Publications
| Title | Abstract | Year Filter | PMID(sorted ascending) Filter |
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| application of smartgene idns software to partial 16s rrna gene sequences for a diverse group of bacteria in a clinical laboratory. | laboratories often receive clinical isolates for bacterial identification that have ambiguous biochemical profiles by conventional testing. with the emergence of 16s rrna gene sequencing as an identification tool, we evaluated the usefulness of smartgene idns, a 16s rrna sequence database and software program for microbial identification. identification by conventional methods of a diverse group of bacterial clinical isolates was compared with gene sequences interrogated by the smartgene and mic ... | 2006 | 17050811 |
| dissecting the pretransitional conformational changes in aminoacylase i thermal denaturation. | aminoacylase i (acyi) catalyzes the stereospecific hydrolysis of l-acylamino acids and is generally assumed to be involved in the final step of the degradation of intracellular n-acetylated proteins. apart from its crucial functions in intracellular amino acid metabolism, acyi also has substantial commercial importance for the optical resolution of n-acylated dl-amino acids. as a zinc-dependent enzyme, acyi is quite stable against heat-induced denaturation and can be regarded as a thermostable e ... | 2006 | 17071653 |
| dissecting the pretransitional conformational changes in aminoacylase i thermal denaturation. | aminoacylase i (acyi) catalyzes the stereospecific hydrolysis of l-acylamino acids and is generally assumed to be involved in the final step of the degradation of intracellular n-acetylated proteins. apart from its crucial functions in intracellular amino acid metabolism, acyi also has substantial commercial importance for the optical resolution of n-acylated dl-amino acids. as a zinc-dependent enzyme, acyi is quite stable against heat-induced denaturation and can be regarded as a thermostable e ... | 2006 | 17071653 |
| crystal structure of an electron transfer complex between aromatic amine dehydrogenase and azurin from alcaligenes faecalis. | the crystal structure of an electron transfer complex of aromatic amine dehydrogenase (aadh) and azurin is presented. electrons are transferred from the tryptophan tryptophylquinone (ttq) cofactor of aadh to the type i copper of the cupredoxin azurin. this structure is compared with the complex of the ttq-containing methylamine dehydrogenase (madh) and the cupredoxin amicyanin. despite significant similarities between the two quinoproteins and the two cupredoxins, each is specific for its respec ... | 2006 | 17087503 |
| site-directed mutagenesis indicates an important role of cysteines 76 and 181 in the catalysis of hydantoin racemase from sinorhizobium meliloti. | hydantoin racemase enzyme plays a crucial role in the reaction cascade known as "hydantoinase process." in conjunction with a stereoselective hydantoinase and a stereospecific carbamoylase, it allows the total conversion from d,l-5-monosubstituted hydantoins, with a low rate of racemization, to optically pure d- or l-amino acids. residues cys76 and cys181 belonging to hydantoin racemase from sinorhizobium meliloti (smehyua) have been proved to be involved in catalysis. here, we report biophysica ... | 2006 | 17132860 |
| an efficient fungal rna-silencing system using the dsred reporter gene. | in filamentous fungi, rna silencing is an attractive alternative to disruption experiments for the functional analysis of genes. we adapted the gene encoding the autofluorescent dsred protein as a reporter to monitor the silencing process in fungal transformants. using the cephalosporin c producer acremonium chrysogenum, strains showing a high level of expression of the dsred gene were constructed, resulting in red fungal colonies. transfer of a hairpin-expressing vector carrying fragments of th ... | 2006 | 17142377 |
| an efficient fungal rna-silencing system using the dsred reporter gene. | in filamentous fungi, rna silencing is an attractive alternative to disruption experiments for the functional analysis of genes. we adapted the gene encoding the autofluorescent dsred protein as a reporter to monitor the silencing process in fungal transformants. using the cephalosporin c producer acremonium chrysogenum, strains showing a high level of expression of the dsred gene were constructed, resulting in red fungal colonies. transfer of a hairpin-expressing vector carrying fragments of th ... | 2006 | 17142377 |
| 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 |
| erythromycin resistance-conferring plasmid prsb105, isolated from a sewage treatment plant, harbors a new macrolide resistance determinant, an integron-containing tn402-like element, and a large region of unknown function. | the erythromycin resistance plasmid prsb105 was previously isolated from an activated sludge bacterial community of a municipal wastewater treatment plant. compilation of the complete prsb105 nucleotide sequence revealed that the plasmid is 57,137 bp in size and has a mean g+c content of 56.66 mol%. the prsb105 backbone is composed of two different replication and/or partitioning modules and a functional mobilization region encoding the mobilization genes mobcde and mobba. the first replicon (re ... | 2007 | 17261525 |
| improvement in ammonium removal efficiency in wastewater treatment by mixed culture of alcaligenes faecalis no. 4 and l1. | to improve ammonium removal efficiency in wastewater treatment, a mixed culture of alcaligenes faecalis no. 4 and its mutant l1, both of which have heterotrophic nitrification and aerobic denitrification abilities, was performed. in a batch culture, no. 4 has a higher denitrification ability than l1, but its ammonium removal rate was lower. in a mixed continuous culture in the ammonium loading range of 750 to 3500 mg-n/l/d, the average ammonium removal rate and the average denitrification ratio ... | 2007 | 17298903 |
