| regulatory system of the protocatechuate 4,5-cleavage pathway genes essential for lignin downstream catabolism. | sphingobium sp. strain syk-6 converts various lignin-derived biaryls with guaiacyl (4-hydroxy-3-methoxyphenyl) and syringyl (4-hydroxy-3,5-dimethoxyphenyl) moieties to vanillate and syringate. these compounds are further catabolized through the protocatechuate (pca) 4,5-cleavage (pca45) pathway. in this article, the regulatory system of the pca45 pathway is described. a lysr-type transcriptional regulator (lttr), ligr, activated the transcription of the ligk-orf1-ligi-lsda and ligjabc operons in ... | 2010 | 20435721 |
| impact of mutation on proton transfer reactions in ketosteroid isomerase: insights from molecular dynamics simulations. | the two proton transfer reactions catalyzed by ketosteroid isomerase (ksi) involve a dienolate intermediate stabilized by hydrogen bonds with tyr14 and asp99. molecular dynamics simulations based on an empirical valence bond model are used to examine the impact of mutating these residues on the hydrogen-bonding patterns, conformational changes, and van der waals and electrostatic interactions during the proton transfer reactions. while the rate constants for the two proton transfer steps are sim ... | 2010 | 20450180 |
| flow cytometry-based method for isolating live bacteria with meta-cleavage activity on dihydroxy compounds of biphenyl. | a new method for isolating targeted live bacterial cells was established with the use of cell sorting by flow cytometry (fcm) based on the fluorescence of the intermediate metabolite of biphenyl degradation. during biphenyl degradation, a pcb degrader, comamonas testosteroni tk102, produces a meta-cleavage intermediate metabolite, 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (hopda), which emits green fluorescence. hopda was produced from 2,3-dihydroxy biphenyl as a substrate, but it was not ap ... | 2010 | 20471608 |
| engineering cofactor preference of ketone reducing biocatalysts: a mutagenesis study on a gamma-diketone reductase from the yeast saccharomyces cerevisiae serving as an example. | the synthesis of pharmaceuticals and catalysts more and more relies on enantiopure chiral building blocks. these can be produced in an environmentally benign and efficient way via bioreduction of prochiral ketones catalyzed by dehydrogenases. a productive source of these biocatalysts is the yeast saccharomyces cerevisiae, whose genome also encodes a reductase catalyzing the sequential reduction of the gamma-diketone 2,5-hexanedione furnishing the diol (2s,5s)-hexanediol and the gamma-hydroxyketo ... | 2010 | 20480039 |
| steroid degradation genes in comamonas testosteroni ta441: isolation of genes encoding a δ4(5)-isomerase and 3α- and 3β-dehydrogenases and evidence for a 100 kb steroid degradation gene hot spot. | in previous studies, we identified two major comamonas testosteroni ta441 gene clusters involved in steroid degradation. because most of the genes included in these clusters were revealed to be involved in degradation of basic steroidal structures and a few were suggested to be involved in the degradation of modified steroid compounds, we investigated the spectrum of steroid compounds degradable for ta441 to better identify the genes involved in steroid degradation. ta441 degraded testosterone, ... | 2010 | 20554032 |
| the comamonas testosteroni steroid biosensor system (coss)--reflection on other methods. | natural and synthetic steroid hormones are released uncontrolled into the environment and are considered as pollutants with regard to their endocrine activity and negative influence on all kind of organisms. due to their widespread presence, endocrine activity even at low concentrations, and their potential adverse effects in both the environment and human health, there is an increasing need for the development of rapid, sensitive and quantitative techniques for measuring trace levels of these s ... | 2010 | 20558289 |
| structural characterization of iscr8, iscr22, and iscr23, subgroups of is91-like insertion elements. | analysis of iscr8 (ispps1) revealed that this group of insertion elements has to be subdivided into three subgroups: iscr8, iscr22, and iscr23. the distinction of three subgroups is supported by phylogenetic analysis of the transposase open reading frames (orfs). comparison of over 20 complete and partial iscr8/22/23 elements identified oriis candidate sequences for all groups and a teris candidate sequence for iscr8. the oriis sequences, their distance to the transposase orfs, and the sequence ... | 2010 | 20625149 |
| transcriptional regulation of the terephthalate catabolism operon in comamonas sp. strain e6. | two almost identical gene clusters, tphr(i)c(i)a2(i)a3(i)b(i)a1(i) and tphr(ii)c(ii)a2(ii)a3(ii)b(ii)a1(ii), are responsible for the conversion of terephthalate (tpa) to protocatechuate in comamonas sp. strain e6. in the present study, we investigated the transcriptional regulation of the tphr(ii)c(ii)a2(ii)a3(ii)b(ii)a1(ii) gene cluster. reverse transcription-pcr analysis suggested that the tphr(ii)c(ii)a2(ii)a3(ii)b(ii)a1(ii) genes form two transcriptional units, the tphc(ii)a2(ii)a3(ii)b(ii)a ... | 2010 | 20656871 |
| isolates of comamonas spp. exhibiting catalase and peroxidase activities and diversity of their responses to oxidative stress. | for survival isolates of comamonas testosteroni ccm 1931, c. testosteroni k3, c. terrigena n3h or n1c and c. terrigena ccm 2409, selected largely from polluted environments, the production of catalase and dianisidine-peroxidase activity was important. electrophoretic resolution of cell-free extracts of aerobically grown strains in luria-bertani medium during the exponential phase revealed distinctive expression of catalatic and peroxidatic activities detected with 3,3'-diaminobenzidine tetrahydr ... | 2010 | 20678795 |
| obstacles of multiplex real-time pcr for bacterial 16s rdna: primer specifity and dna decontamination of taq polymerase. | background: the detection of a broad range of bacteria by pcr is applied for the screening of blood and blood products with special attention to platelet concentrates. for practical use it is desirable that detection systems include gram-positive, gram-negative and non-gram-stainable bacteria. it is quite challenging to achieve high sensitivity along with a clear negative control with pcr reagents, because especially taq polymerase is contaminated with traces of bacterial dna. methods: bacterial ... | 2010 | 20737013 |
| molecular and catalytic properties of the aldehyde dehydrogenase of gluconacetobacter diazotrophicus, a quinoheme protein containing pyrroloquinoline quinone, cytochrome b, and cytochrome c. | several aldehyde dehydrogenase (aldh) complexes have been purified from the membranes of acetic acid bacteria. the enzyme structures and the chemical nature of the prosthetic groups associated with these enzymes remain a matter of debate. we report here on the molecular and catalytic properties of the membrane-bound aldh complex of the diazotrophic bacterium gluconacetobacter diazotrophicus. the purified aldh complex is a heterodimer comprising two subunits of 79.7 and 50 kda, respectively. reve ... | 2010 | 20802042 |
| comparative analysis of myxococcus predation on soil bacteria. | predator-prey relationships among prokaryotes have received little attention but are likely to be important determinants of the composition, structure, and dynamics of microbial communities. many species of the soil-dwelling myxobacteria are predators of other microbes, but their predation range is poorly characterized. to better understand the predatory capabilities of myxobacteria in nature, we analyzed the predation performance of numerous myxococcus isolates across 12 diverse species of bact ... | 2010 | 20802074 |
