bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fungal Community Analysis by Large-Scale Sequencing of Environmental Samples
Authors: O'Brien Heath E. , Parrent Jeri Lynn , Jackson Jason A. , Moncalvo Jean-Marc , Vilgalys Rytas 
Published: September 2005

ABSTRACT
Fungi are an important and diverse component of soil communities, but these communities have proven difficult to study in conventional biotic surveys. We evaluated soil fungal diversity at two sites in a temperate forest using direct isolation of small-subunit and internal transcribed spacer (ITS) rRNA genes by PCR and high-throughput sequencing of cloned fragments. We identified 412 sequence types from 863 fungal ITS sequences, as well as 112 ITS sequences from other eukaryotic microorganisms. Equal proportions of Basidiomycota and Ascomycota sequences were present in both the ITS and small-subunit libraries, while members of other fungal phyla were recovered at much lower frequencies. Many sequences closely matched sequences from mycorrhizal, plant-pathogenic, and saprophytic fungi. Compositional differences were observed among samples from different soil depths, with mycorrhizal species predominating deeper in the soil profile and saprophytic species predominating in the litter layer. Richness was consistently lowest in the deepest soil horizon samples. Comparable levels of fungal richness have been observed following traditional specimen-based collecting and culturing surveys, but only after much more extensive sampling. The high rate at which new sequence types were recovered even after sampling 863 fungal ITS sequences and the dominance of fungi in our libraries relative to other eukaryotes suggest that the abundance and diversity of fungi in forest soils may be much higher than previously hypothesized.
Abundances, Identity, and Growth State of Actinobacteria in Mountain Lakes of Different UV Transparency
Authors: Warnecke Falk , Sommaruga Ruben , Sekar Raju , Hofer Julia S. , Pernthaler Jakob 
Published: September 2005

ABSTRACT

The occurrence, identity, and activity of microbes from the class
Actinobacteria
was studied in the surface waters of 10 oligo- to mesotrophic mountain lakes located between 913 m and 2,799 m above sea level. Oligonucleotide probes were designed to distinguish between individual lineages within this group by means of fluorescence in situ hybridization (FISH). Bacteria of a single phylogenetic lineage (acI) represented >90% of all
Actinobacteria
in the studied lakes, and they constituted up to 70% of the total bacterial abundances. In the subset of eight lakes situated above the treeline, the community contribution of bacteria from the acI lineage was significantly correlated with the ambient levels of solar UV radiation (UV transparency,
r
2
= 0.72;
P
< 0.01). Three distinct genotypic subpopulations were distinguished within acI that constituted varying fractions of all
Actinobacteria
in the different lakes. The abundance of growing actinobacterial cells was estimated by FISH and immunocytochemical detection of bromodeoxyuridine (BrdU) incorporation into de novo-synthesized DNA. The percentages of
Actinobacteria
with visible DNA synthesis approximately corresponded to the average percentages of BrdU-positive cells in the total assemblages.
Actinobacteria
from different subclades of the acI lineage, therefore, constituted an important autochthonous element of the aquatic microbial communities in many of the studied lakes, potentially also due to their higher UV resistance.
Survival of
Campylobacter jejuni
in Waterborne Protozoa
Authors: Snelling W. J. , McKenna J. P. , Lecky D. M. , Dooley J. S. G. 
Published: September 2005

ABSTRACT

The failure to reduce the
Campylobacter
contamination of intensively reared poultry may be partially due to
Campylobacter
resisting disinfection in water after their internalization by waterborne protozoa.
Campylobacter jejuni
and a variety of waterborne protozoa, including ciliates, flagellates, and alveolates, were detected in the drinking water of intensively reared poultry by a combination of culture and molecular techniques. An in vitro assay showed that
C. jejuni
remained viable when internalized by
Tetrahymena pyriformis
and
Acanthamoeba castellanii
for significantly longer (up to 36 h) than when they were in purely a planktonic state. The internalized
Campylobacter
were also significantly more resistant to disinfection than planktonic organisms. Collectively, our results strongly suggest that protozoa in broiler drinking water systems can delay the decline of
Campylobacter
viability and increase
Campylobacter
disinfection resistance, thus increasing the potential of
Campylobacter
to colonize broilers.
Disintegration of
Staphylococcus epidermidis
Biofilms under Glucose-Limiting Conditions Depends on the Activity of the Alternative Sigma Factor σ
B
Authors: Jäger Sebastian , Mack Dietrich , Rohde Holger , Horstkotte Matthias A. , Knobloch Johannes K.-M. 
Published: September 2005

