bluuebunny/crossref_metadata_2025_split huggingface dataset:
Application of Cation-Coated Filter Method to Detection of Noroviruses, Enteroviruses, Adenoviruses, and Torque Teno Viruses in the Tamagawa River in Japan
Authors: Haramoto Eiji , Katayama Hiroyuki , Oguma Kumiko , Ohgaki Shinichiro 
Published: May 2005

ABSTRACT

The occurrence of human enteric viruses in surface water in the Tamagawa River, Japan, was surveyed for 1 year, from April 2003 to March 2004. Sixty-four samples were collected from six sites along the river, and 500 ml of the sample was concentrated using the cation-coated filter method, which was developed in our previous study. This method showed recovery yields of 56% ± 32% (
n
= 37) for surface water samples inoculated with polioviruses. More than one kind of tested virus was detected in 43 (67%) of 64 samples by TaqMan PCR. Noroviruses and adenoviruses were detected in a high positive ratio; 34 (53%), 28 (44%), and 29 (45%) of 64 samples were positive for norovirus genotype 1 and genotype 2 and adenoviruses, respectively. The mean concentrations of norovirus genotype 1 or genotype 2 determined by real-time PCR were 0.087 and 0.61 genome/ml, respectively, showing much higher values in winter (0.21 genome/ml for genotype 1 and 2.3 genomes/ml for genotype 2). Enteroviruses were detected by both direct PCR (6 of 64 samples; 9%) and cell culture PCR (2 of 64 samples; 3%). Torque teno viruses, emerging hepatitis viruses, were also isolated in three samples (5%). The concentration of total coliforms and the presence of F-specific phages showed a high correlation with the presence of viruses, which suggested that the simultaneous use of total coliforms and F-specific phages as indicators of surface water may work to monitor viral contamination.
Processive Endoglucanase Active in Crystalline Cellulose Hydrolysis by the Brown Rot Basidiomycete
Gloeophyllum trabeum
Authors: Cohen Roni , Suzuki Melissa R. , Hammel Kenneth E. 
Published: May 2005

ABSTRACT

Brown rot basidiomycetes have long been thought to lack the processive cellulases that release soluble sugars from crystalline cellulose. On the other hand, these fungi remove all of the cellulose, both crystalline and amorphous, from wood when they degrade it. To resolve this discrepancy, we grew
Gloeophyllum trabeum
on microcrystalline cellulose (Avicel) and purified the major glycosylhydrolases it produced. The most abundant extracellular enzymes in these cultures were a 42-kDa endoglucanase (Cel5A), a 39-kDa xylanase (Xyn10A), and a 28-kDa endoglucanase (Cel12A). Cel5A had significant Avicelase activity—4.5 nmol glucose equivalents released/min/mg protein. It is a processive endoglucanase, because it hydrolyzed Avicel to cellobiose as the major product while introducing only a small proportion of reducing sugars into the remaining, insoluble substrate. Therefore, since
G. trabeum
is already known to produce a β-glucosidase, it is now clear that this brown rot fungus produces enzymes capable of yielding assimilable glucose from crystalline cellulose.
Phenotypic and Genotypic Selection of Microbiota Surviving under Dental Restorations
Authors: Paddick J. S. , Brailsford S. R. , Kidd E. A. M. , Beighton D. 
Published: May 2005

