Publications

evaluation of an immunochromatographic assay kit for rapid identification of mycobacterium tuberculosis complex in clinical isolates.	we evaluated a new immunochromatographic assay (ica) using mouse monoclonal anti-mpt64 antibody for rapid discrimination between mycobacterium tuberculosis and nontuberculous mycobacteria in clinical isolates. a study with mycobacteria and other organisms showed excellent sensitivity (approximately equal 99%) and specificity (100%) and an appropriate detection limit (10(5) cfu/ml) when tested with m. tuberculosis h37rv. this ica can simplify the identification of m. tuberculosis in clinical labo ...	2009	19052177
evaluation of an immunochromatographic assay kit for rapid identification of mycobacterium tuberculosis complex in clinical isolates.	we evaluated a new immunochromatographic assay (ica) using mouse monoclonal anti-mpt64 antibody for rapid discrimination between mycobacterium tuberculosis and nontuberculous mycobacteria in clinical isolates. a study with mycobacteria and other organisms showed excellent sensitivity (approximately equal 99%) and specificity (100%) and an appropriate detection limit (10(5) cfu/ml) when tested with m. tuberculosis h37rv. this ica can simplify the identification of m. tuberculosis in clinical labo ...	2009	19052177
dna aptamers bind specifically and selectively to (1-->3)-beta-d-glucans.	(1-->3)-beta-d-glucans are structural cell wall components of fungi, plants, and some bacteria and have been linked with human respiratory symptoms following aerosol exposure. a clear interpretation of the health impact of (1-->3)-beta-d-glucans is limited by the high cost and uncertainties associated with current glucan quantitation methods. the objective of this research is to develop dna aptamers for the measurement of (1-->3)-beta-d-glucans. aptamers are synthetic dna functional binding mole ...	2009	19061867
dna aptamers bind specifically and selectively to (1-->3)-beta-d-glucans.	(1-->3)-beta-d-glucans are structural cell wall components of fungi, plants, and some bacteria and have been linked with human respiratory symptoms following aerosol exposure. a clear interpretation of the health impact of (1-->3)-beta-d-glucans is limited by the high cost and uncertainties associated with current glucan quantitation methods. the objective of this research is to develop dna aptamers for the measurement of (1-->3)-beta-d-glucans. aptamers are synthetic dna functional binding mole ...	2009	19061867
conformational exchange in pseudoazurin: different kinds of microsecond to millisecond dynamics characterized by their ph and buffer dependence using 15n nmr relaxation.	the dynamics of the reduced form of the blue copper protein pseudoazurin from alcaligenes faecalis s-6 was investigated using (15)n relaxation measurements with a focus on the dynamics of the micro- to millisecond time scale. different types of conformational exchange processes are observed in the protein on this time scale. at low ph, the protonation of the c-terminal copper-ligated histidine, his81, is observed. a comparison of the exchange rates in the presence and absence of added buffers sh ...	2009	19072172
genes involved in arsenic transformation and resistance associated with different levels of arsenic-contaminated soils.	arsenic is known as a toxic metalloid, which primarily exists in inorganic form [as(iii) and as(v)] and can be transformed by microbial redox processes in the natural environment. as(iii) is much more toxic and mobile than as(v), hence microbial arsenic redox transformation has a major impact on arsenic toxicity and mobility which can greatly influence the human health. our main purpose was to investigate the distribution and diversity of microbial arsenite-resistant species in three different a ...	2009	19128515
internalization of dectin-1 terminates induction of inflammatory responses.	dectin-1 is a pattern-recognition receptor recognizing beta-(1,3)-glucans found on fungal cell walls. dectin-1 plays an important role in immunity to fungi by mediating phagocytic clearance of fungal particles and inducing transcription of innate response genes. we show here that the two processes are linked and that dectin-1 signalling for inflammation is attenuated by phagocytosis. blocking dectin-1 ligand-dependent internalization using either actin polymerization or dynamin inhibitors, large ...	2009	19130473
cd40-cd40l cross-talk integrates strong antigenic signals and microbial stimuli to induce development of il-17-producing cd4+ t cells.	il-17-producing cd4(+) t cells have been recognized as key players in organ-related autoimmune disease; however, the parameters that govern their development are yet to be elucidated fully. by using both in vivo and in vitro systems, we have investigated the role of antigen dose, pathogen-associated molecular patterns, and cd40-cd40 ligand (cd40l) cross-talk in th17 differentiation. we found that the strength of antigenic stimulation critically influenced the extent of th17 differentiation, beca ...	2009	19136631
optgraft: a computational procedure for transferring a binding site onto an existing protein scaffold.	one of the many challenging tasks of protein design is the introduction of a completely new function into an existing protein scaffold. in this study, we introduce a new computational procedure optgraft for placing a novel binding pocket onto a protein structure so as its geometry is minimally perturbed. this is accomplished by introducing a two-level procedure where we first identify where are the most appropriate locations to graft the new binding pocket into the protein fold by minimizing the ...	2009	19177362
optgraft: a computational procedure for transferring a binding site onto an existing protein scaffold.	one of the many challenging tasks of protein design is the introduction of a completely new function into an existing protein scaffold. in this study, we introduce a new computational procedure optgraft for placing a novel binding pocket onto a protein structure so as its geometry is minimally perturbed. this is accomplished by introducing a two-level procedure where we first identify where are the most appropriate locations to graft the new binding pocket into the protein fold by minimizing the ...	2009	19177362
atrazine degradation by stable mixed cultures enriched from agricultural soil and their characterization.	the aim of this work was to enrich stable mixed cultures from atrazine-contaminated soil. the cultures were examined for their atrazine biodegradation efficiencies in comparison with j14a, a known atrazine-degrading strain of agrobacterium radiobacter. the cultures were also characterized to identify community structure and bacterial species present.	2009	19191954
crystallization and preliminary x-ray diffraction analysis of a complex between the electron-transfer partners hexameric cu-containing nitrite reductase and pseudoazurin.	the complex between cu-containing nitrite reductase (hdnir) and its electron-donor protein pseudoazurin (hdpaz) from hyphomicrobium denitrificans has been crystallized. the crystals were obtained from a mixture of the two proteins using the hanging-drop vapour-diffusion method in the presence of polyethylene glycol (peg) and 2-methyl-2,4-pentanediol (mpd) as precipitants. sds-page analysis demonstrated that the crystals contained both proteins. the x-ray diffraction experiment was carried out at ...	2009	19193999