ABSTRACT

To evaluate the role of the polysaccharide intercellular adhesin as an energy-storage molecule, we investigated the effect of nutrient limitation on
S. epidermidis
biofilms. The stability of established biofilms depends on σ
B
activity; however, the slow decay of biofilms under conditions of nutrient limitation reveal its use as an energy-storage molecule to be unlikely.
Inactivation of Spores of
Bacillus anthracis
Sterne,
Bacillus cereus
, and
Bacillus thuringiensis
subsp.
israelensis
by Chlorination
Authors: Rice E. W. , Adcock N. J. , Sivaganesan M. , Rose L. J. 
Published: September 2005

ABSTRACT

Three species of
Bacillus
were evaluated as potential surrogates for
Bacillus anthracis
for determining the sporicidal activity of chlorination as commonly used in drinking water treatment. Spores of
Bacillus thuringiensis
subsp.
israelensis
were found to be an appropriate surrogate for spores of
B. anthracis
for use in chlorine inactivation studies.
Biosensor Detection of Botulinum Toxoid A and Staphylococcal Enterotoxin B in Food
Authors: Sapsford Kim E. , Taitt Chris R. , Loo Nicole , Ligler Frances S. 
Published: September 2005

ABSTRACT
Immunoassays were developed for the simultaneous detection of staphylococcal enterotoxin B and botulinum toxoid A in buffer, with limits of detection of 0.1 ng/ml and 20 ng/ml, respectively. The toxins were also spiked and measured in a variety of food samples, including canned tomatoes, sweet corn, green beans, mushrooms, and tuna.
Identification of DNA Sequences Specific for
Vibrio vulnificus
Biotype 2 Strains by Suppression Subtractive Hybridization
Authors: Lee Chung-Te , Amaro Carmen , Sanjuán Eva , Hor Lien-I 
Published: September 2005

ABSTRACT

Vibrio vulnificus
can be divided into three biotypes, and only biotype 2, which is further divided into serovars, contains eel-virulent strains. We compared the genomic DNA of a biotype 2 serovar E isolate (tester) with the genomic DNAs of three biotype 1 strains by suppression subtractive hybridization and then tested the distribution of the tester-specific DNA sequences in a wide collection of bacterial strains. In this way we identified three plasmid-borne DNA sequences that were specific for biotype 2 strains irrespective of the serovar and three chromosomal DNA sequences that were specific for serovar E biotype 2 strains. These sequences have potential for use in the diagnosis of eel vibriosis caused by
V. vulnificus
and in the detection of biotype 2 serovar E strains.
Isolation of Multidrug-Resistant
Stenotrophomonas maltophilia
from Cultured Yellowtail (
Seriola quinqueradiata
) from a Marine Fish Farm
Authors: Furushita Manabu , Okamoto Akira , Maeda Toshimichi , Ohta Michio , Shiba Tsuneo 
Published: September 2005

ABSTRACT

Six strains of multidrug-resistant
Stenotrophomonas maltophilia
were isolated from cultured yellowtail. The strains were divided into two clusters based on the 16S rRNA genes, and all of them contained L1 metallo-β-lactamase and L2 β-lactamase genes. Differences in the intercluster divergence between the lactamase genes suggest that horizontal transfer of the genes occurred.
Surface Attachment of
Listeria monocytogenes
Is Induced by Sublethal Concentrations of Alcohol at Low Temperatures
Authors: Gravesen Anne , Lekkas Charidimos , Knøchel Susanne 
Published: September 2005

ABSTRACT

Sublethal concentrations of ethanol or isopropanol increased attachment of
Listeria monocytogenes
at 10, 20, or 30°C; no induction occurred at 37°C. The alcohol induction phenotype was retained in
sigB
and
cesRK
mutants; however, the degree of induction was affected. These results suggest that alcohol may contribute to the persistence of
L. monocytogenes
.
Biosynthesis of Natural Flavanones in
Saccharomyces cerevisiae
Authors: Yan Yajun , Kohli Abhijeet , Koffas Mattheos A. G. 
Published: September 2005

