Publications

TitleAbstractYear(sorted ascending)
Filter
PMID
Filter
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 ...200717634101
bacterial biosensors for measuring availability of environmental pollutants.traditionally, pollution risk assessment is based on the measurement of a pollutant's total concentration in a sample. the toxicity of a given pollutant in the environment, however, is tightly linked to its bioavailability, which may differ significantly from the total amount. physico-chemical and biological parameters strongly influence pollutant fate in terms of leaching, sequestration and biodegradation. bacterial sensorreporters, which consist of living micro-organisms genetically engineered ...200827879922
the coastal environment and human health: microbial indicators, pathogens, sentinels and reservoirs.innovative research relating oceans and human health is advancing our understanding of disease-causing organisms in coastal ecosystems. novel techniques are elucidating the loading, transport and fate of pathogens in coastal ecosystems, and identifying sources of contamination. this research is facilitating improved risk assessments for seafood consumers and those who use the oceans for recreation. a number of challenges still remain and define future directions of research and public policy. sa ...200819025674
ralstonia pickettii bloodstream infections at a brazilian cancer institution.we describe a series of ralstonia pickettii bloodstream infections (bsi) that occurred in 19 oncohematologic patients admitted to a hospital for patients with cancer, in the city of rio de janeiro, from july 1999 to february 2006. fifty-four r. pickettii isolates were recovered from blood and catheter-tip specimens (1-5 isolates per patient). two patients eventually died of causes unrelated to r. pickettii bsi. eight pulsed-field gel electrophoresis genotypes were resolved (a-h), with two detect ...200817994262
streptomyces griseus enhances denitrification by ralstonia pickettii k50, which is possibly mediated by histidine produced during co-culture.ralstonia pickettii k50 (strain k50) is a denitrifying bacterium that produces low levels of n(2)o under aerobic conditions. in this study, we found that co-culturing of strain k50 with streptomyces griseus significantly enhanced the denitrification activity of strain k50 in an artificial wastewater (aww) system. most factors that enhance denitrification activity were in the high molecular weight fraction of the cell-free broth of s. griseus, and were suggested to be extracellular proteases. fur ...200818175905
protein engineering of toluene monooxygenases for synthesis of chiral sulfoxides.enantiopure sulfoxides are valuable asymmetric starting materials and are important chiral auxiliaries in organic synthesis. toluene monooxygenases (tmos) have been shown previously to catalyze regioselective hydroxylation of substituted benzenes and phenols. here we show that tmos are also capable of performing enantioselective oxidation reactions of aromatic sulfides. mutagenesis of position v106 in the alpha-hydroxylase subunit of toluene ortho-monooxygenase (tom) of burkholderia cepacia g4 a ...200818192418
genetic structures at the origin of acquisition of the beta-lactamase bla kpc gene.genetic structures surrounding the carbapenem-hydrolyzing ambler class a bla kpc gene were characterized in several kpc-positive klebsiella pneumoniae and pseudomonas aeruginosa strains isolated from the united states, colombia, and greece. the bla kpc genes were associated in all cases with transposon-related structures. in the k. pneumoniae yc isolate from the united states, the beta-lactamase bla kpc-2 gene was located on a novel tn3-based transposon, tn4401. tn4401 was 10 kb in size, was del ...200818227185
degradation of 4-fluorophenol by arthrobacter sp. strain if1.a gram-positive bacterial strain capable of aerobic biodegradation of 4-fluorophenol (4-fp) as the sole source of carbon and energy was isolated by selective enrichment from soil samples collected near an industrial site. the organism, designated strain if1, was identified as a member of the genus arthrobacter on the basis of 16s ribosomal rna gene sequence analysis. arthrobacter strain if1 was able to mineralize 4-fp up to concentrations of 5 mm in batch culture. stoichiometric release of fluor ...200818228015
neonatal sepsis caused by ralstonia pickettii. 200818277913
crystalline-structure-dependent enzymatic degradation of polymorphic poly(3-hydroxypropionate).the crystalline structure dependence of enzymatic degradation behavior was investigated for the polymorphic poly(3-hydroxypropionate) (p3hp), which has a basic backbone chemical structure of bacterial poly(3-hydroxyalkanoate)s (p3has). the p3hp films consisting of the beta-, gamma-, and/or delta-form crystal were cast or melt-crystallized as reported previously (macromolecules 2005, 38, 6455; macromolecules 2006, 39, 194-203) by controlling the molecular weight, crystallization temperature, and/ ...200818307304
diversity of the parb and repa genes of the burkholderia cepacia complex and their utility for rapid identification of burkholderia cenocepacia.burkholderia cenocepacia is the most prominent species of the b. cepacia complex (bcc), a group of nine closely related and difficult to identify bacteria that cause serious infections in patients with cystic fibrosis. despite its clinical relevance, identification of b. cenocepacia as a single species is unavailable, as it splits by a widely used reca gene-based pcr identification method into discrete phylogenetic subgroups iiia, iiib, iiic and iiid. with the aim of identifying gene targets sui ...200818328098
secretion pathway for the poly(3-hydroxybutyrate) depolymerase in ralstonia pickettii t1.the extracellular poly(3-hydroxybutyrate) depolymerase from ralstonia pickettii t1 has been purified, its function and character investigated in detail, and its gene cloned and sequenced. however, the mechanism by which this enzyme is secreted has not been elucidated. a mutant unable to degrade poly(3-hydroxybutyrate), n17, was obtained with the random insertion of a mini-transposon, tn5. western analysis using antiserum against the poly(3-hydroxybutyrate) depolymerase of ralstonia pickettii t1, ...200818340545
characterization of a naturally occurring class d beta-lactamase from achromobacter xylosoxidans.a chromosomally encoded class d beta-lactamase, oxa-114, was characterized from achromobacter xylosoxidans strain cip69598. beta-lactamase oxa-114 shared 56% amino acid identity with the naturally occurring class d beta-lactamase of burkholderia cenocepacia and 42% identity with the acquired oxacillinases oxa-9 and oxa-18. oxa-114 has a narrow-spectrum hydrolysis profile, although it includes imipenem, at a very low level. pcr and sequencing revealed that bla(oxa-114)-like genes were identified ...200818362192
