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a comprehensive analysis of gene expression changes provoked by bacterial and fungal infection in c. elegans.while caenorhabditis elegans specifically responds to infection by the up-regulation of certain genes, distinct pathogens trigger the expression of a common set of genes. we applied new methods to conduct a comprehensive and comparative study of the transcriptional response of c. elegans to bacterial and fungal infection. using tiling arrays and/or rna-sequencing, we have characterized the genome-wide transcriptional changes that underlie the host's response to infection by three bacterial (serr ...201121602919
characterization of the structure and function of klebsiella pneumoniae allantoin racemase.the oxidative catabolism of uric acid produces 5-hydroxyisourate (hiu), which is further degraded to (s)-allantoin by two enzymes, hiu hydrolase and 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase. the intermediates of the latter two reactions, hiu and 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline, are unstable in solution and decay nonstereospecifically to allantoin. in addition, nonenzymatic racemization of allantoin has been shown to occur at physiological ph. since the further br ...201121616082
molecular basis of glyphosate resistance-different approaches through protein engineering.glyphosate (n-phosphonomethyl-glycine) is the most widely used herbicide in the world: glyphosate-based formulations exhibit broad-spectrum herbicidal activity with minimal human and environmental toxicity. the extraordinary success of this simple, small molecule is mainly attributable to the high specificity of glyphosate for the plant enzyme enolpyruvyl shikimate-3-phosphate synthase in the shikimate pathway, leading to the biosynthesis of aromatic amino acids. starting in 1996, transgenic gly ...201121668647
genetic approach for the fast discovery of phenazine producing bacteria.a fast and efficient approach was established to identify bacteria possessing the potential to biosynthesize phenazines, which are of special interest regarding their antimicrobial activities. sequences of phze genes, which are part of the phenazine biosynthetic pathway, were used to design one universal primer system and to analyze the ability of bacteria to produce phenazine. diverse bacteria from different marine habitats and belonging to six major phylogenetic lines were investigated. bacter ...201121673888
kinetic, crystallographic, and mechanistic characterization of tomn: elucidation of a function for a 4-oxalocrotonate tautomerase homologue in the tomaymycin biosynthetic pathway.the biosynthesis of the c ring of the anti-tumor antibiotic agent, tomaymycin, is proposed to proceed through five enzyme-catalyzed steps from l-tyrosine. the genes encoding these enzymes have recently been cloned and their functions tentatively assigned, but there is limited biochemical evidence supporting the assignments of the last three steps. one enzyme, tomn, shows 58% pairwise sequence similarity with 4-oxalocrotonate tautomerase (4-ot), an enzyme found in a catabolic pathway for aromatic ...201121809870
mechanisms of nickel toxicity in microorganisms.nickel has long been known to be an important human toxicant, including having the ability to form carcinomas, but until recently nickel was believed to be an issue only to microorganisms living in nickel-rich serpentine soils or areas contaminated by industrial pollution. this assumption was overturned by the discovery of a nickel defense system (rcnr/rcna) found in microorganisms that live in a wide range of environmental niches, suggesting that nickel homeostasis is a general biological conce ...201121799955
xenopus laevis oocytes infected with multi-drug-resistant bacteria: implications for electrical recordings.the xenopus laevis oocyte has been the workhorse for the investigation of ion transport proteins. these large cells have spawned a multitude of novel techniques that are unfathomable in mammalian cells, yet the fickleness of the oocyte has driven many researchers to use other membrane protein expression systems. here, we show that some colonies of xenopus laevis are infected with three multi-drug-resistant bacteria: pseudomonas fluorescens, pseudomonas putida, and stenotrophomonas maltophilia. o ...201121788613
molecular identification of bacteria by total sequence screening: determining the cause of death in ancient human subjects.research of ancient pathogens in ancient human skeletons has been mainly carried out on the basis of one essential historical or archaeological observation, permitting specific pathogens to be targeted. detection of ancient human pathogens without such evidence is more difficult, since the quantity and quality of ancient dna, as well as the environmental bacteria potentially present in the sample, limit the analyses possible. using human lung tissue and/or teeth samples from burials in eastern s ...201121765907
microfluidic fluorescence in situ hybridization and flow cytometry (µflowfish).we describe an integrated microfluidic device (µflowfish) capable of performing 16s rrna fluorescence in situ hybridization (fish) followed by flow cytometric detection for identifying bacteria in natural microbial communities. the device was used for detection of species involved in bioremediation of cr(vi) and other metals in groundwater samples from a highly-contaminated environmental site (hanford, wa, usa). the µflowfish seamlessly integrates two components: a hybridization chamber formed b ...201121755095
novel antiphytopathogenic compound 2-heptyl-5-hexylfuran-3-carboxylic acid, produced by newly isolated pseudomonas sp. strain sjt25.pseudomonas sp. strain sjt25, which strongly antagonizes plant pathogens, was isolated from rice rhizosphere soil by a bioactivity-guided approach. a novel antiphytopathogenic compound was isolated from the fermentation broth of pseudomonas sp. sjt25 and identified as 2-heptyl-5-hexylfuran-3-carboxylic acid. this compound showed antimicrobial activities both in vitro and in vivo.201121742907
repression of the antifungal activity of pseudomonas sp. strain df41 by the stringent response.the stringent response (sr) enables bacteria to adapt to nutrient limitation through production of the nucleotides guanosine tetraphosphate and guanosine pentaphosphate, collectively known as (p)ppgpp. two enzymes are responsible for the intracellular pools of (p)ppgpp: rela acts as a synthetase, while spot can function as either a synthetase or a hydrolase. we investigated how the sr affects the ability of the biological control agent pseudomonas sp. strain df41 to inhibit the fungal pathogen s ...201121705548
kinetics of styrene biodegradation by pseudomonas sp. e-93486.the research into kinetics of styrene biodegradation by bacterial strain pseudomonas sp. e-93486 coming from vtt culture collection (finland) was presented in this work. microbial growth tests in the presence of styrene as the sole carbon and energy source were performed both in batch and continuous cultures. batch experiments were conducted for initial concentration of styrene in the liquid phase changed in the range of 5-90-ágôçëm(-3). the haldane model was found to be the best to fit the kine ...201121833566
