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functional characterization and evaluation of in vitro protective efficacy of murine monoclonal antibodies burk24 and burk37 against burkholderia pseudomallei.burkholderia pseudomallei, the causative agent of melioidosis has been recognized by cdc as a category b select agent. although substantial efforts have been made for development of vaccine molecules against the pathogen, significant hurdles still remain. with no licensed vaccines available and high relapse rate of the disease, there is a pressing need for development of alternate protection strategies. antibody-mediated passive protection is promising in this regard and our primary interest was ...201424614539
lipidblast templates as flexible tools for creating new in-silico tandem mass spectral libraries.tandem mass spectral libraries (ms/ms) are usually built by acquiring experimentally measured mass spectra from chemical reference compounds. we here show the versatility of in-silico or computer generated tandem mass spectra that are directly obtained from compound structures. we use the freely available lipidblast development software to generate 15 000 ms/ms spectra of the glucuronosyldiacylglycerol (glcadg) lipid class, recently discovered for the first time in plants. the generation of such ...201425340521
the dual role of microbes in corrosion.corrosion is the result of a series of chemical, physical and (micro) biological processes leading to the deterioration of materials such as steel and stone. it is a world-wide problem with great societal and economic consequences. current corrosion control strategies based on chemically produced products are under increasing pressure of stringent environmental regulations. furthermore, they are rather inefficient. therefore, there is an urgent need for environmentally friendly and sustainable c ...201425259571
the dual role of microbes in corrosion.corrosion is the result of a series of chemical, physical and (micro) biological processes leading to the deterioration of materials such as steel and stone. it is a world-wide problem with great societal and economic consequences. current corrosion control strategies based on chemically produced products are under increasing pressure of stringent environmental regulations. furthermore, they are rather inefficient. therefore, there is an urgent need for environmentally friendly and sustainable c ...201425259571
a consortium of aggregatibacter actinomycetemcomitans, streptococcus parasanguinis, and filifactor alocis is present in sites prior to bone loss in a longitudinal study of localized aggressive periodontitis.aggregatibacter actinomycetemcomitans-induced localized aggressive periodontitis (lap) in african-american adolescents has been documented but is poorly understood. two thousand fifty-eight adolescents aged 11 to 17 years were screened for their periodontal status and the presence of a. actinomycetemcomitans in their oral cavity. seventy-one a. actinomycetemcomitans-negative and 63 a. actinomycetemcomitans-positive periodontally healthy subjects were enrolled, sampled, examined, and radiographed ...201323784124
enhanced diagnostic yields of bacteremia and candidemia in blood specimens by pcr-electrospray ionization mass spectrometry.a prospective study was performed to determine the value of direct molecular testing of whole blood for detecting the presence of culturable and unculturable bacteria and yeasts in patients with suspected bloodstream infections. a total of 464 adult and pediatric patients with positive blood cultures matched with 442 patients with negative blood cultures collected during the same period were recruited during a 10-month study. pcr amplification coupled with electrospray ionization mass spectromet ...201323966503
pandoraea pulmonicola chronic colonization in a cystic fibrosis patient, france.pandoraea are considered emerging multidrug resistant pathogens in the context of cystic fibrosis. we report herein for the first time the case of a 30-year-old woman with cystic fibrosis, living in france, who was chronically infected with pandoraea pulmonicola and who died of pseudomonas aeruginosa sepsis 3 weeks after bilateral lung transplantation.201325356323
evolution and impact of bacterial drug resistance in the context of cystic fibrosis disease and nosocomial settings.the use of antibiotics is unavoidable in trying to treat acute infections and in the prevention and control of chronic infections. over the years, an ever increasing number of infections has escalated the use of antibiotics, which has necessitated action against an emerging bacterial resistance. there seems to be a continuous acquisition of new resistance mechanisms among bacteria that switch niches between human, animals, and the environment. an antibiotic resistant strain emerges when it acqui ...201324826072
emerging organisms in a tertiary healthcare set up.one-tenth of all infectious diseases are attributable to emerging organisms. as emerging organisms sporadically affect a relatively small percentage of population they are not studied at large. this study was aimed at studying the characteristics of emerging organisms encountered from various clinical samples in an apex tertiary care multispeciality teaching and research hospital.201324843199
emerging organisms in a tertiary healthcare set up.one-tenth of all infectious diseases are attributable to emerging organisms. as emerging organisms sporadically affect a relatively small percentage of population they are not studied at large. this study was aimed at studying the characteristics of emerging organisms encountered from various clinical samples in an apex tertiary care multispeciality teaching and research hospital.201324843199
lysine carboxylation: unveiling a spontaneous post-translational modification.the carboxylation of lysine residues is a post-translational modification (ptm) that plays a critical role in the catalytic mechanisms of several important enzymes. it occurs spontaneously under certain physicochemical conditions, but is difficult to detect experimentally. its full impact is unknown. in this work, the signature microenvironment of lysine-carboxylation sites has been characterized. in addition, a computational method called predictor of lysine carboxylation (prelyscar) for the de ...201324419378
lysine carboxylation: unveiling a spontaneous post-translational modification.the carboxylation of lysine residues is a post-translational modification (ptm) that plays a critical role in the catalytic mechanisms of several important enzymes. it occurs spontaneously under certain physicochemical conditions, but is difficult to detect experimentally. its full impact is unknown. in this work, the signature microenvironment of lysine-carboxylation sites has been characterized. in addition, a computational method called predictor of lysine carboxylation (prelyscar) for the de ...201324419378
direct bacterial identification in positive blood cultures by use of two commercial matrix-assisted laser desorption ionization-time of flight mass spectrometry systems.matrix-assisted laser desorption ionization-time of flight mass spectrometry (maldi-tof ms) for the identification of bacteria and fungi was recently introduced in microbiology laboratories. this technology could greatly improve the clinical management of patients and guidance for chemotherapy. in this study, we used a commercial maldi sepsityper extraction method to evaluate the performance of two commercial maldi-tof ms systems, the vitek ms ivd (biomérieux) and the microflex lt biotyper (bruk ...201323515548
