles clearly showed that strains DR1, MT17, and YTgroup as a single species. “F. acidarmanus” Fer1Tgroups separately, and we propose the new species “F. acidarmanus” Fer1Tsp. nov.
Influence of Environmental Factors and Human Activity on the Presence of
Salmonella
Serovars in a Marine Environment
Authors: Martinez-Urtaza Jaime , Saco Montserrat , de Novoa Jacobo , Perez-Piñeiro Pelayo , Peiteado Jesus , Lozano-Leon Antonio , Garcia-Martin Oscar 
Published: April 2004

ABSTRACT

The temporal and spatial distribution of
Salmonella
contamination in the coastal waters of Galicia (northwestern Spain) relative to contamination events with different environmental factors (temperature, wind, hours of sunlight, rainfall, and river flow) were investigated over a 4-year period. Salmonellae were isolated from 127 of 5,384 samples of molluscs and seawater (2.4%), and no significant differences (
P
< 0.05) between isolates obtained in different years were observed. The incidence of salmonellae was significantly higher in water column samples (2.9%) than in those taken from the marine benthos (0.7%). Of the 127 strains of
Salmonella
isolated, 20 different serovars were identified.
Salmonella enterica
serovar Senftenberg was the predominant serovar, being represented by 54 isolates (42.5%), followed by serovar Typhimurium (19 isolates [15%]) and serovar Agona (12 isolates [9.4%]). Serovar Senftenberg was detected at specific points on the coast and could not be related to any of the environmental parameters analyzed. All serovars except
Salmonella
serovar Senftenberg were found principally in the southern coastal areas close to the mouths of rivers, and their incidence was associated with high southwestern wind and rainfall. Using multiple logistic regression analysis models, the prevalence of salmonellae was best explained by environmental parameters on the day prior to sampling. Understanding this relationship may be useful for the control of molluscan shellfish harvests, with wind and rainfall serving as triggers for closure.
Immunodetection of the Bacteriocin Lacticin RM: Analysis of the Influence of Temperature and Tween 80 on Its Expression and Activity
Authors: Keren Tomer , Yarmus Merav , Halevy Galia , Shapira Roni 
Published: April 2004

ABSTRACT

Immunoassays with specific antibodies offer higher sensitivity than do bioassays with indicator strains in the detection and quantification of several bacteriocins. Here we present the purification of lacticin RM and the production of specific polyclonal antibodies to a synthetic peptide resembling an internal fragment of the mature bacteriocin. The specificity and sensitivity of the generated polyclonal antibodies were evaluated in various immunoassays. The detection limits of lacticin RM were found to be 1.9, 0.16, and 0.18 μg ml
−1
for Western blot, immuno-dot blot, and noncompetitive indirect enzyme-linked immunosorbent assays, respectively. Immunoassay sensitivities were 12.5-fold higher than that of the agar diffusion test (ADT). The production of lacticin RM showed temperature dependency, with 3, 4.2, 12.7, 28.9, 37.8, and 12 μg ml
−1
at 37, 30, 20, 15, 10, and 4°C, respectively. Temperature-stability analysis demonstrated that lacticin RM is sensitive to mild temperature, but the loss of activity does not seem to result from protein degradation. Tween 80 increased the concentration of lacticin RM eightfold and probably affected the results of the ADT either by enhancing the activity of lacticin RM or by increasing the sensitivity of the indicator strain. The use of antibodies for the specific detection and quantification of lacticin RM can expand our knowledge of its production and stability, with important implications for further investigation and future application.
Root Nodule
Bradyrhizobium
spp. Harbor
tfdA
α and
cadA
, Homologous with Genes Encoding 2,4-Dichlorophenoxyacetic Acid-Degrading Proteins
Authors: Itoh Kazuhito , Tashiro Yoshiko , Uobe Kazuko , Kamagata Yoichi , Suyama Kousuke , Yamamoto Hiroki 
Published: April 2004

