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microbiological and clinical aspects of infection associated with stenotrophomonas maltophilia.the gram-negative bacterium stenotrophomonas maltophilia is increasingly recognized as an important cause of nosocomial infection. infection occurs principally, but not exclusively, in debilitated and immunosuppressed individuals. management of s. maltophilia-associated infection is problematic because many strains of the bacterium manifest resistance to multiple antibiotics. these difficulties are compounded by methodological problems in in vitro susceptibility testing for which there are, as y ...19989457429
characterization of chitinase c from a marine bacterium, alteromonas sp. strain o-7, and its corresponding gene and domain structure.one of the chitinase genes of alteromonas sp. strain o-7, the chitinase c-encoding gene (chic), was cloned, and the nucleotide sequence was determined. an open reading frame coded for a protein of 430 amino acids with a predicted molecular mass of 46,680 da. alignment of the deduced amino acid sequence demonstrated that chic contained three functional domains, the n-terminal domain, a fibronectin type iii-like domain, and a catalytic domain. the n-terminal domain (59 amino acids) was similar to ...19989464381
bacterial community dynamics during start-up of a trickle-bed bioreactor degrading aromatic compounds.this study was performed with a laboratory-scale fixed-bed bioreactor degrading a mixture of aromatic compounds (solvesso100). the starter culture for the bioreactor was prepared in a fermentor with a wastewater sample of a care painting facility as the inoculum and solvesso100 as the sole carbon source. the bacterial community dynamics in the fermentor and the bioreactor were examined by a conventional isolation procedure and in situ hybridization with fluorescently labeled rrna-targeted oligon ...19989501433
application of nitrite reductase from alcaligenes faecalis s-6 for nitrite measurement.the enzymatic reaction of nitrite reductase (nir) from alcaligenes faecalis s-6 was applied to the measurement of nitrite. nir was immobilized on the surface of a gold electrode using filter paper and a dialysis membrane, and used as a working electrode in a three-electrode system. amperometric methods were applied using nir and the electron mediator 1-methoxy pms (1-methoxy-5-methylphenazinium methylsulfate). the decrease in cathodic current showed a correlation to nitrite concentration over th ...19989519447
development of a direct in situ pcr method for detection of specific bacteria in natural environments.we applied hnpp (2-hydroxy-3-naphthoic acid-2'-phenylanilide phosphate) to direct in situ pcr for the routine detection of specific bacterial cells at the single-cell level. pcr was performed on glass slides with digoxigenin-labeled dutp. the digoxigenin-labeled pcr products were detected with alkaline phosphatase-labeled antidigoxigenin antibody and hnpp which was combined with fast red tr. a bright red fluorescent signal was produced from conversion to hnp (dephosphorylated form) by alkaline p ...19989546190
protective effects of a human 18-kilodalton cationic antimicrobial protein (cap18)-derived peptide against murine endotoxemia.cap18 (an 18-kda cationic antimicrobial protein) is a granulocyte-derived protein that can bind lipopolysaccharide (lps) and inhibit various activities of lps in vitro. the present study examined the protective effect of a synthetic 27-amino-acid peptide (cap18(109-135)) from the lps-binding domain of cap18 against antibiotic-induced endotoxin shock, using highly lps-sensitive d-(+)-galactosamine (d-galn)-sensitized c3h/hen mice. the antibiotic-induced endotoxin (caz-endotoxin) was prepared from ...19989573062
the adsorption of substrate-binding domain of phb depolymerases to the surface of poly(3-hydroxybutyric acid).the binding characteristic of phb depolymerase has been studied by using glutathione s-transferase (gst) fusion proteins with substrate-binding domain of three bacterial phb depolymerases, alcaligenes faecalis, comamonas acidovorans and comamonas testosteroni. analysis using immuno-gold labeling technique and transmission electron microscopy indicated that a novel gst fusion protein derived from a. faecalis enzyme adsorbed to the surface of poly(3-hydroxybutyric acid) (p(3hb)) single crystals li ...19989585889
in vitro antimicrobial activity of msi-78, a magainin analog.msi-78 is a cationic peptide with broad-spectrum antimicrobial activity and is being developed as a topical agent. we compared the in vitro activity of msi-78 with those of ofloxacin and other antibiotics against fresh clinical isolates. based on mic distribution statistics, strains for which the msi-78 mic was < or = 64 micro/ml were assumed to be susceptible for purposes of this report. of 411 aerobic isolates tested, 91% were susceptible to msi-78, compared to 91% for ofloxacin and 92% for ci ...19989593152
aerobic mineralization of 2,6-dichlorophenol by ralstonia sp. strain rk1.a new aerobic bacterium was isolated from the sediment of a freshwater pond close to a contaminated site at amponville (france). it was enriched in a fixed-bed reactor fed with 2,6-dichlorophenol (2,6-dcp)as the sole carbon and energy source at ph 7.5 and room temperature. the degradation of 2,6-dcp followed monod kinetics at low initial concentrations. at concentrations above 300 microm (50 mg.liter-1), 2,6-dcp increasingly inhibited its own degradation. the base sequence of the 16s ribosomal d ...19989647831
intergeneric transfer of conjugative and mobilizable plasmids harbored by escherichia coli in the gut of the soil microarthropod folsomia candida (collembola).the gut of the soil microarthropod folsomia candida provides a habitat for a high density of bacterial cells (t. thimm, a. hoffmann, h. borkott, j. c. munch, and c. c. tebbe, appl. environ. microbiol. 64:2660-2669, 1998). we investigated whether these gut bacteria act as recipients for plasmids from escherichia coli. filter mating with e. coli donor cells and collected feces of f. candida revealed that the broad-host-range conjugative plasmid prp4-luc (prp4 with a luciferase marker gene) transfe ...19989647844
the gut of the soil microarthropod folsomia candida (collembola) is a frequently changeable but selective habitat and a vector for microorganisms.interaction potentials between soil microarthropods and microorganisms were investigated with folsomia candida (insecta, collembola) in microcosm laboratory experiments. microscopic analysis revealed that the volumes of the simple, rod-shaped guts of adult specimens varied with their feeding activity, from 0.7 to 11.2 nl. a dense layer of bacterial cells, associated with the peritrophic membrane, was detected in the midgut by scanning electron microscopy. depending on the molting stage, which oc ...19989647845
iron starvation of bordetella avium stimulates expression of five outer membrane proteins and regulates a gene involved in acquiring iron from serum.iron starvation of bordetella avium induced expression of five outer membrane proteins with apparent molecular masses of 95, 92, 91.5, 84, and 51 kda. iron-responsive outer membrane proteins (ferps) of similar sizes were detected in six of six strains of b. avium, suggesting that the five ferps are common constituents of the outer membrane of most, if not all, strains of b. avium. iron-regulated genes of b. avium were targeted for mutagenesis with the transposon tnphoa. two mutants with iron-res ...19989673238
