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neutrophil apoptosis: a marker of disease severity in sepsis and sepsis-induced acute respiratory distress syndrome.apoptosis of neutrophils (polymorphonuclear neutrophils [pmns]) may limit inflammatory injury in sepsis and acute respiratory distress syndrome (ards), but the relationship between the severity of sepsis and extent of pmn apoptosis and the effect of superimposed ards is unknown. the objective of this study was to correlate neutrophil apoptosis with the severity of sepsis and sepsis-induced ards.200617092345
questions about the use of antibiotics in acute pancreatitis.the use of antibiotics in acute pancreatitis despite recent clinical trials remains controversial. the aim of this study is to review the latest clinical trials and guidelines about antibiotics in acute pancreatitis and determine its proper use.200616820058
peritonitis - the eastern experience.peritonitis is a common emergency encountered by surgeons the world over. this paper aims to provide an overview of the spectrum of peritonitis seen in the east. studies dealing with the overall spectrum of secondary peritonitis in various countries of this region were identified using pubmed and google. these were analyzed for the site and cause of perforation and the mortality. it was observed that perforation of duodenal ulcers was the most the commonly encountered perforations. these are fol ...200616759427
evaluation of chiral alpha-cyanoesters as general fluorescent substrates for screening enantioselective esterases.esterases play a crucial role in industrial chemical synthesis, maintaining normal physiological metabolism and detoxifying exogenous ester-containing toxicants. to meet the rapidly increasing industrial need for all kinds of esterases, especially enantioselective esterases used to generate highly pure chiral compounds, general substrates are necessary for rapid screening, monitoring, purification, and characterization. in this study, general fluorescent substrates including phenolic derivatives ...200616448170
outcome of life-threatening malaria in african children requiring endotracheal intubation.little is known about children undergoing critical care for malaria. the purpose of this survey was to evaluate the outcome in african children requiring endotracheal intubation for life-threatening malaria.200717470294
conformationally constrained analogues of 2-arachidonoylglycerol.novel monocyclic analogues of 2-arachidonoylglycerol (2-ag) were designed in order to explore the pharmacophoric conformations of this endocannabinoid ligand at the key cannabinergic proteins. all 2-arachidonoyl esters of 1,2,3-cyclohexanetriol [meso-7 (am5504), (+/-)-8 (am5503), and meso-9 (am5505)] were synthesized by regioselective acylation of 2,3-dihydroxycyclohexanone followed by selective reductions. the optically active isomers (+)-8 (am4434) and (-)-8 (am4435) were synthesized from (2s, ...200717826996
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 ...200717623104
similar enzymes, different structures: phthalate dioxygenase is an alpha3alpha3 stacked hexamer, not an alpha3beta3 trimer like "normal" rieske oxygenases.phthalate dioxygenase (pdo) is a member of a class of bacterial oxygenases that contain both rieske [2fe-2s] and fe(ii) mononuclear centers. recent crystal structures of several rieske dioxygenases showed that they exist as alpha(3)beta(3) multimers with subunits arranged head-to-tail in alpha and beta stacked planar rings. the structure of pdo, which consists of only alpha-subunits, remains to be solved. although similar to other rieske dioxygenases in many aspects, pdo was shown to differ in t ...200717764654
finding intermediates in the o2 activation pathways of non-heme iron oxygenases.intermediates in the reaction cycle of an oxygenase are usually very informative with respect to the chemical mechanism of o 2 activation and insertion. however, detection of these intermediates is often complicated by their short lifetime and the regulatory mechanism of the enzyme designed to ensure specificity. here, the methods used to detect the intermediates in an extradiol dioxygenase, a rieske cis-dihydrodiol dioxygenase, and soluble methane monooxygenase are discussed. the methods includ ...200717567087
hydroxyatrazine n-ethylaminohydrolase (atzb): an amidohydrolase superfamily enzyme catalyzing deamination and dechlorination.hydroxyatrazine [2-(n-ethylamino)-4-hydroxy-6-(n-isopropylamino)-1,3,5-triazine] n-ethylaminohydrolase (atzb) is the sole enzyme known to catalyze the hydrolytic conversion of hydroxyatrazine to n-isopropylammelide. atzb, therefore, serves as the point of intersection of multiple s-triazine biodegradative pathways and is completely essential for microbial growth on s-triazine herbicides. here, atzb was cloned from pseudomonas sp. strain adp and its product was purified to homogeneity and charact ...200717660279
adaptation of pseudomonas sp. strain 7-6 to quaternary ammonium compounds and their degradation via dual pathways.pseudomonas sp. strain 7-6, isolated from active sludge obtained from a wastewater facility, utilized a quaternary ammonium surfactant, n-dodecyltrimethylammonium chloride (dtac), as its sole carbon, nitrogen, and energy source. when initially grown in the presence of 10 mm dtac medium, the isolate was unable to degrade dtac. the strain was cultivated in gradually increasing concentrations of the surfactant until continuous exposure led to high tolerance and biodegradation of the compound. based ...200717261523
the role of laterally transferred genes in adaptive evolution.bacterial genomes develop new mechanisms to tide them over the imposing conditions they encounter during the course of their evolution. acquisition of new genes by lateral gene transfer may be one of the dominant ways of adaptation in bacterial genome evolution. lateral gene transfer provides the bacterial genome with a new set of genes that help it to explore and adapt to new ecological niches.200717288581
a gene cluster involved in degradation of substituted salicylates via ortho cleavage in pseudomonas sp. strain mt1 encodes enzymes specifically adapted for transformation of 4-methylcatechol and 3-methylmuconate.pseudomonas sp. strain mt1 has recently been reported to degrade 4- and 5-chlorosalicylate by a pathway assumed to consist of a patchwork of reactions comprising enzymes of the 3-oxoadipate pathway. genes encoding the initial steps in the degradation of salicylate and substituted derivatives were now localized and sequenced. one of the gene clusters characterized (sal) showed a novel gene arrangement, with sala, encoding a salicylate 1-hydroxylase, being clustered with salcd genes, encoding muco ...200717172348
