Publications

introduction of green fluorescent protein gene into phenol-degrading alcaligenes faecalis cells and their monitoring in phenol-contaminated soil.	alcaligenesfaecalis (cct 7145) was isolated from an amazonian soil sample after an enrichment process to select for phenol-degrading microorganisms. the isolate was labeled with the green fluorescent protein (gfp) gene. the gfp-transformed cells were easily detected using a hand-held uv transilluminator and their taxonomy was confirmed by 16s rrna sequencing. polymerase chain reaction (pcr) and southern blot analyses confirmed that the gfp gene was integrated into the chromosome. the addition of ...	2001	11499940
detection of legionellae in hospital water samples by quantitative real-time lightcycler pcr.	contamination of hospital water systems with legionellae is a well-known cause of nosocomial legionellosis. we describe a new real-time lightcycler pcr assay for quantitative determination of legionellae in potable water samples. primers that amplify both a 386-bp fragment of the 16s rrna gene from legionella spp. and a specifically cloned fragment of the phage lambda, added to each sample as an internal inhibitor control, were used. the amplified products were detected by use of a dual-color hy ...	2001	11525995
microbial population structures in soil particle size fractions of a long-term fertilizer field experiment.	soil structure depends on the association between mineral soil particles (sand, silt, and clay) and organic matter, in which aggregates of different size and stability are formed. although the chemistry of organic materials, total microbial biomass, and different enzyme activities in different soil particle size fractions have been well studied, little information is available on the structure of microbial populations in microhabitats. in this study, topsoil samples of different fertilizer treat ...	2001	11526026
identification of strains of alcaligenes and agrobacterium by a polyphasic approach.	the number of stable discriminant biochemical characters is limited in the genera alcaligenes and agrobacterium, whose species are consequently difficult to distinguish from one another by conventional tests. moreover, genomic studies have recently drastically modified the nomenclature of these genera; for example, alcaligenes xylosoxidans was transferred to the genus achromobacter in 1998. twenty-five strains of achromobacter xylosoxidans, three strains of an agrobacterium sp., five strains of ...	2001	11526136
taxonomy and identification of the burkholderia cepacia complex.		2001	11574551
enzymatic degradation of atactic poly(r,s-3-hydroxybutyrate) induced by amorphous polymers and the enzymatic degradation temperature window of an amorphous polymer system.	the phase structure and biodegradability were investigated for amorphous blends of chemosynthetic fully amorphous atactic poly(r,s-3-hydroxybutyrate) (a-phb) with atactic poly(methyl methacrylate) (pmma) and atactic poly(r,s-lactide) (a-pla). the differential scanning calorimetry thermal analysis indicated that a-phb/pmma blends were partially miscible while a-phb/a-pla blends were miscible in the studied composition range. the biodegradations of the blends were carried out in phosphate buffer s ...	2001	11710008
cloning of an intracellular poly[d(-)-3-hydroxybutyrate] depolymerase gene from ralstonia eutropha h16 and characterization of the gene product.	an intracellular poly[d(-)-3-hydroxybutyrate] (phb) depolymerase gene (phaz) has been cloned from ralstonia eutropha h16 by the shotgun method, sequenced, and characterized. nucleotide sequence analysis of a 2.3-kbp dna fragment revealed an open reading frame of 1,260 bp, encoding a protein of 419 amino acids with a predicted molecular mass of 47,316 da. the crude extract of escherichia coli containing the phb depolymerase gene digested artificial amorphous phb granules and released mainly oligo ...	2001	11114905
occurrence of tn4371-related mobile elements and sequences in (chloro)biphenyl-degrading bacteria.	tn4371, a 55-kb transposable element involved in the degradation and biphenyl or 4-chlorobiphenyl identified in ralstonia eutropha a5, displays a modular structure including a phage-like integrase gene (int), a pseudomonas-like (chloro)biphenyl catabolic gene cluster (bph), and rp4- and ti-plasmid-like transfer genes (trb) (c. merlin, d. springael, and a. toussaint, plasmid 41:40-54, 1999). southern blot hybridization was used to examine the presence of different regions of tn4371 in a collectio ...	2001	11133426
polyclonal antibodies recognizing the amob protein of ammonia oxidizers of the beta-subclass of the class proteobacteria.	a 41-kda protein of nitrosomonas eutropha was purified, and the n-terminal amino acid sequence was found to be nearly identical with the sequence of amob, a subunit of ammonia monooxygenase. this protein was used to develop polyclonal antibodies, which were highly specific for the detection of the four genera of ammonia oxidizers of the beta-subclass of proteobacteria (nitrosomonas, including nitrosococcus mobilis, which belongs phylogenetically to nitrosomonas; nitrosospira; nitrosolobus; and n ...	2001	11133435
ralstonia paucula (formerly cdc group iv c-2): unsuccessful strain differentiation with pcr-based methods, study of the 16s-23s spacer of the rrna operon, and comparison with other ralstonia species (r. eutropha, r. pickettii, r. gilardii, and r. solanacearum).	ralstonia paucula (formerly cdc group iv c-2) can cause serious human infections. confronted in 1995 with five cases of nosocomial bacteremia, we found that pulsed-field gel electrophoresis could not distinguish between the isolates and that randomly amplified polymorphic dna analysis was poorly discriminatory. in this study, we used pcr-ribotyping and pcr-restriction fragment length polymorphism analysis of the spacer 16s-23s ribosomal dna (rdna); both methods were unable to differentiate r. pa ...	2001	11136807
nickel-resistance-based minitransposons: new tools for genetic manipulation of environmental bacteria.	the ncc and nre nickel resistance determinants from ralstonia eutropha-like strain 31a were used to construct mini-tn5 transposons. broad host expression of nickel resistance was observed for the nre minitransposons in members of the alpha, beta, and gamma subclasses of the proteobacteria, while the ncc minitransposons expressed nickel resistance only in r. eutropha-like strains.	2001	11157282
comparison of automated and nonautomated systems for identification of burkholderia pseudomallei.	the identification of burkholderia pseudomallei, the causative agent of melioidosis, is usually not difficult in laboratories in areas where it is endemic. with the increase in international travel and the threat of bioterrorism, it has become more likely that laboratories in areas where it is not endemic could encounter this organism. the increase in the use of and dependence upon automated identification systems makes accurate identification of uncommonly encountered organisms such as b. pseud ...	2002	12454163
development and characterization of murine monoclonal antibodies specific for dissimilatoric copper nitrite reductase.	several hybridoma cell lines from mice were established, producing monoclonal antibodies (mabs) directed against the dissimilatoric copper nitrite reductase (dnir) to detect actual denitrifying bacteria at the single cell level under nondestructive conditions in the environment. the mice were immunized with native or recombinant enzyme gained from two different bacteria, ochrobactrum anthropi and alcaligenes faecalis. the antibodies obtained could be divided into two groups according to their di ...	2002	12470477
