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the influence of cultivation methods on shewanella oneidensis physiology and proteome expression.high-throughput analyses that are central to microbial systems biology and ecophysiology research benefit from highly homogeneous and physiologically well-defined cell cultures. while attention has focused on the technical variation associated with high-throughput technologies, biological variation introduced as a function of cell cultivation methods has been largely overlooked. this study evaluated the impact of cultivation methods, controlled batch or continuous culture in bioreactors versus s ...200818030449
ecology and biotechnology of the genus shewanella.the shewanellae are aquatic microorganisms with worldwide distribution. their hallmark features include unparalleled respiratory diversity and the capacity to thrive at low temperatures. as a genus the shewanellae are physiologically diverse, and this review provides an overview of the varied roles they serve in the environment and describes what is known about how they might survive in such extreme and harsh environments. in light of their fascinating physiology, these organisms have several bi ...200718035608
microflora assessments using pcr-denaturing gradient gel electrophoresis of ozone-treated and modified-atmosphere-packaged farmed cod fillets.denaturing gradient gel electrophoresis (dgge) of a pcr-amplified 16s rdna sequence was used to characterize changes in the microbial flora caused by ozone (o3) treatment of farmed cod (gadus morhua). portions of cod were produced under controlled conditions, bathed in fresh water supplemented with 2 ppm of o3 for 30 min, and packaged in modified atmosphere (ma: 60% co2 and 40% n2) before 4 degrees c storage. control samples were packaged in ma or air, without prior o3 treatment. samples were an ...200718044421
speciation-dependent microbial reduction of uranium within iron-coated sands.transport of uranium within surface and subsurface environments is predicated largely on its redox state. uranyl reduction may transpire through either biotic (enzymatic) or abiotic pathways; in either case, reduction of u(vi) to u(iv) results in the formation of sparingly soluble uo2 precipitates. biological reduction of u(vi), while demonstrated as prolific under both laboratory and field conditions, is influenced by competing electron acceptors (such as nitrate, manganese oxides, or iron oxid ...200718044509
fully automated four-column capillary lc-ms system for maximizing throughput in proteomic analyses.we describe a four-column, high-pressure capillary liquid chromatography (lc) system for robust, high-throughput liquid chromatography-mass spectrometry (lc-ms(/ms)) analyses. this system performs multiple lc separations in parallel, but staggers each of them such that the data-rich region of each separation is sampled sequentially. by allowing nearly continuous data acquisition, this design maximizes the use of the mass spectrometer. each analytical column is connected to a corresponding esi em ...200818044960
microbial synthesis of magnetite and mn-substituted magnetite nanoparticles: influence of bacteria and incubation temperature.microbial synthesis of magnetite and metal (co, cr, ni)-substituted magnetites has only recently been reported. the objective of this study was to examine the influence of mn ion on the microbial synthesis of magnetite nanoparticles. the reductive biotransformation of an akaganeite (beta-feooh) or a mn-substituted (2-20 mol%) akaganeite (fe(1-x)mn(x)ooh) by shewanella loiha (pv-4, 25 degrees c) and thermoanaerobacter ethanolicus (tor-39, 60 degrees c) was investigated under anaerobic conditions ...200718047092
shewanella haliotis sp. nov., isolated from the gut microflora of abalone, haliotis discus hannai.a motile, rod-shaped, pink-orange pigmented bacterium, designated strain dw01(t), was isolated from the gut microflora of abalone collected from the south sea (republic of korea). cells were gram-negative, facultatively anaerobic, catalase- and oxidase-positive. the major fatty acids were iso-c(15 : 0) (17.7 %), c(16 : 0) (13.4 %), iso-c(15 : 0) 2-oh and/or c(16 : 1)omega7c (12.5 %) and c(17 : 1)omega8c (10.7 %). the dna g+c content was 53.7 mol%. a phylogenetic tree based on the 16s rrna gene s ...200718048751
