bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection of
Escherichia coli
in Biofilms from Pipe Samples and Coupons in Drinking Water Distribution Networks
Authors: Juhna T. , Birzniece D. , Larsson S. , Zulenkovs D. , Sharipo A. , Azevedo N. F. , Ménard-Szczebara F. , Castagnet S. , Féliers C. , Keevil C. W. 
Published: August 2007

ABSTRACT

Fluorescence in situ hybridization (FISH) was used for direct detection of
Escherichia coli
on pipe surfaces and coupons in drinking water distribution networks. Old cast iron main pipes were removed from water distribution networks in France, England, Portugal, and Latvia, and
E. coli
was analyzed in the biofilm. In addition, 44 flat coupons made of cast iron, polyvinyl chloride, or stainless steel were placed into and continuously exposed to water on 15 locations of 6 distribution networks in France and Latvia and examined after 1 to 6 months exposure to the drinking water. In order to increase the signal intensity, a peptide nucleic acid (PNA) 15-mer probe was used in the FISH screening for the presence or absence of
E. coli
on the surface of pipes and coupons, thus reducing occasional problems of autofluorescence and low fluorescence of the labeled bacteria. For comparison, cells were removed from the surfaces and examined with culture-based or enzymatic (detection of β-
d
-glucuronidase) methods. An additional verification was made by using PCR. Culture method indicated presence of
E. coli
in one of five pipes, whereas all pipes were positive with the FISH methods.
E. coli
was detected in 56% of the coupons using PNA FISH, but no
E. coli
was detected using culture or enzymatic methods. PCR analyses confirmed the presence of
E. coli
in samples that were negative according to culture-based and enzymatic methods. The viability of
E. coli
cells in the samples was demonstrated by the cell elongation after resuscitation in low-nutrient medium supplemented with pipemidic acid, suggesting that the cells were present in an active but nonculturable state, unable to grow on agar media.
E. coli
contributed to ca. 0.001 to 0.1% of the total bacterial number in the samples. The presence and number of
E. coli
did not correlate with any of physical and/or chemical characteristic of the drinking water (e.g., temperature, chlorine, or biodegradable organic matter concentration). We show here that
E. coli
is present in the biofilms of drinking water networks in Europe. Some of the cells are metabolically active but are often not detected due to limitations of traditionally used culture-based methods, indicating that biofilm should be considered as a reservoir that must be investigated further in order to evaluate the risk for human health.
Immunoglobulins to Surface-Associated Biofilm Immunogens Provide a Novel Means of Visualization of Methicillin-Resistant
Staphylococcus aureus
Biofilms
Authors: Brady Rebecca A. , Leid Jeff G. , Kofonow Jennifer , Costerton J. William , Shirtliff Mark E. 
Published: August 2007

ABSTRACT

Antigens from the methicillin-resistant
Staphylococcus aureus
(MRSA) cell wall have been shown to be immunogenic in vivo and upregulated during biofilm growth. In this study, we created purified, recombinant forms of selected antigens and biofilm-upregulated, cell wall-associated proteins. These proteins were shown to cause a robust polyclonal immunoglobulin G (IgG) response when used to immunize rabbits. Antibodies against these recombinant proteins bound to the native forms of each protein as harvested from in vitro grown biofilms of MRSA, as determined both via Western blot analysis and immunofluorescence confocal microscopy. These IgGs could be utilized as imaging tools that localize to areas of specific protein production within a biofilm. This work illustrates that immunogenic, cell wall-associated, biofilm-upregulated proteins are promising for in vitro visualization of biofilm growth, architecture, and space-function relationships.
The Ability ofAneurinibacillus migulanus(Bacillus brevis) To Produce the Antibiotic Gramicidin S Is Correlated with Phenotype Variation
Authors: Berditsch Marina , Afonin Sergii , Ulrich Anne S. 
Published: August 2007

