Publications

utilization of hexamethylenetetramine (urotropine) by bacteria and yeasts.	a slow growing bacterial population able to utilize hexamethylelenetetramine (urotropine) as sole source of carbon, nitrogen and energy was isolated from soil. from this crude enrichment culture two bacteria were isolated and identified as brevundimonas diminuta and a phyllobacterium sp. by sequencing of 16s ribosomal dna. these bacteria also grew on urotropine but at a lower rate than the enrichment culture. addition of glucose to the latter resulted in growth of some yeasts that overgrew the b ...	2007	17043911
isolation and characterization of bacteria capable of tolerating the extreme conditions of clean room environments.	in assessing the bacterial populations present in spacecraft assembly, spacecraft test, and launch preparation facilities, extremophilic bacteria (requiring severe conditions for growth) and extremotolerant bacteria (tolerant to extreme conditions) were isolated. several cultivation approaches were employed to select for and identify bacteria that not only survive the nutrient-limiting conditions of clean room environments but can also withstand even more inhospitable environmental stresses. due ...	2007	17308177
activation of the binuclear metal center through formation of phosphotriesterase-inhibitor complexes.	phosphotriesterase (pte) from pseudomonas diminuta is a binuclear metalloenzyme that catalyzes the hydrolysis of organophosphate nerve agents at rates approaching the diffusion-controlled limit. the proposed catalytic mechanism postulates the interaction of the substrate with the metal center and subsequent nucleophilic attack by the bridging hydroxide. x-band epr spectroscopy was utilized to monitor the active site of mn/mn-substituted pte upon addition of two inhibitors, diisopropyl methyl pho ...	2007	17315951
a new phosphotriesterase from sulfolobus acidocaldarius and its comparison with the homologue from sulfolobus solfataricus.	the phosphotriesterase pte, identified in the soil bacterium pseudomonas diminuta, is thought to have evolved in the last several decades to degrade the pesticide paraoxon with proficiency approaching the limit of substrate diffusion (k(cat)/k(m) of 4 x 10(7)m(-1)s(-1)). it belongs to the amidohydrolase superfamily, but its evolutionary origin remains obscure. the enzyme has important potentiality in the field of the organophosphate decontamination. recently we reported on the characterization o ...	2007	17337320
quorum-quenching microbial infections: mechanisms and implications.		2007	17360274
crystal structures of human carboxylesterase 1 in covalent complexes with the chemical warfare agents soman and tabun.	the organophosphorus nerve agents sarin, soman, tabun, and vx exert their toxic effects by inhibiting the action of human acetylcholinesterase, a member of the serine hydrolase superfamily of enzymes. the current treatments for nerve agent exposure must be administered quickly to be effective, and they often do not eliminate long-term toxic side effects associated with organophosphate poisoning. thus, there is significant need for effective prophylactic methods to protect at-risk personnel from ...	2007	17407327
evaluation of the colorimetric vitek 2 card for identification of gram-negative nonfermentative rods: comparison to 16s rrna gene sequencing.	ninety strains of a collection of well-identified clinical isolates of gram-negative nonfermentative rods collected over a period of 5 years were evaluated using the new colorimetric vitek 2 card. the vitek 2 colorimetric system identified 53 (59%) of the isolates to the species level and 9 (10%) to the genus level; 28 (31%) isolates were misidentified. an algorithm combining the colorimetric vitek 2 card and 16s rrna gene sequencing for adequate identification of gram-negative nonfermentative r ...	2007	17507509
molecular dynamics of organophosphorous hydrolases bound to the nerve agent soman.	the organophosphorous hydrolase (oph) from pseudomonas diminuta is capable of degrading extremely toxic organophosphorous compounds with a high catalytic turnover and broad substrate specificity. although the natural substrate for oph is unknown, its triple-mutant h254g/h257w/l303t exhibits a 3 order of magnitude increase in catalytic efficiency and modified stereospecificity toward the most toxic spsc enantiomer of soman. molecular dynamics simulations and binding free-energy calculations have ...	2007	26633227
quantitative determination of free-dna uptake in river bacteria at the single-cell level by in situ rolling-circle amplification.	detection of plasmid dna uptake in river bacteria at the single-cell level was carried out by rolling-circle amplification (rca). uptake of a plasmid containing the green fluorescent protein gene (gfp) by indigenous bacteria from two rivers in osaka, japan, was monitored for 506 h using this in situ gene amplification technique with optimized cell permeabilization conditions. plasmid uptake determined by in situ rca was compared to direct counts of cells expressing gfp under fluorescence microsc ...	2006	16957252
bacterial diversity in aortic aneurysms determined by 16s ribosomal rna gene analysis.	aortic aneurysms are common vascular conditions that cause considerable morbidity and mortality. understanding of the mechanisms involved in the pathogenesis of the condition remains limited. recently, infection has been suggested as possible contributor in the development of the disease. the aim of the present study was to examine aortic aneurysms for the presence of bacterial dna using polymerase chain reaction (pcr) targeting the 16s ribosomal rna (rrna) gene, followed by cloning and sequenci ...	2006	17098542
brevundimonas terrae sp. nov., isolated from an alkaline soil in korea.	a gram-negative, rod-shaped, brevundimonas-like bacterial strain, ksl-145(t), was isolated from an alkaline soil in korea and subjected to a polyphasic taxonomic investigation. strain ksl-145(t) grew optimally at ph 7.5-8.0 and 30 degrees c without nacl. it was characterized chemotaxonomically as containing q-10 as the predominant ubiquinone and c(18 : 1)omega7c and c(16 : 0) as the major fatty acids. the dna g+c content was 61.8 mol%. a phylogenetic analysis based on 16s rrna gene sequences sho ...	2006	17158998
case report: infective endocarditis caused by brevundimonas vesicularis.	there are few reports in the literature of invasive infection caused by brevundimonas vesicularis in patients without immunosuppression or other predisposing factors. the choice of antimicrobial therapy for bacteremia caused by the pathogen requires more case experience to be determined.	2006	17194310
analogues with fluorescent leaving groups for screening and selection of enzymes that efficiently hydrolyze organophosphorus nerve agents.	enzymes that efficiently hydrolyze highly toxic organophosphorus nerve agents could potentially be used as medical countermeasures. as sufficiently active enzymes are currently unknown, we synthesized twelve fluorogenic analogues of organophosphorus nerve agents with the 3-chloro-7-oxy-4-methylcoumarin leaving group as probes for high-throughput enzyme screening. this set included analogues of the pesticides paraoxon, parathion, and dimefox, and the nerve agents dfp, tabun, sarin, cyclosarin, so ...	2006	16392809