alcaligenes defragrans sp. nov., description of four strains isolated on alkenoic monoterpenes ((+)-menthene, alpha-pinene, 2-carene, and alpha-phellandrene) and nitrate.four pseudomonad strains 51men, 54pin, 62car and 65phen were recently isolated on the monoterpenes (+)-menthene, alpha-pinene, 2-carene and alpha-phellandrene as sole carbon source and nitrate as electron acceptor. these bacteria were characterised. the motile, mesophilic, gram-negative rods had a strictly respiratory metabolism. monoterpenes as carbon sources were completely mineralised to carbon dioxide. the physiology of all strains was very similar, but displayed an individual utilisation pr ...19989704110
new nitrogen-fixing microorganisms detected in oligotrophic oceans by amplification of nitrogenase (nifh) genes.oligotrophic oceanic waters of the central ocean gyres typically have extremely low dissolved fixed inorganic nitrogen concentrations, but few nitrogen-fixing microorganisms from the oceanic environment have been cultivated. nitrogenase gene (nifh) sequences amplified directly from oceanic waters showed that the open ocean contains more diverse diazotrophic microbial populations and more diverse habitats for nitrogen fixers than previously observed by classical microbiological techniques. nitrog ...19989726895
discrimination of psychrotrophic and mesophilic strains of the bacillus cereus group by pcr targeting of major cold shock protein genes.detection of psychrotrophic strains (those able to grow at or below 7 degreesc) of the bacillus cereus group (bacillus cereus, bacillus thuringiensis, and bacillus mycoides) in food products is at present extremely slow with conventional microbiology. this is due to an inability to discriminate these cold-adapted strains from their mesophilic counterparts (those able to grow only above 7 degreesc) by means other than growth at low temperature, which takes 5 to 10 days for detection. here we repo ...19989726910
[evaluation of antibacterial activities of various antibiotics against glucose non-fermentative gram-negative rods other than pseudomonas aeruginosa].mics of piperacillin, sulbactam/cefoperazone, minocycline (mino), gentamicin, amikacin, flomoxef, ceftazidime, cefozopran, cefsulodin and imipenem were determined, against 189 clinical isolated strains of glucose non-fermentative gram-negative rods (nfgnr; acinetobacter baumannii (44), alcaligenes faecalis (5), alcaligenes xylosoxidans (25), burkholderia cepacia (12), chryseobacterium indologenes (23), chryseobacterium meningosepticum (9), pseudomonas fluorescens (8), pseudomonas putida (12), st ...19989755431
development of pcr primer systems for amplification of nitrite reductase genes (nirk and nirs) to detect denitrifying bacteria in environmental samples.a system was developed for the detection of denitrifying bacteria by the amplification of specific nitrite reductase gene fragments with pcr. primer sequences were found for the amplification of fragments from both nitrite reductase genes (nirk and nirs) after comparative sequence analysis. whenever amplification was tried with these primers, the known nir type of denitrifying laboratory cultures could be confirmed. likewise, the method allowed a determination of the nir type of five laboratory ...19989758798
bordetella avium virulence measured in vivo and in vitro.bordetella avium causes an upper-respiratory-tract disease called bordetellosis in birds. bordetellosis shares many of the clinical and histopathological features of disease caused in mammals by bordetella pertussis and bordetella bronchiseptica. in this study we determined several parameters of infection in the domestic turkey, meleagris galapavo, and compared these in vivo findings with an in vitro measure of adherence using turkey tracheal rings. in the in vivo experiments, we determined the ...19989784529
evolution of a pathway for chlorobenzene metabolism leads to natural attenuation in contaminated groundwatercomplete metabolism of chlorinated benzenes is not a feature that is generally found in aerobic bacteria but is thought to be due to a novel recombination of two separate gene clusters. such a recombination could be responsible for adaptation of a natural microbial community in response to contamination with synthetic chemicals. this hypothesis was tested in a chlorobenzene (cb)-contaminated aquifer. cb-degrading bacteria from a contaminated site were characterized for a number of years by exami ...19989797264
comparison of phenotypic and genotypic techniques for identification of unusual aerobic pathogenic gram-negative bacilli.rapid and accurate identification of bacterial pathogens is a fundamental goal of clinical microbiology, but one that is difficult or impossible for many slow-growing and fastidious organisms. we used identification systems based on cellular fatty acid profiles (sherlock; midi, inc., newark, del.), carbon source utilization (microlog; biolog, inc., hayward, calif.), and 16s rrna gene sequence (microseq; perkin-elmer applied biosystems division, foster city, calif.) to evaluate 72 unusual aerobic ...19989817894
phenol-degrading denitrifying bacteria in wastewater sediments.an attempt was made to isolate denitrifying bacteria capable of degrading phenol from anoxic wastewater sediments and compost (vegetable soil). the greatest phenol-degrading activity was shown by autochthonous microflora from petroleum wastewater sediments (pws) and by denitrifying microflora from nitrogenous wastewater reservoir sediment (nwrs). eight strains of denitrifying bacteria able to degrade phenolic compounds were isolated, six of which were from the petroleum wastewater sediments. the ...19989839379
adherence to testing criteria can minimize false-positive results for escherichia coli o157. 19989841245
molecular genetics of the genus paracoccus: metabolically versatile bacteria with bioenergetic flexibility.paracoccus denitrificans and its near relative paracoccus versutus (formerly known as thiobacilllus versutus) have been attracting increasing attention because the aerobic respiratory system of p. denitrificans has long been regarded as a model for that of the mitochondrion, with which there are many components (e.g., cytochrome aa3 oxidase) in common. members of the genus exhibit a great range of metabolic flexibility, particularly with respect to processes involving respiration. prominent exam ...19989841665
allergic alveolitis among agricultural workers in eastern poland: a study of twenty cases.the aim of this study was to identify the specific agents which caused extrinsic allergic alveolitis (eaa) in the selected group of 20 agricultural workers from eastern poland. the microbiological analysis of the samples of plant materials or dusts reported by the patients as causing symptoms has been carried out, followed by allergological tests (inhalation challenge, agar-gel precipitation test, inhibition of leukocyte migration, skin test) with extrinsic microbial antigens. it was found that ...19989852490