ABSTRACT

The effects of sealing infected carious dentine below dental restorations on the phenotypic and genotypic diversity of the surviving microbiota was investigated. It was hypothesized that the microbiota would be subject to nutrient limitation or nutrient simplification, as it would no longer have access to dietary components or salivary secretion for growth. The available nutrients would be limited primarily to serum proteins passing from the pulp through the patent dentinal tubules to the infected dentine. Ten lesions were treated, and infected dentine was sealed below dental restorations for approximately 5 months. Duplicate standardized samples of infected dentine were taken at baseline and after the removal of the restorations. The baseline microbiota were composed primarily of
Lactobacillus
spp.,
Streptococcus mutans
,
Streptococcus parasanguinis
,
Actinomyces israelii
, and
Actinomyces gerencseriae
. None of these taxa were isolated among the microbiota of the dentine samples taken after 5 months, which consisted of only
Actinomyces naeslundii
,
Streptococcus oralis
,
Streptococcus intermedius
, and
Streptococcus mitis.
The microbiota of the final sample exhibited a significantly (
P
< 0.001) increased ability to produce glycosidic enzymes (sialidase, β-
N
-acetylglucosaminidase, and β-galactosidase), which liberate sugars from glycoproteins. The genotypic diversity of
S. oralis
and
A. naeslundii
was significantly (
P
= 0.002 and
P
= 0.001, respectively) reduced in the final samples. There was significantly (
P
< 0.001) greater genotypic diversity within these taxa between the pairs of dentine samples taken at baseline than was found in the 5-month samples, indicating that the dentine was more homogenous than it was at baseline. We propose that during the interval between placement of the restorations and their removal, the available nutrient, primarily serum proteins, or the relative simplicity and homogeneity of the nutrient supply significantly affected the surviving microbiota. The surviving microbiota was less complex, based on compositional, phenotypic, and genotypic analyses, than that isolated from carious lesions which were also exposed to salivary secretions and pH perturbations.
Efficacy of Two Peroxygen-Based Disinfectants for Inactivation of
Cryptosporidium parvum
Oocysts
Authors: Quilez Joaquin , Sanchez-Acedo Caridad , Avendaño Catalina , del Cacho Emilio , Lopez-Bernad Fernando 
Published: May 2005

ABSTRACT

Two commercial peroxygen-based disinfectants containing hydrogen peroxide plus either peracetic acid (Ox-Virin) or silver nitrate (Ox-Agua) were tested for their ability to inactivate
Cryptosporidium parvum
oocysts. Oocysts were obtained from naturally infected goat kids and exposed to concentrations of 2, 5, and 10% Ox-Virin or 1, 3, and 5% Ox-Agua for 30, 60, and 120 min. In vitro excystation, vital dyes (4′,6′-diamidino-2-phenylindole and propidium iodide), and infectivity in neonatal BALB/c mice were used to assess the viability and infectivity of control and disinfectant-treated oocysts. Both disinfectants had a deleterious effect on the survival of
C. parvum
oocysts, since disinfection significantly reduced and in some cases eliminated their viability and infectivity. When in vitro assays were compared with an infectivity assay as indicators of oocyst inactivation, the excystation assay showed 98.6% inactivation after treatment with 10% Ox-Virin for 60 min, while the vital-dye assay showed 95.2% inactivation and the infectivity assay revealed 100% inactivation. Treatment with 3% Ox-Agua for 30 min completely eliminated oocyst infectivity for mice, although we were able to observe only 74.7% inactivation as measured by excystation assays and 24.3% with vital dyes (which proved to be the least reliable method for predicting
C. parvum
oocyst viability). These findings indicate the potential efficacy of both disinfectants for
C. parvum
oocysts in agricultural settings where soil, housing, or tools might be contaminated and support the argument that in comparison to the animal infectivity assay, vital-dye and excystation methods overestimate the viability of oocysts following chemical disinfection.
Application of a pH-Sensitive Fluoroprobe (C-SNARF-4) for pH Microenvironment Analysis in
Pseudomonas aeruginosa
Biofilms
Authors: Hunter Ryan C. , Beveridge Terry J. 
Published: May 2005

ABSTRACT

An important feature of microbial biofilms is the development of four-dimensional physical and chemical gradients in space and time. There is need for novel approaches to probe these so-called microenvironments to determine their effect on biofilm-specific processes. In this study, we describe the use of seminaphthorhodafluor-4F 5-(and-6) carboxylic acid (C-SNARF-4) for pH microenvironment analysis in
Pseudomonas aeruginosa
biofilms. C-SNARF-4 is a fluorescent ratiometric probe that allows pH quantification independent of probe concentration and/or laser intensity. By confocal scanning laser microscopy, C-SNARF-4 revealed pH heterogeneity throughout the biofilm in both the
x
,
y
and
x
,
z
planes, with values ranging from pH 5.6 (within the biofilm) to pH 7.0 (bulk fluid). pH values were typically remarkably different than those just a few micrometers away. Although this probe has been successfully used in a number of eukaryotic systems, problems have been reported which describe spectral emission changes as a result of macromolecular interactions with the fluorophore. To assess how the biofilm environment may influence fluorescent properties of the dye, fluorescence of C-SNARF-4 was quantified via spectrofluorometry while the probe was suspended in various concentrations of representative biofilm matrix components (i.e., proteins, polysaccharides, and bacterial cells) and growth medium. Surprisingly, our data demonstrate that few changes in emission spectra occur as a result of matrix interactions below pH 7. These studies suggest that C-SNARF-4 can be used as a reliable indicator of pH microenvironments, which may help elucidate their influence on the medical and geobiological roles of natural biofilms.
tir
- and
stx
-Positive
Escherichia coli
in Stream Waters in a Metropolitan Area
Authors: Higgins James A. , Belt Kenneth T. , Karns Jeffrey S. , Russell-Anelli Jonathan , Shelton Daniel R. 
Published: May 2005