| a simple and general method for determining the protein and nucleic acid content of viruses by uv absorbance. | uv spectra of viruses are complicated by overlapping protein and rna absorbance and light scattering. we describe and validate methodology for estimating rna and protein concentration from such spectra. importantly, we found that encapsidation did not substantially affect rna absorbance. combining absorbance data with a known t number, we confirmed that brome mosaic virus packages about 3100 nucleotides/capsid, consistent with its genome. e. coli-expressed hepatitis b virus (hbv) packages host r ... | 2010 | 20850162 |
| potential of escherichia coli o157:h7 to persist and form viable but non-culturable cells on a food-contact surface subjected to cycles of soiling and chemical treatment. | our aim was to assess the potential of escherichia coli o157:h7 to persist in a processing environment. we studied e. coli behaviour under conditions modelling those of meat plants to establish one initial bacterial load that allows persistence and another that does not. polyurethane coupons (3.5 cm²) were contaminated once with e. coli in meat exudate before being subjected daily to a cleaning product and a disinfectant, both at half the recommended in-use concentrations, and a further soiling ... | 2010 | 20888655 |
| characterization of the protocatechuate 4,5-cleavage pathway operon in comamonas sp. strain e6 and discovery of a novel pathway gene. | the protocatechuate (pca) 4,5-cleavage (pca45) pathway is the essential catabolic route for the degradation of various aromatic acids in the genus comamonas. all of the pca45 pathway genes, orf1-pmdkefdabc, as well as another pca 4,5-dioxygenase gene, pmda(ii)b(ii), were isolated from a phthalate-degrading bacterium, comamonas sp. strain e6. disruption of pmdb and pmdd in e6, which code for the β subunit of pca 4,5-dioxygenase and 2-pyrone-4,6-dicarboxylate (pdc) hydrolase, respectively, resulte ... | 2010 | 20952641 |
| enhancement of cometabolic biodegradation of 4-chlorophenol induced with phenol and glucose as carbon sources by comamonas testosteroni. | the biological degradation of phenol and 4-chlorophenol (4-cp) by comamonas testosteroni cect 326t has been studied. phenol and 4-cp were treated alone as a sole carbon and energy source, but only phenol was completely degraded by c. testosteroni. since the presence of cosubstrates can enhance the toxic compounds removal by pure cultures, phenol and glucose were added as growth substrates for cometabolic transformation of 4-cp. high efficiencies were obtained in all the experiments carried out i ... | 2010 | 20970917 |
| expression, purification, crystallization and preliminary crystallographic studies of cis-biphenyl-2,3-dihydrodiol-2,3-dehydrogenase from pandoraea pnomenusa b-356. | cis-biphenyl-2,3-dihydrodiol-2,3-dehydrogenase (bphb) is involved in the aerobic biodegradation of biphenyl and polychlorinated biphenyls. bphb from pandoraea pnomenusa strain b-356 was overexpressed in escherichia coli, purified to homogeneity and crystallized. crystals were obtained by the sitting-drop vapour-diffusion method using polyethylene glycol 3350 and 0.2 m sodium malonate. a bphb crystal diffracted to 2.8 å resolution and belonged to space group p4(3)2(1)2, with unit-cell parameters ... | 2010 | 21045310 |
| hydrogen bonding in the active site of ketosteroid isomerase: electronic inductive effects and hydrogen bond coupling. | computational studies are performed to analyze the physical properties of hydrogen bonds donated by tyr16 and asp103 to a series of substituted phenolate inhibitors bound in the active site of ketosteroid isomerase (ksi). as the solution pk(a) of the phenolate increases, these hydrogen bond distances decrease, the associated nuclear magnetic resonance (nmr) chemical shifts increase, and the fraction of protonated inhibitor increases, in agreement with prior experiments. the quantum mechanical/mo ... | 2010 | 21049962 |
| steroid degradation in comamonas testosteroni. | steroid degradation by comamonas testosteroni and nocardia restrictus have been intensively studied for the purpose of obtaining materials for steroid drug synthesis. c. testosteroni degrades side chains and converts single/double bonds of certain steroid compounds to produce androsta-1,4-diene 3,17-dione or the derivative. following 9α-hydroxylation leads to aromatization of the a-ring accompanied by cleavage of the b-ring, and aromatized a-ring is hydroxylated at c-4 position, cleaved at δ4 by ... | 2010 | 21056662 |
| heat resistance mediated by a new plasmid encoded clp atpase, clpk, as a possible novel mechanism for nosocomial persistence of klebsiella pneumoniae. | klebsiella pneumoniae is an important opportunistic pathogen and a frequent cause of nosocomial infections. we have characterized a k. pneumoniae strain responsible for a series of critical infections in an intensive care unit over a two-year period. the strain was found to be remarkably thermotolerant providing a conceivable explanation of its persistence in the hospital environment. this marked phenotype is mediated by a novel type of clp atpase, designated clpk. the clpk gene is encoded by a ... | 2010 | 21085699 |
| biosynthesis of chiral 3-hydroxyvalerate from single propionate-unrelated carbon sources in metabolically engineered e. coli. | the ability to synthesize chiral building block molecules with high optical purity is of considerable importance to the fine chemical and pharmaceutical industries. production of one such compound, 3-hydroxyvalerate (3hv), has previously been studied with respect to the in vivo or in vitro enzymatic depolymerization of biologically-derived co-polymers of poly(3-hydroxybutyrate-co-3-hydroxyvalerate). however, production of this biopolymeric precursor typically necessitates the supplementation of ... | 2010 | 21110891 |
| cloning, expression and characterization of a novel short-chain dehydrogenase/reductase (sdrx) in comamonas testosteroni. | the short-chain dehydrogenase/reductase (sdr) superfamily is a large and diverse group of genes with members found in all forms of life. comamonas testosteroni atcc11996 is a gram-negative bacterium which can use steroids as carbon and energy source. in previous investigations, we have identified 3α-hydroxysteroid dehydrogenase/carbonyl reductase (3α-hsd/cr) from c. testosteroni as a member of the sdr superfamily that catalyzes the reversible interconversion of hydroxyl and oxo groups at positio ... | 2010 | 21111045 |
| the arthrobacter arilaitensis re117 genome sequence reveals its genetic adaptation to the surface of cheese. | arthrobacter arilaitensis is one of the major bacterial species found at the surface of cheeses, especially in smear-ripened cheeses, where it contributes to the typical colour, flavour and texture properties of the final product. the a. arilaitensis re117 genome is composed of a 3,859,257 bp chromosome and two plasmids of 50,407 and 8,528 bp. the chromosome shares large regions of synteny with the chromosomes of three environmental arthrobacter strains for which genome sequences are available: ... | 2010 | 21124797 |