convenient treatment of acetonitrile-containing wastes using the tandem combination of nitrile hydratase and amidase-producing microorganisms.	this study aimed to construct an acetonitrile-containing waste treatment process by using nitrile-degrading microorganisms. to degrade high concentrations of acetonitrile, the microorganisms were newly acquired from soil and water samples. although no nitrilase-producing microorganisms were found to be capable of degrading high concentrations of acetonitrile, the resting cells of rhodococcus pyridinivorans s85-2 containing nitrile hydratase could degrade acetonitrile at concentrations as high as ...	2006	16402166
insight into autoproteolytic activation from the structure of cephalosporin acylase: a protein with two proteolytic chemistries.	cephalosporin acylase (ca), a member of the n-terminal nucleophile hydrolase family, is activated through sequential primary and secondary autoproteolytic reactions with the release of a pro segment. we have determined crystal structures of four ca mutants. two mutants are trapped after the primary cleavage, and the other two undergo secondary cleavage slowly. these structures provide a look at pro-segment conformation during activation in n-terminal nucleophile hydrolases. the highly strained h ...	2006	16446446
16s rrna gene sequencing versus the api 20 ne system and the vitek 2 id-gnb card for identification of nonfermenting gram-negative bacteria in the clinical laboratory.	over a period of 26 months, we have evaluated in a prospective fashion the use of 16s rrna gene sequencing as a means of identifying clinically relevant isolates of nonfermenting gram-negative bacilli (non-pseudomonas aeruginosa) in the microbiology laboratory. the study was designed to compare phenotypic with molecular identification. results of molecular analyses were compared with two commercially available identification systems (api 20 ne, vitek 2 fluorescent card; biomérieux, marcy l'etoil ...	2006	16597863
enhanced stereoselective hydrolysis of toxic organophosphates by directly evolved variants of mammalian serum paraoxonase.	we addressed the ability of various organophosphorus (op) hydrolases to catalytically scavenge toxic op nerve agents. mammalian paraoxonase (pon1) was found to be more active than pseudomonas diminuta op hydrolase (oph) and squid o,o-di-isopropyl fluorophosphatase (dfpase) in detoxifying cyclosarin (o-cyclohexyl methylphosphonofluoridate) and soman (o-pinacolyl methylphosphonofluoridate). subsequently, nine directly evolved pon1 variants, selected for increased hydrolytic rates with a fluorogeni ...	2006	16640555
anomalous scattering analysis of agrobacterium radiobacter phosphotriesterase: the prominent role of iron in the heterobinuclear active site.	bacterial phosphotriesterases are binuclear metalloproteins for which the catalytic mechanism has been studied with a variety of techniques, principally using active sites reconstituted in vitro from apoenzymes. here, atomic absorption spectroscopy and anomalous x-ray scattering have been used to determine the identity of the metals incorporated into the active site in vivo. we have recombinantly expressed the phosphotriesterase from agrobacterium radiobacter (opda) in escherichia coli grown in ...	2006	16686603
evaluation of the duopath legionella lateral flow assay for identification of legionella pneumophila and legionella species culture isolates.	duopath legionella (merck kgaa, darmstadt, germany) is a new immunochromatographic assay for the simultaneous identification of cultured l. pneumophila and legionella species other than l. pneumophila. in tests of 89 l. pneumophila strains and 87 legionella strains other than l. pneumophila representing 41 different species, duopath and a widely used latex agglutination assay detected l. pneumophila with 100% and 98% accuracy, respectively, whereas the percentages differed significantly for othe ...	2006	16751575
l: -stereoselective amino acid amidase with broad substrate specificity from brevundimonas diminuta: characterization of a new member of the leucine aminopeptidase family.	brevundimonas diminuta tpu 5720 produces an amidase acting l-stereoselectively on phenylalaninamide. the enzyme (laaa(bd)) was purified to electrophoretic homogeneity by ammonium sulfate fractionation and four steps of column chromatography. the final preparation gave a single band on sds-page with a molecular weight of approximately 53,000. the native molecular weight of the enzyme was about 288,000 based on gel filtration chromatography, suggesting that the enzyme is active as a homohexamer. i ...	2006	16001251
chemical resistance of the gram-negative bacteria to different sanitizers in a water purification system.	purified water for pharmaceutical purposes must be free of microbial contamination and pyrogens. even with the additional sanitary and disinfecting treatments applied to the system (sequential operational stages), pseudomonas aeruginosa, pseudomonas fluorescens, pseudomonas alcaligenes, pseudomonas picketti, flavobacterium aureum, acinetobacter lowffi and pseudomonas diminuta were isolated and identified from a thirteen-stage purification system. to evaluate the efficacy of the chemical agents u ...	2006	16914053
single-step conversion of cephalosporin-c to 7-aminocephalosporanic acid by free and immobilized cells of pseudomonas diminuta.	7-aminocephalosporanic acid (7-aca), the starting material for the production of a number of clinically used semisynthetic cephalosporins, is produced by deacylation of cephalosporin-c. the production of 7-aca was studied in various modes, at the optimal conditions using free and immobilized whole cells of pseudomonas diminuta.	2005	16014995
improving the activity and stability of gl-7-aca acylase ca130 by site-directed mutagenesis.	in the present study, glutaryl-7-amino cephalosporanic acid acylase from pseudomonas sp. strain 130 (ca130) was mutated to improve its enzymatic activity and stability. based on the crystal structure of ca130, two series of amino acid residues, one from those directly involved in catalytic function and another from those putatively involved in surface charge, were selected as targets for site-directed mutagenesis. in the first series of experiments, several key residues in the substrate-binding ...	2005	16151116
rrna sequence-based scanning electron microscopic detection of bacteria.	a new scanning electron microscopic method was developed for gaining both phylogenetic and morphological information about target microbes using in situ hybridization with rrna-targeted oligonucleotide probes (sem-ish). target cells were hybridized with oligonucleotide probes after gold labeling. gold enhancement was used for amplification of probe signals from hybridized cells. the hybridized cells released a strong backscatter electron signal due to accumulation of gold atoms inside cells. sem ...	2005	16151145
virtual screening against metalloenzymes for inhibitors and substrates.	molecular docking uses the three-dimensional structure of a receptor to screen databases of small molecules for potential ligands, often based on energetic complementarity. for many docking scoring functions, which calculate nonbonded interactions, metalloenzymes are challenging because of the partial covalent nature of metal-ligand interactions. to investigate how well molecular docking can identify potential ligands of metalloenzymes using a "standard" scoring function, we have docked the mdl ...	2005	16156645
