bluuebunny/crossref_metadata_2025_split huggingface dataset:
Isolation of
Salmonella enterica
and Shiga-Toxigenic
Escherichia coli
O157 from Feces of Animals in Public Contact Areas of United States Zoological Parks
Authors: Keen James E. , Durso Lisa M. , Meehan Thomas P. 
Published: December 2006

ABSTRACT

The fecal prevalence of subclinical
Salmonella enterica
and Shiga-toxigenic
Escherichia coli
O157 among animals in human-animal contact exhibits at institutions in the United States accredited by the Association of Zoos and Aquariums was estimated to assess public health risk. The prevalence was less than 0.6% for both zoonotic pathogens among 997 animals sampled at 36 exhibits.
Trigonopsis variabilisd-Amino Acid Oxidase: Control of Protein Quality and Opportunities for Biocatalysis through Production inEscherichia coli
Authors: Dib Iskandar , Stanzer Damir , Nidetzky Bernd 
Published: December 2006

ABSTRACTTrigonopsis variabilisd-amino acid oxidase accounts for 35% ofEscherichia coliprotein when addedd-methionine suppresses the toxic activity of the recombinant product. PermeabilizedE. colicells are reusable and stabilized enzyme preparations. The purified oxidase lacks the microheterogeneity of the natural enzyme. Oriented immobilization of a chimeric oxidase maintains 80% of the original activity in microparticle-bound enzymes.
Communities of
Archaea
and
Bacteria
in a Subsurface Radioactive Thermal Spring in the Austrian Central Alps, and Evidence of Ammonia-Oxidizing
Crenarchaeota
Authors: Weidler Gerhard W. , Dornmayr-Pfaffenhuemer Marion , Gerbl Friedrich W. , Heinen Wolfgang , Stan-Lotter Helga 
Published: December 2006

ABSTRACT

Scanning electron microscopy revealed great morphological diversity in biofilms from several largely unexplored subterranean thermal Alpine springs, which contain radium 226 and radon 222. A culture-independent molecular analysis of microbial communities on rocks and in the water of one spring, the “Franz-Josef-Quelle” in Bad Gastein, Austria, was performed. Four hundred fifteen clones were analyzed. One hundred thirty-two sequences were affiliated with 14 bacterial operational taxonomic units (OTUs) and 283 with four archaeal OTUs. Rarefaction analysis indicated a high diversity of bacterial sequences, while archaeal sequences were less diverse. The majority of the cloned archaeal 16S rRNA gene sequences belonged to the soil-freshwater-subsurface (1.1b) crenarchaeotic group; other representatives belonged to the freshwater-wastewater-soil (1.3b) group, except one clone, which was related to a group of uncultivated
Euryarchaeota
. These findings support recent reports that
Crenarchaeota
are not restricted to high-temperature environments. Most of the bacterial sequences were related to the
Proteobacteria
(α, β, γ, and δ),
Bacteroidetes
, and
Planctomycetes
. One OTU was allied with
Nitrospina
sp. (
δ-Proteobacteria
) and three others grouped with
Nitrospira.
Statistical analyses suggested high diversity based on 16S rRNA gene analyses; the rarefaction plot of archaeal clones showed a plateau. Since
Crenarchaeota
have been implicated recently in the nitrogen cycle, the spring environment was probed for the presence of the ammonia monooxygenase subunit A (
amoA
) gene. Sequences were obtained which were related to crenarchaeotic
amoA
genes from marine and soil habitats. The data suggested that nitrification processes are occurring in the subterranean environment and that ammonia may possibly be an energy source for the resident communities.
Gene Copy Number Polymorphisms in an Arbuscular Mycorrhizal Fungal Population
Authors: Corradi Nicolas , Croll Daniel , Colard Alexandre , Kuhn Gerrit , Ehinger Martine , Sanders Ian R. 
Published: December 2006

