bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of Copper Cast Alloys To Control
Escherichia coli
O157 Cross-Contamination during Food Processing
Authors: Noyce J. O. , Michels H. , Keevil C. W. 
Published: June 2006

ABSTRACT

The most notable method of infection from
Escherichia coli
O157 (
E. coli
O157) is through contaminated food products, usually ground beef. The objective of this study was to evaluate seven cast copper alloys (61 to 95% Cu) for their ability to reduce the viability of
E. coli
O157, mixed with or without ground beef juice, and to compare these results to those for stainless steel.
E. coli
O157 (NCTC 12900) (2 × 10
7
CFU) mixed with extracted beef juice (25%) was inoculated onto coupons of each copper cast alloy or stainless steel and incubated at either 22°C or 4°C for up to 6 h.
E. coli
O157 viability was determined by plate counts in addition to staining in situ with the respiratory indicator fluorochrome 5-cyano-2,3-ditolyl tetrazolium. Without beef extract, three alloys completely killed the inoculum during the 6-h exposure at 22°C. At 4°C, only the high-copper alloys (>85%) significantly reduced the numbers of O157. With beef juice, only one alloy (95% Cu) completely killed the inoculum at 22°C. For stainless steel, no significant reduction in cell numbers occurred. At 4°C, only alloys C83300 (93% Cu) and C87300 (95% Cu) significantly reduced the numbers of
E. coli
O157, with 1.5- and 5-log kills, respectively. Reducing the inoculum to 10
3
CFU resulted in a complete kill for all seven cast copper alloys in 20 min or less at 22°C. These results clearly demonstrate the antimicrobial properties of cast copper alloys with regard to
E. coli
O157, and consequently these alloys have the potential to aid in food safety.
Effect of Growth in Biofilms on Chlorine Susceptibility of
Mycobacterium avium
and
Mycobacterium intracellulare
Authors: Steed Keesha A. , Falkinham Joseph O. 
Published: June 2006

ABSTRACT

Mycobacterium avium
and
Mycobacterium intracellulare
were grown in suspension and in biofilms, and their susceptibilities to chlorine were measured.
M. avium
and
M. intracellulare
readily adhered within 2 h, and numbers increased 10-fold in 30 days at room temperature in biofilms on both polystyrene flasks and glass beads. The chlorine resistance of
M. avium
and
M. intracellulare
cells grown and exposed to chlorine in biofilms was significantly higher than that of cells grown in suspension. Survival curves showed no evidence of a resistant, persisting population after 6 h of exposure to 1 μg chlorine/ml. The chlorine susceptibility of cells grown in biofilms and exposed in suspension (cells detached from bead surfaces) was also significantly higher than that of cells grown and exposed in suspension (planktonic cells), although it was lower than that of cells grown and exposed in biofilms. The higher resistance of the detached biofilm-grown cells was reversed upon their growth in suspension. There was a strong correlation between the chlorine susceptibility of cells of both
M. avium
and
M. intracellulare
and cell surface hydrophobicity measured by contact angle for both biofilm- and suspension-grown cells.
Shifting the pH Profile of
Aspergillus niger
PhyA Phytase To Match the Stomach pH Enhances Its Effectiveness as an Animal Feed Additive
Authors: Kim Taewan , Mullaney Edward J. , Porres Jesus M. , Roneker Karl R. , Crowe Sarah , Rice Sarah , Ko Taegu , Ullah Abul H. J. , Daly Catherine B. , Welch Ross , Lei Xin Gen 
Published: June 2006

ABSTRACT

Environmental pollution by phosphorus from animal waste is a major problem in agriculture because simple-stomached animals, such as swine, poultry, and fish, cannot digest phosphorus (as phytate) present in plant feeds. To alleviate this problem, a phytase from
Aspergillus niger
PhyA is widely used as a feed additive to hydrolyze phytate-phosphorus. However, it has the lowest relative activity at the pH of the stomach (3.5), where the hydrolysis occurs. Our objective was to shift the pH optima of PhyA to match the stomach condition by substituting amino acids in the substrate-binding site with different charges and polarities. Based on the crystal structure of PhyA, we prepared 21 single or multiple mutants at Q50, K91, K94, E228, D262, K300, and K301 and expressed them in
Pichia pastoris
yeast. The wild-type (WT) PhyA showed the unique bihump, two-pH-optima profile, whereas 17 mutants lost one pH optimum or shifted the pH optimum from pH 5.5 to the more acidic side. The mutant E228K exhibited the best overall changes, with a shift of pH optimum to 3.8 and 266% greater (
P
< 0.05) hydrolysis of soy phytate at pH 3.5 than the WT enzyme. The improved efficacy of the enzyme was confirmed in an animal feed trial and was characterized by biochemical analysis of the purified mutant enzymes. In conclusion, it is feasible to improve the function of PhyA phytase under stomach pH conditions by rational protein engineering.
Prevalence of
Chlamydophila psittaci
in Fecal Droppings from Feral Pigeons in Amsterdam, The Netherlands
Authors: Heddema Edou R. , ter Sluis Sietske , Buys Jan A. , Vandenbroucke-Grauls Christina M. J. E. , van Wijnen Joop H. , Visser Caroline E. 
Published: June 2006