initial stages of bacterial fouling during dead-end microfiltration.	constant pressure experiments were performed using track-etched polycarbonate membranes and rod-shaped bacteria (viz., brevundimonas diminuta and serratia marcescens) to study flux decline and backwashing during the early stages of microfiltration. the intermediate blocking law originally derived for spherical particles was modified to account for the approximate cylindrical shape of the selected bacteria. a deposition factor was introduced to empirically account for the morphology of bacterial ...	2005	16190201
integrated recombinant protein expression and purification platform based on ralstonia eutropha.	protein purification of recombinant proteins constitutes a significant cost of biomanufacturing and various efforts have been directed at developing more efficient purification methods. we describe a protein purification scheme wherein ralstonia eutropha is used to produce its own "affinity matrix," thereby eliminating the need for external chromatographic purification steps. this approach is based on the specific interaction of phasin proteins with granules of the intracellular polymer polyhydr ...	2005	16204482
bacterial communities in petroleum oil in stockpiles.	bacterial communities in crude-oil samples from japanese oil stockpiles were investigated by 16s rrna gene cloning, followed by denaturing gradient gel electrophoresis (dgge) analysis. 16s rrna genes were successfully amplified by pcr after isooctane treatment from three kinds of crude-oil sample collected at four oil stockpiles in japan. dgge profiles showed that bacteria related to ochrobactrum anthropi, burkholderia cepacia, stenotrophomonas maltophilia, propionibacterium acnes, and brevundim ...	2005	16233771
evolution of an acylase active on cephalosporin c.	semisynthetic cephalosporins are synthesized from 7-amino cephalosporanic acid, which is produced by chemical deacylation or by a two-step enzymatic process of the natural antibiotic cephalosporin c. the known acylases take glutaryl-7-amino cephalosporanic acid as a primary substrate, and their specificity and activity are too low for cephalosporin c. starting from a known glutaryl-7-amino cephalosporanic acid acylase as the protein scaffold, an acylase gene optimized for expression in escherich ...	2005	16260759
recognition of individual genes in diverse microorganisms by cycling primed in situ amplification.	cycling primed in situ amplification-fluorescent in situ hybridization (cprins-fish) was developed to recognize individual genes in a single bacterial cell. in cprins, the amplicon was long single-stranded dna and thus retained within the permeabilized microbial cells. fish with a multiply labeled fluorescent probe set enabled significant reduction in nonspecific background while maintaining high fluorescence signals of target bacteria. the ampicillin resistance gene in escherichia coli, chloram ...	2005	16269764
evaluation of gel-pad oligonucleotide microarray technology by using artificial neural networks.	past studies have suggested that thermal dissociation analysis of nucleic acids hybridized to dna microarrays would improve discrimination among duplex types by scanning through a broad range of stringency conditions. to more fully constrain the utility of this approach using a previously described gel-pad microarray format, artificial neural networks (nns) were trained to recognize noisy or low-quality data, as might derive from nonspecific fluorescence, poor hybridization, or compromised data ...	2005	16332861
unique kinetic properties of phenol-degrading variovorax strains responsible for efficient trichloroethylene degradation in a chemostat enrichment culture.	a chemostat enrichment of soil bacteria growing on phenol as the sole carbon source has been shown to exhibit quite high trichloroethylene (tce)-degrading activities. to identify the bacterial populations responsible for the high tce-degrading activity, a multidisciplinary survey of the chemostat enrichment was conducted by employing molecular-ecological and culture-dependent approaches. three chemostat enrichment cultures were newly developed under different phenol-loading conditions (0.25, 0.7 ...	2005	15691947
directed evolution of phosphotriesterase from pseudomonas diminuta for heterologous expression in escherichia coli results in stabilization of the metal-free state.	phosphotriesterase from pseudomonas diminuta (pte) is an extremely efficient metalloenzyme that hydrolyses a variety of compounds including organophosphorus nerve agents. study of pte has been hampered by difficulties with efficient expression of the recombinant form of this highly interesting and potentially useful enzyme. we identified a low-level esterolytic activity of pte and then screened pte gene libraries for improvements in 2-naphthyl acetate hydrolysis. however, the attempt to evolve t ...	2005	15790580
brevundimonas diminuta infections and its resistance to fluoroquinolones.	to report infections caused by brevundimonas diminuta and antibiotic studies of this gram-negative bacterium.	2005	15883180
detoxification of organophosphate nerve agents by bacterial phosphotriesterase.	organophosphates have been widely used as insecticides and chemical warfare agents. the health risks associated with these agents have necessitated the need for better detoxification and bioremediation tools. bacterial enzymes capable of hydrolyzing the lethal organophosphate nerve agents are of special interest. phosphotriesterase (pte) isolated from the soil bacteria pseudomonas diminuta displays a significant rate enhancement and substrate promiscuity for the hydrolysis of organophosphate tri ...	2005	15982683
long-term population dynamics of phototrophic sulfur bacteria in the chemocline of lake cadagno, switzerland.	population analyses in water samples obtained from the chemocline of crenogenic, meromictic lake cadagno, switzerland, in october for the years 1994 to 2003 were studied using in situ hybridization with specific probes. during this 10-year period, large shifts in abundance between purple and green sulfur bacteria and among different populations were obtained. purple sulfur bacteria were the numerically most prominent phototrophic sulfur bacteria in samples obtained from 1994 to 2001, when they r ...	2005	16000760
quantitative detection of clostridium perfringens in the broiler fowl gastrointestinal tract by real-time pcr.	strains of clostridium perfringens are a frequent cause of food-borne disease and gas gangrene and are also associated with necrotic enteritis in chickens. to detect and quantify the levels of c. perfringens in the chicken gastrointestinal tract, a quantitative real-time pcr assay utilizing a fluorogenic, hydrolysis-type probe was developed and utilized to assay material retrieved from the broiler chicken cecum and ileum. primers and probe were selected following an alignment of 16s rdna sequenc ...	2005	16000804
