bluuebunny/crossref_metadata_2025_split huggingface dataset:
CRITICAL CARE ISSUES FOR THE NEPHROLOGIST: Acid–base Disturbances in the Intensive Care Unit: Metabolic Acidosis
Authors: Schoolwerth Anton C. , Kaneko Thomas M. , Sedlacek Martin , Block Clay A. , Remillard Brian D. 
Published: December 2006

AbstractThis article will discuss metabolic acidosis and, to a lesser extent, metabolic alkalosis in the ICU setting. A classification and clinical approach will be the focus.
Multiplex Quantitative Real-Time Reverse Transcriptase PCR for F
+
-Specific RNA Coliphages: a Method for Use in Microbial Source Tracking
Authors: Kirs Marek , Smith David C. 
Published: December 2006

ABSTRACT

It is well documented that microbial contamination of coastal waters poses a significant risk to human health through recreational exposure and consumption of shellfish. Identifying the source of microbial contamination (microbial source tracking) plays a dominant role in enabling effective management and remediation strategies. One method used to determine the source of the contamination is quantification of the ratio of the four subgroups of F
+
-specific RNA coliphages (family
Leviviridae
) in impacted water samples. Because of typically low concentrations in the environment, enrichment assays are performed prior to detection, even though differential replication rates have been reported. These assays are also compromised by differential loss of phage infectivity among subgroups after release into the environment, thus obscuring the initial ratio. Here, a culture-independent multiplex real-time reverse transcriptase-PCR (RT-PCR) protocol for the simultaneous quantification of all four subgroups of F
+
-specific RNA coliphages using novel primer sets and molecular beacons is presented. This assay is extremely sensitive, achieving detection with as few as 10 copies of isolated coliphage RNA, and is linear for a minimum of six orders of magnitude. During survival experiments, the real-time RT-PCR technique was able to quantify coliphages in seawater when culture-based double agar layer assay failed. While infectivity was lost at different rates at the subgroup level, decay constants in seawater, calculated using the real-time RT-PCR estimates, did not vary among subgroups. The accurate determination of the in situ concentration of F
+
-specific RNA coliphages using this method will facilitate more effective remediation strategies for impacted environments.
Environmental Stress and Antibiotic Resistance in Food-Related Pathogens
Authors: McMahon M. Ann S. , Xu Jiru , Moore John E. , Blair Ian S. , McDowell David A. 
Published: December 2006

ABSTRACT

This study investigated the possibility that sublethal food preservation stresses (high or low temperature and osmotic and pH stress) can lead to changes in the nature and scale of antibiotic resistance (ABR) expressed by three food-related pathogens (
Escherichia coli
,
Salmonella enterica
serovar Typhimurium, and
Staphylococcus aureus
). The study found that some sublethal stresses significantly altered antibiotic resistance. Incubation at sublethal high temperature (45°C) decreased ABR. Incubation under increased salt (>4.5%) or reduced pH (<5.0) conditions increased ABR. Some of the pathogens continued to express higher levels of ABR after removal of stress, suggesting that in some cases the applied sublethal stress had induced stable increases in ABR. These results indicate that increased use of bacteriostatic (sublethal), rather than bactericidal (lethal), food preservation systems may be contributing to the development and dissemination of ABR among important food-borne pathogens.
Molecular Characterization ofCryptosporidiumIsolates from Humans and Animals in Iran
Authors: Meamar Ahmad Reza , Guyot Karine , Certad Gabriela , Dei-Cas Eduardo , Mohraz Mino , Mohebali Mehdi , Mohammad Kazem , Mehbod Amir Ali , Rezaie Sasan , Rezaian Mostafa 
Published: December 2006

ABSTRACTIsolates ofCryptosporidiumspp. from human and animal hosts in Iran were characterized on the basis of both the 18S rRNA gene and the Laxer locus. ThreeCryptosporidiumspecies,C. hominis,C. parvum, andC. meleagridis, were recognized, and zoonotically transmittedC. parvumwas the predominant species found in humans.
Greater Diversity of Shiga Toxin-Encoding Bacteriophage Insertion Sites among
Escherichia coli
O157:H7 Isolates from Cattle than in Those from Humans
Authors: Besser Thomas E. , Shaikh Nurmohammad , Holt Nicholas J. , Tarr Phillip I. , Konkel Michael E. , Malik-Kale Preeti , Walsh Coilin W. , Whittam Thomas S. , Bono James L. 
Published: December 2006