studies on the mechanism of p-hydroxyphenylacetate 3-hydroxylase from pseudomonas aeruginosa: a system composed of a small flavin reductase and a large flavin-dependent oxygenase.there are two known types of microbial two-component flavin-dependent monooxygenases that catalyze oxygenation of p-hydroxyphenylacetate (hpa), and they are distinguished by having structurally distinct reductases and oxygenases. this paper presents a detailed analysis of the properties of the enzyme from pseudomonas aeruginosa, an example of one group, and compares its properties to those published for the acinetobacter baumannii enzyme, an example of the alternative group. the reductase and ox ...201020000468
the vaginal bacterial communities of japanese women resemble those of women in other racial groups.to determine whether different racial groups shared common types of vaginal microbiota, we characterized the composition and structure of vaginal bacterial communities in asymptomatic and apparently healthy japanese women in tokyo, japan, and compared them with those of white and black women from north america. the composition of vaginal communities was compared based on community profiles of terminal restriction fragments of 16s rrna genes and phylogenetic analysis of cloned 16s rrna gene seque ...201019912342
the vaginal bacterial communities of japanese women resemble those of women in other racial groups.to determine whether different racial groups shared common types of vaginal microbiota, we characterized the composition and structure of vaginal bacterial communities in asymptomatic and apparently healthy japanese women in tokyo, japan, and compared them with those of white and black women from north america. the composition of vaginal communities was compared based on community profiles of terminal restriction fragments of 16s rrna genes and phylogenetic analysis of cloned 16s rrna gene seque ...201019912342
novel insights about class 2 integrons from experimental and genomic epidemiology.in order to contribute to the knowledge of the architecture and epidemiology of class 2 integrons, we performed a class 2 integron molecular survey in which we analyzed 726 isolates in two bacterial populations from environmental and nonepidemiologically related clinical samples, respectively, collected from 1982 to 2007. we recovered the inti2 gene from 130 of 726 isolates, most of which were clinical isolates, and only 1 (a psychrophilic pseudomonas sp.) was from a water sample. unlike the wid ...201019917745
isolation and characterization of a novel 2-sec-butylphenol-degrading bacterium pseudomonas sp. strain ms-1.a novel bacterium capable of utilizing 2-sec-butylphenol as the sole carbon and energy source, pseudomonas sp. strain ms-1, was isolated from freshwater sediment. within 30 h, strain ms-1 completely degraded 1.5 mm 2-sec-butylphenol in basal salt medium, with concomitant cell growth. a pathway for the metabolism of 2-sec-butylphenol by strain ms-1 was proposed on the basis of the identification of 3 internal metabolites-3-sec-butylcatechol, 2-hydroxy-6-oxo-7-methylnona-2,4-dienoic acid, and 2-me ...201019705287
prevalence of renal anomalies after urinary tract infections in hospitalized infants less than 2 months of age.our aim was to determine the incidence of anatomical abnormalities after a urinary tract infection (uti) in infants <2 months of age hospitalized in the neonatal intensive care unit (nicu).201019812586
prevalence of renal anomalies after urinary tract infections in hospitalized infants less than 2 months of age.our aim was to determine the incidence of anatomical abnormalities after a urinary tract infection (uti) in infants <2 months of age hospitalized in the neonatal intensive care unit (nicu).201019812586
electron transfer in the complex of membrane-bound human cytochrome p450 3a4 with the flavin domain of p450bm-3: the effect of oligomerization of the heme protein and intermittent modulation of the spin equilibrium.we studied the kinetics of nadph-dependent reduction of human cyp3a4 incorporated into nanodiscs (cyp3a4-nd) and proteoliposomes in order to probe the effect of p450 oligomerization on its reduction. the flavin domain of cytochrome p450-bm3 (bmr) was used as a model electron donor partner. unlike cyp3a4 oligomers, where only 50% of the enzyme was shown to be reducible by bmr, cyp3a4-nd could be reduced almost completely. high reducibility was also observed in proteoliposomes with a high lipid-to ...201020026040
electron transfer in the complex of membrane-bound human cytochrome p450 3a4 with the flavin domain of p450bm-3: the effect of oligomerization of the heme protein and intermittent modulation of the spin equilibrium.we studied the kinetics of nadph-dependent reduction of human cyp3a4 incorporated into nanodiscs (cyp3a4-nd) and proteoliposomes in order to probe the effect of p450 oligomerization on its reduction. the flavin domain of cytochrome p450-bm3 (bmr) was used as a model electron donor partner. unlike cyp3a4 oligomers, where only 50% of the enzyme was shown to be reducible by bmr, cyp3a4-nd could be reduced almost completely. high reducibility was also observed in proteoliposomes with a high lipid-to ...201020026040
unique extracellular matrix heparan sulfate from the bivalve nodipecten nodosus (linnaeus, 1758) safely inhibits arterial thrombosis after photochemically induced endothelial lesion.heparin-like glycans with diverse disaccharide composition and high anticoagulant activity have been described in several families of marine mollusks. the present work focused on the structural characterization of a new heparan sulfate (hs)-like polymer isolated from the mollusk nodipecten nodosus (linnaeus, 1758) and on its anticoagulant and antithrombotic properties. total glycans were extracted from the mollusk and fractionated by ethanol precipitation. the main component (>90%) was identifie ...201020053999
structure and ligand binding properties of the epoxidase component of styrene monooxygenase .styrene monooxygenase (smo) is a two-component flavoprotein monooxygenase that transforms styrene to styrene oxide in the first step of the styrene catabolic and detoxification pathway of pseudomonas putida s12. the crystal structure of the n-terminally histidine-tagged epoxidase component of this system, nsmoa, determined to 2.3 a resolution, indicates the enzyme exists as a homodimer in which each monomer forms two distinct domains. the overall architecture is most similar to that of p-hydroxy ...201020055497
new structural and functional defects in polyphosphate deficient bacteria: a cellular and proteomic study.inorganic polyphosphate (polyp), a polymer of tens or hundreds of phosphate residues linked by atp-like bonds, is found in all organisms and performs a wide variety of functions. polyp is synthesized in bacterial cells by the actions of polyphosphate kinases (ppk1 and ppk2) and degraded by exopolyphosphatase (ppx). bacterial cells with polyp deficiencies due to knocking out the ppk1 gene are affected in many structural and important cellular functions such as motility, quorum sensing, biofilm fo ...201020067623
