Publications

pseudo-outbreak of brevundimonas diminuta attributed to contamination of culture medium supplement.	we report an epidemiological investigation of a cluster of brevundimonas diminuta isolates cultured from sterile sites. inoculation of supplement medium yielded growth of b. diminuta. molecular typing indicated likely contamination of the lot. no b. diminuta was further isolated after replacement of the supplement with a new lot number. infect control hosp epidemiol 2017;1-4.	2017	28264729
copper-tolerant rhizosphere bacteria-characterization and assessment of plant growth promoting factors.	remediation of heavy metal contaminated soil is a major problem or concern worldwide. heavy metal accumulation in the soil is increasing day by day by industries, mines, agriculture, fuel combustion and municipal waste discharge. such contaminated soils harbour a large number of resistant microbial populations. screening and isolation of such microbes would be utilized for natural remediation of metal contaminated soils. therefore, in the present study, highly copper-tolerant bacteria from rhizo ...	2017	28251535
genome-guided insights reveal organophosphate-degrading brevundimonas diminuta as sphingopyxis wildii and define its versatile metabolic capabilities and environmental adaptations.		2017	28175269
microscopic characterization of brevundimonas diminuta in the hydrated state.	brevundimonas diminuta is the organism most commonly used for challenge testing of sterilizing-grade filter membranes. astm f838-05 and pda technical report 26 rely on b. diminuta atcc #19146 for standard challenge tests used to designate sterilizing-grade filter performance. despite the importance and widespread use of b. diminuta in filter testing and validation, information about this microorganism in its native hydrated state is limited. in this work, we measure, for the first time, the mech ...	2017	26048743
evaluation of the effect of the volume throughput and maximum flux of low-surface-tension fluids on bacterial penetration of 0.2 micron-rated filters during process-specific filter validation testing.	approximately 97% of filter validation tests result in the demonstration of absolute retention of the test bacteria, and thus sterile filter validation failure is rare. however, while brevundimonas diminuta (b. diminuta) penetration of sterilizing-grade filters is rarely detected, the observation that some fluids (such as vaccines and liposomal fluids) may lead to an increased incidence of bacterial penetration of sterilizing-grade filters by b. diminuta has been reported. the goal of the follow ...	2017	25868996
the importance of accurate microorganism identification in microbial challenge tests of membrane filters. part ii. the comparison of hydrogenophaga pseudoflava attc 33668 and curvibacter sp. atcc 700892 by microbial challenge tests with membrane filters.	the astm 838-05 standard describes a bacteria challenge test procedure based on brevundimonas diminuta (atcc 19146) to verify a 0.2 μm rated sterilizing-grade filter. for process validation procedures a correct identification of the challenge organism is essential. the test strain atcc 700892 repeatedly used for microbial challenge tests was incorrectly named hydrogenophaga pseudoflava but is phylogenetically linked to the genus curvibacter, as shown in part i of this series. based on these stud ...	2016	22767883
catalytic efficiencies of directly evolved phosphotriesterase variants with structurally different organophosphorus compounds in vitro.	the nearly 200,000 fatalities following exposure to organophosphorus (op) pesticides each year and the omnipresent danger of a terroristic attack with op nerve agents emphasize the demand for the development of effective op antidotes. standard treatments for intoxicated patients with a combination of atropine and an oxime are limited in their efficacy. thus, research focuses on developing catalytic bioscavengers as an alternative approach using op-hydrolyzing enzymes such as brevundimonas diminu ...	2016	26612364
experimental comparison of point-of-use filters for drinking water ultrafiltration.	waterborne pathogens such as pseudomonas spp. and legionella spp. may persist in hospital water networks despite chemical disinfection. point-of-use filtration represents a physical control measure that can be applied in high-risk areas to contain the exposure to such pathogens. new technologies have enabled an extension of filters' lifetimes and have made available faucet hollow-fibre filters for water ultrafiltration.	2016	28073586
genome-guided insights reveal organophosphate-degrading brevundimonas diminuta as sphingopyxis wildii and define its versatile metabolic capabilities and environmental adaptations.	the complete genome sequence of brevundimonas diminuta represented a chromosome (∼4.15 mb) and two plasmids (pcms1 and pcms2) with sizes of 65,908 bp and 30,654 bp, respectively. the sequence of the genome showed no significant similarity with the known bacterial genome sequences, instead showed weak similarity with the members of different genera of family, sphingomonadaceae. contradicting existing taxonomic position, the core genome guided phylogenetic tree placed b. diminuta in the genus sphi ...	2016	28028121
new and highly active microbial phosphotriesterase sources.	many toxic insecticides used worldwide as well as some chemical warfare agents are phosphotriester derivatives. therefore, detoxification of organophosphorus compounds has become the subject of many studies and in particular bioremediation, based on the phosphotriesterase catalysed hydrolysis of these compounds, has shown to be an effective and ecological methodology. in order to identify new bacterial phosphotriesterases, a simple and sensitive fluorimetric screening method on solid media was e ...	2016	27915249
the role of protein dynamics in the evolution of new enzyme function.	enzymes must be ordered to allow the stabilization of transition states by their active sites, yet dynamic enough to adopt alternative conformations suited to other steps in their catalytic cycles. the biophysical principles that determine how specific protein dynamics evolve and how remote mutations affect catalytic activity are poorly understood. here we examine a 'molecular fossil record' that was recently obtained during the laboratory evolution of a phosphotriesterase from pseudomonas dimin ...	2016	27618189
microbial degradation of high impact polystyrene (hips), an e-plastic with decabromodiphenyl oxide and antimony trioxide.	accumulation of electronic waste has increased catastrophically and out of that various plastic resins constitute one of the leading thrown out materials in the electronic machinery. enrichment medium, containing high impact polystyrene (hips) with decabromodiphenyl oxide and antimony trioxide as sole carbon source, was used to isolate microbial cultures. the viability of these cultures in the e-plastic containing mineral medium was further confirmed by triphenyl tetrazolium chloride (ttc) reduc ...	2016	27434738
