bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conversion of 2-Fluoromuconate tocis-Dienelactone by Purified Enzymes ofRhodococcus opacus1cp
Authors: Solyanikova Inna P. , Moiseeva Olga V. , Boeren Sjef , Boersma Marelle G. , Kolomytseva Marina P. , Vervoort Jacques , Rietjens Ivonne M. C. M. , Golovleva Ludmila A. , van Berkel Willem J. H. 
Published: September 2003

ABSTRACTThe present study describes the19F nuclear magnetic resonance analysis of the conversion of 3-halocatechols to lactones by purified chlorocatechol 1,2-dioxygenase (ClcA2), chloromuconate cycloisomerase (ClcB2), and chloromuconolactone dehalogenase (ClcF) fromRhodococcus opacus1cp grown on 2-chlorophenol. The 3-halocatechol substrates were produced from the corresponding 2-halophenols by either phenol hydroxylase fromTrichosporon cutaneumor 2-hydroxybiphenyl 3-mono-oxygenase fromPseudomonas azelaica. Several fluoromuconates resulting from intradiol ring cleavage by ClcA2 were identified. ClcB2 converted 2-fluoromuconate to 5-fluoromuconolactone and 2-chloro-4-fluoromuconate to 2-chloro-4-fluoromuconolactone. Especially the cycloisomerization of 2-fluoromuconate is a new observation. ClcF catalyzed the dehalogenation of 5-fluoromuconolactone tocis-dienelactone. The ClcB2 and ClcF-mediated reactions are in line with the recent finding of a second cluster of chlorocatechol catabolic genes inR. opacus1cp which provides a new route for the microbial dehalogenation of 3-chlorocatechol.
Stereoselective Microbial Dehalorespiration with Vicinal Dichlorinated Alkanes
Authors: De Wildeman Stefaan , Diekert Gabriele , Van Langenhove Herman , Verstraete Willy 
Published: September 2003

ABSTRACTThe suspected carcinogen 1,2-dichloroethane (1,2-DCA) is the most abundant chlorinated C2groundwater pollutant on earth. However, a reductive in situ detoxification technology for this compound does not exist. Although anaerobic dehalorespiring bacteria are known to catalyze several dechlorination steps in the reductive-degradation pathway of chlorinated ethenes and ethanes, no appropriate isolates that selectively and metabolically convert them into completely dechlorinated end products in defined growth media have been reported. Here we report on the isolation ofDesulfitobacterium dichloroeliminansstrain DCA1, a nutritionally defined anaerobic dehalorespiring bacterium that selectively converts 1,2-dichloroethane and all possible vicinal dichloropropanes and -butanes into completely dechlorinated end products. Menaquinone was identified as an essential cofactor for growth of strain DCA1 in pure culture. Strain DCA1 converts chiral chlorosubstrates, revealing the presence of a stereoselective dehalogenase that exclusively catalyzes an energy-conservingantimechanistic dichloroelimination. Unlike any known dehalorespiring isolate, strain DCA1 does not carry out reductive hydrogenolysis reactions but rather exclusively dichloroeliminates its substrates. This unique dehalorespiratory biochemistry has shown promising application possibilities for bioremediation purposes and fine-chemical synthesis.
Biofilm Formation and the Presence of the Intercellular Adhesion Locus
ica
among Staphylococci from Food and Food Processing Environments
Authors: Møretrø Trond , Hermansen Lene , Holck Askild L. , Sidhu Maan S. , Rudi Knut , Langsrud Solveig 
Published: September 2003

ABSTRACT

In clinical staphylococci, the presence of the
ica
genes and biofilm formation are considered important for virulence. Biofilm formation may also be of importance for survival and virulence in food-related staphylococci. In the present work, staphylococci from the food industry were found to differ greatly in their abilities to form biofilms on polystyrene. A total of 7 and 21 of 144 food-related strains were found to be strong and weak biofilm formers, respectively. Glucose and sodium chloride stimulated biofilm formation. The biofilm-forming strains belonged to nine different coagulase-negative species of
Staphylococcus.
The
icaA
gene of the intercellular adhesion locus was detected by Southern blotting and hybridization in 38 of 67 food-related strains tested. The presence of
icaA
was positively correlated with strong biofilm formation. The
icaA
gene was partly sequenced for 22 food-related strains from nine different species of
Staphylococcus
, and their
icaA
genes were found to have DNA similarities to previously sequenced
icaA
genes of 69 to 100%. Northern blot analysis indicated that the expression of the
ica
genes was higher in strong biofilm formers than that seen with strains not forming biofilms. Biofilm formation on polystyrene was positively correlated with biofilm formation on stainless steel and with resistance to quaternary ammonium compounds, a group of disinfectants.
Novel Eukaryotes from the Permanently Anoxic Cariaco Basin (Caribbean Sea)
Authors: Stoeck Thorsten , Taylor Gordon T. , Epstein Slava S. 
Published: September 2003