direct production of organic acids from starch by cell surface-engineered corynebacterium glutamicum in anaerobic conditions.we produced organic acids, including lactate and succinate, directly from soluble starch under anaerobic conditions using high cell-density cultures of corynebacterium glutamicum displaying α-amylase (amya) from streptococcus bovis 148 on the cell surface. notably, reactions performed under anaerobic conditions at 35 and 40°c, which are higher than the optimal growth temperature of 30°c, showed 32% and 19%, respectively, higher productivity of the organic acids lactate, succinate, and acetate co ...201324342107
quorum sensing and self-quorum quenching in the intracellular pathogen brucellamelitensis.brucella quorum sensing has been described as an important regulatory system controlling crucial virulence determinants such as the virb type iv secretion system and the flagellar genes. however, the basis of quorum sensing, namely the production of autoinducers in brucella has been questioned. here, we report data obtained from the use of a genetic tool allowing the in situ detection of long-chain n-acyl-homoserine lactones (ahl) activity at single bacterium level in brucella melitensis. these ...201324349302
single-molecule resolution of protein structure and interfacial dynamics on biomaterial surfaces.a method was developed to monitor dynamic changes in protein structure and interfacial behavior on surfaces by single-molecule förster resonance energy transfer. this method entails the incorporation of unnatural amino acids to site-specifically label proteins with single-molecule förster resonance energy transfer probes for high-throughput dynamic fluorescence tracking microscopy on surfaces. structural changes in the enzyme organophosphorus hydrolase (oph) were monitored upon adsorption to fus ...201324235137
structural and enzymatic characterization of the phosphotriesterase ophc2 from pseudomonas pseudoalcaligenes.organophosphates (ops) are neurotoxic compounds for which current methods of elimination are unsatisfactory; thus bio-remediation is considered as a promising alternative. here we provide the structural and enzymatic characterization of the recently identified enzyme isolated from pseudomonas pseudoalcaligenes dubbed ophc2. ophc2 belongs to the metallo-β-lactamase superfamily and exhibits an unusual thermal resistance and some op degrading abilities.201324223749
isolation and screening of polyhydroxyalkanoates producing bacteria from pulp, paper, and cardboard industry wastes.background. polyhydroxyalkanoates (phas) are storage materials that accumulate by various bacteria as energy and carbon reserve materials. they are biodegradable, environmentally friendly, and also biocompatible bioplastics. unlike petrochemical-based plastics that take several decades to fully degrade, phas can be completely degraded within a year by variety of microorganisms into co2 and water. in the present study, we aim to utilize pulp, paper, and cardboard industry sludge and waste water f ...201324288534
a treatment plant receiving waste water from multiple bulk drug manufacturers is a reservoir for highly multi-drug resistant integron-bearing bacteria.the arenas and detailed mechanisms for transfer of antibiotic resistance genes between environmental bacteria and pathogens are largely unclear. selection pressures from antibiotics in situations where environmental bacteria and human pathogens meet are expected to increase the risks for such gene transfer events. we hypothesize that waste-water treatment plants (wwtps) serving antibiotic manufacturing industries may provide such spawning grounds, given the high bacterial densities present there ...201324204801
crystallization and preliminary x-ray diffraction analysis of the lactonase vmolac from vulcanisaeta moutnovskia.phosphotriesterase-like lactonases (plls) are native lactonases that are capable of hydrolyzing lactones such as aliphatic lactones or acyl-homoserine lactones, which are involved in bacterial quorum sensing. previously characterized plls are moreover endowed with a promiscuous phosphotriesterase activity and are therefore able to detoxify organophosphate insecticides. a novel pll representative, dubbed vmolac, has been identified from the hyperthermophilic crenarchaeon vulcanisaeta moutnovskia. ...201324192357
draft genome sequence of the dimorphic prosthecate bacterium brevundimonas abyssalis tar-001t.we report the 3.0-mb draft genome sequence of brevundimonas abyssalis strain tar-001(t), isolated from deep-sea floor sediment. the draft genome sequence of strain tar-001(t) consists of 2,979,700 bp in 128 contigs, with a g+c content of 68.2%, 2,946 potential coding sequences (cds), 3 rrnas, and 41 trnas.201324136847
evaluation of the hb&l system for the microbiological screening of storage medium for organ-cultured corneas.aims. to compare hb&l and bactec systems for detecting the microorganisms contaminating the corneal storage liquid preserved at 31°c. methods. human donor corneas were stored at 4°c followed by preservation at 31°c. samples of the storage medium were inoculated in bactec peds plus/f (aerobic microorganisms), bactec plus anaerobic/f (anaerobic microorganisms), and hb&l bottles. the tests were performed (a) after six days of storage, (b) end of storage, and (c) after 24 hours of preservation in de ...201324069532
mixotrophic haptophytes are key bacterial grazers in oligotrophic coastal waters.grazing rate estimates indicate that approximately half of the bacterivory in oligotrophic oceans is due to mixotrophic flagellates (mfs). however, most estimations have considered algae as a single group. here we aimed at opening the black-box of the phytoflagellates (pfs) <20 μm. haptophytes, chlorophytes, cryptophytes and pigmented dinoflagellates were identified using fluorescent in situ hybridization or by standard 4',6-diamidino-2-phenylindole staining. their fluctuations in abundance, cel ...201323924785
mixotrophic haptophytes are key bacterial grazers in oligotrophic coastal waters.grazing rate estimates indicate that approximately half of the bacterivory in oligotrophic oceans is due to mixotrophic flagellates (mfs). however, most estimations have considered algae as a single group. here we aimed at opening the black-box of the phytoflagellates (pfs) <20 μm. haptophytes, chlorophytes, cryptophytes and pigmented dinoflagellates were identified using fluorescent in situ hybridization or by standard 4',6-diamidino-2-phenylindole staining. their fluctuations in abundance, cel ...201323924785
hydrogen atoms in protein structures: high-resolution x-ray diffraction structure of the dfpase.hydrogen atoms represent about half of the total number of atoms in proteins and are often involved in substrate recognition and catalysis. unfortunately, x-ray protein crystallography at usual resolution fails to access directly their positioning, mainly because light atoms display weak contributions to diffraction. however, sub-ångstrom diffraction data, careful modeling and a proper refinement strategy can allow the positioning of a significant part of hydrogen atoms.201323915572
