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chemoselective hydroxyl group transformation: an elusive target.the selective reaction of one functional group in the presence of others is not a trivial task. a noteworthy amount of research has been dedicated to the chemoselective reaction of the hydroxyl moiety. this group is prevalent in many biologically important molecules including natural products and proteins. however, targeting the hydroxyl group is difficult for many reasons including its relatively low nucleophilicity in comparison to other ubiquitous functional groups such as amines and thiols. ...201222695722
significance of bacteria in oviposition and larval development of the sand fly lutzomyia longipalpis.microbial ecology of phlebotomine sand flies is not well understood although bacteria likely play an important role in the sand fly biology and vector capacity for leishmania parasites. in this study, we assessed the significance of the microbial community of rabbit feces in oviposition and larval development of lutzomyia longipalpis as well as bacterial colonization of the gut of freshly emerged flies.201222827861
evaluation of n-butylbenzenesulfonamide (nbbs) neurotoxicity in sprague-dawley male rats following 27-day oral exposure.n-butylbenzenesulfonamide (nbbs) is widely used as a plasticizer in polyacetals, polyamides, and polycarbonates and has been found in ground water and effluent from wastewater treatment sites. the compound is lipophilic and distributes rapidly to the brain but also clears rapidly and shows little evidence of accumulation. limited studies in the literature report neurotoxicity of nbbs in rabbits and rats. adult sprague-dawley male rats (harlan) received corn oil vehicle or nbbs (100, 200, or 400m ...201222824510
the shared antibiotic resistome of soil bacteria and human pathogens.soil microbiota represent one of the ancient evolutionary origins of antibiotic resistance and have been proposed as a reservoir of resistance genes available for exchange with clinical pathogens. using a high-throughput functional metagenomic approach in conjunction with a pipeline for the de novo assembly of short-read sequence data from functional selections (termed parfums), we provide evidence for recent exchange of antibiotic resistance genes between environmental bacteria and clinical pat ...201222936781
an effective strategy for a whole-cell biosensor based on putative effector interaction site of the regulatory dmpr protein.the detection of bioavailable phenol is a very important issue in environmental and human hazard assessment. despite modest developments recently, there is a stern need for development of novel biosensors with high sensitivity for priority phenol pollutants. dmpr (dimethyl phenol regulatory protein), an ntrc-like regulatory protein for the phenol degradation of pseudomonas sp. strain cf600, represents an attractive biosensor regimen. thus, we sought to design a novel biosensor by modifying the p ...201222937060
the role of ca²⁺ in the activity of mycobacterium tuberculosis dna gyrase.dna gyrase is the only type ii topoisomerase in mycobacterium tuberculosis and needs to catalyse dna supercoiling, relaxation and decatenation reactions in order to fulfil the functions normally carried out by gyrase and dna topoisomerase iv in other bacteria. we have obtained evidence for the existence of a ca(2+)-binding site in the gyra subunit of m. tuberculosis gyrase. ca(2+) cannot support topoisomerase reactions in the absence of mg(2+), but partial removal of ca(2+) from gyra by dialysis ...201222844097
optimization of extracellular thermophilic highly alkaline lipase from thermophilic bacillus sp isolated from hotspring of arunachal pradesh, india.studies on lipase production were carried out with a bacterial strain (bacillus sp lbn 2) isolated from soil sample of hotspring of arunachal pradesh, india. the cells were cultivated in a mineral medium with maximum production at 1% groundnut oil. the optimum temperature and initial medium ph for lipase production by the organism were 50(0)c and 9.0 respectively. the molecular mass was found to be 33kda by sds page. the optimal ph and temperature for activity were 10 and 60(0)c respectively. th ...201224031801
midgut microbiota of the malaria mosquito vector anopheles gambiae and interactions with plasmodium falciparum infection.the susceptibility of anopheles mosquitoes to plasmodium infections relies on complex interactions between the insect vector and the malaria parasite. a number of studies have shown that the mosquito innate immune responses play an important role in controlling the malaria infection and that the strength of parasite clearance is under genetic control, but little is known about the influence of environmental factors on the transmission success. we present here evidence that the composition of the ...201222693451
pyrosequencing the bemisia tabaci transcriptome reveals a highly diverse bacterial community and a robust system for insecticide resistance.bemisia tabaci (gennadius) is a phloem-feeding insect poised to become one of the major insect pests in open field and greenhouse production systems throughout the world. the high level of resistance to insecticides is a main factor that hinders continued use of insecticides for suppression of b. tabaci. despite its prevalence, little is known about b. tabaci at the genome level. to fill this gap, an invasive b. tabaci b biotype was subjected to pyrosequencing-based transcriptome analysis to ide ...201222558125
