bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abundance, Diversity, and Activity of Ammonia-Oxidizing Prokaryotes in the Coastal Arctic Ocean in Summer and Winter
Authors: Christman Glenn D. , Cottrell Matthew T. , Popp Brian N. , Gier Elizabeth , Kirchman David L. 
Published: January 2011

ABSTRACT

Ammonia oxidation, the first step in nitrification, is performed by certain
Beta
- and
Gammaproteobacteria
and
Crenarchaea
to generate metabolic energy. Ammonia monooxygenase (
amoA
) genes from both
Bacteria
and
Crenarchaea
have been found in a variety of marine ecosystems, but the relative importance of
Bacteria
versus
Crenarchaea
in ammonia oxidation is unresolved, and seasonal comparisons are rare. In this study, we compared the abundance of betaproteobacterial and crenarchaeal
amoA
genes in the coastal Arctic Ocean during summer and winter over 2 years. Summer and winter betaproteobacterial
amoA
clone libraries were significantly different, although the gene sequences were similar to those found in temperate and polar environments. Betaproteobacterial and crenarchaeal
amoA
genes were 30- to 115-fold more abundant during the winter than during the summer in both years of the study. Archaeal
amoA
genes were more abundant than betaproteobacterial
amoA
genes in the first year, but betaproteobacterial
amoA
was more abundant than archaeal
amoA
the following year. The ratio of archaeal
amoA
gene copies to marine group I crenarchaeal 16S rRNA genes averaged 2.9 over both seasons and years, suggesting that ammonia oxidation was common in
Crenarchaea
at this location. Potential nitrification rates, as well as the total
amoA
gene abundance, were highest in the winter when competition with phytoplankton was minimal and ammonium concentrations were the highest. These results suggest that ammonium concentrations were important in determining the rates of ammonia oxidation and the abundance of ammonia-oxidizing
Betaproteobacteria
and
Crenarchaea
.
Molecular Epidemiology of
Salmonella enterica
Serovar Typhimurium Isolates from Cattle in Hokkaido, Japan: Evidence of Clonal Replacement and Characterization of the Disseminated Clone
Authors: Tamamura Yukino , Uchida Ikuo , Tanaka Kiyoshi , Okazaki Hizuru , Tezuka Satoru , Hanyu Hideki , Kataoka Natsumi , Makino Sou-ichi , Kishima Masato , Kubota Takayuki , Kanno Toru , Hatama Shinichi , Ishihara Ryoko , Hata Eiji , Yamada Hironari , Nakaoka Yuuji , Akiba Masato 
Published: January 2011

ABSTRACT

The molecular epidemiology of 545
Salmonella enterica
serovar Typhimurium isolates collected between 1977 and 2009 from cattle in Hokkaido, Japan, was investigated using pulsed-field gel electrophoresis (PFGE). Nine main clusters were identified from 116 PFGE patterns. Cluster I comprised 248 isolates, 243 of which possessed a sequence specific to definitive phage type 104 (DT104) or U302. The cluster I isolates were dominant in 1993 to 2003, but their numbers declined beginning in 2004. Beginning in 2002, an increase was observed in the number of cluster VII isolates, consisting of 21 PFGE patterns comprising 165 isolates. A total of 116 isolates representative of the 116 PFGE profiles were analyzed by multilocus variable-number tandem-repeat analysis (MLVA). Other than two drug-sensitive isolates, 19 isolates within cluster VII were classified in the same cluster by MLVA. Among the cluster VII isolates, an antibiotic resistance type showing resistance to ampicillin, chloramphenicol, streptomycin, sulfonamides, tetracycline, kanamycin, cefazolin, and sulfamethoxazole-trimethoprim and a resistance type showing resistance to ampicillin, streptomycin, sulfonamides, tetracycline, and kanamycin were found in 23 and 125 isolates, respectively. In the 19 isolates representative of cluster VII, the
bla
TEM-1
gene was found on a
Salmonella
serotype Typhimurium virulence plasmid, which was transferred to
Escherichia coli
by electroporation along with resistance to two to four other antimicrobials. Genomic analysis by subtractive hybridization and plasmid analysis suggested that the
bla
TEM-1
-carrying virulence plasmid has a mosaic structure composed of elements of different origin. These results indicate an emerging multidrug-resistant
S
. Typhimurium clone carrying a virulence-resistance plasmid among cattle in Hokkaido, Japan.
Gene Cluster Conferring Streptomycin, Sulfonamide, and Tetracycline Resistance in
Escherichia coli
O157:H7 Phage Types 23, 45, and 67
Authors: Ziebell K. , Johnson R. P. , Kropinski A. M. , Reid-Smith R. , Ahmed R. , Gannon V. P. , Gilmour M. , Boerlin P. 
Published: January 2011