ABSTRACT

The distribution of
tfdA
α and
cadA
, genes encoding 2,4-dichlorophenoxyacetate (2,4-D)-degrading proteins which are characteristic of the 2,4-D-degrading
Bradyrhizobium
sp. isolated from pristine environments, was examined by PCR and Southern hybridization in several
Bradyrhizobium
strains including type strains of
Bradyrhizobium japonicum
USDA110 and
Bradyrhizobium elkanii
USDA94, in phylogenetically closely related
Agromonas oligotrophica
and
Rhodopseudomonas palustris
, and in 2,4-D-degrading
Sphingomonas
strains. All strains showed positive signals for
tfdA
α, and its phylogenetic tree was congruent with that of 16S rRNA genes in α-
Proteobacteria
, indicating evolution of
tfdA
α without horizontal gene transfer. The nucleotide sequence identities between
tfdA
α and canonical
tfdA
in β- and γ-
Proteobacteria
were 46 to 57%, and the deduced amino acid sequence of TfdAα revealed conserved residues characteristic of the active site of α-ketoglutarate-dependent dioxygenases. On the other hand,
cadA
showed limited distribution in 2,4-D-degrading
Bradyrhizobium
sp. and
Sphingomonas
sp. and some strains of non-2,4-D-degrading
B. elkanii.
The
cadA
genes were phylogenetically separated between 2,4-D-degrading and nondegrading strains, and the cadA genes of 2,4-D degrading strains were further separated between
Bradyrhizobium
sp. and
Sphingomonas
sp., indicating the incongruency of
cadA
with 16S rRNA genes. The nucleotide sequence identities between
cadA
and
tftA
of 2,4,5-trichlorophenoxyacetate-degrading
Burkholderia cepacia
AC1100 were 46 to 53%. Although all root nodule
Bradyrhizobium
strains were unable to degrade 2,4-D, three strains carrying
cadA
homologs degraded 4-chlorophenoxyacetate with the accumulation of 4-chlorophenol as an intermediate, suggesting the involvement of
cadA
homologs in the cleavage of the aryl ether linkage. Based on codon usage patterns and GC content, it was suggested that the
cadA
genes of 2,4-D-degrading and nondegrading
Bradyrhizobium
spp. have different origins and that the genes would be obtained in the former through horizontal gene transfer.
Gas Exchange in the Filamentous Cyanobacterium
Nostoc punctiforme
Strain ATCC 29133 and ItsHydrogenase-Deficient Mutant StrainNHM5
Authors: Lindberg Pia , Lindblad Peter , Cournac Laurent 
Published: April 2004

ABSTRACT

Nostoc
punctiforme
ATCC 29133 is a nitrogen-fixing, heterocystous
cyanobacterium of symbiotic origin. During nitrogen fixation, it
produces molecular hydrogen (H
2
), which is recaptured by an
uptake hydrogenase. Gas exchange in cultures of
N.
punctiforme
ATCC 29133 and its hydrogenase-free mutant strain
NHM5 was studied. Exchange of O
2
, CO
2
,
N
2
, and H
2
was followed simultaneously with a
mass spectrometer in cultures grown under nitrogen-fixing conditions.
Isotopic tracing was used to separate evolution and uptake of
CO
2
and O
2
. The amount of H
2
produced
per molecule of N
2
fixed was found to vary with light
conditions, high light giving a greater increase in H
2
production than N
2
fixation. The ratio under low light and
high light was approximately 1.4 and 6.1 molecules of H
2
produced per molecule of N
2
fixed, respectively. Incubation
under high light for a longer time, until the culture was depleted of
CO
2
, caused a decrease in the nitrogen fixation rate. At the
same time, hydrogen production in the hydrogenase-deficient strain was
increased from an initial rate of approximately 6 μmol (mg of
chlorophyll
a
)
−1
h
−1
to
9 μmol (mg of chlorophyll
a
)
−1
h
−1
after about 50 min. A light-stimulated
hydrogen-deuterium exchange activity stemming from the nitrogenase was
observed in the two strains. The present findings are important for
understanding this nitrogenase-based system, aiming at photobiological
hydrogen production, as we have identified the conditions under which
the energy flow through the nitrogenase can be directed towards
hydrogen production rather than nitrogen
fixation.
Cloning, Deletion, and Characterization of PadR, the Transcriptional Repressor of the Phenolic Acid Decarboxylase-EncodingpadAGene ofLactobacillus plantarum
Authors: Gury Jérôme , Barthelmebs Lise , Tran Ngoc Phuong , Diviès Charles , Cavin Jean-François 
Published: April 2004

