bluuebunny/crossref_metadata_2025_split huggingface dataset:
Measurement of Biologically Available Naphthalene in Gas and Aqueous Phases by Use of a
Pseudomonas putida
Biosensor
Authors: Werlen Christoph , Jaspers Marco C. M. , van der Meer Jan Roelof 
Published: January 2004

ABSTRACT

Genetically constructed microbial biosensors for measuring organic pollutants are mostly applied in aqueous samples. Unfortunately, the detection limit of most biosensors is insufficient to detect pollutants at low but environmentally relevant concentrations. However, organic pollutants with low levels of water solubility often have significant gas-water partitioning coefficients, which in principle makes it possible to measure such compounds in the gas rather than the aqueous phase. Here we describe the first use of a microbial biosensor for measuring organic pollutants directly in the gas phase. For this purpose, we reconstructed a bioluminescent
Pseudomonas putida
naphthalene biosensor strain to carry the NAH7 plasmid and a chromosomally inserted gene fusion between the
sal
promoter and the
luxAB
genes. Specific calibration studies were performed with suspended and filter-immobilized biosensor cells, in aqueous solution and in the gas phase. Gas phase measurements with filter-immobilized biosensor cells in closed flasks, with a naphthalene-contaminated aqueous phase, showed that the biosensor cells can measure naphthalene effectively. The biosensor cells on the filter responded with increasing light output proportional to the naphthalene concentration added to the water phase, even though only a small proportion of the naphthalene was present in the gas phase. In fact, the biosensor cells could concentrate a larger proportion of naphthalene through the gas phase than in the aqueous suspension, probably due to faster transport of naphthalene to the cells in the gas phase. This led to a 10-fold lower detectable aqueous naphthalene concentration (50 nM instead of 0.5 μM). Thus, the use of bacterial biosensors for measuring organic pollutants in the gas phase is a valid method for increasing the sensitivity of these valuable biological devices.
Cultivation and Growth Characteristics of a Diverse Group of Oligotrophic Marine
Gammaproteobacteria
Authors: Cho Jang-Cheon , Giovannoni Stephen J. 
Published: January 2004

ABSTRACT

Forty-four novel strains of
Gammaproteobacteria
were cultivated from coastal and pelagic regions of the Pacific Ocean using high-throughput culturing methods that rely on dilution to extinction in very low nutrient media. Phylogenetic analysis showed that the isolates fell into five rRNA clades, all of which contained rRNA gene sequences reported previously from seawater environmental gene clone libraries (SAR92, OM60, OM182, BD1-7, and KI89A). Bootstrap analyses of phylogenetic reliability did not support collapsing these five clades into a single clade, and they were therefore named the oligotrophic marine
Gammaproteobacteria
(OMG) group. Twelve cultures chosen to represent the five clades were successively purified in liquid culture, and their growth characteristics were determined at different temperatures and dissolved organic carbon concentrations. The isolates in the OMG group were physiologically diverse heterotrophs, and their physiological properties generally followed their phylogenetic relationships. None of the isolates in the OMG group formed colonies on low- or high-nutrient agar upon their first isolation from seawater, while 7 of 12 isolates that were propagated for laboratory testing eventually produced colonies on 1/10 R2A agar. The isolates grew relatively slowly in natural seawater media (1.23 to 2.63 day
−1
), and none of them grew in high-nutrient media (>351 mg of C liter
−1
). The isolates were psychro- to mesophilic and obligately oligotrophic; many of them were of ultramicrobial size (<0.1 μm
3
). This cultivation study revealed that sporadically detected
Gammaproteobacteria
gene clones from seawater are part of a phylogenetically diverse constellation of organisms mainly composed of oligotrophic and ultramicrobial lineages that are culturable under specific cultivation conditions.
Differential Expression of Pine and
Cronartium quercuum
f. sp.
fusiforme
Genes in Fusiform Rust Galls
Authors: Warren Jaimie M. , Covert Sarah F. 
Published: January 2004