ABSTRACTPhenotype instability of bacterial strains can cause significant problems in biotechnological applications, since industrially useful properties may be lost. Here we report such degenerative dissociation forAneurinibacillus migulanus(formerly known asBacillus brevis) an established producer of the antimicrobial peptide gramicidin S (GS). Phenotypic variations within and between various strains maintained in different culture collections are demonstrated. The type strain, ATCC 9999, consists of six colony morphology variants, R, RC, RP, RT, SC, and SP, which were isolated and characterized as pure cultures. Correlations between colony morphology, growth, GS production, spore formation, and resistance to their own antimicrobial peptide were established in this study. We found the original R form to be the best producer, followed by RC, RP, and RT, while SC and SP yielded no GS at all. Currently available ATCC 9999Tcontains only 2% of the original R producer and is dominated by the newly described phenotypes RC and RP. No original R form is detected in the nominally equivalent strain DSM 2895T(=ATCC 9999T), which grows only as SC and SP phenotypes and has thus completely lost its value as a peptide producer. Two other strains from the same collection, DSM 5668 and DSM 5759, contain the unproductive SC variant and the GS-producing RC form, respectively. We describe the growth and maintenance conditions that stabilize certain colony phenotypes and reduce the degree of degenerative dissociation, thus providing a recommendation for how to revert the nonproducing smooth phenotypes to the valuable GS-producing rough ones.
Low-pH Adaptation and the Acid Tolerance Response of
Bifidobacterium longum
Biotype longum
Authors: Sánchez Borja , Champomier-Vergès Marie-Christine , Collado María del Carmen , Anglade Patricia , Baraige Fabienne , Sanz Yolanda , de los Reyes-Gavilán Clara G. , Margolles Abelardo , Zagorec Monique 
Published: August 2007

ABSTRACT

Bifidobacteria are one of the main microbial inhabitants of the human colon. Usually administered in fermented dairy products as beneficial microorganisms, they have to overcome the acidic pH found in the stomach during the gastrointestinal transit to be able to colonize the lower parts of the intestine. The mechanisms underlying acid response and adaptation in
Bifidobacterium longum
biotype longum NCIMB 8809 and its acid-pH-resistant mutant
B. longum
biotype longum 8809dpH were studied. Comparison of protein maps, and protein identification by matrix-assisted laser desorption ionization-time of flight mass spectrometry analysis, allowed us to identify nine different proteins whose production largely changed in the mutant strain. Furthermore, the production of 47 proteins was modulated by pH in one or both strains. These included general stress response chaperones and proteins involved in transcription and translation as well as in carbohydrate and nitrogen metabolism, among others. Significant differences in the levels of metabolic end products and in the redox status of the cells were also detected between the wild-type strain and its acid-pH-resistant mutant in response to, or as a result of, adaptation to acid. Remarkably, the results of this work indicated that adaptation and response to low pH in
B. longum
biotype longum involve changes in the glycolytic flux and in the ability to regulate the internal pH. These changes were accompanied by a higher content of ammonium in the cytoplasm, likely coming from amino acid deamination, and a decrease of the bile salt hydrolase activity.
Microarray-Based Characterization of theListeria monocytogenesCold Regulon in Log- and Stationary-Phase Cells
Authors: Chan Yvonne C. , Raengpradub Sarita , Boor Kathryn J. , Wiedmann Martin 
Published: August 2007

ABSTRACTWhole-genome microarray experiments were performed to define theListeria monocytogenescold growth regulon and to identify genes differentially expressed during growth at 4 and 37°C. Microarray analysis using a stringent cutoff (adjustedP< 0.001; ≥2.0-fold change) revealed 105 and 170 genes that showed higher transcript levels in logarithmic- and stationary-phase cells, respectively, at 4°C than in cells grown at 37°C. A total of 74 and 102 genes showed lower transcript levels in logarithmic- and stationary-phase cells, respectively, grown at 4°C. Genes with higher transcript levels at 4°C in both stationary- and log-phase cells included genes encoding a two-component response regulator (lmo0287), a cold shock protein (cspL), and two RNA helicases (lmo0866 and lmo1722), whereas a number of genes encoding virulence factors and heat shock proteins showed lower transcript levels at 4°C. Selected genes that showed higher transcript levels at 4°C during both stationary and log phases were confirmed by quantitative reverse transcriptase PCR. Our data show that (i) a large number ofL. monocytogenesgenes are differentially expressed at 4 and 37°C, with more genes showing higher transcript levels than lower transcript levels at 4°C, (ii)L. monocytogenesgenes with higher transcript levels at 4°C include a number of genes and operons with previously reported or plausible roles in cold adaptation, and (iii)L. monocytogenesgenes with lower transcript levels at 4°C include a number of virulence and virulence-associated genes as well as some heat shock genes.
Inactivation of
Bacillus anthracis
Spores by Liquid Biocides in the Presence of Food Residue
Authors: Hilgren J. , Swanson K. M. J. , Diez-Gonzalez F. , Cords B. 
Published: August 2007