structural investigations of the ferredoxin and terminal oxygenase components of the biphenyl 2,3-dioxygenase from sphingobium yanoikuyae b1.the initial step involved in oxidative hydroxylation of monoaromatic and polyaromatic compounds by the microorganism sphingobium yanoikuyae strain b1 (b1), previously known as sphingomonas yanoikuyae strain b1 and beijerinckia sp. strain b1, is performed by a set of multiple terminal rieske non-heme iron oxygenases. these enzymes share a single electron donor system consisting of a reductase and a ferredoxin (bpdo-fb1). one of the terminal rieske oxygenases, biphenyl 2,3-dioxygenase (bpdo-ob1), ...200717349044
production of l-carnitine by secondary metabolism of bacteria.abstract: the increasing commercial demand for l-carnitine has led to a multiplication of efforts to improve its production with bacteria. the use of different cell environments, such as growing, resting, permeabilized, dried, osmotically stressed, freely suspended and immobilized cells, to maintain enzymes sufficiently active for l-carnitine production is discussed in the text. the different cell states of enterobacteria, such as escherichia coli and proteus sp., which can be used to produce l- ...200717910757
proteoglycan synthesis by human corneal explants submitted to laser in situ keratomileusis (lasik).to evaluate the acute effects of laser in situ keratomileusis (lasik) upon the synthesis of proteoglycans (pgs) and collagen fibril organization in human corneal explants.200717293778
metabolomic and genetic analysis of biomarkers for peroxisome proliferator-activated receptor alpha expression and activation.peroxisome proliferator-activated receptor alpha (pparalpha) is a nuclear receptor with manifold effects on intermediary metabolism. to define a set of urinary biomarkers that could be used to determine the efficacy of pparalpha agonists, a metabolomic investigation was undertaken in wild-type and pparalpha-null mice fed for 2 wk either a regular diet or a diet containing the pparalpha ligand wy-14,643 ([4-chloro-6-(2,3-xylidino)-2-pyrimidinylthio] acetic acid), and their urine was analyzed by u ...200717550978
dissimilatory iodate reduction by marine pseudomonas sp. strain sct.bacterial iodate (io(3)(-)) reduction is poorly understood largely due to the limited number of available isolates as well as the paucity of information about key enzymes involved in the reaction. in this study, an iodate-reducing bacterium, designated strain sct, was newly isolated from marine sediment slurry. sct is phylogenetically closely related to the denitrifying bacterium pseudomonas stutzeri and reduced 200 microm iodate to iodide (i(-)) within 12 h in an anaerobic culture containing 10 ...200717644635
generation by a widely applicable approach of a hybrid dioxygenase showing improved oxidation of polychlorobiphenyls.recently, a sequence-based approach has been developed for the fast isolation and characterization of class ii aryl-hydroxylating dioxygenase activities (s. kahl and b. hofer, microbiology 149:1475-1481, 2003). it comprises the pcr amplification of segments of alpha subunit genes of unknown sequence that encode the catalytic center and their fusion with sequences of the bpha gene cluster of burkholderia xenovorans lb400. one of the resulting chimeric enzymes, harboring the core segment of a diox ...200717322323
molecular analysis of the subgingival microbiota in health and disease.this investigation provides molecular analyses of the periodontal microbiota in health and disease. subgingival samples from 47 volunteers with healthy gingivae or clinically diagnosed chronic periodontitis were characterized by pcr-denaturing gradient gel electrophoresis (dgge) with primers specific for the v2-v3 region of the eubacterial 16s rrna gene. a hierarchical dendrogram was constructed from band patterns. all unique pcr amplicons (dgge bands) were sequenced for identity. samples were a ...200717085691
biochemical and crystallographic analysis of substrate binding and conformational changes in acetyl-coa synthetase.the adenylate-forming enzymes, including acyl-coa synthetases, the adenylation domains of non-ribosomal peptide synthetases (nrps), and firefly luciferase, perform two half-reactions in a ping-pong mechanism. we have proposed a domain alternation mechanism for these enzymes whereby, upon completion of the initial adenylation reaction, the c-terminal domain of these enzymes undergoes a 140 degrees rotation to perform the second thioester-forming half-reaction. structural and kinetic data of mutan ...200717497934
biochemical and genetic investigation of initial reactions in aerobic degradation of the bile acid cholate in pseudomonas sp. strain chol1.bile acids are surface-active steroid compounds with toxic effects for bacteria. recently, the isolation and characterization of a bacterium, pseudomonas sp. strain chol1, growing with bile acids as the carbon and energy source was reported. in this study, initial reactions of the aerobic degradation pathway for the bile acid cholate were investigated on the biochemical and genetic level in strain chol1. these reactions comprised a-ring oxidation, activation with coenzyme a (coa), and beta-oxida ...200717693490
a novel sampling method for the investigation of gut mirobiota.in order to characterize the qualitative and quantitative microorganisms in different sites of the lower digestive tract (ldt) in healthy volunteers, a specific technique was developed for collecting mucous of the distal ileum, colon and rectum.200717663516
c-myc interacts with trf1/pin2 and regulates telomere length.telomere, the end of linear chromosome, is protected by dna-protein complexes. these complexes cap the linear chromosome and play an important role in the maintenance of genomic stability. trf1/pin2, a double-stranded dna-binding protein is known to regulate telomere length by not only protecting telomere but also blocking the access of telomerase to telomere in cis. to better understand the mechanism through which trf1/pin2 regulates telomere length, we performed the yeast two-hybrid screening ...200717765874
