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gene targeting in gram-negative bacteria by use of a mobile group ii intron ("targetron") expressed from a broad-host-range vector.mobile group ii introns ("targetrons") can be programmed for insertion into virtually any desired dna target with high frequency and specificity. here, we show that targetrons expressed via an m-toluic acid-inducible promoter from a broad-host-range vector containing an rk2 minireplicon can be used for efficient gene targeting in a variety of gram-negative bacteria, including escherichia coli, pseudomonas aeruginosa, and agrobacterium tumefaciens. targetrons expressed from donor plasmids introdu ...200717322321
genetic characterization of 2,4,6-trichlorophenol degradation in cupriavidus necator jmp134.the degradation pathway of 2,4,6-trichlorophenol (2,4,6-tcp), a hazardous pollutant, in the aerobic bacterium cupriavidus necator jmp134(pjp4) (formerly ralstonia eutropha jmp134) is encoded by the tcp genes. these genes are located in a genetic context, tcprxabcyd, which resembles a putative catabolic operon. in this work, these gene sequences were individually disrupted and mutant strains were evaluated for their ability to grow on or degrade 2,4,6-tcp. the tcpx and tcpa mutants completely fai ...200717322325
differential response of etiolated pea seedlings to inoculation with rhizobacteria capable of utilizing 1-aminocyclopropane-1-carboxylate or l-methionine.the majority of soil microorganisms can derive ethylene from l-methionine (l-met), while some rhizobacteria can hydrolyze 1-aminocyclopropane-1-carboxylate (acc) due to their acc-deaminase activity. in this study, three strains having either acc-deaminase activity (pseudomonas putida biotype a, a7), or the ability to produce ethylene from l-met (acinetobacter calcoaceticus, m9) or both (pseudomonas fluorescens, am3) were used for inoculation. the highly ethylene specific bioassay of a classical ...200717342050
insertion sequence diversity in archaea.insertion sequences (iss) can constitute an important component of prokaryotic (bacterial and archaeal) genomes. over 1,500 individual iss are included at present in the isfinder database (www-is.biotoul.fr), and these represent only a small portion of those in the available prokaryotic genome sequences and those that are being discovered in ongoing sequencing projects. in spite of this diversity, the transposition mechanisms of only a few of these ubiquitous mobile genetic elements are known, a ...200717347521
adeabc multidrug efflux pump is associated with decreased susceptibility to tigecycline in acinetobacter calcoaceticus-acinetobacter baumannii complex.to investigate the role of the adeabc multidrug efflux pump in the decreased susceptibility of clinical isolates of acinetobacter calcoaceticus-acinetobacter baumannii complex to tigecycline.200717363424
a detailed analysis of 16s ribosomal rna gene segments for the diagnosis of pathogenic bacteria.bacterial 16s ribosomal rna (rrna) genes contain nine "hypervariable regions" (v1-v9) that demonstrate considerable sequence diversity among different bacteria. species-specific sequences within a given hypervariable region constitute useful targets for diagnostic assays and other scientific investigations. no single region can differentiate among all bacteria; therefore, systematic studies that compare the relative advantage of each region for specific diagnostic goals are needed. we characteri ...200717391789
a marine mesorhizobium sp. produces structurally novel long-chain n-acyl-l-homoserine lactones.our study focused on a mesorhizobium sp. that is phylogenetically affiliated by 16s rrna gene sequence to other marine and saline bacteria of this genus. liquid chromatography-mass spectrometry investigations of the extract obtained from solid-phase extraction of cultures of this bacterium indicated the presence of several n-acyl homoserine lactones (ahls), with chain lengths of c(10) to c(16). chromatographic separation of the active bacterial extract yielded extraordinarily large amounts of tw ...200717400774
peptoniphilus gorbachii sp. nov., peptoniphilus olsenii sp. nov., and anaerococcus murdochii sp. nov. isolated from clinical specimens of human origin.three groups of previously unknown gram-positive, anaerobic, coccus-shaped bacteria were characterized using phenotypic and molecular taxonomic methods. phenotypic and genotypic data demonstrate that these organisms are distinct, and each group represents a previously unknown subline within clostridium cluster xiii. two groups are most closely related to peptoniphilus harei in the genus peptoniphilus, and the other group is most closely related to anaerococcus lactolyticus in the genus anaerococ ...200717428937
potential of the adhesion of bacteria isolated from drinking water to materials.heterotrophic bacteria (11 genera, 14 species, 25 putative strains) were isolated from drinking water, identified either biochemically or by partial 16s rdna gene sequencing and their adherence characteristics were determined by two methods: i. thermodynamic prediction of adhesion potential by measuring hydrophobicity (contact angle measurements) and ii. by measuring adherence to eight different substrata (asi 304 and 316 stainless steel, copper, polyvinyl chloride, polypropylene, polyethylene, ...200717440920
pantoea agglomerans, a plant pathogen causing human disease.we present 53 pediatric cases of pantoea agglomerans infections cultured from normally sterile sites in patients seen at a children's hospital over 6 years. isolates included 23 from the bloodstream, 14 from abscesses, 10 from joints/bones, 4 from the urinary tract, and 1 each from the peritoneum and the thorax. p. agglomerans was most associated with penetrating trauma by vegetative material and catheter-related bacteremia.200717442803
a polyomic approach to elucidate the fluoranthene-degradative pathway in mycobacterium vanbaalenii pyr-1.mycobacterium vanbaalenii pyr-1 is capable of degrading a wide range of high-molecular-weight polycyclic aromatic hydrocarbons (pahs), including fluoranthene. we used a combination of metabolomic, genomic, and proteomic technologies to investigate fluoranthene degradation in this strain. thirty-seven fluoranthene metabolites including potential isomers were isolated from the culture medium and analyzed by high-performance liquid chromatography, gas chromatography-mass spectrometry, and uv-visibl ...200717449607