accuracy of rapid tests for malaria and treatment outcomes for malaria and non-malaria cases among under-five children in rural ghana.who now recommends test-based management of malaria across all transmission settings. the accuracy of rapid diagnostic test (rdt) and the outcome of treatment based on the result of tests will influence acceptability of and adherence to the new guidelines.201222514617
mineralization of acephate, a recalcitrant organophosphate insecticide is initiated by a pseudomonad in environmental samples.an aerobic bacterium capable of breaking down the pesticide acephate (o,s-dimethyl acetyl phosphoramidothioic acid) was isolated from activated sludge collected from a pesticide manufacturing facility. a phylogenetic tree based on the 16 s rrna gene sequence determined that the isolate lies within the pseudomonads. the isolate was able to grow in the presence of acephate at concentrations up to 80 mm, with maximum growth at 40 mm. hplc and lc-ms/ms analysis of spent medium from growth experiment ...201222496729
changes in bacterial composition of zucchini flowers exposed to refrigeration temperatures.microbial spoilage is one of the main factors affecting the quality of fresh fruits and vegetables, leading to off-flavor, fermented aroma, and tissue decay. the knowledge of microbial growth kinetics is essential for estimating a correct risk assessment associated with consuming raw vegetables and better managing the development of spoilage microorganisms. this study shows, for the first time, that only a part of total microbial community, originally present on fresh harvested female zucchini f ...201222566759
two separate gene clusters encode the biosynthetic pathway for the meroterpenoids austinol and dehydroaustinol in aspergillus nidulans.meroterpenoids are a class of fungal natural products that are produced from polyketide and terpenoid precursors. an understanding of meroterpenoid biosynthesis at the genetic level should facilitate engineering of second-generation molecules and increasing production of first-generation compounds. the filamentous fungus aspergillus nidulans has previously been found to produce two meroterpenoids, austinol and dehydroaustinol. using targeted deletions that we created, we have determined that, su ...201222329759
engineering of acetyl-coa metabolism for the improved production of polyhydroxybutyrate in saccharomyces cerevisiae.through metabolic engineering microorganisms can be engineered to produce new products and further produce these with higher yield and productivities. here, we expressed the bacterial polyhydroxybutyrate (phb) pathway in the yeast saccharomyces cerevisiae and we further evaluated the effect of engineering the formation of acetyl coenzyme a (acetyl-coa), an intermediate of the central carbon metabolism and precursor of the phb pathway, on heterologous phb production by yeast. we engineered the ac ...201223009357
detection of mycobacterium tuberculosis glcb or hspx antigens or devr dna impacts the rapid diagnosis of tuberculous meningitis in children.tuberculous meningitis (tbm) is the most common form of neurotuberculosis and the fifth most common form of extrapulmonary tb. early diagnosis and prompt treatment are the cornerstones of effective disease management. the accurate diagnosis of tbm poses a challenge due to an extensive differential diagnosis, low bacterial load and paucity of cerebrospinal fluid (csf) especially in children.201222984534
interspecies modulation of bacterial development through iron competition and siderophore piracy.while soil-dwelling actinomycetes are renowned for secreting natural products, little is known about the roles of these molecules in mediating actinomycete interactions. in a previous co-culture screen, we found that one actinomycete, amycolatopsis sp. aa4, inhibited aerial hyphae formation in adjacent colonies of streptomyces coelicolor. a siderophore, amychelin, mediated this developmental arrest. here we present genetic evidence that confirms the role of the amc locus in the production of amy ...201222931126
changes in gram negative microorganisms' resistance pattern during 4 years period in a referral teaching hospital; a surveillance study. 201223351308
biological activities of various extracts and chemical composition of trigonella monantha c. a. mey. subsp. monantha grown in iran.the objective of this research was to study the biological activities of various extracts and the chemical composition of the essential oil trigonella monantha c. a. mey. subsp. monantha by gas chromatography (gc) and gas chromatography-mass spectroscopy (gc-ms), from the compounds derived from the aerial parts. the overall results of t. monantha tests allow us to conclude various extracts [hexane extract (he), methanol extract (me) and chloroform extract (ce)] of the test total phenolic, abts a ...201224250546
characterization of bacteria associated with pinewood nematode bursaphelenchus xylophilus.pine wilt disease (pwd) is a complex disease integrating three major agents: the pathogenic agent, the pinewood nematode bursaphelenchus xylophilus; the insect-vector monochamus spp.; and the host pine tree, pinus sp. since the early 80's, the notion that another pathogenic agent, namely bacteria, may play a role in pwd has been gaining traction, however the role of bacteria in pwd is still unknown. the present work supports the possibility that some b. xylophilus-associated bacteria may play a ...201223091599
convergent development of anodic bacterial communities in microbial fuel cells.microbial fuel cells (mfcs) are often inoculated from a single wastewater source. the extent that the inoculum affects community development or power production is unknown. the stable anodic microbial communities in mfcs were examined using three inocula: a wastewater treatment plant sample known to produce consistent power densities, a second wastewater treatment plant sample, and an anaerobic bog sediment. the bog-inoculated mfcs initially produced higher power densities than the wastewater-in ...201222572637
