bluuebunny/crossref_metadata_2025_split huggingface dataset:
Isolation and Identification ofRickettsia massiliaefromRhipicephalus sanguineusTicks Collected in Arizona
Authors: Eremeeva Marina E. , Bosserman Elizabeth A. , Demma Linda J. , Zambrano Maria L. , Blau Dianna M. , Dasch Gregory A. 
Published: August 2006

ABSTRACTTwentyRhipicephalus sanguineusticks collected in eastern Arizona were tested by PCR assay to establish their infection rate with spotted fever group rickettsiae. With a nested PCR assay which detects a fragment of theRickettsiagenus-specific 17-kDa antigen gene (htrA), five ticks (25%) were found to contain rickettsial DNA. One rickettsial isolate was obtained from these ticks by inoculating a suspension of a triturated tick into monolayers of Vero E6 monkey kidney cells and XTC-2 clawed toad cells, and its cell culture and genotypic characteristics were determined. Fragments of the 16S rRNA, GltA, rOmpA, rOmpB, and Sca4 genes had 100%, 100%, 99%, 99%, and 99%, respectively, nucleotide similarity toRickettsia massiliaestrain Bar29, previously isolated fromR. sanguineusin Catalonia, Spain (L. Beati et al., J. Clin. Microbiol.34:2688-2694, 1996). The new isolate, AZT80, does not elicit cytotoxic effects in Vero cells and causes a persistent infection in XTC-2 cells. The AZT80 strain is susceptible to doxycycline but resistant to rifampin and erythromycin. WhetherR. massiliaeAZT80 is pathogenic or infectious for dogs and humans or can cause seroconversion to spotted fever group antigens in the United States is unknown.
Molecular Profiling of theClostridium leptumSubgroup in Human Fecal Microflora by PCR-Denaturing Gradient Gel Electrophoresis and Clone Library Analysis
Authors: Shen Jian , Zhang Baorang , Wei Guifang , Pang Xiaoyan , Wei Hua , Li Min , Zhang Yan , Jia Wei , Zhao Liping 
Published: August 2006

ABSTRACTA group-specific PCR-based denaturing gradient gel electrophoresis (DGGE) method was developed and combined with group-specific clone library analysis to investigate the diversity of theClostridium leptumsubgroup in human feces. PCR products (length, 239 bp) were amplified usingC. leptumcluster-specific primers and were well separated by DGGE. The DGGE patterns of fecal amplicons from 11 human individuals revealed host-specific profiles; the patterns for fecal samples collected from a child for 3 years demonstrated the structural succession of the population in the first 2 years and its stability in the third year. A clone library was constructed with 100 clones consisting of 1,143-bp inserts of 16S rRNA gene fragments that were amplified from one adult fecal DNA with one forward universal bacterial primer and one reverse group-specific primer. Eighty-six of the clones produced the 239-bpC. leptumcluster-specific amplicons, and the remaining 14 clones did not produce these amplicons but still phylogenetically belong to the subgroup. Sixty-four percent of the clones were related toFaecalibacterium prausnitzii(similarity, 97 to 99%), 6% were related toSubdoligranulum variabile(similarity, ∼99%), 2% were related to butyrate-producing bacterium A2-207 (similarity, 99%), and 28% were not identified at the species level. The identities of most bands in the DGGE profiles for the same adult were determined by comigration analysis with the 86 clones that harbored the 239-bp group-specific fragments. Our results suggest that DGGE combined with clone library analysis is an effective technique for monitoring and analyzing the composition of this important population in the human gut flora.
Biodegradation of Ether Pollutants by
Pseudonocardia
sp. Strain ENV478
Authors: Vainberg Simon , McClay Kevin , Masuda Hisako , Root Duane , Condee Charles , Zylstra Gerben J. , Steffan Robert J. 
Published: August 2006

