Publications

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growth kinetics, effect of carbon substrate in biosynthesis of mcl-pha by pseudomonas putida bet001.growth associated biosynthesis of medium chain length poly-3-hydroxyalkanoates (mcl-pha) in pseudomonas putida bet001 isolated from palm oil mill effluent was studied. models with substrate inhibition terms described well the kinetics of its growth. selected fatty acids (c8:0 to c18:1) and ammonium were used as carbon and nitrogen sources during growth and pha biosynthesis, resulting in pha accumulation of about 50 to 69% (w/w) and pha yields ranging from 10.12 g l(-1) to 15.45 g l(-1), respecti ...201425242925
biofertilizers function as key player in sustainable agriculture by improving soil fertility, plant tolerance and crop productivity.current soil management strategies are mainly dependent on inorganic chemical-based fertilizers, which caused a serious threat to human health and environment. the exploitation of beneficial microbes as a biofertilizer has become paramount importance in agriculture sector for their potential role in food safety and sustainable crop production. the eco-friendly approaches inspire a wide range of application of plant growth promoting rhizobacteria (pgprs), endo- and ectomycorrhizal fungi, cyanobac ...201424885352
silencing by h-ns potentiated the evolution of salmonella.the bacterial h-ns protein silences expression from sequences with higher at-content than the host genome and is believed to buffer the fitness consequences associated with foreign gene acquisition. loss of h-ns results in severe growth defects in salmonella, but the underlying reasons were unclear. an experimental evolution approach was employed to determine which secondary mutations could compensate for the loss of h-ns in salmonella. six independently derived s. typhimurium hns mutant strains ...201425375226
inhibition of batrachochytrium dendrobatidis caused by bacteria isolated from the skin of boreal toads, anaxyrus (bufo) boreas boreas, from grand teton national park, wyoming, usa.the chytrid fungus batrachochytrium dendrobatidis is a significant cause of the worldwide decline in amphibian populations; however, various amphibian species are capable of coexisting with b. dendrobatidis. among them are boreal toads (anaxyrus (bufo) boreas boreas) located in grand teton national park (gtnp) in wyoming, usa. the purpose of this study was to identify cultivable bacterial isolates from the skin microbiota of boreal toads from gtnp and determine if they were capable of inhibiting ...201424826077
draft genome sequence analysis of a pseudomonas putida w15oct28 strain with antagonistic activity to gram-positive and pseudomonas sp. pathogens.pseudomonas putida is a member of the fluorescent pseudomonads known to produce the yellow-green fluorescent pyoverdine siderophore. p. putida w15oct28, isolated from a stream in brussels, was found to produce compound(s) with antimicrobial activity against the opportunistic pathogens staphylococcus aureus, pseudomonas aeruginosa, and the plant pathogen pseudomonas syringae, an unusual characteristic for p. putida. the active compound production only occurred in media with low iron content and w ...201425369289
interactions of non-natural halogenated substrates with d-specific dehalogenase (dehd) mutants using in silico studies.the d-2-haloacid dehalogenase of d-specific dehalogenase (dehd) from rhizobium sp. rc1 catalyses the hydrolytic dehalogenation of d-haloalkanoic acids, inverting the substrate-product configuration and thereby forming the corresponding l-hydroxyalkanoic acids. our investigations were focused on dehd mutants: r134a and y135a. we examined the possible interactions between these mutants with haloalkanoic acids and characterized the key catalytic residues in the wild-type dehalogenase, to design deh ...201426019583
chromobacterium csp_p reduces malaria and dengue infection in vector mosquitoes and has entomopathogenic and in vitro anti-pathogen activities.plasmodium and dengue virus, the causative agents of the two most devastating vector-borne diseases, malaria and dengue, are transmitted by the two most important mosquito vectors, anopheles gambiae and aedes aegypti, respectively. insect-bacteria associations have been shown to influence vector competence for human pathogens through multi-faceted actions that include the elicitation of the insect immune system, pathogen sequestration by microbes, and bacteria-produced anti-pathogenic factors. t ...201425340821
novel assay to measure the plasmid mobilizing potential of mixed microbial communities.mobilizable plasmids lack necessary genes for complete conjugation and are therefore non-self-transmissible. instead, they rely on the conjugation system of conjugal plasmids to be horizontally transferred to new recipients. while community permissiveness, the fraction of a mixed microbial community that can receive self-transmissible conjugal plasmids, has been studied, the intrinsic ability of a community to mobilize plasmids that lack conjugation systems is unexplored. here, we present a nove ...201425566238
p. aeruginosa sgnh hydrolase-like proteins algj and algx have similar topology but separate and distinct roles in alginate acetylation.the o-acetylation of polysaccharides is a common modification used by pathogenic organisms to protect against external forces. pseudomonas aeruginosa secretes the anionic, o-acetylated exopolysaccharide alginate during chronic infection in the lungs of cystic fibrosis patients to form the major constituent of a protective biofilm matrix. four proteins have been implicated in the o-acetylation of alginate, algijf and algx. to probe the biological function of algj, we determined its structure to 1 ...201425165982
soil salinity: a serious environmental issue and plant growth promoting bacteria as one of the tools for its alleviation.salinity is one of the most brutal environmental factors limiting the productivity of crop plants because most of the crop plants are sensitive to salinity caused by high concentrations of salts in the soil, and the area of land affected by it is increasing day by day. for all important crops, average yields are only a fraction - somewhere between 20% and 50% of record yields; these losses are mostly due to drought and high soil salinity, environmental conditions which will worsen in many region ...201425737642
bacterial degradation of chlorophenols and their derivatives.chlorophenols (cps) and their derivatives are persistent environmental pollutants which are used in the manufacture of dyes, drugs, pesticides and other industrial products. cps, which include monochlorophenols, polychlorophenols, chloronitrophenols, chloroaminophenols and chloromethylphenols, are highly toxic to living beings due to their carcinogenic, mutagenic and cytotoxic properties. several physico-chemical and biological methods have been used for removal of cps from the environment. bact ...201424589366