humic substances act as electron acceptor and redox mediator for microbial dissimilatory azoreduction by shewanella decolorationis s12.the potential for humic substances to serve as terminal electron acceptors in microbial respiration and the effects of humic substances on microbial azoreduction were investigated. the dissimilatory azoreducing microorganism shewanella decolorationis s12 was able to conserve energy to support growth from electron transport to humics coupled to the oxidation of various organic substances or h2. batch experiments suggested that when the concentration of anthraquinone-2-sulfonate (aqs), a humics an ...200718050946
secretion of flavins by shewanella species and their role in extracellular electron transfer.fe(iii)-respiring bacteria such as shewanella species play an important role in the global cycle of iron, manganese, and trace metals and are useful for many biotechnological applications, including microbial fuel cells and the bioremediation of waters and sediments contaminated with organics, metals, and radionuclides. several alternative electron transfer pathways have been postulated for the reduction of insoluble extracellular subsurface minerals, such as fe(iii) oxides, by shewanella specie ...200818065612
significance of antioxidative functions of eicosapentaenoic and docosahexaenoic acids in marine microorganisms. 200818065628
biogenic formation of photoactive arsenic-sulfide nanotubes by shewanella sp. strain hn-41.microorganisms facilitate the formation of a wide range of minerals that have unique physical and chemical properties as well as morphologies that are not produced by abiotic processes. here, we report the production of an extensive extracellular network of filamentous, arsenic-sulfide (as-s) nanotubes (20-100 nm in diameter by approximately 30 mum in length) by the dissimilatory metal-reducing bacterium shewanella sp. hn-41. the as-s nanotubes, formed via the reduction of as(v) and s(2)o(3)(2-) ...200718077394
accelerated decolorization of structurally different azo dyes by newly isolated bacterial strains.wastewater effluents from the textile and other dye-stuff industries contain significant amounts of synthetic dyes that require treatment to prevent groundwater contamination. in research aimed at biotechnology for treatment of azo dyes, this study examined 288 strains of azo-dye degrading bacteria to identify efficient strains and determine incubation times required for decolorization. initial enrichment cultures were carried out using a mixture of four structurally different dyes (acid red 88, ...200818084755
utilization of dna as a sole source of phosphorus, carbon, and energy by shewanella spp.: ecological and physiological implications for dissimilatory metal reduction.the solubility of orthophosphate (po4(3-)) in iron-rich sediments can be exceedingly low, limiting the bioavailability of this essential nutrient to microbial populations that catalyze critical biogeochemical reactions. here we demonstrate that dissolved extracellular dna can serve as a sole source of phosphorus, as well as carbon and energy, for metal-reducing bacteria of the genus shewanella. shewanella oneidensis mr-1, shewanella putrefaciens cn32, and shewanella sp. strain w3-18-1 all grew w ...200818156329
structure of the molybdenum site of escherichia coli trimethylamine n-oxide reductase.we report a structural characterization of the molybdenum site of recombinant escherichia coli trimethylamine n-oxide (tmao) reductase using x-ray absorption spectroscopy. the enzyme active site shows considerable similarity to that of dimethyl sulfoxide (dmso) reductase, in that, like dmso reductase, the tmao reductase active site can exist in multiple forms. examination of the published crystal structure of tmao oxidase from shewanella massilia indicates that the postulated mo coordination str ...200818163615
microbial and endotoxin contamination of water-soluble metalworking fluids.the present study is a part of a larger project on assessment of exposure to biological agents and respiratory health effects among metal workers.200718165196
systematic assessment of the benefits and caveats in mining microbial post-translational modifications from shotgun proteomic data: the response of shewanella oneidensis to chromate exposure.microbes are known to regulate both gene expression and protein activity through the use of post-translational modifications (ptms). common ptms involved in cellular signaling and gene control include methylations, acetylations, and phosphorylations, whereas oxidations have been implicated as an indicator of stress. shewanella oneidensis mr-1 is a gram-negative bacterium that demonstrates both respiratory versatility and the ability to sense and adapt to diverse environmental conditions. the dat ...200818171020
