bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exposure of Phytopathogenic
Xanthomonas
spp. to Lethal Concentrations of Multiple Oxidants Affects Bacterial Survival in a Complex Manner
Authors: Sriprang Rutchadaporn , Vattanaviboon Paiboon , Mongkolsuk Skorn 
Published: July 2002

ABSTRACT

During plant-microbe interactions and in the environment,
Xanthomonas campestris
pv. phaseoli is likely to be exposed to high concentrations of multiple oxidants. Here, we show that simultaneous exposures of the bacteria to multiple oxidants affects cell survival in a complex manner. A superoxide generator (menadione) enhanced the lethal effect of an organic peroxide (
tert
-butyl hydroperoxide) by 1,000-fold; conversely, treatment of cells with menadione plus H
2
O
2
resulted in 100-fold protection compared to that for cells treated with the individual oxidants. Treatment of
X. campestris
with a combination of H
2
O
2
and
tert
-butyl hydroperoxide elicited no additive or protective effect. High levels of catalase alone are sufficient to protect cells against the lethal effect of menadione plus H
2
O
2
and
tert
-butyl hydroperoxide plus H
2
O
2
. These data suggest that H
2
O
2
is the lethal agent responsible for killing the bacteria as a result of these treatments. However, increased expression of individual genes for peroxide (alkyl hydroperoxide reductase, catalase)- and superoxide (superoxide dismutase)-scavenging enzymes or concerted induction of oxidative stress-protective genes by menadione gave no protection against killing by a combination of menadione plus
tert
-butyl hydroperoxide. However,
X. campestris
cells in the stationary phase and a spontaneous H
2
O
2
-resistant mutant (
X. campestris
pv. phaseoli HR) were more resistant to killing by menadione plus
tert
-butyl hydroperoxide. These findings give new insight into oxidant killing of
Xanthomonas
spp. that could be generally applied to other bacteria.
Pigment Production by
Streptococcus agalactiae
in Quasi-Defined Media
Authors: Rosa-Fraile Manuel , Sampedro Antonio , Rodrı́guez-Granger Javier , Garcı́a-Peña Maria Luisa , Ruiz-Bravo Alfonso , Haı̈dour Ali 
Published: July 2002

ABSTRACT

A quasi-defined medium that supports the growth of
Streptococcus agalactiae
as pigmented colonies has been developed. The medium contains starch, a peptic digest of albumin, amino acids, nucleosides, vitamins, and salts. The presence of free cysteine, which could be replaced with other sulphur-containing compounds and to a lesser degree by reducing agents, was required for pigment formation.
Cross-Epithelial Hydrogen Transfer from the Midgut Compartment Drives Methanogenesis in the Hindgut of Cockroaches
Authors: Lemke Thorsten , van Alen Theo , Hackstein Johannes H. P. , Brune Andreas 
Published: July 2002

ABSTRACT

In the intestinal tracts of animals, methanogenesis from CO
2
and other C
1
compounds strictly depends on the supply of electron donors by fermenting bacteria, but sources and sinks of reducing equivalents may be spatially separated. Microsensor measurements in the intestinal tract of the omnivorous cockroach
Blaberus
sp. showed that molecular hydrogen strongly accumulated in the midgut (H
2
partial pressures of 3 to 26 kPa), whereas it was not detectable (<0.1 kPa) in the posterior hindgut. Moreover, living cockroaches emitted large quantities of CH
4
[105 ± 49 nmol (g of cockroach)
−1
h
−1
] but only traces of H
2
. In vitro incubation of isolated gut compartments, however, revealed that the midguts produced considerable amounts of H
2
, whereas hindguts emitted only CH
4
[106 ± 58 and 71 ± 50 nmol (g of cockroach)
−1
h
−1
, respectively]. When ligated midgut and hindgut segments were incubated in the same vials, methane emission increased by 28% over that of isolated hindguts, whereas only traces of H
2
accumulated in the headspace. Radial hydrogen profiles obtained under air enriched with H
2
(20 kPa) identified the hindgut as an efficient sink for externally supplied H
2
. A cross-epithelial transfer of hydrogen from the midgut to the hindgut compartment was clearly evidenced by the steep H
2
concentration gradients which developed when ligated fragments of midgut and hindgut were placed on top of each other—a configuration that simulates the situation in vivo. These findings emphasize that it is essential to analyze the compartmentalization of the gut and the spatial organization of its microbiota in order to understand the functional interactions among different microbial populations during digestion.
Homologous Expression of the Lipase and ABC Transporter Gene Cluster,
tliDEFA
, Enhances Lipase Secretion in
Pseudomonas
spp
Authors: Ahn Jung Hoon , Pan Jae Gu , Rhee Joon Shick 
Published: July 2002

