Publications

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metabolism dependent chemotaxis of pseudomonas aeruginosa n1 towards anionic detergent sodium dodecyl sulfate.sodium dodecyl sulfate (sds) is one of the most commonly used detergent, which exhibits excellent biocidal activity against various bacteria and fungi. it is commonly employed in many detergent formulations and is employed for disinfection purposes. it is shown to be toxic to fishes, aquatic animals and is also inhibitory to microbes and cyanobacteria. we had isolated a strain belonging to pseudomonas aeruginosa n1, from a detergent contaminated pond situated in varanasi city india, which was ab ...201325320412
metabolism dependent chemotaxis of pseudomonas aeruginosa n1 towards anionic detergent sodium dodecyl sulfate.sodium dodecyl sulfate (sds) is one of the most commonly used detergent, which exhibits excellent biocidal activity against various bacteria and fungi. it is commonly employed in many detergent formulations and is employed for disinfection purposes. it is shown to be toxic to fishes, aquatic animals and is also inhibitory to microbes and cyanobacteria. we had isolated a strain belonging to pseudomonas aeruginosa n1, from a detergent contaminated pond situated in varanasi city india, which was ab ...201325320412
metabolic potential of the organic-solvent tolerant pseudomonas putida dot-t1e deduced from its annotated genome.pseudomonas putida dot-t1e is an organic solvent tolerant strain capable of degrading aromatic hydrocarbons. here we report the dot-t1e genomic sequence (6,394,153 bp) and its metabolic atlas based on the classification of enzyme activities. the genome encodes for at least 1751 enzymatic reactions that account for the known pattern of c, n, p and s utilization by this strain. based on the potential of this strain to thrive in the presence of organic solvents and the subclasses of enzymes encoded ...201323815283
microbial production of isoquinoline alkaloids as plant secondary metabolites based on metabolic engineering research.plants produce a variety of secondary metabolites that possess strong physiological activities. unfortunately, however, their production can suffer from a variety of serious problems, including low levels of productivity and heterogeneous quality, as well as difficulty in raw material supply. in contrast, microorganisms can be used to produce their primary and some of their secondary metabolites in a controlled environment, thus assuring high levels of efficiency and uniform quality. in an attem ...201323666088
explaining bacterial dispersion on leaf surfaces with an individual-based model (phyllosim).we developed the individual-based model phyllosim to explain observed variation in the size of bacterial clusters on plant leaf surfaces (the phyllosphere). specifically, we tested how different 'waterscapes' impacted the diffusion of nutrients from the leaf interior to the surface and the growth of individual bacteria on these nutrients. in the 'null' model or more complex 'patchy' models, the surface was covered with a continuous water film or with water drops of equal or different volumes, re ...201324124501
discovery of plant phenolic compounds that act as type iii secretion system inhibitors or inducers of the fire blight pathogen, erwinia amylovora.erwinia amylovora causes a devastating disease called fire blight in rosaceous plants. the type iii secretion system (t3ss) is one of the important virulence factors utilized by e. amylovora in order to successfully infect its hosts. by using a green fluorescent protein (gfp) reporter construct combined with a high-throughput flow cytometry assay, a library of phenolic compounds and their derivatives was studied for their ability to alter the expression of the t3ss. based on the effectiveness of ...201323770912
exopolymer diversity and the role of levan in bacillus subtilis biofilms.exopolymeric substances (eps) are important for biofilm formation and their chemical composition may influence biofilm properties. to explore these relationships the chemical composition of eps from bacillus subtilis ncib 3610 biofilms grown in sucrose-rich (sym) and sucrose-poor (msgg and czapek) media was studied. we observed marked differences in composition of eps polymers isolated from all three biofilms or from spent media below the biofilms. the polysaccharide levan dominated the eps of s ...201323637960
de-novo assembly and characterization of the transcriptome of metschnikowia fructicola reveals differences in gene expression following interaction with penicillium digitatum and grapefruit peel.the yeast metschnikowia fructicola is an antagonist with biological control activity against postharvest diseases of several fruits. we performed a transcriptome analysis, using rna-seq technology, to examine the response of m. fructicola with citrus fruit and with the postharvest pathogen, penicillium digitatum.201323496978
plant-associated bacteria and their role in the success or failure of metal phytoextraction projects: first observations of a field-related experiment.phytoextraction has been reported as an economically and ecologically sound alternative for the remediation of metal-contaminated soils. willow is a metal phytoextractor of interest because it allows to combine a gradual contaminant removal with production of biomass that can be valorized in different ways. in this work two willow clones growing on a metal-contaminated site were selected: 'belgisch rood' (br) with a moderate metal extraction capacity and 'tora' (to) with a twice as high metal ac ...201323425076
epidemiological study of hazelnut bacterial blight in central italy by using laboratory analysis and geostatistics.incidence of xanthomonas arboricola pv. corylina, the causal agent of hazelnut bacterial blight, was analyzed spatially in relation to the pedoclimatic factors. hazelnut grown in twelve municipalities situated in the province of viterbo, central italy was studied. a consistent number of bacterial isolates were obtained from the infected tissues of hazelnut collected in three years (2010-2012). the isolates, characterized by phenotypic tests, did not show any difference among them. spatial patter ...201323424654
diverse microhabitats experienced by halomonas variabilis on salt-secreting leaves.the leaf surfaces of the salt-excreting tree tamarix aphylla harbor a wide diversity of halophilic microorganisms, including halomonas sp., but little is known of the factors that shape community composition in this extreme habitat. we isolated a strain of halomonas variabilis from the leaf surface of t. aphylla and used it to determine the heterogeneity of salt concentrations experienced by bacteria in this environment. this halophilic strain was transformed with a prou::gfp reporter gene fusio ...201323160133