ABSTRACTPresent knowledge of microbial diversity is decidedly incomplete (S. J. Giovannoni and M. S. Rappé, p. 47-84,inD. Kirchman, ed.,Microbial Ecology of the Oceans, 2000; E. Stackebrandt and T. M. Embley, p. 57-75,inR. R. Colwell and D. J. Grimes, ed.,Nonculturable Microorganisms in the Environment, 2000). Protistan phylogenies are particularly deficient and undoubtedly exclude clades of principal ecological and evolutionary importance (S. L. Baldauf, Science 300:1703-1706, 2003). The rRNA approach has been extraordinarily successful in expanding the global prokaryotic record (S. J. Giovannoni and M. S. Rappé, p. 47-84,inD. Kirchman, ed.,Microbial Ecology of the Oceans, 2000; E. Stackebrandt and T. M. Embley, p. 57-75,inR. R. Colwell and D. J. Grimes, ed.,Nonculturable Microorganisms in the Environment, 2000) but has rarely been used in protistan discovery. Here we report the first application of the 18S rRNA approach to a permanently anoxic environment, the Cariaco Basin off the Venezuelan coast. On the basis of rRNA sequences, we uncovered a substantial number of novel protistan lineages. These included new clades of the highest taxonomic level unrelated to any known eukaryote as well as deep branches within established protistan groups. Three novel lineages branch at the base of the eukaryotic evolutionary tree preceding, contemporary with, or immediately following the earliest eukaryotic branches. These newly discovered protists may retain traits reminiscent of an early eukaryotic ancestor(s).
Toward an International Standard for PCR-BasedDetection of Food-Borne Thermotolerant Campylobacters: AssayDevelopment and AnalyticalValidation
Authors: Lübeck P.S. , Wolffs P. , On S. L. W. , Ahrens P. , Rådström P. , Hoorfar J. 
Published: September 2003

ABSTRACT

As
part of a European research project (FOOD-PCR), we developed a
standardized and robust PCR detection assay specific for the three most
frequently reported food-borne pathogenic
Campylobacter
species,
C. jejuni
,
C. coli
, and
C. lari
.
Fifteen published and unpublished PCR primers targeting the 16S rRNA
gene were tested in all possible pairwise combinations, as well as two
published primers targeting the 23S rRNA gene. A panel of 150 strains
including target and nontarget strains was used in an in-house
validation. Only one primer pair, OT1559 plus 18-1, was found to be
selective. The inclusivity and exclusivity were 100 and 97%,
respectively. In an attempt to find a thermostable DNA polymerase more
resistant than
Taq
to PCR inhibitors present in chicken
samples, three DNA polymerases were evaluated. The DNA polymerase
T
th
was not inhibited at a concentration of 2%
(vol/vol) chicken carcass rinse, unlike both
Taq
DNA
polymerase and DyNAzyme. Based on these results, T
th
was
selected as the most suitable enzyme for the assay. The standardized
PCR test described shows potential for use in large-scale screening
programs for food-borne
Campylobacter
species under the assay
conditions
specified.
Toward an International Standard for PCR-Based Detection of Food-Borne Thermotolerant Campylobacters: Validation in a Multicenter Collaborative Trial
Authors: Lübeck P. S. , Cook N. , Wagner M. , Fach P. , Hoorfar J. 
Published: September 2003

ABSTRACT

As part of a European research project, the performance of a PCR assay to detect food-borne thermotolerant campylobacters (
Campylobacter jejuni
,
C. coli
, and
C. lari
) was evaluated through an international collaborative trial involving 12 participating laboratories. DNA from 10 target and 8 nontarget strains was tested, and the results were reported as the presence of a positive signal after gel electrophoresis. The overall inclusivity (sensitivity) was 93.7%, and the exclusivity (specificity) was 100%. The results indicate that the assay can become an international standard and can be confidently applied in microbiological laboratories.
Use of DNA and Peptide Nucleic Acid Molecular Beacons for Detection and Quantification of rRNA in Solution and in Whole Cells
Authors: Xi Chuanwu , Balberg Michal , Boppart Stephen A. , Raskin Lutgarde 
Published: September 2003