ABSTRACT

In many cities, the feral rock dove is an abundant bird species that can harbor
Chlamydophila psittaci
. We determined the prevalence and genotype of
C. psittaci
in fresh fecal samples from feral pigeons in Amsterdam, The Netherlands. The prevalence was 7.9% overall (26/331; 95% confidence interval, 5 to 11). Ten genotyped PCR-positive samples were all genotype B.
Internally Controlled Real-Time PCR Method for Quantitative Species-Specific Detection and
vapA
Genotyping of
Rhodococcus equi
Authors: Rodríguez-Lázaro David , Lewis Deborah A. , Ocampo-Sosa Alain A. , Fogarty Ursula , Makrai László , Navas Jesús , Scortti Mariela , Hernández Marta , Vázquez-Boland José A. 
Published: June 2006

ABSTRACT

We developed a novel quantitative real-time PCR (Q-PCR) method for the soil actinomycete
Rhodococcus equi
, an important horse pathogen and emerging human pathogen. Species-specific quantification was achieved by targeting the chromosomal monocopy gene
choE
, universally conserved in
R. equi
. The
choE
Q-PCR included an internal amplification control (IAC) for identification of false negatives. A second Q-PCR targeted the virulence plasmid gene
vapA
, carried by most horse isolates but infrequently found in isolates from other sources. The
choE
-IAC and
vapA
assays were 100% sensitive and specific as determined using 178
R. equi
isolates, 77 nontarget bacteria, and a panel of 60
R. equi
isolates with known
vapA
+
and
vapA
-negative (including
vapB
+
) plasmid genotypes. The
vapA
+
frequency among isolate types was as follows: horse, 85%; human, 20%; bovine and pig, 0%; others, 27%. The
choE
-IAC Q-PCR could detect up to one genome equivalent using
R. equi
DNA or 100 bacteria/ml using DNA extracted from artificially contaminated horse bronchoalveolar lavage (BAL) fluid. Quantification was linear over a 6-log dynamic range down to ≈10 target molecules (or 1,000 CFU/ml BAL fluid) with PCR efficiency
E
of >0.94. The
vapA
assay had similar performance but appeared unsuitable for accurate (
vapA
+
)
R. equi
quantification due to variability in target gene or plasmid copy number (1 to 9). The dual-reaction Q-PCR system here reported offers a useful tool to both medical and veterinary diagnostic laboratories for the quantitative detection of
R. equi
and (optional)
vapA
+
“horse-pathogenic” genotype determination.
Pure and Mixed Genetic Lines of
Saccharomyces bayanus
and
Saccharomyces pastorianus
and Their Contribution to the Lager Brewing Strain Genome
Authors: Rainieri Sandra , Kodama Yukiko , Kaneko Yoshinobu , Mikata Kozaburo , Nakao Yoshihiro , Ashikari Toshihiko 
Published: June 2006

ABSTRACT

The yeast species
Saccharomyces bayanus
and
Saccharomyces pastorianus
are of industrial importance since they are involved in the production process of common beverages such as wine and lager beer; however, they contain strains whose variability has been neither fully investigated nor exploited in genetic improvement programs. We evaluated this variability by using PCR-restriction fragment length polymorphism analysis of 48 genes and partial sequences of 16. Within these two species, we identified “pure” strains containing a single type of genome and “hybrid” strains that contained portions of the genomes from the “pure” lines, as well as alleles termed “Lager” that represent a third genome commonly associated with lager brewing strains. The two pure lines represent
S. uvarum
and
S. bayanus
, the latter a novel group of strains that may be of use in strain improvement programs. Hybrid lines identified include (i)
S. cerevisiae
/
S. bayanus
/Lager, (ii)
S. bayanus
/
S. uvarum
/Lager, and (iii)
S. cerevisiae
/
S. bayanus
/
S. uvarum
/Lager. The genome of the lager strains may have resulted from chromosomal loss, replacement, or rearrangement within the hybrid genetic lines. This study identifies brewing strains that could be used as novel genetic sources in strain improvement programs and provides data that can be used to generate a model of how naturally occurring and industrial hybrid strains may have evolved.
Estimating High-Affinity Methanotrophic Bacterial Biomass, Growth, and Turnover in Soil by Phospholipid Fatty Acid
13
C Labeling
Authors: Maxfield P. J. , Hornibrook E. R. C. , Evershed R. P. 
Published: June 2006