statistically optimized biotransformation protocol for continuous production of l-dopa using mucuna monosperma callus culture.l-dopa (3,4-dihydroxyphenyl-l-alanine), a modified amino acid, is an expansively used drug for the parkinson's disease treatment. in the present study, optimization of nutritional parameters influencing l-dopa production was attempted using the response surface methodology (rsm) from mucuna monosperma callus. optimization of the four factors was carried out using the box-behnken design. the optimized levels of factors predicted by the model include tyrosine 0.894 g l(-1), ph 4.99, ascorbic acid ...201325674405
screening of sds-degrading bacteria from car wash wastewater and study of the alkylsulfatase enzyme activity.sodium dodecyl sulfate (sds) is one of the main surfactant components in detergents and cosmetics, used in high amounts as a detergent in products such as shampoos, car wash soap and toothpaste. therefore, its bioremediation by suitable microorganisms is important. alkylsulfatase is an enzyme that hydrolyses sulfate -ester bonds to give inorganic sulfate and alcohol. the purpose of this study was to isolate sds-degrading bacteria from tehran city car wash wastewater, study bacterial alkylsulfata ...201323825734
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
the role of the intestinal microbiota in the pathogenesis of necrotizing enterocolitis.development of necrotizing enterocolitis (nec) requires a susceptible host, typically a premature infant or an infant with congenital heart disease, enteral feedings and bacterial colonization. although there is little doubt that microbes are critically involved in the pathogenesis of nec, the identity of specific causative pathogens remains elusive. unlike established normal adult gut microbiota, which is quite complex, uniform, and stable, early postnatal bacterial populations are simple, dive ...201323611609
whole cell biotransformation for reductive amination reactions.whole cell biotransformation systems with enzyme cascading increasingly find application in biocatalysis to complement or replace established chemical synthetic routes for production of, e.g., fine chemicals. recently, we established an escherichia coli whole cell biotransformation system for reductive amination by coupling a transaminase and an amino acid dehydrogenase with glucose catabolism for cofactor recycling. transformation of 2-keto-3-methylvalerate to l-isoleucine by e. coli cells was ...201324406456
whole cell biotransformation for reductive amination reactions.whole cell biotransformation systems with enzyme cascading increasingly find application in biocatalysis to complement or replace established chemical synthetic routes for production of, e.g., fine chemicals. recently, we established an escherichia coli whole cell biotransformation system for reductive amination by coupling a transaminase and an amino acid dehydrogenase with glucose catabolism for cofactor recycling. transformation of 2-keto-3-methylvalerate to l-isoleucine by e. coli cells was ...201324406456
production of pharmaceutical proteins in solanaceae food crops.the benefits of increased safety and cost-effectiveness make vegetable crops appropriate systems for the production and delivery of pharmaceutical proteins. in particular, solanaceae edible crops could be inexpensive biofactories for oral vaccines and other pharmaceutical proteins that can be ingested as minimally processed extracts or as partially purified products. the field of crop plant biotechnology is advancing rapidly due to novel developments in genetic and genomic tools being made avail ...201323434646
microbial alkyl- and aryl-sulfatases: mechanism, occurrence, screening and stereoselectivities.this review gives an overview on the occurrence of sulfatases in prokaryota, eukaryota and archaea. the mechanism of enzymes acting with retention or inversion of configuration during sulfate ester hydrolysis is discussed taking two complementary examples. methods for the discovery of novel alkyl sulfatases are described by way of sequence-based search and enzyme induction. a comprehensive list of organisms with their respective substrate scope regarding prim- and sec-alkyl sulfate esters allows ...201324352732
microbial alkyl- and aryl-sulfatases: mechanism, occurrence, screening and stereoselectivities.this review gives an overview on the occurrence of sulfatases in prokaryota, eukaryota and archaea. the mechanism of enzymes acting with retention or inversion of configuration during sulfate ester hydrolysis is discussed taking two complementary examples. methods for the discovery of novel alkyl sulfatases are described by way of sequence-based search and enzyme induction. a comprehensive list of organisms with their respective substrate scope regarding prim- and sec-alkyl sulfate esters allows ...201324352732
the near-quantitative sampling of genomic dna from various food-borne eubacteria.the disruption of the bacterial cell wall plays an important part in achieving quantitative extraction of dna from eubacteria essential for accurate analyses of genetic material recovered from environmental samples.201425551371
detection, identification and differentiation of pectobacterium and dickeya species causing potato blackleg and tuber soft rot: a review.the soft rot enterobacteriaceae (sre) pectobacterium and dickeya species (formerly classified as pectinolytic erwinia spp.) cause important diseases on potato and other arable and horticultural crops. they may affect the growing potato plant causing blackleg and are responsible for tuber soft rot in storage thereby reducing yield and quality. efficient and cost-effective detection and identification methods are essential to investigate the ecology and pathogenesis of the sre as well as in seed c ...201425684775
detection, identification and differentiation of pectobacterium and dickeya species causing potato blackleg and tuber soft rot: a review.the soft rot enterobacteriaceae (sre) pectobacterium and dickeya species (formerly classified as pectinolytic erwinia spp.) cause important diseases on potato and other arable and horticultural crops. they may affect the growing potato plant causing blackleg and are responsible for tuber soft rot in storage thereby reducing yield and quality. efficient and cost-effective detection and identification methods are essential to investigate the ecology and pathogenesis of the sre as well as in seed c ...201425684775
spatial scales of interactions among bacteria and between bacteria and the leaf surface.microbial life on plant leaves is characterized by a multitude of interactions between leaf colonizers and their environment. while the existence of many of these interactions has been confirmed, their spatial scale or reach often remained unknown. in this study, we applied spatial point pattern analysis to 244 distribution patterns of pantoea agglomerans and pseudomonas syringae on bean leaves. the results showed that bacterial colonizers of leaves interact with their environment at different s ...201425764562
spatial scales of interactions among bacteria and between bacteria and the leaf surface.microbial life on plant leaves is characterized by a multitude of interactions between leaf colonizers and their environment. while the existence of many of these interactions has been confirmed, their spatial scale or reach often remained unknown. in this study, we applied spatial point pattern analysis to 244 distribution patterns of pantoea agglomerans and pseudomonas syringae on bean leaves. the results showed that bacterial colonizers of leaves interact with their environment at different s ...201425764562