| decolorisation and detoxification of direct blue-15 by a bacterial consortium. | studies were carried out on decolorisation and biotransformation of the dye direct blue-15 into 3,3'-dimethoxybenzidine (o'-dianisidine) and a sulphonated derivative by a five-member bacterial consortium. chromatographic studies revealed further complete biodegradation of 3,3'-dimethoxybenzidine coupled with release of ammonia, but the recalcitrant sulphonated derivative persisted. the microorganisms identified in the mixed consortium by 16s rdna sequence analysis were alcaligenes faecalis, sphi ... | 2007 | 17321737 |
| characterization of sodc, a periplasmic superoxide dismutase from burkholderia cenocepacia. | burkholderia cenocepacia is a gram-negative, non-spore-forming bacillus and a member of the burkholderia cepacia complex. b. cenocepacia can survive intracellularly in phagocytic cells and can produce at least one superoxide dismutase (sod). the inability of o2- to cross the cytoplasmic membrane, coupled with the periplasmic location of cu,znsods, suggests that periplasmic sods protect bacteria from superoxide that has an exogenous origin (for example, when cells are faced with reactive oxygen i ... | 2007 | 17325048 |
| beta-1,4-glucanase-like protein from the cyanobacterium synechocystis pcc6803 is a beta-1,3-1,4-glucanase and functions in salt stress tolerance. | in the present study, we characterized the gene (cyanobase accession number slr0897) designated ssglc encoding a beta-1,4-glucanase-like protein (ssglc) from synechocystis pcc6803. the deduced amino acid sequence for ssglc showed a high degree of similarity to sequences of gh (glycoside hydrolase) family 9 beta-1,4-glucanases (cellulases) from various sources. surprisingly, the recombinant protein obtained from the escherichia coli expression system was able to hydrolyse barley beta-glucan and l ... | 2007 | 17331074 |
| structure and function of a hexameric copper-containing nitrite reductase. | dissimilatory nitrite reductase (nir) is a key enzyme in denitrification, catalyzing the first step that leads to gaseous products (no, n(2)o, and n(2)). we have determined the crystal structure of a cu-containing nir from a methylotrophic denitrifying bacterium, hyphomicrobium denitrificans, at 2.2-a resolution. the overall structure of this h. denitrificans nir reveals a trigonal prism-shaped molecule in which a monomer consisting of 447 residues and three cu atoms is organized into a unique h ... | 2007 | 17360521 |
| [reaction of microorganisms to the digestive fluid of the earthworms]. | the reaction of soil bacteria and fungi to the digestive fluid of the earthworm aporrectodea caliginosa was studied. the fluid was obtained by centrifugation of the native enzymes of the digestive tract. the inhibition of growth of certain bacteria, spores, and fungal hyphae under the effect of extracts from the anterior and middle sections of the digestive tract of a. caliginosa was discovered for the first time. in bacteria, microcolony formation was inhibited as early as 20-30 s after the app ... | 2007 | 17410875 |
| bacterial decolorization of acid orange 7 in the presence of ionic and non-ionic surfactants. | the effects of the non-ionic surfactant triton x-100, the cationic surfactant cetyltri-methylammonium bromide (ctab) and the anionic surfactant sodium n-lauroyl sarcosinate (sls) on the decolorization of the reaction medium containing the monoazo dye acid orange 7 (ao7) by alcaligenes faecalis and rhodococcus erythropolis were studied. it was found that the surfactants influenced in different ways the rate of decolorization. at all concentrations tested the non-ionic surfactant triton x-100 decr ... | 2007 | 17425112 |
| a tale of two oxidation states: bacterial colonization of arsenic-rich environments. | microbial biotransformations have a major impact on contamination by toxic elements, which threatens public health in developing and industrial countries. finding a means of preserving natural environments-including ground and surface waters-from arsenic constitutes a major challenge facing modern society. although this metalloid is ubiquitous on earth, thus far no bacterium thriving in arsenic-contaminated environments has been fully characterized. in-depth exploration of the genome of the beta ... | 2007 | 17432936 |
| biochemical characterization of per-2 and genetic environment of blaper-2. | per-2 was the first detected and the second most prevalent extended-spectrum beta-lactamase in clinical pathogens isolated in argentina and was also reported only in other south american countries. citrobacter freundii 33587 was isolated in 1999 in buenos aires and was resistant to all tested beta-lactams except cephamycins and carbapenems. the strain produced both plasmid-borne tem-1 and per-2 (pi 5.4), which could be transferred by conjugation. by pcr screening, thermal asymmetric interlaced p ... | 2007 | 17438050 |
| evaluation of the colorimetric vitek 2 card for identification of gram-negative nonfermentative rods: comparison to 16s rrna gene sequencing. | ninety strains of a collection of well-identified clinical isolates of gram-negative nonfermentative rods collected over a period of 5 years were evaluated using the new colorimetric vitek 2 card. the vitek 2 colorimetric system identified 53 (59%) of the isolates to the species level and 9 (10%) to the genus level; 28 (31%) isolates were misidentified. an algorithm combining the colorimetric vitek 2 card and 16s rrna gene sequencing for adequate identification of gram-negative nonfermentative r ... | 2007 | 17507509 |
| posttraumatic endophthalmitis due to a rare pathogen, alcaligenes faecalis. | 2007 | 17508059 | |
| nucleotide sequence of plasmid pcnb1 from comamonas strain cnb-1 reveals novel genetic organization and evolution for 4-chloronitrobenzene degradation. | the nucleotide sequence of a new plasmid pcnb1 from comamonas sp. strain cnb-1 that degrades 4-chloronitrobenzene (4cnb) was determined. pcnb1 belongs to the incp-1beta group and is 91,181 bp in length. a total of 95 open reading frames appear to be involved in (i) the replication, maintenance, and transfer of pcnb1; (ii) resistance to arsenate and chromate; and (iii) the degradation of 4cnb. the 4cnb degradative genes and arsenate resistance genes were located on an extraordinarily large transp ... | 2007 | 17526790 |