structural basis for catalysis by the mono- and dimetalated forms of the dape-encoded n-succinyl-l,l-diaminopimelic acid desuccinylase.biosynthesis of lysine and meso-diaminopimelic acid in bacteria provides essential components for protein synthesis and construction of the bacterial peptidoglycan cell wall. the dape operon enzymes synthesize both meso-diaminopimelic acid and lysine and, therefore, represent potential targets for novel antibacterials. the dape-encoded n-succinyl-l,l-diaminopimelic acid desuccinylase functions in a late step of the pathway and converts n-succinyl-l,l-diaminopimelic acid to l,l-diaminopimelic aci ...201020138056
mycobacterium tuberculosis nucleoid-associated dna-binding protein h-ns binds with high-affinity to the holliday junction and inhibits strand exchange promoted by reca protein.a number of studies have shown that the structure and composition of bacterial nucleoid influences many a processes related to dna metabolism. the nucleoid-associated proteins modulate not only the dna conformation but also regulate the dna metabolic processes such as replication, recombination, repair and transcription. understanding of how these processes occur in the context of mycobacterium tuberculosis nucleoid is of considerable medical importance because the nucleoid structure may be cons ...201020176569
anthranilate-activating modules from fungal nonribosomal peptide assembly lines.fungal natural products containing benzodiazepinone- and quinazolinone-fused ring systems can be assembled by nonribosomal peptide synthetases (nrps) using the conformationally restricted beta-amino acid anthranilate as one of the key building blocks. we validated that the first module of the acetylaszonalenin synthetase of neosartorya fischeri nrrl 181 activates anthranilate to anthranilyl-amp. with this as a starting point, we then used bioinformatic predictions about fungal adenylation domain ...201020225828
annual variations in the diversity, viability, and origin of airborne bacteria.the presence of bacteria in aerosols has been known for centuries, but information on their identity and role in dispersing microbial traits is still limited. this study monitored the airborne bacterial community during an annual survey using samples collected from a 25-m tower near the baltic sea coast. the number of cfu was estimated using agar plates while the most probable number (mpn) of viable bacteria was estimated using dilution-to-extinction culturing assays (dcas). the mpn and cfu valu ...201020228096
a novel hydrolytic dehalogenase for the chlorinated aromatic compound chlorothalonil.dehalogenases play key roles in the detoxification of halogenated aromatics. interestingly, only one hydrolytic dehalogenase for halogenated aromatics, 4-chlorobenzoyl-coenzyme a (coa) dehalogenase, has been reported. here, we characterize another novel hydrolytic dehalogenase for a halogenated aromatic compound from the 2,4,5,6-tetrachloroisophthalonitrile (chlorothalonil)-degrading strain of pseudomonas sp. ctn-3, which we have named chd. chd catalyzes a hydroxyl substitution at the 4-chlorine ...201020363940
bacterial community dynamics during the application of a myxococcus xanthus-inoculated culture medium used for consolidation of ornamental limestone.in this study, we investigated under laboratory conditions the bacterial communities inhabiting quarry and decayed ornamental carbonate stones before and after the application of a myxococcus xanthus-inoculated culture medium used for consolidation of the stones. the dynamics of the community structure and the prevalence of the inoculated bacterium, m. xanthus, were monitored during the time course of the consolidation treatment (30 days). for this purpose, we selected a molecular strategy combi ...201020393845
phenolic acids act as signaling molecules in plant-microbe symbioses.phenolic acids are the main polyphenols made by plants. these compounds have diverse functions and are immensely important in plant-microbe interactions/symbiosis. phenolic compounds act as signaling molecules in the initiation of legumerhizobia symbioses, establishment of arbuscular mycorrhizal symbioses and can act as agents in plant defense. flavonoids are a diverse class of polyphenolic compounds that have received considerable attention as signaling molecules involved in plant-microbe inter ...201020400851
bacteriological study of aerobic isolates from plantar ulcers of paucibacillary leprosy patients.plantar ulcers commonly occur in leprosy patients, which usually recur and cause morbidity in such cases.201020418976
expression, purification, crystallization and preliminary x-ray analysis of pseudomonas aeruginosa algx.algx is a periplasmic protein required for the production of the exopolysaccharide alginate in pseudomonas sp. and azotobacter vinelandii. algx has been overexpressed and purified and diffraction-quality crystals have been grown using iterative seeding and the hanging-drop vapor-diffusion method. the crystals grew as flat plates with unit-cell parameters a = 46.4, b = 120.6, c = 86.9 a, beta = 95.7 degrees . the crystals exhibited the symmetry of space group p2(1) and diffracted to a minimum d-s ...201020445266
kinetic and structural characterization of a heterohexamer 4-oxalocrotonate tautomerase from chloroflexus aurantiacus j-10-fl: implications for functional and structural diversity in the tautomerase superfamily .4-oxalocrotonate tautomerase (4-ot) isozymes play prominent roles in the bacterial utilization of aromatic hydrocarbons as sole carbon sources. these enzymes catalyze the conversion of 2-hydroxy-2,4-hexadienedioate (or 2-hydroxymuconate) to 2-oxo-3-hexenedioate, where pro-1 functions as a general base and shuttles a proton from the 2-hydroxyl group of the substrate to the c-5 position of the product. 4-ot, a homohexamer from pseudomonas putida mt-2, is the most extensively studied 4-ot isozyme a ...201020465238
incidence, relevance and response for ralsfonia respiratory infections.cases of ralstonia colonization/infection occasionally reported by hospitals has generated increased interest in an organism previously little known to most clinicians. our goal was to determine the incidence of respiratory colonizations and infections involving ralstonia and the association of mechanical ventilation (limited to reports on respiratory-related occurrences in the u.s.a.) and propose a decision chart to assist response.201020499534
thioesterases: a new perspective based on their primary and tertiary structures.thioesterases (tes) are classified into ec 3.1.2.1 through ec 3.1.2.27 based on their activities on different substrates, with many remaining unclassified (ec 3.1.2.-). analysis of primary and tertiary structures of known tes casts a new light on this enzyme group. we used strong primary sequence conservation based on experimentally proved proteins as the main criterion, followed by verification with tertiary structure superpositions, mechanisms, and catalytic residue positions, to accurately de ...201020506386