direct comparison of the bd phoenix system with the microscan walkaway system for identification and antimicrobial susceptibility testing of enterobacteriaceae and nonfermentative gram-negative organisms.the phoenix automated microbiology system (bd diagnostics, sparks, md) is designed for the rapid identification (id) and antimicrobial susceptibility testing (ast) of clinically significant human bacterial pathogens. we evaluated the performance of the phoenix instrument in comparison with that of the microscan walkaway system (dade behring, west sacramento, ca) in the id and ast of gram-negative clinical strains and challenge isolates of enterobacteriaceae (n = 150) and nonfermentative gram-neg ...200818495856
fsle is necessary for siderophore-mediated iron acquisition in francisella tularensis schu s4.strains of francisella tularensis secrete a siderophore in response to iron limitation. siderophore production is dependent on fsla, the first gene in an operon that appears to encode biosynthetic and export functions for the siderophore. transcription of the operon is induced under conditions of iron limitation. the fsl genes lie adjacent to the fur homolog on the chromosome, and there is a canonical fur box sequence in the promoter region of fsla. we generated a deltafur mutant of the schu s4 ...200818539739
fourier transform infrared spectroscopy for rapid identification of nonfermenting gram-negative bacteria isolated from sputum samples from cystic fibrosis patients.the accurate and rapid identification of bacteria isolated from the respiratory tract of patients with cystic fibrosis (cf) is critical in epidemiological studies, during intrahospital outbreaks, for patient treatment, and for determination of therapeutic options. while the most common organisms isolated from sputum samples are pseudomonas aeruginosa, staphylococcus aureus, and haemophilus influenzae, in recent decades an increasing fraction of cf patients has been colonized by other nonfermenti ...200818550747
outer-membrane transport of aromatic hydrocarbons as a first step in biodegradation.bacterial biodegradation of hydrocarbons, an important process for environmental remediation, requires the passage of hydrophobic substrates across the cell membrane. here, we report crystal structures of two outer membrane proteins, pseudomonas putida todx and ralstonia pickettii tbux, which have been implicated in hydrocarbon transport and are part of a subfamily of the fadl fatty acid transporter family. the structures of todx and tbux show significant differences with those previously determ ...200818559855
a novel transposon, tn6009, composed of a tn916 element linked with a staphylococcus aureus mer operon.the aim of this study was to characterize a novel conjugative transposon tn6009 composed of a tn916 linked to a staphylococcus aureus mer operon in representative gram-positive and gram-negative bacteria isolated in nigeria and portugal.200818583328
acinetobacter baylyi as a pathogen for opportunistic infection.there are no previous reports of human infection due to acinetobacter baylyi. in this study, we report on six patients with bacteremia due to a. baylyi, based on analysis of the 16s-23s rrna intergenic spacer and the 16s rrna gene. all six patients had multiple underlying diseases. the infection was nosocomially acquired in five patients. the six clinical isolates had similar ribopatterns, suggesting a clonal relationship. compared to the reference strain, the clinical isolates were more resista ...200818632910
misidentification of pandoraea sputorum isolated from sputum of a patient with cystic fibrosis and review of pandoraea species infections in transplant patients.pandoraea species are considered emerging pathogens in cystic fibrosis (cf) patients, but few data exist regarding outcomes of patients colonized with these organisms. we report a case of pandoraea sputorum colonization in a cf patient under consideration for lung transplantation and review five cases of lung transplantation involving pandoraea species.200818650348
matrix-assisted laser desorption ionization-time of flight mass spectrometry for identification of nonfermenting gram-negative bacilli isolated from cystic fibrosis patients.the identification of nonfermenting gram-negative bacilli isolated from cystic fibrosis (cf) patients is usually achieved by using phenotype-based techniques and eventually molecular tools. these techniques remain time-consuming, expensive, and technically demanding. we used a method based on matrix-assisted laser desorption ionization-time of flight mass spectrometry (maldi-tof-ms) for the identification of these bacteria. a set of reference strains belonging to 58 species of clinically relevan ...200818685005
crystal structures of nadh:fmn oxidoreductase (emob) at different stages of catalysis.edta has become a major organic pollutant in the environment because of its extreme usage and resistance to biodegradation. recently, two critical enzymes, edta monooxygenase (emoa) and nadh:fmn oxidoreductase (emob), belonging to the newly established two-component flavin-diffusible monooxygenase family, were identified in the edta degradation pathway in mesorhizobium sp. bnc1. emoa is an fmnh2-dependent enzyme that requires emob to provide fmnh2 for the conversion of edta to ethylenediaminedia ...200818701448
isolation and characterization of alicycliphilus denitrificans strain bc, which grows on benzene with chlorate as the electron acceptor.a bacterium, strain bc, was isolated from a benzene-degrading chlorate-reducing enrichment culture. strain bc degrades benzene in conjunction with chlorate reduction. cells of strain bc are short rods that are 0.6 microm wide and 1 to 2 microm long, are motile, and stain gram negative. strain bc grows on benzene and some other aromatic compounds with oxygen or in the absence of oxygen with chlorate as the electron acceptor. strain bc is a denitrifying bacterium, but it is not able to grow on ben ...200818791031
influence of soil components on the biodegradation of benzene, toluene, ethylbenzene, and o-, m-, and p-xylenes by the newly isolated bacterium pseudoxanthomonas spadix bd-a59.a bacterium designated strain bd-a59, able to degrade all six benzene, toluene, ethylbenzene, and o-, m-, and p-xylene (btex) compounds, was isolated by plating gasoline-contaminated sediment from a gasoline station in geoje, republic of korea, without enrichment, on minimal salts basal (msb) agar containing 0.01% yeast extract, with btex as the sole carbon and energy source. taxonomic analyses showed that the isolate belonged to pseudoxanthomonas spadix, and until now, the genus pseudoxanthomon ...200818835999