purification and characterization of arsenite oxidase from arthrobacter sp.	the chemolithoautotroph, arthrobacter sp.15b oxidizes arsenite to arsenate using a membrane bound arsenite oxidase. the enzyme arsenite oxidase is purified to its homogeneity and identified using maldi-tof ms analysis. upon further characterization, it was observed that the enzyme is a heterodimer showing native molecular mass as approximately 100 kda and appeared as two subunits of approximately 85 kda lsu and 14 kda ssu on sds-page. the v(max) and k(m) values of the enzyme was found to be 2.45 ...	2009	19214757
crystal structure of a two-domain multicopper oxidase: implications for the evolution of multicopper blue proteins.	the two-domain multicopper oxidases are proposed to be key intermediates in the evolution of three-domain multicopper oxidases. a number of two-domain multicopper oxidases have been identified from genome sequences and are classified as type a, type b, or type c on the basis of the predicted location of the type 1 copper center. the crystal structure of blue copper oxidase, a type c two-domain multicopper oxidase from nitrosomonas europaea, has been determined to 1.9 a resolution. blue copper ox ...	2009	19224923
characterization of a polycyclic aromatic hydrocarbon degradation gene cluster in a phenanthrene-degrading acidovorax strain.	acidovorax sp. strain na3 was isolated from polycyclic aromatic hydrocarbon (pah)-contaminated soil that had been treated in a bioreactor and enriched with phenanthrene. the 16s rrna gene of the isolate possessed 99.8 to 99.9% similarity to the dominant sequences recovered during a previous stable-isotope probing experiment with [u-(13)c]phenanthrene on the same soil (d. r. singleton, s. n. powell, r. sangaiah, a. gold, l. m. ball, and m. d. aitken, appl. environ. microbiol. 71:1202-1209, 2005). ...	2009	19270134
a tn5051-like mer-containing transposon identified in a heavy metal tolerant strain achromobacter sp. ao22.	achromobacter sp. ao22 (formerly alcaligenes sp. ao22), a bacterial strain isolated from a lead-contaminated industrial site in australia, was previously found to be resistant to moderate to high levels of mercury, copper and other heavy metals. however, the nature and location of the genetic basis for mercuric ion resistance in this strain, had not been previously identified.	2009	19284535
arsenite oxidation by immobilized cells of alcaligenes faecalis strain o1201 in a fluidized-bed reactor.	arsenic(iii) oxidation was evaluated in a continuous-flow fluidized-bed reactor (fbr) with alcaligenes faecalis strain 01201 immobilized in gel beads. the fbr was operated under 300 mg/l citrate and a range of influent as(iii) concentrations (75 to 3000 mg/l) at short hydraulic retention times (1.06 to 3.17 hours). the ph and temperature in the fbr were maintained at optimal growth conditions for strain o1201 (ph 7 and 30 degrees c) throughout the study. a total of 10 quasi-steady-state operatin ...	2009	19323288
widespread distribution of cell defense against d-aminoacyl-trnas.	several l-aminoacyl-trna synthetases can transfer a d-amino acid onto their cognate trna(s). this harmful reaction is counteracted by the enzyme d-aminoacyl-trna deacylase. two distinct deacylases were already identified in bacteria (dtd1) and in archaea (dtd2), respectively. evidence was given that dtd1 homologs also exist in nearly all eukaryotes, whereas dtd2 homologs occur in plants. on the other hand, several bacteria, including most cyanobacteria, lack genes encoding a dtd1 homolog. here w ...	2009	19332551
structure of d-3-hydroxybutyrate dehydrogenase prepared in the presence of the substrate d-3-hydroxybutyrate and nad+.	d-3-hydroxybutyrate dehydrogenase from alcaligenes faecalis catalyzes the reversible conversion between d-3-hydroxybutyrate and acetoacetate. the enzyme was crystallized in the presence of the substrate d-3-hydroxybutyrate and the cofactor nad(+) at the optimum ph for the catalytic reaction. the structure, which was solved by x-ray crystallography, is isomorphous to that of the complex with the substrate analogue acetate. the product as well as the substrate molecule are accommodated well in the ...	2009	19342772
[denitrifying bacteria isolated from river sediment and its nitrogen and phosphorus removal capacity from river water].	20 strains of bacteria were isolated from river sediment using enrichment culture medium for denitrification, and the denitrification intensity was determined. f10, one of bacteria strain, was identified having the highest denitrifying intensity, and further used to test its role in the removing of nitrogen and phosphorus from wastewater in laboratory. by checking the individual morphology, colony culture characteristics, dna sequencing and 16s rdna gene bank, f10 was identified as alcaligenes f ...	2009	19353863
pseudomonas aeruginosa las quorum sensing autoinducer suppresses growth and biofilm production in legionella species.	bacteria commonly communicate with each other by a cell-to-cell signalling mechanism known as quorum sensing (qs). recent studies have shown that the las qs autoinducer n-(3-oxododecanoyl)-l-homoserine lactone (3-oxo-c(12)-hsl) of pseudomonas aeruginosa performs a variety of functions not only in intraspecies communication, but also in interspecies and interkingdom interactions. in this study, we report the effects of pseudomonas 3-oxo-c(12)-hsl on the growth and suppression of virulence factors ...	2009	19383702
mammalian nitrilase 1 homologue nit1 is a negative regulator in t cells.	the mammalian nit1 protein is homologous to plant and bacterial nitrilases. in flies and worms, nit1 is fused to the 5' end of fhit, suggesting that nit1 may functionally interact with the fhit pathway. fhit has been shown to play a role of a tumor suppressor. somatic loss of fhit in human tissues is associated with a wide variety of cancers. deletion of fhit results in a predisposition to induced and spontaneous tumors in mice. it has been suggested that nit1 collaborates with fhit in tumor sup ...	2009	19395373
conjugative type 4 secretion system of a novel large plasmid from the chemoautotroph tetrathiobacter kashmirensis and construction of shuttle vectors for alcaligenaceae.	tetrathiobacter spp. and other members of the alcaligenaceae are metabolically versatile and environmentally significant. a novel, approximately 60-kb conjugative plasmid, pbtk445, from the sulfur chemolithoautotroph tetrathiobacter kashmirensis, was identified and characterized. this plasmid exists at a low copy number of 2 to 3 per host chromosome. the portion of pbtk445 sequenced so far ( approximately 25 kb) harbors genes putatively involved in replication, transfer functions, partition, and ...	2009	19411426
strain-specific virulence of bordetella hinzii in poultry.	bordetella hinzii is commonly acquired from the respiratory tract of diseased poultry but is generally regarded as nonpathogenic in avian hosts because attempts to demonstrate disease following experimental infection of chickens and turkeys have failed. recently, with the availability of highly specific dna-based methods for identification of this agent, it was recognized that some isolates used in previous studies were misidentified at the time of their acquisition as bordetella avium, b. avium ...	2009	19432003