screening of genes regulated by cold shock in shewanella piezotolerans wp3 and time course expression of cold-regulated genes.the differential gene transcription of a deep-sea bacterium shewanella piezotolerans wp3 in response to cold shock was analyzed by rna arbitrarily primed pcr. ninety primer sets were used to scan two different rna pools derived from the culture of cold shock and its control (culture at its optimal grown temperature). ninety-four putative differentially expressed fragments were identified and cloned. six out of the 94 fragments were confirmed to be truly differentially transcribed in terms of col ...200818193200
potential for luxs related signalling in marine bacteria and production of autoinducer-2 in the genus shewanella.the autoinducer-2 (ai-2) group of signalling molecules are produced by both gram positive and gram negative bacteria as the by-product of a metabolic transformation carried out by the luxs enzyme. they are the only non species-specific quorum sensing compounds presently known in bacteria. the luxs gene coding for the ai-2 synthase enzyme was found in many important pathogens. here, we surveyed its occurrence in a collection of 165 marine isolates belonging to abundant marine phyla using conserve ...200818215278
probing regulon of arca in shewanella oneidensis mr-1 by integrated genomic analyses.the arc two-component system is a global regulator controlling many genes involved in aerobic/anaerobic respiration and fermentative metabolism in escherichia coli. shewanella oneidensis mr-1 contains a gene encoding a putative arca homolog with ~81% amino acid sequence identity to the e. coli arca protein but not a full-length arcb gene.200818221523
isolation and molecular characterization of shewanella sp. g5, a producer of cold-active beta-d-glucosidases.beta -glucosidase is a highly desired glycosidase, especially for hydrolysis of glycoconjugated precursors in musts and wines for the release of active aromatic compounds. a shewanella sp. g5 strain was isolated from the intestinal content of benthonic organism (munida subrrugosa) from different coastal areas of the beagle channel, tierra del fuego (argentina). this marine bacterium was able to grow at a temperature range between 4 to 20 degrees c using different beta-glycoside substrates, such ...200818247390
correlated biofilm imaging, transport and metabolism measurements via combined nuclear magnetic resonance and confocal microscopy.bacterial biofilms are complex, three-dimensional communities found nearly everywhere in nature and are also associated with many human diseases. detailed metabolic information is critical to understand and exploit beneficial biofilms as well as combat antibiotic-resistant, disease-associated forms. however, most current techniques used to measure temporal and spatial metabolite profiles in these delicate structures are invasive or destructive. here, we describe imaging, transport and metabolite ...200818253132
efficient site-specific labeling of proteins via cysteines.methods for chemical modifications of proteins have been crucial for the advancement of proteomics. in particular, site-specific covalent labeling of proteins with fluorophores and other moieties has permitted the development of a multitude of assays for proteome analysis. a common approach for such a modification is solvent-accessible cysteine labeling using thiol-reactive dyes. cysteine is very attractive for site-specific conjugation due to its relative rarity throughout the proteome and the ...200818275130
the use of electrochemical impedance spectroscopy (eis) in the evaluation of the electrochemical properties of a microbial fuel cell.electrochemical impedance spectroscopy (eis) has been used to determine several electrochemical properties of the anode and cathode of a mediator-less microbial fuel cell (mfc) under different operational conditions. these operational conditions included a system with and without the bacterial catalyst and eis measurements at the open-circuit potential of the anode and the cathode or at an applied cell voltage. in all cases the impedance spectra followed a simple one-time-constant model (otcm) i ...200818294928
biodegradation of pyridine by the new bacterial isolates s. putrefaciens and b. sphaericus.in this study, two bacterial strains capable of utilizing pyridine as a sole carbon source were isolated from biofilters. based on the biochemical test, the organisms were identified as shewanella putrefaciens and bacillus sphaericus. in liquid cultures, s. putrefaciens and b. sphaericus degraded pyridine quite effectively up to 500 mg l(-1). s. putrefaciens degrades 500 mg l(-1) of pyridine completely within 140 h, whereas the b. sphaericus degrades 500 mg l(-1) of pyridine only nearly 75% and ...200818295401