protein engineering of wzc to generate new emulsan analogs.acinetobacter venetianus rag1 produces an extracellular, polymeric lipoheteropolysaccharide termed apoemulsan. this polymer is putatively produced via a wzy-dependent pathway. according to this model, the length of the polymer is regulated by polysaccharide-copolymerase (pcp) protein. a highly conserved proline and glycine motif was identified in all members of the pcp family of proteins and is involved in regulation of polymer chain length. in order to control the structure of apoemulsan, defin ...200717449706
lipid composition and transcriptional response of mycobacterium tuberculosis grown under iron-limitation in continuous culture: identification of a novel wax ester.the low level of available iron in vivo is a major obstacle for microbial pathogens and is a stimulus for the expression of virulence genes. in this study, mycobacterium tuberculosis h37rv was grown aerobically in the presence of limited iron availability in chemostat culture to determine the physiological response of the organism to iron-limitation. a previously unidentified wax ester accumulated under iron-limited growth, and changes in the abundance of triacylglycerol and menaquinone were als ...200717464057
hexadecane and tween 80 stimulate lipase production in burkholderia glumae by different mechanisms.burkholderia glumae strain pg1 produces a lipase of biotechnological relevance. lipase production by this strain and its derivative lu8093, which was obtained through classical strain improvement, was investigated under different conditions. when 10% hexadecane was included in the growth medium, lipolytic activity in both strains could be increased approximately 7-fold after 24 h of growth. hexadecane also stimulated lipase production in a strain containing the lipase gene fused to the tac promo ...200717468265
comparison of one-tube multiplex pcr, automated ribotyping and intergenic spacer (its) sequencing for rapid identification of acinetobacter baumannii.acinetobacter baumannii has emerged as a serious cause of nosocomial infections. rapid identification of this pathogen is required so that appropriate therapy can be given and outbreaks controlled. this study evaluated a multiplex pcr and an automated ribotyping system for the rapid identification of acinetobacter baumannii. in total, 22 different reference strains and 138 clinical isolates of acinetobacter spp., identified by 16s-23s rrna intergenic spacer (its) sequence analysis, were evaluate ...200717488329
substrate specificity of a long-chain alkylamine-degrading pseudomonas sp isolated from activated sludge.a bacterium strain bert, which utilizes primary long-chain alkylamines as nitrogen, carbon and energy source, was isolated from activated sludge. this rod-shaped motile, gram-negative strain was identified as a pseudomonas sp. the substrate spectrum of this pseudomonas strain bert includes primary alkylamines with alkyl chains ranging from c(3) to c(18), and dodecyl-1,3-diaminopropane. amines with alkyl chains ranging from 8 to 14 carbons were the preferred substrates. growth on dodecanal, dodec ...200817492358
substrate specificity of a long-chain alkylamine-degrading pseudomonas sp isolated from activated sludge.a bacterium strain bert, which utilizes primary long-chain alkylamines as nitrogen, carbon and energy source, was isolated from activated sludge. this rod-shaped motile, gram-negative strain was identified as a pseudomonas sp. the substrate spectrum of this pseudomonas strain bert includes primary alkylamines with alkyl chains ranging from c(3) to c(18), and dodecyl-1,3-diaminopropane. amines with alkyl chains ranging from 8 to 14 carbons were the preferred substrates. growth on dodecanal, dodec ...200817492358
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 ...200717507509
acinetobacter skin carriage among us army soldiers deployed in iraq.skin carriage of acinetobacter calcoaceticus-baumannii complex was not detected among a representative sample of 102 us army soldiers stationed in iraq. this observation refutes the hypothesis that preinjury skin carriage serves as the reservoir for the acinetobacter infections seen in us military combat casualties.200717520547
enhanced production of epsilon-caprolactone by overexpression of nadph-regenerating glucose 6-phosphate dehydrogenase in recombinant escherichia coli harboring cyclohexanone monooxygenase gene.whole-cell conversion of cyclohexanone to epsilon-caprolactone was attempted by recombinant escherichia coli bl21(de3) expressing cyclohexanone monooxygenase (chmo) of acinetobacter calcoaceticus ncimb 9871. high concentrations of cyclohexanone and epsilon-caprolactone reduced chmo-mediated bioconversion of cyclohexanone to epsilon-caprolactone in the resting recombinant e. coli cells. metabolically active cells were employed by adopting a fed-batch culture to improve the production of epsilon-c ...200717541782
an ecology-based analysis of irreversible biofouling in membrane bioreactors.to provide the first step towards a microbial ecology-based understanding of irreversible membrane biofouling, four laboratory-scale membrane bioreactors (mbrs) were operated to investigate the identity of bacterial populations highly correlated with irreversible membrane biofouling. the conventional mbr was divided into two separate experimental units. unit one consisted of four suspended-growth, activated sludge, sequencing batch bioreactors treating a synthetic paper mill wastewater. unit two ...200717547010
prevalence of antimicrobial resistance in acinetobacter calcoaceticus-baumannii complex in a saudi arabian hospital.during the period from 1998 through 2004, a total of 476 isolates of acinetobacter calcoaceticus-baumannii complex were recovered. the organism showed high rates of resistance to ampicillin (86% of isolates), cefoxitin (89%), and nitrofurantoin (89%). the rate of resistance to imipenem was 3%; to ticarcillin-clavulanic acid, 16.5%; to gentamicin, 26%; and to ceftazidime, 38%. multidrug resistance was observed in 14%-35.8% of acinetobacter species isolates.200717564992
three novel highly charged copper-based biocides: safety and efficacy against healthcare-associated organisms.we investigated three novel highly charged copper-based inorganic biocidal formulations for their activity against organisms highly relevant to healthcare-associated infection.200717567632
parallel analysis of antimicrobial activities in microbial community by sscp based on ce.conventional antimicrobial activity analyses such as the broth dilution method and disk diffusion test are considerably demanding processes for new antimicrobial agent discovery and sensitive diagnosis of infectious diseases. here, we developed a new antimicrobial activity analysis system using ce-based sscp (ce-sscp) combined with 16s rrna gene-specific pcr (pcr/ce-sscp). using this method, the population change in the microbial community in response to specific antimicrobial agents could be qu ...200717577886