high ice nucleation activity located in blueberry stem bark is linked to primary freeze initiation and adaptive freezing behaviour of the bark.controlled ice nucleation is an important mechanism in cold-hardy plant tissues for avoiding excessive supercooling of the protoplasm, for inducing extracellular freezing and/or for accommodating ice crystals in specific tissues. to understand its nature, it is necessary to characterize the ice nucleation activity (ina), defined as the ability of a tissue to induce heterogeneous ice nucleation. few studies have addressed the precise localization of ina in wintering plant tissues in respect of it ...201425082142
the role of abiotic environmental conditions and herbivory in shaping bacterial community composition in floral nectar.identifying the processes that drive community assembly has long been a central theme in ecology. for microorganisms, a traditional prevailing hypothesis states that "everything is everywhere, but the environment selects". although the bacterial community in floral nectar may be affected by both atmosphere (air-borne bacteria) and animals as dispersal vectors, the environmental and geographic factors that shape microbial communities in floral nectar are unknown. we studied culturable bacterial c ...201424922317
intervention of phytohormone pathways by pathogen effectors.the constant struggle between plants and microbes has driven the evolution of multiple defense strategies in the host as well as offense strategies in the pathogen. to defend themselves from pathogen attack, plants often rely on elaborate signaling networks regulated by phytohormones. in turn, pathogens have adopted innovative strategies to manipulate phytohormone-regulated defenses. tactics frequently employed by plant pathogens involve hijacking, evading, or disrupting hormone signaling pathwa ...201424920334
analysis of the pantoea ananatis pan-genome reveals factors underlying its ability to colonize and interact with plant, insect and vertebrate hosts.pantoea ananatis is found in a wide range of natural environments, including water, soil, as part of the epi- and endophytic flora of various plant hosts, and in the insect gut. some strains have proven effective as biological control agents and plant-growth promoters, while other strains have been implicated in diseases of a broad range of plant hosts and humans. by analysing the pan-genome of eight sequenced p. ananatis strains isolated from different sources we identified factors potentially ...201424884520
xanthomonas perforans colonization influences salmonella enterica in the tomato phyllosphere.salmonella enterica rarely grows on healthy, undamaged plants, but its persistence is influenced by bacterial plant pathogens. the interactions between s. enterica, xanthomonas perforans (a tomato bacterial spot pathogen), and tomato were characterized. we observed that virulent x. perforans, which establishes disease by suppressing pathogen-associated molecular pattern (pamp)-triggered immunity that leads to effector-triggered susceptibility, created a conducive environment for persistence of s ...201424632252
measurement of ice nucleation-active bacteria on plants and in precipitation by quantitative pcr.ice nucleation-active (ina) bacteria may function as high-temperature ice-nucleating particles (inp) in clouds, but their effective contribution to atmospheric processes, i.e., their potential to trigger glaciation and precipitation, remains uncertain. we know little about their abundance on natural vegetation, factors that trigger their release, or persistence of their ice nucleation activity once airborne. to facilitate these investigations, we developed two quantitative pcr (qpcr) tests of th ...201424317082
characterization of acrd, a resistance-nodulation-cell division-type multidrug efflux pump from the fire blight pathogen erwinia amylovora.multidrug efflux pumps are membrane translocases that have the ability to extrude a variety of structurally unrelated compounds from the cell. acrd, a resistance-nodulation-cell division (rnd) transporter, was shown to be involved in efflux of highly hydrophilic aminoglycosides and a limited number of amphiphilic compounds in e. coli. here, a homologue of acrd in the plant pathogen and causal agent of fire blight disease erwinia amylovora was identified.201424443882
identification of multidrug-resistant bacteria and bacillus cereus from healthcare workers and environmental surfaces in a hospital. 201425280977
bioinformatics based structural characterization of glucose dehydrogenase (gdh) gene and growth promoting activity of leclercia sp. qau-66.glucose dehydrogenase (gdh; ec 1.1. 5.2) is the member of quinoproteins group that use the redox cofactor pyrroloquinoline quinoine, calcium ions and glucose as substrate for its activity. in present study, leclercia sp. qau-66, isolated from rhizosphere of vigna mungo, was characterized for phosphate solubilization and the role of gdh in plant growth promotion of phaseolus vulgaris. the strain qau-66 had ability to solubilize phosphorus and significantly (p ≤ 0.05) promoted the shoot and root l ...201425242947
purification of chitinase enzymes from bacillus subtilis bacteria tv-125, investigation of kinetic properties and antifungal activity against fusarium culmorum.chitin is the main structural component of cell walls of fungi, exoskeletons of insects and other arthropods and shells of crustaceans. chitinase enzyme is capable of degrading chitin, and this enzyme can be used as a biological fungicide against phytopathogenic fungi, as well as an insecticide against insect pests.201425112904
molecular method for detection of total coliforms in drinking water samples.this work demonstrates the ability of a bacterial concentration and recovery procedure combined with three different pcr assays targeting the lacz, wecg, and 16s rrna genes, respectively, to detect the presence of total coliforms in 100-ml samples of potable water (presence/absence test). pcr assays were first compared to the culture-based colilert and mi agar methods to determine their ability to detect 147 coliform strains representing 76 species of enterobacteriaceae encountered in fecal and ...201424771030
isolation, plant colonization potential, and phenanthrene degradation performance of the endophytic bacterium pseudomonas sp. ph6-gfp.this investigation provides a novel method of endophyte-aided removal of polycyclic aromatic hydrocarbons (pahs) from plant bodies. a phenanthrene-degrading endophytic bacterium pseudomonas sp. ph6 was isolated from clover (trifolium pratense l.) grown in a pah-contaminated site. after being marked with the gfp gene, the colonization and distribution of strain ph6-gfp was directly visualized in plant roots, stems, and leaves for the first time. after ryegrass (lolium multiflorum lam.) roots inoc ...201424964867