ABSTRACT

Multidrug resistance to streptomycin, sulfonamide, and tetracycline (AMR-SSuT) was identified in 156 of 171 isolates of
Escherichia coli
O157:H7 of phage types 23, 45, and 67. In 154 AMR-SSuT isolates, resistance was encoded by
strA
,
strB
,
sul2
, and
tet
(B), which in 59 of 63 tested isolates were found clustered together on the chromosome within the
cdiA
locus.
Inhibition of
Streptococcus mutans
Biofilm Formation by
Streptococcus salivarius
FruA
Authors: Ogawa Ayako , Furukawa Soichi , Fujita Shuhei , Mitobe Jiro , Kawarai Taketo , Narisawa Naoki , Sekizuka Tsuyoshi , Kuroda Makoto , Ochiai Kuniyasu , Ogihara Hirokazu , Kosono Saori , Yoneda Saori , Watanabe Haruo , Morinaga Yasushi , Uematsu Hiroshi , Senpuku Hidenobu 
Published: January 2011

ABSTRACT

The oral microbial flora consists of many beneficial species of bacteria that are associated with a healthy condition and control the progression of oral disease. Cooperative interactions between oral streptococci and the pathogens play important roles in the development of dental biofilms in the oral cavity. To determine the roles of oral streptococci in multispecies biofilm development and the effects of the streptococci in biofilm formation, the active substances inhibiting
Streptococcus mutans
biofilm formation were purified from
Streptococcus salivarius
ATCC 9759 and HT9R culture supernatants using ion exchange and gel filtration chromatography. Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry analysis was performed, and the results were compared to databases. The
S. salivarius
HT9R genome sequence was determined and used to indentify candidate proteins for inhibition. The candidates inhibiting biofilms were identified as
S. salivarius
fructosyltransferase (FTF) and exo-beta-
d
-fructosidase (FruA). The activity of the inhibitors was elevated in the presence of sucrose, and the inhibitory effects were dependent on the sucrose concentration in the biofilm formation assay medium. Purified and commercial FruA from
Aspergillus niger
(31.6% identity and 59.6% similarity to the amino acid sequence of FruA from
S. salivarius
HT9R) completely inhibited
S. mutans
GS-5 biofilm formation on saliva-coated polystyrene and hydroxyapatite surfaces. Inhibition was induced by decreasing polysaccharide production, which is dependent on sucrose digestion rather than fructan digestion. The data indicate that
S. salivarius
produces large quantities of FruA and that FruA alone may play an important role in multispecies microbial interactions for sucrose-dependent biofilm formation in the oral cavity.
Detection of Shiga Toxin-Producing
Escherichia coli
Serotypes O26:H11, O103:H2, O111:H8, O145:H28, and O157:H7 in Raw-Milk Cheeses by Using Multiplex Real-Time PCR
Authors: Madic Jordan , Vingadassalon Noémie , de Garam Carine Peytavin , Marault Muriel , Scheutz Flemming , Brugère Hubert , Jamet Emmanuel , Auvray Frédéric 
Published: January 2011