molecular engineering of organophosphate hydrolysis activity from a weak promiscuous lactonase template.rapid evolution of enzymes provides unique molecular insights into the remarkable adaptability of proteins and helps to elucidate the relationship between amino acid sequence, structure, and function. we interrogated the evolution of the phosphotriesterase from pseudomonas diminuta (pdpte), which hydrolyzes synthetic organophosphates with remarkable catalytic efficiency. pte is thought to be an evolutionarily "young" enzyme, and it has been postulated that it has evolved from members of the phos ...201323837603
the structure of microbial community and degradation of diatoms in the deep near-bottom layer of lake baikal.insight into the role of bacteria in degradation of diatoms is important for understanding the factors and components of silica turnover in aquatic ecosystems. using microscopic methods, it has been shown that the degree of diatom preservation and the numbers of diatom-associated bacteria in the surface layer of bottom sediments decrease with depth; in the near-bottom water layer, the majority of bacteria are associated with diatom cells, being located either on the cell surface or within the ce ...201323560063
a new class of plant lipid is essential for protection against phosphorus depletion.phosphorus supply is a major factor responsible for reduced crop yields. as a result, plants utilize various adaptive mechanisms against phosphorus depletion, including lipid remodelling. here we report the involvement of a novel plant lipid, glucuronosyldiacylglycerol, against phosphorus depletion. lipidomic analysis of arabidopsis plants cultured in phosphorus-depleted conditions revealed inducible accumulation of glucuronosyldiacylglycerol. investigation using a series of sulfolipid sulfoquin ...201323443538
environmental dynamics as a structuring factor for microbial carbon utilization in a subtropical coastal lagoon.laguna de rocha belongs to a series of shallow coastal lagoons located along south america. it is periodically connected to the sea through a sand bar, exhibiting a hydrological cycle where physicochemical and biological gradients are rapidly established and destroyed. its most frequent state is the separation of a northern zone with low salinity, high turbidity and nutrient load, and extensive macrophyte growth, and a southern zone with higher salinity and light penetration, and low nutrient co ...201323423262
the effect of conformational variability of phosphotriesterase upon n-acyl-l-homoserine lactone and paraoxon binding: insights from molecular dynamics studies.the organophosphorous hydrolase (pte) from brevundimonas diminuta is capable of degrading extremely toxic organophosphorous compounds with a high catalytic turnover and broad substrate specificity. although the natural substrate for pte is unknown, its loop remodeling (loop 7-2/h254r) led to the emergence of a homoserine lactonase (hsl) activity that is undetectable in pte (kcat/km values of up to 2 × 10(4)), with only a minor decrease in pte paraoxonase activity. in this study, homology modelin ...201324352010
production of nano zinc, zinc sulphide and nanocomplex of magnetite zinc oxide by brevundimonas diminuta and pseudomonas stutzeri.zno (zincite) nanoparticle has many industrial applications and is mostly produced by chemical reactions, usually prepared by decomposition of zinc acetate or hot-injection and heating-up method. synthesis of semi-conductor nanoparticles such as zns (sphalerite) by ultrasonic was previously reported. in this work, high-zinc tolerant bacteria were isolated and used for nano zinc production. among all isolated microorganisms, a gram negative bacterium which was identified as brevundimonas diminuta ...201324206770
engineering v-type nerve agents detoxifying enzymes using computationally focused libraries.vx and its russian (rvx) and chinese (cvx) analogues rapidly inactivate acetylcholinesterase and are the most toxic stockpile nerve agents. these organophosphates have a thiol leaving group with a choline-like moiety and are hydrolyzed very slowly by natural enzymes. we used an integrated computational and experimental approach to increase brevundimonas diminuta phosphotriesterase's (pte) detoxification rate of v-agents by 5000-fold. computational models were built of the complex between pte and ...201324041203
high-level expression of glutaryl-7-aminocephalosporanic acid acylase from pseudomonas diminuta nk703 in escherichia coli by combined optimization strategies.in this work, a glutaryl-7-aminocephalosporanic acid acylase (gla) coding gene was cloned from pseudomonas diminuta nk703 which was screened from oilfield. the concerted effects of the expression system, inducing condition and culture medium on the expression of nk703 gla in e. coli were firstly investigated. the best combination was the recombinant e. coli strain of pet-28a+gla/bl21(de3) with 2.0% (w/v) lactose inducing in yt medium at 25°c. then, by optimizing the components of culture medium, ...201323994688
expression and subcellular localization of organophosphate hydrolase in acephate-degrading pseudomonas sp. strain ind01 and its use as a potential biocatalyst for elimination of organophosphate insecticides.organophosphate hydrolase (oph), the product of an organophosphate-degrading (opd) gene cloned from brevundimonas diminuta, hydrolyses the triester linkage found in neurotoxic organophosphate (op) insecticides and nerve agents. despite the fact that ophs have a broad substrate range, op compounds with a p-s linkage, such as insecticides like acephate, are poor substrates for the enzyme. expression of oph in acephate-utilizing pseudomonas sp. ind01 generated a live biocatalyst capable of degradin ...201323574004
catalytic biofilms on structured packing for the production of glycolic acid.while structured packing modules are known to be efficient for surface wetting and gas-liquid exchange in abiotic surface catalysis, this model study explores structured packing as a growth surface for catalytic biofilms. microbial biofilms have been proposed as self-immobilized and self-regenerating catalysts for the production of chemicals. a concern is that the complex and dynamic nature of biofilms may cause fluctuations in their catalytic performance over time or may affect process reproduc ...201323412062
evidence for grow-through penetration of 0.2-μm-pore-size filters by serratia marcescens and brevundimonas diminuta.we find that both brevundimonas diminuta and serratia marcescens can grow through sterilizing grade filter membranes of different membrane polymer compositions. although this passage does not occur on a consistent basis, generation of "grow-through positive" results indicate that grow-through can occur stochastically at basal levels. this observation argues that the following risk mitigation strategies during pharmaceutical aseptic processing are warranted: minimization of processing times, and ...201323385852
pleuritis due to brevundimonas diminuta in a previously healthy man.brevundimonas diminuta is rarely associated with invasive infections. we report the case of a previously healthy young man with pleural effusion, in which b. diminuta was recovered but incorrectly identified as kingella kingae when it was freshly isolated. consequently, the misidentification resulted in initial treatment failure. the correct identification was achieved through further incubation, sequencing of the 16s rrna gene and ms.201323180480