high frequency of multidrug-resistant gram-negative rods in 2 neonatal intensive care units in the philippines.	although hospital-acquired infections appear to be a growing threat to the survival of newborns in the developing world, the epidemiology of this problem remains poorly characterized.	2009	19435448
microflora of the penile skin-lined neovagina of transsexual women.	the microflora of the penile skin-lined neovagina in male-to-female transsexuals is a recently created microbial niche which thus far has been characterized only to a very limited extent. yet the knowledge of this microflora can be considered as essential to the follow-up of transsexual women. the primary objective of this study was to map the neo-vaginal microflora in a group of 50 transsexual women for whom a neovagina was constructed by means of the inverted penile skin flap technique. second ...	2009	19457233
impact of antifungals producing rhizobacteria on the performance of vigna radiata in the presence of arbuscular mycorrhizal fungi.	plant growth-promoting rhizobacteria (pgpr) that produce antifungal metabolites are potential threats for the arbuscular mycorrhizal (am) fungi known for their beneficial symbiosis with plants that is crucially important for low-input sustainable agriculture. to address this issue, we used a compartmented container system where test plants, vigna radiata, could only reach a separate nutrient-rich compartment indirectly via the hyphae of am fungi associated with their roots. in this system, where ...	2009	19458967
functions of manduca sexta hemolymph proteinases hp6 and hp8 in two innate immune pathways.	serine proteinases in insect plasma have been implicated in two types of immune responses; that is, activation of prophenoloxidase (propo) and activation of cytokine-like proteins. we have identified more than 20 serine proteinases in hemolymph of the tobacco hornworm, manduca sexta, but functions are known for only a few of them. we report here functions of two additional m. sexta proteinases, hemolymph proteinases 6 and 8 (hp6 and hp8). hp6 and hp8 are each composed of an amino-terminal clip d ...	2009	19487692
[evaluation of occurrence of alcaligenes faecalis in clinical samples of patients of the university hospital in bydgoszcz].	alcaligenes faecalis is an aerobic gram-negative, non-fermentative rod. it's saprophyte of water and soil. it may be recovered from wet places of hospital environment. it is considered as an opportunistic pathogen. the aim of this review was evaluation of occurrence in clinical samples and susceptibility to antibiotics of 72 a. faecalis strains isolated in years 2003-2008. over 30% of strains were isolated from patients in surgical ward, 19.6% from patients in outpatient clinic and almost 14% fr ...	2009	19517818
annotating enzymes of uncertain function: the deacylation of d-amino acids by members of the amidohydrolase superfamily.	the catalytic activities of three members of the amidohydrolase superfamily were discovered using amino acid substrate libraries. bb3285 from bordetella bronchiseptica, gox1177 from gluconobacter oxidans, and sco4986 from streptomyces coelicolor are currently annotated as d-aminoacylases or n-acetyl-d-glutamate deacetylases. these three enzymes are 22-34% identical to one another in amino acid sequence. substrate libraries containing nearly all combinations of n-formyl-d-xaa, n-acetyl-d-xaa, n-s ...	2009	19518059
identification of an aox system that requires cytochrome c in the highly arsenic-resistant bacterium ochrobactrum tritici scii24.	microbial biotransformations have a major impact on environments contaminated with toxic elements, including arsenic, resulting in an increasing interest in strategies responsible for how bacteria cope with arsenic. in the present work, we investigated the metabolism of this metalloid in the bacterium ochrobactrum tritici scii24. this heterotrophic organism contains two different ars operons and is able to oxidize arsenite to arsenate. the presence of arsenite oxidase genes in this organism was ...	2009	19525272
novel denitrifying bacterium ochrobactrum anthropi yd50.2 tolerates high levels of reactive nitrogen oxides.	most studies of bacterial denitrification have used nitrate (no3-) as the first electron acceptor, whereas relatively less is understood about nitrite (no2-) denitrification. we isolated novel bacteria that proliferated in the presence of high levels of no2- (72 mm). strain yd50.2, among several isolates, was taxonomically positioned within the alpha subclass of proteobacteria and identified as ochrobactrum anthropi yd50.2. this strain denitrified no2-, as well as no3-. the gene clusters for den ...	2009	19542343
broad-range pcr, cloning and sequencing of the full 16s rrna gene for detection of bacterial dna in synovial fluid samples of tunisian patients with reactive and undifferentiated arthritis.	broad-range rdna pcr provides an alternative, cultivation-independent approach for identifying bacterial dna in reactive and other form of arthritis. the aim of this study was to use broad-range rdna pcr targeting the 16s rrna gene in patients with reactive and other forms of arthritis and to screen for the presence of dna from any given bacterial species in synovial fluid (sf) samples.	2009	19570210
identification of amino acid residues responsible for the enantioselectivity and amide formation capacity of the arylacetonitrilase from pseudomonas fluorescens ebc191.	the nitrilase from pseudomonas fluorescens ebc191 converted (r,s)-mandelonitrile with a low enantioselectivity to (r)-mandelic acid and (s)-mandeloamide in a ratio of about 4:1. in contrast, the same substrate was hydrolyzed by the homologous nitrilase from alcaligenes faecalis atcc 8750 almost exclusively to (r)-mandelic acid. a chimeric enzyme between both nitrilases was constructed, which represented in total 16 amino acid exchanges in the central part of the nitrilase from p. fluorescens ebc ...	2009	19581475
demonstration of proton-coupled electron transfer in the copper-containing nitrite reductases.	the reduction of nitrite (no2-) into nitric oxide (no), catalyzed by nitrite reductase, is an important reaction in the denitrification pathway. in this study, the catalytic mechanism of the copper-containing nitrite reductase from alcaligenes xylosoxidans (axnir) has been studied using single and multiple turnover experiments at ph 7.0 and is shown to involve two protons. a novel steady-state assay was developed, in which deoxyhemoglobin was employed as an no scavenger. a moderate solvent kinet ...	2009	19586913
airway infection with a novel cupriavidus species in persons with cystic fibrosis.	we describe the recovery and identification of a bacterium that represents a new species of the genus cupriavidus from cultures of respiratory tract specimens from two patients with cystic fibrosis (cf). the elucidation of the role of this species in cf lung disease will require an evaluation of a greater number of cases.	2009	19605576
synergy between ficolin-2 and pentraxin 3 boosts innate immune recognition and complement deposition.	the long pentraxin 3 (ptx3) is a multifunctional soluble pattern recognition molecule that is crucial in innate immune protection against opportunistic fungal pathogens such as aspergillus fumigatus. the mechanisms that mediate downstream effects of ptx3 are largely unknown. however, ptx3 interacts with c1q from the classical pathway of the complement. the ficolins are recognition molecules of the lectin complement pathway sharing structural and functional characteristics with c1q. thus, we inve ...	2009	19632990
