bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogenetic Analysis of and Oligonucleotide Probe Development for Eikelboom Type 021N Filamentous Bacteria Isolated from Bulking Activated Sludge
Authors: Kanagawa Takahiro , Kamagata Yoichi , Aruga Shinobu , Kohno Tetsuro , Horn Matthias , Wagner Michael 
Published: July 2002

ABSTRACT

Fifteen filamentous strains, morphologically classified as Eikelboom type 021N bacteria, were isolated from bulking activated sludges. Based on comparative 16S ribosomal DNA (rDNA) sequence analysis, all strains form a monophyletic cluster together with all recognized
Thiothrix
species (88.3 to 98.7% 16S rDNA sequence similarity) within the gamma-subclass of
Proteobacteria
. The investigated Eikelboom type 021N isolates were subdivided into three distinct groups (I to III) demonstrating a previously unrecognized genetic diversity hidden behind the uniform morphology of the filaments. For in situ detection of these bacteria, 16S rRNA-targeted oligonucleotide probes specific for the entire Eikelboom type 021N-
Thiothrix
cluster and the Eikelboom type 021N groups I, II, and III, respectively, were designed, evaluated, and successfully applied in activated sludge.
Simultaneous Detection of
Salmonella
Strains and
Escherichia coli
O157:H7 with Fluorogenic PCR and Single-Enrichment-Broth Culture
Authors: Sharma Vijay K. , Carlson Steve A. 
Published: July 2002

ABSTRACT

A multiplex fluorogenic PCR assay for simultaneous detection of pathogenic
Salmonella
strains and
Escherichia coli
O157:H7 was developed and evaluated for use in detecting very low levels of these pathogens in meat and feces. Two sets of primers were used to amplify a junctional segment of virulence genes
sipB
and
sipC
of
Salmonella
and an intragenic segment of gene
eae
of
E. coli
O157:H7. Fluorogenic reporter probes were included in the PCR assay for automated and specific detection of amplified products. The assay could detect <10 CFU of
Salmonella enterica
serovar Typhimurium or
E. coli
O157:H7 per g of meat or feces artificially inoculated with these pathogens and cultured for 6 to 18 h in a single enrichment broth. Detection of amplification products could be completed in ≤4 h after enrichment.
Estimation of the Yield Coefficient of
Pseudomonas
sp. Strain DP-4 with a Low Substrate (2,4-Dichlorophenol [DCP]) Concentration in a Mineral Medium from Which Uncharacterized Organic Compounds Were Eliminated by a Non-DCP-Degrading Organism
Authors: Tarao Mitsunori , Seto Masayuki 
Published: July 2002

ABSTRACT

The yield coefficient (YC) of
Pseudomonas
sp. strain DP-4, a 2,4-dichlorophenol (DCP)-degrading organism, was estimated from the number of CFU produced at the expense of 1 unit amount of DCP at low concentrations. At a low concentration of DCP, the YC can be overestimated in pure culture, because DP-4 assimilated not only DCP but also uncharacterized organic compounds contaminating a mineral salt medium. The concentration of these uncharacterized organic compounds was nutritionally equivalent to 0.7 μg of DCP-C ml
−1
. A mixed culture with non-DCP-degrading organisms resulted in elimination of ca. 99.9% of the uncharacterized organic compounds, and then DP-4 assimilated only DCP as a substrate. In a mixed culture, DP-4 degraded an initial concentration of 0.1 to 10 μg of C ml of DCP
−1
and the number of CFU of DP-4 increased. In the mixed culture, DCP at an initial concentration of 0.07 μg of C ml
−1
was degraded. However, the number of CFU of DP-4 did not increase. DCP at an extremely low initial concentration of 0.01 μg of C ml
−1
was not degraded in mixed culture even by a high density, 10
5
CFU ml
−1
, of DP-4. When glucose was added to this mixed culture to a final concentration of 1 μg of C ml
−1
, the initial concentration of 0.01 μg of C ml of DCP
−1
was degraded. These results suggested that DP-4 required cosubstrates to degrade DCP at an extremely low initial concentration of 0.01 μg of C ml
−1
. The YCs of DP-4 at the expense of DCP alone decreased discontinuously with the decrease of the initial concentration of DCP, i.e., 1.5, 0.19, or 0 CFU per pg of DCP-C when 0.7 to 10, 0.1 to 0.5, or 0.07 μg of C ml of DCP
−1
was degraded, respectively. In this study, we developed a new method to eliminate uncharacterized organic compounds, and we estimated the YC of DP-4 at the expense of DCP as a sole source of carbon.
Bacteriocin Production with
Lactobacillus amylovorus
DCE 471 Is Improved and Stabilized by Fed-Batch Fermentation
Authors: Callewaert Raf , De Vuyst Luc 
Published: July 2002