optimization of biomass and biokinetic constant in mazut biodegradation by indigenous bacteria bbrc10061.optimization based on appropriate parameters can be applied to improve a process. mazut degradation as a critical issue in environment requires optimization to be efficiently done. to provide biodegradation conditions, experiments were designed on the least interactions among levels of parameters consisting of ph, tween 80, glucose, phosphorous source, nitrogen source, and time. kinetic constants and biomass were calculated based on 16 assays, designed using taguchi method, which constructed var ...201425013725
microbial tyrosinases: promising enzymes for pharmaceutical, food bioprocessing, and environmental industry.tyrosinase is a natural enzyme and is often purified to only a low degree and it is involved in a variety of functions which mainly catalyse the o-hydroxylation of monophenols into their corresponding o-diphenols and the oxidation of o-diphenols to o-quinones using molecular oxygen, which then polymerizes to form brown or black pigments. the synthesis of o-diphenols is a potentially valuable catalytic ability and thus tyrosinase has attracted a lot of attention with respect to industrial applica ...201424895537
expression and properties of the highly alkalophilic phenylalanine ammonia-lyase of thermophilic rubrobacter xylanophilus.the sequence of a phenylalanine ammonia-lyase (pal; ec: 4.3.1.24) of the thermophilic and radiotolerant bacterium rubrobacter xylanophilus (rxpal) was identified by screening the genomes of bacteria for members of the phenylalanine ammonia-lyase family. a synthetic gene encoding the rxpal protein was cloned and overexpressed in escherichia coli top 10 in a soluble form with an n-terminal his6-tag and the recombinant rxpal protein was purified by ni-nta affinity chromatography. the activity assay ...201424475062
enzyme recruitment and its role in metabolic expansion.although more than 10(9) years have passed since the existence of the last universal common ancestor, proteins have yet to reach the limits of divergence. as a result, metabolic complexity is ever expanding. identifying and understanding the mechanisms that drive and limit the divergence of protein sequence space impact not only evolutionary biologists investigating molecular evolution but also synthetic biologists seeking to design useful catalysts and engineer novel metabolic pathways. investi ...201424483367
vegetable microbiomes: is there a connection among opportunistic infections, human health and our 'gut feeling'?the highly diverse microbiomes of vegetables are reservoirs for opportunistic and emerging pathogens. in recent years, an increased consumption, larger scale production and more efficient distribution of vegetables together with an increased number of immunocompromised individuals resulted in an enhanced number of documented outbreaks of human infections associated with the consumption of vegetables. here we discuss the occurrence of potential pathogens in vegetable microbiomes, the impact of fa ...201425186140
n-acyl homoserine lactone-mediated quorum sensing with special reference to use of quorum quenching bacteria in membrane biofouling control.membrane biofouling remains a severe problem to be addressed in wastewater treatment systems affecting reactor performance and economy. the finding that many wastewater bacteria rely on n-acyl homoserine lactone-mediated quorum sensing to synchronize their activities essential for biofilm formations; the quenching bacterial quorum sensing suggests a promising approach for control of membrane biofouling. a variety of quorum quenching compounds of both synthetic and natural origin have been identi ...201425147787
susceptibility to antibiotics in urinary tract infections in a secondary care setting from 2005-2006 and 2010-2011, in são paulo, brazil: data from 11,943 urine cultures.urinary tract infection (uti) has a high incidence and recurrence, therefore, treatment is empirical in the majority of cases.201425076433
molecular epidemiology of methicillin-resistant staphylococcus aureus isolated in serial cultures from the respiratory tract of children with cystic fibrosis.little is known about strain relatedness of methicillin-resistant staphyloccocus aureus (mrsa) isolated at serial time points from the respiratory tract of patients with cystic fibrosis (cf). the objectives are to interrogate the genetic diversity of mrsa recovered in serial cultures from children with cf and to correlate strain relatedness with clinical characteristics.201424220228
linking bacterial endophytic communities to essential oils: clues from lavandula angustifolia mill.endophytic bacteria play a crucial role in plant life and are also drawing much attention for their capacity to produce bioactive compounds of relevant biotechnological interest. here we present the characterisation of the cultivable endophytic bacteria of lavandula angustifolia mill.-a species used since antiquity for its therapeutic properties-since the production of bioactive metabolites from medical plants may reside also in the activity of bacterial endophytes through their direct productio ...201424971151
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.201424822114
microbial production of short chain diols.short chain diols (propanediols, butanediols, pentanediols) have been widely used in bulk and fine chemical industries as fuels, solvents, polymer monomers and pharmaceutical precursors. the chemical production of short chain diols from fossil resources has been developed and optimized for decades. consideration of the exhausting fossil resources and the increasing environment issues, the bio-based process to produce short chain diols is attracting interests. currently, a variety of biotechnolog ...201425491899
rapid identification of positive blood cultures by matrix-assisted laser desorption ionization-time of flight mass spectrometry using prewarmed agar plates.this study describes an inexpensive and straightforward method for identifying bacteria by matrix-assisted laser desorption ionization-time of flight mass spectrometry (maldi-tof ms) directly from positive blood cultures using prewarmed agar plates. different inoculation methods and incubation times were evaluated to determine the optimal conditions. the two methods using pelleted material from positive culture bottles performed best. in particular, the pellet streak method correctly identified ...201425232166
evaluation of a modified cefsulodin-irgasan-novobiocin agar for isolation of yersinia spp.y. enterocolitica and y. pseudotuberculosis are important food borne pathogens. however, the presence of competitive microbiota makes the isolation of y. enterocolitica and y. pseudotuberculosis from naturally contaminated foods difficult. we attempted to evaluate the performance of a modified cefsulodin-irgasan-novobiocin (cin) agar in the differentiation of y. enterocolitica from non-yersinia species, particularly the natural intestinal microbiota. the modified cin enabled the growth of y. ent ...201425170941