| formation of amyloid fibrils via longitudinal growth of oligomers. | mature amyloid fibrils are believed to be formed by the lateral association of discrete structural units designated as protofibrils, but this lateral association of protofibrils has never been directly observed. we have recently characterized a thioesterase from alcaligenes faecalis, which was shown to exist as homomeric oligomers with an average diameter of 21.6 nm consisting of 22 kda subunits in predominantly beta-sheet structure. in this study, we have shown that upon incubation in a 75% eth ... | 2007 | 17536835 |
| n-acetyl-d-glucosamine-6-phosphate deacetylase: substrate activation via a single divalent metal ion. | naga is a member of the amidohydrolase superfamily and catalyzes the deacetylation of n-acetyl-d-glucosamine-6-phosphate. the catalytic mechanism of this enzyme was addressed by the characterization of the catalytic properties of metal-substituted derivatives of naga from escherichia coli with a variety of substrate analogues. the reaction mechanism is of interest since naga from bacterial sources is found with either one or two divalent metal ions in the active site. this observation indicates ... | 2007 | 17567047 |
| protein film voltammetry of copper-containing nitrite reductase reveals reversible inactivation. | the cu-containing nitrite reductase from alcaligenes faecalis s-6 catalyzes the one-electron reduction of nitrite to nitric oxide (no). electrons enter the enzyme at the so-called type-1 cu site and are then transferred internally to the catalytic type-2 cu site. protein film voltammetry experiments were carried out to obtain detailed information about the catalytic cycle. the homotrimeric structure of the enzyme is reflected in a distribution of the heterogeneous electron-transfer rates around ... | 2007 | 17579406 |
| biodegradation of phenol at high initial concentration by alcaligenes faecalis. | strain alcaligenes faecalis was isolated and identified as a member of the genus alcaligenes by using biolog and 16s rdna sequence analysis. the phenol biodegradation tests showed that the phenol-degrading potential of a. faecalis related greatly to the different physiological phases of inoculum. the maximum phenol degradation occurred at the late phase of the exponential growth stages, where 1600 mg l(-1) phenol was completely degraded within 76 h. a. faecalis secreted and accumulated a vast qu ... | 2007 | 17597295 |
| a survey of orphan enzyme activities. | using computational database searches, we have demonstrated previously that no gene sequences could be found for at least 36% of enzyme activities that have been assigned an enzyme commission number. here we present a follow-up literature-based survey involving a statistically significant sample of such "orphan" activities. the survey was intended to determine whether sequences for these enzyme activities are truly unknown, or whether these sequences are absent from the public sequence databases ... | 2007 | 17623104 |
| relative abundances of proteobacterial membrane-bound and periplasmic nitrate reductases in selected environments. | dissimilatory nitrate reduction is catalyzed by a membrane-bound and a periplasmic nitrate reductase. we set up a real-time pcr assay to quantify these two enzymes, using the narg and napa genes, encoding the catalytic subunits of the two types of nitrate reductases, as molecular markers. the narg and napa gene copy numbers in dna extracted from 18 different environments showed high variations, with most numbers ranging from 2 x 10(2) to 6.8 x 10(4) copies per ng of dna. this study provides evid ... | 2007 | 17630306 |
| comparison of hand-held test kits, immunofluorescence microscopy, enzyme-linked immunosorbent assay, and flow cytometric analysis for rapid presumptive identification of yersinia pestis. | an in-house immunochromatographic test, plague biothreat alert test strips, abicap columns, enzyme-linked immunosorbent assay, flow cytometry, and immunofluorescence microscopy were compared for the detection of the fraction 1 capsular antigen of yersinia pestis, using spiked buffer and clinical specimens. hand-held test kits proved to be excellent benchtop tools. | 2007 | 17652472 |
| temperature effect on bacterial azo bond reduction kinetics: an arrhenius plot analysis. | studied was the effect of temperature in the range 12-46 degrees c on the rate of bacterial decolorization of the mono-azo dye acid orange 7 by alcaligenes faecalis 6132 and rhodococcus erythropolis 24. with both strains the raise of temperature led to a corresponding raise of decolorization rate better manifested by r. erythropolis. the analysis of the arrhenius plot revealed a break near the middle of the temperature range. the regression analysis showed practically complete identity of the ob ... | 2008 | 17653820 |
| investigation of the redox centres of periplasmic selenate reductase from thauera selenatis by epr spectroscopy. | periplasmic ser (selenate reductase) from thauera selenatis is classified as a member of the tat (twin-arginine translocase)-translocated (type ii) molybdoenzymes and comprises three subunits each containing redox cofactors. variable-temperature x-band epr spectra of the purified ser complex showed features attributable to centres [3fe-4s]1+, [4fe-4s]1+, mo(v) and haem-b. epr-monitored redox-potentiometric titration of the serabc complex (sera-serb-serc, a hetero-trimetric complex of alphabetaga ... | 2007 | 17688424 |
| influence of different carboxy-terminal mutations on the substrate-, reaction- and enantiospecificity of the arylacetonitrilase from pseudomonas fluorescens ebc191. | different members of the nitrilase superfamily (d-carbamoylases, nit-fhit proteins, amidases, cyanide dihydratases and nitrilases) were compared by multiple sequence alignments and a long carboxy-terminal extension (about 50 amino acids) identified in all nitrilases and cyanide dihydratases which was not present in other members of the nitrilase superfamily. the function of this c-terminal part was experimentally analysed in the arylacetonitrilase of pseudomonas fluorescens ebc191 by the constru ... | 2007 | 17693456 |
