bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biocatalytic Synthesis of Vanillin
Authors: Li Tao , Rosazza John P. N. 
Published: July 2002

ABSTRACT

The conversions of vanillic acid and
O
-benzylvanillic acid to vanillin were examined by using whole cells and enzyme preparations of
Nocardia
sp. strain NRRL 5646. With growing cultures, vanillic acid was decarboxylated (69% yield) to guaiacol and reduced (11% yield) to vanillyl alcohol. In resting
Nocardia
cells in buffer, 4-
O
-benzylvanillic acid was converted to the corresponding alcohol product without decarboxylation. Purified
Nocardia
carboxylic acid reductase, an ATP and NADPH-dependent enzyme, quantitatively reduced vanillic acid to vanillin. Structures of metabolites were established by
1
H nuclear magnetic resonance and mass spectral analyses.
Selective Inhibition of the Oxidation of Ferrous Iron or Sulfur in
Thiobacillus ferrooxidans
Authors: Harahuc Lesia , Lizama Hector M. , Suzuki Isamu 
Published: July 2002

ABSTRACT

The oxidation of either ferrous iron or sulfur by
Thiobacillus ferrooxidans
was selectively inhibited or controlled by various anions, inhibitors, and osmotic pressure. Iron oxidation was more sensitive than sulfur oxidation to inhibition by chloride, phosphate, and nitrate at low concentrations (below 0.1 M) and also to inhibition by azide and cyanide. Sulfur oxidation was more sensitive than iron oxidation to the inhibitory effect of high osmotic pressure. These differences were evident not only between iron oxidation by iron-grown cells and sulfur oxidation by sulfur-grown cells but also between the iron and sulfur oxidation activities of the same iron-grown cells. Growth experiments with ferrous iron or sulfur as an oxidizable substrate confirmed the higher sensitivity of iron oxidation to inhibition by phosphate, chloride, azide, and cyanide. Sulfur oxidation was actually stimulated by 50 mM phosphate or chloride. Leaching of Fe and Zn from pyrite (FeS
2
) and sphalerite (ZnS) by
T. ferrooxidans
was differentially affected by phosphate and chloride, which inhibited the solubilization of Fe without significantly affecting the solubilization of Zn.
Highly Ordered Vertical Structure of
Synechococcus
Populations within the One-Millimeter-Thick Photic Zone of a Hot Spring Cyanobacterial Mat
Authors: Ramsing Niels Birger , Ferris Mike J. , Ward David M. 
Published: July 2002

ABSTRACT

A variety of contemporary techniques were used to investigate the vertical distribution of thermophilic unicellular cyanobacteria,
Synechococcus
spp., and their activity within the upper 1-mm-thick photic zone of the mat community found in an alkaline siliceous hot spring in Yellowstone National Park in Wyoming. Detailed measurements were made over a diel cycle at a 61°C site. Net oxygenic photosynthesis measured with oxygen microelectrodes was highest within the uppermost 100- to 200-μm-thick layer until midmorning, but as the day progressed, the peak of net activity shifted to deeper layers, stabilizing at a depth of 300 μm from midday throughout the afternoon. Examination of vertical thin sections by bright-field and autofluorescence microscopy revealed the existence of different populations of
Synechococcus
which form discrete bands at different vertical positions. Denaturing gradient gel electrophoresis analysis of PCR-amplified 16S rRNA gene segments from horizontal cryosections obtained at 100-μm-thick vertical intervals also suggested vertical stratification of cyanobacterial, green sulfur bacterium-like, and green nonsulfur bacterium-like populations. There was no evidence of diel migration. However, image analysis of vertical thin sections revealed the presence of a narrow band of rod-shaped
Synechococcus
cells in which the cells assumed an upright position. These upright cells, located 400 to 800 μm below the surface, were observed only in mat samples obtained around noon. In mat samples obtained at other time points, the cells were randomly oriented throughout the mat. These combined observations reveal the existence of a highly ordered structure within the very thin photic zone of this hot spring microbial mat, consisting of morphologically similar
Synechococcus
populations that are likely to be differentially adapted, some co-occurring with green sulfur bacterium-like populations, and all overlying green nonsulfur bacterium-like populations.
Significance of Inoculum Size in the Lag Time of
Listeria monocytogenes
Authors: Augustin Jean-Christophe , Brouillaud-Delattre Agnès , Rosso Laurent , Carlier Vincent 
Published: July 2002

