bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic Deletion Marking an Emerging Subclone of
Francisella tularensis
subsp.
holarctica
in France and the Iberian Peninsula
Authors: Dempsey M. P. , Dobson M. , Zhang C. , Zhang M. , Lion C. , Gutiérrez-Martín C. B. , Iwen P. C. , Fey P. D. , Olson M. E. , Niemeyer D. , Francesconi S. , Crawford R. , Stanley M. , Rhodes J. , Wagner D. M. , Vogler A. J. , Birdsell D. , Keim P. , Johansson A. , Hinrichs S. H. , Benson A. K. 
Published: September 2007

ABSTRACT

Francisella tularensis
subsp.
holarctica
is widely disseminated in North America and the boreal and temperate regions of the Eurasian continent. Comparative genomic analyses identified a 1.59-kb genomic deletion specific to
F. tularensis
subsp.
holarctica
isolates from Spain and France. Phylogenetic analysis of strains carrying this deletion by multiple-locus variable-number tandem repeat analysis showed that the strains comprise a highly related set of genotypes, implying that these strains were recently introduced or recently emerged by clonal expansion in France and the Iberian Peninsula.
Differences in Virulence among
Escherichia coli
O157:H7 Strains Isolated from Humans during Disease Outbreaks and from Healthy Cattle
Authors: Baker Diane R. , Moxley Rodney A. , Steele Mike B. , LeJeune Jeffrey T. , Christopher-Hennings Jane , Chen Ding-Geng , Hardwidge Philip R. , Francis David H. 
Published: September 2007

ABSTRACT

Escherichia coli
O157:H7 causes life-threatening outbreaks of diarrhea, hemorrhagic colitis, and hemolytic-uremic syndrome in humans and significant economic loss in agriculture and could be a potential agent of bioterrorism. Although the prevalence of
E. coli
O157:H7 in cattle and other species with which humans have frequent contact is high, human infections are relatively uncommon, despite a low infectious dose. A plausible explanation for the low disease incidence is the possibility that not all strains are virulent in humans. If there are substantial differences in virulence among strains in nature, then human disease may select for high virulence. We used a gnotobiotic piglet model to investigate the virulence of isolates from healthy cattle and from humans in disease outbreaks and to determine the correlation between production of Shiga toxin 1 (Stx1) and Stx2 and virulence. Overall,
E. coli
O157:H7 strains isolated from healthy cattle were less virulent in gnotobiotic piglets than strains isolated from humans during disease outbreaks. The amount of Stx2 produced by
E. coli
O157:H7 strains correlated with strain virulence as measured by a reduction in piglet survival and signs of central nervous system disease due to brain infarction. The amount of Stx1 produced in culture was not correlated with the length of time of piglet survival or with signs of central nervous system disease. We suggest that disease outbreaks select for producers of high levels of Stx2 among
E. coli
O157:H7 strains shed by animals and further suggest that Stx1 expression is unlikely to be significant in human outbreaks.
Aspergillus Volatiles Regulate Aflatoxin Synthesis and Asexual Sporulation in
Aspergillus parasiticus
Authors: Roze Ludmila V. , Beaudry Randolph M. , Arthur Anna E. , Calvo Ana M. , Linz John E. 
Published: September 2007