construction and use of new cloning vectors for the rapid isolation of recombinant proteins from escherichia coli.we describe the construction and use of two sets of vectors for the over-expression and purification of protein from escherichia coli. the set of ptev plasmids (ptev3, 4, 5) directs the synthesis of a recombinant protein with a n-terminal hexahistidine (his(6)) tag that is removable by the tobacco etch virus (tev) protease. the set of pkld plasmids (pkld66, 116) directs the synthesis of a recombinant protein that contains a n-terminal his(6) and maltose-binding protein tag in tandem, which can a ...200818295882
in vivo identification of the outer membrane protein omca-mtrc interaction network in shewanella oneidensis mr-1 cells using novel hydrophobic chemical cross-linkers.outer membrane (om) cytochromes omca (so1779) and mtrc (so1778) are the integral components of electron transfer used by shewanella oneidensis for anaerobic respiration of metal (hydr)oxides. here the omca-mtrc interaction was identified in vivo using a novel hydrophobic chemical cross-linker (mrn) combined with immunoprecipitation techniques. in addition, identification of other om proteins from the cross-linked complexes allows first visualization of the omca-mtrc interaction network. further ...200818303833
microarray-based whole-genome hybridization as a tool for determining procaryotic species relatedness.the definition and delineation of microbial species are of great importance and challenge due to the extent of evolution and diversity. whole-genome dna-dna hybridization is the cornerstone for defining procaryotic species relatedness, but obtaining pairwise dna-dna reassociation values for a comprehensive phylogenetic analysis of procaryotes is tedious and time consuming. a previously described microarray format containing whole-genomic dna (the community genome array or cga) was rigorously eva ...200818309358
shewanella secretes flavins that mediate extracellular electron transfer.bacteria able to transfer electrons to metals are key agents in biogeochemical metal cycling, subsurface bioremediation, and corrosion processes. more recently, these bacteria have gained attention as the transfer of electrons from the cell surface to conductive materials can be used in multiple applications. in this work, we adapted electrochemical techniques to probe intact biofilms of shewanella oneidensis mr-1 and shewanella sp. mr-4 grown by using a poised electrode as an electron acceptor. ...200818316736
is vanadium a more versatile target in the activity of primordial life forms than hitherto anticipated?the two predominant forms of vanadium occurring in the geo-, aqua- and biosphere, soluble vanadate(v) and insoluble oxovanadium(iv) (vanadyl), are subject to bacterial activity and transformation. bacteria belonging to genera such as shewanella, pseudomonas and geobacter can use vanadate as a primary electron acceptor in dissimilation or respiration, an important issue in the context of biomineralisation and soil detoxification. azotobacter, which can employ vanadium as an essential element in n ...200818327316
empirical evaluation of a new method for calculating signal-to-noise ratio for microarray data analysis.signal-to-noise-ratio (snr) thresholds for microarray data analysis were experimentally determined with an oligonucleotide array that contained perfect-match (pm) and mismatch (mm) probes based upon four genes from shewanella oneidensis mr-1. a new snr calculation, called the signal-to-both-standard-deviations ratio (ssdr), was developed and evaluated, along with other two methods, the signal-to-standard-deviation ratio (ssr) and the signal-to-background ratio (sbr). at a low stringency, the thr ...200818344333
identification of bacteria from the normal flora of perch, perca fluviatilis l., and evaluation of their inhibitory potential towards aeromonas species.pathogenic aeromonas sobria has been identified as a causative agent of ulcerative disease in farmed european perch, perca fluviatilis l. to study the effect of the normal intestinal bacterial flora of perch against a. sobria, we sampled 193 bacterial isolates from the perch digestive tract. the isolates were identified by sequence analysis of the 16s rrna gene and their inhibitory potential against a. sobria was evaluated in vitro. nineteen of the strains isolated showed inhibition and were als ...200818355180