| characterization of the steroid degrading bacterium s19-1 from the baltic sea at kiel, germany. | steroid contamination of sea water is an ever growing problem and impacts population dynamics of all kinds of sea animals. we have long experience with the soil bacterium comamonas testosteroni atcc11996 which is able to catabolize a variety of steroids and polycyclic aromatic hydrocarbons, and which might be used in the bioremediation of contaminated places. in c. testosteroni about 20 enzymes which are involved in steroid degradation could be induced by 0.5mm testosterone. in this work, we iso ... | 2010 | 21185812 |
| why two are not enough: degradation of p-toluenesulfonate by a bacterial community from a pristine site in moorea, french polynesia. | in previous work, only one culture (strain ta12) from a pristine site was reported to utilize the xenobiotic compound p-toluenesulfonate (tsa) as a sole source of carbon and energy for aerobic growth. 'strain ta12' has now been recognized as a community of three bacteria: achromobacter xylosoxidans ta12-a, ensifer adhaerens ta12-b and pseudomonas nitroreducens ta12-c. achromobacter xylosoxidans ta12-a and e. adhaerens ta12-b were identified as the tsa degraders. these two organisms contain sever ... | 2011 | 21204940 |
| catheter-related bacteremia caused by comamonas testosteroni in a hemodialysis patient. | comamonas testosteroni has rarely been implicated as a human pathogen. in general, the outcome of c. testosteroni infections is favorable. we report a case of fatal bacteremia caused by c. testosteroni in a 64-year-old woman on hemodialysis. | 2011 | 21223488 |
| steroid degradation and two steroid-inducible enzymes in the marine bacterium h5. | natural and synthetic steroid hormones excreted into the environment are potentially threatening the population dynamics of all kinds of animals and public health. we have previously isolated a steroid degrading bacterial strain (h5) from the baltic sea, at kiel, germany. 16s-rrna analysis showed that bacterial strain h5 belongs to the genus vibrio, family vibrionaceae and class gamma-proteobacteria. bacterial strain h5 can degrade steroids such as testosterone and estrogens, which was shown in ... | 2011 | 21281621 |
| identification of a new steroid degrading bacterial strain h5 from the baltic sea and isolation of two estradiol inducible genes. | the presence of steroid hormones in the aquatic environment is potentially threatening the population dynamics of all kinds of sea animals and public health. environmental estrogens in water have been reported to be associated with abnormal sexual development and abnormal feminizing responses in some animals. new approaches for the bioremediation of steroid hormones from the environment are therefore urgently sought. we have previously isolated a steroid degrading bacterial strain (h5) from the ... | 2011 | 21310233 |
| identification of a thiolase gene essential for ß-oxidation of the acyl side chain of the steroid compound cholate in pseudomonas sp. strain chol1. | bile salts such as cholate are steroid compounds occurring ubiquitously in the environment through excretion by animals. cholate degradation by pseudomonas sp. strain chol1 is initiated by a-ring oxidation and ß-oxidation of the acyl side chain. a transposon mutant of strain chol1 was isolated that could not grow with cholate, but transformed it into several steroid compounds accumulating in culture supernatants. the main product was identified as (22e)-7a,12a-dihydroxy-3-oxochola-1,4,22-triene- ... | 2011 | 21362022 |
| novel regulator mphx represses activation of phenol hydroxylase genes caused by a xylr/dmpr-type regulator mphr in acinetobacter calcoaceticus. | acinetobacter calcoaceticus phea-2 utilizes phenol as its sole carbon and energy source and has a multi-component phenol hydroxylase-encoding gene operon (mphklmnop) for phenol degradation. two additional genes, mphr and mphx, were found upstream and downstream of mphklmnop, respectively. the mphr gene encodes a xylr/dmpr-type regulator-like protein and is transcribed in the opposite direction to mphklmnop. the mphx gene is transcribed in the same direction as mphklmnop and encodes a protein wit ... | 2011 | 21455294 |
| bioinformatic characterization of the trimeric intracellular cation-specific channel protein family. | trimeric intracellular cation-specific (tric) channels are integral to muscle excitation-contraction coupling. tric channels provide counter-ionic flux when calcium is rapidly transported from intracellular stores to the cell cytoplasm. until recently, knowledge of the presence of these proteins was limited to animals. we analyzed the tric family and identified a profusion of prokaryotic family members with topologies and motifs similar to those of their eukaryotic counterparts. prokaryotic memb ... | 2011 | 21519847 |
| isomerization of the phytohormone precursor opda in the insect gut: a mechanistic and computational study. | 12-oxophytodienoic acid (opda) is isomerized in the gut of herbivorous insects to tetrahydrodicranenone b (iso-opda). the transformation is achieved by a glutathione-s-transferase present in the gut epithelium. experiments with 9-[2h]-iso-opda demonstrated the complete retention of the deuterium atom in the product 11-[2h]-opda consistent with an intramolecular 1,3-hydrogen shift. homology-modeling based on the x-ray structure of a glutathione s-trans-ferase from anopheles gambiae revealed that ... | 2011 | 21527631 |
| comamonas testosteroni infection in taiwan: reported two cases and literature review. | comamonas testosteroni is a widely distributed aerobic gram-negative bacillus. infection by c testosteroni is infrequent, and no such cases have been reported in taiwan. here, we would like to present a 54-year-old alcoholic patient from taiwan, and his left leg was injured during a fishing trip, resulting in left leg cellulitis and c testosteroni bacteremia. the patient's fever subsided after initial treatment with extended-spectrum cephalosporin, whereas his erythematous swelling did not resol ... | 2011 | 21531356 |
| patchwork assembly of nag-like nitroarene dioxygenase genes and 3-chlorocatechol degradation cluster for the pathway evolution of 2-chloronitrobenzene catabolism in pseudomonas stutzeri zwlr2-1. | pseudomonas stutzeri zwlr2-1 utilizes 2-chloronitrobenzene (2cnb) as a sole source of carbon, nitrogen and energy. to identify genes involved in this pathway, a 16.2-kb dna fragment containing putative 2-chloronitrobenzene dioxygenase genes was cloned and sequenced. of the products from the 19 open reading frames that resulted from this fragment, cnbac and cnbad exhibited striking identities to the respective α- and β- subunits of the nag-like ring-hydroxylating dioxygenases involved in the meta ... | 2011 | 21602392 |
| comamonas testosteronan synthase, a bifunctional glycosyltransferase that produces a unique heparosan polysaccharide analog. | glycosaminoglycans [gags] are linear hexosamine-containing polysaccharides. these polysaccharides are synthesized by some pathogenic bacteria to form an extracellular coating or capsule. this strategy forms the basis of molecular camouflage since vertebrates possess naturally-occurring gags that are essential for life. a recent sequence database search identified a putative protein from the opportunistic pathogen comamonas testosteroni that exhibits similarity to the pasteurella multocida glycos ... | 2011 | 21610195 |