ABSTRACT

The lag time of
Listeria monocytogenes
growing under suboptimal conditions (low nutrient concentrations, pH 6, and 6.5°C) was extended when the inoculum was severely stressed by starvation and the inoculum size was very small. Predictive microbiology should deal with bacterial stress and stochastic approaches to improve its value for the agro-food industry.
Prey Range Characterization, Ribotyping, and Diversity of Soil and Rhizosphere
Bdellovibrio
spp. Isolated on Phytopathogenic Bacteria
Authors: Jurkevitch E. , Minz D. , Ramati Barak , Barel Gili 
Published: July 2002

ABSTRACT

Thirty new
Bdellovibrio
strains were isolated from an agricultural soil and from the rhizosphere of plants grown in that soil. Using a combined molecular and culture-based approach, we found that the soil bdellovibrios included subpopulations of organisms that differed from rhizosphere bdellovibrios. Thirteen soil and seven common bean rhizosphere
Bdellovibrio
strains were isolated when
Pseudomonas corrugata
was used as prey; seven and two soil strains were isolated when
Erwinia carotovora
subsp.
carotovora
and
Agrobacterium tumefaciens
, respectively, were used as prey; and one tomato rhizosphere strain was isolated when
A. tumefaciens
was used as prey. In soil and in the rhizosphere, depending on the prey cells used, the concentrations of bdellovibrios were between 3 × 10
2
to 6 × 10
3
and 2.8 × 10
2
to 2.3 × 10
4
PFU g
−1
. A prey range analysis of five soil and rhizosphere
Bdellovibrio
isolates performed with 22 substrate species, most of which were plant-pathogenic and plant growth-enhancing bacteria, revealed unique utilization patterns and differences between closely related prey cells. An approximately 830-bp fragment of the 16S rRNA genes of all of the
Bdellovibrio
strains used was obtained by PCR amplification by using a
Bdellovibrio
-specific primer combination. Soil and common bean rhizosphere strains produced two and one restriction patterns for this PCR product, respectively. The 16S rRNA genes of three soil isolates and three root-associated isolates were sequenced. One soil isolate belonged to the
Bdellovibrio stolpii-Bdellovibrio starrii
clade, while all of the other isolates clustered with
Bdellovibrio bacteriovorus
and formed two distantly related, heterogeneous groups.
Genes Expressed in
Pseudomonas putida
during Colonization of a Plant-Pathogenic Fungus
Authors: Lee Seon-Woo , Cooksey Donald A. 
Published: July 2002

ABSTRACT

In vivo expression technology (IVET) was employed to study colonization of
Phytophthora parasitica
by a biological control bacterium,
Pseudomonas putida
06909, based on a new selection marker. The
pyrB
gene, which encodes aspartate transcarbamoylase, an enzyme used for pyrimidine biosynthesis, was cloned from
P. putida
06909. A
pyrB
-disrupted mutant did not grow in pyrimidine-deficient media unless it was complemented with
pyrBC
′ behind an active promoter. Thirty clones obtained from
P. putida
06909 that were expressed on fungal hyphae but not on culture media were isolated by IVET based on the promoterless transcriptional fusion between
pyrBC
′ and
lacZ
. Nineteen of these clones were induced during late-stage bacterial growth in vitro, while 11 of the clones were expressed only when they were inoculated onto fungal hyphae. Restriction analysis of these 11 clones revealed that there were five unique clones. Sequence analyses of three of the five unique clones showed that the 3′ ends of the clones fused to
pyrB
were similar to genes encoding diacylglycerol kinase (DAGK), bacterial ABC transporters, and outer membrane porins. The sequences of the two other clones were not similar to the sequences of any of the genes in the database used. A LuxR family response regulator was found upstream of DAGK, and a LysR family response regulator was found upstream of the ABC transporter. The location of the inducible promoter of two clones suggested that DAGK and the ABC transporter are induced and may play a role in colonization of the fungus
P. parasitica
by
P. putida
06909.
Molecular Diversity of Plasmids Bearing Genes That Encode Toluene and Xylene Metabolism in
Pseudomonas
Strains Isolated from Different Contaminated Sites in Belarus
Authors: Sentchilo Vladimir S. , Perebituk Alexander N. , Zehnder Alexander J. B. , van der Meer Jan Roelof 
Published: July 2002