ABSTRACT

Gene copy number polymorphism was studied in a population of the arbuscular mycorrhizal fungus
Glomus intraradices
by using a quantitative PCR approach on four different genomic regions. Variation in gene copy number was found for a pseudogene and for three ribosomal genes, providing conclusive evidence for a widespread occurrence of macromutational events in the population.
Multiple-Level Regulation of Genes for Protocatechuate Degradation in
Acinetobacter baylyi
Includes Cross-Regulation
Authors: Siehler Simone Yasmin , Dal Süreyya , Fischer Rita , Patz Patricia , Gerischer Ulrike 
Published: December 2006

ABSTRACT

The bacterium
Acinetobacter baylyi
uses the branched β-ketoadipate pathway to metabolize aromatic compounds. Here, the multiple-level regulation of expression of the
pca-qui
operon encoding the enzymes for protocatechuate and quinate degradation was studied. It is shown that both activities of the IclR-type regulator protein PcaU at the structural gene promoter
pcaIp
, namely protocatechuate-dependent activation of
pca-qui
operon expression as well as repression in the absence of protocatechuate, can be observed in a different cellular background (
Escherichia coli
) and therefore are intrinsic to PcaU. The regulation of PcaU expression is demonstrated to be carbon source dependent according to the same pattern as the
pca-qui
operon. The increase of the
pcaU
gene copy number leads to a decrease of the basal expression at
pcaIp
, indicating that the occupancy of the PcaU binding site is well balanced and depends on the concentration of PcaU in the cell. Luciferase is used as a reporter to demonstrate strong repression of
pcaIp
when benzoate, a substrate of the catechol branch of the pathway, is present in addition to substrates of the protocatechuate branch (cross-regulation). The same repression pattern was observed for promoter
pcaUp
. Thus, three promoters involved in gene expression of enzymes of the protocatechuate branch (
pobAp
upstream of
pobA
,
pcaIp
, and
pcaUp
) are strongly repressed in the presence of benzoate. The negative effect of protocatechuate on
pobA
expression is not based on a direct sensing of the metabolite by PobR, the specific regulator of
pobA
expression.
Lytic Activity of Recombinant Bacteriophage φ11 and φ12 Endolysins on Whole Cells and Biofilms of
Staphylococcus aureus
Authors: Sass Peter , Bierbaum Gabriele 
Published: December 2006

ABSTRACT
The recombinant φ11 endolysin hydrolyzed heat-killed staphylococci as well as staphylococcal biofilms. Cell wall targeting appeared to be a prerequisite for lysis of whole cells, and the combined action of the endopeptidase and amidase domains was necessary for maximum activity. In contrast, the φ12 endolysin was inactive and caused aggregation of the cells.
Identification and Characterization of Conjugative Transposons CTn86 and CTn9343 in
Bacteroides fragilis
Strains
Authors: Buckwold Simy L. , Shoemaker Nadja B. , Sears Cynthia L. , Franco Augusto A. 
Published: December 2006

ABSTRACT

The related genetic elements flanking the
Bacteroides fragilis
pathogenicity island (PAI) in enterotoxigenic
B. fragilis
(ETBF) 86-5443-2-2 and also present in pattern III nontoxigenic
B. fragilis
(NTBF) NCTC 9343 were defined as putative conjugative transposons (CTns), designated CTn86 and CTn9343, respectively (A. A. Franco, J. Bacteriol. 181:6623-6633, 2004). CTn86 and CTn9343 have the same basic structures except that their encoded transposases have low similarity and CTn9343 lacks the
B. fragilis
PAI and contains an extra 7-kb region not present in CTn86. In this study, using DNA hybridization and PCR analysis, we characterized the genetic element flanking the PAI in a collection of ETBF strains and the related genetic elements in a collection of NTBF pattern III strains. We found that in all 123 ETBF strains, the PAI is contained in a genetic element similar to CTn86. Of 73 pattern III strains, 26 (36%) present a genetic element similar to CTn9343, 38 (52%) present a genetic element similar to CTn9343 but lack the 7-kb region that is also absent in CTn86 (CTn9343-like element), and 9 (12%) present a genetic element similar to CTn86 but lacking the PAI (CTn86-like element). In addition to containing CTn86, ETBF strains can also contain CTn9343, CTn9343-like, or CTn86-like elements. CTn86, CTn9343, CTn86-like, and CTn9343-like elements were found exclusively in
B. fragilis
strains and predominantly in division I,
cepA
-positive strains.
Identification of Acetate-Assimilating Microorganisms under Methanogenic Conditions in Anoxic Rice Field Soil by Comparative Stable Isotope Probing of RNA
Authors: Hori Tomoyuki , Noll Matthias , Igarashi Yasuo , Friedrich Michael W. , Conrad Ralf 
Published: December 2006

