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investigation of the role of arg301 identified in the x-ray structure of phosphite dehydrogenase.phosphite dehydrogenase (ptdh) from pseudomonas stutzeri catalyzes the nicotinamide adenine dinucleotide-dependent oxidation of phosphite to phosphate. the enzyme belongs to the family of d-hydroxy acid dehydrogenases (dhdhs). a search of the protein databases uncovered many additional putative phosphite dehydrogenases. the genes encoding four diverse candidates were cloned and expressed, and the enzymes were purified and characterized. all oxidized phosphite to phosphate and had similar kinetic ...201222564138
bacteria from ips sexdentatus (coleoptera: curculionidae) and their biocontrol potential.ips sexdentatus (coleoptera: curculionidae) is one of the most destructive pests of the spruce trees in europe. in this study, we have isolated and characterized culturable bacteria from i. sexdentatus and tested their insecticidal activity against the last instar larvae of the pest as a possible biocontrol agent. a total of eight bacterial isolates was determined and four of them were identified at species level, and the others were identified at genus level. isolates were identified as stenotr ...201222581609
isolation and characterization of a heterotrophic nitrifier from coke plant wastewater.this study investigated some factors affecting ammonium removal and nitrite accumulation by alcaligenes faecalis c16, which was isolated from the activated sludge of a coking wastewater treatment plant. nitrite was produced from ammonium only in the presence of citrate, acetate, meat extract, peptone or ethanol. the highest amount of nitrite was found with citrate as carbon source. a. faecalis c16 could not use glucose, fructose, sucrose and methanol. under the optimum conditions of initial ph 6 ...201222592482
performances of the vitek ms matrix-assisted laser desorption ionization-time of flight mass spectrometry system for rapid identification of bacteria in routine clinical microbiology.rapid and cost-effective matrix-assisted laser desorption ionization-time of flight mass spectrometry (maldi-tof ms)-based systems will replace conventional phenotypic methods for routine identification of bacteria. we report here the first evaluation of the new maldi-tof ms-based vitek ms system in a large clinical microbiology laboratory. this system uses an original spectrum classifier algorithm and a specific database designed for the identification of clinically relevant species. we have te ...201222593596
induction of immune-related gene expression in ctenopharyngodon idella kidney cells by secondary metabolites from immunostimulatory alcaligenes faecalis fy-3.this study was undertaken to isolate active secondary metabolites from immunostimulatory alcaligenes faecalis fy-3 and evaluate their activities using grass carp ctenopharyngodon idella kidney (cik) cells. by applying chromatography techniques and successive recrystallization, three purified metabolites were obtained and identified by spectral data (mass spectrometry and nuclear magnetic resonance) as: (1) phenylacetic acid, (2) p-hydroxyphenylacetylamide and (3) cyclo-(gly-(l)-pro). cik cells w ...201222606987
biotechnological tools for environmental sustainability: prospects and challenges for environments in nigeria-a standard review.the environment is a very important component necessary for the existence of both man and other biotic organisms. the degree of sustainability of the physical environment is an index of the survival and well-being of the entire components in it. additionally, it is not sufficient to try disposing toxic/deleterious substances with any known method. the best method of sustaining the environment is such that returns back all the components (wastes) in a recyclable way so that the waste becomes usef ...201222611499
expression, and molecular and enzymatic characterization of cu-containing nitrite reductase from a marine ammonia-oxidizing gammaproteobacterium, nitrosococcus oceani.ammonia-oxidizing bacteria (aob) remove intracellular nitrite to prevent its toxicity by a nitrifier denitrification pathway involving two denitrifying enzymes, nitrite reductase and nitric oxide reductase. here, a cu-containing nitrite reductase from nitrosococcus oceani strain ns58, a gammaproteobacterial marine aob, was expressed in escherichia coli and purified to homogeneity. sequence homology analysis indicated that the nitrite reductase from n. oceani was phylogenetically closer to its co ...201222641151
penicillin acylase-catalyzed effective and stereoselective acylation of 1-phenylethylamine in aqueous medium using non-activated acyl donor.until recently, the biocatalytic preparation of enantiomerically pure amines was based on stereoselective acyl transfer in an organic medium using activated acyl donors. the possibility of performing an effective and enantioselective enzymatic acylation of amines in an aqueous medium without using activated acyl donors was demonstrated for the first time as the example of direct condensation of phenylacetic acid and racemic 1-phenylethylamine. direct condensation of the acid and the amine took p ...201022649633
protein engineering of penicillin acylase.penicillin acylases (pa) are widely used for the production of semi-synthetic β-lactam antibiotics and chiral compounds. in this review, the latest achievements in the production of recombinant enzymes are discussed, as well as the results of pa type g protein engineering.201022649651
comparison of the potency of a variety of β-glucans to induce cytokine production in human whole blood.β-glucans are components of fungal cell walls and potent stimulants of innate immunity. the majority of research on biological activities of glucans has focused on β-(1→3)-glucans, which have been implicated in relation to fungal exposure-associated respiratory symptoms and as important stimulatory agents in anti-fungal immune responses. fungi-and bacteria and plants-produce a wide variety of glucans with vast differences in the proportion and arrangement of their β-(1→3)-, -(1→4)- and -(1→6)-gl ...201222653750
comparison of the potency of a variety of β-glucans to induce cytokine production in human whole blood.β-glucans are components of fungal cell walls and potent stimulants of innate immunity. the majority of research on biological activities of glucans has focused on β-(1→3)-glucans, which have been implicated in relation to fungal exposure-associated respiratory symptoms and as important stimulatory agents in anti-fungal immune responses. fungi-and bacteria and plants-produce a wide variety of glucans with vast differences in the proportion and arrangement of their β-(1→3)-, -(1→4)- and -(1→6)-gl ...201222653750
chemical characterization, crossfeeding and uptake studies on hydroxamate siderophore of alcaligenes faecalis.we report the production of two types of siderophores namely catecholate and hydroxamate in modified succinic acid medium (sm) from alcaligenes faecalis. two fractions of siderophores were purified on amberlite xad, major fraction was hydroxamate type having a λ(max) at 224 nm and minor fraction appeared as catecholate with a λ(max) of 264 nm. the recovery yield obtained from major and minor fractions was 297 and 50 mg ml(-1) respectively. the ief pattern of xad-4 purified siderophore suggested ...201122654161
