bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization ofPseudomonasspp. Associated with Spoilage of Gilt-Head Sea Bream Stored under Various Conditions
Authors: Tryfinopoulou P. , Tsakalidou E. , Nychas G.-J. E. 
Published: July 2002

ABSTRACTThe population dynamics of pseudomonads in gilt-head sea bream Mediterranean fish (Sparusaurata) stored under different conditions were studied. Phenotypic analysis and sodium dodecyl sulfate-polyacrylamide gel electrophoresis of whole-cell proteins were performed to identify a total of 106Pseudomonasstrains isolated fromS.auratastored under different temperatures (at 0, 10, and 20°C) and packaging conditions (air and a modified atmosphere of 40% CO2-30% N2-30% O2).Pseudomonas lundensiswas the predominant species, followed byPseudomonas fluorescens, whilePseudomonas fragiandPseudomonas putidawere detected less frequently. FluorescentPseudomonasstrains dominated under air conditions, while proteolytic and less lipolytic strains dominated under modified-atmosphere packaging. Different storage conditions appear to govern the selection of pseudomonads in gilt-head sea bream fish.
Molecular Cloning of
XYL3
(
d
-Xylulokinase) from
Pichia stipitis
and Characterization of Its Physiological Function
Authors: Jin Yong-Su , Jones Sharon , Shi Nian-Qing , Jeffries Thomas W. 
Published: July 2002

ABSTRACT

XYL3
, which encodes a
d
-xylulokinase (EC 2.7.1.17), was isolated from
Pichia stipitis
CBS 6054 genomic DNA by using primers designed against conserved motifs. Disruption of
XYL3
eliminated
d
-xylulokinase activity, but
d
-ribulokinase activity was still present. Southern analysis of
P. stipitis
genomic DNA with
XYL3
as a probe confirmed the disruption and did not reveal additional related genes. Disruption of
XYL3
stopped ethanol production from xylose, but the resulting mutant still assimilated xylose slowly and formed xylitol and arabinitol. These results indicate that
XYL3
is critical for ethanol production from xylose but that
P. stipitis
has another pathway for xylose assimilation. Expression of
XYL3
using its
P. stipitis
promoter increased
Saccharomyces cerevisiae
d
-xylulose consumption threefold and enabled the transformants to produce ethanol from a mixture of xylose and xylulose, whereas the parental strain only accumulated xylitol. In vitro,
d
-xylulokinase activity in recombinant
S. cerevisiae
was sixfold higher with a multicopy than with a single-copy
XYL3
plasmid, but ethanol production decreased with increased copy number. These results confirmed the function of
XYL3
in
S. cerevisiae
.
Use of Fe(III) as an Electron Acceptor To Recover Previously Uncultured Hyperthermophiles: Isolation and Characterization of
Geothermobacterium ferrireducens
gen. nov., sp. nov
Authors: Kashefi Kazem , Holmes Dawn E. , Reysenbach Anna-Louise , Lovley Derek R. 
Published: July 2002

ABSTRACT

It has recently been recognized that the ability to use Fe(III) as a terminal electron acceptor is a highly conserved characteristic in hyperthermophilic microorganisms. This suggests that it may be possible to recover as-yet-uncultured hyperthermophiles in pure culture if Fe(III) is used as an electron acceptor. As part of a study of the microbial diversity of the Obsidian Pool area in Yellowstone National Park, Wyo., hot sediment samples were used as the inoculum for enrichment cultures in media containing hydrogen as the sole electron donor and poorly crystalline Fe(III) oxide as the electron acceptor. A pure culture was recovered on solidified, Fe(III) oxide medium. The isolate, designated FW-1a, is a hyperthermophilic anaerobe that grows exclusively by coupling hydrogen oxidation to the reduction of poorly crystalline Fe(III) oxide. Organic carbon is not required for growth. Magnetite is the end product of Fe(III) oxide reduction under the culture conditions evaluated. The cells are rod shaped, about 0.5 μm by 1.0 to 1.2 μm, and motile and have a single flagellum. Strain FW-1a grows at circumneutral pH, at freshwater salinities, and at temperatures of between 65 and 100°C with an optimum of 85 to 90°C. To our knowledge this is the highest temperature optimum of any organism in the
Bacteria
. Analysis of the 16S ribosomal DNA (rDNA) sequence of strain FW-1a places it within the
Bacteria
, most closely related to abundant but uncultured microorganisms whose 16S rDNA sequences have been previously recovered from Obsidian Pool and a terrestrial hot spring in Iceland. While previous studies inferred that the uncultured microorganisms with these 16S rDNA sequences were sulfate-reducing organisms, the physiology of the strain FW-1a, which does not reduce sulfate, indicates that these organisms are just as likely to be Fe(III) reducers. These results further demonstrate that Fe(III) may be helpful for recovering as-yet-uncultured microorganisms from hydrothermal environments and illustrate that caution must be used in inferring the physiological characteristics of at least some thermophilic microorganisms solely from 16S rDNA sequences. Based on both its 16S rDNA sequence and physiological characteristics, strain FW-1a represents a new genus among the
Bacteria.
The name
Geothermobacterium ferrireducens
gen. nov., sp. nov., is proposed (ATCC BAA-426).
Intracellular Carbon Fluxes in Riboflavin-Producing
Bacillus
subtilis
during Growth on Two-Carbon Substrate Mixtures
Authors: Dauner Michael , Sonderegger Marco , Hochuli Michel , Szyperski Thomas , Wüthrich Kurt , Hohmann Hans-Peter , Sauer Uwe , Bailey James E. 
Published: July 2002