ABSTRACT

Cronartium quercuum
f. sp.
fusiforme
is the causative agent of fusiform rust disease of southern pines in the United States. This disease is characterized by the formation of woody branch and stem galls. Differential display was used to identify pine genes whose expression is altered by
C. quercuum
f. sp.
fusiforme
infection and to identify
C. quercuum
f. sp.
fusiforme
genes that are expressed in fusiform rust galls. Six pine cDNAs that appeared to be differentially expressed in galled and healthy stems and 13
C. quercuum
f. sp.
fusiforme
cDNAs expressed in galled tissues were identified. A probe that hybridizes specifically to
C. quercuum
f. sp.
fusiforme
18S rRNA was used to estimate that 14% of the total RNA in fusiform rust galls was from
C. quercuum
f. sp.
fusiforme
. This finding was used to calibrate gene expression levels in galls when comparing them to expression levels in uninfected pines or in isolated
C. quercuum
f. sp.
fusiforme
cultures. According to Northern analysis and reverse transcriptase PCR analysis, all six of the pine clones were expressed at lower levels in galls than in healthy tissues. Seven of the nine
C. quercuum
f. sp.
fusiforme
clones that were assayed were expressed at higher levels in galls than in axenic culture. A number of the cDNAs encode proteins that are similar to those that play roles in plant development, plant defense, or fungal stress responses.
Phylogenetic Analysis of the Hypervariable Region of the 18S rRNA Gene ofCryptosporidiumOocysts in Feces of Canada Geese (Branta canadensis): Evidence for Five Novel Genotypes
Authors: Jellison Kristen L. , Distel Daniel L. , Hemond Harold F. , Schauer David B. 
Published: January 2004

ABSTRACTTo assess genetic diversity inCryptosporidiumoocysts from Canada geese, 161 fecal samples from Canada geese in the United States were analyzed. Eleven (6.8%) were positive forCryptosporidiumspp. following nested PCR amplification of the hypervariable region of the 18S rRNA gene. Nine PCR products from geese were cloned and sequenced, and all nine diverged from previously reportedCryptosporidium18S rRNA gene sequences. Five sequences were very similar or identical to each other but genetically distinct from that ofCryptosporidium baileyi; two were most closely related to, but genetically distinct from, the first five; and two were distinct from any other sequence analyzed. One additional sequence in the hypervariable region of the 18S rRNA gene isolated from a cormorant was identical to that ofC. baileyi. Phylogenetic analysis provided evidence for new genotypes ofCryptosporidiumspecies in Canada geese. Results of this study suggest that the taxonomy ofCryptosporidiumspecies in geese is complex and that a more complete understanding of genetic diversity among these parasites will facilitate our understanding of oocyst sources and species in the environment.
Characterization of Secretory Genes
ypt1
/
yptA
and
nsf1
/
nsfA
from Two Filamentous Fungi: Induction of Secretory Pathway Genes of
Trichoderma reesei
under Secretion Stress Conditions
Authors: Saloheimo Markku , Wang Huaming , Valkonen Mari , Vasara Tuija , Huuskonen Anne , Riikonen Marjukka , Pakula Tiina , Ward Michael , Penttilä Merja 
Published: January 2004

ABSTRACT

Two genes involved in protein secretion, encoding the Rab protein YPT1/YPTA and the general fusion factor NSFI/NSFA, were characterized from two filamentous fungi,
Trichoderma reesei
and
Aspergillus niger
var.
awamori
. The isolated genes showed a high level of conservation with their
Saccharomyces cerevisiae
and mammalian counterparts, and
T. reesei ypt1
was shown to complement yeast Ypt1p depletion. The transcriptional regulation of the
T. reesei ypt1
,
nsf1
, and
sar1
genes, involved in protein trafficking, was studied with mycelia treated with the folding inhibitor dithiothreitol (DTT) and with brefeldin A, which inhibits membrane traffic between the endoplasmic reticulum and Golgi complex. The well-known inducer of the yeast and
T. reesei
unfolded protein response (UPR), DTT, induced the
nsf1
gene and the protein disulfide isomerase gene,
pdi1
, in both of the experiments, and
sar1
mRNA increased in only one experiment under strong UPR induction. The
ypt1
mRNA did not show a clear increase during DTT treatment. Brefeldin A strongly induced
pdi1
and all of the intracellular trafficking genes studied. These results suggest the possibility that the whole secretory pathway of
T. reesei
could be induced at the transcriptional level by stress responses caused by protein accumulation in the secretory pathway.
Bacterial Diversity in Agricultural Soils during Litter Decomposition
Authors: Dilly Oliver , Bloem Jaap , Vos An , Munch Jean Charles 
Published: January 2004

