bluuebunny/crossref_metadata_2025_split huggingface dataset:
Procedure for Rapid Concentration and Detection of Enteric Viruses from Berries and Vegetables
Authors: Butot S. , Putallaz T. , Sánchez G. 
Published: December 2006

ABSTRACT

Several hepatitis A virus (HAV) and norovirus (NV) outbreaks due to consumption of berries and vegetables have been reported during recent years. To facilitate the detection of enteric viruses that may be present on different fresh and frozen products, we developed a rapid and sensitive detection method for HAV, NV, and rotavirus (RV). Initial experiments focused on optimizing the composition of the elution buffer, improving the viral concentration method, and evaluating the performance of various extraction kits. Viruses were extracted from the food surface by a direct elution method in a glycine-Tris (pH 9.5) buffer containing 1% beef extract and concentrated by ultrafiltration. Occasionally, PCR inhibitors were present in the processed berry samples, which gave relatively poor detection limits. However, this problem was overcome by adding a pectinase treatment in the protocol, which markedly improved the sensitivity of the method. After optimization, this concentration method was applied in combination with real-time reverse transcription-PCR (RT-PCR) using specific primers in various types of berries and vegetables. The average detection limits were 1 50% tissue culture infective dose (TCID
50
), 54 RT-PCR units, and 0.02 TCID
50
per 15 g of food for HAV, NV, and RV, respectively. Based on our results, it is concluded that this procedure is suitable to detect and quantify enteric viruses within 6 h and can be applied for surveillance of enteric viruses in fresh and frozen products.
Efficient Production of
l
-Lactic Acid from Xylose by
Pichia stipitis
Authors: Ilmén Marja , Koivuranta Kari , Ruohonen Laura , Suominen Pirkko , Penttilä Merja 
Published: December 2006

ABSTRACT

Microbial conversion of renewable raw materials to useful products is an important objective in industrial biotechnology.
Pichia stipitis
, a yeast that naturally ferments xylose, was genetically engineered for
l
-(+)-lactate production. We constructed a
P. stipitis
strain that expressed the
l
-lactate dehydrogenase (LDH) from
Lactobacillus helveticus
under the control of the
P. stipitis
fermentative
ADH1
promoter. Xylose, glucose, or a mixture of the two sugars was used as the carbon source for lactate production. The constructed
P. stipitis
strain produced a higher level of lactate and a higher yield on xylose than on glucose. Lactate accumulated as the main product in xylose-containing medium, with 58 g/liter lactate produced from 100 g/liter xylose. Relatively efficient lactate production also occurred on glucose medium, with 41 g/liter lactate produced from 94 g/liter glucose. In the presence of both sugars, xylose and glucose were consumed simultaneously and converted predominantly to lactate. Lactate was produced at the expense of ethanol, whose production decreased to ∼15 to 30% of the wild-type level on xylose-containing medium and to 70 to 80% of the wild-type level on glucose-containing medium. Thus, LDH competed efficiently with the ethanol pathway for pyruvate, even though the pathway from pyruvate to ethanol was intact. Our results show, for the first time, that lactate production from xylose by a yeast species is feasible and efficient. This is encouraging for further development of yeast-based bioprocesses to produce lactate from lignocellulosic raw material.
Shiga Toxin and Shiga Toxin-Encoding Phage Do Not Facilitate
Escherichia coli
O157:H7 Colonization in Sheep
Authors: Cornick Nancy A. , Helgerson Amy F. , Sharma Vijay 
Published: December 2006

ABSTRACT

Isogenic strains of
Escherichia coli
O157:H7, missing either
stx
2
or the entire Stx2-encoding phage, were compared with the parent strain for their abilities to colonize sheep. The absence of the phage or of the Shiga toxin did not significantly impact the magnitude or duration of shedding of
E. coli
O157:H7.
Fluidization of Membrane Lipids Enhances the Tolerance of
Saccharomyces cerevisiae
to Freezing and Salt Stress
Authors: Rodríguez-Vargas Sonia , Sánchez-García Alicia , Martínez-Rivas Jose Manuel , Prieto Jose Antonio , Randez-Gil Francisca 
Published: December 2006