bacterial communities in semen from men of infertile couples: metagenomic sequencing reveals relationships of seminal microbiota to semen quality.some previous studies have identified bacteria in semen as being a potential factor in male infertility. however, only few types of bacteria were taken into consideration while using pcr-based or culturing methods. here we present an analysis approach using next-generation sequencing technology and bioinformatics analysis to investigate the associations between bacterial communities and semen quality. ninety-six semen samples collected were examined for bacterial communities, measuring seven cli ...201425340531
new insights into 1-aminocyclopropane-1-carboxylate (acc) deaminase phylogeny, evolution and ecological significance.the main objective of this work is the study of the phylogeny, evolution and ecological importance of the enzyme 1-aminocyclopropane-1-carboxylate (acc) deaminase, the activity of which represents one of the most important and studied mechanisms used by plant growth-promoting microorganisms. the acc deaminase gene and its regulatory elements presence in completely sequenced organisms was verified by multiple searches in diverse databases, and based on the data obtained a comprehensive analysis w ...201424905353
the quest for a unified view of bacterial land colonization.exploring molecular mechanisms underlying bacterial water-to-land transition represents a critical start toward a better understanding of the functioning and stability of the terrestrial ecosystems. here, we perform comprehensive analyses based on a large variety of bacteria by integrating taxonomic, phylogenetic and metagenomic data, in the quest for a unified view that elucidates genomic, evolutionary and ecological dynamics of the marine progenitors in adapting to nonaquatic environments. we ...201424451209
natural rice rhizospheric microbes suppress rice blast infections.the natural interactions between plant roots and their rhizospheric microbiome are vital to plant fitness, modulating both growth promotion and disease suppression. in rice (oryza sativa), a globally important food crop, as much as 30% of yields are lost due to blast disease caused by fungal pathogen magnaporthe oryzae. capitalizing on the abilities of naturally occurring rice soil bacteria to reduce m. oryzae infections could provide a sustainable solution to reduce the amount of crops lost to ...201424884531
parallel histories of horizontal gene transfer facilitated extreme reduction of endosymbiont genomes in sap-feeding insects.bacteria confined to intracellular environments experience extensive genome reduction. in extreme cases, insect endosymbionts have evolved genomes that are so gene-poor that they blur the distinction between bacteria and endosymbiotically derived organelles such as mitochondria and plastids. to understand the host's role in this extreme gene loss, we analyzed gene content and expression in the nuclear genome of the psyllid pachypsylla venusta, a sap-feeding insect that harbors an ancient endosym ...201424398322
cyanuric acid hydrolase from azorhizobium caulinodans ors 571: crystal structure and insights into a new class of ser-lys dyad proteins.cyanuric acid hydrolase (cah) catalyzes the hydrolytic ring-opening of cyanuric acid (2,4,6-trihydroxy-1,3,5-triazine), an intermediate in s-triazine bacterial degradation and a by-product from disinfection with trichloroisocyanuric acid. in the present study, an x-ray crystal structure of the cah-barbituric acid inhibitor complex from azorhizobium caulinodans ors 571 has been determined at 2.7 å resolution. the cah protein fold consists of three structurally homologous domains forming a β-barre ...201424915109
newly identified pathogens associated with periodontitis: a systematic review.there is substantial evidence supporting the role of certain oral bacteria species in the onset and progression of periodontitis. nevertheless, results of independent-culture diagnostic methods introduced about a decade ago have pointed to the existence of new periodontal pathogens. however, the data of these studies have not been evaluated together, which may generate some misunderstanding on the actual role of these microorganisms in the etiology of periodontitis. the aim of this systematic re ...201425074492
electronic waste - an emerging threat to the environment of urban india.electronic waste or e-waste is one of the emerging problems in developed and developing countries worldwide. it comprises of a multitude of components with valuable materials, some containing toxic substances, that can have an adverse impact on human health and the environment. previous studies show that india has generated 0.4 million tons of e-waste in 2010 which may increase to 0.5 to 0.6 million tons by 2013-2014. coupled with lack of appropriate infrastructural facilities and procedures for ...201424444377
efficient asymmetric synthesis of 1-cyano-tetrahydroisoquinolines from lipase dual activity and opposite enantioselectivities in α-aminonitrile resolution.dual promiscuous racemization/amidation activities of lipases leading to efficient dynamic kinetic resolution protocols of racemic α-aminonitrile compounds are described. α-amidonitrile products of high enantiomeric purity could be formed in high yields. several lipases from different sources were shown to exhibit the dual catalytic activities, where opposite enantioselectivities could be recorded for certain substrates.201425055970
two structurally different dienelactone hydrolases (tfdei and tfdeii) from cupriavidus necator jmp134 plasmid pjp4 catalyse cis- and trans-dienelactones with similar efficiency.in this study, dienelactone hydrolases (tfdei and tfdeii) located on plasmid pjp4 of cupriavidus necator jmp134 were cloned, purified, characterized and three dimensional structures were predicted. tfdei and tfdeii genes were cloned into pet21b vector and expressed in e. coli bl21(de3). the enzymes were purified by applying ultra-membrane filtration, anion-exchange qff and gel-filtration columns. the enzyme activity was determined by using cis-dienelactone. the three-dimensional structure of enz ...201425054964
rate of positive urine culture and double-j catheters colonization on the basis of microorganism dna analysis.the aim of the trial was to estimate the relationship between colonization of the double-j catheter, and the microorganisms cultured from urine.201424982789
burkholderia ambifaria and b. caribensis promote growth and increase yield in grain amaranth (amaranthus cruentus and a. hypochondriacus) by improving plant nitrogen uptake.grain amaranth is an emerging crop that produces seeds having high quality protein with balanced amino-acid content. however, production is restricted by agronomic limitations that result in yields that are lower than those normally produced by cereals. in this work, the use of five different rhizobacteria were explored as a strategy to promote growth and yields in amaranthus hypochondriacus cv. nutrisol and a. cruentus cv. candil, two commercially important grain amaranth cultivars. the plants ...201424533068