structure of a novel phosphotriesterase from sphingobium sp. tcm1: a familiar binuclear metal center embedded in a seven-bladed β-propeller protein fold.	a novel phosphotriesterase was recently discovered and purified from sphingobium sp. tcm1 (sb-pte) and shown to catalyze the hydrolysis of a broad spectrum of organophosphate esters with a catalytic efficiency that exceeds 10(6) m(-1) s(-1) for the hydrolysis of triphenyl phosphate. the enzyme was crystallized and the three-dimensional structure determined to a resolution of 2.1 å using single-wavelength anomalous diffraction (protein data bank entry 5hrm ). the enzyme adopts a seven-bladed β-pr ...	2016	27353520
organophosphate hydrolase is a lipoprotein and interacts with pi-specific transport system to facilitate growth of brevundimonas diminuta using op insecticide as source of phosphate.	organophosphate hydrolase (oph), encoded by the organophosphate degradation (opd) island, hydrolyzes the triester bond found in a variety of organophosphate insecticides and nerve agents. oph is targeted to the inner membrane ofbrevundimonas diminutain a pre-folded conformation by thetwinargininetransport (tat) pathway. the oph signal peptide contains an invariant cysteine residue at the junction of the signal peptidase (spase) cleavage site along with a well conserved lipobox motif. treatment o ...	2016	26861877
brevundimonas diminuta mediated alleviation of arsenic toxicity and plant growth promotion in oryza sativa l.	arsenic (as), a toxic metalloid adversely affects plant growth in polluted areas. in the present study, we investigated the possibility of improving phytostablization of arsenic through application of new isolated strain brevundimonas diminuta (nbri012) in rice plant [oryza sativa (l.) var. sarju 52] at two different concentrations [10ppm (low toxic) and 50ppm (high toxic)] of as. the plant growth promoting traits of bacterial strains revealed the inherent ability of siderophores, phosphate solu ...	2016	26650422
comprehensive analysis of draft genomes of two closely related pseudomonas syringae phylogroup 2b strains infecting mono- and dicotyledon host plants.	in recent years, the damage caused by bacterial pathogens to major crops has been increasing worldwide. pseudomonas syringae is a widespread bacterial species that infects almost all major crops. different p. syringae strains use a wide range of biochemical mechanisms, including phytotoxins and effectors of the type iii and type iv secretion systems, which determine the specific nature of the pathogen virulence.	2016	28105943
a case of flavobacterium ceti meningitis.		2016	27578519
a microbial sensor for organophosphate hydrolysis exploiting an engineered specificity switch in a transcription factor.	a whole-cell biosensor utilizing a transcription factor (tf) is an effective tool for sensitive and selective detection of specialty chemicals or anthropogenic molecules, but requires access to an expanded repertoire of tfs. using homology modeling and ligand docking for binding pocket identification, assisted by conservative mutations in the pocket, we engineered a novel specificity in an acinetobacter tf, pobr, to 'sense' a chemical p-nitrophenol (pnp) and measured the response via a fluoresce ...	2016	27536006
a metaproteomic analysis of the response of a freshwater microbial community under nutrient enrichment.	eutrophication can lead to an uncontrollable increase in algal biomass, which has repercussions for the entire microbial and pelagic community. studies have shown how nutrient enrichment affects microbial species succession, however details regarding the impact on community functionality are rare. here, we applied a metaproteomic approach to investigate the functional changes to algal and bacterial communities, over time, in oligotrophic and eutrophic conditions, in freshwater microcosms. sample ...	2016	27536273
influence of chicken manure fertilization on antibiotic-resistant bacteria in soil and the endophytic bacteria of pakchoi.	animal manure is commonly used as fertilizer for agricultural crops worldwide, even though it is believed to contribute to the spread of antibiotic resistance from animal intestines to the soil environment. however, it is unclear whether and how there is any impact of manure fertilization on populations and community structure of antibiotic-resistant endophytic bacteria (areb) in plant tissues. to investigate the effect of manure and organic fertilizer on endophytic bacterial communities, pot ex ...	2016	27376311
composition and predicted metabolic capacity of upper and lower airway microbiota of healthy dogs in relation to the fecal microbiota.	the upper and lower airways of healthy humans are reported to harbor stable and consistent bacterial populations, and the composition of these communities is altered in individuals affected with several respiratory diseases. data regarding the presence of airway microbiota in other animals are scant and a better understanding of the composition and metabolic function of such bacterial populations is essential for the development of novel therapeutic and diagnostic modalities for use in both vete ...	2016	27136381
protecting enzymatic function through directed packaging into bacterial outer membrane vesicles.	bacteria possess innate machinery to transport extracellular cargo between cells as well as package virulence factors to infect host cells by secreting outer membrane vesicles (omvs) that contain small molecules, proteins, and genetic material. these robust proteoliposomes have evolved naturally to be resistant to degradation and provide a supportive environment to extend the activity of encapsulated cargo. in this study, we sought to exploit bacterial omv formation to package and maintain the a ...	2016	27117743
bioinformatics data supporting revelatory diversity of cultivable thermophiles isolated and identified from two terrestrial hot springs, unkeshwar, india.	a total of 21 thermophilic bacteria were isolated and identified using 16s rrna gene sequencing method. sequences were submitted to ncbi website. short dna sequences jn392966-jn392972; kc120909-kc120919; km998072-km998074 and kp053645 strains were downloaded from ncbi biosample database. endmemo gc calculating tool was used for calculation of maximum, minimum and average gc percentage and graphical representation of gc content. data generated indicate 20 short dna sequences have maximum gc conte ...	2016	27182549
vim-47, a new variant of the autochthonous metallo-β-lactamase vim-13 from the balearic islands in spain.		2016	26976859
besifloxacin: efficacy and safety in treatment and prevention of ocular bacterial infections.	this comprehensive review summarizes the mechanism of action, pharmacokinetics, efficacy, and safety of besifloxacin ophthalmic suspension, 0.6% and examines its role in the treatment of ocular surface bacterial infections. besifloxacin possesses balanced activity against bacterial topoisomerase ii (also called dna gyrase) and topoisomerase iv. it has shown a low potential to select for bacterial resistance in vitro and demonstrated strong in vitro activity against many gram-positive, gram-negat ...	2016	27010720
optical sensing of microbial life on surfaces.	the label-free detection of microbial cells attached to a surface is an active field of research. the field is driven by the need to understand and control the growth of biofilms in a number of applications, including basic research in natural environments, industrial facilities, and clinical devices, to name a few. despite significant progress in the ability to monitor the growth of biofilms and related living cells, the sensitivity and selectivity of such sensors are still a challenge. we beli ...	2016	26637605
