Publications

molecular fingerprinting of dairy microbial ecosystems by use of temporal temperature and denaturing gradient gel electrophoresis.	numerous microorganisms, including bacteria, yeasts, and molds, constitute the complex ecosystem present in milk and fermented dairy products. our aim was to describe the bacterial ecosystem of various cheeses that differ by production technology and therefore by their bacterial content. for this purpose, we developed a rapid, semisystematic approach based on genetic profiling by temporal temperature gradient electrophoresis (ttge) for bacteria with low-g+c-content genomes and denaturing gradien ...	2004	15345452
1h, 13c and 15n resonance assignment of cu(i)-pseudoazurin from alcaligenes faecalis s-6.		2004	15243189
characterization of slac: a small laccase from streptomyces coelicolor with unprecedented activity.	laccases and other four-copper oxidases are usually constructed of three domains: domains one and three house the copper sites, and the second domain often helps form a substrate-binding cleft. in contrast to this arrangement, the genome of streptomyces coelicolor was found to encode a small, four-copper oxidase that lacks the second domain. this protein is representative of a new family of enzymes--the two-domain laccases. disruption of the corresponding gene abrogates laccase activity in the g ...	2004	15295117
multifocal detection of multidrug-resistant pseudomonas aeruginosa producing the per-1 extended-spectrum beta-lactamase in northern italy.	forty-four nonreplicate clinical isolates of pseudomonas aeruginosa that were resistant to extended-spectrum cephalosporins (ceftazidime and cefepime) and aztreonam, that putatively produced an acquired extended- spectrum beta-lactamase (esbl), according to the results of a double-disk synergy test, and that had been involved in nosocomial outbreaks were obtained from six different hospitals in northern italy and screened for the presence of bla(per) esbl determinants. twenty isolates, associate ...	2004	15184430
characterization of beta-glucan recognition site on c-type lectin, dectin 1.	dectin 1 is a mammalian cell surface receptor for (1-->3)-beta-d-glucans. since (1-->3)-beta-d-glucans are commonly present on fungal cell walls, it has been suggested that dectin 1 is important for recognizing fungal invasion. in this study we tried to deduce the amino acid residues in dectin 1 responsible for beta-glucan recognition. hek293 cells transfected with mouse dectin 1 cdna could bind to a gel-forming (1-->3)-beta-d-glucan, schizophyllan (spg). the binding of spg to a dectin 1 transfe ...	2004	15213161
growth inhibition of foodborne pathogens and food spoilage organisms by select raw honeys.	twenty-seven honey samples from different floral sources and geographical locations were evaluated for their ability to inhibit the growth of seven food spoilage organisms (alcaligenes faecalis, aspergillus niger, bacillus stearothermophilus, geotrichum candidum, lactobacillus acidophilus, penicillium expansum, pseudomonas fluorescens) and five foodborne pathogens (bacillus cereus, escherichia coli o157:h7, listeria monocytogenes, salmonella enterica ser. typhimurium, and staphylococcus aureus) ...	2004	15527912
the functional role of the binuclear metal center in d-aminoacylase: one-metal activation and second-metal attenuation.	our structural comparison of the tim barrel metal-dependent hydrolase(-like) superfamily suggests a classification of their divergent active sites into four types: alphabeta-binuclear, alpha-mononuclear, beta-mononuclear, and metal-independent subsets. the d-aminoacylase from alcaligenes faecalis da1 belongs to the beta-mononuclear subset due to the fact that the catalytically essential zn(2+) is tightly bound at the beta site with coordination by cys(96), his(220), and his(250), even though it ...	2004	14736882
electrochemical studies of arsenite oxidase: an unusual example of a highly cooperative two-electron molybdenum center.	arsenite oxidase from alcaligenes faecalis, an unusual molybdoenzyme that does not exhibit a mo(v) epr signal during oxidative-reductive titrations, has been investigated by protein film voltammetry. a film of the enzyme on a pyrolytic graphite edge electrode produces a sharp two-electron signal associated with reversible reduction of the oxidized mo(vi) molybdenum center to mo(iv). that reduction or oxidation of the active site occurs without accumulation of mo(v) is consistent with the failure ...	2004	14769044
bacterium-based no2- biosensor for environmental applications.	a sensitive no2- biosensor that is based on bacterial reduction of no2- to n2o and subsequent detection of the n2o by a built-in electrochemical n2o sensor was developed. four different denitrifying organisms lacking no3- reductase activity were assessed for use in the biosensor. the relevant physiological aspects examined included denitrifying characteristics, growth rate, no2- tolerance, and temperature and salinity effects on the growth rate. two organisms were successfully used in the biosen ...	2004	15528518
molybdenum-containing arsenite oxidase of the chemolithoautotrophic arsenite oxidizer nt-26.	the chemolithoautotroph nt-26 oxidizes arsenite to arsenate by using a periplasmic arsenite oxidase. purification and preliminary characterization of the enzyme revealed that it (i) contains two heterologous subunits, aroa (98 kda) and arob (14 kda); (ii) has a native molecular mass of 219 kda, suggesting an alpha2beta2 configuration; and (iii) contains two molybdenum and 9 or 10 iron atoms per alpha2beta2 unit. the genes that encode the enzyme have been cloned and sequenced. sequence analyses r ...	2004	14996791
l-alanine auxotrophy of lactobacillus johnsonii as demonstrated by physiological, genomic, and gene complementation approaches.	using a chemically defined medium without l-alanine, lactobacillus johnsonii was demonstrated to be strictly auxotrophic for that amino acid. a comparative genetic analysis showed that all known genes involved in l-alanine biosynthesis are absent from the genome of l. johnsonii. this auxotrophy was complemented by heterologous expression of the bacillus subtilis l-alanine dehydrogenase.	2004	15006820
surface glycans of candida albicans and other pathogenic fungi: physiological roles, clinical uses, and experimental challenges.	although fungi have always been with us as commensals and pathogens, fungal infections have been increasing in frequency over the past few decades. there is a growing body of literature describing the involvement of carbohydrate groups in various aspects of fungal disease. carbohydrates comprising the cell wall or capsule, or as a component of glycoproteins, are the fungal cell surface entities most likely to be exposed to the surrounding environment. thus, the fungus-host interaction is likely ...	2004	15084502
mapping of the binding site on pseudoazurin in the transient 152 kda complex with nitrite reductase.	nitrite reductase (nir) catalyzes the reduction of nitrite to nitrite oxide as a part of the denitrification process. in alcaligenes faecalis s-6, the copper protein pseudoazurin acts as electron donor to nir. the binding surface of pseudoazurin involved in the formation of the 152 kda complex with nir has been determined by nmr using cross saturation from nir to perdeuterated pseudoazurin. due to the transient nature of the complex, saturation effects can be observed on the resonances of the un ...	2004	15125645