ABSTRACTLactobacillus plantarumdisplays a substrate-induciblepadAgene encoding a phenolic acid decarboxylase enzyme (PadA) that is considered a specific chemical stress response to the inducing substrate. The putative regulator ofpadAwas located in thepadAlocus based on its 52% identity with PadR, thepadAgene transcriptional regulator ofPediococcus pentosaceus(L. Barthelmebs, B. Lecomte, C. Diviès, and J.-F. Cavin, J. Bacteriol.182:6724-6731, 2000). Deletion of theL. plantarum padRgene clearly demonstrates that the protein it encodes is the transcriptional repressor of divergently orientedpadA. ThepadRgene is cotranscribed with a downstream open reading frame (ORF1), the product of which may belong to a group of universal stress proteins (Usp). ThepadRdeletion mutant overexpressedpadAconstitutively, and thepadApromoter appears to be tightly regulated in this bacterium. Gel mobility shift assays using thepadAgene promoter region and purified PadR expressed inEscherichia coliindicated that operator DNA binding by PadR was not eliminated by addition ofp-coumarate. Gel mobility shift assays using partially purified extracts of native PadR protein from both phenolic acid-induced and noninducedL. plantarumcells demonstrate that inactivation of PadR by phenolic acids requires the integrity ofL. plantarumand mediation by a specific protein absent inE. coli.
Detection of Noroviruses in Tap Water in Japan by Means of a New Method for Concentrating Enteric Viruses in Large Volumes of Freshwater
Authors: Haramoto Eiji , Katayama Hiroyuki , Ohgaki Shinichiro 
Published: April 2004

ABSTRACT

A virus concentration method using a cation-coated filter was developed for large-volume freshwater applications. Poliovirus type 1 (LSc 2ab Sabin strain) inoculated into 40 ml of MilliQ (ultrapure) water was adsorbed effectively to a negatively charged filter (Millipore HA, 0.45-μm pore size) coated with aluminum ions, 99% (range, 81 to 114%) of which were recovered by elution with 1.0 mM NaOH (pH 10.8) following an acid rinse with 0.5 mM H
2
SO
4
(pH 3.0). More than 80% poliovirus recovery yields were obtained from 500-ml, 1,000-ml, and 10-liter MilliQ water samples and from tap water samples. This method, followed by TaqMan PCR detection, was applied to determine the presence of noroviruses in tap water in Tokyo, Japan. In a 14-month survey, 4 (4.1%) and 7 (7.1%) of 98 tap water samples (100 to 532 liters) contained a detectable amount of noroviruses of genotype 1 and genotype 2, respectively. This method was proved to be useful for surveying the occurrence of enteric viruses, including noroviruses, in large volumes of freshwater.
Characterization of
Bacillus
Probiotics Available for Human Use
Authors: Duc Le H. , Hong Huynh A. , Barbosa Teresa M. , Henriques Adriano O. , Cutting Simon M. 
Published: April 2004

ABSTRACT

Bacillus
species (
Bacillus cereus
,
Bacillus clausii
,
Bacillus pumilus
) carried in five commercial probiotic products consisting of bacterial spores were characterized for potential attributes (colonization, immunostimulation, and antimicrobial activity) that could account for their claimed probiotic properties. Three
B. cereus
strains were shown to persist in the mouse gastrointestinal tract for up to 18 days postadministration, demonstrating that these organisms have some ability to colonize. Spores of one
B. cereus
strain were extremely sensitive to simulated gastric conditions and simulated intestinal fluids. Spores of all strains were immunogenic when they were given orally to mice, but the
B. pumilus
strain was found to generate particularly high anti-spore immunoglobulin G titers. Spores of
B. pumilus
and of a laboratory strain of
B. subtilis
were found to induce the proinflammatory cytokine interleukin-6 in a cultured macrophage cell line, and in vivo, spores of
B. pumilus
and
B. subtilis
induced the proinflammatory cytokine tumor necrosis factor alpha and the Th1 cytokine gamma interferon. The
B. pumilus
strain and one
B. cereus
strain (
B. cereus
var. vietnami) were found to produce a bacteriocin-like activity against other
Bacillus
species. The results that provided evidence of colonization, immunostimulation, and antimicrobial activity support the hypothesis that the organisms have a potential probiotic effect. However, the three
B. cereus
strains were also found to produce the Hbl and Nhe enterotoxins, which makes them unsafe for human use.
Multilocus Sequence Typing of
Listeria monocytogenes
by Use of Hypervariable Genes Reveals Clonal and Recombination Histories of Three Lineages
Authors: Meinersmann Richard J. , Phillips Robert W. , Wiedmann Martin , Berrang Mark E. 
Published: April 2004