ABSTRACT

Amylovorin L471 is a small, heat-stable, and hydrophobic bacteriocin produced by
Lactobacillus amylovorus
DCE 471. The nutritional requirements for amylovorin L471 production were studied with fed-batch fermentations. A twofold increase in bacteriocin titer was obtained when substrate addition was controlled by the acidification rate of the culture, compared with the titers reached with constant substrate addition or pH-controlled batch cultures carried out under the same conditions. An interesting feature of fed-batch cultures observed under certain culture conditions (constant feed rate) is the apparent stabilization of bacteriocin activity after obtaining maximum production. Finally, a mathematical model was set up to simulate cell growth, glucose and complex nitrogen source consumption, and lactic acid and bacteriocin production kinetics. The model showed that bacterial growth was dependent on both the energy and the complex nitrogen source. Bacteriocin production was growth associated, with a simultaneous bacteriocin adsorption on the producer cells dependent on the lactic acid accumulated and hence the viability of the cells. Both bacteriocin production and adsorption were inhibited by high concentrations of the complex nitrogen source.
Selected Bacterial Strains Protect
Artemia
spp. from the Pathogenic Effects of
Vibrio proteolyticus
CW8T2
Authors: Verschuere Laurent , Heang Hanglamong , Criel Godelieve , Sorgeloos Patrick , Verstraete Willy 
Published: July 2002

ABSTRACT

In this study
Vibrio proteolyticus
CW8T2 has been identified as a virulent pathogen for
Artemia
spp. Its infection route has been visualized with transmission electron microscopy. The pathogen affected microvilli and gut epithelial cells, disrupted epithelial cell junctions, and reached the body cavity, where it devastated cells and tissues. In vivo antagonism tests showed that preemptive colonization of the culture water with nine selected bacterial strains protected
Artemia
juveniles against the pathogenic effects. Two categories of the selected strains could be distinguished: (i) strains providing total protection, as no mortality occurred 2 days after the experimental infection with
V. proteolyticus
CW8T2, with strain LVS8 as a representative, and (ii) strains providing partial protection, as significant but not total mortality was observed, with strain LVS2 as a representative. The growth of
V. proteolyticus
CW8T2 in the culture medium was slowed down in the presence of strains LVS2 and LVS8, but growth suppression was distinctly higher with LVS8 than with LVS2. It was striking that the strains that gave only partial protection against the pathogen in the in vivo antagonism test showed also a restricted capability to colonize the
Artemia
compared to the strains providing total protection. The in vivo antagonism tests and the filtrate experiments showed that probably no extracellular bacterial compounds were involved in the protective action but that the living cells were required to protect
Artemia
against
V. proteolyticus
CW8T2.
A New Shiga Toxin 2 Variant (Stx2f) from
Escherichia coli
Isolated from Pigeons
Authors: Schmidt Herbert , Scheef Jürgen , Morabito Stefano , Caprioli Alfredo , Wieler Lothar H. , Karch Helge 
Published: July 2002

ABSTRACT

We have isolated Shiga toxin (Stx)-producing
Escherichia coli
(STEC) strains from the feces of feral pigeons which contained a new Stx2 variant gene designated

stx
2f

. This gene is most similar to
sltIIva
of patient
E. coli
O128:B12 isolate H.I.8. Stx2f reacted only weakly with commercial immunoassays. The prevalence of STEC organisms carrying the

stx
2f

gene in pigeon droppings was 12.5%. The occurrence of a new Stx2 variant in STEC from pigeons enlarges the pool of Stx2 variants and raises the question whether horizontal gene transfer to
E. coli
pathogenic to humans may occur.
Interspecific Variability in Sensitivity to UV Radiation and Subsequent Recovery in Selected Isolates of Marine Bacteria
Authors: Arrieta Jesús María , Weinbauer Markus G. , Herndl Gerhard J. 
Published: July 2002