effect of packaging atmosphere on the microbial attributes of pearlspot (etroplus suratensis bloch) stored at 0-2 degrees c.effect of packaging atmosphere (air and under different modified atmospheres (mas), 40% co2/60% o2, 50%/50% o2, 60% co2/40% o2, 70% co2/30% o2 and 40% co2/30% o2/30% n2) on the microbial and biochemical attributes of fresh pearlspot (etroplus suratensis bloch) stored at 0-2 degrees c was investigated. trimethylamine nitrogen (tma-n) and thiobarbituric acid (tba) values remained lower than the proposed acceptability limits throughout the storage period. results demonstrated that storage of pearls ...200818355677
characterization of the shewanella oneidensis fur gene: roles in iron and acid tolerance response.iron homeostasis is a key metabolism for most organisms. in many bacterial species, coordinate regulation of iron homeostasis depends on the protein product of a fur gene. fur also plays roles in virulence, acid tolerance, redox-stress responses, flagella chemotaxis and metabolic pathways.200818366600
phylogenetic and enzymatic diversity of deep subseafloor aerobic microorganisms in organics- and methane-rich sediments off shimokita peninsula."a meta-enzyme approach" is proposed as an ecological enzymatic method to explore the potential functions of microbial communities in extreme environments such as the deep marine subsurface. we evaluated a variety of extra-cellular enzyme activities of sediment slurries and isolates from a deep subseafloor sediment core. using the new deep-sea drilling vessel "chikyu", we obtained 365 m of core sediments that contained approximately 2% organic matter and considerable amounts of methane from offs ...200818368287
bacteria flora and heavy metals in cultivated oysters crassostrea iredalei of setiu wetland, east coast peninsular malaysia.slipper oyster crassostrea iredalei is a species of good demand for its sweet flavor and white coloured flesh. the filter feeding nature predisposes oysters to accumulation of pathogenic and heavy metals in waters impacted by sewage pollutions and may thus render the oysters unfit for human consumption. a study was undertaken to investigate the presence of bacteria flora and heavy metal concentrations in cultivated oysters crassostrea iredalei at setiu wetland, terengganu, the only source of cul ...200818369732
regulation of hexahydro-1,3,5-trinitro-1,3,5-triazine (rdx) metabolism in shewanella halifaxensis haw-eb4 by terminal electron acceptor and involvement of c-type cytochrome.shewanella halifaxensis haw-eb4 was previously isolated for its potential to mineralize hexahydro-1,3,5-trinitro-1,3,5-triazine (rdx) from a uxo (unexploded ordnance)-contaminated marine sediment site near halifax harbor. the present study was undertaken to determine the effect of terminal electron acceptors (tea) on the growth of strain haw-eb4 and on the enzymic processes involved in rdx metabolism. the results showed that aerobic conditions were optimal for bacterial growth, but that anaerobi ...200818375796
shewanella and photobacterium spp. in oysters and seawater from the delaware bay.shewanella algae, s. putrefaciens, and photobacterium damselae subsp. damselae are indigenous marine bacteria and human pathogens causing cellulitis, necrotizing fasciitis, abscesses, septicemia, and death. infections are rare and are most often associated with the immunocompromised host. a study was performed on the microbiological flora of oysters and seawater from commercial oyster harvesting sites in the delaware bay, new jersey. from 276 water and shellfish samples tested, 1,421 bacterial i ...200818378645
identification of mobile elements and pseudogenes in the shewanella oneidensis mr-1 genome.shewanella oneidensis mr-1 is the first of 22 different shewanella spp. whose genomes have been or are being sequenced and thus serves as the model organism for studying the functional repertoire of the shewanella genus. the original mr-1 genome annotation revealed a large number of transposase genes and pseudogenes, indicating that many of the genome's functions may be decaying. comparative analyses of the sequenced shewanella strains suggest that 209 genes in mr-1 have in-frame stop codons, fr ...200818378659
pyomelanin is produced by shewanella algae bry and affected by exogenous iron.melanin production by shewanella algae bry occurred during late- and (or) post-exponential growth in lactate basal salts liquid medium supplemented with tyrosine or phenylalanine. the antioxidant ascorbate inhibited melanin production but not production of the melanin precursor homogentisic acid. in the absence of ascorbate, melanin production was inhibited by the 4-hydroxyphenylpyruvate dioxygenase inhibitor sulcotrione and by concentrations of fe >or= 0.38 mmol l(-1). these data support the hy ...200818389008
extracellular electron transfer: wires, capacitors, iron lungs, and more. 200818393985