rapid real-time pcr assays for detection of klebsiella pneumoniae with the rmpa or maga genes associated with the hypermucoviscosity phenotype: screening of nonhuman primates.	the relationship of mucoviscosity-associated (maga) and/or regulator of mucoid phenotype (rmpa) genes to the klebsiella pneumoniae hypermucoviscosity (hmv) phenotype has been reported. we previously demonstrated that rmpa+ k. pneumoniae can cause serious disease in african green monkeys and isolated rmpa+ and maga+ hmv k. pneumoniae from other species of non-human primates. to rapidly screen african green monkeys/non-human primates for these infections, we developed three real-time pcr assays. t ...	2009	19644019
characterization of sucrose-glutamic acid maillard products (sgmps) degrading bacteria and their metabolites.	two aerobic bacteria rnbs1 and rnbs3 capable to degrade and utilize sucrose-glutamic acid maillard products (sgmps) as carbon, nitrogen and energy source were isolated and characterized as alcaligenes faecalis (dq659619) and bacillus cereus (dq659620) respectively by 16s rrna gene sequence analysis. in present study, mixed bacterial culture was found more effective compared to axenic culture rnbs1 and rnbs3 decolourizing 73.79%, 66.80% and 62.56% sgmps, respectively. the sgmps catabolizing enzym ...	2009	19665891
maternal and early onset neonatal bacterial sepsis: burden and strategies for prevention in sub-saharan africa.	maternal and child health are high priorities for international development. through a review of published work, we show substantial gaps in current knowledge on incidence (cases per live births), aetiology, and risk factors for both maternal and early onset neonatal bacterial sepsis in sub-saharan africa. although existing published data suggest that sepsis causes about 10% of all maternal deaths and 26% of neonatal deaths, these are likely to be considerable underestimates because of methodolo ...	2009	19555902
nitrilase enzymes and their role in plant-microbe interactions.	nitrilase enzymes (nitrilases) catalyse the hydrolysis of nitrile compounds to the corresponding carboxylic acid and ammonia, and have a wide range of industrial and biotechnological applications, including the synthesis of industrially important carboxylic acids and bioremediation of cyanide and toxic nitriles. nitrilases are produced by a wide range of organisms, including plants, bacteria and fungi, but despite their biotechnological importance, the role of these enzymes in living organisms i ...	2009	21255276
the pha depolymerase engineering database: a systematic analysis tool for the diverse family of polyhydroxyalkanoate (pha) depolymerases.	polyhydroxyalkanoates (phas) can be degraded by many microorganisms using intra- or extracellular pha depolymerases. pha depolymerases are very diverse in sequence and substrate specificity, but share a common alpha/beta-hydrolase fold and a catalytic triad, which is also found in other alpha/beta-hydrolases.	2009	19296857
biodegradability of plastics.	plastic is a broad name given to different polymers with high molecular weight, which can be degraded by various processes. however, considering their abundance in the environment and their specificity in attacking plastics, biodegradation of plastics by microorganisms and enzymes seems to be the most effective process. when plastics are used as substrates for microorganisms, evaluation of their biodegradability should not only be based on their chemical structure, but also on their physical pro ...	2009	19865515
genetic diversity of siderophore-producing bacteria of tobacco rhizosphere.	the genetic diversity of siderophore-producing bacteria of tobacco rhizosphere was studied by amplified ribosomal dna restriction analysis (ardra), 16s rrna sequence homology and phylogenetics analysis methods. studies demonstrated that 85% of the total 354 isolates produced siderophores in iron limited liquid medium. a total of 28 ardra patterns were identified among the 299 siderophore-producing bacterial isolates. the 28 ardra patterns represented bacteria of 14 different genera belonging to ...	2009	24031358
beta-(1,3)-glucan exposure assessment by passive airborne dust sampling and new sensitive immunoassays.	associations between house dust-associated beta-(1,3)-glucan exposure and airway inflammatory reactions have been reported, while such exposures in early childhood have been suggested to protect against asthma and wheezing. most epidemiological studies have used reservoir dust samples and an inhibition enzyme immunoassay (eia) for beta-(1,3)-glucan exposure assessment. the objective of this study was to develop inexpensive but highly sensitive enzyme immunoassays to measure airborne beta-(1,3)-g ...	2009	20038709
beta-(1,3)-glucan exposure assessment by passive airborne dust sampling and new sensitive immunoassays.	associations between house dust-associated beta-(1,3)-glucan exposure and airway inflammatory reactions have been reported, while such exposures in early childhood have been suggested to protect against asthma and wheezing. most epidemiological studies have used reservoir dust samples and an inhibition enzyme immunoassay (eia) for beta-(1,3)-glucan exposure assessment. the objective of this study was to develop inexpensive but highly sensitive enzyme immunoassays to measure airborne beta-(1,3)-g ...	2009	20038709
hypochlorite digestion method for efficient recovery of phb from alcaligenes faecalis.	we reported the optimum amount of phb accumulated by alcaligenes faecalis during its 24 h growth under nitrogen deficient conditions. after 24 h incubation decrease in the amount of phb was recorded. hypochlorite digestion of biomass of organism followed by extraction with a solvent system consisting of 1:1 mixture of ethanol and acetone resulted in efficient recovery of phb vis-à-vis earlier methods. this solvent system gave a high recovery yield, i.e. 5.6 gl(-1) vis-à-vis earlier reported yiel ...	2009	23100774
free radical scavenging and antimicrobial properties of extracts of wild mushrooms.	antioxidant and antimicrobial potentials of extracts obtained from four wild mushrooms, termitomyces clypeatus (tce), termitomyces robustus (tre), lentinus subnudus (lse) and lenzites species (lze) collected in nigeria were investigated. lse and lze displayed good scavenging activity against 2, 2-diphenyl-1-picrylhydrazyl (dpph) and ferrous ion radicals at concentration of 2 mg/ml. however, tre and tce exhibited better superoxide anion scavenging effect at 2 mg/ml. all extracts (tce, tre, lse an ...	2009	24031376
advances in marine microbial symbionts in the china sea and related pharmaceutical metabolites.	marine animals and plants such as sponges, sea squirts, corals, worms and algae host diverse and abundant symbiotic microorganisms. marine microbial symbionts are possible the true producers or take part in the biosynthesis of some bioactive marine natural products isolated from the marine organism hosts. investigation of the pharmaceutical metabolites may reveal the biosynthesis mechanisms of related natural products and solve the current problem of supply limitation in marine drug development. ...	2009	19597576