ABSTRACT

Biocide inactivation of
Bacillus anthracis
spores in the presence of food residues after a 10-min treatment time was investigated. Spores of nonvirulent
Bacillus anthracis
strains 7702, ANR-1, and 9131 were mixed with water, flour paste, whole milk, or egg yolk emulsion and dried onto stainless-steel carriers. The carriers were exposed to various concentrations of peroxyacetic acid, sodium hypochlorite (NaOCl), or hydrogen peroxide (H
2
O
2
) for 10 min at 10, 20, or 30°C, after which time the survivors were quantified. The relationship between peroxyacetic acid concentration, H
2
O
2
concentration, and spore inactivation followed a sigmoid curve that was accurately described using a four-parameter logistic model. At 20°C, the minimum concentrations of peroxyacetic acid, H
2
O
2
, and NaOCl (as total available chlorine) predicted to inactivate 6 log
10
CFU of
B. anthracis
spores with no food residue present were 1.05, 23.0, and 0.78%, respectively. At 10°C, sodium hypochlorite at 5% total available chlorine did not inactivate more than 4 log
10
CFU. The presence of the food residues had only a minimal effect on peroxyacetic acid and H
2
O
2
sporicidal efficacy, but the efficacy of sodium hypochlorite was markedly inhibited by whole-milk and egg yolk residues. Sodium hypochlorite at 5% total available chlorine provided no greater than a 2-log
10
CFU reduction when spores were in the presence of egg yolk residue. This research provides new information regarding the usefulness of peroxygen biocides for
B. anthracis
spore inactivation when food residue is present. This work also provides guidance for adjusting decontamination procedures for food-soiled and cold surfaces.
Fine-Scale Genetic Diversity among
Burkholderia pseudomallei
Soil Isolates in Northeast Thailand
Authors: U'Ren Jana M. , Hornstra Heidie , Pearson Talima , Schupp James M. , Leadem Benjamin , Georgia Shalamar , Sermswan Rasana W. , Keim Paul 
Published: August 2007

ABSTRACT

Burkholderia pseudomallei
soil isolates from northeast Thailand were genotyped using multiple-locus variable-number tandem repeat (VNTR) analysis (MLVA) and multilocus sequence typing (MLST). MLVA identified 19 genotypes within three clades, while MLST revealed two genotypes. These close genetic relationships imply a recent colonization followed by localized expansion, similar to what occurs in an outbreak situation.
Cryptosporidium
Genotypes in Wildlife from a New York Watershed
Authors: Feng Yaoyu , Alderisio Kerri A. , Yang Wenli , Blancero Lisa A. , Kuhne William G. , Nadareski Christopher A. , Reid Michael , Xiao Lihua 
Published: August 2007

ABSTRACT

To identify the animal sources for
Cryptosporidium
contamination, we genotyped
Cryptosporidium
spp. in wildlife from the watershed of the New York City drinking water supply, using a small-subunit rRNA gene-based PCR-restriction fragment length polymorphism analysis and DNA sequencing. A total of 541 specimens from 38 species of wildlife were analyzed. One hundred and eleven (20.5%) of the wildlife specimens were PCR positive. Altogether, 21
Cryptosporidium
genotypes were found in wildlife samples, 11 of which were previously found in storm runoff in the watershed, and six of these 11 were from storm water genotypes of unknown animal origin. Four new genotypes were found, and the animal hosts for four storm water genotypes were expanded. With the exception of the cervine genotype, most genotypes were found in a limited number of animal species and have no major public health significance.
Comparison of Ergot Alkaloid Biosynthesis Gene Clusters in
Claviceps
Species Indicates Loss of Late Pathway Steps in Evolution of
C. fusiformis
Authors: Lorenz Nicole , Wilson Ella V. , Machado Caroline , Schardl Christopher L. , Tudzynski Paul 
Published: August 2007

ABSTRACT

The grass parasites
Claviceps purpurea
and
Claviceps fusiformis
produce ergot alkaloids (EA) in planta and in submerged culture. Whereas EA synthesis (EAS) in
C. purpurea
proceeds via clavine intermediates to lysergic acid and the complex ergopeptines,
C. fusiformis
produces only agroclavine and elymoclavine. In
C. purpurea
the EAS gene (
EAS
) cluster includes
dmaW
(encoding the first pathway step),
cloA
(elymoclavine oxidation to lysergic acid), and the
lpsA/lpsB
genes (ergopeptine formation). We analyzed the corresponding
C. fusiformis EAS
cluster to investigate the evolutionary basis for chemotypic differences between the
Claviceps
species. Other than three peptide synthetase genes (
lpsC
and the tandem paralogues
lpsA1
and
lpsA2
), homologues of all
C. purpurea EAS
genes were identified in
C. fusiformis
, including homologues of
lpsB
and
cloA
, which in
C. purpurea
encode enzymes for steps after clavine synthesis. Rearrangement of the cluster was evident around
lpsB
, which is truncated in
C. fusiformis
. This and several frameshift mutations render Cf
lpsB
a pseudogene (Cf
lpsB