actinobacterial nitrate reducers and proteobacterial denitrifiers are abundant in n2o-metabolizing palsa peat.palsa peats are characterized by elevated, circular frost heaves (peat soil on top of a permanently frozen ice lens) and are strong to moderate sources or even temporary sinks for the greenhouse gas nitrous oxide (n(2)o). palsa peats are predicted to react sensitively to global warming. the acidic palsa peat skalluvaara (approximate ph 4.4) is located in the discontinuous permafrost zone in northwestern finnish lapland. in situ n(2)o fluxes were spatially variable, ranging from 0.01 to -0.02 μmo ...201222660709
production and downstream processing of (1→3)-β-d-glucan from mutant strain of agrobacterium sp. atcc 31750.we isolated a mutant that produced higher levels of curdlan than the wild strain agrobacterium sp. atcc 31750 by chemical mutagenesis using n-methyl-n-nitro-nitrosoguanidine. the mutant strain produced 66 g/l of curdlan in 120 h with a yield of (0.88) while, the wild strain produced 41 g/l in 120 h with a yield of (0.62) in a stirred bioreactor. the mutant could not produce curdlan when the ph was shifted from 7.0 to 5.5 after nitrogen depletion as followed for wild strain. in contrast, ph optim ...201222681895
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
macrophage dectin-1 expression is controlled by leukotriene b4 via a gm-csf/pu.1 axis.pattern recognition receptors for fungi include dectin-1 and mannose receptor, and these mediate phagocytosis, as well as production of cytokines, reactive oxygen species, and the lipid mediator leukotriene b(4) (ltb(4)). the influence of g protein-coupled receptor ligands such as ltb(4) on fungal pattern recognition receptor expression is unknown. in this study, we investigated the role of ltb(4) signaling in dectin-1 expression and responsiveness in macrophages. genetic and pharmacologic appro ...201222696442
purification, characterization, and primary structure of a novel n-acyl-d-amino acid amidohydrolase from microbacterium natoriense tnjl143-2.a novel n-acyl-d-amino acid amidohydrolase (daa) was purified from the cells of a novel species of the genus microbacterium. the purified enzyme, termed acym, was a monomeric protein with an apparent molecular weight of 56,000. it acted on n-acylated hydrophobic d-amino acids with the highest preference for n-acetyl-d-phenylalanine (nadf). optimum temperature and ph for the hydrolysis of nadf were 45°c and ph 8.5, respectively. the k(cat) and k(m) values for nadf were 41 s⁻¹ and 2.5 mm at 37°c a ...201222721690
characterization of contaminants from a sanitized milk processing plant.milk processing lines offer a wide variety of microenvironments where a diversity of microorganisms can proliferate. we sampled crevices and junctions where, due to deficient reach by typical sanitizing procedures, bacteria can survive and establish biofilms. the sampling sites were the holding cell, cold storage tank, pasteurizer and storage tank--transfer pump junction. the culturable bacteria that were isolated after the sanitation procedure were predominantly pseudomonas spp., serratia spp, ...201222761957
comparative study of bacterial status from conjunctival sac of the elder qiang minority and han people with dry eye in sichuan, china.to compare the status of bacteria in the conjunctival sac from the elder qiang minority and han people with dry eyes in sichuan, china.201222773985
pcr offers no advantage over culture for microbiologic diagnosis in cellulitis.most cases of cellulitis are traditionally attributed to β-hemolytic streptococcus and staphylococcus species, although in most cases, no organism is identified. development of pcr using the conserved bacterial 16 s rrna dna permits identification of bacteria independent of conventional culture approaches and prior use of antibiotics.201222802097
the importance of rhamnolipid-biosurfactant-induced changes in bacterial membrane lipids of bacillus subtilis for the antimicrobial activity of thiosulfonates.the antimicrobial properties of methyl (mts) and ethyl (ets) esters of thiosulfonic acid alone and in combination with rhamnolipid-biosurfactant (rl) have been characterized for their ability to disrupt the normal physiological functions of living pathogens. bactericidal and fungicidal activities of mts and ets and their combination with rhamnolipid were demonstrated on strains of pseudomonas aeruginosa, bacillus subtilis, alcaligenes faecalis, and rhizopus ngtricans. it was found that the combi ...201222810959
cloning and expression analysis of genes encoding lytic endopeptidases l1 and l5 from lysobacter sp. strain xl1.lytic enzymes are the group of hydrolases that break down structural polymers of the cell walls of various microorganisms. in this work, we determined the nucleotide sequences of the lysobacter sp. strain xl1 alpa and alpb genes, which code for, respectively, secreted lytic endopeptidases l1 (alpa) and l5 (alpb). in silico analysis of their amino acid sequences showed these endopeptidases to be homologous proteins synthesized as precursors similar in structural organization: the mature enzyme se ...201222865082
functional expression of a penicillin acylase from the extreme thermophile thermus thermophilus hb27 in escherichia coli.penicillin acylases (pacs) are enzymes of industrial relevance in the manufacture of β-lactam antibiotics. development of a pac with a longer half-life under the reaction conditions used is essential for the improvement of the operational stability of the process. a gene encoding a homologue to escherichia coli pac was found in the genome of the thermophilic bacterium thermus thermophilus (tth) hb27. because of the nature of this pac and its complex maturation that is crucial to reach its functi ...201222876915
bacterial contamination of dental unit waterlines.safety of patients and dental personnel requires the appropriate microbiological water quality in dental units. during treatment, patients and dental workers are exposed both to direct contact with bacteria-contaminated water in the form of splatter and with contaminated water aerosol emitted during work by unit handpieces, including rotating and ultrasonic instruments. the aim of the study was to determine the qualitative and quantitative contamination of water in dental unit reservoirs with ae ...201222899458
bacterial contamination of dental unit waterlines.safety of patients and dental personnel requires the appropriate microbiological water quality in dental units. during treatment, patients and dental workers are exposed both to direct contact with bacteria-contaminated water in the form of splatter and with contaminated water aerosol emitted during work by unit handpieces, including rotating and ultrasonic instruments. the aim of the study was to determine the qualitative and quantitative contamination of water in dental unit reservoirs with ae ...201222899458