ABSTRACT

Shiga toxin (Stx)-producing
Escherichia coli
(STEC) strains are a diverse group of food-borne pathogens with various levels of virulence for humans. In this study, we describe the use of a combination of multiple real-time PCR assays for the screening of 400 raw-milk cheeses for the five main pathogenic STEC serotypes (O26:H11, O103:H2, O111:H8, O145:H28, and O157:H7). The prevalences of samples positive for
stx
, intimin-encoding gene (
eae
), and at least one of the five O group genetic markers were 29.8%, 37.3%, and 55.3%, respectively. The H2, H7, H8, H11, and H28
fliC
alleles were highly prevalent and could not be used as reliable targets for screening. Combinations of
stx
,
eae
variants, and O genetic markers, which are typical of the five targeted STEC serotypes, were detected by real-time PCR in 6.5% of the cheeses (26 samples) and included
stx-wzx
O26
-
eae-
β
1
(4.8%; 19 samples),
stx
-
wzx
O103
-
eae-
ε (1.3%; five samples),
stx
-
ihp1
O145
-
eae-
γ
1
(0.8%; three samples), and
stx
-
rfbE
O157
-
eae
-γ
1
(0.3%; one sample). Twenty-eight immunomagnetic separation (IMS) assays performed on samples positive for these combinations allowed the recovery of seven
eae
β
1
-positive STEC O26:H11 isolates, whereas no STEC O103:H2, O145:H28, or O157:H7 strains could be isolated. Three
stx
-negative and
eae
β
1
-positive
E. coli
O26:[H11] strains were also isolated from cheeses by IMS. Colony hybridization allowed us to recover STEC from
stx
-positive samples for 15 out of 45 assays performed, highlighting the difficulties encountered in STEC isolation from dairy products. The STEC O26:H11 isolates shared the same virulence genetic profile as enterohemorrhagic
E. coli
(EHEC) O26:H11, i.e., they carried the virulence-associated genes EHEC-
hlyA
,
katP
, and
espP
, as well as genomic O islands 71 and 122. Except for one strain, they all contained the
stx1
variant only, which was reported to be less frequently associated with human cases than
stx2
. Pulsed-field gel electrophoresis (PFGE) analysis showed that they displayed high genetic diversity; none of them had patterns identical to those of human O26:H11 strains investigated here.
Fate ofMycobacterium aviumsubsp.paratuberculosisafter Application of Contaminated Dairy Cattle Manure to Agricultural Soils
Authors: Salgado M. , Collins M. T. , Salazar F. , Kruze J. , Bölske G. , Söderlund R. , Juste R. , Sevilla I. A. , Biet F. , Troncoso F. , Alfaro M. 
Published: January 2011

ABSTRACTDetails regarding the fate ofMycobacterium aviumsubsp.paratuberculosis(basonym,Mycobacterium paratuberculosis) after manure application on grassland are unknown. To evaluate this, intact soil columns were collected in plastic pipes (lysimeters) and placed under controlled conditions to test the effect of a loamy or sandy soil composition and the amount of rainfall on the fate ofM. paratuberculosisapplied to the soil surface with manure slurry. The experiment was organized as a randomized design with two factors and three replicates.M. paratuberculosis-contaminated manure was spread on the top of the 90-cm soil columns. After weekly simulated rainfall applications, water drainage samples (leachates) were collected from the base of each lysimeter and cultured forM. paratuberculosisusing Bactec MGIT ParaTB medium and supplements. Grass was harvested, quantified, and tested from each lysimeter soil surface. The identity of all probableM. paratuberculosisisolates was confirmed by PCR for IS900and F57 genetic elements. There was a lag time of 2 months after each treatment beforeM. paratuberculosiswas found in leachates. The greatest proportions ofM. paratuberculosis-positive leachates were from sandy-soil lysimeters in the manure-treated group receiving the equivalent of 1,000 mm annual rainfall. Under the higher rainfall regimen (2,000 mm/year),M. paratuberculosiswas detected more often from lysimeters with loamy soil than sandy soil. Among all lysimeters,M. paratuberculosiswas detected more often in grass clippings than in lysimeter leachates. At the end of the trial, lysimeters were disassembled and soil cultured at different depths, and we found thatM. paratuberculosiswas recovered only from the uppermost levels of the soil columns in the treated group. Factors associated withM. paratuberculosispresence in leachates were soil type and soil pH (P< 0.05). ForM. paratuberculosispresence in grass clippings, only manure application showed a significant association (P< 0.05). From these findings we conclude that this pathogen tends to move slowly through soils (faster through sandy soil) and tends to remain on grass and in the upper layers of pasture soil, representing a clear infection hazard for grazing livestock and a potential for the contamination of runoff after heavy rains.
Persistent Infection or Successive Reinfection of Deer Mice withBartonella vinsoniisubsp.arupensis
Authors: Bai Ying , Calisher Charles H. , Kosoy Michael Y. , Root J. Jeffrey , Doty Jeffrey B. 
Published: January 2011