dissimilatory iron reduction in escherichia coli: identification of cyma of shewanella oneidensis and napc of e. coli as ferric reductases.over geological time scales, microbial reduction of chelated fe(iii) or fe(iii) minerals has profoundly affected today's composition of our bio- and geosphere. however, the electron transfer reactions that are specific and defining for dissimilatory iron(iii)-reducing (dir) bacteria are not well understood. using a synthetic biology approach involving the reconstruction of the putative electron transport chain of the dir bacterium shewanella oneidensis mr-1 in escherichia coli, we showed that ex ...200818394146
environmental adaptation: genomic analysis of the piezotolerant and psychrotolerant deep-sea iron reducing bacterium shewanella piezotolerans wp3.shewanella species are widespread in various environments. here, the genome sequence of shewanella piezotolerans wp3, a piezotolerant and psychrotolerant iron reducing bacterium from deep-sea sediment was determined with related functional analysis to study its environmental adaptation mechanisms. the genome of wp3 consists of 5,396,476 base pairs (bp) with 4,944 open reading frames (orfs). it possesses numerous genes or gene clusters which help it to cope with extreme living conditions such as ...200818398463
evaluation of antifouling activity of eight commercially available organic chemicals against the early foulers marine bacteria and ulva spores.environmental impacts caused by tin and copper based commercial antifouling (af) paints were proved to be detrimental to aquatic ecosystems. therefore, a search of environmental friendly af compounds to be used in marine paint to protect the surface of maritime developmental structures from the unwanted biofouling is a burning issue of the present time. commercially available eight organic chemicals--allyl isothiocyanate, beta-myrecene, cis-3-hexenyl acetate, citral, ethyl heptanoate, eugenol, m ...200718405125
oxygen-dependent autoaggregation in shewanella oneidensis mr-1.in aerobic chemostat cultures maintained at 50% dissolved o(2) tension (3.5 mg l(-1) dissolved o(2)), shewanella oneidensis strain mr-1 rapidly aggregated upon addition of 0.68 mm cacl(2) and retained this multicellular phenotype at high dilution rates. confocal microscopy analysis of the extracellular matrix material contributing to the stability of the aggregate structures revealed the presence of extracellular dna, protein and glycoconjugates. upon onset of o(2)-limited growth (dissolved o(2) ...200818412550
microbial fuel cell technology for measurement of microbial respiration of lactate as an example of bioremediation amendment.microbial fuel cell (mfc) based sensing was explored to provide for the development of an in situ bioremediation monitoring approach for substrate concentrations and microbial respiration rates. mfc systems were examined in column systems where shewanella oneidensis mr1 used an external electron acceptor (an electrode) to metabolize lactate (a bioremediation additive) to acetate. column systems were operated with varying influent lactate concentrations (0-41 mm) and monitored for current generat ...200818414805
comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes.recent proliferation of low-cost dna sequencing techniques will soon lead to an explosive growth in the number of sequenced genomes and will turn manual annotations into a luxury. mass spectrometry recently emerged as a valuable technique for proteogenomic annotations that improves on the state-of-the-art in predicting genes and other features. however, previous proteogenomic approaches were limited to a single genome and did not take advantage of analyzing mass spectrometry data from multiple g ...200818426904
predicting sigma28 promoters in eleven shewanella genomes.an iterative position-specific score matrix (pssm)-based approach was used to predict sigma(28) promoters in 11 shewanella genomes. the shewanella correlation browser was used to distinguish true-positive predictions from false-positive predictions in shewanella oneidensis mr-1 by generating a sigma(28)-regulated transcriptional network from transcriptional profiling data. this dual-pronged approach identified several genes that have sigma(28) promoters and that may be involved with motility or ...200818430000
the molecular density of states in bacterial nanowires.the recent discovery of electrically conductive bacterial appendages has significant physiological, ecological, and biotechnological implications, but the mechanism of electron transport in these nanostructures remains unclear. we here report quantitative measurements of transport across bacterial nanowires produced by the dissimilatory metal-reducing bacterium, shewanella oneidensis mr-1, whose electron transport system is being investigated for renewable energy recovery in microbial fuel cells ...200818441026