on the purification and preliminary crystallographic analysis of isoquinoline 1-oxidoreductase from brevundimonas diminuta 7.	isoquinoline 1-oxidoreductase (ior) from brevundimonas diminuta is a mononuclear molybdoenzyme of the xanthine-dehydrogenase family of proteins and catalyzes the conversion of isoquinoline to isoquinoline-1-one. its primary sequence and behaviour, specifically in its substrate specificity and lipophilicity, differ from other members of the family. a crystal structure of the enzyme is expected to provide an explanation for these differences. this paper describes the crystallization and preliminar ...	2005	16508115
protein subunit interfaces: heterodimers versus homodimers.	protein dimers are either homodimers (complexation of identical monomers) or heterodimers (complexation of non-identical monomers). these dimers are common in catalysis and regulation. however, the molecular principles of protein dimer interactions are difficult to understand mainly due to the geometrical and chemical characteristics of proteins. nonetheless, the principles of protein dimer interactions are often studied using a dataset of 3d structural complexes determined by x-ray crystallogra ...	2005	17597849
structural features differentiate the mechanisms between 2s (2 state) and 3s (3 state) folding homodimers.	the formation of homodimer complexes for interface stability, catalysis and regulation is intriguing. the mechanisms of homodimer complexations are even more interesting. some homodimers form without intermediates (two-state (2s)) and others through the formation of stable intermediates (three-state (3s)). here, we analyze 41 homodimer (25 2s and 16 3s) structures determined by x-ray crystallography to estimate structural differences between them. the analysis suggests that a combination of stru ...	2005	17597851
evaluation of the new vitek 2 card for identification of clinically relevant gram-negative rods.	the vitek 2 card for gram-negative bacteria (biomérieux,marcy-l'etoile, france) has been redesigned to improve the identification of fermenting and nonfermenting bacilli. forty-seven biochemical tests, including 19 enzymatic tests, are present in the new card and interpreted in a kinetic mode. final identification results are available within 10 h. the database allows the identification of 159 different taxa. six hundred fifty-five gram-negative rods (gnr; 511 fermenters and 144 nonfermenters), ...	2004	15364991
pcr-based positive hybridization to detect genomic diversity associated with bacterial secondary metabolism.	a pcr-based positive hybridization (pph) method was developed to explore toxic-specific genes in common between toxigenic strains of anabaena circinalis, a cyanobacterium able to produce saxitoxin (stx). the pph technique is based on the same principles of suppression subtractive hybridization (ssh), although with the former no driver dna is required and two tester genomic dnas are hybridized at high stringency. the aim was to obtain genes associated with cyanobacterial stx production. the genet ...	2004	14718552
biodegradation of dna and nucleotides to nucleosides and free bases.	thirty-two different microorganisms were examined in order to check their ability to degrade an exogenous dna. bacteria from species: stenotrophomonas maltophilia, brevundimonas diminuta, bacillus subtilis, mycobacterium butyricum and fungus fusarium moniliforme were capable to degrade dna to nucleic bases or their derivatives. degradation of dna by s. maltophilia resulted in formation of free bases, such as hypoxanthine, thymine, uracil and xanthine. the optimum concentration of dna seemed to b ...	2004	14751311
rapid detection and enumeration of legionella pneumophila in hot water systems by solid-phase cytometry.	a new method for the rapid and sensitive detection of legionella pneumophila in hot water systems has been developed. the method is based on an if assay combined with detection by solid-phase cytometry. this method allowed the enumeration of l. pneumophila serogroup 1 and l. pneumophila serogroups 2 to 6, 8 to 10, and 12 to 15 in tap water samples within 3 to 4 h. the sensitivity of the method was between 10 and 100 bacteria per liter and was principally limited by the filtration capacity of mem ...	2004	15006790
occurrence and phylogenetic diversity of sphingomonas strains in soils contaminated with polycyclic aromatic hydrocarbons.	bacterial strains of the genus sphingomonas are often isolated from contaminated soils for their ability to use polycyclic aromatic hydrocarbons (pah) as the sole source of carbon and energy. the direct detection of sphingomonas strains in contaminated soils, either indigenous or inoculated, is, as such, of interest for bioremediation purposes. in this study, a culture-independent pcr-based detection method using specific primers targeting the sphingomonas 16s rrna gene combined with denaturing ...	2004	15066784
mechanism for the hydrolysis of organophosphates by the bacterial phosphotriesterase.	phosphotriesterase (pte) from pseudomonas diminuta is a zinc metalloenzyme that hydrolyzes a variety of organophosphorus compounds. the kinetic parameters of zn/zn pte, cd/cd pte, and a mixed-metal zn/cd hybrid pte were obtained with a variety of substrates to determine the role of each metal ion in binding and catalysis. ph-rate profiles for the hydrolysis of diethyl p-nitrophenyl phosphate (i) and diethyl p-chlorophenyl phosphate (ii) demonstrated that the ionization of a single group in the p ...	2004	15134445
a core catalytic domain of the tyra protein family: arogenate dehydrogenase from synechocystis.	the tyra protein family includes prephenate dehydrogenases, cyclohexadienyl dehydrogenases and tyra(a)s (arogenate dehydrogenases). tyra(a) from synechocystis sp. pcc 6803, encoding a 30 kda tyra(a) protein, was cloned into an overexpression vector in escherichia coli. tyra(a) was then purified to apparent homogeneity and characterized. this protein is a model structure for a catalytic core domain in the tyra superfamily, uncomplicated by allosteric or fused domains. competitive inhibitors actin ...	2004	15171683
altering the substrate specificity of organophosphorus hydrolase for enhanced hydrolysis of chlorpyrifos.	chlorpyrifos is one of the most popular pesticides used for agriculture crop protection, and widespread contamination is a potential concern. however, chlorpyrifos is hydrolyzed almost 1,000-fold slower than the preferred substrate, paraoxon, by organophosphorus hydrolase (oph), an enzyme that can degrade a broad range of organophosphate pesticides. we have recently demonstrated that directed evolution can be used to generate oph variants with up to 25-fold improvement in hydrolysis of methyl pa ...	2004	15294802
biodegradation of chlorpyrifos by enterobacter strain b-14 and its use in bioremediation of contaminated soils.	six chlorpyrifos-degrading bacteria were isolated from an australian soil and compared by biochemical and molecular methods. the isolates were indistinguishable, and one (strain b-14) was selected for further analysis. this strain showed greatest similarity to members of the order enterobacteriales and was closest to members of the enterobacter asburiae group. the ability of the strain to mineralize chlorpyrifos was investigated under different culture conditions, and the strain utilized chlorpy ...	2004	15294824