Ψ

). No obvious inactivating mutation was identified in Cf
cloA
. All
C. fusiformis EAS
genes, including Cf
lpsB

Ψ

and Cf
cloA
, were expressed in culture. Cross-complementation analyses demonstrated that Cf
cloA
and Cf
lpsB

Ψ

were expressed in
C. purpurea
but did not encode functional enzymes. In contrast, Cp
cloA
catalyzed lysergic acid biosynthesis in
C. fusiformis
, indicating that
C. fusiformis
terminates its EAS pathway at elymoclavine because the
cloA
gene product is inactive. We propose that the
C. fusiformis EAS
cluster evolved from a more complete cluster by loss of some
lps
genes and by rearrangements and mutations inactivating
lpsB
and
cloA
.
Zoo Animals as Reservoirs of Gram-Negative Bacteria Harboring Integrons and Antimicrobial Resistance Genes
Authors: Ahmed Ashraf M. , Motoi Yusuke , Sato Maiko , Maruyama Akito , Watanabe Hitoshi , Fukumoto Yukio , Shimamoto Tadashi 
Published: August 2007

ABSTRACT

A total of 232 isolates of gram-negative bacteria were recovered from mammals, reptiles, and birds housed at Asa Zoological Park, Hiroshima prefecture, Japan. Forty-nine isolates (21.1%) showed multidrug resistance phenotypes and harbored at least one antimicrobial resistance gene. PCR and DNA sequencing identified class 1 and class 2 integrons and many β-lactamase-encoding genes, in addition to a novel AmpC β-lactamase gene,
bla
CMY-26
. Furthermore, the plasmid-mediated quinolone resistance genes
qnr
and
aac
(
6
′)-
Ib-cr
were also identified.
Fermentative Production ofl-Alanyl-l-Glutamine by a Metabolically EngineeredEscherichia coliStrain Expressingl-Amino Acid α-Ligase
Authors: Tabata Kazuhiko , Hashimoto Shin-ichi 
Published: August 2007

ABSTRACTIn spite of its clinical and nutritional importance,l-alanyl-l-glutamine (Ala-Gln) has not been widely used due to the absence of an efficient manufacturing method. Here, we present a novel method for the fermentative production of Ala-Gln using anEscherichia colistrain expressingl-amino acid α-ligase (Lal), which catalyzes the formation of dipeptides by combining two amino acids in an ATP-dependent manner. Two metabolic manipulations were necessary for the production of Ala-Gln: reduction of dipeptide-degrading activity by combinatorial disruption of thedppandpepgenes and enhancement of the supply of substrate amino acids by deregulation of glutamine biosynthesis and overexpression of heterologousl-alanine dehydrogenase (Ald). Since expression of Lal was found to hamper cell growth, it was controlled using a stationary-phase-specific promoter. The final strain constructed was designated JKYPQ3 (pepA pepB pepD pepN dpp glnE glnB putA) containing pPE167 (lalandaldexpressed under the control of theuspApromoter) or pPE177 (lalandaldexpressed under the control of therpoHpromoter). Either strain produced more than 100 mM Ala-Gln extracellularly, in fed-batch cultivation on glucose-ammonium salt medium, without added alanine and glutamine. Because of the characteristics of Lal, no longer peptides (such as tripeptides) or dipeptides containingd-amino acids were formed.
Incubation of Environmental Samples in a Diffusion Chamber Increases the Diversity of Recovered Isolates
Authors: Bollmann Annette , Lewis Kim , Epstein Slava S. 
Published: August 2007

