bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genotypic and Physiological Characterization of
Saccharomyces boulardii
, the Probiotic Strain of
Saccharomyces cerevisiae
Authors: Edwards-Ingram Laura , Gitsham Paul , Burton Nicola , Warhurst Geoff , Clarke Ian , Hoyle David , Oliver Stephen G. , Stateva Lubomira 
Published: February 2007

ABSTRACT

Saccharomyces boulardii
, a yeast that was isolated from fruit in Indochina, has been used as a remedy for diarrhea since 1950 and is now a commercially available treatment throughout Europe, Africa, and South America. Though initially classified as a separate species of
Saccharomyces
, recent publications have shown that the genome of
S. boulardii
is so similar to
Saccharomyces cerevisiae
that the two should be classified as conspecific. This raises the question of the distinguishing molecular and phenotypic characteristics present in
S. boulardii
that make it perform more effectively as a probiotic organism compared to other strains of
S. cerevisiae
. This investigation reports some of these distinguishing characteristics including enhanced ability for pseudohyphal switching upon nitrogen limitation and increased resistance to acidic pH. However, these differences did not correlate with increased adherence to epithelial cells or transit through mouse gut. Pertinent characteristics of the
S. boulardii
genome such as trisomy of chromosome IX, altered copy number of a number of individual genes, and sporulation deficiency have been revealed by comparative genome hybridization using oligonucleotide-based microarrays coupled with a rigorous statistical analysis. The contributions of the different genomic and phenotypic features of
S. boulardii
to its probiotic nature are discussed.
New Mathematical Modeling Approach for Predicting Microbial Inactivation by High Hydrostatic Pressure
Authors: Klotz Bernadette , Pyle D. Leo , Mackey Bernard M. 
Published: February 2007

ABSTRACT

A new primary model based on a thermodynamically consistent first-order kinetic approach was constructed to describe non-log-linear inactivation kinetics of pressure-treated bacteria. The model assumes a first-order process in which the specific inactivation rate changes inversely with the square root of time. The model gave reasonable fits to experimental data over six to seven orders of magnitude. It was also tested on 138 published data sets and provided good fits in about 70% of cases in which the shape of the curve followed the typical convex upward form. In the remainder of published examples, curves contained additional shoulder regions or extended tail regions. Curves with shoulders could be accommodated by including an additional time delay parameter and curves with tails shoulders could be accommodated by omitting points in the tail beyond the point at which survival levels remained more or less constant. The model parameters varied regularly with pressure, which may reflect a genuine mechanistic basis for the model. This property also allowed the calculation of (a) parameters analogous to the decimal reduction time
D
and
z
, the temperature increase needed to change the
D
value by a factor of 10, in thermal processing, and hence the processing conditions needed to attain a desired level of inactivation; and (b) the apparent thermodynamic volumes of activation associated with the lethal events. The hypothesis that inactivation rates changed as a function of the square root of time would be consistent with a diffusion-limited process.
Helicobacter pylori
EstV: Identification, Cloning, and Characterization of the First Lipase Isolated from an Epsilon-Proteobacterium
Authors: Ruiz Cristian , Falcocchio Serena , Pastor F. I. Javier , Saso Luciano , Diaz Pilar 
Published: February 2007

ABSTRACT

Bacterial lipases are attracting an enormous amount of attention due to their wide biotechnological applications and due to their roles as virulence factors in some bacteria.
Helicobacter pylori
is a significant and widespread pathogen which produces a lipase(s) and phospholipases that seem to play a role in mucus degradation and the release of proinflammatory and cytotoxic compounds. However, no
H. pylori
lipase(s) has been isolated and described previously. Therefore, a search for putative lipase-encoding genes was performed by comparing the amino acid sequences of 53 known lipolytic enzymes with the deduced proteome of
H. pylori
. As a result, we isolated, cloned, purified, and characterized EstV, a novel lipolytic enzyme encoded by open reading frame HP0739 of
H. pylori
26695, and classified it in family V of the bacterial lipases. This enzyme has the properties of a small, cell-bound carboxylesterase (EC 3.1.1.1) that is active mostly with short-chain substrates and does not exhibit interfacial activation. EstV is stable and does not require additional cofactors, and the maximum activity occurs at 50°C and pH 10. This unique enzyme is the first lipase isolated from
H. pylori
that has been described, and it might contribute to ulcer development, as inhibition by two antiulcer substances (β-aescin and glycyrrhizic acid) suggests. EstV is also the first lipase from an epsilon-proteobacterium to be described. Furthermore, this enzyme is a new member of family V, probably the least-known family of bacterial lipases, and the first lipase of this family for which kinetic behavior, inhibition by natural substances, and other key biochemical features are reported.
Molecular Fingerprinting of the Fecal Microbiota of Children Raised According to Different Lifestyles
Authors: Dicksved Johan , Flöistrup Helen , Bergström Anna , Rosenquist Magnus , Pershagen Göran , Scheynius Annika , Roos Stefan , Alm Johan S. , Engstrand Lars , Braun-Fahrländer Charlotte , von Mutius Erika , Jansson Janet K. 
Published: February 2007