| effects of entrapment on nucleic acid content, cell morphology, cell surface property, and stress of pure cultures commonly found in biological wastewater treatment. | the effects of cell entrapment on nucleic acid content, cell morphology, cell surface property, and stress of major groups of bacteria (betaproteobacteria and gammaproteobacteria) in biological municipal wastewater treatment were investigated. three different entrapment media (alginate, carrageenan, and polyvinyl alcohol) were examined. results indicated that the entrapment and type of entrapment media affected nucleic acid content, cell morphology, cell surface property, and stress of the three ... | 2011 | 21660542 |
| most mutant occr proteins that are defective in positive control hold operator dna in a locked high angle bend. | occr is a lysr-type transcriptional regulator of agrobacterium tumefaciens that positively regulates the octopine catabolism operon of the ti plasmid. positive control of the occ genes occurs in response to octopine, a nutrient released from crown gall tumors. occr also functions as an autorepressor in the presence or absence of octopine. occr binds to a site between occq and occr in the presence or absence of octopine, although octopine triggers a conformational change that shortens the dna foo ... | 2011 | 21804007 |
| recurrent intravascular catheter-related bacteremia caused by delftia acidovorans in a hemodialysis patient. | we report the first case of recurrent intravascular catheter-related bacteremia in a pediatric hemodialysis patient caused by delftia acidovorans, previously called comamonas acidovorans or pseudomonas acidovorans. the patient had a history of multiple infections of central vascular catheters with other organisms, requiring courses of antibiotics and catheter replacements. previously reported cases of d. acidovorans infections are reviewed. in vitro susceptibility testing for cephalosporins is n ... | 2011 | 21775546 |
| a novel testosterone catabolic pathway in bacteria. | forty years ago, coulter and talalay (a. w. coulter and p. talalay, j. biol. chem. 243:3238-3247, 1968) established the oxygenase-dependent pathway for the degradation of testosterone by aerobes. the oxic testosterone catabolic pathway involves several oxygen-dependent reactions and is not available for anaerobes. since then, a variety of anaerobic bacteria have been described for the ability to degrade testosterone in the absence of oxygen. here, a novel, oxygenase-independent testosterone cata ... | 2011 | 21725000 |
| virulence determinants, drug resistance and mobile genetic elements of laribacter hongkongensis: a genome-wide analysis. | | 2011 | 21711902 |
| emerging roles for the ro 60-kda autoantigen in noncoding rna metabolism. | all cells contain an enormous variety of ribonucleoprotein (rnp) complexes that function in diverse processes. although the mechanisms by which many of these rnps contribute to cell metabolism are well understood, the roles of others are only now beginning to be revealed. a member of this latter category, the ro 60-kda protein and its associated noncoding y rnas, was discovered because the protein component is a frequent target of the autoimmune response in patients with the rheumatic diseases s ... | 2011 | 21823229 |
| genome analysis and characterization of zinc efflux systems of a highly zinc-resistant bacterium, comamonas testosteroni s44. | a novel and multiple metal(loid)-resistant strain comamonas testosteroni s44 with a high zn(2+) resistance level (10-ámm) was isolated. to understand the molecular basis for the high zinc resistance, whole genome sequencing was performed and revealed a large number of genes encoding putative metal(loid) resistance proteins, mobile genetic elements (mges) and horizontal gene transfer (hgt) events that may have occurred to adapt to a metal(loid)-contaminated environment. in particular, 9 putative ... | 2011 | 21704702 |
| the steroid catabolic pathway of the intracellular pathogen rhodococcus equi is important for pathogenesis and a target for vaccine development. | rhodococcus equi causes fatal pyogranulomatous pneumonia in foals and immunocompromised animals and humans. despite its importance, there is currently no effective vaccine against the disease. the actinobacteria r. equi and the human pathogen mycobacterium tuberculosis are related, and both cause pulmonary diseases. recently, we have shown that essential steps in the cholesterol catabolic pathway are involved in the pathogenicity of m. tuberculosis. bioinformatic analysis revealed the presence o ... | 2011 | 21901092 |
| glygly-cterm and rhombosortase: a c-terminal protein processing signal in a many-to-one pairing with a rhomboid family intramembrane serine protease. | the rhomboid family of serine proteases occurs in all domains of life. its members contain at least six hydrophobic membrane-spanning helices, with an active site serine located deep within the hydrophobic interior of the plasma membrane. the model member glpg from escherichia coli is heavily studied through engineered mutant forms, varied model substrates, and multiple x-ray crystal studies, yet its relationship to endogenous substrates is not well understood. here we describe an apparent membr ... | 2011 | 22194940 |
| Cloning, overexpression, purification, crystallization and preliminary X-ray analysis of 3-ketosteroid ?(4)-(5a)-dehydrogenase from Rhodococcus jostii RHA1. | 3-Ketosteroid dehydrogenases are flavoproteins which play key roles in steroid ring degradation. The enzymes are abundantly present in actinobacteria, including the catabolic powerhouse Rhodococcus jostii and the pathogenic species R. equi and Mycobacterium tuberculosis. The gene for 3-ketosteroid ?(4)-(5a)-dehydrogenase [?(4)-(5a)-KSTD] from R. jostii RHA1 was cloned and overexpressed in Escherichia coli. His-tagged ?(4)-(5a)-KSTD enzyme was purified by Ni(2+)-NTA affinity chromatography, anion ... | 2011 | 22102045 |
| in the nadr regulon, adhesins and diverse meningococcal functions are regulated in response to signals in human saliva. | the neisseria meningitidis regulator nadr was shown to repress expression of the nada adhesin and play a major role in nada phase-variable expression. in this study, we identified through microarray analysis over 30 genes coregulated with nada in the nadr mutant and defined members of the nadr regulon through in vitro dna-binding assays. two distinct types of promoter architectures (i and ii) were identified for nadr targets, differing in both the number and position of nadr-binding sites. all n ... | 2012 | 22081399 |
| role of incp-1β plasmids pwdl7::rfp and pnb8c in chloroaniline catabolism as determined by genomic and functional analyses. | broad-host-range catabolic plasmids play an important role in bacterial degradation of man-made compounds. to gain insight into the role of these plasmids in chloroaniline degradation, we determined the first complete nucleotide sequences of an incp-1 chloroaniline degradation plasmid, pwdl7::rfp and its close relative pnb8c, as well as the expression pattern, function, and bioaugmentation potential of the putative 3-chloroaniline (3-ca) oxidation genes. based on phylogenetic analysis of backbon ... | 2011 | 22101050 |
| Vanillin Catabolism in Rhodococcus jostii RHA1. | Genes encoding vanillin dehydrogenase (vdh) and vanillate O-demethylase (vanAB) were identified in Rhodococcus jostii RHA1 using gene disruption and enzyme activities. During growth on vanillin or vanillate, vanA was highly upregulated while vdh was not. This study contributes to our understanding of lignin degradation by RHA1 and other actinomycetes. | 2012 | 22057861 |
