bluuebunny/crossref_metadata_2025_split huggingface dataset:
Halotolerant Cyanobacterium
Aphanothece halophytica
Contains NapA-Type Na
+
/H
+
Antiporters with Novel Ion Specificity That Are Involved in Salt Tolerance at Alkaline pH
Authors: Wutipraditkul Nuchanat , Waditee Rungaroon , Incharoensakdi Aran , Hibino Takashi , Tanaka Yoshito , Nakamura Tatsunosuke , Shikata Masamitsu , Takabe Tetsuko , Takabe Teruhiro 
Published: August 2005

ABSTRACT

Aphanothece halophytica
is a halotolerant alkaliphilic cyanobacterium which can grow at NaCl concentrations up to 3.0 M and at pH values up to 11. The genome sequence revealed that the cyanobacterium
Synechocystis
sp. strain PCC 6803 contains five putative Na
+
/H
+
antiporters, two of which are homologous to NhaP of
Pseudomonas aeruginosa
and three of which are homologous to NapA of
Enterococcus hirae
. The physiological and functional properties of NapA-type antiporters are largely unknown. One of NapA-type antiporters in
Synechocystis
sp. strain PCC 6803 has been proposed to be essential for the survival of this organism. In this study, we examined the isolation and characterization of the homologous gene in
Aphanothece halophytica
. Two genes encoding polypeptides of the same size, designated Ap-
napA1
-
1
and Ap-
napA1
-
2
, were isolated. Ap-NapA1-1 exhibited a higher level of homology to the
Synechocystis
ortholog (Syn-NapA1) than Ap-NapA1-2 exhibited. Ap-NapA1-1, Ap-NapA1-2, and Syn-NapA1 complemented the salt-sensitive phenotypes of an
Escherichia coli
mutant and exhibited strongly pH-dependent Na
+
/H
+
and Li
+
/H
+
exchange activities (the highest activities were at alkaline pH), although the activities of Ap-NapA1-2 were significantly lower than the activities of the other polypeptides. Only one these polypeptides, Ap-NapA1-2, complemented a K
+
uptake-deficient
E. coli
mutant and exhibited K
+
uptake activity. Mutagenesis experiments suggested the importance of Glu129, Asp225, and Asp226 in the putative transmembrane segment and Glu142 in the loop region for the activity. Overexpression of Ap-NapA1-1 in the freshwater cyanobacterium
Synechococcus
sp. strain PCC 7942 enhanced the salt tolerance of cells, especially at alkaline pH. These findings indicate that
A. halophytica
has two NapA1-type antiporters which exhibit different ion specificities and play an important role in salt tolerance at alkaline pH.
Inhibition of
Clostridium perfringens
by a Novel Strain of
Bacillus subtilis
Isolated from the Gastrointestinal Tracts of Healthy Chickens
Authors: Teo Alex Yeow-Lim , Tan Hai-Meng 
Published: August 2005

ABSTRACT

The objectives of this study were to isolate beneficial strains of microorganisms from the gastrointestinal tracts of healthy chickens and to screen them against
Clostridium perfringens
, a causative agent of necrotic enteritis in poultry. One of the bacteria isolated, a strain of
Bacillus subtilis
, was found to possess an anticlostridial factor that could inhibit the
C. perfringens
ATCC 13124 used in this study. The anticlostridial factor produced by
B. subtilis
PB6 was found to be fully or partially inactivated in the presence of pronase, trypsin, and pepsin. In contrast, the antimicrobial activity of the anticlostridial factor was not affected by treatment at 100 or 121°C or by treatment with any of the organic solvents used in the study. The optimum growth temperature and optimum pH for production of the anticlostridial factor were 37°C and 6.20, respectively. Using the mass spectroscopy-mass spectroscopy technique, the apparent molecular mass of the anticlostridial factor was estimated to be in the range from 960 to 983 Da. In terms of the antimicrobial spectrum, the anticlostridial factor was inhibitory toward various strains of
C. perfringens
implicated in necrotic enteritis in poultry,
Clostridium difficile
,
Streptococcus pneumoniae
,
Campylobacter jejuni
, and
Campylobacter coli.
Use of Enrichment Culture for Directed Evolution of the
Vibrio fluvialis
JS17 ω-Transaminase, Which Is Resistant to Product Inhibition by Aliphatic Ketones
Authors: Yun Hyungdon , Hwang Bum-Yeol , Lee Jae-Hun , Kim Byung-Gee 
Published: August 2005