development of two pcr-based techniques for detecting helical and coccoid forms of helicobacter pylori.	the primary mode of transmission of helicobacter pylori, a human pathogen carried by more than half the population worldwide, is still unresolved. some epidemiological data suggest water as a possible transmission route. h. pylori in the environment transforms into a nonculturable, coccoid form, which frequently results in the failure to detect this bacterium in environmental samples by conventional culture techniques. to overcome limitations associated with culturing, molecular approaches based ...	2004	15297506
transcarboxylase 5s structures: assembly and catalytic mechanism of a multienzyme complex subunit.	transcarboxylase is a 1.2 million dalton (da) multienzyme complex from propionibacterium shermanii that couples two carboxylation reactions, transferring co(2)(-) from methylmalonyl-coa to pyruvate to yield propionyl-coa and oxaloacetate. crystal structures of the 5s metalloenzyme subunit, which catalyzes the second carboxylation reaction, have been solved in free form and bound to its substrate pyruvate, product oxaloacetate, or inhibitor 2-ketobutyrate. the structure reveals a dimer of beta(8) ...	2004	15329673
strain-specific differences in the grazing sensitivities of closely related ultramicrobacteria affiliated with the polynucleobacter cluster.	ultramicrobacteria (cell volume < 0.1 microm(3)) are the numerically dominant organisms in the plankton of marine and freshwater habitats. flagellates and other protists are assumed to be the most important predators of these ultramicrobacteria as well as of larger planktonic bacteria. however, due to controversial observations conducted previously, it is not clear as to whether fractions of the ultramicrobacteria are resistant to flagellate predation. furthermore, it is not known if closely rel ...	2004	15466515
mrna differential display in a microbial enrichment culture: simultaneous identification of three cyclohexanone monooxygenases from three species.	mrna differential display has been used to identify cyclohexanone oxidation genes in a mixed microbial community derived from a wastewater bioreactor. thirteen dna fragments randomly amplified from the total rna of an enrichment subculture exposed to cyclohexanone corresponded to genes predicted to be involved in the degradation of cyclohexanone. nine of these dna fragments are part of genes encoding three distinct baeyer-villiger cyclohexanone monooxygenases from three different bacterial speci ...	2003	12514013
isolation of novel ultramicrobacteria classified as actinobacteria from five freshwater habitats in europe and asia.	we describe the first freshwater members of the class actinobacteria that have been isolated. nine ultramicro-size (<0.1 microm(3)) strains were isolated from five freshwater habitats in europe and asia. these habitats represent a broad spectrum of ecosystems, ranging from deep oligotrophic lakes to shallow hypertrophic lakes. even when the isolated strains were grown in very rich media, the cell size was <0.1 microm(3) and was indistinguishable from the cell sizes of bacteria belonging to the s ...	2003	12620827
mixed culture bioconversion of 16-dehydropregnenolone acetate to androsta-1,4-diene-3,17-dione: optimization of parameters.	bioconversion of 16-dehydropregnenolone acetate (16-dpa) to androsta-1,4-diene-3,17-dione (add), an intermediate for the production of female sex hormones, by mixed culture of pseudomonas diminuta mtcc 3361 and comamonas acidovorans mtcc 3362 is reported. various physicochemical parameters for the bioconversion of 16-dpa to add have been optimized in shake flask cultures. nutrient broth inoculated with actively growing co-culture proved ideal for bacterial growth and bioconversion. a temperature ...	2003	12675614
evolution of an organophosphate-degrading enzyme: a comparison of natural and directed evolution.	organophosphate-degrading enzyme from agrobacterium radiobacter p230 (opda) is a recently discovered enzyme that degrades a broad range of organophosphates. it is very similar to oph first isolated from pseudomonas diminuta mg. despite a high level of sequence identity, oph and opda exhibit different substrate specificities. we report here the structure of opda and identify regions of the protein that are likely to give it a preference for substrates that have shorter alkyl substituents. directe ...	2003	12676982
burkholderia is highly resistant to human beta-defensin 3.	the bactericidal activity of the novel beta-defensin hbd-3 against 28 species and 55 strains of gram-positive cocci and gram-negative fermentative and nonfermentative rods was tested. all strains proved to be highly or intermediately susceptible to hbd-3 (minimal bactericidal concentration [mbc], </=50 micro g/ml), except for burkholderia cepacia, for all 23 tested strains of which mbcs were >100 micro g/ml.	2003	12709350
transposon-like organization of the plasmid-borne organophosphate degradation (opd) gene cluster found in flavobacterium sp.	several bacterial strains that can use organophosphate pesticides as a source of carbon have been isolated from soil samples collected from diverse geographical regions. all these organisms synthesize an enzyme called parathion hydrolase, and in each case the enzyme is encoded by a gene (opd) located on a large indigenous plasmid. these plasmids show considerable genetic diversity, but the region containing the opd gene is highly conserved. two opd plasmids, ppdl2 from flavobacterium sp. and pcm ...	2003	12732518
evaluation of the vitek 2 id-gnb assay for identification of members of the family enterobacteriaceae and other nonenteric gram-negative bacilli and comparison with the vitek gni+ card.	we evaluated the vitek 2 id-gnb identification card (biomérieux, inc., durham, n.c.) for its ability to identify members of the family enterobacteriaceae and other gram-negative bacilli that are isolated in clinical microbiology laboratories. using 482 enteric stock cultures and 103 strains of oxidase-positive, gram-negative glucose-fermenting and nonfermenting bacilli that were maintained at -70 degrees c and passaged three times before use, we inoculated cards according to the manufacturer's d ...	2003	12734254
ultrasound increases the rate of bacterial cell growth.	ultrasound was employed to increase the growth rate of bacterial cells attached to surfaces. staphylococcus epidermidis, pseudomonas aeruginosa, and escherichia coli cells adhered to and grew on a polyethylene surface in the presence of ultrasound. it was found that low-frequency ultrasound (70 khz) of low acoustic intensity (<2 w/cm(2)) increased the growth rate of the cells compared to growth without ultrasound. however, at high intensity levels, cells were partially removed from the surface. ...	2003	12790676
crystal structure of d-hydantoinase from burkholderia pickettii at a resolution of 2.7 angstroms: insights into the molecular basis of enzyme thermostability.	d-hydantoinase (d-hyd) is an industrial enzyme that is widely used in the production of d-amino acids which are precursors for semisynthesis of antibiotics, peptides, and pesticides. this report describes the crystal structure of d-hydantoinase from burkholderia pickettii (hyd(bp)) at a 2.7-a resolution. the structure of hyd(bp) consists of a core (alpha/beta)(8) triose phosphate isomerase barrel fold and a beta-sheet domain, and the catalytic active site consists of two metal ions and six highl ...	2003	12837777
reevaluation of production of paralytic shellfish toxin by bacteria associated with dinoflagellates of the portuguese coast.	paralytic 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 autonomo ...	2003	12957964