adsorption characteristics of p(3hb) depolymerase as evaluated by surface plasmon resonance and atomic force microscopy.molecular recognition of poly[(r)-3-hydroxybutyrate] (p(3hb)) depolymerase from ralstonia pickettii t1 to the surfaces of biodegradable aliphatic polyesters such as p(3hb) and poly(l-lactic acid) (plla) was examined from the viewpoints of kinetics and dynamics. to determine the kinetic parameters on the interaction between the substrate-binding domain (sbd) of p(3hb) depolymerase and various polymer substrates with different chemical structures, surface plasmon resonance (spr) measurements were ...200818939805
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 ...200817626295
the quest for biofuels fuels genome sequencing. 200818821974
pulmonary bacterial pathogens in cystic fibrosis patients and antibiotic therapy: a tool for the health workers.cystic fibrosis is the most common and best known genetic disease involving a defect in transepithelial cl- transport by mutations in the cf gene on chromosome 7, which codes for the cystic fibrosis transmembrane conductance regulator protein (cftr). the most serious symptoms are observed in the lungs, augmenting the risk of bacterial infection. the objective of this review was to describe the bacterial pathogens colonizing patients with cystic fibrosis. a systematic search was conducted using t ...200818992146
healthcare-associated infections in pediatric cancer patients: results of a prospective surveillance study from university hospitals in germany and switzerland.pediatric cancer patients face an increased risk of healthcare-associated infection (hai). to date, no prospective multicenter studies have been published on this topic.200818500998
clinical practice guidelines for the diagnosis and management of intravascular catheter-related infection: 2009 update by the infectious diseases society of america. 200919489710
approaches to analyse dynamic microbial communities such as those seen in cystic fibrosis lung.microbial communities play vital roles in many aspects of our lives, although our understanding of microbial biogeography and community profiles remains unclear. the number of microbes or the diversity of the microbes, even in small environmental niches, is staggering. current microbiological methods used to analyse these communities are limited, in that many microorganisms cannot be cultured. even for the isolates that can be cultured, the expense of identifying them definitively is much too hi ...200919403459
guidelines for preventing infectious complications among hematopoietic cell transplantation recipients: a global perspective. 200919747629
data correction pre-processing for electronically stored blood culture results: implications on microbial spectrum and empiric antibiotic therapy.the outcome of patients with bacteraemia is influenced by the initial selection of adequate antimicrobial therapy. the objective of our study was to clarify the influence of different crude data correction methods on a) microbial spectrum and ranking of pathogens, and b) cumulative antimicrobial susceptibility pattern of blood culture isolates obtained from patients from intensive care units (icus) using a computer based tool, moni.200919500418
novel tn4371-ice like element in ralstonia pickettii and genome mining for comparative elements.integrative conjugative elements (ices) are important factors in the plasticity of microbial genomes. an element related to the ice tn4371 was discovered during a bioinformatic search of the ralstonia pickettii 12j genome. this element was analysed and further searches carried out for additional elements.a pcr method was designed to detect and characterise new elements of this type based on this scaffold and a culture collection of fifty-eight ralstonia pickettii and ralstonia insidiosa strains ...200919941653
improving the thermostability of n-carbamyl-d-amino acid amidohydrolase by error-prone pcr.to facilitate the easier production of d-amino acids using n-carbamyl-d-amino acid amidohydrolase (dcase) in an immobilized form, we improved the enzymatic thermostability of highly soluble dcase-m3 of ralstonia pickettii using directed mutagenesis. six novel mutation sites were identified in this study, apart from several thermostability-related amino acid sites reported previously. the most thermostable mutant, in which the 12th amino acid had been changed from glutamine to leucine, showed a 7 ...200918985337
benzene degradation by ralstonia pickettii pko1 in the presence of the alternative substrate succinate.the regulation of benzene degradation by ralstonia pickettii pko1 in the presence of the alternative substrate succinate was investigated in batch and continuous culture. in batch culture, r. pickettii pko1 achieved a maximum specific growth rate with benzene of 0.18 h(-1), while succinate allowed much faster growth (mu(max) = 0.5 h(-1)). under carbon excess conditions succinate repressed benzene consumption resulting in diauxic growth whereas under carbon-limited conditions in the chemostat bot ...200919039669
evaluation of an immunochromatographic assay kit for rapid identification of mycobacterium tuberculosis complex in clinical isolates.we evaluated a new immunochromatographic assay (ica) using mouse monoclonal anti-mpt64 antibody for rapid discrimination between mycobacterium tuberculosis and nontuberculous mycobacteria in clinical isolates. a study with mycobacteria and other organisms showed excellent sensitivity (approximately equal 99%) and specificity (100%) and an appropriate detection limit (10(5) cfu/ml) when tested with m. tuberculosis h37rv. this ica can simplify the identification of m. tuberculosis in clinical labo ...200919052177
evaluation of an immunochromatographic assay kit for rapid identification of mycobacterium tuberculosis complex in clinical isolates.we evaluated a new immunochromatographic assay (ica) using mouse monoclonal anti-mpt64 antibody for rapid discrimination between mycobacterium tuberculosis and nontuberculous mycobacteria in clinical isolates. a study with mycobacteria and other organisms showed excellent sensitivity (approximately equal 99%) and specificity (100%) and an appropriate detection limit (10(5) cfu/ml) when tested with m. tuberculosis h37rv. this ica can simplify the identification of m. tuberculosis in clinical labo ...200919052177
insights on escherichia coli biofilm formation and inhibition from whole-transcriptome profiling.biofilms transform independent cells into specialized cell communities. here are presented some insights into biofilm formation ascertained with the best-characterized strain, escherichia coli. investigations of biofilm formation and inhibition with this strain using whole-transcriptome profiling coupled to phenotypic assays, in vivo dna binding studies and isogenic mutants have led to discoveries related to the role of stress, to the role of intra- and interspecies cell signalling, to the impac ...200919125816