ABSTRACT

Metabolic responses to cofeeding of different carbon substrates in carbon-limited chemostat cultures were investigated with riboflavin-producing
Bacillus
subtilis
. Relative to the carbon content (or energy content) of the substrates, the biomass yield was lower in all cofeeding experiments than with glucose alone. The riboflavin yield, in contrast, was significantly increased in the acetoin- and gluconate-cofed cultures. In these two scenarios, unusually high intracellular ATP-to-ADP ratios correlated with improved riboflavin yields. Nuclear magnetic resonance spectra recorded with amino acids obtained from biosynthetically directed fractional
13
C labeling experiments were used in an isotope isomer balancing framework to estimate intracellular carbon fluxes. The glycolysis-to-pentose phosphate (PP) pathway split ratio was almost invariant at about 80% in all experiments, a result that was particularly surprising for the cosubstrate gluconate, which feeds directly into the PP pathway. The in vivo activities of the tricarboxylic acid cycle, in contrast, varied more than twofold. The malic enzyme was active with acetate, gluconate, or acetoin cofeeding but not with citrate cofeeding or with glucose alone. The in vivo activity of the gluconeogenic phosphoenolpyruvate carboxykinase was found to be relatively high in all experiments, with the sole exception of the gluconate-cofed culture.
Synthesis of Pyruvate Dehydrogenase in
Staphylococcus aureus
Is Stimulated by Osmotic Stress
Authors: Vilhelmsson Oddur , Miller Karen J. 
Published: July 2002

ABSTRACT

The pyruvate dehydrogenase multienzyme complex (PDHC) was found to be upregulated by osmotic stress in the osmotolerant pathogen
Staphylococcus aureus
. Upregulation was detectable in the levels of both activity and protein and was judged to be about fourfold when sodium chloride was used to adjust the water activity (a
w
) of the growth medium to 0.94. The upregulation of the PDHC was also found to be humectant dependent and was greatest when impermeant, nonmetabolizable humectants were used to adjust a
w
. Further experiments provided evidence that in addition to osmotic upregulation, the PDHC complex is also subject to catabolite repression, thus providing a possible explanation for the observation that high concentrations of carbohydrates are generally more inhibitory to the growth of this bacterial pathogen than are high concentrations of salts.
Modulation of Gene Expression Made Easy
Authors: Solem Christian , Jensen Peter Ruhdal 
Published: July 2002

ABSTRACT

A new approach for modulating gene expression, based on randomization of promoter (spacer) sequences, was developed. The method was applied to chromosomal genes in
Lactococcus lactis
and shown to generate libraries of clones with broad ranges of expression levels of target genes. In one example, overexpression was achieved by introducing an additional gene copy into a phage attachment site on the chromosome. This resulted in a series of strains with phosphofructokinase activities from 1.4 to 11 times the wild-type activity level. In this example, the
pfk
gene was cloned upstream of a
gusA
gene encoding β-glucuronidase, resulting in an operon structure in which both genes are transcribed from a common promoter. We show that there is a linear correlation between the expressions of the two genes, which facilitates screening for mutants with suitable enzyme activities. In a second example, we show that the method can be applied to modulating the expression of native genes on the chromosome. We constructed a series of strains in which the expression of the
las
operon, containing the genes
pfk
,
pyk
, and
ldh
, was modulated by integrating a truncated copy of the
pfk
gene. Importantly, the modulation affected the activities of all three enzymes to the same extent, and enzyme activities ranging from 0.5 to 3.5 times the wild-type level were obtained.
Biochemical and Genetic Characterization of the Two-Peptide Bacteriocin Enterocin 1071 Produced by
Enterococcus faecalis
FAIR-E 309
Authors: Franz Charles M. A. P. , Grube Alexandra , Herrmann Anette , Abriouel Hikmate , Stärke Joachim , Lombardi Angiolella , Tauscher Bernhard , Holzapfel Wilhelm H. 
Published: July 2002