molecular characterization of a class i p450 electron transfer system from novosphingobium aromaticivorans dsm12444.cytochrome p450 (cyp) enzymes of the cyp101 and cyp111 families from the oligotrophic bacterium novosphingobium aromaticivorans dsm12444 are heme monooxygenases that receive electrons from nadh via arx, a [2fe-2s] ferredoxin, and arr, a ferredoxin reductase. these systems show fast nadh turnovers (k(cat) = 39-91 s(-1)) that are efficiently coupled to product formation. the three-dimensional structures of arr, arx, and cyp101d1, which form a physiological class i p450 electron transfer chain, hav ...201020576606
identification and characterization of a novel estrogenic ligand actinopolymorphol a.xenoestrogenic compounds are abundant in the modern environment including phytoestrogens from plants, chemical by-products from industry, and secondary metabolites from microbes; all can profoundly affect human health. consequently mechanism-based screens are urgently needed to improve the rate at which the xenoestrogens are discovered. estrogen receptor (er) dimerization is required for target gene transcription. the three er dimer pairs (eralpha/alpha homodimers, erbeta/beta homodimers, and er ...201020599778
innate immunology of bovine respiratory disease.there are a variety of factors and conditions that predispose cattle to pneumonia. cattle have anatomic and cellular differences from humans and other species and are managed in groups/herds, all of which can increase susceptibility to microbial pathogens. this article highlights the basic innate immune response of the respiratory tract and newer developments in the understanding of adaptive immune responses of the bovine respiratory tract, placing special emphasis on features unique to cattle.201020619180
stya1 and stya2b from rhodococcus opacus 1cp: a multifunctional styrene monooxygenase system.two-component flavoprotein monooxygenases are emerging biocatalysts that generally consist of a monooxygenase and a reductase component. here we show that rhodococcus opacus 1cp encodes a multifunctional enantioselective flavoprotein monooxygenase system composed of a single styrene monooxygenase (smo) (stya1) and another styrene monooxygenase fused to an nadh-flavin oxidoreductase (stya2b). stya1 and stya2b convert styrene and chemical analogues to the corresponding epoxides at the expense of f ...201020675468
scarless and sequential gene modification in pseudomonas using pcr product flanked by short homology regions.the lambda red recombination system has been used to inactivate chromosomal genes in various bacteria and fungi. the procedure consists of electroporating a polymerase chain reaction (pcr) fragment containing antibiotic cassette flanked by homology regions to the target locus into a strain that can express the lambda red proteins (gam, bet, exo).201020682065
moenomycin family antibiotics: chemical synthesis, biosynthesis, and biological activity. 201020730219
partial purification and characterization of the mode of action of enterocin s37: a bacteriocin produced by enterococcus faecalis s37 isolated from poultry feces.the aim of this research was to purify and characterize the mode of action of enterocin s37, a bacteriocin produced by enterococcus faecalis s37, a strain recently isolated from the chicken feces. enterocin s37 has a molecular weight comprised between 4 and 5 kda. it remained active after 1 h at 80(o)c and at ph values ranging from 4.0 to 9.0. furthermore, cell-free supernatant of enterococcus faecalis s37 and purified enterocin s37 were active against gram-positive bacteria including listeria m ...201020811593
isolation and characterization of bacteria from the gut of bombyx mori that degrade cellulose, xylan, pectin and starch and their impact on digestion.bombyx mori l. (lepidoptera: bombycidae) have been domesticated and widely used for silk production. it feeds on mulberry leaves. mulberry leaves are mainly composed of pectin, xylan, cellulose and starch. some of the digestive enzymes that degrade these carbohydrates might be produced by gut bacteria. eleven isolates were obtained from the digestive tract of b. mori, including the gram positive bacillus circulans and gram negative proteus vulgaris, klebsiella pneumoniae, escherichia coli, citro ...201020874394
lipoic acid synthesis: a new family of octanoyltransferases generally annotated as lipoate protein ligases.bacillus subtilis lacks a recognizable homologue of the lipb octanoyltransferase, an enzyme essential for lipoic acid synthesis in escherichia coli. lipb transfers the octanoyl moiety from octanoyl-acyl carrier protein to the lipoyl domains of the 2-oxoacid dehydrogenases via a thioester-linked octanoyl-lipb intermediate. the octanoylated dehydrogenase is then converted to the enzymatically active lipoylated species by insertion of two sulfur atoms into the octanoyl moiety by the s-adenosyl-l-me ...201020882995
activity and interactions of antibiotic and phytochemical combinations against pseudomonas aeruginosa in vitro.in this study the in vitro activities of seven antibiotics (ciprofloxacin, ceftazidime, tetracycline, trimethoprim, sulfamethoxazole, polymyxin b and piperacillin) and six phytochemicals (protocatechuic acid, gallic acid, ellagic acid, rutin, berberine and myricetin) against five p. aeruginosa isolates, alone and in combination are evaluated. all the phytochemicals under investigation demonstrate potential inhibitory activity against p. aeruginosa. the combinations of sulfamethoxazole plus proto ...201020941374
expression of an organic solvent stable lipase from staphylococcus epidermidis at2.an organic solvent tolerant lipase gene from staphylococcus epidermidis at2 was successfully cloned and expressed with ptrchis2 in e. coli top10. sequence analysis revealed an open reading frame (orf) of 1,933 bp in length which coded for a polypeptide of 643 amino acid residues. the polypeptide comprised of a signal peptide (37 amino acids), pro-peptide and a mature protein of 390 amino acids. expression of at2 lipase resulted in an 18-fold increase in activity, upon the induction of 0.6 mm ipt ...201020957088
keratitis after implantation of intrastromal corneal rings with spontaneous extrusion of the segment.purpose: to report a case of bacterial keratitis in a patient with a history of intrastromal corneal ring segments (intacs®) implantation to correct keratoconus. methods: the patient's history, clinical presentation, pathological analysis and therapeutic management were reviewed. results: a 36-year-old-man was referred to our department due to decreased vision and intense pain in his left eye, 40 days after intacs® implantation for keratoconus. slit-lamp examination revealed epithelial defects a ...201021060771
thny is a ferredoxin reductase-like iron-sulfur flavoprotein that has evolved to function as a regulator of tetralin biodegradation gene expression.previous genetic studies in sphingomonas macrogolitabida strain tfa have established that expression of genes involved in tetralin biodegradation (thn genes) requires the function of the lysr type activator thnr and also thny. sequence comparison indicated that thny is homologous to bacterial oxygenase-coupled nad(p)h-dependent ferredoxin reductases. however, thny showed substitutions in highly conserved positions of the pyridine nucleotide binding domain of these ferredoxin reductases. thny exp ...201021068394