carbon fiber as an excellent support material for wastewater treatment biofilms.fibrous materials made of carbon fiber (cf), aromatic polyamide (ap), preoxidized polyacrylonitrile (pan), and polyethylene (pe), which are widely used in the textile industry, were evaluated as biofilm supports for wastewater treatment. we found that cf has a high capacity for adsorbing nitrifying bacterial sludge. the adhesion rate of four pure strains-cytophaga hutchinsonii, alcaligenes faecalis, bacillus subtilis, and escherichia coli-was highest to cf. the ζ-potentials of the fibrous suppor ...201222906194
draft genome sequence of alcaligenes faecalis subsp. faecalis ncib 8687 (ccug 2071).alcaligenes faecalis subsp. faecalis ncib 8687, the betaproteobacterium from which arsenite oxidase had its structure solved and the first "arsenate gene island" identified, provided a draft genome of 3.9 mb in 186 contigs (with the largest 15 comprising 90% of the total) for this opportunistic pathogen species.201222933773
isolation of kerstersia gyiorum from a patient with cholesteatomatous chronic otitis media.we describe the first case of a kerstersia gyiorum strain isolated from a patient with cholesteatomatous chronic otitis media. we emphasize the isolation of members of the family alcaligenaceae in serious infections and unusual sites and the importance of polyphasic identification addressing the definitive identification.201222972825
bio-activity of natural polymers from the genus pistacia: a validated model for their antimicrobial action.the polymers from mastic gum of pistacia lentiscose and subspecies of pistacia atlantica, (sp. kurdica, mutica and cabolica) have been isolated and characterised by gel permeation chromatography (gpc) and 13c nmr spectroscopy as cis-1,4-poly-?-myrcenes. they were screened against helicobacter pylori and other gram-negative and gram-positive bacteria to evaluate their antimicrobial action. in order to further test their hypothesised mode of action, two polymer types were synthesized: one from myr ...201122980106
isolation, analysis and antimicrobial activity of the acidic fractions of mastic, kurdica, mutica and cabolica gums from genus pistacia.the chemical entities of mastic, kurdica, mutica and cabolica gums from genus pistacia have been isolated and characterised by gc-mass spectrometry, high performance liquid chromatography and column chromatography. these chemical entities were screened for anti-microbial activities against nine strains of helicobacter pylori and some other gram-negative and gram-positive bacteria. the most bioactive components were structurally analysed. these components mimic steroid compounds, in particular, t ...201122980113
phylogenetically novel luxi/luxr-type quorum sensing systems isolated using a metagenomic approach.a great deal of research has been done to understand bacterial cell-to-cell signaling systems, but there is still a large gap in our current knowledge because the majority of microorganisms in natural environments do not have cultivated representatives. metagenomics is one approach to identify novel quorum sensing (qs) systems from uncultured bacteria in environmental samples. in this study, fosmid metagenomic libraries were constructed from a forest soil and an activated sludge from a coke plan ...201222983963
evaluation of serological diagnostic tests for typhoid fever in papua new guinea using a composite reference standard.typhoid fever remains a major global health problem. a major impediment to improving outcomes is the lack of appropriate diagnostic tools, which have not significantly improved in low-income settings for 100 years. we evaluated two commercially available rapid diagnostic tests (tubex and typhidot), a prototype (typhirapid tr-02), and the commonly used single-serum widal test in a previously reported high-burden area of papua new guinea. samples were collected from 530 outpatients with axillary t ...201222993409
genome sequence of a highly efficient aerobic denitrifying bacterium, pseudomonas stutzeri t13.pseudomonas stutzeri t13 is a highly efficient aerobic denitrifying bacterium. information about the genome of this aerobic denitrifying bacterium has been limited until now. we present the draft genome of p. stutzeri t13. the results could provide further insight into the aerobic denitrification mechanism in strain t13.201223012292
bacteria in crude oil survived autoclaving and stimulated differentially by exogenous bacteria.autoclaving of crude oil is often used to evaluate the hydrocarbon-degrading abilities of bacteria. this may be potentially useful for bioaugmentation and microbial enhanced oil recovery (meor). however, it is not entirely clear if "endogenous" bacteria (e.g., spores) in/on crude oil survive the autoclaving process, or influence subsequent evaluation of the hydrocarbon-degradation abilities of the "exogenous" bacterial strains. to test this, we inoculated autoclaved crude oil medium with six exo ...201223028421
genetic contexts of blandm-1. 201223074228
effect of nitrogen source on curdlan production by alcaligenes faecalis atcc 31749.this study aims to investigate the effect of nitrogen source on curdlan production by alcaligenes faecalis atcc 31749. curdlan production fell when excess nitrogen source was present, while biomass accumulation increased as the level of nitrogen source raised. curdlan production and biomass accumulation were greater with urea compared with those with other nitrogen sources. the highest production of curdlan and biomass accumulation by a. faecalis atcc 31749 was 28.16 g l(-1) and 9.58 g l(-1), re ...201323085490
hypochlorite digestion method for efficient recovery of phb from alcaligenes faecalis.we reported the optimum amount of phb accumulated by alcaligenes faecalis during its 24 h growth under nitrogen deficient conditions. after 24 h incubation decrease in the amount of phb was recorded. hypochlorite digestion of biomass of organism followed by extraction with a solvent system consisting of 1:1 mixture of ethanol and acetone resulted in efficient recovery of phb vis-à-vis earlier methods. this solvent system gave a high recovery yield, i.e. 5.6 gl(-1) vis-à-vis earlier reported yiel ...200923100774
growth and siderophores production in alcaligenes faecalis is regulated by metal ions.during stationary phase of growth under low stress of iron in succinic acid medium, alcaligenes feacalis bccm id 2374 produced microbial iron chelators. increase in iron concentration supported bacterial growth but suppressed siderophores production, 1 μm and 2 μm of iron was optimum for maximum siderophore yield, i.e. 354 and 360 μg/ml in untreated and deferrated medium, respectively. threshold level of iron, which suppressed siderophores production in a. feacalis bccm id 2374, was 20 μm. ten m ...201023100825
draft genome sequence of achromobacter piechaudii strain hle.achromobacter piechaudii strain hle is a betaproteobacterium (previously known as alcaligenes faecalis) that was an early isolate with arsenite oxidase activity. this draft genome of 6.89 mb is the second available genome for this species in the opportunistic pathogen alcaligenaceae family.201223105084
