| ppsx: a novel vector for the cloning and heterologous expression of antitumor antibiotic gene clusters. | a cosmid cloning vector has been constructed that demonstrates high levels of segregational stability in escherichia coli k12. ppsx is a 14-kilobase vector derived from the incw plasmid pr388. ppsx is highly stable in e. coli in the absence of antibiotic selection, even while expressing the toxic indolocarbazole antitumor antibiotic violacein. the incorporation of the lambdacos sequence enables construction of cosmid libraries with inserts ranging from 24 to 36kb. the inclusion of a laczalpha mu ... | 2007 | 17218012 |
| isolation and gene quantification of heterotrophic n2-fixing bacterioplankton in the baltic sea. | cyanobacteria are regarded as the main n(2)-fixing organisms in marine waters. however, recent clone libraries from various oceans show a wide distribution of the dinitrogenase reductase gene (nifh) originating from heterotrophic bacterioplankton. we isolated heterotrophic n(2)-fixing bacteria from baltic sea bacterioplankton using low-nitrogen plates and semi-solid diazotroph medium (ssdm) tubes. isolates were analysed for the nitrogenase (nifh) gene and active n(2) fixation by nested polymeras ... | 2007 | 17227420 |
| desaturase reactions complicate the use of norcarane as a mechanistic probe. unraveling the mixture of twenty-plus products formed in enzyme-catalyzed oxidations of norcarane. | norcarane, bicyclo[4.1.0]heptane, has been widely used as a mechanistic probe in studies of oxidations catalyzed by several iron-containing enzymes. we report here that, in addition to oxygenated products, norcarane is also oxidized by iron-containing enzymes in desaturase reactions that give 2-norcarene and 3-norcarene. furthermore, secondary products from further oxidation reactions of the norcarenes are produced in yields that are comparable to those of the minor products from oxidation of th ... | 2007 | 17288366 |
| products from enzyme-catalyzed oxidations of norcarenes. | recent studies revealed that norcarane (bicyclo[4.1.0]heptane) is oxidized to 2-norcarene (bicyclo[4.1.0]-hept-2-ene) and 3-norcarene (bicyclo[4.1.0]hept-3-ene) by iron-containing enzymes and that secondary oxidation products from the norcarenes complicate mechanistic probe studies employing norcarane as the substrate (newcomb, m.; chandrasena, r. e. p.; lansakara-p., d. s. p.; kim, h.-y.; lippard, s. j.; beauvais, l. g.; murray, l. j.; izzo, v.; hollenberg, p. f.; coon, m. j. j. org. chem. 2007 ... | 2007 | 17288367 |
| high nitrogen removal from wastewater with several new aerobic bacteria isolated from diverse ecosystems. | three new bacteria hs-03, hs-043 and hs-047 isolated from different ecosystems were found capable of aerobic denitrification. the potential application of these strains in wastewater treatment under aerobic conditions was investigated. these three bacteria all presented high nitrogen removal from wastewater that more than 98% of 10 mmol/l nitrate could be removed in 12-24 h by adding cheap external carbon source and low concentration of iron as well as molybdate. the mechanism at molecular level ... | 2006 | 17294651 |
| construction of pha-operon-defined knockout mutants of pseudomonas putida kt2442 and their applications in poly(hydroxyalkanoate) production. | pseudomonas putida kt2442 could accumulate medium-chain-length poly(hydroxyalkanoate)s (pha) consisting of 3-hydroxyhexanoate, 3-hydroxyoctanoate, 3-hydroxydecanoate, and 3-hydroxydodecanoate from a wide range of carbon sources. in this study, the pha synthase pha operon (phac1-phaz-phac2) was knocked out and the vgb gene encoding vitreoscilla hemoglobin protein (vhb), which could enhance oxygen uptake rate especially at low oxygen concentration, was integrated into the p. putida kt2442 genome t ... | 2007 | 17295412 |
| isolation and characterization of bacteria capable of tolerating the extreme conditions of clean room environments. | in assessing the bacterial populations present in spacecraft assembly, spacecraft test, and launch preparation facilities, extremophilic bacteria (requiring severe conditions for growth) and extremotolerant bacteria (tolerant to extreme conditions) were isolated. several cultivation approaches were employed to select for and identify bacteria that not only survive the nutrient-limiting conditions of clean room environments but can also withstand even more inhospitable environmental stresses. due ... | 2007 | 17308177 |
| kinetics of decolourisation and biotransformation of direct black 38 by c. hominis and p. stutzeri. | in the present study, a consortium of cardiobacterium hominis and pseudomonas stutzeri was isolated from an effluent treatment plant of a textile industry, based on its ability to decolourise azo dyes including direct black 38 (db38), a benzidine-based azo dye. the role of each culture in the decolourisation process was elucidated, and c. hominis was found to decolourise the dye. although p. stutzeri could not decolourise the dye, it was found to synergistically enhance dye decolourisation activ ... | 2007 | 17318544 |
| role of soil rhizobacteria in phytoremediation of heavy metal contaminated soils. | heavy metal pollution of soil is a significant environmental problem and has its negative impact on human health and agriculture. rhizosphere, as an important interface of soil and plant, plays a significant role in phytoremediation of contaminated soil by heavy metals, in which, microbial populations are known to affect heavy metal mobility and availability to the plant through release of chelating agents, acidification, phosphate solubilization and redox changes, and therefore, have potential ... | 2007 | 17323432 |
| the anaerobic regulatory network required for pseudomonas aeruginosa nitrate respiration. | in pseudomonas aeruginosa, the nark(1)k(2)ghji operon encodes two nitrate/nitrite transporters and the dissimilatory nitrate reductase. the nark(1) promoter is anaerobically induced in the presence of nitrate by the dual activity of the oxygen regulator anr and the n-oxide regulator dnr in cooperation with the nitrate-responsive two-component regulatory system narxl. the dna bending protein ihf is essential for this process. similarly, narxl gene transcription is enhanced under anaerobic conditi ... | 2007 | 17400734 |
| culture-independent analysis of bacterial diversity in a child-care facility. | child-care facilities appear to provide daily opportunities for exposure and transmission of bacteria and viruses. however, almost nothing is known about the diversity of microbial contamination in daycare facilities or its public health implications. recent culture-independent molecular studies of bacterial diversity in indoor environments have revealed an astonishing diversity of microorganisms, including opportunistic pathogens and many uncultured bacteria. in this study, we used culture and ... | 2007 | 17411442 |
| microbial diversity in natural asphalts of the rancho la brea tar pits. | bacteria commonly inhabit subsurface oil reservoirs, but almost nothing is known yet about microorganisms that live in naturally occurring terrestrial oil seeps and natural asphalts that are comprised of highly recalcitrant petroleum hydrocarbons. here we report the first survey of microbial diversity in ca. 28,000-year-old samples of natural asphalts from the rancho la brea tar pits in los angeles, ca. microbiological studies included analyses of 16s rrna gene sequences and dna encoding aromati ... | 2007 | 17416692 |