cloning, overexpression, and characterization of a novel thermostable penicillin g acylase from achromobacter xylosoxidans: probing the molecular basis for its high thermostability.	the gene encoding a novel penicillin g acylase (pga), designated pgaw, was cloned from achromobacter xylosoxidans and overexpressed in escherichia coli. the pgaw gene contains an open reading frame of 2586 nucleotides. the deduced protein sequence encoded by pgaw has about 50% amino acid identity to several well-characterized pgas, including those of providencia rettgeri, kluyvera cryocrescens, and escherichia coli. biochemical studies showed that the optimal temperature for this novel pga (pga6 ...	2004	15128530
arsenite oxidation by the heterotroph hydrogenophaga sp. str. nt-14: the arsenite oxidase and its physiological electron acceptor.	heterotrophic arsenite oxidation by hydrogenophaga sp. str. nt-14 is coupled to the reduction of oxygen and appears to yield energy for growth. purification and partial characterization of the arsenite oxidase revealed that it (1). contains two heterologous subunits, aroa (86 kda) and arob (16 kda), (2). has a native molecular mass of 306 kda suggesting an alpha(3)beta(3) configuration, and (3). contains molybdenum and iron as cofactors. although the hydrogenophaga sp. str. nt-14 arsenite oxidas ...	2004	15178476
effect of alcaligenes faecalis on nitrous oxide emission and nitrogen removal in three phase fluidized bed process.	nitrous oxide (n2o), one of the greenhouse effect gases, has not been known that how much n2o is produced from municipal wastewater treatment and what its management should be. in this study, for controlling nitrous oxide emission and removing nitrogen from municipal wastewater, we experimented the three phase fluidized bed process equipped with draft tube along with immobilized alcaligenes faecalis, a typical heterotrophic nitrifer and a predominant genus. also we evaluated the optimum treatmen ...	2004	15242127
bidirectional catalysis by copper-containing nitrite reductase.	the copper-containing nitrite reductase from alcaligenes faecalis s-6 was found to catalyze the oxidation of nitric oxide to nitrite, the reverse of its physiological reaction. thermodynamic and kinetic constants with the physiological electron donor pseudoazurin were determined for both directions of the catalyzed reaction in the ph range of 6-8. for this, nitric oxide was monitored by a clark-type electrode, and the redox state of pseudoazurin was measured by optical spectroscopy. the equilibr ...	2004	15301545
microdiversity of phenol hydroxylase genes among phenol-degrading isolates of alcaligenes sp. from an activated sludge system.	enterobacterial repetitive intergenic consensus (eric)-pcr fingerprinting classified 97 phenol-degrading isolates with identical amplified ribosomal dna restriction analysis (ardra) patterns into six genotypic groups. the 16s rrna gene of the representative isolate of each group had higher than 99.47% common identity with each other and higher than 98% identity with the type strain of alcaligenes faecalis. pcr-tgge (temperature gradient gel electrophoresis) analysis of the genes of the largest s ...	2004	15321685
bacteremia caused by achromobacter and alcaligenes species in 46 patients with cancer (1989-2003).	achromobacter and alcaligenes are emerging infectious gram-negative bacterial species that can affect immunosuppressed patients. the authors sought to determine the incidence and characteristics of bloodstream infections caused by these organisms in patients with underlying malignancies.	2004	15389476
beta-1,3 glucan sulfate, but not beta-1,3 glucan, induces the salicylic acid signaling pathway in tobacco and arabidopsis.	sulfate substituents naturally occurring in biomolecules, such as oligosaccharides and polysaccharides, can play a critical role in major physiological functions in plants and animals. we show that laminarin, a beta-1,3 glucan with elicitor activity in tobacco (nicotiana tabacum), becomes, after chemical sulfation, an inducer of the salicylic acid (sa) signaling pathway in tobacco and arabidopsis thaliana. in tobacco cell suspensions, the oxidative burst induced by the laminarin sulfate ps3 was ...	2004	15494557
high-rate nitrification at low ph in suspended- and attached-biomass reactors.	this article reports on high-rate nitrification at low ph in biofilm and suspended-biomass reactors by known chemolithotrophic bacteria. in the biofilm reactor, at low ph (4.3 +/- 0.1) and low bulk ammonium concentrations (9.3 +/- 3.3 mg.liter(-1)), a very high nitrification rate of 5.6 g of n oxidized.liter(-1).day(-1) was achieved. the specific nitrification rate (0.55 g of n.g of biomass(-1).day(-1)) was similar to values reported for nitrifying reactors at optimal ph. in the suspended-biomas ...	2004	15528509
hydrolysis of nitriles using an immobilized nitrilase: applications to the synthesis of methionine hydroxy analogue derivatives.	mild and selective hydrolysis of a large range of nitriles leading to carboxylic acids was achieved under neutral conditions by an immobilized and genetically modified enzyme preparation from alcaligenes faecalis atcc8750. this immobilized nitrilase has been shown to be an effective catalyst for the stereoselective hydrolysis of mandelonitrile 1a to r-(-)-mandelic acid 1c. this method is particularly useful for the production of hydroxy analogues of methionine derivatives 2c-4c that could have a ...	2004	15612811
comparison of aerobic denitrifying activity among three cultural species with various carbon sources.	abilities of three aerobic denitrifiers such as alcaligenes faecalis, microvirgula aerodenitrificans and paracoccus pantotrophus were compared from the viewpoints of nitrate removal efficiency and organic matter utilization. first, the effect of carbon source was investigated. although nitrate reduction was observed in all strains under aerobic conditions, a change of carbon source considerably affected the denitrification ability. in the case of p. pantotrophus, nitrate and nitrite were complet ...	2004	15566182
identification of the bacterial community of maple sap by using amplified ribosomal dna (rdna) restriction analysis and rdna sequencing.	the bacterial community of maple sap was characterized by analysis of samples obtained at the taphole of maple trees for the 2001 and 2002 seasons. among the 190 bacterial isolates, 32 groups were formed according to the similarity of the banding patterns obtained by amplified ribosomal dna restriction analysis (ardra). a subset of representative isolates for each ardra group was identified by 16s rrna gene fragment sequencing. results showed a wide variety of organisms, with 22 different genera ...	2004	15066796
[constitutive expression and purification of alcaligenes faecalis penicillin g acylase in escherichia coli].	considering alcaligenes faecalis pencillin g acylase(afpga), which possesses the attractive characteristics for beta-lactam antibiotics conversions, the gene of pga was cloned into an expressing vector pkkfpga. the recombinant plasmid contained multicopy replicon(cole 1), trc promoter, afpga gene, rrnb transcript terminator and ampicillin marker transformed escherichia coli dh5alpha. as both the recombinant plasmid and the host dh5alpha had no laclq gene, the trc promoter was always active and t ...	2004	15974000