characterization of a facultatively psychrophilic bacterium, vibrio rumoiensis sp. nov., that exhibits high catalase activitya novel facultatively psychrophilic bacterium, strain s-1, which exhibits extraordinarily high catalase activity was isolated from the drain pool of a fish product processing plant that uses h2o2 as a bleaching and microbicidal agent. the catalase activity of the isolate was 1 or 2 orders of magnitude higher than those of corynebacterium glutamicum, staphylococcus aureus, pseudomonas fluorescens, and five other species tested in this study. the strain seemed to possess only one kind of catalase, ...19999872761
cloning and characterization of the polyhydroxybutyrate depolymerase gene of pseudomonas stutzeri and analysis of the function of substrate-binding domains.the extracellular polyhydroxybutyrate (phb) depolymerase gene (phazpst) of pseudomonas stutzeri was cloned and sequenced. phazpst was composed of 1,728 bp encoding a protein of 576 amino acids. analyses of the n-terminal amino acid sequence and the matrix-assisted laser desorption/ionization-time-of-flight (maldi-tof) mass spectrum of the purified enzyme showed that the mature enzyme consisted of 538 amino acids with a deduced molecular mass of 57,506 da. analysis of the deduced amino acid seque ...19999872779
purification and characterization of a novel 5-oxoprolinase (without atp-hydrolyzing activity) from alcaligenes faecalis n-38a.a novel type of 5-oxoprolinase was found in a cell extract of strain n-38a, which was later identified as alcaligenes faecalis. the enzyme in the cell extract was purified to a homogeneous state with a yield of 16.6%. the molecular weight of the purified enzyme was estimated to be 47,000 by both sodium dodecyl sulfate-polyacrylamide gel electrophoresis and gel filtration, suggesting that the enzyme is a monomeric protein. the enzyme specifically catalyzed a decyclization of l-pyroglutamate witho ...19999925605
nested duplex pcr to detect bordetella pertussis and bordetella parapertussis and its application in diagnosis of pertussis in nonmetropolitan southeast queensland, australia.a duplex pcr to detect bordetella pertussis and bordetella parapertussis was developed with the insertion sequences is481 (b. pertussis) and is1001 (b. parapertussis) and evaluated with specimens from 520 consecutive patients presenting with possible pertussis. no culture-positive-pcr-negative results occurred, giving the method a sensitivity of 100%. for b. pertussis, 58 of 520 patients (11.2%) were positive by pcr compared to 17 of 520 patients positive (3.3%) by culture. for b. parapertussis, ...19999986820
hydroxylamine oxidation and subsequent nitrous oxide production by the heterotrophic ammonia oxidizer alcaligenes faecalis.nitrous oxide (n2o), a greenhouse gas, is emitted during autotrophic and heterotrophic ammonia oxidation. this emission may result from either coupling to aerobic denitrification, or it may be formed in the oxidation of hydroxylamine (nh2oh) to nitrite (no2(-). therefore, the n2o production during nh2oh oxidation was studied with alcaligenes faecalis strain tud. continuous cultures of a. faecalis showed increased n2o production when supplemented with increasing nh2oh concentrations. 15n-labeling ...199910091333
in vitro antibacterial properties of pexiganan, an analog of magainin.pexiganan, a 22-amino-acid antimicrobial peptide, is an analog of the magainin peptides isolated from the skin of the african clawed frog. pexiganan exhibited in vitro broad-spectrum antibacterial activity when it was tested against 3,109 clinical isolates of gram-positive and gram-negative, anaerobic and aerobic bacteria. the pexiganan mic at which 90% of isolates are inhibited (mic90) was 32 micrograms/ml or less for staphylococcus spp., streptococcus spp., enterococcus faecium, corynebacteriu ...199910103181
pcr detection of genes encoding nitrite reductase in denitrifying bacteria.using consensus regions in gene sequences encoding the two forms of nitrite reductase (nir), a key enzyme in the denitrification pathway, we designed two sets of pcr primers to amplify cd1- and cu-nir. the primers were evaluated by screening defined denitrifying strains, denitrifying isolates from wastewater treatment plants, and extracts from activated sludge. sequence relationships of nir genes were also established. the cd1 primers were designed to amplify a 778 to 799-bp region of cd1-nir in ...199910103263
the blue copper-containing nitrite reductase from alcaligenes xylosoxidans: cloning of the nira gene and characterization of the recombinant enzyme.the nira gene encoding the blue dissimilatory nitrite reductase from alcaligenes xylosoxidans has been cloned and sequenced. to our knowledge, this is the first report of the characterization of a gene encoding a blue copper-containing nitrite reductase. the deduced amino acid sequence exhibits a high degree of similarity to other copper-containing nitrite reductases from various bacterial sources. the full-length protein included a 24-amino-acid leader peptide. the nira gene was overexpressed i ...199910197991
in vitro and in vivo antimicrobial activities of t-3811me, a novel des-f(6)-quinolone.the in vitro and in vivo activities of t-3811me, a novel des-f(6)-quinolone, were evaluated in comparison with those of some fluoroquinolones, including a newly developed one, trovafloxacin. t-3811, a free base of t-3811me, showed a wide range of antimicrobial spectra, including activities against chlamydia trachomatis, mycoplasma pneumoniae, and mycobacterium tuberculosis. in particular, t-3811 exhibited potent activity against various gram-positive cocci, with mics at which 90% of the isolates ...199910223917
classification of alcaligenes faecalis-like isolates from the environment and human clinical samples as ralstonia gilardii sp. nov.a polyphasic taxonomic study that included dna-dna hybridizations, dna base ratio determinations, 16s rdna sequence analysis, whole-cell protein and fatty acid analyses, aflp (amplified fragment length polymorphism) fingerprinting and an extensive biochemical characterization was performed on 10 strains provisionally identified as alcaligenes faecalis-like bacteria. the six environmental and four human isolates belonged to the genus ralstonia and were assigned to a new species for which the name ...199910319461
phylogenetic analysis of ara+ and ara- burkholderia pseudomallei isolates and development of a multiplex pcr procedure for rapid discrimination between the two biotypes.a burkholderia pseudomallei-like organism has recently been identified among some soil isolates of b. pseudomallei in an area with endemic melioidosis. this organism is almost identical to b. pseudomallei in terms of morphological and biochemical profiles, except that it differs in ability to assimilate l-arabinose. these ara+ isolates are also less virulent than the ara- isolates in animal models. in addition, clinical isolates of b. pseudomallei available to date are almost exclusively ara-. t ...199910325345
antigenic and molecular conservation of the gonococcal nspa protein.a low-molecular-weight protein named nspa (neisserial surface protein a) was recently identified in the outer membrane of all neisseria meningitidis strains tested. antibodies directed against this protein were shown to protect mice against an experimental meningococcal infection. hybridization experiments clearly demonstrated that the nspa gene was also present in the genomes of the 15 neisseria gonorrhoeae strains tested. cloning and sequencing of the nspa gene of n. gonorrhoeae b2 revealed an ...199910338491