ABSTRACTBartonella infections are common in rodents. From 1994 to 2006, longitudinal studies of a rodent community, consisting mainly of deer mice (Peromyscus maniculatus), were conducted in southwestern Colorado to study hantaviruses. Blood samples from deer mice captured one or more times during the period 2003 to 2006 (n= 737) were selected to study bartonellae in deer mice. Bartonellae were found to be widely distributed in that population, with an overall prevalence of 82.4% (607/737 mice). No correlation was found between bartonella prevalence and deer mouse weight or sex. Persistent or successive infections with bartonellae were observed in deer mice captured repeatedly, with a prevalence of 83.9% (297/354), and the infection appeared to last for more than 1 year in some of them. Persistent infection with bartonellae may explain the high prevalence of these bacteria in deer mice at this site and, perhaps, elsewhere. Genetic analysis demonstrated that deer mouse-borne bartonella isolates at this site belong to the same species,B. vinsoniisubsp.arupensis, demonstrating a specific relationship betweenB. vinsoniisubsp.arupensisand deer mice.
Comprehensive Approaches to Molecular Biomarker Discovery for Detection and Identification of
Cronobacter
spp. (
Enterobacter sakazakii
) and
Salmonella
spp
Authors: Yan Xianghe , Gurtler Joshua , Fratamico Pina , Hu Jing , Gunther Nereus W. , Juneja Vijay , Huang Lihan 
Published: January 2011

ABSTRACT

Cronobacter
spp. (formerly
Enterobacter sakazakii
) and
Salmonella
spp. are increasingly implicated internationally as important microbiological contaminants in low-moisture food products, including powdered infant formula. Estimates indicate that 40 to 80% of infants infected with
Cronobacter sakazakii
and/or
Salmonella
in the United States may not survive the illness. A systematic approach, combining literature-based data mining, comparative genome analysis, and the direct sequencing of PCR products of specific biomarker genes, was used to construct an initial collection of genes to be targeted. These targeted genes, particularly genes encoding virulence factors and genes responsible for unique phenotypes, have the potential to function as biomarker genes for the identification and differentiation of
Cronobacter
spp. and
Salmonella
from other food-borne pathogens in low-moisture food products. In this paper, a total of 58 unique
Salmonella
gene clusters and 126 unique potential
Cronobacter
biomarkers and putative virulence factors were identified. A chitinase gene, a well-studied virulence factor in fungi, plants, and bacteria, was used to confirm this approach. We found that the chitinase gene has very low sequence variability and/or polymorphism among
Cronobacter
,
Citrobacter
, and
Salmonella
, while differing significantly in other food-borne pathogens, either by sequence blasting or experimental testing, including PCR amplification and direct sequencing. This computational analysis for
Cronobacter
and
Salmonella
biomarker identification and the preliminary laboratory studies are only a starting point; thus, PCR and array-based biomarker verification studies of these and other food-borne pathogens are currently being conducted.
The EIIABManPhosphotransferase System Permease Regulates Carbohydrate Catabolite Repression inStreptococcus gordonii
Authors: Tong Huichun , Zeng Lin , Burne Robert A. 
Published: January 2011