p-coumaric acid influenced cucumber rhizosphere soil microbial communities and the growth of fusarium oxysporum f.sp. cucumerinum owen.autotoxicity of cucumber root exudates or decaying residues may be the cause of the soil sickness of cucumber. however, how autotoxins affect soil microbial communities is not yet fully understood.201223118972
cold-adapted arsenite oxidase from a psychrotolerant polaromonas species.polaromonas sp. str. gm1 is an aerobic, psychrotolerant, heterotrophic member of the betaproteobacteria and is the only isolate capable of oxidising arsenite at temperatures below 10 °c. sequencing of the aio gene cluster in gm1 revealed the presence of the aiob and aioa genes, which encode the arsenite oxidase but the regulatory genes typically found upstream of aiob in other members of the proteobacteria were absent. the gm1 aio was purified to homogeneity and was found to be a heterodimer. th ...201323150098
brucella β 1,2 cyclic glucan is an activator of human and mouse dendritic cells.bacterial cyclic glucans are glucose polymers that concentrate within the periplasm of alpha-proteobacteria. these molecules are necessary to maintain the homeostasis of the cell envelope by contributing to the osmolarity of gram negative bacteria. here, we demonstrate that brucella β 1,2 cyclic glucans are potent activators of human and mouse dendritic cells. dendritic cells activation by brucella β 1,2 cyclic glucans requires tlr4, myd88 and trif, but not cd14. the brucella cyclic glucans show ...201223166489
role of the moth fly clogmia albipunctata (diptera: psychodinae) as a mechanical vector of bacterial pathogens in german hospitals.the formerly mediterranean moth fly species clogmia albipunctata (diptera: psychodidae) is now present in germany, where it has become a common, year-round pest in hospital buildings.201323182212
microbial population responses to ph and salt shock during phenols degradation under high salt conditions revealed by risa and afdra.the responses of microbial community to ph and salt shock during phenols degradation under high salt conditions were revealed by two dna fingerprint methods, i.e. ribosomal intergenic spacer analysis (risa) and amplified functional dna restriction analysis (afdra), together with 16s rdna clone library analysis. it was shown that the phenols removal rate was improved with increasing nacl concentration from 0 to 50 mg/l, and could remain at a high level even in the presence of 100 mg/l nacl. the d ...201323202556
bacterial exopolysaccharides: functionality and prospects.diverse structural, functional and valuable polysaccharides are synthesized by bacteria of all taxa and secreted into the external environment. these polysaccharides are referred to as exopolysaccharides and they may either be homopolymeric or heteropolymeric in composition and of diverse high molecular weights (10 to 1000 kda). the material properties of exopolysaccharides have revolutionized the industrial and medical sectors due to their retinue of functional applications and prospects. these ...201223203046
bacterial bio-resources for remediation of hexachlorocyclohexane.in the last few decades, highly toxic organic compounds like the organochlorine pesticide (op) hexachlorocyclohexane (hch) have been released into the environment. all hch isomers are acutely toxic to mammals. although nowadays its use is restricted or completely banned in most countries, it continues posing serious environmental and health concerns. since hch toxicity is well known, it is imperative to develop methods to remove it from the environment. bioremediation technologies, which use mic ...201223203113
isolation and identification of the microbiota of danish farmhouse and industrially produced surface-ripened cheeses.for studying the microbiota of four danish surface-ripened cheeses produced at three farmhouses and one industrial dairy, both a culture-dependent and culture-independent approach were used. after dereplication of the initial set of 433 isolates by (gtg)5-pcr fingerprinting, 217 bacterial and 25 yeast isolates were identified by sequencing of the 16s rrna gene or the d1/d2 domain of the 26s rrna gene, respectively. at the end of ripening, the cheese core microbiota of the farmhouse cheeses consi ...201223224222
isolation and identification of the microbiota of danish farmhouse and industrially produced surface-ripened cheeses.for studying the microbiota of four danish surface-ripened cheeses produced at three farmhouses and one industrial dairy, both a culture-dependent and culture-independent approach were used. after dereplication of the initial set of 433 isolates by (gtg)5-pcr fingerprinting, 217 bacterial and 25 yeast isolates were identified by sequencing of the 16s rrna gene or the d1/d2 domain of the 26s rrna gene, respectively. at the end of ripening, the cheese core microbiota of the farmhouse cheeses consi ...201223224222
designing a functional type 2 copper center that has nitrite reductase activity within α-helical coiled coils.one of the ultimate objectives of de novo protein design is to realize systems capable of catalyzing redox reactions on substrates. this goal is challenging as redox-active proteins require design considerations for both the reduced and oxidized states of the protein. in this paper, we describe the spectroscopic characterization and catalytic activity of a de novo designed metallopeptide cu(i/ii)(tril23h)(3)(+/2+), where cu(i/ii) is embeded in α-helical coiled coils, as a model for the cu(t2) ce ...201223236170
assignment of pterin deaminase activity to an enzyme of unknown function guided by homology modeling and docking.of the over 22 million protein sequences in the nonredundant trembl database, fewer than 1% have experimentally confirmed functions. structure-based methods have been used to predict enzyme activities from experimentally determined structures; however, for the vast majority of proteins, no such structures are available. here, homology models of a functionally uncharacterized amidohydrolase from agrobacterium radiobacter k84 (arad3529) were computed on the basis of a remote template structure. th ...201323256477
engineering the substrate specificity of a thermophilic penicillin acylase from thermus thermophilus.a homologue of the escherichia coli penicillin acylase is encoded in the genomes of several thermophiles, including in different thermus thermophilus strains. although the natural substrate of this enzyme is not known, this acylase shows a marked preference for penicillin k over penicillin g. three-dimensional models were created in which the catalytic residues and the substrate binding pocket were identified. through rational redesign, residues were replaced to mimic the aromatic binding site o ...201223263966
marked changes in electron transport through the blue copper protein azurin in the solid state upon deuteration.measuring solid-state electron transport (etp) across proteins allows studying electron transfer (et) mechanism(s), while minimizing solvation effects on the process. etp is, however, sensitive to any static (conformational) or dynamic (vibrational) changes in the protein. our macroscopic measurements allow extending etp studies to low temperatures, with the concomitant resolution of lower current densities, because of the larger electrode contact areas. thus, earlier we reported temperature-ind ...201223267087