ABSTRACT

Aspergillus parasiticus
is one primary source of aflatoxin contamination in economically important crops. To prevent the potential health and economic impacts of aflatoxin contamination, our goal is to develop practical strategies to reduce aflatoxin synthesis on susceptible crops. One focus is to identify biological and environmental factors that regulate aflatoxin synthesis and to manipulate these factors to control aflatoxin biosynthesis in the field or during crop storage. In the current study, we analyzed the effects of aspergillus volatiles on growth, development, aflatoxin biosynthesis, and promoter activity in the filamentous fungus
A. parasiticus
. When colonies of
Aspergillus nidulans
and
A. parasiticus
were incubated in the same growth chamber, we observed a significant reduction in aflatoxin synthesis and asexual sporulation by
A. parasiticus
. Analysis of the headspace gases demonstrated that
A. nidulans
produced much larger quantities of 2-buten-1-ol (CA) and 2-ethyl-1-hexanol (EH) than
A. parasiticus
. In its pure form, EH inhibited growth and increased aflatoxin accumulation in
A. parasiticus
at all doses tested; EH also stimulated aflatoxin transcript accumulation. In contrast, CA exerted dose-dependent up-regulatory or down-regulatory effects on aflatoxin accumulation, conidiation, and aflatoxin transcript accumulation. Experiments with reporter strains carrying
nor-1
promoter deletions and mutations suggested that the differential effects of CA were mediated through separate regulatory regions in the
nor-1
promoter. The potential efficacy of CA as a tool for analysis of transcriptional regulation of aflatoxin biosynthesis is discussed. We also identify a novel, rapid, and reliable method to assess norsolorinic acid accumulation in solid culture using a Chroma Meter CR-300 apparatus.
Culturable Psychrotrophic Bacterial Communities in Raw Milk and Their Proteolytic and Lipolytic Traits
Authors: Hantsis-Zacharov Elionora , Halpern Malka 
Published: September 2007

ABSTRACT

During cold storage after milk collection, psychrotrophic bacterial populations dominate the microflora, and their extracellular enzymes, mainly proteases and lipases, contribute to the spoilage of dairy products. The diversity, dynamics, and enzymatic traits of culturable psychrotrophs in raw milk from four farms were investigated over a 10-month period. About 20% of the isolates were found to be novel species, indicating that there is still much to be learned about culturable psychrotrophs in raw milk. The psychrotrophic isolates were identified and classified in seven classes. Three classes were predominant, with high species richness (18 to 21 species per class) in different seasons of the year:
Gammaproteobacteria
in spring and winter,
Bacilli
in summer, and
Actinobacteria
in autumn. The four minor classes were
Alphaproteobacteria
,
Betaproteobacteria
,
Flavobacteria
, and
Sphingobacteria
. The dominant classes were found in all four dairies, although every dairy had its own unique “bacterial profile.” Most but not all bacterial isolates had either lipolytic or both lipolytic and proteolytic activities. Only a few isolates showed proteolytic activity alone. The dominant genera,
Pseudomonas
and
Acinetobacter
(
Gammaproteobacteria
), showed mainly lipolytic activity,
Microbacterium
(
Actinobacteria
) was highly lipolytic and proteolytic, and the lactic acid bacteria (
Lactococcus
and
Leuconostoc
) displayed very minor enzymatic ability. Hence, the composition of psychrotrophic bacterial flora in raw milk has an important role in the determination of milk quality. Monitoring the dominant psychrotrophic species responsible for the production of heat-stable proteolytic and lipolytic enzymes offers a sensitive and efficient tool for maintaining better milk quality in the milk industry.
Multiplex Assay Based on Single-Nucleotide Polymorphisms for Rapid Identification of
Brucella
Isolates at the Species Level
Authors: Scott Julie C. , Koylass Mark S. , Stubberfield Michael R. , Whatmore Adrian M. 
Published: September 2007

ABSTRACT

The genus
Brucella
includes a number of species that are major animal pathogens worldwide and significant causes of zoonotic infections of humans. Traditional methods of identifying
Brucella
to the species level can be time-consuming, can be subjective, and can pose a hazard to laboratory personnel in the absence of suitable biocontainment facilities. Using a robust phylogenetic framework, a number of single-nucleotide polymorphisms (SNPs) that define particular species within the genus were identified. These SNPs were used to develop a multiplex SNP detection assay, based on primer extension technology, that can rapidly and unambiguously identify an isolate as a member of one of the six classical
Brucella
species or as a member of the recently identified marine mammal group.
Diversity Analysis of Dairy and Nondairy
Lactococcus lactis
Isolates, Using a Novel Multilocus Sequence Analysis Scheme and (GTG)
5
-PCR Fingerprinting
Authors: Rademaker Jan L. W. , Herbet Hélène , Starrenburg Marjo J. C. , Naser Sabri M. , Gevers Dirk , Kelly William J. , Hugenholtz Jeroen , Swings Jean , van Hylckama Vlieg Johan E. T. 
Published: September 2007