ABSTRACT

In this population-based study, 90 children from three European countries were examined to determine the impact of lifestyle on the fecal microbiota. The study was designed to assess the impact of two extreme lifestyles that we hypothesized could impact the microbial composition in the gut: i.e., an anthroposophic lifestyle (restricted use of antibiotics, greater consumption of fermented vegetables, etc.) versus living on a farm (greater consumption of farm milk, contact with animals, etc.). In previous studies, these lifestyles correlated with lower prevalence of allergies. Terminal restriction fragment length polymorphism (T-RFLP) was used to assess the bacterial composition in fecal samples since recent studies have shown that the majority of this community cannot be cultivated. The T-RFLP data were used to calculate richness and evenness of the fecal microbiota. Children that were attending Steiner schools (anthroposophic children) had a significantly higher diversity of microbes in their feces than farm children, who in turn also had lower diversity than the control groups. Specific primers were also used to focus on the
Lactobacillus
-like community (lactic acid bacteria [LAB]). Large differences were found in the LAB subpopulations in the sampled groups. In some children, the LAB subpopulation was dominated by a species that has not yet been cultivated.
Widespread Occurrence and Genomic Context of Unusually Small Polyketide Synthase Genes in Microbial Consortia Associated with Marine Sponges
Authors: Fieseler Lars , Hentschel Ute , Grozdanov Lubomir , Schirmer Andreas , Wen Gaiping , Platzer Matthias , Hrvatin Siniša , Butzke Daniel , Zimmermann Katrin , Piel Jörn 
Published: February 2007

ABSTRACT

Numerous
marine sponges harbor enormous amounts of as-yet-uncultivated bacteria
in their tissues. There is increasing evidence that these symbionts
play an important role in the synthesis of protective metabolites, many
of which are of great pharmacological interest. In this study, genes
for the biosynthesis of polyketides, one of the most important classes
of bioactive natural products, were systematically investigated in 20
demosponge species from different oceans. Unexpectedly, the sponge
metagenomes were dominated by a ubiquitously present, evolutionarily
distinct, and highly sponge-specific group of polyketide synthases
(PKSs). Open reading frames resembling animal fatty acid genes were
found on three corresponding DNA regions isolated from the metagenomes
of
Theonella swinhoei
and
Aplysina aerophoba
. Their
architecture suggests that methyl-branched fatty acids are the
metabolic product. According to a phylogenetic analysis of housekeeping
genes, at least one of the PKSs belongs to a bacterium of the
Deinococcus-Thermus
phylum. The results provide new insights
into the chemistry of sponge symbionts and allow inference of a
detailed phylogeny of the diverse functional PKS types present in
sponge metagenomes. Based on these qualitative and quantitative data,
we propose a significantly simplified strategy for the targeted
isolation of biomedically relevant PKS genes from complex
sponge-symbiont
associations.
Expression Profiles of Bovine Genes in the Rectoanal Junction Mucosa during Colonization with
Escherichia coli
O157:H7
Authors: Li Jie , Hovde Carolyn J. 
Published: February 2007

ABSTRACT

A bovine-specific cDNA microarray was used to characterize gene expression in the bovine rectoanal junction mucosa in response to
Escherichia coli
O157:H7 colonization, and results were confirmed using quantitative real-time PCR. The results showed involvement of cell processes including immune response, cell structure/dynamics, signal transduction, intercellular communication, and metabolism.
A Derepression System Based on the
Bacillus subtilis
Sporulation Pathway Offers Dynamic Control of Heterologous Gene Expression
Authors: Nijland Reindert , Veening Jan-Willem , Kuipers Oscar P. 
Published: February 2007