| a novel hydrolase identified by genomic-proteomic analysis of phenylurea herbicide mineralization by variovorax sp. strain srs16. | the soil bacterial isolate variovorax sp. strain srs16 mineralizes the phenylurea herbicide linuron. the proposed pathway initiates with hydrolysis of linuron to 3,4-dichloroaniline (dca) and n,o-dimethylhydroxylamine, followed by conversion of dca to krebs cycle intermediates. differential proteomic analysis showed a linuron-dependent upregulation of several enzymes that fit into this pathway, including an amidase (liba), a multicomponent chloroaniline dioxygenase, and enzymes associated with a ... | 2011 | 22003008 |
| Identification and Characterization of the LysR-type Transcriptional Regulator HsdR for Steroid-inducible Expression of the 3a-Hydroxysteroid Dehydrogenase/Carbonyl Reductase Gene in Comamonas testosteroni. | 3a-hydroxysteroid dehydrogenase/carbonyl reductase (3a-HSD/CR) from Comamonas testosteroni (C. testosteroni) is a key enzyme in steroid degradation in soil and water. 3a-HSD/CR gene (hsdA) expression can be induced by steroids like testosterone and progesterone. Previously, we have shown that induction of hsdA expression by steroids is a derepression where steroidal inducers bind to two repressors, RepA and RepB, thereby preventing blocking of hsdA transcription and translation, respectively. In ... | 2011 | 22156416 |
| nonlinear changes in the activity of the oxygen-dependent demethylase system in rhodococcus erythropolis cells in the presence of low and very low doses of formaldehyde. | abstract: the effect of exogenous, highly diluted formaldehyde on the rate of demethylation/re-methylation of veratric acid by the bacteria rhodococcus erythropolis was studied using electrophoretic and microscopic techniques. the activity of 4-o-demethylase, responsible for accumulation of vanillic acid, and the levels of veratric and vanillic acids were determined using capillary electrophoresis. formaldehyde was serially diluted at 1:100 ratios, and the total number of iterations was 20. afte ... | 2011 | 22104369 |
| Mainstreams of horizontal gene exchange in enterobacteria: consideration of the outbreak of enterohemorrhagic E. coli O104:H4 in Germany in 2011. | Escherichia coli O104:H4 caused a severe outbreak in Europe in 2011. The strain TY-2482 sequenced from this outbreak allowed the discovery of its closest relatives but failed to resolve ways in which it originated and evolved. On account of the previous statement, may we expect similar upcoming outbreaks to occur recurrently or spontaneously in the future? The inability to answer these questions shows limitations of the current comparative and evolutionary genomics methods. | 2011 | 22022434 |
| isolation and partial characterization of extracellular nadph-dependent phenol hydroxylase oxidizing phenol to catechol in comamonas testosteroni. | comamonas testosteroni pb50 is a microorganism that possesses high tolerance for phenol and shows strong phenol degrading activity. this bacterial strain is capable of utilizing phenol as the sole carbon and energy source. although examples are known in which the c. testosteroni utilizes phenol for growth or metabolism, much less information are known on the nature of the phenol-oxidizing enzymes in this microorganism. therefore, the occurrence and cellular location of phenol hydroxylase (ec 1.1 ... | 2011 | 22167219 |
| analysis of the bacterial diversity existing on animal hide and wool: development of a preliminary pcr-restriction fragment length polymorphism fingerprint database for identifying isolates. | twenty-one bacterial strains were isolated from imported cattle hide and rabbit wool using two types of media, nutrient broth, and nutrient broth with serum. the bacteria identified were brevibacillus laterosporus, leclercia adecarboxylata, peptococcus niger, bacillus circulans, raoultella ornithinolytica, bacillus subtilis, bacillus cereus, bacillus thermobacillus, bacillus choshinensis, bacillus sphaericus, acinetobacter haemolyticus, sphingomonas paucimobilis, bacillus thuringiensis, staphylo ... | 2012 | 23451394 |
| role of sex steroid hormones in bacterial-host interactions. | sex steroid hormones play important physiological roles in reproductive and nonreproductive tissues, including immune cells. these hormones exert their functions by binding to either specific intracellular receptors that act as ligand-dependent transcription factors or membrane receptors that stimulate several signal transduction pathways. the elevated susceptibility of males to bacterial infections can be related to the usually lower immune responses presented in males as compared to females. t ... | 2012 | 23509808 |
| role of sex steroid hormones in bacterial-host interactions. | sex steroid hormones play important physiological roles in reproductive and nonreproductive tissues, including immune cells. these hormones exert their functions by binding to either specific intracellular receptors that act as ligand-dependent transcription factors or membrane receptors that stimulate several signal transduction pathways. the elevated susceptibility of males to bacterial infections can be related to the usually lower immune responses presented in males as compared to females. t ... | 2012 | 23509808 |
| a novel tripartite aromatic acids transporter is essential for terephthalate uptake in comamonas sp. strain e6. | a novel type of aromatic acids transporter, which is similar to the tripartite tricarboxylate transporter (ttt), has been suggested to be involved in terephthalate (tpa) uptake by comamonas sp. strain e6. this suggestion was based on the presence of the putative tpa-binding protein gene, tphc, in the tpa catabolic operon. the tphc gene is essential for growth on tpa, and similar to the genes encoding ttt-like substrate-binding proteins. here we identified the two sets of e6 genes as tctba and tp ... | 2013 | 23913423 |
| bioinformatic characterization of the 4-toluene sulfonate uptake permease (tsup) family of transmembrane proteins. | the ubiquitous sequence diverse 4-toluene sulfonate uptake permease (tsup) family contains few characterized members and is believed to catalyze the transport of several sulfur-based compounds. prokaryotic members of the tsup family outnumber the eukaryotic members substantially, and in prokaryotes, but not eukaryotes, extensive lateral gene transfer occurred during family evolution. despite unequal representation, homologues from the three taxonomic domains of life share well-conserved motifs. ... | 2012 | 22192777 |
| bioinformatic characterization of the 4-toluene sulfonate uptake permease (tsup) family of transmembrane proteins. | the ubiquitous sequence diverse 4-toluene sulfonate uptake permease (tsup) family contains few characterized members and is believed to catalyze the transport of several sulfur-based compounds. prokaryotic members of the tsup family outnumber the eukaryotic members substantially, and in prokaryotes, but not eukaryotes, extensive lateral gene transfer occurred during family evolution. despite unequal representation, homologues from the three taxonomic domains of life share well-conserved motifs. ... | 2012 | 22192777 |
| protein subunit interfaces: heterodimers versus homodimers. | protein dimers are either homodimers (complexation of identical monomers) or heterodimers (complexation of non-identical monomers). these dimers are common in catalysis and regulation. however, the molecular principles of protein dimer interactions are difficult to understand mainly due to the geometrical and chemical characteristics of proteins. nonetheless, the principles of protein dimer interactions are often studied using a dataset of 3d structural complexes determined by x-ray crystallogra ... | 2005 | 17597849 |