evaluation of the new vitek 2 card for identification of clinically relevant gram-negative rods.	the vitek 2 card for gram-negative bacteria (biomérieux,marcy-l'etoile, france) has been redesigned to improve the identification of fermenting and nonfermenting bacilli. forty-seven biochemical tests, including 19 enzymatic tests, are present in the new card and interpreted in a kinetic mode. final identification results are available within 10 h. the database allows the identification of 159 different taxa. six hundred fifty-five gram-negative rods (gnr; 511 fermenters and 144 nonfermenters), ...	2004	15364991
type v protein secretion pathway: the autotransporter story.	gram-negative bacteria possess an outer membrane layer which constrains uptake and secretion of solutes and polypeptides. to overcome this barrier, bacteria have developed several systems for protein secretion. the type v secretion pathway encompasses the autotransporter proteins, the two-partner secretion system, and the recently described type vc or at-2 family of proteins. since its discovery in the late 1980s, this family of secreted proteins has expanded continuously, due largely to the adv ...	2004	15590781
nitrous oxide reductase (nosz) gene fragments differ between native and cultivated michigan soils.	the effect of standard agricultural management on the genetic heterogeneity of nitrous oxide reductase (nosz) fragments from denitrifying prokaryotes in native and cultivated soil was explored. thirty-six soil cores were composited from each of the two soil management conditions. nosz gene fragments were amplified from triplicate samples, and pcr products were cloned and screened by restriction fragment length polymorphism (rflp). the total nosz rflp profiles increased in similarity with soil sa ...	2004	14711656
cpndb: a chaperonin sequence database.	type i chaperonins are molecular chaperones present in virtually all bacteria, some archaea and the plastids and mitochondria of eukaryotes. sequences of cpn60 genes, encoding 60-kda chaperonin protein subunits (cpn60, also known as groel or hsp60), are useful for phylogenetic studies and as targets for detection and identification of organisms. conveniently, a 549-567-bp segment of the cpn60 coding region can be amplified with universal pcr primers. here, we introduce cpndb, a curated collectio ...	2004	15289485
propionate oxidation by and methanol inhibition of anaerobic ammonium-oxidizing bacteria.	anaerobic ammonium oxidation (anammox) is a recently discovered microbial pathway and a cost-effective way to remove ammonium from wastewater. anammox bacteria have been described as obligate chemolithoautotrophs. however, many chemolithoautotrophs (i.e., nitrifiers) can use organic compounds as a supplementary carbon source. in this study, the effect of organic compounds on anammox bacteria was investigated. it was shown that alcohols inhibited anammox bacteria, while organic acids were convert ...	2005	15691967
characteristics and adaptability of iron- and sulfur-oxidizing microorganisms used for the recovery of metals from minerals and their concentrates.	microorganisms are used in large-scale heap or tank aeration processes for the commercial extraction of a variety of metals from their ores or concentrates. these include copper, cobalt, gold and, in the past, uranium. the metal solubilization processes are considered to be largely chemical with the microorganisms providing the chemicals and the space (exopolysaccharide layer) where the mineral dissolution reactions occur. temperatures at which these processes are carried out can vary from ambie ...	2005	15877814
biofilm reactors for industrial bioconversion processes: employing potential of enhanced reaction rates.	this article describes the use of biofilm reactors for the production of various chemicals by fermentation and wastewater treatment. biofilm formation is a natural process where microbial cells attach to the support (adsorbent) or form flocs/aggregates (also called granules) without use of chemicals and form thick layers of cells known as "biofilms." as a result of biofilm formation, cell densities in the reactor increase and cell concentrations as high as 74 gl(-1) can be achieved. the reactor ...	2005	16122390
health considerations regarding horizontal transfer of microbial transgenes present in genetically modified crops.	the potential effects of horizontal gene transfer on human health are an important item in the safety assessment of genetically modified organisms. horizontal gene transfer from genetically modified crops to gut microflora most likely occurs with transgenes of microbial origin. the characteristics of microbial transgenes other than antibiotic-resistance genes in market-approved genetically modified crops are reviewed. these characteristics include the microbial source, natural function, function ...	2005	16489267
enzymatic transformation of bacterial polyhydroxyalkanoates into repolymerizable oligomers directed towards chemical recycling.	the enzymatic transformation into an oligomer was carried out with the objective of developing the chemical recycling of bacterial polyesters. poly(r-3-hydroxyalkanoate)s (phas), such as poly[(r-3-hydroxybutyrate)-co-12%(r-3-hydroxyhexanoate)] and poly[(r-3-hydroxybutyrate)-co-12%(r-3-hydroxyvalerate)], were degraded by granulated candida antarctica lipase b immobilized on hydrophilic silica (lipase gca) in a diluted organic solvent at 70 degrees c. the degradation products were cyclic oligomers ...	2005	15988790
alcaligenes faecalis kw-a biofilm for denitrification of nitrate-rich effluent.	alcaligenes faecalis kw-a selected for possessing good denitrification efficiency was used for biofilm development. the biofilm could be developed on a glass surface within 12 hr when 5%, ix 10(8) cells/ml was used as inoculum. the microcolonies were seen in 6 hr and glycocalyx in 9 hr stage. at 24 hr the biofilm was developed fully and hence was visualised as dense mass. the biofilm protein content showed 48.5% increase in shake flask than in static condition. the exopoplymer is produced in lar ...	2005	15991580
release of an enantioselective nitrilase from alcaligenes faecalis mtcc 126: a comparative study.	nitrilases constitute an important class of hydrolases, however, cheap and ready availability of enzyme sources limit their practical synthetic applications. the present investigation was directed to compare the applicability of various physical cell disintegration methods namely, solid shear, liquid shear and sonication, for the release of an enantioselective nitrilase from alcaligenes faecalis mtcc 126. different parameters associated with each method were optimized in order to ensure maximal ...	2005	16080003
calorimetric and spectroscopic investigations of the thermal denaturation of wild type nitrite reductase.	nitrite reductase (nir) is a multicopper protein, with a trimeric structure containing two types of copper site: type 1 is present in each subunit whereas type 2 is localized at the subunits interface. the paper reports on the thermal behaviour of wild type nir from alcaligenes faecalis s-6. the temperature-induced changes of the copper centres are characterized by optical spectroscopy and electron paramagnetic resonance spectroscopy, and by establishing the thermal stability by differential sca ...	2005	16085470
nitrification and denitrification in high-strength ammonium by alcaligenes faecalis.	alcaligenes faecalis sp. no. 4, that has the ability of heterotrophic nitrification and aerobic denitrification in high-strength ammonium at about 1200 mg-n/l, converted about one-half of removed nh4+-n to intracellular nitrogen and nitrified only 3% of the removed nh4+. from the nitrogen balance, 40-50% of removed nh4+-n was estimated to be denitrified. production of n2 was confirmed by gc-ms and 90% of denitrified products was n2. the maximum ammonium removal rate, 29 mg-n/l h and its denitrif ...	2005	16086258