control of biogenic amines in food--existing and emerging approaches.	biogenic amines have been reported in a variety of foods, such as fish, meat, cheese, vegetables, and wines. they are described as low molecular weight organic bases with aliphatic, aromatic, and heterocyclic structures. the most common biogenic amines found in foods are histamine, tyramine, cadaverine, 2-phenylethylamine, spermine, spermidine, putrescine, tryptamine, and agmatine. in addition octopamine and dopamine have been found in meat and meat products and fish. the formation of biogenic a ...	2010	21535566
protein engineering of penicillin acylase.	penicillin acylases (pa) are widely used for the production of semi-synthetic β-lactam antibiotics and chiral compounds. in this review, the latest achievements in the production of recombinant enzymes are discussed, as well as the results of pa type g protein engineering.	2010	22649651
growth and siderophores production in alcaligenes faecalis is regulated by metal ions.	during stationary phase of growth under low stress of iron in succinic acid medium, alcaligenes feacalis bccm id 2374 produced microbial iron chelators. increase in iron concentration supported bacterial growth but suppressed siderophores production, 1 μm and 2 μm of iron was optimum for maximum siderophore yield, i.e. 354 and 360 μg/ml in untreated and deferrated medium, respectively. threshold level of iron, which suppressed siderophores production in a. feacalis bccm id 2374, was 20 μm. ten m ...	2010	23100825
penicillin acylase-catalyzed effective and stereoselective acylation of 1-phenylethylamine in aqueous medium using non-activated acyl donor.	until recently, the biocatalytic preparation of enantiomerically pure amines was based on stereoselective acyl transfer in an organic medium using activated acyl donors. the possibility of performing an effective and enantioselective enzymatic acylation of amines in an aqueous medium without using activated acyl donors was demonstrated for the first time as the example of direct condensation of phenylacetic acid and racemic 1-phenylethylamine. direct condensation of the acid and the amine took p ...	2010	22649633
biosynthesis and biodegradation of 3-hydroxypropionate-containing polyesters.	3-hydroxypropionate (3hp) is an important compound in the chemical industry, and the polymerized 3hp can be used as a bioplastic. in this review, we focus on polyesters consisting of 3hp monomers, including the homopolyester poly(3-hydroxypropionate) and copolyesters poly(3-hydroxybutyrate-co-3-hydroxypropionate), poly(3-hydroxypropionate-co-3-hydroxybutyrate-co-3-hydroxyhexanoate-co-3-hydroxyoctanoate), poly(4-hydroxybutyrate-co-3-hydroxypropionate-co-lactate), and poly(3-hydroxybutyrate-co-3-h ...	2010	20543057
marine drugs from sponge-microbe association--a review.	the subject of this review is the biodiversity of marine sponges and associated microbes which have been reported to produce therapeutically important compounds, along with the contextual information on their geographic distribution. class demospongiae and the orders halichondrida, poecilosclerida and dictyoceratida are the richest sources of these compounds. among the microbial associates, members of the bacterial phylum actinobacteria and fungal division ascomycota have been identified to be t ...	2010	20479984
bioactivity of syzygium jambos methanolic extracts: antibacterial activity and toxicity.	methanol extracts from s. jambos leaves were tested for antimicrobial activity and toxicity. s. jambos leaf extract inhibited the growth of 4 of the 14 bacteria tested (29%). both gram-positive and gram-negative bacterial growths were inhibited by s. jambos leaf extract, although gram-positive bacteria appeared more susceptible. two of the 10 gram-negative bacteria (20%) and 2 of the 4 gram-positive bacteria (50%) tested had their growths inhibited by the extract. the leaf extract also proved to ...	2010	21808530
paenalcaligenes hominis gen. nov., sp. nov., a new member of the family alcaligenaceae.	a beige-pigmented bacterium (strain ccug 53761a(t)) was isolated from human blood from an 85-year-old man in göteborg, sweden. comparative analysis of 16s rrna gene sequences showed that this bacterium displayed <95 % similarity to all described species of the genera of the family alcaligenaceae. it grouped within the radiation of the genus alcaligenes, but showed only 93.0-94.8 % similarity to type strains of members of this genus (alcaligenes faecalis subsp. parafaecalis, 94.8 %; alcaligenes f ...	2010	19684310
molecular and kinetic characterization of mixed cultures degrading natural and synthetic estrogens.	the biodegradation of estradiol (e2), estrone (e1), and ethinylestradiol (ee2) was investigated using mixed bacterial cultures enriched from activated sludge. enrichments were carried out on e2 or ee2 in batch conditions with acetonitrile as additional carbon source. degradation experiments were performed both using hormones as sole carbon source or with an additional source. the hormones were completely degraded by these cultures. estradiol was rapidly converted to e1 within 24 h. thereafter, e ...	2010	19685239
fatal infection caused by cupriavidus gilardii in a child with aplastic anemia.	cupriavidus gilardii is a gram-negative bacterium that has rarely been associated with human infections. we report a fatal case of sepsis caused by c. gilardii in a previously healthy 12-year-old female.	2010	20071544
directed evolution of copper nitrite reductase to a chromogenic reductant.	directed evolution methods were developed for cu-containing nitrite reductase (nir) from alcaligenes faecalis s-6. the pcr cloning strategy allows for the efficient production of libraries of 100 000 clones by a modification of a megaprimer-based whole-plasmid synthesis reaction. the high-throughput screen includes colony lift onto a nylon membrane and subsequent lysis of nir-expressing colonies in the presence of cu(2+) ions for copper incorporation into intracellularly expressed nir. addition ...	2010	20083495
c-type lectin langerin is a beta-glucan receptor on human langerhans cells that recognizes opportunistic and pathogenic fungi.	langerhans cells (lcs) lining the stratified epithelia and mucosal tissues are the first antigen presenting cells to encounter invading pathogens, such as viruses, bacteria and fungi. fungal infections form a health threat especially in immuno-compromised individuals. lcs express c-type lectin langerin that has specificity for mannose, fucose and glcnac structures. little is known about the role of human langerin in fungal infections. our data show that langerin interacts with both mannan and be ...	2010	20097424
heterologous expression of leader-less pga gene in pichia pastoris: intracellular production of prokaryotic enzyme.	penicillin g acylase of escherichia coli (pgaec) is a commercially valuable enzyme for which efficient bacterial expression systems have been developed. the enzyme is used as a catalyst for the hydrolytic production of beta-lactam nuclei or for the synthesis of semi-synthetic penicillins such as ampicillin, amoxicillin and cephalexin. to become a mature, periplasmic enzyme, the inactive prepropeptide of pga has to undergo complex processing that begins in the cytoplasm (autocatalytic cleavage), ...	2010	20128906