ABSTRACT

The majority of microorganisms from natural environments cannot be grown in the laboratory. The diffusion-chamber-based approach is an alternative method that allows microorganisms to grow in their natural environment. An inoculum is sandwiched between semipermeable (0.03-μm-pore-size) membranes of the chamber, which is then returned to the source environment. The chamber allows for a free exchange of chemicals with the external milieu by diffusion while restricting the movement of cells. We used freshwater pond sediment to inoculate diffusion chambers and petri dishes. The diffusion chambers were incubated on top of the sediment for 4 weeks. Both chamber and petri dish cultivation resulted in the isolation of numerous representatives of
Alpha
-,
Beta
-, and
Gammaproteobacteria
;
Actinobacteria
;
Firmicutes
; and
Bacteroidetes
. However, the diffusion-chamber-based approach also led to the isolation of species from rarely cultivated groups, such as
Deltaproteobacteria, Verrucomicrobia, Spirochaetes
, and
Acidobacteria
. Material from the chambers was also transferred to new chambers in order to learn whether this will increase the recovery of isolates. Several isolates could be obtained only from material transferred through multiple diffusion chambers. This suggests that continuous cultivation in diffusion chambers adapts some microorganisms for growth under otherwise prohibitive in vitro conditions.
Isolation, Characterization, and Ecology of Sulfur-Respiring
Crenarchaea
Inhabiting Acid-Sulfate-Chloride-Containing Geothermal Springs in Yellowstone National Park
Authors: Boyd Eric S. , Jackson Robert A. , Encarnacion Gem , Zahn James A. , Beard Trevor , Leavitt William D. , Pi Yundan , Zhang Chuanlun L. , Pearson Ann , Geesey Gill G. 
Published: August 2007

ABSTRACT

Elemental sulfur (S
0
) is associated with many geochemically diverse hot springs, yet little is known about the phylogeny, physiology, and ecology of the organisms involved in its cycling. Here we report the isolation, characterization, and ecology of two novel, S
0
-reducing
Crenarchaea
from an acid geothermal spring referred to as Dragon Spring. Isolate 18U65 grows optimally at 70 to 72°C and at pH 2.5 to 3.0, while isolate 18D70 grows optimally at 81°C and pH 3.0. Both isolates are chemoorganotrophs, dependent on complex peptide-containing carbon sources, S
0
, and anaerobic conditions for respiration-dependent growth. Glycerol dialkyl glycerol tetraethers (GDGTs) containing four to six cyclopentyl rings were present in the lipid fraction of isolates 18U65 and 18D70. Physiological characterization suggests that the isolates are adapted to the physicochemical conditions of Dragon Spring and can utilize the natural organic matter in the spring as a carbon and energy source. Quantitative PCR analysis of 16S rRNA genes associated with the S
0
flocs recovered from several acid geothermal springs using isolate-specific primers indicates that these two populations together represent 17 to 37% of the floc-associated DNA. The physiological characteristics of isolates 18U65 and 18D70 are consistent with their potential widespread distribution and putative role in the cycling of sulfur in acid geothermal springs throughout the Yellowstone National Park geothermal complex. Based on phenotypic and genetic characterization, the designations
Caldisphaera draconis
sp. nov. and
Acidilobus sulfurireducens
sp. nov. are proposed for isolates 18U65 and 18D70, respectively.
Genetic Screen for Regulatory Mutations in
Methanococcus maripaludis
and Its Use in Identification of Induction-Deficient Mutants of the Euryarchaeal Repressor NrpR
Authors: Lie Thomas J. , Leigh John A. 
Published: August 2007

ABSTRACT

NrpR is an euryarchaeal transcriptional repressor of nitrogen assimilation genes. Previous studies with
Methanococcus maripaludis
demonstrated that NrpR binds to palindromic operator sequences, blocking transcription initiation. The metabolite 2-oxoglutarate, an indicator of cellular nitrogen deficiency, induces transcription by lowering the affinity of NrpR for operator DNA. In this report we build on existing genetic tools for
M. maripaludis
to develop a screen for change-of-function mutations in a transcriptional regulator and demonstrate the use of an X-Gal (5-bromo-4-chloro-3-indolyl-β-
d
-galactopyranoside) screen for strict anaerobes. We use the approach to address the primary structural requirements for the response of NrpR to 2-oxoglutarate.
nrpR
genes from the mesophilic
M. maripaludis
and the hyperthermophilic
Methanopyrus kandleri
were targeted for mutagenesis.
M. maripaludis nrpR
encodes a protein with two homologous NrpR domains while the
M. kandleri nrpR
homolog encodes a single NrpR domain. Random point mutagenesis and alanine replacement mutagenesis identified two amino acid residues of
M. kandleri
NrpR involved in induction of gene expression under nitrogen-deficient conditions and thus in the response to 2-oxoglutarate. Mutagenesis of the corresponding regions in either domain of
M. maripaludis
NrpR resulted in a similar effect, demonstrating a conserved structure-function relationship between the two repressors. The results indicate that in
M. maripaludis
, both NrpR domains participate in the 2-oxoglutarate response. The approach used here has wide adaptability to other regulatory systems in methanogenic
Archaea
and other strict anaerobes.