ABSTRACT

Escherichia coli
O157:H7, a zoonotic human pathogen for which domestic cattle are a reservoir host, produces a Shiga toxin(s) (Stx) encoded by bacteriophages. Chromosomal insertion sites of these bacteriophages define three principal genotypes (clusters 1 to 3) among clinical isolates of
E. coli
O157:H7. Stx-encoding bacteriophage insertion site genotypes of 282 clinical and 80 bovine isolates were evaluated. A total of 268 (95.0%) of the clinical isolates, but only 41 (51.3%) of the bovine isolates, belonged to cluster 1, 2, or 3 (
P
< 0.001). Thirteen additional genotypes were identified in isolates from both cattle and humans (four genotypes), from only cattle (seven genotypes), or from only humans (two genotypes). Two other markers previously associated with isolates from cattle or with clinical isolates showed similar associations with genotype groups within bovine isolates; the
tir
allele sp-1 and the
Q
933W
allele were under- and overrepresented, respectively, among cluster 1 to 3 genotypes. Stx-encoding bacteriophage insertion site typing demonstrated that there is broad genetic diversity of
E. coli
O157:H7 in the bovine reservoir and that numerous genotypes are significantly underrepresented among clinical isolates, consistent with the possibility that there is reduced virulence or transmissibility to humans of some bovine
E. coli
O157:H7 genotypes.
Diversity of Fungi, Bacteria, and Actinomycetes on Leaves Decomposing in a Stream
Authors: Das Mitali , Royer Todd V. , Leff Laura G. 
Published: December 2006

ABSTRACT
Although fungi, bacteria, and specific bacterial taxa, such as the actinomycetes, have been studied extensively in various habitats, few studies have examined them simultaneously, especially on decomposing leaves in streams. In this study, sugar maple and white oak leaves were incubated in a stream in northeastern Ohio for 181 days during which samples were collected at regular intervals. Following DNA extraction, PCR-denaturing gradient gel electrophoresis (DGGE) was performed using fungus-, bacterium-, and actinomycete-specific primers. In addition, fungal and bacterial biomass was estimated. Fungal biomass differed on different days but not between leaves of the two species and was always greater than bacterial biomass. There were significant differences in bacterial biomass through time and between leaf types on some days. Generally, on the basis of DGGE, few differences in community structure were found for different leaf types. However, the ribotype richness of fungi was significantly greater than those of the bacteria and actinomycetes, which were similar to each other. Ribotype richness decreased toward the end of the study for each group except bacteria. Lack of differences between the two leaf types suggests that the microorganisms colonizing the leaf biofilm were primarily generalists that could exploit the resources of the leaves of either species equally well. Thus, we conclude that factors, such as the ecological role of the taxa (generalists versus specialists), stage of decay, and time of exposure, appeared to be more important determinants of microbial community structure than leaf quality.
Mixed-Valence Cytoplasmic Iron Granules Are Linked to Anaerobic Respiration
Authors: Glasauer S. , Langley S. , Boyanov M. , Lai B. , Kemner K. , Beveridge T. J. 
Published: December 2006

ABSTRACT

Intracellular granules containing ferric and ferrous iron formed in
Shewanella putrefaciens
CN32 during dissimilatory reduction of solid-phase ferric iron. It is the first in situ detection at high resolution (150 nm) of a mixed-valence metal particle residing within a prokaryotic cell. The relationship of the internal particles to Fe(III) reduction may indicate a respiratory role.
Correlation of Functional Instability and Community Dynamics in Denitrifying Dispersed-Growth Reactors
Authors: Gentile M. E. , Jessup C. M. , Nyman J. L. , Criddle C. S. 
Published: December 2006

ABSTRACT

Understanding the relationship between microbial community dynamics and functional instability is an important step towards designing reliable biological water treatment systems. In this study, the community dynamics of two dispersed-growth denitrifying reactors were examined during periods of functional stability and instability. In both reactors during the period of functional instability, the effluent chemistry changed over time, with periods of high nitrate concentrations followed by periods of fluctuating nitrite concentrations. Community structure was examined by clone library analysis of the 16S rRNA gene. Community dynamics were investigated with terminal restriction fragment (T-RF) length polymorphism, and the functional diversity represented by T-RFs was assessed through nitrate reduction assays of representative isolates. During the period of functional instability, the community structure changed considerably, and the dynamics correlated significantly with effluent chemistry. The nitrite concentration was significantly correlated with the relative abundances of the nitrate-reducing
Delftia
- and
Achromobacter
-like T-RFs. The isolate representing the
Acidovorax
-like T-RF reduced nitrate directly to nitrogen in batch assays without the accumulation of any intermediates. The
Acidovorax
-like T-RF relative abundance was significantly negatively correlated with nitrite concentration, indicating that it was associated with good functional performance. The results of this study reveal a clear relationship between community dynamics and functional instability and the importance of diversity among nitrate-reducing populations within a denitrifying community.
Role of Microbial Immigration in the Colonization of Apple Leaves by
Aureobasidium pullulans
Authors: McGrath Molly J. , Andrews John H. 
Published: December 2006