ABSTRACT

The diversity of a collection of 102 lactococcus isolates including 91
Lactococcus lactis
isolates of dairy and nondairy origin was explored using partial small subunit rRNA gene sequence analysis and limited phenotypic analyses. A subset of 89 strains of
L. lactis
subsp.
cremoris
and
L. lactis
subsp.
lactis
isolates was further analyzed by (GTG)
5
-PCR fingerprinting and a novel multilocus sequence analysis (MLSA) scheme. Two major genomic lineages within
L. lactis
were found. The
L. lactis
subsp.
cremoris
type-strain-like genotype lineage included both
L. lactis
subsp.
cremoris
and
L. lactis
subsp.
lactis
isolates. The other major lineage, with a
L. lactis
subsp.
lactis
type-strain-like genotype, comprised
L. lactis
subsp.
lactis
isolates only. A novel third genomic lineage represented two
L. lactis
subsp.
lactis
isolates of nondairy origin. The genomic lineages deviate from the subspecific classification of
L. lactis
that is based on a few phenotypic traits only. MLSA of six partial genes (
atpA
, encoding ATP synthase alpha subunit;
pheS
, encoding phenylalanine tRNA synthetase;
rpoA
, encoding RNA polymerase alpha chain;
bcaT
, encoding branched chain amino acid aminotransferase;
pepN
, encoding aminopeptidase N; and
pepX
, encoding X-prolyl dipeptidyl peptidase) revealed 363 polymorphic sites (total length, 1,970 bases) among 89
L. lactis
subsp.
cremoris
and
L. lactis
subsp.
lactis
isolates with unique sequence types for most isolates. This allowed high-resolution cluster analysis in which dairy isolates form subclusters of limited diversity within the genomic lineages. The
pheS
DNA sequence analysis yielded two genetic groups dissimilar to the other genotyping analysis-based lineages, indicating a disparate acquisition route for this gene.
Synthesis of γ-Aminobutyric Acid by Lactic Acid Bacteria Isolated from a Variety of Italian Cheeses
Authors: Siragusa S. , De Angelis M. , Di Cagno R. , Rizzello C. G. , Coda R. , Gobbetti M. 
Published: September 2007

ABSTRACT

The concentrations of γ-aminobutyric acid (GABA) in 22 Italian cheese varieties that differ in several technological traits markedly varied from 0.26 to 391 mg kg
−1
. Presumptive lactic acid bacteria were isolated from each cheese variety (total of 440 isolates) and screened for the capacity to synthesize GABA. Only 61 isolates showed this activity and were identified by partial sequencing of the 16S rRNA gene. Twelve species were found.
Lactobacillus paracasei
PF6,
Lactobacillus delbrueckii
subsp.
bulgaricus
PR1,
Lactococcus lactis
PU1,
Lactobacillus plantarum
C48, and
Lactobacillus brevis
PM17 were the best GABA-producing strains during fermentation of reconstituted skimmed milk. Except for
L. plantarum
C48, all these strains were isolated from cheeses with the highest concentrations of GABA. A core fragment of glutamate decarboxylase (GAD) DNA was isolated from
L. paracasei
PF6,
L. delbrueckii
subsp.
bulgaricus
PR1,
L. lactis
PU1, and
L. plantarum
C48 by using primers based on two highly conserved regions of GAD. A PCR product of ca. 540 bp was found for all the strains. The amino acid sequences deduced from nucleotide sequence analysis showed 98, 99, 90, and 85% identity to GadB of
L. plantarum
WCFS1 for
L. paracasei
PF6,
L. delbrueckii
subsp.
bulgaricus
PR1,
L. lactis
PU1, and
L. plantarum
C48, respectively. Except for
L. lactis
PU1, the three lactobacillus strains survived and synthesized GABA under simulated gastrointestinal conditions. The findings of this study provide a potential basis for exploiting selected cheese-related lactobacilli to develop health-promoting dairy products enriched in GABA.
Design and Application of Highly Responsive Fluorescence Resonance Energy Transfer Biosensors for Detection of Sugar in LivingSaccharomyces cerevisiaeCells
Authors: Ha Jae-Seok , Song Jae Jun , Lee Young-Mi , Kim Su-Jin , Sohn Jung-Hoon , Shin Chul-Soo , Lee Seung-Goo 
Published: September 2007