ABSTRACT
DNA and peptide nucleic acid (PNA) molecular beacons were successfully used to detect rRNA in solution. In addition, PNA molecular beacon hybridizations were found to be useful for the quantification of rRNA: hybridization signals increased in a linear fashion with the 16S rRNA concentrations used in this experiment (between 0.39 and 25 nM) in the presence of 50 nM PNA MB. DNA and PNA molecular beacons were successfully used to detect whole cells in fluorescence in situ hybridization (FISH) experiments without a wash step. The FISH results with the PNA molecular beacons were superior to those with the DNA molecular beacons: the hybridization kinetics were much faster, the signal-to-noise ratio was much higher, and the specificity was much better for the PNA molecular beacons. Finally, it was demonstrated that the combination of the use of PNA molecular beacons in FISH and flow cytometry makes it possible to rapidly collect quantitative FISH data. Thus, PNA molecular beacons might provide a solution for limitations of traditional FISH methods, such as variable target site accessibility, poor sensitivity for target cells with low rRNA content, background fluorescence, and applications of FISH in microfluidic devices.
Unusual Water Flux in the Extracellular Polysaccharide of the Cyanobacterium
Nostoc commune
Authors: Shaw Eric , Hill Donna R. , Brittain Nicole , Wright Debbie J. , Täuber Uwe , Marand Hervé , Helm Richard F. , Potts Malcolm 
Published: September 2003

ABSTRACT

The speed of water uptake by desiccated
Nostoc commune
was found to depend upon the duration of desiccation. The rehydration of desiccated colonies led to marked, time-dependent changes in structure and ultrastructure and fluctuations in the composition of the transcriptome. Physical evaporative water loss is an active process that was influenced by inhibitors of transcription and translation.
Factors Influencing the Chlorine Susceptibility of
Mycobacterium avium
,
Mycobacterium intracellulare
, and
Mycobacterium scrofulaceum
Authors: Falkinham Joseph O. 
Published: September 2003

ABSTRACT

The susceptibility of representative strains of
Mycobacterium avium
,
Mycobacterium intracellulare
, and
Mycobacterium scrofulaceum
(the MAIS group) to chlorine was studied to identify factors related to culture conditions and growth phase that influenced susceptibility.
M. avium
and
M. intracellulare
strains were more resistant to chlorine than were strains of
M. scrofulaceum
. Transparent and unpigmented colony variants were more resistant to chlorine than were their isogenic opaque and pigmented variants (respectively). Depending on growth stage and growth rate, MAIS strains differed in their chlorine susceptibilities. Cells from strains of all three species growing in early log phase at the highest growth rates were more susceptible than cells in log and stationary phase. Rapidly growing cells were more susceptible to chlorine than slowly growing cells. The chlorine susceptibility of
M. avium
cells grown at 30°C was increased when cells were exposed to chlorine at 40°C compared to susceptibility after exposure at 30°C. Cells of
M. avium
grown in 6% oxygen were significantly more chlorine susceptible than cells grown in air. Chlorine-resistant MAIS strains were more hydrophobic and resistant to Tween 80,
para
-nitrobenzoate, hydroxylamine, and nitrite than were the chlorine-sensitive strains.
Prevalence and Characteristics of
eae
-Positive
Escherichia coli
from Healthy Cattle in Japan
Authors: Kobayashi Hideki , Miura Akihiko , Hayashi Hiroko , Ogawa Torata , Endô Takayuki , Hata Eiji , Eguchi Masashi , Yamamoto Kôsi 
Published: September 2003

ABSTRACT

The prevalence of
eae
-positive
Escherichia coli
(
eae
EC) in Japan was examined using rectal stool samples taken from 35 calves less than 1 month old, 107 calves more than 1 to 3 months old, 88 heifers more than 3 to 6 months old, 214 heifers over 6 months old, and cows from 95 farms. Screening with
eae
PCR revealed the prevalence to be, with increasing age, 31.4, 8.4, 26.1, and 14.5%, respectively. Of 51 selected
eae
EC strains, more than 40% were serotyped as O26, O103, O111, O145, or O157, which are frequently detected as enterohemorrhagic
E
.
coli
types. Four strains were identified as recently reported intimin types η, ι, and κ.
Reevaluation of Production of Paralytic Shellfish Toxin by Bacteria Associated with Dinoflagellates of the Portuguese Coast
Authors: Martins Claudia A. , Alvito Paula , Tavares Maria João , Pereira Paulo , Doucette Gregory , Franca Susana 
Published: September 2003