dynamics of bacterial populations during bench-scale bioremediation of oily seawater and desert soil bioaugmented with coastal microbial mats.	this study describes a bench-scale attempt to bioremediate kuwaiti, oily water and soil samples through bioaugmentation with coastal microbial mats rich in hydrocarbonoclastic bacterioflora. seawater and desert soil samples were artificially polluted with 1% weathered oil, and bioaugmented with microbial mat suspensions. oil removal and microbial community dynamics were monitored. in batch cultures, oil removal was more effective in soil than in seawater. hydrocarbonoclastic bacteria associated ...	2016	26751253
strategies for decreasing contamination of homemade nasal saline irrigation solutions.	saline nasal irrigations (sni) are an important adjunct in the treatment of rhinosinusitis, and many patients prepare and store these solutions in their homes without an awareness of the potential for contamination. the objectives of this study were to determine if such contamination occurs and the effect of preparation methods on contamination.	2016	26290494
identification and characterization of endophytic bacteria isolated from in vitro cultures of peach and pear rootstocks.	endophytes are microorganisms which live symbiotically with almost all varieties of plant and in turn helping the plant in a number of ways. instead of satisfactory surface sterilization approaches, repeatedly occurring bacterial growth on in vitro rootstock cultures of peach and pear was identified and isolated as endophytic bacteria in our present study. five different isolates from peach rootstocks were molecularly identified by 16s rrna gene sequencing as brevundimonas diminuta, leifsonia sh ...	2016	28330195
isolation of aluminum-tolerant bacteria capable of nitrogen removal in activated sludge.	four strains of bacteria capable of withstanding 20mm concentration of aluminum were isolated from activated sludge in a bioreactor. 16s rrna identification and morphological characteristics indicated that these strains were chryseobacterium sp. b1, brevundimonas diminuta b3, hydrogenophaga sp. b4, and bacillus cereus b5. phylogenetic analysis revealed the position and interrelationships of these bacteria. b. diminuta b3 and hydrogenophaga sp. b4 could achieve nitrate nitrogen removal of 94.0% a ...	2016	27038879
comparative study of plasma endotoxin with procalcitonin levels in diagnosis of bacteremia in intensive care unit patients.	both procalcitonin (pct) and plasma endotoxin levels cannot be solely used for a definite diagnosis of bacteremia or sepsis, and there has been few study comparing the values of the two biomarkers for the diagnosis of bacteremia. the aim of this study was to identify bacteria causing bacteremia and evaluate the role of the two biomarkers in the diagnosis of bacteremia in intensive care unit (icu).	2016	26879015
detection of extended spectrum beta-lactamases resistance genes among bacteria isolated from selected drinking water distribution channels in southwestern nigeria.	extended spectrum beta-lactamases (esbl) provide high level resistance to beta-lactam antibiotics among bacteria. in this study, previously described multidrug resistant bacteria from raw, treated, and municipal taps of dwds from selected dams in southwestern nigeria were assessed for the presence of esbl resistance genes which include bla tem, bla shv, and bla ctx by pcr amplification. a total of 164 bacteria spread across treated (33), raw (66), and municipal taps (68), belonging to α-proteoba ...	2016	27563674
diversity takes shape: understanding the mechanistic and adaptive basis of bacterial morphology.	the modern age of metagenomics has delivered unprecedented volumes of data describing the genetic and metabolic diversity of bacterial communities, but it has failed to provide information about coincident cellular morphologies. much like metabolic and biosynthetic capabilities, morphology comprises a critical component of bacterial fitness, molded by natural selection into the many elaborate shapes observed across the bacterial domain. in this essay, we discuss the diversity of bacterial morpho ...	2016	27695035
the use of pcr/electrospray ionization-time-of-flight-mass spectrometry (pcr/esi-tof-ms) to detect bacterial and fungal colonization in healthy military service members.	the role of microbial colonization in disease is complex. novel molecular tools to detect colonization offer theoretical improvements over traditional methods. we evaluated pcr/electrospray ionization-time-of-flight-mass spectrometry (pcr/esi-tof-ms) as a screening tool to study colonization of healthy military service members.	2016	27448413
nicotine dehydrogenase complexed with 6-hydroxypseudooxynicotine oxidase involved in the hybrid nicotine-degrading pathway in agrobacterium tumefaciens s33.	nicotine, a major toxic alkaloid in tobacco wastes, is degraded by bacteria, mainly via pyridine and pyrrolidine pathways. previously, we discovered a new hybrid of the pyridine and pyrrolidine pathways in agrobacterium tumefaciens s33 and characterized its key enzyme 6-hydroxy-3-succinoylpyridine (hsp) hydroxylase. here, we purified the nicotine dehydrogenase initializing the nicotine degradation from the strain and found that it forms a complex with a novel 6-hydroxypseudooxynicotine oxidase. ...	2016	26729714
functional metagenomics of spacecraft assembly cleanrooms: presence of virulence factors associated with human pathogens.	strict planetary protection practices are implemented during spacecraft assembly to prevent inadvertent transfer of earth microorganisms to other planetary bodies. therefore, spacecraft are assembled in cleanrooms, which undergo strict cleaning and decontamination procedures to reduce total microbial bioburden. we wanted to evaluate if these practices selectively favor survival and growth of hardy microorganisms, such as pathogens. three geographically distinct cleanrooms were sampled during the ...	2016	27667984
metabolic network modeling of microbial interactions in natural and engineered environmental systems.	we review approaches to characterize metabolic interactions within microbial communities using stoichiometric metabolic network (smn) models for applications in environmental and industrial biotechnology. smn models are computational tools used to evaluate the metabolic engineering potential of various organisms. they have successfully been applied to design and optimize the microbial production of antibiotics, alcohols and amino acids by single strains. to date however, such models have been ra ...	2016	27242701
novel conopeptides of largely unexplored indo pacific conus sp.	cone snails are predatory creatures using venom as a weapon for prey capture and defense. since this venom is neurotoxic, the venom gland is considered as an enormous collection of pharmacologically interesting compounds having a broad spectrum of targets. as such, cone snail peptides represent an interesting treasure for drug development. here, we report five novel peptides isolated from the venom of conus longurionis, conus asiaticus and conus australis. lo6/7a and lo6/7b were retrieved from c ...	2016	27801785