ABSTRACT

A bacterium designated
Pseudonocardia
sp. strain ENV478 was isolated by enrichment culturing on tetrahydrofuran (THF) and was screened to determine its ability to degrade a range of ether pollutants. After growth on THF, strain ENV478 degraded THF (63 mg/h/g total suspended solids [TSS]), 1,4-dioxane (21 mg/h/g TSS), 1,3-dioxolane (19 mg/h/g TSS),
bis
-2-chloroethylether (BCEE) (12 mg/h/g TSS), and methyl
tert
-butyl ether (MTBE) (9.1 mg/h/g TSS). Although the highest rates of 1,4-dioxane degradation occurred after growth on THF, strain ENV478 also degraded 1,4-dioxane after growth on sucrose, lactate, yeast extract, 2-propanol, and propane, indicating that there was some level of constitutive degradative activity. The BCEE degradation rates were about threefold higher after growth on propane (32 mg/h/g TSS) than after growth on THF, and MTBE degradation resulted in accumulation of
tert
-butyl alcohol. Degradation of 1,4-dioxane resulted in accumulation of 2-hydroxyethoxyacetic acid (2HEAA). Despite its inability to grow on 1,4-dioxane, strain ENV478 degraded this compound for >80 days in aquifer microcosms. Our results suggest that the inability of strain ENV478 and possibly other THF-degrading bacteria to grow on 1,4-dioxane is related to their inability to efficiently metabolize the 1,4-dioxane degradation product 2HEAA but that strain ENV478 may nonetheless be useful as a biocatalyst for remediating 1,4-dioxane-contaminated aquifers.
Quantitative Detection of the
nosZ
Gene, Encoding Nitrous Oxide Reductase, and Comparison of the Abundances of 16S rRNA,
narG
,
nirK
, and
nosZ
Genes in Soils
Authors: Henry S. , Bru D. , Stres B. , Hallet S. , Philippot L. 
Published: August 2006

ABSTRACT

Nitrous oxide (N
2
O) is an important greenhouse gas in the troposphere controlling ozone concentration in the stratosphere through nitric oxide production. In order to quantify bacteria capable of N
2
O reduction, we developed a SYBR green quantitative real-time PCR assay targeting the
nosZ
gene encoding the catalytic subunit of the nitrous oxide reductase. Two independent sets of
nosZ
primers flanking the
nosZ
fragment previously used in diversity studies were designed and tested (K. Kloos, A. Mergel, C. Rösch, and H. Bothe, Aust. J. Plant Physiol. 28:991-998, 2001). The utility of these real-time PCR assays was demonstrated by quantifying the
nosZ
gene present in six different soils. Detection limits were between 10
1
and 10
2
target molecules per reaction for all assays. Sequence analysis of 128 cloned quantitative PCR products confirmed the specificity of the designed primers. The abundance of
nosZ
genes ranged from 10
5
to 10
7
target copies g
−1
of dry soil, whereas genes for 16S rRNA were found at 10
8
to 10
9
target copies g
−1
of dry soil. The abundance of
narG
and
nirK
genes was within the upper and lower limits of the 16S rRNA and
nosZ
gene copy numbers. The two sets of
nosZ
primers gave similar gene copy numbers for all tested soils. The maximum abundance of
nosZ
and
nirK
relative to 16S rRNA was 5 to 6%, confirming the low proportion of denitrifiers to total bacteria in soils.
Screening for and Identification of Starch-, Amylopectin-, and Pullulan-Degrading Activities in Bifidobacterial Strains
Authors: Ryan Sinéad M. , Fitzgerald Gerald F. , van Sinderen Douwe 
Published: August 2006