marked changes in electron transport through the blue copper protein azurin in the solid state upon deuteration.measuring solid-state electron transport (etp) across proteins allows studying electron transfer (et) mechanism(s), while minimizing solvation effects on the process. etp is, however, sensitive to any static (conformational) or dynamic (vibrational) changes in the protein. our macroscopic measurements allow extending etp studies to low temperatures, with the concomitant resolution of lower current densities, because of the larger electrode contact areas. thus, earlier we reported temperature-ind ...201223267087
exploring residues crucial for nitrilase function by site directed mutagenesis to gain better insight into sequence-function relationships.nitrilases represent a very important class of enzymes having an array of applications. in the present scenario, where the indepth information about nitrilases is limited, the present work is an attempt to shed light on the residues crucial for the nitrilase activity. the nitrilase sequences demonstrating varying degree of identity with p. putida nitrilase were explored. a stretch of residues, fairly conserved throughout the range of higher (96%) to lower (27%) sequence identity among different ...201223301203
enantioselective acylation of β-phenylalanine acid and its derivatives catalyzed by penicillin g acylase from alcaligenes faecalis.this study developed a simple, efficient method for producing racemic β-phenylalanine acid (bpa) and its derivatives via the enantioselective acylation catalyzed by the penicillin g acylase from alcaligenes faecalis (af-pga). when the reaction was run at 25°c and ph 10 in an aqueous medium containing phenylacetamide and bpa in a molar ratio of 2:1, 8 u/ml enzyme and 0.1 m bpa, the maximum bpa conversion efficiency at 40 min only reached 36.1%, which, however, increased to 42.9% as the ph value a ...201323302108
high-throughput system for screening of cephalosporin c high-yield strain by 48-deep-well microtiter plates.improvement of microbial strains for the high-production of industrial products has been the hallmark of all commercial fermentation processes. strain improvement has been conventionally achieved through mutation and selection. however, most of the screenings were performed in shake flasks, which made the screening procedure very complex, time-consuming, and inefficient. most mutant spore suspension had no chance to be screened due to the low-throughput of shake flasks and had to be sacrificed. ...201323334835
heterotrophic nitrifying and oxygen tolerant denitrifying bacteria from greenwater system of coastal aquaculture.in this work, herbivorous fish mugil cephalus has been cultured to secrete protein rich green slime, which helps nitrifying and oxygen tolerant denitrifying bacteria to grow and colonize. four strains representing alcaligenaceae family have been isolated from greenwater system and characterized using biochemical test, fatty acid methyl ester (gc-fame) analysis, 16s rrna and functional gene approaches. they were tested for an ability to nitrify ammonia and nitrite aerobically. two strains showed ...201323354499
degradation of poly(ε-caprolactone) by thermophilic streptomyces thermoviolaceus subsp. thermoviolaceus 76t-2.a thermophilic streptomyces thermoviolaceus subsp. thermoviolaceus isolate 76t-2 that can degrade poly(ε-caprolactone) (pcl) was isolated from soil in taiwan. isolate 76t-2 grew well in urea fructose oatmeal medium and exhibited clear zones on agar plates containing pcl, indicating the presence of extracellular pcl depolymerases. the pcl powder present in culture medium was completely degraded within 6 h of culture at 45°c. two pcl-degrading enzymes were purified to homogeneity from the culture ...201323360778
discovery and characterization of a highly efficient enantioselective mandelonitrile hydrolase from burkholderia cenocepacia j2315 by phylogeny-based enzymatic substrate specificity prediction.a nitrilase-mediated pathway has significant advantages in the production of optically pure (r)-(-)-mandelic acid. however, unwanted byproduct, low enantioselectivity, and specific activity reduce its value in practical applications. an ideal nitrilase that can efficiently hydrolyze mandelonitrile to optically pure (r)-(-)-mandelic acid without the unwanted byproduct is needed.201323414071
isolation and identification of hydrocarbon degrading bacteria from ennore creek.the widespread problem caused due to petroleum products, is their discharge and accidental spillage in marine environment proving to be hazardous to the surroundings as well as life forms. thus remediation of these hydrocarbons by natural decontamination process is of utmost importance. bioremediation is a non-invasive and cost effective technique for the clean-up of these petroleum hydrocarbons. in this study we have investigated the ability of microorganisms present in the sediment sample to d ...201323424279
the tryptophan synthase α2β2 complex: a model for substrate channeling, allosteric communication, and pyridoxal phosphate catalysis.i reflect on my research on pyridoxal phosphate (plp) enzymes over fifty-five years and on how i combined research with marriage and family. my ph.d. research with esmond e. snell established one aspect of plp enzyme mechanism. my postdoctoral work first with hans l. kornberg and then with alton meister characterized the structure and function of another plp enzyme, l-aspartate β-decarboxylase. my independent research at the national institutes of health (nih) since 1966 has focused on the bacte ...201323426371
chlamydomonas reinhardtii thermal tolerance enhancement mediated by a mutualistic interaction with vitamin b12-producing bacteria.temperature is one of the most important environmental factors affecting the growth and survival of microorganisms and in light of current global patterns is of particular interest. here, we highlight studies revealing how vitamin b12 (cobalamin)-producing bacteria increase the fitness of the unicellular alga chlamydomonas reinhardtii following an increase in environmental temperature. heat stress represses c. reinhardtii cobalamin-independent methionine synthase (mete) gene expression coincidin ...201323486253
specific and sensitive detection of alcaligenes species from an agricultural environment.a quantitative real-time pcr assay to specifically detect and quantify the genus alcaligenes in samples from the agricultural environment, such as vegetables and farming soils, was developed. the minimum detection sensitivity was 106 fg of pure culture dna, corresponding to dna extracted from two cells of alcaligenes faecalis. to evaluate the detection limit of a. faecalis, serially diluted genomic dna from this organism was mixed with dna extracted from soil and vegetables and then a standard c ...201323489084