| control of microorganisms and reduction of biogenic amines in chicken breast and thigh by irradiation and organic acids. | the effect of irradiation or organic acid treatment of raw chicken breast and thigh meat to control inoculated microorganisms and the production of biogenic amines (ba) was studied. bacillus cereus, enterobacter cloacae, and alcaligenes faecalis were selected and inoculated into raw ground chicken breast and thigh meat at approximately 10(7) cfu/g. the samples were irradiated at 0, 0.5, 1, and 2 kgy or mixed with a 0.2 m solution of acetic, citric, or lactic acid (1 ml for 10 g of meat sample) f ... | 2007 | 17704395 |
| genomic analysis reveals widespread occurrence of new classes of copper nitrite reductases. | recently, the structure of a cu-containing nitrite reductase (nir) from hyphomicrobium denitrificans (hdnir) has been reported, establishing the existence of a new family of cu-nir where an additional type 1 cu (t1cu) containing cupredoxin domain is located at the n-terminus (nojiri et al. in proc. natl. acad. sci. usa 104:4315-4320, 2007). hdnir retains the well-characterised coupled t1cu-type 2 cu (t2cu) core, where the t2cu catalytic site is also built utilising ligands from neighbouring mono ... | 2007 | 17712582 |
| reconstitution of a branch of the manduca sexta prophenoloxidase activation cascade in vitro: snake-like hemolymph proteinase 21 (hp21) cleaved by hp14 activates prophenoloxidase-activating proteinase-2 precursor. | upon wounding or infection, a serine proteinase cascade in insect hemolymph leads to prophenoloxidase (propo) activation and melanization, a defense response against invading microbes. in the tobacco hornworm manduca sexta, this response is initiated via hemolymph proteinase 14 (hp14), a mosaic protein that interacts with bacterial peptidoglycan or fungal beta-1,3-glucan to autoactivate. in this paper, we report the expression, purification, and functional analysis of m. sexta hp21 precursor, an ... | 2007 | 17785189 |
| convergent evolution of a new arsenic binding site in the arsr/smtb family of metalloregulators. | acidithiobacillus ferrooxidans has an arsenic resistance operon that is controlled by an as(iii)-responsive transcriptional repressor, afarsr, a member of the arsr/smtb family of metalloregulators. afarsr lacks the as(iii) binding site of the arsrs from plasmid r773 and escherichia coli, which have a cys(32)-val-cys(34)-asp-leu-cys(37) sequence in the dna binding site. in contrast, it has three cysteine residues, cys(95), cys(96), and cys(102), that are not present in the r773 and e. coli arsrs. ... | 2007 | 17897948 |
| stable copper-nitrosyl formation by nitrite reductase in either oxidation state. | nitrite reductase (nir) is an enzyme that uses type 1 and type 2 copper sites to reduce nitrite to nitric oxide during bacterial denitrification. a copper-nitrosyl intermediate is a proposed, yet poorly characterized feature of the nir catalytic cycle. this intermediate is formally described as cu(i)-no+ and is proposed to be formed at the type 2 copper site after nitrite binding and electron transfer from the type 1 copper site. in this study, copper-nitrosyl complexes were formed by prolonged ... | 2007 | 17924665 |
| pre-steady-state studies of phosphite dehydrogenase demonstrate that hydride transfer is fully rate limiting. | phosphite dehydrogenase (ptdh) is a unique nad-dependent enzyme that catalyzes the oxidation of inorganic phosphite to phosphate. the enzyme has great potential for cofactor regeneration, and mechanistic studies have provided some insight into the residues that are important for catalysis. in this investigation, pre-steady-state studies were performed on the his6-tagged wild-type (wt) enzyme, several active site mutants, a thermostable mutant (12x-ptdh), and a thermostable mutant with dual cofac ... | 2007 | 17949110 |
| synergy within structural biology of single crystal optical spectroscopy and x-ray crystallography. | advances in the adaptation of optical spectroscopy to monitor photo-induced or enzyme-catalyzed reactions in the crystalline state have enabled x-ray crystal structures to be accurately linked with spectroscopically defined intermediates. this, in turn, has led to a deeper understanding of the role protein structural changes play in function. the integration of optical spectroscopy with x-ray crystallography is growing and now extends beyond linking crystal structure to reaction intermediate. re ... | 2007 | 17959373 |
| antibacterial activity of guava (psidium guajava l.) and neem (azadirachta indica a. juss.) extracts against foodborne pathogens and spoilage bacteria. | the antibacterial activity of guava (psidium guajava) and neem (azadirachta indica) extracts against 21 strains of foodborne pathogens were determined--listeria monocytogenes (five strains), staphylococcus aureus (four strains), escherichia coli o157:h7 (six strains), salmonella enteritidis (four strains), vibrio parahaemolyticus, and bacillus cereus, and five food spoilage bacteria: pseudomonas aeroginosa, p. putida, alcaligenes faecalis, and aeromonas hydrophila (two strains). guava and neem e ... | 2007 | 18041957 |
| the autodisplay story, from discovery to biotechnical and biomedical applications. | among the pathways used by gram-negative bacteria for protein secretion, the autotransporter pathway represents a solution of impressive simplicity. proteins are transported, independent of their nature as recombinant or native passengers, as long as the coding nucleotide sequence is inserted in frame between those of an n-terminal signal peptide and a c-terminal domain, referred to as the beta-barrel of the outer membrane translocation unit. the immunoglobulin a1 (iga1) protease from neisseria ... | 2007 | 18063719 |
| high incidence of plant growth-stimulating bacteria associated with the rhizosphere of wheat grown on salinated soil in uzbekistan. | soil salinization is increasing steadily in many parts of the world and causes major problems for plant productivity. under these stress conditions, root-associated beneficial bacteria can help improve plant growth and nutrition. in this study, salt-tolerant bacteria from the rhizosphere of uzbek wheat with potentially beneficial traits were isolated and characterized. eight strains which initially positively affect the growth of wheat plants in vitro were investigated in detail. all eight strai ... | 2008 | 18211262 |