ABSTRACT

By rewiring the sporulation gene-regulatory network of
Bacillus subtilis
, we generated a novel expression system relying on derepression. The gene of interest is placed under the control of the
abrB
promoter, which is active only when Spo0A is absent, and Spo0A is controlled via an IPTG (isopropyl-β-
d
-thiogalactopyranoside)-inducible promoter.
Detection and Identification by PCR of a Highly Virulent Phylogenetic Subgroup among Extraintestinal Pathogenic
Escherichia coli
B2 Strains
Authors: Bidet Philippe , Metais Arnaud , Mahjoub-Messai Farah , Durand Lionel , Dehem Marie , Aujard Yannick , Bingen Edouard , Nassif Xavier , Bonacorsi Stéphane 
Published: February 2007

ABSTRACT

Closely related
Escherichia coli
B2 strains O1:K1, O2:K1, O18:K1, and O45:K1 constitute a major subgroup causing extraintestinal infections. A DNA pathoarray analysis was used to develop a PCR specific for this subgroup that was included in the multiplex phylogenetic-grouping PCR method. Our PCR may serve to identify this virulent subgroup among different ecological niches.
Clonal Population Structure and Specific Genotypes of Multidrug-Resistant
Campylobacter coli
from Turkeys
Authors: D'lima C. B. , Miller W. G. , Mandrell R. E. , Wright S. L. , Siletzky R. M. , Carver D. K. , Kathariou S. 
Published: February 2007

ABSTRACT

Commercial turkey flocks in North Carolina have been found to be colonized frequently with
Campylobacter coli
strains that are resistant to several antimicrobials (tetracycline, streptomycin, erythromycin, kanamycin, and ciprofloxacin/nalidixic acid). Such strains have been designated multidrug resistant (MDR). However, the population structure of MDR
C. coli
from turkeys remains poorly characterized. In this study, an analysis of multilocus sequence typing (MLST)-based sequence types (STs) of 59 MDR strains from turkeys revealed that the majority of these strains corresponded to one of 14 different STs, with three STs accounting for 41 (69%) of the strains. The major STs were turkey specific, and most (87%) of the strains with these STs were resistant to the entire panel of antibiotics mentioned above. Some (13%) of the strains with these STs were susceptible to just one or two of the antibiotics in this panel. Further subtyping using
fla
typing and pulsed-field gel electrophoresis with SmaI and KpnI revealed that the major MDR STs corresponded to strains of related but distinct subtypes, providing evidence for genomic diversification within these STs. These findings suggest that MDR strains of
C. coli
from turkeys have a clonal population structure characterized by the presence of a relatively small number of clonal groups that appear to be disseminated in the turkey production system. In addition, the observed correlation between STs and the MDR profiles of the microbes indicates that MLST-based typing holds potential for source-tracking applications specific to the animal source (turkeys) and the antimicrobial resistance profile (MDR status) of
C. coli
.
Enhancement of Biodesulfurization in Two-Liquid Systems by Heterogeneous Expression of
Vitreoscilla
Hemoglobin
Authors: Xiong Xiaochao , Xing Jianmin , Li Xin , Bai Xuejing , Li Wangliang , Li Yuguang , Liu Huizhou 
Published: February 2007

ABSTRACT

The
vgb
gene, encoding
Vitreoscilla
hemoglobin (VHb), was introduced into a specific desulfurization bacterium,
Rhodococcus erythropolis
LSSE8-1. The VHb-specific spectrum was observed for the recombinant. Compared to the wild type, the strain bearing
vgb
showed a higher biomass yield and desulfurizing activity.
Weissellicin 110, a Newly Discovered Bacteriocin from
Weissella cibaria
110, Isolated from Plaa-Som, a Fermented Fish Product from Thailand
Authors: Srionnual Sirinat , Yanagida Fujitoshi , Lin Li-Hsiu , Hsiao Kuang-Nan , Chen Yi-sheng 
Published: February 2007

ABSTRACT

Weissella cibaria
110, isolated from the Thai fermented fish product plaa-som, was found to produce a bacteriocin active against some gram-positive bacteria. Bacteriocin activity was not eliminated by exposure to high temperatures or catalase but was destroyed by exposure to the proteolytic enzymes proteinase K and trypsin. The bacteriocin from
W. cibaria
110 was purified, and sodium dodecyl sulfate-polyacrylamide gel electrophoresis showed that the purified bacteriocin contained one protein band that was approximately 2.5 kDa in size. Mass spectrometry analysis showed the mass of the peptide to be approximately 3,487.8 Da. N-terminal amino acid sequence analysis was performed, and 27 amino acids were identified. Because it has no similarity to other known bacteriocins, this bacteriocin was defined as a new bacteriocin and termed weissellicin 110.
The SAR92 Clade: an Abundant Coastal Clade of Culturable Marine Bacteria Possessing Proteorhodopsin
Authors: Stingl Ulrich , Desiderio Russell A. , Cho Jang-Cheon , Vergin Kevin L. , Giovannoni Stephen J. 
Published: February 2007