genetic characterization of wild-type and mutant fur genes of bordetella avium.for most, if not all, organisms, iron (fe) is an essential element. in response to the nutritional requirement for fe, bacteria evolved complex systems to acquire the element from the environment. the genes encoding these systems are often coordinately regulated in response to the fe concentration. recent investigations revealed that bordetella avium, a respiratory pathogen of birds, expressed a number of fe-regulated genes (t. d. connell, a. dickenson, a. j. martone, k. t. militello, m. j. fili ...199910338537
purification and characterization of an alpha-glucosidase from rhizobium sp. (robinia pseudoacacia l.) strain usda 4280.a novel alpha-glucosidase with an apparent subunit mass of 59 +/- 0. 5 kda was purified from protein extracts of rhizobium sp. strain usda 4280, a nodulating strain of black locust (robinia pseudoacacia l), and characterized. after purification to homogeneity (475-fold; yield, 18%) by ammonium sulfate precipitation, cation-exchange chromatography, hydrophobic chromatography, dye chromatography, and gel filtration, this enzyme had a pi of 4.75 +/- 0.05. the enzyme activity was optimal at ph 6.0 t ...199910388682
the rice inoculant strain alcaligenes faecalis a15 is a nitrogen-fixing pseudomonas stutzeri.the taxonomic position of the nitrogen-fixing rice isolate a15, previously classified as alcaligenes faecalis, was reinvestigated. on the basis of its small subunit ribosomal rna (16s rrna) sequence this strain identifies as pseudomonas stutzeri. phenotyping and fatty acid profiling confirm this result. dna:dna hybridisations, using the optical renaturation rate method, between strain a15 and pseudomonas stutzeri lmg 11199t revealed a mean dna-binding of 77%. the identification was further corro ...199910390872
factors influencing capacitance-based monitoring of microbial growth.microbiological impedance devices are routinely used by food and manufacturing industries, and public health agencies to measure microbiological growth. factors contributing to increases and decreases in capacitance at the culture medium-electrode interface are poorly understood. to objectively evaluate the effects of temperature, cell density and medium conductivity on capacitance, admittance values from an impedance device were standardized; capacitance was converted to susceptance to allow un ...199910395464
heterologous expression of correctly assembled methylamine dehydrogenase in rhodobacter sphaeroides.the biosynthesis of methylamine dehydrogenase (madh) from paracoccus denitrificans requires four genes in addition to those that encode the two structural protein subunits, maub and maua. the accessory gene products appear to be required for proper export of the protein to the periplasm, synthesis of the tryptophan tryptophylquinone (ttq) prosthetic group, and formation of several structural disulfide bonds. to accomplish the heterologous expression of correctly assembled madh, eight genes from ...199910400578
substrate and binding specificities of bacterial polyhydroxybutyrate depolymerases.the substrate specificities of three extracellular polyhydroxybutyrate (phb) depolymerases from alcaligenes faecalis (phaz afa), pseudomonas stutzeri (phaz pst), and comamonas acidovorans (phaz cac), which are grouped into types a and b based on the position of a lipase box sequence in the catalytic domain, were examined for films of 12 different aliphatic polyesters. each of these phb depolymerases used was capable of hydrolyzing poly(3-hydroxybutyrate) (p(3hb)), poly(3-hydroxypropionate) (p(3h ...199910408639
properties and biodegradability of ultra-high-molecular-weight poly[(r)-hydroxybutyrate] produced by a recombinant escherichia coli.ultra-high-molecular-weight poly[(r)-3-hydroxybutyrate] (p(3hb)) (mw = 3-11 x 10(6)) was produced from glucose by a recombinant escherichia coli xl1-blue (psyl105) harboring ralstonia eutropha h16 polyhydroxyalkanoate (pha) biosynthesis genes. morphology of ultra-high-molecular-weight p(3hb) granules in the recombinant cells was studied by transmission electron microscopy. the recombinant e. coli contained several p(3hb) granules within a cell. freeze-fracture morphology of ultra-high-molecular- ...199910416654
structure and enzymatic degradation of poly(3-hydroxybutyrate) copolymer single crystals with an extracellular phb depolymerase from alcaligenes faecalis t1.lamellar single crystals of four random copolymers of (r)-3-hydroxybutyrate with different hydroxyalkanoates: poly(3-hydroxybutyrate-co-8 mol%-3-hydroxyvalerate) (p(3hb-co-8%-3hv)), poly(3-hydroxybutyrate-co-10 mol%-4-hydroxybutyrate) (p(3hb-co-10%-4hb)), poly(3-hydroxybutyrate-co-8 mol%-3-hydroxyhexanoate) (p(3hb-co-8%-3hh)) and poly(3-hydroxybutyrate-co-10 mol%-6-hydroxyhexanoate) (p(3hb-co-10%-6hh)), were grown from dilute solutions of chloroform and ethanol. all single crystals have lath-sha ...199910416664
structural effects on enzymatic degradabilities for poly[(r)-3-hydroxybutyric acid] and its copolymers.poly[(r)-3-hydroxybutyric acid] and its copolymers were prepared by biosynthetic and chemosynthetic methods. the films of polyesters were prepared by both the solution-cast and melt-crystallized techniques. the enzymatic degradation of polyester films was carried out at 37 degrees c in an aqueous solution (ph 7.4) of phb depolymerase from alcaligenes faecalis. the rate of enzymatic erosion on the solution-cast films increased markedly with an increase in the fraction of second monomer units up t ...199910416666
community analysis of biofilters using fluorescence in situ hybridization including a new probe for the xanthomonas branch of the class proteobacteria.domain-, class-, and subclass-specific rrna-targeted probes were applied to investigate the microbial communities of three industrial and three laboratory-scale biofilters. the set of probes also included a new probe (named xan818) specific for the xanthomonas branch of the class proteobacteria; this probe is described in this study. the members of the xanthomonas branch do not hybridize with previously developed rrna-targeted oligonucleotide probes for the alpha-, beta-, and gamma-proteobacteri ...199910427047
comparison of pcr, culture, and direct fluorescent-antibody testing for detection of bordetella pertussis.we prospectively compared the performance of culture, direct fluorescent-antibody testing (dfa), and an in-house-developed pcr test targeting the repeated insertion sequence is481 for the detection of bordetella pertussis in nasopharyngeal swab specimens. we tested 319 consecutive paired specimens on which all three tests were performed. a total of 59 specimens were positive by one or more tests. of these, 5 were positive by all three tests, 2 were positive by culture and pcr, 16 were positive b ...199910449467
processing and functional display of the 86 kda heterodimeric penicillin g acylase on the surface of phage fd.the large heterodimeric penicillin g acylase from alcaligenes faecalis was displayed on the surface of phage fd. we fused the coding sequence (alpha subunit-internal peptide-beta subunit) to the gene of a phage coat protein. a modified g3p signal sequence was used to direct the polypeptide to the periplasm. here we show that a heterodimeric enzyme can be expressed as a fusion protein that matures to an active biocatalyst connected to the coat protein of phage fd, resulting in a phage to which th ...199910455029