brevundimonas abyssalis sp. nov., a dimorphic prosthecate bacterium isolated from deep-subsea floor sediment.a novel gram-negative, aerobic, psychrotolerant, alkali-tolerant, heterotrophic and dimorphic prosthecate bacterium, designated strain tar-001(t), was isolated from deep-sea floor sediment in japan. cells of this strain had a dimorphic life cycle and developed an adhesive stalk at a site not coincident with the centre of the cell pole, and the other type of cell, a swarm cell, had a polar flagellum. colonies were glossy, viscous and yellowish-white in colour. the temperature, ph and salt concent ...201323041635
identification and characterization of novel catalytic bioscavengers of organophosphorus nerve agents.in an effort to discover novel catalytic bioscavengers of organophosphorus (op) nerve agents, cell lysates from a diverse set of bacterial strains were screened for their capacity to hydrolyze the op nerve agents vx, vr, and soman (gd). the library of bacterial strains was identified using both random and rational approaches. specifically, two representative strains from eight categories of extremophiles were chosen at random. for the rational approach, the protein sequence of organophosphorus h ...201323041042
a further biochemical characterization of drpll the thermophilic lactonase from deinococcus radiodurans.recently, the cloning of the orf dr0930 from deinococcus radiodurans displaying, as primary activity, a lactonase activity and a promiscuous phosphotriesterase activity was reported. the crystal structure of the resulting recombinant enzyme has been solved, and many mutants have been generated in order to increase the phosphotriesterase activity, with the aim to reach the level of activity of the related ppte from pseudomonas diminuta. in this paper we report an additional biochemical characteri ...201322789107
hydrolysis of phosphotriesters: a theoretical analysis of the enzymatic and solution mechanisms.a theoretical study on the alkaline hydrolysis of paraoxon, one of the most popular organophosphorus pesticides, in aqueous solution and in the active site of pseudomonas diminuta phosphotriesterase (pte) is presented. simulations by means of hybrid quantum mechanics/molecular mechanics (qm/mm) potentials show that the hydrolysis of paraoxon takes place through an a(n)d(n) or associative mechanism both in solution and in the active site of pte. the results correctly reproduce the magnitude of th ...201222745111
molecular cloning of brevundimonas diminuta for efficacy assessment of reverse osmosis devices.brevundimonas diminuta is the test organism specified in the united states environmental protection agency's (usepa) reverse osmosis (ro) treatment device verification protocol. as non-selective growth medium is employed, enumeration of b. diminuta may be impaired due to interference by indigenous heterotrophic bacteria. thus the microbial removal capability of the filtration system may be incorrectly assessed. as these treatment devices are used in emergency situations, the health of the public ...201222717753
catalytic mechanisms for phosphotriesterases.phosphotriesters are one class of highly toxic synthetic compounds known as organophosphates. wide spread usage of organophosphates as insecticides as well as nerve agents has lead to numerous efforts to identify enzymes capable of detoxifying them. a wide array of enzymes has been found to have phosphotriesterase activity including phosphotriesterase (pte), methyl parathion hydrolase (mph), organophosphorus acid anhydrolase (opaa), diisopropylfluorophosphatase (dfp), and paraoxonase 1 (pon1). t ...201222561533
catalytic mechanisms for phosphotriesterases.phosphotriesters are one class of highly toxic synthetic compounds known as organophosphates. wide spread usage of organophosphates as insecticides as well as nerve agents has lead to numerous efforts to identify enzymes capable of detoxifying them. a wide array of enzymes has been found to have phosphotriesterase activity including phosphotriesterase (pte), methyl parathion hydrolase (mph), organophosphorus acid anhydrolase (opaa), diisopropylfluorophosphatase (dfp), and paraoxonase 1 (pon1). t ...201222561533
application of a battery of biotests for the determination of leachate toxicity to bacteria and invertebrates from sewage sludge-amended soil.the objective of the study was to determine the leachates toxicity from sewage sludge-amended soils (sandy and loamy). samples originated from a plot experiment realized over a period of 29 months. two types of soil were fertilized with sewage sludges at the dose of 3 % (90 t/ha). soil samples were taken after 0, 7, 17, and 29 months from the application of sewage sludges. leachates were obtained according to the en 12457-2 protocol. the following commercial tests were applied for the estimation ...201223132406
application of a battery of biotests for the determination of leachate toxicity to bacteria and invertebrates from sewage sludge-amended soil.the objective of the study was to determine the leachates toxicity from sewage sludge-amended soils (sandy and loamy). samples originated from a plot experiment realized over a period of 29 months. two types of soil were fertilized with sewage sludges at the dose of 3 % (90 t/ha). soil samples were taken after 0, 7, 17, and 29 months from the application of sewage sludges. leachates were obtained according to the en 12457-2 protocol. the following commercial tests were applied for the estimation ...201223132406
microbes and asthma: the missing cellular and molecular links.in this review, we describe the 'state-of-the-art' in our knowledge of asthma and what gaps exist, which can be exploited in the future for effective translation of our knowledge from the bench or population studies to diagnosis and therapy.201222113000
the lung tissue microbiome in chronic obstructive pulmonary disease.based on surface brushings and bronchoalveolar lavage fluid, hilty and coworkers demonstrated microbiomes in the human lung characteristic of asthma and chronic obstructive pulmonary disease (copd), which have now been confirmed by others.201222427533
quorum quenching revisited--from signal decays to signalling confusion.in a polymicrobial community, while some bacteria are communicating with neighboring cells (quorum sensing), others are interrupting the communication (quorum quenching), thus creating a constant arms race between intercellular communication. in the past decade, numerous quorum quenching enzymes have been found and initially thought to inactivate the signalling molecules. though this is widely accepted, the actual roles of these quorum quenching enzymes are now being uncovered. recent evidence e ...201222666051
crystallization and preliminary x-ray diffraction analysis of the organophosphorus hydrolase ophc2 from pseudomonas pseudoalcaligenes.enzymes that are capable of degrading neurotoxic organophosphorus compounds are of increasing interest because of the lack of efficient and clean methods for their removal. recently, a novel organophosphorus hydrolase belonging to the metallo-β-lactamase superfamily was identified and isolated from the mesophilic bacterium pseudomonas pseudoalcaligenes. this enzyme, named ophc2, is endowed with significant thermal and ph stability, making it an appealing candidate for engineering studies to deve ...201223295492