biodegradation of the herbicide trifluralin by bacteria isolated from soil.	trifluralin (alpha,alpha,alpha-trifluoro-2,6-dinitro-n,n-dipropyl-p-toluidine; tfl) is a pre-emergence, soil-incorporated herbicide that has been in agricultural use since the early 1960s and is moderately persistent in soil. the purpose of this study was to isolate and characterise tfl-resistant bacteria from a soil in which this pesticide has been used for the last four decades and to determine their ability to degrade tfl using hplc. eight bacteria were isolated by repeated subculture in liqu ...	2003	19719679
ability of the microscan rapid gram-negative id type 3 panel to identify nonenteric glucose-fermenting and nonfermenting gram-negative bacilli.	the microscan rapid neg id3 panel is designed for the identification of enterobacteriaceae and nonenteric glucose-fermenting and nonfermenting gram-negative bacilli. we evaluated this panel for its ability to identify gram-negative non-enterobacteriaceae bacteria. a total of 134 strains, representing 26 genera and 42 species, were taken from storage at -70(o)c, passaged three times before testing, and inoculated into the panels according to the manufacturer's directions before being inserted int ...	2002	12354875
precursor structure of cephalosporin acylase. insights into autoproteolytic activation in a new n-terminal hydrolase family.	autocatalytic proteolytic cleavage is a frequently observed post-translational modification in proteins. cephalosporin acylase (ca) is a recently identified member of the n-terminal hydrolase family that is activated from an inactive precursor by autoproteolytic processing, generating a new n-terminal residue, which is either a ser or a thr. the n-terminal ser or thr becomes a nucleophilic catalytic center for intramolecular and intermolecular amide cleavages. the gene structure of the open read ...	2002	11706000
microbial enantioselective ester hydrolysis for the preparation of optically active 4,1-benzoxazepine-3-acetic acid derivatives as squalene synthase inhibitors.	microbial enantioselective ester hydrolysis for the preparation of optically active (3r,5s)-(-)-5-phenyl-4,1-benzoxazepine-3-acetic acid derivatives as potent squalene synthase inhibitors was investigated. pseudomonas diminuta and pseudomonas taetrolens hydrolyzed the racemic ethyl ester of the 5-(2-chlorophenyl) analogue to yield the (-)-carboxylic acid with excellent enantiomeric excess (>99% ee). we found that the (-)-enantiomer was an active inhibitor. bulkiness of the ester moiety did not a ...	2002	11824586
the wild type bacterial co(2+)/co(2+)-phosphotriesterase shows a middle-range thermostability.	the phosphotriesterase (pte) from pseudomonas diminuta, a metalloenzyme that catalyses the hydrolysis of organophosphorus pesticides and nerve agents, has been described as a remarkably heat-stable protein [grimsley et al., biochemistry 36 (1997), 14366-14374]. because substitution of the naturally occurring zinc ions by cobalt ions was found to enhance the enzyme catalytic activity, we investigated the thermal stability of the co(2+)/co(2+)-pte. this study, carried out using capillary electroph ...	2002	11904217
bacterial cell surface display of organophosphorus hydrolase for selective screening of improved hydrolysis of organophosphate nerve agents.	organophosphorus hydrolase (oph) is a bacterial enzyme that has been shown to degrade a wide range of neurotoxic organophosphate nerve agents. however, the effectiveness of degradation varies dramatically, ranging from highly efficient with paraoxon to relatively slow with methyl parathion. sequential cycles of dna shuffling and screening were used to fine-tune and enhance the activity of oph towards poorly degraded substrates. because of the inaccessibility of these pesticides across the cell m ...	2002	11916726
enzymatic synthesis of chiral organophosphothioates from prochiral precursors.	the phosphotriesterase from pseudomonas diminuta has been shown to selectively cleave the pro-r p-nitrophenolate substituent from bis-p-nitrophenyl alkyl phosphothioate esters. when the alkyl substituent is methyl, ethyl, or isopropyl the enantiomeric excess of the product is >/=99%. manipulation of the active site through mutagenesis has enabled the preparation of protein variants that preferentially hydrolyze the pro-s substituent of the target substrates. this methodology thus permits the pre ...	2002	11929226
biofilms: survival mechanisms of clinically relevant microorganisms.	though biofilms were first described by antonie van leeuwenhoek, the theory describing the biofilm process was not developed until 1978. we now understand that biofilms are universal, occurring in aquatic and industrial water systems as well as a large number of environments and medical devices relevant for public health. using tools such as the scanning electron microscope and, more recently, the confocal laser scanning microscope, biofilm researchers now understand that biofilms are not unstru ...	2002	11932229
changes in the cell size of brevundimonas diminuta using different growth agitation rates.	brevundimonas diminuta (atcc 19146) is a standard organism for validation of sterilizing-grade membrane filters. cell size is critical for the determination of retention characteristics of 0.2 micron rated membrane filters. in this study, cell size changes of b. diminuta cultured under different physiologic states and variable agitations at 50, 100 and 200 rpm were measured by a particle size analyzer and scanning electron microscope (sem). the smallest cells were obtained at initial stationary ...	2002	11977409
expression of the iorab genes from brevundimonas diminuta 7 encoding the molybdenum hydroxylase isoquinoline 1-oxidoreductase in pseudomonas putida.	isoquinoline 1-oxidoreductase (ior) from brevundimonas diminuta 7, encoded by iorab, is a molybdenum hydroxylase containing a molybdopterin cytosine dinucleotide molybdenum cofactor (mo-mcd) and two distinct [2fe2s] clusters. the iorab genes were inserted into pjb653, generating pil1. pseudomonas putida kt2440, and p. putida 86 which produces a mo-mcd-containing quinoline 2-oxidoreductase when grown on quinoline, were used as recipients for pil1. upon induction of gene expression, both clones pr ...	2002	12023088
prevalent bacterial species and novel phylotypes in advanced noma lesions.	the purpose of this study was to determine the bacterial diversity in advanced noma lesions using culture-independent molecular methods. 16s ribosomal dna bacterial genes from dna isolated from advanced noma lesions of four nigerian children were pcr amplified with universally conserved primers and spirochetal selective primers and cloned into escherichia coli. partial 16s rrna sequences of approximately 500 bases from 212 cloned inserts were used initially to determine species identity or close ...	2002	12037085
identification of an opd (organophosphate degradation) gene in an agrobacterium isolate.	we isolated a bacterial strain, agrobacterium radiobacter p230, which can hydrolyze a wide range of organophosphate (op) insecticides. a gene encoding a protein involved in op hydrolysis was cloned from a. radiobacter p230 and sequenced. this gene (called opda) had sequence similarity to opd, a gene previously shown to encode an op-hydrolyzing enzyme in flavobacterium sp. strain atcc 27551 and brevundimonas diminuta mg. insertional mutation of the opda gene produced a strain lacking the ability ...	2002	12089017