marine bacterial isolates display diverse responses to uv-b radiation.the molecular and biological consequences of uv-b radiation were investigated by studying five species of marine bacteria and one enteric bacterium. laboratory cultures were exposed to an artificial uv-b source and subjected to various post-uv irradiation treatments. significant differences in survival subsequent to uv-b radiation were observed among the isolates, as measured by culturable counts. uv-b-induced dna photodamage was investigated by using a highly specific radioimmunoassay to measur ...199910473381
bacterial growth state distinguished by single-cell protein profiling: does chlorination kill coliforms in municipal effluent?municipal effluent is the largest reservoir of human enteric bacteria. its public health significance, however, depends upon the physiological status of the wastewater bacterial community. a novel immunofluorescence assay was developed and used to examine the bacterial growth state during wastewater disinfection. quantitative levels of three highly conserved cytosolic proteins (dnak, dps, and fis) were determined by using enterobacterium-specific antibody fluorochrome-coupled probes. enterobacte ...199910473432
capillary electrophoresis-single-strand conformation polymorphism analysis for rapid identification of pseudomonas aeruginosa and other gram-negative nonfermenting bacilli recovered from patients with cystic fibrosis.we used capillary electrophoresis-single-strand conformation polymorphism (ce-sscp) analysis of pcr-amplified 16s rrna gene fragments for rapid identification of pseudomonas aeruginosa and other gram-negative nonfermenting bacilli isolated from patients with cystic fibrosis (cf). target sequences were amplified by using forward and reverse primers labeled with various fluorescent dyes. the labeled pcr products were denatured by heating and separated by capillary gel electrophoresis with an autom ...199910488211
localization of periplasmic redox proteins of alcaligenes faecalis by a modified general method for fractionating gram-negative bacteria.a lysozyme-osmotic shock method is described for fractionation of alcaligenes faecalis which uses glucose to adjust osmotic strength and multiple osmotic shocks. during phenylethylamine-dependent growth, aromatic amine dehydrogenase, azurin, and a single cytochrome c were localized in the periplasm. their induction patterns are different from those for the related quinoprotein methylamine dehydrogenase and its associated redox proteins.199910515948
the use of chromogenic reference substrates for the kinetic analysis of penicillin acylases.determination of kinetic parameters of penicillin acylases for phenylacetylated compounds is complicated due to the low k(m) values for these substrates, the lack of a spectroscopic signal, and the strong product inhibition by phenylacetic acid. to overcome these difficulties, a spectrophotometric method was developed, with which kinetic parameters could be determined by measuring the effects on the hydrolysis of the chromogenic reference substrate 2-nitro-5-[(phenylacetyl)amino]benzoic acid (ni ...199910542108
application of a dna hybridization-hydrophobic-grid membrane filter method for detection and isolation of verotoxigenic escherichia coli.verotoxigenic escherichia coli (vtec) strains were isolated from food and animal fecal samples by using pcr to screen for the presence of vtec after broth enrichment and then filtering vtec-positive cultures through hydrophobic-grid membrane filters (hgmfs) which were incubated on macconkey agar. the filters were probed with a digoxigenin-labeled pcr product generated by amplification of a conserved verotoxin gene sequence. replication of the growth on filters allowed probe-positive colonies to ...199910543785
metabolism of acrylate to beta-hydroxypropionate and its role in dimethylsulfoniopropionate lyase induction by a salt marsh sediment bacterium, alcaligenes faecalis m3a.dimethylsulfoniopropionate (dmsp) is degraded to dimethylsulfide (dms) and acrylate by the enzyme dmsp lyase. dms or acrylate can serve as a carbon source for both free-living and endophytic bacteria in the marine environment. in this study, we report on the mechanism of dmsp-acrylate metabolism by alcaligenes faecalis m3a. suspensions of citrate-grown cells expressed a low level of dmsp lyase activity that could be induced to much higher levels in the presence of dmsp, acrylate, and its metabol ...199910543825
isolation of terrabacter sp. strain dde-1, which metabolizes 1, 1-dichloro-2,2-bis(4-chlorophenyl)ethylene when induced with biphenyl.terrabacter sp. strain dde-1, able to metabolize 1,1-dichloro-2, 2-bis(4-chlorophenyl)ethylene (dde) in pure culture when induced with biphenyl, was enriched from a 1-1-1-trichloro-2, 2-bis(4-chlorophenyl)ethane residue-contaminated agricultural soil. gas chromatography-mass spectrometry analysis of culture extracts revealed a number of dde catabolites, including 2-(4'-chlorophenyl)-3,3-dichloropropenoic acid, 2-(4'-chlorophenyl)-2-hydroxy acetic acid, 2-(4'-chlorophenyl) acetic acid, and 4-chlo ...199910584027
[isolation of bacteria which could perform nitrification and denitrification simultaneously by gene probe].the bacteria which could perform nitrification and denitrification simultaneously from nitrogen containing wastes in taiwan were isolated by using the probes made from random dna fragments of thiosphaera pantotropha. two isolates were identified and named alcaligenes faecalis subsp. faecalis strain 1 and strain 2 respectively. the effects on nitrification and denitrification by different medium ph, oxygen content, addition of different electron donors or inhibitors were studied. the isolates not ...199710592830
characterization of a novel, antifungal, chitin-binding protein from streptomyces tendae tü901 that interferes with growth polarity.the afp1 gene, which encodes the antifungal protein afp1, was cloned from nikkomycin-producing streptomyces tendae tü901, using a nikkomycin-negative mutant as a host and screening transformants for antifungal activity against paecilomyces variotii in agar diffusion assays. the 384-bp afp1 gene has a low g+c content (63%) and a transcription termination structure with a poly(t) region, unusual attributes for streptomyces genes. afp1 was purified from culture filtrate of s. tendae carrying the af ...199910601197
a new chemolithoautotrophic arsenite-oxidizing bacterium isolated from a gold mine: phylogenetic, physiological, and preliminary biochemical studies.a previously unknown chemolithoautotrophic arsenite-oxidizing bacterium has been isolated from a gold mine in the northern territory of australia. the organism, designated nt-26, was found to be a gram-negative motile rod with two subterminal flagella. in a minimal medium containing only arsenite as the electron donor (5 mm), oxygen as the electron acceptor, and carbon dioxide-bicarbonate as the carbon source, the doubling time for chemolithoautotrophic growth was 7.6 h. arsenite oxidation was f ...200010618208
application of 16s rrna gene sequencing to identify bordetella hinzii as the causative agent of fatal septicemia.we report on the first case of fatal septicemia caused by bordetella hinzii. the causative organism exhibited a biochemical profile identical to that of bordetella avium with three commercial identification systems (api 20e, api 20 ne, and vitek gni+ card). however, its cellular fatty acid profile was not typical for either b. avium or previously reported strains of b. hinzii. presumptive identification of the patient's isolate was accomplished by traditional biochemical testing, and definitive ...200010655386
