Publications

the structure of the o-specific polysaccharide from ralstonia pickettii.	the following structure of the ralstonia pickettii have been determined using nmr and chemical methods: -->4)-alpha-d-rha-(1-->4)-alpha-l-galnaca-(1-->3)-beta-d-bacnac-(1-->.	2004	15261599
a novel p-nitrophenol degradation gene cluster from a gram-positive bacterium, rhodococcus opacus sao101.	p-nitrophenol (4-np) is recognized as an environmental contaminant; it is used primarily for manufacturing medicines and pesticides. to date, several 4-np-degrading bacteria have been isolated; however, the genetic information remains very limited. in this study, a novel 4-np degradation gene cluster from a gram-positive bacterium, rhodococcus opacus sao101, was identified and characterized. the deduced amino acid sequences of npcb, npca, and npcc showed identity with phenol 2-hydroxylase compon ...	2004	15262926
failure of ceftriaxone in an intravenous drug user with invasive infection due to ralstonia pickettii.	we report a case of septic arthritis due to ralstonia pickettii in an intravenous drug user with unfavorable clinical course under antibiotic therapy with ceftriaxone despite in vitro susceptibility to the drug. the treatment failure may have been due to a discrepancy between in vitro and in vivo susceptibility of r. pickettii, or to resistance development mediated by a recently described inducible beta-lactamase.	2004	15293083
change in bacterial community structure during in situ biostimulation of subsurface sediment cocontaminated with uranium and nitrate.	previous studies have demonstrated that metal-reducing microorganisms can effectively promote the precipitation and removal of uranium from contaminated groundwater. microbial communities were stimulated in the acidic subsurface by ph neutralization and addition of an electron donor to wells. in single-well push-pull tests at a number of treated sites, nitrate, fe(iii), and uranium were extensively reduced and electron donors (glucose, ethanol) were consumed. examination of sediment chemistry in ...	2004	15294831
development of two pcr-based techniques for detecting helical and coccoid forms of helicobacter pylori.	the primary mode of transmission of helicobacter pylori, a human pathogen carried by more than half the population worldwide, is still unresolved. some epidemiological data suggest water as a possible transmission route. h. pylori in the environment transforms into a nonculturable, coccoid form, which frequently results in the failure to detect this bacterium in environmental samples by conventional culture techniques. to overcome limitations associated with culturing, molecular approaches based ...	2004	15297506
beta-lactamase production and antimicrobial susceptibility of subgingival bacteria from refractory periodontitis.	this study assessed the extent of beta-lactamase-producing bacteria in subgingival plaque samples obtained from 25 patients with refractory marginal periodontitis in the usa. beta-lactamase-positive isolates were characterized using commercial diagnostic kits and partial sequencing of the 16s rrna gene. the susceptibilities to different antimicrobial agents were tested and, in addition, the isolates were screened for the presence of extended spectrum beta-lactamases (esbls). beta-lactamase-produ ...	2004	15327642
direct observation of poly(3-hydroxybutyrate) depolymerase adsorbed on polyester thin film by atomic force microscopy.	poly[(r)-3-hydroxybutyrate] (phb) depolymerases adsorbed on poly(l-lactide) (plla) thin film were directly observed by atomic force microscopy (afm). a plla thin film of 100 nm thickness was prepared on a silicon wafer by spin-cast method. the plla thin film was treated at 220 degrees c and quenched to room temperature, resulting in the formation of a completely amorphous film with a smooth surface. then, the phb depolymerases from pseudomonas stutzeri ym1006 and ralstonia pickettii t1 were disp ...	2004	15360268
morphology and enzymatic degradation of oriented thin film of ultrahigh molecular weight poly[(r)-3-hydroxybutyrate].	thin films of ultrahigh molecular weight poly[(r)-3-hydroxybutyrate] (p(3hb)) were sheared and isothermally crystallized at 100 degrees c. transmission electron microscopy and atomic force microscopy (afm) observations revealed that thick fibrous textures, on which lamellae are overgrown normal to the long axis of the fibril, run parallel to the shearing direction. a selected area electron diffraction pattern taken from the fibrils exhibits a fiber pattern of p(3hb) alpha-modification, and the c ...	2004	15360288
bioremediation of quinoline-contaminated soil using bioaugmentation in slurry-phase reactor.	to investigate the possibility of using bioaugmentation as a strategy for remediating quinoline-contaminated soil.	2004	15386944
thermophilic, reversible gamma-resorcylate decarboxylase from rhizobium sp. strain mtp-10005: purification, molecular characterization, and expression.	we found the occurrence of thermophilic reversible gamma-resorcylate decarboxylase (gamma-rdc) in the cell extract of a bacterium isolated from natural water, rhizobium sp. strain mtp-10005, and purified the enzyme to homogeneity. the molecular mass of the enzyme was determined to be about 151 kda by gel filtration, and that of the subunit was 37.5 kda by sodium dodecyl sulfate-polyacrylamide gel electrophoresis; in other words, the enzyme was a homotetramer. the enzyme was induced specifically ...	2004	15466039
in-situ atomic force microscopy observation of enzymatic degradation in poly(hydroxyalkanoic acid) thin films: normal and constrained conditions.	the enzymatic degradation of lamellar crystals in poly(hydroxyalkanoic acid) thin films has been visualized by using in-situ dynamic force mode (tapping mode) atomic force microscopy (afm) in buffer solution. it was found that poly(hydroxybutyric acid) (phb) depolymerase from ralstonia pickettii t1 degraded the thin surface layers formed at room temperature first, and that lamellar crystals formed at the crystallization temperature (110 degrees c) were eroded from the crystallographic a-axis to ...	2004	15468218
tour-mediated effector-independent growth phase-dependent activation of the sigma54 ptou promoter of pseudomonas stutzeri ox1.	transcription of the catabolic touabcdef operon, encoding the toluene-o-xylene monooxygenase of pseudomonas stutzeri ox1, is driven by the sigma(54)-dependent ptou promoter, whose activity is controlled by the phenol-responsive ntrc-like activator tour. in this paper we describe for the first time a peculiar characteristic of this system, namely, that ptou transcription is activated in a growth phase-dependent manner in the absence of genuine effectors of the cognate tour regulator. this phenome ...	2004	15489447
[case report: nosocomial ralstonia pickettii infection in neonatal intensive care unit].	although ralstonia pickettii was known as a saprophytic species, it has been isolated in nosocomial infections in recent years. in this case report, r. pickettii infection of a neonate in the neonatal intensive care unit (icu) was presented. r. pickettii was isolated from the blood cultures of the neonate and also from the incubator and distilled water of the incubator. the isolates revealed identical biochemical and physiological characteristics. the strains were identified by conventional test ...	2004	15490846