ABSTRACT

The structural genes for the two-peptide bacteriocin enterocin 1071 (Ent1071) in
Enterococcus faecalis
FAIR-E 309 were cloned. DNA sequence analysis showed that the enterocin 1071A (Ent1071A) peptide of strain FAIR-E 309 differed by two amino acids from the Ent1071A reported for
E. faecalis
BFE 1071 (E. Balla, L. M. T. Dicks, M. Du Toit, M. J. van der Merwe, and W. H. Holzapfel, Appl. Environ. Microbiol. 66:1298-1304, 2000), while the Ent1071B gene encoded identical peptides in these strains. However, resequencing of
ent1071A
from
E. faecalis
BFE 1071 showed that the Ent1071A peptide sequence reported previously was incorrect in two amino acids. Also,
ent1071B
in
E. faecalis
FAIR-E 309 encoded a prepeptide that was three amino acids shorter than that previously reported for
E. faecalis
BFE 1071 Ent1071B. A presumptive immunity gene (
eni1071
) was located downstream of the bacteriocin structural genes. This gene was cloned into the heterologous host
E. faecalis
ATCC 19433 and was shown to confer immunity. A truncated ABC transporter gene was located upstream of the Ent1071 structural genes.
An Antifungal Protein from the Marine Bacterium
Streptomyces
sp. Strain AP77 Is Specific for
Pythium porphyrae
, a Causative Agent of Red Rot Disease in
Porphyra
spp
Authors: Woo Jung-Hee , Kitamura Etsushi , Myouga Hisashi , Kamei Yuto 
Published: July 2002

ABSTRACT

A novel antifungal protein (SAP) was found in the culture supernatant of a marine bacterium,
Streptomyces
sp. strain AP77, and was purified. This protein was characterized by chemical, biochemical, and biological analyses. By using gel filtration, the molecular mass of SAP was estimated to be 160 kDa. Structural analysis of SAP by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and matrix-assisted laser desorption ionization-time of flight mass spectrometry suggested that SAP is composed of three heterologous protein subunits of 41.7 kDa (SAP1), 21.7 kDa (SAP2), and 18.7 kDa (SAP3) at a molar ratio of 1:1:5 (or 1:1:6). N-terminal amino acid sequence analysis and a homology search revealed that SAP1, SAP2, and SAP3 exhibit 64.3, 68.4, and 86.7% similarity to three
Streptomyces coelicolor
polypeptides, puromycin resistance protein (Pur8), a conserved hypothetical protein, and bacterioferritin, respectively. The MIC of purified SAP against
Pythium porphyrae
was determined to be 1.6 μg/disk, whereas no inhibitory effect was observed at concentrations up to 100 μg/disk against most of the fungal and bacterial strains tested; the only exception was relatively strong antifungal activity against
Pythium ultimum
(MIC, 6.3 μg/disk). In vitro and in vivo toxicity tests demonstrated that SAP showed no toxicity against
Porphyra yezoensis
cells, human normal dermal fibroblasts, and mice at doses up to 700 μg/ml (for 24 h), 250 μg/ml (for 12 h), and 75 mg/kg (for 35 days), respectively. SAP was labile when it was subjected to a heated-air drying treatment, which is a great advantage in food production procedures. These results indicated that
Streptomyces
sp. strain AP77 might be useful as a gene source for safe transgenic
Porphyra
breeding for tolerance to
Pythium
infection.
High Prevalence of Vancomycin-Resistant Enterococci in Swedish Sewage
Authors: Iversen Aina , Kühn Inger , Franklin Anders , Möllby Roland 
Published: July 2002