| fumaric acid production by fermentation. | the potential of fumaric acid as a raw material in the polymer industry and the increment of cost of petroleum-based fumaric acid raises interest in fermentation processes for production of this compound from renewable resources. although the chemical process yields 112% w/w fumaric acid from maleic anhydride and the fermentation process yields only 85% w/w from glucose, the latter raw material is three times cheaper. besides, the fermentation fixes co2. production of fumaric acid by rhizopus sp ... | 2008 | 18214471 |
| development and evaluation of immunochromatographic assay for simple and rapid detection of campylobacter jejuni and campylobacter coli in human stool specimens. | an immunochromatographic assay (campy-ica) using a newly generated single monoclonal antibody against a 15-kda cell surface protein of campylobacter jejuni was developed. when cell suspensions of 86 c. jejuni strains and 27 campylobacter coli strains were treated with a commercially available bacterial protein extraction reagent and the resulting extracts were tested with the campy-ica, they all yielded positive results. the minimum detectable limits for the c. jejuni strains ranged from 1.8 x 1 ... | 2008 | 18256225 |
| detoxification of toxic heavy metals by marine bacteria highly resistant to mercury. | pollution in industrial areas is a serious environmental concern, and interest in bacterial resistance to heavy metals is of practical significance. mercury (hg), cadmium (cd), and lead (pb) are known to cause damage to living organisms, including human beings. several marine bacteria highly resistant to mercury (bhrm) capable of growing at 25 ppm (mg l(-1)) or higher concentrations of mercury were tested during this study to evaluate their potential to detoxify cd and pb. results indicate their ... | 2008 | 18288535 |
| fed batch bioconversion of 2-propanol by a solvent tolerant strain of alcaligenes faecalis entrapped in ca-alginate gel. | a gram-negative, rod-shaped, aerobe, capable of converting 2-propanol (isopropanol, ipa) to acetone was isolated from an oil/sump, and identified by 16 s rdna analysis as alcaligenes faecalis. investigations showed this strain to be extremely solvent-tolerant and it was subsequently named st1. in this study, a. faecalis st1 cells were immobilized by entrapment in ca-alginate beads (3 mm in diameter), and used in the bioconversion of high concentration ipa. the biodegradation rates and the corres ... | 2008 | 18293022 |
| the enzyme mechanism of nitrite reductase studied at single-molecule level. | a generic method is described for the fluorescence "readout" of the activity of single redox enzyme molecules based on förster resonance energy transfer from a fluorescent label to the enzyme cofactor. the method is applied to the study of copper-containing nitrite reductase from alcaligenes faecalis s-6 immobilized on a glass surface. the parameters extracted from the single-molecule fluorescence time traces can be connected to and agree with the macroscopic ensemble averaged kinetic constants. ... | 2008 | 18303118 |
| enzymatic preparation of cefaclor with immobilized penicillin acylase. | enzymatic syntheses of cefaclor by immobilized penicillin acylase under kinetic control were carried out. according to the initial reaction rate ratio of synthesis to hydrolysis (vs/vh), penicillin acylase from alcaligenes faecalis was chosen as the suitable catalyst for the synthesis of cefaclor. the reaction conditions, such as temperature, ph, and substrate concentration were investigated based on their vs/vh values. in the process of preparing cefaclor, in situ product removal (ispr) and acy ... | 2008 | 18320464 |
| survey of bacterial diversity in chronic wounds using pyrosequencing, dgge, and full ribosome shotgun sequencing. | chronic wound pathogenic biofilms are host-pathogen environments that colonize and exist as a cohabitation of many bacterial species. these bacterial populations cooperate to promote their own survival and the chronic nature of the infection. few studies have performed extensive surveys of the bacterial populations that occur within different types of chronic wound biofilms. the use of 3 separate16s-based molecular amplifications followed by pyrosequencing, shotgun sanger sequencing, and denatur ... | 2008 | 18325110 |
| conserved active site residues limit inhibition of a copper-containing nitrite reductase by small molecules. | the interaction of copper-containing dissimilatory nitrite reductase from alcaligenes faecalis s-6 ( afnir) with each of five small molecules was studied using crystallography and steady-state kinetics. structural studies revealed that each small molecule interacted with the oxidized catalytic type 2 copper of afnir. three small molecules (formate, acetate and nitrate) mimic the substrate by having at least two oxygen atoms for bidentate coordination to the type 2 copper atom. these three anions ... | 2008 | 18358002 |
| novel aromatic ring-hydroxylating dioxygenase genes from coastal marine sediments of patagonia. | polycyclic aromatic hydrocarbons (pahs), widespread pollutants in the marine environment, can produce adverse effects in marine organisms and can be transferred to humans through seafood. our knowledge of pah-degrading bacterial populations in the marine environment is still very limited, and mainly originates from studies of cultured bacteria. in this work, genes coding catabolic enzymes from pah-biodegradation pathways were characterized in coastal sediments of patagonia with different levels ... | 2008 | 18366740 |
| riboswitches that sense s-adenosylhomocysteine and activate genes involved in coenzyme recycling. | we have identified a highly conserved rna motif that occurs upstream of genes involved in s-adenosyl-l-methionine (sam) recycling in many gram-positive and gram-negative species of bacteria. the phylogenetic distribution and the conserved structural features of representatives of this motif are indicative of riboswitch function. riboswitches are widespread metabolite-sensing gene control elements that are typically found in the 5' untranslated regions (utrs) of bacterial mrnas. we experimentally ... | 2008 | 18374645 |