potential for plant growth promotion by a consortium of stress-tolerant 2,4-dinitrotoluene-degrading bacteria: isolation and characterization of a military soil.the presence of explosives in soils and the interaction with drought stress and nutrient limitation are among the environmental factors that severely affect plant growth on military soils. in this study, we seek to isolate and identify the cultivable bacteria of a 2,4-dinitrotoluene (dnt) contaminated soil (ds) and an adjacent grassland soil (gs) of a military training area aiming to isolate new plant growth-promoting (pgp) and 2,4-dnt-degrading strains. metabolic profiling revealed disturbances ...201424467368
cloning and characterization of ef-tu and ef-ts from pseudomonas aeruginosa.we have cloned genes encoding elongation factors ef-tu and ef-ts from pseudomonas aeruginosa and expressed and purified the proteins to greater than 95% homogeneity. sequence analysis indicated that p. aeruginosa ef-tu and ef-ts are 84% and 55% identical to e. coli counterparts, respectively. p. aeruginosa ef-tu was active when assayed in gdp exchange assays. kinetic parameters for the interaction of ef-tu with gdp in the absence of ef-ts were observed to be k m = 33 μm, k cat (obs) = 0.003 s(-1 ...201323984384
prevent infection linked to the dialysis water in a hemodialysis center in fez city (morocco).water treatment systems are a critical variable in dialysis therapy. rigorous control of hemodialysis water quality is particularly important in order to guarantee a better quality of life of the hemodialysis patients. the objective of the study was to evaluate the chemical, microbiological quality and antimicrobial resistance of bacteria isolated from water and dialysate in a public hd center.201324839530
genome analysis and physiological comparison of alicycliphilus denitrificans strains bc and k601(t.).the genomes of the betaproteobacteria alicycliphilus denitrificans strains bc and k601(t) have been sequenced to get insight into the physiology of the two strains. strain bc degrades benzene with chlorate as electron acceptor. the cyclohexanol-degrading denitrifying strain k601(t) is not able to use chlorate as electron acceptor, while strain bc cannot degrade cyclohexanol. the 16s rrna sequences of strains bc and k601(t) are identical and the fatty acid methyl ester patterns of the strains are ...201323825601
the catalytic roles of p185 and t188 and substrate-binding loop flexibility in 3α-hydroxysteroid dehydrogenase/carbonyl reductase from comamonas testosteroni.3α-hydroxysteroid dehydrogenase/carbonyl reductase from comamonas testosteroni reversibly catalyzes the oxidation of androsterone with nad(+) to form androstanedione and nadh. structurally the substrate-binding loop of the residues, t188-k208, is unresolved, while binding with nad(+) causes the appearance of t188-p191 in the binary complex. this study determines the functional roles of the flexible substrate-binding loop in conformational changes and enzyme catalysis. a stopped-flow study reveal ...201323717450
identification of genes and pathways related to phenol degradation in metagenomic libraries from petroleum refinery wastewater.two fosmid libraries, totaling 13,200 clones, were obtained from bioreactor sludge of petroleum refinery wastewater treatment system. the library screening based on pcr and biological activity assays revealed more than 400 positive clones for phenol degradation. from these, 100 clones were randomly selected for pyrosequencing in order to evaluate the genetic potential of the microorganisms present in wastewater treatment plant for biodegradation, focusing mainly on novel genes and pathways of ph ...201323637911
genomic and functional analyses of the 2-aminophenol catabolic pathway and partial conversion of its substrate into picolinic acid in burkholderia xenovorans lb400.2-aminophenol (2-ap) is a toxic nitrogen-containing aromatic pollutant. burkholderia xenovorans lb400 possess an amn gene cluster that encodes the 2-ap catabolic pathway. in this report, the functionality of the 2-aminophenol pathway of b. xenovorans strain lb400 was analyzed. the amnrjbacdfehg cluster located at chromosome 1 encodes the enzymes for the degradation of 2-aminophenol. the absence of haba and habb genes in lb400 genome correlates with its no growth on nitrobenzene. rt-pcr analyses ...201324124510
ultrasound assessment of thrombotic complications in pediatric patients with tunneled central venous catheters.central venous access consists in inserting a vascular catheter to the vena cava and placing its tip in the vicinity of the opening to the right atrium. in the patients of the clinic of pediatrics, hematology and oncology at the academic clinical centre of the medical university in gdańsk, such implantation procedures are conducted 40-50 times in a year using broviac/hickman catheters that are placed in the subclavian vein. in the ultrasound and biopsy laboratory at the clinic mentioned above, a ...201326673005
comparative evaluation of the in-vitro activity of six β-lactam/β-lactamase inhibitor combinations against gram negative bacilli.the extensive use of the β-lactam antibiotics in hospitals and in the community has created major resistance problems which has led to increased morbidity, mortality and healthcare costs. the use of the β-lactamase inhibitors in combination with the β-lactam antibiotics is currently the most successful strategy used for circumventing the resistance mechanisms.201323543071
crystal structure of the γ-hydroxymuconic semialdehyde dehydrogenase from pseudomonas sp. strainwbc-3, a key enzyme involved in para-nitrophenol degradation.para-nitrophenol (pnp) is a highly toxic compound with threats to mammalian health. the pnpe-encoded γ-hydroxymuconic semialdehyde dehydrogenase catalyzes the reduction of γ-hydroxymuconic semialdehyde to maleylacetate in pseudomonas sp. strain wbc-3, playing a key role in the catabolism of pnp to krebs cycle intermediates. however, the catalyzing mechanism by pnpe has not been well understood.201324252642
a treatment plant receiving waste water from multiple bulk drug manufacturers is a reservoir for highly multi-drug resistant integron-bearing bacteria.the arenas and detailed mechanisms for transfer of antibiotic resistance genes between environmental bacteria and pathogens are largely unclear. selection pressures from antibiotics in situations where environmental bacteria and human pathogens meet are expected to increase the risks for such gene transfer events. we hypothesize that waste-water treatment plants (wwtps) serving antibiotic manufacturing industries may provide such spawning grounds, given the high bacterial densities present there ...201324204801