enzymatic reduction of levulinic acid by engineering the substrate specificity of 3-hydroxybutyrate dehydrogenase.enzymatic reduction of levulinic acid (la) was performed for the synthesis of 4-hydroxyvaleric acid (4hv)--a monomer of bio-polyester and a precursor of bio-fuels--using 3-hydroxybutyrate dehydrogenase (3hbdh) from alcaligenes faecalis. due to the catalytic inactivity of the wild-type enzyme toward la, engineering of the substrate specificity of the enzyme was performed. a rational design approach with molecular docking simulation was applied, and a double mutant, his144leu/trp187phe, which has ...201323489571
dectin-1 regulates il-10 production via a msk1/2 and creb dependent pathway and promotes the induction of regulatory macrophage markers.in response to infection by fungal pathogens, the innate immune system recognises specific fungal pathogen associated molecular patterns (pamps) via pattern recognition receptors including the c-type lectin dectin-1 and members of the toll like receptor (tlr) family. stimulation of these receptors leads to the induction of both pro- and anti-inflammatory cytokines. the protein kinases msk1 and 2 are known to be important in limiting inflammatory cytokine production by macrophages in response to ...201323533666
kinetics of arsenite removal by halobacteria from a highland andean chilean salar.the purpose of this study was to identify arsenite-oxidizing halobacteria in samples obtained from salar de punta negra, ii region of chile. seven bacterial isolates, numbered as isolates i to vii, grown in a culture medium with 100 ppm as naaso2 (as (iii)) were tested. bacterial growth kinetics and the percent of arsenite removal (par) were performed simultaneously with the detection of an arsenite oxidase enzyme through dot blot analysis.201323547876
detection of new delhi metallo-β-lactamase (encoded by blandm-1) in acinetobacter schindleri during routine surveillance.a carbapenem-resistant alcaligenes faecalis strain was isolated from a surveillance swab of a service member injured in afghanistan. the isolate was positive for bla(ndm) by real-time pcr. species identification was reevaluated on three identification systems but was inconclusive. genome sequencing indicated that the closest relative was acinetobacter schindleri and that bla(ndm-1) was carried on a plasmid that shared >99% identity with one identified in an acinetobacter lwoffii isolate. the iso ...201323554204
production of indole acetic acid by pseudomonas sp.: effect of coinoculation with mesorhizobium sp. cicer on nodulation and plant growth of chickpea (cicer arietinum).pseudomonas isolates obtained from the rhizosphere of chickpea (cicer arietinum l.) and green gram (vigna radiata) were found to produce significant amount of indole acetic acid (iaa) when grown in a lb medium broth supplemented with l-tryptophan. seed bacterization of chickpea cultivar c235 with different pseudomonas isolates showed stunting effect on the development of root and shoot at 5 and 10 days of seedling growth except the strains mps79 and mps90 that showed stimulation of root growth, ...201123572992
assessing bacterial diversity in a seawater-processing wastewater treatment plant by 454-pyrosequencing of the 16s rrna and amoa genes.the bacterial community composition of activated sludge from a wastewater treatment plant (almería, spain) with the particularity of using seawater was investigated by applying 454-pyrosequencing. the results showed that deinococcus-thermus, proteobacteria, chloroflexi and bacteroidetes were the most abundant retrieved sequences, while other groups, such as actinobacteria, chlorobi, deferribacteres, firmicutes, planctomycetes, spirochaetes and verrumicrobia were reported at lower proportions. ra ...201323574645
a prospective study of the causes of febrile illness requiring hospitalization in children in cambodia.febrile illnesses are pre-eminent contributors to morbidity and mortality among children in south-east asia but the causes are poorly understood. we determined the causes of fever in children hospitalised in siem reap province, cambodia.201323593267
two cases of kerstersia gyiorum isolated from sites of chronic infection.kerstersia gyiorum is infrequently associated with human infection. we report the isolation of kerstersia gyiorum from two patients: the first, a patient with chronic ear infections, and the second, a patient with a chronic leg wound. both isolates were resistant to ciprofloxacin, which has not been previously reported.201323596236
paracoccus denitrificans pd1222 utilizes hypotaurine via transamination followed by spontaneous desulfination to yield acetaldehyde and, finally, acetate for growth.hypotaurine (ht; 2-aminoethane-sulfinate) is known to be utilized by bacteria as a sole source of carbon, nitrogen, and energy for growth, as is taurine (2-aminoethane-sulfonate); however, the corresponding ht degradation pathway has remained undefined. genome-sequenced paracoccus denitrificans pd1222 utilized ht (and taurine) quantitatively for heterotrophic growth and released the ht sulfur as sulfite (and sulfate) and ht nitrogen as ammonium. enzyme assays with cell extracts suggested that an ...201323603744
multicenter evaluation of the vitek ms matrix-assisted laser desorption ionization-time of flight mass spectrometry system for identification of gram-positive aerobic bacteria.matrix-assisted laser desorption ionization-time of flight mass spectrometry (maldi-tof) is gaining momentum as a tool for bacterial identification in the clinical microbiology laboratory. compared with conventional methods, this technology can more readily and conveniently identify a wide range of organisms. here, we report the findings from a multicenter study to evaluate the vitek ms v2.0 system (biomérieux, inc.) for the identification of aerobic gram-positive bacteria. a total of 1,146 uniq ...201323658261
secondary bacterial infections of buruli ulcer lesions before and after chemotherapy with streptomycin and rifampicin.buruli ulcer (bu), caused by mycobacterium ulcerans is a chronic necrotizing skin disease. it usually starts with a subcutaneous nodule or plaque containing large clusters of extracellular acid-fast bacilli. surrounding tissue is destroyed by the cytotoxic macrolide toxin mycolactone produced by microcolonies of m. ulcerans. skin covering the destroyed subcutaneous fat and soft tissue may eventually break down leading to the formation of large ulcers that progress, if untreated, over months and ...201323658847
halomonas sp. bs4, a biosurfactant producing halophilic bacterium isolated from solar salt works in india and their biomedical importance.halophilic bacteria were isolated from thamaraikulam solar salt works in india. after routine biosurfactant screening by various methods, the biosurfactant producing bacteria, halomonas sp bs4 was confirmed by 16 s rrna sequencing. the growth optimization of halomonas sp bs4 revealed their optimum growth at 8% nacl and 6-8 ph in the growth medium. further the partially purified biosurfactants were characterized by tlc, ftir and gc-ms analysis. gc-ms results revealed that, the partial purified bi ...201323667807