controlling the regiospecific oxidation of aromatics via active site engineering of toluene para-monooxygenase of ralstonia pickettii pko1.	a primary goal of protein engineering is to control catalytic activity. here we show that through mutagenesis of three active site residues, the catalytic activity of a multicomponent monooxygenase is altered so that it hydroxylates all three positions of toluene as well as both positions of naphthalene. hence, for the first time, an enzyme has been engineered so that its regiospecific oxidation of a substrate can be controlled. through the a107g mutation in the alpha-subunit of toluene para-mon ...	2005	15498762
oxa-60, a chromosomal, inducible, and imipenem-hydrolyzing class d beta-lactamase from ralstonia pickettii.	a chromosomally encoded oxacillinase, oxa-22, had been characterized from ralstonia pickettii pic-1 that did not explain by itself the resistance profile of this strain to beta-lactams. thus, further analysis of the genetic background of this species led to the identification of another oxacillinase, oxa-60, that was expressed only after beta-lactam induction. this chromosomally encoded oxacillinase shared 19% amino acid identity with oxa-22. it has a narrow-spectrum hydrolysis profile that incl ...	2004	15504844
characterization of bacterial community diversity in cystic fibrosis lung infections by use of 16s ribosomal dna terminal restriction fragment length polymorphism profiling.	progressive loss of lung function resulting from the inflammatory response to bacterial colonization is the leading cause of mortality in cystic fibrosis (cf) patients. a greater understanding of these bacterial infections is needed to improve lung disease management. as culture-based diagnoses are associated with fundamental drawbacks, we used terminal restriction fragment (t-rf) length polymorphism profiling and 16s rrna clone data to characterize, without prior cultivation, the bacterial comm ...	2004	15528712
enzymatic degradation processes of lamellar crystals in thin films for poly[(r)-3-hydroxybutyric acid] and its copolymers revealed by real-time atomic force microscopy.	enzymatic degradation processes of flat-on lamellar crystals in melt-crystallized thin films of poly[(r)-3-hydroxybutyric acid] (p(3hb)) and its copolymers were characterized by real-time atomic force microscopy (afm) in a phosphate buffer solution containing phb depolymerase from ralstonia pickettii t1. fiberlike crystals with regular intervals were generated along the crystallographic a axis at the end of lamellar crystals during the enzymatic degradation. the morphologies and sizes of the fib ...	2004	15530032
ralstonia solanacearum iron scavenging by the siderophore staphyloferrin b is controlled by phca, the global virulence regulator.	phca is a transcriptional regulator that activates expression of multiple virulence genes in the plant pathogen ralstonia solanacearum. relative to their wild-type parents, phca mutants overproduced iron-scavenging activity detected with chrome azurol s siderophore detection medium. transposon mutagenesis of strain aw1-pc (phca1) generated strain gb6, which was siderophore negative but retained weak iron-scavenging activity. the ssd gene inactivated in gb6 encodes a protein similar to group iv a ...	2004	15547261
real-time pcr assay for a unique chromosomal sequence of bacillus anthracis.	real-time pcr has become an important method for the rapid identification of bacillus anthracis since the 2001 anthrax mailings. most real-time pcr assays for b. anthracis have been developed to detect virulence genes located on the pxo1 and pxo2 plasmids. in contrast, only two published chromosomal targets exist, the rpob gene and the gyra gene. in the present study, subtraction-hybridization with a plasmid-cured b. anthracis tester strain and a bacillus cereus driver was used to find a unique ...	2004	15583318
manual and automated instrumentation for identification of enterobacteriaceae and other aerobic gram-negative bacilli.	identification of gram-negative bacilli, both enteric and nonenteric, by conventional methods is not realistic for clinical microbiology laboratories performing routine cultures in today's world. the use of commercial kits, either manual or automated, to identify these organisms is a common practice. the advent of rapid or "spot" testing has eliminated the need for some commonly isolated organisms to be identified with the systems approach. commercially available systems provide more in-depth id ...	2005	15653824
two cases of ralstonia pickettii bacteremias in a pediatric oncology unit requiring removal of the port-a-caths.	ralstonia pickettii is an aerobic, gram-negative bacterium causing bacteremia following the use of contaminated saline vials, respiratory therapy solutions, skin disinfectants, blood culture mediums, and water supplies. it is rarely associated with human infections. the authors report two cases of r. pickettii bacteremia in patients with port-a-caths that could be treated only by removal of the ports.	2005	15654276
aerobic biodegradation of n-nitrosodimethylamine (ndma) by axenic bacterial strains.	the water contaminant n-nitrosodimethylamine (ndma) is a probable human carcinogen whose appearance in the environment is related to the release of rocket fuel and to chlorine-based disinfection of water and wastewater. although this compound has been shown to be biodegradable, there is minimal information about the organisms capable of this degradation, and little is understood of the mechanisms or biochemistry involved. this study shows that bacteria expressing monooxygenase enzymes functional ...	2005	15672376
regiospecific oxidation of naphthalene and fluorene by toluene monooxygenases and engineered toluene 4-monooxygenases of pseudomonas mendocina kr1.	the regiospecific oxidation of the polycyclic aromatic hydrocarbons naphthalene and fluorene was examined with escherichia coli strains expressing wildtype toluene 4-monooxygenase (t4mo) from pseudomonas mendocina kr1, toluene para-monooxygenase (tpmo) from ralstonia pickettii pko1, toluene ortho-monooxygenase (tom) from burkholderia cepacia g4, and toluene/ortho-xylene monooxygenase (tomo) from p. stutzeri ox1. t4mo oxidized toluene (12.1+/-0.8 nmol/min/mg protein at 109 microm), naphthalene (7 ...	2005	15723332
species abundance and diversity of burkholderia cepacia complex in the environment.	despite considerable interest in studying burkholderia cepacia complex in the environment, we still do not have efficient methods to detect, isolate, and screen large numbers of b. cepacia isolates. to better describe the ecology and diversity of b. cepacia complex, a colony hybridization assay was developed to detect specifically all species of the complex based on polymorphism of the variable v3 region of the 16s rrna sequence. the sensitivity of the assay was dramatically enhanced by using a ...	2005	15746318