ABSTRACTA protein sensor with a highly responsive fluorescence resonance energy transfer (FRET) signal for sensing sugars in livingSaccharomyces cerevisiaecells was developed by combinatorial engineering of the domain linker and the binding protein moiety. Although FRET sensors based on microbial binding proteins have previously been created for visualizing various sugars in vivo, such sensors are limited due to a weak signal intensity and a narrow dynamic range. In the present study, the length and composition of the linker moiety of a FRET-based sensor consisting of CFP-linker1-maltose-binding protein-linker2-YFP were redesigned, which resulted in a 10-fold-higher signal intensity. Molecular modeling of the composite linker moieties, including the connecting peptide and terminal regions of the flanking proteins, suggested that an ordered helical structure was preferable for tighter coupling of the conformational change of the binding proteins to the FRET response. When the binding site residue Trp62 of the maltose-binding protein was diversified by saturation mutagenesis, the Leu mutant exhibited an increased binding constant (82 μM) accompanied by further improvement in the signal intensity. Finally, the maltose sensor with optimized linkers was redesigned to create a sugar sensor with a new specificity and a wide dynamic range. When the optimized maltose sensors were employed as in vivo sensors, highly responsive FRET images were generated from real-time analysis of maltose uptake ofSaccharomyces cerevisiae(baker's yeast).
Mucosa-Associated Bacterial Diversity in Relation to Human Terminal Ileum and Colonic Biopsy Samples
Authors: Ahmed Shakil , Macfarlane George T. , Fite Alemu , McBain Andrew J. , Gilbert Peter , Macfarlane Sandra 
Published: September 2007

ABSTRACT

Little is known about bacterial communities that colonize mucosal surfaces in the human gastrointestinal tract, but they are believed to play an important role in host physiology. The objectives of this study were to investigate the compositions of these populations in the distal small bowel and colon. Healthy mucosal tissue from either the terminal ileum (
n
= 6) or ascending (
n
= 8), transverse (
n
= 8), or descending colon (
n
= 4) of 26 patients (age, 68.5 ± 1.2 years [mean ± standard deviation]) undergoing emergency resection of the large bowel was used to study these communities. Mucosa-associated eubacteria were characterized by using PCR-denaturing gradient gel electrophoresis (DGGE), while real-time PCR was employed for quantitative analysis. Mucosal communities were also visualized in situ using confocal laser scanning microscopy. DGGE banding profiles from all the gut regions exhibited at least 45% homology, with five descending colon profiles clustering at ca. 75% concordance. Real-time PCR showed that mucosal bacterial population densities were highest in the terminal ileum and that there were no significant differences in overall bacterial numbers in different parts of the colon. Bifidobacterial numbers were significantly higher in the large bowel than in the terminal ileum (
P
= 0.006), whereas lactobacilli were more prominent in the distal large intestine (
P
= 0.019).
Eubacterium rectale
(
P
= 0.0004) and
Faecalibacterium prausnitzii
(
P
= 0.001) were dominant in the ascending and descending colon. Site-specific colonization in the gastrointestinal tract may be contributory in the etiology of some diseases of the large intestine.
Enhancement of the Stability of a Prolipase from
Rhizopus oryzae
toward Aldehydes by Saturation Mutagenesis
Authors: Di Lorenzo Mirella , Hidalgo Aurelio , Molina Rafael , Hermoso Juan A. , Pirozzi Domenico , Bornscheuer Uwe T. 
Published: September 2007