ABSTRACT

The ABC transporter TliDEF was found to be an efficient secretory apparatus for extracellular lipase TliA in
Pseudomonas fluorescens
. For the enhanced secretion of the lipase, we tried to coexpress
tliA
and
tliDEF
in various
Pseudomonas
species. Whereas the coexpression of
tliA
and
tliDEF
was required for the lipase secretion in
P. fragi
, the expression of
tliA
was sufficient for the lipase secretion in
P. fluorescens
,
P. syringae
, and
P. putida
, indicating the existence of compatible ABC transporter in these species. However,
P. fluorescens
harboring
tliDEFA
secreted much more lipase than
P. fluorescens
harboring only
tliA
, but the
tliDEF
was functional only at temperatures below 30°C. The recombinant
P. fluorescens
overexpressing
tliDEFA
showed the highest secretion level, 217 U/ml · OD (optical density) (28 μg/ml · OD) of lipase in Luria-Bertani medium under microaerated conditions. With the increase of aeration, the lipase production was decreased and the lipase seemed to be degraded as the cells entered the cell death phase. These results demonstrate that
P. fluorescens
can be used as a host system for the secretory production of the lipase using the ABC transporter, thus producing lipase in over 14% of the total protein.
Development and Evaluation of Functional Gene Arrays for Detection of Selected Genes in the Environment
Authors: Wu Liyou , Thompson Dorothea K. , Li Guangshan , Hurt Richard A. , Tiedje James M. , Zhou Jizhong 
Published: July 2002

ABSTRACT

To determine the potential of DNA array technology for assessing functional gene diversity and distribution, a prototype microarray was constructed with genes involved in nitrogen cycling: nitrite reductase (
nirS
and
nirK
) genes, ammonia mono-oxygenase (
amoA
) genes, and methane mono-oxygenase (
pmoA
) genes from pure cultures and those cloned from marine sediments. In experiments using glass slide microarrays, genes possessing less than 80 to 85% sequence identity were differentiated under hybridization conditions of high stringency (65°C). The detection limit for
nirS
genes was approximately 1 ng of pure genomic DNA and 25 ng of soil community DNA using our optimized protocol. A linear quantitative relationship (
r
2
= 0.89 to 0.94) was observed between signal intensity and target DNA concentration over a range of 1 to 100 ng for genomic DNA (or genomic DNA equivalent) from both pure cultures and mixed communities. However, the quantitative capacity of microarrays for measuring the relative abundance of targeted genes in complex environmental samples is less clear due to divergent target sequences. Sequence divergence and probe length affected hybridization signal intensity within a certain range of sequence identity and size, respectively. This prototype functional gene array did reveal differences in the apparent distribution of
nir
and
amo
A and
pmo
A gene families in sediment and soil samples. Our results indicate that glass-based microarray hybridization has potential as a tool for revealing functional gene composition in natural microbial communities; however, more work is needed to improve sensitivity and quantitation and to understand the associated issue of specificity.
Burkholderia cepacia
Genomovar III Is a Common Plant-Associated Bacterium
Authors: Balandreau Jacques , Viallard Veronique , Cournoyer Benoit , Coenye Tom , Laevens Severine , Vandamme Peter 
Published: July 2002

ABSTRACT

A polyphasic taxonomic study involving DNA-DNA hybridization, whole-cell protein electrophoresis, and 16S ribosomal DNA sequence analysis revealed that a group of
Burkholderia cepacia
-like organisms isolated from the rhizosphere or tissues of maize, wheat, and lupine belong to
B. cepacia
genomovar III, a genomic species associated with “cepacia syndrome” in cystic fibrosis patients. The present study also revealed considerable protein electrophoretic heterogeneity within this species and demonstrated that the
B. cepacia
complex consists of two independent phylogenetic lineages.
Applications of Gene Replacement Technology to
Streptomyces clavuligerus
Strain Development for Clavulanic Acid Production
Authors: Paradkar A. S. , Mosher R. H. , Anders C. , Griffin A. , Griffin J. , Hughes C. , Greaves P. , Barton B. , Jensen S. E. 
Published: July 2002