thny is a ferredoxin reductase-like iron-sulfur flavoprotein that has evolved to function as a regulator of tetralin biodegradation gene expression.previous genetic studies in sphingomonas macrogolitabida strain tfa have established that expression of genes involved in tetralin biodegradation (thn genes) requires the function of the lysr type activator thnr and also thny. sequence comparison indicated that thny is homologous to bacterial oxygenase-coupled nad(p)h-dependent ferredoxin reductases. however, thny showed substitutions in highly conserved positions of the pyridine nucleotide binding domain of these ferredoxin reductases. thny exp ...201021068394
structural insight into the expanded pcb-degrading abilities of a biphenyl dioxygenase obtained by directed evolution.the biphenyl dioxygenase of burkholderia xenovorans lb400 is a multicomponent rieske-type oxygenase that catalyzes the dihydroxylation of biphenyl and many polychlorinated biphenyls (pcbs). the structural bases for the substrate specificity of the enzyme's oxygenase component (bphae(lb400)) are largely unknown. bphae(p4), a variant previously obtained through directed evolution, transforms several chlorobiphenyls, including 2,6-dichlorobiphenyl, more efficiently than bphae(lb400), yet differs fr ...201021073881
structural insight into the expanded pcb-degrading abilities of a biphenyl dioxygenase obtained by directed evolution.the biphenyl dioxygenase of burkholderia xenovorans lb400 is a multicomponent rieske-type oxygenase that catalyzes the dihydroxylation of biphenyl and many polychlorinated biphenyls (pcbs). the structural bases for the substrate specificity of the enzyme's oxygenase component (bphae(lb400)) are largely unknown. bphae(p4), a variant previously obtained through directed evolution, transforms several chlorobiphenyls, including 2,6-dichlorobiphenyl, more efficiently than bphae(lb400), yet differs fr ...201021073881
hydrogenosome-localization of arginine deiminase in trichomonas vaginalis.the arginine dihydrolase (adh) pathway has an analogous function to the urea cycle in mitochondria-containing cells, by removing nitrogen from amino acids and generating atp. subcellular localization of the adh pathway enzymes in trichomonas vaginalis revealed that arginine deiminase (adi) localizes to the hydrogenosome, a mitochondrion-like organelle of anaerobic protists. however the other enzymes of the adh pathway, ornithine carbamyltransferase and carbamate kinase localize to the cytosol. t ...201021074581
hydrogenosome-localization of arginine deiminase in trichomonas vaginalis.the arginine dihydrolase (adh) pathway has an analogous function to the urea cycle in mitochondria-containing cells, by removing nitrogen from amino acids and generating atp. subcellular localization of the adh pathway enzymes in trichomonas vaginalis revealed that arginine deiminase (adi) localizes to the hydrogenosome, a mitochondrion-like organelle of anaerobic protists. however the other enzymes of the adh pathway, ornithine carbamyltransferase and carbamate kinase localize to the cytosol. t ...201021074581
giardia duodenalis 14-3-3 protein is polyglycylated by a tubulin tyrosine ligase-like member and deglycylated by two metallocarboxypeptidases.the flagellated protozoan giardia duodenalis is a parasite of the upper part of the small intestine of mammals, including humans, and an interesting biological model. giardia harbors a single 14-3-3 isoform, a multifunctional protein family, that is modified at the c terminus by polyglycylation, an unusual post-translational modification consisting of the covalent addition of one or multiple glycines on the γ-carboxyl groups of specific glutamic acids. polyglycylation affects the intracellular l ...201021135098
giardia duodenalis 14-3-3 protein is polyglycylated by a tubulin tyrosine ligase-like member and deglycylated by two metallocarboxypeptidases.the flagellated protozoan giardia duodenalis is a parasite of the upper part of the small intestine of mammals, including humans, and an interesting biological model. giardia harbors a single 14-3-3 isoform, a multifunctional protein family, that is modified at the c terminus by polyglycylation, an unusual post-translational modification consisting of the covalent addition of one or multiple glycines on the γ-carboxyl groups of specific glutamic acids. polyglycylation affects the intracellular l ...201021135098
nature of the reaction intermediates in the flavin adenine dinucleotide-dependent epoxidation mechanism of styrene monooxygenase.styrene monooxygenase (smo) is a two-component flavoenzyme composed of an nadh-specific flavin reductase (smob) and fad-specific styrene epoxidase (nsmoa). nsmoa binds tightly to reduced fad and catalyzes the stereospecific addition of one atom of molecular oxygen to the vinyl side chain of styrene in the enantioselective synthesis of s-styrene oxide. in this mechanism, molecular oxygen first reacts with nsmoa(fad(red)) to yield an fad c(4a)-peroxide intermediate. this species is nonfluorescent ...201021166448
nature of the reaction intermediates in the flavin adenine dinucleotide-dependent epoxidation mechanism of styrene monooxygenase.styrene monooxygenase (smo) is a two-component flavoenzyme composed of an nadh-specific flavin reductase (smob) and fad-specific styrene epoxidase (nsmoa). nsmoa binds tightly to reduced fad and catalyzes the stereospecific addition of one atom of molecular oxygen to the vinyl side chain of styrene in the enantioselective synthesis of s-styrene oxide. in this mechanism, molecular oxygen first reacts with nsmoa(fad(red)) to yield an fad c(4a)-peroxide intermediate. this species is nonfluorescent ...201021166448
screening of ethanol, petroleum ether and chloroform extracts of medicinal plants, lawsonia inermis l. and mimosa pudica l. for antibacterial activity.organic extracts (ethanol, petroleum ether and chloroform) of two medicinal plants lawsonia inermis l. and mimosa pudica l. were proven for antibacterial properties against 15 gram-positive and gram-negative human pathogenic bacteria. among the three types of extracts tested, ethanol extract was found to possess maximum antibacterial activity. the diameter of the zone of inhibition of bacterial growth showed that gram-negative bacteria are more sensitive than gram-positive bacteria to plant extr ...201021188055
real-time solvent tolerance analysis of pseudomonas sp. strain vlb120{delta}c catalytic biofilms.biofilms are ubiquitous surface-associated microbial communities embedded in an extracellular polymeric (eps) matrix, which gives the biofilm structural integrity and strength. it is often reported that biofilm-grown cells exhibit enhanced tolerance toward adverse environmental stress conditions, and thus there has been a growing interest in recent years to use biofilms for biotechnological applications. we present a time- and locus-resolved, noninvasive, quantitative approach to study biofilm d ...201021193676
