bluuebunny/crossref_metadata_2025_split huggingface dataset:
Occurrence and Genetic Diversity of Uncultured
Legionella
spp. in Drinking Water Treated at Temperatures below 15°C
Authors: Wullings Bart A. , van der Kooij Dick 
Published: January 2006

ABSTRACT

Representatives of the genus
Legionella
were detected by use of a real-time PCR method in all water samples collected directly after treatment from 16 surface water (SW) supplies prior to postdisinfection and from 81 groundwater (GW) supplies.
Legionella
concentrations ranged from 1.1 × 10
3
to 7.8 × 10
5
cells liter
−1
and were significantly higher in SW treated with multiple barriers at 4°C than in GW treated at 9 to 12°C with aeration and filtration but without chemical disinfection. No Legionellae (<50 CFU liter
−1
) were detected in treated water by the culture method.
Legionella
was also observed in untreated SW and in untreated aerobic and anaerobic GW. Filtration processes in SW and GW treatment had little effect or increased the
Legionella
concentration, but ozonation in SW treatment caused about 1-log-unit reduction. A phylogenetic analysis of 16S rRNA gene sequences of 202 clones, obtained from a selection of samples, showed a high similarity (>91%) with
Legionella
sequences in the GenBank database. A total of 40 (33%) of the 16S rRNA gene sequences obtained from treated water were identified as described
Legionella
species and types, including
L. bozemanii
,
L. worsleiensis
,
Legionella
-like amoebal pathogen types,
L. quateirensis
,
L. waltersii
, and
L. pneumophila
. 16S rRNA gene sequences with a similarity of below 97% from described species were positioned all over the phylogenetic tree of
Legionella
. Hence, a large diversity of yet-uncultured Legionellae are common members of the microbial communities in SW and GW treated at water temperatures of below 15°C.
Deoxysugar Transfer during Chromomycin A
3
Biosynthesis in
Streptomyces griseus
subsp.
griseus
: New Derivatives with Antitumor Activity
Authors: Menéndez Nuria , Nur-e-Alam Mohammad , Fischer Carsten , Braña Alfredo F. , Salas José A. , Rohr Jürgen , Méndez Carmen 
Published: January 2006

ABSTRACT

Chromomycin A
3
is an antitumor drug produced by
Streptomyces griseus
subsp.
griseus
. It consists of a tricyclic aglycone with two aliphatic side chains and two O-glycosidically linked saccharide chains, a disaccharide of 4-
O
-acetyl-
d
-oliose (sugar A) and 4-
O
-methyl-
d
-oliose (sugar B), and a trisaccharide of
d
-olivose (sugar C),
d
-olivose (sugar D), and 4-
O
-acetyl-
l
-chromose B (sugar E). The chromomycin gene cluster contains four glycosyltransferase genes (
cmmGI
,
cmmGII
,
cmmGIII
, and
cmmGIV
), which were independently inactivated through gene replacement, generating mutants C60GI, C10GII, C10GIII, and C10GIV. Mutants C10GIV and C10GIII produced the known compounds premithramycinone and premithramycin A1, respectively, indicating the involvement of CmmGIV and CmmGIII in the sequential transfer of sugars C and D and possibly also of sugar E of the trisaccharide chain, to the 12a position of the tetracyclic intermediate premithramycinone. Mutant C10GII produced two new tetracyclic compounds lacking the disaccharide chain at the 8 position, named prechromomycin A3 and prechromomycin A2. All three compounds accumulated by mutant C60GI were tricyclic and lacked sugar B of the disaccharide chain, and they were named prechromomycin A4, 4A-
O
-deacetyl-3A-
O
-acetyl-prechromomycin A4, and 3A-
O
-acetyl-prechromomycin A4. CmmGII and CmmGI are therefore responsible for the formation of the disaccharide chain by incorporating, in a sequential manner, two
d
-oliosyl residues to the 8 position of the biosynthetic intermediate prechromomycin A3. A biosynthetic pathway is proposed for the glycosylation events in chromomycin A
3
biosynthesis.
Effect of Inhibition of Acetoclastic Methanogenesis on Growth of Archaeal Populations in an Anoxic Model Environment
Authors: Penning Holger , Conrad Ralf 
Published: January 2006