| identification of anaerobic selenate-respiring bacteria from aquatic sediments. | the diversity population of microorganisms with the capability to use selenate as a terminal electron acceptor, reducing it to selenite and elemental selenium by the process known as dissimilatory selenate reduction, is largely unknown. the overall objective of this study was to gain an in-depth understanding of anaerobic biotransformation of selenium in the environment, particularly anaerobic respiration, and to characterize the microorganisms catalyzing this process. here, we demonstrate the i ... | 2007 | 17435005 |
| nitric oxide reductase-targeted real-time pcr quantification of denitrifier populations in soil. | the quantification of denitrifying bacteria is a component in the further understanding of denitrification processes in the environment. real-time pcr primers were designed to target two segments of the denitrifier population (cnorb(p) [pseudomonas mandelii and closely related strains] and cnorb(b) [bosea, bradyrhizobium, and ensifer spp.]) in agricultural soils based on functional cnorb (nitric oxide reductase) gene sequences. total population numbers were measured using 16s rrna gene real-time ... | 2007 | 17449686 |
| the outer membrane secretin pilq from neisseria meningitidis binds dna. | neisseria meningitidis is naturally competent for transformation throughout its growth cycle. transformation in neisserial species is coupled to the expression of type iv pili, which are present on the cell surface as bundled filamentous appendages, and are assembled, extruded and retracted by the pilus biogenesis components. during the initial phase of the transformation process, binding and uptake of dna takes place with entry through a presumed outer-membrane channel into the periplasm. this ... | 2007 | 17464074 |
| nitrate respiration in pseudomonas stutzeri a15 and its involvement in rice and wheat root colonization. | unlike most bacteria, the nitrogen-fixing rice-associated pseudomonas stutzeri a15 disposes of three different nitrate reductases that enable conversion of nitrate to nitrite through three physiologically distinct processes, called nitrate assimilation, nitrate respiration and nitrate dissimilation. to study the role of nitrate respiration in rhizosphere fitness, a pseudomonas stutzeri narg mutant was constructed and characterized by assessing its growth characteristics and whole-cell nitrate re ... | 2009 | 17467964 |
| identification of siderophores of pseudomonas stutzeri. | we have identified two types of siderophores produced by pseudomonas, one of which has never before been found in the genus. twelve strains of pseudomonas stutzeri belonging to genomovars 1, 2, 3, 4, 5, and 9 produced proferrioxamines, the hydroxamate-type siderophores. pseudomonas stutzeri jm 300 (genomovar 7) and dsm 50238 (genomovar 8) and pseudomonas balearica dsm 6082 produced amonabactins, catecholate-type siderophores. the major proferrioxamines detected were the cyclic proferrioxamines e ... | 2006 | 17473886 |
| solution conformation of the his-47 to ala-47 mutant of pseudomonas stutzeri zobell ferrocytochrome c-551. | in the cytochrome c-551 family, the heme 17-propionate caboxylate group is always hydrogen bonded to an invariant trp-56 and conserved residues (his and arg mainly, lys occasionally) at position 47. the mutation of his-47 to ala-47 for pseudomas stutzeri zobell cytochrome c-551 removes this otherwise invariant hydrogen bond. the solution structure of ferrous h47a has been solved based on nmr-derived constraints. results indicate that the mutant has very similar main chain folding compared to wil ... | 2007 | 17496029 |
| 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 |
| type iv fimbrial biogenesis is required for protease secretion and natural transformation in dichelobacter nodosus. | the objective of this study was to develop an understanding of the molecular mechanisms by which type iv fimbrial biogenesis, natural transformation, and protease secretion are linked in the ovine foot rot pathogen, dichelobacter nodosus. we have shown that like the d. nodosus fimbrial subunit fima, the pilin-like protein pile and the fimn, fimo, and fimp proteins, which are homologs of pilb, pilc, and pild from pseudomonas aeruginosa, are essential for fimbrial biogenesis and natural transforma ... | 2007 | 17513472 |
| metabolomic and genetic analysis of biomarkers for peroxisome proliferator-activated receptor alpha expression and activation. | peroxisome proliferator-activated receptor alpha (pparalpha) is a nuclear receptor with manifold effects on intermediary metabolism. to define a set of urinary biomarkers that could be used to determine the efficacy of pparalpha agonists, a metabolomic investigation was undertaken in wild-type and pparalpha-null mice fed for 2 wk either a regular diet or a diet containing the pparalpha ligand wy-14,643 ([4-chloro-6-(2,3-xylidino)-2-pyrimidinylthio] acetic acid), and their urine was analyzed by u ... | 2007 | 17550978 |
| pseudomonas aeruginosa type iv pilus expression in neisseria gonorrhoeae: effects of pilin subunit composition on function and organelle dynamics. | type iv pili (tfp) play central roles in the expression of many phenotypes including motility, multicellular behavior, sensitivity to bacteriophages, natural genetic transformation, and adherence. in neisseria gonorrhoeae, these properties require ancillary proteins that act in conjunction with tfp expression and influence organelle dynamics. here, the intrinsic contributions of the pilin protein itself to tfp dynamics and associated phenotypes were examined by expressing the pseudomonas aerugin ... | 2007 | 17573479 |
| molecular characterization of a novel ortho-nitrophenol catabolic gene cluster in alcaligenes sp. strain nyz215. | alcaligenes sp. strain nyz215 was isolated for its ability to grow on ortho-nitrophenol (onp) as the sole source of carbon, nitrogen, and energy and was shown to degrade onp via a catechol ortho-cleavage pathway. a 10,152-bp dna fragment extending from a conserved region of the catechol 1,2-dioxygenase gene was obtained by genome walking. of seven complete open reading frames deduced from this fragment, three (onpabc) have been shown to encode the enzymes involved in the initial reactions of onp ... | 2007 | 17616586 |
| activation of the cytochrome cd1 nitrite reductase from paracoccus pantotrophus. reaction of oxidized enzyme with substrate drives a ligand switch at heme c. | cytochromes cd(1) are dimeric bacterial nitrite reductases, which contain two hemes per monomer. on reduction of both hemes, the distal ligand of heme d(1) dissociates, creating a vacant coordination site accessible to substrate. heme c, which transfers electrons from donor proteins into the active site, has histidine/methionine ligands except in the oxidized enzyme from paracoccus pantotrophus where both ligands are histidine. during reduction of this enzyme, tyr(25) dissociates from the distal ... | 2007 | 17623666 |
| quantification of 2,4-diacetylphloroglucinol-producing pseudomonas fluorescens strains in the plant rhizosphere by real-time pcr. | a real-time pcr sybr green assay was developed to quantify populations of 2,4-diacetylphloroglucinol (2,4-dapg)-producing (phld+) strains of pseudomonas fluorescens in soil and the rhizosphere. primers were designed and pcr conditions were optimized to specifically amplify the phld gene from four different genotypes of phld+ p. fluorescens. using purified genomic dna and genomic dna extracted from washes of wheat roots spiked with bacteria, standard curves relating the threshold cycles (c(t)s) a ... | 2007 | 17630311 |