evaluation and biochemical characterization of a distinctive pyoverdin from a pseudomonas isolated from chickpea rhizosphere.microbial siderophores confiscate the available ferric ions around the roots and trigger a reaction resulting in plant growth promotion. in our study, a high level of siderophore production was observed from a newly isolated pseudomonas sp. from the rhizosphere of chickpea plants. under an iron depleted condition in standard succinic acid medium a 1000 μgml(-1) of siderophore production was achieved. increasing the concentration of iron showed an inverse relationship between growth and sideropho ...201224031875
plant-growth promoting effect of newly isolated rhizobacteria varies between two arabidopsis ecotypes.various rhizobacteria are known for their beneficial effects on plants, i. e. promotion of growth and induction of systemic resistance against pathogens. these bacteria are categorized as plant growth promoting rhizobacteria (pgpr) and are associated with plant roots. knowledge of the underlying mechanisms of plant growth promotion in vivo is still very limited, but interference of bacteria with plant hormone metabolism is suggested to play a major role. to obtain new growth promoting bacteria, ...201222580689
investigation of the biosynthetic potential of endophytes in traditional chinese anticancer herbs.traditional chinese medicine encompasses a rich empirical knowledge of the use of plants for the treatment of disease. in addition, the microorganisms associated with medicinal plants are also of interest as the producers of the compounds responsible for the observed plant bioactivity. the present study has pioneered the use of genetic screening to assess the potential of endophytes to synthesize bioactive compounds, as indicated by the presence of non-ribosomal peptide synthetase (nrps) and pol ...201222629306
re-evaluation of a bacterial antifreeze protein as an adhesin with ice-binding activity.a novel role for antifreeze proteins (afps) may reside in an exceptionally large 1.5-mda adhesin isolated from an antarctic gram-negative bacterium, marinomonas primoryensis. mpafp was purified from bacterial lysates by ice adsorption and gel electrophoresis. we have previously reported that two highly repetitive sequences, region ii (rii) and region iv (riv), divide mpafp into five distinct regions, all of which require mm ca(2+) levels for correct folding. also, the antifreeze activity is conf ...201223144980
biosynthesis and characterization of polyhydroxyalkanoates copolymers produced by pseudomonas putida bet001 isolated from palm oil mill effluent.the biosynthesis and characterization of medium chain length poly-3-hydroxyalkanoates (mcl-pha) produced by pseudomonas putida bet001 isolated from palm oil mill effluent was studied. the biosynthesis of mcl-pha in this newly isolated microorganism follows a growth-associated trend. mcl-pha accumulation ranging from 49.7 to 68.9% on cell dry weight (cdw) basis were observed when fatty acids ranging from octanoic acid (c(8:0)) to oleic acid (c(18:1)) were used as sole carbon and energy source. mo ...201223028854
an ultrasensitive enzymatic method for measuring mevalonic acid in serum.we have developed a simple, precise, and ultrasensitive enzymatic method for measuring serum mevalonic acid (mva) concentration, which is thought to be a good indicator of the in vivo cholesterol biosynthesis rate. this assay is based on an enzyme cycling reaction and makes use of hmg-coa reductase (hmgr), thio-nad, nadh, and coa. mva participates in the hmgr cycling reaction, and its level is measured based on the production of thio-nadh, which is determined from the change in absorbance at 405 ...201222715156
identification of the para-nitrophenol catabolic pathway, and characterization of three enzymes involved in the hydroquinone pathway, in peudomonas sp. 1-7.para-nitrophenol (pnp), a priority environmental pollutant, is hazardous to humans and animals. however, the information relating to the pnp degradation pathways and their enzymes remain limited.201222380602
reduction of chromium-vi by chromium resistant lactobacilli: a prospective bacterium for bioremediation.chromium is a toxic heavy metal, which primarily exists in two inorganic forms, cr (vi) and cr (iii). highly soluble hexavalent chromium is carcinogenic due to its oxidizing nature. it is well established that the intestinal bacteria including lactobacilli have regulatory effect on intestinal homeostasis and a breakdown in the relationship between intestinal cells and bacteria results in the manifestation of gastrointestinal (gi) disorders. in this study cr (vi) resistance was developed in lacto ...201222736899
a conjugative 38 kb plasmid is present in multiple subspecies of xylella fastidiosa.a ≈ 38kb plasmid (pxf-riv5) was present in the riv5 strain of xylella fastidiosa subsp. multiplex isolated from ornamental plum in southern california. the complete nucleotide sequence of pxf-riv5 is almost identical to that of pxfas01 from x. fastidiosa subsp. fastidiosa strain m23; the two plasmids vary at only 6 nucleotide positions. blast searches and phylogenetic analyses indicate pxf-riv5 and pxfas01 share some similarity to chromosomal and plasmid (pxf51) sequences of x. fastidiosa subsp. ...201223251694
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 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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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