plp catabolism: identification of the 4-pyridoxic acid dehydrogenase gene in mesorhizobium loti maff303099.the function of the mlr6793 gene from mesorhizobium loti maff303099 has been identified. this gene encodes 4-pyridoxic acid dehydrogenase, an enzyme involved in the catabolism of plp (vitamin b6). this enzyme was overexpressed in escherichia coli and characterized. 4-pyridoxic acid dehydrogenase is a 33kda protein that catalyzes the four electron oxidation of 4-pyridoxic acid to 3-hydroxy-2-methylpyridine-4,5-dicarboxylate, using nicotinamide adenine dinucleotide as a cofactor. the k cat for nad ...200717868768
a comprehensive set of plasmids for vanillate- and xylose-inducible gene expression in caulobacter crescentus.caulobacter crescentus is widely used as a powerful model system for the study of prokaryotic cell biology and development. analysis of this organism is complicated by a limited selection of tools for genetic manipulation and inducible gene expression. this study reports the identification and functional characterization of a vanillate-regulated promoter (p(van)) which meets all requirements for application as a multi-purpose expression system in caulobacter, thus complementing the established x ...200717959646
gene identification and structural characterization of the pyridoxal 5'-phosphate degradative protein 3-hydroxy-2-methylpyridine-4,5-dicarboxylate decarboxylase from mesorhizobium loti maff303099.the function of the mlr6791 gene from mesorhizobium loti maff303099 has been identified. this gene encodes 3-hydroxy-2-methylpyridine-4,5-dicarboxylate decarboxylase (hmpddc), an enzyme involved in the catabolism of pyridoxal 5'-phosphate (vitamin b6). this enzyme was overexpressed in escherichia coli and characterized. hmpddc is a 26 kda protein that catalyzes the decarboxylation of 3-hydroxy-2-methylpyridine-4,5-dicarboxylate to 3-hydroxy-2-methylpyridine-5-carboxylate. the km and kcat were fo ...200717973403
novel macrolide resistance module carried by the incp-1beta resistance plasmid prsb111, isolated from a wastewater treatment plant.the macrolide resistance plasmid prsb111 was isolated from bacteria residing in the final effluents of a wastewater treatment plant. the 47-kb plasmid confers resistance to azithromycin, clarithromycin, erythromycin, roxithromycin, and tylosin when it is carried by pseudomonas sp. strain b13 and is very similar to prototype incp-1beta plasmid pb3, which was previously isolated from an activated-sludge bacterial community of a wastewater treatment plant. the two plasmids differ in their accessory ...200717101677
a genome-scale metabolic reconstruction of pseudomonas putida kt2440: ijn746 as a cell factory.pseudomonas putida is the best studied pollutant degradative bacteria and is harnessed by industrial biotechnology to synthesize fine chemicals. since the publication of p. putida kt2440's genome, some in silico analyses of its metabolic and biotechnology capacities have been published. however, global understanding of the capabilities of p. putida kt2440 requires the construction of a metabolic model that enables the integration of classical experimental data along with genomic and high-through ...200818793442
variability in in vitro macrophage activation by commercially diverse bulk echinacea plant material is predominantly due to bacterial lipoproteins and lipopolysaccharides.we previously reported that the majority of in vitro monocyte/macrophage activation exhibited by extracts of echinacea and other botanicals depends upon bacterial lipopolysaccharides and braun-type bacterial lipoproteins. we determined the contribution made by these bacterial components to the overall immune-enhancing activity detected in e. purpurea and e. angustifolia bulk root and aerial material obtained from six major growers/suppliers in north america. substantial variation in activity (up ...200818942831
crystal structure of a carbonyl reductase from candida parapsilosis with anti-prelog stereospecificity.a novel short-chain (s)-1-phenyl-1,2-ethanediol dehydrogenase (scr) from candida parapsilosis exhibits coenzyme specificity for nadph over nadh. it catalyzes an anti-prelog type reaction to reduce 2-hydroxyacetophenone into (s)-1-phenyl-1,2-ethanediol. the coding gene was overexpressed in escherichia coli and the purified protein was crystallized. the crystal structure of the apo-form was solved to 2.7 a resolution. this protein forms a homo-tetramer with a broken 2-2-2 symmetry. the overall fol ...200818566346
arsenic accumulation by pseudomonas stutzeri and its response to some thiol chelators.the aim of this study is to examine arsenic accumulation by pseudomonas stutzeri and its response to some thiol chelators, dmps and miadmsa.200819568912
the plant-associated bacterium stenotrophomonas rhizophila expresses a new enzyme for the synthesis of the compatible solute glucosylglycerol.the rhizobacterium stenotrophomonas rhizophila accumulates the compatible solutes glucosylglycerol (gg) and trehalose under salt stress conditions. the complete gene for the gg synthesis enzyme was cloned and sequenced. this enzyme from s. rhizophila represented a novel fusion protein composed of a putative c-terminal gg-phosphate synthase domain and an n-terminal putative gg-phosphate phosphatase domain, which was named ggpps. a similar gene was cloned from pseudomonas sp. strain oa146. the ggp ...200818586931
poly-3-hydroxybutyrate synthase from the periplasm of escherichia coli.this is the first report of a poly-3-hydroxybutyrate (phb) synthase in escherichia coli. the enzyme was isolated from the periplasm using ammonium sulfate fractionation, hydrophobic, and size-exclusion chromatography and identified by lc/ms/ms as ydcs, a component of a putative abc transporter. green fluorescent protein-tagged ydcs, purified by 2d native gel electrophoresis, also exhibited phb synthase activity. optimal conditions for enzyme activity were 37 degrees c, ph 6.8-7.5, 100 mm kcl. k( ...200818640095
structure of a sigma28-regulated nonflagellar virulence protein from campylobacter jejuni.campylobacter jejuni, a gram-negative motile bacterium, is a leading cause of human gastrointestinal infections. although the mechanism of c.jejuni-mediated enteritis appears to be multifactorial, flagella play complex roles in the virulence of this human pathogen. cj0977 is a recently identified virulence factor in c. jejuni and is expressed by a sigma(28) promoter that controls late genes in the flagellar regulon. a cj0977 mutant strain is fully motile but significantly reduced in the invasion ...200818835274