| dissimilatory iodate reduction by marine pseudomonas sp. strain sct. | bacterial iodate (io(3)(-)) reduction is poorly understood largely due to the limited number of available isolates as well as the paucity of information about key enzymes involved in the reaction. in this study, an iodate-reducing bacterium, designated strain sct, was newly isolated from marine sediment slurry. sct is phylogenetically closely related to the denitrifying bacterium pseudomonas stutzeri and reduced 200 microm iodate to iodide (i(-)) within 12 h in an anaerobic culture containing 10 ... | 2007 | 17644635 |
| cloning, sequencing, overexpression and characterization of l-rhamnose isomerase from bacillus pallidus y25 for rare sugar production. | the l-rhamnose isomerase gene (l-rhi) encoding for l-rhamnose isomerase (l-rhi) from bacillus pallidus y25, a facultative thermophilic bacterium, was cloned and overexpressed in escherichia coli with a cooperation of the 6xhis sequence at a c-terminal of the protein. the open reading frame of l-rhi consisted of 1,236 nucleotides encoding 412 amino acid residues with a calculated molecular mass of 47,636 da, showing a good agreement with the native enzyme. mass-produced l-rhi was achieved in a la ... | 2007 | 17653540 |
| characterization of the osmoprotectant transporter opuc from pseudomonas syringae and demonstration that cystathionine-beta-synthase domains are required for its osmoregulatory function. | the plant pathogen pseudomonas syringae may cope with osmotic stress on plants, in part, by importing osmoprotective compounds. in this study, we found that p. syringae pv. tomato strain dc3000 was distinct from most bacterial species in deriving greater osmoprotection from exogenous choline than from glycine betaine. this superior osmoprotection was correlated with a higher capacity for uptake of choline than for uptake of glycine betaine. of four putative osmoregulatory abc transporters in dc3 ... | 2007 | 17660277 |
| siderophore production by pseudomonas stutzeri under aerobic and anaerobic conditions. | the siderophore production of the facultative anaerobe pseudomonas stutzeri, strain ccug 36651, grown under both aerobic and anaerobic conditions, was investigated by liquid chromatography and mass spectrometry. the bacterial strain has been isolated at a 626-m depth at the aspö hard rock laboratory, where experiments concerning the geological disposal of nuclear waste are performed. in bacterial culture extracts, the iron in the siderophore complexes was replaced by gallium to facilitate sidero ... | 2007 | 17675442 |
| identification of discriminative characteristics for clusters from biologic data with inforbio software. | there are a number of different methods for generation of trees and algorithms for phylogenetic analysis in the study of bacterial taxonomy. genotypic information, such as ssu rrna gene sequences, now plays a more prominent role in microbial systematics than does phenotypic information. however, the integration of genotypic and phenotypic information for polyphasic studies is necessary for the classification and identification of microbes. thus, we devised an algorithm that objectively identifie ... | 2007 | 17683520 |
| pseudomonas stutzeri: a rare cause of neonatal septicaemia. | | 2007 | 17687848 |
| identification of the functional periplasmic nitrate reductase (nap) gene cluster from the deep-sea denitrifier pseudomonas sp. strain mt-1. | the nap gene cluster encoding periplasmic nitrate reductase was identified from pseudomonas sp. strain mt-1, a deep-sea denitrifier isolated from the mariana trench. the orfs identified were highly homologous with those of pseudomonas stutzeri, but the cluster included only four orfs (napdabc), less than those in other organisms. for other bacteria, some additional small orfs (such as nape, napf, napg, naph, and napk) are found in the nap gene cluster, although their physiological function is st ... | 2007 | 17690469 |
| cj0011c, a periplasmic single- and double-stranded dna-binding protein, contributes to natural transformation in campylobacter jejuni. | campylobacter jejuni is an important bacterial pathogen causing gastroenteritis in humans. c. jejuni is capable of natural transformation, which is considered a major mechanism mediating horizontal gene transfer and generating genetic diversity. despite recent efforts to elucidate the transformation mechanisms of c. jejuni, the process of dna binding and uptake in this organism is still not well understood. in this study, we report a previously unrecognized dna-binding protein (cj0011c) in c. je ... | 2007 | 17693521 |
| probing the environment of cu(b) in heme-copper oxidases. | time-resolved step-scan ftir (trs2-ftir) and density functional theory have been applied to probe the structural dynamics of cub in heme-copper oxidases at room temperature. the trs2-ftir data of cbb3 from pseudomonas stutzeri indicate a small variation in the frequency of the transient co bound to cub in the ph/pd 7-9 range. this observation in conjunction with density functional theory calculations, in which significant frequency shifts of the nu(co) are observed upon deprotonation and/or deta ... | 2007 | 17696387 |
| siderophore-based iron acquisition and pathogen control. | high-affinity iron acquisition is mediated by siderophore-dependent pathways in the majority of pathogenic and nonpathogenic bacteria and fungi. considerable progress has been made in characterizing and understanding mechanisms of siderophore synthesis, secretion, iron scavenging, and siderophore-delivered iron uptake and its release. the regulation of siderophore pathways reveals multilayer networks at the transcriptional and posttranscriptional levels. due to the key role of many siderophores ... | 2007 | 17804665 |
| membrane-bound l- and d-lactate dehydrogenase activities of a newly isolated pseudomonas stutzeri strain. | pseudomonas stutzeri sdm was newly isolated from soil, and two stereospecific nad-independent lactate dehydrogenase (ildh) activities were detected in membrane of the cells cultured in a medium containing dl-lactate as the sole carbon source. neither enzyme activities was constitutive, but both of them might be induced by either enantiomer of lactate. p. stutzeri sdm preferred to utilize lactate to growth, when both l-lactate and glucose were available, and the consumption of glucose was observe ... | 2007 | 17805529 |
| purification and characterization of a three-component salicylate 1-hydroxylase from sphingomonas sp. strain chy-1. | in the bacterial degradation of polycyclic aromatic hydrocarbons (pahs), salicylate hydroxylases catalyze essential reactions at the junction between the so-called upper and lower catabolic pathways. unlike the salicylate 1-hydroxylase from pseudomonads, which is a well-characterized flavoprotein, the enzyme found in sphingomonads appears to be a three-component fe-s protein complex, which so far has not been characterized. here, the salicylate 1-hydroxylase from sphingomonas sp. strain chy-1 wa ... | 2007 | 17905882 |
| insight into the haem d1 biosynthesis pathway in heliobacteria through bioinformatics analysis. | haem d(1) is a unique tetrapyrrole molecule that serves as a prosthetic group of cytochrome cd(1), which reduces nitrite to nitric oxide during the process of denitrification. very little information is available regarding the biosynthesis of haem d(1). the extreme difficulty in studying the haem d(1) biosynthetic pathway can be partly attributed to the lack of a theoretical basis for experimental investigation. we report here a gene cluster encoding enzymes involved in the biosynthesis of haem ... | 2007 | 17906152 |