high isolation rates of multidrug-resistant bacteria from water and carpets of mosques.there is little information regarding the isolation of antimicrobial-resistant potentially pathogenic bacteria from water and carpets of mosques worldwide. the objective of the present investigation is to determine the bacteriological quality of water and carpets of mosques in elkhomes city in libya.201425128691
isolation and identification of an enterobacter cloacae strain producing a novel subtype of shiga toxin type 1.we describe here the isolation and identification of a shiga toxin 1 (stx1)-producing enterobacter cloacae strain, m12x01451, from a human clinical specimen. the bacterial isolate was identified as e. cloacae using a polyphasic approach that included phenotypic, genetic, and proteomic analyses. the m12x01451 stx1 was sequenced, and the holotoxin was found to share only 87% amino acid sequence identity with the nearest stx1 subtype reference sequence. sequence analysis of the regions immediately ...201424759708
a culture-based method for determining the production of secreted protease inhibitors.we have developed a culture-based method for determining the production of secreted protease inhibitors. the assay utilizes standard proteolysis detection plates to support microbial growth followed by infiltrating the plate with a protease and subsequently detecting the remaining protein by trichloroacetic acid (tca) precipitation, or by bromocreosol green (bcg) or ponseau s (ps) staining. the presence of a protease inhibitor can be observed in the form of a protected zone of protein around the ...201424632514
activities of selected medicinal plants against multi-drug resistant gram-negative bacteria in cameroon.medicinal plants are used worldwide for several human ailments including bacterial infections. the present work was designed to assess the in vitro antibacterial activities of some cameroonian medicinal plants including entada abyssinica, entada africana, pentaclethra macrophylla, allexis cauliflora, anthocleista leibrechtsiana, carapa procera, carica papaya and persea americana against gram-negative bacteria expressing multidrug resistant (mdr) phenotypes.201426060474
adjunctive management of central line-associated bloodstream infections with 70% ethanol-lock therapy.ethanol is bactericidal against most pathogens implicated in central line-associated bloodstream infections (clabsis) and biofilms. current infectious diseases society of america guidelines cite insufficient evidence to support adjunctive ethanol-lock therapy (elt) for central venous catheter (cvc) salvage in patients with clabsi in combination with systemic antimicrobial treatment. we evaluated the safety and potential efficacy of 70% elt for clabsi at our institution after implementation of a ...201424526514
marennine, promising blue pigments from a widespread haslea diatom species complex.in diatoms, the main photosynthetic pigments are chlorophylls a and c, fucoxanthin, diadinoxanthin and diatoxanthin. the marine pennate diatom haslea ostrearia has long been known for producing, in addition to these generic pigments, a water-soluble blue pigment, marennine. this pigment, responsible for the greening of oysters in western france, presents different biological activities: allelopathic, antioxidant, antibacterial, antiviral, and growth-inhibiting. a method to extract and purify mar ...201424879542
biosynthesis of β-carotene in engineered e. coli using the mep and mva pathways.β-carotene is a carotenoid compound that has been widely used not only in the industrial production of pharmaceuticals but also as nutraceuticals, animal feed additives, functional cosmetics, and food colorants. currently, more than 90% of commercial β-carotene is produced by chemical synthesis. due to the growing public concern over food safety, the use of chemically synthesized β-carotene as food additives or functional cosmetic agents has been severely controlled in recent years. this has rei ...201425403509
discovery of pantoea rodasii strain nd03 that produces n-(3-oxo-hexanoyl)-l-homoserine lactone.proteobacteria use quorum sensing to regulate target gene expression in response to population density. quorum sensing (qs) is achieved via so-called signalling molecules and the best-studied qs signalling system uses n-acyl homoserine lactones (ahls). this study aimed to identify and characterize the production of ahls by a bacterium nd03 isolated from a malaysian tropical rainforest waterfall. molecular identification showed that nd03 is a pantoea sp. closely related to pantoea rodasii. we use ...201424859023
heterologous expression of pyrroloquinoline quinone (pqq) gene cluster confers mineral phosphate solubilization ability to herbaspirillum seropedicae z67.gluconic acid secretion mediated by the direct oxidation of glucose by pyrroloquinoline quinone (pqq)-dependent glucose dehydrogenase (gdh) is responsible for mineral phosphate solubilization in gram-negative bacteria. herbaspirillum seropedicae z67 (atcc 35892) genome encodes gdh apoprotein but lacks genes for the biosynthesis of its cofactor pqq. in this study, pqqe of erwinia herbicola (in plasmid pjnk1) and pqq gene clusters of pseudomonas fluorescens b16 (pok53) and acinetobacter calcoaceti ...201424682480
probiotic bacillus pumilus se5 shapes the intestinal microbiota and mucosal immunity in grouper epinephelus coioides.the health benefits of probiotics are thought to occur, at least in part, through an improved intestinal microbial balance in fish, although the molecular mechanisms whereby probiotics modulate the intestinal microbiota by means of activation of mucosal immunity are rarely explored. in this study, the effects of viable and heat-inactivated probiotic bacillus pumilus se5 on the intestinal dominant microbial community and mucosal immune gene expression were evaluated. the fish were fed for 60 d wi ...201425266899
structure and dynamics of a polysaccharide matrix: aqueous solutions of bacterial levan.the polysaccharide levan is a homopolymer of fructose and appears in nature as an important structural component of some bacterial biofilms. this paper reports the structural and dynamic properties of aqueous solutions of levan of various origin obtained from dynamic rheological, small-angle x-ray scattering, static and dynamic light scattering, as well as density and sound velocity measurements, determination of polymer branching after per-o-methylation, and microscopy. besides samples of comme ...201424654746
control of diatraea saccharalis by the endophytic pantoea agglomerans 33.1 expressing cry1ac7.despite the fact that bacillus thuringiensis (bt) is found in more than 90 % of the products used against insects, it has some difficulty reaching the internal regions where the larvae feed. to solve this problem, many genetically modified microorganisms that colonize the same pests have been developed. thus, the endophytic bacterium pantoea agglomerans (33.1), which has been recently described as a promising sugarcane growth promoter, was genetically modified with the pjtt vector (which carries ...201424531524