complete conversion of nitrate into dinitrogen gas in co-cultures of denitrifying bacteria.	in the past 10 years many molecular aspects of microbial nitrate reduction have been elucidated, but the ecophysiology of this process is hardly understood. in this contribution, our efforts to study the complex microbial communities and interactions involved in the reduction of nitrate to dinitrogen gas are summarized. the initial work concentrated on emission of the greenhouse gas nitrous oxide during incomplete denitrification by alcaligenes faecalis. as more research methods became available ...	2005	15667308
sensing nitrite through a pseudoazurin-nitrite reductase electron transfer relay.	nitrite is converted to nitric oxide by haem or copper-containing enzymes in denitrifying bacteria during the process of denitrification. in designing an efficient biosensor, this enzymic turnover must be quantitatively assessed. the enzyme nitrite reductase from alcaligenes faecalis contains a redox-active blue copper centre and a nonblue enzyme-active copper centre. it can be covalently tethered to modified gold-electrode surfaces in configurations in which direct electron transfer is possible ...	2005	15900523
atomic resolution structures of resting-state, substrate- and product-complexed cu-nitrite reductase provide insight into catalytic mechanism.	copper-containing nitrite reductases catalyze the reduction of nitrite to nitric oxide (no), a key step in denitrification that results in the loss of terrestrial nitrogen to the atmosphere. they are found in a wide variety of denitrifying bacteria and fungi of different physiology from a range of soil and aquatic ecosystems. structural analysis of potential intermediates in the catalytic cycle is an important goal in understanding enzyme mechanism. using "crystal harvesting" and substrate-soaki ...	2005	16093314
alcaligenes faecalis subsp. phenolicus subsp. nov. a phenol-degrading, denitrifying bacterium isolated from a graywater bioprocessor.	a gram (-) coccobacillary bacterium, j(t), was isolated from a graywater bioprocessor. 16s rrna and biochemical analysis has revealed strain j(t) closely resembles alcaligenes faecalis atcc 8750t and a. faecalis subsp. parafaecalis dsm 13975t, but is a distinct, previously uncharacterized isolate. strain j(t), along with the type strain of a. faecalis and its previously described subspecies share the ability to aerobically degrade phenol. the degradation rates of phenol for strain j(t) and refer ...	2005	16094869
isolation and characterization of a chlorpyrifos and 3,5,6-trichloro-2-pyridinol degrading bacterium.	a bacterium, isolated from contaminated soils around a chemical factory and named strain dsp3 was capable of biodegrading both chlorpyrifos and 3,5,6-trichloro-2-pyridinol. based on the results of phenotypic features, phylogenetic similarity of 16s rrna gene sequences, dna g+c content, and dna homology between strain dsp3 and reference strains, strain dsp3 was identified as alcaligenes faecalis. chlorpyrifos was utilized as the sole source of carbon and phosphorus by strain dsp3. we examined the ...	2005	16143458
characteristics of ammonium removal by heterotrophic nitrification-aerobic denitrification by alcaligenes faecalis no. 4.	alcaligenes faecalis no. 4 has heterotrophic nitrification and aerobic denitrification abilities. by taking the nitrogen balance under different culture conditions, 40-50% of removed nh4+-n was denitrified and about one-half of removed nh4+-n was converted to intracellular nitrogen. the maximum ammonium removal rate of no. 4 (28.9 mg-n/l/h) and its denitrification rate at high-strength nh4+-n of about 1200 ppm in aerated batch experiments at a c/n ratio of 10 were 5-40 times higher than those of ...	2005	16198262
tryptophan tryptophylquinone cofactor biogenesis in the aromatic amine dehydrogenase of alcaligenes faecalis. cofactor assembly and catalytic properties of recombinant enzyme expressed in paracoccus denitrificans.	the heterologous expression of tryptophan trytophylquinone (ttq)-dependent aromatic amine dehydrogenase (aadh) has been achieved in paracoccus denitrificans. the aaubeda genes and orf-2 from the aromatic amine utilization (aau) gene cluster of alcaligenes faecalis were placed under the regulatory control of the mauf promoter from p. denitrificans and introduced into p. denitrificans using a broad-host-range vector. the physical, spectroscopic and kinetic properties of the recombinant aadh were i ...	2005	16279953
alcaligenes aquatilis sp. nov., a novel bacterium from sediments of the weser estuary, germany, and a salt marsh on shem creek in charleston harbor, usa.	four nitrite-dissimilating strains, isolated from weser estuary sediments, were investigated using a polyphasic taxonomic approach. phylogenetic analysis based on 16s rrna gene sequences indicated that these strains belong to the 'betaproteobacteria' and are related to the genus alcaligenes. the highest level of sequence similarity (100 %) was found with strain m3a (=atcc 700596), a dimethyl sulfide-producing marine isolate that was included in this study. dna-dna hybridizations between the five ...	2005	16280529
[influence of nitrogen source nh4 cl concentration on curdlan production in alcaligenes faecalis].	the effect of initial ammonium chloride level on production of curdlan in alcaligenesfaecalis was investigated. it was found that ammonium chloride was the limiting substrate for cell growth during the batch fermentation process. however, the cell growth and curdlan production could not be enhanced by solely increasing the initial ammonium chloride level. the ph drop in the broth due to the consumption of ammonium chloride also effected the cell growth and curdlan production. by simultaneously i ...	2005	16013500
the substrate-bound type 2 copper site of nitrite reductase: the nitrogen hyperfine coupling of nitrite revealed by pulsed epr.	a pulsed electron paramagnetic resonance study has been performed on the type 2 copper site of nitrite reductase (nir) from alcaligenes faecalis. the h145a mutant, in which histidine 145 is replaced by alanine, was studied by eseem and hyscore experiments at 9 ghz on frozen solutions. this mutant contains a reduced type 1 copper site which allowed a selective investigation of the type 2 site of h145a and of its nitrite-bound form h145a (no2(-)). the experiments yielded hyperfine and quadrupole p ...	2005	16285722
[isolation and characterization of a chlorpyrifos degrading bacteria and its bioremediation application in the soil].	a strain dsp3 capable of utilizing chlorpyrifos as the sole carbon and energy sources was isolated. based on the results of phenotypic features, phylogenetic of 16s rdna sequence, dna (g + c) mol% and dna homology between strain dsp3 and reference strains, the strain dsp3 is identified as alcaligenes faecalis. the degradation rate of chlorpyrifos was at 98.6% (100 mg/l) in liquid culture medium within 18 days and nearly 100% (100 mg/kg) in soil within 20 days respectively. an addition of strain ...	2005	16496701
analytical verification of a pcr assay for identification of bordetella avium.	bordetella avium is the etiologic agent of turkey coryza or bordetellosis, a respiratory disease responsible for substantial economic losses to the turkey industry. at present, identification of this bacterium relies on isolation and biochemical testing. although a pcr for the detection of b. avium was proposed a number of years ago, lack of analytical verification precludes its use as a diagnostic tool. furthermore, a number of details pertaining to the reaction conditions used are missing or u ...	2005	16272488