ABSTRACT

Cephamycin C production was blocked in wild-type cultures of the clavulanic acid-producing organism
Streptomyces clavuligerus
by targeted disruption of the gene (
lat
) encoding lysine ɛ-aminotransferase. Specific production of clavulanic acid increased in the
lat
mutants derived from the wild-type strain by 2- to 2.5-fold. Similar beneficial effects on clavulanic acid production were noted in previous studies when gene disruption was used to block the production of the non-clavulanic acid clavams produced by
S. clavuligerus
. Therefore, mutations in
lat
and in
cvm1
, a gene involved in clavam production, were introduced into a high-titer industrial strain of
S. clavuligerus
to create a double mutant with defects in production of both cephamycin C and clavams. Production of both cephamycin C and non-clavulanic acid clavams was eliminated in the double mutant, and clavulanic acid titers increased about 10% relative to those of the parental strain. This represents the first report of the successful use of genetic engineering to eliminate undesirable metabolic pathways in an industrial strain used for the production of an antibiotic important in human medicine.
Quantitative Shedding of Two Genotypes of
Cryptosporidium parvum
in California Ground Squirrels (
Spermophilus beecheyi
)
Authors: Atwill Edward R. , Camargo Sergio Maldonado , Phillips Ralph , Alonso Laura Herrera , Tate Kenneth W. , Jensen Wayne A. , Bennet Joe , Little Scott , Salmon Terrell P. 
Published: July 2002

ABSTRACT

Sixteen percent of California ground squirrels (
Spermophilus beecheyi
) were found to be shedding an average of 53,875
Cryptosporidium parvum
oocysts/g of feces. Male squirrels had a higher prevalence and higher intensity of shedding than did female squirrels. The majority of
C. parvum
isolates matched a bovine-murine genotype, with a few isolates resembling a porcine genotype. Higher intensities of shedding by males may enhance dissemination and genotypic mixing of this protozoa given males' proclivity to disperse to nonnatal colonies.
Nitrogen-Fixing Nodules with
Ensifer adhaerens
Harboring
Rhizobium tropici
Symbiotic Plasmids
Authors: Rogel M. Antonio , Hernández-Lucas Ismael , Kuykendall L. David , Balkwill David L. , Martinez-Romero Esperanza 
Published: July 2002

ABSTRACT

Ensifer adhaerens
is a soil bacterium that attaches to other bacteria and may cause lysis of these other bacteria. Based on the sequence of its small-subunit rRNA gene,
E. adhaerens
is related to
Sinorhizobium
spp.
E. adhaerens
ATCC 33499 did not nodulate
Phaseolus vulgaris
(bean) or
Leucaena leucocephala
, but with symbiotic plasmids from
Rhizobium tropici
CFN299 it formed nitrogen-fixing nodules on both hosts. The nodule isolates were identified as
E. adhaerens
isolates by growth on selective media.
Quantitative Analysis of Bacterial Gene Expression by Using the
gusA
Reporter Gene System
Authors: Sun Jun , Smets Ilse , Bernaerts Kristel , Van Impe Jan , Vanderleyden Jos , Marchal Kathleen 
Published: July 2002

ABSTRACT

An
Azospirillum brasilense
Sp7 strain containing a plasmid-borne translational
cytN-gusA
fusion was grown in a continuous culture to quantitatively evaluate the influence of extracellular signals (such as O
2
) on expression of the
cytNOQP
operon. The dissolved oxygen concentration was shifted at regular time intervals before the steady state was reached. The measured β-glucuronidase activity was used to monitor
cytN
gene expression. However, as the β-glucuronidase activity in the experimental setup not only depended on altered transcription of the hybrid gene when the signal was varied but was also influenced by cellular accumulation, degradation, and dilution of the hybrid fusion protein, a mathematical method was developed to describe the intrinsic properties of the dynamic bioprocess. After identification and validation of the mathematical model, the apparent specific rate of expression of the fusion, which was independent of the experimental setup, could be deduced from the model and used to quantify gene expression regulated by extracellular environmental signals. In principle, this approach can be generalized to assess the effects of external signals on bacterial gene expression.
Brown Pigments Produced by
Yarrowia lipolytica
Result from Extracellular Accumulation of Homogentisic Acid
Authors: Carreira Alexandra , Ferreira Luı́sa M. , Loureiro Virgı́lio 
Published: July 2002