ci-990 (pd 131112): a new quinolone prodrug.in vitro susceptibility of 1021 strains of recent clinical isolates was determined against the new fluoroquinolone ci-990 (pd 131112) and compared with ci-960, ciprofloxacin, fleroxacin, lomefloxacin, norfloxacin, perfloxacin, sparfloxacin, and temafloxacin. the minimum inhibitory concentrations (mic) of ci-990 in mg/l required for >90% isolates were 0.03-0.5 for members of enterobacteriaceae, 0.12-2.0 for pseudomonas aeruginosa, 0.03-1.0 for aeromonas hydrophilia, 1.0-2.0 for acinetobacter calc ...199317588022
bioremediation of eutrophicated water by acinetobacter calcoaceticus.removal of phosphorus and nitrogen from eutrophicated water was carried out by in situ bioremediation. with the addition of acinetobacter calcoaceticus, 65.0% +/- 4.0% of total phosphorus (tp), 37.0% +/- 4.0% of total nitrogen (tn), 75.0% +/- 7.0% nitrite (no(2) (-)-n), and 87.0% +/- 4.0% of ammonia (nh(4) (+)-n) were removed. furthermore, chlorophyll a removal in the inoculated treatments reached 83.7% +/- 1.5%, and algae in the water was basically controlled.200717619803
atmospheric movement of microorganisms in clouds of desert dust and implications for human health.billions of tons of desert dust move through the atmosphere each year. the primary source regions, which include the sahara and sahel regions of north africa and the gobi and takla makan regions of asia, are capable of dispersing significant quantities of desert dust across the traditionally viewed oceanic barriers. while a considerable amount of research by scientists has addressed atmospheric pathways and aerosol chemistry, very few studies to determine the numbers and types of microorganisms ...200717630335
global challenge of multidrug-resistant acinetobacter baumannii. 200717646423
bacterial communities of leachate from tire monofill disposal sites.the disposal of used automobile tires is problematic due to the large number generated each year. newer methods of tire disposal have been developed in which tires are shredded and used for construction materials or buried in dedicated tire monofill sites. in this study, the bacterial assemblage associated with aqueous leachate collected from tire monofill sites was examined and compared to the bacterial assemblage of reference streams. leachate from two tire monofill sites in ohio (usa) was col ...200717651788
biofilm interactions between distinct bacterial genera isolated from drinking water.in the environment, multiple microorganisms coexist as communities, competing for resources and often associated as biofilms. in this study, single- and dual-species biofilm formation by, and specific activities of, six heterotrophic intergeneric bacteria were determined using 96-well polystyrene plates over a 72-h period. these bacteria were isolated from drinking water and identified by partial 16s rrna gene sequencing. a series of planktonic studies was also performed, assessing the bacterial ...200717675433
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 ...200717683520
comprehensive analysis of transport proteins encoded within the genome of bdellovibrio bacteriovorus.bdellovibrio bacteriovorus is a bacterial parasite with an unusual lifestyle. it grows and reproduces in the periplasm of a host prey bacterium. the complete genome sequence of b. bacteriovorus has recently been reported. we have reanalyzed the transport proteins encoded within the b. bacteriovorus genome according to the current content of the transporter classification database. a comprehensive analysis is given on the types and numbers of transport systems that b. bacteriovorus has. in this r ...200717706914
carbapenemase and efflux pump genes in acinetobacter calcoaceticus acinetobacter baumannii complex strains from singapore. 200717768175
a pcr-based method to differentiate between acinetobacter baumannii and acinetobacter genomic species 13tu.a new pcr-based method that exploits differences in gyrb gene sequences was developed to distinguish between acinetobacter baumannii and acinetobacter genomic sp. 13tu. among 118 clinical and reference acinetobacter strains, 102 of which were previously speciated by amplified rdna restriction analysis as belonging to the acinetobacter calcoaceticus-a. baumannii complex, the method correctly identified 31 a. baumannii and 54 acinetobacter genomic sp. 13tu isolates to the species level. the method ...200717850345
regulation of a novel acidithiobacillus caldus gene cluster involved in metabolism of reduced inorganic sulfur compounds.acidithiobacillus caldus has been proposed to play a role in the oxidation of reduced inorganic sulfur compounds (riscs) produced in industrial biomining of sulfidic minerals. here, we describe the regulation of a new cluster containing the gene encoding tetrathionate hydrolase (teth), a key enzyme in the risc metabolism of this bacterium. the cluster contains five cotranscribed genes, isac1, rsrr, rsrs, teth, and doxd, coding for a transposase, a two-component response regulator (rsrr and rsrs) ...200717873067
development of colistin-dependent acinetobacter baumannii-acinetobacter calcoaceticus complex. 200717876007
assessment of technological options and economical feasibility for cyanophycin biopolymer and high-value amino acid production.major transitions can be expected within the next few decades aiming at the reduction of pollution and global warming and at energy saving measures. for these purposes, new sustainable biorefinery concepts will be needed that will replace the traditional mineral oil-based synthesis of specialty and bulk chemicals. an important group of these chemicals are those that comprise n-functionalities. many plant components contained in biomass rest or waste stream fractions contain these n-functionaliti ...200717876577
production of l-carnitine by secondary metabolism of bacteria.abstract: the increasing commercial demand for l-carnitine has led to a multiplication of efforts to improve its production with bacteria. the use of different cell environments, such as growing, resting, permeabilized, dried, osmotically stressed, freely suspended and immobilized cells, to maintain enzymes sufficiently active for l-carnitine production is discussed in the text. the different cell states of enterobacteria, such as escherichia coli and proteus sp., which can be used to produce l- ...200717910757
clonal spread of imipenem-resistant acinetobacter baumannii among different cities of china.a total of 342 imipenem-resistant acinetobacter baumannii isolates (irabs) were collected from 16 chinese cities. six predominant clones had spread widely, and four clones were detected in distant hospitals. the majority of the irabs contain bla(oxa-23), with isaba1 upstream of the gene. these results suggested that clonal spread played an important role in the outbreak of irabs in china.200717942662