ABSTRACT

Forty-two bifidobacterial strains were screened for α-amylase and/or pullulanase activity by investigating their capacities to utilize starch, amylopectin, or pullulan. Of the 42 bifidobacterial strains tested, 19 were capable of degrading potato starch. Of these 19 strains, 11 were able to degrade starch and amylopectin, as well as pullulan. These 11 strains, which were shown to produce extracellular starch-degrading activities, included 5 strains of
Bifidobacterium breve
, 1
B. dentium
strain, 1
B. infantis
strain, 3 strains of
B. pseudolongum
, and 1 strain of
B. thermophilum
. Quantitative and qualitative enzyme activities were determined by measuring the concentrations of released reducing sugars and by high-performance thin-layer chromatography, respectively. These analyses confirmed both the inducible nature and the extracellular nature of the starch- and pullulan-degrading enzyme activities and showed that the five
B. breve
strains produced an activity that is consistent with type II pullulanase (amylopullulanase) activity, while the remaining six strains produced an activity with properties that resemble those of type III pullulan hydrolase.
Deletion Mutations Caused by DNA Strand Slippage in
Acinetobacter baylyi
Authors: Gore Jeremy M. , Ran F. Ann , Ornston L. Nicholas 
Published: August 2006

ABSTRACT

Short nucleotide sequence repetitions in DNA can provide selective benefits and also can be a source of genetic instability arising from deletions guided by pairing between misaligned strands. These findings raise the question of how the frequency of deletion mutations is influenced by the length of sequence repetitions and by the distance between them. An experimental approach to this question was presented by the heat-sensitive phenotype conferred by
pcaG1102
, a 30-bp deletion in one of the structural genes for
Acinetobacter baylyi
protocatechuate 3,4-dioxygenase, which is required for growth with quinate. The original
pcaG1102
deletion appears to have been guided by pairing between slipped DNA strands from nearby repeated sequences in wild-type
pcaG
. Placement of an in-phase termination codon between the repeated sequences in
pcaG
prevents growth with quinate and permits selection of sequence-guided deletions that excise the codon and permit quinate to be used as a growth substrate at room temperature. Natural transformation facilitated introduction of 68 different variants of the wild-type repeat structure within
pcaG
into the
A. baylyi
chromosome, and the frequency of deletion between the repetitions was determined with a novel method, precision plating. The deletion frequency increases with repeat length, decreases with the distance between repeats, and requires a minimum amount of similarity to occur at measurable rates. Deletions occurred in a
recA
-deficient background. Their frequency was unaffected by deficiencies in
mutS
and was increased by inactivation of
recG
.
Occurrence of Ammonia-Oxidizing Archaea in Wastewater Treatment Plant Bioreactors
Authors: Park Hee-Deung , Wells George F. , Bae Hyokwan , Criddle Craig S. , Francis Christopher A. 
Published: August 2006

ABSTRACT

We report molecular evidence that ammonia-oxidizing archaea (AOA) occur in activated sludge bioreactors used to remove ammonia from wastewater. Using PCR primers targeting archaeal ammonia monooxygenase subunit A (
amoA
) genes, we retrieved and compared 75 sequences from five wastewater treatment plants operating with low dissolved oxygen levels and long retention times. All of these sequences showed similarity to sequences previously found in soil and sediments, and they were distributed primarily in four major phylogenetic clusters. One of these clusters contained virtually identical
amoA
sequences obtained from all five activated sludge samples (from Oregon, Wisconsin, Pennsylvania, and New Jersey) and accounted for 67% of all the sequences, suggesting that this AOA phylotype may be widespread in nitrifying bioreactors.
Hyperthermophilic DNA Methyltransferase M.PabI from the Archaeon
Pyrococcus abyssi
Authors: Watanabe Miki , Yuzawa Harumi , Handa Naofumi , Kobayashi Ichizo 
Published: August 2006