screen-printed carbon electrodes modified by rhodium dioxide and glucose dehydrogenase.the described glucose biosensor is based on a screen-printed carbon electrode (spce) modified by rhodium dioxide, which functions as a mediator. the electrode is further modified by the enzyme glucose dehydrogenase, which is immobilized on the electrode's surface through electropolymerization with m-phenylenediamine. the enzyme biosensor was optimized and tested in model glucose samples. the biosensor showed a linear range of 500-5000 mg l(-1) of glucose with a detection limit of 210 mg l(-1) (e ...201021528113
screen-printed carbon electrodes modified by rhodium dioxide and glucose dehydrogenase.the described glucose biosensor is based on a screen-printed carbon electrode (spce) modified by rhodium dioxide, which functions as a mediator. the electrode is further modified by the enzyme glucose dehydrogenase, which is immobilized on the electrode's surface through electropolymerization with m-phenylenediamine. the enzyme biosensor was optimized and tested in model glucose samples. the biosensor showed a linear range of 500-5000 mg l(-1) of glucose with a detection limit of 210 mg l(-1) (e ...201021528113
single turnover kinetics of tryptophan hydroxylase: evidence for a new intermediate in the reaction of the aromatic amino acid hydroxylases.tryptophan hydroxylase (trph) uses a non-heme mononuclear iron center to catalyze the tetrahydropterin-dependent hydroxylation of tryptophan to 5-hydroxytryptophan. the reactions of the trph.fe(ii), trph.fe(ii).tryptophan, trph.fe(ii).6meph(4).tryptophan, and trph.fe(ii).6meph(4).phenylalanine complexes with o(2) were monitored by stopped-flow absorbance spectroscopy and rapid quench methods. the second-order rate constant for the oxidation of trph.fe(ii) has a value of 104 m(-1) s(-1) irrespect ...201020687613
favored and disfavored pathways of protein crosslinking by glucose: glucose lysine dimer (glucold) and crossline versus glucosepane.we describe the isolation and molecular characterization of a novel glucose-lysine dimer crosslink 1,3-bis-(5-amino-5-carboxypentyl)-4-(1',2',3',4'-tetrahydroxybutyl)-3h-imidazolium salt, named glucold. glucold was easily formed from the amadori product (fructose-lysine). however, when bsa was incubated with 100 mm glucose for 25 days, the levels of the lysine-lysine glucose crosslinks glucold and crossline were only 21 and <1 pmol/mg, respectively, compared to 611 pmol/mg protein for the lysine ...201020607325
favored and disfavored pathways of protein crosslinking by glucose: glucose lysine dimer (glucold) and crossline versus glucosepane.we describe the isolation and molecular characterization of a novel glucose-lysine dimer crosslink 1,3-bis-(5-amino-5-carboxypentyl)-4-(1',2',3',4'-tetrahydroxybutyl)-3h-imidazolium salt, named glucold. glucold was easily formed from the amadori product (fructose-lysine). however, when bsa was incubated with 100 mm glucose for 25 days, the levels of the lysine-lysine glucose crosslinks glucold and crossline were only 21 and <1 pmol/mg, respectively, compared to 611 pmol/mg protein for the lysine ...201020607325
enzymatic determination of diglyceride using an iridium nano-particle based single use, disposable biosensor.a single use, disposable iridium-nano particle contained biosensor had been developed for the determination of diglyceride (dg). in this study hydrogen peroxide, formed through the enzymatic breakdown of dg via lipase, glycerol kinase and glycerol 3-phosphate oxidase, was electrochemically oxidized at an applied potential of +0.5 v versus the ag/agcl reference electrode. the oxidation current was then used to quantify the diglyceride concentration. optimum enzyme concentrations and the surfactan ...201022219685
hydroxylated metabolites of 4-monochlorobiphenyl and its metabolic pathway in whole poplar plants.4-monochlorobiphenyl (cb3), mainly an airborne pollutant, undergoes rapid biotransformation to produce hydroxylated metabolites (oh-cb3s). however, up to now, hydroxylation of cb3 has not been studied in living organisms. in order to explore the formation of hydroxylated metabolites of cb3 in whole plants, poplars (populus deltoides x nigra, dn34) were exposed to cb3 for 10 days. poplars are a model plant with complete genomic sequence, and they are widely used in phytoremediation. results showe ...201020402517
risk factors and prevention of late-onset sepsis in premature infants.late-onset sepsis in premature infants is a major cause of morbidity, mortality, and increased medical costs. risk factors include low birth weight, low gestational age, previous antimicrobial exposure, poor hand hygiene, and central venous catheters. methods studied to prevent late-onset sepsis include early feedings, immune globulin administration, prophylactic antimicrobial administration, and improved hand hygiene. in this review, we will outline the risk factors for development of late-onse ...201020116186
macrocyclic histone deacetylase inhibitors.histone deacetylase inhibitors (hdaci) are an emerging class of novel anti-cancer drugs that cause growth arrest, differentiation, and apoptosis of tumor cells. in addition, they have shown promise as anti-parasitic, anti-neurodegenerative, anti-rheumatologic and immunosuppressant agents. to date, several structurally distinct small molecule hdaci have been reported including aryl hydroxamates, benzamides, short-chain fatty acids, electrophilic ketones, and macrocyclic peptides. macrocyclic hdac ...201020536416
degradation of h-acid by free and immobilized cells of alcaligenes latus.alcaligenes latus, isolated from industrial effluent, was able to grow in mineral salts medium with 50 ppm (0.15 mm) of h-acid as a sole source of carbon. immobilization of alcaligenes latus in ca-alginate and polyurethane foam resulted in cells embedded in the matrices. when free cells and immobilized cells were used for biodegradation studies at concentration ranging from 100 ppm (0.3 mm) to 500 ppm (1.15 mm) degradation rate was enhanced with immobilized cells. cells immobilized in polyuretha ...201024031573
prevalence of uropathogens in diabetic patients and their corresponding resistance pattern: results of a survey conducted at diagnostic centers in dhaka, bangladesh.urinary tract infection is the second most common clinical indication for empirical antibiotic treatment in primary and secondary health care settings. the incidence of diabetes mellitus throughout the world is increasing strikingly and in the long run, it has some major effects on the genitourinary system which makes diabetic patients more liable to urinary tract infection. this study is designed to reveal the distribution of uropathogens in diabetic patients according to age and sex, and corre ...201022043358
gene duplications in prokaryotes can be associated with environmental adaptation.gene duplication is a normal evolutionary process. if there is no selective advantage in keeping the duplicated gene, it is usually reduced to a pseudogene and disappears from the genome. however, some paralogs are retained. these gene products are likely to be beneficial to the organism, e.g. in adaptation to new environmental conditions. the aim of our analysis is to investigate the properties of paralog-forming genes in prokaryotes, and to analyse the role of these retained paralogs by relati ...201020961426