ABSTRACT
Denaturing gradient gel electrophoresis (DGGE) of amplified fragments of genes coding for 16S rRNA was used to study the development of bacterial communities during decomposition of crop residues in agricultural soils. Ten strains were tested, and eight of these strains produced a single band. Furthermore, a mixture of strains yielded distinguishable bands. Thus, DGGE DNA band patterns were used to estimate bacterial diversity. A field experiment performed with litter in nylon bags was used to evaluate the bacterial diversity during the decomposition of readily degradable rye and more refractory wheat material in comparable luvisols and cambisols in northern, central, and southern Germany. The amount of bacterial DNA in the fresh litter was small. The DNA content increased rapidly after the litter was added to the soil, particularly in the rapidly decomposing rye material. Concurrently, diversity indices, such as the Shannon-Weaver index, evenness, and equitability, which were calculated from the number and relative abundance (intensity) of the bacterial DNA bands amplified from genes coding for 16S rRNA, increased during the course of decomposition. This general trend was not significant for evenness and equitability at any time. The indices were higher for the more degradation-resistant wheat straw than for the more easily decomposed rye grass. Thus, the DNA band patterns indicated that there was increasing bacterial diversity as decomposition proceeded and substrate quality decreased. The bacterial diversity differed for the sites in northern, central, and southern Germany, where the same litter material was buried in the soil. This shows that in addition to litter type climate, vegetation, and indigenous microbes in the surrounding soil affected the development of the bacterial communities in the litter.
Species Differentiation of a Diverse Suite of
Bacillus
Spores by Mass Spectrometry-Based Protein Profiling
Authors: Dickinson Danielle N. , La Duc Myron T. , Haskins William E. , Gornushkin Igor , Winefordner James D. , Powell David H. , Venkateswaran Kasthuri 
Published: January 2004

ABSTRACT

In this study, we demonstrate the versatility of matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOFMS) protein profiling for the species differentiation of a diverse suite of
Bacillus
spores. MALDI-TOFMS protein profiles of 11 different strains of
Bacillus
spores, encompassing nine different species, were evaluated.
Bacillus
species selected for MALDI-TOFMS analysis represented the spore-forming bacterial diversity of typical class 100K clean room spacecraft assembly facilities. A one-step sample treatment and MALDI-TOFMS preparation were used to minimize the sample preparation time. A library of MALDI-TOFMS spectra was created from these nine
Bacillus
species, the most diverse protein profiling study of the genus reported to date. Linear correlation analysis was used to successfully differentiate the MALDI-TOFMS protein profiles from all strains evaluated in this study. The MALDI-TOFMS protein profiles were compared with 16S rDNA sequences for their bacterial systematics and molecular phylogenetic affiliations. The MALDI-TOFMS profiles were found to be complementary to the 16S rDNA analysis. Proteomic studies of
Bacillus subtilis
168 were pursued to identify proteins represented by the biomarker peaks in the MALDI-TOFMS spectrum. Four small, acid-soluble proteins (A, B, C, and D), one DNA binding protein, hypothetical protein ymf J, and four proteins associated with the spore coat and spore coat formation (coat JB, coat F, coat T, and spoIVA) were identified. The ability to visualize higher-molecular-mass coat proteins (10 to 25 kDa) as well as smaller proteins (<10 kDa) with MALDI-TOFMS profiling is critical for the complete and effective species differentiation of the
Bacillus
genus.
Molecular and Metabolic Characterization of Cold-Tolerant Alpine Soil
Pseudomonas
Sensu Stricto
Authors: Meyer A. F. , Lipson D. A. , Martin A. P. , Schadt C. W. , Schmidt S. K. 
Published: January 2004