| a new classification system for bacterial rieske non-heme iron aromatic ring-hydroxylating oxygenases. | rieske non-heme iron aromatic ring-hydroxylating oxygenases (rhos) are multi-component enzyme systems that are remarkably diverse in bacteria isolated from diverse habitats. since the first classification in 1990, there has been a need to devise a new classification scheme for these enzymes because many rhos have been discovered, which do not belong to any group in the previous classification. here, we present a scheme for classification of rhos reflecting new sequence information and interactio ... | 2008 | 18387195 |
| an amino acid at position 142 in nitrilase from rhodococcus rhodochrous atcc 33278 determines the substrate specificity for aliphatic and aromatic nitriles. | nitrilase from rhodococcus rhodochrous atcc 33278 hydrolyses both aliphatic and aromatic nitriles. replacing tyr-142 in the wild-type enzyme with the aromatic amino acid phenylalanine did not alter specificity for either substrate. however, the mutants containing non-polar aliphatic amino acids (alanine, valine and leucine) at position 142 were specific only for aromatic substrates such as benzonitrile, m-tolunitrile and 2-cyanopyridine, and not for aliphatic substrates. these results suggest th ... | 2008 | 18412544 |
| analysis of bacterial dna in synovial tissue of tunisian patients with reactive and undifferentiated arthritis by broad-range pcr, cloning and sequencing. | bacteria and/or their antigens have been implicated in the pathogenesis of reactive arthritis (rea). several studies have reported the presence of bacterial antigens and nucleic acids of bacteria other than those specified by diagnostic criteria for rea in joint specimens from patients with rea and various arthritides. the present study was conducted to detect any bacterial dna and identify bacterial species that are present in the synovial tissue of tunisian patients with reactive arthritis and ... | 2008 | 18412942 |
| the structures of alcaligenes faecalis d-3-hydroxybutyrate dehydrogenase before and after nad+ and acetate binding suggest a dynamical reaction mechanism as a member of the sdr family. | d-3-hydroxybutyrate dehydrogenase, which catalyzes the reversible reaction between d-3-hydroxybutyrate and acetoacetate, has been classified into the short-chain dehydrogenase/reductase family and is a useful marker in the assay of diabetes mellitus and/or ketoacidosis. the enzyme from alcaligenes faecalis was crystallized in the apo form and in the holo form with acetate as a substrate analogue. the crystal structures of both forms were determined at 2.2 angstroms resolution. the enzyme is a te ... | 2008 | 18453685 |
| assessment of gut bacteria for a paratransgenic approach to control dermolepida albohirtum larvae. | bacteria from the hindguts of dermolepida albohirtum larvae were assessed for their potential to be used in paratransgenic strategies that target scarab pests of sugarcane. bacteria isolated in pure culture from the hindguts of d. albohirtum larvae were from the proteobacteria, firmicutes, and actinobacteria phyla and matched closely with taxa from intestinal and rhizosphere environments. however, these isolates were not the most common gut-associated bacteria identified in denaturing gradient g ... | 2008 | 18456847 |
| nitrogen fixation island and rhizosphere competence traits in the genome of root-associated pseudomonas stutzeri a1501. | the capacity to fix nitrogen is widely distributed in phyla of bacteria and archaea but has long been considered to be absent from the pseudomonas genus. we report here the complete genome sequencing of nitrogen-fixing root-associated pseudomonas stutzeri a1501. the genome consists of a single circular chromosome with 4,567,418 bp. comparative genomics revealed that, among 4,146 protein-encoding genes, 1,977 have orthologs in each of the five other pseudomonas representative species sequenced to ... | 2008 | 18495935 |
| diversity surveys and evolutionary relationships of aoxb genes in aerobic arsenite-oxidizing bacteria. | a new primer set was designed to specifically amplify ca. 1,100 bp of aoxb genes encoding the as(iii) oxidase catalytic subunit from taxonomically diverse aerobic as(iii)-oxidizing bacteria. comparative analysis of aoxb protein sequences showed variable conservation levels and highlighted the conservation of essential amino acids and structural motifs. aoxb phylogeny of pure strains showed well-discriminated taxonomic groups and was similar to 16s rrna phylogeny. alphaproteobacteria-, betaproteo ... | 2008 | 18502920 |
| anaerobic growth of alcaligenes faecalis var. denitrificans at the expense of ether glycols and nonionic detergents. | 1983 | 18548680 | |
| dectin-1 synergizes with tlr2 and tlr4 for cytokine production in human primary monocytes and macrophages. | the beta-glucan receptor dectin-1 and toll-like receptors tlr2 and tlr4 are the main receptors for recognition of candida albicans by the innate immune system. it has been reported that dectin-1 amplifies tlr2-dependent induction of cytokines in mouse models. in the present study we hypothesized that dectin-1 has potent synergistic effects with both tlr2 and tlr4 in human pbmcs and macrophages. human pbmcs and monocyte-derived macrophages were stimulated with curdlan, a linear beta-1,3-glucan-po ... | 2008 | 18549457 |
| enzymatic properties of immobilized alcaligenes faecalis cells with cell-associated beta-glucosidase activity. | enzymatic properties of alcaligenes faecalis cells immobilized in polyacrylamide were characterized and compared with those reported for the extracted enzyme, and with those measured for free cells. many of the properties reflected those of the extracted enzyme rather than those measured in the free whole cells prior to immobilization, suggesting cell disruption during immobilization. these properties included the ph activity profile, a slightly broader ph stability profile, and the activation e ... | 1984 | 18553373 |
| sequencing and expression of two arsenic resistance operons with different functions in the highly arsenic-resistant strain ochrobactrum tritici scii24t. | arsenic (as) is a natural metalloid, widely used in anthropogenic activities, that can exist in different oxidation states. throughout the world, there are several environments contaminated with high amounts of arsenic where many organisms can survive. the most stable arsenical species are arsenate and arsenite that can be subject to chemically and microbiologically oxidation, reduction and methylation reactions. organisms surviving in arsenic contaminated environments can have a diversity of me ... | 2008 | 18554386 |