ABSTRACT

Acetate is the most abundant intermediate of organic matter degradation in anoxic rice field soil and is converted to CH
4
and/or CO
2
. Aceticlastic methanogens are the primary microorganisms dissimilating acetate in the absence of sulfate and reducible ferric iron. In contrast, very little is known about bacteria capable of assimilating acetate under methanogenic conditions. Here, we identified active acetate-assimilating microorganisms by using a combined approach of frequent label application at a low concentration and comparative RNA-stable isotope probing with
13
C-labeled and unlabeled acetate. Rice field soil was incubated anaerobically at 25°C for 12 days, during which
13
C-labeled acetate was added at a concentration of 500 μM every 3 days.
13
C-labeled CH
4
and CO
2
were produced from the beginning of the incubation and accounted for about 60% of the supplied acetate
13
C. RNA was extracted from the cells in each sample taken and separated by isopycnic centrifugation according to molecular weight. Bacterial and archaeal populations in each density fraction were screened by reverse transcription-PCR-mediated terminal restriction fragment polymorphism analysis. No differences in the bacterial populations were observed throughout the density fractions of the unlabeled treatment. However, in the heavy fractions of the
13
C treatment, terminal restriction fragments (T-RFs) of 161 bp and 129 bp in length predominated. These T-RFs were identified by cloning and sequencing of 16S rRNA as from a
Geobacter
sp. and an
Anaeromyxobacter
sp., respectively. Apparently these bacteria, which are known as dissimilatory iron reducers, were able to assimilate acetate under methanogenic conditions, i.e., when CO
2
was the predominant electron acceptor. We hypothesize that ferric iron minerals with low bioavailability might have served as electron acceptors for
Geobacter
spp. and
Anaeromyxobacter
spp. under these conditions.
Removal of Astrovirus from Water and Sewage Treatment Plants, Evaluated by a Competitive Reverse Transcription-PCR
Authors: Morsy El-Senousy Waled , Guix Susana , Abid Islem , Pintó Rosa M. , Bosch Albert 
Published: December 2006

ABSTRACT

Quantification of human astrovirus genogroups A and B was undertaken with sewage and water samples, collected from the Greater Cairo area in Egypt from November 1998 to October 1999, by a competitive reverse transcription (RT)-PCR with an internal control. The number of RNA copies of genogroup A/liter in quantifiable samples ranged from 3.4 × 10
3
to 5.6 × 10
6
in raw sewage and from 3.4 × 10
3
to 1.1 × 10
4
in treated effluents, while the number of infectious units per liter in these samples as determined by cell culture RT-PCR (CC-RT-PCR U/liter) ranged from 3.3 × 10
1
to 3.3 × 10
3
in raw sewage and was 3.3 × 10
0
in treated effluents. On the other hand, the number of RNA copies/liter in quantifiable genogroup B samples ranged from 1.1 × 10
4
to 8.7 × 10
6
in raw sewage and from 1.1 × 10
3
to 6.2 × 10
5
in treated effluents, while the number of infectious units ranged from 3.3 × 10
1
to 3.3 × 10
5
CC-RT-PCR U/liter in raw sewage and from 3.3 × 10
1
to 3.3 × 10
2
CC-RT-PCR U/liter in treated effluents. These higher numbers of both RNA copies/liter and infectious particles of genogroup B may indicate the emergence of genogroup B in the area. Additionally, genogroup B astrovirus exhibited a higher resistance to removal treatments with regard to the number of RNA copies per ml. When the equipment for real-time approaches is unavailable, a competitive PCR or RT-PCR with an internal control may be employed for virus quantification in validations of the efficiency of virus removal treatments.
Folate Production by Bifidobacteria as a Potential Probiotic Property
Authors: Pompei Anna , Cordisco Lisa , Amaretti Alberto , Zanoni Simona , Matteuzzi Diego , Rossi Maddalena 
Published: December 2006