ABSTRACT

Genome sequence comparisons among multiple species of
Pyrococcus
, a hyperthermophilic archaeon, revealed a linkage between a putative restriction-modification gene complex and several large genome polymorphisms/rearrangements. From a region apparently inserted into the
Pyrococcus abyssi
genome, a hyperthermoresistant restriction enzyme [PabI; 5′-(GTA/C)] with a novel structure was discovered. In the present work, the neighboring methyltransferase homologue, M.PabI, was characterized. Its N-terminal half showed high similarities to the M subunit of type I systems and a modification enzyme of an atypical type II system, M.AhdI, while its C-terminal half showed high similarity to the S subunit of type I systems. M.PabI expressed within
Escherichia coli
protected PabI sites from RsaI, a PabI isoschizomer. M.PabI, purified following overexpression, was shown to generate 5′-GTm6AC, which provides protection against PabI digestion. M.PabI was found to be highly thermophilic; it showed methylation at 95°C and retained at least half the activity after 9 min at 95°C. This hyperthermophilicity allowed us to obtain activation energy and other thermodynamic parameters for the first time for any DNA methyltransferases. We also determined the kinetic parameters of
k
cat
,

K
m

, DNA
, and

K
m

, AdoMet
. The activity of M.PabI was optimal at a slightly acidic pH and at an NaCl concentration of 200 to 500 mM and was inhibited by Zn
2+
but not by Mg
2+
, Ca
2+
, or Mn
2+
. These and previous results suggest that this unique methyltransferase and PabI constitute a type II restriction-modification gene complex that inserted into the
P. abyssi
genome relatively recently. As the most thermophilic of all the characterized DNA methyltransferases, M.PabI may help in the analysis of DNA methylation and its application to DNA engineering.
Diversity of
Bacillus anthracis
Strains in Georgia and of Vaccine Strains from the Former Soviet Union
Authors: Merabishvili Maya , Natidze Merab , Rigvava Sergo , Brusetti Lorenzo , Raddadi Noura , Borin Sara , Chanishvili Nina , Tediashvili Marina , Sharp Richard , Barbeschi Maurizio , Visca Paolo , Daffonchio Daniele 
Published: August 2006

ABSTRACT

Despite the increased number of anthrax outbreaks in Georgia and the other Caucasian republics of the former Soviet Union, no data are available on the diversity of the
Bacillus anthracis
strains involved. There is also little data available on strains from the former Soviet Union, including the strains previously used for vaccine preparation. In this study we used eight-locus variable-number tandem repeat analyses to genotype 18 strains isolated from infected animals and humans at different sites across Georgia, where anthrax outbreaks have occurred in the last 10 years, and 5 strains widely used for preparation of human and veterinary vaccines in the former Soviet Union. Three different genotypes affiliated with the A3.a cluster were detected for the Georgian isolates. Two genotypes were previously shown to include Turkish isolates, indicating that there is a regional strain pattern in the South Caucasian-Turkish region. Four of the vaccine strains were polymorphic, exhibiting three different patterns of the cluster A1.a genotype and the cluster A3.b genotype. The genotype of vaccine strain 71/12, which is considered an attenuated strain in spite of the presence of both of the virulence pXO plasmids, appeared to be a novel genotype in the A1.a cluster.
Occurrence of
Cryptosporidium
Oocysts and
Giardia
Cysts in Sewage in Norway
Authors: Robertson L. J. , Hermansen L. , Gjerde B. K. 
Published: August 2006

ABSTRACT

Samples of sewage influent from 40 sewage treatment works (STW) throughout Norway were examined for
Cryptosporidium
oocysts and
Giardia duodenalis
cysts. Both parasites were detected frequently (80% of STW were
Cryptosporidium
positive; 93% of STW were
Giardia
positive) and at maximum concentrations of >20,000 parasites/liter. The data suggest giardiasis is more widespread, and/or occurs with greater infection intensity, than cryptosporidiosis in Norway. STW serving higher person equivalents were more likely to be positive and had higher parasite concentrations. Parasite concentrations were used to estimate the proportion of contributing populations that could be clinically infected. For
Cryptosporidium
, the highest estimates were up to 5 per 100,000 individuals for two populations in eastern Norway. For
Giardia
, the highest estimate was 40 infected per 100,000 persons (approximately five times the usual national annual average) contributing to an STW in western Norway. As this population experienced a large waterborne giardiasis outbreak 6 months after sampling, it can be speculated that regular challenge with
Giardia
may occur here. Most
Giardia
isolates in sewage influent were assemblage A, although some assemblage B isolates were detected. There was substantial heterogeneity, but most samples contained isolates similar to genotype A3. Removal efficiencies at two STW with secondary treatment processes were estimated to be approximately 50% for
Cryptosporidium
and >80% for
Giardia
. An STW with minimal treatment had negligible removal of both parasites. Many STW in Norway have minimal treatment and discharge effluent into rivers and lakes, thus, risk of contamination of water courses by
Cryptosporidium
and
Giardia
is considerable.
Discovery of a Marine Bacterium Producing 4-Hydroxybenzoate and Its Alkyl Esters, Parabens
Authors: Peng Xue , Adachi Kyoko , Chen Choryu , Kasai Hiroaki , Kanoh Kaneo , Shizuri Yoshikazu , Misawa Norihiko 
Published: August 2006