the 1.6 a crystal structure of mycobacterium smegmatis mshc: the penultimate enzyme in the mycothiol biosynthetic pathway.mycobacterium smegmatis mshc catalyzes the atp-dependent condensation of glcn-ins and l-cysteine to form l-cys-glcn-ins, the penultimate step in mycothiol biosynthesis. attempts to crystallize the native, full-length mshc have been unsuccessful. however, incubation of the enzyme with the cysteinyl adenylate analogue, 5'-o-[n-(l-cysteinyl)-sulfamonyl]adenosine (csa), followed by a 24-h limited trypsin proteolysis yielded an enzyme preparation that readily crystallized. the three-dimensional struc ...200819053270
a modeling study by response surface methodology and artificial neural network on culture parameters optimization for thermostable lipase production from a newly isolated thermophilic geobacillus sp. strain arm.thermostable bacterial lipases occupy a place of prominence among biocatalysts owing to their novel, multifold applications and resistance to high temperature and other operational conditions. the capability of lipases to catalyze a variety of novel reactions in both aqueous and nonaqueous media presents a fascinating field for research, creating interest to isolate novel lipase producers and optimize lipase production. the most important stages in a biological process are modeling and optimizat ...200819105837
anenpi: identification and annotation of analogous enzymes.enzymes are responsible for the catalysis of the biochemical reactions in metabolic pathways. analogous enzymes are able to catalyze the same reactions, but they present no significant sequence similarity at the primary level, and possibly different tertiary structures as well. they are thought to have arisen as the result of independent evolutionary events. a detailed study of analogous enzymes may reveal new catalytic mechanisms, add information about the origin and evolution of biochemical pa ...200819091081
performance of a yeast-mediated biological fuel cell.saccharomyces cerevisiae present in common baker's yeast was used in a microbial fuel cell in which glucose was the carbon source. methylene blue was used as the electronophore in the anode compartment, while potassium ferricyanide and methylene blue were tested as electron acceptors in the cathode compartment. microbes in a mediator-free environment were used as the control. the experiment was performed in both open and closed circuit configurations under different loads ranging from 100 komega ...200819325724
distribution of bacterial keratitis and emerging resistance to antibiotics in china from 2001 to 2004.to study on the distribution of bacterial keratitis isolates and the resistance to antibiotics in china from 2001 to 2004.200819668756
function-biased choice of additives for optimization of protein crystallization - the case of the putative thioesterase pa5185 from pseudomonas aeruginosa pao1.the crystal structure of pa5185, a putative thioesterase from pseudomonas aeruginosa strain pao1, was solved using multi-wavelength anomalous diffraction to 2.4 a. analysis of the structure and information about the putative function of the protein were used to optimize crystallization conditions. the crystal growth was optimized by applying additives with chemical similarity to a fragment of a putative pa5185 substrate (coa or its derivative). using new crystallization conditions containing thi ...200819898606
sub-grouping and sub-functionalization of the rifin multi-copy protein family.parasitic protozoans possess many multicopy gene families which have central roles in parasite survival and virulence. the number and variability of members of these gene families often make it difficult to predict possible functions of the encoded proteins. the families of extra-cellular proteins that are exposed to a host immune response have been driven via immune selection to become antigenically variant, and thereby avoid immune recognition while maintaining protein function to establish a ...200818197962
functional role of the additional domains in inulosucrase (isla) from leuconostoc citreum cw28.inulosucrase (isla) from leuconostoc citreum cw28 belongs to a new subfamily of multidomain fructosyltransferases (ftfs), containing additional domains from glucosyltransferases. it is not known what the function of the additional domains in this subfamily is.200818237396
action for child survival: elimination of haemophilus influenzae type b meningitis in uganda.to guide immunization policy, we determined the public health benefit of introducing haemophilus influenzae type b (hib) vaccine in uganda and estimated the vaccine effectiveness.200818438518
the majority of in vitro macrophage activation exhibited by extracts of some immune enhancing botanicals is due to bacterial lipoproteins and lipopolysaccharides.we have identified potent monocyte/macrophage activating bacterial lipoproteins within commonly used immune enhancing botanicals such as echinacea, american ginseng and alfalfa sprouts. these bacterial lipoproteins, along with lipopolysaccharides, were substantially more potent than other bacterially derived components when tested in in vitro monocyte/macrophage activation systems. in experiments using raw 264.7 and mouse peritoneal macrophages the majority (85-98%) of the activity within extrac ...200818486914
the binary protein interactome of treponema pallidum--the syphilis spirochete.protein interaction networks shed light on the global organization of proteomes but can also place individual proteins into a functional context. if we know the function of bacterial proteins we will be able to understand how these species have adapted to diverse environments including many extreme habitats. here we present the protein interaction network for the syphilis spirochete treponema pallidum which encodes 1,039 proteins, 726 (or 70%) of which interact via 3,649 interactions as revealed ...200818509523