ABSTRACT

Unsaturated fatty acids play an essential role in the biophysical characteristics of cell membranes and determine the proper function of membrane-attached proteins. Thus, the ability of cells to alter the degree of unsaturation in their membranes is an important factor in cellular acclimatization to environmental conditions. Many eukaryotic organisms can synthesize dienoic fatty acids, but
Saccharomyces cerevisiae
can introduce only a single double bond at the Δ
9
position. We expressed two sunflower (
Helianthus annuus
) oleate Δ
12
desaturases encoded by
FAD2-1
and
FAD2-3
in yeast cells of the wild-type W303-1A strain (
trp1
) and analyzed their effects on growth and stress tolerance. Production of the heterologous desaturases increased the content of dienoic fatty acids, especially 18:2Δ
9,12
, the unsaturation index, and the fluidity of the yeast membrane. The total fatty acid content remained constant, and the level of monounsaturated fatty acids decreased. Growth at 15°C was reduced in the
FAD2
strains, probably due to tryptophan auxotrophy, since the
trp1
(
TRP1
) transformants that produced the sunflower desaturases grew as well as the control strain did. Our results suggest that changes in the fluidity of the lipid bilayer affect tryptophan uptake and/or the correct targeting of tryptophan transporters. The expression of the sunflower desaturases, in either Trp
+
or Trp
−
strains, increased NaCl tolerance. Production of dienoic fatty acids increased the tolerance to freezing of wild-type cells preincubated at 30°C or 15°C. Thus, membrane fluidity is an essential determinant of stress resistance in
S. cerevisiae
, and engineering of membrane lipids has the potential to be a useful tool of increasing the tolerance to freezing in industrial strains.
Respiration and Growth of
Shewanella decolorationis
S12 with an Azo Compound as the Sole Electron Acceptor
Authors: Hong Yiguo , Xu Meiying , Guo Jun , Xu Zhicheng , Chen Xingjuan , Sun Guoping 
Published: December 2006

ABSTRACT

The ability of
Shewanella decolorationis
S12 to obtain energy for growth by coupling the oxidation of various electron donors to dissimilatory azoreduction was investigated. This microorganism can reduce a variety of azo dyes by use of formate, lactate, pyruvate, or H
2
as the electron donor. Furthermore, strain S12 grew to a maximal density of 3.0 × 10
7
cells per ml after compete reduction of 2.0 mM amaranth in a defined medium. This was accompanied by a stoichiometric consumption of 4.0 mM formate over time when amaranth and formate were supplied as the sole electron acceptor and donor, respectively, suggesting that microbial azoreduction is an electron transport process and that this electron transport can yield energy to support growth. Purified membranous, periplasmic, and cytoplasmic fractions from S12 were analyzed, but only the membranous fraction was capable of reducing azo dyes with formate, lactate, pyruvate, or H
2
as the electron donor. The presence of 5 μM Cu
2+
ions, 200 μM dicumarol, 100 μM stigmatellin, and 100 μM metyrapone inhibited anaerobic azoreduction activity by both whole cells and the purified membrane fraction, showing that dehydrogenases, cytochromes, and menaquinone are essential electron transfer components for azoreduction. These results provide evidence that the microbial anaerobic azoreduction is linked to the electron transport chain and suggest that the dissimilatory azoreduction is a form of microbial anaerobic respiration. These findings not only expand the number of potential electron acceptors known for microbial energy conservation but also elucidate the mechanisms of microbial anaerobic azoreduction.
Bacterial Population Dynamics in Dairy Waste during Aerobic and Anaerobic Treatment and Subsequent Storage
Authors: McGarvey Jeffery A. , Miller William G. , Zhang Ruihong , Ma Yanguo , Mitloehner Frank 
Published: December 2006

ABSTRACTThe objective of this study was to model a typical dairy waste stream, monitor the chemical and bacterial population dynamics that occur during aerobic or anaerobic treatment and subsequent storage in a simulated lagoon, and compare them to those of waste held without treatment in a simulated lagoon. Both aerobic and anaerobic treatment methods followed by storage effectively reduced the levels of total solids (59 to 68%), biological oxygen demand (85 to 90%), and sulfate (56 to 65%), as well as aerobic (83 to 95%), anaerobic (80 to 90%), and coliform (>99%) bacteria. However, only aerobic treatment reduced the levels of ammonia, and anaerobic treatment was more effective at reducing total sulfur and sulfate. The bacterial population structure of waste before and after treatment was monitored using 16S rRNA gene sequence libraries. Both treatments had unique effects on the bacterial population structure of waste. Aerobic treatment resulted in the greatest change in the type of bacteria present, with the levels of eight out of nine phyla being significantly altered. The most notable differences were the >16-fold increase in the phylumProteobacteriaand the approximately 8-fold decrease in the phylumFirmicutes. Anaerobic treatment resulted in fewer alterations, but significant decreases in the phylaActinobacteriaandBacteroidetes, and increases in the phylaPlanctomycetes,Spirochetes, and TM7 were observed.
Vertical Distribution of Denitrification in an Estuarine Sediment: Integrating Sediment Flowthrough Reactor Experiments and Microprofiling via Reactive Transport Modeling
Authors: Laverman Anniet M. , Meile Christof , Van Cappellen Philippe , Wieringa Elze B. A. 
Published: December 2006