| tmrdb (tmrna database). | maintained at the university of texas health science center at tyler, texas, the tmrna database (tmrdb) is accessible at the url http://psyche.uthct.edu/dbs/tmrdb/tmrdb.html with mirror sites located at auburn university, auburn, alabama (http://www.ag.auburn.edu/mirror/tmrdb/) and the bioinformatics research center, aarhus, denmark (http://www.bioinf.au.dk/tmrdb/). the tmrdb collects and distributes information relevant to the study of tmrna. in trans-translation, this molecule combines propert ... | 2003 | 12520048 |
| isolation and metabolic characteristics of previously uncultured members of the order aquificales in a subsurface gold mine. | culture-dependent and -independent techniques were combined to characterize the physiological properties and the ecological impacts of culture-resistant phylotypes of thermophiles within the order aquificales from a subsurface hot aquifer of a japanese gold mine. thermophilic bacteria phylogenetically associated with previously uncultured phylotypes of aquificales were successfully isolated. 16s ribosomal dna clone analysis of the entire microbial dna assemblage and fluorescence in situ whole-ce ... | 2002 | 12039766 |
| novel dehalogenase mechanism for 2,3-dichloro-1-propanol utilization in pseudomonas putida strain mc4. | a pseudomonas putida strain (mc4) that can utilize 2,3-dichloro-1-propanol (dcp) and several aliphatic haloacids and haloalcohols as sole carbon and energy source for growth was isolated from contaminated soil. degradation of dcp was found to start with oxidation and concomitant dehalogenation catalyzed by a 72-kda monomeric protein (dppa) that was isolated from cell lysate. the dppa gene was cloned from a cosmid library and appeared to encode a protein equipped with a signal peptide and that po ... | 2012 | 22752160 |
| a persistent and diverse airway microbiota present during chronic obstructive pulmonary disease exacerbations. | acute exacerbations of chronic obstructive pulmonary disease (copd) are a major source of morbidity and contribute significantly to healthcare costs. although bacterial infections are implicated in nearly 50% of exacerbations, only a handful of pathogens have been consistently identified in copd airways, primarily by culture-based methods, and the bacterial microbiota in acute exacerbations remains largely uncharacterized. the aim of this study was to comprehensively profile airway bacterial com ... | 2010 | 20141328 |
| distribution of genes encoding nucleoid-associated protein homologs in plasmids. | bacterial nucleoid-associated proteins (naps) form nucleoprotein complexes and influence the expression of genes. recent studies have shown that some plasmids carry genes encoding nap homologs, which play important roles in transcriptional regulation networks between plasmids and host chromosomes. in this study, we determined the distributions of the well-known naps fis, h-ns, hu, ihf, and lrp and the newly found naps mvat and ndpa among the whole-sequenced 1382 plasmids found in gram-negative b ... | 2011 | 21350637 |
| across bacterial phyla, distantly-related genomes with similar genomic gc content have similar patterns of amino acid usage. | the gc content of bacterial genomes ranges from 16% to 75% and wide ranges of genomic gc content are observed within many bacterial phyla, including both gram negative and gram positive phyla. thus, divergent genomic gc content has evolved repeatedly in widely separated bacterial taxa. since genomic gc content influences codon usage, we examined codon usage patterns and predicted protein amino acid content as a function of genomic gc content within eight different phyla or classes of bacteria. w ... | 2011 | 21423704 |
| enumeration and detection of anaerobic ferrous iron-oxidizing, nitrate-reducing bacteria from diverse european sediments. | anaerobic, nitrate-dependent microbial oxidation of ferrous iron was recently recognized as a new type of metabolism. in order to study the occurrence of three novel groups of ferrous iron-oxidizing, nitrate-reducing bacteria (represented by strains brg1, brg2, and brg3), 16s rrna-targeted oligonucleotide probes were developed. in pure-culture experiments, these probes were shown to be suitable for fluorescent in situ hybridization, as well as for hybridization analysis of denaturing gradient ge ... | 1998 | 9835573 |
| 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 |
| molecular diagnosis of actinomadura madurae infection by 16s rrna deep sequencing. | next-generation dna sequencing can be used to catalog individual organisms within complex, polymicrobial specimens. here, we utilized deep sequencing of 16s rrna to implicate actinomadura madurae as the cause of mycetoma in a diabetic patient when culture and conventional molecular methods were overwhelmed by overgrowth of other organisms. | 2013 | 24108607 |
| rapid 16s rrna next-generation sequencing of polymicrobial clinical samples for diagnosis of complex bacterial infections. | classifying individual bacterial species comprising complex, polymicrobial patient specimens remains a challenge for culture-based and molecular microbiology techniques in common clinical use. we therefore adapted practices from metagenomics research to rapidly catalog the bacterial composition of clinical specimens directly from patients, without need for prior culture. we have combined a semiconductor deep sequencing protocol that produces reads spanning 16s ribosomal rna gene variable regions ... | 2013 | 23734239 |
| effects of microbial species, organic loading and substrate degradation rate on the power generation capability of microbial fuel cells. | four microbial fuel cells (mfcs) inoculated with different bacterial species were constructed. the species were pseudomonas putida, comamonas testosteroni, corynebacterium gultamicum, and arthrobacter polychromogenes. the mfcs were operated under identical continuous flow conditions. the factors affecting the capabilities of the mfcs for treating organic matter and generating power were evaluated and compared. the factors include microbial species type, organic loading, and substrate degradation ... | 2011 | 21750995 |
| ability of the microscan rapid gram-negative id type 3 panel to identify nonenteric glucose-fermenting and nonfermenting gram-negative bacilli. | the microscan rapid neg id3 panel is designed for the identification of enterobacteriaceae and nonenteric glucose-fermenting and nonfermenting gram-negative bacilli. we evaluated this panel for its ability to identify gram-negative non-enterobacteriaceae bacteria. a total of 134 strains, representing 26 genera and 42 species, were taken from storage at -70(o)c, passaged three times before testing, and inoculated into the panels according to the manufacturer's directions before being inserted int ... | 2002 | 12354875 |
| microbial community analysis in biocathode microbial fuel cells packed with different materials. | biocathode mfcs using microorganisms as catalysts have important advantages in lowering cost and improving sustainability. electrode materials and microbial synergy determines biocathode mfcs performance. in this study, four materials, granular activated carbon (gac), granular semicoke (gs), granular graphite (gg) and carbon felt cube (cfc) were used as packed cathodic materials. the microbial composition on each material and its correlation with the electricity generation performance of mfcs we ... | 2012 | 22458430 |