inquilinus limosus in patients with cystic fibrosis, germany.	we identified inquilinus limosus, a recently described ?-proteobacterium, in sputum of 2 patients with cystic fibrosis whose respiratory tracts were persistently colonized for >9 months. we present data on the epidemiology, antimicrobial susceptibility, and molecular characteristics of i. limosus.	2005	15757565
the effect of simulated microgravity on bacteria from the mir space station.	the effects of simulated microgravity on two bacterial isolates, sphingobacterium thalpophilium and ralstonia pickettii (formerly burkholderia pickettii), originally recovered from water systems aboard the mir space station were examined. these bacteria were inoculated into water, high and low concentrations of nutrient broth and subjected to simulated microgravity conditions. s. thalpophilium (which was motile and had flagella) showed no significant differences between simulated microgravity an ...	2004	15773020
ralstonia pickettii and burkholderia cepacia complex bloodstream infections related to infusion of contaminated water for injection.	ralstonia pickettii and burkholderia cepacia complex isolates are causes of healthcare-associated infection related to contamination of intravenously administered products. based on microbiological and epidemiological data and molecular typing by pulsed-field gel electrophoresis, we report the occurrence of two outbreaks of r. pickettii and b. cepacia complex bloodstream infections. the first outbreak occurred from august 1995 to september 1996, and the second outbreak occurred from 28 march to ...	2005	15823657
oxa-46, a new class d beta-lactamase of narrow substrate specificity encoded by a blavim-1-containing integron from a pseudomonas aeruginosa clinical isolate.	a novel oxa-type enzyme, named oxa-46, was found to be encoded by a gene cassette inserted into a class 1 integron from a multidrug-resistant pseudomonas aeruginosa clinical isolate. the variable region of the integron also contained a bla(vim-1) metallo-beta-lactamase cassette and a duplicated aaca4 aminoglycoside acetyltransferase cassette. oxa-46 belongs to the oxa-2 lineage of class d beta-lactamases. it exhibits 78% sequence identity with oxa-2 and the highest similarity (around 92% identit ...	2005	15855521
burkholderia pickettii spondylitis.	case report describing burkholderia pickettii spondylitis in a healthy adult.	2005	15867939
use of pcr analyses to define the distribution of ralstonia species recovered from patients with cystic fibrosis.	two new pcr assays (for ralstonia species and ralstonia respiraculi), together with previously published pcr assays, were used to assess ralstonia isolates recovered from 111 cystic fibrosis patients. ralstonia mannitolilytica accounted for 46% of isolates, while r. respiraculi and ralstonia pickettii accounted for 19% and 18%, respectively. ralstonia basilensis and ralstonia metallidurans, species not previously recovered from human samples, were also identified.	2005	16000479
dynamics of an oligotrophic bacterial aquifer community during contact with a groundwater plume contaminated with benzene, toluene, ethylbenzene, and xylenes: an in situ mesocosm study.	an in situ mesocosm system was designed to monitor the in situ dynamics of the microbial community in polluted aquifers. the mesocosm system consists of a permeable membrane pocket filled with aquifer material and placed within a polypropylene holder, which is inserted below groundwater level in a monitoring well. after a specific time period, the microcosm is recovered from the well and its bacterial community is analyzed. using this system, we examined the effect of benzene, toluene, ethylbenz ...	2005	16000793
enzymatic degradation processes of poly[(r)-3-hydroxybutyric acid] and poly[(r)-3-hydroxybutyric acid-co-(r)-3-hydroxyvaleric acid] single crystals revealed by atomic force microscopy: effects of molecular weight and second-monomer composition on erosion rates.	enzymatic degradation processes of poly[(r)-3-hydroxybutyric acid] (p(3hb)) and poly[(r)-3-hydroxybutyric acid-co-(r)-3-hydroxyvaleric acid] (p(3hb-co-3hv)) single crystals in the presence of phb depolymerase from ralstonia pickettii t1 were studied by real-time and static atomic force microscopy (afm) observations. fibril-like crystals were generated along the long axis of single crystals during the enzymatic degradation, and then the dimensions of fibril-like crystals were analyzed quantitativ ...	2005	16004439
novel intracellular 3-hydroxybutyrate-oligomer hydrolase in wautersia eutropha h16.	wautersia eutropha h16 (formerly ralstonia eutropha) mobilizes intracellularly accumulated poly(3-hydroxybutyrate) (phb) with intracellular poly(3-hydroxybutyrate) depolymerases. in this study, a novel intracellular 3-hydroxybutyrate-oligomer hydrolase (phazc) gene was cloned and overexpressed in escherichia coli. then phazc was purified and characterized. immunoblot analysis with polyclonal antiserum against phazc revealed that most phazc is present in the cytosolic fraction and a small amount ...	2005	16030206
comparison of biomérieux api 20ne and remel rapid nf plus, identification systems of type strains of ralstonia pickettii.	a : comparison of two commercial miniaturized rapid systems for the identification of ralstonia pickettii strains.	2005	16033510
pulsed field gel electrophoresis and random amplified polymorphic dna molecular characterization of ralstonia pickettii isolates from patients with nosocomial central venous catheter related bacteremia.	over a period of 18 months 3 clusters of central venous catheter-related ralstonia pickettii bacteremia occurred in 3 different units of the same hospital. in order to investigate the relatedness of the clinical isolates we studied 15 strains using pulsed-field gel electrophoresis (pfge) and randomly amplified polymorphic dna (rapd) techniques. the combined analysis of the results obtained by these two methods led us to conclude that all the patients except one were infected by a single clone co ...	2005	16035259
superiority of molecular techniques for identification of gram-negative, oxidase-positive rods, including morphologically nontypical pseudomonas aeruginosa, from patients with cystic fibrosis.	phenotypic identification of gram-negative bacteria from cystic fibrosis (cf) patients carries a high risk of misidentification. therefore, we compared the results of biochemical identification by api 20ne with 16s rrna gene sequencing in 88 gram-negative, oxidase-positive rods, other than morphologically and biochemically typical p. aeruginosa, from respiratory secretions of cf patients. the api 20ne allowed correct identification of the bacterial species in 15 out of 88 (17%) isolates investig ...	2005	16081953
allophanate hydrolase, not urease, functions in bacterial cyanuric acid metabolism.	growth substrates containing an s-triazine ring are typically metabolized by bacteria to liberate 3 mol of ammonia via the intermediate cyanuric acid. over a 25-year period, a number of original research papers and reviews have stated that cyanuric acid is metabolized in two steps to the 2-nitrogen intermediate urea. in the present study, allophanate, not urea, was shown to be the 2-nitrogen intermediate in cyanuric acid metabolism in all the bacteria examined. six different experimental results ...	2005	16085834