precipitin response of potato processing workers to work-related microbial allergens.	serum samples from 61 potato processing workers and 30 urban dwellers not exposed to organic dusts (as a reference group) were examined in agar-gel precipitation test performed by ouchterlony double diffusion method with the antigens of 12 microorganisms associated with organic dusts. each serum was tested twice: not concentrated, and three-fold concentrated, for the detection of low levels of precipitins. the antibody response of workers to the antigen of coryneform bacterium agromyces ramosus ...	2002	12498593
hyperthermostable endoglucanase from pyrococcus horikoshii.	an endoglucanase homolog from the hyperthermophilic archaeon pyrococcus horikoshii was expressed in escherichia coli, and its enzymatic characteristics were examined. the expressed protein was a hyperthermostable endoglucanase which hydrolyzes celluloses, including avicel and carboxymethyl cellulose, as well as beta-glucose oligomers. this enzyme is the first endoglucanase belonging to glycosidase family 5 found from pyrococcus species and is also the first hyperthermostable endoglucanase to whi ...	2002	11772658
aerobic-type ribonucleotide reductase in the anaerobe bacteroides fragilis.	bacteroides fragilis, a component of the normal intestinal flora, is an obligate anaerobe capable of long-term survival in the presence of air. survival is attributed to an elaborate oxidative stress response that controls the induction of more than 28 peptides, but there is limited knowledge concerning the identities of these peptides. in this report, rna fingerprinting by arbitrarily primed pcr identified five new genes whose expression increased following exposure to o2. nucleotide sequence a ...	2002	11807048
coexistence of two distinct copies of naphthalene degradation genes in pseudomonas strains isolated from the western mediterranean region.	we analyzed the occurrence of the naphthalene degradation upper-pathway (nah) genes in the western mediterranean region. the amplification, restriction, and sequence analysis of internal fragments for several nah genes (nahac, nahb, nahc, and nahe) from naphthalene-degrading strains isolated from this geographical area proved the coexistence of two distinct sets of nah genes.	2002	11823244
crystal structure of the soluble domain of the major anaerobically induced outer membrane protein (ania) from pathogenic neisseria: a new class of copper-containing nitrite reductases.	the major anaerobically induced outer membrane protein (ania) from pathogenic neisseria gonorrhoeae is essential for cell growth under oxygen limiting conditions in the presence of nitrite and is protective against killing by human sera. a phylogenic analysis indicates that ania is a member of a new class of copper-containing nitrite reductases. expression of the soluble domain of ania yields a protein capable of reducing nitrite with specific activity of 160 units/mg, approximately 50 % of that ...	2002	11827480
postkeratoplasty endophthalmitis by alcaligenes faecalis: a case report.	to describe a postkeratoplasty endophthalmitis owing to alcaligenes faecalis that resolved with medical management.	2002	11862104
side-chain effect of second monomer units on crystalline morphology, thermal properties, and enzymatic degradability for random copolyesters of (r)-3-hydroxybutyric acid with (r)-3-hydroxyalkanoic acids.	three types of random copolymers with 94 mol % (r)-3-hydroxybutyric acid (3hb) and 6 mol % (r)-3-hydroxyalkanoic acids with different side-chain lengths, (r)-3-hydroxypentanoic acid (3hv), (r)-3-hydroxyhexanoic acid (3hhx), and medium-chain-length (r)-3-hydroxyalkanoic acids (mcl-3ha, c8-c12), were prepared by biological synthetic techniques. the solid-state structure and thermal properties of melt-crystallized films for copolymers were characterized by means of wide-angle x-ray diffraction, sma ...	2002	11866565
nonhydrolytic fragmentation of a poly[(r)-3-hydroxybutyrate] single crystal revealed by use of a mutant of polyhydroxybutyrate depolymerase.	this paper reports the initial process of the enzymatic degradation of solution-grown lamellar single crystals of bacterial poly[(r)-3-hydroxybutyrate] (p(3hb)) with an extracellular polyhydroxybutyrate (phb) depolymerase purified from alcaligenes faecalis t1. we used a hydrolytic-activity-disrupted mutant of the phb depolymerase in order to avoid the influence of hydrolytic reaction in the system. the effect of addition of the mutant enzyme upon the p(3hb) single crystals was investigated by tu ...	2002	11888317
purification and characterization of alkaline protease from alcaligenes faecalis.	extracellular alkaline protease from the alkalophilic bacterium alcaligenes faecalis was purified by a combination of ion-exchange and size-exclusion chromatographic methods, and its properties were examined. the purified enzyme had a specific activity of 563.8 micromol of tyrosine/min per mg of protein and gave a single band on native page and sds/page with a molecular mass of 67 kda. gelatin zymogram also revealed one clear zone of proteolytic activity which corresponded to the band obtained w ...	2002	11916457
molecular method to assess the diversity of burkholderia species in environmental samples.	in spite of the importance of many members of the genus burkholderia in the soil microbial community, no direct method to assess the diversity of this genus has been developed so far. the aim of this work was the development of soil dna-based pcr-denaturing gradient gel electrophoresis (dgge), a powerful tool for studying the diversity of microbial communities, for detection and analysis of the burkholderia diversity in soil samples. primers specific for the genus burkholderia were developed bas ...	2002	11916673
molecular biological detection and characterization of clostridium populations in municipal landfill sites.	primer sets specific for 16s rrna genes were designed for four phylogenetic groups of clostridia known to contain mesophilic cellulolytic species. specific amplification of these groups from landfill leachate dna extracts demonstrated the widespread occurrence of clostridia from the clostridium thermocellum and c. leptum groups. in contrast, the c. botulinum group was never detected, and the c. coccoides-c. lentocellum group was only occasionally detected. amplification products were analyzed by ...	2002	11916731
ribosomal dna-directed pcr for identification of achromobacter (alcaligenes) xylosoxidans recovered from sputum samples from cystic fibrosis patients.	the opportunistic human pathogen achromobacter (alcaligenes) xylosoxidans has been recovered with increasing frequency from respiratory tract culture of persons with cystic fibrosis (cf). however, confusion of this species with other closely related respiratory pathogens has limited studies to better elucidate its epidemiology, natural history, and pathogenic role in cf. misidentification of a. xylosoxidans as burkholderia cepacia complex is especially problematic and presents a challenge to eff ...	2002	11923333