crystallization and preliminary x-ray diffraction analysis of the organophosphorus hydrolase ophc2 from pseudomonas pseudoalcaligenes.enzymes that are capable of degrading neurotoxic organophosphorus compounds are of increasing interest because of the lack of efficient and clean methods for their removal. recently, a novel organophosphorus hydrolase belonging to the metallo-β-lactamase superfamily was identified and isolated from the mesophilic bacterium pseudomonas pseudoalcaligenes. this enzyme, named ophc2, is endowed with significant thermal and ph stability, making it an appealing candidate for engineering studies to deve ...201223295492
multiple mechanisms contribute to lateral transfer of an organophosphate degradation (opd) island in sphingobium fuliginis atcc 27551.the complete sequence of ppdl2 (37,317 bp), an indigenous plasmid of sphingobium fuliginis atcc 27551 that encodes genes for organophosphate degradation (opd), revealed the existence of a site-specific integrase (int) gene with an attachment site attp, typically seen in integrative mobilizable elements (ime). in agreement with this sequence information, site-specific recombination was observed between ppdl2 and an artificial plasmid having a temperature-sensitive replicon and a cloned attb site ...201223275877
advances in toxicology and medical treatment of chemical warfare nerve agents.organophosphorous (op) nerve agents (nas) are known as the deadliest chemical warfare agents. they are divided into two classes of g and v agents. most of them are liquid at room temperature. nas chemical structures and mechanisms of actions are similar to op pesticides, but their toxicities are higher than these compounds. the main mechanism of action is irreversible inhibition of acetyl choline esterase (ache) resulting in accumulation of toxic levels of acetylcholine (ach) at the synaptic jun ...201223351280
characterisation of the organophosphate hydrolase catalytic activity of ssopox.ssopox is a lactonase endowed with promiscuous phosphotriesterase activity isolated from sulfolobus solfataricus that belongs to the phosphotriesterase-like lactonase family. because of its intrinsic thermal stability, ssopox is seen as an appealing candidate as a bioscavenger for organophosphorus compounds. a comprehensive kinetic characterisation of ssopox has been performed with various phosphotriesters (insecticides) and phosphodiesters (nerve agent analogues) as substrates. we show that sso ...201223139857
why does the g117h mutation considerably improve the activity of human butyrylcholinesterase against sarin? insights from quantum mechanical/molecular mechanical free energy calculations.human butyrylcholinesterase (bche) is recognized as the most promising bioscavenger for organophosphorus (op) warfare nerve agents. the g117h mutant of human bche has been identified as a potential catalytic bioscavenger with a remarkably improved activity against op nerve agents such as sarin, but it still does not satisfy the clinical use. for further design of the higher-activity mutants against op nerve agents, it is essential to understand how the g117h mutation improves the activity. the r ...201223092211
structural and enzymatic characterization of the lactonase sislac from sulfolobus islandicus.a new member of the phosphotriesterase-like lactonases (pll) family from the hyperthermophilic archeon sulfolobus islandicus (sislac) has been characterized. sislac is a native lactonase that exhibits a high promiscuous phosphotriesterase activity. sislac thus represents a promising target for engineering studies, exhibiting both detoxification and bacterial quorum quenching abilities, including human pathogens such as pseudomonas aeruginosa.201223071703
first report of an extensively drug-resistant vim-2 metallo-β-lactamase-producing brevundimonas diminuta clinical isolate.in the literature, only three brevundimonas diminuta environmental isolates carrying metallo-β-lactamase genes were recently published. however, so far, no b. diminuta clinical isolates carrying these carbapenem resistance genes have been described. here we report the first vim-2 metallo-β-lactamase-producing b. diminuta clinical isolate obtained from an immunocompromised patient.201222692741
the ecology of bacterial genes and the survival of the new.much of the observed variation among closely related bacterial genomes is attributable to gains and losses of genes that are acquired horizontally as well as to gene duplications and larger amplifications. the genomic flexibility that results from these mechanisms certainly contributes to the ability of bacteria to survive and adapt in varying environmental challenges. however, the duplicability and transferability of individual genes imply that natural selection should operate, not only at the ...201222900231
lipid body-phagosome interaction in macrophages during infectious diseases: host defense or pathogen survival strategy?phagocytosis of invading microorganisms by specialized cells such as macrophages and neutrophils is a key component of the innate immune response. these cells capture and engulf pathogens and subsequently destroy them in intracellular vacuoles-the phagosomes. pathogen phagocytosis and progression and maturation of pathogen-containing phagosomes, a crucial event to acquire microbicidal features, occurs in parallel with accentuated formation of lipid-rich organelles, termed lipid bodies (lbs), or ...201222792061
purification and characterization of a novel chlorpyrifos hydrolase from cladosporium cladosporioides hu-01.chlorpyrifos is of great environmental concern due to its widespread use in the past several decades and its potential toxic effects on human health. thus, the degradation study of chlorpyrifos has become increasing important in recent years. a fungus capable of using chlorpyrifos as the sole carbon source was isolated from organophosphate-contaminated soil and characterized as cladosporium cladosporioides hu-01 (collection number: cctcc m 20711). a novel chlorpyrifos hydrolase from cell extract ...201222693630
detection of bacteria using fluorogenic dnazymes.outbreaks linked to food-borne and hospital-acquired pathogens account for millions of deaths and hospitalizations as well as colossal economic losses each and every year. prevention of such outbreaks and minimization of the impact of an ongoing epidemic place an ever-increasing demand for analytical methods that can accurately identify culprit pathogens at the earliest stage. although there is a large array of effective methods for pathogen detection, none of them can satisfy all the following ...201222688431
the chemical composition of endotoxin isolated from intestinal strain of desulfovibrio desulfuricans.desulfovibrio desulfuricans anaerobes are constituents of human alimentary tract microflora. there are suggestions that they take part in the pathogenesis of periodontitis and some gastrointestinal inflammatory disorders, such as ulcerative colitis or crohn's disease. endotoxin is one of gram-negative bacteria cellular components that influence these microorganisms pathogenicity. endotoxin is a lipid-polisaccharide heteropolymer consisting of three elements: lipid a, core oligosaccharide, and o- ...201222629175
fluorescence-based rapid detection of microbiological contaminants in water samples.microbiological contamination of process waters is a current issue for pharmaceutical industries. traditional methods require several days to obtain results; therefore, rapid microbiological methods are widely requested to shorten time-to-result. milliflex quantum was developed for the rapid detection and enumeration of microorganisms in filterable samples. it combines membrane filtration to universal fluorescent staining of viable microorganisms. this new alternative method was validated using ...201222623887
