bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimization of Analytical Parameters for Inferring Relationships among
Escherichia coli
Isolates from Repetitive-Element PCR by Maximizing Correspondence with Multilocus Sequence Typing Data
Authors: Goldberg Tony L. , Gillespie Thomas R. , Singer Randall S. 
Published: September 2006

ABSTRACT

Repetitive-element PCR (rep-PCR) is a method for genotyping bacteria based on the selective amplification of repetitive genetic elements dispersed throughout bacterial chromosomes. The method has great potential for large-scale epidemiological studies because of its speed and simplicity; however, objective guidelines for inferring relationships among bacterial isolates from rep-PCR data are lacking. We used multilocus sequence typing (MLST) as a “gold standard” to optimize the analytical parameters for inferring relationships among
Escherichia coli
isolates from rep-PCR data. We chose 12 isolates from a large database to represent a wide range of pairwise genetic distances, based on the initial evaluation of their rep-PCR fingerprints. We conducted MLST with these same isolates and systematically varied the analytical parameters to maximize the correspondence between the relationships inferred from rep-PCR and those inferred from MLST. Methods that compared the shapes of densitometric profiles (“curve-based” methods) yielded consistently higher correspondence values between data types than did methods that calculated indices of similarity based on shared and different bands (maximum correspondences of 84.5% and 80.3%, respectively). Curve-based methods were also markedly more robust in accommodating variations in user-specified analytical parameter values than were “band-sharing coefficient” methods, and they enhanced the reproducibility of rep-PCR. Phylogenetic analyses of rep-PCR data yielded trees with high topological correspondence to trees based on MLST and high statistical support for major clades. These results indicate that rep-PCR yields accurate information for inferring relationships among
E. coli
isolates and that accuracy can be enhanced with the use of analytical methods that consider the shapes of densitometric profiles.
Two 2[5H]-Furanones as Possible Signaling Molecules inLactobacillus helveticus
Authors: Ndagijimana Maurice , Vallicelli Melania , Cocconcelli P. Sandro , Cappa Fabrizio , Patrignani Francesca , Lanciotti Rosalba , Guerzoni M. Elisabetta 
Published: September 2006

ABSTRACTTwo 2[5H]-furanones, in association with medium-chain fatty acids, were released in whey byLactobacillus helveticusexposed to oxidative and heat stresses. This species plays an important role in cheese technology, particularly for Swiss-type cheeses and Grana cheese. Moreover, it significantly contributes to cheese ripening by means of an early autolysis and the release of enzymes during processing. Experimental evidence of the involvement of the two 2[5H]-furanones, detected by a gas chromatography-mass spectrometry/solid-phase microextraction technique, in the autolysis phenomenon has been obtained. Zymograms performed by using renaturing sodium dodecyl sulfate-polyacrylamide gels were used to detect the bioactivity of the supernatants containing the two furanones on fresh cells of the same strain. In addition to bands corresponding to known autolysins, new autolysins were detected concomitant with the exposure ofLactobacillus helveticusto the supernatants, which can be regarded as conditioned media (CM), and to a commercial furanone, 5-ethyl-3-hydroxy-4-methyl-2[5H]-furanone (HEMFi), having spectral data similar to those of the newly described 2[5H]-furanones. Morphological changes were observed when fresh cells were exposed to CM containing the two 2[5H]-furanones and HEMFi. The two furanones produced byLactobacillus helveticus, which met a number of criteria to be included in cell-cell signaling molecules, have a presumptive molecular mass lower than those of already known 3[2H]-furanones having an autolytic activity and being produced by gram-negative bacteria. Moreover, they present a different chemical structure with respect to the furanones already identified as products ofLactococcus lactissubsp.cremorisor to those identified in some cheeses withLactobacillus helveticusas a starter culture.
Proteomic Profiling and Identification of Immunodominant Spore Antigens of
Bacillus anthracis
,
Bacillus cereus
, and
Bacillus thuringiensis
Authors: DelVecchio Vito G. , Connolly Joseph P. , Alefantis Timothy G. , Walz Alexander , Quan Marian A. , Patra Guy , Ashton John M. , Whittington Jessica T. , Chafin Ryan D. , Liang Xudong , Grewal Paul , Khan Akbar S. , Mujer Cesar V. 
Published: September 2006