identification and characterization of bacterial cutinase.cutinase, which exists in both fungi and bacteria, catalyzes the cleavage of the ester bonds of cutin. fungal cutinases have been extensively studied, however, reports on bacterial cutinases have been limited due to the lack of knowledge concerning the identity of their open reading frames. in the present study, the cutinase from thermobifida fusca was induced by cutin and purified to homogeneity by following p-nitrophenyl butyrate hydrolyzing activity. peptide mass fingerprinting analysis of th ...200818658138
a novel transposon, tn6009, composed of a tn916 element linked with a staphylococcus aureus mer operon.the aim of this study was to characterize a novel conjugative transposon tn6009 composed of a tn916 linked to a staphylococcus aureus mer operon in representative gram-positive and gram-negative bacteria isolated in nigeria and portugal.200818583328
genes and enzymes of azetidine-2-carboxylate metabolism: detoxification and assimilation of an antibiotic.l-(-)-azetidine-2-carboxylate (ac) is a toxic, natural product analog of l-proline. this study revealed the genes and biochemical strategy employed by pseudomonas sp. strain a2c to detoxify and assimilate ac as its sole nitrogen source. the gene region from pseudomonas sp. strain a2c required for detoxification was cloned into escherichia coli and sequenced. the 7.0-kb region contained eight identifiable genes. four encoded putative transporters or permeases for gamma-amino acids or drugs. anoth ...200818487339
the transcriptional repressor protein nsrr senses nitric oxide directly via a [2fe-2s] cluster.the regulatory protein nsrr, a member of the rrf2 family of transcription repressors, is specifically dedicated to sensing nitric oxide (no) in a variety of pathogenic and non-pathogenic bacteria. it has been proposed that no directly modulates nsrr activity by interacting with a predicted [fe-s] cluster in the nsrr protein, but no experimental evidence has been published to support this hypothesis. here we report the purification of nsrr from the obligate aerobe streptomyces coelicolor. we demo ...200818989365
a novel caffeine dehydrogenase in pseudomonas sp. strain cbb1 oxidizes caffeine to trimethyluric acid.a unique heterotrimeric caffeine dehydrogenase was purified from pseudomonas sp. strain cbb1. this enzyme oxidized caffeine to trimethyluric acid stoichiometrically and hydrolytically, without producing hydrogen peroxide. the enzyme was not nad(p)(+) dependent; coenzyme q(0) was the preferred electron acceptor. the enzyme was specific for caffeine and theobromine and showed no activity with xanthine.200817981969
nadh availability limits asymmetric biocatalytic epoxidation in a growing recombinant escherichia coli strain.styrene can efficiently be oxidized to (s)-styrene oxide by recombinant escherichia coli expressing the styrene monooxygenase genes styab from pseudomonas sp. strain vlb120. targeting microbial physiology during whole-cell redox biocatalysis, we investigated the interdependency of styrene epoxidation, growth, and carbon metabolism on the basis of mass balances obtained from continuous two-liquid-phase cultures. full induction of styab expression led to growth inhibition, which could be attenuate ...200818192422
efficient display of active lipase lipb52 with a pichia pastoris cell surface display system and comparison with the lipb52 displayed on saccharomyces cerevisiae cell surface.for industrial bioconversion processes, the utilization of surface-displayed lipase in the form of whole-cell biocatalysts is more advantageous, because the enzymes are displayed on the cell surface spontaneously, regarded as immobilized enzymes.200818221563
survey of bacterial diversity in chronic wounds using pyrosequencing, dgge, and full ribosome shotgun sequencing.chronic wound pathogenic biofilms are host-pathogen environments that colonize and exist as a cohabitation of many bacterial species. these bacterial populations cooperate to promote their own survival and the chronic nature of the infection. few studies have performed extensive surveys of the bacterial populations that occur within different types of chronic wound biofilms. the use of 3 separate16s-based molecular amplifications followed by pyrosequencing, shotgun sanger sequencing, and denatur ...200818325110
novel aromatic ring-hydroxylating dioxygenase genes from coastal marine sediments of patagonia.polycyclic aromatic hydrocarbons (pahs), widespread pollutants in the marine environment, can produce adverse effects in marine organisms and can be transferred to humans through seafood. our knowledge of pah-degrading bacterial populations in the marine environment is still very limited, and mainly originates from studies of cultured bacteria. in this work, genes coding catabolic enzymes from pah-biodegradation pathways were characterized in coastal sediments of patagonia with different levels ...200818366740
biphenyl dioxygenase from an arctic isolate is not cold adapted.biphenyl dioxygenase from the psychrotolerant bacterium pseudomonas sp. strain cam-1 (bpdo(cam-1)) was purified and found to have an apparent k(cat) for biphenyl of 1.1 +/- 0.1 s(-1) (mean +/- standard deviation) at 4 degrees c. in contrast, bpdo(lb400) from the mesophile burkholderia xenovorans lb400 had no detectable activity at this temperature. at 57 degrees c, the half-life of the bpdo(cam-1) oxygenase was less than half that of the bpdo(lb400) oxygenase. nevertheless, bpdo(cam-1) appears t ...200818424535
substrate specificity of a long-chain alkylamine-degrading pseudomonas sp isolated from activated sludge.a bacterium strain bert, which utilizes primary long-chain alkylamines as nitrogen, carbon and energy source, was isolated from activated sludge. this rod-shaped motile, gram-negative strain was identified as a pseudomonas sp. the substrate spectrum of this pseudomonas strain bert includes primary alkylamines with alkyl chains ranging from c(3) to c(18), and dodecyl-1,3-diaminopropane. amines with alkyl chains ranging from 8 to 14 carbons were the preferred substrates. growth on dodecanal, dodec ...200817492358
[in process citation].le pronostic des brûlures est souvent tributaire de complications infectieuses. les objectifs de cette étude préliminaire rétrospective sont une évaluation de la flore microbienne et ses fluctuations selon la durée d'hospitalisation chez les patients du centre des brûlés adultes de annaba (algérie). ce travail porte sur 633 prélèvements microbiologiques positifs obtenus entre juin 2003 (inauguration du service) et décembre 2005. selon le site de prélèvement la répartition est: cutané (78%), hémo ...200821991102