ABSTRACT

Proteorhodopsin (PR) is a protein that is abundant in marine bacterioplankton. PR is hypothesized to be a light-dependent proton pump, thus creating a proton gradient that can be used for energy production without electron transport. Currently, the only culture that has been reported to possesses PR is the highly abundant alphaproteobacterium “
Candidatus
Pelagibacter ubique” (SAR11 clade), but surprisingly, its growth in batch culture was not enhanced by light. Here, we present the first cultured gammaproteobacterium that possesses a PR gene. Genome sequencing and analysis of HTCC2207 showed that the PR gene is present as a lone transcriptional unit directly followed by an operon containing genes that are presumably involved in the synthesis of retinal, the chromophore of PR. Half-time decay times of different PR intermediates in native HTCC2207 cells ranged between 2 and 15 ms, and the absorbance maximum of PR was determined to be 528 nm. Proteorhodopsin was identified in three additional strains, using a specific PCR assay on other cultured members of the SAR92 clade. Phylogenetic analyses of the PR genes determined that they form a deeply rooting cluster not closely related to any PR genes recovered so far. Fluorescence in situ hybridization and RNA blots showed that the SAR92 clade reaches up to 10% of the total bacterial population in surface waters close to the Oregon coast and decreases over depth and distance from the shore. Although the growth of HTCC2207 is limited by the amount of available carbon that is present in the medium applied, these cultures do not grow at higher rates nor do they have higher growth yields when incubated under light.
Simultaneous Detection of
Pseudomonas fragi
,
P. lundensis
, and
P. putida
from Meat by Use of a Multiplex PCR Assay Targeting the
carA
Gene
Authors: Ercolini Danilo , Russo Federica , Blaiotta Giuseppe , Pepe Olimpia , Mauriello Gianluigi , Villani Francesco 
Published: February 2007

ABSTRACT

Species-specific primers and a multiplex PCR assay were developed for the simultaneous identification and differentiation of
Pseudomonas fragi
,
P. lundensis
, and
P. putida
based on the coamplification of different portions of the small subunit of the carbamoyl phosphate synthase gene (
carA
). The
carA
multiplex PCR was used to detect the presence of the three
Pseudomonas
species from beef, chicken, and pork samples and proved to be effective in showing their evolution during the storage of meat.
Assessing Adhesion Forces of Type I and Type IV Pili of
Xylella fastidiosa
Bacteria by Use of a Microfluidic Flow Chamber
Authors: De La Fuente Leonardo , Montanes Emilie , Meng Yizhi , Li Yaxin , Burr Thomas J. , Hoch H. C. , Wu Mingming 
Published: February 2007

ABSTRACT

Xylella fastidiosa
, a bacterium responsible for Pierce's disease in grapevines, possesses both type I and type IV pili at the same cell pole. Type IV pili facilitate twitching motility, and type I pili are involved in biofilm development. The adhesiveness of the bacteria and the roles of the two pili types in attachment to a glass substratum were evaluated using a microfluidic flow chamber in conjunction with pilus-defective mutants. The average adhesion force necessary to detach wild-type
X. fastidiosa
cells was 147 ± 11 pN. Mutant cells possessing only type I pili required a force of 204 ± 22 pN for removal, whereas cells possessing only type IV pili required 119 ± 8 pN to dislodge these cells. The experimental results demonstrate that microfluidic flow chambers are useful and convenient tools for assessing the drag forces necessary for detaching bacterial cells and that with specific pilus mutants, the role of the pilus type can be further assessed.
An NAD(P)H-Nicotine Blue Oxidoreductase Is Part of the Nicotine Regulon and May Protect
Arthrobacter nicotinovorans
from Oxidative Stress during Nicotine Catabolism
Authors: Mihasan Marius , Chiribau Calin-Bogdan , Friedrich Thorsten , Artenie Vlad , Brandsch Roderich 
Published: February 2007