| production of bioemulsifier by bacillus subtilis, alcaligenes faecalis and enterobacter species in liquid culture. | three bacterial strains isolated from waste crude oil were selected due to their capacity of growing in the presence of hydrocarbons and production of bioemulsifier. the genetic identification (pcr of the 16s rdna gene using fd1 and rd1 primers) of these strains showed their affiliation to bacillus subtilis, alcaligenes faecalis and enterobacter sp. these strains were able to emulsify n-octane, toluene, xylene, mineral oils and crude oil, look promising for bioremediation application. finally, c ... | 2008 | 18554901 |
| expanded-spectrum beta-lactamase per-1 in an environmental aeromonas media isolate from switzerland. | 2008 | 18644966 | |
| misidentification of pandoraea sputorum isolated from sputum of a patient with cystic fibrosis and review of pandoraea species infections in transplant patients. | pandoraea species are considered emerging pathogens in cystic fibrosis (cf) patients, but few data exist regarding outcomes of patients colonized with these organisms. we report a case of pandoraea sputorum colonization in a cf patient under consideration for lung transplantation and review five cases of lung transplantation involving pandoraea species. | 2008 | 18650348 |
| characterization of the proteins of bordetella isolates from turkeys in the uk by polyacrylamide gel electrophoresis. | the proteins of seven bordetella bronchiseptica-like isolates were examined by polyacrylamide gel electrophoresis (page). they were compared with three similar isolates from overseas, one of which is the type strain of bordetella avium, and with bordetella bronchiseptica nctc 452t and alcaligenes faecalis nctc 415. apart from alcaligenes faecalis, there was strong homology between the isolates suggesting their close relationship, but minor differences were apparent, too. the significance of thes ... | 1992 | 18670923 |
| rapid identification of bordetella avium and related organisms on the basis of their cellular carbohydrate patterns. | whole cell hydrolysates of bordetella avium, b. bronchiseptica, b. pertussis, b. parapertussis, alcaligenes faecalis, a. xylosoxidans ssp. denitrificans, a. xylosoxidans ssp. xylosoxidans, and a. piechaudii were analysed for their cellular carbohydrates by capillary gas-chromatography of per-acetylated aldononitriles and o-methyloximes, respectively. all alcaligenaceae species could be discriminated on the basis of their carbohydrate profiles and a few conventional features. taxometric evaluatio ... | 1991 | 18680060 |
| yeast cell factories for fine chemical and api production. | abstract: this review gives an overview of different yeast strains and enzyme classes involved in yeast whole-cell biotransformations. a focus was put on the synthesis of compounds for fine chemical and api (= active pharmaceutical ingredient) production employing single or only few-step enzymatic reactions. accounting for recent success stories in metabolic engineering, the construction and use of synthetic pathways was also highlighted. examples from academia and industry and advances in the f ... | 2008 | 18684335 |
| structure of diethyl phosphate bound to the binuclear metal center of phosphotriesterase. | the bacterial phosphotriesterase (pte) from pseudomonas diminuta catalyzes the hydrolysis of organophosphate esters at rates close to the diffusion limit. x-ray diffraction studies have shown that a binuclear metal center is positioned in the active site of pte and that this complex is responsible for the activation of the nucleophilic water from solvent. in this paper, the three-dimensional structure of pte was determined in the presence of the hydrolysis product, diethyl phosphate (dep), and a ... | 2008 | 18702530 |
| efficacy of intraoperative vancomycin in irrigating solutions on aqueous contamination during phacoemulsification. | to study the efficacy of adding vancomycin in irrigating solutions, in comparison to topical antibiotic given preoperatively for a day, during phacoemulsification, in reducing the anterior chamber (ac) contamination. | 2008 | 18711269 |
| the characterisation of bordetella/alcaligenes-like organisms and their effects on turkey poults and chicks. | eight isolates of the bordetella or alcaligenes-like organisms associated with turkey rhino-tracheitis were examined. five of these isolates had been recovered from the united kingdom and three were foreign isolates. four of the uk isolates came from flocks with mild respiratory disease. the fifth isolate came from birds with no respiratory signs and this appears to be the first report of the recovery of bordetella/alcaligenes from apparently normal turkeys. the field isolates and type strains a ... | 1986 | 18766500 |
| identification of bordetella avium sp. nov. by the api 20 ne system. | the reactions of 47 bordetella avium strains in the api 20 ne micro-test system were compared to those of the species bordetella bronchiseptica, alcaligenes faecalis and alcaligenes denitrificans. the api 20 ne microtest system allowed separation between b. avium and the other species of gram-negative nonfermentative rods investigated. | 1986 | 18766558 |
| a comparative study of avian bordetella-like strains, bordetella bronchiseptica, alcaligenes faecalis and other related nonfermentable bacteria. | cultural and biochemical characteristics, electrophoretic patterns of soluble proteins, and pathogenicity in turkey poults, of 30 avian gram-negative nonfermentable bacterial strains acquired from various geographical regions, of which 26 had been isolated from turkeys and one each from a chicken, duck, goose and sharp-tailed munia, were compared to those of bordetella bronchiseptica, alcaligenes faecalis, alcaligenes denitrificans, achromobacter xylosoxidans and bordetella parapertussis. with t ... | 1983 | 18766782 |