aldehyde oxidase carrying an unusual subunit structure from pseudomonas sp. mx-058.pseudomonas sp. mx-058 produces aldehyde oxidase catalysing glyoxal to glyoxylic acid. two aldehyde oxidases (f10 and f13) were purified to homogeneity from pseudomonas sp. mx-058. f10 and f13 had subunit structures, a heterotetramer and heteropentamer respectively. the n-terminal amino acid sequences of all subunits were highly homologous to amino acid sequences of the putative oxidoreductases of pseudomonas strains. all of these homologous oxidoreductases have a heterotrimer structure consisti ...200821261859
[in process citation].le pseudomonasest un agent pathogène à l'origine d'infections nosocomiales graves dans les centres des brûlés. son opportunisme et sa virulence en font une préoccupation majeure. ce travail se propose d'évaluer la place de cette bactérie dans l'écologie bactérienne locale et d'en apprécier la sensibilité aux antibiotiques. cette étude rétrospective préliminaire porte sur la période de juin 2003 à décembre 2005. elle intéresse l'ensemble des prélèvements bactériologiques ayant pu être réalisés au ...200821991140
structural characterization of a 140 degrees domain movement in the two-step reaction catalyzed by 4-chlorobenzoate:coa ligase.members of the adenylate-forming family of enzymes play a role in the metabolism of halogenated aromatics and of short, medium, and long chain fatty acids, as well as in the biosynthesis of menaquinone, peptide antibiotics, and peptide siderophores. this family includes a subfamily of acyl- and aryl-coa ligases that catalyze thioester synthesis through two half-reactions. a carboxylate substrate first reacts with atp to form an acyl-adenylate. subsequent to the release of the product pp i, the e ...200818620418
versatility of biological non-heme fe(ii) centers in oxygen activation reactions.oxidase and oxygenase enzymes allow the use of relatively unreactive o2 in biochemical reactions. many of the mechanistic strategies used in nature for this key reaction are represented within the 2-histidine-1-carboxylate facial triad family of non-heme fe(ii)-containing enzymes. the open face of the metal coordination sphere opposite the three endogenous ligands participates directly in the reaction chemistry. here, data from several studies are presented showing that reductive o2 activation w ...200818277980
a new classification system for bacterial rieske non-heme iron aromatic ring-hydroxylating oxygenases.rieske non-heme iron aromatic ring-hydroxylating oxygenases (rhos) are multi-component enzyme systems that are remarkably diverse in bacteria isolated from diverse habitats. since the first classification in 1990, there has been a need to devise a new classification scheme for these enzymes because many rhos have been discovered, which do not belong to any group in the previous classification. here, we present a scheme for classification of rhos reflecting new sequence information and interactio ...200818387195
microbial biodiversity and in situ bioremediation of endosulfan contaminated soil.molecular characterization based on 16s rdna gene sequence analysis of bacterial colonies isolated from endosulfan contaminated soil showed the presence of ochrobacterum sp, burkholderia sp, pseudomonas alcaligenes, pseudomonas sp and arthrobacter sp which degraded 57-90% of α-endosulfan and 74-94% of β-endosulfan after 7days. whole cells of pseudomonas sp and pseudomonas alcaligenes showed 94 and 89% uptake of α-isomer and 86 and 89% of β-endosulfan respectively in 120 min. in pseudomonas sp, e ...200823100706
first total synthesis of the potent anticancer natural product dideoxypetrosynol a: preparation of the "skipped" (z)-enediyne moiety by oxidative coupling of homopropargyl phosphonium ylide.dideoxypetrosynol a is a c30 polyacetylenic alcohol with c2 symmetry. the first total synthesis of both enantiomers of the potent anti-cancer natural product (+)- and (-)-dideoxypetrosynol a is reported. the key step is an oxidative coupling of a homopropargyl phosphonium ylide to prepare the "skipped" (z)-enediyne moiety. the natural dideoxypetrosynol a was isolated as a racemic mixture as shown in structure 1. the absolute configurations of the chiral centers are established for the (+)- and ( ...200823519828
neonatal conjunctivitis - a review.ophthalmia neonatorum remains a significant cause of ocular morbidity, blindness and even death in underdeveloped countries. the organisms causing ophthalmia neonatorum are acquired mainly from the mother's birth canal during delivery and a small percentage of cases are acquired by other ways. chlamydia and neisseria are the most common pathogens responsible for the perinatal infection. fortunately in most cases, laboratory studies can identify the causative organism and unlike other form of con ...200825606121
intermediate in the o-o bond cleavage reaction of an extradiol dioxygenase.the reactive oxy intermediate of the catalytic cycle of extradiol aromatic ring-cleaving dioxygenases is formed by binding the catecholic substrate and o2 in adjacent ligand positions of the active site metal [usually fe(ii)]. this intermediate and the following fe(ii)-alkylperoxo intermediate resulting from oxygen attack on the substrate have been previously characterized in a crystal of homoprotocatechuate 2,3-dioxygenase (hpcd). here a subsequent intermediate in which the o-o bond is broken t ...200818826259
pruning nature: biodiversity-derived discovery of novel sodium channel blocking conotoxins from conus bullatus.described herein is a general approach to identify novel compounds using the biodiversity of a megadiverse group of animals; specifically, the phylogenetic lineage of the venomous gastropods that belong to the genus conus ("cone snails"). cone snail biodiversity was exploited to identify three new mu-conotoxins, buiiia, buiiib and buiiic, encoded by the fish-hunting species conus bullatus. buiiia, buiiib and buiiic are strikingly divergent in their amino acid composition compared to previous mu- ...200818950653