identification and characterization of a novel thermostable pyrethroid-hydrolyzing enzyme isolated through metagenomic approach.pyrethroid pesticides are broad-spectrum pest control agents in agricultural production. both agricultural and residential usage is continuing to grow, leading to the development of insecticide resistance in the pest and toxic effects on a number of nontarget organisms. thus, it is necessary to hunt suitable enzymes including hydrolases for degrading pesticide residues, which is an efficient "green" solution to biodegrade polluting chemicals. although many pyrethroid esterases have consistently ...201222409882
origin and evolution of antibiotic resistance: the common mechanisms of emergence and spread in water bodies.the environment, and especially freshwater, constitutes a reactor where the evolution and the rise of new resistances occur. in water bodies such as waste water effluents, lakes, and rivers or streams, bacteria from different sources, e.g., urban, industrial, and agricultural waste, probably selected by intensive antibiotic usage, are collected and mixed with environmental species. this may cause two effects on the development of antibiotic resistances: first, the contamination of water by antib ...201222303296
comprehensive analysis of secondary dental root canal infections: a combination of culture and culture-independent approaches reveals new insights.persistence of microorganisms or reinfections are the main reasons for failure of root canal therapy. very few studies to date have included culture-independent methods to assess the microbiota, including non-cultivable microorganisms. the aim of this study was to combine culture methods with culture-independent cloning methods to analyze the microbial flora of root-filled teeth with periradicular lesions. twenty-one samples from previously root-filled teeth were collected from patients with per ...201223152922
comparative analysis of two phenotypically-similar but genomically-distinct burkholderia cenocepacia-specific bacteriophages.genomic analysis of bacteriophages infecting the burkholderia cepacia complex (bcc) is an important preliminary step in the development of a phage therapy protocol for these opportunistic pathogens. the objective of this study was to characterize kl1 (vb_bces_kl1) and ah2 (vb_bces_ah2), two novel burkholderia cenocepacia-specific siphoviruses isolated from environmental samples.201222676492
factors influencing the microbial composition of metalworking fluids and potential implications for machine operator's lung.hypersensitivity pneumonitis, also known as "machine operator's lung" (mol), has been related to microorganisms growing in metalworking fluids (mwfs), especially mycobacterium immunogenum. we aimed to (i) describe the microbiological contamination of mwfs and (ii) look for chemical, physical, and environmental parameters associated with variations in microbiological profiles. we microbiologically analyzed 180 mwf samples from nonautomotive plants (e.g., screw-machining or metal-cutting plants) i ...201222057869
influence of substrate mineralogy on bacterial mineralization of calcium carbonate: implications for stone conservation.the influence of mineral substrate composition and structure on bacterial calcium carbonate productivity and polymorph selection was studied. bacterial calcium carbonate precipitation occurred on calcitic (iceland spar single crystals, marble, and porous limestone) and silicate (glass coverslips, porous sintered glass, and quartz sandstone) substrates following culturing in liquid medium (m-3p) inoculated with different types of bacteria (myxococcus xanthus, brevundimonas diminuta, and a carbona ...201222447589
characterization of trapped lignin-degrading microbes in tropical forest soil.lignin is often the most difficult portion of plant biomass to degrade, with fungi generally thought to dominate during late stage decomposition. lignin in feedstock plant material represents a barrier to more efficient plant biomass conversion and can also hinder enzymatic access to cellulose, which is critical for biofuels production. tropical rain forest soils in puerto rico are characterized by frequent anoxic conditions and fluctuating redox, suggesting the presence of lignin-degrading orga ...201121559391
comparison of bruker biotyper matrix-assisted laser desorption ionization-time of flight mass spectrometer to bd phoenix automated microbiology system for identification of gram-negative bacilli.we compared the bd phoenix automated microbiology system to the bruker biotyper (version 2.0) matrix-assisted laser desorption ionization-time of flight (maldi-tof) mass spectrometry (ms) system for identification of gram-negative bacilli, using biochemical testing and/or genetic sequencing to resolve discordant results. the bd phoenix correctly identified 363 (83%) and 330 (75%) isolates to the genus and species level, respectively. the bruker biotyper correctly identified 408 (93%) and 360 (82 ...201121209160
assessment of denitrifying bacterial composition in activated sludge.the abundance and structure of denitrifying bacterial community in different activated sludge samples were assessed, where the abundance of denitrifying functional genes showed nirs in the range of 10(4)-10(5), nosz with 10(4)-10(6) and 16s rrna gene in the range 10(9)-10(10) copy number per ml of sludge. the culturable approach revealed pseudomonas sp. and alcaligenes sp. to be numerically high, whereas culture independent method showed betaproteobacteria to dominate the sludge samples. comamon ...201121868215
environmental microbiota represents a natural reservoir for dissemination of clinically relevant metallo-beta-lactamases.a total of 10 metallo-β-lactamase-producing isolates of six different species, including brevundimonas diminuta (n = 3), rhizobium radiobacter (n = 2), pseudomonas monteilii (n = 1), pseudomonas aeruginosa (n = 2), ochrobactrum anthropi (n = 1), and enterobacter ludwigii (n = 1), were detected in the sewage water of a hospital. the presence of bla(vim-13) associated with a tn1721-class 1 integron structure was detected in all but one of the isolates (e. ludwigii, which produced vim-2), and in tw ...201121859934
molecular modeling and conformational analysis of native and refolded viral genome-linked protein of cardamom mosaic virus.the viral genome-linked protein (vpg) of potyviruses is covalently attached to the 5' end of the genomic rna. towards biophysical characterization, the vpg coding region of cardamom mosaic virus (cdmv) was amplified from the cdna and expressed in e. coli. most of the expressed vpg aggregated as inclusion bodies that were solubilized with urea and refolded with l-arginine hydrochloride. the various forms of cdmv vpg (native, denatured and refolded) were purified and the conformational variations ...201122165292