| pseudomonas stutzeri knee arthritis in a child: case report and review. | we report a child with pseudomonas stutzeri-associated right knee arthritis following knife puncture wound. only four children with p. stutzeri-associated infections have been reported in the english literature in the last 40 years of whom one suffered from calcaneal osteomyelitis caused by this pathogen. in both cases, the suggested mechanism of the infection was local rather than bacterium invasion. | 2007 | 17909340 |
| isolation and characterization of a benzoylformate decarboxylase and a nad+/nadp+-dependent benzaldehyde dehydrogenase involved in d-phenylglycine metabolism in pseudomonas stutzeri st-201. | following induction with d-phenylglycine both d-phenylglycine aminotransferase activity and benzoylformate decarboxylase activity were observed in cultures of pseudomonas stutzeri st-201. induction with benzoylformate, on the other hand, induced only benzoylformate decarboxylase activity. purification of the benzoylformate decarboxylase, followed by n-terminal sequencing, enabled the design of probes for hybridization with p. stutzeri st-201 genomic dna libraries. sequencing of two overlapping g ... | 2007 | 17916405 |
| molecular epidemiology and mechanisms of carbapenem resistance in pseudomonas aeruginosa isolates from spanish hospitals. | all (236) pseudomonas aeruginosa isolates resistant to imipenem and/or meropenem collected during a multicenter (127-hospital) study in spain were analyzed. carbapenem-resistant isolates were found to be more frequently resistant to all beta-lactams and non-beta-lactam antibiotics than carbapenem-susceptible isolates (p < 0.001), and up to 46% of the carbapenem-resistant isolates met the criteria used to define multidrug resistance (mdr). pulsed-field gel electrophoresis revealed remarkable clon ... | 2007 | 17938181 |
| cystic fibrosis patient with burkholderia pseudomallei infection acquired in brazil. | burkholderia pseudomallei is rarely isolated from cystic fibrosis patients outside known areas of endemicity. we report the recovery of b. pseudomallei from the sputum of a cystic fibrosis patient who lives in brazil. we highlight the importance of careful attention to unusual nonfermentative gram-negative rods in cystic fibrosis patients. | 2007 | 17942657 |
| a new method to extract dental pulp dna: application to universal detection of bacteria. | dental pulp is used for pcr-based detection of dna derived from host and bacteremic microorganims. current protocols require odontology expertise for proper recovery of the dental pulp. dental pulp specimen exposed to laboratory environment yields contaminants detected using universal 16s rdna-based detection of bacteria. | 2007 | 17957246 |
| soluble expression and purification of the oxidoreductase component of toluene 4-monooxygenase. | toluene 4-monooxygenase (t4mo) is a member of the bacterial multicomponent monooxygenases, an enzyme family that utilizes a soluble diiron hydroxylase to oxidize a variety of hydrocarbons as the initial step in their metabolism. the hydroxylases obtain reducing equivalents from nad(p)h via an electron transfer chain that is initiated by an oxidoreductase containing an n-terminal ferredoxin domain and c-terminal flavin- and nad-binding domains. t4mof, the nadh oxidoreductase of t4mo, was expresse ... | 2008 | 17964805 |
| soluble expression and purification of the oxidoreductase component of toluene 4-monooxygenase. | toluene 4-monooxygenase (t4mo) is a member of the bacterial multicomponent monooxygenases, an enzyme family that utilizes a soluble diiron hydroxylase to oxidize a variety of hydrocarbons as the initial step in their metabolism. the hydroxylases obtain reducing equivalents from nad(p)h via an electron transfer chain that is initiated by an oxidoreductase containing an n-terminal ferredoxin domain and c-terminal flavin- and nad-binding domains. t4mof, the nadh oxidoreductase of t4mo, was expresse ... | 2008 | 17964805 |
| [phenotyping of bacteria isolated in blood cultures from critical patients]. | bloodstream infections are a serious complication among critical patients. the detection of microbial pathogens in blood cultures is an important diagnostic tool. this study aimed to isolate and characterize bacteria from the blood of patients admitted to the clinical intensive care unit of a teaching hospital, between april 2003 and april 2004. the bacteria isolated were identified by biochemical/enzymatic tests and detection of the antimicrobial susceptibility profile using the disk diffusion ... | 2007 | 17992409 |
| role of hypermutability in the evolution of the genus oenococcus. | oenococcus oeni is an alcohol-tolerant, acidophilic lactic acid bacterium primarily responsible for malolactic fermentation in wine. a recent comparative genomic analysis of o. oeni psu-1 with other sequenced lactic acid bacteria indicates that psu-1 lacks the mismatch repair (mmr) genes muts and mutl. consistent with the lack of mmr, mutation rates for o. oeni psu-1 and a second oenococcal species, o. kitaharae, were higher than those observed for neighboring taxa, pediococcus pentosaceus and l ... | 2008 | 17993526 |
| role of hypermutability in the evolution of the genus oenococcus. | oenococcus oeni is an alcohol-tolerant, acidophilic lactic acid bacterium primarily responsible for malolactic fermentation in wine. a recent comparative genomic analysis of o. oeni psu-1 with other sequenced lactic acid bacteria indicates that psu-1 lacks the mismatch repair (mmr) genes muts and mutl. consistent with the lack of mmr, mutation rates for o. oeni psu-1 and a second oenococcal species, o. kitaharae, were higher than those observed for neighboring taxa, pediococcus pentosaceus and l ... | 2008 | 17993526 |
| secretion of flavins by shewanella species and their role in extracellular electron transfer. | fe(iii)-respiring bacteria such as shewanella species play an important role in the global cycle of iron, manganese, and trace metals and are useful for many biotechnological applications, including microbial fuel cells and the bioremediation of waters and sediments contaminated with organics, metals, and radionuclides. several alternative electron transfer pathways have been postulated for the reduction of insoluble extracellular subsurface minerals, such as fe(iii) oxides, by shewanella specie ... | 2008 | 18065612 |
| secretion of flavins by shewanella species and their role in extracellular electron transfer. | fe(iii)-respiring bacteria such as shewanella species play an important role in the global cycle of iron, manganese, and trace metals and are useful for many biotechnological applications, including microbial fuel cells and the bioremediation of waters and sediments contaminated with organics, metals, and radionuclides. several alternative electron transfer pathways have been postulated for the reduction of insoluble extracellular subsurface minerals, such as fe(iii) oxides, by shewanella specie ... | 2008 | 18065612 |