beneficial cyanobacteria and eubacteria synergistically enhance bioavailability of soil nutrients and yield of okra.	microorganisms in the rhizosphere mediate the cycling of nutrients, their enhanced mobilisation and facilitate their uptake, leading to increased root growth, biomass and yield of plants. we examined the promise of beneficial cyanobacteria and eubacteria as microbial inoculants, applied singly or in combination as consortia or biofilms, to improve growth and yields of okra. interrelationships among the microbial activities and the micro/macro nutrient dynamics in soils and okra yield characteris ...	2016	27441245
rapid identification and multiple susceptibility testing of pathogens from positive-culture sterile body fluids by a combined maldi-tof mass spectrometry and vitek susceptibility system.	infections of the bloodstream, central nervous system, peritoneum, joints, and other sterile areas are associated with high morbidity and sequelae risk. timely initiation of effective antimicrobial therapy is crucial to improving patient prognosis. however, standard final identification and antimicrobial susceptibility tests (asts) are reported 16-48 h after a positive alert. for a rapid, effective and low-cost diagnosis, we combined matrix-assisted laser desorption/ionization time of flight mas ...	2016	27148212
comprehensive laboratory evaluation of a highly specific lateral flow assay for the presumptive identification of bacillus anthracis spores in suspicious white powders and environmental samples.	we conducted a comprehensive, multiphase laboratory evaluation of the anthrax biothreat alert(®) test strip, a lateral flow immunoassay (lfa) for the rapid detection of bacillus anthracis spores. the study, conducted at 2 sites, evaluated this assay for the detection of spores from the ames and sterne strains of b. anthracis, as well as those from an additional 22 strains. phylogenetic near neighbors, environmental background organisms, white powders, and environmental samples were also tested. ...	2016	27661796
modularity and determinants of a (bi-)polarization control system from free-living and obligate intracellular bacteria.	although free-living and obligate intracellular bacteria are both polarized it is unclear whether the underlying polarization mechanisms and effector proteins are conserved. here we dissect at the cytological, functional and structural level a conserved polarization module from the free living α-proteobacterium caulobacter crescentus and an orthologous system from an obligate intracellular (rickettsial) pathogen. the nmr solution structure of the zinc-finger (znr) domain from the bifunctional an ...	2016	28008852
whole-genome sequencing of brevundimonas diminuta xgc1, isolated from a tuberculosis patient in gujarat, india.	we report the draft genome of brevundimonas diminuta strain xgc1, isolated from a tuberculosis-infected patient in gujarat, india. this study also reveals that the b. diminuta xgc1 strain has acquired mutation to confer resistance to quinolone drugs.	2015	26112790
infectious causes of cholesteatoma and treatment of infected ossicles prior to reimplantation by hydrostatic high-pressure inactivation.	chronic inflammation, which is caused by recurrent infections, is one of the factors contributing to the pathogenesis of cholesteatoma. if reimplantation of autologous ossicles after a surgical intervention is intended, inactivation of planktonic bacteria and biofilms is desirable. high hydrostatic pressure treatment is a procedure, which has been used to inactivate cholesteatoma cells on ossicles. here we discuss the potential inactivating effect of high hydrostatic pressure on microbial pathog ...	2015	25705686
the influence of smoking on the peri-implant microbiome.	smokers are at high risk for 2 bacterially driven oral diseases: peri-implant mucositis and peri-implantitis. therefore, the purpose of this investigation was to use a deep-sequencing approach to identify the effect of smoking on the peri-implant microbiome in states of health and disease. peri-implant biofilm samples were collected from 80 partially edentulous subjects with peri-implant health, peri-implant mucositis, and peri-implantitis. bacterial dna was isolated and 16s ribsomal rna gene li ...	2015	26124222
whole-genome sequence of chryseobacterium oranimense, a colistin-resistant bacterium isolated from a cystic fibrosis patient in france.	for the first time, we report the whole-genome sequence analysis of chryseobacterium oranimense g311, a multidrug-resistant bacterium, from a cystic fibrosis patient in france, including resistance to colistin. whole-genome sequencing of c. oranimense g311 was performed using ion torrent pgm, and rast, the embl-ebi server, and the antibiotic resistance gene-annotation (arg-annot) database were used for annotation of all genes, including antibiotic resistance (ar) genes. general features of the c ...	2015	25583710
high voltage electrochemiluminescence (ecl) as a new method for detection of pah during screening for pah-degrading microbial consortia.	the search for new bacterial consortia capable of removing pah from the environment is associated with the need to employ novel, simple, and economically efficient detection methods. a fluorimetric method (fl) as well as high voltage electrochemiluminescence (ecl) on a modified surface of an aluminum electrode were used in order to determine the changes in the concentrations of pah in the studied aqueous solutions. the ecl signal (the spectrum and emission intensity for a given wavelength) was d ...	2015	26213425
bacterial degradation of monocyclic aromatic amines.	aromatic amines are an important group of industrial chemicals, which are widely used for manufacturing of dyes, pesticides, drugs, pigments, and other industrial products. these compounds have been considered highly toxic to human beings due to their carcinogenic nature. three groups of aromatic amines have been recognized: monocyclic, polycyclic, and heterocyclic aromatic amines. bacterial degradation of several monocyclic aromatic amines has been studied in a variety of bacteria, which utiliz ...	2015	26347719
challenge study of the pathogen reduction capacity of the theraflex mb-plasma technology.	although most pathogen reduction systems for plasma primarily target viruses, bacterial contamination may also occur. this study aimed to investigate the bacterial reduction capacity of a methylene blue (mb) treatment process and its virus inactivation capacity in lipaemic plasma.	2015	25899343
interrogation of the substrate profile and catalytic properties of the phosphotriesterase from sphingobium sp. strain tcm1: an enzyme capable of hydrolyzing organophosphate flame retardants and plasticizers.	the most familiar organophosphorus compounds are the neurotoxic insecticides and nerve agents. a related group of organophosphorus compounds, the phosphotriester plasticizers and flame retardants, has recently become widely used. unlike the neurotoxic phosphotriesters, the plasticizers and flame retardants lack an easily hydrolyzable bond. while the hydrolysis of the neurotoxic organophosphates by phosphotriesterase enzymes is well-known, the lack of a labile bond in the flame retardants and pla ...	2015	26629649