ABSTRACT

Yarrowia lipolytica
produces brown extracellular pigments that correlate with tyrosine catabolism. During tyrosine depletion, the yeast accumulated homogentisic acid,
p
-hydroxyphenylethanol, and
p
-hydroxyphenylacetic acid in the medium. Homogentisic acid accumulated under all aeration conditions tested, but its concentration decreased as aeration decreased. With moderate aeration, equimolar concentrations of alcohol and
p
-hydroxyphenylacetic acid (1:1) were detected, but with lower aeration the alcohol concentration was twice that of the acid (2:1).
p
-Hydroxyphenylethanol and
p
-hydroxyphenylacetic acid may result from the spontaneous disproportionation of the corresponding aldehyde,
p
-hydroxyphenylacetaldehyde. The catabolic pathway of tyrosine in
Y. lipolytica
involves the formation of
p
-hydroxyphenylacetaldehyde, which is oxidized to
p
-hydroxyphenylacetic acid and then further oxidized to homogentisic acid. Brown pigments are produced when homogentisic acid accumulates in the medium. This acid can spontaneously oxidize and polymerize, leading to the formation of pyomelanins. Mn
2+
accelerated and intensified the oxidative polymerization of homogentisic acid, and lactic acid enhanced the stimulating role of Mn
2+
. Alkaline conditions also accelerated pigment formation. The proposed tyrosine catabolism pathway appears to be unique for yeast, and this is the first report of a yeast producing pigments involving homogentisic acid.
Isolation of an Insertion Sequence from
Ralstonia solanacearum
Race 1 and Its Potential Use for Strain Characterization and Detection
Authors: Lee Yung-An , Fan Shu-Chung , Chiu Ling-Ya , Hsia Kuo-Chiang 
Published: July 2002

ABSTRACT

A new insertion sequence (IS), IS
1405
, was isolated and characterized from a
Ralstonia solanacearum
race 1 strain by the method of insertional inactivation of the
sacB
gene. Sequence analysis indicated that the IS is closely related to the members of IS
5
family, but the extent of nucleotide sequence identity in 5′ and 3′ noncoding regions between IS
1405
and other members of IS5 family is only 23 to 31%. Nucleotide sequences of these regions were used to design specific oligonucleotide primers for detection of race 1 strains by PCR. The PCR amplified a specific DNA fragment for all
R. solanacearum
race 1 strains tested, and no amplification was observed with some other plant-pathogenic bacteria. Analysis of nucleotide sequences flanking IS
1405
and additional five endogenous IS
1405
s that reside in the chromosome of
R. solanacearum
race 1 strains indicated that IS
1405
prefers a target site of CTAR and has two different insertional orientations with respect to this target site. Restriction fragment length polymorphism (RFLP) pattern analysis using IS
1405
as a probe revealed extensive genetic variation among strains of
R. solanacearum
race 1 isolated from eight different host plants in Taiwan. The RFLP patterns were then used to subdivide the race 1 strains into two groups and several subgroups, which allowed for tracking different subgroup strains of
R. solanacearum
through a host plant community. Furthermore, specific insertion sites of IS
1405
in certain subgroups were used as a genetic marker to develop subgroup-specific primers for detection of
R. solanacearum
, and thus, the subgroup strains can be easily identified through a rapid PCR assay rather than RFLP analysis.
Susceptibility of a Field-Derived,
Bacillus thuringiensis
-Resistant Strain of Diamondback Moth to In Vitro-Activated Cry1Ac Toxin
Authors: Sayyed Ali H. , Gatsi Roxani , Kouskoura Thaleia , Wright Denis J. , Crickmore Neil 
Published: July 2002

ABSTRACT

Resistant and susceptible populations of the diamondback moth (
Plutella xylostella
) were tested with crystalline, solubilized, and partially and fully activated forms of the
Bacillus thuringiensis
Cry1Ac δ-endotoxin. Fully activated toxin greatly reduced the resistance ratio (ratio of the 50% lethal concentration for the resistant population to that for the susceptible population) of the resistant population, suggesting that a defect in toxin activation is a major resistance mechanism.
Microbial Diversity of a Heavily Polluted Microbial Mat and Its Community Changes following Degradation of Petroleum Compounds
Authors: Abed Raeid M. M. , Safi Nimer M. D. , Köster Jürgen , de Beer Dirk , El-Nahhal Yasser , Rullkötter Jürgen , Garcia-Pichel Ferran 
Published: July 2002