interactions of pathogens and irritant chemicals in land-applied sewage sludges (biosolids).	fertilisation of land with processed sewage sludges, which often contain low levels of pathogens, endotoxins, and trace amounts of industrial and household chemicals, has become common practice in western europe, the us, and canada. local governments, however, are increasingly restricting or banning the practice in response to residents reporting adverse health effects. these self-reported illnesses have not been studied and methods for assessing exposures of residential communities to contamina ...	2002	12097151
bioconversion of 3 beta-acetoxypregna-5,16-diene-20-one to androsta-1,4-diene-3,17-dione by mixed bacterial culture.	to isolate a bacterium capable of degrading 3 beta-acetoxypregna-5,16-diene-20-one (16-dpa) to androsta-1,4-diene-3,17-dione (add) and to decipher the biodegradation pathway.	2002	12100580
performance of a novel viresolve nfr virus filter.	mammalian cell-expressed therapeutic proteins are particularly vulnerable to contamination by endogenous retrovirus-like particles (rvlps). the viresolve nfr filter was designed to meet the critical requirement of manufacturing a safe and virus-free therapeutic by retaining rvlps by a minimum of six log reduction value (lrv). the nfr designation refers to retrovirus removal in a normal flow format. to qualify the product, we tested two model viruses: the 78 nm diameter phi6 bacteriophage and the ...	2002	12153313
identification of bacteria in drinking and purified water during the monitoring of a typical water purification system.	a typical purification system that provides purified water which meets ionic and organic chemical standards, must be protected from microbial proliferation to minimize cross-contamination for use in cleaning and preparations in pharmaceutical industries and in health environments.	2002	12182763
microbial retention characteristics of sterilizing-grade membrane filters with alginate substituted for oil-based products.	for oil-based products, fda recommends substitution of the oil with a compound which has similar viscosity and physical characteristics. in this study, a substitute for oil-based products was screened by measuring the viscosity and filterability, and examined for the presence of cell clumps in the various test fluids using an optical microscopy. the viscosity of the test fluids measured in the range of about 60-75 cp. brevundimonas diminuta (formerly pseudomonas diminuta), a standard challenge t ...	2002	12404720
a novel high-cell-density protein expression system based on ralstonia eutropha.	we describe the development of a novel protein expression system based on the industrial fermentation organism ralstonia eutropha (formerly known as alcaligenes eutrophus) ncimb 40124. this new system overcomes some of the shortcomings of traditional escherichia coli-based protein expression systems, particularly the propensity of such systems to form inclusion bodies during high-level expression. using a proteomics approach, we identified promoters that can be induced by simple process paramete ...	2002	12450812
biochemical and susceptibility tests useful for identification of nonfermenting gram-negative rods.	six hundred nineteen strains of nonfermenting gram-negative rods were tested for alkaline phosphatase, benzyl-arginine arylamidase, pyrrolidonyl arylamidase, ethylene glycol acidification, and susceptibility to desferrioxamine and colistin. the results were highly discriminant. therefore, the proposed tests may be helpful for the identification of this group of organisms.	2002	11880447
unveiling the organisms behind novel eukaryotic ribosomal dna sequences from the ocean.	despite the fact that the smallest eukaryotes (cells less than 5 micro m in diameter) play key roles in marine food webs, particularly in open oligotrophic areas, the study of their in situ diversity started just one year ago. perhaps the most remarkable finding of the most recent studies has been the discovery of completely new phylogenetic lineages, such as novel clades belonging to the stramenopile and alveolate phyla. the two new groups account for a significant fraction of clones in genetic ...	2002	12200313
case of catheter sepsis with ralstonia gilardii in a child with acute lymphoblastic leukemia.	acute lymphoblastic leukemia was diagnosed in a 7-year-old girl. two months after insertion of a central venous catheter, she developed fever and complained of headache and abdominal pain. physical examination revealed no focus of infection. a gram-negative nonfermenting bacillus was recurrently cultured from blood. extensive biochemical testing and 16s ribosomal dna sequencing led to the identification of ralstonia gilardii.	2001	11724891
method for qualifying microbial removal performance of 0.1 micron rated filters. part ii: preliminary characterization of hydrogenophaga (formerly pseudomonas) pseudoflava for use as a standard challenge organism to qualify 0.1 micron rated filters.	in this article, we report on the preliminary characterization of hydrogenophaga (formerly pseudomonas) pseudoflava for potential use as a standard challenge organism to qualify 0.1 microm rated filters. filter-cloned h. pseudoflava (atcc 700892) was easily cultured in a low nutrient broth (r2a broth) under standard laboratory conditions, reaching high titers of 10(8)-10(9) cfu/ml within 48-65 hours of incubation at 25+/-5 degrees c. under these conditions, h. pseudoflava is a rod-shaped bacteri ...	2001	11766823
method for qualifying microbial removal performance of 0.1 micron rated filters. part iii: bacterial challenge tests on 0.2/0.22 and 0.1 micron rated filter cartridges with hydrogenophaga (formerly pseudomonas) pseudoflava.	we have previously reported on the preliminary characterization of hydrogenophaga (formerly pseudomonas) pseudoflava for potential use as a standard challenge organism to qualify 0.1 microm rated filters. this article reports on the retention efficiencies of a large panel of 0.2/0.22 microm and 0.1 microm rated filter cartridges for h. pseudoflava (atcc 700892) versus the retention capabilities of the same filters for brevundimonas diminuta (atcc 19146). a total of thirty-two 0.2/0.22 microm rat ...	2001	11766824
[auxotrophy and utilization of oxidized and reduced mineral sulfur forms by brevundimonas diminuta strains].	connection between auxotrophy of brevundimonas diminuta strains for sulphur-containing amino acids and presence of oxidized or reduced sulphur forms in the medium has been shown. when grown in synthetic medium supplied with sulphate or sulphite b. diminuta strains required cystine, biotin, pantothenate and vitamin b12 for growth and utilized very limited spectrum--from 8 to 12--carbon sources. in the presence of 5 g/l of thiosulphate in the medium instead of mentioned sulphur-containing salts st ...	2001	11785417