ABSTRACT

Twenty different
Pseudomonas
strains utilizing
m
-toluate were isolated from oil-contaminated soil samples near Minsk, Belarus. Seventeen of these isolates carried plasmids ranging in size from 78 to about 200 kb (assigned pSVS plasmids) and encoding the
meta
cleavage pathway for toluene metabolism. Most plasmids were conjugative but of unknown incompatibility groups, except for one, which belonged to the IncP9 group. The organization of the genes for toluene catabolism was determined by restriction analysis and hybridization with
xyl
gene probes of pWW0. The majority of the plasmids carried
xyl
-type genes highly homologous to those of pWW53 and organized in a similar manner (M. T. Gallegos, P. A. Williams, and J. L. Ramos, J. Bacteriol. 179:5024–5029, 1997), with two distinguishable
meta
pathway operons, one upper pathway operon, and three
xylS
-homologous regions. All of these plasmids also possessed large areas of homologous DNA outside the catabolic genes, suggesting a common ancestry. Two other pSVS plasmids carried only one
meta
pathway operon, one upper pathway operon, and one copy each of
xylS
and
xylR
. The backbones of these two plasmids differed greatly from those of the others. Whereas these parts of the plasmids, carrying the
xyl
genes, were mostly conserved between plasmids of each group, the noncatabolic parts had undergone intensive DNA rearrangements. DNA sequencing of specific regions near and within the
xylTE
and
xylA
genes of the pSVS plasmids confirmed the strong homologies to the
xyl
genes of pWW53 and pWW0. However, several recombinations were discovered within the upper pathway operons of the pSVS plasmids and pWW0. The main genetic mechanisms which are thought to have resulted in the present-day configuration of the
xyl
operons are discussed in light of the diversity analysis carried out on the pSVS plasmids.
A New Method To Monitor Airborne Inoculum of the Fungal Plant Pathogens
Mycosphaerella brassicicola
and
Botrytis cinerea
Authors: Kennedy R. , Wakeham A. J. , Byrne K. G. , Meyer U. M. , Dewey F. M. 
Published: July 2002

ABSTRACT

We describe a new microtiter immunospore trapping device (MTIST device) that uses a suction system to directly trap air particulates by impaction in microtiter wells. This device can be used for rapid detection and immunoquantification of ascospores of
Mycosphaerella brassicicola
and conidia of
Botrytis cinerea
by an enzyme-linked immunosorbent assay (ELISA) under controlled environmental conditions. For ascospores of
M. brassicicola
correlation coefficients (
r
2
) of 0.943 and 0.9514 were observed for the number of MTIST device-impacted ascospores per microtiter well and the absorbance values determined by ELISA, respectively. These values were not affected when a mixed fungal spore population was used. There was a relationship between the number of MTIST device-trapped ascospores of
M. brassicicola
per liter of air sampled and the amount of disease expressed on exposed plants of
Brassica oleracea
(Brussels sprouts). Similarly, when the MTIST device was used to trap conidia of
B. cinerea
, a correlation coefficient of 0.8797 was obtained for the absorbance values generated by the ELISA and the observed number of conidia per microtiter well. The relative collection efficiency of the MTIST device in controlled plant growth chambers with limited airflow was 1.7 times greater than the relative collection efficiency of a Burkard 7-day volumetric spore trap for collection of
M. brassicicola
ascospores. The MTIST device can be used to rapidly differentiate, determine, and accurately quantify target organisms in a microflora. The MTIST device is a portable, robust, inexpensive system that can be used to perform multiple tests in a single sampling period, and it should be useful for monitoring airborne particulates and microorganisms in a range of environments.
Roles of Fe Superoxide Dismutase and Catalase in Resistance of
Campylobacter coli
to Freeze-Thaw Stress
Authors: Stead Don , Park Simon F. 
Published: July 2002

ABSTRACT

We demonstrated that oxidative stress plays a role in freeze-thaw-induced killing of
Campylobacter coli
following analysis of mutants deficient in key antioxidant functions. Superoxide anions, but not H
2
O
2
, were formed during the freeze-thaw process. However, a failure to detoxify superoxide anions may lead to spontaneous disproportionation of the radicals to H
2
O
2
.
Requirement of Autolytic Activity for Bacteriocin-Induced Lysis
Authors: Martínez-Cuesta M. Carmen , Kok Jan , Herranz Elisabet , Peláez Carmen , Requena Teresa , Buist Girbe 
Published: July 2002