ABSTRACT

Chemically synthesized 4-hydroxybenzoate (4HBA) is widely used in the chemical and electrical industries as a material for producing polymers such as those of the liquid crystal type. Its alkyl esters, called parabens, have been the most widely used preservatives by the food and cosmetic industries. We report here for the first time a microorganism, a marine bacterium, which biosynthesizes these petrochemical products. The marine bacterial strain, A4B-17, which was found to belong to the genus
Microbulbifer
on the basis of its rRNA and
gyrB
sequences, was isolated from an ascidian in the coastal waters of Palau. Strain A4B-17 was, surprisingly, found to produce 10 mg/liter of 4HBA, together with its butyl (24 mg/liter), heptyl (0.4 mg/liter), and nonyl (6 mg/liter) esters. We therefore characterized 23 other marine bacteria belonging to the genus
Microbulbifer
, which our institute had previously isolated from various marine environments, and found that these bacteria also produced 4HBA, although with low production levels (less than one-fifth of that produced by A4B-17). We also show that the alkyl esters of 4HBA produced by strain A4B-17 were effective in preventing the growth of yeasts, molds, and gram-positive bacteria.
Eukaryotic Community Distribution and Its Relationship to Water Physicochemical Parameters in an Extreme Acidic Environment, Río Tinto (Southwestern Spain)
Authors: Aguilera Angeles , Manrubia Susanna C. , Gómez Felipe , Rodríguez Nuria , Amils Ricardo 
Published: August 2006

ABSTRACT

The correlation between water physicochemical parameters and eukaryotic benthic composition was examined in Río Tinto. Principal component analysis showed a high inverse relationship between pH and most of the heavy metals analyzed as well as
Dunaliella
sp., while
Chlamydomonas
sp. abundance was positively related. Zn, Cu, and Ni clustered together and showed a strong inverse correlation with the diversity coefficient and most of the species analyzed. These eukaryotic communities seem to be more influenced by the presence of heavy metals than by the pH.
Engineering of Promoter Replacement Cassettes for Fine-Tuning of Gene Expression in
Saccharomyces cerevisiae
Authors: Nevoigt Elke , Kohnke Jessica , Fischer Curt R. , Alper Hal , Stahl Ulf , Stephanopoulos Gregory 
Published: August 2006

ABSTRACT

The strong overexpression or complete deletion of a gene gives only limited information about its control over a certain phenotype or pathway. Gene function studies based on these methods are therefore incomplete. To effect facile manipulation of gene expression across a full continuum of possible expression levels, we recently created a library of mutant promoters. Here, we provide the detailed characterization of our yeast promoter collection comprising 11 mutants of the strong constitutive
Saccharomyces cerevisiae TEF1
promoter. The activities of the mutant promoters range between about 8% and 120% of the activity of the unmutated
TEF1
promoter. The differences in reporter gene expression in the 11 mutants were independent of the carbon source used, and real-time PCR confirmed that these differences were due to varying levels of transcription (i.e., caused by varying promoter strengths). In addition to a CEN/ARS plasmid-based promoter collection, we also created promoter replacement cassettes. They enable genomic integration of our mutant promoter collection upstream of any given yeast gene, allowing detailed genotype-phenotype characterizations. To illustrate the utility of the method, the
GPD1
promoter of
S. cerevisiae
was replaced by five
TEF1
promoter mutants of different strengths, which allowed analysis of the impact of glycerol 3-phosphate dehydrogenase activity on the glycerol yield.
The Lactic Acid-Induced Acid Tolerance Response in
Salmonella enterica
Serovar Typhimurium Induces Sensitivity to Hydrogen Peroxide
Authors: Greenacre E. J. , Lucchini S. , Hinton J. C. D. , Brocklehurst T. F. 
Published: August 2006