ABSTRACT

The ability of 76
Bifidobacterium
strains to produce folate was investigated. In order to evaluate folic acid productivity, bifidobacteria were cultivated in the folate-free semisynthetic medium SM7. Most of the tested strains needed folate for growth. The production and the extent of vitamin accumulation were not a function of species but were distinctive features of individual strains. Six strains among the 17 that grew without folate produced significantly higher concentrations of vitamin (between 41 and 82 ng ml
−1
). The effects of exogenous folate and
p
-aminobenzoic acid (PABA) concentrations on folate production were evaluated. In contrast to most of the other strains, the folate yield of
B. adolescentis
MB 239 was not negatively affected by either PABA or exogenous folic acid. Folate production by
B. adolescentis
MB 239 was studied in the pH range of the colonic environment, and a comparison of folate production on raffinose, lactose, and fructo-oligosaccharides, which belong to three important groups of fermentable intestinal carbon sources, was established. Differences in folate biosynthesis by
B. adolescentis
MB 239 were not observed as a function either of the pH or of the carbon source. Fecal culture experiments demonstrated that the addition of
B. adolescentis
MB 239 may increase the folate concentration in the colonic environment.
Rapid Separation and Concentration of Food-Borne Pathogens in Food Samples Prior to Quantification by Viable-Cell Counting and Real-Time PCR
Authors: Fukushima Hiroshi , Katsube Kazunori , Hata Yukiko , Kishi Ryoko , Fujiwara Satomi 
Published: December 2006

ABSTRACT

Buoyant density gradient centrifugation has been used to separate bacteria from complex food matrices, as well as to remove compounds that inhibit rapid detection methods, such as PCR, and to prevent false-positive results due to DNA originating from dead cells. Applying a principle of buoyant density gradient centrifugation, we developed a method for rapid separation and concentration following filtration and low- and high-speed centrifugation, as well as flotation and sedimentation buoyant density centrifugation, for 12 food-borne pathogens (
Salmonella enterica
,
Escherichia coli
,
Yersinia enterocolitica
,
Campylobacter jejuni
,
Vibrio cholerae
O139,
Vibrio parahaemolyticus
O3K6,
Vibrio vulnificus
,
Providencia alcalifaciens
,
Aeromonas hydrophila
,
Bacillus cereus
,
Staphylococcus aureus
, and
Clostridium perfringens
) in 13 different food homogenates. This method can be used prior to real-time quantitative PCR (RTi-qPCR) and viable-cell counting. Using this combined method, the target organisms in the food samples theoretically could be concentrated 250-fold and detected at cell concentrations as low as 10
1
to 10
3
CFU/g using the RTi-qPCR assay, and amounts as small as 10
0
to 10
1
CFU/g could be isolated using plate counting. The combined separation and concentration methods and RTi-qPCR confirmed within 3 h the presence of 10
1
to 10
2
CFU/g of
Salmonella
and
C. jejuni
directly in naturally contaminated chicken and the presence of
S. aureus
directly in remaining food items in a poisoning outbreak. These results illustrated the feasibility of using these assays for rapid inspection of bacterial food contamination during a real-world outbreak.
Biotransformation of Hg(II) by Cyanobacteria
Authors: Lefebvre Daniel D. , Kelly David , Budd Kenneth 
Published: December 2006