a catalytic dna activated by a specific strain of bacterial pathogen.	pathogenic strains of bacteria are known to cause various infectious diseases and there is a growing demand for molecular probes that can selectively recognize them. here we report a special dnazyme (catalytic dna), rfd-cd1, that shows exquisite specificity for a pathogenic strain of clostridium difficile (c. difficile). rfd-cd1 was derived by an in vitro selection approach where a random-sequence dna library was allowed to react with an unpurified molecular mixture derived from this strain of c ...	2015	26676768
a catalytic dna activated by a specific strain of bacterial pathogen.	pathogenic strains of bacteria are known to cause various infectious diseases and there is a growing demand for molecular probes that can selectively recognize them. here we report a special dnazyme (catalytic dna), rfd-cd1, that shows exquisite specificity for a pathogenic strain of clostridium difficile (c. difficile). rfd-cd1 was derived by an in vitro selection approach where a random-sequence dna library was allowed to react with an unpurified molecular mixture derived from this strain of c ...	2015	26676768
the cytoplasmic and periplasmic expression levels and folding of organophosphorus hydrolase enzyme in escherichia coli.	organophosphorus hydrolase (oph) is a type of organophosphate-degrading enzyme which is widely used in the bioremediation process.	2015	26870308
allergy associations with the adult fecal microbiota: analysis of the american gut project.	alteration of the gut microbial population (dysbiosis) may increase the risk for allergies and other conditions. this study sought to clarify the relationship of dysbiosis with allergies in adults.	2015	26870828
allergy associations with the adult fecal microbiota: analysis of the american gut project.	alteration of the gut microbial population (dysbiosis) may increase the risk for allergies and other conditions. this study sought to clarify the relationship of dysbiosis with allergies in adults.	2015	26870828
digital data for quick response (qr) codes of thermophiles to identify and compare the bacterial species isolated from unkeshwar hot springs (india).	16s rrna sequences of morphologically and biochemically identified 21 thermophilic bacteria isolated from unkeshwar hot springs (19°85'n and 78°25'e), dist. nanded (india) has been deposited in ncbi repository. the 16s rrna gene sequences were used to generate qr codes for sequences (fasta format and full gene bank information). diversity among the isolates is compared with known isolates and evaluated using cgr, fcgr and pca i.e. visual comparison and evaluation respectively. considerable biodi ...	2015	26793757
digital data for quick response (qr) codes of thermophiles to identify and compare the bacterial species isolated from unkeshwar hot springs (india).	16s rrna sequences of morphologically and biochemically identified 21 thermophilic bacteria isolated from unkeshwar hot springs (19°85'n and 78°25'e), dist. nanded (india) has been deposited in ncbi repository. the 16s rrna gene sequences were used to generate qr codes for sequences (fasta format and full gene bank information). diversity among the isolates is compared with known isolates and evaluated using cgr, fcgr and pca i.e. visual comparison and evaluation respectively. considerable biodi ...	2015	26793757
lipid remodelling is a widespread strategy in marine heterotrophic bacteria upon phosphorus deficiency.	upon phosphorus (p) deficiency, marine phytoplankton reduce their requirements for p by replacing membrane phospholipids with alternative non-phosphorus lipids. it was very recently demonstrated that a sar11 isolate also shares this capability when phosphate starved in culture. yet, the extent to which this process occurs in other marine heterotrophic bacteria and in the natural environment is unknown. here, we demonstrate that the substitution of membrane phospholipids for a variety of non-phos ...	2015	26565724
lipid remodelling is a widespread strategy in marine heterotrophic bacteria upon phosphorus deficiency.	upon phosphorus (p) deficiency, marine phytoplankton reduce their requirements for p by replacing membrane phospholipids with alternative non-phosphorus lipids. it was very recently demonstrated that a sar11 isolate also shares this capability when phosphate starved in culture. yet, the extent to which this process occurs in other marine heterotrophic bacteria and in the natural environment is unknown. here, we demonstrate that the substitution of membrane phospholipids for a variety of non-phos ...	2015	26565724
molybdenum-containing nicotine hydroxylase genes in a nicotine degradation pathway that is a variant of the pyridine and pyrrolidine pathways.	ochrobactrum sp. strain sjy1 utilizes nicotine as a sole source of carbon, nitrogen, and energy via a variant of the pyridine and pyrrolidine pathways (the vpp pathway). several strains and genes involved in the vpp pathway have recently been reported; however, the first catalyzing step for enzymatic turnover of nicotine is still unclear. in this study, a nicotine hydroxylase for the initial hydroxylation step of nicotine degradation was identified and characterized. the nicotine hydroxylase (vp ...	2015	26407884
chemotaxis and degradation of organophosphate compound by a novel moderately thermo-halo tolerant pseudomonas sp. strain bur11: evidence for possible existence of two pathways for degradation.	an organophosphate (op) degrading chemotactic bacterial strain bur11 isolated from an agricultural field was identified as a member of pseudomonas genus on the basis of its 16s rrna gene sequence. the strain could utilize parathion, chlorpyrifos and their major hydrolytic intermediates as sole source of carbon for its growth and exhibited positive chemotactic response towards most of them. optimum concentration of parathion for its growth was recorded to be 200 ppm and 62% of which was degraded ...	2015	26587344
decreased phototoxic effects of tio₂ nanoparticles in consortium of bacterial isolates from domestic waste water.	this study is aimed to explore the toxicity of tio2 nanoparticles at low concentrations (0.25, 0.50 & 1.00 μg/ml); on five bacterial isolates and their consortium in waste water medium both in dark and uva conditions. to critically examine the toxic effects of nanoparticles and the response mechanism(s) offered by microbes, several aspects were monitored viz. cell viability, ros generation, sod activity, membrane permeability, eps release and biofilm formation. a dose and time dependent loss in ...	2015	26496250
high-throughput screening in protein engineering: recent advances and future perspectives.	over the last three decades, protein engineering has established itself as an important tool for the development of enzymes and (therapeutic) proteins with improved characteristics. new mutagenesis techniques and computational design tools have greatly aided in the advancement of protein engineering. yet, one of the pivotal components to further advance protein engineering strategies is the high-throughput screening of variants. compartmentalization is one of the key features allowing miniaturiz ...	2015	26492240