ABSTRACTCommensal oral streptococci play critical roles in oral biofilm formation and promote dental health by competing with, and antagonizing the growth of, pathogenic organisms, such asStreptococcus mutans. Efficient utilization of the spectrum of carbohydrates in the oral cavity by commensal streptococci is essential for their persistence, and yet very little is known about the regulation of carbohydrate catabolism by these organisms. Carbohydrate catabolite repression (CCR) in the abundant oral commensalStreptococcus gordoniistrain DL-1 was investigated using the exo-β-d-fructosidase gene (fruA) and a fructose/mannose sugar:phosphotransferase (PTS) enzyme II operon (levDEFG) as model systems. Functional studies confirmed the predicted roles of FruA and LevD inS. gordonii. ManL, the AB domain of a fructose/mannose-type enzyme II PTS permease, contributed to utilization of glucose, mannose, galactose, and fructose and exerted primary control over CCR of thefruAandlevDoperons. Unlike inS. mutans, ManL-dependent CCR was not sugar specific, and galactose was very effective at eliciting CCR inS. gordonii. Inactivation of the apparentccpAhomologue ofS. gordoniiactually enhanced CCR offruAandlevD, an effect likely due to its demonstrated role in repression ofmanLexpression. Thus, there are some similarities and fundamental differences in CCR control mechanisms between the oral pathogenS. mutansand the oral commensalS. gordoniithat may eventually be exploited to enhance the competitiveness of health-associated commensals in oral biofilms.
Detection of
Cryptosporidium molnari
Oocysts from Fish by Fluorescent-Antibody Staining Assays for
Cryptosporidium
spp. Affecting Humans
Authors: Barugahare Rona , Dennis Michelle M. , Becker Joy A. , Šlapeta Jan 
Published: January 2011

ABSTRACT

Three direct fluorescent-antibody staining assay kits for the detection of zoonotic
Cryptosporidium
species were used to detect
Cryptosporidium molnari
from Murray cod, and the cryptosporidia were characterized by using small-subunit (SSU) ribosomal DNA (rDNA). To facilitate rapid diagnosis of infection, this study demonstrated that all three kits detected fresh
C. molnari
and two kits detected formalin-fixed oocysts.
Ammonium Availability Affects the Ratio of Ammonia-Oxidizing Bacteria to Ammonia-Oxidizing Archaea in Simulated Creek Ecosystems
Authors: Herrmann Martina , Scheibe Andrea , Avrahami Sharon , Küsel Kirsten 
Published: January 2011

ABSTRACT

The ammonia-oxidizing microbial community colonizing clay tiles in flow channels changed in favor of ammonia-oxidizing bacteria during a 12-week incubation period even at originally high ratios of ammonia-oxidizing archaea to ammonia-oxidizing bacteria (AOB). AOB predominance was established more rapidly in flow channels incubated at 350 μM NH
4
+
than in those incubated at 50 or 20 μM NH
4
+
. Biofilm-associated potential nitrification activity was first detected after 28 days and was positively correlated with bacterial but not archaeal
amoA
gene copy numbers.
Role of Glucose in the Expression of Cryptococcus neoformans Antiphagocytic Protein 1, App1
Authors: Williams Virginia , Del Poeta Maurizio 
Published: January 2011