[ralstonia pickettii osteomyelitis of the trapezium].	an immunocompromised 29-year-old man presented with a ralstonia pickettii osteomyelitis affecting the trapezium bone. the patient underwent two surgical debridement stages, including trapezectomy and long-term drainage. the type of the contaminant organism and the trapezium localization make this observation atypical.	2005	16121624
characterization of the naturally occurring oxacillinase of acinetobacter baumannii.	a chromosomally encoded oxacillinase, oxa-69, was characterized from acinetobacter baumannii aye. beta-lactamase oxa-69 shared 97% amino acid identity with the recently described oxa-51 enzyme of a. baumannii and 62 and 56% amino acid identity with the carbapenem-hydrolyzing oxacillinases oxa-24 and oxa-23, respectively. biochemical characterization of the purified oxa-69 revealed a narrow-spectrum hydrolysis profile but including, at a low level, imipenem and meropenem. by pcr and sequencing bl ...	2005	16189095
properties of a novel intracellular poly(3-hydroxybutyrate) depolymerase with high specific activity (phazd) in wautersia eutropha h16.	a novel intracellular poly(3-hydroxybutyrate) (phb) depolymerase (phazd) of wautersia eutropha (formerly ralstonia eutropha) h16 which shows similarity with the catalytic domain of the extracellular phb depolymerase in ralstonia pickettii t1 was identified. the positions of the catalytic triad (ser190-asp266-his330) and oxyanion hole (his108) in the amino acid sequence of phazd deduced from the nucleotide sequence roughly accorded with those of the extracellular phb depolymerase of r. pickettii ...	2005	16199568
cloning and sequence analysis of hydroxyquinol 1,2-dioxygenase gene in 2,4,6-trichlorophenol-degrading ralstonia pickettii dtp0602 and characterization of its product.	a gene encoding hydroxyquinol 1,2-dioxygenase was cloned from 2,4,6-trichlorophenol-degrading ralstonia (pseudomonas) pickettii strain dtp0602. cell-free extracts of escherichia coli containing a cloned 1.4-kb stui-xhoi dna fragment of r. pickettii dtp0602 hydroxyquinol 1,2-dioxygenase converted hydroxyquinol into maleylacetate and also degraded 6-chlorohydroxyquinol. the 1.4-kb dna fragment contained one open reading frame (designated hadc) composed of 948 nucleotides. the molecular mass of 34, ...	1999	16232466
cloning of an intracellular d(-)-3-hydroxybutyrate-oligomer hydrolase gene from ralstonia eutropha h16 and identification of the active site serine residue by site-directed mutagenesis.	an intracellular d(-)-3-hydroxybutyrate (3hb)-oligomer hydrolase gene from ralstonia eutropha (formerly alcaligenes eutrophus) h16 was cloned, sequenced, and characterized. as a hybridization probe to screen restriction digests of chromosomal dna, an extracellular 3hb-oligomer hydrolase gene from ralstonia pickettii strain (formerly pseudomonas sp. strain) a1 was used. a specific hybridization signal was obtained and a 6.5-kbp smai fragment was cloned in an escherichia coli phagemid vector. the ...	2002	16233278
[from the mailing list sin: epidemic of infections caused by 'aquatic' bacteria in patients undergoing hemodialysis via central venous catheters].	bacteremia due to central venous catheter (cvc) infection is the most frequent complication of cvc use as vascular access for hemodialysis (hd). we report a case of an epidemic of cvc infections caused by 3 strains of unusual bacteria: ralstonia pickettii (rp), leifsonia xyli/leifsonia aquatica (lxa), tsuckamurella strandjordae (ts). from 20/8/01 to 30/9/01, 23 of 35 patients dialyzed via cvcs experienced intra-hd pyrogenic reactions. their hemocultures were positive for: rp (14 pts), lxa (3 pts ...	2005	16267809
antimicrobial susceptibility patterns of unusual nonfermentative gram-negative bacilli isolated from latin america: report from the sentry antimicrobial surveillance program (1997-2002).	the antimicrobial susceptibility of 176 unusual non-fermentative gram-negative bacilli (nf-gnb) collected from latin america region through the sentry program between 1997 and 2002 was evaluated by broth microdilution according to the national committee for clinical laboratory standards (nccls) recommendations. nearly 74% of the nf-bgn belonged to the following genera/species: burkholderia spp. (83), achromobacter spp. (25), ralstonia pickettii (16), alcaligenes spp. (12), and cryseobacterium sp ...	2005	16302068
interaction between poly[(r)-3-hydroxybutyrate] depolymerase and biodegradable polyesters evaluated by atomic force microscopy.	adsorption of phb depolymerase from ralstonia pickettii t1 to biodegradable polyesters such as poly[(r)-3-hydroxybutyrate] (phb) and poly(l-lactic acid) (plla) was investigated by atomic force microscopy (afm). the substrate-binding domain (sbd) with histidines within the n-terminus was prepared and immobilized on the afm tip surface via a self-assembled monolayer with a nitrilotriacetic acid group. using the functionalized afm tips, the force-distance measurements for polyesters were carried ou ...	2005	16316121
symbiotic association in chlorella culture.	chlorella sorokiniana iam c-212 has long been maintained in slant culture as a mixed strain, representing an associated natural microbial consortium. in this study, the consortium was separated and five nonalgal constituents, a fungal strain (cssf-1), and four bacterial strains (cssb-1, cssb-2, cssb-3, and cssb-4) were isolated and identified. 16s rdna sequence analysis revealed that strains cssb-1, cssb-2, cssb-3, and cssb-4 were close to ralstonia pickettii (99.8% identity), sphingomonas sp. d ...	2005	16329867
distribution of typical freshwater bacterial groups is associated with ph, temperature, and lake water retention time.	the distribution of 15 typical freshwater bacterial groups in 15 diverse lakes in northern europe was investigated using reverse line blot hybridization. statistical evaluation of the data in relation to the characteristics of the lakes showed that ph, temperature, and the theoretical hydrological retention time of the lakes were most strongly related to variations in the distribution of bacterial taxa. this suggests that ph and temperature are steering factors in the selection of taxa and suppo ...	2005	16332803
growth and multiplexed analysis of microorganisms on a subdivided, highly porous, inorganic chip manufactured from anopore.	a highly porous inorganic material (anopore) was shown to be an effective support for culturing and imaging a wide range of microorganisms. an inert barrier grid was printed on the rigid surface of anopore to create a "living chip" of 336 miniaturized compartments (200/cm2) with broad applications in microbial culture.	2005	16332904
ralstonia pickettii: a persistent gram-negative nosocomial infectious organism.	non-fermenting gram-negative bacilli create a significant problem in clinical settings, being a widespread cause of nosocomial infections. they are opportunistic pathogens that take advantage of underlying conditions and diseases. ralstonia pickettii, a non-fermenting gram-negative bacillus, is regarded as being of minor clinical significance; however, many instances of infections with this organism are reported in the literature. infections can include bacteraemia/septicaemia caused by contamin ...	2006	16337309