ABSTRACTDenitrifying activity in a sediment from the freshwater part of a polluted estuary in northwest Europe was quantified using two independent approaches. High-resolution N2O microprofiles were recorded in sediment cores to which acetylene was added to the overlying water and injected laterally into the sediment. The vertical distribution of the rate of denitrification supported by nitrate uptake from the overlying water was then derived from the time series N2O concentration profiles. The rates obtained for the core incubations were compared to the rates predicted by a forward reactive transport model, which included rate expression for denitrification calibrated with potential rate measurements obtained in flowthrough reactors containing undisturbed, 1-cm-thick sediment slices. The two approaches yielded comparable rate profiles, with a near-surface, 2- to 3-mm narrow zone of denitrification and maximum in situ rates on the order of 200 to 300 nmol cm−3h−1. The maximum in situ rates were about twofold lower than the maximum potential rate for the 0- to 1-cm depth interval of the sediment, indicating that in situ denitrification was nitrate limited. The experimentally and model-derived rates of denitrification implied that there was nitrate uptake by the sediment at a rate that was on the order of 50 (± 10) nmol cm−2h−1, which agreed well with direct nitrate flux measurements for core incubations. Reactive transport model calculations showed that benthic uptake of nitrate at the site is particularly sensitive to the nitrate concentration in the overlying water and the maximum potential rate of denitrification in the sediment.
A Single-Nucleotide-Polymorphism-Based Multilocus Genotyping Assay for Subtyping Lineage I Isolates of
Listeria monocytogenes
Authors: Ducey Thomas F. , Page Brent , Usgaard Thomas , Borucki Monica K. , Pupedis Kitty , Ward Todd J. 
Published: December 2006

ABSTRACT

Listeria monocytogenes
is a facultative intracellular pathogen responsible for food-borne disease with high mortality rates in humans and is the leading microbiological cause of food recalls. Lineage I isolates of
L. monocytogenes
are a particular public health concern because they are responsible for most sporadic cases of listeriosis and the vast majority of epidemic outbreaks. Rapid, reproducible, and sensitive methods for differentiating pathogens below the species level are required for effective pathogen control programs, and the CDC PulseNet Task Force has called for the development and validation of DNA sequence-based methods for subtyping food-borne pathogens. Therefore, we developed a multilocus genotyping (MLGT) assay for
L. monocytogenes
lineage I isolates based on nucleotide variation identified by sequencing 23,251 bp of DNA from 22 genes distributed across seven genomic regions in 65
L. monocytogenes
isolates. This single-well assay of 60 allele-specific probes captured 100% of the haplotype information contained in approximately 1.5 Mb of comparative DNA sequence and was used to reproducibly type a total of 241 lineage I isolates. The MLGT assay provided high discriminatory power (Simpson's index value, 0.91), uniquely identified isolates from the eight listeriosis outbreaks examined, and differentiated serotypes 1/2b and 4b as well as epidemic clone I (ECI), ECIa, and ECII. In addition, the assay included probes for a previously characterized truncation mutation in
inlA
, providing for the identification of a specific virulence-attenuated subtype. These results demonstrate that MLGT represents a significant new tool for use in pathogen surveillance, outbreak detection, risk assessment, population analyses, and epidemiological investigations.
Effects of Target Length on the Hybridization Efficiency and Specificity of rRNA-Based Oligonucleotide Microarrays
Authors: Liu Wen-Tso , Guo Huiling , Wu Jer-Horng 
Published: December 2006