changes in denitrifier abundance, denitrification gene mrna levels, nitrous oxide emissions, and denitrification in anoxic soil microcosms amended with glucose and plant residues.	in agricultural cropping systems, crop residues are sources of organic carbon (c), an important factor influencing denitrification. the effects of red clover, soybean, and barley plant residues and of glucose on denitrifier abundance, denitrification gene mrna levels, nitrous oxide (n(2)o) emissions, and denitrification rates were quantified in anoxic soil microcosms for 72 h. nosz gene abundances and mrna levels significantly increased in response to all organic carbon treatments over time. in ...	2010	20154105
novel duplex real-time pcr assay detects bordetella holmesii in specimens from patients with pertussis-like symptoms in ontario, canada.	bordetella holmesii is a human pathogen found mainly in immunocompromised patients. a specific real-time pcr assay was developed and successfully used to identify specimens from which b. holmesii was misidentified as bordetella pertussis and to establish the prevalence of b. holmesii in ontario patients with pertussis-like symptoms.	2010	20181919
rapid differentiation of francisella species and subspecies by fluorescent in situ hybridization targeting the 23s rrna.	francisella (f.) tularensis is the causative agent of tularemia. due to its low infectious dose, ease of dissemination and high case fatality rate, f. tularensis was the subject in diverse biological weapons programs and is among the top six agents with high potential if misused in bioterrorism. microbiological diagnosis is cumbersome and time-consuming. methods for the direct detection of the pathogen (immunofluorescence, pcr) have been developed but are restricted to reference laboratories.	2010	20205957
molecular epidemiology of metallo-beta-lactamase-producing pseudomonas aeruginosa isolates from norway and sweden shows import of international clones and local clonal expansion.	scandinavia is considered a region with a low prevalence of antimicrobial resistance. however, the number of multidrug-resistant (mdr) gram-negative bacteria is increasing, including metallo-beta-lactamase (mbl)-producing pseudomonas aeruginosa. in this study mbl-producing p. aeruginosa isolates identified in norway (n = 4) and sweden (n = 9) from 1999 to 2007 were characterized. two international clonal complexes (cc), cc111 (n = 8) and cc235 (n = 2), previously associated with mbl-producing is ...	2010	19884381
molecular epidemiology of metallo-beta-lactamase-producing pseudomonas aeruginosa isolates from norway and sweden shows import of international clones and local clonal expansion.	scandinavia is considered a region with a low prevalence of antimicrobial resistance. however, the number of multidrug-resistant (mdr) gram-negative bacteria is increasing, including metallo-beta-lactamase (mbl)-producing pseudomonas aeruginosa. in this study mbl-producing p. aeruginosa isolates identified in norway (n = 4) and sweden (n = 9) from 1999 to 2007 were characterized. two international clonal complexes (cc), cc111 (n = 8) and cc235 (n = 2), previously associated with mbl-producing is ...	2010	19884381
outbreak of alcaligenes faecalis pseudobacteraemia in neonatology and paediatric units.		2010	19900735
got black swimming dots in your cell culture? identification of achromobacter as a novel cell culture contaminant.	cell culture model systems are utilized for their ease of use, relative inexpensiveness, and potentially limitless sample size. reliable results cannot be obtained, however, when cultures contain contamination. this report discusses the observation and identification of mobile black specks observed in multiple cell lines. cultures of the contamination were grown, and dna was purified from isolated colonies. the 16s rdna gene was pcr amplified using primers that will amplify the gene from many ge ...	2010	19926304
got black swimming dots in your cell culture? identification of achromobacter as a novel cell culture contaminant.	cell culture model systems are utilized for their ease of use, relative inexpensiveness, and potentially limitless sample size. reliable results cannot be obtained, however, when cultures contain contamination. this report discusses the observation and identification of mobile black specks observed in multiple cell lines. cultures of the contamination were grown, and dna was purified from isolated colonies. the 16s rdna gene was pcr amplified using primers that will amplify the gene from many ge ...	2010	19926304
international spread and persistence of tem-24 is caused by the confluence of highly penetrating enterobacteriaceae clones and an inca/c2 plasmid containing tn1696::tn1 and is5075-tn21.	tem-24 remains one of the most widespread tem-type extended-spectrum beta-lactamases (esbls) among enterobacteriaceae. to analyze the reasons influencing its spread and persistence, a multilevel population genetics study was carried out on 28 representative tem-24 producers from belgium, france, portugal, and spain (13 enterobacter aerogenes isolates, 6 escherichia coli isolates, 6 klebsiella pneumoniae isolates, 2 proteus mirabilis isolates, and 1 klebsiella oxytoca isolate, from 1998 to 2004). ...	2010	19995930
international spread and persistence of tem-24 is caused by the confluence of highly penetrating enterobacteriaceae clones and an inca/c2 plasmid containing tn1696::tn1 and is5075-tn21.	tem-24 remains one of the most widespread tem-type extended-spectrum beta-lactamases (esbls) among enterobacteriaceae. to analyze the reasons influencing its spread and persistence, a multilevel population genetics study was carried out on 28 representative tem-24 producers from belgium, france, portugal, and spain (13 enterobacter aerogenes isolates, 6 escherichia coli isolates, 6 klebsiella pneumoniae isolates, 2 proteus mirabilis isolates, and 1 klebsiella oxytoca isolate, from 1998 to 2004). ...	2010	19995930
protonation of type-1 cu bound histidines: a quantum chemical study.	the protonation of the solvent-exposed histidine ligands of the type-1 cu sites in five proteins, thiobacillus ferrooxidans rusticyanin, pseudomonas aeruginosa azurin, fern plastocyanin, alcaligenes faecalis pseudoazurin, and paracoccus versutus amicyanin, were studied with quantum chemical methods and conductorlike polarizable continuum model (cpcm). active site model molecules consisting of approximately 140 atoms were extracted from x-ray crystal structures and optimized with the homogeneous ...	2010	20000723
method to detect only viable cells in microbial ecology.	propidium monoazide can limit the analysis of microbial communities derived from genetic fingerprints to viable cells with intact cell membranes. however, pma treatment cannot completely suppress polymerase chain reaction (pcr) amplification when the targeted gene is too short. pma treatment in combination with two-step nested pcr was designed to overcome this problem. four experiments were performed to determine the limitation of pma treatment and to evaluate the suitability of the method by ap ...	2010	20024544
actinobaculum schaalii, a common uropathogen in elderly patients, denmark.	actinobaculum schaalii can cause urinary tract infections and septicemia but is difficult to identify by cultivation. to obtain a fast diagnosis and identify a. schaalii, we developed a taqman real-time quantitative pcr. routine urine samples were obtained from 177 hospitalized patients and 75 outpatients in viborg county, denmark, in 2008-2009. the pcr detected a. schaalii in 22% of samples from patients >60 years of age. this assay showed that a. schaalii is more common than implied by routine ...	2010	20031046