ABSTRACT
The interspecific variability in the sensitivity of marine bacterial isolates to UV-B (295- to 320-nm) radiation and their ability to recover from previous UV-B stress were examined. Isolates originating from different microenvironments of the northern Adriatic Sea were transferred to aged seawater and exposed to artificial UV-B radiation for 4 h and subsequently to different radiation regimens excluding UV-B to determine the recovery from UV-B stress. Bacterial activity was assessed by thymidine and leucine incorporation measurements prior to and immediately after the exposure to UV-B and after the subsequent exposure to the different radiation regimens. Large interspecific differences among the 11 bacterial isolates were found in the sensitivity to UV-B, ranging from 21 to 92% inhibition of leucine incorporation compared to the bacterial activity measured in dark controls and from 14 to 84% for thymidine incorporation. Interspecific differences in the recovery from the UV stress were also large. An inverse relation was detectable between the ability to recover under dark conditions and the recovery under photosynthetic active radiation (400 to 700 nm). The observed large interspecific differences in the sensitivity to UV-B radiation and even more so in the subsequent recovery from UV-B stress are not related to the prevailing radiation conditions of the microhabitats from which the bacterial isolates originate. Based on our investigations on the 11 marine isolates, we conclude that there are large interspecific differences in the sensitivity to UV-B radiation and even larger differences in the mechanisms of recovery from previous UV stress. This might lead to UV-mediated shifts in the bacterioplankton community composition in marine surface waters.
A Binding Site for
Bacillus thuringiensis
Cry1Ab Toxin Is Lost during Larval Development in Two Forest Pests
Authors: Rausell Carolina , Martínez-Ramírez Amparo Consuelo , García-Robles Inmaculada , Real María Dolores 
Published: July 2002

ABSTRACT

The insecticidal activity and receptor binding properties of
Bacillus thuringiensis
Cry1A toxins towards the forest pests
Thaumetopoea pityocampa
(processionary moth) and
Lymantria monacha
(nun moth) were investigated. Cry1Aa, Cry1Ab, and Cry1Ac were highly toxic (corresponding 50% lethal concentration values: 956, 895, and 379 pg/μl, respectively) to first-instar
T. pityocampa
larvae. During larval development, Cry1Ab and Cry1Ac toxicity decreased with increasing age, although the loss of activity was more pronounced for Cry1Ab. Binding assays with
125
I-labelled Cry1Ab and brush border membrane vesicles from
T. pityocampa
first- and last-instar larvae detected a remarkable decrease in the overall Cry1Ab binding affinity in last-instar larvae, although saturable Cry1Ab binding to both instars was observed. Homologous competition experiments demonstrated the loss of one of the two Cry1Ab high-affinity binding sites detected in first-instar larvae. Growth inhibition assays with sublethal doses of Cry1Aa, Cry1Ab, and Cry1Ac in
L. monacha
showed that all three toxins were able to delay molting from second instar to third instar. Specific saturable binding of Cry1Ab was detected only in first- and second-instar larvae. Cry1Ab binding was not detected in last-instar larvae, although specific binding of Cry1Aa and Cry1Ac was observed. These results demonstrate a loss of Cry1Ab binding sites during development on the midgut epithelium of
T. pityocampa
and
L. monacha
, correlating in
T. pityocampa
with a decrease in Cry1Ab toxicity with increasing age.
Anaerobic Naphthalene Degradation by Microbial Pure Cultures under Nitrate-Reducing Conditions
Authors: Rockne Karl J. , Chee-Sanford Joanne C. , Sanford Robert A. , Hedlund Brian P. , Staley James T. , Strand Stuart E. 
Published: July 2002

ABSTRACT

Pure bacterial cultures were isolated from a highly enriched denitrifying consortium previously shown to anaerobically biodegrade naphthalene. The isolates were screened for the ability to grow anaerobically in liquid culture with naphthalene as the sole source of carbon and energy in the presence of nitrate. Three naphthalene-degrading pure cultures were obtained, designated NAP-3-1, NAP-3-2, and NAP-4. Isolate NAP-3-1 tested positive for denitrification using a standard denitrification assay. Neither isolate NAP-3-2 nor isolate NAP-4 produced gas in the assay, but both consumed nitrate and NAP-4 produced significant amounts of nitrite. Isolates NAP-4 and NAP-3-1 transformed 70 to 90% of added naphthalene, and the transformation was nitrate dependent. No significant removal of naphthalene occurred under nitrate-limited conditions or in cell-free controls. Both cultures exhibited partial mineralization of naphthalene, representing 7 to 20% of the initial added
14
C-labeled naphthalene. After 57 days of incubation, the largest fraction of the radiolabel in both cultures was recovered in the cell mass (30 to 50%), with minor amounts recovered as unknown soluble metabolites. Nitrate consumption, along with the results from the
14
C radiolabel study, are consistent with the oxidation of naphthalene coupled to denitrification for NAP-3-1 and nitrate reduction to nitrite for NAP-4. Phylogenetic analyses based on 16S ribosomal DNA sequences of NAP-3-1 showed that it was closely related to
Pseudomonas stutzeri
and that NAP-4 was closely related to
Vibrio pelagius
. This is the first report we know of that demonstrates nitrate-dependent anaerobic degradation and mineralization of naphthalene by pure cultures.
Involvement of Two Plasmids in Fenitrothion Degradation by
Burkholderia
sp. Strain NF100
Authors: Hayatsu Masahito , Hirano Motoko , Tokuda Shinichi 
Published: July 2002