ABSTRACT

In Europe the use of the growth promoter avoparcin is considered to have selected for vancomycin-resistant enterococci (VRE). Sweden ceased using avoparcin in 1986, and only occasional cases of VRE from hospitals have been reported since 1995. Within the framework of a European study, samples from urban raw sewage, treated sewage, surface water, and hospital sewage in Sweden (
n
= 118) were screened for VRE. Surprisingly, VRE were isolated from 21 of 35 untreated sewage samples (60%), from 5 of 14 hospital sewage samples (36%), from 6 of 32 treated sewage samples (19%), and from 1 of 37 surface water samples. Thirty-five isolates from 33 samples were further characterized by geno- and phenotyping, MIC determination, and PCR analysis. Most isolates (30 of 35) carried the
vanA
gene, and the majority (24 of 35) of the isolates were
Enterococcus faecium
. Most of the VRE were multiresistant. The typing revealed high diversity of the isolates. However, one major cluster with seven identical or similar isolates was found. These isolates came from three different sewage treatment plants and were collected at different occasions during 1 year. All VRE from hospital sewage originated from one of the two hospitals studied. That hospital also had vancomycin consumption that was 10-fold that of the other. We conclude that VRE were commonly found in sewage samples in Sweden. The origin might be both healthy individuals and individuals in hospitals. Possibly, antimicrobial drugs or chemicals released into the sewage system may sustain VRE in the system.
Development of a Flow Cytometric Method To Analyze Subpopulations of Bacteria in Probiotic Products and Dairy Starters
Authors: Bunthof Christine J. , Abee Tjakko 
Published: July 2002

ABSTRACT

Flow cytometry (FCM) is a rapid and sensitive technique that can determine cell numbers and measure various physiological characteristics of individual cells by using appropriate fluorescent probes. Previously, we developed an FCM assay with the viability probes carboxyfluorescein diacetate (cFDA) and TOTO-1 {1′-(4,4,7,7-tetramethyl-4,7-diazaundecamethylene)-bis-4-[3-methyl-2,3dihydro(benzo-1,3-oxazole)-2-methylidene]-1-(3′-trimethylammoniumpropyl)-pyridinium tetraiodide} for (stressed) lactic acid bacteria (C. J. Bunthof, K. Bloemen, P. Breeuwer, F. M. Rombouts, and T. Abee, Appl. Environ. Microbiol.
67:
2326-2335, 2001). cFDA stains intact cells with enzymatic activity, and TOTO-1 stains membrane-permeabilized cells. Here we used this assay to study the viability of bacterial suspensions in milk, dairy fermentation starters, and probiotic products. To facilitate FCM analysis of bacteria in milk, a commercially available milk-clearing solution was used. The procedure was optimized to increase the signal-to-noise ratio. FCM enumerations were accurate down to a concentration of 10
5
cells ml
−1
. The level of retrieval of
Lactobacillus plantarum
WCFS 1 suspended in milk was high, and viability was not affected by the procedure. The plate counts for cleared samples of untreated cell suspensions were nearly as high as the total FCM counts, and the correlation was strong (
r
> 0.99). In dairy fermentation starters and in probiotic products the FCM total cell counts were substantially higher than the numbers of CFU. Three functional populations could be distinguished: culturable cells, cells that are intact and metabolically active but not culturable, and permeabilized cells. The proportions of the populations differed in the products tested. This FCM method provides tools to assess the functionality of different populations in fermentation starters and probiotic products.
Identification and Isolation of Genes Involved in Poly(β-Hydroxybutyrate) Biosynthesis in
Azospirillum brasilense
and Characterization of a
phbC
Mutant
Authors: Kadouri Daniel , Burdman Saul , Jurkevitch Edouard , Okon Yaacov 
Published: July 2002

ABSTRACT

Like many other prokaryotes, rhizobacteria of the genus
Azospirillum
produce high levels of poly(β-hydroxybutyrate) (PHB) under suboptimal growth conditions. Utilization of PHB by bacteria under stress has been proposed as a mechanism that favors their compatible establishment in competitive environments, thus showing great potential for the improvement of bacterial inoculants for plants and soils. The three genes that are considered to be essential in the PHB biosynthetic pathway,
phbA
(β-ketothiolase),
phbB
(acetoacetyl coenzyme A reductase), and
phbC
(PHB synthase), were identified in
Azospirillum brasilense
strain Sp7, cloned, and sequenced. The
phbA
, -
B
, and -
C
genes were found to be linked together and located on the chromosome. An
A. brasilense phbC
mutant was obtained by insertion of a kanamycin resistance cassette within the
phbC
gene. No PHB production was detected in this mutant. The capability of the wild-type strain to endure starvation conditions was higher than that of the mutant strain. However, motility, cell aggregation, root adhesion, and exopolysaccharide (EPS) and capsular polysaccharide (CPS) production were higher in the
phbC
mutant strain than in the wild type.
Immunomagnetic Separation (IMS)-Fluorescent Antibody Detection and IMS-PCR Detection of Seeded
Cryptosporidium parvum
Oocysts in Natural Waters and Their Limitations
Authors: Sturbaum Gregory D. , Klonicki Patricia T. , Marshall Marilyn M. , Jost B. Helen , Clay Brec L. , Sterling Charles R. 
Published: July 2002