ABSTRACT

A four-step flavanone biosynthetic pathway was constructed and introduced into
Saccharomyces cerevisiae
. The recombinant yeast strain was fed with phenylpropanoid acids and produced the flavanones naringenin and pinocembrin 62 and 22 times more efficiently compared to previously reported recombinant prokaryotic strains. Microbial biosynthesis of the flavanone eriodictyol was also achieved.
Comparative Inactivation of Adenovirus Serotypes by UV Light Disinfection
Authors: Nwachuku Nena , Gerba Charles P. , Oswald Amy , Mashadi Faezeh D. 
Published: September 2005

ABSTRACT
The results of this study confirm that adenoviruses are the most resistant enteric viruses to inactivation by UV light and that adenovirus 40 appears to be the most resistant. The effect of freeze-thawing and storage in water may affect the sensitivity of some adenoviruses to inactivation by UV light.
Nitrogenase Switch-Off by Ammonium Ions in
Azospirillum brasilense
Requires the GlnB Nitrogen Signal-Transducing Protein
Authors: Klassen Giseli , Souza Emanuel M. , Yates M. Geoffrey , Rigo Liu Un , Costa Roberta M. , Inaba Juliana , Pedrosa Fábio O. 
Published: September 2005

ABSTRACT

Nitrogenase activity in several diazotrophs is switched off by ammonium and reactivated after consumption. The signaling pathway to this system in
Azospirillum brasilense
is not understood. We show that ammonium-dependent switch-off through ADP-ribosylation of Fe protein was partial in a
glnB
mutant of
A. brasilense
but absent in a
glnB glnZ
double mutant. Triggering of inactivation by anaerobic conditions was not affected in either mutant. The results suggest that
glnB
is necessary for full ammonium-dependent nitrogenase switch-off in
A. brasilense
.
Extracellular Protease of
Pseudomonas fluorescens
CHA0, a Biocontrol Factor with Activity against the Root-Knot Nematode
Meloidogyne incognita
Authors: Siddiqui Imran Ali , Haas Dieter , Heeb Stephan 
Published: September 2005

ABSTRACT

In
Pseudomonas fluorescens
CHA0, mutation of the GacA-controlled
aprA
gene (encoding the major extracellular protease) or the
gacA
regulatory gene resulted in reduced biocontrol activity against the root-knot nematode
Meloidogyne incognita
during tomato and soybean infection. Culture supernatants of strain CHA0 inhibited egg hatching and induced mortality of
M. incognita
juveniles more strongly than did supernatants of
aprA
and
gacA
mutants, suggesting that AprA protease contributes to biocontrol.
Characterization of a Multicopper Oxidase Gene from
Staphylococcus aureus
Authors: Sitthisak S. , Howieson K. , Amezola C. , Jayaswal R. K. 
Published: September 2005

ABSTRACT

A multicopper oxidase gene from
Staphylococcus aureus
was cloned and overexpressed. Purified recombinant multicopper oxidase oxidized the substrate 3,3′-dimethoxybenzidine in the presence of copper. Disruption of
mco
showed copper sensitivity and H
2
O
2
resistance, suggesting roles for
mco
in copper homeostasis and oxidative stress response. Northern blot analysis showed copper-induced
mco
transcription.
Genetic Loci of Major Antigenic Protein Genes ofEdwardsiella tarda
Authors: Verjan Noel , Hirono Ikuo , Aoki Takashi 
Published: September 2005

ABSTRACTSeven antigenic proteins ofEdwardsiella tardawere identified by using a rabbit polyclonal antiserum. Four of these proteins also reacted with a Japanese flounder antiserum. The amino acid sequences had identity to lipoproteins, periplasmic proteins, and exported and secreted proteins with roles in transport of metabolites across the cell membrane, stress response, and motility. These genes and their products are useful for developing DNA or recombinant subunit vaccines to control edwardsiellosis.
Release of Ca
2+
from the Endoplasmic Reticulum Contributes to Ca
2+
Signaling in
Dictyostelium discoideum
Authors: Wilczynska Zofia , Happle Kathrin , Müller-Taubenberger Annette , Schlatterer Christina , Malchow Dieter , Fisher Paul R. 
Published: September 2005