ABSTRACT

A bacterium capable of utilizing fenitrothion (
O
,
O
-dimethyl
O
-4-nitro-
m
-tolyl phosphorothioate) as a sole carbon source was isolated from fenitrothion-treated soil. This bacterium was characterized taxonomically as being a member of the genus
Burkholderia
and was designated strain NF100. NF100 first hydrolyzed an organophosphate bond of fenitrothion, forming 3-methyl-4-nitrophenol, which was further metabolized to methylhydroquinone. The ability to degrade fenitrothion was found to be encoded on two plasmids, pNF1 and pNF2.
Metabolic Analysis of
Escherichia coli
in the Presence and Absence of the Carboxylating Enzymes Phosphoenolpyruvate Carboxylase and Pyruvate Carboxylase
Authors: Gokarn R. R. , Eiteman M. A. , Altman E. 
Published: July 2002

ABSTRACT

Fermentation patterns of
Escherichia coli
with and without the phosphoenolpyruvate carboxylase (PPC) and pyruvate carboxylase (PYC) enzymes were compared under anaerobic conditions with glucose as a carbon source. Time profiles of glucose and fermentation product concentrations were determined and used to calculate metabolic fluxes through central carbon pathways during exponential cell growth. The presence of the
Rhizobium etli pyc
gene in
E. coli
(JCL1242/pTrc99A-
pyc
) restored the succinate producing ability of
E. coli ppc
null mutants (JCL1242), with PYC competing favorably with both pyruvate formate lyase and lactate dehydrogenase. Succinate formation was slightly greater by JCL1242/pTrc99A-
pyc
than by cells which overproduced PPC (JCL1242/pPC201,
ppc
+
), even though PPC activity in cell extracts of JCL1242/pPC201 (
ppc
+
) was 40-fold greater than PYC activity in extracts of JCL1242/pTrc99a-
pyc
. Flux calculations indicate that during anaerobic metabolism the
pyc
+
strain had a 34% greater specific glucose consumption rate, a 37% greater specific rate of ATP formation, and a 6% greater specific growth rate compared to the
ppc
+
strain. In light of the important position of pyruvate at the juncture of NADH-generating pathways and NADH-dissimilating branches, the results show that when PPC or PYC is expressed, the metabolic network adapts by altering the flux to lactate and the molar ratio of ethanol to acetate formation.
Toluene Monooxygenase-Catalyzed Epoxidation of Alkenes
Authors: McClay Kevin , Fox Brian G. , Steffan Robert J. 
Published: July 2002

ABSTRACT

Several toluene monooxygenase-producing organisms were tested for their ability to oxidize linear alkenes and chloroalkenes three to eight carbons long. Each of the wild-type organisms degraded all of the alkenes that were tested. Epoxides were produced during the oxidation of butene, butadiene, and pentene but not hexene or octadiene. A strain of
Escherichia coli
expressing the cloned toluene-4-monooxygenase (T4MO) of
Pseudomonas mendocina
KR1 was able to oxidize butene, butadiene, pentene, and hexene but not octadiene, producing epoxides from all of the substrates that were oxidized. A T4MO-deficient variant of
P. mendocina
KR1 oxidized alkenes that were five to eight carbons long, but no epoxides were detected, suggesting the presence of multiple alkene-degrading enzymes in this organism. The alkene oxidation rates varied widely (ranging from 0.01 to 0.33 μmol of substrate/min/mg of cell protein) and were specific for each organism-substrate pair. The enantiomeric purity of the epoxide products also varied widely, ranging from 54 to >90% of a single epoxide enantiomer. In the absence of more preferred substrates, such as toluene or alkenes, the epoxides underwent further toluene monooxygenase-catalyzed transformations, forming products that were not identified.
Cryptosporidiumspp. in Domestic Dogs: the “Dog” Genotype
Authors: Morgan Una M. , Xiao Lihua , Monis Paul , Fall Abbie , Irwin Peter J. , Fayer Ronald , Denholm Karen M. , Limor Josef , Lal Altaf , Thompson R. C. Andrew 
Published: July 2002