ABSTRACT

A prolipase from
Rhizopus oryzae
(proROL) was engineered in order to increase its stability toward lipid oxidation products such as aldehydes with the aim of improving its performance in oleochemical industries. Out of 22 amino acid residues (15 Lys and 7 His) prone to react with aldehydes, 6 Lys and all His residues (except for the catalytic histidine) were chosen and subjected to saturation mutagenesis. In order to quickly and reliably identify stability mutants within the resulting libraries, active variants were prescreened by an activity staining method on agar plates. Active mutants were expressed in
Escherichia coli
Origami in a 96-well microtiterplate format, and a stability test using octanal as a model deactivating agent was performed. The most stable histidine mutant (H201S) conferred a stability increase of 60%, which was further enhanced to 100% by combination with a lysine mutant (H201S/K168I). This increase in stability was also confirmed for other aldehydes. Interestingly, the mutations did not affect specific activity, as this was still similar to the wild-type enzyme.
Real-Time Quantitative PCR Measurement of Ileal
Lactobacillus salivarius
Populations from Broiler Chickens To Determine the Influence of Farming Practices
Authors: Harrow Sally A. , Ravindran Velmurugu , Butler Ruth C. , Marshall John W. , Tannock Gerald W. 
Published: September 2007

ABSTRACT

A real-time quantitative PCR assay targeting a 16S-23S intergenic spacer region sequence was devised to measure the sizes of populations of
Lactobacillus salivarius
present in ileal digesta collected from broiler chickens. This species has been associated with deconjugation of bile salts in the small bowel and reduced broiler productivity. The assay was tested as a means of monitoring the sizes of
L. salivarius
populations from broilers fed diets with different compositions, maintained at different stocking densities, or given the antimicrobial drugs bacitracin and monensin in the feed. Stocking densities did not influence the numbers of
L. salivarius
cells in the ileum. A diet containing meat and bone meal reduced the size of the
L. salivarius
population relative to that of chickens given the control diet, as did administration of bacitracin and monensin in the feed. These changes in the target bacterial population were associated with improved broiler weight gain.
Microarray Analysis of
Escherichia coli
Strains from Interstitial Beach Waters of Lake Huron (Canada)
Authors: Kon T. , Weir S. C. , Trevors J. T. , Lee H. , Champagne J. , Meunier L. , Brousseau R. , Masson L. 
Published: September 2007

ABSTRACT

DNA microarray analyses revealed that clusters of repetitive extragenic palindromic PCR-related
Escherichia coli
isolates were isogenic only within interstitial Lake Huron beach water samples and not in surrounding waters. This suggested that adaptation and growth occurred within the interstitial water sites tested. All isolates were nonpathogenic, and three lake isolates possessed tetracycline resistance genes.
Identification of
opdA
, a Gene Involved in Biodegradation of the Endocrine Disrupter Octylphenol
Authors: Porter A. W. , Hay A. G. 
Published: September 2007