distinct microbiological signatures associated with triple negative breast cancer.	infectious agents are the third highest human cancer risk factor and may have a greater role in the origin and/or progression of cancers, and related pathogenesis. thus, knowing the specific viruses and microbial agents associated with a cancer type may provide insights into cause, diagnosis and treatment. we utilized a pan-pathogen array technology to identify the microbial signatures associated with triple negative breast cancer (tnbc). this technology detects low copy number and fragmented ge ...	2015	26469225
first report of wohlfahrtiimonas chitiniclastica isolation from a patient with cellulitis in the united states.	we report the first documented isolation of wohlfahrtiimonas chitiniclastica from a human in the united states. initially misidentified as acinetobacter lwoffii by vitek-2, the isolate was subsequently identified as w. chitiniclastica by matrix-assisted laser desorption ionization-time of flight mass spectrometry (maldi-tof ms) and 16s rrna gene sequencing. while the clinical significance of the isolate in this case is unclear, it highlights the superior performance of maldi-tof ms for bacterial ...	2015	26378273
rapid bursts and slow declines: on the possible evolutionary trajectories of enzymes.	the evolution of enzymes is often viewed as following a smooth and steady trajectory, from barely functional primordial catalysts to the highly active and specific enzymes that we observe today. in this review, we summarize experimental data that suggest a different reality. modern examples, such as the emergence of enzymes that hydrolyse human-made pesticides, demonstrate that evolution can be extraordinarily rapid. experiments to infer and resurrect ancient sequences suggest that some of the f ...	2015	25926697
recent advances in qm/mm free energy calculations using reference potentials.	recent years have seen enormous progress in the development of methods for modeling (bio)molecular systems. this has allowed for the simulation of ever larger and more complex systems. however, as such complexity increases, the requirements needed for these models to be accurate and physically meaningful become more and more difficult to fulfill. the use of simplified models to describe complex biological systems has long been shown to be an effective way to overcome some of the limitations asso ...	2015	25038480
function discovery and structural characterization of a methylphosphonate esterase.	pmi1525, an enzyme of unknown function from proteus mirabilis hi4320 and the amidohydrolase superfamily, was cloned, purified to homogeneity, and functionally characterized. the three-dimensional structure of pmi1525 was determined with zinc and cacodylate bound in the active site (pdb id: 3rhg ). the structure was also determined with manganese and butyrate in the active site (pdb id: 4qsf ). pmi1525 folds as a distorted (β/α)8-barrel that is typical for members of the amidohydrolase superfamil ...	2015	25873441
gmp-compliant (68)ga radiolabelling in a conventional small-scale radiopharmacy: a feasible approach for routine clinical use.	the number of routine care patient examinations with (68)ga radiopharmaceuticals is still relatively limited, probably caused by the presumed need for large investments in hot cells, automated synthesis modules, laboratory equipment and validation efforts. our aim was to set up the preparation of (68)ga-dota-noc in compliance with all current european union-good manufacturing practices (eu-gmp), current good radiopharmacy practice (cgrpp) and european pharmacopoeia (ph. eur.) guidance but withou ...	2015	25932354
flavobacterium ceti from blood samples of a korean patient with alcoholic liver cirrhosis.		2015	25932454
efficacy of ph elevation as a bactericidal strategy for treating ballast water of freight carriers.	treatment of ship ballast water with sodium hydroxide (naoh) is one method currently being developed to minimize the risk to introduce aquatic invasive species. the bactericidal capability of sodium hydroxide was determined for 148 bacterial strains from ballast water collected in 2009 and 2010 from the m/v indiana harbor, a bulk-freight carrier plying the laurentian great lakes, usa. primary culture of bacteria was done using brain heart infusion agar and a developmental medium. strains were ch ...	2015	26257948
demonstrating the efficacy of the foneastra pasteurization monitor for human milk pasteurization in resource-limited settings.	human milk provides crucial nutrition and immunologic protection for infants. when a mother's own milk is unavailable, donated human milk, pasteurized to destroy bacteria and viruses, is a lifesaving replacement. flash-heat pasteurization is a simple, low-cost, and commonly used method to make milk safe, but currently there is no system to monitor milk temperature, which challenges quality control. foneastra, a smartphone-based mobile pasteurization monitor, removes this barrier by guiding users ...	2015	25668396
active site loop conformation regulates promiscuous activity in a lactonase from geobacillus kaustophilus hta426.	enzyme promiscuity is a prerequisite for fast divergent evolution of biocatalysts. a phosphotriesterase-like lactonase (pll) from geobacillus kaustophilus hta426 (gkap) exhibits main lactonase and promiscuous phosphotriesterase activities. to understand its catalytic and evolutionary mechanisms, we investigated a "hot spot" in the active site by saturation mutagenesis as well as x-ray crystallographic analyses. we found that position 99 in the active site was involved in substrate discrimination ...	2015	25706379
overexpression of penicillin v acylase from streptomyces lavendulae and elucidation of its catalytic residues.	the pva gene from streptomyces lavendulae atcc 13664, encoding a novel penicillin v acylase (slpva), has been isolated and characterized. the gene encodes an inactive precursor protein containing a secretion signal peptide that is activated by two internal autoproteolytic cleavages that release a 25-amino-acid linker peptide and two large domains of 18.79 kda (alpha-subunit) and 60.09 kda (beta-subunit). based on sequence alignments and the three-dimensional model of slpva, the enzyme contains a ...	2015	25501472
brevundimonas diminuta bacteremia in a man with myelodysplastic syndromes.	brevundimonas diminuta are ubiquitous in the environment, but are infrequently isolated from clinical samples. here we report a case of b. diminuta bacteremia in a man with myelodysplastic syndromes (mds) at a teaching hospital in china and review the previously reported cases. the organism was confirmed by culture and 16s rrna sequence analysis with highly sensitivity to broad-spectrum antibiotics. our report and other cases demonstrated that the optimal therapeutic duration for b. diminuta inf ...	2015	26275273
laboratory replication of filtration procedures associated with serratia marcescens bloodstream infections in patients receiving compounded amino acid solutions.	specific deviations from united states pharmacopeia standards were analyzed to investigate the factors allowing an outbreak of serratia marcescens bloodstream infections in patients receiving compounded amino acid solutions.	2015	26195654