bacterial communities associated with the surfaces of fresh fruits and vegetables.fresh fruits and vegetables can harbor large and diverse populations of bacteria. however, most of the work on produce-associated bacteria has focused on a relatively small number of pathogenic bacteria and, as a result, we know far less about the overall diversity and composition of those bacterial communities found on produce and how the structure of these communities varies across produce types. moreover, we lack a comprehensive view of the potential effects of differing farming practices on ...201323544058
microarray-based identification of differentially expressed genes in intracellular brucella abortus within raw264.7 cells.brucella spp. is a species of facultative intracellular gram-negative bacteria that induces abortion and causes sterility in domesticated mammals and chronic undulant fever in humans. important determinants of brucella's virulence and potential for chronic infection include the ability to circumvent the host cell's internal surveillance system and the capability to proliferate within dedicated and non-dedicated phagocytes. hence, identifying genes necessary for intracellular survival may hold th ...201323950864
evolution of rep diversity: a comparative study.repetitive extragenic palindromic elements (reps) constitute a group of bacterial genomic repeats known for their high abundance and several roles in host cells´ physiology. we analyzed the phylogenetic distribution of particular rep classes in genomic sequences of sixty-three bacterial strains belonging to the pseudomonas fluorescens species complex and ten strains of stenotrophomonas sp., in order to assess intraspecific rep diversity and to gain insight into long-term rep evolution.201323758774
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
the surface properties of shewanella putrefaciens 200 and s. oneidensis mr-1: the effect of ph and terminal electron acceptors.we investigated the surface characteristics of two strains of shewanella sp., s. oneidensis mr-1 and s. putrefaciens 200, that were grown under aerobic conditions as well as under anaerobic conditions with trimethylamine oxide (tmao) as the electron acceptor. the investigation focused on the experimental determination of electrophoretic mobility (epm) under a range of ph and ionic strength, as well as by subsequent modeling in which shewanella cells were considered to be soft particles with wate ...201323566080
promise for plant pest control: root-associated pseudomonads with insecticidal activities.insects are an important and probably the most challenging pest to control in agriculture, in particular when they feed on belowground parts of plants. the application of synthetic pesticides is problematic owing to side effects on the environment, concerns for public health and the rapid development of resistance. entomopathogenic bacteria, notably bacillus thuringiensis and photorhabdus/xenorhabdus species, are promising alternatives to chemical insecticides, for they are able to efficiently k ...201323914197
phosphate solubilizing microbes: sustainable approach for managing phosphorus deficiency in agricultural soils.phosphorus is the second important key element after nitrogen as a mineral nutrient in terms of quantitative plant requirement. although abundant in soils, in both organic and inorganic forms, its availability is restricted as it occurs mostly in insoluble forms. the p content in average soil is about 0.05% (w/w) but only 0.1% of the total p is available to plant because of poor solubility and its fixation in soil (illmer and schinner, soil biol biochem 27:257-263, 1995). an adequate supply of p ...201325674415
functional genes to assess nitrogen cycling and aromatic hydrocarbon degradation: primers and processing matter.targeting sequencing to genes involved in key environmental processes, i.e., ecofunctional genes, provides an opportunity to sample nature's gene guilds to greater depth and help link community structure to process-level outcomes. vastly different approaches have been implemented for sequence processing and, ultimately, for taxonomic placement of these gene reads. the overall quality of next generation sequence analysis of functional genes is dependent on multiple steps and assumptions of unknow ...201324062736
purification and identification of trichloroethylene induced proteins from stenotrophomonas maltophilia pm102 by immuno-affinity-chromatography and maldi-tof mass spectrometry.a novel bacterial isolate capable of growth on trichloroethylene as the sole carbon source was identified as stenotrophomonas maltophilia pm102 by 16s rdna sequencing (genbank acc.no. jq797560). serum was obtained from a rabbit immunized with the total protein extracted from the pm102 isolate grown in 0.2% tce with 0.2% peptone. antibodies to the common antigens were removed by preadsorbing the serum antibody on total protein extracted from the pm102 strain grown in 0.2% peptone. western blot wi ...201323741645
current status on biochemistry and molecular biology of microbial degradation of nicotine.bioremediation is one of the most promising methods to clean up polluted environments using highly efficient potent microbes. microbes with specific enzymes and biochemical pathways are capable of degrading the tobacco alkaloids including highly toxic heterocyclic compound, nicotine. after the metabolic conversion, these nicotinophilic microbes use nicotine as the sole carbon, nitrogen, and energy source for their growth. various nicotine degradation pathways such as demethylation pathway in fun ...201324470788
community acquired bacteremia by sphingomonas paucimobilis: two rare case reports.s.paucimobilis has a diverse nutritional substrate spectrum and found in both environmental and hospital settings. sphingomonas paucimobilis is rarely isolated from clinical specimen. this low virulence organism since has been reported to cause a variety of diseases since 1979. it has been reported to be associated with both community acquired and nosocomial diseases including bacteremia, catheter related sepsis, diarrhoeal diseases, peritonitis, meningitis, cutaneous infections, endopthalmitis, ...201324551684
microbial community dynamics and effect of environmental microbial reservoirs on red-backed salamanders (plethodon cinereus).beneficial cutaneous bacteria on amphibians can protect against the lethal disease chytridiomycosis, which has devastated many amphibian species and is caused by the fungus batrachochytrium dendrobatidis. we describe the diversity of bacteria on red-backed salamanders (plethodon cinereus) in the wild and the stability of these communities through time in captivity using culture-independent illumina 16s rrna gene sequencing. after field sampling, salamanders were housed with soil from the field o ...201324335825