ABSTRACT

An NAD(P)H-nicotine blue (quinone) oxidoreductase was discovered as a member of the nicotine catabolic pathway of
Arthrobacter nicotinovorans
. Transcriptional analysis and electromobility shift assays showed that the enzyme gene was expressed in a nicotine-dependent manner under the control of the transcriptional activator PmfR and thus was part of the nicotine regulon of
A. nicotinovorans
. The flavin mononucleotide-containing enzyme uses NADH and, with lower efficiency, NADPH to reduce, by a two-electron transfer, nicotine blue to the nicotine blue leuco form (hydroquinone). Besides nicotine blue, several other quinones were reduced by the enzyme. The NAD(P)H-nicotine blue oxidoreductase may prevent intracellular one-electron reductions of nicotine blue which may lead to semiquinone radicals and potentially toxic reactive oxygen species.
Characterization of the Sporulation Control Protein SsgA by Use of an Efficient Method To Create and Screen Random Mutant Libraries in Streptomycetes
Authors: Traag Bjørn A. , Seghezzi Nicolas , Vijgenboom Erik , van Wezel Gilles P. 
Published: February 2007

ABSTRACT

Filamentous actinomycetes are commercially widely used as producers of natural products. However, the mycelial lifestyle of actinomycetes has been a major bottleneck in their commercialization, and screening is difficult due to their poor growth on microtiter plates. We previously demonstrated that the enhanced expression of the cell division activator protein SsgA results in the fragmented growth of streptomycetes, with enhanced growth rates and improved product formation. We here describe a novel and efficient method to create, maintain, and screen mutant libraries in streptomycetes and the application of this method for the functional analysis of
Streptomyces coelicolor ssgA
. The variants were amplified directly from deep-frozen biomass suspensions. Around 800
ssgA
variants, including single-amino-acid-substitution mutants corresponding to more than half of all SsgA residues, were analyzed for their abilities to restore sporulation to an
ssgA
mutant. The essential residues were clustered in three main sections, and hardly any were in the carboxy-terminal third of the protein. The majority of the crucial residues were conserved among all SsgA-like proteins (SALPs). However, the essential residues L29, D58, and S89 were conserved only in SsgA orthologues and not in other SALPs, suggesting an SsgA-specific function.
Induction of Glutathione
S
-Transferase in Biofilms and Germinating Spores of
Mucor hiemalis
Strain EH5 from Cold Sulfidic Spring Waters
Authors: Hoque Enamul , Pflugmacher Stephan , Fritscher Johannes , Wolf Manfred 
Published: February 2007

ABSTRACT

The occurrence and activation of glutathione
S
-transferase (GST) and the GST activities in biofilms in cold sulfidic spring waters were compared to the occurrence and activation of GST and the GST activities of the aquatic fungal strains EH5 and EH7 of
Mucor hiemalis
isolated for the first time from such waters. Using fluorescently labeled polyclonal anti-GST antibodies and GST activity measurements, we demonstrated that a high level of GST occurred in situ in natural biofilms and pure cultures of strain EH5. Measurement of microsomal and cytosolic soluble GST activities using different xenobiotic substrates, including 1-chloro-2,4-dinitrobenzene (CDNB), 1,2-dichloro-4-nitrobenzene, 1,2-epoxy-3-(4-nitrophenoxy)propane, 1-iodo-2,4-dinitrobenzene, and fluorodifen, showed that the overall biotransforming abilities of biofilms were at least sixfold greater than that of strain EH5 alone. Increasing the level of sodium thiosulfate (STS) in the medium stimulated the microsomal and cytosolic GST activities with CDNB of strain EH5 about 44- and 94-fold, respectively, compared to the activities in the control. The induction of microsomal GST activity with fluorodifen by STS was strongly linear, but the initial strong linear increase in cytosolic GST activity with fluorodifen showed saturation-like effects at STS concentrations higher than approximately 1 mM. Using laser scanning confocal and conventional fluorescence microscopy, abundant fluorescently labeled GST proteins were identified in germinating sporangiospores of strain EH5 after activation by STS. High-performance size exclusion chromatography and sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed the presence of at least two main GSTs (∼27.8- and ∼25.6-kDa subunits) in the cytosol of EH5, whereas the major 27.8-kDa subunit was the only GST in microsomes. We suggest that differential cellular GST expression takes place in strain EH5 depending on spore and hyphal development. Our results may contribute to our understanding of induction of GST by sulfurous compounds, as well as to the immunofluorescence visualization of GST in aquatic fungus and fungus-bacterium biofilms.