ABSTRACT

Methyl fluoride is frequently used to specifically inhibit acetoclastic methanogenesis, thus allowing determination of the relative contribution of acetate versus H
2
/CO
2
to total CH
4
production in natural environments. However, the effect of the inhibitor on growth of the target archaeal population has not yet been studied. Therefore, we incubated rice roots as an environmental model system under anoxic conditions in the presence and absence of CH
3
F, measured the activity and Gibbs free energy (Δ
G
) of CH
4
production, and determined the abundance of individual archaeal populations by using a combination of quantitative (real-time) PCR and analysis of terminal restriction fragment length polymorphism targeting the 16S rRNA gene. It was shown that CH
3
F specifically inhibited not only acetoclastic methanogenic activity but also the proliferation of
Methanosarcina
spp, which were the prevalent acetoclastic methanogens in our environmental model system. Therefore, inhibition experiments with CH
3
F seem to be a suitable method for quantifying acetoclastic CH
4
production. It is furthermore shown that the growth and final population size of methanogens were consistent with energetic conditions that at least covered the maintenance requirements of the population.
Genetic Variability and Distribution of Mating Type Alleles in Field Populations of
Leptosphaeria maculans
from France
Authors: Gout Lilian , Eckert Maria , Rouxel Thierry , Balesdent Marie-Hélène 
Published: January 2006

ABSTRACT

Leptosphaeria maculans
is the most ubiquitous fungal pathogen of
Brassica
crops and causes the devastating stem canker disease of oilseed rape worldwide. We used minisatellite markers to determine the genetic structure of
L. maculans
in four field populations from France. Isolates were collected at three different spatial scales (leaf, 2-m
2
field plot, and field) enabling the evaluation of spatial distribution of the mating type alleles and of genetic variability within and among field populations. Within each field population, no gametic disequilibrium between the minisatellite loci was detected and the mating type alleles were present at equal frequencies. Both sexual and asexual reproduction occur in the field, but the genetic structure of these populations is consistent with annual cycles of randomly mating sexual reproduction. All
L. maculans
field populations had a high level of gene diversity (
H
= 0.68 to 0.75) and genotypic diversity. Within each field population, the number of genotypes often was very close to the number of isolates. Analysis of molecular variance indicated that >99.5% of the total genetic variability was distributed at a small spatial scale, i.e., within 2-m
2
field plots. Population differentiation among the four field populations was low (

G
ST

< 0.02), suggesting a high degree of gene exchange between these populations. The high gene flow evidenced here in French populations of
L. maculans
suggests a rapid countrywide diffusion of novel virulence alleles whenever novel resistance sources are used.
New Insights into the Lifestyle of the Cold-Loving SM1 Euryarchaeon: Natural Growth as a Monospecies Biofilm in the Subsurface
Authors: Henneberger Ruth , Moissl Christine , Amann Thomas , Rudolph Christian , Huber Robert 
Published: January 2006

ABSTRACT
In the surface waters of sulfidic springs near Regensburg, Bavaria, Germany, the SM1 euryarchaeon, together with filamentous bacteria, forms the recently described unique string-of-pearls community. In addition to naturally occurring string-of-pearls communities, the growth of these communities was also observed on polyethylene nets provided as an artificial attachment material in the streamlets of springs. In order to learn more about the distribution and origin of the SM1 euryarchaeon and its possible occurrence in the subsurface, polyethylene nets were incubated as deeply as possible in different spring holes. After a short residence time, slime-like, milky drops, almost completely composed of SM1 euryarchaeon, were attached to the nets, indicating that this organism grows independent of a partner in deeper earth layers. A newly designed in situ biofilm trapping system allowed the quantitative harvesting of organisms exhibiting this newly discovered lifestyle of the SM1 euryarchaeon for detailed biological studies. The discovery of naturally occurring archaeal biofilms extends our knowledge of the biology and ecological significance of archaea in their environments.
Development and Validation of a Real-Time PCR Method To Quantify Rumen Protozoa and Examination of Variability between
Entodinium
Populations in Sheep Offered a Hay-Based Diet
Authors: Skillman Lucy C. , Toovey Andrew F. , Williams Andrew J. , Wright André-Denis G. 
Published: January 2006