ABSTRACT

The effect of target size on microarray hybridization efficiencies and specificity was investigated using a set of 166 oligonucleotide probes targeting the 16S rRNA gene of
Escherichia coli
. The targets included unfragmented native rRNA, fragmented rRNA (∼20 to 100 bp), PCR amplicons (93 to 1,480 bp), and three synthetic single-stranded DNA oligonucleotides (45 to 56 bp). Fluorescence intensities of probes hybridized with targets were categorized into classes I (81 to 100% relative to the control probe), II (61 to 80%), III (41 to 60%), IV (21 to 40%), V (6 to 20%), and VI (0 to 5%). Good hybridization efficiency was defined for those probes conferring intensities in classes I to IV; those in classes V and VI were regarded as weak and false-negative signals, respectively. Using unfragmented native rRNA, 13.9% of the probes had fluorescence intensities in classes I to IV, whereas the majority (57.8%) exhibited false-negative signals. Similar trends were observed for the 1,480-bp PCR amplicon (6.6% of the probes were in classes I to IV). In contrast, after hybridization of fragmented rRNA, the percentage of probes in classes I to IV rose to 83.1%. Likewise, when DNA target sizes were reduced from 1,480 bp to 45 bp, this percentage increased approximately 14-fold. Overall, microarray hybridization efficiencies and specificity were improved with fragmented rRNA (20 to 100 bp), short PCR amplicons (<150 bp), and synthetic targets (45 to 56 bp). Such an understanding is important to the application of DNA microarray technology in microbial community studies.
Spatial and Temporal Expression of
Lactobacillus plantarum
Genes in the Gastrointestinal Tracts of Mice
Authors: Marco Maria L. , Bongers Roger S. , de Vos Willem M. , Kleerebezem Michiel 
Published: December 2006

ABSTRACT

Lactobacillus plantarum
is a common inhabitant of mammalian gastrointestinal tracts, and
L. plantarum
strain WCFS1 is a human isolate with a known genome sequence.
L. plantarum
WCFS1 survives intestinal passage in an active form, and its transit time and transcriptional activities were monitored in 15 BALB/c mice at 2, 4, 6, 8, and 24 h after being fed a single intragastric dose of this organism. Enumeration of viable cells isolated from fecal material revealed that the majority of the
L. plantarum
inoculum transited the mouse intestine within 4 h after ingestion. Three mice were sacrificed at each time point, and total RNA was isolated from the mouse intestinal compartments (stomach through colon). Quantification of
L. plantarum
16S rRNA by quantitative real-time reverse-transcription-PCR revealed that
L. plantarum
was present at elevated levels in the stomach and small intestine for at least 4 h following ingestion and for over 8 h in the cecum and colon. We also examined the expression of 9
L. plantarum
housekeeping genes and 15
L. plantarum
in vivo-inducible (
ivi
) genes previously identified by recombination-based in vivo expression technology to be induced in the mouse gastrointestinal tract. The relative expression levels of the
ivi
genes increased up to 350-fold in the mouse intestine compared to levels observed for
L. plantarum
WCFS1 cells grown in a rich laboratory medium. Moreover, several genes displayed intestinal compartment-specific (small intestine versus colon) activities. These results confirm that
L. plantarum
displays specific and differential responses at various sites along the mammalian intestine.
Sources of Variation in the Ampicillin-Resistant
Escherichia coli
Concentration in the Feces of Organic Broiler Chickens
Authors: Pleydell E. J. , Brown P. E. , Woodward M. J. , Davies R. H. , French N. P. 
Published: December 2006

ABSTRACT

Currently, there are limited published data for the population dynamics of antimicrobial-resistant commensal bacteria. This study was designed to evaluate both the proportions of the
Escherichia coli
populations that are resistant to ampicillin at the level of the individual chicken on commercial broiler farms and the feasibility of obtaining repeated measures of fecal
E. coli
concentrations. Short-term temporal variation in the concentration of fecal
E. coli
was investigated, and a preliminary assessment was made of potential factors involved in the shedding of high numbers of ampicillin-resistant
E. coli
by growing birds in the absence of the use of antimicrobial drugs. Multilevel linear regression modeling revealed that the largest component of random variation in log-transformed fecal
E. coli
concentrations was seen between sampling occasions for individual birds. The incorporation of fixed effects into the model demonstrated that the older, heavier birds in the study were significantly more likely (
P
= 0.0003) to shed higher numbers of ampicillin-resistant
E. coli
. This association between increasing weight and high shedding was not seen for the total fecal
E. coli
population (
P
= 0.71). This implies that, in the absence of the administration of antimicrobial drugs, the proportion of fecal
E. coli
that was resistant to ampicillin increased as the birds grew. This study has shown that it is possible to collect quantitative microbiological data on broiler farms and that such data could make valuable contributions to risk assessments concerning the transfer of resistant bacteria between animal and human populations.
Longitudinal Study of Finnish
Campylobacter jejuni
and
C. coli
Isolates from Humans, Using Multilocus Sequence Typing, Including Comparison with Epidemiological Data and Isolates from Poultry and Cattle
Authors: Kärenlampi Rauni , Rautelin Hilpi , Schönberg-Norio Daniela , Paulin Lars , Hänninen Marja-Liisa 
Published: December 2006