outbreak of ralstonia pickettii bacteremia in a neonatal intensive care unit.	ralstonia pickettii is a gram-negative bacillus commonly found in soil and moist environments; however, r. pickettii is rarely isolated from clinical specimens. in august 2001, a cluster of r. pickettii bacteremia occurred among neonatal intensive care unit (nicu) infants at a california hospital.	2005	16371873
ralstonia pickettii-innocent bystander or a potential threat?		2006	16441445
cloning and functional characterization of the stye gene, involved in styrene transport in pseudomonas putida ca-3.	a 1.5-kb region immediately downstream of the styabcd operon involved in styrene degradation in pseudomonas putida ca-3 has been cloned. sequence analysis revealed a 1,296-bp open reading frame, designated stye, and blast p database comparisons of the deduced stye amino acid sequence revealed 33 to 98% identity with several membrane-associated atpase-dependent kinase proteins involved in the active transport of aromatic hydrocarbons across bacterial membranes and also with fadl, an outer membran ...	2006	16461680
crystallization and x-ray diffraction analysis of dihydropyrimidinase from saccharomyces kluyveri.	dihydropyrimidinase (ec 3.5.2.2) catalyzes the second step in the reductive pathway of pyrimidine degradation, the hydrolysis of 5,6-dihydrouracil and 5,6-dihydrothymine to the corresponding n-carbamylated beta-amino acids. crystals of the recombinant enzyme from the yeast saccharomyces kluyveri diffracting to 2.6 a at a synchrotron-radiation source have been obtained by the hanging-drop vapour-diffusion method. they belong to space group p2(1) (unit-cell parameters a = 91.0, b = 73.0, c = 161.4 ...	2005	16511040
differentiation of species combined into the burkholderia cepacia complex and related taxa on the basis of their fatty acid patterns.	using the established commercial system sherlock (midi, inc.), cellular fatty acid methyl ester analysis for differentiation among burkholderia cepacia complex species was proven. the identification key based on the diagnostic fatty acids is able to discern phenotypically related ralstonia pickettii and pandoraea spp. and further distinguish burkholderia pyrrocinia, burkholderia ambifaria, and burkholderia vietnamiensis.	2006	16517920
novel carbapenem-hydrolyzing oxacillinase oxa-62 from pandoraea pnomenusa.	pandoraea spp. are gram-negative, glucose nonfermenting rods detectable in blood cultures and sputa of cystic fibrosis patients. they are resistant to various antibiotic groups, with imipenem being the only active beta-lactam. we isolated an imipenem-resistant (mic, 64 microg/ml) pandoraea pnomenusa strain from a cystic fibrosis patient. cloning and sequencing identified two beta-lactamases of bush group 2d, namely, the known oxa-33, located on an integron, and the novel carbapenem-hydrolyzing o ...	2006	16569848
16s rrna gene sequencing versus the api 20 ne system and the vitek 2 id-gnb card for identification of nonfermenting gram-negative bacteria in the clinical laboratory.	over a period of 26 months, we have evaluated in a prospective fashion the use of 16s rrna gene sequencing as a means of identifying clinically relevant isolates of nonfermenting gram-negative bacilli (non-pseudomonas aeruginosa) in the microbiology laboratory. the study was designed to compare phenotypic with molecular identification. results of molecular analyses were compared with two commercially available identification systems (api 20 ne, vitek 2 fluorescent card; biomérieux, marcy l'etoil ...	2006	16597863
biodegradation of vinyl chloride and cis-dichloroethene by a ralstonia sp. strain trw-1.	an aerobic bacterium, ralstonia sp. strain trw-1, that assimilates vinyl chloride (vc) or ethene (eth) as the sole carbon source was isolated from a chloroethene-degrading enrichment culture. phylogenetic analysis of 16s rdna sequence of the isolate revealed almost 99% sequence similarity to ralstonia pickettii. to our knowledge, this is the first report describing the isolation of a member of ralstonia that can degrade vc as the growth substrate. the measured growth yield values for vc and eth ...	2006	16642331
diazotrophic burkholderia species associated with field-grown maize and sugarcane.	until recently, diazotrophy was known in only one of the 30 formally described species of burkholderia. novel n(2)-fixing plant-associated burkholderia species such as b. unamae, b. tropica, and b. xenovorans have been described, but their environmental distribution is scarcely known. in the present study, the occurrence of n(2)-fixing burkholderia species associated with different varieties of sugarcane and maize growing in regions of mexico and brazil was analyzed. only 111 out of more than 90 ...	2006	16672447
characterization of the siderophore of francisella tularensis and role of fsla in siderophore production.	we determined that lvs and schu s4 strains of the human pathogen francisella tularensis express a siderophore when grown under iron-limiting conditions. we purified this siderophore by conventional column chromatography and high-pressure liquid chromatography and used mass spectrometric analysis to demonstrate that it is structurally similar to the polycarboxylate siderophore rhizoferrin. the siderophore promoted the growth of lvs and schu s4 strains in iron-limiting media. we identified a poten ...	2006	16707671
outbreak of ralstonia pickettii pseudobacteremia among patients with hematological malignancies.		2006	16755490
biology of pseudomonas stutzeri.	pseudomonas stutzeri is a nonfluorescent denitrifying bacterium widely distributed in the environment, and it has also been isolated as an opportunistic pathogen from humans. over the past 15 years, much progress has been made in elucidating the taxonomy of this diverse taxonomical group, demonstrating the clonality of its populations. the species has received much attention because of its particular metabolic properties: it has been proposed as a model organism for denitrification studies; many ...	2006	16760312
evaluation of pyrrolidonyl arylamidase for the identification of nonfermenting gram-negative rods.	to evaluate the activity of pyrrolidonyl arylamidase (pyr) for the differentiation and identification of nonfermenting gram negative rods (nfgnr), 293 isolates were tested. a 24 h culture of each test organism was prepared. from this a 108-109 cfu/ml suspension was added to 0.25 ml of sterile physiologic solution. a pyr disk was then added and the test was incubated for 30 minutes at 35-37 degrees c, at environmental atmosphere. reading was done by adding 1 drop of cinnamaldehyde reagent. strain ...	2007	16822636
bacterial decontamination of duwl biofilm using oxygenal 6.	the aim of this study was bacteriological assessment of the dental unit waterlines (duwl) biofilm - concentration and composition of the aerobe and facultative anaerobe bacterial microflora, and evaluation of the influence of a disinfecting product, oxygenal 6, on the biofilm composition. tubing fragments were taken from 25 units twice, before and after disinfection, and bacterial suspension of the biofilm was obtained from the samples. the bacterial flora was determined with the plate culture m ...	2006	16841887
the prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like beta-grasp domains.	ubiquitin (ub)-mediated signaling is one of the hallmarks of all eukaryotes. prokaryotic homologs of ub (this and moad) and e1 ligases have been studied in relation to sulfur incorporation reactions in thiamine and molybdenum/tungsten cofactor biosynthesis. however, there is no evidence for entire protein modification systems with ub-like proteins and deconjugation by deubiquitinating enzymes in prokaryotes. hence, the evolutionary assembly of the eukaryotic ub-signaling apparatus remains unclea ...	2006	16859499
surveillance bronchoscopy in children during the first year after lung transplantation: is it worth it?	since january 2002, routine surveillance bronchoscopy with bronchoalveolar lavage (bal) and transbronchial biopsy has been performed in all paediatric recipients of lung and heart-lung transplants at the great ormond street hospital for children, london, uk, using a newly revised treatment protocol.	2006	16928706
surveillance bronchoscopy in children during the first year after lung transplantation: is it worth it?	since january 2002, routine surveillance bronchoscopy with bronchoalveolar lavage (bal) and transbronchial biopsy has been performed in all paediatric recipients of lung and heart-lung transplants at the great ormond street hospital for children, london, uk, using a newly revised treatment protocol.	2006	16928706
characterization of two 3-hydroxybutyrate dehydrogenases in poly(3-hydroxybutyrate)-degradable bacterium, ralstonia pickettii t1.	two d-(-)-3-hydroxybutyrate (3hb) dehydrogenases, bdh1 and bdh2, were isolated and purified from a poly(3-hydroxybutyrate) (phb)-degradable bacterium, ralstonia pickettii t1. bdh1 activity increased in r. pickettii t1 cells grown on several organic acids as a carbon source but not on 3hb, whereas bdh2 activity markedly increased in the same cells grown on 3hb or phb. to examine their biochemical properties, bdh1 and bdh2 were cloned and overexpressed in escherichia coli, and their purified produ ...	2006	16935252
identification and characterization of the bacillus thuringiensis phaz gene, encoding new intracellular poly-3-hydroxybutyrate depolymerase.	a gene that codes for a novel intracellular poly-3-hydroxybutyrate (phb) depolymerase has now been identified in the genome of bacillus thuringiensis subsp. israelensis atcc 35646. this gene, previously annotated as a hypothetical 3-oxoadipate enol-lactonase (pcad) gene and now designated phaz, encodes a protein that shows no significant similarity with any known phb depolymerase. purified his-tagged phaz could efficiently degrade trypsin-activated native phb granules as well as artificial amorp ...	2006	16936025
regulation of class d beta-lactamase gene expression in ralstonia pickettii.	ralstonia pickettii, an environmental bacterium that may also be responsible for human infections, produces two unrelated, inducible and chromosomally encoded oxacillinases, oxa-22 and oxa-60. in order to study the molecular basis of the induction process of these oxacillinase genes, the induction kinetics, the promoter/operator regions necessary for expression and induction, and the role of several orfs located upstream and downstream of the bla(oxa) genes were investigated. the beta-lactamase ...	2006	16946261
biotransformation of n-nitrosodimethylamine by pseudomonas mendocina kr1.	n-nitrosodimethylamine (ndma) is a potent carcinogen and an emerging contaminant in groundwater and drinking water. the metabolism of ndma in mammalian cells has been widely studied, but little information is available concerning the microbial transformation of this compound. the objective of this study was to elucidate the pathway(s) of ndma biotransformation by pseudomonas mendocina kr1, a strain that possesses toluene-4-monooxygenase (t4mo). p. mendocina kr1 was observed to initially oxidize ...	2006	16950909
phenotypic detection of carbapenem-susceptible metallo-beta-lactamase-producing gram-negative bacilli in the clinical laboratory.	rapid detection of metallo-beta-lactamase (mbl)-producing gram-negative pathogens is critical to prevent their widespread dissemination. thus far, no standardized phenotypic method is available, and previously reported techniques have poor sensitivity for detecting carbapenem-susceptible mbl-carrying isolates, an increasingly described phenomenon. we developed a phenotypic detection method using both a double-disk synergy test and a combined-disk test with imipenem and 292 microg edta on one aga ...	2006	16954239
fluorescence in situ hybridization for rapid identification of achromobacter xylosoxidans and alcaligenes faecalis recovered from cystic fibrosis patients.	achromobacter xylosoxidans is frequently isolated from the respiratory secretions of cystic fibrosis (cf) patients, but identification with biochemical tests is unreliable. we describe fluorescence in situ hybridization assays for the rapid identification of achromobacter xylosoxidans and alcaligenes faecalis. both assays showed high sensitivities and high specificities with a collection of 155 nonfermenters from cf patients.	2006	16954289
effects of mutations in the substrate-binding domain of poly[(r)-3-hydroxybutyrate] (phb) depolymerase from ralstonia pickettii t1 on phb degradation.	poly[(r)-3-hydroxybutyrate] (phb) depolymerase from ralstonia pickettii t1 (phaz(rpit1)) adsorbs to denatured phb (dphb) via its substrate-binding domain (sbd) to enhance dphb degradation. to evaluate the amino acid residues participating in dphb adsorption, phaz(rpit1) was subjected to a high-throughput screening system consisting of pcr-mediated random mutagenesis targeted to the sbd gene and a plate assay to estimate the effects of mutations in the sbd on dphb degradation by phaz(rpit1). gene ...	2006	16963553
metabolism of thioamides by ralstonia pickettii ta.	information on bacterial thioamide metabolism has focused on transformation of the antituberculosis drug ethionamide and related compounds by mycobacterium tuberculosis. to study this metabolism more generally, a bacterium that grew using thioacetamide as the sole nitrogen source was isolated via enrichment culture. the bacterium was identified as ralstonia pickettii and designated strain ta. cells grown on thioacetamide also transformed other thioamide compounds. transformation of the thioamide ...	2006	16997975
kinetics of 1,4-dioxane biodegradation by monooxygenase-expressing bacteria.	1,4-dioxane is a probable human carcinogen, and an important emerging water contaminant. in this study, the biodegradation of dioxane by 20 bacterial isolates was evaluated, and 13 were found to be capable of transforming dioxane. dioxane served as a growth substrate for pseudonocardia dioxanivorans cb1190 and pseudonocardia benzenivorans b5, with yields of 0.09 g protein g dioxane(-1) and 0.03 g protein g dioxane(-1), respectively. cometabolic transformation of dioxane was observed for monooxyg ...	2006	16999122