microbial community dynamics and effect of environmental microbial reservoirs on red-backed salamanders (plethodon cinereus).beneficial cutaneous bacteria on amphibians can protect against the lethal disease chytridiomycosis, which has devastated many amphibian species and is caused by the fungus batrachochytrium dendrobatidis. we describe the diversity of bacteria on red-backed salamanders (plethodon cinereus) in the wild and the stability of these communities through time in captivity using culture-independent illumina 16s rrna gene sequencing. after field sampling, salamanders were housed with soil from the field o ...201324335825
prevalence and antibiogram of extended spectrum β-lactamase (esbl) producing gram negative bacilli and further molecular characterization of esbl producing escherichia coli and klebsiella spp.resistance to a wide variety of common antimicrobials has made the proliferation of extended spectrum β-lactmase (esbl) producing strains a serious global health concern that has complicated treatment strategies. the high proportion of esbl producers among the enterobacteriaceae and the complex molecular epidemiology with diverse types of esbl genes are alarming. this study was undertaken to identify esbl production in various gram negative bacilli isolated and to further characterize esbl produ ...201324298468
3d structure modeling of alpha-amino acid ester hydrolase from xanthomonas rubrilineans.alpha-amino acid ester hydrolase (ec 3.1.1.43, aeh) is a promising biocatalyst for the production of semi-synthetic β-lactam antibiotics, penicillins and cephalosporins. the aeh gene from xanthomonas rubrilineans (xraeh) was recently cloned in this laboratory. the three-dimensional structure of xraeh was simulated using the homology modeling method for rational design experiments. the analysis of the active site was performed, and its structure was specified. the key amino acid residues in the a ...201324455184
infectious scleritis: clinical spectrum and management outcomes in india.in this retrospective case series, we studied the predisposing factors, causative organisms, clinical spectrum, and outcomes of 12 cases of culture-proven infectious scleritis. nine of 12 patients had a history of preceding trauma (surgical or accidental). past surgical history included small-incision cataract surgery (4), pterygium surgery (1), and trabeculectomy (1). six patients had multifocal scleral abscesses due to pseudomonas, klebsiella, or nocardia. only 2 patients retained useful visio ...201324212312
food, pathogen, signal: the multifaceted nature of a bacterial diet.c. elegans, both in the wild and in the lab, live on a diet of live bacteria. the bacterial diet provides nutrients for c. elegans, but can also play a number of other roles in c. elegans physiology. recently, we compared the effects of different bacterial diets on life history traits and gene expression. here, we discuss our recent findings in the context of other dietary studies and highlight challenges in understanding dietary effects. for instance, since bacteria can be pathogenic it can be ...201324744980
identification of a histidine metal ligand in the arge-encoded n-acetyl-l-ornithine deacetylase from escherichia coli.the h355a, h355k, h80a, and h80k mutant enzymes of the arge-encoded n-acetyl-l-ornithine deacetylase (arge) from escherichia coli were prepared, however, only the h355a enzyme was found to be soluble. kinetic analysis of the co(ii)-loaded h355a exhibited activity levels that were 380-fold less than co(ii)-loaded wt arge. electronic absorption spectra of co(ii)-loaded h355a-arge indicate that the bound co(ii) ion resides in a distorted, five-coordinate environment and isothermal titration calorim ...201325674394
light based anti-infectives: ultraviolet c irradiation, photodynamic therapy, blue light, and beyond.owing to the worldwide increase in antibiotic resistance, researchers are investigating alternative anti-infective strategies to which it is supposed microorganisms will be unable to develop resistance. prominent among these strategies, is a group of approaches which rely on light to deliver the killing blow. as is well known, ultraviolet light, particularly uvc (200-280 nm), is germicidal, but it has not been much developed as an anti-infective approach until recently, when it was realized that ...201324060701
characterization of epiphytic bacterial communities from grapes, leaves, bark and soil of grapevine plants grown, and their relations.despite its importance in plant health and crop quality, the diversity of epiphytic bacteria on grape berries and other plant parts, like leaves and bark, remains poorly described, as does the role of telluric bacteria in plant colonization. in this study, we compare the bacterial community size and structure in vineyard soils, as well as on grapevine bark, leaves and berries. analyses of culturable bacteria revealed differences in the size and structure of the populations in each ecosystem. the ...201324023666
loss of competition in the outside host environment generates outbreaks of environmental opportunist pathogens.environmentally transmitted pathogens face ecological interactions (e.g., competition, predation, parasitism) in the outside-host environment and host immune system during infection. despite the ubiquitousness of environmental opportunist pathogens, traditional epidemiology focuses on obligatory pathogens incapable of environmental growth. here we ask how competitive interactions in the outside-host environment affect the dynamics of an opportunist pathogen. we present a model coupling the class ...201324244752
bacteriuria amongst pregnant women in the buea health district, cameroon: prevalence, predictors, antibiotic susceptibility patterns and diagnosis.bacteriuria is associated with significant maternal and foetal risks. however, its prevalence is not known in our community.201323976983
randomized controlled trial to reduce bacterial colonization of surgical drains after breast and axillary operations.to determine whether bacterial colonization of drains can be reduced by local antiseptic interventions.201323518704
culture-independent investigation of the microbiome associated with the nematode acrobeloides maximus.symbioses between metazoans and microbes are widespread and vital to many ecosystems. recent work with several nematode species has suggested that strong associations with microbial symbionts may also be common among members of this phylu. in this work we explore possible symbiosis between bacteria and the free living soil bacteriovorous nematode acrobeloides maximus.201323894287
responses of soil bacterial and fungal communities to extreme desiccation and rewetting.the microbial response to summer desiccation reflects adaptation strategies, setting the stage for a large rainfall-induced soil co2 pulse upon rewetting, an important component of the ecosystem carbon budget. in three california annual grasslands, the present (dna-based) and potentially active (rna-based) soil bacterial and fungal communities were tracked over a summer season and in response to controlled rewetting of intact soil cores. phylogenetic marker genes for bacterial (16s) and fungal ( ...201323823489