novel cyclic lipodepsipeptide from pseudomonas syringae pv. lachrymans strain 508 and syringopeptin antimicrobial activities.	the syringopeptins are a group of antimicrobial cyclic lipodepsipeptides produced by several plant-associated pseudomonads. a novel syringopeptin, sp508, was shown to be produced as two homologs (a and b) by pseudomonas syringae pv. lachrymans strain 508 from apple and to structurally resemble syringopeptin sp22. sp508 differed from sp22 and other syringopeptins by having three instead of four alpha,beta-unsaturated amino acids and a longer beta-hydroxy acyl chain. both sp508 and sp22 displayed ...	2005	16304170
class 1 integrons and tetracycline resistance genes in alcaligenes, arthrobacter, and pseudomonas spp. isolated from pigsties and manured soil.	the presence of tetracycline resistance (tc(r)) genes and class i integrons (in-1), and their ability to cotransfer were investigated in tc(r) gram-negative (185 strains) and gram-positive (72 strains) bacteria from danish farmland and pigsties. the isolates belonged to the groups or species escherichia coli, enterobacter spp., arthrobacter spp., alcaligenes spp., pseudomonas spp., and corynebacterium glutamicum. the 257 isolates were screened for in-1. eighty-one of the gram-negative isolates w ...	2005	16332771
genetic diversity and horizontal transfer of genes involved in oxidation of reduced phosphorus compounds by alcaligenes faecalis wm2072.	enrichment was performed to isolate organisms that could utilize reduced phosphorus compounds as their sole phosphorus sources. one isolate that grew well with either hypophosphite or phosphite was identified by 16s rrna gene analysis as a strain of alcaligenes faecalis. the genes required for oxidation of hypophosphite and phosphite by this organism were identified by using transposon mutagenesis and include homologs of the ptxd and htxa genes of pseudomonas stutzeri wm88, which encode an nad-d ...	2005	15640200
pancreatic abscess secondary to alcaligenes faecalis.	we report a patient with pancreatic abscesses and necrosis secondary to alcaligenes faecalis infection. he initially presented with alcohol-induced acute pancreatitis. twenty days after the initial presentation, he re-presented with increasing pain and was found to have pancreatic necrosis and abscesses. treatment was initiated with meropenem. because of persistent fevers, computed tomography-guided drainage was performed. the fluid grew a faecalis resistant to meropenem and the patient continue ...	2005	15654182
genes and enzymes involved in bacterial oxidation and reduction of inorganic arsenic.		2005	15691908
genomic analysis of anaerobic respiration in the archaeon halobacterium sp. strain nrc-1: dimethyl sulfoxide and trimethylamine n-oxide as terminal electron acceptors.	we have investigated anaerobic respiration of the archaeal model organism halobacterium sp. strain nrc-1 by using phenotypic and genetic analysis, bioinformatics, and transcriptome analysis. nrc-1 was found to grow on either dimethyl sulfoxide (dmso) or trimethylamine n-oxide (tmao) as the sole terminal electron acceptor, with a doubling time of 1 day. an operon, dmsreabcd, encoding a putative regulatory protein, dmsr, a molybdopterin oxidoreductase of the dmso reductase family (dmseabc), and a ...	2005	15716436
a role for fungal {beta}-glucans and their receptor dectin-1 in the induction of autoimmune arthritis in genetically susceptible mice.	a combination of genetic and environmental factors can cause autoimmune disease in animals. skg mice, which are genetically prone to develop autoimmune arthritis, fail to develop the disease under a microbially clean condition, despite active thymic production of arthritogenic autoimmune t cells and their persistence in the periphery. however, in the clean environment, a single intraperitoneal injection of zymosan, a crude fungal beta-glucan, or purified beta-glucans such as curdlan and laminari ...	2005	15781585
suppression of neutrophil accumulation in mice by cutaneous application of geranium essential oil.	background: previous studies suggested that essential oils suppressed the adherence response of human neutrophils in vitro and that intraperitoneal application of geranium oil suppressed the neutrophil accumulation into peritoneal cavity in vivo. usually, essential oils are applied through skin in aromatherapy in inflammatory symptoms. the purpose of this study is to assess the effects of cutaneous application of essential oils on the accumulation of neutrophils in inflammatory sites in skin of ...	2005	15813994
pro-sequence and ca2+-binding: implications for folding and maturation of ntn-hydrolase penicillin amidase from e. coli.	penicillin amidase (pa) is a bacterial periplasmic enzyme synthesized as a pre-pro-pa precursor. the pre-sequence mediates membrane translocation. the intramolecular pro-sequence is expressed along with the a and b chains but is rapidly removed in an autocatalytic manner. in extensive studies we show here that the pro-peptide is required for the correct folding of pa. pro-pa and pa unfold via a biphasic transition that is more pronounced in the case of pa. according to size-exclusion chromatogra ...	2005	15843029
ligand loop effects on the free energy change of redox and ph-dependent equilibria in cupredoxins probed on amicyanin variants.	in this work, we have determined the thermodynamic parameters of the reduction of four different variants of thiobacillus versutus amicyanin by electrochemical techniques. in addition, the thermodynamic parameters were determined of the low-ph conformational change involving protonation of the c-terminal histidine ligand and the concomitant dissociation of this histidine from the cu(i) ion. in these variants, the native c-terminal loop containing the cys, his, and met copper ligands has been rep ...	2005	16026167
tn5393d, a complex tn5393 derivative carrying the per-1 extended-spectrum beta-lactamase gene and other resistance determinants.	in alcaligenes faecalis fl-424/98, a clinical isolate that produces the per-1 extended-spectrum beta-lactamase, the bla(per-1) gene was found to be carried on a 44-kb nonconjugative plasmid, named pfl424, that was transferred to escherichia coli by electroporation. investigation of the genetic context of the bla(per-1) gene in pfl424 by means of a combined cloning and pcr mapping approach revealed that the gene is associated with a transposonlike element of the tn3 family. this 14-kb element is ...	2005	16048938
use of shell-vial cell culture assay for isolation of bacteria from clinical specimens: 13 years of experience.	the shell-vial culture assay is performed routinely in our laboratory. recently we revisited our experience of using the shell-vial culture assay for the isolation of microorganisms from various clinical samples. over a 13-year period, we have isolated 580 bacterial strains (5%) from 11,083 clinical samples tested. over the same period, 285 isolates of rickettsiae, bartonellae, or coxiella burnetii were cultured from a total of 7,102 samples tested. these isolates include 55 rickettsia sp. isola ...	2005	16207953