ABSTRACT

The bacteriocin produced by
Lactococcus lactis
IFPL105 is bactericidal against several
Lactococcus
and
Lactobacillus
strains. Addition of the bacteriocin to exponential-growth-phase cells resulted in all cases in bacteriolysis. The bacteriolytic response of the strains was not related to differences in sensitivity to the bacteriocin and was strongly reduced in the presence of autolysin inhibitors (Co
2+
and sodium dodecyl sulfate). When
L. lactis
MG1363 and its derivative deficient in the production of the major autolysin AcmA (MG1363
acmAΔ1
) were incubated with the bacteriocin, the latter did not lyse and no intracellular proteins were released into the medium. Incubation of cell wall fragments of
L. lactis
MG1363, or of
L. lactis
MG1363
acmAΔ1
to which extracellular AcmA was added, in the presence or absence of the bacteriocin had no effect on the speed of cell wall degradation. This result indicates that the bacteriocin does not degrade cell walls, nor does it directly activate the autolysin AcmA. The autolysin was also responsible for the observed lysis of
L. lactis
MG1363 cells during incubation with nisin or the mixture of lactococcins A, B, and M. The results presented here show that lysis of
L. lactis
after addition of the bacteriocins is caused by the resulting cell damage, which promotes uncontrolled degradation of the cell walls by AcmA.
Distribution and Diversity of Archaea Corresponding to the Limnological Cycle of a Hypersaline Stratified Lake (Solar Lake, Sinai, Egypt)
Authors: Cytryn Eddie , Minz Dror , Oremland Ronald S. , Cohen Yehuda 
Published: July 2002

ABSTRACT

The vertical and seasonal distribution and diversity of archaeal sequences was investigated in a hypersaline, stratified, monomictic lake, Solar Lake, Sinai, Egypt, during the limnological development of stratification and mixing. Archaeal sequences were studied via phylogenetic analysis of 16S rDNA sequences as well as denaturing gradient gel electrophoresis analysis. The 165 clones studied were grouped into four phylogenetically different clusters. Most of the clones isolated from both the aerobic epilimnion and the sulfide-rich hypolimnion were defined as cluster I, belonging to the
Halobacteriaceae
family. The three additional clusters were all isolated from the anaerobic hypolimnion. Cluster II is phylogenetically located between the genera
Methanobacterium
and
Methanococcus
. Clusters III and IV relate to two previously documented groups of uncultured euryarchaeota, remotely related to the genus
Thermoplasma
. No crenarchaeota were found in the water column of the Solar Lake. The archaeal community in the Solar Lake under both stratified and mixed conditions was dominated by halobacteria in salinities higher than 10%. During stratification, additional clusters, some of which may possibly relate to uncultured halophilic methanogens, were found in the sulfide- and methane-rich hypolimnion.
Community Structure, Cellular rRNA Content, and Activity of Sulfate-Reducing Bacteria in Marine Arctic Sediments
Authors: Ravenschlag Katrin , Sahm Kerstin , Knoblauch Christian , Jørgensen Bo B. , Amann Rudolf 
Published: July 2002

ABSTRACT

The community structure of sulfate-reducing bacteria (SRB) of a marine Arctic sediment (Smeerenburgfjorden, Svalbard) was characterized by both fluorescence in situ hybridization (FISH) and rRNA slot blot hybridization by using group- and genus-specific 16S rRNA-targeted oligonucleotide probes. The SRB community was dominated by members of the
Desulfosarcina-Desulfococcus
group. This group accounted for up to 73% of the SRB detected and up to 70% of the SRB rRNA detected. The predominance was shown to be a common feature for different stations along the coast of Svalbard. In a top-to-bottom approach we aimed to further resolve the composition of this large group of SRB by using probes for cultivated genera. While this approach failed, directed cloning of probe-targeted genes encoding 16S rRNA was successful and resulted in sequences which were all affiliated with the
Desulfosarcina-Desulfococcus
group. A group of clone sequences (group SVAL1) most closely related to
Desulfosarcina variabilis
(91.2% sequence similarity) was dominant and was shown to be most abundant in situ, accounting for up to 54.8% of the total SRB detected. A comparison of the two methods used for quantification showed that FISH and rRNA slot blot hybridization gave comparable results. Furthermore, a combination of the two methods allowed us to calculate specific cellular rRNA contents with respect to localization in the sediment profile. The rRNA contents of
Desulfosarcina
-
Desulfococcus
cells were highest in the first 5 mm of the sediment (0.9 and 1.4 fg, respectively) and decreased steeply with depth, indicating that maximal metabolic activity occurred close to the surface. Based on SRB cell numbers, cellular sulfate reduction rates were calculated. The rates were highest in the surface layer (0.14 fmol cell
−1
day
−1
), decreased by a factor of 3 within the first 2 cm, and were relatively constant in deeper layers.
Amplified Fragment Length Polymorphism Analysis of
Campylobacter jejuni
Strains Isolated from Chickens and from Patients with Gastroenteritis or Guillain-Barré or Miller Fisher Syndrome
Authors: Duim Birgitta , Ang C. Wim , van Belkum Alex , Rigter Alan , van Leeuwen Nan W. J. , Endtz Hubert P. , Wagenaar Jaap A. 
Published: July 2002