ABSTRACT

Ca
2+
responses to two chemoattractants, folate and cyclic AMP (cAMP), were assayed in
Dictyostelium D. discoideum
mutants deficient in one or both of two abundant Ca
2+
-binding proteins of the endoplasmic reticulum (ER), calreticulin and calnexin. Mutants deficient in either or both proteins exhibited enhanced cytosolic Ca
2+
responses to both attractants. Not only were the mutant responses greater in amplitude, but they also exhibited earlier onsets, faster rise rates, earlier peaks, and faster fall rates. Correlations among these kinetic parameters and the response amplitudes suggested that key events in the Ca
2+
response are autoregulated by the magnitude of the response itself, i.e., by cytosolic Ca
2+
levels. This autoregulation was sufficient to explain the altered kinetics of the mutant responses: larger responses are faster in both mutant and wild-type cells in response to both folate (vegetative cells) and cAMP (differentiated cells). Searches of the predicted
D. discoideum
proteome revealed three putative Ca
2+
pumps and four putative Ca
2+
channels. All but one contained sequence motifs for Ca
2+
- or calmodulin-binding sites, consistent with Ca
2+
signals being autoregulatory. Although cytosolic Ca
2+
responses in the calnexin and calreticulin mutants are enhanced, the influx of Ca
2+
from the extracellular medium into the mutant cells was smaller. Compared to wild-type cells, Ca
2+
release from the ER in the mutants thus contributes more to the total cytosolic Ca
2+
response while influx from the extracellular medium contributes less. These results provide the first molecular genetic evidence that release of Ca
2+
from the ER contributes to cytosolic Ca
2+
responses in
D. discoideum
.
Characterization of Farnesylated Protein Tyrosine Phosphatase TcPRL-1 from
Trypanosoma cruzi
Authors: Cuevas Ileana C. , Rohloff Peter , Sánchez Daniel O. , Docampo Roberto 
Published: September 2005

ABSTRACT

Protein tyrosine kinases and phosphatases play important roles in the regulation of cell growth, development, and differentiation. We report here the identification in
Trypanosoma cruzi
of a gene (
TcPRL-1
) encoding a protein tyrosine phosphatase. The predicted protein (TcPRL-1) shares ca. 35% identity with the mammalian protein tyrosine phosphatase known as phosphatase of regenerating liver 1 (PRL-1). Four copies of this protein tyrosine phosphatase are present in the
T. cruzi
genome, and Northern blot assays showed a transcript of ∼750 bases. TcPRL-1 was detected by Western blot analysis only in amastigote extracts as a 21-kDa protein. TcPRL-1 was expressed in
Escherichia coli
, and its phosphatase activity was determined by using
p
-nitrophenylphosphate and a phosphorylated protein as substrates. In contrast to other PRLs, TcPRL-1 activity was not affected by pentamidine, and it was inhibited by very low concentrations of
o
-vanadate. TcPRL-1 has a C-terminal CAAX motif (CAVM) and is farnesylated in vitro by
T. cruzi
epimastigote extracts and in vivo according to the transfection results. After transfection of
T. cruzi
with a vector that expresses TcPRL-1 as a C-terminal fusion to green fluorescent protein, GFP-TcPRL-1 was detected in the endocytic pathway of epimastigotes, amastigotes, and trypomastigotes by colocalization with cruzipain and concanavalin A. Interestingly, a mutant form without the CAAX motif localized to the cytoplasm, in contrast to its mammalian counterparts that localize to the nucleus. The results of these studies on TcPRL-1 reveal that, even though the animal and parasite PRLs share similar kinetic properties, their susceptibilities to inhibitors, as well as their localization, are distinct, implying that they may be involved in different cellular processes.
Genome-Wide Transcription Profiling of the Early Phase of Biofilm Formation by
Candida albicans
Authors: Murillo Luis A. , Newport George , Lan Chung-Yu , Habelitz Stefan , Dungan Jan , Agabian Nina M. 
Published: September 2005

ABSTRACT

The ability to adhere to surfaces and develop as a multicellular community is an adaptation used by most microorganisms to survive in changing environments. Biofilm formation proceeds through distinct developmental phases and impacts not only medicine but also industry and evolution. In organisms such as the opportunistic pathogen
Candida albicans
, the ability to grow as biofilms is also an important mechanism for persistence, facilitating its growth on different tissues and a broad range of abiotic surfaces used in medical devices. The early stage of
C. albicans
biofilm is characterized by the adhesion of single cells to the substratum, followed by the formation of an intricate network of hyphae and the beginning of a dense structure. Changes in the transcriptome begin within 30 min of contact with the substrate and include expression of genes related to sulfur metabolism, in particular
MET3
, and the equivalent gene homologues of the Ribi regulon in
Saccharomyces cerevisiae
. Some of these changes are initiated early and maintained throughout the process; others are restricted to the earliest stages of biofilm formation. We identify here a potential alternative pathway for cysteine metabolism and the biofilm-associated expression of genes involved in glutathione production in
C. albicans
.
Characterization of a Molecular Chaperone Present in the Eukaryotic Flagellum
Authors: Shapiro Jessica , Ingram Jessica , Johnson Karl A. 
Published: September 2005