ABSTRACT

A novel high-throughput screening method that overcame product inhibition was used to isolate a mutant ω-transaminase from
Vibrio fluvialis
JS17. An enzyme library was generated using error-prone PCR mutagenesis and then enriched on minimal medium containing 2-aminoheptane as the sole nitrogen source and 2-butanone as an inhibitory ketone. An identified mutant enzyme, ω-TAmla, showed significantly reduced product inhibition by aliphatic ketone. The product inhibition constants of the mutant with 2-butanone and 2-heptanone were 6- and 4.5-fold higher than those of the wild type, respectively. Using ω-TAmla (50 U/ml) overexpressed in
Escherichia coli
BL21, 150 mM 2-aminoheptane was successfully resolved to (
R
)-2-aminoheptane (enantiomeric excess, >99%) with 53% conversion with an enantioselectivity of >100.
Study of Adhesion and Survival of Lactobacilli and Bifidobacteria on Table Olives with the Aim of Formulating a New Probiotic Food
Authors: Lavermicocca Paola , Valerio Francesca , Lonigro Stella Lisa , De Angelis Maria , Morelli Lorenzo , Callegari Maria Luisa , Rizzello Carlo G. , Visconti Angelo 
Published: August 2005

ABSTRACT

With the aim of developing new functional foods, a traditional product, the table olive, was used as a vehicle for incorporating probiotic bacterial species. Survival on table olives of
Lactobacillus rhamnosus
(three strains),
Lactobacillus paracasei
(two strains),
Bifidobacterium bifidum
(one strain), and
Bifidobacterium longum
(one strain) at room temperature was investigated. The results obtained using a selected olive sample demonstrated that bifidobacteria and one strain of
L. rhamnosus
(
Lactobacillus
GG) showed a good survival rate, with a recovery of about 10
6
CFU g
−1
after 30 days. The
Lactobacillus
GG population remained unvaried until the end of the experiment, while a slight decline (to about 10
5
CFU g
−1
) was observed for bifidobacteria. High viability, with more than 10
7
CFU g
−1
, was observed throughout the 3-month experiment for
L. paracasei
IMPC2.1. This strain, selected for its potential probiotic characteristics and for its lengthy survival on olives, was used to validate table olives as a carrier for transporting bacterial cells into the human gastrointestinal tract.
L. paracasei
IMPC2.1 was recovered from fecal samples in four out of five volunteers fed 10 to 15 olives per day carrying about 10
9
to 10
10
viable cells for 10 days.
Role for HtrA in Stress Induction and Virulence Potential in
Listeria monocytogenes
Authors: Stack Helena M. , Sleator Roy D. , Bowers Megan , Hill Colin , Gahan Cormac G. M. 
Published: August 2005

ABSTRACT

In silico analysis of the
Listeria monocytogenes
genome revealed
lmo0292
, a gene predicted to encode a HtrA-like serine protease. A stable insertion mutant was constructed, revealing a requirement for
htrA
in the listerial response to heat, acid, and penicillin stress. Transcriptional analysis revealed that
htrA
is not induced in response to heat shock but is induced in response to low pH and penicillin G stress. Furthermore,
htrA
expression was shown to be dependent upon the LisRK two-component sensor-kinase, a system known to respond to changes in integrity of the cell envelope. In addition, we demonstrated that a second in-frame start codon, upstream of that previously annotated for
L. monocytogenes htrA
, incorporating a putative signal sequence appears to influence virulence potential. Finally, a significant virulence defect was observed for the
htrA
mutant, indicating that this gene is required for full virulence in mice. Our findings suggest that
L. monocytogenes lmo0292
encodes an HtrA-like serine protease that is not part of the classical heat shock response but is involved in stress responses and virulence.
Elucidation of a Carotenoid Biosynthesis Gene Cluster Encoding a Novel Enzyme, 2,2′-β-Hydroxylase, from
Brevundimonas
sp. Strain SD212 and Combinatorial Biosynthesis of New or Rare Xanthophylls
Authors: Nishida Yasuhiro , Adachi Kyoko , Kasai Hiroaki , Shizuri Yoshikazu , Shindo Kazutoshi , Sawabe Akiyoshi , Komemushi Sadao , Miki Wataru , Misawa Norihiko 
Published: August 2005