ABSTRACT

PCR and real-time PCR primers for the 18S rRNA gene of rumen protozoa (
Entodinium
and
Dasytricha
spp.) were designed, and their specificities were tested against a range of rumen microbes and protozoal groups. External standards were prepared from DNA extracts of a rumen matrix containing known numbers and species of protozoa. The efficiency of PCR (ε) was calculated following amplification of serial dilutions of each standard and was used to calculate the numbers of protozoa in each sample collected; serial dilutions of DNA were used similarly to calculate PCR efficiency. Species of
Entodinium
, the most prevalent of the rumen protozoa, were enumerated in rumen samples collected from 100 1-year-old merino wethers by microscopy and real-time PCR. Both the counts developed by the real-time PCR method and microscopic counts were accurate and repeatable, with a strong correlation between them (
R
2
= 0.8), particularly when the PCR efficiency was close to optimal (i.e., two copies per cycle). The advantages and disadvantages of each procedure are discussed.
Entodinium
represented on average 98% of the total protozoa, and populations within the same sheep were relatively stable, but greater variation occurred between different sheep (10
0
and 10
6
entodinia per gram of rumen contents). With this inherent variability, it was estimated that, to detect a statistically significant (
P
= 0.05) 20% change in
Entodinium
populations, 52 sheep per treatment group would be required.
Evaluation of Affymetrix Severe Acute Respiratory Syndrome Resequencing GeneChips in Characterization of the Genomes of Two Strains of Coronavirus Infecting Humans
Authors: Sulaiman Irshad M. , Liu Xin , Frace Michael , Sulaiman Nikhat , Olsen-Rasmussen Melissa , Neuhaus Elizabeth , Rota Paul A. , Wohlhueter Robert M. 
Published: January 2006

ABSTRACT
Severe acute respiratory syndrome (SARS) was discovered during a recent global outbreak of atypical pneumonia. A number of immunologic and molecular studies of the clinical samples led to the conclusion that a novel coronavirus (SARS-CoV) was associated with the outbreak. Later, a SARS resequencing GeneChip was developed by Affymetrix to characterize the complete genome of SARS-CoV on a single GeneChip. The present study was carried out to evaluate the performance of SARS resequencing GeneChips. Two human SARS-CoV strains (CDC#200301157 and Urbani) were resequenced by the SARS GeneChips. Five overlapping PCR amplicons were generated for each strain and hybridized with these GeneChips. The successfully hybridized GeneChips generated nucleotide sequences of nearly complete genomes for the two SARS-CoV strains with an average call rate of 94.6%. Multiple alignments of nucleotide sequences obtained from SARS GeneChips and conventional sequencing revealed full concordance. Furthermore, the GeneChip-based analysis revealed no additional polymorphic sites. The results of this study suggest that GeneChip-based genome characterization is fast and reproducible. Thus, SARS resequencing GeneChips may be employed as an alternate tool to obtain genome sequences of SARS-CoV strains pathogenic for humans in order to further understand the transmission dynamics of these viruses.
Selective Phylogenetic Analysis Targeted at 16S rRNA Genes of Thermophiles and Hyperthermophiles in Deep-Subsurface Geothermal Environments
Authors: Kimura Hiroyuki , Sugihara Maki , Kato Kenji , Hanada Satoshi 
Published: January 2006

ABSTRACT
Deep-subsurface samples obtained by deep drilling are likely to be contaminated with mesophilic microorganisms in the drilling fluid, and this could affect determination of the community structure of the geothermal microflora using 16S rRNA gene clone library analysis. To eliminate possible contamination by PCR-amplified 16S rRNA genes from mesophiles, a combined thermal denaturation and enzyme digestion method, based on a strong correlation between the G+C content of the 16S rRNA gene and the optimum growth temperatures of most known prokaryotic cultures, was used prior to clone library construction. To validate this technique, hot spring fluid (76°C) and river water (14°C) were used to mimic a deep-subsurface sample contaminated with drilling fluid. After DNA extraction and PCR amplification of the 16S rRNA genes from individual samples separately, the amplified products from river water were observed to be denatured at 82°C and completely digested by exonuclease I (Exo I), while the amplified products from hot spring fluid remained intact after denaturation at 84°C and enzyme digestion with Exo I. DNAs extracted from the two samples were mixed and used as a template for amplification of the 16S rRNA genes. The amplified rRNA genes were denatured at 84°C and digested with Exo I before clone library construction. The results indicated that the 16S rRNA gene sequences from the river water were almost completely eliminated, whereas those from the hot spring fluid remained.
Structure and Function of Bacterial Communities Emerging from Different Sources under Identical Conditions
Authors: Langenheder Silke , Lindström Eva S. , Tranvik Lars J. 
Published: January 2006