ABSTRACT

Alpine soils undergo dramatic temporal changes in their microclimatic properties, suggesting that the bacteria there encounter uncommon shifting selection gradients. Pseudomonads constitute important members of the alpine soil community. In order to characterize the alpine
Pseudomonas
community and to assess the impact of shifting selection on this community, we examined the ability of cold-tolerant
Pseudomonas
isolates to grow on a variety of carbon sources, and we determined their phylogenetic relationships based on 16S ribosomal DNA sequencing. We found a high prevalence of
Pseudomonas
in our soil samples, and isolates from these soils exhibited extensive metabolic diversity. In addition, our data revealed that many of our isolates form a unique cold-adapted clade, representatives of which are also found in the Swedish tundra and Antarctica. Our data also show a lack of concordance between the metabolic properties and 16S phylogeny, indicating that the metabolic diversity of these organisms cannot be predicted by phylogeny.
Nutrient Shock and Incubation Atmosphere Influence Recovery of Culturable
Helicobacter pylori
from Water
Authors: Azevedo N. F. , Pacheco A. P. , Keevil C. W. , Vieira M. J. 
Published: January 2004

ABSTRACT

Three different media—Columbia agar, Wilkins-Chalgren agar, and
Helicobacter pylori
special peptone agar—were prepared in a diluted version and compared to the standard medium formulation in order to study a possible nutrient shock effect observed when recovering
H. pylori
from water by counting the number of CFU. This same parameter was subsequently used to evaluate the influence of the incubation atmosphere by using a modular atmosphere-controlled system to provide different atmospheres and by employing an established gas generation kit as a control. Both a low nutrient content of the media and a rapidly achieved microaerophilic incubation atmosphere proved to increase the numbers of environment-stressed
H. pylori
organisms recovered. An atmosphere of 5% CO
2
, 5% O
2
, and 3% H
2
is recommended, although other atmospheres with a low oxygen concentration are also acceptable. Besides highlighting and assessing the importance of several factors in the culturability of
H. pylori
, this paper demonstrates the potential ability to develop an optimized technique for recovery of this pathogen from water.
Improved Method for Polynucleotide Probe-Based Cell Sorting, Using DNA-Coated Microplates
Authors: Zwirglmaier K. , Ludwig W. , Schleifer K.-H. 
Published: January 2004

ABSTRACT
We developed an improved method for cultivation-independent sorting of bacterial cells. The technique is based on labeling the target cells by in situ hybridization with polynucleotide transcript probes. Due to the probes' length, part of the probe remains outside the cell and can subsequently be used to capture the cells. Target cells are immobilized during a second hybridization step in microplates that are coated with DNA that is complementary to the probe sequence. The method was applied successfully to artificial mixtures of cells with polynucleotide probes targeting either rRNA, a plasmid-borne beta-lactamase gene, or a chromosome-borne glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene. Cells could be separated based on phylogenetic parameters (using rRNA-targeted probes) as well as on other DNA-encoded traits.
Rapid Detection ofVibrio vulnificusin Shellfish and Gulf of Mexico Water by Real-Time PCR
Authors: Panicker Gitika , Myers Michael L. , Bej Asim K. 
Published: January 2004

ABSTRACTIn this paper we describe optimization of SYBR Green I-based real-time PCR parameters and testing of a large number of microbial species withvvh-specific oligonucleotide primers to establish a rapid, specific, and sensitive method for detection ofVibrio vulnificusin oyster tissue homogenate and Gulf of Mexico water (gulf water). Selected oligonucleotide primers for thevvhgene were tested for PCR amplification of a 205-bp DNA fragment with a melting temperature of approximately 87°C for 84 clinical and environmental strains ofV. vulnificus. No amplification was observed with other vibrios or nonvibrio strains with these primers. The minimum level of detection by the real-time PCR method was 1 pg of purified genomic DNA or 102V. vulnificuscells in 1 g of unenriched oyster tissue homogenate or 10 ml of gulf water. It was possible to improve the level of detection to oneV. vulnificuscell in samples that were enriched for 5 h. The standard curves prepared from the real-time PCR cycle threshold values revealed that there was a strong correlation between the number of cells in unenriched samples and the number of cells in enriched samples. Detection of a single cell ofV. vulnificusin 1 g of enriched oyster tissue homogenate is in compliance with the recent Interstate Shellfish Sanitation Conference guidelines. The entire detection method, including sample processing, enrichment, and real-time PCR amplification, was completed within 8 h, making it a rapid single-day assay. Rapid and sensitive detection ofV. vulnificuswould ensure a steady supply of postharvest treated oysters to consumers, which should help decrease the number of illnesses or outbreaks caused by this pathogen.
Biodegradation of Nitro-Substituted Explosives 2,4,6-Trinitrotoluene, Hexahydro-1,3,5-Trinitro-1,3,5-Triazine, and Octahydro-1,3,5,7-Tetranitro-1,3,5-Tetrazocine by a Phytosymbiotic
Methylobacterium
sp. Associated with Poplar Tissues (
Populus deltoides
×
nigra
DN34)
Authors: Van Aken Benoit , Yoon Jong Moon , Schnoor Jerald L. 
Published: January 2004