ABSTRACT

A carotenoid biosynthesis gene cluster mediating the production of 2-hydroxyastaxanthin was isolated from the marine bacterium
Brevundimonas
sp. strain SD212 by using a common
crtI
sequence as the probe DNA. A sequence analysis revealed this cluster to contain 12 open reading frames (ORFs), including the 7 known genes,
crtW
,
crtY
,
crtI
,
crtB
,
crtE
,
idi
, and
crtZ
. The individual ORFs were functionally analyzed by complementation studies using
Escherichia coli
that accumulated various carotenoid precursors due to the presence of other bacterial
crt
genes. In addition to functionally identifying the known
crt
genes, we found that one (ORF11, named
crtG
) coded for a novel enzyme, carotenoid 2,2′-β-hydroxylase, which showed intriguingly partial homology with animal sterol-C5-desaturase. When this
crtG
gene was introduced into
E. coli
accumulating zeaxanthin and canthaxanthin, the resulting transformants produced their 2-hydroxylated and 2,2′-dihydroxylated products which were structurally novel or rare xanthophylls, as determined by their nuclear magnetic resonance and high-performance liquid chromatography/photodiode array detector/atmospheric pressure chemical ionization mass spectrometry spectral data. The new carotenoid produced was suggested to have a strong inhibitory effect on lipid peroxidation.
Discrimination of Enterobacterial Repetitive Intergenic Consensus PCR Types of
Campylobacter coli
and
Campylobacter jejuni
by Fourier Transform Infrared Spectroscopy
Authors: Mouwen D. J. M. , Weijtens M. J. B. M. , Capita R. , Alonso-Calleja C. , Prieto M. 
Published: August 2005

ABSTRACT

Fourier transform infrared spectroscopy (FT-IR) has been used together with pattern recognition methodology to study isolates belonging to the species
Campylobacter coli
and
Campylobacter jejuni
and to compare FT-IR typing schemes with established genomic profiles based on enterobacterial repetitive intergenic consensus PCR (ERIC-PCR). Seventeen isolates were cultivated under standardized conditions for 2, 3, and 4 days to study variability and improve reproducibility. ERIC-PCR profiles and FT-IR spectra were obtained from strains belonging to the species
Campylobacter coli
and
C. jejuni
, normalized, and explored by hierarchical clustering and stepwise discriminant analysis. Strains could be differentiated by using mainly the first-derivative FT-IR spectral range, 1,200 to 900 cm
−1
(described as the carbohydrate region). The reproducibility index varied depending on the ages of the cultures and on the spectral ranges investigated. Classification obtained by FT-IR spectroscopy provided valuable taxonomic information and was mostly in agreement with data from the genotypic method, ERIC-PCR. The classification functions obtained from the discriminant analysis allowed the identification of 98.72% of isolates from the validation set. FT-IR can serve as a valuable tool in the classification, identification, and typing of thermophilic
Campylobacter
isolates, and a number of types can be differentiated by means of FT-IR spectroscopy.
Responses of Baltic Sea Ice and Open-Water Natural Bacterial Communities to Salinity Change
Authors: Kaartokallio Hermanni , Laamanen Maria , Sivonen Kaarina 
Published: August 2005

ABSTRACT

To investigate the responses of Baltic Sea wintertime bacterial communities to changing salinity (5 to 26 practical salinity units), an experimental study was conducted. Bacterial communities of Baltic seawater and sea ice from a coastal site in southwest Finland were used in two batch culture experiments run for 17 or 18 days at 0°C. Bacterial abundance, cell volume, and leucine and thymidine incorporation were measured during the experiments. The bacterial community structure was assessed using denaturing gradient gel electrophoresis (DGGE) of PCR-amplified partial 16S rRNA genes with sequencing of DGGE bands from initial communities and communities of day 10 or 13 of the experiment. The sea ice-derived bacterial community was metabolically more active than the open-water community at the start of the experiment. Ice-derived bacterial communities were able to adapt to salinity change with smaller effects on physiology and community structure, whereas in the open-water bacterial communities, the bacterial cell volume evolution, bacterial abundance, and community structure responses indicated the presence of salinity stress. The closest relatives for all eight partial 16S rRNA gene sequences obtained were either organisms found in polar sea ice and other cold habitats or those found in summertime Baltic seawater. All sequences except one were associated with the α- and γ-proteobacteria or the
Cytophaga
-
Flavobacterium-Bacteroides
group. The overall physiological and community structure responses were parallel in ice-derived and open-water bacterial assemblages, which points to a linkage between community structure and physiology. These results support previous assumptions of the role of salinity fluctuation as a major selective factor shaping the sea ice bacterial community structure.
Genetic Characterization of Accumulation of Polyhydroxyalkanoate from Styrene in
Pseudomonas putida
CA-3
Authors: O'Leary Niall D. , O'Connor Kevin E. , Ward Patrick , Goff Miriam , Dobson Alan D. W. 
Published: August 2005