high-throughput identification of bacteria and yeast by matrix-assisted laser desorption ionization-time of flight mass spectrometry in conventional medical microbiology laboratories.	matrix-assisted laser desorption ionization-time of flight mass spectrometry (maldi-tof ms) is suitable for high-throughput and rapid diagnostics at low costs and can be considered an alternative for conventional biochemical and molecular identification systems in a conventional microbiological laboratory. first, we evaluated maldi-tof ms using 327 clinical isolates previously cultured from patient materials and identified by conventional techniques (vitek-ii, api, and biochemical tests). discre ...	2010	20053859
first reported case of alcaligenes faecalis peritonitis.		2010	20056996
characterization of phenol degradation by high-efficiency binary mixed culture.	two new high phenol-degrading strains, micrococcus sp. and alcaligenes faecalis jh 1013, were isolated. the two isolates could grow aerobically in mineral salts medium containing phenol as a sole carbon source at concentration of 3,000 mg l(-1). it was found that the binary mixed culture of the two isolates possessed good potential for phenol removal.	2010	20300870
denitrifying bacteria isolated from terrestrial subsurface sediments exposed to mixed-waste contamination.	in terrestrial subsurface environments where nitrate is a critical groundwater contaminant, few cultivated representatives are available to verify the metabolism of organisms that catalyze denitrification. in this study, five species of denitrifying bacteria from three phyla were isolated from subsurface sediments exposed to metal radionuclide and nitrate contamination as part of the u.s. department of energy's oak ridge integrated field research challenge (or-ifrc). isolates belonged to the gen ...	2010	20305024
high levels of beta-d-glucan in immunocompromised children with proven invasive fungal disease.	the plasmatic levels of 1,3-beta-d-glucan (bdg) were >523 pg/ml in 4 children, 2 low-birth-weight neonates and 2 stem cell transplant recipients, with the following invasive fungal diseases (ifd) proven apart from this bdg test: 3 cases of candida parapsilosis candidemias and 1 case of disseminated aspergillosis. the bdg test may be useful for identification of ifd in pediatrics.	2010	20335432
identification and differentiation of taylorella equigenitalis and taylorella asinigenitalis by lipopolysaccharide o-antigen serology using monoclonal antibodies.	lipopolysaccharides (lpss) from taylorella equigenitalis, the causative agent of contagious equine metritis, and t. asinigenitalis were compared by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (sds-page). lipopolysaccharide profiles of 11 t. equigenitalis strains were similar, but different from the profiles of 3 t. asinigenitalis strains, and the profiles of 2 t. asinigenitalis strains were similar to each other. the serological specificities of the lpss from these 14 strains were ...	2010	20357953
indigenous opportunistic bacteria inhabit mammalian gut-associated lymphoid tissues and share a mucosal antibody-mediated symbiosis.	the indigenous bacteria create natural cohabitation niches together with mucosal abs in the gastrointestinal (gi) tract. here we report that opportunistic bacteria, largely alcaligenes species, specifically inhabit host peyer's patches (pps) and isolated lymphoid follicles, with the associated preferential induction of antigen-specific mucosal iga abs in the gi tract. alcaligenes were identified as the dominant bacteria on the interior of pps from naïve, specific-pathogen-free but not from germ- ...	2010	20360558
construction and application of variants of the pseudomonas fluorescens ebc191 arylacetonitrilase for increased production of acids or amides.	the arylacetonitrilase from pseudomonas fluorescens ebc191 differs from previously studied arylacetonitrilases by its low enantiospecificity during the turnover of mandelonitrile and by the large amounts of amides that are formed in the course of this reaction. in the sequence of the nitrilase from p. fluorescens, a cysteine residue (cys163) is present in direct neighborhood (toward the amino terminus) to the catalytic active cysteine residue, which is rather unique among bacterial nitrilases. t ...	2010	20382812
biocatalytic synthesis of (r)-(-)-mandelic acid from racemic mandelonitrile by cetyltrimethylammonium bromide-permeabilized cells of alcaligenes faecalis ecu0401.	the nitrilase from alcaligenes faecalis ecu0401 belongs to the category of arylacetonitrilase, which could hydrolyze 2-chloromandelonitrile, 3,4-dimethoxyphenylacetonitrile, mandelonitrile, and phenylacetonitrile into the corresponding arylacetic acids. to overcome the permeability barrier and prepare whole cell biocatalysts with high activities, permeabilization of alcaligenes faecalis ecu0401 in relation to nitrilase activity was optimized by using cetyltrimethylammonium bromide (ctab) as perm ...	2010	20411403
discovery and structure determination of the orphan enzyme isoxanthopterin deaminase .	two previously uncharacterized proteins have been identified that efficiently catalyze the deamination of isoxanthopterin and pterin 6-carboxylate. the genes encoding these two enzymes, nysgxrc-9339a ( gi\|44585104 ) and nysgxrc-9236b ( gi\|44611670 ), were first identified from dna isolated from the sargasso sea as part of the global ocean sampling project. the genes were synthesized, and the proteins were subsequently expressed and purified. the x-ray structure of sgx9339a was determined at 2.7 ...	2010	20415463
calcineurin regulates innate antifungal immunity in neutrophils.	patients taking immunosuppressive drugs, like cyclosporine a (csa), that inhibit calcineurin are highly susceptible to disseminated fungal infections, although it is unclear how these drugs suppress resistance to these opportunistic pathogens. we show that in a mouse model of disseminated candida albicans infection, csa-induced susceptibility to fungal infection maps to the innate immune system. to further define the cell types targeted by csa, we generated mice with a conditional deletion of ca ...	2010	20421389
the small subunit arob of arsenite oxidase: lessons on the [2fe-2s] rieske protein superfamily.	here, we describe the characterization of the [2fe-2s] clusters of arsenite oxidases from rhizobium sp. nt-26 and ralstonia sp. 22. both reduced rieske proteins feature epr signals similar to their homologs from rieske-cyt b complexes, with g values at 2.027, 1.88, and 1.77. redox titrations in a range of ph values showed that both [2fe-2s] centers have constant e(m) values up to ph 8 at approximately +210 mv. above this ph value, the e(m) values of both centers are ph-dependent, similar to what ...	2010	20421651
arsenite oxidase from ralstonia sp. 22: characterization of the enzyme and its interaction with soluble cytochromes.	we characterized the aro arsenite oxidation system in the novel strain ralstonia sp. 22, a beta-proteobacterium isolated from soil samples of the salsigne mine in southern france. the inducible aro system consists of a heterodimeric membrane-associated enzyme reacting with a dedicated soluble cytochrome c(554). our biochemical results suggest that the weak association of the enzyme to the membrane probably arises from a still unknown interaction partner. analysis of the phylogeny of the aro gene ...	2010	20421652