ABSTRACT

The high-resolution genotyping method of amplified fragment length polymorphism (AFLP) analysis was used to study the genetic relationships between
Campylobacter jejuni
strains infecting chickens (
n
= 54) and those causing gastroenteritis in humans (
n
= 53). In addition,
C. jejuni
strains associated with the development of Guillain-Barré syndrome (GBS) (
n
= 14) and Miller Fisher syndrome (MFS) (
n
= 4), two related acute paralytic syndromes in human, were included. Strains were isolated between 1989 and 1998 in The Netherlands. The AFLP banding patterns were analyzed with correlation-based and band-based similarity coefficients and UPGMA (unweighted pair group method using average linkages) cluster analysis. All
C. jejuni
strains showed highly heterogeneous fingerprints, and no fingerprints exclusive for chicken strains or for human strains were obtained. All strains were separated in two distinct genetic groups. In group A the percentage of human strains was significantly higher and may be an indication that genotypes of this group are more frequently associated with human diseases. We conclude that
C. jejuni
from chickens cannot be distinguished from human strains and that GBS or MFS related strains do not belong to a distinct genetic group.
In Situ Reproductive Rate of Freshwater
Caulobacter
spp
Authors: Poindexter Jeanne S. , Pujara Kanan P. , Staley James T. 
Published: July 2002

ABSTRACT

Electron microscope grids were submerged in Lake Washington, Seattle, Wash., in June 1996 as bait to which
Caulobacter
sp. swarmers would attach and on which they would then reproduce in situ. Enumeration of bands in the stalks of attached cells implied that the caulobacters were completing approximately three reproductive cycles per day. A succession of morphological types of caulobacters occurred, as well as an episode of bacteriovore grazing that slowed the accumulation of caulobacters and prevented the aging of the population.
Transformation of Triclosan by
Trametes versicolor
and
Pycnoporus cinnabarinus
Authors: Hundt Kai , Martin Dierk , Hammer Elke , Jonas Ulrike , Kindermann Markus Karl , Schauer Frieder 
Published: July 2002

ABSTRACT

We investigated the ability of
Trametes versicolor
and
Pycnoporous cinnabarinus
to metabolize triclosan.
T. versicolor
produced three metabolites, 2-
O
-(2,4,4′-trichlorodiphenyl ether)-β-
d
-xylopyranoside, 2-
O
-(2,4,4′-trichlorodiphenyl ether)-β-
d
-glucopyranoside, and 2,4-dichlorophenol.
P. cinnabarinus
converted triclosan to 2,4,4′-trichloro-2′-methoxydiphenyl ether and the glucoside conjugate known from
T. versicolor
. The conjugates showed a distinctly lower cytotoxic and microbicidal activity than triclosan did.
Prevalence and Characteristics of Shiga Toxin-Producing
Escherichia coli
from Healthy Cattle in Japan
Authors: Kobayashi Hideki , Shimada Jun , Nakazawa Muneo , Morozumi Tetsuo , Pohjanvirta Tarja , Pelkonen Sinikka , Yamamoto Koshi 
Published: July 2002

ABSTRACT

The prevalence of Shiga toxin-producing
Escherichia coli
(STEC) in Japan was examined by using stool samples from 87 calves, 88 heifers, and 183 cows on 78 farms. As determined by screening with
stx
-PCR, the prevalence was 46% in calves, 66% in heifers, and 69% in cows; as determined by nested
stx
-PCR, the prevalence was 100% in all animal groups. Of the 962 isolates picked by colony
stx
hybridization, 92 isolates from 54 farms were characterized to determine their O serogroups, virulence factor genes, and antimicrobial resistance. Of these 92 isolates, 74 (80%) could be classified into O serogroups; 50% of these 74 isolates belonged to O serogroups O8, O26, O84, O113, and O116 and 1 isolate belonged to O serogroup O157. Locus of enterocyte effacement genes were detected in 24% of the isolates, and enterohemorrhagic
E. coli
(EHEC)
hlyA
genes were detected in 72% of the isolates. Neither the bundle-forming pilus gene nor the enteropathogenic
E. coli
adherence factor plasmid was found. STEC strains with characteristics typical of isolates from human EHEC infections, which were regarded as potential EHEC strains, were present on 11.5% of the farms.