biopesticides from plants: calceolaria integrifolia s.l.the effects of persistent organic pollutants (pops) on humans and biodiversity are multiple and varied. nowadays environmentally-friendly pesticides are strongly preferred to pops. it is noteworthy that the crop protection role of pesticides and other techniques, i.e. biopesticides, plant extracts, prevention methods, organic methods, evaluation of plant resistance to certain pests under an integrated pest management (ipm), could improve the risks and benefits which must be assessed on a sound s ...201424893349
spectrally-resolved fluorescence cross sections of aerosolized biological live agents and simulants using five excitation wavelengths in a bsl-3 laboratory.a system for measuring spectrally-resolved fluorescence cross sections of single bioaerosol particles has been developed and employed in a biological safety level 3 (bsl-3) facility at edgewood chemical and biological center (ecbc). it is used to aerosolize the slurry or solution of live agents and surrogates into dried micron-size particles, and to measure the fluorescence spectra and sizes of the particles one at a time. spectrally-resolved fluorescence cross sections were measured for (1) bac ...201424718194
ceftobiprole activity against over 60,000 clinical bacterial pathogens isolated in europe, turkey, and israel from 2005 to 2010.ceftobiprole medocaril is a newly approved drug in europe for the treatment of hospital-acquired pneumonia (hap) (excluding patients with ventilator-associated pneumonia but including ventilated hap patients) and community-acquired pneumonia in adults. the aim of this study was to evaluate the in vitro antimicrobial activity of ceftobiprole against prevalent gram-positive and -negative pathogens isolated in europe, turkey, and israel during 2005 through 2010. a total of 60,084 consecutive, nondu ...201424777091
risk assessment of the schmutzdecke of biosand filters: identification of an opportunistic pathogen in schmutzdecke developed by an unsafe water source.the biosand filter (bsf) is widely applied in developing counties as an appropriate technology-based product for supplying "safe" water. biosand filters exhibit relatively high purifying efficiency because of the schmutzdecke (biofilm) embedded in them. however, schmutzdecke should be cleaned or discarded on a regular basis to maintain the purifying efficiency of the bsf. due to its role in bsfs, the purifying function of schmutzdecke, rather than its potential risk when not properly discarded, ...201424534769
pulmonary disease potentially associated with nicoletella semolina in 3 young horses. 201424689696
evaluation of a real-time polymerase chain reaction assay of the outer membrane protein p2 gene for the detection of haemophilus parasuis in clinical samples.a real-time polymerase chain reaction (pcr) assay of the outer membrane protein (omp) p2 gene was developed and used to test 97 putative haemophilus parasuis pure cultures and 175 clinical tissue samples. with standard culture isolation as the gold standard, the diagnostic sensitivity and specificity of the pcr assay were determined to be 83% and 80%, respectively.201424688178
comprehensive profiling of the vaginal microbiome in hiv positive women using massive parallel semiconductor sequencing.infections by hiv increase the risk of acquiring secondary viral and bacterial infections and methods are needed to determine the spectrum of co-infections for proper treatment. we used rolling circle amplification (rca) and ion proton sequencing to investigate the vaginal microbiome of 20 hiv positive women from south africa. a total of 46 different human papillomavirus (hpv) types were found, many of which are not detected by existing genotyping assays. moreover, the complete genomes of two no ...201424637939
evaluation of various factors affecting bioconversion of l-tyrosine to l-dopa by yeast yarrowia lipolytica-ncim 3450 using response surface methodology.3,4-dihydroxy l-phenylalanine (l-dopa) is considered a potent drug for the treatment of parkinson disease. physical and nutritional parameters where optimized by using yarrowia lipolytica-ncim 3450 to accomplished the highest production of l-dopa. screenings of critical components were completed by using a plackett-burman design, while further optimization was carried out using the box-behnken design. the optimized factor levels predicted by the model were ph 6.1, 1.659 g l(-1) yeast extract, 1. ...201424955295
rapid identification of pathogens from pediatric blood cultures by use of the filmarray blood culture identification panel.the performance of the filmarray blood culture identification (bcid) panel has been studied in adult patients. we describe here an evaluation of this assay for the rapid identification of pathogens in bactec peds plus/f and bactec standard anaerobic/f bottles that contained blood samples from pediatric patients at a tertiary care children's hospital.201425274998
crispr is an optimal target for the design of specific pcr assays for salmonella enterica serotypes typhi and paratyphi a.serotype-specific pcr assays targeting salmonella enterica serotypes typhi and paratyphi a, the causal agents of typhoid and paratyphoid fevers, are required to accelerate formal diagnosis and to overcome the lack of typing sera and, in some situations, the need for culture. however, the sensitivity and specificity of such assays must be demonstrated on large collections of strains representative of the targeted serotypes and all other bacterial populations producing similar clinical symptoms.201424498453
validation of antibiotic susceptibility testing guidelines in a routine clinical microbiology laboratory exemplifies general key challenges in setting clinical breakpoints.this study critically evaluated the new european committee for antimicrobial susceptibility testing (eucast) antibiotic susceptibility testing guidelines on the basis of a large set of disk diffusion diameters determined for clinical isolates. we report several paradigmatic problems that illustrate key issues in the selection of clinical susceptibility breakpoints, which are of general importance not only for eucast but for all guidelines systems, i.e., (i) the need for species-specific determin ...201424777093
1,3-propanediol production with citrobacter werkmanii dsm17579: effect of a dhad knock-out.1,3-propanediol (pdo) is a substantially industrial metabolite used in the polymer industry. although several natural pdo production hosts exist, e.g. klebsiella sp., citrobacter sp. and clostridium sp., the pdo yield on glycerol is insufficient for an economically viable bio-process. enhancing this yield via strain improvement can be achieved by disconnecting the production and growth pathways. in the case of pdo formation, this approach results in a microorganism metabolizing glycerol strictly ...201424885849