identification of a novel arsenite oxidase gene, arxa, in the haloalkaliphilic, arsenite-oxidizing bacterium alkalilimnicola ehrlichii strain mlhe-1.	although arsenic is highly toxic to most organisms, certain prokaryotes are known to grow on and respire toxic metalloids of arsenic (i.e., arsenate and arsenite). two enzymes are known to be required for this arsenic-based metabolism: (i) the arsenate respiratory reductase (arra) and (ii) arsenite oxidase (aoxb). both catalytic enzymes contain molybdopterin cofactors and form distinct phylogenetic clades (arra and aoxb) within the dimethyl sulfoxide (dmso) reductase family of enzymes. here we r ...	2010	20453090
potential of aerobic denitrification by pseudomonas stutzeri tr2 to reduce nitrous oxide emissions from wastewater treatment plants.	in contrast to most denitrifiers studied so far, pseudomonas stutzeri tr2 produces low levels of nitrous oxide (n(2)o) even under aerobic conditions. we compared the denitrification activity of strain tr2 with those of various denitrifiers in an artificial medium that was derived from piggery wastewater. strain tr2 exhibited strong denitrification activity and produced little n(2)o under all conditions tested. its growth rate under denitrifying conditions was near comparable to that under aerobi ...	2010	20495048
through ageing, and beyond: gut microbiota and inflammatory status in seniors and centenarians.	age-related physiological changes in the gastrointestinal tract, as well as modifications in lifestyle, nutritional behaviour, and functionality of the host immune system, inevitably affect the gut microbiota, resulting in a greater susceptibility to infections.	2010	20498852
the 1.4 a resolution structure of paracoccus pantotrophus pseudoazurin.	pseudoazurins are small type 1 copper proteins that are involved in the flow of electrons between various electron donors and acceptors in the bacterial periplasm, mostly under denitrifying conditions. the previously determined structure of paracoccus pantotrophus pseudoazurin in the oxidized form was improved to a nominal resolution of 1.4 a, with r and r(free) values of 0.188 and 0.206, respectively. this high-resolution structure makes it possible to analyze the interactions between the monom ...	2010	20516588
emergence of gentamicin-resistant bacteremia in hemodialysis patients receiving gentamicin lock catheter prophylaxis.	antibiotic locks in catheter-dependent chronic hemodialysis patients reduce the rate of catheter-related blood stream infections (cris), but there are no data regarding the long-term consequences of this practice.	2010	20595689
identification and heterologous expression of genes involved in anaerobic dissimilatory phosphite oxidation by desulfotignum phosphitoxidans.	desulfotignum phosphitoxidans is a strictly anaerobic, gram-negative bacterium that utilizes phosphite as the sole electron source for homoacetogenic co2 reduction or sulfate reduction. a genomic library of d. phosphitoxidans, constructed using the fosmid vector pjk050, was screened for clones harboring the genes involved in phosphite oxidation via pcr using primers developed based on the amino acid sequences of phosphite-induced proteins. sequence analysis of two positive clones revealed a puta ...	2010	20622064
exobiopolymer production of ophiocordyceps dipterigena bcc 2073: optimization, production in bioreactor and characterization.	biopolymers have various applications in medicine, food and petroleum industries. the ascomycetous fungus ophiocordyceps dipterigena bcc 2073 produces an exobiopolymer, a (1-->3)-beta-d-glucan, in low quantity under screening conditions. optimization of o. dipterigena bcc 2073 exobiopolymer production using experimental designs, a scale-up in 5 liter bioreactor, analysis of molecular weight at different cultivation times, and levels of induction of interleukin-8 synthesis are described in this s ...	2010	20624309
comparative impact of cadmium on two phenanthrene-degrading bacteria isolated from cadmium and phenanthrene co-contaminated soil in china.	alcaligenes faecalis strain j08 and brevundimonas sp. strain x08 were isolated from soils co-contaminated by cadmium (cd) and polycyclic aromatic hydrocarbons (pahs) in northeast china. the two strains of bacteria were identified by phenotypic tests and 16s rdna. different cd treatments (0.01 mm, 0.1mm, 0.5mm) showed no significant influence (p>0.05) on the biodegradation of phenanthrene by a. faecalis strain j08. brevundimonas sp. strain x08 also presented no significant differences in the biod ...	2010	19853994
biochip system for rapid and accurate identification of mycobacterial species from isolates and sputum.	the accurate detection of mycobacterial species from isolates and clinical samples is important for pathogenic diagnosis and treatment and for disease control. there is an urgent need for the development of a rapid, simple, and accurate detection method. we established a biochip assay system, including a biochip, sample preparation apparatus, hybridization instrument, chip washing machine, and laser confocal scanner equipped with interpretation software for automatic diagnosis. the biochip simul ...	2010	20686082
anaerobic oxidation of arsenite linked to chlorate reduction.	microorganisms play a significant role in the speciation and mobility of arsenic in the environment. in this study, the oxidation of arsenite [as(iii)] to arsenate [as(v)] linked to chlorate (clo₃⁻) reduction was shown to be catalyzed by sludge samples, enrichment cultures (ecs), and pure cultures incubated under anaerobic conditions. no activity was observed in treatments lacking inoculum or with heat-killed sludge, or in controls lacking clo₃⁻. the as(iii) oxidation was linked to the complete ...	2010	20729322
component identification of electron transport chains in curdlan-producing agrobacterium sp. atcc 31749 and its genome-specific prediction using comparative genome and phylogenetic trees analysis.	agrobacterium sp. atcc 31749 (formerly named alcaligenes faecalis var. myxogenes) is a non-pathogenic aerobic soil bacterium used in large scale biotechnological production of curdlan. however, little is known about its genomic information. dna partial sequence of electron transport chains (etcs) protein genes were obtained in order to understand the components of etc and genomic-specificity in agrobacterium sp. atcc 31749. degenerate primers were designed according to etc conserved sequences in ...	2010	20730594
evaluation of matrix-assisted laser desorption ionization-time of flight mass spectrometry for identification of nocardia species.	the identification of nocardia species, usually based on biochemical tests together with phenotypic in vitro susceptibility and resistance patterns, is a difficult and lengthy process owing to the slow growth and limited reactivity of these bacteria. in this study, a panel of 153 clinical and reference strains of nocardia spp., altogether representing 19 different species, were characterized by matrix-assisted laser desorption ionization-time of flight mass spectrometry (maldi-tof ms). as refere ...	2010	20861335