ABSTRACTParalytic shellfish toxins (PSTs) are potent neurotoxins produced by certain dinoflagellate and cyanobacterial species. The autonomous production of PSTs by bacteria remains controversial. In this study, PST production by two bacterial strains, isolated previously from toxic dinoflagellates, was evaluated using biological and analytical methods. Analyses were performed under conditions determined previously to be optimal for toxin production and detection. Our data are inconsistent with autonomous bacterial PST production under these conditions, thereby challenging previous findings for the same strains.
Phenotypic Changes Resulting from Distinct Point Mutations in the
Azospirillum brasilense glnA
Gene, Encoding Glutamine Synthetase
Authors: Van Dommelen Anne , Keijers Veerle , Wollebrants An , Vanderleyden Jozef 
Published: September 2003

ABSTRACT

Sequencing the
glnA
genes of two chemically induced
Azospirillum brasilense
glutamine synthetase mutants revealed an Arg→Cys mutation, corresponding to the glutamate binding site, in one mutant and an Asp→Asn mutation, corresponding to the ammonium binding site, in the second mutant. The phenotypic changes in these mutants are discussed in relation to their genotypes.
Diversion of Electron Flow from Methanogenesis to Crystalline Fe(III) Oxide Reduction in Carbon-Limited Cultures of Wetland Sediment Microorganisms
Authors: Roden Eric E. 
Published: September 2003

ABSTRACT
Electron flow in acetate-limited cultures of wetland sediment microorganisms was diverted from methane production to Fe(III) reduction in the presence of crystalline Fe(III) oxides at surface area loadings equivalent to that of amorphous Fe(III) oxide. The results indicate that inferences regarding the ability of microbial Fe(III) oxide reduction to compete with other terminal electron-accepting processes in anoxic soils and sediments should be based on estimates of bulk microbially available surface site abundance rather than assumed thermodynamic properties of the dominant oxide phase(s) in the soil or sediment.
Survival of F-Specific RNA Coliphage, Feline Calicivirus, andEscherichia coliin Water: a Comparative Study
Authors: Allwood Paul B. , Malik Yashpal S. , Hedberg Craig W. , Goyal Sagar M. 
Published: September 2003

ABSTRACTThe relationship between the survival of enteric viral pathogens and their indicators (coliform bacteria and coliphages) is not well understood. We compared the survival rates of feline calicivirus (FCV),Escherichia coli, and a male-specific RNA coliphage MS2 at 4, 25, and 37°C for up to 28 days in dechlorinated water. The survival rates ofE. coliand FCV, a surrogate of noroviruses (NV), had a high degree of correlation at 4 and 25°C, while MS2 phage survived significantly longer (P< 0.05) at these two temperatures. At 37°C, the survival rates for all three organisms were highly correlated. Decimal reduction values indicating the number of days needed for 90% reduction in titer (D values) decreased for all three organisms as storage temperatures increased. FCV had the shortest D value among all three organisms at all temperatures investigated. These findings indicate that F-specific RNA phages may be useful indicators of NV in the environment.
Role for Mannose-Sensitive Hemagglutinin in Promoting Interactions between
Vibrio cholerae
El Tor and Mussel Hemolymph
Authors: Zampini Massimiliano , Canesi Laura , Betti Michele , Ciacci Caterina , Tarsi Renato , Gallo Gabriella , Pruzzo Carla 
Published: September 2003

ABSTRACT

The role of mannose-sensitive hemagglutinin (MSHA) in
Vibrio cholerae
O1 El Tor interactions with hemolymph of the mussel
Mytilus galloprovincialis
was studied. Bacterial adherence to and association with hemocytes were evaluated at 4 and 18°C, respectively. In hemolymph serum, the wild-type strain N16961 adhered to and associated with hemocytes about twofold more efficiently than its mutant lacking MSHA. In artificial seawater (ASW), no significant differences between the two strains were observed. N16961 was also more sensitive to hemocyte bactericidal activity than its MSHA mutant; in fact, the percentages of killed bacteria after 120 min of incubation were 60 and 34%, respectively. The addition of
d
-mannose abolished the serum-mediated increase in adherence, association, and sensitivity to killing of the wild-type strain without affecting the interactions of the mutant. A similar increase in N16961 adherence to hemocytes was observed when serum was adsorbed with MSHA-deficient bacteria. In contrast, serum adsorbed with either wild-type
V. cholerae
El Tor or wild-type
Escherichia coli
carrying type 1 fimbriae was no longer able to increase adherence of N16961 to hemocytes. The results indicate that hemolymph-soluble factors are involved in interactions between hemocytes and mannose-sensitive adhesins.
Dispersal and Phylogenetic Diversity of Nonmarine Picocyanobacteria, Inferred from 16S rRNA Gene and
cpcBA
-Intergenic Spacer Sequence Analyses
Authors: Crosbie Nicholas D. , Pöckl Matthias , Weisse Thomas 
Published: September 2003