| structure and function of pa4872 from pseudomonas aeruginosa, a novel class of oxaloacetate decarboxylase from the pep mutase/isocitrate lyase superfamily. | pseudomonas aeruginosa pa4872 was identified by sequence analysis as a structurally and functionally novel member of the pep mutase/isocitrate lyase superfamily and therefore targeted for investigation. substrate screens ruled out overlap with known catalytic functions of superfamily members. the crystal structure of pa4872 in complex with oxalate (a stable analogue of the shared family alpha-oxyanion carboxylate intermediate/transition state) and mg2+ was determined at 1.9 a resolution. as with ... | 2008 | 18081320 |
| structure and function of pa4872 from pseudomonas aeruginosa, a novel class of oxaloacetate decarboxylase from the pep mutase/isocitrate lyase superfamily. | pseudomonas aeruginosa pa4872 was identified by sequence analysis as a structurally and functionally novel member of the pep mutase/isocitrate lyase superfamily and therefore targeted for investigation. substrate screens ruled out overlap with known catalytic functions of superfamily members. the crystal structure of pa4872 in complex with oxalate (a stable analogue of the shared family alpha-oxyanion carboxylate intermediate/transition state) and mg2+ was determined at 1.9 a resolution. as with ... | 2008 | 18081320 |
| differential regulation of high-affinity phosphate transport systems of mycobacterium smegmatis: identification of phnf, a repressor of the phndce operon. | the uptake of phosphate into the cell via high-affinity, phosphate-specific transport systems has been studied with several species of mycobacteria. all of these species have been shown to contain several copies of such transport systems, which are synthesized in response to phosphate limitation. however, the mechanisms leading to the expression of the genes encoding these transporters have not been studied. this study reports on the investigation of the regulation of the pstscab and the phndce ... | 2008 | 18083811 |
| differential regulation of high-affinity phosphate transport systems of mycobacterium smegmatis: identification of phnf, a repressor of the phndce operon. | the uptake of phosphate into the cell via high-affinity, phosphate-specific transport systems has been studied with several species of mycobacteria. all of these species have been shown to contain several copies of such transport systems, which are synthesized in response to phosphate limitation. however, the mechanisms leading to the expression of the genes encoding these transporters have not been studied. this study reports on the investigation of the regulation of the pstscab and the phndce ... | 2008 | 18083811 |
| the isolation, purification and biological activity of a novel antibacterial compound produced by pseudomonas stutzeri. | a novel compound designated zafrin [4beta-methyl-5, 6, 7, 8 tetrahydro-1 (4beta-h)-phenanthrenone] was isolated from a crude extract of a marine bacterium identified as pseudomonas stutzeri. zafrin showed strong antibacterial activity against both gram-positive and gram-negative bacteria. the compound was purified and its structure was elucidated by spectroscopic methods including 1h-nuclear magnetic resonance (nmr), 13c-nmr, 1d-nmr and 2d-nmr spectroscopy. it could be demonstrated that a purifi ... | 2008 | 18093138 |
| prosthetic knee septic arthritis due to pseudomonas stutzeri. | prosthetic joint infection is usually caused by staphylococcus aureus, coagulase-negative staphylococci and, less commonly, by gram-negative bacilli and anaerobes. a case of prosthetic joint infection due to pseudomonas stutzeri in a 73-year-old female with acute promyelocytic leukemia is presented, and the pertinent literature is reviewed. although the patient had prolonged neutropenia, the infection was successfully treated with antibiotics and without artificial joint replacement. | 2000 | 18159309 |
| 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 ... | 2008 | 18192418 |
| resonance raman spectroscopy of nitric oxide reductase and cbb(3) heme-copper oxidase. | elucidating the structure and properties of the active sites in cbb3 heme-copper oxidase and in nitric oxide reductase (nor) is crucial in understanding the reaction mechanisms of oxygen and nitric oxide reduction by both enzymes. in the work here, we have applied resonance raman (rr) spectroscopy to investigate the structure and properties of the binuclear heme b3-cub center of cbb3 heme-copper oxidase from pseudomonas stutzeri and the dinuclear heme b3-feb center of nor from paracoccus denitri ... | 2008 | 18211060 |
| binding of the major phasin, phap1, from ralstonia eutropha h16 to poly(3-hydroxybutyrate) granules. | the surface of polyhydroxybutyrate (phb) storage granules in bacteria is covered mainly by proteins referred to as phasins. the layer of phasins stabilizes the granules and prevents coalescence of separated granules in the cytoplasm and nonspecific binding of other proteins to the hydrophobic surfaces of the granules. phasin phap1(reu) is the major surface protein of phb granules in ralstonia eutropha h16 and occurs along with three homologues (phap2, phap3, and phap4) that have the capacity to ... | 2008 | 18223073 |
| the structure of the o-specific polysaccharide from the lipopolysaccharide of pseudomonas sp. ox1 cultivated in the presence of the azo dye orange ii. | the gram-negative bacterium pseudomonas sp. ox1, previously known as pseudomonas stutzeri ox1, is endowed with a high metabolic versatility. in fact, it is able to utilize a wide range of toxic organic compounds as the only source of carbon and energy for growth. it has been recently observed that, while growing on a glucose-containing liquid medium, pseudomonas sp. ox1 can reduce azo dyes, ubiquitous pollutants particularly resistant to chemical and physical degradation, with this azoreduction ... | 2008 | 18258222 |
| solvent stress response of the denitrifying bacterium "aromatoleum aromaticum" strain ebn1. | the denitrifying betaproteobacterium "aromatoleum aromaticum" strain ebn1 degrades several aromatic compounds, including ethylbenzene, toluene, p-cresol, and phenol, under anoxic conditions. the hydrophobicity of these aromatic solvents determines their toxic properties. here, we investigated the response of strain ebn1 to aromatic substrates at semi-inhibitory (about 50% growth inhibition) concentrations under two different conditions: first, during anaerobic growth with ethylbenzene (0.32 mm) ... | 2008 | 18263750 |
| involvement of glnk, a pii protein, in control of nitrogen fixation and ammonia assimilation in pseudomonas stutzeri a1501. | the nitrogen-fixing, root-associated strain pseudomonas stutzeri a1501 carries a single gene encoding a protein from the pii family, designated glnk. the glnk gene is co-transcribed with two distantly related copies of amtb genes encoding putative ammonium channels. transcription of glnk was decreased in the presence of ammonia and was partly dependent on ntrc and rpon under nitrogen-limiting conditions. inactivation of glnk led to a mutant strain devoid of nitrogenase activity, auxotrophic for ... | 2008 | 18274728 |
| highly enantioselective dynamic kinetic resolution of 1,2-diarylethanols by a lipase-ruthenium couple. | a practical procedure has been developed for the dynamic kinetic resolution of 1,2-diarylethanols. this procedure employs a highly enantioselective lipase from pseudomonas stutzeri (trade name, lipase tl) as the resolution catalyst and a ruthenium complex as the racemization catalyst. sixteen 1,2-diarylethanols have been efficiently resolved to provide their acetyl derivatives with good yields (95-97%) and high enantiomeric excesses (96-99%). | 2008 | 18303906 |