ABSTRACT

Chlamydomonas
flagella contain a molecular chaperone now identified as HSP70A, a major cytoplasmic isoform. HSP70A synthesis is upregulated by deflagellation, and its distribution in the flagellum overlaps with the IFT kinesin-II motor FLA10. HSP70A may chaperone flagellar proteins during transport, participating in the assembly and maintenance of the flagellum.
Genetic Analysis of the TOR Pathway in
Aspergillus nidulans
Authors: Fitzgibbon Gregory J. , Morozov Igor Y. , Jones Meriel G. , Caddick Mark X. 
Published: September 2005

ABSTRACT

We identified five genes encoding components of the TOR signaling pathway within
Aspergillus nidulans
. Unlike the situation in
Saccharomyces cerevisiae
, there is only a single Tor kinase, as in plant and animal systems, and mutant phenotypes suggest that the TOR pathway plays only a minor role in regulating nitrogen metabolism.
Incomplete quality of life data in lung transplant research: comparing cross sectional, repeated measures ANOVA, and multi-level analysis
Authors: Vermeulen Karin M , Post Wendy J , Span Mark M , van der Bij Wim , Koëter Gerard H , TenVergert Elisabeth M 
Published: September 2005

AbstractBackgroundIn longitudinal studies on Health Related Quality of Life (HRQL) it frequently occurs that patients have one or more missing forms, which may cause bias, and reduce the sample size. Aims of the present study were to address the problem of missing data in the field of lung transplantation (LgTX) and HRQL, to compare results obtained with different methods of analysis, and to show the value of each type of statistical method used to summarize data.MethodsResults from cross-sectional analysis, repeated measures on complete cases (ANOVA), and a multi-level analysis were compared. The scores on the dimension 'energy' of the Nottingham Health Profile (NHP) after transplantation were used to illustrate the differences between methods.ResultsCompared to repeated measures ANOVA, the cross-sectional and multi-level analysis included more patients, and allowed for a longer period of follow-up. In contrast to the cross sectional analyses, in the complete case analysis, and the multi-level analysis, the correlation between different time points was taken into account. Patterns over time of the three methods were comparable. In general, results from repeated measures ANOVA showed the most favorable energy scores, and results from the multi-level analysis the least favorable. Due to the separate subgroups per time point in the cross-sectional analysis, and the relatively small number of patients in the repeated measures ANOVA, inclusion of predictors was only possible in the multi-level analysis.ConclusionResults obtained with the various methods of analysis differed, indicating some reduction of bias took place. Multi-level analysis is a useful approach to study changes over time in a data set where missing data, to reduce bias, make efficient use of available data, and to include predictors, in studies concerning the effects of LgTX on HRQL.
GASH: An improved algorithm for maximizing the number of equivalent residues between two protein structures
Authors: Standley Daron M , Toh Hiroyuki , Nakamura Haruki 
Published: September 2005

Abstract
Background
We introduce GASH, a new, publicly accessible program for structural alignment and superposition. Alignments are scored by the Number of Equivalent Residues (NER), a quantitative measure of structural similarity that can be applied to any structural alignment method. Multiple alignments are optimized by conjugate gradient maximization of the NER score within the genetic algorithm framework. Initial alignments are generated by the program Local ASH, and can be supplemented by alignments from any other program.

Results
We compare GASH to DaliLite, CE, and to our earlier program Global ASH on a difficult test set consisting of 3,102 structure pairs, as well as a smaller set derived from the Fischer-Eisenberg set. The extent of alignment crossover, as well as the completeness of the initial set of alignments are examined. The quality of the superpositions is evaluated both by NER and by the number of aligned residues under three different RMSD cutoffs (2,4, and 6Å). In addition to the numerical assessment, the alignments for several biologically related structural pairs are discussed in detail.

Conclusion
Regardless of which criteria is used to judge the superposition accuracy, GASH achieves the best overall performance, followed by DaliLite, Global ASH, and CE. In terms of CPU usage, DaliLite CE and GASH perform similarly for query proteins under 500 residues, but for larger proteins DaliLite is faster than GASH or CE. Both an http interface and a simple object application protocol (SOAP) interface to the GASH program are available at http://www.pdbj.org/GASH/.