fusion of binding domains to thermobifida cellulosilytica cutinase to tune sorption characteristics and enhancing pet hydrolysis.a cutinase from thermomyces cellullosylitica (thc_cut1), hydrolyzing the synthetic polymer polyethylene terephthalate (pet), was fused with two different binding modules to improve sorption and thereby hydrolysis. the binding modules were from cellobiohydrolase i from hypocrea jecorina (cbm) and from a polyhydroxyalkanoate depolymerase from alcaligenes faecalis (pbm). although both binding modules have a hydrophobic nature, it was possible to express the proteins in e. coli . both fusion enzymes ...201323718548
antibacterial activity of honey on cariogenic bacteria.honey has antibacterial activity. the aim of this study was to evaluate the antibacterial activity of honey on streptococcus mutans and lactobacillus.201323724198
isolation of cellulolytic bacillus subtilis strains from agricultural environments.the bioconversion of cellulose and hemicellulose to soluble sugars is important for global stabilization and a sustainable human society. here, hundreds of cellulolytic bacteria were screened and isolated from soil, compost, and animal waste slurry in jeju island, south korea. among the isolates, three strains, sl9-9, c5-16, and s52-2, showing higher potential for practical uses were purified on carboxymethyl cellulose (cmc) agar plates and identified as bacillus subtilis strains by morphologica ...201223724328
reduction of contaminants (physical, chemical, and microbial) in domestic wastewater through hybrid constructed wetland.the current research was focused mainly on the designing and construction of efficient laboratory scale hybrid constructed wetland (hcw) for the treatment of domestic wastewater. parameters like cod, bod5, po4, so4, no3, no2, and pathogenic indicator microbes were monitored after hydraulic retention time (hrt) of 4, 8, 12, 16, and 20 days. treatment efficiency of hcw kept on increasing with the increase in hydraulic retention time. maximum efficiency of hcw was observed with a 20-day hrt, that i ...201323724336
unified theory of bacterial sialometabolism: how and why bacteria metabolize host sialic acids.sialic acids are structurally diverse nine-carbon ketosugars found mostly in humans and other animals as the terminal units on carbohydrate chains linked to proteins or lipids. the sialic acids function in cell-cell and cell-molecule interactions necessary for organismic development and homeostasis. they not only pose a barrier to microorganisms inhabiting or invading an animal mucosal surface, but also present a source of potential carbon, nitrogen, and cell wall metabolites necessary for bacte ...201323724337
genome implosion elicits host-confinement in alcaligenaceae: evidence from the comparative genomics of tetrathiobacter kashmirensis, a pathogen in the making.this study elucidates the genomic basis of the evolution of pathogens alongside free-living organisms within the family alcaligenaceae of betaproteobacteria. towards that end, the complete genome sequence of the sulfur-chemolithoautotroph tetrathiobacter kashmirensis wt001(t) was determined and compared with the soil isolate achromobacter xylosoxidans a8 and the two pathogens bordetella bronchiseptica rb50 and taylorella equigenitalis mce9. all analyses comprehensively indicated that the rb50 an ...201323741407
characterization of alcaligenes faecalis strain ad15 indicating biocontrol activity against plant pathogens.bacterial strain possessing both bacteriostatic and fungistatic activity (biocontrol activity) against pathogens of cyclamen (cyclamen sp.) was isolated from the soil in gifu prefecture, japan, and characterized with respect to its taxonomic and biocontrol properties. the sequence of its 16s rrna gene, morphology, biochemistry, and fatty acid composition demonstrated that it is a strain most closely related to alcaligenes faecalis subsp. faecalis lmg 1229(t). the isolate was named a. faecalis st ...201323759862
emergence of vim-6 metallo-beta-lactamase-producing alcaligenes faecalis clinical isolates in a hospital in india. 201323771294
colonization of alcaligenes faecalis strain jbw4 in natural soils and its detoxification of endosulfan.alcaligenes faecalis strain jbw4, a strain of bacteria that is capable of degrading endosulfan, was inoculated into sterilized and natural soils spiked with endosulfan. jbw4 degraded 75.8 and 87.0 % of α-endosulfan and 58.5 and 69.5 % of β-endosulfan in sterilized and natural soils, respectively, after 77 days. endosulfan ether and endosulfan lactone were the major metabolites that were detected by gas chromatography-mass spectrometry. this result suggested that a. faecalis strain jbw4 degrades ...201423812277
comparison of a novel, rapid chromogenic biochemical assay, the carba np test, with the modified hodge test for detection of carbapenemase-producing gram-negative bacilli.we compared carbapenemase detection among 271 gram-negative bacilli (of which 131 were carbapenemase producers) using a novel chromogenic rapid test--the carba np test (cnp)--and the modified hodge test (mht). sensitivities were comparable (cnp, 100%, versus mht, 98%; p = 0.08), but cnp was more specific (100% versus 80%; p < 0.0001) and faster.201323824767
β-d-glucan testing is important for diagnosis of invasive fungal infections.invasive fungal infections are a significant cause of morbidity and mortality in patients who receive immunosuppressive therapy, such as solid organ and hematopoietic stem cell transplant (hsct) recipients. many of the fungi associated with these infections are angioinvasive and are best diagnosed by visualizing the organism in or culturing the organism from deep tissue. however, obtaining such tissue often requires an invasive procedure. many hsct recipients are thrombocytopenic, making such pr ...201323850953
characterization of a nitrite reductase involved in nitrifier denitrification.nitrifier denitrification is the conversion of nitrite to nitrous oxide by ammonia-oxidizing organisms. this process, which is distinct from denitrification, is active under aerobic conditions in the model nitrifier nitrosomonas europaea. the central enzyme of the nitrifier dentrification pathway is a copper nitrite reductase (cunir). to understand how a cunir, typically inactivated by oxygen, functions in this pathway, the enzyme isolated directly from n. europaea (nenir) was biochemically and ...201323857587
identification of opportunistic pathogenic bacteria in drinking water samples of different rural health centers and their clinical impacts on humans.international drinking water quality monitoring programs have been established in order to prevent or to reduce the risk of contracting water-related infections. a survey was performed on groundwater-derived drinking water from 13 different hospitals in the mahabubnagar district. a total of 55 bacterial strains were isolated which belonged to both gram-positive and gram-negative bacteria. all the taxa were identified based on the 16s rrna gene sequence analysis based on which they are phylogenet ...201323862144