| twitching motility is essential for virulence in dichelobacter nodosus. | type iv fimbriae are essential virulence factors of dichelobacter nodosus, the principal causative agent of ovine foot rot. the fima fimbrial subunit gene is required for virulence, but fima mutants exhibit several phenotypic changes and it is not certain if the effects on virulence result from the loss of type iv fimbria-mediated twitching motility, cell adherence, or reduced protease secretion. we showed that mutation of either the pilt or pilu gene eliminated the ability to carry out twitchin ... | 2008 | 18310333 |
| 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 ... | 2008 | 18328098 |
| comparative analysis of acinetobacters: three genomes for three lifestyles. | acinetobacter baumannii is the source of numerous nosocomial infections in humans and therefore deserves close attention as multidrug or even pandrug resistant strains are increasingly being identified worldwide. here we report the comparison of two newly sequenced genomes of a. baumannii. the human isolate a. baumannii aye is multidrug resistant whereas strain sdf, which was isolated from body lice, is antibiotic susceptible. as reference for comparison in this analysis, the genome of the soil- ... | 2008 | 18350144 |
| quantification, distribution, and possible source of bacterial biofilm in mouse automated watering systems. | the use of automated watering systems for providing drinking water to rodents has become commonplace in the research setting. little is known regarding bacterial biofilm growth within the water piping attached to the racks (manifolds). the purposes of this project were to determine whether the mouse oral flora contributed to the aerobic bacterial component of the rack biofilm, quantify bacterial growth in rack manifolds over 6 mo, assess our rack sanitation practices, and quantify bacterial biof ... | 2008 | 18351724 |
| antimicrobial biocides in the healthcare environment: efficacy, usage, policies, and perceived problems. | biocides are heavily used in the healthcare environment, mainly for the disinfection of surfaces, water, equipment, and antisepsis, but also for the sterilization of medical devices and preservation of pharmaceutical and medicinal products. the number of biocidal products for such usage continuously increases along with the number of applications, although some are prone to controversies. there are hundreds of products containing low concentrations of biocides, including various fabrics such as ... | 2005 | 18360573 |
| novel aromatic ring-hydroxylating dioxygenase genes from coastal marine sediments of patagonia. | polycyclic aromatic hydrocarbons (pahs), widespread pollutants in the marine environment, can produce adverse effects in marine organisms and can be transferred to humans through seafood. our knowledge of pah-degrading bacterial populations in the marine environment is still very limited, and mainly originates from studies of cultured bacteria. in this work, genes coding catabolic enzymes from pah-biodegradation pathways were characterized in coastal sediments of patagonia with different levels ... | 2008 | 18366740 |
| a single residue mutation of 5-enoylpyruvylshikimate-3-phosphate synthase in pseudomonas stutzeri enhances resistance to the herbicide glyphosate. | a novel class ii 5-enoylpyruvylshikimate-3-phosphate synthase (epsps) was identified from pseudomonas stutzeri a1501 by complementation of an escherichia coli auxotrophic aroa mutant. the single amino acid substitution of serine (ser) for asparagine (asn)-130 of the a1501 epsps enhanced resistance to 200 mm glyphosate. the mutated epsps had a 2.5-fold increase for ic(50) [glyphosate] value, a 2-fold increase for k (i) [glyphosate] value, but a k (m) [pep] value similar to that of wild type. the ... | 2008 | 18368293 |
| characterization of diazotrophs containing mo-independent nitrogenases, isolated from diverse natural environments. | molybdenum-independent nitrogenases were first described in the nitrogen-fixing bacterium azotobacter vinelandii and have since been described in other diazotrophic bacteria. previously, we reported the isolation of seven diazotrophs with mo-independent nitrogenases from aquatic environments. in the present study, we extend these results to include diazotrophs isolated from wood chip mulch, soil, "paraffin dirt," and sediments from mangrove swamps. mo-deficient, n-free media under both aerobic a ... | 2008 | 18378646 |
| cloning, expression and physicochemical characterization of a di-heme cytochrome c (4) from the psychrophilic bacterium pseudoalteromonas haloplanktis tac 125. | the 20-kda di-heme cytochrome c (4) from the psycrophilic bacterium pseudoalteromonas haloplanktis tac 125 was cloned and expressed in escherichia coli and investigated through uv-vis and (1)h nmr spectroscopies and protein voltammetry. the model structure was computed using the x-ray structure of pseudomonas stutzeri cytochrome c (4) as a template. the protein shows unprecedented properties within the cytochrome c (4) family, including (1) an almost nonpolar surface charge distribution, (2) the ... | 2008 | 18386080 |
| saturation mutagenesis of putative catalytic residues of benzoylformate decarboxylase provides a challenge to the accepted mechanism. | benzoylformate decarboxylase from pseudomonas putida (ppbfdc) is a thiamin diphosphate-dependent enzyme that carries out the nonoxidative decarboxylation of aromatic 2-keto acids. the x-ray structure of ppbfdc suggested that ser-26, his-70, and his-281 would play important roles in its catalytic mechanism, and the s26a, h70a, and h281a variants all exhibited greatly impaired catalytic activity. based on stopped-flow studies with the alanine mutants, it was proposed that the histidine residues ac ... | 2008 | 18398009 |
| description of a novel indole-oxidizing bacterium pseudomonas indoloxydans sp. nov., isolated from a pesticide-contaminated site. | a gram-negative, deep brown-pigmented gammaproteobacteria, strain ipl-1(t), capable of oxidizing indole was isolated from a lindane-contaminated site and subjected to a polyphasic taxonomic study. most of the physiological and biochemical properties, major fatty acids (c(18:1)omega7c, c(16:1)omega7c/iso c(15:0) 2oh and c(16:0)), estimated dna g+c content (67.2mol%) and 16s rrna gene sequence analysis showed that strain ipl-1(t) belonged to the genus pseudomonas. strain ipl-1(t) exhibited highest ... | 2008 | 18406094 |
| whole-genome pyrosequencing of an epidemic multidrug-resistant acinetobacter baumannii strain belonging to the european clone ii group. | the whole-genome sequence of an epidemic, multidrug-resistant acinetobacter baumannii strain (strain acicu) belonging to the european clone ii group and carrying the plasmid-mediated bla(oxa)(-)(58) carbapenem resistance gene was determined. the a. baumannii acicu genome was compared with the genomes of a. baumannii atcc 17978 and acinetobacter baylyi adp1, with the aim of identifying novel genes related to virulence and drug resistance. a. baumannii acicu has a single chromosome of 3,904,116 bp ... | 2008 | 18411315 |
| enzymatic resolution and evaluation of enantiomers of cis-5'-hydroxythalidomide. | the straightforward synthesis of both enantiomers of cis-5'-hydroxythalidomide, a major metabolite of thalidomide, has been accomplished by enzymatic kinetic resolution of a racemic substrate catalyzed by pseudomonas stutzeri lipase tl. cis-5'-hydroxythalidomide shows resistance to racemization (and epimerization) at physiological ph. a tube formation assay to assess the ability to inhibit angiogenesis revealed that cis-5'-hydroxythalidomides are inactive. | 2008 | 18421383 |