isolation and identification of cellulose-binding proteins from sheep rumen contents.to extend our understanding of the mechanisms of plant cell wall degradation in the rumen, cellulose-binding proteins (cbps) from the contents of a sheep rumen were directly isolated and identified using a metaproteomics approach. the rumen cbps were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and some cbps revealed endoglucanase activities toward carboxymethyl cellulose. using mass spectrometry analyses, four cbps were identified and annotated as known proteins from ...200919151184
ralstonia pickettii septicemia in a dog with immune-mediated thrombocytopenia. 200919175738
transmembrane passage of hydrophobic compounds through a protein channel wall.membrane proteins that transport hydrophobic compounds have important roles in multi-drug resistance and can cause a number of diseases, underscoring the importance of protein-mediated transport of hydrophobic compounds. hydrophobic compounds readily partition into regular membrane lipid bilayers, and their transport through an aqueous protein channel is energetically unfavourable. alternative transport models involving acquisition from the lipid bilayer by lateral diffusion have been proposed f ...200919182779
characterization of a novel 3-hydroxybutyrate dehydrogenase from ralstonia pickettii t1.we previously reported that the activities of two 3-hydroxybutyrate dehydrogenases (bdh1 and bdh2) were greatly influenced by culture conditions when ralstonia pickettii t1, a strain growing on extracellular poly-3-hydroxybutyrate (phb), was grown on different carbon sources such as 3hb and succinate. in this study, knockout mutants of bdh1 or bdh2 were constructed and characterized under different culture conditions. in addition, a novel bdh (bdh3) was found in bdh2 mutants, and bdh3 was cloned ...200919219638
development of non-antibiotic-resistant, chromosomally based, constitutive and inducible expression systems for aroa-attenuated salmonella enterica serovar typhimurium.live-vaccine delivery systems expressing two model antigens from mycoplasma hyopneumoniae, f2(p97) (adh) and nrdf, were constructed using salmonella enterica serovar typhimurium aroa (stm-1), and immunogenicity in mice was evaluated. recombinant plasmid-based expression (pbe) and chromosomally based expression (cbe) systems were constructed. the pbe system was formed by cloning both antigen genes into pjla507 to create an operon downstream of temperature-inducible promoters. constitutive cbe was ...200919223478
principles of bone marrow transplantation (bmt): providing optimal veterinary and husbandry care to irradiated mice in bmt studies.bone marrow transplantation (bmt) is the treatment of choice for many leukemias, solid tumors, and metabolic diseases. the field of bone marrow research is highly dependent on in vivo experimentation, because in vitro techniques do not mimic these complicated in vivo systems. therefore, understanding the medical and husbandry care needs of these transiently immunodeficient bone marrow recipient animals is crucial for researchers, veterinary and animal care personnel. here we discuss the principl ...200919245745
low rates of pseudomonas aeruginosa misidentification in isolates from cystic fibrosis patients.pseudomonas aeruginosa is an important cause of pulmonary infection in cystic fibrosis (cf). its correct identification ensures effective patient management and infection control strategies. however, little is known about how often cf sputum isolates are falsely identified as p. aeruginosa. we used p. aeruginosa-specific duplex real-time pcr assays to determine if 2,267 p. aeruginosa sputum isolates from 561 cf patients were correctly identified by 17 australian clinical microbiology laboratorie ...200919261796
siderophore production by marine-derived fungi.siderophore production by marine-derived fungi has not been extensively explored. three studies have investigated the ability of marine-derived fungi to produce siderophores in response to iron limitation [(vala et al. in indian j mar sci 29:339-340, 2000; can j microbiol 52:603-607, 2006); baakza et al. in j exp mar biol ecol 311:1-9, 2004]. in all, 24 of 28 marine fungal strains were found to secrete hydroxamate or carboxylate siderophores; no evidence was found for production of catecholate s ...200919350395
genetic and biochemical analyses of chlorobenzene degradation gene clusters in pandoraea sp. strain mcb032.pandoraea sp. strain mcb032 was isolated as an emerging chlorobenzene degrader from a functionally stable bioreactor where species succession had occurred. in this study, two gene clusters encoding chlorobenzene metabolic functions have been cloned. within the cbs gene cluster, cbsa and cbsb are similar to the chlorobenzene dioxygenase and the cis-chlorobenzene dihydrodiol dehydrogenase in ralstonia sp. js705 and shown to transform chlorobenzene to 3-chlorocatechol. the clc gene cluster shows st ...200919365620
outbreak of ralstonia pickettii bacteraemia in patients with haematological malignancies and haematopoietic stem cell transplant recipients. 200919376610
ralstonia pickettii-induced ataxia in immunodeficient mice.we report here the characterization of an asymmetric ataxia syndrome (head tilt and circling, with death in the most severe cases) demonstrated by profoundly immunodeficient mice housed at the institut curie spf facility. the immune system of the affected mice had been genetically modified so that they were deficient in both b and t cells. extensive bacteriologic, parasitic, serologic, and histopathologic analysis of the affected animals and their healthy controls led us to identify ralstonia pi ...200919389312
microbial co-habitation and lateral gene transfer: what transposases can tell us.determining the habitat range for various microbes is not a simple, straightforward matter, as habitats interlace, microbes move between habitats, and microbial communities change over time. in this study, we explore an approach using the history of lateral gene transfer recorded in microbial genomes to begin to answer two key questions: where have you been and who have you been with?200919393086
[comparison between agar dilution and three other methods for determining the susceptibility of 228 clinical isolates of non-fermenting gram-negative rods].susceptibility testing for non-fermenting gram-negative rods (nfgnr) is problematic; valid methods are needed for this purpose.200919406523