ABSTRACT

The cryptococcus-specific protein antiphagocytic protein 1 (App1) regulates
Cryptococcus neoformans
virulence by controlling macrophage-driven fungal phagocytosis. This is accomplished through complement receptors (CR), specifically CR3. When inhaled,
C. neoformans
can cause a life-threatening meningoencephalitis in immunocompromised patients. Because glucose starvation can significantly change the gene expression and virulence of
C. neoformans
and because App1 is critical for phagocytosis in the lung—a low-glucose environment—we investigated the role of glucose in App1 expression. We found that App1 was upregulated dramatically under low-glucose conditions, and it was upregulated when
C. neoformans
cells were incubated in bronchoalveolar lavage (BAL) fluid, serum, and cerebrospinal fluid, which are low-glucose environments. Characterization of App1's regulation based on mammalian lung physiology revealed that App1 is upregulated via both increases in transcription and increases in mRNA stability. Our data provide new insights regarding
C. neoformans
adaptations to low-glucose environments.
Nhe1 Is Essential for Potassium but Not Calcium Facilitation of Cell Motility and the Monovalent Cation Requirement for Chemotactic Orientation in Dictyostelium discoideum
Authors: Lusche Daniel F. , Wessels Deborah , Ryerson Daniel E. , Soll David R. 
Published: January 2011

ABSTRACTInDictyostelium discoideum, extracellular K+or Ca2+at a concentration of 40 or 20 mM, respectively, facilitates motility in the absence or presence of a spatial gradient of chemoattractant. Facilitation results in maximum velocity, cellular elongation, persistent translocation, suppression of lateral pseudopod formation, and myosin II localization in the posterior cortex. A lower threshold concentration of 15 mM K+or Na or 5 mM Ca2+is required for chemotactic orientation. Although the common buffer solutions used byD. discoideumresearchers to study chemotaxis contain sufficient concentrations of cations for chemotactic orientation, the majority contain insufficient levels to facilitate motility. Here it has been demonstrated that Nhe1, a plasma membrane protein, is required for K+but not Ca2+facilitation of cell motility and for the lower K+but not Ca2+requirement for chemotactic orientation.
Bistability in
myo
-Inositol Utilization by
Salmonella enterica
Serovar Typhimurium
Authors: Kröger Carsten , Srikumar Shabarinath , Ellwart Joachim , Fuchs Thilo M. 
Published: January 2011

ABSTRACT

The capability of
Salmonella enterica
serovar Typhimurium strain 14028 (
S
. Typhimurium 14028) to utilize
myo
-inositol (MI) is determined by the genomic island GEI4417/4436 carrying the
iol
genes that encode enzymes, transporters, and a repressor responsible for the MI catabolic pathway. In contrast to all bacteria investigated thus far,
S
. Typhimurium 14028 growing on MI as the sole carbon source is characterized by a remarkable long lag phase of 40 to 60 h. We report here that on solid medium with MI as the sole carbon source, this human pathogen exhibits a bistable phenotype characterized by a dissection into large colonies and a slow-growing bacterial background. This heterogeneity is reversible and therefore not caused by mutation, and it is not observed in the absence of the
iol
gene repressor IolR nor in the presence of at least 0.55% CO
2
. Bistability is correlated with the activity of the
iolE
promoter (P

iolE

), but not of P

iolC

or P

iolD

, as shown by promoter-
gfp
fusions. On the single-cell level, fluorescence microscopy and flow cytometry analysis revealed a gradual switch of P

iolE

from the “off” to the “on” status during the late lag phase and the transition to the log phase. Deletion of
iolR
or the addition of 0.1% NaHCO
3
induced an early growth start of
S
. Typhimurium 14028 in minimal medium with MI. The addition of ethoxyzolamide, an inhibitor of carboanhydrases, elongated the lag phase in the presence of bicarbonate. The positive-feedback loop via repressor release and positive induction by bicarbonate-CO
2
might allow
S
. Typhimurium 14028 to adapt to rapidly changing environments. The phenomenon described here is a novel example of bistability in substrate degradation, and, to our knowledge, is the first demonstration of gene regulation by bicarbonate-CO
2
in
Salmonella
.