ABSTRACT

A time series phospholipid fatty acid (PLFA)
13
C-labeling study was undertaken to determine methanotrophic taxon, calculate methanotrophic biomass, and assess carbon recycling in an upland brown earth soil from Bronydd Mawr (Wales, United Kingdom). Laboratory incubations of soils were performed at ambient CH
4
concentrations using synthetic air containing 2 parts per million of volume of
13
CH
4
. Flowthrough chambers maintained a stable CH
4
concentration throughout the 11-week incubation. Soils were analyzed at weekly intervals by gas chromatography (GC), GC-mass spectrometry, and GC-combustion-isotope ratio mass spectrometry to identify and quantify individual PLFAs and trace the incorporation of
13
C label into the microbial biomass. Incorporation of the
13
C label was seen throughout the experiment, with the rate of incorporation decreasing after 9 weeks. The δ
13
C values of individual PLFAs showed that
13
C label was incorporated into different components to various extents and at various rates, reflecting the diversity of PLFA sources. Quantitative assessments of
13
C-labeled PLFAs showed that the methanotrophic population was of constant structure throughout the experiment. The dominant
13
C-labeled PLFA was 18:1ω7c, with 16:1ω5 present at lower abundance, suggesting the presence of novel type II methanotrophs. The biomass of methane-oxidizing bacteria at optimum labeling was estimated to be about 7.2 × 10
6
cells g
−1
of soil (dry weight). While recycling of
13
C label from the methanotrophic biomass must occur, it is a slower process than initial
13
CH
4
incorporation, with only about 5 to 10% of
13
C-labeled PLFAs reflecting this process. Thus,
13
C-labeled PLFA distributions determined at any time point during
13
CH
4
incubation can be used for chemotaxonomic assessments, although extended incubations are required to achieve optimum
13
C labeling for methanotrophic biomass determinations.
Prevalence of
Escherichia coli
O157 in Saskatchewan Cattle: Characterization of Isolates by Using Random Amplified Polymorphic DNA PCR, Antibiotic Resistance Profiles, and Pathogenicity Determinants
Authors: Vidovic Sinisa , Korber Darren R. 
Published: June 2006

ABSTRACT

The prevalence of
Escherichia coli
O157 associated with feedlot cattle in Saskatchewan was determined in a 10-month longitudinal study (3 feedlots) and a point prevalence study (20 feedlots). The prevalence of
E. coli
O157 at the three different sites in the horizontal study varied from 2.5 to 45%. The point prevalence of
E. coli
O157 among Saskatchewan cattle from 20 different feedlots ranged from 0% to a high of 57%. A statistically significant (
P
= 0.003) positive correlation was determined to exist between the density of cattle and the
E. coli
O157 prevalence rate. A significant correlation (
P
= 0.006) was also found between the
E. coli
O157 percent prevalence and the number of cattle housed/capacity ratio. All 194
E. coli
O157 isolates obtained were highly virulent, and random amplified polymorphic DNA PCR analysis revealed that the isolates grouped into 39 different
E. coli
O157 subtypes, most of which were indigenous to specific feedlots. Two of the most predominant subtypes were detected in 11 different feedlots and formed distinct clusters in two geographic regions in the province. Antimicrobial susceptibility testing of the
E. coli
O157 isolates revealed that 10 were multidrug resistant and that 73 and 5 were resistant to sulfisoxazole and tetracycline, respectively.
Atypical
Helicobacter canadensis
Strains Associated with Swine
Authors: Inglis G. Douglas , McConville Malcolm , de Jong Anno 
Published: June 2006