comparative evaluation of the bd phoenix and vitek 2 automated instruments for identification of isolates of the burkholderia cepacia complex.	we evaluated two new automated identification systems, the bd phoenix (becton dickinson) and the vitek 2 (biomérieux), for identification of isolates of the burkholderia cepacia complex (bcc). the test sample included 42 isolates of the highly virulent and epidemic genomovar iii, 45 isolates of b. multivorans, and 47 isolates of other members of the bcc. rates of correct identification by the bd phoenix and vitek 2 were similar when all bcc isolates were considered (50 and 53%, respectively) but ...	2002	11980954
base-specific fragmentation of amplified 16s rrna genes analyzed by mass spectrometry: a tool for rapid bacterial identification.	a rapid approach to the 16s rrna gene (16s rdna)-based bacterial identification has been developed that combines uracil-dna-glycosylase (udg)-mediated base-specific fragmentation of pcr products with matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (maldi-tof ms). 16s rdna signature sequences were pcr-amplified from both cultured and as-yet-uncultured bacteria in the presence of dutp instead of dttp. these pcr products then were immobilized onto a streptavidin-coated ...	2002	11983869
plasmid-encoded asp operon confers a proton motive metabolic cycle catalyzed by an aspartate-alanine exchange reaction.	tetragenococcus halophila d10 catalyzes the decarboxylation of l-aspartate with nearly stoichiometric release of l-alanine and co(2). this trait is encoded on a 25-kb plasmid, pd1. we found in this plasmid a putative asp operon consisting of two genes, which we designated aspd and aspt, encoding an l-aspartate-beta-decarboxylase (aspd) and an aspartate-alanine antiporter (aspt), respectively, and determined the nucleotide sequences. the sequence analysis revealed that the genes of the asp operon ...	2002	12003930
in vitro antiseptic susceptibility of clinical isolates from nosocomial infections.	to evaluate the susceptibility of a large number of strains to various antiseptics, we elaborated a simple, qualitative broth turbidity method in which we could quickly judge the efficacy visually. for this method, we prepared a modified neutralizer broth, consisting of trypticase soy broth containing 15% tween 80, 1% soybean lecithin and 0.5% sodium thiosulfate. the susceptibilities of serratia marcescens no. 26 to 4 antiseptics obtained from the turbidity method showed a good agreement with th ...	2002	12011516
a broad host range plasmid vector that does not encode replication proteins.	the 640-bp minimal replication region derived from a plasmid dna preparation from an acidothiobacillus ferrooxidans strain capable of autonomous replication in a range of gram-negative bacteria (escherichia coli, pseudomonas aeruginosa, acinetobacter calcoaceticus and alcaligenes faecalis) was identified. this dna fragment (named tfk replicon) does not encode rep proteins and appears to be unrelated to other known replicons.	2002	12052556
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
a quantitative pcr (taqman) assay for pathogenic leptospira spp.	leptospirosis is an emerging infectious disease. the differential diagnosis of leptospirosis is difficult due to the varied and often "flu like" symptoms which may result in a missed or delayed diagnosis. there are over 230 known serovars in the genus leptospira. confirmatory serological diagnosis of leptospirosis is usually made using the microscopic agglutination test (mat) which relies on the use of live cultures as the source of antigen, often performed using a panel of antigens representati ...	2002	12100734
active site titration as a tool for the evaluation of immobilization procedures of penicillin acylase.	native and immobilized preparations of penicillin acylase from escherichia coli and alcaligenes faecalis were studied using an active site titration technique. knowledge of the number of active sites allowed the calculation of the average turnover rate of the enzyme in the various preparations and allowed us to quantify the contribution of irreversible inactivation of the enzyme to the loss of catalytic activity during the immobilization procedure. in most cases a loss of active sites as well as ...	2002	12115439
sat, the secreted autotransporter toxin of uropathogenic escherichia coli, is a vacuolating cytotoxin for bladder and kidney epithelial cells.	the secreted autotransporter toxin (sat) of uropathogenic escherichia coli exhibits cytopathic activity upon incubation with hep-2 cells. we further investigated the effects of sat on cell lines more relevant to the urinary tract, namely, those derived from bladder and kidney epithelium. sat elicited elongation of cells and apparent loosening of cellular junctions upon incubation with vero kidney cells. additionally, incubation with sat triggered significant vacuolation within the cytoplasm of b ...	2002	12117966
plasmid-borne genes code for an angular dioxygenase involved in dibenzofuran degradation by terrabacter sp. strain yk3.	the genes responsible for angular dioxygenation of dibenzofuran in actinomycetes were cloned by using a degenerate set of pcr primers designed by using conserved sequences of the dioxygenase alpha subunit genes. one sequence of alpha subunit genes was commonly amplified from four dibenzofuran-utilizing actinomycetes: terrabacter sp. strains yk1 and yk3, rhodococcus sp. strain yk2, and microbacterium sp. strain yk18. a 5.2-kb psti fragment encoding the alpha and beta subunits of the terminal diox ...	2002	12147464
biodiversity of denitrifying and dinitrogen-fixing bacteria in an acid forest soil.	isolated soil dna from an oak-hornbeam forest close to cologne, germany, was suitable for pcr amplification of gene segments coding for the 16s rrna and nitrogenase reductase (nifh), nitrous oxide reductase (nosz), cytochrome cd(1)-containing nitrite reductase (nirs), and cu-containing nitrite reductase (nirk) of denitrification. for each gene segment, diverse pcr products were characterized by cloning and sequencing. none of the 16s rrna gene sequences was identical to any deposited in the data ...	2002	12147477
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
genetic analysis of pigment biosynthesis in xanthobacter autotrophicus py2 using a new, highly efficient transposon mutagenesis system that is functional in a wide variety of bacteria.	a highly efficient method of transposon mutagenesis was developed for genetic analysis of xanthobacter autotrophicus py2. the method makes use of a transposon delivery vector that encodes a hyperactive tn 5 transposase that is 1,000-fold more active than the wild-type transposase. in this construct, the transposase is expressed from the promoter of the teta gene of plasmid rp4, which is functional in a wide variety of organisms. the transposon itself contains a kanamycin resistance gene as a sel ...	2002	12189420
crystallization and preliminary crystallographic analysis of a d-aminoacylase from alcaligenes faecalis da1.	d-aminoacylases catalyze the hydrolysis of n-acyl-d-amino acids into d-amino acids with the aid of zinc ions. the first d-aminoacylase crystal from alcaligenes faecalis has been obtained in hanging drops at ph 5.6 by the vapour-diffusion method using 30% polyethylene glycol 4000 as precipitant. it belongs to space group p2(1)2(1)2(1), with unit-cell parameters a = 60.2, b = 76.6, c = 135.3 a. reflections to 1.2 a resolution are observable. an initial atomic model with 472 residues has been built ...	2002	12198309