ABSTRACT

Transcriptome analyses of
Salmonella enterica
serovar Typhimurium revealed that 15 genes were significantly up-regulated after 2 h of adaptation with lactic acid.
cadB
was the most highly up-regulated gene and was shown to be an essential component. Lactic acid-adapted cells exhibited sensitivity to hydrogen peroxide, likely due to down-regulation of the OxyR regulon.
Ecological Advantages of Autolysis during the Development and Dispersal of
Pseudoalteromonas tunicata
Biofilms
Authors: Mai-Prochnow Anne , Webb Jeremy S. , Ferrari Belinda C. , Kjelleberg Staffan 
Published: August 2006

ABSTRACT

In the ubiquitous marine bacterium
Pseudoalteromonas tunicata
, subpopulations of cells are killed by the production of an autocidal protein, AlpP, during biofilm development. Our data demonstrate an involvement of this process in two parameters, dispersal and phenotypic diversification, which are of importance for the ecology of this organism and for its survival within the environment. Cell death in
P. tunicata
wild-type biofilms led to a major reproducible dispersal event after 192 h of biofilm development. The dispersal was not observed with a ΔAlpP mutant strain. Using flow cytometry and the fluorescent dye DiBAC
4
(3), we also show that
P. tunicata
wild-type cells that disperse from biofilms have enhanced metabolic activity compared to those cells that disperse from ΔAlpP mutant biofilms, possibly due to nutrients released from dead cells. Furthermore, we report that there was considerable phenotypic variation among cells dispersing from wild-type biofilms but not from the ΔAlpP mutant. Wild-type cells that dispersed from biofilms showed significantly increased variations in growth, motility, and biofilm formation, which may be important for successful colonization of new surfaces. These findings suggest for the first time that the autocidal events mediated by an antibacterial protein can confer ecological advantages to the species by generating a metabolically active and phenotypically diverse subpopulation of dispersal cells.
Bacteria Associated with Mucus and Tissues of the Coral
Oculina patagonica
in Summer and Winter
Authors: Koren Omry , Rosenberg Eugene 
Published: August 2006

ABSTRACT

The relative abundance of bacteria in the mucus and crushed tissue of the Mediterranean coral
Oculina patagonica
was determined by analyses of the 16S rRNA genes of isolated colonies and from a 16S rRNA clone library of extracted DNA. By SYBR gold staining, the numbers of bacteria in mucus and tissue samples were 6.2 × 10
7
and 8.3 × 10
8
/cm
2
of coral surface, respectively, 99.8% of which failed to produce colonies on Marine Agar. From analysis of mucus DNA, the most-abundant bacterium was
Vibrio splendidus
, representing 68% and 50% of the clones from the winter and summer, respectively. After removal of mucus from coral by centrifugation, analyses of DNA from the crushed tissue revealed a large diversity of bacteria, with
Vibrio
species representing less than 5% of the clones. The most-abundant culturable bacteria were a
Pseudomonas
sp. (8 to 14%) and two different α-proteobacteria (6 to 18%). Out of a total 1,088 16S rRNA genes sequenced, 400 different operational taxonomic units were identified (>99.5% identity). Of these, 295 were novel (<99% identical to any sequences in the GenBank database). This study provides a comprehensive database for future examinations of changes in the bacterial community during bleaching events.