directed evolution and structural analysis of n-carbamoyl-d-amino acid amidohydrolase provide insights into recombinant protein solubility in escherichia coli.	one of the greatest bottlenecks in producing recombinant proteins in escherichia coli is that over-expressed target proteins are mostly present in an insoluble form without any biological activity. dcase (n-carbamoyl-d-amino acid amidohydrolase) is an important enzyme involved in semi-synthesis of beta-lactam antibiotics in industry. in the present study, in order to determine the amino acid sites responsible for solubility of dcase, error-prone pcr and dna shuffling techniques were applied to r ...	2007	17121498
whole-genome analysis of the methyl tert-butyl ether-degrading beta-proteobacterium methylibium petroleiphilum pm1.	methylibium petroleiphilum pm1 is a methylotroph distinguished by its ability to completely metabolize the fuel oxygenate methyl tert-butyl ether (mtbe). strain pm1 also degrades aromatic (benzene, toluene, and xylene) and straight-chain (c(5) to c(12)) hydrocarbons present in petroleum products. whole-genome analysis of pm1 revealed an approximately 4-mb circular chromosome and an approximately 600-kb megaplasmid, containing 3,831 and 646 genes, respectively. aromatic hydrocarbon and alkane deg ...	2007	17158667
whole-genome analysis of the methyl tert-butyl ether-degrading beta-proteobacterium methylibium petroleiphilum pm1.	methylibium petroleiphilum pm1 is a methylotroph distinguished by its ability to completely metabolize the fuel oxygenate methyl tert-butyl ether (mtbe). strain pm1 also degrades aromatic (benzene, toluene, and xylene) and straight-chain (c(5) to c(12)) hydrocarbons present in petroleum products. whole-genome analysis of pm1 revealed an approximately 4-mb circular chromosome and an approximately 600-kb megaplasmid, containing 3,831 and 646 genes, respectively. aromatic hydrocarbon and alkane deg ...	2007	17158667
control of 2-chlorophenol vapour emissions by a trickling biofilter.	this research work investigates the biodegradation of 2-chlorophenol vapours in a trickling biofilter packed with a ceramic material, and seeded with a pure strain of pseudomonas pickettii. the process was tested at laboratory scale over 260 days of operation under varying loading conditions. more than 98% degradation efficiencies were achieved for loading rates up to 82.5gm(-3)h(-1). process analysis, performed using data on 2-chlorophenol concentration profiles along the biofilter bed, shows t ...	2007	17222935
redox and functional analysis of the rieske ferredoxin component of the toluene 4-monooxygenase.	toluene 4-monooxygenase catalyzes the nadh- and o2-dependent hydroxylation of toluene to form p-cresol. the four-protein complex consists of a diiron hydroxylase, an oxidoreductase, a catalytic effector protein, and a rieske-type ferredoxin (t4moc). phylogenetic analysis suggests that t4moc is part of a clade specialized for reaction with diiron hydroxylases, possibly reflected in the conservation of w69, whose indole side chain makes close contacts with a bridging sulfide. in order to further i ...	2007	17240981
monitoring bacterial communities in raw milk and cheese by culture-dependent and -independent 16s rrna gene-based analyses.	the diversity and dynamics of bacterial populations in saint-nectaire, a raw-milk, semihard cheese, were investigated using a dual culture-dependent and direct molecular approach combining single-strand conformation polymorphism (sscp) fingerprinting and sequencing of 16s rrna genes. the dominant clones, among 125 16s rrna genes isolated from milk, belonged to members of the firmicutes (58% of the total clones) affiliated mainly with the orders clostridiales and the lactobacillales, followed by ...	2007	17259356
characterization of a pseudomonad 2-nitrobenzoate nitroreductase and its catabolic pathway-associated 2-hydroxylaminobenzoate mutase and a chemoreceptor involved in 2-nitrobenzoate chemotaxis.	pseudomonas fluorescens strain ku-7 is a prototype microorganism that metabolizes 2-nitrobenzoate (2-nba) via the formation of 3-hydroxyanthranilate (3-haa), a known antioxidant and reductant. the initial two steps leading to the sequential formation of 2-hydroxy/aminobenzoate and 3-haa are catalyzed by a nadph-dependent 2-nba nitroreductase (nbaa) and 2-hydroxylaminobenzoate mutase (nbab), respectively. the 216-amino-acid protein nbaa is 78% identical to a plasmid-encoded hypothetical conserved ...	2007	17277060
genetic characterization of 2,4,6-trichlorophenol degradation in cupriavidus necator jmp134.	the degradation pathway of 2,4,6-trichlorophenol (2,4,6-tcp), a hazardous pollutant, in the aerobic bacterium cupriavidus necator jmp134(pjp4) (formerly ralstonia eutropha jmp134) is encoded by the tcp genes. these genes are located in a genetic context, tcprxabcyd, which resembles a putative catabolic operon. in this work, these gene sequences were individually disrupted and mutant strains were evaluated for their ability to grow on or degrade 2,4,6-tcp. the tcpx and tcpa mutants completely fai ...	2007	17322325
spatial distribution and physiological state of bacteria in a sand column experiment during the biodegradation of toluene.	toxic organic contaminants frequently serve as growth substrates for bacteria. however, long-term exposure to the organic contaminants can result in significant stress or "injury" to bacterial cells such that bacteria may lose, either temporarily or permanently, their capacity to degrade a specific toxic organic contaminant. in order to understand the relationship between biodegradability and physiological conditions of bacteria after a prolonged exposure to a contaminant, biomass samples collec ...	2007	17397899
positively selected codons in immune-exposed loops of the vaccine candidate omp-p1 of haemophilus influenzae.	the high levels of variation in surface epitopes can be considered as an evolutionary hallmark of immune selection. new computational tools enable analysis of this variation by identifying codons that exhibit high rates of amino acid changes relative to the synonymous substitution rate. in the outer membrane protein p1 of haemophilus influenzae, a vaccine candidate for nontypeable strains, we identified four codons with this attribute in domains that did not correspond to known or assumed b- and ...	2007	17479342
enterohemorrhagic escherichia coli biofilms are inhibited by 7-hydroxyindole and stimulated by isatin.	since indole is present at up to 500 microm in the stationary phase and is an interspecies biofilm signal (j. lee, a. jayaraman, and t. k. wood, bmc microbiol. 7:42, 2007), we investigated hydroxyindoles as biofilm signals and found them also to be nontoxic interspecies biofilm signals for enterohemorrhagic escherichia coli o157:h7 (ehec), e. coli k-12, and pseudomonas aeruginosa. the genetic basis of ehec biofilm formation was also explored, and notably, virulence genes in biofilm cells were re ...	2007	17483266