evidence for natural horizontal transfer of the pcpb gene in the evolution of polychlorophenol-degrading sphingomonads.	the chlorophenol degradation pathway in sphingobium chlorophenolicum is initiated by the pcpb gene product, pentachlorophenol-4-monooxygenase. the distribution of the gene was studied in a phylogenetically diverse group of polychlorophenol-degrading bacteria isolated from contaminated groundwater in kärkölä, finland. all the sphingomonads isolated were shown to share pcpb gene homologs with 98.9 to 100% sequence identity. the gene product was expressed when the strains were induced by 2,3,4,6-te ...	2002	12200305
pathogenic effects of bacteria isolated from larvae of hylesia metabus crammer (lepidoptera: saturniidae).	hylesia metabus larvae are susceptible to several pathogens indigenous to the area in which they are found. some larvae show symptoms characteristic of bacterial infection; they become flaccid and lethargic, and show a marked loss of appetite. we isolated and identified 29 bacterial strains from live, dead and experimentally infected h. metabus larvae, and evaluated their pathogenic activity. the bacteria which caused mortality in the larvae were: pseudomonas aeruginosa (60-93.3%), proteus vulga ...	2002	12234536
the active site of arsenite oxidase from alcaligenes faecalis.	arsenite oxidase, a member of the dmso reductase family of molybdenum enzymes, has two molecules of guanosine dinucleotide molybdenum cofactor coordinating the molybdenum at the active site. x-ray absorption spectroscopy indicates that the mo-s bonds shorten from 2.47 to 2.37 a upon reduction with the physiological substrate. it also indicates the presence of an oxo ligand at 1.70 a in both oxidized and reduced forms of the enzyme, together with a short, 1.83 a, mo-o bond in the oxidized form th ...	2002	12236735
microbial diversity in an in situ reactor system treating monochlorobenzene contaminated groundwater as revealed by 16s ribosomal dna analysis.	a molecular approach based on the construction of 16s ribosomal dna clone libraries was used to investigate the microbial diversity of an underground in situ reactor system filled with the original aquifer sediments. after chemical steady state was reached in the monochlorobenzene concentration between the original inflowing groundwater and the reactor outflow, samples from different reactor locations and from inflowing and outflowing groundwater were taken for dna extraction. small-subunit rrna ...	2002	12353878
use of 16s rrna gene sequencing for identification of nonfermenting gram-negative bacilli recovered from patients attending a single cystic fibrosis center.	during 1999, we used partial 16s rrna gene sequencing for the prospective identification of atypical nonfermenting gram-negative bacilli isolated from patients attending our cystic fibrosis center. of 1,093 isolates of nonfermenting gram-negative bacilli recovered from 148 patients, 46 (4.2%) gave problematic results with conventional phenotypic tests. these 46 isolates were genotypically identified as pseudomonas aeruginosa (19 isolates, 12 patients), achromobacter xylosoxidans (10 isolates, 8 ...	2002	12354883
structural analysis of the curdlan-like exopolysaccharide produced by cellulomonas flavigena ku.	cellulomonas flavigena ku produces large quantities of an insoluble exopolysaccharide (eps) under certain growth conditions. the eps has previously been shown to be a glucose polymer and to have solubility properties similar to curdlan, a beta-1,3-d-glucan produced by alcaligenes faecalis var. myxogenes 10c3k. furthermore, eps purified by alkaline extraction stains with aniline blue, a dye specific for curdlan-type polysaccharides. however, eps-producing colonies of c. flavigena ku do not stain ...	2002	12355320
structural-based mutational analysis of d-aminoacylase from alcaligenes faecalis da1.	d-aminoacylase is an attractive candidate for commercial production of d-amino acids through its catalysis in the zinc-assistant hydrolysis of n-acyl-d-amino acids. we report here the cloning, expression, and structural-based mutation of the d-aminoacylase from alcaligenes faecalis da1. a 1,007-bp pcr product amplified with degenerate primers, was used to isolate a 4-kb genomic fragment, encoding a 484-residue d-aminoacylase. the enzyme amino-terminal segment shared significant homology within a ...	2002	12381838
microbiological evaluation of a commercial transport system for urine samples.	the aim of this study was to evaluate a commercial tube prepared with boric acid, sodium formate and sorbitol (hemogard vacutainer tubes, becton-dickinson, hg tubes). fourteen bacterial strains were incubated in urine in hg tubes and conventional tubes. during a 24-h period, most of the microorganisms grew readily in conventional tubes at room temperature, whereas the bacterial counts were comparatively unchanged when chilled or kept in hg tubes. the bacterial counts of alcaligenes faecalis and ...	2002	12387577
effect of soil ammonium concentration on n2o release and on the community structure of ammonia oxidizers and denitrifiers.	the effect of ammonium addition (6.5, 58, and 395 microg of nh4+-n g [dry weight] of soil(-1)) on soil microbial communities was explored. for medium and high ammonium concentrations, increased n2o release rates and a shift toward a higher contribution of nitrification to n2o release occurred after incubation for 5 days at 4 degrees c. communities of ammonia oxidizers were assayed after 4 weeks of incubation by denaturant gradient gel electrophoresis (dgge) of the amoa gene coding for the small ...	2002	12406765
mutants of streptomyces clavuligerus with disruptions in different genes for clavulanic acid biosynthesis produce large amounts of holomycin: possible cross-regulation of two unrelated secondary metabolic pathways.	a streptomyces clavuligerus ccar::aph strain, which has a disruption in the regulatory gene ccar, does not produce cephamycin c or clavulanic acid, but does produce a bioactive compound that was identified as holomycin by high-performance liquid chromatography (hplc) and infrared and mass spectrometry. s. clavuligerus strains with disruptions in different genes of the clavulanic acid pathway fall into three groups with respect to holomycin biosynthesis. (i) mutants with mutations in the early st ...	2002	12426344
purification and characterization of carbazole 1,9a-dioxygenase, a three-component dioxygenase system of pseudomonas resinovorans strain ca10.	the carbazole 1,9a-dioxygenase (cardo) system of pseudomonas resinovorans strain ca10 consists of terminal oxygenase (caraa), ferredoxin (carac), and ferredoxin reductase (carad). each component of cardo was expressed in escherichia coli strain bl21(de3) as a native form (caraa) or a his-tagged form (carac and carad) and was purified to apparent homogeneity. caraa was found to be trimeric and to have one rieske type [2fe-2s] cluster and one mononuclear iron center in each monomer. both his-tagge ...	2002	12450807
disruption of narh, narj, and moae inhibits heterotrophic nitrification in pseudomonas strain m19.	interruptions in three nitrate reductase-related genes, narh, narj, and moae, inhibited heterotrophic nitrification in pseudomonas strain m19. no nitrate was detected in the medium, and nitrification proceeded in the presence of a nitrate reductase inhibitor. heterotrophic nitrification was greatly stimulated by the addition of nitrate.	2002	12450879