ABSTRACT

Differentially expressed and immunogenic spore proteins of the
Bacillus cereus
group of bacteria, which includes
Bacillus anthracis
,
Bacillus cereus
, and
Bacillus thuringiensis
, were identified. Comparative proteomic profiling of their spore proteins distinguished the three species from each other as well as the virulent from the avirulent strains. A total of 458 proteins encoded by 232 open reading frames were identified by matrix-assisted laser desorption ionization-time-of-flight mass spectrometry analysis for all the species. A number of highly expressed proteins, including elongation factor Tu (EF-Tu), elongation factor G, 60-kDa chaperonin, enolase, pyruvate dehydrogenase complex, and others exist as charge variants on two-dimensional gels. These charge variants have similar masses but different isoelectric points. The majority of identified proteins have cellular roles associated with energy production, carbohydrate transport and metabolism, amino acid transport and metabolism, posttranslational modifications, and translation. Novel vaccine candidate proteins were identified using
B. anthracis
polyclonal antisera from humans postinfected with cutaneous anthrax. Fifteen immunoreactive proteins were identified in
B. anthracis
spores, whereas 7, 14, and 7 immunoreactive proteins were identified for
B. cereus
and in the virulent and avirulent strains of
B. thuringiensis
spores, respectively. Some of the immunodominant antigens include charge variants of EF-Tu, glyceraldehyde-3-phosphate dehydrogenase, dihydrolipoamide acetyltransferase, Δ-1-pyrroline-5-carboxylate dehydrogenase, and a dihydrolipoamide dehydrogenase. Alanine racemase and neutral protease were uniquely immunogenic to
B. anthracis
. Comparative analysis of the spore immunome will be of significance for further nucleic acid- and immuno-based detection systems as well as next-generation vaccine development.
Virulence of
Serratia
Strains against
Costelytra zealandica
Authors: Tan Binglin , Jackson Trevor A. , Hurst Mark R. H. 
Published: September 2006

ABSTRACT

Strains of
Serratia
spp. showed a high level of virulence when injected into the hemocoel of larvae
Costelytra zealandica
, with
Serratia entomophila
,
S. plymuthica
, and
S. marcescens
showing significantly higher virulence than
S. proteamaculans
. Toxicity was independent of the amber disease-causing plasmid pADAP, suggesting a generalized
Serratia
toxin.
Global Transcriptional and Physiological Responses of
Saccharomyces cerevisiae
to Ammonium,
l
-Alanine, or
l
-Glutamine Limitation
Authors: Usaite Renata , Patil Kiran R. , Grotkjær Thomas , Nielsen Jens , Regenberg Birgitte 
Published: September 2006

ABSTRACT

The yeast
Saccharomyces cerevisiae
encounters a range of nitrogen sources at various concentrations in its environment. The impact of these two parameters on transcription and metabolism was studied by growing
S. cerevisiae
in chemostat cultures with
l
-glutamine,
l
-alanine, or
l
-ammonium in limitation and by growing cells in an excess of ammonium. Cells grown in
l
-alanine-limited cultures had higher biomass yield per nitrogen mole (19%) than those from ammonium-limited cultures. Whole-genome transcript profiles were analyzed with a genome-scale metabolic model that suggested increased anabolic activity in
l
-alanine-limited cells. The changes in these cells were found to be focused around pyruvate, acetyl coenzyme A, glyoxylate, and α-ketoglutarate via increased levels of
ALT1
,
DAL7
,
PYC1
,
GDH2
, and
ADH5
and decreased levels of
GDH3
,
CIT2
, and
ACS1
transcripts. The transcript profiles were then clustered. Approximately 1,400 transcripts showed altered levels when amino acid-grown cells were compared to those from ammonium. Another 400 genes had low transcript levels when ammonium was in excess. Overrepresentation of the GATAAG element in their promoters suggests that nitrogen catabolite repression (NCR) may be responsible for this regulation. Ninety-one genes had transcript levels on both
l
-glutamine and ammonium that were decreased compared to those on
l
-alanine, independent of the concentration. The GATAAG element in these genes suggests two groups of NCR-responsive genes, those that respond to high levels of nitrogen and those that respond to levels below 30 μM. In conclusion, our results reveal that the nitrogen source has substantial influence on the transcriptome of yeasts and that transcriptional changes may be correlated to physiology via a metabolic model.
New Screening Software Shows that Most Recent Large 16S rRNA Gene Clone Libraries Contain Chimeras
Authors: Ashelford Kevin E. , Chuzhanova Nadia A. , Fry John C. , Jones Antonia J. , Weightman Andrew J. 
Published: September 2006