evaluation of microorganisms cultured from injured and repressed tissue regeneration sites in endangered giant aquatic ozark hellbender salamanders.investigation into the causes underlying the rapid, global amphibian decline provides critical insight into the effects of changing ecosystems. hypothesized and confirmed links between amphibian declines, disease, and environmental changes are increasingly represented in published literature. however, there are few long-term amphibian studies that include data on population size, abnormality/injury rates, disease, and habitat variables to adequately assess changes through time. we cultured and i ...201122205979
Tn125-related acquisition of blaNDM-like genes in Acinetobacter baumannii.A multidrug-resistant Acinetobacter baumannii isolate recovered from a patient hospitalized in Switzerland after a transfer from Serbia produced the NDM-1 carbapenemase. The bla(NDM-1) gene was part of a chromosomally-located Tn125 composite transposon bracketed by two copies of the same insertion sequence ISAba125. This transposon was also associated to the acquisition and the expression of the bla(NDM-2) gene in an A. baumannii isolate in Germany. Tn125 appears to be the main vehicle for disse ...201122143526
Development of a protocol for supercritical carbon dioxide extraction of ubiquinone-10 from dried biomass of Pseudomonas diminuta.Ubiquinone (Coenzyme Q10, CoQ10), a yellow-to-orange-colored lipophilic substance having nutraceutical value, was extracted from dried biomass of Pseudomonas diminuta using supercritical carbon dioxide (SC-CO(2)). The effect of different operational parameters (temperature, pressure, and extraction time) and addition of co-solvent on SC-CO(2) extraction of CoQ10 was studied in detail. The solubility parameter of CoQ10, CO(2), and CO(2) with ethanol and methanol as co-solvents was calculated and ...201122160186
Complete sequencing of the bla(NDM-1)-positive IncA/C plasmid from Escherichia coli ST38 isolate suggests a possible origin from plant pathogens.The complete sequence of the plasmid pNDM-1_Dok01 carrying New Delhi metallo-ß-lactamase (NDM-1) was determined by whole genome shotgun sequencing using Escherichia coli strain NDM-1_Dok01 (multilocus sequence typing type: ST38) and the transconjugant E. coli DH10B. The plasmid is an IncA/C incompatibility type composed of 225 predicted coding sequences in 195.5 kb and partially shares a sequence with bla(CMY-2)-positive IncA/C plasmids such as E. coli AR060302 pAR060302 (166.5 kb) and Salmonell ...201121966500
evaluation of an innovative antimicrobial surgical glove technology to reduce the risk of microbial passage following intraoperative perforation.surgical gloves provide a protective barrier for patients and members of the surgical team. although glove integrity is important in an era of blood-borne pathogens, little data exist on bacterial passage after glove perforation. this study evaluated the impact of antimicrobial surgical gloves in reducing microbial passage after glove puncture in a model of wound contamination.201120864217
catalytic mechanism and three-dimensional structure of adenine deaminase.adenine deaminase (ade) catalyzes the conversion of adenine to hypoxanthine and ammonia. the enzyme isolated from escherichia coli using standard expression conditions was low for the deamination of adenine (k(cat) = 2.0 s(-1); k(cat)/k(m) = 2.5 × 10(3) m(-1) s(-1)). however, when iron was sequestered with a metal chelator and the growth medium was supplemented with mn(2+) prior to induction, the purified enzyme was substantially more active for the deamination of adenine with k(cat) and k(cat)/ ...201121247091
prevalence and significance of fluoroquinolone resistant escherichia coli in patients undergoing transrectal ultrasound guided prostate needle biopsy.we estimated the prevalence of fluoroquinolone resistant escherichia coli in patients undergoing repeat transrectal ultrasound guided prostate needle biopsy and identified high risk groups.201121334021
indigenous organophosphate-degrading (opd) plasmid pcms1 of brevundimonasdiminuta is self-transmissible and plays a key role in horizontal mobility of the opd gene.a fosmid library of the 66kb indigenous organophosphate-degrading (opd) plasmid pcms1 of brevundimonas diminuta was tagged with mini-transposon eztn5 <r6k?ori/kan-2>, to determine its sequence using transposon-specific primers. the sequence revealed the presence of a number of tra genes suggesting their role in conjugal transfer of pcms1. consistent with the presence of the tra genes, the b. diminuta plasmid, pcms1::tet, generated by replacing the opd gene with opd::tet, served as a donor for tr ...201121354204
crystallization and preliminary x-ray diffraction analysis of the hyperthermophilic sulfolobus islandicus lactonase.phosphotriesterase-like lactonases (plls) constitute an interesting family of enzymes that are of paramount interest in biotechnology with respect to their catalytic functions. as natural lactonases, they may act against pathogens such as-ápseudomonas aeruginosa by shutting down their quorum-sensing system (quorum quenching) and thus decreasing pathogen virulence. owing to-átheir promiscuous phosphotriesterase activity, which can inactivate toxic organophosphorus compounds such as pesticides and ...201121393842
identification of an n-terminal formylated, two-peptide bacteriocin from enterococcus faecalis 710c.enterococcus faecalis 710c, isolated from beef product, has a broad antimicrobial activity spectrum against foodborne pathogens. two bacteriocins, enterocin 7a (ent7a) and enterocin 7b (ent7b), were purified from the culture supernatant of e. faecalis 710c and characterized using matrix-assisted laser desorption ionization-time-of-flight mass spectrometry and electrospray infusion tandem mass spectrometry analyses. these data and subsequent genetic analysis showed that ent7a and ent7b are produc ...201121469734
first case of fulminant sepsis due to wohlfahrtiimonas chitiniclastica.we report the first case of fulminant sepsis due to wohlfahrtiimonas chitiniclastica. this case is also the first one reported in south america. we emphasize the importance of recognizing bacteria that live in the larvae of a parasitic fly as the causative agent of severe infections in homeless patients.201121471333
microbiology of animal bite wound infections.the microbiology of animal bite wound infections in humans is often polymicrobial, with a broad mixture of aerobic and anaerobic microorganisms. bacteria recovered from infected bite wounds are most often reflective of the oral flora of the biting animal, which can also be influenced by the microbiome of their ingested prey and other foods. bacteria may also originate from the victim's own skin or the physical environment at the time of injury. our review has focused on bite wound infections in ...201121482724
the importance of accurate microorganism identification in microbial challenge tests of membrane filters--part i.microbial challenge testing is a common procedure to determine the retention efficiency, performance, and validity of a sterilizing-grade filter. the astm 838-05 standard describes a bacteria challenge test procedure based on brevundimonas diminuta (atcc 19146), routinely used to verify a 0.2 μm rated sterilizing-grade filter. process validation procedures most often also utilize b. diminuta (atcc 19146), but instead of the standard procedures and fluids, process, and product parameters are empl ...201121502070