ABSTRACT

Octylphenol (OP) is an estrogenic detergent breakdown product. Structurally similar nonylphenols are transformed via type II
ispo
substitution, resulting in the production of hydroquinone and removal of the branched side chain. Nothing is known, however, about the gene(s) encoding this activity. We report here on our efforts to clone the gene(s) encoding OP degradation activity from
Sphingomonas
sp. strain PWE1, which we isolated for its ability to grow on OP. A fosmid library of PWE1 DNA yielded a single clone, aew4H12, which accumulated a brown polymerization product in the presence of OP. Sequence analysis of loss-of-function transposon mutants of aew4H12 revealed a single open reading frame,
opdA
, that conferred OP degradation activity.
Escherichia coli
subclones expressing
opdA
caused OP disappearance, with the concomitant production of hydroquinone and 2,4,4-trimethyl-1-pentene as well as small amounts of 2,4,4-trimethyl-2-pentanol. These metabolites are consistent with a type II
ipso
substitution reaction, the same mechanism described for nonylphenol biodegradation in other sphingomonads. Based on
opdA
's sequence homology to a unique group of putative flavin monooxygenases and the recovery of hydroxylated OP intermediates from
E. coli
expressing
opdA
, we conclude that this gene encodes the observed type II
ipso
substitution activity responsible for the initial step in OP biodegradation.
Comparative Transcriptome Analysis of
Methylibium petroleiphilum
PM1 Exposed to the Fuel Oxygenates Methyl
tert
-Butyl Ether and Ethanol
Authors: Hristova Krassimira R. , Schmidt Radomir , Chakicherla Anu Y. , Legler Tina C. , Wu Janice , Chain Patrick S. , Scow Kate M. , Kane Staci R. 
Published: September 2007

ABSTRACT

High-density whole-genome cDNA microarrays were used to investigate substrate-dependent gene expression of
Methylibium petroleiphilum
PM1, one of the best-characterized aerobic methyl
tert
-butyl ether (MTBE)-degrading bacteria. Differential gene expression profiling was conducted with PM1 grown on MTBE and ethanol as sole carbon sources. Based on microarray high scores and protein similarity analysis, an MTBE regulon located on the megaplasmid was identified for further investigation. Putative functions for enzymes encoded in this regulon are described with relevance to the predicted MTBE degradation pathway. A new unique dioxygenase enzyme system that carries out the hydroxylation of
tert
-butyl alcohol to 2-methyl-2-hydroxy-1-propanol in
M. petroleiphilum
PM1 was discovered. Hypotheses regarding the acquisition and evolution of MTBE genes as well as the involvement of IS elements in these complex processes were formulated. The pathways for toluene, phenol, and alkane oxidation via toluene monooxygenase, phenol hydroxylase, and propane monooxygenase, respectively, were upregulated in MTBE-grown cells compared to ethanol-grown cells. Four out of nine putative cyclohexanone monooxygenases were also upregulated in MTBE-grown cells. The expression data allowed prediction of several hitherto-unknown enzymes of the upper MTBE degradation pathway in
M. petroleiphilum
PM1 and aided our understanding of the regulation of metabolic processes that may occur in response to pollutant mixtures and perturbations in the environment.
Genomic Diversity in
Staphylococcus xylosus
Authors: Dordet-Frisoni Emilie , Dorchies Géraud , De Araujo Cécilia , Talon Régine , Leroy Sabine 
Published: September 2007

ABSTRACT

Staphylococcus xylosus
is a commensal of the skin of humans and animals and a ubiquitous bacterium naturally present in food. It is one of the major starter cultures used for meat fermentation, but a few strains could potentially be hazardous and are related to animal opportunistic infections. To better understand the genetic diversity of
S. xylosus
intraspecies, suppressive and subtractive hybridization (SSH) was carried out with the
S. xylosus
C2a strain, a commensal of human skin, used as the driver for three tester strains, S04002 used as a starter culture, S04009 isolated from cow mastitis, and 00-1747, responsible for mouse dermatitis. SSH revealed 122 tester-specific fragments corresponding to 149 open reading frames (ORFs). A large proportion of these ORFs resembled genes involved in specific metabolisms. Analysis of the distribution of the tester-specific fragments in 20
S. xylosus
strains of various origins showed that the
S. xylosus
species could be divided into two clusters with one composed only of potentially hazardous strains. The genetic content diversity of this species is colocalized in a region near the origin of replication of the chromosome. This region of speciation previously observed in the
Staphylococcus
genus corresponded in
S. xylosus
species to a strain-specific region potentially implicated in ecological fitness.