identification and population structure of burkholderia stabilis sp. nov. (formerly burkholderia cepacia genomovar iv).the burkholderia cepacia complex currently comprises five genomic species, i.e., b. cepacia genomovar i, b. multivorans (formerly known as b. cepacia genomovar ii), b. cepacia genomovar iii, b. cepacia genomovar iv, and b. vietnamiensis (also known as b. cepacia genomovar v). in the absence of straightforward diagnostic tests for the identification of b. cepacia genomovars i, iii, and iv, the last two genomic species were not formally classified as novel burkholderia species (genomovar i contain ...200010698993
evaluation of autoscan-w/a and the vitek gni+ automicrobic system for identification of non-glucose-fermenting gram-negative bacilli.the autoscan-w/a (w/a; dade behring microscan inc., west sacramento, calif.) and vitek automicrobic system (vitek ams; biomérieux vitek systems, inc., hazelwood, mo.) are both fully automated microbiology systems. we evaluated the accuracy of these two systems in identifying nonglucose-fermenting gram-negative bacilli. we used the w/a with conventional-panel neg combo type 12 and vitek gni+ identification systems. a total of 301 isolates from 25 different species were tested. of these, 299 isola ...200010699007
a novel phenanthrene dioxygenase from nocardioides sp. strain kp7: expression in escherichia coli.nocardioides sp. strain kp7 grows on phenanthrene but not on naphthalene. this organism degrades phenanthrene via 1-hydroxy-2-naphthoate, o-phthalate, and protocatechuate. the genes responsible for the degradation of phenanthrene to o-phthalate (phd) were found by southern hybridization to reside on the chromosome. a 10.6-kb dna fragment containing eight phd genes was cloned and sequenced. the phda, phdb, phdc, and phdd genes, which encode the alpha and beta subunits of the oxygenase component, ...200010735855
poly(3-hydroxyvalerate) depolymerase of pseudomonas lemoignei.pseudomonas lemoignei is equipped with at least five polyhydroxyalkanoate (pha) depolymerase structural genes (phaz1 to phaz5) which enable the bacterium to utilize extracellular poly(3-hydroxybutyrate) (phb), poly(3-hydroxyvalerate) (phv), and related polyesters consisting of short-chain-length hxdroxyalkanoates (pha(scl)) as the sole sources of carbon and energy. four genes (phaz1, phaz2, phaz3, and phaz5) encode phb depolymerases c, b, d, and a, respectively. it was speculated that the remain ...200010742216
[immobilization of cells by entrapping in aubasidan].a new technique of immobilization of microbial cells by entrapping in aubasidan, a microbial polysaccharide, was developed. this technique was applied to three cultures: erwinia aroidea, pseudomonas sp., and alcaligenes faecalis, the producers of aspartase and l-aspartate beta-decarboxylase. the new method is effective. after immobilization, microbial cells retained 79-91% of their initial enzymatic activity.200010752090
septic arthritis caused by a gram-negative bacterium representing a new species related to the bordetella-alcaligenes complex.a knee-joint exudate culture yielded on two occasions a gram-negative bacterium. regular methods for speciation did not provide an identification. the infection was successfully treated with ciprofloxacin. the unknown isolate, ccug 36768, was subjected to further investigation, including 16s rdna sequencing, protein profiling, cellular fatty acid analysis, and various biochemical tests, in order to produce a species identification. the 1469 bp-long 16s rdna sequence did not reveal identity with ...200010752687
molecular and phenotypic characterization of pseudomonas spp. isolated from milk.putative pseudomonas spp. isolated predominantly from raw and processed milk were characterized by automated ribotyping and by biochemical reactions. isolates were biochemically profiled using the biolog system and api 20 ne and by determining the production of proteases, lipases, and lecithinases for each isolate. isolates grouped into five coherent clusters, predominated by the species p. putida (cluster a), p. fluorescens (cluster b), p. fragi (as identified by biolog) or p. fluorescens (as i ...200010788386
nitrite reductase genes (nirk and nirs) as functional markers to investigate diversity of denitrifying bacteria in pacific northwest marine sediment communities.genetic heterogeneity of denitrifying bacteria in sediment samples from puget sound and two sites on the washington continental margin was studied by pcr approaches amplifying nirk and nirs genes. these structurally different but functionally equivalent single-copy genes coding for nitrite reductases, a key enzyme of the denitrification process, were used as a molecular marker for denitrifying bacteria. nirs sequences could be amplified from samples of both sampling sites, whereas nirk sequences ...200010788387
molecular analysis of maleate cis-trans isomerase from thermophilic bacteria.several strains of thermophilic bacteria containing maleate cis-trans isomerase were isolated from soil samples and identified as bacillus stearothermophilus, bacillus circulans, bacillus brevis, and deleya halophila. the maleate cis-trans isomerase was purified and characterized from one of the isolated strains, b. stearothermophilus mi-102. the purified enzyme of strain mi-102 showed higher thermal stability than the enzyme of a mesophile, alcaligenes faecalis ifo13111. the seven maleate cis-t ...200010803955
catalytic roles for two water bridged residues (asp-98 and his-255) in the active site of copper-containing nitrite reductase.two active site residues, asp-98 and his-255, of copper-containing nitrite reductase (nir) from alcaligenes faecalis have been mutated to probe the catalytic mechanism. three mutations at these two sites (d98n, h255d, and h255n) result in large reductions in activity relative to native nir, suggesting that both residues are involved intimately in the reaction mechanism. crystal structures of these mutants have been determined using data collected to better than 1. 9-a resolution. in the native s ...200010811642
gene organization for nitric oxide reduction in alcaligenes faecalis s-6.norb and norc encoding the cytochrome b-containing subunit and the cytochrome c-containing subunit, respectively, of the nitric oxide reductase (nor) in alcaligenes faecalis s-6 were cloned and sequenced. both norb and norc showed more than 40% sequence identity to the corresponding subunits of cytochrome bc-type nors in other denitrifying bacteria. norcb was in a gene cluster containing seven other genes; these were named dnr, orf2, orf3, nore, norf, norq, and nord on the basis of their similar ...200010830505
distribution of aldoxime dehydratase in microorganisms.the distribution of phenylacetaldoxime-degrading and pyridine-3-aldoxime-degrading ability was examined with intact cells of 975 microorganisms, including 45 genera of bacteria, 11 genera of actinomyces, 22 genera of yeasts, and 37 genera of fungi, by monitoring the decrease of the aldoximes by high-pressure liquid chromatography. the abilities were found to be widely distributed in bacteria, actinomyces, fungi, and some yeasts: 98 and 107 strains degraded phenylacetaldoxime and pyridine-3-aldox ...200010831401