the n-terminal nucleophile serine of cephalosporin acylase executes the second autoproteolytic cleavage and acyl-peptide hydrolysis.cephalosporin acylase precursor is translated as a single polypeptide chain and folds into a self-activating pre-protein. activation requires two peptide bond cleavages that excise an internal spacer to form the mature αβ heterodimer. using q-tof lc/ms, we located the second cleavage site between e159 and g160, and detected the corresponding 10 aa spacer g160dppdladqg169 of ca mutants. the site of the second cleavage depended on e159: moving e into the spacer or removing 5-10 residues from the s ...201121576250
brevundimonas diminuta keratitis.purpose:: to report the first documented case of keratitis secondary to the gram-negative bacillus brevundimonas diminuta. methods:: a 66-year-old woman with an ocular history of bilateral soft contact lens wear presented with a large, 6×9-mm, culture-positive pseudomonas aeruginosa-induced corneal ulcer. after weeks of therapy, she developed secondary keratitis. repeat cultures grew a rare, gram-negative bacillus, b. diminuta. results:: targeted therapy followed by adjustments based on repeat b ...201121617535
crystallization and preliminary crystallographic analysis of the phosphotriesterase-like lactonase from geobacillus kaustophilus.gk1506 from the thermophilic bacterium geobacillus kaustophilus is a member of the phosphotriesterase-like lactonases, which can catalyze the hydrolysis of a broad range of compounds with different chemical properties. it is of particular interest because of its high thermostability and its dual activity towards organophosphate compounds and some lactones. these properties make gk1506 an attractive target for future enzyme engineering and use in practical applications. in order to resolve the cr ...201121795796
synthesis and exploration of qsar model of 2-methyl-3-[2-(2-methylprop-1-en-1-yl)-1h-benzimidazol-1-yl]pyrimido[1,2-a]benzimidazol-4(3h)-one as potential antibacterial agents.present communication deals with the synthesis of novel 2-methyl-3-[2-(2-methylprop-1-en-1-yl)-1h-benzimidazol-1-yl]pyrimido[1,2-a]benzimidazol-4(3h)-one derivatives under phase transfer catalysis (ptc) conditions using benzyl triethyl ammonium chloride (bteac) as ptc. it also elicits the studies on in vitro antimicrobial evaluation of synthesized compounds against a representative genera of gram-negative and gram-positive bacteria i.e., bacillus subtilis, staphylococcus aureus, pseudomonas dimi ...201121699375
genome sequences of eight morphologically diverse alphaproteobacteria.the alphaproteobacteriacomprise morphologically diverse bacteria, including many species of stalked bacteria. here we announce the genome sequences of eight alphaproteobacteria, including the first genome sequences of species belonging to the genera asticcacaulis, hirschia, hyphomicrobium, and rhodomicrobium.201121705585
differential radial capillary action of ligand assay for high-throughput detection of protein-metabolite interactions.interactions of proteins with low-molecular-weight ligands, such as metabolites, cofactors, and allosteric regulators, are important determinants of metabolism, gene regulation, and cellular homeostasis. pharmaceuticals often target these interactions to interfere with regulatory pathways. we have developed a rapid, precise, and high-throughput method for quantitatively measuring protein-ligand interactions without the need to purify the protein when performed in cells with low background activi ...201121876132
clinical significance of microbial infection and adaptation in cystic fibrosis.a select group of microorganisms inhabit the airways of individuals with cystic fibrosis. once established within the pulmonary environment in these patients, many of these microbes adapt by altering aspects of their structure and physiology. some of these microbes and adaptations are associated with more rapid deterioration in lung function and overall clinical status, whereas others appear to have little effect. here we review current evidence supporting or refuting a role for the different mi ...201121233507
the evolution of new enzyme function: lessons from xenobiotic metabolizing bacteria versus insecticide-resistant insects.here, we compare the evolutionary routes by which bacteria and insects have evolved enzymatic processes for the degradation of four classes of synthetic chemical insecticide. for insects, the selective advantage of such degradative activities is survival on exposure to the insecticide, whereas for the bacteria the advantage is simply a matter of access to additional sources of nutrients. nevertheless, bacteria have evolved highly efficient enzymes from a wide variety of enzyme families, whereas ...201125567970
conformational variability of organophosphorus hydrolase upon soman and paraoxon binding.the bacterial enzyme organophosphorus hydrolase (oph) exhibits both catalytic and substrate promiscuity. it hydrolyzes bonds in a variety of phosphotriester (p-o), phosphonothioate (p-s), phosphofluoridate (p-f), and phosphonocyanate (f-cn) compounds. however, its catalytic efficiency varies markedly for different substrates, limiting the broad-range application of oph as catalyst in the bioremediation of pesticides and chemical war agents. in the present study, pk(a) calculations and multiple e ...201122098575
clinically defined chemotherapy-associated bowel syndrome predicts severe complications and death in cancer patients.neutropenic patients are at risk of abdominal complications and yet the incidence and impact of these complications on patients' morbidity and mortality have not been sufficiently evaluated. we aimed to assess a clinical rule for early detection of abdominal complications leading to death or transfer to intensive care in patients with chemotherapy-associated neutropenia.201121859736
toward a systems biology perspective on enzyme evolution.large superfamilies of enzymes derived from a common progenitor have emerged by duplication and divergence of genes encoding metabolic enzymes. division of the functions of early generalist enzymes enhanced catalytic power and control over metabolic fluxes. later, novel enzymes evolved from inefficient secondary activities in specialized enzymes. enzymes operate in the context of complex metabolic and regulatory networks. the potential for evolution of a new enzyme depends upon the collection of ...201122069330
toward a systems biology perspective on enzyme evolution.large superfamilies of enzymes derived from a common progenitor have emerged by duplication and divergence of genes encoding metabolic enzymes. division of the functions of early generalist enzymes enhanced catalytic power and control over metabolic fluxes. later, novel enzymes evolved from inefficient secondary activities in specialized enzymes. enzymes operate in the context of complex metabolic and regulatory networks. the potential for evolution of a new enzyme depends upon the collection of ...201122069330
divergence and convergence in enzyme evolution: parallel evolution of paraoxonases from quorum-quenching lactonases.we discuss the basic features of divergent versus convergent evolution and of the common scenario of parallel evolution. the example of quorum-quenching lactonases is subsequently described. three different quorum-quenching lactonase families are known, and they belong to three different superfamilies. their key active-site architectures have converged and are strikingly similar. curiously, a promiscuous organophosphate hydrolase activity is observed in all three families. we describe the struct ...201122069329
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