| microbial production of medium-chain-length 3-hydroxyalkanoic acids by recombinant pseudomonas putida kt2442 harboring genes fadl, fadd and phaz. | monomers of microbial polyhydroxyalkanoates, mainly 3-hydroxyhexanoic acid (3hhx) and 3-hydroxyoctanoic acid (3ho), were produced by overexpressing polyhydroxyalkanoates depolymerase gene phaz, together with putative long-chain fatty acid transport protein fadl of pseudomonas putida kt2442 and acyl-coa synthetase (fadd) of escherichia coli mg1655 in p. putida kt2442. fadl(pp), which is responsible for free fatty acid transportation from the extracellular environment to the cytoplasm, and fadd(ec ... | 2008 | 18422622 |
| molecular structure of endotoxins from gram-negative marine bacteria: an update. | marine bacteria are microrganisms that have adapted, through millions of years, to survival in environments often characterized by one or more extreme physical or chemical parameters, namely pressure, temperature and salinity. the main interest in the research on marine bacteria is due to their ability to produce several biologically active molecules, such as antibiotics, toxins and antitoxins, antitumor and antimicrobial agents. nonetheless, lipopolysaccharides (lpss), or their portions, from g ... | 2007 | 18463721 |
| a family of insertion sequences that impacts integrons by specific targeting of gene cassette recombination sites, the is1111-attc group. | integrons facilitate the evolution of complex phenotypes by physical and transcriptional linkage of genes. they can be categorized as chromosomal integrons (cis) or mobile resistance integrons (mris). the significance of mris for the problem of multiple antibiotic resistance is well established. cis are more widespread, but their only demonstrated significance is as a reservoir of gene cassettes for mris. in characterizing cis associated with pseudomonas, we discovered a subfamily of insertion s ... | 2008 | 18487340 |
| nitrogen fixation island and rhizosphere competence traits in the genome of root-associated pseudomonas stutzeri a1501. | the capacity to fix nitrogen is widely distributed in phyla of bacteria and archaea but has long been considered to be absent from the pseudomonas genus. we report here the complete genome sequencing of nitrogen-fixing root-associated pseudomonas stutzeri a1501. the genome consists of a single circular chromosome with 4,567,418 bp. comparative genomics revealed that, among 4,146 protein-encoding genes, 1,977 have orthologs in each of the five other pseudomonas representative species sequenced to ... | 2008 | 18495935 |
| competitive oxidation of volatile fatty acids by sulfate- and nitrate-reducing bacteria from an oil field in argentina. | acetate, propionate, and butyrate, collectively referred to as volatile fatty acids (vfa), are considered among the most important electron donors for sulfate-reducing bacteria (srb) and heterotrophic nitrate-reducing bacteria (hnrb) in oil fields. samples obtained from a field in the neuquén basin, western argentina, had significant activity of mesophilic srb, hnrb, and nitrate-reducing, sulfide-oxidizing bacteria (nr-sob). in microcosms, containing vfa (3 mm each) and excess sulfate, srb first ... | 2008 | 18502934 |
| role of cj1211 in natural transformation and transfer of antibiotic resistance determinants in campylobacter jejuni. | campylobacter jejuni, an important food-borne human pathogen, is increasingly resistant to antimicrobials. natural transformation is considered to be a main mechanism for mediating the transfer of genetic materials encoding antibiotic resistance determinants in c. jejuni, but direct evidence for this notion is still lacking. in this study, we determined the role of cj1211 in natural transformation and in the development of antibiotic resistance in c. jejuni. insertional mutagenesis of cj1211, a ... | 2008 | 18505858 |
| bifurcational and dynamical analysis of a continuous biofilm reactor. | a dynamical model of a continuous biofilm reactor is presented. the reactor consists of a three-phase internal loop airlift operated continuously with respect to the liquid and gaseous phases, and batchwise with respect to the immobilized cells. the model has been applied to the conversion of phenol by means of immobilized cells of pseudomonas sp. ox1 whose metabolic activity was previously characterized (viggiani, a., olivieri, g., siani, l., di donato, a., marzocchella, a., salatino, p., barbi ... | 2008 | 18511142 |
| insights and inferences about integron evolution from genomic data. | integrons are mechanisms that facilitate horizontal gene transfer, allowing bacteria to integrate and express foreign dna. these are important in the exchange of antibiotic resistance determinants, but can also transfer a diverse suite of genes unrelated to pathogenicity. here, we provide a systematic analysis of the distribution and diversity of integron inti genes and integron-containing bacteria. | 2008 | 18513439 |
| coupled effect of chemotaxis and growth on microbial distributions in organic-amended aquifer sediments: observations from laboratory and field studies. | the inter-relationship of growth and chemotactic response exhibited bytwo common soil-inhabiting bacteria was investigated to determine its impact on bacterial migration. filter-chambers were used to simulate aquifer sediments characterized by vertical gradients of organic contaminants in both artificial groundwater flow systems in the laboratory and within the screened intervals of observation wells in a sandy aquifer. a labile model contaminant (acetate) was added to the top compartments of th ... | 2008 | 18546689 |
| indole production by pseudomonas stutzeri strain nap-3 during anaerobic naphthalene biodegradation in the presence of dimethyl formamide. | we previously reported on the denitrifier pseudomonas stutzeri strain nap-3 that degrades naphthalene without oxygen. in our present studies, naphthalene biodegradation by nap-3 was slow or nearly absent when acetate was not present, suggesting a stimulating effect by the non-fermentable substrate. nap-3 was sensitive to the amount of naphthalene in the culture; with naphthalene removal and nitrate utilization rates higher when present at 20 mg l(-1) compared to 40 mg l(-1). electron equivalents ... | 2008 | 18569316 |
| expression of cell wall related genes in basal and ear internodes of silking brown-midrib-3, caffeic acid o-methyltransferase (comt) down-regulated, and normal maize plants. | silage maize is a major forage and energy resource for cattle feeding, and several studies have shown that lignin content and structure are the determining factors in forage maize feeding value. in maize, four natural brown-midrib mutants have modified lignin content, lignin structure and cell wall digestibility. the greatest lignin reduction and the highest cell wall digestibility were observed in the brown-midrib-3 (bm3) mutant, which is disrupted in the caffeic acid o-methyltransferase (comt) ... | 2008 | 18582385 |