autodisplay: functional display of active beta-lactamase on the surface of escherichia coli by the aida-i autotransporter.members of the protein family of immunoglobulin a1 protease-like autotransporters comprise multidomain precursors consisting of a c-terminal autotransporter domain that promotes the translocation of n-terminally attached passenger domains across the cell envelopes of gram-negative bacteria. several autotransporter domains have recently been shown to efficiently promote the export of heterologous passenger domains, opening up an effective tool for surface display of heterologous proteins. here we ...200010850987
per-1 extended-spectrum beta-lactamase production in an alcaligenes faecalis clinical isolate resistant to expanded-spectrum cephalosporins and monobactams from a hospital in northern italy.an alicaligenes faecalis (fl-424/98) resistant to expanded-spectrum cephalosporins and aztreonam was isolated from the urine of an inpatient at the intensive care unit of the varese hospital (northern italy) after antimicrobial chemotherapy with cefazolin, vancomycin, and amikacin. clavulanic acid restored the activity of expanded-spectrum cephalosporins, suggesting the production of an extended-spectrum beta-lactamase (esbetal). a crude extract of fl-424/98 showed the presence of two beta-lacta ...200010868812
a promoter region binding protein and dna gyrase regulate anaerobic transcription of nifla in enterobacter cloacae.our work provides evidence that a sequence characteristic of fnr binding sites, when interacted with by a trans-acting factor, activates anaerobic transcription of the nifla operon in enterobacter cloacae. dna gyrase activity has been found to be important for the anaerobic transcription of the nifla promoter. our results suggest that anaerobic regulation of the nifla operon is mediated through the control of the promoter region-binding trans-acting factor at the transcriptional level, while dna ...200010869067
biotransformation of lantadene a (22 beta-angeloyloxy-3-oxoolean-12-en-28-oic acid), the pentacyclic triterpenoid, by alcaligenes faecalis.a bacterial strain capable of biotransformation of lantadene a (22 beta-angeloyloxy-3-oxo-olean-12-en-28-oic acid), the pentacyclic hepatotoxin of lantana (lantana camara var. aculeata) has been isolated from soil using lantadene a as the sole carbon source. the organism is gram negative, rod shaped, motile, catalase positive and has been identified as alcaligenes faecalis. the isolate has been found to be specific for lantadene a and did not utilize lantadene b. in studies using sucrose as an a ...199910870553
bioaugmentation of activated sludge by an indigenous 3-chloroaniline-degrading comamonas testosteroni strain, i2gfp.a strain identified as comamonas testosteroni i2 was isolated from activated sludge and found to be able to mineralize 3-chloroaniline (3-ca). during the mineralization, a yellow intermediate accumulated temporarily, due to the distal meta-cleavage of chlorocatechol. this strain was tested for its ability to clean wastewater containing 3-ca upon inoculation into activated sludge. to monitor its survival, the strain was chromosomally marked with the gfp gene and designated i2gfp. after inoculatio ...200010877785
fluorescent whole-cell hybridization with 16s rrna-targeted oligonucleotide probes to identify brucella spp. by flow cytometry.a whole-cell hybridization assay with fluorescent oligonucleotide probes derived from the 16s rrna sequence of brucella abortus in combination with flow cytometry has been developed. with the three fluorescent probes selected, a positive signal was observed with all the representative strains of the species and biovars of brucella and with a total of nine different brucella clinical isolates. using the b9 probe in the hybridization assay, it was possible to discriminate between brucella suis bio ...200010878084
high efficiency separation of microbial aggregates using capillary electrophoresis.recent advances in the technique of capillary electrophoresis have demonstrated fast, highly efficient separation of mixtures of intact microbes. this paper describes the application of this technique for the separation of microbial aggregates of micrococcus luteus, saccharomyces cerevisiae, or alcaligenes faecalis. the aggregates of these microbes were resolved into several highly efficient peaks with analysis times under 10 min and efficiencies approaching 1000000 plates m(-1) in some cases. a ...200010913863
molecular cloning, sequencing, and expression in escherichia coli of the gene encoding a novel 5-oxoprolinase without atp-hydrolyzing activity from alcaligenes faecalis n-38a.the gene encoding a novel 5-oxoprolinase without atp-hydrolyzing activity from alcaligenes faecalis n-38a was cloned and characterized. the coding region of this gene is 1,299 bp long. the predicted primary protein is composed of 433 amino acid residues, with a 31-amino-acid signal peptide. the mature protein is composed of 402 amino acid residues with a molecular mass of 46,163 da. the derived amino acid sequence of the enzyme showed no significant sequence similarity to any other proteins repo ...200010919770
analysis of oxidation sensitivity of maleate cis-trans isomerase from serratia marcescens.the maleate cis-trans isomerase gene (maia) from serratia marcescens ifo3736 was cloned and sequenced. serratia maia has 62.4% amino acid identity with alcaligenes faecalis ifo13111 maia and 64.9% with bacillus stearothermophilus mi-102 maia. all known ten amino acid sequences of maia had significant conserved regions containing cysteine residues, which were previously suggested to be involved in an active site of the enzyme. the maia gene was expressed in escherichia coli, and expressed product ...200010945267
molecular analysis of diazotroph diversity in the rhizosphere of the smooth cordgrass, spartina alterniflora.n(2) fixation by diazotrophic bacteria associated with the roots of the smooth cordgrass, spartina alterniflora, is an important source of new nitrogen in many salt marsh ecosystems. however, the diversity and phylogenetic affiliations of these rhizosphere diazotrophs are unknown. denaturing gradient gel electrophoresis (dgge) of pcr-amplified nifh sequence segments was used in previous studies to examine the stability and dynamics of the spartina rhizosphere diazotroph assemblages in the north ...200010966395
bacteria in the leaf ecosystem with emphasis on pseudomonas syringae-a pathogen, ice nucleus, and epiphyte.the extremely large number of leaves produced by terrestrial and aquatic plants provide habitats for colonization by a diversity of microorganisms. this review focuses on the bacterial component of leaf microbial communities, with emphasis on pseudomonas syringae-a species that participates in leaf ecosystems as a pathogen, ice nucleus, and epiphyte. among the diversity of bacteria that colonize leaves, none has received wider attention than p. syringae, as it gained notoriety for being the firs ...200010974129