ABSTRACT

Diarrheagenic
Escherichia coli
, which may include the enteropathogenic
E. coli
and the enterohemorrhagic
E. coli
, are a significant cause of diarrheal disease among infants and children in both developing and developed areas. Disease outbreaks related to freshwater exposure have been documented, but the presence of these organisms in the urban aquatic environment is not well characterized. From April 2002 through April 2004 we conducted weekly surveys of streams in the metropolitan Baltimore, Md., area for the prevalence of potentially pathogenic
E. coli
by using PCR assays targeting the
tir
and
stx
1
and
stx
2
genes. Coliforms testing positive for the presence of the
tir
gene were cultured from 653 of 1,218 samples (53%), with a greater prevalence associated with urban, polluted streams than in suburban and forested watershed streams. Polluted urban streams were also more likely to test positive for the presence of one of the
stx
genes. Sequence analysis of the
tir
amplicon, as well as the entire
tir
gene from three isolates, indicated that the pathogenic
E. coli
present in the stream waters has a high degree of sequence homology with the
E. coli
O157:H7 serotype. Our data indicate that pathogenic
E. coli
are continually deposited into a variety of stream habitats and suggest that this organism may be a permanent member of the gastrointestinal microflora of humans and animals in the metropolitan Baltimore area.
Suppressive Subtractive Hybridization of and Differences in Gene Expression Content of Calcifying and Noncalcifying Cultures ofEmiliania huxleyiStrain 1516
Authors: Nguyen Binh , Bowers Robert M. , Wahlund Thomas M. , Read Betsy A. 
Published: May 2005

ABSTRACTThe marine coccolithophoridEmiliania huxleyiis a cosmopolitan alga intensely studied in relation to global carbon cycling, biogeochemistry, marine ecology, and biomineralization processes. The biomineralization capabilities of coccolithophorids have attracted the attention of scientists interested in exploiting this ability for the development of materials science and biomedical and biotechnological applications. Although it has been well documented that biomineralization inE. huxleyiis promoted by growth under phosphate-limited conditions, the genes and proteins that govern the processes of calcification and coccolithogenesis remain unknown. Suppressive subtractive hybridization (SSH) libraries were constructed from cultures grown in phosphate-limited and phosphate-replete media as tester and driver populations for reciprocal SSH procedures. Positive clones from each of the two libraries were randomly selected, and dot blotting was performed for the analysis of expression patterns. A total of 513 clones from the phosphate-replete library and 423 clones from the phosphate-limited library were sequenced, assembled, and compared to sequences in GenBank using BLASTX. Of the 103 differentially expressed gene fragments from the phosphate-replete library, 34% showed significant homology to other known proteins, while only 23% of the 65 differentially expressed gene fragments from the phosphate-limited library showed homology to other proteins. To further assess mRNA expression, real-time RT-PCR analysis was employed and expression profiles were generated over a 14-day time course for three clones from the phosphate-replete library and five clones from the phosphate-limited library. The fragments isolated provide the basis for future cloning of full-length genes and functional analysis.
Methane-Oxidizing Bacteria in a California Upland Grassland Soil: Diversity and Response to Simulated Global Change
Authors: Horz Hans-Peter , Rich Virginia , Avrahami Sharon , Bohannan Brendan J. M. 
Published: May 2005