ABSTRACTA new computer program, called Mallard, is presented for screening entire 16S rRNA gene libraries of up to 1,000 sequences for chimeras and other artifacts. Written in the Java computer language and capable of running on all major operating systems, the program provides a novel graphical approach for visualizing phylogenetic relationships among 16S rRNA gene sequences. To illustrate its use, we analyzed most of the large libraries of cloned bacterial 16S rRNA gene sequences submitted to the public repository during 2005. Defining a large library as one containing 100 or more sequences of 1,200 bases or greater, we screened 25 of the 28 libraries and found that all but three contained substantial anomalies. Overall, 543 anomalous sequences were found. The average anomaly content per clone library was 9.0%, 4% higher than that previously estimated for the public repository overall. In addition, 90.8% of anomalies had characteristic chimeric patterns, a rise of 25.4% over that found previously. One library alone was found to contain 54 chimeras, representing 45.8% of its content. These figures far exceed previous estimates of artifacts within public repositories and further highlight the urgent need for all researchers to adequately screen their libraries prior to submission. Mallard is freely available from our website athttp://www.cardiff.ac.uk/biosi/research/biosoft/.
Inhibition of Fungal Colonization by
Pseudoalteromonas tunicata
Provides a Competitive Advantage during Surface Colonization
Authors: Franks A. , Egan S. , Holmström C. , James S. , Lappin-Scott H. , Kjelleberg S. 
Published: September 2006

ABSTRACT

The marine epiphytic bacterium
Pseudoalteromonas tunicata
produces a range of extracellular secondary metabolites that inhibit an array of common fouling organisms, including fungi. In this study, we test the hypothesis that the ability to inhibit fungi provides
P. tunicata
with an advantage during colonization of a surface. Studies on a transposon-generated antifungal-deficient mutant of
P. tunicata
, FM3, indicated that a long-chain fatty acid-coenzyme A ligase is involved in the production of a broad-range antifungal compound by
P. tunicata
. Flow cell experiments demonstrated that production of an antifungal compound provided
P. tunicata
with a competitive advantage against a marine yeast isolate during surface colonization. This compound enabled
P. tunicata
to disrupt an already established fungal biofilm by decreasing the number of yeast cells attached to the surface by 66% ± 9%. For in vivo experiments, the wild-type and FM3 strains of
P. tunicata
were used to inoculate the surface of the green alga
Ulva australis
. Double-gradient denaturing gradient gel electrophoresis analysis revealed that after 48 h, the wild-type
P. tunicata
had outcompeted the surface-associated fungal community, whereas the antifungal-deficient mutant had no effect on the fungal community. Our data suggest that
P. tunicata
is an effective competitor against fungal surface communities in the marine environment.
Methane- and Sulfur-Metabolizing Microbial Communities Dominate the Lost City Hydrothermal Field Ecosystem
Authors: Brazelton William J. , Schrenk Matthew O. , Kelley Deborah S. , Baross John A. 
Published: September 2006