detection and characterization of a bacteriocin, putadicin t01, produced by pseudomonas putida isolated from hot spring water.	pseudomonas strains isolated from hot spring water were tested for bacteriocin-like substance (bls) production using a target panel of closely related microorganisms and other gram-positive and gram-negative bacteria. molecular identification was carried out through specific pcr and 16s rna sequence analysis. isolates were identified as brevundimonas diminuta and pseudomonas putida, the latter exhibited antimicrobial activity. pseudomonas putida strains produce an inhibitory substance against ot ...	2015	25556393
characterization of bacterial community of raw milk from dairy cows during subacute ruminal acidosis challenge by high-throughput sequencing.	four cannulated primiparous holstein dairy cows (84 ± 25 dim) were used in a 2 × 2 crossover experimental design. the two diets contained 40% (low-concentrate diet, or control diet, lc) and 70% (high-concentrate diet, or sara induction diet, hc) concentrate feeds respectively. milk samples were collected on days 17, 18 and 19 of each experimental period. dna was extracted from each milk sample, and pyrosequencing was applied to analyse the milk microbial community.	2015	24961605
[peculiarities of the brevundimonas diminuta gl7aca-acylase quaternary structure formation and obtaining stable enzyme analogues].	the physicochemical and enzymatic properties of hybrid analogues of the brevundimonas diminuta gl7aca-acylase (brdgia), containing the n-terminal chitin-binding domain of the bacterial chitinase (brdg1a/nmchbd) or the c-terminal oligohistidine sequence (brdgia/h), were studied. an enhanced thermostability level of brdg1a/nmchbd could suggest the stabilizing effect of the chitin-binding domain. an analysis of ph profiles of the enzymatic activity of recombinat brdgia analogues did not reveal sign ...	2014	25507777
[peculiarities of the brevundimonas diminuta gl7aca-acylase quaternary structure formation and obtaining stable enzyme analogues].	the physicochemical and enzymatic properties of hybrid analogues of the brevundimonas diminuta gl7aca-acylase (brdgia), containing the n-terminal chitin-binding domain of the bacterial chitinase (brdg1a/nmchbd) or the c-terminal oligohistidine sequence (brdgia/h), were studied. an enhanced thermostability level of brdg1a/nmchbd could suggest the stabilizing effect of the chitin-binding domain. an analysis of ph profiles of the enzymatic activity of recombinat brdgia analogues did not reveal sign ...	2014	25434179
comparative investigation of the reaction mechanisms of the organophosphate-degrading phosphotriesterases from agrobacterium radiobacter (opda) and pseudomonas diminuta (oph).	metal ion-dependent, organophosphate-degrading enzymes have acquired increasing attention due to their ability to degrade and thus detoxify commonly used pesticides and nerve agents such as sarin. the best characterized of these enzymes are from pseudomonas diminuta (oph) and agrobacterium radiobacter (opda). despite high sequence homology (>90 % identity) and conserved metal ion coordination these enzymes display considerable variations in substrate specificity, metal ion affinity/preference an ...	2014	25104333
preparation of electrochemical biosensor for detection of organophosphorus pesticides.	polyvinyl chloride (pvc) can be used to develop reaction beaker which acts as electrochemical cell for the measurement of op pesticides. being chemically inert, corrosion resistant, and easy in molding to various shapes and size, pvc can be used for the immobilization of enzyme. organophosphorus hydrolase was immobilized covalently onto the chemically activated inner surface of pvc beaker by using glutaraldehyde as a coupling agent. the carbon nanotubes paste working electrode was constructed fo ...	2014	25667593
maldi-tof mass spectrometry and identification of new bacteria species in air samples from makkah, saudi arabia.	during the hajj season, respiratory symptoms are very common among pilgrims. here, we investigated the viable bacterial population in air samples collected around the slaughterhouses used during the hajj.	2014	25491533
first case reports of ignatzschineria (schineria) indica associated with myiasis.	we report three cases of infection due to the gram-negative rod ignatzschineria (schineria) indica involving bacteremia and the urinary tract. two cases were clearly associated with maggot infestation, and the third could conceivably have had unrecognized maggot infestation of the urinary tract. we believe these cases to be the first i. indica infections reported in association with maggot infestation and myiasis.	2014	25297331
factors influencing persistence of legionella pneumophila serogroup 1 in laboratory cocultures.	risk for infections from legionella pneumophila for immunocompromised individuals increases greatly when this species is present within the biofilm of the water distribution systems of hospitals or other health facilities. multiplication and persistence of legionella may dependent also upon planktonic growth in alternative to sessile growth. here we compared the persistence of l. pneumophila serogroup 1 in experimental planktonic co-cultures subsided with iron, pseudomonas aeruginosa and other n ...	2014	25277877
haloalkylphosphorus hydrolases purified from sphingomonas sp. strain tdk1 and sphingobium sp. strain tcm1.	phosphotriesterases catalyze the first step of organophosphorus triester degradation. the bacterial phosphotriesterases purified and characterized to date hydrolyze mainly aryl dialkyl phosphates, such as parathion, paraoxon, and chlorpyrifos. in this study, we purified and cloned two novel phosphotriesterases from sphingomonas sp. strain tdk1 and sphingobium sp. strain tcm1 that hydrolyze tri(haloalkyl)phosphates, and we named these enzymes haloalkylphosphorus hydrolases (tdk-had and tcm-had, r ...	2014	25038092
new pcr-based open reading frame typing method for easy, rapid, and reliable identification of acinetobacter baumannii international epidemic clones without performing multilocus sequence typing.	antimicrobial resistance issues have become a global health concern. the rapid identification of multidrug-resistant microbes, which depends on microbial genomic information, is essential for overcoming growing antimicrobial resistance challenges. however, genotyping methods, such as multilocus sequence typing (mlst), for identifying international epidemic clones of acinetobacter baumannii are not easily performed as routine tests in ordinary clinical laboratories. in this study, we aimed to dev ...	2014	24899031
computational design of a ph stable enzyme: understanding molecular mechanism of penicillin acylase's adaptation to alkaline conditions.	protein stability provides advantageous development of novel properties and can be crucial in affording tolerance to mutations that introduce functionally preferential phenotypes. consequently, understanding the determining factors for protein stability is important for the study of structure-function relationship and design of novel protein functions. thermal stability has been extensively studied in connection with practical application of biocatalysts. however, little work has been done to ex ...	2014	24959852