evaluation of the colorimetric vitek 2 card for identification of gram-negative nonfermentative rods: comparison to 16s rrna gene sequencing.	ninety strains of a collection of well-identified clinical isolates of gram-negative nonfermentative rods collected over a period of 5 years were evaluated using the new colorimetric vitek 2 card. the vitek 2 colorimetric system identified 53 (59%) of the isolates to the species level and 9 (10%) to the genus level; 28 (31%) isolates were misidentified. an algorithm combining the colorimetric vitek 2 card and 16s rrna gene sequencing for adequate identification of gram-negative nonfermentative r ...	2007	17507509
indole is an inter-species biofilm signal mediated by sdia.	as a stationary phase signal, indole is secreted in large quantities into rich medium by escherichia coli and has been shown to control several genes (e.g., astd, tnab, gabt), multi-drug exporters, and the pathogenicity island of e. coli; however, its impact on biofilm formation has not been well-studied.	2007	17511876
inhibition of hydrogen uptake in escherichia coli by expressing the hydrogenase from the cyanobacterium synechocystis sp. pcc 6803.	molecular hydrogen is an environmentally-clean fuel and the reversible (bi-directional) hydrogenase of the cyanobacterium synechocystis sp. pcc 6803 as well as the native escherichia coli hydrogenase 3 hold great promise for hydrogen generation. these enzymes perform the simple reaction 2h+ + 2e- <--> h2 (g).	2007	17521447
description, etiology, and prevention of an outbreak of diffuse lamellar keratitis after lasik.	to describe an outbreak of diffuse lamellar keratitis (dlk) and provide a hypothesis about the etiology.	2007	17523510
adsorption and hydrolysis reactions of poly(hydroxybutyric acid) depolymerases secreted from ralstonia pickettii t1 and penicillium funiculosum onto poly[(r)-3-hydroxybutyric acid].	reaction processes of poly[(r)-3-hydroxybutyric acid] (p(3hb)) with two types of poly(hydroxybutyric acid) (phb) depolymerases secreted from ralstonia pickettii t1 and penicillium funiculosum were characterized by means of atomic force microscopy (afm) and quartz crystal microbalance (qcm). the phb depolymerase from r. pickettii t1 consists of catalytic, linker, and substrate-binding domains, whereas the one from p. funiculosum lacks a substrate-binding domain. we succeeded in observing the adso ...	2007	17547455
the tomato rhizosphere, an environment rich in nitrogen-fixing burkholderia species with capabilities of interest for agriculture and bioremediation.	burkholderia strains are promising candidates for biotechnological applications. unfortunately, most of these strains belong to species of the burkholderia cepacia complex (bcc) involved in human infections, hampering potential applications. novel diazotrophic burkholderia species, phylogenetically distant from the bcc species, have been discovered recently, but their environmental distribution and relevant features for agro-biotechnological applications are little known. in this work, the occur ...	2007	17601817
ralstonia pickettii bacteremia associated with pediatric extracorporeal membrane oxygenation therapy in a canadian hospital.	we describe 2 pediatric patients with ralstonia pickettii bacteremia associated with extracorporeal membrane oxygenation (ecmo) therapy. investigation revealed a common environmental source--the ecmo temperature-control units. we created guidelines for disinfecting these units that do not void the manufacturer's warranty and have prevented additional cases of bacteremia due to this organism.	2007	17620255
degradation of toluene by a mixed population of archetypal aerobes, microaerophiles, and denitrifiers: laboratory sand column experiment and multispecies biofilm model formulation.	an experiment was conducted in a saturated sand column with three bacterial strains that have different growth characteristics on toluene, pseudomonas putida f1 which degrades toluene only under aerobic conditions, thauera aromatica t1 which degrades toluene only under denitrifying conditions, and ralstonia pickettii pko1 has a facultative nature and can perform nitrate-enhanced biodegradation of toluene under hypoxic conditions (do <2 mg/l). steady-state concentration profiles showed that oxyge ...	2008	17626295
carbapenemases: the versatile beta-lactamases.	carbapenemases are beta-lactamases with versatile hydrolytic capacities. they have the ability to hydrolyze penicillins, cephalosporins, monobactams, and carbapenems. bacteria producing these beta-lactamases may cause serious infections in which the carbapenemase activity renders many beta-lactams ineffective. carbapenemases are members of the molecular class a, b, and d beta-lactamases. class a and d enzymes have a serine-based hydrolytic mechanism, while class b enzymes are metallo-beta-lactam ...	2007	17630334
putative prophages related to lytic tailless marine dsdna phage pm2 are widespread in the genomes of aquatic bacteria.	the origin and evolution of viruses is currently a heavily discussed issue. one element in this discussion is the innate viral "self" concept, which suggests that viral structures and functions can be divided into two categories. the first category consists of genetic determinants that are inherited from a viral ancestor and encode the viral "self". the second group consists of another set of structures and functions, the "nonself", which is interchangeable between different viruses and can be o ...	2007	17634101
bacterial contamination of water in dental unit reservoirs.	the aim of this study was bacteriological assessment of water in dental unit reservoirs--concentration and composition of the aerobe and facultative anaerobe bacterial microflora. reservoir water samples were taken from 25 units. bacterial flora were determined with the plate culture method. bacteria were identified with biochemical microtests: api 20e, api 20ne (biomérieux, france) and gp2 microplatetm (biolog, usa). the concentration of total bacteria isolated from one site was 201,039 cfu/ml, ...	2007	17655191
genomic analysis reveals widespread occurrence of new classes of copper nitrite reductases.	recently, the structure of a cu-containing nitrite reductase (nir) from hyphomicrobium denitrificans (hdnir) has been reported, establishing the existence of a new family of cu-nir where an additional type 1 cu (t1cu) containing cupredoxin domain is located at the n-terminus (nojiri et al. in proc. natl. acad. sci. usa 104:4315-4320, 2007). hdnir retains the well-characterised coupled t1cu-type 2 cu (t2cu) core, where the t2cu catalytic site is also built utilising ligands from neighbouring mono ...	2007	17712582
host-plant selectivity of rhizobacteria in a crop/weed model system.	belowground microorganisms are known to influence plants' performance by altering the soil environment. plant pathogens such as cyanide-producing strains of the rhizobacterium pseudomonas may show strong host-plant selectivity. we analyzed interactions between different host plants and pseudomonas strains and tested if these can be linked to the cyanide sensitivity of host plants, the cyanide production of bacterial strains or the plant identity from which strains had been isolated. eight strain ...	2007	17786217
identification of isolates within the burkholderia cepacia complex by a multiplex reca and 16s rrna gene real-time pcr assay.		2007	17855569