pruning nature: biodiversity-derived discovery of novel sodium channel blocking conotoxins from conus bullatus.described herein is a general approach to identify novel compounds using the biodiversity of a megadiverse group of animals; specifically, the phylogenetic lineage of the venomous gastropods that belong to the genus conus ("cone snails"). cone snail biodiversity was exploited to identify three new mu-conotoxins, buiiia, buiiib and buiiic, encoded by the fish-hunting species conus bullatus. buiiia, buiiib and buiiic are strikingly divergent in their amino acid composition compared to previous mu- ...200818950653
mechanism of extradiol aromatic ring-cleaving dioxygenases.the extradiol aromatic ring-cleaving dioxygenases activate molecular oxygen by binding both o(2) and the catecholic substrate to a reduced active site metal, generally fe(ii). progress has been made in understanding the mechanism of this reaction through the combined use of kinetic, computational, biomimetic, structural, and diagnostic chemical approaches. it appears that o(2) is activated by accepting an electron transferred from the substrate through the metal, thereby simultaneously activatin ...200819007887
unconventional serine proteases: variations on the catalytic ser/his/asp triad configuration.serine proteases comprise nearly one-third of all known proteases identified to date and play crucial roles in a wide variety of cellular as well as extracellular functions, including the process of blood clotting, protein digestion, cell signaling, inflammation, and protein processing. their hallmark is that they contain the so-called "classical" catalytic ser/his/asp triad. although the classical serine proteases are the most widespread in nature, there exist a variety of "nonclassical" serine ...200818824507
isolation and preliminary characterization of a o-nitrobenzaldehyde-degrading alcaligenes sp. nd1.this paper reports the isolation and characterization of a new o-nitrobenzaldehyde (onba)-degrading bacterium, alcaligenes sp. nd1. nd1 degraded almost all onba (100 mg l(-1)) in m9 medium within 36 hours. the key enzyme(s) involved in the initial biodegradation was a constitutively intracellular enzyme(s). this bacterium has great potential utility for bioremediation.200824031306
lumbar periradicular abscess mimicking a fragmented lumbar disc herniation : an unusual case.we herein describe the case of a focal spontaneous spinal epidural abscess who was initially diagnosed to have a free fragment of a lumbar disc. a 71-year-old woman presented with history of low back and right leg pain. magnetic resonance imaging suggested a peripherally enhancing free fragment extending down from s1 nerve root axilla. preoperative laboratory investigation showed elevation of c-reactive protein (crp), erythrocyte sedimentation rate (esr) levels. she was taken for surgery and a f ...200819137084
fast quantitative determination of microbial rhamnolipids from cultivation broths by atr-ftir spectroscopy.vibrational spectroscopic techniques are becoming increasingly important and popular because they have the potential to provide rapid and convenient solutions to routine analytical problems. using these techniques, a variety of substances can be characterized, identified and also quantified rapidly.200818840269
"hot cores" in proteins: comparative analysis of the apolar contact area in structures from hyper/thermophilic and mesophilic organisms.a wide variety of stabilizing factors have been invoked so far to elucidate the structural basis of protein thermostability. these include, amongst the others, a higher number of ion-pairs interactions and hydrogen bonds, together with a better packing of hydrophobic residues. it has been frequently observed that packing of hydrophobic side chains is improved in hyperthermophilic proteins, when compared to their mesophilic counterparts. in this work, protein crystal structures from hyper/thermop ...200818312638
redox-linked conformational dynamics in apoptosis-inducing factor.apoptosis-inducing factor (aif) is a bifunctional mitochondrial flavoprotein critical for energy metabolism and induction of caspase-independent apoptosis, whose exact role in normal mitochondria remains unknown. upon reduction with nadh, aif undergoes dimerization and forms tight, long-lived fadh(2)-nad charge-transfer complexes (ctc) that are proposed to be functionally important. to obtain a deeper insight into structure/function relations and redox mechanism of this vitally important protein ...200919447115
16s rrna gene-based analysis of fecal microbiota from preterm infants with and without necrotizing enterocolitis.neonatal necrotizing enterocolitis (nec) is an inflammatory intestinal disorder affecting preterm infants. intestinal bacteria have an important function; however no causative pathogen has been identified. the purpose of this study was to determine if there are differences in microbial patterns that may be critical to the development of this disease. fecal samples from 20 preterm infants, 10 with nec and 10 matched controls (including 4 twin pairs) were obtained from patients in a single site le ...200919369970
aerobic bacterial microflora of broad-snouted caiman (caiman latirostris) oral cavity and cloaca, originating from parque zoológico arruda câmara, paraíba, brazil.the objective of this study was to isolate and identify the aerobic bacterial microflora from the oral cavity mucosa and cloaca's samples, collected from broad-snouted caiman (caiman latirostris), born and bred in captivity at parque zoológico arruda câmara, joão pessoa, paraíba, brazil. the most common bacteria were staphylococcus sp. (14.74%), corynebacterium sp. (13.68%), escherichia coli (13.68%) and shigella sp.(11.58%), and the less common were citrobacter sp. (1.05%), klebsiella pneumonia ...200924031343
conformational dynamics in the acyl-coa synthetases, adenylation domains of non-ribosomal peptide synthetases, and firefly luciferase.the anl superfamily of adenylating enzymes contains acyl- and aryl-coa synthetases, firefly luciferase, and the adenylation domains of the modular non-ribosomal peptide synthetases (nrpss). members of this family catalyze two partial reactions: the initial adenylation of a carboxylate to form an acyl-amp intermediate, followed by a second partial reaction, most commonly the formation of a thioester. recent biochemical and structural evidence has been presented that supports the use by this enzym ...200919610673