ABSTRACT

We investigated the diversity of methane-oxidizing bacteria (i.e., methanotrophs) in an annual upland grassland in northern California, using comparative sequence analysis of the
pmoA
gene. In addition to identifying type II methanotrophs commonly found in soils, we discovered three novel
pmoA
lineages for which no cultivated members have been previously reported. These novel
pmoA
clades clustered together either with clone sequences related to “RA 14” or “WB5FH-A,” which both represent clusters of environmentally retrieved sequences of putative atmospheric methane oxidizers. Conservation of amino acid residues and rates of nonsynonymous versus synonymous nucleotide substitution in these novel lineages suggests that the
pmoA
genes in these clades code for functionally active methane monooxygenases. The novel clades responded to simulated global changes differently than the type II methanotrophs. We observed that the relative abundance of type II methanotrophs declined in response to increased precipitation and increased atmospheric temperature, with a significant antagonistic interaction between these factors such that the effect of both together was less than that expected from their individual effects. Two of the novel clades were not observed to respond significantly to these environmental changes, while one of the novel clades had an opposite response, increasing in relative abundance in response to increased precipitation and atmospheric temperature, with a significant antagonistic interaction between these factors.
Production of Autoinducer 2 in
Salmonella enterica
Serovar Thompson Contributes to Its Fitness in Chickens but Not on Cilantro Leaf Surfaces
Authors: Brandl M. T. , Miller W. G. , Bates A. H. , Mandrell R. E. 
Published: May 2005

ABSTRACT

Food-borne illness caused by
Salmonella enterica
has been linked traditionally to poultry products but is associated increasingly with fresh fruits and vegetables. We have investigated the role of the production of autoinducer 2 (AI-2) in the ability of
S. enterica
serovar Thompson to colonize the chicken intestine and the cilantro phyllosphere. A mutant of
S. enterica
serovar Thompson that is defective in AI-2 production was constructed by insertional mutagenesis of
luxS
. The population size of the
S. enterica
serovar Thompson parental strain was significantly higher than that of its LuxS
−
mutant in the intestine, spleen, and droppings of chicks 12 days after their oral inoculation with the strains in a ratio of 1:1. In contrast, no significant difference in the population dynamics of the parental and LuxS
−
strain was observed after their inoculation singly or in mixtures onto cilantro plants. Digital image analysis revealed that 54% of
S. enterica
serovar Thompson cells were present in large aggregates on cilantro leaves but that the frequency distributions of the size of aggregates formed by the parental strain and the LuxS
−
mutant were not significantly different. Carbon utilization profiles indicated that the AI-2-producing strain utilized a variety of amino and organic acids more efficiently than its LuxS
−
mutant but that most sugars were utilized similarly in both strains. Thus, inherent differences in the nutrients available to
S. enterica
in the phyllosphere and in the chicken intestine may underlie the differential contribution of AI-2 synthesis to the fitness of
S. enterica
in these environments.
Polychlorinated Biphenyl Rhizoremediation by
Pseudomonas fluorescens
F113 Derivatives, Using a
Sinorhizobium meliloti nod
System To Drive
bph
Gene Expression
Authors: Villacieros Marta , Whelan Clare , Mackova Martina , Molgaard Jesper , Sánchez-Contreras María , Lloret Javier , Aguirre de Cárcer Daniel , Oruezábal Roke I. , Bolaños Luis , Macek Thomas , Karlson Ulrich , Dowling David N. , Martín Marta , Rivilla Rafael 
Published: May 2005

ABSTRACT

Rhizoremediation of organic chemicals requires high-level expression of biodegradation genes in bacterial strains that are excellent rhizosphere colonizers.
Pseudomonas fluorescens
F113 is a biocontrol strain that was shown to be an excellent colonizer of numerous plant rhizospheres, including alfalfa. Although a derivative of F113 expressing polychlorinated biphenyl (PCB) biodegradation genes (F113pcb) has been reported previously, this strain shows a low level of
bph
gene expression, limiting its rhizoremediation potential. Here, a high-level expression system was designed from rhizobial
nod
gene regulatory relays. Nod promoters were tested in strain F113 by using β-galactosidase transcriptional fusions. This analysis showed that nodbox 4 from
Sinorhizobium meliloti
has a high level of expression in F113 that is dependent on an intact
nodD1
gene. A transcriptional fusion of a nodbox cassette containing the
nodD1
gene and nodbox 4 fused to a
gfp
gene was expressed in the alfalfa rhizosphere. The
bph
operon from
Burkholderia
sp. strain LB400 was cloned under the control of the nodbox cassette and was inserted as a single copy into the genome of F113, generating strain F113L::1180. This new genetically modified strain has a high level of BphC activity and grows on biphenyl as a sole carbon and energy source at a growth rate that is more than three times higher than that of F113pcb. Degradation of PCBs 3, 4, 5, 17, and 25 was also much faster in F113L::1180 than in F113pcb. Finally, the modified strain cometabolized PCB congeners present in Delor103 better than strain LB400, the donor of the
bph
genes used.
Changes in Nitrogen-Fixing and Ammonia-Oxidizing Bacterial Communities in Soil of a Mixed Conifer Forest after Wildfire
Authors: Yeager Chris M. , Northup Diana E. , Grow Christy C. , Barns Susan M. , Kuske Cheryl R. 
Published: May 2005