postoperative differences between colonization and infection after pediatric cardiac surgery-a propensity matched analysis.the objective of this study was to identify the postoperative risk factors associated with the conversion of colonization to postoperative infection in pediatric patients undergoing cardiac surgery.201323819455
quality parameters, fatty acid profiling and estimation of umbelliferone in grahaṇimihira tailam: an ayurvedic oil preparation.grahaṇimihira tailam is an unexplored ayurvedic oil preparation which consists of 34 ingredients. the efficacy of this traditional ayurvedic medicine is undisputable. proper clinical standardization of this formulation will go a long way in securing greater recognition for it. the main objective of this study was to develop standardization parameters for the formulation in a multidisciplinary way.201325161324
a novel approach for pathogen reduction in wastewater treatment.many sewage waste treatment systems are aiming for complete pathogen removal which necessitates search for novel approaches that does not harm the environment. one such novel approach is exploring the possibilities of bacteriophages for pathogen removal. hospital wastewater was collected from different locations of tamil nadu and used for the study. the total heterotroph and total coliform population ranged from 1.6 × 105 to 8.3 × 106 per ml and from 1.2 × 103 to 1.6 × 103/ 100 ml of sample resp ...201324499588
structural and kinetic characterization of two 4-oxalocrotonate tautomerases in methylibium petroleiphilum strain pm1.methylibium petroleiphilum strain pm1 uses various petroleum products including the fuel additive methyl tert-butyl ether and straight chain and aromatic hydrocarbons as sole carbon and energy sources. it has two operons, dmpi and dmpii, that code for the enzymes in a pair of parallel meta-fission pathways. in order to understand the roles of the pathways, the 4-oxalocrotonate tautomerase (4-ot) isozyme from each pathway was characterized. tautomerase i and tautomerase ii have the lowest pairwis ...201323831510
relationship of femtosecond-picosecond dynamics to enzyme-catalyzed h-transfer.at physiological temperatures, enzymes exhibit a broad spectrum of conformations, which interchange via thermally activated dynamics. these conformations are sampled differently in different complexes of the protein and its ligands, and the dynamics of exchange between these conformers depends on the mass of the group that is moving and the length scale of the motion, as well as restrictions imposed by the globular fold of the enzymatic complex. many of these motions have been examined and their ...201323539379
bioaugmentation with petroleum-degrading consortia has a selective growth-promoting impact on crop plants germinated in diesel oil-contaminated soil.rhizoremediation is a complex type of green clean-up technology that involves both plants and the rhizosphere-associated microorganisms to decompose hazardous compounds. the success of the strategy strongly depends on plant tolerance towards the pollutant, as well as plant's interactions with the rhizospheric microbes. the microorganisms may be stimulated by the secreted root exudates, which results in an increased breakdown of contaminants in the rhizosphere. the main goal of this study was to ...201324078757
structural and enzymatic characterization of the phosphotriesterase ophc2 from pseudomonas pseudoalcaligenes.organophosphates (ops) are neurotoxic compounds for which current methods of elimination are unsatisfactory; thus bio-remediation is considered as a promising alternative. here we provide the structural and enzymatic characterization of the recently identified enzyme isolated from pseudomonas pseudoalcaligenes dubbed ophc2. ophc2 belongs to the metallo-β-lactamase superfamily and exhibits an unusual thermal resistance and some op degrading abilities.201324223749
isolation and 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
biosurfactants in agriculture.agricultural productivity to meet growing demands of human population is a matter of great concern for all countries. use of green compounds to achieve the sustainable agriculture is the present necessity. this review highlights the enormous use of harsh surfactants in agricultural soil and agrochemical industries. biosurfactants which are reported to be produced by bacteria, yeasts, and fungi can serve as green surfactants. biosurfactants are considered to be less toxic and eco-friendly and thu ...201323280539
permanent draft genome sequence of comamonas testosteroni kf-1.comamonas testosteroni kf-1 is a model organism for the elucidation of the novel biochemical degradation pathways for xenobiotic 4-sulfophenylcarboxylates (spc) formed during biodegradation of synthetic 4-sulfophenylalkane surfactants (linear alkylbenzenesulfonates, las) by bacterial communities. here we describe the features of this organism, together with the complete genome sequence and annotation. the 6,026,527 bp long chromosome (one sequencing gap) exhibits an average g+c content of 61.79% ...201323991256
biosynthesis of rare hexoses using microorganisms and related enzymes.rare sugars, referred to as monosaccharides and their derivatives that rarely exist in nature, can be applied in many areas ranging from foodstuffs to pharmaceutical and nutrition industry, or as starting materials for various natural products and drug candidates. unfortunately, an important factor restricting the utilization of rare sugars is their limited availability, resulting from limited synthetic methods. nowadays, microbial and enzymatic transformations have become a very powerful tool i ...201324367410
wide screening of phage-displayed libraries identifies immune targets in planta.microbe-associated molecular patterns and virulence effectors are recognized by plants as a first step to mount a defence response against potential pathogens. this recognition involves a large family of extracellular membrane receptors and other immune proteins located in different sub-cellular compartments. we have used phage-display technology to express and select for arabidopsis proteins able to bind bacterial pathogens. to rapidly identify microbe-bound phage, we developed a monitoring met ...201323372747
prevention and treatment of biofilms by hybrid- and nanotechnologies.bacteria growing as adherent biofilms are difficult to treat and frequently develop resistance to antimicrobial agents. to counter biofilms, various approaches, including prevention of bacterial surface adherence, application of device applicators, and assimilation of antimicrobials in targeted drug delivery machinery, have been utilized. these methods are also combined to achieve synergistic bacterial killing. this review discusses various multimodal technologies, presents general concepts, and ...201323946652