ABSTRACT

We studied the microbial diversity of benthic cyanobacterial mats inhabiting a heavily polluted site in a coastal stream (Wadi Gaza) and monitored the microbial community response induced by exposure to and degradation of four model petroleum compounds in the laboratory.
Phormidium-
and
Oscillatoria
-like cyanobacterial morphotypes were dominant in the field. Bacteria belonging to different groups, mainly the
Cytophaga
-
Flavobacterium
-
Bacteriodes
group, the γ and β subclasses of the class
Proteobacteria
, and the green nonsulfur bacteria, were also detected. In slurry experiments, these communities efficiently degraded phenanthrene and dibenzothiophene completely in 7 days both in the light and in the dark.
n
-Octadecane and pristane were degraded to 25 and 34% of their original levels, respectively, within 7 days, but there was no further degradation until 40 days. Both cyanobacterial and bacterial communities exhibited noticeable changes concomitant with degradation of the compounds. The populations enriched by exposure to petroleum compounds included a cyanobacterium affiliated phylogenetically with
Halomicronema
. Bacteria enriched both in the light and in the dark, but not bacteria enriched in any of the controls, belonged to the newly described
Holophaga
-
Geothrix
-
Acidobacterium
phylum. In addition, another bacterial population, found to be a member of green nonsulfur bacteria, was detected only in the bacteria treated in the light. All or some of the populations may play a significant role in metabolizing the petroleum compounds. We concluded that the microbial mats from Wadi Gaza are rich in microorganisms with high biodegradative potential.
Identification and Characterization of
Leuconostoc fallax
Strains Isolated from an Industrial Sauerkraut Fermentation
Authors: Barrangou Rodolphe , Yoon Sung-Sik , Breidt, Frederick , Fleming Henry P. , Klaenhammer Todd R. 
Published: July 2002

ABSTRACT

Lactic acid bacterial strains were isolated from brines sampled after 7 days of an industrial sauerkraut fermentation, and six strains were selected on the basis of susceptibility to bacteriophages. Bacterial growth in cabbage juice was monitored, and the fermentation end products were identified, quantified, and compared to those of
Leuconostoc mesenteroides
. Identification by biochemical fingerprinting, endonuclease digestion of the 16S-23S intergenic transcribed spacer region, and sequencing of variable regions V1 and V2 of the 16S rRNA gene indicated that the six selected sauerkraut isolates were
Leuconostoc fallax
strains. Random amplification of polymorphic DNA fingerprints indicated that the strains were distinct from one another. The growth and fermentation patterns of the
L. fallax
isolates were highly similar to those of
L. mesenteroides
. The final pH of cabbage juice fermentation was 3.6, and the main fermentation end products were lactic acid, acetic acid, and mannitol for both species. However, none of the
L. fallax
strains exhibited the malolactic reaction, which is characteristic of most
L. mesenteroides
strains. These results indicated that in addition to
L. mesenteroides
, a variety of
L. fallax
strains may be present in the heterofermentative stage of sauerkraut fermentation. The microbial ecology of sauerkraut fermentation appears to be more complex than previously indicated, and the prevalence and roles of
L. fallax
require further investigation.
oriC
Region and Replication Termination Site,
dif
, of the
Xanthomonas campestris
pv. campestris 17 Chromosome
Authors: Yen Ming-Ren , Lin Nien-Tsung , Hung Chih-Hsin , Choy Ka-Tim , Weng Shu-Fen , Tseng Yi-Hsiung 
Published: July 2002

ABSTRACT

A 13-kb DNA fragment containing
oriC
and the flanking genes
thdF
,
orf900
,
yidC
,
rnpA
,
rpmH
,
oriC
,
dnaA
,
dnaN
,
recF
, and
gyrB
was cloned from the gram-negative plant pathogen
Xanthomonas campestris
pv. campestris 17. These genes are conserved in order with other eubacterial
oriC
genes and code for proteins that share high degrees of identity with their homologues, except for
orf900
, which has a homologue only in
Xylella fastidiosa
. The
dnaA
/
dnaN
intergenic region (273 bp) identified to be the minimal
oriC
region responsible for autonomous replication has 10 pure AT clusters of four to seven bases and only three consensus DnaA boxes. These findings are in disagreement with the notion that typical
oriC
s contain four or more DnaA boxes located upstream of the
dnaA
gene. The
X. campestris
pv. campestris 17
attB
site required for site-specific integration of cloned fragments from filamentous phage φLf replicative form DNA was identified to be a
dif
site on the basis of similarities in nucleotide sequence and function with the
Escherichia coli dif
site required for chromosome dimer resolution and whose deletion causes filamentation of the cells. The
oriC
and
dif
sites were located at 12:00 and 6:00, respectively, on the circular
X. campestris
pv. campestris 17 chromosome map, similar to the locations found for
E. coli
sites. Computer searches revealed the presence of both the
dif
site and XerC/XerD recombinase homologues in 16 of the 42 fully sequenced eubacterial genomes, but eight of the
dif
sites are located far away from the 6:00 point instead of being placed opposite the cognate
oriC
. The differences in the relative position suggest that mechanisms different from that of
E. coli
may participate in the control of chromosome replication.