colistin heteroresistance in acinetobacter and its association with previous colistin therapy.colistin heteroresistance has been reported among acinetobacter isolates; however, its association with prior colistin therapy has not been not described. a population analysis profile identified resistant acinetobacter subpopulations from colistin-susceptible clinical isolates. the proportion of cells exhibiting heteroresistance was significantly higher among isolates recovered from patients treated with colistin.200817954699
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.200717957246
epidemiological and microbiological analysis of ventilator-associated pneumonia patients in a public teaching hospital.ventilator-associated pneumonia (vap) is the most commonly-acquired infection in patients in intensive care units. we analyzed epidemiological and microbiological characteristics and the outcome, in a cohort of critically-ill patients with confirmed diagnosis of vap. all patients who had been on mechanical ventilation (mv) for more than 48 hours were included in our study; material collection for microbiological analysis was done within the first 24 hours after beginning treatment or after chang ...200717962875
discovery of three novel lipase ( lipa1 , lipa2 , and lipa3) and lipase-specific chaperone ( lipb) genes present in acinetobacter sp. dyl129.a microbe isolated from a soil sample obtained on deog-yu mountain in korea, was found to produce an extracellular lipase. this microbe, which was designated as dyl129, was identified as an acinetobacter sp. based on phylogenetic analysis of its 16s rdna. a genomic library was constructed by using dyl129 fragment digested with hindiii and a recombinant plasmid, plip-1, was selected for further analysis by colony polymerase chain reaction (pcr). sequencing of a 3.8-kb insert in the plip-1 clone r ...200817962933
sequential outbreaks of infections by distinct acinetobacter baumannii strains in a public teaching hospital in houston, texas.invasive disease due to acinetobacter baumannii is an increasing problem in health care settings worldwide. whether certain clones of a. baumannii are more likely to cause invasive disease in hospitalized patients is unknown. we studied all patients at a public teaching hospital in houston, texas, from whom the acinetobacter calcoaceticus-acinetobacter baumannii complex was isolated over a 14-month period in 2005 to 2006. one hundred seven unique patient isolates were identified, with 87 of the ...200818003801
biochemical and structural characterization of a novel family of cystathionine beta-synthase domain proteins fused to a zn ribbon-like domain.we have identified a novel family of proteins, in which the n-terminal cystathionine beta-synthase (cbs) domain is fused to the c-terminal zn ribbon domain. four proteins were overexpressed in escherichia coli and purified: ta0289 from thermoplasma acidophilum, tv1335 from thermoplasma volcanium, pf1953 from pyrococcus furiosus, and ph0267 from pyrococcus horikoshii. the purified proteins had a red/purple color in solution and an absorption spectrum typical of rubredoxins (rds). metal analysis o ...200818021800
biochemical and structural characterization of a novel family of cystathionine beta-synthase domain proteins fused to a zn ribbon-like domain.we have identified a novel family of proteins, in which the n-terminal cystathionine beta-synthase (cbs) domain is fused to the c-terminal zn ribbon domain. four proteins were overexpressed in escherichia coli and purified: ta0289 from thermoplasma acidophilum, tv1335 from thermoplasma volcanium, pf1953 from pyrococcus furiosus, and ph0267 from pyrococcus horikoshii. the purified proteins had a red/purple color in solution and an absorption spectrum typical of rubredoxins (rds). metal analysis o ...200818021800
pyrroloquinoline quinone is a plant growth promotion factor produced by pseudomonas fluorescens b16.pseudomonas fluorescens b16 is a plant growth-promoting rhizobacterium. to determine the factors involved in plant growth promotion by this organism, we mutagenized wild-type strain b16 using omegakm elements and isolated one mutant, k818, which is defective in plant growth promotion, in a rockwool culture system. a cosmid clone, pok40, which complements the mutant k818, was isolated from a genomic library of the parent strain. tn3-gusa mutagenesis of pok40 revealed that the genes responsible fo ...200818055583
determination of specific growth rate by measurement of specific rate of ribosome synthesis in growing and nongrowing cultures of acinetobacter calcoaceticus.rt-ribosyn measures the specific rate of ribosome synthesis in distinct microbial populations by measuring the generation rate of precursor 16s rrna relative to that of mature 16s rrna when precursor 16s rrna processing is inhibited. good agreement was demonstrated between specific rate of ribosome synthesis and specific growth rate of acinetobacter calcoaceticus.200818083876
acinetobacter pneumonia: a review.acinetobacter species are becoming a major cause of nosocomial infections, including hospital-acquired and ventilator-associated pneumonia. acinetobacter species have become increasingly resistant to antibiotics over the past several years and currently present a significant challenge in treating these infections. physicians now rely on older agents, such as polymyxins (colistin), for treatment. this paper reviews the epidemiology, treatment, and prevention of this emerging pathogen.200718092011
rhau of rhizobium leguminosarum is a rhamnose mutarotase.of the nine genes comprising the l-rhamnose operon of rhizobium leguminosarum, rhau has not been assigned a function. the construction of a delta rhau strain revealed a growth phenotype that was slower than that of the wild-type strain, although the ultimate cell yields were equivalent. the transport of l-rhamnose into the cell and the rate of its phosphorylation were unaffected by the mutation. rhau exhibits weak sequence similarity to the formerly hypothetical protein yiil of escherichia coli ...200818156270
rhau of rhizobium leguminosarum is a rhamnose mutarotase.of the nine genes comprising the l-rhamnose operon of rhizobium leguminosarum, rhau has not been assigned a function. the construction of a delta rhau strain revealed a growth phenotype that was slower than that of the wild-type strain, although the ultimate cell yields were equivalent. the transport of l-rhamnose into the cell and the rate of its phosphorylation were unaffected by the mutation. rhau exhibits weak sequence similarity to the formerly hypothetical protein yiil of escherichia coli ...200818156270