[influence of ph control on the production of curdlan by alcaligenes faecalis strain].	a two-stage ph control method was employed in batch fermentation of curdlan by alcaligenes faecalis wx-c12 where cell-growth stage was constantly controlled at ph 7.0 and stationary stage was controlled at a constant ph as well. the influence of ph control on the curdlan production was investigated. the optimal ph control of batch process for curdlan production was obtained when cell-growth stage was controlled at ph 7.0 and stationary stage was constantly controlled at ph 5.6. production and pr ...	2002	12561215
bacteriological analysis of blood culture isolates from neonates in a tertiary care hospital in india.	this study was undertaken to determine the profile and antibiotic sensitivity patterns of aerobic isolates from blood cultures of neonates in a tertiary care hospital in new delhi, india. all blood culture reports (n = 1,828), obtained during august 1995-september 1996 from newborns admitted to the department of pediatrics and the neonatal intensive care unit at the university college of medical sciences and gtb hospital, delhi, were analyzed, and the sensitivity patterns were recorded. the posi ...	2002	12659415
dimethylsulfoniopropionate: its sources, role in the marine food web, and biological degradation to dimethylsulfide.		2002	12450799
rapid and sensitive enumeration of viable diluted cells of members of the family enterobacteriaceae in freshwater and drinking water.	water quality assessment involves the specific, sensitive, and rapid detection of bacterial indicators and pathogens in water samples, including viable but nonculturable (vbnc) cells. this work evaluates the specificity and sensitivity of a new method which combines a fluorescent in situ hybridization (fish) approach with a physiological assay (direct viable count [dvc]) for the direct enumeration, at the single-cell level, of highly diluted viable cells of members of the family enterobacteriace ...	2002	12324357
in vitro activities of bal9141, a novel broad-spectrum pyrrolidinone cephalosporin, against gram-negative nonfermenters.	the activities of bal9141 (formerly ro 63-9141), a novel pyrrolidinone-3-ylidenemethyl cephalosporin, against 244 strains of gram-negative nonfermenters were evaluated. the overall mic at which 50% of isolates are inhibited (mic50) and the overall mic90 were 2 and 64 microg/ml, respectively, which are similar to those of imipenem, lower than those of the other cephalosporins tested, amoxicillin, and the ticarcillin-clavulanic acid combination, and much higher than those of ciprofloxacin. bal9141 ...	2002	11850276
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
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
diversity of nitrite reductase (nirk and nirs) gene fragments in forested upland and wetland soils.	the genetic heterogeneity of nitrite reductase gene (nirk and nirs) fragments from denitrifying prokaryotes in forested upland and marsh soil was investigated using molecular methods. nirk gene fragments could be amplified from both soils, whereas nirs gene fragments could be amplified only from the marsh soil. pcr products were cloned and screened by restriction fragment length polymorphism (rflp), and representative fragments were sequenced. the diversity of nirk clones was lower than the dive ...	2002	11916709
nitrous oxide formation in the colne estuary, england: the central role of nitrite.	nitrate and nitrite concentrations in the water and nitrous oxide and nitrite fluxes across the sediment-water interface were measured monthly in the river colne estuary, england, from december 1996 to march 1998. water column concentrations of n(2)o in the colne were supersaturated with respect to air, indicating that the estuary was a source of n(2)o for the atmosphere. at the freshwater end of the estuary, nitrous oxide effluxes from the sediment were closely correlated with the nitrite conce ...	2002	11872474
nitric oxide reductase (norb) genes from pure cultures and environmental samples.	a pcr-based approach was developed to recover nitric oxide (no) reductase (norb) genes as a functional marker gene for denitrifying bacteria. norb database sequences grouped in two very distinct branches. one encodes the quinol-oxidizing single-subunit class (qnorb), while the other class is a cytochrome bc-type complex (cnorb). the latter oxidizes cytochrome c, and the gene is localized adjacent to norc. while both norb types occur in denitrifying strains, the qnorb type was also found in a var ...	2003	12788753
detection and enumeration of aromatic oxygenase genes by multiplex and real-time pcr.	our abilities to detect and enumerate pollutant-biodegrading microorganisms in the environment are rapidly advancing with the development of molecular genetic techniques. techniques based on multiplex and real-time pcr amplification of aromatic oxygenase genes were developed to detect and quantify aromatic catabolic pathways, respectively. pcr primer sets were identified for the large subunits of aromatic oxygenases from alignments of known gene sequences and tested with genetically well-charact ...	2003	12788736
tmrdb (tmrna database).	maintained at the university of texas health science center at tyler, texas, the tmrna database (tmrdb) is accessible at the url http://psyche.uthct.edu/dbs/tmrdb/tmrdb.html with mirror sites located at auburn university, auburn, alabama (http://www.ag.auburn.edu/mirror/tmrdb/) and the bioinformatics research center, aarhus, denmark (http://www.bioinf.au.dk/tmrdb/). the tmrdb collects and distributes information relevant to the study of tmrna. in trans-translation, this molecule combines propert ...	2003	12520048
nitrite reductase genes in halobenzoate degrading denitrifying bacteria.	abstract diversity of the functional genes encoding dissimilatory nitrite reductase was investigated for the first time in denitrifying halobenzoate degrading bacteria and in two 4-chlorobenzoate degrading denitrifying consortia. nitrite reductase genes were pcr-amplified with degenerate primers (specific to the two different types of respiratory nitrite reductase, nirs and nirk), cloned and sequenced to determine which type of nitrite reductase was present in each isolate and consortium. halobe ...	2003	19719666
controlled clinical comparison of bact/alert standard aerobic medium with bactec standard aerobic medium for culturing blood.	standard aerobic media are widely used for culturing blood with the bact/alert (biomérieux, inc., durham, n.c.) (bm) and bactec 9240 (bd diagnostic systems, sparks, md.) (bd) automated continuously monitoring instrument systems. although similarly composed of soybean-casein digest broths, the formulations of the standard aerobic media available for these instruments differ from each other in supplements and in sodium polyanetholesulfonate concentration. therefore, we compared the standard aerobi ...	2003	12791854