ABSTRACT
The aim of this study was to compare two major hypotheses concerning the formation of bacterial community composition (BCC) at the local scale, i.e., whether BCC is determined by the prevailing local environmental conditions or by “metacommunity processes.” A batch culture experiment where bacteria from eight distinctly different aquatic habitats were regrown under identical conditions was performed to test to what extent similar communities develop under similar selective pressure. Differently composed communities emerged from different inoculum communities, as determined by terminal restriction fragment length polymorphism analysis of the 16S rRNA gene. There was no indication that similarity increased between communities upon growth under identical conditions compared to that for growth at the ambient sampling sites. This suggests that the history and distribution of taxa within the source communities were stronger regulating factors of BCC than the environmental conditions. Moreover, differently composed communities were different with regard to specific functions, such as enzyme activities, but maintained similar broad-scale functions, such as biomass production and respiration.
Effect of Simultaneous Inoculation with Yeast and Bacteria on Fermentation Kinetics and Key Wine Parameters of Cool-Climate Chardonnay
Authors: Jussier Delphine , Dubé Morneau Amélie , Mira de Orduña Ramón 
Published: January 2006

ABSTRACTInoculating grape musts with wine yeast and lactic acid bacteria (LAB) concurrently in order to induce simultaneous alcoholic fermentation (AF) and malolactic fermentation (MLF) can be an efficient alternative to overcome potential inhibition of LAB in wines because of high ethanol concentrations and reduced nutrient content. In this study, the simultaneous inoculation of yeast and LAB into must was compared with a traditional vinification protocol, where MLF was induced after completion of AF. For this, two suitable commercial yeast-bacterium combinations were tested in cool-climate Chardonnay must. The time courses of glucose and fructose, acetaldehyde, several organic acids, and nitrogenous compounds were measured along with the final values of other key wine parameters. Sensory evaluation was done after 12 months of storage. The current study could not confirm a negative impact of simultaneous AF/MLF on fermentation success and kinetics or on final wine parameters. While acetic acid concentrations were slightly increased in wines after simultaneous AF/MLF, the differences were of neither practical nor legal significance. No statistically significant differences were found with regard to the final values of pH or total acidity and the concentrations of ethanol, acetaldehyde, glycerol, citric and lactic acids, and the nitrogen compounds arginine, ammonia, urea, citrulline, and ornithine. Sensory evaluation by a semiexpert panel confirmed the similarity of the wines. However, simultaneous inoculation led to considerable reductions in overall fermentation durations. Furthermore, differences of physiological and microbiological relevance were found. Specifically, we report the vinification of “super-dry” wines devoid of glucose and fructose after simultaneous inoculation of yeast and bacteria.
Fourier Transform Infrared and Raman Spectroscopy for Characterization of
Listeria monocytogenes
Strains
Authors: Oust Astrid , Møretrø Trond , Naterstad Kristine , Sockalingum Ganesh D. , Adt Isabelle , Manfait Michel , Kohler Achim 
Published: January 2006

ABSTRACT

The purpose of this study was to characterize the variation in biochemical composition of 89 strains of
Listeria monocytogenes
with different susceptibilities towards sakacin P, using Fourier transform infrared (FTIR) spectroscopy and Raman spectroscopy. The strains were also analyzed using amplified fragment length polymorphism (AFLP) analysis. Based on their susceptibilities to sakacin P, the 89 strains have previously been divided into two groups. Using the FTIR spectra and AFLP data, the strains were basically differentiated into the same two groups. Analyses of the FTIR and Raman spectra revealed that the strains in the two groups contained differences in the compositions of carbohydrates and fatty acids. The relevance of the variation in the composition of carbohydrates with respect to the variation in the susceptibility towards sakacin P for the
L. monocytogenes
strains is discussed.
Effects of
Lactococcus lactis
on Composition of Intestinal Microbiota: Role of Nisin
Authors: Bernbom Nete , Licht Tine Rask , Brogren Carl-Henrik , Jelle Birthe , Johansen Anette H. , Badiola Iker , Vogensen Finn K. , Nørrung Birgit 
Published: January 2006