intergeneric coaggregation among drinking water bacteria: evidence of a role for acinetobacter calcoaceticus as a bridging bacterium.intergeneric coaggregation of drinking water bacteria was tested. acinetobacter calcoaceticus was found not only to autoaggregate but also to coaggregate with four of the five other isolates (burkholderia cepacia, methylobacterium sp., mycobacterium mucogenicum, sphingomonas capsulata, and staphylococcus sp.). in its absence, no coaggregation was found. interactions were lectin-saccharide mediated. the putative bridging function of a. calcoaceticus was evidenced by multispecies biofilm studies, ...200818156333
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
lipase expression in pseudomonas alcaligenes is under the control of a two-component regulatory system.preliminary observations in a large-scale fermentation process suggested that the lipase expression of pseudomonas alcaligenes can be switched on by the addition of certain medium components, such as soybean oil. in an attempt to elucidate the mechanism of induction of lipase expression, we have set up a search method for genes controlling lipase expression by use of a cosmid library containing fragments of p. alcaligenes genomic dna. a screen for lipase hyperproduction resulted in the selection ...200818192420
single-culture aerobic granules with acinetobacter calcoaceticus.aerobic granules are cultivated by a single bacterial strain, acinetobacter calcoaceticus, in a sequencing batch reactor (sbr). this strain presents as a good phenol reducer and an efficient auto coagulator in the presence of phenol, mediated by heat-sensitive adhesins proteins. stable 2.3-mm granules were formed in the sbr following a 7-week cultivation. these granules exhibit excellent settling attributes and degrade phenol efficiently at concentrations of 250-2,000 mg l(-1). the corresponding ...200818193420
comprehensive bactericidal activity of an ethanol-based hand gel in 15 seconds.some studies indicate that the commonly recommended 30 s application time for the post contamination treatment of hands may not be necessary as the same effect may be achieved with some formulations in a shorter application time such as 15 s.200818211682
development and evaluation of immunochromatographic assay for simple and rapid detection of campylobacter jejuni and campylobacter coli in human stool specimens.an immunochromatographic assay (campy-ica) using a newly generated single monoclonal antibody against a 15-kda cell surface protein of campylobacter jejuni was developed. when cell suspensions of 86 c. jejuni strains and 27 campylobacter coli strains were treated with a commercially available bacterial protein extraction reagent and the resulting extracts were tested with the campy-ica, they all yielded positive results. the minimum detectable limits for the c. jejuni strains ranged from 1.8 x 1 ...200818256225
in vitro activity of tigecycline and comparators against carbapenem-susceptible and resistant acinetobacter baumannii clinical isolates in italy.in a recent multi-centre italian survey (2003-2004), conducted in 45 laboratories throughout italy with the aim of monitoring microorganisms responsible for severe infections and their antibiotic resistance, acinetobacter baumannii was isolated from various wards of 9 hospitals as one of the most frequent pathogens. one hundred and seven clinically significant strains of a. baumannii isolates were included in this study to determine the in vitro activity of tigecycline and comparator agents.200818261233
plasticity of the systemic inflammatory response to acute infection during critical illness: development of the riboleukogram.diagnosis of acute infection in the critically ill remains a challenge. we hypothesized that circulating leukocyte transcriptional profiles can be used to monitor the host response to and recovery from infection complicating critical illness.200818270561
direct aspiration of capsular bag material in a case of sequestered endophthalmitis.chronic recurrent endophthalmitis can occur following uncomplicated cataract surgery with intraocular lens implantation secondary to organisms sequestered in the capsular bag. there is a need to identify these sequestered organisms to facilitate appropriate management. frequently, specimens from the anterior chamber and vitreous cavity could be unyielding, especially in the early cases in which the vitreous is still uninvolved. this article highlights the technique of directly sampling the capsu ...200818292631
comparative molecular biological analysis of membrane transport genes in organisms.comparative analyses of membrane transport genes revealed many differences in the features of transport homeostasis in eight diverse organisms, ranging from bacteria to animals and plants. in bacteria, membrane-transport systems depend mainly on single genes encoding proteins involved in an atp-dependent pump and secondary transport proteins that use h(+) as a co-transport molecule. animals are especially divergent in their channel genes, and plants have larger numbers of p-type atpase and secon ...200818293089
outcomes of bacteremia in burn patients involved in combat operations overseas.burn patients constitute approximately 5% of casualties injured in support of us military operations in iraq (operation iraqi freedom [oif]) and afghanistan (operation enduring freedom [oef]). since the onset of these conflicts, there have been numerous casualties infected with multidrug-resistant bacteria. it is currently unclear if bacteremia with these multidrug-resistant organisms in oif/oef burn casualties is associated with increased mortality.200818308213
characterisation of carbapenem-resistant acinetobacter calcoaceticus--a. baumannii complex isolates in a third-level hospital in bogotá, colombia. 200818308519
a complete collection of single-gene deletion mutants of acinetobacter baylyi adp1.we have constructed a collection of single-gene deletion mutants for all dispensable genes of the soil bacterium acinetobacter baylyi adp1. a total of 2594 deletion mutants were obtained, whereas 499 (16%) were not, and are therefore candidate essential genes for life on minimal medium. this essentiality data set is 88% consistent with the escherichia coli data set inferred from the keio mutant collection profiled for growth on minimal medium, while 80% of the orthologous genes described as esse ...200818319726
multidrug-resistant organisms in military wounds from iraq and afghanistan.mortality from battlefield wounds has historically declined, thanks to better surgical management, faster transport of casualties, and improved antibiotics. today, one of the major challenges facing u.s. military caregivers is the presence of multidrug-resistant organisms in orthopaedic extremity wounds. the most frequently identified resistant strains of bacteria are staphylococcus aureus, klebsiella pneumoniae, pseudomonas aeruginosa, and acinetobacter calcoaceticus-baumannii complex. overuse ...200818347888