interstrain inhibition in the sweet potato pathogen streptomyces ipomoeae: purification and characterization of a highly specific bacteriocin and cloning of its structural gene.	strains of the sweet potato soil rot pathogen streptomyces ipomoeae had previously been divided into three groups based on their ability to inhibit one another during pairwise cocultivation. while group i strains are not antagonistic to members of the other groups, group ii and group iii strains produce separate substances that are inhibitory to strains outside their respective cognate groups. here, we purified the group iii inhibitory substance from the culture supernatant of a representative s ...	2003	12676701
reconstitution of the type-1 active site of the h145g/a variants of nitrite reductase by ligand insertion.	variants of the copper-containing nitrite reductase (nir) of alcaligenes faecalis s6 were constructed by site-directed mutagenesis, by which the c-terminal histidine ligand (his145) of the cu in the type-1 site was replaced by an alanine or a glycine. the type-1 sites in the nir variants as isolated, are in the reduced form, but can be oxidized in the presence of external ligands, like (substituted) imidazoles and chloride. the reduction potential of the type-1 site of nir-h145a reconstituted wi ...	2003	12680761
comparison of ribotyping and restriction enzyme analysis for inter- and intraspecies discrimination of bordetella avium and bordetella hinzii.	bordetella avium is an avian respiratory disease pathogen responsible for substantial economic losses to the turkey industry. the inability to distinguish isolates has hampered outbreak investigations and prevents a complete understanding of transmission mechanisms. isolates of bordetella hinzii, often referred to as b. avium-like or as alcaligenes faecalis type ii prior to 1995, have also been acquired from the respiratory tracts of diseased poultry but are not believed to be pathogenic for bir ...	2003	12682138
correlation between structure of the lactones and substrate specificity in enzyme-catalyzed polymerization for the synthesis of polyesters.	small-size (4-membered) and medium-size (5-, 6-, and 7-membered) unsubstituted lactones as well as unsubstituted macrolides (12 and 13 membered) were subjected to the ring-opening polymerization using the extracellular phb depolymerase from alcaligenes faecalis t1 (phaz(afa)). the characteristic reactivities of the lactones were discussed based on a tertiary structure model of the active site of the phaz(afa). with respect to the ring-size of the lactones, the 4-membered beta-propiolactone and 6 ...	2003	12741767
long-term analysis of diesel fuel consumption in a co-culture of acinetobacter venetianus, pseudomonas putida and alcaligenes faecalis.	the dynamics of a microbial population isolated from superficial waters of venice lagoon and the ability to utilise diesel fuel (n-alkanes mixture c12-c28) as the sole carbon and energy source were studied in a long-term reconstruction experiment. the reconstructed microbial population consisted of three bacterial strains belonging to the species acinetobacter venetianus, pseudomonas putida, and alcaligenes faecalis, which were able to oxidise n-alkanes to alkanoates, n-alkanols to alkanoates, o ...	2003	12755474
purification and characterization of alcaligenes faecalis penicillin g acylase expressed in bacillus subtilis.	the alcaligenes faecalis pga gene encoding heterodimeric penicillin g acylase (pga) was cloned and successfully expressed in escherichia coli and bacillus subtilis respectively. in contrast to e.coli hosts where the enzymes were retained in the periplasm, b. subtilis cell secreted the recombinant enzyme into the medium. contrary to limited expression yield of e. coli (petapga), pga extracellularly expressed by b. subtilis (pbapga) and b. subtilis (pmapga) reached the highest yield of 653 u/l. th ...	2003	12766801
purification and properties of an intracellular 3-hydroxybutyrate-oligomer hydrolase (phaz2) in ralstonia eutropha h16 and its identification as a novel intracellular poly(3-hydroxybutyrate) depolymerase.	an intracellular 3-hydroxybutyrate (3hb)-oligomer hydrolase (phaz2(reu)) of ralstonia eutropha was purified from escherichia coli harboring a plasmid containing phaz2(reu). the purified enzyme hydrolyzed linear and cyclic 3hb-oligomers. although it did not degrade crystalline poly(3-hydroxybutyrate) (phb), the purified enzyme degraded artificial amorphous phb at a rate similar to that of the previously identified intracellular phb (iphb) depolymerase (phaz1(reu)). the enzyme appeared to be an en ...	2003	12775684
molecular diversity of denitrifying genes in continental margin sediments within the oxygen-deficient zone off the pacific coast of mexico.	to understand the composition and structure of denitrifying communities in the oxygen-deficient zone off the pacific coast of mexico, the molecular diversity of nir genes from sediments obtained at four stations was examined by using a pcr-based cloning approach. a total of 50 operational taxonomic units (otus) for nirk and 82 otus for nirs were obtained from all samples. forty-four of the nirs clones and 31 of the nirk clones were sequenced; the levels of similarity of the nirs clones were 52 t ...	2003	12788762
phylogeny and characterization of three nifh-homologous genes from paenibacillus azotofixans.	in this paper, we report the cloning and characterization of three paenibacillus azotofixans dna regions containing genes involved in nitrogen fixation. sequencing analysis revealed the presence of nifb1h1d1k1 gene organization in the 4,607-bp saci dna fragment. this is the first report of linkage of a nifb open reading frame upstream of the structural nif genes. the second (nifb2h2) and third (nifh3) nif homologues are confined within the 6,350-bp hindiii and 2,840-bp ecori dna fragments, respe ...	2003	12788777
a homology model of penicillin acylase from alcaligenes faecalis and in silico evaluation of its selectivity.	a three-dimensional model of the relatively unknown penicillin acylase from alcaligenes faecalis (pa-af) was built up by means of homology modeling based on three different crystal structures of penicillin acylase from various sources. an in silico selectivity study was performed to compare this homology model to the structure of the escherichia coli enzyme (pa-ec) in order to find any selectivity differences between the two enzymes. the program grid was applied in combination with the principal ...	2003	12851931
phylogenetic analysis of bacterial and archaeal arsc gene sequences suggests an ancient, common origin for arsenate reductase.	the ars gene system provides arsenic resistance for a variety of microorganisms and can be chromosomal or plasmid-borne. the arsc gene, which codes for an arsenate reductase is essential for arsenate resistance and transforms arsenate into arsenite, which is extruded from the cell. a survey of genbank shows that arsc appears to be phylogenetically widespread both in organisms with known arsenic resistance and those organisms that have been sequenced as part of whole genome projects.	2003	12877744
bioreactor cultivation of escherichia coli for production of recombinant penicillin g amidase from alcaligenes faecalis.	the penicillin g amidase (pga) from alcaligenes faecalis, which has interesting properties for use in combinatorial biochemistry, was produced by recombinant expression in escherichia coli. the corresponding gene was cloned into a multicopy vector under the strict regulatory control of the rhamnose inducible promoter. cells were grown in a synthetic minimal medium in a bioreactor (5 l working vol.), and production of pga was induced by repeated addition of the inducer rhamnose, that served also ...	2003	12882560