accounting for mating pair formation in plasmid population dynamics.plasmids are important vehicles for horizontal gene transfer and rapid adaptation in bacteria, including the spread of antibiotic resistance genes. conjugative transfer of a plasmid from a plasmid-bearing to a plasmid-free bacterial cell requires contact and attachment of the cells followed by plasmid dna transfer prior to detachment. we introduce a system of differential equations for plasmid transfer in well-mixed populations that accounts for attachment, dna transfer, and detachment dynamics. ...200919835890
accounting for mating pair formation in plasmid population dynamics.plasmids are important vehicles for horizontal gene transfer and rapid adaptation in bacteria, including the spread of antibiotic resistance genes. conjugative transfer of a plasmid from a plasmid-bearing to a plasmid-free bacterial cell requires contact and attachment of the cells followed by plasmid dna transfer prior to detachment. we introduce a system of differential equations for plasmid transfer in well-mixed populations that accounts for attachment, dna transfer, and detachment dynamics. ...200919835890
evolution of efficient pathways for degradation of anthropogenic chemicals.anthropogenic compounds used as pesticides, solvents and explosives often persist in the environment and can cause toxicity to humans and wildlife. the persistence of anthropogenic compounds is due to their recent introduction into the environment; microbes in soil and water have had relatively little time to evolve efficient mechanisms for degradation of these new compounds. some anthropogenic compounds are easily degraded, whereas others are degraded very slowly or only partially, leading to a ...200919620997
the preparation of 2-o-[1'-c]arachidonoyl-1-o-stearoyl-sn-glycerol.2-o-arachidonoyl-1-o-stearoyl-sn-glycerol is the most abundant molecular species of the 1,2-diacyl-sn-glycerol signaling lipids in neural tissue. the facile preparation of 2-o-[1'-(14)c]arachidonoyl-1-o-stearoyl-sn-glycerol from 2-o-[1'-(14)c]arachidonoyl-1-o-stearoyl-sn-glycero-3-phosphocholine at a hexane and phosphate buffer interface with phospholipase c was demonstrated on a 20 µci scale in 83% radiochemical yield. the specific activity of the product 2-o-[1'-(14)c]arachidonoyl-1-o-stearoyl ...200921423828
examination of enzymatic h-tunneling through kinetics and dynamics.in recent years, kinetic measurements of isotope effects of enzyme-catalyzed reactions and their temperature dependence led to the development of theoretical models that were used to rationalize the findings. these models suggested that motions at the femto- to picosecond (fs to ps) time scale modulate the environment of the catalyzed reaction. due to the fast nature of motions that directly affect the cleavage of a covalent bond, it is challenging to correlate the enzyme kinetics and dynamics r ...200919621965
fabrication and modeling of dynamic multipolymer nanofibrous scaffolds.aligned nanofibrous scaffolds hold tremendous potential for the engineering of dense connective tissues. these biomimetic micropatterns direct organized cell-mediated matrix deposition and can be tuned to possess nonlinear and anisotropic mechanical properties. for these scaffolds to function in vivo, however, they must either recapitulate the full dynamic mechanical range of the native tissue upon implantation or must foster cell infiltration and matrix deposition so as to enable construct matu ...200919831482
atomic resolution crystal structure of nad(+)-dependent formate dehydrogenase from bacterium moraxella sp. c-1.the crystal structure of the ternary complex of nad+-dependent formate dehydrogenase from the methylotrophic bacterium moraxella sp. c-1 with the cofactor (nad+) and the inhibitor (azide ion) was established at 1.1 a resolution. the complex mimics the structure of the transition state of the enzymatic reaction. the structure was refined with anisotropic displacitalicents parameters for non-hydrogen atoms to a r factor of 13.4%. most of the nitrogen, oxygen, and carbon atoms were distinguished ba ...200922649619
managing corneal disease: focus on suppurative keratitis. 200920212926
taking a corneal scrape and making a diagnosis. 200920212927
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
x-ray structure of ill2, an auxin-conjugate amidohydrolase from arabidopsis thaliana.the plant hormone indole-3-acetic acid (iaa) is the most abundant natural auxin involved in many aspects of plant development and growth. the iaa levels in plants are modulated by a specific group of amidohydrolases from the peptidase m20d family that release the active hormone from its conjugated storage forms. here, we describe the x-ray crystal structure of iaa-amino acid hydrolase iaa-leucine resistantlike gene 2 (ill2) from arabidopsis thaliana at 2.0 a resolution. ill2 preferentially hydro ...200918543330
investigation of atomic level patterns in protein--small ligand interactions.shape complementarity and non-covalent interactions are believed to drive protein-ligand interaction. to date protein-protein, protein-dna, and protein-rna interactions were systematically investigated, which is in contrast to interactions with small ligands. we investigate the role of covalent and non-covalent bonds in protein-small ligand interactions using a comprehensive dataset of 2,320 complexes.200919221587
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
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
constitutive and regulated expression vectors to construct polyphosphate deficient bacteria.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 an exopolyphosphatase (ppx). bacterial cells with polyp deficiencies are impaired in many structural and important cellular functions such as motility, quorum sensing, biofilm formation and virulence. knockout ...200919323822
medical bioremediation of age-related diseases.abstract: catabolic insufficiency in humans leads to the gradual accumulation of a number of pathogenic compounds associated with age-related diseases, including atherosclerosis, alzheimer's disease, and macular degeneration. removal of these compounds is a widely researched therapeutic option, but the use of antibodies and endogenous human enzymes has failed to produce effective treatments, and may pose risks to cellular homeostasis. another alternative is "medical bioremediation," the use of m ...200919358742
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
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