involvement of two transport systems and a specific porin in the uptake of phthalate by burkholderia spp.burkholderia spp. that degrade phthalate have an abc transporter-type phthalate transport system (ophfgh) and a specific porin (ophp) in addition to a permease-type phthalate transporter (ophd). ophfgh has a lower k(m) and higher v(max) than ophd, which affects how the bacteria grow. ophp is involved in both mechanisms of transport.200919429613
ralstonia pickettii meningitis in a child with hydrocephalus. 200919449287
interactions between hyphosphere-associated bacteria and the fungus cladosporium herbarum on aquatic leaf litter.we investigated microbial interactions of aquatic bacteria associated with hyphae (the hyphosphere) of freshwater fungi on leaf litter. bacteria were isolated directly from the hyphae of fungi from sedimented leaves of a small stream in the national park "lower oder," germany. to investigate interactions, bacteria and fungi were pairwise co-cultivated on leaf-extract medium and in microcosms loaded with leaves. the performance of fungi and bacteria was monitored by measuring growth, enzyme produ ...200919452199
isolation and molecular characterization of a novel d-hydantoinase from jannaschia sp. ccs1.hydantoinases (hyds) are important enzymes for industrial production of optically pure amino acids, which are widely used as precursors for various semi-synthetic antibiotics. by a process coupling genomic data mining with activity screening, a new hydantoinase, tentatively designated hyd(js), was identified from jannaschia sp. ccs1 and overexpressed in escherichia coli. the specific activity of hyd(js) on d,l-p-hydroxyphenylhydantoin as the substrate was three times higher than that of the hyda ...200919490017
metabolic capacity of sinorhizobium (ensifer) meliloti strains as determined by phenotype microarray analysis.sinorhizobium meliloti is a soil bacterium that fixes atmospheric nitrogen in plant roots. the high genetic diversity of its natural populations has been the subject of extensive analysis. recent genomic studies of several isolates revealed a high content of variable genes, suggesting a correspondingly large phenotypic differentiation among strains of s. meliloti. here, using the phenotype microarray (pm) system, hundreds of different growth conditions were tested in order to compare the metabol ...200919561177
glycosylation of fluorophenols by plant cell cultures.fluoroaromatic compounds are used as agrochemicals and released into environment as pollutants. glycosylation of 2-, 3-, and 4-fluorophenols using plant cell cultures of nicotiana tabacum was investigated to elucidate their potential to metabolize these compounds. cultured n. tabacum cells converted 2-fluorophenol into its beta-glucoside (60%) and beta-gentiobioside (10%). 4-fluorophenol was also glycosylated to its beta-glucoside (32%) and beta-gentiobioside (6%) by n. tabacum cells. on the oth ...200919564930
metagenomics reveals diversity and abundance of meta-cleavage pathways in microbial communities from soil highly contaminated with jet fuel under air-sparging bioremediation.the extradiol dioxygenase diversity of a site highly contaminated with aliphatic and aromatic hydrocarbons under air-sparging treatment was assessed by functional screening of a fosmid library in escherichia coli with catechol as substrate. the 235 positive clones from inserts of dna extracted from contaminated soil were equivalent to one extradiol dioxygenase-encoding gene per 3.6 mb of dna screened, indicating a strong selection for genes encoding this function. three subfamilies were identifi ...200919575758
airway infection with a novel cupriavidus species in persons with cystic fibrosis.we describe the recovery and identification of a bacterium that represents a new species of the genus cupriavidus from cultures of respiratory tract specimens from two patients with cystic fibrosis (cf). the elucidation of the role of this species in cf lung disease will require an evaluation of a greater number of cases.200919605576
[acute bacterial prostatitis by ralstonia pickettii: clinical and epidemiological considerations of excepcional observation]. 200919615483
investigation of shell disease in map turtles (graptemys spp.).nineteen map turtles (graptemys spp.) maintained under natural conditions were investigated because of chronic shell abnormalities. animals were evaluated using a novel shell scoring system that divided the 54 scutes into six regions, with each region scored for lesion extent and severity, and summated to produce a total shell disease score (tsds). complete blood counts and various biochemistry analytes (total protein, albumin, globulin, urea, uric acid, 25-hydroxycholecalciferol, phosphorus, an ...200919617474
[a community acquired pneumonia case caused by ralstonia pickettii].ralstonia pickettii, formerly known as burkholderia pickettii, is a non-fermentative gram-negative bacillus. it is emerging as an opportunistic pathogen both in the hospital setting and in the environment, leading to outbreaks especially in the intensive care units. the available literature revealed two case reports of pneumonia associated with r. pickettii in adults. in this report, a case of pneumoniae due to r. pickettii, in a patient with chronic obstructive pulmonary disease was presented. ...200919621622
rapid real-time pcr assays for detection of klebsiella pneumoniae with the rmpa or maga genes associated with the hypermucoviscosity phenotype: screening of nonhuman primates.the relationship of mucoviscosity-associated (maga) and/or regulator of mucoid phenotype (rmpa) genes to the klebsiella pneumoniae hypermucoviscosity (hmv) phenotype has been reported. we previously demonstrated that rmpa+ k. pneumoniae can cause serious disease in african green monkeys and isolated rmpa+ and maga+ hmv k. pneumoniae from other species of non-human primates. to rapidly screen african green monkeys/non-human primates for these infections, we developed three real-time pcr assays. t ...200919644019
diversity, abundance, and consistency of microbial oxygenase expression and biodegradation in a shallow contaminated aquifer.the diversity of rieske dioxygenase genes and short-term temporal variability in the abundance of two selected dioxygenase gene sequences were examined in a naphthalene-rich, coal tar waste-contaminated subsurface study site. using a previously published pcr-based approach (s. m. ní chadhain, r. s. norman, k. v. pesce, j. j. kukor, and g. j. zylstra, appl. environ. microbiol. 72:4078-4087, 2006) a broad suite of genes was detected, ranging from dioxygenase sequences associated with rhodococcus a ...200919700556