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- ...200818350144
moxifloxacin in the treatment of skin and skin structure infections.moxifloxacin is a recent addition to the fluoroquinolone class, differing from ciprofloxacin and other older agents in having much better in vitro activity against gram-positive aerobes while retaining potent activity against gram-negative aerobes. it is also active against the pathogens of human and animal bite wounds and those species of atypical mycobacteria associated with dermatologic infections. its activity against anaerobes is quite variable. moxifloxacin penetrates well into inflammator ...200618360653
the pyrroloquinoline quinone biosynthesis pathway revisited: a structural approach.the biosynthesis pathway of pyrroloquinoline quinone, a bacterial redox active cofactor for numerous alcohol and aldose dehydrogenases, is largely unknown, but it is proven that at least six genes in klebsiella pneumoniae (pqqa-f) are required, all of which are located in the pqq-operon.200818371220
cytological and transcript analyses reveal fat and lazy persister-like bacilli in tuberculous sputum.tuberculous sputum provides a sample of bacilli that must be eliminated by chemotherapy and that may go on to transmit infection. a preliminary observation that mycobacterium tuberculosis cells contain triacylglycerol lipid bodies in sputum, but not when growing in vitro, led us to investigate the extent of this phenomenon and its physiological basis.200818384229
oligonucleotide array-based identification of species in the acinetobacter calcoaceticus-a. baumannii complex in isolates from blood cultures and antimicrobial susceptibility testing of the isolates.acinetobacter calcoaceticus, a. baumannii, acinetobacter genomic species (gen. sp.) 3, and acinetobacter gen. sp. 13tu, which are included in the a. calcoaceticus-a. baumannii complex, are difficult to distinguish by phenotypic methods. an array with six oligonucleotide probes based on the 16s-23s rrna gene intergenic spacer (its) region was developed to differentiate species in the a. calcoaceticus-a. baumannii complex. validation of the array with a reference collection of 52 strains of the a. ...200818385442
diversity of predominant endophytic bacteria in european deciduous and coniferous trees.the diversity of endophytic bacteria residing in root, stem, and leaf tissues was examined in coniferous and deciduous tree species, scots pine (pinus sylvestris l.), silver birch (betula pendula roth), and rowan (sorbus aucuparia l.). using cultivation-dependent and -independent analyses, the bacterial communities were observed to be significantly different in the belowground (roots and rhizosphere) and aboveground (leaves and stems) samples of the respective host trees. no significant differen ...200818388988
[(3)h]adenine is a suitable radioligand for the labeling of g protein-coupled adenine receptors but shows high affinity to bacterial contaminations in buffer solutions.[(3)h]adenine has previously been used to label the newly discovered g protein-coupled murine adenine receptors. recent reports have questioned the suitability of [(3)h]adenine for adenine receptor binding studies because of curious results, e.g. high specific binding even in the absence of mammalian protein. in this study, we showed that specific [(3)h]adenine binding to various mammalian membrane preparations increased linearly with protein concentration. furthermore, we found that tris-buffer ...200718404448
intergeneric coaggregation of strains isolated from phenol-degrading aerobic granules.this work aims at exploring the intergeneric coaggregation of the pairs of strains, acinetobacter calcoaceticus i6 and bacillus thuringiensis i2 or candida tropicalis i9 (with genbank accession numbers eu250016, eu036759, and dq515822) isolated from phenol-degrading aerobic granules. the i2 and i6 are functionally similar stains, while the i6 and i9 are functionally dissimilar strains. the lectin-saccharide interaction controlled the coaggregation of both the i2+i6 and i6+i9 pairs, with the prot ...200818414847
biofilm formation and interactions of bacterial strains found in wastewater treatment systems.biofilm formation and adherence properties of 13 bacterial strains commonly found in wastewater treatment systems were studied in pure and mixed cultures using a crystal violet microtiter plate assay. four different culture media were used, wastewater, acetate medium, glucose medium and diluted nutrient broth. the medium composition strongly affected biofilm formation. all strains were able to form pure culture biofilms within 24 h in at least one of the tested culture media and three strains we ...200818422628
acquisition of a plasmid-borne blaoxa-58 gene with an upstream is1008 insertion conferring a high level of carbapenem resistance to acinetobacter baumannii.the oxacillinase gene was reported to confer limited resistance to carbapenem in acinetobacter baumannii. in this study, we have demonstrated that an a. baumannii clinical isolate harboring a plasmid, ptvicu53, has 11,037 bp encoding 13 open reading frames. a bla(oxa-58) gene with an upstream insertion of truncated isaba3 (deltaisaba3) and is1008 was found in this plasmid. deltaisaba3and is1008 provided two independent promoters for the transcription control of the bla(oxa-58) gene. the transfor ...200818443121
characterization of the carbapenem-hydrolyzing oxacillinase oxa-58 in an acinetobacter genospecies 3 clinical isolate.based on imipenem resistance in an acinetobacter genospecies 3 clinical isolate, we were able to identify, for the first time in this genomic species, a plasmid-encoded bla(oxa-58) gene that was 100% homologous to the same gene in acinetobacter baumannii.200818505859
purification and partial characterization of lignin peroxidase from acinetobacter calcoaceticus ncim 2890 and its application in decolorization of textile dyes.lignin peroxidase was purified (72-fold) from acinetobacter calcoaceticus ncim 2890. the purified lignin peroxidase (55-65 kda) showed dimeric nature. the maximum enzyme activity was observed at ph 1.0, between a broad temperature range of 50 and 70 degrees c, at h2o2 concentration (40 mm) and the substrate concentration (n-propanol, 100 mm). purified lignin peroxidase was able to oxidize a variety of substrates including mn2+, tryptophan, mimosine, l-dopa, hydroquinone, xylidine, n-propanol, ve ...200918506630