ABSTRACT

In an attempt to develop a method to discriminate among isolates of
Listeria monocytogenes
, the sequences of all of the annotated genes from the fully sequenced strain
L. monocytogenes
EGD-e (serotype 1/2a) were compared by BLASTn to a file of the unfinished genomic sequence of
L. monocytogenes
ATCC 19115 (serotype 4b). Approximately 7% of the matching genes demonstrated 90% or lower identity between the two strains, and the lowest observed identity was 80%. Nine genes (
hisJ
,
cbiE
,
truB
,
ribC
,
comEA
,
purM
,
aroE
,
hisC
, and
addB
) in the 80 to 90% identity group and two genes (
gyrB
and
rnhB
) with approximately 97% identity were selected for multilocus sequence analysis in two sets of
L. monocytogenes
isolates (a 15-strain diversity set and a set of 19 isolates from a single food-processing plant). Based on concatenated sequences, a total of 33 allotypes were differentiated among the 34 isolates tested. Population genetics analyses revealed three lineages of
L. monocytogenes
that differed in their history of apparent recombination. Lineage I appeared to be completely clonal, whereas representatives of the other lineages demonstrated evidence of horizontal gene transfer and recombination. Although most of the gene sequences for lineage II strains were distinct from those of lineage I, a few strains with the majority of genes characteristic of lineage II had some that were characteristic of lineage I. Genes from lineage III organisms were mostly similar to lineage I genes, with instances of genes appearing to be mosaics with lineage II genes. Even though lineage I and lineage II generally demonstrated very distinct sequences, the sequences for the 11 selected genes demonstrated little discriminatory power within each lineage. In the
L. monocytogenes
isolate set obtained from one food-processing plant, lineage I and lineage II were found to be almost equally prevalent. While it appears that different lineages of
L. monocytogenes
can share habitats, they appear to differ in their histories of horizontal gene transfer.
Identification ofStreptococcus thermophilusCNRZ368 Genes Involved in Defense against Superoxide Stress
Authors: Thibessard Annabelle , Borges Frédéric , Fernandez Annabelle , Gintz Brigitte , Decaris Bernard , Leblond-Bourget Nathalie 
Published: April 2004

ABSTRACTTo better understand the defense mechanism ofStreptococcus thermophilusagainst superoxide stress, molecular analysis of 10 menadione-sensitive mutants, obtained by insertional mutagenesis, was undertaken. This analysis allowed the identification of 10 genes that, with respect to their putative functions, were classified into five categories: (i) those involved in cell wall metabolism, (ii) those involved in exopolysaccharide translocation, (iii) those involved in RNA modification, (iv) those involved in iron homeostasis, and (v) those whose functions are still unknown. The behavior of the 10 menadione-sensitive mutants exposed to heat shock was investigated. Data from these experiments allowed us to distinguish genes whose action might be specific to oxidative stress defense (tgt,ossF, andossG) from those whose action may be generalized to other stressful conditions (mreD,rodA,pbp2b,cpsX, andiscU). Among the mutants, two harbored an independently inserted copy of pGh9:ISS1in two loci close to each other. More precisely, these two loci are homologous to thesufDandiscUgenes, which are involved in the biosynthesis of iron-sulfur clusters. This region, called thesufregion, was further characterized inS. thermophilusCNRZ368 by sequencing and by construction of ΔsufDandiscU97nonpolar mutants. The streptonigrin sensitivity levels of both mutants suggest that these two genes are involved in iron metabolism.
Survey of Archaeal Diversity Reveals an Abundance of HalophilicArchaeain a Low-Salt, Sulfide- and Sulfur-Rich Spring
Authors: Elshahed Mostafa S. , Najar Fares Z. , Roe Bruce A. , Oren Aharon , Dewers Thomas A. , Krumholz Lee R. 
Published: April 2004