ABSTRACT

The biotransformation of Hg(II) by cyanobacteria was investigated under aerobic and pH-controlled culture conditions. Mercury was supplied as HgCl
2
in amounts emulating those found under heavily impacted environmental conditions where bioremediation would be appropriate. The analytical procedures used to measure mercury within the culture solution, including that in the cyanobacterial cells, used reduction under both acid and alkaline conditions in the presence of SnCl
2
. Acid reduction detected free Hg(II) ions and its complexes, whereas alkaline reduction revealed that
meta
-cinnabar (β-HgS) constituted the major biotransformed and cellularly associated mercury pool. This was true for all investigated species of cyanobacteria:
Limnothrix planctonica
(Lemm.),
Synechococcus leopoldiensis
(Racib.) Komarek, and
Phormidium limnetica
(Lemm.). From the outset of mercury exposure, there was rapid synthesis of β-HgS and Hg(0); however, the production rate for the latter decreased quickly. Inhibitory studies using dimethylfumarate and iodoacetamide to modify intra- and extracellular thiols, respectively, revealed that the former thiol pool was required for the conversion of Hg(II) into β-HgS. In addition, increasing the temperature enhanced the amount of β-HgS produced, with a concomitant decrease in Hg(0) volatilization. These findings suggest that in the environment, cyanobacteria at the air-water interface could act to convert substantial amounts of Hg(II) into β-HgS. Furthermore, the efficiency of conversion into β-HgS by cyanobacteria may lead to the development of applications in the bioremediation of mercury.
Identification and Quantification of Methanogenic Archaea in Adult Chicken Ceca
Authors: Saengkerdsub Suwat , Anderson Robin C. , Wilkinson Heather H. , Kim Woo-Kyun , Nisbet David J. , Ricke Steven C. 
Published: December 2006

ABSTRACT

By using molecular methods for the identification and quantification of methanogenic archaea in adult chicken ceca, 16S rRNA genes of 11 different phylotypes, 10 of which were 99% similar to
Methanobrevibacter woesei
, were found. Methanogen populations, as assessed by cultivation, and the 16S rRNA copy number were between 6.38 and 8.23 cells/g (wet weight) and 5.50 and 7.19 log
10
/g (wet weight), respectively.
Localization of Functional Polypeptides in Bacterial Inclusion Bodies
Authors: García-Fruitós Elena , Arís Anna , Villaverde Antonio 
Published: December 2006

ABSTRACT
Bacterial inclusion bodies, while showing intriguing amyloid-like features, such as a β-sheet-based intermolecular organization, binding to amyloid-tropic dyes, and origin in a sequence-selective deposition process, hold an important amount of native-like secondary structure and significant amounts of functional polypeptides. The aggregation mechanics supporting the occurrence of both misfolded and properly folded protein is controversial. Single polypeptide chains might contain both misfolded stretches driving aggregation and properly folded protein domains that, if embracing the active site, would account for the biological activities displayed by inclusion bodies. Alternatively, soluble, functional polypeptides could be surface adsorbed by interactions weaker than those driving the formation of the intermolecular β-sheet architecture. To explore whether the fraction of properly folded active protein is a natural component or rather a mere contaminant of these aggregates, we have explored their localization by image analysis of inclusion bodies formed by green fluorescent protein. Since the fluorescence distribution is not homogeneous and the core of inclusion bodies is particularly rich in active protein forms, such protein species cannot be passively trapped components and their occurrence might be linked to the reconstruction dynamics steadily endured in vivo by such bacterial aggregates. Intriguingly, even functional protein species in inclusion bodies are not excluded from the interface with the solvent, probably because of the porous structure of these particular protein aggregates.
Conjugative Transfer Facilitates Stable Maintenance of IncP-1 Plasmid pKJK5 in
Escherichia coli
Cells Colonizing the Gastrointestinal Tract of the Germfree Rat
Authors: Bahl Martin Iain , Hansen Lars Hestbjerg , Licht Tine Rask , Sørensen Søren J. 
Published: December 2006