ABSTRACT

This study examined the ability of (i) pure nisin, (ii) nisin-producing
Lactococcus lactis
strain CHCC5826, and (iii) the non-nisin-producing
L. lactis
strain CHCH2862 to affect the composition of the intestinal microbiota of human flora-associated rats. The presence of both the nisin-producing and the non-nisin-producing
L. lactis
strains significantly increased the number of
Bifidobacterium
cells in fecal samples during the first 8 days but decreased the number of enterococci/streptococci in duodenum, ileum, cecum, and colon samples as detected by selective cultivation. No significant changes in the rat fecal microbiota were observed after dosage with nisin. Pearson cluster analysis of denaturing gradient gel electrophoresis profiles of the 16S rRNA genes present in the fecal microbial population revealed that the microbiota of animals dosed with either of the two
L. lactis
strains were different from that of control animals dosed with saline. However, profiles of the microbiota from animals dosed with nisin did not differ from the controls. The concentrations of nisin estimated by competitive enzyme-linked immunosorbent assay (ELISA) were approximately 10-fold higher in the small intestine and 200-fold higher in feces than the corresponding concentrations estimated by a biological assay. This indicates that nisin was degraded or inactivated in the gastrointestinal tract, since fragments of this bacteriocin are detected by ELISA while an intact molecule is needed to retain biological activity.
A Lithium-Sensitive and Sodium-Tolerant 3′-Phosphoadenosine-5′-Phosphatase Encoded by
halA
from the Cyanobacterium
Arthrospira platensis
Is Closely Related to Its Counterparts from Yeasts and Plants
Authors: Zhang Ju-Yuan , Zou Jie , Bao Qiyu , Chen Wen-Li , Wang Li , Yang Huanming , Zhang Cheng-Cai 
Published: January 2006

ABSTRACT

3′-Phosphoadenosine-5′-phosphatase (PAPase) is required for the removal of toxic 3′-phosphoadenosine-5′-phosphate (PAP) produced during sulfur assimilation in various eukaryotic organisms. This enzyme is a well-known target of lithium and sodium toxicity and has been used for the production of salt-resistant transgenic plants. In addition, PAPase has also been proposed as a target in the treatment of manic-depressive patients. One gene,
halA
, which could encode a protein closely related to the PAPases of yeasts and plants, was identified from the cyanobacterium
Arthrospira
(
Spirulina
)
platensis
. Phylogenic analysis indicated that proteins related to PAPases from several cyanobacteria were found in different clades, suggesting multiple origins of PAPases in cyanobacteria. The HalA polypeptide from
A. platensis
was overproduced in
Escherichia coli
and used for the characterization of its biochemical properties. HalA was dependent on Mg
2+
for its activity and could use PAP or 3′-phosphoadenosine-5′-phosphosulfate as a substrate. HalA is sensitive to Li
+
(50% inhibitory concentration [IC
50
] = 3.6 mM) but only slightly sensitive to Na
+
(IC
50
= 600 mM). The salt sensitivity of HalA was thus different from that of most of its eukaryotic counterparts, which are much more sensitive to both Li
+
and Na
+
, but was comparable to the PAPase AtAHL (Hal2p-like protein) from
Arabidopsis thaliana
. The properties of HalA could help us to understand the structure-function relationship underlying the salt sensitivity of PAPases. The expression of
halA
improved the Li
+
tolerance of
E. coli
, suggesting that the sulfur-assimilating pathway is a likely target of salt toxicity in bacteria as well.
Long Serial Analysis of Gene Expression for Gene Discovery and Transcriptome Profiling in the Widespread Marine Coccolithophore
Emiliania huxleyi
Authors: Dyhrman Sonya T. , Haley Sheean T. , Birkeland Shanda R. , Wurch Louie L. , Cipriano Michael J. , McArthur Andrew G. 
Published: January 2006

ABSTRACT

The abundant and widespread coccolithophore
Emiliania huxleyi
plays an important role in mediating CO
2
exchange between the ocean and the atmosphere through its impact on marine photosynthesis and calcification. Here, we use long serial analysis of gene expression (SAGE) to identify
E. huxleyi
genes responsive to nitrogen (N) or phosphorus (P) starvation. Long SAGE is an elegant approach for examining quantitative and comprehensive gene expression patterns without a priori knowledge of gene sequences via the detection of 21-bp nucleotide sequence tags.
E. huxleyi
appears to have a robust transcriptional-level response to macronutrient deficiency, with 42 tags uniquely present or up-regulated twofold or greater in the N-starved library and 128 tags uniquely present or up-regulated twofold or greater in the P-starved library. The expression patterns of several tags were validated with reverse transcriptase PCR. Roughly 48% of these differentially expressed tags could be mapped to publicly available genomic or expressed sequence tag (EST) sequence data. For example, in the P-starved library a number of the tags mapped to genes with a role in P scavenging, including a putative phosphate-repressible permease and a putative polyphosphate synthetase. In short, the long SAGE analyses have (i) identified many new differentially regulated gene sequences, (ii) assigned regulation data to EST sequences with no database homology and unknown function, and (iii) highlighted previously uncharacterized aspects of
E. huxleyi
N and P physiology. To this end, our long SAGE libraries provide a new public resource for gene discovery and transcriptional analysis in this biogeochemically important marine organism.