ABSTRACT

The role of microbial immigration in the veinal colonization pattern of
Aureobasidium pullulans
on the adaxial surface of apple leaves was investigated in two experiments at two periods (early and late seasons) in 2004 by applying green fluorescent protein (GFP)-tagged blastospores to the foliage of orchard trees. Individual leaves were resampled by a semidestructive method immediately after inoculation (
t
0
) and about 1 (
t
1
), 2 (
t
2
), and 3 (
t
3
) weeks later. At
t
0
, there were no significant (
P
≤ 0.05) differences in densities (cells/mm
2
) on veinal (excluding midvein) sites and those on interveinal sites, but at all points thereafter, densities were significantly higher on veins. GFP-tagged
A. pullulans
cells remained primarily as singletons on interveinal regions (≥90% at all points), while ≥20% of cells over veins at
t
3
were in colonies of ≥4 cells. The colonies that developed from single cells placed on midveins and other veins were significantly larger than those that developed on interveinal regions of detached field and seedling leaves incubated under controlled conditions. Colonies primarily developed linearly along veins, reaching average colony sizes (72 h) of 24.4 ± 12.7 (mean ± standard deviation) cells. In contrast, colonies on interveinal regions tended to average only 2.9 ± 1.3 cells, with less linearity. To examine the potential role of
A. pullulans
growth-inhibiting factors associated with interveinal features, single GFP-tagged
A. pullulans
cells in droplets previously incubated on interveinal sites were placed on midveins and compared to midvein colonies derived from cells in a water-only suspension. No differences in colony size resulted. Our results indicate that immigration limitation and growth-inhibiting factors are not the primary factors responsible for
A. pullulans
veinal colonization patterns in the field. Rather, indirect evidence suggests that growth-promoting substances occur locally in the veinal areas.
Role of Broiler Carcasses and Processing Plant Air in Contamination of Modified-Atmosphere-Packaged Broiler Products with Psychrotrophic Lactic Acid Bacteria
Authors: Vihavainen Elina , Lundström Hanna-Saara , Susiluoto Tuija , Koort Joanna , Paulin Lars , Auvinen Petri , Björkroth K. Johanna 
Published: December 2006

ABSTRACT

Some psychrotrophic lactic acid bacteria (LAB) are specific meat spoilage
organisms in modified-atmosphere-packaged (MAP), cold-stored meat
products. To determine if incoming broilers or the production plant
environment is a source of spoilage LAB, a total of 86, 122, and 447
LAB isolates from broiler carcasses, production plant air, and MAP
broiler products, respectively, were characterized using a library
of HindIII restriction fragment length polymorphism (RFLP)
patterns of the 16 and 23S rRNA genes as operational taxonomic units in
numerical analyses. Six hundred thirteen LAB isolates from the total of
655 clustered in 29 groups considered to be species specific.
Sixty-four percent of product isolates clustered either with
Carnobacterium divergens
or with
Carnobacterium
maltaromaticum
type strains. The third major product-associated
cluster (17% of isolates) was formed by unknown LAB. Representative
strains from these three clusters were analyzed for the phylogeny of
their 16S rRNA genes. This analysis verified that the two largest RFLP
clusters consisted of carnobacteria and showed that the unknown LAB
group consisted of
Lactococcus
spp. No product-associated LAB
were detected in broiler carcasses sampled at the beginning of
slaughter, whereas carnobacteria and lactococci, along with some other
specific meat spoilage LAB, were recovered from processing plant air at
many sites. This study reveals that incoming broiler chickens are not
major sources of psychrotrophic spoilage LAB, whereas the detection of
these organisms from the air of the processing environment highlights
the role of processing facilities as sources of LAB
contamination.
Chronic
Helicobacter pylori
Infection Does Not Significantly Alter the Microbiota of the Murine Stomach
Authors: Tan Mai Ping , Kaparakis Maria , Galic Maja , Pedersen John , Pearse Martin , Wijburg Odilia L. C. , Janssen Peter H. , Strugnell Richard A. 
Published: December 2006