control of metalloprotein reduction potential: compensation phenomena in the reduction thermodynamics of blue copper proteins.	the reduction thermodynamics (delta h degrees '(rc) and delta s degrees '(rc)) for native paracoccus versutus amicyanin, for alcaligenes faecalis s-6 pseudoazurin, and for the g45p, m64e, and k27c variants of pseudomonas aeruginosa azurin were measured electrochemically. comparison with the data available for other native and mutated blue copper proteins indicates that the features of metal coordination and the electrostatic potential due to the protein matrix and the solvent control the reducti ...	2003	12885256
cloning of a nitrilase gene from the cyanobacterium synechocystis sp. strain pcc6803 and heterologous expression and characterization of the encoded protein.	the gene encoding a putative nitrilase was identified in the genome sequence of the photosynthetic cyanobacterium synechocystis sp. strain pcc6803. the gene was amplified by pcr and cloned into an expression vector. the encoded protein was heterologously expressed in the native form and as a his-tagged protein in escherichia coli, and the recombinant strains were shown to convert benzonitrile to benzoate. the active enzyme was purified to homogeneity and shown by gel filtration to consist probab ...	2003	12902216
nitrogen fixation genetics and regulation in a pseudomonas stutzeri strain associated with rice.	the pseudomonas stutzeri strain a1501 (formerly known as alcaligenes faecalis) fixes nitrogen under microaerobic conditions in the free-living state and colonizes rice endophytically. the authors characterized a region in strain a1501, corresponding to most of the nif genes and the rnf genes, involved in electron transport to nitrogenase in rhodobacter capsulatus. the region contained three groups of genes arranged in the same order as in azotobacter vinelandii: (1) nifb fdx orf3 nifq orf5 orf6; ...	2003	12904565
isolation of strains belonging to the cosmopolitan polynucleobacter necessarius cluster from freshwater habitats located in three climatic zones.	more than 40 bacterial strains belonging to the cosmopolitan polynucleobacter necessarius cluster (betaproteobacteria) were isolated from a broad spectrum of freshwater habitats located in three climatic zones. sequences affiliated with the freshwater p. necessarius cluster are among the most frequently detected in studies on bacterial diversity in freshwater ecosystems. despite this frequent detection with culture-independent techniques and the cosmopolitan occurrence of members affiliated with ...	2003	12957910
the nomenclatural type of the genus deleya and the consequences of deleya aesta and alcaligenes aquamarinus being synonyms.	the genus deleya was created to encompass a number of marine organisms that had previously been classified in diverse genera. deleya aesta was designated as the type species of the genus. subsequent work indicated that deleya aesta, alcaligenes aquamarinus and alcaligenes faecalis subsp. homari were heterotypic synonyms. consequently, akagawa & yamasato (int j syst bacteriol 39, 462-466, 1989) concluded that, based on rules 23a and 51b of the bacteriological code (1975 revision), the oldest legi ...	2003	13130071
modulation of pps10 host range by plasmid-encoded repa initiator protein.	we report here the isolation and analysis of novel repa host range mutants of pps10, a plasmid originally found in pseudomonas savastanoi. upon hydroxylamine treatment, five plasmid mutants were selected for their establishment in escherichia coli at 37 degrees c, a temperature at which the wild-type form cannot be established. the mutations were located in different functional regions of the plasmid repa initiation protein, and the mutants differ in their stable maintenance, copy number, and ab ...	2003	12562807
non-fermenters in human infections.	one thousand and one hundred thirty non-fermenting gram negative bacteria were isolated from various samples. of these, pseudomonas aeruginosa was the commonest isolate (72.83%) followed by acinetobacter anitratus (8.4%), alcaligenes faecalis (7.6%), acinetobacter lwoffi (4.4%), pseudomonas flourescens (2.4%), schwanella putrefaciens (1.6%), stenotrophomonas maltophilia (1.6%), pseudomonas putida (0.4%), bravundimonas vesicularis (0.4%) and flavobacterium meningosepticum (0.4%). antibiotic sensi ...	2003	15022936
influence of growth phase on bacterial cell electrokinetic characteristics examined by soft particle electrophoresis theory.	the influence of incubation time on the electrokinetic properties of escherichia coli, pseudomonas putida, alcaligenes faecalis, and alcaligenes sp., was examined by electrophoretic mobility measurements and the results were discussed based on ohshima's soft particle theory. the electrophoretic mobility of e. coli plotted against incubation time revealed that the mobility gradually increased from the outset of incubation to 7 h, which corresponded to the exponential growth and early stationary p ...	2003	16256681
multiplex real-time pcr method to identify shiga toxin genes stx1 and stx2 and escherichia coli o157:h7/h- serotype.	a multiplex real-time pcr method to simultaneously detect the stx1 and stx2 genes of shiga toxin-producing escherichia coli and a unique conserved single-nucleotide polymorphism in the e. coli o157:h7/h- uida gene has been developed. there is more than 98.6% sensitivity and 100% specificity for all three gene targets based on a panel of 138 isolates. the pcr efficiencies were >/= 1.89, and as few as 6 cfu/reaction could be detected.	2003	14532101
extended-spectrum beta-lactamases in klebsiella pneumoniae bloodstream isolates from seven countries: dominance and widespread prevalence of shv- and ctx-m-type beta-lactamases.	a huge variety of extended-spectrum beta-lactamases (esbls) have been detected during the last 20 years. the majority of these have been of the tem or shv lineage. we have assessed esbls occurring among a collection of 455 bloodstream isolates of klebsiella pneumoniae, collected from 12 hospitals in seven countries. multiple beta-lactamases were produced by isolates with phenotypic evidence of esbl production (mean of 2.7 beta-lactamases per isolate; range, 1 to 5). shv-type esbls were the most ...	2003	14576117
molecular characterization and substrate preference of a polycyclic aromatic hydrocarbon dioxygenase from cycloclasticus sp. strain a5.	cycloclasticus sp. strain a5 is able to grow with petroleum polycyclic aromatic hydrocarbons (pahs), including unsubstituted and substituted naphthalenes, dibenzothiophenes, phenanthrenes, and fluorenes. a set of genes responsible for the degradation of petroleum pahs was isolated by using the ability of the organism to oxidize indole to indigo. this 10.5-kb dna fragment was sequenced and found to contain 10 open reading frames (orfs). seven orfs showed homology to previously characterized genes ...	2003	14602629
diversity and succession of the intestinal bacterial community of the maturing broiler chicken.	the diversity of bacterial floras in the ilea and ceca of chickens that were fed a vegetarian corn-soy broiler diet devoid of feed additives was examined by analysis of 1,230 partial 16s rrna gene sequences. nearly 70% of sequences from the ileum were related to those of lactobacillus, with the majority of the rest being related to clostridiaceae (11%), streptococcus (6.5%), and enterococcus (6.5%). in contrast, clostridiaceae-related sequences (65%) were the most abundant group detected in the ...	2003	14602645