ABSTRACT

A pink-pigmented symbiotic bacterium was isolated from hybrid poplar tissues (
Populus deltoides
×
nigra
DN34). The bacterium was identified by 16S and 16S-23S intergenic spacer ribosomal DNA analysis as a
Methylobacterium
sp. (strain BJ001). The isolated bacterium was able to use methanol as the sole source of carbon and energy, which is a specific attribute of the genus
Methylobacterium
. The bacterium in pure culture was shown to degrade the toxic explosives 2,4,6-trinitrotoluene (TNT), hexahydro-1,3,5-trinitro-1,3,5-triazene (RDX), and octahydro-1,3,5,7-tetranitro-1,3,5-tetrazocine (HMX). [U-ring-
14
C]TNT (25 mg liter
−1
) was fully transformed in less than 10 days. Metabolites included the reduction derivatives amino-dinitrotoluenes and diamino-nitrotoluenes. No significant release of
14
CO
2
was recorded from [
14
C]TNT. In addition, the isolated methylotroph was shown to transform [U-
14
C]RDX (20 mg liter
−1
) and [U-
14
C]HMX (2.5 mg liter
−1
) in less than 40 days. After 55 days of incubation, 58.0% of initial [
14
C]RDX and 61.4% of initial [
14
C]HMX were mineralized into
14
CO
2
. The radioactivity remaining in solution accounted for 12.8 and 12.7% of initial [
14
C]RDX and [
14
C]HMX, respectively. Metabolites detected from RDX transformation included a mononitroso RDX derivative and a polar compound tentatively identified as methylenedinitramine. Since members of the genus
Methylobacterium
are distributed in a wide diversity of natural environments and are very often associated with plants,
Methylobacterium
sp. strain BJ001 may be involved in natural attenuation or in situ biodegradation (including phytoremediation) of explosive-contaminated sites.
In Vitro and In Vivo Inhibition of
Helicobacter pylori
by
Lactobacillus casei
Strain Shirota
Authors: Sgouras D. , Maragkoudakis P. , Petraki K. , Martinez-Gonzalez B. , Eriotou E. , Michopoulos S. , Kalantzopoulos G. , Tsakalidou E. , Mentis Α. 
Published: January 2004

ABSTRACT

We studied the potential inhibitory effect of
Lactobacillus casei
strain Shirota (from the fermented milk product Yakult [Yakult Ltd., Tokyo, Japan]) on
Helicobacter pylori
by using (i) in vitro inhibition assays with
H. pylori
SS1 (Sydney strain 1) and nine
H. pylori
clinical isolates and (ii) the in vivo
H. pylori
SS1 mouse model of infection over a period of 9 months. In vitro activity against
H. pylori
SS1 and all of the clinical isolates was observed in the presence of viable
L. casei
strain Shirota cells but not in the cell-free culture supernatant, although there was profound inhibition of urease activity. In vivo experiments were performed by oral administration of
L. casei
strain Shirota in the water supply over a period of 9 months to 6-week-old C57BL/6 mice previously infected with
H. pylori
SS1 (study group;
n
= 25). Appropriate control groups of
H. pylori
-infected but untreated animals (
n
= 25) and uninfected animals given
L. casei
strain Shirota (
n
= 25) also were included in the study.
H. pylori
colonization and development of gastritis were assessed at 1, 2, 3, 6, and 9 months postinfection. A significant reduction in the levels of
H. pylori
colonization was observed in the antrum and body mucosa in vivo in the lactobacillus-treated study group, as assessed by viable cultures, compared to the levels in the
H. pylori
-infected control group. This reduction was accompanied by a significant decline in the associated chronic and active gastric mucosal inflammation observed at each time point throughout the observation period. A trend toward a decrease in the anti-
H. pylori
immunoglobulin G response was measured in the serum of the animals treated with lactobacillus, although this decrease was not significant.