ABSTRACT

We examined the impact of
Helicobacter pylori
infection on the murine gastric microbiota by culture and terminal-restriction fragment length polymorphism and found that neither acute nor chronic
H. pylori
infection substantially affected the gastric microbial composition. Interestingly, the total
H. pylori
burden detected by real-time PCR was significantly higher than that revealed by viable counts, suggesting that the antigenic load sustaining
H. pylori
-induced gastritis could be considerably higher than previously believed.
Identification and Expression of Benzylsuccinate Synthase Genes in a Toluene-Degrading Methanogenic Consortium
Authors: Washer Cheryl E. , Edwards Elizabeth A. 
Published: December 2006

ABSTRACT

Benzylsuccinate synthase (BSS) initiates anaerobic toluene biodegradation, and BSS genes have been found in several nitrate- and iron-reducing organisms. Here, two new putative
bssA
genes were identified in a methanogenic toluene-degrading culture. Transcription was upregulated with toluene but not with benzoate, consistent with the proposed function. These are the first
bss
sequences from a methanogenic culture.
Identification of Bacterial Groups Preferentially Associated with Mycorrhizal Roots of
Medicago truncatula
Authors: Offre P. , Pivato B. , Siblot S. , Gamalero E. , Corberand T. , Lemanceau P. , Mougel C. 
Published: December 2006

ABSTRACT

The genetic structures of bacterial communities associated with
Medicago truncatula
Gaertn. cv. Jemalong line J5 (Myc
+
Nod
+
) and its symbiosis-defective mutants TRV48 (Myc
+
Nod
−
) and TRV25 (Myc
−
Nod
−
) were compared. Plants were cultivated in a fertile soil (Châteaurenard, France) and in soil from the Mediterranean basin showing a low fertility (Mas d'Imbert, France). Plant growth, root architecture, and the efficiency of root symbiosis of the three plant genotypes were characterized in the two soils. Structures of the bacterial communities were assessed by automated-ribosomal intergenic spacer analysis (A-RISA) fingerprinting from DNA extracted from the rhizosphere soil and root tissues. As expected, the TRV25 mutant did not develop endomycorrhizal symbiosis in any of the soils, whereas mycorrhization of line J5 and the TRV48 mutant occurred in both soils but at a higher intensity in the Mas d'Imbert (low fertility) than in the Châteaurenard soil. However, modifications of plant growth and root architecture, between mycorrhizal (J5 and TRV48) and nonmycorrhizal (TRV25) plants, were recorded only when cultivated in the Mas d'Imbert soil. Similarly, the genetic structures of bacterial communities associated with mycorrhizal and nonmycorrhizal plants differed significantly in the Mas d'Imbert soil but not in the Châteaurenard soil. Multivariate analysis of the patterns allowed the identification of molecular markers, explaining these differences, and markers were further sequenced. Molecular marker analysis allowed the delineation of 211 operational taxonomic units. Some of those belonging to the
Comamonadaceae
and
Oxalobacteraceae
(β-
Proteobacteria
) families were found to be significantly more represented within bacterial communities associated with the J5 line and the TRV48 mutant than within those associated with the TRV25 mutant, indicating that these bacterial genera were preferentially associated with mycorrhizal roots in the Mas d'Imbert soil.
Succession of Sulfur-Oxidizing Bacteria in the Microbial Community on Corroding Concrete in Sewer Systems
Authors: Okabe Satoshi , Odagiri Mitsunori , Ito Tsukasa , Satoh Hisashi 
Published: December 2006