epidemiology and molecular characterization of extended-spectrum beta-lactamase-producing enterobacter spp., pantoea agglomerans, and serratia marcescens isolates from a bulgarian hospital.forty-two extended-spectrum beta-lactamase (esbl)-producing isolates of enterobacter aerogenes, enterobacter cloacae, pantoea agglomerans, and serratia marcescens, collected consecutively during the period january-november 2011 from the university hospital in varna, bulgaria, were studied to characterize their esbls by isoelectric focusing, group-specific pcr, and sequencing. the epidemiological relationship was evaluated by random amplified polymorphic dna analysis (rapd). transferability of es ...201424171449
extended spectrum ß-lactamase- and constitutively ampc-producing enterobacteriaceae on fresh produce and in the agricultural environment.the attribution of fresh produce to the overall community-associated exposure of humans to esbl- or ampc-producing bacteria is currently unknown. to address this issue, the prevalence of esbl- and ampc-producing enterobacteriaceae on fresh produce produced in the netherlands was determined. seven vegetable types that are consumed raw were selected: blanched celery, bunched carrots, chicory, endive, iceberg lettuce, mushrooms, and radish. the vegetables were mostly obtained from supermarkets. to ...201424211774
microbiological quality of packaged ice from various sources in georgia.this study determined the microbiological and chemical quality of ice produced and bagged on premises in retail establishments and in free-standing self-service ice vending machines in the state of georgia and compared the results with that from ice produced by manufacturing companies monitored by the international packaged ice association. two hundred fifty bags of packaged ice samples were obtained from retail locations and self-service ice vending machines, along with 25 bags of packaged manu ...201425198846
the astaxanthin dideoxyglycoside biosynthesis pathway in sphingomonas sp. pb304.a major carotenoid in sphingomonas sp. pb304, originally isolated from a river in daejon city, south korea, was identified as astaxanthin dideoxyglycoside. gene clusters encoding the astaxanthin dideoxyglycoside biosynthetic enzymes were identified by screening sphingomonas sp. pb304 fosmid libraries using degenerate probes that harbor highly conserved sequences from the sphigomonas elodea-derived crti and nostoc sp. pcc 7120-dervied crtw genes. selected positive gene clusters were fully sequenc ...201425193422
β-carotene-producing bacteria residing in the intestine provide vitamin a to mouse tissues in vivo.vitamin a deficiency (vad) is an overwhelming public health problem that affects hundreds of millions of people worldwide. a definitive solution to vad has yet to be identified. because it is an essential nutrient, vitamin a or its carotenoid precursor β-carotene can only be obtained from food or supplements. in this study, we wanted to establish whether β-carotene produced in the mouse intestine by bacteria synthesizing the provitamin a carotenoid could be delivered to various tissues within th ...201424598882
phenotypic comparison of clinical and plant-beneficial strains of pantoea agglomerans.certain strains of pantoea are used as biocontrol agents for the suppression of plant diseases. however, their commercial registration is hampered in some countries because of biosafety concerns. this study compares clinical and plant-beneficial strains of p. agglomerans and related species using a phenotypic analysis approach in which plant-beneficial effects, adverse effects in nematode models, and toxicity were evaluated. plant-beneficial effects were determined as the inhibition of apple fru ...201426418852
[electron microscopy and restriction analysis of bacteriophages isolated from quince and pear with symptoms of fire blight].phage populations of isolates from quince and pear affected with fire blight disease were studied using electron microscopy, restriction analysis and both agarose gel electrophoresis of particles and host range scoping method. the isolate from quince (pma1) comprises at least three phage populations and two phage variants that can be detected on different bacterial indicators. after titration of this isolate on erwinia amylovora the bacteriophage key of b1 morphotype with the genome size of 82.4 ...201424479316
pantoea agglomerans as a rare cause of catheter-related infection in hemodialysis patients. 201423599132
alteration of flower color in iris germanica l. 'fire bride' through ectopic expression of phytoene synthase gene (crtb) from pantoea agglomerans.genetic modulation of the carotenogenesis in i. germanica 'fire bride' by ectopic expression of a crtb gene causes several flower parts to develop novel orange and pink colors. flower color in tall bearded irises (iris germanica l.) is determined by two distinct biochemical pathways; the carotenoid pathway, which imparts yellow, orange and pink hues and the anthocyanin pathway, which produces blue, violet and maroon flowers. red-flowered i. germanica do not exist in nature and conventional breed ...201424801678
development of pma real-time pcr method to quantify viable cells of pantoea agglomerans cpa-2, an antagonist to control the major postharvest diseases on oranges.dilution plating is the quantification method commonly used to estimate the population level of postharvest biocontrol agents, but this method does not permit a distinction among introduced and indigenous strains. recently, molecular techniques based on dna amplification such as quantitative real-time pcr (qpcr) have been successfully applied for their high strain-specific detection level. however, the ability of qpcr to distinguish viable and nonviable cells is limited. a promising strategy to ...201424786552
optimization of packaging and storage conditions of a freeze-dried pantoea agglomerans formulation for controlling postharvest diseases in fruit.this study aimed to evaluate different packaging strategies to extend the shelf life of a freeze-dried formulation of the biocontrol agent pantoea agglomerans strain cpa-2.201424698363
pantoea agglomerans endophthalmitis: clinical features and outcomes.to determine the clinical profile and outcomes of patients with pantoea agglomerans endophthalmitis as seen at a tertiary eye care center in india.201424671031
rapid isolation of a facultative anaerobic electrochemically active bacterium capable of oxidizing acetate for electrogenesis and azo dyes reduction.in this study, 27 strains of electrochemically active bacteria (eab) were rapidly isolated and their capabilities of extracellular electron transfer were identified using a photometric method based on wo3 nanoclusters. these strains caused color change of wo3 from white to blue in a 24-well agar plate within 40 h. most of the isolated eab strains belonged to the genera of aeromonas and shewanella. one isolate, pantoea agglomerans s5-44, was identified as an eab that can utilize acetate as the ca ...201424648142
detection and quantification by pcr assay of the biocontrol agent pantoea agglomerans cpa-2 on apples.the registration of biological control agents requires the development of monitoring systems to detect and quantify the agent in the environment. pantoea agglomerans cpa-2 is an effective biocontrol agent for postharvest diseases of citrus and pome fruits. the monitoring of cpa-2 in postharvest semi-commercial trials was evaluated by rodac impression plates and the colonies isolated were confirmed by conventional pcr using the scar primers paga1 and pagb1. samples were taken from different surfa ...201424534396