midgut microbial community of culex quinquefasciatus mosquito populations from india.the mosquito culex quinquefasciatus is a ubiquitous species that serves as a major vector for west nile virus and lymphatic filariasis. ingestion of bloodmeal by females triggers a series of physiological processes in the midgut and also exposes them to infection by these pathogens. the bacteria normally harbored in the midgut are known to influence physiology and can also alter the response to various pathogens. the midgut bacteria in female cx. quinquefasciatus mosquitoes collected over a larg ...201324312223
pivotal role of p450-p450 interactions in cyp3a4 allostery: the case of α-naphthoflavone.we investigated the relationship between oligomerization of cyp3a4 (cytochrome p450 3a4) and its response to anf (α-naphthoflavone), a prototypical heterotropic activator. the addition of anf resulted in over a 2-fold increase in the rate of cyp3a4-dependent debenzylation of 7-bfc [7-benzyloxy-4-(trifluoromethyl)coumarin] in hlm (human liver microsomes), but failed to produce activation in bd supersomes or baculosomes containing recombinant cyp3a4 and nadph-cpr (cytochrome p450 reductase). howev ...201323651100
diversity and phylogenetic analyses of bacteria from a shallow-water hydrothermal vent in milos island (greece).studies of shallow-water hydrothermal vents have been lagging behind their deep-sea counterparts. hence, the importance of these systems and their contribution to the local and regional diversity and biogeochemistry is unclear. this study analyzes the bacterial community along a transect at the shallow-water hydrothermal vent system of milos island, greece. the abundance and biomass of the prokaryotic community is comparable to areas not affected by hydrothermal activity and was, on average, 1.3 ...201323847607
cryotolerance strategies of pseudomonads isolated from the rhizosphere of himalayan plants.the cold stress biology of psychrotrophic pseudomonas strains isolated from the rhizosphere of himalayan plants have been explored to evaluate their cryotolerance characteristcs. pseudomonas strains were examined for stress metabolites, viz., exopolysaccharide (eps) production, intracellular sugar, polyols and amino acid content, ice nucleation activity, and their freezing survival at -10 and -40°c, respectively. high freezing survival was observed for the pseudomonas strains that were grown at ...201324363982
new and alternative approaches to tackling antibiotic resistance.multidrug-resistant bacteria are becoming more common and due to their multiplicity of mechanisms, they are frequently resistant to many if not all of the current antibiotics. this daunting spectre has been the target of many research efforts into conventional antibiotics and alternative approaches. this review focuses on the more recent advances in these fields with an overview on peptidomimetics, nanoparticles and their derivatives, fimh inhibitors, quorum sensing inhibition molecules, neoglyc ...201324381727
computational mass spectrometry for small molecules.: the identification of small molecules from mass spectrometry (ms) data remains a major challenge in the interpretation of ms data. this review covers the computational aspects of identifying small molecules, from the identification of a compound searching a reference spectral library, to the structural elucidation of unknowns. in detail, we describe the basic principles and pitfalls of searching mass spectral reference libraries. determining the molecular formula of the compound can serve as a ...201323453222
african mistletoes (loranthaceae); ethnopharmacology, chemistry and medicinal values: an update.mistletoes of the loranthaceae and viscaceae are hemiparasitic plants and their preparations in the form of injectable extracts, infusions, tinctures, fluid extracts or tea bags are widely used in various cultures in almost every continent to treat or manage various health problems including hypertension, diabetes mellitus, inflammatory conditions, irregular menstruations, menopause, epilepsy, arthritis, cancer, etc. the medicinal values of some species of mistletoes (loranthaceae) growing in th ...201324146518
the ethnobotanical, phytochemical and mineral analyses of phragmanthera incana (klotzsch), a species of mistletoe growing on three plant hosts in south-western nigeria.mistletoe is collected wildly on various plants and phragmanthera incana is noted to grow on different plant hosts. this study was designed to carry out the ethnobotanical survey, phytochemical and mineral analyses of phragmanthera incana, a species of mistletoe growing on three plant hosts namely cocoa (theobroma cacao), kolanut (cola nitida) and bush mango (irvingia gabonensis). mistletoe samples were identified at the forestry research institute of nigeria herbarium. phragmanthera incana was ...201323675287
antibacterial activity of rhizome of curcuma aromatica and partial purification of active compounds.the hexane extract of curcuma aromatica, a plant belonging to the family zingiberaceae was tested on 10 bacterial strains (clinical isolates and standard strains). agar diffusion method was adopted for determining the antibacterial activity of the extract. the hexane extract was found to be active against all gram-positive strains tested, but inactive against gram-negative strains. the minimum inhibitory concentration and minimum bactericidal concentration were determined and found to be 539 μg/ ...201324591751
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
structure of the flavoprotein tryptophan 2-monooxygenase, a key enzyme in the formation of galls in plants.the flavoprotein tryptophan 2-monooxygenase catalyzes the oxidative decarboxylation of tryptophan to yield indole-3-acetamide. this is the initial step in the biosynthesis of the plant growth hormone indole-acetic acid by bacterial pathogens that cause crown gall and related diseases. the structure of the enzyme from pseudomonas savastanoi has been determined by x-ray diffraction methods to a resolution of 1.95 å. the overall structure of the protein shows that it has the same fold as members of ...201323521653
a microfluidic bioreactor with in situ sers imaging for the study of controlled flow patterns of biofilm precursor materials.a microfluidic bioreactor with an easy to fabricate nano-plasmonic surface is demonstrated for studies of biofilms and their precursor materials via surface enhanced raman spectroscopy (sers). the system uses a novel design to induce sheath flow confinement of a sodium citrate biofilm precursor stream against the sers imaging surface to measure spatial variations in the concentration profile. the unoptimised sers enhancement was approximately 2.5 × 10(4), thereby improving data acquisition time, ...201324172286
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
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