evaluation of a rapid direct assay for identification of bacteria and the mec a and van genes from positive-testing blood cultures.	we performed the first evaluation of a dna strip assay (genotype blood culture; hain lifescience, nehren, germany) for the detection of the most relevant bacterial sepsis pathogens directly from positive bactec blood culture bottles (becton dickinson, heidelberg, germany). the test comprises two panels, one for the direct species identification of important gram-positive cocci and the other for gram-negative rods. additionally, detection of the mec a and the van genes are implemented. the genoty ...	2005	16207992
extended-spectrum beta-lactamases: a clinical update.	extended-spectrum beta-lactamases (esbls) are a rapidly evolving group of beta-lactamases which share the ability to hydrolyze third-generation cephalosporins and aztreonam yet are inhibited by clavulanic acid. typically, they derive from genes for tem-1, tem-2, or shv-1 by mutations that alter the amino acid configuration around the active site of these beta-lactamases. this extends the spectrum of beta-lactam antibiotics susceptible to hydrolysis by these enzymes. an increasing number of esbls ...	2005	16223952
dissimilatory iron reduction and odor indicator abatement by biofilm communities in swine manure microcosms.	animal waste odors arising from products of anaerobic microbial metabolism create community relations problems for livestock producers. we investigated a novel approach to swine waste odor reduction: the addition of fecl(3), a commonly used coagulant in municipal wastewater treatment, to stimulate degradation of odorous compounds by dissimilatory iron-reducing bacteria (dirb). two hypotheses were tested: (i) fecl(3) is an effective source of redox-active ferric iron (fe(3+)) for dissimilatory re ...	2005	16151075
new chitosan-degrading strains that produce chitosanases similar to choa of mitsuaria chitosanitabida.	the betaproteobacterium mitsuaria chitosanitabida (formerly matsuebacter chitosanotabidus) 3001 produces a chitosanase (choa) that is classified in glycosyl hydrolase family 80. while many chitosanase genes have been isolated from various bacteria to date, they show limited homology to the m. chitosanitabida 3001 chitosanase gene (choa). to investigate the phylogenetic distribution of chitosanases analogous to choa in nature, we identified 67 chitosan-degrading strains by screening and investiga ...	2005	16151097
presence of two different active nirs nitrite reductase genes in a denitrifying thauera sp. from a high-nitrate-removal-rate reactor.	the nirs nitrite reductase genes were studied in two strains (strains 27 and 28) isolated from two denitrifying reactors and characterized as thauera according to their 16s rrna gene sequences. strain 28 contains a single nirs sequence, which is related to the nirs of thauera mechernichensis, and strain 27 contains two nirs sequences; one is similar to the nirs sequence from thauera mechernichensis (gene 2), but the second one (gene 8) is from a separate clade with nirs from pseudomonas stutzeri ...	2005	16151169
antibacterial activity of essential oils from australian native plants.	to date, of the australian essential oils, only tea tree (melaleuca alternifolia) and eucalyptus spp. have undergone extensive investigation. in this study a range of australian essential oils, including those from anethole anisata, callistris glaucophyllia, melaleuca spp. and thyptomine calycina, were assayed for in vitro antibacterial activity. m. alternifolia was also included for comparison purposes. activity was determined using standard disc diffusion assays with each oil assayed at 100%, ...	2005	16161028
shared genotypes of achromobacter xylosoxidans strains isolated from patients at a cystic fibrosis rehabilitation center.	during a study examining transmission of pseudomonas aeruginosa among 76 cystic fibrosis patients in a rehabilitation center, where patients stay in close contact during prolonged periods, several clusters of patients carrying genotypically identical p. aeruginosa, as well as two clusters of 4 and 10 patients, respectively, colonized with genotypically identical achromobacter xylosoxidans strains, were discovered.	2005	15956444
genetic environment and expression of the extended-spectrum beta-lactamase blaper-1 gene in gram-negative bacteria.	the genetic location of the gene coding for the expanded-spectrum beta-lactamase per-1 was analyzed in a series of gram-negative isolates. it was identified as part of a composite transposon bracketed by two novel insertion elements, ispa12 and ispa13, belonging to the is4 family that possess transposases that share 63% amino acid identity and that are chromosomally located in pseudomonas aeruginosa, providencia stuartii, and acinetobacter baumannii. on the contrary, the bla(per-1) gene was iden ...	2005	15855485
metallo-beta-lactamases: the quiet before the storm?	the ascendancy of metallo-beta-lactamases within the clinical sector, while not ubiquitous, has nonetheless been dramatic; some reports indicate that nearly 30% of imipenem-resistant pseudomonas aeruginosa strains possess a metallo-beta-lactamase. acquisition of a metallo-beta-lactamase gene will invariably mediate broad-spectrum beta-lactam resistance in p. aeruginosa, but the level of in vitro resistance in acinetobacter spp. and enterobacteriaceae is less dependable. their clinical significan ...	2005	15831827
bacterial zoonoses and infective endocarditis, algeria.	blood culture-negative endocarditis is common in algeria. we describe the etiology of infective endocarditis in this country. samples from 110 cases in 108 patients were collected in algiers. blood cultures were performed in algeria. serologic and molecular analysis of valves was performed in france. infective endocarditis was classified as definite in 77 cases and possible in 33. causative agents were detected by blood cultures in 48 cases. all 62 blood culture-negative endocarditis cases were ...	2005	15752438
identification and characterization of sulfolobus solfataricus d-gluconate dehydratase: a key enzyme in the non-phosphorylated entner-doudoroff pathway.	the extremely thermoacidophilic archaeon sulfolobus solfataricus utilizes d-glucose as a sole carbon and energy source through the non-phosphorylated entner-doudoroff pathway. it has been suggested that this micro-organism metabolizes d-gluconate, the oxidized form of d-glucose, to pyruvate and d-glyceraldehyde by using two unique enzymes, d-gluconate dehydratase and 2-keto-3-deoxy-d-gluconate aldolase. in the present study, we report the purification and characterization of d-gluconate dehydrat ...	2005	15509194
development and evaluation of a real-time pcr assay targeting the type iii secretion system of burkholderia pseudomallei.	here we report on the development of a discriminatory real-time assay for the rapid identification of burkholderia pseudomallei isolates and the evaluation of this assay for sensitivity against related species and detection in spiked human blood samples. the assay targets a 115-base-pair region within orf2 of the b. pseudomallei type iii secretion system gene cluster and distinguishes b. pseudomallei from other microbial species. assay performance was evaluated with 224 geographically, temporall ...	2006	16390953
plasmid-mediated high-level gentamicin resistance among enteric bacteria isolated from pet turtles in louisiana.	the sale of small turtles is banned by the food and drug administration from the u.s. market due to concerns about their excretion of salmonella spp. to produce a safe pet for the export market, the louisiana pet turtle industry uses gentamicin sulfate baths (1,000 microg/ml) to eradicate salmonella spp. from turtle eggs. in 1999, we analyzed bacterial samples recovered from turtle farms and found that strains of salmonella enterica subsp. arizonae and other bacteria, such as enterobacter cloaca ...	2006	16391058