purification of protease from pseudomonas thermaerum gw1 isolated from poultry waste site.an extracellular protease was purified from pseudomonas thermaerum gw1 a new strain identified by morphological, biochemical and 16s rdna sequencing. it was isolated from soil of poultry waste site at ghazipur near ghaziabad, delhi. the strain produces extra cellular protease in the culture media that was maintained at 37°c, 140 rpm. the media was harvested for protease after 48 hrs of incubation at 37°c in basal media supplemented with 1% casein. we report 6.08 fold purification of enzyme follo ...201021379398
clinical and antimicrobial efficacy of nitradine ™-based disinfecting cleaning tablets in complete denture wearers.this study evaluated the efficacy of nitradine ™-based disinfecting cleaning tablets for complete denture, in terms of denture biofilm removal and antimicrobial action.201021308285
engineering of a psychrophilic bacterium for the bioremediation of aromatic compounds.microbial degradation of aromatic hydrocarbons has been studied with the aim of developing applications for the removal of toxic compounds. efforts have been directed toward the genetic manipulation of mesophilic bacteria to improve their ability to degrade pollutants, even though many pollution problems occur in sea waters and in effluents of industrial processes which are characterized by low temperatures. from these considerations the idea of engineering a psychrophilic microorganism for the ...201021326928
functional promiscuity of homologues of the bacterial arsa atpases.the arsa atpase of e. coli plays an essential role in arsenic detoxification. published evidence implicates arsa in the energization of as(iii) efflux via the formation of an oxyanion-translocating complex with arsb. in addition, eukaryotic arsa homologues have several recognized functions unrelated to arsenic resistance. by aligning arsa homologues, constructing phylogenetic trees, examining arsa encoding operons, and estimating the probable coevolution of these homologues with putative transpo ...201020981284
prediction and analysis of the modular structure of cytochrome p450 monooxygenases.cytochrome p450 monooxygenases (cyps) form a vast and diverse family of highly variable sequences. they catalyze a wide variety of oxidative reactions and are therefore of great relevance in drug development and biotechnological applications. despite their differences in sequence and substrate specificity, the structures of cyps are highly similar. although being in research focus for years, factors mediating selectivity and activity remain vague.201020950472
rhamnolipid biosurfactants as new players in animal and plant defense against microbes.rhamnolipids are known as very efficient biosurfactant molecules. they are used in a wide range of industrial applications including food, cosmetics, pharmaceutical formulations and bioremediation of pollutants. the present review provides an overview of the effect of rhamnolipids in animal and plant defense responses. we describe the current knowledge on the stimulation of plant and animal immunity by these molecules, as well as on their direct antimicrobial properties. given their ecological a ...201021614194
whole-cell fluorescent biosensors for bioavailability and biodegradation of polychlorinated biphenyls.whole-cell microbial biosensors are one of the newest molecular tools used in environmental monitoring. such biosensors are constructed through fusing a reporter gene such as lux, gfp or lacz, to a responsive promoter. there have been many reports of the applications of biosensors, particularly their use in assaying pollutant toxicity and bioavailability. this paper reviews the basic concepts behind the construction of whole-cell microbial biosensors for pollutant monitoring, and describes the a ...201022205873
functional gene diversity of soil microbial communities from five oil-contaminated fields in china.to compare microbial functional diversity in different oil-contaminated fields and to know the effects of oil contaminant and environmental factors, soil samples were taken from typical oil-contaminated fields located in five geographic regions of china. geochip, a high-throughput functional gene array, was used to evaluate the microbial functional genes involved in contaminant degradation and in other major biogeochemical/metabolic processes. our results indicated that the overall microbial com ...201020861922
functional gene diversity of soil microbial communities from five oil-contaminated fields in china.to compare microbial functional diversity in different oil-contaminated fields and to know the effects of oil contaminant and environmental factors, soil samples were taken from typical oil-contaminated fields located in five geographic regions of china. geochip, a high-throughput functional gene array, was used to evaluate the microbial functional genes involved in contaminant degradation and in other major biogeochemical/metabolic processes. our results indicated that the overall microbial com ...201020861922
microbial degradation of petroleum hydrocarbon contaminants: an overview.one of the major environmental problems today is hydrocarbon contamination resulting from the activities related to the petrochemical industry. accidental releases of petroleum products are of particular concern in the environment. hydrocarbon components have been known to belong to the family of carcinogens and neurotoxic organic pollutants. currently accepted disposal methods of incineration or burial insecure landfills can become prohibitively expensive when amounts of contaminants are large. ...201021350672
microbial degradation of petroleum hydrocarbon contaminants: an overview.one of the major environmental problems today is hydrocarbon contamination resulting from the activities related to the petrochemical industry. accidental releases of petroleum products are of particular concern in the environment. hydrocarbon components have been known to belong to the family of carcinogens and neurotoxic organic pollutants. currently accepted disposal methods of incineration or burial insecure landfills can become prohibitively expensive when amounts of contaminants are large. ...201021350672
assessment of formate dehydrogenase stress stability in vivo using inactivation by hydrogen peroxide.kinetic studies on hydrogen peroxide-induced inactivation of mutant formate dehydrogenase from pseudomonas sp. 101 (psefdh cys255ala) suggest a simple bimolecular mechanism for enzyme reaction with the inactivation agent. in the excess of hydrogen peroxide, the decrease in enzyme activity follows first-order kinetics. therefore, the first-order effective inactivation kinetic constants determined for various fdh forms at a constant h(2)o(2) concentration can be used as a quantitative measure of t ...201022649634