ABSTRACT

Detection and enumeration of
Cryptosporidium parvum
in both treated and untreated waters are important to facilitate prevention of future cryptosporidiosis incidents. Immunomagnetic separation (IMS)-fluorescent antibody (FA) detection and IMS-PCR detection efficiencies were evaluated in two natural waters seeded with nominal seed doses of 5, 10, and 15 oocysts. IMS-FA detected oocysts at concentrations at or below the three nominal oocyst seed doses, illustrating that IMS-FA is sensitive enough to detect low oocyst numbers. However, the species of the oocysts could not be determined with this technique. IMS-PCR, targeting the 18S rRNA gene in this study, yielded positive amplification for 17 of the 18 seeded water samples, and the amplicons were subjected to restriction fragment length polymorphism digestion and DNA sequencing for species identification. Interestingly, the two unseeded, natural water samples were also PCR positive; one amplicon was the same base pair size as the
C. parvum
amplicon, and the other amplicon was larger. These two amplified products were determined to be derived from DNA of
Cryptosporidium muris
and a dinoflagellate. These IMS-PCR results illustrate that (i) IMS-PCR is able to detect low oocyst numbers in natural waters, (ii) PCR amplification alone is not confirmatory for detection of target DNA when environmental samples are used, (ii) PCR primers, especially those designed against the rRNA gene region, need to be evaluated for specificity with organisms closely related to the target organism, and (iv) environmental amplicons should be subjected to appropriate species-specific confirmatory techniques.
Characterization of Cholylglycine Hydrolase from a Bile-Adapted Strain of
Xanthomonas maltophilia
and Its Application for Quantitative Hydrolysis of Conjugated Bile Salts
Authors: Dean Mariangela , Cervellati Carlo , Casanova Elena , Squerzanti Monica , Lanzara Vincenzo , Medici Alessandro , Polverino de Laureto Patrizia , Bergamini Carlo M. 
Published: July 2002

ABSTRACT

Purified bile salt hydrolase from bile-adapted
Xanthomonas maltophilia
displays Michaelis-Menten kinetics on cholylglycine and cholyltaurine and hydrolyzes bile salts also in crude bovine bile. The protein is a dimer and is resistant to proteinases and to heating at 55 to 60°C for up to 60 min, in agreement with calorimetric data.
Comparative Study of Vaginal
Lactobacillus
Phages Isolated from Women in the United States and Turkey: Prevalence, Morphology, Host Range, and DNA Homology
Authors: Kiliç Ali O. , Pavlova Sylvia I. , Alpay Sengul , Kiliç S. Sirri , Tao Lin 
Published: July 2002

ABSTRACT

Lactobacilli play an important role in maintaining vaginal health. However, during bacterial vaginosis lactobacilli decrease for unknown reasons. Our preliminary study showed that phages could infect vaginal lactobacilli. Therefore, the aim of this study was to analyze the distribution, virulence, and types of vaginal
Lactobacillus
phages isolated from women of two countries: the United States and Turkey. A total of 209 vaginal lactobacilli were isolated from reproductive-aged women in the United States (
n
= 107) and Turkey (
n
= 102). By analysis of 16S rRNA gene sequence and by comparison of protein profiles, most lactobacilli were identified as
L. crispatus
,
L. gasseri
, and
L. jensenii
. After mitomycin C induction, 28% of American lactobacilli and 36% of Turkish lactobacilli released phages. A total of 67 phages were isolated and further characterized by their host range, electron microscopy, and DNA homology. All 67 phages were infective against lactobacilli from both collections. The host ranges of most phages were broad, including multiple
Lactobacillus
species. Even though the phages were all temperate, they were able to cause lytic infection in various strains. The electron micrographs of these phages showed a hexagon-shaped head and a long tail with or without a contractile tail sheath. Based on their morphology, these phages belonged to Bradley's phage groups A and B, and could be further classified into four morphotypes. All four types were found among American phages, but only three were found among Turkish isolates. DNA hybridization with labeled probes of the four types of phages revealed that additional genetic types existed within each morphotype among these phages. The phage genomic sizes ranged between 34 and 55 kb. Many of the lysogenic
Lactobacillus
strains released phages spontaneously at a high frequency of 10
−3
to 10
−4
PFU/cell. In conclusion, lysogeny in vaginal lactobacilli is widely spread. Some lysogenic lactobacilli spontaneously release phages with a broad host range, which can be lytic against other vaginal lactobacilli regardless of their geographic origin.