selection and identification of bacterial strains with methyl-tert-butyl ether, ethyl-tert-butyl ether, and tert-amyl methyl ether degrading capacities.nine bacterial strains isolated from two hydrocarbon-contaminated soils were selected because of their capacity for growth in culture media amended with 200 mg/l of one of the following gasoline oxygenates: methyl-tert-butyl ether (mtbe), ethyl-tert-butyl ether (etbe), and tert-amyl methyl ether (tame). these strains were identified by amplification of their 16s rrna gene, using fdl and rd1 primers, and were tested for their capacity to grow and biotransform these oxygenates in both mineral and ...200818522454
the surface activity of acinetobacter calcoaceticus sp. 2ca2.the hydrocarbon metabolizing acinetobacter calcoaceticus sp. 2ca2 reduces the surface tension of the culture broth during growth on liquid hydrocarbons. this activity, which is not evident during growth on soluble substrates, is associated with the whole cells. removing the cells from the culture broth increases the surface tension of the liquid phase. the cells when resuspended in water result in a dramatic lowering of the surface tension. acinetobacter sp. 2ca2 tends to partition between the t ...198418553533
utilization of short chain monocarboxylic acids in an effluent of a petrochemical industry by acinetobacter calcoaceticus.the aqueous effluent generated by the fischer--tropsch process, containing a total of 13 g/l c(2)-c(5) monocarboxylic acids, was investigated as a potential substrate for the production of single-cell protein (scp). a bacterial isolate, acinetobacter calcoaceticus, could utilize all the acids in the effluent simultaneously in chemostat cultures, and no residual acids were detected in the culture below a dilution rate of 0.78 h(-1). the critical dilution rate was 1.04 h(-1). the maintenance energ ...198518553646
acinetobacter baumannii: a universal threat to public health?acinetobacter spp. are non-fermentative, strictly aerobic, gram-negative microorganisms with a confusing taxonomic history. the acinetobacter baumannii-acinetobacter calcoaceticus complex is the species most commonly isolated from clinical specimens. it is ubiquitous in nature and has been found as part of the normal skin, throat and rectal flora as well as in food and body lice. it colonises patients in intensive care units and contaminates inanimate hospital surfaces and devices as well as wou ...200818571905
quantification of the degree of acclimation of a mixed culture to an industrial landfill leachate.quantification of the degree of acclimation of a mixed culture is demonstrated. an industrial landfill leachate was used as a model mixed substrate. the biodegradable fraction, the specific rate of substrate uptake, and the apparent reaction order were measured. the method of acclimation did not appear to affect the biodegradable fraction. the apparent reaction order is shown to be related to the difference between the rates of uptake of the various leachate components. this difference is define ...198718581494
cell adsorption and local accumulation of extracellular polysaccharide in an immobilized acinetobacter calcoaceticus system.acinetobacter calcoaceticus can be immobilized on celite by adsorption. the salt concentrations suitable for immobilized cell fermentation are between 10 and 50 mm phosphate concentration. low salt concentrations cause desorption of immobilized cells while high salt concentrations inhibit the adsorption of cells on celite. it is also found that cell adsorption is better at lower ph than at higher ph. an airlift fermentation using immobilized cells at 300 g/l celite loading shows that about 70% o ...198918588066
mechanisms for biopolymer accumulation in immobilized acinetobacter calcoaceticus system.the gram-positive bacteria, acinetobacter calcoaceticus, is capable of accumulating biopolymer in the carrier matrix of an immobilized cell system. several possible mechanisms for the biopolymer accumulation are evaluated. it appears that direct solid surface polymer adsorption and polymer diffusion limitation within the pore space are minor factors in biopolymer accumulation. calculations demonstrate that the cell bound polymer to dry cell weight ratio is much higher for immobilized cells than ...199018595094
modeling and experimental validation of carbon dioxide evolution in alkalophilic cultures.the chemical reactions involving carbon dioxide in mineral culture media are considered. a mathematic model is set up, based on published data, which is valid at ph values below 9, and in which the nonideality of the solution is taken into account. the crucial parameter is the constant expressing the equilibrium between carbon dioxide and bicarbonate, k(1).the reactions were studied in three different aqueous solutions: water, mineral salt medium, and a suspension with nongrowing bacterial cells ...199218600908
hydrocarbon degradation by acinetobacter calcoaceticus rag-1 using the self-cycling fermentation technique.the use of self-cycling fermentations (scfs) as a method for dealing with insoluble carbon substrates was examined. the emulsan-producing acinetobacter calcoaceticus rag-1 was used as the test organism. limiting concentrations of hexadecane, 1-hexadecene, or 1-chlorohexadecane were used as the carbon substrate. the parameters monitored were residual hydrocarbon concentration, cycle time (doubling time), biomass concentration and emulsan concentration. cycle-to-cycle variations of the measured pa ...199218601183
self-cycling fermentation in a stirred tank reactor.self-cycling fermentations (scfs) were conducted in a stirred tank apparatus using bacillus subtilis and acinetobacter calcoaceticus. the systems were very stable and the experiments lasted through many cycles. the variation of parameters such as biomass and doubling time from cycle to cycle was small. the stirred tank reactor (str) allowed a much better control of the working volume in the fermentor from cycle to cycle, compared to the cyclone column, and it was not necessary to make periodic c ...199318609666
polymicrobial bacteremia in cancer patients: analysis of risk factors, etiology and outcome in 214 episodes.two hundred and fourteen episodes of polymicrobial bacteremia in 182 cancer patients in a period of 6 years in a 360-bed national cancer institute were analyzed for etiology, risk factors and outcome. variables were compared with 187 episodes of monomicrobial bacteremias in 147 cancer patients to find statistical significance among risk factors, etiology and outcome. urinary catheters and breakthrough bacteremia were the only risk factors associated with polymicrobial in comparison to monomicrob ...199618611744