the role of hydrophobic interactions on alcohol binding in the active center of penicillin acylases.inhibition of penicillin acylases from escherichia coli and alcaligenes faecalis by aliphatic and aromatic alcohols was studied. it was shown that the inhibition of both enzymes has competitive nature and they bind the alcohols at the acyl group binding site of the enzyme active center. the free energy of alcohol sorption was shown to be linearly dependent on the hydrophobicity of the inhibitor with slopes of 1.6 and 1.7, demonstrating extremely effective hydrophobic interactions. to rationalize ...200011002191
mobilization of poly(3-hydroxybutyrate) in ralstonia eutropha.ralstonia eutropha h16 degraded (mobilized) previously accumulated poly(3-hydroxybutyrate) (phb) in the absence of an exogenous carbon source and used the degradation products for growth and survival. isolated native phb granules of mobilized r. eutropha cells released 3-hydroxybutyrate (3hb) at a threefold higher rate than did control granules of nonmobilized bacteria. no 3hb was released by native phb granules of recombinant escherichia coli expressing the phb biosynthetic genes. native phb gr ...200011004196
isolation of moraxella canis from an ulcerated metastatic lymph node.moraxella canis was isolated in large numbers from an ulcerated supraclavicular lymph node of a terminal patient, who died a few days later. although the patient presented with septic symptoms and with a heavy growth of gram-negative diplococci in the lymph node, blood cultures remained negative. m. canis is an upper-airway commensal from dogs and cats and is considered nonpathogenic for humans, although this is the third reported human isolate of this species.200011015424
discovery, purification, and characterization of a temperate transducing bacteriophage for bordetella avium.we discovered and characterized a temperate transducing bacteriophage (ba1) for the avian respiratory pathogen bordetella avium. ba1 was initially identified along with one other phage (ba2) following screening of four strains of b. avium for lysogeny. of the two phage, only ba1 showed the ability to transduce via an allelic replacement mechanism and was studied further. with regard to host range, ba1 grew on six of nine clinical isolates of b. avium but failed to grow on any tested strains of b ...200011029434
sequencing bands of ribosomal intergenic spacer analysis fingerprints for characterization and microscale distribution of soil bacterium populations responding to mercury spiking.two major emerging bands (a 350-bp band and a 650-bp band) within the risa (ribosomal intergenic spacer analysis) profile of a soil bacterial community spiked with hg(ii) were selected for further identification of the populations involved in the response of the community to the added metal. the bands were cut out from polyacrylamide gels, cloned, characterized by restriction analysis, and sequenced for phylogenetic affiliation of dominant clones. the sequences were the intergenic spacer between ...200011097911
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 ...200111114905
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 ...200111133426
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 ...200111133435
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 ...200111136807
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.200111157282
survival rate of microbes after freeze-drying and long-term storage.the survival rates of 10 species of microorganisms were investigated after freeze-drying and preserving in a vacuum at 5 degrees c. the survival rates varied with species. the survival rates immediately after freeze-drying were different among yeast, gram-positive bacteria, and gram-negative bacteria, and the change in the 10-year survival rate was species-specific. the survival rate of yeast, saccharomyces cerevisiae, was about 10% immediately after drying, and the rate did not decrease signifi ...200011161557
phylogenetic analysis of culturable dimethyl sulfide-producing bacteria from a spartina-dominated salt marsh and estuarine water.dimethylsulfoniopropionate (dmsp), an abundant osmoprotectant found in marine algae and salt marsh cordgrass, can be metabolized to dimethyl sulfide (dms) and acrylate by microbes having the enzyme dmsp lyase. a suite of dms-producing bacteria isolated from a salt marsh and adjacent estuarine water on dmsp agar plates differed markedly from the pelagic strains currently in culture. while many of the salt marsh and estuarine isolates produced dms and methanethiol from methionine and dimethyl sulf ...200111229912
phenotypic methods for determining genomovar status of the burkholderia cepacia complex.recent taxonomic advances have demonstrated that burkholderia cepacia is a cluster of at least seven closely related genomic species (or genomovars) collectively referred to as the b. cepacia complex, all of which may cause infections among cystic fibrosis patients and other vulnerable individuals. thus, it is important for clinical microbiologists to be able to differentiate genomovars. prior to this study, 361 b. cepacia complex isolates and 51 isolates easily confused with b. cepacia complex ...200111230429
crystal structure of the 100 kda arsenite oxidase from alcaligenes faecalis in two crystal forms at 1.64 a and 2.03 a.arsenite oxidase from alcaligenes faecalis ncib 8687 is a molybdenum/iron protein involved in the detoxification of arsenic. it is induced by the presence of aso(2-) (arsenite) and functions to oxidize as(iii)o(2-), which binds to essential sulfhydryl groups of proteins and dithiols, to the relatively less toxic as(v)o(4)(3-) (arsenate) prior to methylation.200111250197
hydrogen peroxide-forming nadh oxidase belonging to the peroxiredoxin oxidoreductase family: existence and physiological role in bacteria.amphibacillus xylanus and sporolactobacillus inulinus nadh oxidases belonging to the peroxiredoxin oxidoreductase family show extremely high peroxide reductase activity for hydrogen peroxide and alkyl hydroperoxides in the presence of the small disulfide redox protein, ahpc (peroxiredoxin). in order to investigate the distribution of this enzyme system in bacteria, 15 bacterial strains were selected from typical aerobic, facultatively anaerobic, and anaerobic bacteria. ahpc-linked alkyl hydroper ...200111274101
phylogenetic diversity of bacterial and archaeal communities in the anoxic zone of the cariaco basin.microbial community samples were collected from the anoxic zone of the cariaco basin at depths of 320, 500, and 1,310 m on a november 1996 cruise and were used to construct 16s ribosomal dna libraries. of 60 nonchimeric sequences in the 320-m library, 56 belonged to the epsilon subdivision of the proteobacteria (epsilon-proteobacteria) and 53 were closely related to ectosymbionts of rimicaris exoculata and alvinella pompejana, which are referred to here as epsilon symbiont relatives (esr). the 5 ...200111282619
in vitro activities of rwj-54428 (mc-02,479) against multiresistant gram-positive bacteria.rwj-54428 (mc-02,479) is a new cephalosporin with a high level of activity against gram-positive bacteria. in a broth microdilution susceptibility test against methicillin-resistant staphylococcus aureus (mrsa), rwj-54428 was as active as vancomycin, with an mic at which 90% of isolates are inhibited (mic(90)) of 2 microg/ml. for coagulase-negative staphylococci, rwj-54428 was 32 times more active than imipenem, with an mic(90) of 2 microg/ml. rwj-54428 was active against s. aureus, staphylococc ...200111302805
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