| genomic analysis reveals key aspects of prokaryotic symbiosis in the phototrophic consortium "chlorochromatium aggregatum". | 'chlorochromatium aggregatum' is a phototrophic consortium, a symbiosis that may represent the highest degree of mutual interdependence between two unrelated bacteria not associated with a eukaryotic host. 'chlorochromatium aggregatum' is a motile, barrel-shaped aggregate formed from a single cell of 'candidatus symbiobacter mobilis", a polarly flagellated, non-pigmented, heterotrophic bacterium, which is surrounded by approximately 15 epibiont cells of chlorobium chlorochromatii, a non-motile p ... | 2013 | 24267588 |
| multidrug-resistant gram-negative bacteria colonization of healthy us military personnel in the us and afghanistan. | the us military has seen steady increases in multidrug-resistant (mdr) gram-negative bacteria (gnb) infections in casualties from iraq and afghanistan. this study evaluates the prevalence of mdr gnb colonization in us military personnel. | 2013 | 23384348 |
| set-domain bacterial effectors target heterochromatin protein 1 to activate host rdna transcription. | transcription of rrna genes (rdnas) in the nucleolus is regulated by epigenetic chromatin modifications including histone h3 lysine (de)methylation. here we show that legas4, a legionella pneumophila type iv secretion system (tfss) effector, is targeted to specific rdna chromatin regions in the host nucleolus. legas4 promotes rdna transcription, through its set-domain (named after drosophila su(var)3-9, enhancer of zeste [e(z)], and trithorax [trx]) histone lysine methyltransferase (hkmtase) act ... | 2013 | 23797873 |
| a subset of the diverse cog0523 family of putative metal chaperones is linked to zinc homeostasis in all kingdoms of life. | cog0523 proteins are, like the nickel chaperones of the ureg family, part of the g3e family of gtpases linking them to metallocenter biosynthesis. even though the first cog0523-encoding gene, cobw, was identified almost 20 years ago, little is known concerning the function of other members belonging to this ubiquitous family. | 2009 | 19822009 |
| two enzymes of a complete degradation pathway for linear alkylbenzenesulfonate (las) surfactants: 4-sulfoacetophenone baeyer-villiger monooxygenase and 4-sulfophenylacetate esterase in comamonas testosteroni kf-1. | complete biodegradation of the surfactant linear alkylbenzenesulfonate (las) is accomplished by complex bacterial communities in two steps. first, all las congeners are degraded into about 50 sulfophenylcarboxylates (spc), one of which is 3-(4-sulfophenyl)butyrate (3-c(4)-spc). second, these spcs are mineralized. 3-c(4)-spc is mineralized by comamonas testosteroni kf-1 in a process involving 4-sulfoacetophenone (sap) as a metabolite and an unknown inducible baeyer-villiger monooxygenase (bvmo) t ... | 2012 | 23001656 |
| characterization of bacteria in ballast water using maldi-tof mass spectrometry. | to evaluate a rapid and cost-effective method for monitoring bacteria in ballast water, several marine bacterial isolates were characterized by matrix-assisted laser desorption ionization-time of flight mass spectrometry (maldi-tof ms). since international maritime organization (imo) regulations are concerned with the unintended transportation of pathogenic bacteria through ballast water, emphasis was placed on detecting species of vibrio, enterococci and coliforms. seawater samples collected fr ... | 2012 | 22685576 |
| gene cluster encoding cholate catabolism in rhodococcus spp. | bile acids are highly abundant steroids with important functions in vertebrate digestion. their catabolism by bacteria is an important component of the carbon cycle, contributes to gut ecology, and has potential commercial applications. we found that rhodococcus jostii rha1 grows well on cholate, as well as on its conjugates, taurocholate and glycocholate. the transcriptome of rha1 growing on cholate revealed 39 genes upregulated on cholate, occurring in a single gene cluster. reverse transcript ... | 2012 | 23024343 |
| the essential function of genes for a hydratase and an aldehyde dehydrogenase for growth of pseudomonas sp. strain chol1 with the steroid compound cholate indicates an aldolytic reaction step for deacetylation of the side chain. | in the bacterial degradation of steroid compounds, the enzymes initiating the breakdown of the steroid rings are well known, while the reactions for degrading steroid side chains attached to c-17 are largely unknown. a recent in vitro analysis with pseudomonas sp. strain chol1 has shown that the degradation of the c5 acyl side chain of the c24 steroid compound cholate involves the c22 intermediate 7α,12α-dihydroxy-3-oxopregna-1,4-diene-20s-carbaldehyde (dhopdca) with a terminal aldehyde group. i ... | 2013 | 23708132 |
| identification of 9α-hydroxy-17-oxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid in steroid degradation by comamonas testosteroni ta441 and its conversion to the corresponding 6-en-5-oyl coenzyme a (coa) involving open reading frame 28 (orf28)- and orf30-encoded acyl-coa dehydrogenases. | comamonas testosteroni ta441 degrades steroids via aromatization and meta-cleavage of the a ring, followed by hydrolysis, and produces 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid as an intermediate compound. herein, we identify a new intermediate compound, 9α-hydroxy-17-oxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid. open reading frame 28 (orf28)- and orf30-encoded acyl coenzyme a (acyl-coa) dehydrogenase was shown to convert the coa ester of 9α-hydroxy-17-oxo-1,2,3,4,10,19-hexanorandros ... | 2014 | 25092028 |
| identification of comamonas testosteroni as an androgen degrader in sewage. | numerous studies have reported the masculinization of freshwater wildlife exposed to androgens in polluted rivers. microbial degradation is a crucial mechanism for eliminating steroid hormones from contaminated ecosystems. the aerobic degradation of testosterone was observed in various bacterial isolates. however, the ecophysiological relevance of androgen-degrading microorganisms in the environment is unclear. here, we investigated the biochemical mechanisms and corresponding microorganisms of ... | 2016 | 27734937 |
| 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 |
| biochemical and susceptibility tests useful for identification of nonfermenting gram-negative rods. | six hundred nineteen strains of nonfermenting gram-negative rods were tested for alkaline phosphatase, benzyl-arginine arylamidase, pyrrolidonyl arylamidase, ethylene glycol acidification, and susceptibility to desferrioxamine and colistin. the results were highly discriminant. therefore, the proposed tests may be helpful for the identification of this group of organisms. | 2002 | 11880447 |
| performances of vitek 2 colorimetric cards for identification of gram-positive and gram-negative bacteria. | the purpose of this study was to evaluate the new vitek 2 identification cards that use colorimetric reading to identify gram-positive and gram-negative bacteria (gp and gn cards, respectively) in comparison to fluorimetric cards (id-gpc and id-gnb, respectively). a total of 580 clinical isolates and stock collection strains belonging to 116 taxa were included in the study. of the 249 gram-positive strains tested with both the id-gpc and gp cards, 218 (87.5%) and 235 (94.4%) strains were correct ... | 2005 | 16145083 |