ABSTRACTThe archaeal community in a sulfide- and sulfur-rich spring with a stream water salinity of 0.7 to 1.0% in southwestern Oklahoma was studied by cloning and sequencing of 16S rRNA genes. Two clone libraries were constructed from sediments obtained at the hydrocarbon-exposed source of the spring and the microbial mats underlying the water flowing from the spring source. Analysis of 113 clones from the source library and 65 clones from the mat library revealed that the majority of clones belonged to the kingdomEuryarchaeota, whileCrenarchaeotarepresented less than 10% of clones. Euryarchaeotal clones belonged to the ordersMethanomicrobiales,Methanosarcinales, andHalobacteriales, as well as several previously described lineages with no pure-culture representatives. Those within theHalobacterialesrepresented 36% of the mat library and 4% of the source library. All cultivated members of this order are obligately aerobic halophiles. The majority of halobacterial clones encountered were not affiliated with any of the currently described genera of the familyHalobacteriaceae. Measurement of the salinity at various locations at the spring, as well as along vertical gradients, revealed that soils adjacent to spring mats have a much higher salinity (NaCl concentrations as high as 32%) and a lower moisture content than the spring water, presumably due to evaporation. By use of a high-salt-plus-antibiotic medium, several halobacterial isolates were obtained from the microbial mats. Analysis of 16S rRNA genes indicated that all the isolates were members of the genusHaloferax. All isolates obtained grew at a wide range of salt concentrations, ranging from 6% to saturation, and all were able to reduce elemental sulfur to sulfide. We reason that the unexpected abundance of halophilicArchaeain such a low-salt, highly reduced environment could be explained by their relatively low salt requirement, which could be satisfied in specific locations of the shallow spring via evaporation, and their ability to grow under the prevalent anaerobic conditions in the spring, utilizing zero-valent sulfur compounds as electron acceptors. This study demonstrates that members of theHalobacterialesare not restricted to their typical high-salt habitats, and we propose a role for theHalobacterialesin sulfur reduction in natural ecosystems.
Prevalence of the Genes Encoding Propionicin T1 andProtease-Activated Antimicrobial Peptide and Their Expressionin ClassicalPropionibacteria
Authors: Faye Therese , Brede Dag Anders , Langsrud Thor , Nes Ingolf F. , Holo Helge 
Published: April 2004

ABSTRACT

The
purpose of this study was to investigate the frequency
of production of the bacteriocin propionicin T1 and the
protease-activated antimicrobial peptide (PAMP) and their corresponding
genes in 64 isolates of classical propionibacteria. This study revealed
that these genes are widespread in
Propionibacterium jensenii
and
Propionibacterium thoenii
but absent from the remaining
species of classical propionibacteria that were studied. The
pro-PAMP-encoding gene (
pamA
) was found in 63% of the
P. jensenii
strains and 61% of the
P. thoenii
strains, and all of these strains displayed PAMP activity. The
propionicin T1-encoding gene (
pctA
) was present in 89%
of the
P. thoenii
strains and 54% of the
P.
jensenii
strains. All
P. thoenii
strains containing the
pctA
gene exhibited antimicrobial activity corresponding to
propionicin T1 activity, whereas only 38% of the
pctA
-containing
P. jensenii
strains displayed this
activity. Sequencing of the
pctA
genes revealed the existence
of two allelic variants that differed in a single nucleotide in six
strains of
P. jensenii
; in these strains the glycine at
position 55 of propionicin T1 was replaced by an aspartate residue (A
variant). No strains harboring the A variant showed any antimicrobial
activity against propionicin T1-sensitive bacteria. An open reading
frame (
orf2
) located immediately downstream from the
pctA
gene was absent in three strains containing the G variant
of propionicin T1. Two of these strains showed low antimicrobial
activity, while the third strain showed no antimicrobial activity at
all. The protein encoded by
orf2
showed strong homology to ABC
transporters, and it has been proposed previously that this protein is
involved in the producer immunity against propionicin T1. The limited
antimicrobial activity exhibited by the strains lacking
orf2
further suggests that this putative ABC transporter plays an important
role in propionicin T1
activity.