ingestion of a marked bacterial pathogen of cotton conclusively demonstrates feeding by first instar southern green stink bug (hemiptera: pentatomidae).long-held dogma dictates that first instars of nezara viridula (l.) do not feed, yet recent observations of stylet activity within a food source suggest otherwise. as a cosmopolitan pest of cotton and other high-value cash crops, confirmation of feeding by first instars may ultimately influence the knowledge on biology and management strategies for this pest. to determine whether first instars feed, newly hatched nymphs were provided sterile green beans (control) or beans infected with a rifampi ...201424342007
[construction of saccharomyces cerevisiae cell factories for lycopene production].for microbial production of lycopene, the lycopene synthetic genes from pantoea agglomerans were integrated into saccharomyces cerevisiae strain by4742, to obtain strain zd-l-000 for production of 0.17 mg · l(-1) lycopene. improving supplies of isoprenoid precursors was then investigated for increasing lycopene production. four key genes were chosen to be overexpressed, inclu- ding truncated 3-hydroxy-3-methylglutaryl-coa reductase gene (thmg1), which is the major rate-limiting enzyme in the mev ...201425751950
[production of β-carotene by metabolically engineered saccharomyces cerevisiae].β-carotene has a wide range of application in food, pharmaceutical and cosmetic industries. for microbial production of β-carotene in saccharomyces cerevisiae, the supply of geranylgeranyl diphosphate (ggpp) was firstly increased in s. cerevisiae by4742 to obtain strain by4742-t2 through over-expressing truncated 3-hydroxy-3-methylglutaryl-coa reductase (thmgr), which is the major rate-limiting enzyme in the mevalonate (mva) pathway, and ggpp synthase (ggps), which is a key enzyme in the diterpe ...201425507473
emergence of ndm-1 in a clinical isolate of pantoea agglomerans from india. 201427873700
draft genome sequence of pantoea agglomerans r190, a producer of antibiotics against phytopathogens and foodborne pathogens.pantoea agglomerans r190, isolated from an apple orchard, showed antibacterial activity against various spoilage bacteria, including pectobacterium carotovorum subsp. carotovorum, and foodborne pathogens such as escherichia coli o157:h7. here, we report the genome sequence of p. agglomerans r190. this report will raise the value of p. agglomerans as an agent for biocontrol of disease.201425087741
immigrant pantoea agglomerans embedded within indigenous microbial aggregates: a novel spatial distribution of epiphytic bacteria.immigrant bacteria located on leaf surfaces are important to the health of plants as well as to people who consume fresh fruits and vegetables. however, the spatial distribution and organization of these immigrant bacteria on leaf surfaces are still poorly understood. to examine the spatial organization of these strains, two bacterial strains on tobacco leaves: (1) an indigenous strain, pseudomonas stutzeri nov. y2011 labeled with green fluorescent protein, and (2) an immigrant strain pantoea ag ...201425076531
usefulness of oral administration of lipopolysaccharide for disease prevention through the induction of priming in macrophages.many publications show that macrophages are closely involved in etiology of diseases, such as cancer, diabetes, arteriosclerosis, and alzheimer's disease. recent studies show that waste products (e.g. dead cells, denatured proteins, oxidized lipids, and advanced glycation end-products) are the real causative agents of lifestyle-associated diseases. from the standpoint of health maintenance, macrophages eliminate foreign objects and waste products from an animal's body and appear to be quite impo ...201425075092
an unusual cause of peritonitis in peritoneal dialysis patients: pantoea agglomerans.peritonitis is a serious infection and early diagnosis and treatment is mandatory. a variety of microorganisms are identified in these cases and during recent years a new one was included, pantoea agglomerans. in this case report, a female patient on continuous ambulatory peritoneal dialysis therapy with a peritonitis episode caused by this organism is described. the source of infection was thought to be due to contact of catheter with non-sterile surfaces. in microbiologic culture, this organis ...201425022305
[production of β-carotene by metabolically engineered saccharomyces cerevisiae].β-carotene has a wide range of application in food, pharmaceutical and cosmetic industries. for microbial production of β-carotene in saccharomyces cerevisiae, the supply of geranylgeranyl diphosphate (ggpp) was firstly increased in s. cerevisiae by4742 to obtain strain by4742-t2 through over-expressing truncated 3-hydroxy-3-methylglutaryl-coa reductase (thmgr), which is the major rate-limiting enzyme in the mevalonate (mva) pathway, and ggpp synthase (ggps), which is a key enzyme in the diterpe ...201425423750
the combination enterobacter agglomerans is to be cited as enterobacter agglomerans (beijerinck 1888) ewing and fife 1972 and the combination pantoea agglomerans is to be cited as pantoea agglomerans (beijerinck 1888) gavini et al. 1989. opinion 90. judicial commission of the international committee on systematics of prokaryotes.the judicial commission affirms that, according to information presented to it, the combination enterobacter agglomerans is to be cited as enterobacter agglomerans (beijerinck 1888) ewing and fife 1972 and the combination pantoea agglomerans is to be cited as pantoea agglomerans (beijerinck 1888) gavini et al. 1989.201425288660
[seven cases of port-a-cath contamination caused by pantoea agglomerans in the oncological service of iseo hospital, brescia (italy)].pantoea agglomerans, a gram negative bacillus in the enterobacteriaceae family, has been isolated from feculent material, plants and soil. soft tissue and bone-joint infections due to p. agglomerans following penetrating trauma by vegetation and bacteraemia in association with intravenous fluid, total parenteral nutrition, blood products and anaesthetic agent contamination have been reported. between october 2009 and january 2010 seven cases of port a cath contamination caused by p. agglomerans ...201424955805
plant growth promoting capability and genetic diversity of bacteria isolated from mud volcano and lime cave of andaman and nicobar islands.twenty four bacterial strains from four different regions of mud volcano and lime cave were isolated to estimate their diversity, plant growth promoting and biocontrol activities to use them as inoculant strains in the fields. an excellent antagonistic effect against four plant pathogens and plant growth promoting properties such as iaa production, hcn production, phosphate solubilization, siderophore production, starch hydrolysis and hydrolytic enzymes syntheses were identified in om5 (pantoea ...201425763031
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