| experimental studies on turkey coryza. | disease with severe respiratory symptoms, nasal discharge, swelling of sinuses, conjunctivitis with foamy discharge and mortality has been observed in turkey flocks in israel. of the pathogenic agents isolated from field cases, three, paramyxovirus, yucaipa (yucaipa virus), alcaligenes faecalis (a. faecalis) and mycoplasma gallisepticum (mg) were used to infect turkey poults, singly or in combination, in our attempt to reproduce the field disease symptoms. yucaipa virus alone caused mild symptom ... | 1984 | 18766831 |
| body temperature response of turkey poults infected with alcaligenes faecalis. | experiments were conducted to investigate the colonic temperature (tc) response to alcaligenes faecalis infection in turkeys. one-day-old poults were inoculated intranasally with 0.05 ml of a 24 hour brain heart infusion (bhi) broth culture with a bacterial concentration of 1.0 x 10(9) cells/ml. within 2 hours after inoculation tc was depressed significantly in challenged poults. this depression was significant through day 14 in experiment 1 and day 6 in experiment 2. further studies with steril ... | 1984 | 18766888 |
| the effect of combined and separate infection by alcaligenes faecalis and paramyxovirus (yucaipa) on the surface morphology of the trachea in turkey poults. | sixty-seven 1-day-old turkey poults were inoculated in the infra orbital sinus with 3 x 10(8) alcaligenes faecalis bacteria and/or by 10(5.8)eid 50/ ml of yucaipa virus. twenty-five similar birds served as controls. identification of the agents inoculated was made during the development of disease by means of isolation and serological tests. during the development of the disease, the surface morphology of the trachea in the affected animals revealed cellular oedema associated with a mucus coatin ... | 1985 | 18766948 |
| recent clinical overview of renal and perirenal abscesses in 56 consecutive cases. | the aim of this study was to examine the recent clinical trends and antibiotic susceptibilities of the causative microorganisms in renal and perirenal abscesses, and to elucidate the factors associated with treatment strategies. | 2008 | 18787367 |
| effective mutagenesis of vibrio fischeri by using hyperactive mini-tn5 derivatives. | we have developed a transposon mutagenesis system for vibrio fischeri es114 that utilizes a hyperactive mutant tn5 transposase (e54k and m56a) and optimized transposon ends. using a conjugation-based procedure, we obtained independent single-insertion mini-tn5 mutants at a rate of approximately 10(-6). this simple and inexpensive technique represents a significant improvement over previous methods for transposon mutagenesis of v. fischeri and should be applicable to many other bacteria. | 2008 | 18805998 |
| [enhanced production of curdlan by alcaligenes faecalis by selective feeding with ammonia water during the cell growth phase of fermentation]. | curdlan is a water insoluble exopolysaccharide produced by alcaligenes faecalis under nitrogen-limiting conditions. after excretion, the polysaccharide is attached the cell wall. thus enhancement of biomass production during the cell growth phase is important to curdlan production. a strategy of increasing nitrogen source to improve biomass production was adopted for curdlan production by alcaligenes faecalis (atcc 31749). in the batch fermentation of curdlan, a relatively higher nh4cl level of ... | 2008 | 18807988 |
| the missing link: bordetella petrii is endowed with both the metabolic versatility of environmental bacteria and virulence traits of pathogenic bordetellae. | bordetella petrii is the only environmental species hitherto found among the otherwise host-restricted and pathogenic members of the genus bordetella. phylogenetically, it connects the pathogenic bordetellae and environmental bacteria of the genera achromobacter and alcaligenes, which are opportunistic pathogens. b. petrii strains have been isolated from very different environmental niches, including river sediment, polluted soil, marine sponges and a grass root. recently, clinical isolates asso ... | 2008 | 18826580 |
| structure, membrane orientation, mechanism, and function of pexiganan--a highly potent antimicrobial peptide designed from magainin. | the growing problem of bacterial resistance to conventional antibiotic compounds and the need for new antibiotics have stimulated interest in the development of antimicrobial peptides (amps) as human therapeutics. development of topically applied agents, such as pexiganan (also known as msi-78, an analog of the naturally occurring magainin2, extracted from the skin of the african frog xenopus laevis) has been the focus of pharmaceutical development largely because of the relative safety of topic ... | 2009 | 19010301 |
| structure, membrane orientation, mechanism, and function of pexiganan--a highly potent antimicrobial peptide designed from magainin. | the growing problem of bacterial resistance to conventional antibiotic compounds and the need for new antibiotics have stimulated interest in the development of antimicrobial peptides (amps) as human therapeutics. development of topically applied agents, such as pexiganan (also known as msi-78, an analog of the naturally occurring magainin2, extracted from the skin of the african frog xenopus laevis) has been the focus of pharmaceutical development largely because of the relative safety of topic ... | 2009 | 19010301 |
| bacterial contamination in drinking water: a case study in rural areas of northern rajasthan, india. | the objective of this study was to determine the bacterial contaminations in drinking water samples collected form some rural habitations of northern rajasthan, india. a total of ten bacterial species: escherichia coli, pseudomonas aeruginosa, enterobacter aerogenes, klebsiella sp, proteus vulgaris, alcaligenes faecalis, bacillus cereus, staphylococcus aureus, streptococcus lactis and micrococcus luteum were identified form drinking water samples. the bacteria belonging to the family enterobacte ... | 2009 | 19023670 |
| impact of enhanced infection control at 2 neonatal intensive care units in the philippines. | the growing burden of neonatal mortality associated with hospital-acquired neonatal sepsis in the developing world creates an urgent need for cost-effective infection-control measures in resource-limited settings. | 2009 | 19025496 |
| 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 |