ABSTRACT

Forty-two
Helicobacter
isolates were isolated from swine feces in The Netherlands and Denmark. All 12 isolates sequenced (16S rRNA gene) formed a robust clade with
Helicobacter canadensis
(∼99% similarity). Species-specific PCR indicated that all of the isolates were
H. canadensis
isolates. Although the appearance of the porcine isolates was similar to the appearance of
H. canadensis
, only one of these isolates was able to hydrolyze indoxyl acetate, a cardinal characteristic of this taxon. Examination of the 23S rRNA and
hsp60
genes revealed high levels of similarity between the porcine isolates and
H. canadensis
. However, amplified fragment length polymorphism genomic typing showed that isolates recovered from swine feces were genetically distinct from
H. canadensis
strains obtained from humans and geese.
Microbial Diversity in Water and Sediment of Lake Chaka, an Athalassohaline Lake in Northwestern China
Authors: Jiang Hongchen , Dong Hailiang , Zhang Gengxin , Yu Bingsong , Chapman Leah R. , Fields Matthew W. 
Published: June 2006

ABSTRACTWe employed culture-dependent and -independent techniques to study microbial diversity in Lake Chaka, a unique hypersaline lake (32.5% salinity) in northwest China. It is situated at 3,214 m above sea level in a dry climate. The average water depth is 2 to 3 cm. Halophilic isolates were obtained from the lake water, and halotolerant isolates were obtained from the shallow sediment. The isolates exhibited resistance to UV and gamma radiation. Microbial abundance in the sediments ranged from 108cells/g at the water-sediment interface to 107cells/g at a sediment depth of 42 cm. A major change in the bacterial community composition was observed across the interface. In the lake water, clone sequences affiliated with theBacteroideteswere the most abundant, whereas in the sediments, sequences related to low G+C gram-positive bacteria were predominant. A similar change was also present in the archaeal community. While all archaeal clone sequences in the lake water belonged to theHalobacteriales, the majority of the sequences in the sediments were related to those previously obtained from methanogenic soils and sediments. The observed changes in the microbial community structure across the water-sediment interface were correlated with a decrease in salinity from the lake water (32.5%) to the sediments (approximately 4%). Across the interface, the redox state also changed from oxic to anoxic and may also have contributed to the observed shift in the microbial community.
Analysis of Quantitative Interactions between Two Species of Arbuscular Mycorrhizal Fungi,Glomus mosseaeandG. intraradices, by Real-Time PCR
Authors: Alkan Noam , Gadkar Vijay , Yarden Oded , Kapulnik Yoram 
Published: June 2006

ABSTRACTArbuscular mycorrhizal fungi (AMF) are obligate biotrophs, known to play an important role in ecological processes. Conventional light microscopy is the most common method used to detect their presence in planta, but this method fails to discern the presence of multiple AMF species and is not quantitative. These two factors are critically important in ecological studies, where the symbiotic contribution of each isolate needs to be defined. This paper describes the use of quantitative real-time PCR (qRT-PCR) as a detection system to address this issue. We used twoGlomusspp., namely,G. intraradicesandG. mosseae, to show that it is possible to study the interactions between these two isolates during the cocolonization of a single root system. Three different physiological studies were set up to assess how the interactions affected the occupancy of these fungi intraradically on a temporal basis. These treatments included saline and phosphorus stress, spatial distribution in the root zone, and preference for a particular host. qRT-PCR could prove a valuable tool in the area of AMF field ecology, where such data are critically important for defining the role of each species in the community structure.
Induction of Autophagy by Second-Fermentation Yeasts during Elaboration of Sparkling Wines
Authors: Cebollero Eduardo , Gonzalez Ramon 
Published: June 2006

ABSTRACTAutophagy is a transport system mediated by vesicles, ubiquitous in eukaryotic cells, by which bulk cytoplasm is targeted to a lysosome or vacuole for degradation. In the yeastSaccharomyces cerevisiae, autophagy is triggered by nutritional stress conditions (e.g., carbon- or nitrogen-depleted medium). In this study we showed that there is induction of autophagy in second-fermentation yeasts during sparkling wine making. Two methods were employed to detect autophagy: a biochemical approach based on depletion of the protein acetaldehyde dehydrogenase Ald6p and a morphological strategy consisting of visualization of autophagic bodies and autophagosomes, which are intermediate vesicles in the autophagic process, by transmission electron microscopy. This study provides the first demonstration of autophagy in second-fermentation yeasts under enological conditions. The correlation between autophagy and yeast autolysis during sparkling wine production is discussed, and genetic engineering of autophagy-related genes in order to accelerate the aging steps in wine making is proposed.
Evaluation of a Macrofoam Swab Protocol for the Recovery of
Bacillus anthracis
Spores from a Steel Surface
Authors: Hodges L. R. , Rose L. J. , Peterson A. , Noble-Wang J. , Arduino M. J. 
Published: June 2006