regulation of homocysteine metabolism by mycobacterium tuberculosis s-adenosylhomocysteine hydrolase.mycobacterium tuberculosis modulates expression of various metabolism-related genes to adapt in the adverse host environment. the gene coding for m. tuberculosis s-adenosylhomocysteine hydrolase (mtb-sahh) is essential for optimal growth and the protein product is involved in intermediary metabolism. however, the relevance of sahh in mycobacterial physiology is unknown. in this study, we analyze the role of mtb-sahh in regulating homocysteine concentration in surrogate host mycobacterium smegmat ...201323877358
endophthalmitis caused by alcaligenes faecalis: a case series.to profile the etiology, clinical outcomes and drug sensitivity patterns in endophthalmitis caused by alcaligenes faecalis.201323895234
antifungal activity of phlorotannins against dermatophytes and yeasts: approaches to the mechanism of action and influence on candida albicans virulence factor.in the last few decades, fungal infections, particularly nosocomial, increased all around the world. this increment stimulated the search for new antifungal agents, especially those derived from nature. among natural products, those from marine sources have gained prominence in the last years. purified phlorotannins extracts from three brown seaweeds (cystoseira nodicaulis (withering) m. roberts, cystoseira usneoides (linnaeus) m. roberts and fucus spiralis linnaeus) were screened for their anti ...201323951297
acrylyl-coenzyme a reductase, an enzyme involved in the assimilation of 3-hydroxypropionate by rhodobacter sphaeroides.the anoxygenic phototroph rhodobacter sphaeroides uses 3-hydroxypropionate as a sole carbon source for growth. previously, we showed that the gene (rsp_1434) known as acui, which encodes a protein of the medium-chain dehydrogenase/reductase (mdr) superfamily, was involved in 3-hydroxypropionate assimilation via the reductive conversion to propionyl-coenzyme a (coa). based on these results, we speculated that acui encoded acrylyl-coa reductase. in this work, we characterize the in vitro enzyme ac ...201323955006
rapid and direct real-time detection of blakpc and blandm from surveillance samples.we assessed the performance of a duplex real-time pcr assay for bla(kpc) and bla(ndm) performed directly (d-pcr) on perianal and perirectal swabs and stool. spiked specimens and 126 clinical surveillance swabs (comprising a sensitivity panel of 46 perirectal double swabs previously determined to be culture positive for bla(kpc)-pcr-positive enterobacteriaceae and a specificity panel of 80 perianal swabs from patients at risk of carbapenemase-producing enterobacteriaceae [cpe] colonization) were ...201323966498
identification of bacteria in enrichment cultures of sulfate reducers in the cariaco basin water column employing denaturing gradient gel electrophoresis of 16s ribosomal rna gene fragments.the cariaco basin is characterized by pronounced and predictable vertical layering of microbial communities dominated by reduced sulfur species at and below the redox transition zone. marine water samples were collected in may, 2005 and 2006, at the sampling stations a (10°30' n, 64°40' w), b (10°40' n, 64°45' w) and d (10°43'n, 64°32'w) from different depths, including surface, redox interface, and anoxic zones. in order to enrich for sulfate reducing bacteria (srb), water samples were inoculat ...201323981583
isolation of an indigenous imidacloprid-degrading bacterium and imidacloprid bioremediation under simulated in situ and ex situ conditions.the bacterial community structure and its complexity of the enrichment culture during the isolation and screening of imidacloprid-degrading strain were studied using denaturating gradient gel electrophoresis analysis. the dominant bacteria in the original tea rhizosphere soil were uncultured bacteria, rhizobium sp., sinorhizobium, ochrobactrum sp., alcaligenes, bacillus sp., bacterium, klebsiella sp., and ensifer adhaerens. the bacterial community structure was altered extensively and its comple ...201323985542
effect of tween 80 on the production of curdlan by alcaligenes faecalis atcc 31749.this study aims to investigate the effects of tween 80 on curdlan production, cell growth, and glucosyltransferase activity. the addition of tween 80 to the culture medium increased curdlan production. however, curdlan production did not increase further when excessive tween 80 (>0.3% tween 80) was added to the culture medium. the addition of tween 80 to the culture medium did not affect cell growth. the glucosyltransferase activity involved in the curdlan synthesis increased with the increase o ...201323987333
designing functional metalloproteins: from structural to catalytic metal sites.metalloenzymes efficiently catalyze some of the most important and difficult reactions in nature. for many years, coordination chemists have effectively used small molecule models to understand these systems. more recently, protein design has been shown to be an effective approach for mimicking metal coordination environments. since the first designed proteins were reported, much success has been seen for incorporating metal sites into proteins and attaining the desired coordination environment ...201323997273
the tetr family of regulators.the most common prokaryotic signal transduction mechanisms are the one-component systems in which a single polypeptide contains both a sensory domain and a dna-binding domain. among the >20 classes of one-component systems, the tetr family of regulators (tfrs) are widely associated with antibiotic resistance and the regulation of genes encoding small-molecule exporters. however, tfrs play a much broader role, controlling genes involved in metabolism, antibiotic production, quorum sensing, and ma ...201324006471
thermus oshimai jl-2 and t. thermophilus jl-18 genome analysis illuminates pathways for carbon, nitrogen, and sulfur cycling.the complete genomes of thermus oshimai jl-2 and t. thermophilus jl-18 each consist of a circular chromosome, 2.07 mb and 1.9 mb, respectively, and two plasmids ranging from 0.27 mb to 57.2 kb. comparison of the t. thermophilus jl-18 chromosome with those from other strains of t. thermophilus revealed a high degree of synteny, whereas the megaplasmids from the same strains were highly plastic. the t. oshimai jl-2 chromosome and megaplasmids shared little or no synteny with other sequenced thermu ...201324019992
the respiratory arsenite oxidase: structure and the role of residues surrounding the rieske cluster.the arsenite oxidase (aio) from the facultative autotrophic alphaproteobacterium rhizobium sp. nt-26 is a bioenergetic enzyme involved in the oxidation of arsenite to arsenate. the enzyme from the distantly related heterotroph, alcaligenes faecalis, which is thought to oxidise arsenite for detoxification, consists of a large α subunit (aioa) with bis-molybdopterin guanine dinucleotide at its active site and a 3fe-4s cluster, and a small β subunit (aiob) which contains a rieske 2fe-2s cluster. th ...201324023621
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