alpha- and beta-proteobacteria control the consumption and release of amino acids on lake snow aggregates.	we analyzed the composition of aggregate (lake snow)-associated bacterial communities in lake constance from 1994 until 1996 between a depth of 25 m and the sediment surface at 110 m by fluorescent in situ hybridization with rrna-targeted oligonucleotide probes of various specificity. in addition, we experimentally examined the turnover of dissolved amino acids and carbohydrates together with the microbial colonization of aggregates formed in rolling tanks in the lab. generally, between 40 and m ...	2001	11157226
genetic diversity among 3-chloroaniline- and aniline-degrading strains of the comamonadaceae.	we examined the diversity of the plasmids and of the gene tdnq, involved in the oxidative deamination of aniline, in five bacterial strains that are able to metabolize both aniline and 3-chloroaniline (3-ca). three strains have been described and identified previously, i.e., comamonas testosteroni i2 and delftia acidovorans ca28 and bn3.1. strains lme1 and b8c were isolated in this study from linuron-treated soil and from a wastewater treatment plant, respectively, and were both identified as d. ...	2001	11229899
multiple antibiotic resistance (mar) locus in salmonella enterica serovar typhimurium dt104.	in order to understand the role of the mar locus in salmonella with regard to multiple antibiotic resistance, cyclohexane resistance, and outer membrane protein f (ompf) regulation, a mara::gfp reporter mutant was constructed in an antibiotic-sensitive salmonella enterica serovar typhimurium dt104 background. salicylate induced mara, whereas a number of antibiotics, disinfectants, and various growth conditions did not. increased antibiotic resistance was observed upon salicylate induction, altho ...	2001	11229910
high resolution x-ray structures of different metal-substituted forms of phosphotriesterase from pseudomonas diminuta.	phosphotriesterase, isolated from the soil-dwelling bacterium pseudomonas diminuta, catalyzes the detoxification of organophosphate-based insecticides and chemical warfare agents. the enzyme has attracted significant research attention in light of its possible employment as a bioremediation tool. as naturally isolated, the enzyme is dimeric. each subunit contains a binuclear zinc center that is situated at the c-terminal portion of a "tim" barrel motif. the two zincs are separated by approximate ...	2001	11258882
determination of dna content of aquatic bacteria by flow cytometry.	the distribution of dna among bacterioplankton and bacterial isolates was determined by flow cytometry of dapi (4',6'-diamidino-2-phenylindole)-stained organisms. conditions were optimized to minimize error from nonspecific staining, at bias, dna packing, changes in ionic strength, and differences in cell permeability. the sensitivity was sufficient to characterize the small 1- to 2-mb-genome organisms in freshwater and seawater, as well as low-dna cells ("dims"). the dims could be formed from l ...	2001	11282616
retention of water-borne bacteria by membrane filters. part i: bacterial challenge tests on 0.2 and 0.22 micron rated filters.	the results of bacterial challenge tests conducted on several 0.2 and 0.22 micron rated "sterilizing grade" filter cartridge types with bacteria from a natural water source are presented. eight different 0.2/0.22 micron rated "sterilizing grade" filter types from four different filter manufacturers, claimed to be capable of retaining brevundimonas diminuta at a challenge level of 10(7) cfu/cm2, were tested. the filters tested included nylon 6.6 and polyamide filters from two manufacturers, modif ...	2001	11310322
degradation of substituted phenylurea herbicides by arthrobacter globiformis strain d47 and characterization of a plasmid-associated hydrolase gene, puha.	arthrobacter globiformis d47 was shown to degrade a range of substituted phenylurea herbicides in soil. this strain contained two plasmids of approximately 47 kb (phrim620) and 34 kb (phrim621). plasmid-curing experiments produced plasmid-free strains as well as strains containing either the 47- or the 34-kb plasmid. the strains were tested for their ability to degrade diuron, which demonstrated that the degradative genes were located on the 47-kb plasmid. studies on the growth of these strains ...	2001	11319111
biological properties of lipid a isolated from flavobacterium meningosepticum.	the biological properties of the lipid a from flavobacterium meningosepticum, which we recently isolated and whose complete chemical structure has been determined (h. kato, t. iida, y. haishima, a. tanaka, and k. tanamoto. j. bacteriol. 180:3891--3899, 1998), were studied. the lipid a exhibited generally moderate activity compared to salmonella enterica subsp. enterica serovar abortus equi lipopolysaccharide (lps) used as a control in the assay systems tested; lethal toxicity in galactosamine-se ...	2001	11329451
isolation of methyl parathion-degrading strain m6 and cloning of the methyl parathion hydrolase gene.	a degradative bacterium, m6, was isolated and presumptively identified as plesiomonas sp. strain m6 was able to hydrolyze methyl parathion to p-nitrophenol. a novel organophosphate hydrolase gene designated mpd was selected from its genomic library prepared by shotgun cloning. the nucleotide sequence of the mpd gene was determined. the gene could be effectively expressed in escherichia coli.	2001	11571204
culture-dependent and culture-independent characterization of microbial assemblages associated with high-temperature petroleum reservoirs.	recent investigations of oil reservoirs in a variety of locales have indicated that these habitats may harbor active thermophilic prokaryotic assemblages. in this study, we used both molecular and culture-based methods to characterize prokaryotic consortia associated with high-temperature, sulfur-rich oil reservoirs in california. enrichment cultures designed for anaerobic thermophiles, both autotrophic and heterotrophic, were successful at temperatures ranging from 60 to 90 degrees c. heterotro ...	2000	10653739
in situ analysis of sulfate-reducing bacteria related to desulfocapsa thiozymogenes in the chemocline of meromictic lake cadagno (switzerland).	comparative sequence analysis of a 16s rrna gene clone library from the chemocline of the meromictic lake cadagno (switzerland) retrieved two clusters of sequences resembling sulfate-reducing bacteria within the family desulfovibrionaceae. in situ hybridization showed that, similar to sulfate-reducing bacteria of the family desulfobacteriaceae, bacteria of one cluster with similarity values to the closest cultured relatives of between 92.6 and 93.1% resembled free cells or cells loosely attached ...	2000	10653757
reductive cleavage of demeton-s-methyl by corynebacterium glutamicum in cometabolism on more readily metabolizable substrates.	corynebacterium glutamicum is able to biotransform demeton-s-methyl, an organophosphorus compound, during cometabolism with more readily metabolizable substrates. among the cosubstrates used, fructose is the growth substrate that is most favorable for demeton-s-methyl biotransformation. the reaction mechanism of demeton-s-methyl biotransformation involves reductive cleavage of an s-c bond, which leads to accumulation of dimethyl thiophosphate in the culture medium.	2000	10698792
interference of pseudomonas strains in the identification of helicobacter pylori.		2000	10722321
involvement of two plasmids in fenitrothion degradation by burkholderia sp. strain nf100.	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 ...	2000	10742273