characterization of regulatory element rp3 of regulation of beta-lactamases from ralstonia pickettii.the two chromosomally encoded beta-lactamases, oxa-22 and oxa-60, from ralstonia pickettii are inducible by beta-lactam molecules. disruption of rp3 abolished induction of both beta-lactamases and the resistance to ph, osmolarity and survival in the stationary phase, suggesting that rp3 might be a global regulator. interactions between rp3, oxa-22 and oxa-60 were investigated at a transcript and protein level using 5'-rapid amplification of cdna ends experiments, real-time reverse transcription ...200919817868
an immunocompetent patient presenting with severe septic arthritis due to ralstonia pickettii identified by molecular-based assays: a case report.ralstonia pickettii is an infrequent pathogen of invasive infections in healthy individuals. the microorganism is supposed to be of relatively low virulence, but can cause infections, mainly of the respiratory tract, in immunocompromised and cystic fibrosis patients. ralstonia pickettii has also been associated with hospital outbreaks related to contamination of products used for medical care and laboratory diagnosis.200919830053
analysis of two gene clusters involved in the degradation of 4-fluorophenol by arthrobacter sp. strain if1.arthrobacter sp. strain if1 is able to grow on 4-fluorophenol (4-fp) as a sole source of carbon and energy. to clone the 4-fp degradation genes, dna libraries were constructed and screened with a probe obtained by pcr using primers designed on the basis of conserved regions of aromatic two-component monooxygenases. sequencing of positive clones yielded two gene clusters, each harboring a gene encoding a monooxygenase with high sequence similarity to the oxygenase component of 4-nitrophenol and 4 ...200919837837
the pha depolymerase engineering database: a systematic analysis tool for the diverse family of polyhydroxyalkanoate (pha) depolymerases.polyhydroxyalkanoates (phas) can be degraded by many microorganisms using intra- or extracellular pha depolymerases. pha depolymerases are very diverse in sequence and substrate specificity, but share a common alpha/beta-hydrolase fold and a catalytic triad, which is also found in other alpha/beta-hydrolases.200919296857
first investigation of the microbiology of the deepest layer of ocean crust.the gabbroic layer comprises the majority of ocean crust. opportunities to sample this expansive crustal environment are rare because of the technological demands of deep ocean drilling; thus, gabbroic microbial communities have not yet been studied. during the integrated ocean drilling program expeditions 304 and 305, igneous rock samples were collected from 0.45-1391.01 meters below seafloor at hole 1309d, located on the atlantis massif (30 °n, 42 °w). microbial diversity in the rocks was anal ...201021079766
enzymatic functionalization of carbon-hydrogen bonds.the development of new catalytic methods to functionalize carbon-hydrogen (c-h) bonds continues to progress at a rapid pace due to the significant economic and environmental benefits of these transformations over traditional synthetic methods. in nature, enzymes catalyze regio- and stereoselective c-h bond functionalization using transformations ranging from hydroxylation to hydroalkylation under ambient reaction conditions. the efficiency of these enzymes relative to analogous chemical processe ...201021079862
enzymatic functionalization of carbon-hydrogen bonds.the development of new catalytic methods to functionalize carbon-hydrogen (c-h) bonds continues to progress at a rapid pace due to the significant economic and environmental benefits of these transformations over traditional synthetic methods. in nature, enzymes catalyze regio- and stereoselective c-h bond functionalization using transformations ranging from hydroxylation to hydroalkylation under ambient reaction conditions. the efficiency of these enzymes relative to analogous chemical processe ...201021079862
the changing microbial epidemiology in cystic fibrosis.infection of the airways remains the primary cause of morbidity and mortality in persons with cystic fibrosis (cf). this review describes salient features of the epidemiologies of microbial species that are involved in respiratory tract infection in cf. the apparently expanding spectrum of species causing infection in cf and recent changes in the incidences and prevalences of infection due to specific bacterial, fungal, and viral species are described. the challenges inherent in tracking and int ...201020375354
effects of nonionic surfactant addition on populations of polycyclic aromatic hydrocarbon-degrading bacteria in a bioreactor treating contaminated soil.we studied the effects of two polyethoxylated nonionic surfactants, brij 30 and c(12)e(8), on populations of polycyclic aromatic hydrocarbon- (pah-) degrading bacteria from a bioreactor treating pah-contaminated soil. each surfactant was evaluated at doses that corresponded to aqueous-phase concentrations both above and below the critical micelle concentration (cmc) after mixing with reactor slurry. real-time quantitative pcr was used to quantify 16s rrna (rrna) gene sequences representing degra ...201020707373
biosynthesis and biodegradation of 3-hydroxypropionate-containing polyesters.3-hydroxypropionate (3hp) is an important compound in the chemical industry, and the polymerized 3hp can be used as a bioplastic. in this review, we focus on polyesters consisting of 3hp monomers, including the homopolyester poly(3-hydroxypropionate) and copolyesters poly(3-hydroxybutyrate-co-3-hydroxypropionate), poly(3-hydroxypropionate-co-3-hydroxybutyrate-co-3-hydroxyhexanoate-co-3-hydroxyoctanoate), poly(4-hydroxybutyrate-co-3-hydroxypropionate-co-lactate), and poly(3-hydroxybutyrate-co-3-h ...201020543057
general trends in trace element utilization revealed by comparative genomic analyses of co, cu, mo, ni, and se.trace elements are used by all organisms and provide proteins with unique coordination and catalytic and electron transfer properties. although many trace element-containing proteins are well characterized, little is known about the general trends in trace element utilization. we carried out comparative genomic analyses of copper, molybdenum, nickel, cobalt (in the form of vitamin b(12)), and selenium (in the form of selenocysteine) in 747 sequenced organisms at the following levels: (i) transpo ...201019887375
general trends in trace element utilization revealed by comparative genomic analyses of co, cu, mo, ni, and se.trace elements are used by all organisms and provide proteins with unique coordination and catalytic and electron transfer properties. although many trace element-containing proteins are well characterized, little is known about the general trends in trace element utilization. we carried out comparative genomic analyses of copper, molybdenum, nickel, cobalt (in the form of vitamin b(12)), and selenium (in the form of selenocysteine) in 747 sequenced organisms at the following levels: (i) transpo ...201019887375