| continuous production of maltotetraose using immobilized pseudomonas stutzeri amylase. | a continuous production process of maltotetraose was investigated by using immobilized maltotetraose (g(4))- forming amylase (1,4-alpha-d-glucan maltotetraohydrolase, ec3.2.1.60) from pseudomonas stutzeri adsorbed on a macroporous hydrophobic resin. the maximum reaction rate was obtained at 55 degrees c and the activation energy of hydrolysis by immobilized g(4)-forming amylase was calculated to be 8.45 kcal/mol. the maltotetraose yield was greatly influenced by the flow rate of substrate soluti ... | 1988 | 18587768 |
| stability of immobilized maltotetraose-forming amylase from pseudomonas stutzeri. | the stability of immobilized maltotetraose (g(4))-forming amylase (1,4-alpha-d-glucan maltoteraohydrolase, ec 3.2.1.60) from pseudomonas stutzeri was investigated in both batch and continuous processes. the inactivation process of the immobilized enzyme seemed to obey first-order kinetics, and the immobilized enzyme became more stable when coexisting with 20-30 wt % substrate and calcium ions. from intensive studies on the operational stability in the continuous process, the apparent half-life o ... | 1989 | 18587992 |
| nitrite removal performance and community structure of nitrite-oxidizing and heterotrophic bacteria suffered with organic matter. | although ammonia oxidation and ammonia-oxidizing bacteria (aob) have been extensively studied, nitrite oxidation and nitrite-oxidizing bacteria (nob) are still not well understood. in this article, the effect of organic matter on nob and heterotrophic bacteria was investigated with functional performance analysis and bacterial community shift analysis. the results showed that at low concentrations of initial sodium acetate [initial sodium acetate (isa) = 0.5 or 1 g/l], the nitrite removal rate w ... | 2008 | 18594908 |
| ispst9, an isl3-like insertion sequence from pseudomonas stutzeri an10 involved in catabolic gene inactivation. | a novel insertion sequence (is), ispst9, from pseudomonas stutzeri an10 was cloned and characterized. ispst9 is a typical bacterial is, consisting of a 2472-bp element flanked by 24-bp perfect inverted repeats that generates 8-bp at-rich target duplications upon insertion. the sequence also contains a gene that encodes an active transposase (tnpa) with significant amino acid identity to members of the isl3 family. southern blot analysis of digested genomic dna of strain an10 and its 4-chlorosali ... | 2008 | 18645960 |
| isolation and characterization of acc deaminase gene from two plant growth-promoting rhizobacteria. | lowering of plant ethylene by deamination of its immediate precursor 1-aminocyclopropane-1-carboxylate (acc) is a key trait found in many rhizobacteria. we isolated and screened bacteria from the rhizosphere of wheat for their acc-degrading ability. the acc deaminase gene (acds) isolated from two bacterial isolates through pcr amplification was cloned and sequenced. nucleotide sequence alignment of these genes with previously reported genes of pseudomonas sp. strain acp and enterobacter cloacae ... | 2008 | 18654819 |
| molecular detection of multiple emerging pathogens in sputa from cystic fibrosis patients. | there is strong evidence that culture-based methods detect only a small proportion of bacteria present in the respiratory tracts of cystic fibrosis (cf) patients. | 2008 | 18682840 |
| [detection methods and changes in metallo-beta-lactamase-producing gram-negative rod isolates at nagasaki university hospital from 1991 to 2005]. | since plasmid-mediated metallo-beta-lactamase (mbl)-producing pseudimonas aeruginosa was reported in japan, mbl-producing gram-negative rods (gnrs) have emerged worldwide. we developed a way to detect mbl-producing gnrs in routine examination using broth microdilution with the mbl inhibitor sodium mercaptoacetate (sma) in frozen plates. between 1996 and 2005, we evaluated this and other methods, including broth microdilution with another mbl inhibitor dipicolinic acid (dpa) in dry plates, conven ... | 2008 | 18697478 |
| adaptation of aerobically growing pseudomonas aeruginosa to copper starvation. | restricted bioavailability of copper in certain environments can interfere with cellular respiration because copper is an essential cofactor of most terminal oxidases. the global response of the metabolically versatile bacterium and opportunistic pathogen pseudomonas aeruginosa to copper limitation was assessed under aerobic conditions. expression of cioab (encoding an alternative, copper-independent, cyanide-resistant ubiquinol oxidase) was upregulated, whereas numerous iron uptake functions (i ... | 2008 | 18708503 |
| anaerobic degradation of long-chain alkylamines by a denitrifying pseudomonas stutzeri. | the anaerobic degradation of tetradecylamine and other long-chain alkylamines by a newly isolated denitrifying bacterium was studied. strain zn6 was isolated from a mixture of soil and active sludge and was identified as representing pseudomonas stutzeri, based on partial 16s rrna gene sequence analysis. strain zn6 was a mesophilic, motile, gram-negative rod-shaped bacterium and was able to grow on a variety of compounds including even-numbered primary fatty amines with alkyl chains ranging from ... | 2008 | 18721145 |
| formation of nanoscale elemental silver particles via enzymatic reduction by geobacter sulfurreducens. | geobacter sulfurreducens reduced ag(i) (as insoluble agcl or ag(+) ions), via a mechanism involving c-type cytochromes, precipitating extracellular nanoscale ag(0). these results extend the range of metals known to be reduced by geobacter species and offer a method for recovering silver from contaminated water as potentially useful silver nanoparticles. | 2008 | 18723646 |
| multilocus sequence typing and phylogenetic analyses of pseudomonas aeruginosa isolates from the ocean. | recent isolation of pseudomonas aeruginosa strains from the open ocean and subsequent pulsed-field gel electrophoresis analyses indicate that these strains have a unique genotype (n. h. khan, y. ishii, n. kimata-kino, h. esaki, t. nishino, m. nishimura, and k. kogure, microb. ecol. 53:173-186, 2007). we hypothesized that ocean p. aeruginosa strains have a unique phylogenetic position relative to other strains. the objective of this study was to clarify the intraspecies phylogenetic relationship ... | 2008 | 18757570 |
| identification and functional characterization of nifa variants that are independent of glnb activation in the photosynthetic bacterium rhodospirillum rubrum. | the activity of nifa, the transcriptional activator of the nitrogen fixation (nif) gene, is tightly regulated in response to ammonium and oxygen. however, the mechanisms for the regulation of nifa activity are quite different among various nitrogen-fixing bacteria. unlike the well-studied nifl-nifa regulatory systems in klebsiella pneumoniae and azotobacter vinelandii, in rhodospirillum rubrum nifa is activated by a direct protein-protein interaction with the uridylylated form of glnb, which in ... | 2008 | 18757802 |
| differences in nitric oxide steady states between arginine, hypoxanthine, uracil auxotrophs (ahu) and non-ahu strains of neisseria gonorrhoeae during anaerobic respiration in the presence of nitrite. | neisseria gonorrhoeae can grow by anaerobic respiration using nitrite as an alternative electron acceptor. under these growth conditions, n. gonorrhoeae produces and degrades nitric oxide (no), an important host defense molecule. laboratory strain f62 has been shown to establish and maintain a no steady-state level that is a function of the nitrite reductase/no reductase ratio and is independent of cell number. the nitrite reductase activities (122-197 nmol no2 reduced x min(-1) x od600(-1)) and ... | 2008 | 18772926 |