ABSTRACTGenetic and phylogenetic characterization ofCryptosporidiumisolates at two loci (18S rRNA gene and heat shock gene) from both Australian and United States dogs demonstrated that dog-derivedCryptosporidiumisolates had a distinct genotype which is conserved across geographic areas. Phylogenetic analysis provided support for the idea that the “dog” genotype is, in fact, a valid species.
Isolation and Characterization of Strains CVO and FWKO B, Two Novel Nitrate-Reducing, Sulfide-Oxidizing Bacteria Isolated from Oil Field Brine
Authors: Gevertz Diane , Telang Anita J. , Voordouw Gerrit , Jenneman Gary E. 
Published: July 2002

ABSTRACT

Bacterial strains CVO and FWKO B were isolated from produced brine at the Coleville oil field in Saskatchewan, Canada. Both strains are obligate chemolithotrophs, with hydrogen, formate, and sulfide serving as the only known energy sources for FWKO B, whereas sulfide and elemental sulfur are the only known electron donors for CVO. Neither strain uses thiosulfate as an energy source. Both strains are microaerophiles (1% O
2
). In addition, CVO grows by denitrification of nitrate or nitrite whereas FWKO B reduces nitrate only to nitrite. Elemental sulfur is the sole product of sulfide oxidation by FWKO B, while CVO produces either elemental sulfur or sulfate, depending on the initial concentration of sulfide. Both strains are capable of growth under strictly autotrophic conditions, but CVO uses acetate as well as CO
2
as its sole carbon source. Neither strain reduces sulfate; however, FWKO B reduces sulfur and displays chemolithoautotrophic growth in the presence of elemental sulfur, hydrogen, and CO
2
. Both strains grow at temperatures between 5 and 40°C. CVO is capable of growth at NaCl concentrations as high as 7%. The present 16s rRNA analysis suggests that both strains are members of the epsilon subdivision of the division
Proteobacteria
, with CVO most closely related to
Thiomicrospira denitrifcans
and FWKO B most closely related to members of the genus
Arcobacter
. The isolation of these two novel chemolithotrophic sulfur bacteria from oil field brine suggests the presence of a subterranean sulfur cycle driven entirely by hydrogen, carbon dioxide, and nitrate.
Detection of Astroviruses, Enteroviruses, and Adenovirus Types 40 and 41 in Surface Waters Collected and Evaluated by the Information Collection Rule and an Integrated Cell Culture-Nested PCR Procedure
Authors: Chapron Christopher D. , Ballester Nicola A. , Fontaine Justin H. , Frades Christine N. , Margolin Aaron B. 
Published: July 2002

ABSTRACT
We evaluated the use of an integrated cell culture-reverse transcription-PCR (ICC-RT-PCR) procedure coupled with nested PCR to detect human astroviruses, enteroviruses, and adenovirus types 40 and 41 in surface water samples that were collected and evaluated by using the Information Collection Rule (ICR) method. The results obtained with the ICC-RT-PCR–nested PCR method were compared to the results obtained with the total culturable virus assay–most-probable-number (TCVA-MPN) method, the method recommended by the U.S. Environmental Protection Agency for monitoring viruses in surface and finished waters. Twenty-nine ICR surface water samples were analyzed. Viruses were concentrated by using filter adsorption-beef extract elution and organic flocculation techniques, and then the preparations were evaluated for viruses by visualizing cytopathic effects in the Buffalo green monkey kidney (BGMK) cell line. In the ICC-RT-PCR–nested PCR technique we used Caco-2 cells to propagate astroviruses and enteroviruses (ICC step), and we used BGMK cells to propagate adenovirus types 40 and 41, as well as enteroviruses. Fifteen of the 29 samples (51.7%) were positive for astrovirus as determined by the ICC-RT-PCR–nested PCR method, and eight of these samples (27.5%) contained infectious astrovirus. Seventeen of the 29 samples (58.6%) were positive for enteroviruses when the BGMK cell line was used, and six (27.6%) of these samples were determined to be infectious. Fourteen of the 29 samples (48.3%) were positive for adenovirus types 40 and 41, and 11 (37.9%) of these samples were determined to be infectious. Twenty-seven of the 29 samples (93.1%) were positive for a virus, and 19 (68.9%) of the samples were positive for an infectious virus. Only 5 of the 29 samples (17.2%) were positive as determined by the TCVA-MPN method. The ICC-RT-PCR–nested PCR method provided increased sensitivity compared to the TCVA-MPN method.