genomic and biological analysis of phage xfas53 and related prophages of xylella fastidiosa.we report the plaque propagation and genomic analysis of xfas53, a temperate phage of xylella fastidiosa. xfas53 was isolated from supernatants of x. fastidiosa strain 53 and forms plaques on the sequenced strain temecula. xfas53 forms short-tailed virions, morphologically similar to podophage p22. the 36.7-kb genome is predicted to encode 45 proteins. the xfas53 terminase and structural genes are related at a protein and gene order level to p22. the left arm of the xfas53 genome has over 90% nu ...201019897657
genomic and biological analysis of phage xfas53 and related prophages of xylella fastidiosa.we report the plaque propagation and genomic analysis of xfas53, a temperate phage of xylella fastidiosa. xfas53 was isolated from supernatants of x. fastidiosa strain 53 and forms plaques on the sequenced strain temecula. xfas53 forms short-tailed virions, morphologically similar to podophage p22. the 36.7-kb genome is predicted to encode 45 proteins. the xfas53 terminase and structural genes are related at a protein and gene order level to p22. the left arm of the xfas53 genome has over 90% nu ...201019897657
novel insights about class 2 integrons from experimental and genomic epidemiology.in order to contribute to the knowledge of the architecture and epidemiology of class 2 integrons, we performed a class 2 integron molecular survey in which we analyzed 726 isolates in two bacterial populations from environmental and nonepidemiologically related clinical samples, respectively, collected from 1982 to 2007. we recovered the inti2 gene from 130 of 726 isolates, most of which were clinical isolates, and only 1 (a psychrophilic pseudomonas sp.) was from a water sample. unlike the wid ...201019917745
novel insights about class 2 integrons from experimental and genomic epidemiology.in order to contribute to the knowledge of the architecture and epidemiology of class 2 integrons, we performed a class 2 integron molecular survey in which we analyzed 726 isolates in two bacterial populations from environmental and nonepidemiologically related clinical samples, respectively, collected from 1982 to 2007. we recovered the inti2 gene from 130 of 726 isolates, most of which were clinical isolates, and only 1 (a psychrophilic pseudomonas sp.) was from a water sample. unlike the wid ...201019917745
a beta-barrel outer membrane protein facilitates cellular uptake of polychlorophenols in cupriavidus necator.the tcprxabcyd operon of cupriavidus necator jmp134 is involved in the degradation of 2,4,6-trichlorophenol (tcp). all of the gene products except tcpy have assigned functions in tcp metabolism. sequence comparison identified tcpy as a member of cog4313, a group of hypothetical proteins. tcpy has a signal peptide, indicating it is a membrane or secreted protein. secondary structure and topology analysis indicated tcpy as a beta-barrel outer membrane protein, similar to the escherichia coli outer ...201019937267
a beta-barrel outer membrane protein facilitates cellular uptake of polychlorophenols in cupriavidus necator.the tcprxabcyd operon of cupriavidus necator jmp134 is involved in the degradation of 2,4,6-trichlorophenol (tcp). all of the gene products except tcpy have assigned functions in tcp metabolism. sequence comparison identified tcpy as a member of cog4313, a group of hypothetical proteins. tcpy has a signal peptide, indicating it is a membrane or secreted protein. secondary structure and topology analysis indicated tcpy as a beta-barrel outer membrane protein, similar to the escherichia coli outer ...201019937267
use of hydrogenophaga pseudoflava penetration to quantitatively assess the impact of filtration parameters for 0.2-micrometer-pore-size filters.filters rated as having a 0.2-microm pore size (0.2-microm-rated filters) are used in laboratory and manufacturing settings for diverse applications of bacterial and particle removal from process fluids, analytical test articles, and gasses. using hydrogenophaga pseudoflava, a diminutive bacterium with an unusual geometry (i.e., it is very thin), we evaluated passage through 0.2-microm-rated filters and the impact of filtration process parameters and bacterial challenge density. we show that con ...201019966023
use of hydrogenophaga pseudoflava penetration to quantitatively assess the impact of filtration parameters for 0.2-micrometer-pore-size filters.filters rated as having a 0.2-microm pore size (0.2-microm-rated filters) are used in laboratory and manufacturing settings for diverse applications of bacterial and particle removal from process fluids, analytical test articles, and gasses. using hydrogenophaga pseudoflava, a diminutive bacterium with an unusual geometry (i.e., it is very thin), we evaluated passage through 0.2-microm-rated filters and the impact of filtration process parameters and bacterial challenge density. we show that con ...201019966023
degradation and adsorption characteristics of phb depolymerase as revealed by kinetics of mutant enzymes with amino acid substitution in substrate-binding domain.extracelluar poly[(r)-3-hydroxybutyrate] (phb) depolymerase (phaz(rpit1)) from ralstonia pickettii t1 adsorbs to phb surface via its substrate-binding domain (sbd) to enhance phb degradation. our previous study combining pcr random mutagenesis with the determination of phb degradation levels of mutant enzymes suggested that ser, tyr, val, ala, and leu residues in sbd are probably involved in the enzymatic adsorption to and degradation of phb. in the present study, the effects of mutations at leu ...201020058938
an automated system for rapid non-destructive enumeration of growing microbes.the power and simplicity of visual colony counting have made it the mainstay of microbiological analysis for more than 130 years. a disadvantage of the method is the long time required to generate visible colonies from cells in a sample. new rapid testing technologies generally have failed to maintain one or more of the major advantages of culture-based methods.201020062794
fatal infection caused by cupriavidus gilardii in a child with aplastic anemia.cupriavidus gilardii is a gram-negative bacterium that has rarely been associated with human infections. we report a fatal case of sepsis caused by c. gilardii in a previously healthy 12-year-old female.201020071544