ABSTRACT

We describe a study on the application of multilocus sequence typing for the analysis of
Campylobacter jejuni
and
C. coli
isolates from human domestically acquired infections in the Helsinki-Uusimaa area of Finland in 1996, 2002, and 2003. In addition, isolates from poultry meat and fecal samples of cattle from the seasonal peak (July to September) in 2003 were included in the study. In total, 361 Finnish
C. jejuni
and
C. coli
strains were typed. Sequence type 45 (ST-45) (45%), ST-21 (21%), and ST-677 (11%) clonal complexes were the most prevalent. The ST-45 and ST-677 complexes were overrepresented in comparison with previous studies. The longitudinal study revealed an association between
C. coli
(ST-828 complex) infection and elderly patients (≥60 years). Analysis of exposure factors, determined by a previous case-control study conducted during the seasonal peak in 2002, revealed that the ST-48 complex was significantly (
P
< 0.05) associated with the tasting or eating of raw minced meat. New and unassigned STs were associated with swimming in natural bodies of water, whereas the ST-677 complex was related to drinking nonchlorinated water from a small water plant or water from natural sources. The ST-45 complex was associated with contact with pet cats and dogs. In 2003, ST-45 occurrence was significantly associated with poultry whereas ST-50 was associated with isolates from humans. In contrast, ST-53, ST-58, ST-61, and ST-883 were significantly associated with isolates from cattle. Further studies are needed to reveal the significance of the observed associations.
Potential of the
Bacillus thuringiensis
Toxin Reservoir for the Control of
Lobesia botrana
(Lepidoptera: Tortricidae), a Major Pest of Grape Plants
Authors: Ruiz de Escudero Iñigo , Estela Anna , Escriche Baltasar , Caballero Primitivo 
Published: December 2006

ABSTRACT

The potential of
Bacillus thuringiensis
Cry proteins to control the grape pest
Lobesia botrana
was explored by testing first-instar larvae with Cry proteins belonging to the Cry1, Cry2, and Cry9 groups selected for their documented activities against Lepidoptera. Cry9Ca, a toxin from
B. thuringiensis
, was the protein most toxic to
L. botrana
larvae, followed in decreasing order by Cry2Ab, Cry1Ab, Cry2Aa, and Cry1Ia7, with 50% lethal concentration values of 0.09, 0.1, 1.4, 3.2, and 8.5 μg/ml of diet, respectively. In contrast, Cry1Fa and Cry1JA were not active at the assayed concentration (100 μg/ml). In vitro binding and competition experiments showed that none of the toxins tested (Cry1Ia, Cry2Aa, Cry2Ab, and Cry9C) shared binding sites with Cry1Ab. We conclude that either Cry1Ia or Cry9C could be used in combination with Cry1Ab to control this pest, either as the active components of
B. thuringiensis
sprays or expressed together in transgenic plants.
Comparison of Media for the Isolation of
Enterobacter sakazakii
Authors: Iversen Carol , Forsythe Stephen J. 
Published: December 2006

ABSTRACT

Enterobacter sakazakii
is associated with neonatal infections and is occasionally present at low levels (<1 CFU/g) in powdered infant formula milk (IFM). It has been previously reported that some
E. sakazakii
strains do not grow in standard media for
Enterobacteriaceae
and coliform bacteria; therefore, a reliable method is needed for recovery of the organism. Three
E. sakazakii
enrichment broths—
Enterobacteriaceae
enrichment broth (EE),
E. sakazakii
selective broth (ESSB), and modified lauryl sulfate broth (mLST)—were compared with a novel broth designed for maximum recovery of
E. sakazakii
,
E. sakazakii
enrichment broth (ESE). One hundred seventy-seven strains (100%) grew in ESE, whereas between 2 and 6% of strains did not grow in EE, mLST, or ESSB.
E. sakazakii
possesses α-glucosidase activity, and a number of selective, chromogenic agars for
E. sakazakii
isolation based on this enzyme have been developed.
E. sakazakii
isolation agar produced fewer false-positive colonies than did Druggan-Forsythe-Iversen agar. However, the latter supported the growth of more
E. sakazakii
strains. It was also determined that 2% of
E. sakazakii
strains did not produce yellow pigmentation on tryptone soya agar at 25°C, a characteristic frequently cited in the identification of
E. sakazakii
. The recovery of desiccated
E. sakazakii
(0.2 to 2000 CFU/25 g) from powdered IFM in the presence of a competing flora was determined with various enrichment broths and differential selective media. Current media designed for the isolation and presumptive identification of
E. sakazakii
do not support the growth of all currently known
E. sakazakii
phenotypes; therefore, improvements in the proposed methods are desirable.