ABSTRACT

More than 20
Synechococcus
and
Cyanobium
isolates were obtained from central European subalpine lakes and sequenced for their 16S rRNA gene and part of the phycocyanin operon (
cpc
), specifically the intergenic spacer (IGS) between
cpcB
and
cpcA
, and corresponding flanking regions (
cpcBA
-IGS). Maximum-likelihood analyses revealed the existence of at least six to seven clusters of nonmarine picocyanobacteria within the picophytoplankton clade and support the conjecture of global dispersal for some closely related picocyanobacterial genotypes.
Precipitation of Barite by
Myxococcus xanthus
: Possible Implications for the Biogeochemical Cycle of Barium
Authors: González-Muñoz Maria Teresa , Fernández-Luque Belén , Martínez-Ruiz Francisca , Ben Chekroun Kaoutar , Arias José María , Rodríguez-Gallego Manuel , Martínez-Cañamero Magdalena , de Linares Concepción , Paytan Adina 
Published: September 2003

ABSTRACT

Bacterial precipitation of barite (BaSO
4
) under laboratory conditions is reported for the first time. The bacterium
Myxococcus xanthus
was cultivated in a solid medium with a diluted solution of barium chloride. Crystallization occurred as a result of the presence of live bacteria and the bacterial metabolic activity. A phosphorous-rich amorphous phase preceded the more crystalline barite formation. These experiments may indicate the involvement of bacteria in the barium biogeochemical cycle, which is closely related to the carbon cycle.
Molecular Detection and Quantitation of the Red TideDinoflagellate
Karenia brevis
in the MarineEnvironment
Authors: Gray M. , Wawrik B. , Paul J. , Casper E. 
Published: September 2003

ABSTRACT

A
real-time reverse transcription-PCR method targeting the
rbcL
gene was developed for the detection and quantitation of
the Florida red tide organism,
Karenia brevis.
The assay was
sensitive to less than 1 cell per reaction, did not detect
rbcL
from 38 nontarget taxa, and accurately quantitated
K.
brevis
organisms in red tide samples from around Florida. These
studies have resulted in a sensitive and specific method for
K.
brevis
detection in the marine
environment.
Selective Plating Underestimates Abundance and Shows Differential Recovery of Bifidobacterial Species from Human Feces
Authors: Apajalahti Juha H. A. , Kettunen Anu , Nurminen Päivi H. , Jatila Hanna , Holben William E. 
Published: September 2003

ABSTRACT

The aim of the present work was to compare the efficacies and levels of selectivity of different culture-dependent and -independent methods for analyzing bifidobacteria in human stool samples. The three different culture media used here significantly differed from each other, particularly with regard to the recovery of
Bifidobacterium adolescentis
.
Bifidobacterium
medium failed to recover
B. adolescentis
; Beerens medium recovered some
B. adolescentis
organisms (17% of total bifidobacteria), whereas tomato-Eugon medium recovered mainly
B. adolescentis
organisms (58% of total bifidobacteria). A culture-independent method that combines GC fractionation of bacterial community DNA and 16S rRNA sequencing indicated that
B. adolescentis
organisms accounted for 85% of all bifidobacteria. Methodological biases, such as those described in this paper, should be taken into account in interpreting earlier studies and designing future experiments.
Development and Clinical Evaluation of an Internally Controlled, Single-Tube Multiplex Real-Time PCR Assay for Detection of
Legionella pneumophila
and Other
Legionella
Species
Authors: Templeton Kate E. , Scheltinga Sitha A. , Sillekens Peter , Crielaard Jantine W. , van Dam Alje P. , Goossens Herman , Claas Eric C. J. 
Published: September 2003

ABSTRACT

A multiplex real-time PCR assay for detection of
Legionella pneumophila
and
Legionella
spp. and including an internal control was designed.
Legionella
species,
L. pneumophila
, and the internal control were detected simultaneously by probes labeled with 6-carboxy-fluorescein, hexachlorofluorescein, and indodicarbocyanine, respectively. Therefore, no postamplification analysis was required in order to distinguish the targets. The sensitivity of both assays was 2.5 CFU/ml, and from analysis of 10 culture-positive and 74 culture-negative samples from patients investigated for legionellosis, 100% agreement was observed by both assays in comparison to culture. Four additional positives were found by the multiplex real-time PCR assay in the
Legionella
culture-negative samples.