ABSTRACT

A protocol to recover
Bacillus anthracis
spores from a steel surface using macrofoam swabs was evaluated for its accuracy, precision, reproducibility, and limit of detection. Macrofoam swabs recovered 31.7 to 49.1% of spores from 10-cm
2
steel surfaces with a ≤32.7% coefficient of variation in sampling precision and reproducibility for inocula of ≥38 spores.
Evidence for an Intermediate Colony Morphology of
Vibrio vulnificus
Authors: Rosche Thomas M. , Smith Ben , Oliver James D. 
Published: June 2006

ABSTRACT

Vibrio vulnificus
causes both food-borne disease and wound infections. Most
V. vulnificus
strains express capsular polysaccharide (CPS), which is required for the virulence of this organism. Under standard growth conditions, CPS expression is lost at a relatively high frequency (10
−3
to 10
−4
), resulting in a switch from an opaque (Op, CPS
+
) colony morphology to a translucent (Tr, CPS
−
) colony morphology. The
wzb
gene, which encodes a phosphatase required for CPS expression, has been proposed to be involved in this switch through a site-specific deletion of the entire gene. In an examination of five strains, we found that the frequency of
wzb
deletion in Tr colonies varies by strain and therefore does not account for all the Tr colonies that are seen. In addition, we have identified a third, intermediate (Int) colony morphotype, in which the colonies appear less opaque but are not fully translucent. PCR studies have demonstrated that Int colonies still contain the
wzb
gene, while reverse transcriptase PCR studies have shown that although Int strains retain expression of
wzb
, in some cases the transcription of
wzb
is reduced. Int strains switch to a true Tr (
wzb
negative) morphotype at a very high frequency (nearly 100%) under certain conditions. Finally, Int colonies, which in some cases can easily be mistaken for Tr colonies, have been observed to occasionally revert to Op, while Tr colonies containing a
wzb
deletion presumably are unable to revert to the encapsulated form.
Cellulose Acetate Containing Toluidine Blue and Rose Bengal Is an Effective Antimicrobial Coating when Exposed to White Light
Authors: Decraene Valérie , Pratten Jonathan , Wilson Michael 
Published: June 2006

ABSTRACT

Simple methods of reducing the microbial load on surfaces in hospitals are needed to reduce the risk of hospital-associated infections. Here we report on the ability of a cellulose acetate coating containing the photosensitizers toluidine blue and rose bengal to kill microbes (
Staphylococcus aureus
,
Escherichia coli
,
Clostridium difficile
, a bacteriophage, and
Candida albicans
) on its surface when illuminated with white light.
Microbial Dioxygenase Gene Population Shifts during Polycyclic Aromatic Hydrocarbon Biodegradation
Authors: Ní Chadhain Sinéad M. , Norman R. Sean , Pesce Karen V. , Kukor Jerome J. , Zylstra Gerben J. 
Published: June 2006

ABSTRACT
The degradation of polycyclic aromatic hydrocarbons (PAHs) by bacteria has been widely studied. While many pure cultures have been isolated and characterized for their ability to grow on PAHs, limited information is available on the diversity of microbes involved in PAH degradation in the environment. We have designed generic PCR primers targeting the gene fragment encoding the Rieske iron sulfur center common to all PAH dioxygenase enzymes. These Rieske primers were employed to track dioxygenase gene population shifts in soil enrichment cultures following exposure to naphthalene, phenanthrene, or pyrene. PAH degradation was monitored by gas chromatograph with flame ionization detection. DNA was extracted from the enrichment cultures following PAH degradation. 16S rRNA and Rieske gene fragments were PCR amplified from DNA extracted from each enrichment culture and an unamended treatment. The PCR products were cloned and sequenced. Molecular monitoring of the enrichment cultures before and after PAH degradation using denaturing gradient gel electrophoresis and 16S rRNA gene libraries suggests that specific phylotypes of bacteria were associated with the degradation of each PAH. Sequencing of the cloned Rieske gene fragments showed that different suites of genes were present in soil microbe populations under each enrichment culture condition. Many of the Rieske gene fragment sequences fell into clades which are distinct from the reference dioxygenase gene sequences used to design the PCR primers. The ability to profile not only the bacterial community but also the dioxygenases which they encode provides a powerful tool for both assessing bioremediation potential in the environment and for the discovery of novel dioxygenase genes.