characterization of a cryptic plasmid pd403 from lactobacillus plantarum and construction of shuttle vectors based on its replicon.a cryptic plasmid pd403 was isolated from lactobacillus plantarum d403 derived from fermented dairy products. it was 2,791 bp in size with a g+c content of 37%. nucleotide sequence analysis revealed two open reading frames, orf1 and orf2. orf1 (318 amino acids) was identified as a replication protein (repa). orf2 (137 amino acids) shared 31% similarity with the transcriptional regulator of ralstonia pickettii 12d. functional investigation indicated that orf2 (tra) had the ability of improving th ...201020077035
efficient biocatalytic production of d-4-hydroxyphenylglycine by whole cells of recombinant ralstonia pickettii.the first establishment of a homologous expression system in the host ralstonia pickettii cgmcc1596 using the compatible broad-host-range plasmid pwb5 is described. when whole cells of the recombinant strain r. pickettii mmyy01 (cgmcc1596/pyy05) were used as the biocatalyst to transform dl-4-hydroxyphenylhydantoin (dl-hph) to d-4-hydroxyphenylglycine (d-hpg), the conversion rate reached 94 % in first 9 h, at a production rate of 2.8 g l(-1) h(-1), with the rapid reduction of the intermediate [n- ...201020140718
effects of bovine milk lactoperoxidase system on some bacteria.bovine lactoperoxidase (lpo) was purified from skimmed milk using amberlite cg-50-h+ resin, cm sephadex c-50 ion-exchange chromatography, and sephadex g-100 gel filtration chromatography. lactoperoxidase was purified 20.45-fold with a yield of 28.8%. purity of enzyme checked by sodium dodecyl sulphate-polyacrylamide gel electrophoresis method and a single band was observed. km was 0.25 mm at 20 degrees c, vmax value was 7.95 micromol/ml min at 20 degrees c (ph 6.0). antibacterial study was done ...201020198919
rapid differentiation of francisella species and subspecies by fluorescent in situ hybridization targeting the 23s rrna.francisella (f.) tularensis is the causative agent of tularemia. due to its low infectious dose, ease of dissemination and high case fatality rate, f. tularensis was the subject in diverse biological weapons programs and is among the top six agents with high potential if misused in bioterrorism. microbiological diagnosis is cumbersome and time-consuming. methods for the direct detection of the pathogen (immunofluorescence, pcr) have been developed but are restricted to reference laboratories.201020205957
the complete multipartite genome sequence of cupriavidus necator jmp134, a versatile pollutant degrader.cupriavidus necator jmp134 is a gram-negative beta-proteobacterium able to grow on a variety of aromatic and chloroaromatic compounds as its sole carbon and energy source.201020339589
identification of diverse antimicrobial resistance determinants carried on bacterial, plasmid, or viral metagenomes from an activated sludge microbial assemblage.using both sequence- and function-based metagenomic approaches, multiple antibiotic resistance determinants were identified within metagenomic libraries constructed from dna extracted from bacterial chromosomes, plasmids, or viruses within an activated sludge microbial assemblage. metagenomic clones and a plasmid that in escherichia coli expressed resistance to chloramphenicol, ampicillin, or kanamycin were isolated, with many cloned dna sequences lacking any significant homology to known antibi ...201020382816
comonomer compositional distribution, physical properties, and enzymatic degradability of bacterial poly(3-hydroxybutyrate-co-3-hydroxy-4-methylvalerate) copolyesters.poly(3-hydroxybutyrate-co-3-hydroxy-4-methylvalerate) (p(3hb-co-3h4mv)) was synthesized by using ralstonia eutropha strain phb(-)4 (pha-negative mutant) harboring with the n149s/d171g double mutation of pha synthase gene from aeromonas caviae (phac(ac) nsdg mutant) with 4-methylvaleric acid and fructose as the carbon sources. because the microbially synthesized p(3hb-co-3h4mv) samples were found to have broad comonomer compositional distribution, p(3hb-co-3h4mv) samples with 3h4mv content of 7, ...201020441146
pseudo-outbreak of cupriavidus pauculus infection at an outpatient clinic related to rinsing culturette swabs in tap water.cupriavidus pauculus is a water microorganism rarely isolated from clinical specimens. we describe a pseudo-outbreak in which multiple strains that were associated with moistening of culturette swabs with tap water were isolated from a single clinic before collecting the patient specimen.201020444965
the complete genome sequence of cupriavidus metallidurans strain ch34, a master survivalist in harsh and anthropogenic environments.many bacteria in the environment have adapted to the presence of toxic heavy metals. over the last 30 years, this heavy metal tolerance was the subject of extensive research. the bacterium cupriavidus metallidurans strain ch34, originally isolated by us in 1976 from a metal processing factory, is considered a major model organism in this field because it withstands milli-molar range concentrations of over 20 different heavy metal ions. this tolerance is mostly achieved by rapid ion efflux but al ...201020463976
potential of aerobic denitrification by pseudomonas stutzeri tr2 to reduce nitrous oxide emissions from wastewater treatment plants.in contrast to most denitrifiers studied so far, pseudomonas stutzeri tr2 produces low levels of nitrous oxide (n(2)o) even under aerobic conditions. we compared the denitrification activity of strain tr2 with those of various denitrifiers in an artificial medium that was derived from piggery wastewater. strain tr2 exhibited strong denitrification activity and produced little n(2)o under all conditions tested. its growth rate under denitrifying conditions was near comparable to that under aerobi ...201020495048
incidence, relevance and response for ralsfonia respiratory infections.cases of ralstonia colonization/infection occasionally reported by hospitals has generated increased interest in an organism previously little known to most clinicians. our goal was to determine the incidence of respiratory colonizations and infections involving ralstonia and the association of mechanical ventilation (limited to reports on respiratory-related occurrences in the u.s.a.) and propose a decision chart to assist response.201020499534
nitroaromatic compounds, from synthesis to biodegradation.nitroaromatic compounds are relatively rare in nature and have been introduced into the environment mainly by human activities. this important class of industrial chemicals is widely used in the synthesis of many diverse products, including dyes, polymers, pesticides, and explosives. unfortunately, their extensive use has led to environmental contamination of soil and groundwater. the nitro group, which provides chemical and functional diversity in these molecules, also contributes to the recalc ...201020508249
Refresh
firstprev
12345678
nextlast
Displaying items 401 - 500 of 787