complex regulation of arsenite oxidation in agrobacterium tumefaciens.	seminal regulatory controls of microbial arsenite [as(iii)] oxidation are described in this study. transposon mutagenesis of agrobacterium tumefaciens identified genes essential for as(iii) oxidation, including those coding for a two-component signal transduction pair. the transposon interrupted a response regulator gene (referred to as aoxr), which encodes an ntrc-like protein and is immediately downstream of a gene (aoxs) encoding a protein with primary structural features found in sensor hist ...	2006	16428412
a na+:h+ antiporter and a molybdate transporter are essential for arsenite oxidation in agrobacterium tumefaciens.	transposon tn5-b22 mutagenesis was used to identify genetic determinants required for arsenite [as(iii)] oxidation in an agrobacterium tumefaciens soil isolate, strain 5a. in one mutant, the transposon interrupted modb, which codes for the permease component of a high-affinity molybdate transporter. in a second mutant, the transposon insertion occurred in mrpb, which is part of a seven-gene operon encoding an mrp-type na+:h+ antiporter complex. complementation experiments with mod and mrp operon ...	2006	16452441
l-cysteate sulpho-lyase, a widespread pyridoxal 5'-phosphate-coupled desulphonative enzyme purified from silicibacter pomeroyi dss-3(t).	quantitative utilization of l-cysteate (2-amino-3-sulphopropionate) as the sole source of carbon and energy for growth of the aerobic, marine bacterium silicibacter pomeroyi dss-3(t) was observed. the sulphonate moiety was recovered in the medium largely as sulphite, and the appropriate amount of the ammonium ion was also observed. genes [suyab (3-sulpholactate sulpho-lyase)] encoding the known desulphonation reaction in cysteate degradation were absent from the genome, but a homologue of a puta ...	2006	16302849
tem-21 extended-spectrum beta-lactamase in a clinical isolate of alcaligenes faecalis from a nursing home.		2006	16344284
ligands for the beta-glucan receptor, dectin-1, assigned using "designer" microarrays of oligosaccharide probes (neoglycolipids) generated from glucan polysaccharides.	dectin-1 is a c-type lectin-like receptor on leukocytes that mediates phagocytosis and inflammatory mediator production in innate immunity to fungal pathogens. dectin-1 lacks residues involved in calcium ligation that mediates carbohydrate-binding by classical c-type lectins; nevertheless, it binds zymosan, a particulate beta-glucan-rich extract of saccharomyces cerevisiae, and binding is inhibited by polysaccharides rich in beta1,3- or both beta1,3- and beta1,6-linked glucose. the oligosacchari ...	2006	16371356
interaction of beta-1,3-glucan with its recognition protein activates hemolymph proteinase 14, an initiation enzyme of the prophenoloxidase activation system in manduca sexta.	a serine proteinase pathway in insect hemolymph leads to prophenoloxidase activation, an innate immune response against pathogen infection. in the tobacco hornworm manduca sexta, recombinant hemolymph proteinase 14 precursor (pro-hp14) interacts with peptidoglycan, autoactivates, and initiates the proteinase cascade (ji, c., wang, y., guo, x., hartson, s., and jiang, h. (2004) j. biol. chem. 279, 34101-34106). here, we report the purification and characterization of pro-hp14 from the hemolymph o ...	2006	16461344
structure-based stabilization of an enzyme: the case of penicillin acylase from alcaligenes faecalis.	the modeled structure of penicillin acylase from alcaligenes faecali (afpga) was constructed by comparative modeling with the modeller program. candidate positions that could be replaced with cysteine were estimated by scanning the modeled structure of afpga with the program modip (modeling disulfide bond in protein). the mutant q3c/p751c had a higher optimum temperature by three degrees than that of the wild type afpga. the half life of the double mutant q3c/p751c at 55 degrees c was increased ...	2006	16472081
resistance determinants of a highly arsenic-resistant strain of leptospirillum ferriphilum isolated from a commercial biooxidation tank.	two sets of arsenic resistance genes were isolated from the highly arsenic-resistant leptospirillum ferriphilum fairview strain. one set is located on a transposon, tnlfars, and is related to the previously identified tnatcars from acidithiobacillus caldus isolated from the same arsenopyrite biooxidation tank as l. ferriphilum. tnlfars conferred resistance to arsenite and arsenate and was transpositionally active in escherichia coli. tnlfars and tnatcars were sufficiently different for them not ...	2006	16517682
the sulfonated osmolyte n-methyltaurine is dissimilated by alcaligenes faecalis and by paracoccus versutus with release of methylamine.	selective enrichments yielded bacterial cultures able to utilize the osmolyte n-methyltaurine as sole source of carbon and energy or as sole source of fixed nitrogen for aerobic growth. strain mt1, which degraded n-methyltaurine as a sole source of carbon concomitantly with growth, was identified as a strain of alcaligenes faecalis. stoichiometric amounts of methylamine, whose identity was confirmed by matrix-assisted, laser-desorption ionization time-of-flight mass spectrometry, and of sulfate ...	2006	16549680
enhancing enzymatic activity of penicillin g acylase by coexpressing pcm gene.	penicillin g acylase (pga; e.c. 3.5.1.11) is an important enzyme which has broad applications in industries of beta-lactim antibiotics production. in this study, a promising pga gene from alcaligenes faecalis (afpga) and another pcm gene encoding protein isoaspartate methyltransferase (pimt) were constructed into pet43.1a((+)) and pet28a((+)), respectively. the recombinant plasmids petafpga and petpcm were transformed into the same host cell escherichia coli bl21 (de3). results suggested that th ...	2006	16550378
castellaniella gen. nov., to accommodate the phylogenetic lineage of alcaligenes defragrans, and proposal of castellaniella defragrans gen. nov., comb. nov. and castellaniella denitrificans sp. nov.	comparative 16s rrna gene sequence analysis indicates that two distinct sublineages exist within the genus alcaligenes: the alcaligenes faecalis lineage, comprising alcaligenes aquatilis and a. faecalis (with the three subspecies a. faecalis subsp. faecalis, a. faecalis subsp. parafaecalis and a. faecalis subsp. phenolicus), and the alcaligenes defragrans lineage, comprising a. defragrans. this phylogenetic discrimination is supported by phenotypic and chemotaxonomic differences. it is proposed ...	2006	16585701
cloning and sequencing of the ompa gene of enterobacter sakazakii and development of an ompa-targeted pcr for rapid detection of enterobacter sakazakii in infant formula.	enterobacter sakazakii is an emerging, infant formula-borne pathogen that causes severe meningitis, meningoencephalitis, sepsis, and necrotizing enterocolitis in neonates and infants, with a high fatality rate. traditional detection methods take up to 7 days to identify e. sakazakii. the outer membrane protein a gene (ompa), along with its flanking sequences from e. sakazakii (atcc 51329), was cloned in the pgem-t easy vector and sequenced. comparison of the nucleotide and deduced amino acid seq ...	2006	16597955