cholesterol oxidase: physiological functions.an important aspect of catalysis performed by cholesterol oxidase (3beta-hydroxysteroid oxidase) concerns the nature of its association with the lipid bilayer that contains the sterol substrate. efficient catalytic turnover is affected by the association of the protein with the membrane as well as the solubility of the substrate in the lipid bilayer. in this review, the binding of cholesterol oxidase to the lipid bilayer, its turnover of substrates presented in different physical environments, a ...200919843168
cloning and characterisation of (r)-3-hydroxyacyl-acyl carrier protein-coenzyme a transferase gene (phag) from pseudomonas sp. usm 4-55.the (r)-3-hydroxyacyl-acp-coa transferase catalyses the conversion of (r)-3-hydroxyacyl-acp to (r)-3-hydroxyacyl-coa derivatives, which serves as the ultimate precursor for polyhydroxyalkanoate (pha) polymerisation from unrelated substrates in pseudomonads. phag was found to be responsible for channelling precursors for polyhydroxyalkanoate (pha) synthase from a de novo fatty acid biosynthesis pathway when cultured on carbohydrates, such as glucose or gluconate. the phag gene was cloned from pse ...200924575175
caenorhabditis elegans genomic response to soil bacteria predicts environment-specific genetic effects on life history traits.with the post-genomic era came a dramatic increase in high-throughput technologies, of which transcriptional profiling by microarrays was one of the most popular. one application of this technology is to identify genes that are differentially expressed in response to different environmental conditions. these experiments are constructed under the assumption that the differentially expressed genes are functionally important in the environment where they are induced. however, whether differential e ...200919503598
the pha depolymerase engineering database: a systematic analysis tool for the diverse family of polyhydroxyalkanoate (pha) depolymerases.polyhydroxyalkanoates (phas) can be degraded by many microorganisms using intra- or extracellular pha depolymerases. pha depolymerases are very diverse in sequence and substrate specificity, but share a common alpha/beta-hydrolase fold and a catalytic triad, which is also found in other alpha/beta-hydrolases.200919296857
isolation and identification of profenofos degrading bacteria.an enrichment culture technique was used to isolate bacterial strains responsible for the biodegradation of profenofos in a soil from hubei province of central china. two pure bacterial cultures, named w and y, were isolated and subsequently characterized by sequencing of 16s rrna genes and biochemical tests. isolate w showed 96% similarity to the 16s rrna gene of a pseudomonas putida unlike y which showed 99% similarity to the 16s rrna gene of burkholderia gladioli. both strains grew well at ph ...200924031438
metagenomic approaches to natural products from free-living and symbiotic organisms. 200919844642
recombinant organisms for production of industrial products.a revolution in industrial microbiology was sparked by the discoveries of ther double-stranded structure of dna and the development of recombinant dna technology. traditional industrial microbiology was merged with molecular biology to yield improved recombinant processes for the industrial production of primary and secondary metabolites, protein biopharmaceuticals and industrial enzymes. novel genetic techniques such as metabolic engineering, combinatorial biosynthesis and molecular breeding te ...200921326937
recombinant organisms for production of industrial products.a revolution in industrial microbiology was sparked by the discoveries of ther double-stranded structure of dna and the development of recombinant dna technology. traditional industrial microbiology was merged with molecular biology to yield improved recombinant processes for the industrial production of primary and secondary metabolites, protein biopharmaceuticals and industrial enzymes. novel genetic techniques such as metabolic engineering, combinatorial biosynthesis and molecular breeding te ...200921326937
sphingomyelin metabolism at the plasma membrane: implications for bioactive sphingolipids.the plasma membrane (pm) is a major resource for production of bioactive lipids and contains a large proportion of the cellular sphingomyelin (sm) content. consequently, the regulation of sm levels at the pm by enzymes such as sphingomyelinase (smase) and sm synthase 2 (sms2) can have profound effects - both on biophysical properties of the membrane, but also on cellular signaling. over the past 20 years, there has been considerable research into the physiological and cellular functions associat ...200919857494
sphingomyelin metabolism at the plasma membrane: implications for bioactive sphingolipids.the plasma membrane (pm) is a major resource for production of bioactive lipids and contains a large proportion of the cellular sphingomyelin (sm) content. consequently, the regulation of sm levels at the pm by enzymes such as sphingomyelinase (smase) and sm synthase 2 (sms2) can have profound effects - both on biophysical properties of the membrane, but also on cellular signaling. over the past 20 years, there has been considerable research into the physiological and cellular functions associat ...200919857494
atrazine biodegradation in the lab and in the field: enzymatic activities and gene regulation.atrazine is an herbicide of the s-triazine family that is used primarily as a nitrogen source by degrading microorganisms. while many catabolic pathways for xenobiotics are subjected to catabolic repression by preferential carbon sources, atrazine utilization is repressed in the presence of preferential nitrogen sources. this phenomenon appears to restrict atrazine elimination in nitrogen-fertilized soils by indigenous organisms or in bioaugmentation approaches. the mechanisms of nitrogen contro ...200921261912
massive comparative genomic analysis reveals convergent evolution of specialized bacteria.genome size and gene content in bacteria are associated with their lifestyles. obligate intracellular bacteria (i.e., mutualists and parasites) have small genomes that derived from larger free-living bacterial ancestors; however, the different steps of bacterial specialization from free-living to intracellular lifestyle have not been studied comprehensively. the growing number of available sequenced genomes makes it possible to perform a statistical comparative analysis of 317 genomes from bacte ...200919361336
an in vitro spectroscopic analysis to determine whether para-chloroaniline is produced from mixing sodium hypochlorite and chlorhexidine.the purpose of this in vitro study was to determine whether para-chloroaniline (pca) is formed through the reaction of mixing sodium hypochlorite (naocl) and chlorhexidine (chx).200920113799
an in vitro spectroscopic analysis to determine whether para-chloroaniline is produced from mixing sodium hypochlorite and chlorhexidine.the purpose of this in vitro study was to determine whether para-chloroaniline (pca) is formed through the reaction of mixing sodium hypochlorite (naocl) and chlorhexidine (chx).200920113799
taking a corneal scrape and making a diagnosis. 200920212927
managing corneal disease: focus on suppurative keratitis. 200920212926
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