ABSTRACT

This study was undertaken to examine the effects of forest fire on two important groups of N-cycling bacteria in soil, the nitrogen-fixing and ammonia-oxidizing bacteria. Sequence and terminal restriction fragment length polymorphism (T-RFLP) analysis of
nifH
and
amoA
PCR amplicons was performed on DNA samples from unburned, moderately burned, and severely burned soils of a mixed conifer forest. PCR results indicated that the soil biomass and proportion of nitrogen-fixing and ammonia-oxidizing species was less in soil from the fire-impacted sites than from the unburned sites. The number of dominant
nifH
sequence types was greater in fire-impacted soils, and
nifH
sequences that were most closely related to those from the spore-forming taxa
Clostridium
and
Paenibacillus
were more abundant in the burned soils. In T-RFLP patterns of the ammonia-oxidizing community, terminal restriction fragments (TRFs) representing
amoA
cluster 1, 2, or 4
Nitrosospira
spp. were dominant (80 to 90%) in unburned soils, while TRFs representing
amoA
cluster 3A
Nitrosospira
spp. dominated (65 to 95%) in fire-impacted soils. The dominance of
amoA
cluster 3A
Nitrosospira
spp. sequence types was positively correlated with soil pH (5.6 to 7.5) and NH
3
-N levels (0.002 to 0.976 ppm), both of which were higher in burned soils. The decreased microbial biomass and shift in nitrogen-fixing and ammonia-oxidizing communities were still evident in fire-impacted soils collected 14 months after the fire.
The Gene
yggE
Functions in Restoring Physiological Defects of
Escherichia coli
Cultivated under Oxidative Stress Conditions
Authors: Kim SunYoung , Nishioka Motomu , Hayashi Shuhei , Honda Hiroyuki , Kobayashi Takeshi , Taya Masahito 
Published: May 2005

ABSTRACT

DNA microarray analysis showed that
yfiD
,
yggB
, and
yggE
genes were up-regulated when superoxide dismutase (SOD)-deficient
Escherichia coli
IM303 (I4) was cultivated under the oxidative stress generated by photoexcited TiO
2
, and pYFD, pYGB, and pYGE were constructed by inserting the respective genes into a pUC 19 vector. The content of reactive oxygen species (ROS) in IM303 (I4) cells carrying pYGE was reduced to 31% of ROS content in the control cells with pUC 19. In the culture of wild-type strain,
E. coli
MM294, in the medium with paraquat (10 μmol/l), maximum specific growth rate of the cells with pYGE was about five times higher than that of the control cells, with a decreased ROS content in the former cells. The introduction of pYGE also suppressed the occurrence of the cells with altered amino acid requirement in the culture of MM294 cells with paraquat.
Molecular Analysis of Human, Porcine, and Poultry
Enterococcus faecium
Isolates and Their
erm
(B) Genes
Authors: De Leener E. , Martel A. , De Graef E. M. , Top J. , Butaye P. , Haesebrouck F. , Willems R. , Decostere A. 
Published: May 2005

ABSTRACT

Fifty-nine
erm
(B)-positive
Enterococcus faecium
strains isolated from pigs, broilers, and humans were typed using multilocus sequence typing (MLST), and the coding sequence of the
erm
(B) gene was determined. Identical
erm
(B) gene sequences were detected in genetically unrelated isolates. Furthermore, genetically indistinguishable strains were found to contain different
erm
(B) alleles. This may suggest that horizontal exchange of the
erm
(B) gene between animal and human
E. faecium
strains or the existence of a common reservoir of
erm
(B) genes might be more important than direct transmission of resistant strains.