ABSTRACT

Quantitative determination of IncP-1 plasmid loss from
Escherichia coli
cells colonizing the gastrointestinal tracts of germfree rats was achieved by flow cytometry. Results show that the plasmid's ability to conjugate counteracts plasmid loss and is thus an important mechanism for the stable maintenance of IncP-1 plasmids within the gastrointestinal environment.
Increased Insect Virulence in
Beauveria bassiana
Strains Overexpressing an Engineered Chitinase
Authors: Fan Yanhua , Fang Weiguo , Guo Shujuan , Pei Xiaoqiong , Zhang Yongjun , Xiao Yuehua , Li Demou , Jin Kai , Bidochka Michael J. , Pei Yan 
Published: December 2006

ABSTRACT

Entomopathogenic fungi are currently being used for the control of several insect pests as alternatives or supplements to chemical insecticides. Improvements in virulence and speed of kill can be achieved by understanding the mechanisms of fungal pathogenesis and genetically modifying targeted genes, thus improving the commercial efficacy of these biocontrol agents. Entomopathogenic fungi, such as
Beauveria bassiana
, penetrate the insect cuticle utilizing a plethora of hydrolytic enzymes, including chitinases, which are important virulence factors. Two chitinases (Bbchit1 and Bbchit2) have previously been characterized in
B. bassiana
, neither of which possesses chitin-binding domains. Here we report the construction and characterization of several
B. bassiana
hybrid chitinases where the chitinase Bbchit1 was fused to chitin-binding domains derived from plant, bacterial, or insect sources. A hybrid chitinase containing the chitin-binding domain (BmChBD) from the silkworm
Bombyx mori
chitinase fused to Bbchit1 showed the greatest ability to bind to chitin compared to other hybrid chitinases. This hybrid chitinase gene (Bb
chit1
-Bm
ChBD
) was then placed under the control of a fungal constitutive promoter (
gpd
-Bb
chit1
-Bm
ChBD
) and transformed into
B. bassiana
. Insect bioassays showed a 23% reduction in time to death in the transformant compared to the wild-type fungus. This transformant also showed greater virulence than another construct (
gpd
-Bb
chit1
) with the same constitutive promoter but lacking the chitin-binding domain. We utilized a strategy where genetic components of the host insect can be incorporated into the fungal pathogen in order to increase host cuticle penetration ability.
Highly Prevalent
Coxiella
sp. Bacterium in the Tick Vector
Amblyomma americanum
Authors: Jasinskas Algimantas , Zhong Jianmin , Barbour Alan G. 
Published: December 2006

ABSTRACT

Laboratory-reared and field-collected
Amblyomma americanum
ticks were hosts of a
Coxiella
sp. and a
Rickettsia
sp. While the
Coxiella
sp. was detected in 50 of 50 field-collected ticks, the
Rickettsia
sp. was absent from 32% of ticks. The
Coxiella
sp. showed evidence of a reduced genome and may be an obligate endosymbiont.
Evidence that Accumulation of Mutants in a Biofilm Reflects Natural Selection Rather than Stress-Induced Adaptive Mutation
Authors: Banas Jeffrey A. , Miller Justin D. , Fuschino Meghan E. , Hazlett Karsten R. O. , Toyofuku Wendy , Porter Kristen A. , Reutzel Sarah B. , Florczyk Matthew A. , McDonough Kathleen A. , Michalek Suzanne M. 
Published: December 2006

ABSTRACT

The accumulation of mutant genotypes within a biofilm evokes the controversy over whether the biofilm environment induces adaptive mutation or whether the accumulation can be explained by natural selection. A comparison of the virulence of two strains of the dental pathogen
Streptococcus mutans
showed that rats infected with one of the strains accumulated a high proportion (average, 22%) of organisms that had undergone a deletion between two contiguous and highly homologous genes. To determine if the accumulation of deletion mutants was due to selection or to an increased mutation rate, accumulations of deletion mutants within in vitro planktonic and biofilm cultures and within rats inoculated with various proportions of deletion organisms were quantified. We report here that natural selection was the primary force behind the accumulation of the deletion mutants.