| quantitative determination of free-dna uptake in river bacteria at the single-cell level by in situ rolling-circle amplification. | detection of plasmid dna uptake in river bacteria at the single-cell level was carried out by rolling-circle amplification (rca). uptake of a plasmid containing the green fluorescent protein gene (gfp) by indigenous bacteria from two rivers in osaka, japan, was monitored for 506 h using this in situ gene amplification technique with optimized cell permeabilization conditions. plasmid uptake determined by in situ rca was compared to direct counts of cells expressing gfp under fluorescence microsc ... | 2006 | 16957252 |
| reciprocal tripartite interactions between the aedes aegypti midgut microbiota, innate immune system and dengue virus influences vector competence. | dengue virus is one of the most important arboviral pathogens and the causative agent of dengue fever, dengue hemorrhagic fever, and dengue shock syndrome. it is transmitted between humans by the mosquitoes aedes aegypti and aedes albopictus, and at least 2.5 billion people are at daily risk of infection. during their lifecycle, mosquitoes are exposed to a variety of microbes, some of which are needed for their successful development into adulthood. however, recent studies have suggested that th ... | 2012 | 22413032 |
| surveillance cultures of samples obtained from biopsy channels and automated endoscope reprocessors after high-level disinfection of gastrointestinal endoscopes. | the instrument channels of gastrointestinal (gi) endoscopes may be heavily contaminated with bacteria even after high-level disinfection (hld). the british society of gastroenterology guidelines emphasize the benefits of manually brushing endoscope channels and using automated endoscope reprocessors (aers) for disinfecting endoscopes. in this study, we aimed to assess the effectiveness of decontamination using reprocessors after hld by comparing the cultured samples obtained from biopsy channels ... | 2012 | 22943739 |
| nasopharyngeal carriage of klebsiella pneumoniae and other gram-negative bacilli in pneumonia-prone age groups in semarang, indonesia. | gram-negative bacilli (gnb) cause many cases of pneumonia in indonesia. we investigated nasopharyngeal carriage of gnb in semarang, indonesia. klebsiella pneumoniae carriage in adults (15%) was higher than in children (7%) (p = 0.004), while that of other gnb was comparable. poor food and water hygiene are determinants of carriage of these bacteria. | 2013 | 23486716 |
| characterization and genomic analysis of kraft lignin biodegradation by the beta-proteobacterium cupriavidus basilensis b-8. | | 2013 | 23298573 |
| an outbreak of nonflocculating catabolic populations caused the breakdown of a phenol-digesting activated-sludge process. | activated sludge was fed phenol as the sole carbon source, and the phenol-loading rate was increased stepwise from 0.5 to 1.0 g liter-1 day-1 and then to 1.5 g liter-1 day-1. after the loading rate was increased to 1.5 g liter-1 day-1, nonflocculating bacteria outgrew the sludge, and the activated-sludge process broke down within 1 week. the bacterial population structure of the activated sludge was analyzed by temperature gradient gel electrophoresis (tgge) of pcr-amplified 16s ribosomal dna (r ... | 1999 | 10388669 |
| microbial biomass and activity in lead-contaminated soil | microbial community diversity, potential microbial activity, and metal resistance were determined in three soils whose lead contents ranged from 0.00039 to 48 mmol of pb kg of soil-1. biomass levels were directly related to lead content. a molecular analysis of 16s rrnas suggested that each soil contained a complex, diverse microbial community. a statistical analysis of the phospholipid fatty acids indicated that the community in the soil having the highest lead content was not related to the co ... | 1999 | 10224032 |
| selection of clc, cba, and fcb chlorobenzoate-catabolic genotypes from groundwater and surface waters adjacent to the hyde park, niagara falls, chemical landfill. | the frequency of isolation of three nonhomologous chlorobenzoate catabolic genotypes (clc, cba, and fcb) was determined for 464 isolates from freshwater sediments and groundwater in the vicinity of the hyde park industrial landfill site in the niagara watershed. samples were collected from both contaminated and noncontaminated sites during spring, summer, and fall and enriched at 4, 22, or 32 degrees c with micromolar to millimolar concentrations of chlorobenzoates and 3-chlorobiphenyl (m. c. pe ... | 1999 | 10103260 |
| catalytic role of enzymes: short strong h-bond-induced partial proton shuttles and charge redistributions. | a two-step reaction mechanism (catalyzed alternatively by acid and base) with partial proton shuttles and charge redistributions promoted by short strong h bonds (sshbs) (playing a dual role as an amphi-acid/base catalyst) is proposed to explain the enormous rate enhancement observed in enzymatic reactions involving carbanion intermediates. the sshbs in the two-step reactions are found to be responsible for enhancing enzyme-substrate interactions in favor of the transition state structure over t ... | 2000 | 10841545 |
| bacteria are not what they eat: that is why they are so diverse. | | 2000 | 10629168 |
| use of sublimation to prepare solid microbial media with water-insoluble substrates. | a method was developed to deposit a visible layer of water-insoluble compounds via sublimation onto the surface of solid media. the compound is sublimed from a heated aluminum dish containing the compound onto the surface of an inverted, ice-cooled, inoculated agar petri dish. the method results in the deposition of a thin, even layer on the agar surface without the use of solvent. after incubation, clearing zones around colonies indicate the presence of compound-degrading microorganisms. | 2000 | 10618263 |
| phylogenetic analysis of tmrna genes within a bacterial subgroup reveals a specific structural signature. | bacterial tmrna mediates a trans-translation reaction, which permits the recycling of stalled ribosomes and probably also contributes to the regulated expression of a subset of genes. its action results in the addition of a small number of c-terminal amino acids to protein whose synthesis had stalled and these constitute a proteolytic recognition tag for the degradation of these incompletely synthesized proteins. previous work has identified pseudoknots and stem-loops that are widely conserved i ... | 2001 | 11266563 |
| recent advances in petroleum microbiology. | recent advances in molecular biology have extended our understanding of the metabolic processes related to microbial transformation of petroleum hydrocarbons. the physiological responses of microorganisms to the presence of hydrocarbons, including cell surface alterations and adaptive mechanisms for uptake and efflux of these substrates, have been characterized. new molecular techniques have enhanced our ability to investigate the dynamics of microbial communities in petroleum-impacted ecosystem ... | 2003 | 14665675 |
| detection and enumeration of aromatic oxygenase genes by multiplex and real-time pcr. | our abilities to detect and enumerate pollutant-biodegrading microorganisms in the environment are rapidly advancing with the development of molecular genetic techniques. techniques based on multiplex and real-time pcr amplification of aromatic oxygenase genes were developed to detect and quantify aromatic catabolic pathways, respectively. pcr primer sets were identified for the large subunits of aromatic oxygenases from alignments of known gene sequences and tested with genetically well-charact ... | 2003 | 12788736 |