the medium-chain dehydrogenase/reductase engineering database: a systematic analysis of a diverse protein family to understand sequence-structure-function relationship.the medium-chain dehydrogenase/reductase engineering database (mdred, http://www.mdred.uni-stuttgart.de) has been established to serve as an analysis tool for a systematic investigation of sequence-structure-function relationships. it includes sequence and structure information of 2684 and 42 medium-chain dehydrogenases/reductases (mdrs), respectively. although mdrs are very diverse in sequence, they have a conserved tertiary structure. mdrs are assigned to 199 homologous families and 29 superfa ...200818614751
identification of the wax ester synthase/acyl-coenzyme a: diacylglycerol acyltransferase wsd1 required for stem wax ester biosynthesis in arabidopsis.wax esters are neutral lipids composed of aliphatic alcohols and acids, with both moieties usually long-chain (c(16) and c(18)) or very-long-chain (c(20) and longer) carbon structures. they have diverse biological functions in bacteria, insects, mammals, and terrestrial plants and are also important substrates for a variety of industrial applications. in plants, wax esters are mostly found in the cuticles coating the primary shoot surfaces, but they also accumulate to high concentrations in the ...200818621978
mathematical model of self-cycling fermentation.this article presents a mathematical model for biomass, limiting substrate, and dissolved oxygen concentrations during stable operation of self-cycling fermentation (scf). laboratory experiments using the bacterium acinetobacter calcoaceticus rag-1 and ethanol as the limiting substrate were performed to validate the model. a computer simulation developed from the model successfully matched experimental scf intracycle trends and end-of-cycle results and, most importantly, settled into an unimpose ...199518623278
classification, error detection, and reconciliation of process information in complex biochemical systems.bioprocess identification starts with collection of process information. usually there is a variety of information available, consisting of actual measurement data, historical data, empirical kinetic and yield correlations, and general knowledge available from literature. a central problem is to find out how the various pieces of information should be integrated. in addition, one should know how to deal with missing, inconsistent, or too inaccurate data. recently, a general systematic method for ...199618623590
acinetobacter baumannii: emergence of a successful pathogen.acinetobacter baumannii has emerged as a highly troublesome pathogen for many institutions globally. as a consequence of its immense ability to acquire or upregulate antibiotic drug resistance determinants, it has justifiably been propelled to the forefront of scientific attention. apart from its predilection for the seriously ill within intensive care units, a. baumannii has more recently caused a range of infectious syndromes in military personnel injured in the iraq and afghanistan conflicts. ...200818625687
native bacterial endophytes promote host growth in a species-specific manner; phytohormone manipulations do not result in common growth responses.all plants in nature harbor a diverse community of endophytic bacteria which can positively affect host plant growth. changes in plant growth frequently reflect alterations in phytohormone homoeostasis by plant-growth-promoting (pgp) rhizobacteria which can decrease ethylene (et) levels enzymatically by 1-aminocyclopropane-1-carboxylate (acc) deaminase or produce indole acetic acid (iaa). whether these common pgp mechanisms work similarly for different plant species has not been rigorously teste ...200818628963
acinetobacter sp. strain ths, a novel psychrotolerant and alkalitolerant bacterium that utilizes hydrocarbon.a novel psychrotolerant, alkalitolerant bacterium, strain ths, was isolated from a soil sample immersed in hot spring water containing hydrocarbons and grown on a chemically defined medium containing n-tetradecane as the sole carbon source. the isolate grew at 0 degrees c but not at temperatures higher than 45 degrees c; its optimum growth temperature was 27 degrees c. it grew in the ph range of 7-9. the strain utilized c(13)-c(30) n-alkane and fluorene at ph 9 and 4 degrees c. to our knowledge, ...200818629434
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
phytotoxic effects of (+/-)-catechin in vitro, in soil, and in the field.exploring the residence time of allelochemicals released by plants into different soils, episodic exposure of plants to allelochemicals, and the effects of allelochemicals in the field has the potential to improve our understanding of interactions among plants.200818648546
7alpha- and 12alpha-hydroxysteroid dehydrogenases from acinetobacter calcoaceticus lwoffii: a new integrated chemo-enzymatic route to ursodeoxycholic acid.we report the very efficient biotransformation of cholic acid to 7-keto- and 7,12-diketocholic acids with acinetobacter calcoaceticus lwoffii. the enzymes responsible of the biotransformation (i.e. 7alpha- and 12alpha-hydroxysteroid dehydrogenases) are partially purified and employed in a new chemo-enzymatic synthesis of ursodeoxycholic acid starting from cholic acid. the first step is the 12alpha-hsdh-mediated total oxidation of sodium cholate followed by the wolf-kishner reduction of the carbo ...200818674553
observations on carbapenem resistance by minimum inhibitory concentration in nosocomial isolates of acinetobacter species: an experience at a tertiary care hospital in north india.acinetobacter species are emerging as an important nosocomial pathogen. multidrug-resistant acinetobacter spp. has limited the option for effective treatment. although carbapenems are effective for the treatment of such infections, resistance to this drug has recently been reported. this study was undertaken to assess resistance to carbapenem in clinical isolates of acinetobacter spp. from hospitalized patients by both disc-diffusion and minimum inhibitory concentration (mic) methods. all clinic ...200818686551
in vitro antibacterial activity of vertilmicin and its susceptibility to modifications by the recombinant aac6'-aph2'' enzyme.vertilmicin is a new semisynthetic aminoglycoside with a structure similar to that of netilmicin except for a methyl group at the c-6' position. in the present study, the in vitro antibacterial activity of vertilmicin was studied, and its susceptibility to modifications by the recombinant aminoglycoside bifunctional modifying enzyme aac(6')-aph(2'') was compared with those of verdamicin and netilmicin. a total of 1,185 clinical isolates collected from hospitals in beijing between 2000 and 2001 w ...200818710917
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