ABSTRACT

Hydrothermal venting and the formation of carbonate chimneys in the Lost City hydrothermal field (LCHF) are driven predominantly by serpentinization reactions and cooling of mantle rocks, resulting in a highly reducing, high-pH environment with abundant dissolved hydrogen and methane. Phylogenetic and terminal restriction fragment length polymorphism analyses of 16S rRNA genes in fluids and carbonate material from this site indicate the presence of organisms similar to sulfur-oxidizing, sulfate-reducing, and methane-oxidizing
Bacteria
as well as methanogenic and anaerobic methane-oxidizing
Archaea
. The presence of these metabolic groups indicates that microbial cycling of sulfur and methane may be the dominant biogeochemical processes active within this ultramafic rock-hosted environment. 16S rRNA gene sequences grouping within the
Methylobacter
and
Thiomicrospira
clades were recovered from a chemically diverse suite of carbonate chimney and fluid samples. In contrast, 16S rRNA genes corresponding to the Lost City
Methanosarcinales
phylotype were found exclusively in high-temperature chimneys, while a phylotype of anaerobic methanotrophic
Archaea
(ANME-1) was restricted to lower-temperature, less vigorously venting sites. A hyperthermophilic habitat beneath the LCHF may be reflected by 16S rRNA gene sequences belonging to
Thermococcales
and uncultured
Crenarchaeota
identified in vent fluids. The finding of a diverse microbial ecosystem supported by the interaction of high-temperature, high-pH fluids resulting from serpentinization reactions in the subsurface provides insight into the biogeochemistry of what may be a pervasive process in ultramafic subseafloor environments.
Assessment of Genes Associated with
Streptococcus mutans
Biofilm Morphology
Authors: Motegi Mizuho , Takagi Yuzo , Yonezawa Hideo , Hanada Nobuhiro , Terajima Jun , Watanabe Haruo , Senpuku Hidenobu 
Published: September 2006

ABSTRACT

Streptococcus mutans
, the major pathogen responsible for dental caries in humans, is a biofilm-forming bacterium. In the present study, 17 different pulsed-field gel electrophoresis patterns of genomic DNA were identified in
S. mutans
organisms isolated clinically from whole saliva. The
S. mutans
isolates showed different abilities to form biofilms on polystyrene surfaces in semidefined minimal medium cultures. Following cultivation in a flow cell system in tryptic soy broth with 0.25% sucrose and staining using a BacLight LIVE/DEAD system, two strains, designated FSC-3 and FSC-4, showed the greatest and least, respectively, levels of biofilm formation when examined with confocal laser scanning microscopy. Further, image analyses of spatial distribution and architecture were performed to quantify the merged green (live cells) and red (dead cells) light. The light intensity of the FSC-3 biofilm was greater than that of the FSC-4 biofilm in the bottom area but not in the top area.
S. mutans
whole-genome array results showed that approximately 3.8% of the genes were differentially expressed in the two strains, of which approximately 2.2%, including bacitracin transport ATP-binding protein gene
glrA
and a BLpL-like putative immunity protein gene, were activated in FSC-3. In addition, about 1.6% of the genes, including those associated with phosphotransferase system genes, were repressed. Analyses of the
glrA
-deficient strains and reverse transcription-PCR confirmed the role of the gene in biofilm formation. Differential assessment of biofilm-associated genes in clinical strains may provide useful information for understanding the morphological development of streptococcal biofilm, as well as for colonization of
S. mutans
.
Lysine-Oriented Charges Trigger the Membrane Binding and Activity of Nukacin ISK-1
Authors: Asaduzzaman Sikder M. , Nagao Jun-ichi , Aso Yuji , Nakayama Jiro , Sonomoto Kenji 
Published: September 2006

ABSTRACT

The antibacterial activities and membrane binding of nukacin ISK-1 and its fragments and mutants were evaluated to delineate the determinants governing structure-function relationships. The tail region (nukacin
1-7
) and ring region (nukacin
7-27
) were shown to have no antibacterial activity and also had no synergistic effect on each other or even on nukacin ISK-1. Both a fragment with three lysines in the N terminus deleted (nukacin
4-27
) and a mutant with three lysines in the N terminus replaced with alanine (K1-3A nukacin ISK-1) imparted very low activity (32-fold lower than nukacin ISK-1) and also exhibited a similar antagonistic effect on nukacin ISK-1. Addition of two lysine residues at the N terminus (+2K nukacin ISK-1) provided no further increased antibacterial activity. Surface plasmon resonance sensorgrams and kinetic rate constants determined by a BIAcore biosensor revealed that nukacin ISK-1 has remarkably higher binding affinity to anionic model membrane than to zwitterionic model membrane. Similar trends of strong binding responses and kinetics were indicated by the high affinities of nukacin ISK-1 and +2K nukacin ISK-1, but there was no binding of tail region, ring region, nukacin
4-27
, and K1-3A nukacin ISK-1 to the anionic model membrane. Our findings therefore suggest that the complete structure of nukacin ISK-1 is necessary for its full activity, in which the N-terminus three lysine residues play a crucial role in electrostatic binding to the target membrane and therefore nukacin ISK-1's ability to exert its potent antibacterial activity.
Application of the [
3
H]Leucine Incorporation Technique for Quantification of Bacterial Secondary Production Associated with Decaying Wetland Plant Litter
Authors: Gillies Jane E. , Kuehn Kevin A. , Francoeur Steven N. , Neely Robert K. 
Published: September 2006