ABSTRACT

Microbially induced concrete corrosion (MICC) in sewer systems has been a serious problem for a long time. A better understanding of the succession of microbial community members responsible for the production of sulfuric acid is essential for the efficient control of MICC. In this study, the succession of sulfur-oxidizing bacteria (SOB) in the bacterial community on corroding concrete in a sewer system in situ was investigated over 1 year by culture-independent 16S rRNA gene-based molecular techniques. Results revealed that at least six phylotypes of SOB species were involved in the MICC process, and the predominant SOB species shifted in the following order:
Thiothrix
sp.,
Thiobacillus plumbophilus
,
Thiomonas intermedia
,
Halothiobacillus neapolitanus
,
Acidiphilium acidophilum
, and
Acidithiobacillus thiooxidans. A. thiooxidans
, a hyperacidophilic SOB, was the most dominant (accounting for 70% of EUB338-mixed probe-hybridized cells) in the heavily corroded concrete after 1 year. This succession of SOB species could be dependent on the pH of the concrete surface as well as on trophic properties (e.g., autotrophic or mixotrophic) and on the ability of the SOB to utilize different sulfur compounds (e.g., H
2
S, S
0
, and S
2
O
3
2−
). In addition, diverse heterotrophic bacterial species (e.g., halo-tolerant, neutrophilic, and acidophilic bacteria) were associated with these SOB. The microbial succession of these microorganisms was involved in the colonization of the concrete and the production of sulfuric acid. Furthermore, the vertical distribution of microbial community members revealed that
A. thiooxidans
was the most dominant throughout the heavily corroded concrete (gypsum) layer and that
A. thiooxidans
was most abundant at the highest surface (1.5-mm) layer and decreased logarithmically with depth because of oxygen and H
2
S transport limitations. This suggested that the production of sulfuric acid by
A. thiooxidans
occurred mainly on the concrete surface and the sulfuric acid produced penetrated through the corroded concrete layer and reacted with the sound concrete below.
Inhibition of
Staphylococcus aureus
Growth on Tellurite-Containing Media by
Lactobacillus reuteri
Is Dependent on CyuC and Thiol Production
Authors: Turner Mark S. , Lo Raquel , Giffard Philip M. 
Published: December 2006

ABSTRACT

Lactobacillus reuteri
inhibits
Staphylococcus aureus
growth on Baird-Parker agar. This activity required the presence of tellurite and was not shared with other lactic acid bacteria or an
L. reuteri
mutant defective in cystine metabolism. Secreted products generated from
L. reuteri
cystine metabolism and thiols were shown to augment tellurite toxicity.
Inactivation of a Norovirus by High-Pressure Processing
Authors: Kingsley David H. , Holliman Daniel R. , Calci Kevin R. , Chen Haiqiang , Flick George J. 
Published: December 2006

ABSTRACT

Murine norovirus (strain MNV-1), a propagable norovirus, was evaluated for susceptibility to high-pressure processing. Experiments with virus stocks in Dulbecco's modified Eagle medium demonstrated that at room temperature (20°C) the virus was inactivated over a pressure range of 350 to 450 MPa, with a 5-min, 450-MPa treatment being sufficient to inactivate 6.85 log
10
PFU of MNV-1. The inactivation of MNV-1 was enhanced when pressure was applied at an initial temperature of 5°C; a 5-min pressure treatment of 350 MPa at 30°C inactivated 1.15 log
10
PFU of virus, while the same treatment at 5°C resulted in a reduction of 5.56 log
10
PFU. Evaluation of virus inactivation as a function of treatment times ranging from 0 to 150 s and 0 to 900 s at 5°C and 20°C, respectively, indicated that a decreasing rate of inactivation with time was consistent with Weibull or log-logistic inactivation kinetics. The inactivation of MNV-1 directly within oyster tissues was demonstrated; a 5-min, 400-MPa treatment at 5°C was sufficient to inactivate 4.05 log
10
PFU. This work is the first demonstration that norovirus can be inactivated by high pressure and suggests good prospects for inactivation of nonpropagable human norovirus strains in foods.
An Efficient Fungal RNA-Silencing System Using the
DsRed
Reporter Gene
Authors: Janus Danielle , Hoff Birgit , Hofmann Eckhard , Kück Ulrich 
Published: December 2006

ABSTRACT

In filamentous fungi, RNA silencing is an attractive alternative to disruption experiments for the functional analysis of genes. We adapted the gene encoding the autofluorescent DsRed protein as a reporter to monitor the silencing process in fungal transformants. Using the cephalosporin C producer
Acremonium chrysogenum
, strains showing a high level of expression of the
DsRed
gene were constructed, resulting in red fungal colonies. Transfer of a hairpin-expressing vector carrying fragments of the
DsRed
gene allowed efficient silencing of
DsRed
expression. Monitoring of this process by Northern hybridization, real-time PCR quantification, and spectrofluorometric measurement of the DsRed protein confirmed that downregulation of gene expression can be observed at different expression levels. The usefulness of the DsRed silencing system was demonstrated by investigating cosilencing of
DsRed
together with
pcbC
, encoding the isopenicillin N synthase, an enzyme involved in cephalosporin C biosynthesis. Downregulation of
pcbC
can be detected easily by a bioassay measuring the antibiotic activity of individual strains. In addition, the presence of the isopenicillin N synthase was investigated by Western blot hybridization. All transformants having a colorless phenotype showed simultaneous downregulation of the
pcbC
gene, albeit at different levels. The RNA-silencing system presented here should be a powerful genetic tool for strain improvement and genome-wide analysis of this biotechnologically important filamentous fungus.