ABSTRACT

Pseudomonas putida
CA-3 is capable of accumulating medium-chain-length polyhydroxyalkanoates (MCL-PHAs) when growing on the toxic pollutant styrene as the sole source of carbon and energy. In this study, we report on the molecular characterization of the metabolic pathways involved in this novel bioconversion. With a mini-Tn
5
random mutagenesis approach, acetyl-coenzyme A (CoA) was identified as the end product of styrene metabolism in
P. putida
CA-3. Amplified flanking-region PCR was used to clone functionally expressed phenylacetyl-CoA catabolon genes upstream from the
sty
operon in
P. putida
CA-3, previously reported to generate acetyl-CoA moieties from the styrene catabolic intermediate, phenylacetyl-CoA. However, the essential involvement of a (non-phenylacetyl-CoA) catabolon-encoded 3-hydroxyacyl-CoA dehydrogenase is also reported. The link between de novo fatty acid synthesis and PHA monomer accumulation was investigated, and a functionally expressed 3-hydroxyacyl-acyl carrier protein-CoA transacylase (
phaG
) gene in
P. putida
CA-3 was identified. The deduced PhaG amino acid sequence shared >99% identity with a transacylase from
P. putida
KT2440, involved in 3-hydroxyacyl-CoA MCL-PHA monomer sequestration from de novo fatty acid synthesis under inorganic nutrient-limited conditions. Similarly, with
P. putida
CA-3, maximal
phaG
expression was observed only under nitrogen limitation, with concomitant PHA accumulation. Thus, β-oxidation and fatty acid de novo synthesis appear to converge in the generation of MCL-PHA monomers from styrene in
P. putida
CA-3. Cloning and functional characterization of the
pha
locus, responsible for PHA polymerization/depolymerization is also reported and the significance and future prospects of this novel bioconversion are discussed.
Lactobacillus oligofermentans
sp. nov., Associated with Spoilage of Modified-Atmosphere-Packaged Poultry Products
Authors: Koort Joanna , Murros Anna , Coenye Tom , Eerola Susanna , Vandamme Peter , Sukura Antti , Björkroth Johanna 
Published: August 2005

ABSTRACT

Unidentified lactic acid bacterium (LAB) isolates which had mainly been detected in spoiled, marinated, modified atmosphere packaged (MAP) broiler meat products during two previous studies, were identified and analyzed for their phenotypic properties and the capability to produce biogenic amines. To establish the taxonomic position of these isolates, 16S rRNA gene sequence analysis, numerical analysis of ribopatterns, and DNA-DNA hybridization experiments were done. Unexpectedly for a meat-spoilage-associated LAB, the strains utilized glucose very weakly. According to the API 50 CHL test, arabinose and xylose were the only carbohydrates strongly fermented. None of the six strains tested for production of histamine, tyramine, tryptamine, phenylethylamine, putrescine, and cadaverine were able to produce these main meat-associated biogenic amines in vitro. The polyphasic taxonomy approach showed that these strains represent a new
Lactobacillus
species. The six isolates sequenced for the 16S rRNA encoding genes shared the highest similarity (95.0 to 96.3%) with the sequence of the
Lactobacillus durianis
type strain. In the phylogenetic tree, these isolates formed a distinct cluster within the
Lactobacillus reuteri
group, which also includes
L. durianis
. Numerical analyses of HindIII-EcoRI ribotypes placed all isolates together in a cluster with seven subclusters well separated from the
L. reuteri
group reference strains. The DNA-DNA hybridization levels between
Lactobacillus
sp. nov. isolates varied from 67 to 96%, and low hybridization levels (3 to 15%) were obtained with the
L. durianis
type strain confirming that these isolates belong to the same species different from
L. durianis
. The name
Lactobacillus oligofermentans
sp. nov. is proposed, with strain LMG 22743
T
(also known as DSM 15707
T
or AMKR18
T
) as the type strain.
Distribution of
Cryptosporidium
Genotypes in Storm Event Water Samples from Three Watersheds in New York
Authors: Jiang Jianlin , Alderisio Kerri A. , Xiao Lihua 
Published: August 2005