ABSTRACT

The radiolabeled leucine incorporation technique for quantifying rates of bacterial production has increased in popularity since its original description for bacterioplankton communities. Prior studies addressing incorporation conditions (e.g., substrate saturation) for bacterial communities in other habitats, such as decaying plant litter, have reported a wide range of final leucine concentrations (400 nM to 50 μM) required to achieve saturation-level uptake. We assessed the application of the [
3
H]leucine incorporation procedure for measuring bacterial production on decaying wetland plant litter. Substrate saturation experiments (nine concentrations, 10 nM to 50 μM final leucine concentration) were conducted on three dates for microbial communities colonizing the submerged litter of three emergent plant species (
Typha angustifolia
,
Schoenoplectus validus
, and
Phragmites australis
). A modified [
3
H]leucine protocol was developed by coupling previously described incubation and alkaline extraction protocols with microdialysis (500 molecular weight cutoff membrane) of the final radiolabeled protein extract. The incorporation of [
3
H]leucine into protein exhibited a biphasic saturation curve, with lower apparent

K
m

values ranging from 400 nM to 4.2 μM depending on the plant species studied. Upper apparent

K
m

values ranged from 1.3 to 59 μM. These results suggest differential uptake by litter-associated microbial assemblages, with the lower apparent

K
m

values possibly representing bacterial uptake and higher apparent

K
m

values representing a combination of both bacterial and nonbacterial (e.g., eukaryotic) uptake.
Temporal Changes in Microscale Colonization of the Phylloplane by
Aureobasidium pullulans
Authors: McGrath Molly J. , Andrews John H. 
Published: September 2006

ABSTRACT

Colonization of apple leaves by the yeastlike fungus
Aureobasidium pullulans
was followed quantitatively and spatially at a microscale level throughout two growing seasons. Ten field leaves were sampled on 11 dates in 2003 and 15 dates in 2004. Using an
A. pullulans
-specific fluorescence in situ hybridization probe and epifluorescence microscopy, we enumerated total cells, swollen-cells and chlamydospores (SCC), and blastospores/mm
2
on leaf features, including the midvein, other (smaller) veins, and the interveinal regions. By 7 July 2003 and 7 June 2004, the total numbers of
A. pullulans
cells/mm
2
were significantly higher (
P
< 0.05) on the midvein and other veins than in the interveinal regions. This pattern remained consistent thereafter. The primary colonizing morphotype in all regions at all dates was the SCC form, although blastospores always occurred in low numbers. Occupancy was quantified based on the percentage of microscope fields of a particular leaf feature containing ≥1
A. pullulans
cell. In general, as seasons progressed, the percent occupancy of features increased and, for most midvein and veinal features, approximated 100% at the end of both growing seasons. Except for early collections, when
A. pullulans
cell numbers were low, the percent occupancy of interveinal regions was lower than that of the midvein or other veinal regions.
A. pullulans
was distributed primarily as single cells throughout the seasons in interveinal regions. On the midvein and other veins, colonies of ≥4 cells developed over time, and more cells occurred in colonies than as singletons by August. Our results demonstrate that
A. pullulans
primarily colonizes veins, where populations appear to increase by growth in situ. This pattern is established early in the growing season and persists.
Granadaene: Proposed Structure of the Group B Streptococcus Polyenic Pigment
Authors: Rosa-Fraile Manuel , Rodríguez-Granger Javier , Haidour-Benamin Ali , Cuerva Juan Manuel , Sampedro Antonio 
Published: September 2006

ABSTRACT

The goal of this work was to determine the chemical nature of the red pigment produced by
Streptococcus agalactiae
, which has been thought to be a carotene. We extracted the pigment with 0.1 M KOH and purified it by column chromatography on Sephadex LH. Data from elemental analysis and mass and nuclear magnetic resonance spectra lead us to propose the structure to be that of a new ornithine rhamno-polyene with 12 conjugated double bonds, to which we have assigned the trivial name granadaene.