columnaris disease in fish: a review with emphasis on bacterium-host interactions.flavobacterium columnare (f. columnare) is the causative agent of columnaris disease. this bacterium affects both cultured and wild freshwater fish including many susceptible commercially important fish species. f. columnare infections may result in skin lesions, fin erosion and gill necrosis, with a high degree of mortality, leading to severe economic losses. especially in the last decade, various research groups have performed studies aimed at elucidating the pathogenesis of columnaris disease ...201323617544
transcriptional profile of p. syringae pv. phaseolicola nps3121 at low temperature: physiology of phytopathogenic bacteria.low temperatures play key roles in the development of most plant diseases, mainly because of their influence on the expression of various virulence factors in phytopathogenic bacteria. thus far, studies regarding this environmental parameter have focused on specific themes and little is known about phytopathogenic bacteria physiology under these conditions. to obtain a global view regarding phytopathogenic bacteria strategies in response to physiologically relevant temperature changes, we used d ...201323587016
fluopsin c induces oncosis of human breast adenocarcinoma cells.fluopsin c, an antibiotic isolated from pseudomonas jinanesis, has shown antitumor effects on several cancer cell lines. in the current study, the oncotic cell death induced by fluopsin c was investigated in human breast adenocarcinoma cells in vitro.201323708552
atrazine removal from aqueous solutions using submerged biological aerated filter.atrazine is widely used in the agriculture as an herbicide. due to its high mobility, atrazine leaks into the groundwaters, surface waters, and drinking water wells. many physical and chemical methods have been suggested for removing atrazine from aquatic environments. however, these methods are very costly, have many performance problems, produce a lot of toxic intermediates which are very harmful and dangerous, and cannot completely mineralize atrazine. in this study, biodegradation of atrazin ...201324499572
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
outpatient management following intensive induction or salvage chemotherapy for acute myeloid leukemia.adults with newly diagnosed or relapsed acute myeloid leukemia (aml) commonly receive intensive chemotherapy to achieve disease remission. in the united states and many other countries, it is standard practice that these patients remain hospitalized "preemptively" until blood count recovery, owing to the risk for overwhelming infections and bleeding during pancytopenia. this care policy requires hospitalization for an average of 3 to 4 weeks after completion of chemotherapy. however, highly effe ...201324518520
antimicrobial activity of heterotrophic bacterial communities from the marine sponge erylus discophorus (astrophorida, geodiidae).heterotrophic bacteria associated with two specimens of the marine sponge erylus discophorus were screened for their capacity to produce bioactive compounds against a panel of human pathogens (staphylococcus aureus wild type and methicillin-resistant s. aureus (mrsa), bacillus subtilis, pseudomonas aeruginosa, acinetobacter baumanii, candida albicans and aspergillus fumigatus), fish pathogen (aliivibrio fischeri) and environmentally relevant bacteria (vibrio harveyi). the sponges were collected ...201324236081
utilization of oleo-chemical industry by-products for biosurfactant production.biosurfactants are the surface active compounds produced by micro-organisms. the eco-friendly and biodegradable nature of biosurfactants makes their usage more advantageous over chemical surfactants. biosurfactants encompass the properties of dropping surface tension, stabilizing emulsions, promoting foaming and are usually non- toxic and biodegradable. biosurfactants offer advantages over their synthetic counterparts in many applications ranging from environmental, food, and biomedical, cosmeti ...201324262384
commensal bacteria-dependent indole production enhances epithelial barrier function in the colon.microbiota have been shown to have a great influence on functions of intestinal epithelial cells (ecs). the role of indole as a quorum-sensing (qs) molecule mediating intercellular signals in bacteria has been well appreciated. however, it remains unknown whether indole has beneficial effects on maintaining intestinal barriers in vivo. in this study, we analyzed the effect of indole on ecs using a germ free (gf) mouse model. gf mice showed decreased expression of junctional complex molecules in ...201324278294
antioxidative, antimicrobial and cytotoxic properties of isatis floribunda boiss. ex bornm. extracts.the isatis species has antibacterial, anticancer and antiviral properties and these important endemic plants grow widely in various parts of anatolian-turkey. in the present study, the antioxidant activities of isatis floribunda boiss. ex bornm. flower and root extracts were determined with total antioxidant activity, free radical scavenging activity, ferric ion reducing power, and cupric ion reducing antioxidant capacity assay. the total phenolic compounds and flavonoids were also examined for ...201326417224
the spectrum of acute bacterial meningitis in elderly patients.we conducted a prospective, observational study in barcelona to determine the epidemiology, clinical features, and outcome of elderly patients with acute bacterial meningitis (abm) compared with younger adults.201323446215
blood stream infection is associated with altered heptavalent pneumococcal conjugate vaccine immune responses in very low birth weight infants.sepsis in older children and adults modifies immune system function. we compared serotype-specific antibody responses to heptavalent pneumococcal conjugate vaccine (pcv7) in very low birth weight infants (<1500 g,vlbws) with and without blood stream infection (bsi) during their birth hospitalization.201323370608
low level laser therapy (algainp) applied at 5j/cm2 reduces the proliferation of staphylococcus aureus mrsa in infected wounds and intact skin of rats.laser therapy is a low cost, non-invasive procedure with good healing results. doubts exist as to whether laser therapy action on microorganisms can justify research aimed at investigating its possible effects on bacteria-infected wounds.201323539003
new approaches to the study of sepsis.models of sepsis have been instructive in understanding the sequence of events in animals and, to an extent, in humans with sepsis. events developing early in sepsis suggest that a hyperinflammatory state exists, accompanied by a buildup of oxidants in tissues reflective of a redox imbalance. development of immunosuppression and degraded innate and adaptive immune responses are well-established complications of sepsis. in addition, there is robust activation of the complement system, which contr ...201223208733
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