sacpox from the thermoacidophilic crenarchaeon sulfolobus acidocaldarius is a proficient lactonase.	sacpox, an enzyme from the extremophilic crenarchaeal sulfolobus acidocaldarius (sac), was isolated by virtue of its phosphotriesterase (or paraoxonase; pox) activity, i.e. its ability to hydrolyze the neurotoxic organophosphorus insecticides. later on, sacpox was shown to belong to the phosphotriesterase-like lactonase family that comprises natural lactonases, possibly involved in quorum sensing, and endowed with promiscuous, phosphotriesterase activity.	2014	24894602
structural characterization and function determination of a nonspecific carboxylate esterase from the amidohydrolase superfamily with a promiscuous ability to hydrolyze methylphosphonate esters.	the uncharacterized protein rsp3690 from rhodobacter sphaeroides is a member of the amidohydrolase superfamily of enzymes. in this investigation the gene for rsp3690 was expressed in escherichia coli and purified to homogeneity, and the three-dimensional structure was determined to a resolution of 1.8 å. the protein folds as a distorted (β/α)8-barrel, and the subunits associate as a homotetramer. the active site is localized to the c-terminal end of the β-barrel and is highlighted by the formati ...	2014	24832101
in vivo self-assembly of stable green fluorescent protein fusion particles and their uses in enzyme immobilization.	bacterial inclusion bodies are aggregations of mostly inactive and misfolded proteins. however, previously the in vivo self-assembly of green fluorescent protein (gfp) fusions into fluorescent particles which displayed specific binding sites suitable for applications in bioseparation and diagnostics was demonstrated. here, the suitability of gfp particles for enzyme immobilization was assessed. the enzymes tested were a thermostable α-amylase from bacillus licheniformis, n-acetyl-d-neuraminic ac ...	2014	24610847
phosphotriesterase-related protein sensed albuminuria and conferred renal tubular cell activation in membranous nephropathy.	membranous nephropathy (mn) is a common cause of nephrotic syndrome that may progress to end-stage renal disease (esrd). the formation of mn involves the in situ formation of subepithelial immune deposits and leads to albuminuria; however, the underlying mechanism of how mn leads to esrd remains unclear. the aim of this study was to investigate the expression and biological functions of phosphotriesterase-related protein (pter) in mn.	2014	24750591
hydrolysis of dfp and the nerve agent (s)-sarin by dfpase proceeds along two different reaction pathways: implications for engineering bioscavengers.	organophosphorus (op) nerve agents such as (s)-sarin are among the most highly toxic compounds that have been synthesized. engineering enzymes that catalyze the hydrolysis of nerve agents ("bioscavengers") is an emerging prophylactic approach to diminish their toxic effects. although its native function is not known, diisopropyl fluorophosphatase (dfpase) from loligo vulgaris catalyzes the hydrolysis of op compounds. here, we investigate the mechanisms of diisopropylfluorophosphate (dfp) and (s) ...	2014	24720808
a 5000-fold increase in the specificity of a bacterial phosphotriesterase for malathion through combinatorial active site mutagenesis.	phosphotriesterases (ptes) have been isolated from a range of bacterial species, including agrobcaterium radiobacter (ptear), and are efficient enzymes with broad substrate ranges. the turnover rate of ptear for the common organophosphorous insecticide malathion is lower than expected based on its physical properties; principally the pka of its leaving group. in this study, we rationalise the turnover rate of ptear for malathion using computational docking of the substrate into a high resolution ...	2014	24721933
significance and biological importance of pyrimidine in the microbial world.	microbes are unique creatures that adapt to varying lifestyles and environment resistance in extreme or adverse conditions. the genetic architecture of microbe may bear a significant signature not only in the sequences position, but also in the lifestyle to which it is adapted. it becomes a challenge for the society to find new chemical entities which can treat microbial infections. the present review aims to focus on account of important chemical moiety, that is, pyrimidine and its various deri ...	2014	25383216
biomarkers and molecular analysis to improve bloodstream infection diagnostics in an emergency care unit.	molecular pathogen detection from blood is still expensive and the exact clinical value remains to be determined. the use of biomarkers may assist in preselecting patients for immediate molecular testing besides blood culture. in this study, 140 patients with ≥ 2 sirs criteria and clinical signs of infection presenting at the emergency department of our hospital were included. c-reactive protein (crp), neutrophil-lymphocyte count ratio (nlcr), procalcitonin (pct) and soluble urokinase plasminoge ...	2014	24475269
effects of polyethoxylate lauryl ether (brij 35) addition on phenanthrene biodegradation in a soil/water system.	non-ionic surfactants usually are often selected for use in surfactant flushing technology, which is a process that can be used as part of pah-contaminated soil bioremediation. phenanthrene (phe) biodegradation in the presence of polyethoxylate lauryl ether (brij 35) was studied in two soil/water systems. the natural soil organic matter content (som) and the present of brij 35, both above the critical micelle concentration (cmc) and below the cmc, changed the rate of phe biodegradation in the pr ...	2014	25320854
temporal changes in the bacterial community of animal feces and their correlation with stable fly oviposition, larval development, and adult fitness.	stable flies are blood-feeding insects with a great negative impact on animals world wide. larvae develop primarily in animal manure and bacteria are essential for larval development; however, the principle of this dependence is not understood. we hypothesized that as the microbial community of animal manure changes over time, it plays an important role in stable fly fitness. two-choice bioassays were conducted using 2 week old horse manure (control) and aging horse manure (fresh to 5 week old) ...	2014	25426108
novel selective medium for isolation of staphylococcus lugdunensis from wound specimens.	we compared a novel selective staphylococcus lugdunensis (ssl) medium with routine media (blood and chocolate agars) for the detection of s. lugdunensis in 990 clinical specimens (from tissue, pus, or wound swabs). significantly more s. lugdunensis isolates were detected on ssl medium (34/990) than on routine medium (7/990) (p = 0.001, mcnemar's test).	2014	24759715
performance of mass spectrometric identification of bacteria and yeasts routinely isolated in a clinical microbiology laboratory using maldi-tof ms.	matrix-assisted laser desorption ionization-time of flight mass spectrometry (maldi-tof ms) is an emerging technology newly applied to identifying bacterial and yeast strains. the aim of this study was to evaluate the clinical performance of the vitek(®) ms system in the identification of bacteria and yeast strains routinely isolated from clinical samples.	2014	24822114