stereoselective nitrile hydrolysis by immobilized whole-cell biocatalyst.	the present work attempts to deal with the stability and reusability aspect of nitrilase from alcaligenes faecalis for the production of (r)-(-)-mandelic acid. four entrapment matrixes were screened to search for a suitable support, and alginate was found to have significant process advantages over its other counterparts. thermodynamic analysis allowed us to account for decreased enantioselectivity (e) as a result of immobilization. the system was also characterized based on the thiele modulus ( ...	2006	16677036
characterization of a novel long-chain acyl-coa thioesterase from alcaligenes faecalis.	a novel long-chain acyl-coa thioesterase from alcaligenes faecalis has been isolated and characterized. the protein was extracted from the cells with 1 m nacl, which required 1.5-fold, single-step purification to yield near-homogeneous preparations. in solution, the protein exists as homomeric aggregates, of mean diameter 21.6 nm, consisting of 22-kda subunits. ms/ms data for peptides obtained by trypsin digestion of the thiosterase did not match any peptide from escherichia coli thioesterases o ...	2006	16704412
mutant afm 2 of alcaligenes faecalis for phenol biodegradation using he-ne laser irradiation.	he-ne laser technology was utilized in this study to investigate the response of alcaligenes faecalis to laser stimulation. the irradiation experiments were conducted by the adjustment of the output power from 5 to 25 mw and the exposure time from 5 to 25 min. the results showed that the survival rate changed regularly with the variety of irradiation dose, and high positive mutation frequency was determined by both the energy density and the output power. the mutant strain afm 2 was obtained. ph ...	2006	16730779
tetrathiobacter mimigardefordensis sp. nov., isolated from compost, a betaproteobacterium capable of utilizing the organic disulfide 3,3'-dithiodipropionic acid.	in this study, a novel betaproteobacterium, strain dpn7(t), was isolated under mesophilic conditions from compost because of its capacity to utilize the organic disulfide 3,3'-dithiodipropionic acid. analysis of the 16s rrna gene sequence of strain dpn7(t) revealed 98.5 % similarity to that of tetrathiobacter kashmirensis lmg 22695(t). values for sequence similarity to members of the genera alcaligenes, castellaniella and taylorella, the nearest neighbours of the genus tetrathiobacter, were abou ...	2006	16738107
biology of pseudomonas stutzeri.	pseudomonas stutzeri is a nonfluorescent denitrifying bacterium widely distributed in the environment, and it has also been isolated as an opportunistic pathogen from humans. over the past 15 years, much progress has been made in elucidating the taxonomy of this diverse taxonomical group, demonstrating the clonality of its populations. the species has received much attention because of its particular metabolic properties: it has been proposed as a model organism for denitrification studies; many ...	2006	16760312
immobilization of permeabilized whole cell penicillin g acylase from alcaligenes faecalis using pore matrix crosslinked with glutaraldehyde.	the activity of penicillin g acylase from alcaligenes faecalis increased 7.5-fold when cells were permeabilized with 0.3% (w/v) ctab. the treated cells were entrapped by polyvinyl alcohol crosslinked with boric acid, and crosslinked with 2% (v/v) glutaraldehyde to increase the stability. the conversion yield of penicillin g to 6-aminopenicillanic acid was 75% by immobilized system in batch reaction. no activity was lost after 15 cycles and about 65% enzyme activity was retained at the end of the ...	2006	16799762
quantitative detection of the nosz gene, encoding nitrous oxide reductase, and comparison of the abundances of 16s rrna, narg, nirk, and nosz genes in soils.	nitrous oxide (n2o) is an important greenhouse gas in the troposphere controlling ozone concentration in the stratosphere through nitric oxide production. in order to quantify bacteria capable of n2o reduction, we developed a sybr green quantitative real-time pcr assay targeting the nosz gene encoding the catalytic subunit of the nitrous oxide reductase. two independent sets of nosz primers flanking the nosz fragment previously used in diversity studies were designed and tested (k. kloos, a. mer ...	2006	16885263
fluorescence in situ hybridization for rapid identification of achromobacter xylosoxidans and alcaligenes faecalis recovered from cystic fibrosis patients.	achromobacter xylosoxidans is frequently isolated from the respiratory secretions of cystic fibrosis (cf) patients, but identification with biochemical tests is unreliable. we describe fluorescence in situ hybridization assays for the rapid identification of achromobacter xylosoxidans and alcaligenes faecalis. both assays showed high sensitivities and high specificities with a collection of 155 nonfermenters from cf patients.	2006	16954289
effects of mutations in the substrate-binding domain of poly[(r)-3-hydroxybutyrate] (phb) depolymerase from ralstonia pickettii t1 on phb degradation.	poly[(r)-3-hydroxybutyrate] (phb) depolymerase from ralstonia pickettii t1 (phaz(rpit1)) adsorbs to denatured phb (dphb) via its substrate-binding domain (sbd) to enhance dphb degradation. to evaluate the amino acid residues participating in dphb adsorption, phaz(rpit1) was subjected to a high-throughput screening system consisting of pcr-mediated random mutagenesis targeted to the sbd gene and a plate assay to estimate the effects of mutations in the sbd on dphb degradation by phaz(rpit1). gene ...	2006	16963553
piggery wastewater treatment using alcaligenes faecalis strain no. 4 with heterotrophic nitrification and aerobic denitrification.	alcaligenes faecalis strain no. 4, which has heterotrophic nitrification and aerobic denitrification abilities, was used to treat actual piggery wastewater containing high-strength ammonium under aerobic conditions. in a continuous experiment using a solids-free wastewater (sfw) mixed with feces, almost all of the 2000 nh4+ -n mg/l and 12,000 cod mg/l in the wastewater was removed and the ammonium removal rate was approximately 30 mg-n/l/h, which was 5-10 times higher than the rates achieved by ...	2006	16893560
effect of ph, temperature and substrate on n2o, no and co2 production by alcaligenes faecalis p.	to study the effect of ph, temperature and substrate on the magnitude of n(2)o and no production by heterotrophic nitrifiers.	2006	16907816
evaluation of the duopath legionella lateral flow assay for identification of legionella pneumophila and legionella species culture isolates.	duopath legionella (merck kgaa, darmstadt, germany) is a new immunochromatographic assay for the simultaneous identification of cultured l. pneumophila and legionella species other than l. pneumophila. in tests of 89 l. pneumophila strains and 87 legionella strains other than l. pneumophila representing 41 different species, duopath and a widely used latex agglutination assay detected l. pneumophila with 100% and 98% accuracy, respectively, whereas the percentages differed significantly for othe ...	2006	16751575
a robotic dna purification protocol and real-time pcr for the detection of enterobacter sakazakii in powdered infant formulae.	enterobacter sakazakii is the causative agent of rare but severe food-borne infections associated with meningitis, necrotizing enterocolitis and sepsis in infants. rehydrated powdered infant formulae have been implicated as the source of infection in several outbreaks and sporadic cases. in this work, a real time fluorescence resonance energy transfer pcr assay incorporating an internal amplification control (iac) was developed for the specific detection of e. sakazakii in foods. performance of ...	2006	17166252