ABSTRACT

To assess the source and public health significance of
Cryptosporidium
oocyst contamination in storm runoff, a PCR-restriction fragment length polymorphism technique based on the small-subunit rRNA gene was used in the analysis of 94 storm water samples collected from the Malcolm Brook and N5 stream basins in New York over a 3-year period. The distribution of
Cryptosporidium
in this study was compared with the data obtained from 27 storm water samples from the Ashokan Brook in a previous study. These three watersheds represented different levels of human activity. Among the total of 121 samples analyzed from the three watersheds, 107 were PCR positive, 101 of which (94.4%) were linked to animal sources. In addition,
C. hominis
(W14) was detected in six samples collected from the Malcolm Brook over a 2-week period. Altogether, 22
Cryptosporidium
species or genotypes were found in storm water samples from these three watersheds, only 11 of which could be attributed to known species/groups of animals. Several
Cryptosporidium
spp. were commonly found in these three watersheds, including the W1 genotype from an unknown animal source, the W4 genotype from deer, and the W7 genotype from muskrats. Some genotypes were found only in a particular watershed. Aliquots of 113 samples were also analyzed by the Environmental Protection Agency (EPA) Method 1623; 63 samples (55.7%) were positive for
Cryptosporidium
by microscopy, and 39 (78%) of the 50 microscopy-negative samples were positive by PCR. Results of this study demonstrate that molecular techniques can complement traditional detection methods by providing information on the source of contamination and the human-infective potential of
Cryptosporidium
oocysts found in water.
Host Species-Specific Metabolic Fingerprint Database for Enterococci and
Escherichia coli
and Its Application To Identify Sources of Fecal Contamination in Surface Waters
Authors: Ahmed W. , Neller R. , Katouli M. 
Published: August 2005

ABSTRACT

A metabolic fingerprint database of enterococci and
Escherichia coli
from 10 host groups of animals was developed to trace the sources of fecal contamination in surface waters. In all, 526 biochemical phenotypes (BPTs) of enterococci and 530
E. coli
BPTs were obtained from 4,057 enterococci and 3,728
E. coli
isolates tested. Of these, 231
Enterococcus
BPTs and 257
E. coli
BPTs were found in multiple host groups. The remaining 295
Enterococcus
BPTs and 273
E. coli
BPTs were unique to individual host groups. The database was used to trace the sources of fecal contamination in a local creek. The mean diversities (Di) of enterococci (Di = 0.76 ± 0.05) and
E. coli
(Di = 0.88 ± 0.04) were high (maximum 1) in water samples, indicating diverse sources of fecal contamination. Overall, 71% of BPTs of enterococci and 67% of
E. coli
BPTs from water samples were identified as human and animal sources. Altogether, 248
Enterococcus
BPTs and 282
E. coli
BPTs were found in water samples. Among enterococci, 26 (10%) BPTs were identical to those of humans and 152 BPTs (61%) were identical to those of animals (animal BPTs). Among
E. coli
isolates, 36 (13%) BPTs were identical to those of humans and 151 (54%) BPTs were identical to those of animals. Of the animal BPTs, 101 (66%)
Enterococcus
BPTs and 93 (62%)
E. coli
BPTs were also unique to individual animal groups. On the basis of these unique
Enterococcus
BPTs, chickens contributed 14% of contamination, followed by humans (10%), dogs (7%), and horses (6%). For
E. coli
, humans contributed 13% of contamination, followed by ducks (9%), cattle (7%), and chickens (6%). The developed metabolic fingerprint database was able to distinguish between human and animal sources as well as among animal species in the studied catchment.
Identification and Characterization of Putative Virulence Genes and Gene Clusters in
Aeromonas hydrophila
PPD134/91
Authors: Yu H. B. , Zhang Y. L. , Lau Y. L. , Yao F. , Vilches S. , Merino S. , Tomas J. M. , Howard S. P. , Leung K. Y. 
Published: August 2005

ABSTRACT

Aeromonas hydrophila
is a gram-negative opportunistic pathogen of animals and humans. The pathogenesis of
A. hydrophila
is multifactorial. Genomic subtraction and markers of genomic islands (GIs) were used to identify putative virulence genes in
A. hydrophila
PPD134/91. Two rounds of genomic subtraction led to the identification of 22 unique DNA fragments encoding 19 putative virulence factors and seven new open reading frames, which are commonly present in the eight virulence strains examined. In addition, four GIs were found, including O-antigen, capsule, phage-associated, and type III secretion system (TTSS) gene clusters. These putative virulence genes and gene clusters were positioned on a physical map of
A. hydrophila
PPD134/91 to determine their genetic organization in this bacterium. Further in vivo study of insertion and deletion mutants showed that the TTSS may be one of the important virulence factors in
A. hydrophila
pathogenesis. Furthermore, deletions of multiple virulence factors such as S-layer, serine protease, and metalloprotease also increased the 50% lethal dose to the same level as the TTSS mutation (about 1 log) in a blue gourami infection model. This observation sheds light on the multifactorial and concerted nature of pathogenicity in
A. hydrophila
. The large number of putative virulence genes identified in this study will form the basis for further investigation of this emerging pathogen and help to develop effective vaccines, diagnostics, and novel therapeutics.