development and application of a dapb-based in vivo expression technology system to study colonization of rice by the endophytic nitrogen-fixing bacterium pseudomonas stutzeri a15.	pseudomonas stutzeri a15 is a nitrogen-fixing bacterium isolated from paddy rice. strain a15 is able to colonize and infect rice roots. this strain may provide rice plants with fixed nitrogen and hence promote plant growth. in this article, we describe the use of dapb-based in vivo expression technology to identify p. stutzeri a15 genes that are specifically induced during colonization and infection (cii). we focused on the identification of p. stutzeri a15 genes that are switched on during rice ...	2003	14602651
fragments of pro-peptide activate mature penicillin amidase of alcaligenes faecalis.	penicillin amidase from alcaligenes faecalis is a recently identified n-terminal nucleophile hydrolase, which possesses the highest specificity constant (kcat/km) for the hydrolysis of benzylpenicillin compared with penicillin amidases from other sources. similar to the escherichia coli penicillin amidase, the a. faecalis penicillin amidase is maturated in vivo from an inactive precursor into the catalytically active enzyme, containing one tightly bound ca2+ ion, via a complex post-translational ...	2003	14622260
achromobacter insolitus sp. nov. and achromobacter spanius sp. nov., from human clinical samples.	a polyphasic taxonomic study (employing whole-cell protein and fatty acid analyses, 16s rdna sequencing, dna-dna hybridization, determination of dna g+c content, antibiotic susceptibility testing and extensive phenotypic characterization) was performed on 10 isolates that appeared to be related to alcaligenes faecalis. the isolates were recovered from diverse environments that included human clinical samples. 16s rdna sequence analysis indicated that these isolates belonged to the genus achromob ...	2003	14657110
kerstersia gyiorum gen. nov., sp. nov., a novel alcaligenes faecalis-like organism isolated from human clinical samples, and reclassification of alcaligenes denitrificans rüger and tan 1983 as achromobacter denitrificans comb. nov.	a polyphasic taxonomic study was performed on nine isolates recovered from various human clinical samples. phenotypically, these isolates resembled alcaligenes faecalis. whole-cell protein analysis distinguished two different species, and this was confirmed by dna-dna hybridizations. cellular fatty acid analysis and 16s rdna sequence analysis indicated that these isolates were related to the genera alcaligenes, bordetella, achromobacter and pigmentiphaga and belonged to the family alcaligenaceae ...	2003	14657111
pcr typing of genetic determinants for metallo-beta-lactamases and integrases carried by gram-negative bacteria isolated in japan, with focus on the class 3 integron.	from january 2001 to december 2002, 587 strains of gram-negative bacterial isolates demonstrating resistance to ceftazidime and a combination of sulbactam and cefoperazone were subjected to a disk diffusion screening test using sodium mercaptoacetic acid; 431 strains (73.4%) appeared to produce metallo-beta-lactamase (mbl). of these 431 strains, 357 were found by pcr to carry genes for imp-1 type mbl (bla(imp-1)), while only 7 and 67 strains carried the imp-2 gene (bla(imp-2)) and the vim-2 gene ...	2003	14662918
crystal structure of d-aminoacylase from alcaligenes faecalis da1. a novel subset of amidohydrolases and insights into the enzyme mechanism.	d-aminoacylase is an attractive candidate for commercial production of d-amino acids through its catalysis in the hydrolysis of n-acyl-d-amino acids. we report here the first d-aminoacylase crystal structure from a. faecalis at 1.5-a resolution. the protein comprises a small beta-barrel, and a catalytic (betaalpha)(8)-barrel with a 63-residue insertion. the enzyme structure shares significant similarity to the alpha/beta-barrel amidohydrolase superfamily, in which the beta-strands in both barrel ...	2003	12454005
genetic analysis and characterization of poly(aspartic acid) hydrolase-1 from sphingomonas sp. kt-1.	sphingomonas sp. kt-1 hydrolyzes poly(aspartic acid) (paa) containing alpha- and beta-amide units and has at least two different types of paa hydrolases. the paa hydrolase-1 hydrolyzes selectively beta-beta amide units in paa. molecular cloning of paa hydrolase-1 from sphingomonas sp. kt-1 has been carried out to characterize its gene products. genetic analysis shows that the deduced amino acid sequence of paa hydrolase-1 has a similarity with those of the catalytic domain of poly(3-hydroxybutyr ...	2003	12523851
directing the mode of nitrite binding to a copper-containing nitrite reductase from alcaligenes faecalis s-6: characterization of an active site isoleucine.	unlike the heme cd(1)-based nitrite reductase enzymes, the molecular mechanism of copper-containing nitrite reductases remains controversial. a key source of controversy is the productive binding mode of nitrite in the active site. to identify and characterize the molecular determinants associated with nitrite binding, we applied a combinatorial mutagenesis approach to generate a small library of six variants at position 257 in nitrite reductase from alcaligenes faecalis s-6. the activities of t ...	2003	12538888
molecular diversity and characterization of nitrite reductase gene fragments (nirk and nirs) from nitrate- and uranium-contaminated groundwater.	nitrate-contaminated groundwater samples were analysed for nirk and nirs gene diversity. the samples differed with respect to nitrate, uranium, heavy metals, organic carbon content, ph and dissolved oxygen levels. a total of 958 nirk and 1162 nirs clones were screened by restriction fragment length polymorphism (rflp) analysis: 48 and 143 distinct nirk and nirs clones, respectively, were obtained. a single dominant nirk restriction pattern was observed for all six samples and was 83% identical t ...	2003	12542709
arsenite oxidase aox genes from a metal-resistant beta-proteobacterium.	the beta-proteobacterial strain ulpas1, isolated from an arsenic-contaminated environment, is able to efficiently oxidize arsenite [as(iii)] to arsenate [as(v)]. mutagenesis with a lacz-based reporter transposon yielded two knockout derivatives deficient in arsenite oxidation. sequence analysis of the dna flanking the transposon insertions in the two mutants identified two adjacent open reading frames, named aoxa and aoxb, as well as a putative promoter upstream of the aoxa gene. reverse transcr ...	2003	12486049
the functional role of the binuclear metal center in d-aminoacylase: one-metal activation and second-metal attenuation.	our structural comparison of the tim barrel metal-dependent hydrolase(-like) superfamily suggests a classification of their divergent active sites into four types: alphabeta-binuclear, alpha-mononuclear, beta-mononuclear, and metal-independent subsets. the d-aminoacylase from alcaligenes faecalis da1 belongs to the beta-mononuclear subset due to the fact that the catalytically essential zn(2+) is tightly bound at the beta site with coordination by cys(96), his(220), and his(250), even though it ...	2004	14736882