the role of tandem acyl carrier protein domains in polyunsaturated fatty acid biosynthesis.acyl carrier protein (acp) plays an essential role in fatty acid and polyketide biosynthesis, and most of the fatty acid synthases (fass) and polyketide synthases (pkss) known to date are characterized with a single acp for each cycle of chain elongation. polyunsaturated fatty acid (pufa) biosynthesis is catalyzed by the pufa synthase, and all pufa synthases known to date contain tandem acps (ranging from 5 to 9). using the pfa pufa synthase from shewanella japonica as a model system, we report ...200818444614
investigations of structure and metabolism within shewanella oneidensis mr-1 biofilms.biofilms possess spatially and temporally varying metabolite concentration profiles at the macroscopic and microscopic scales. this results in varying growth environments that may ultimately drive species diversity, determine biofilm structure and the spatial distribution of the community members. using non-invasive nuclear magnetic resonance (nmr) microscopic imaging/spectroscopy and confocal imaging, we investigated the kinetics and stratification of anaerobic metabolism within live biofilms o ...200818448180
biosorption of metals (cu(2+), zn(2+)) and anions (f(-), h(2)po(4)(-)) by viable and autoclaved cells of the gram-negative bacterium shewanella putrefaciens.microbial biomass represents a potentially cost-effective sorbent for water treatment applications. high sorption capacities for both cations and anions are demonstrated here for viable and autoclaved cell suspensions of the gram-negative bacterium shewanella putrefaciens. ftir absorption spectra and ph-dependent zeta-potentials are similar for the viable and killed bacterial cells. potentiometric titrations, however, reveal a two to three times higher oh(-) buffering capacity for the living cel ...200818450432
physiology of microbes in biofilms.microbial biofilms are governed by an intricate interplay between physical-chemical factors and the physiological and genetic properties of the inhabiting microbes. many of the physiological traits that are exhibited in a biofilm environment have been observed and studied previously in detail in planktonic cultures. however, their differential and combinatorial phenotypic expression in distinct subpopulations localized to different regions in a biofilm is the cause for the overall biofilm hetero ...200818453270
a support vector machine model for the prediction of proteotypic peptides for accurate mass and time proteomics.the standard approach to identifying peptides based on accurate mass and elution time (amt) compares profiles obtained from a high resolution mass spectrometer to a database of peptides previously identified from tandem mass spectrometry (ms/ms) studies. it would be advantageous, with respect to both accuracy and cost, to only search for those peptides that are detectable by ms (proteotypic).200818453551
in search of the microbe/mineral interface: quantitative analysis of bacteria on metal surfaces using vertical scanning interferometry.to understand the development of biofilms on metal surfaces, analysis of initial bacterial attachment to surfaces is crucial. here we present the results of a study, using shewanella oneidensis mr-1 as a model organism, in which vertical scanning interferometry (vsi) was used to investigate the initial stages of cell attachment to glass, steel and aluminium surfaces. it was found that while vsi gave unambiguous results with opaque surfaces, when reflective surfaces were used, an artifact sometim ...200818459964
decolorization of azo dyes by shewanella sp. under saline conditions.wastewaters from textile processing and dye-stuff manufacture industries contain substantial amounts of salts in addition to azo dye residues. to examine salinity effects on dye-degrading bacteria, a study was carried out with four azo dyes in the presence of varying concentrations of nacl (0-100 g l(-1)) with a previously isolated bacterium, shewanella putrefaciens strain as96. under static, low oxygen conditions, the bacterium decolorized 100 mg dye l(-1) at salt concentrations up to 60 g nacl ...200818461315
antimicrobial and antioxidative activities of bioactive constituents from hydnophytum formicarum jack.hydnophytum formicarum jack. (rubiaceae) is a medicinal plant whose tubers possesses cardiovascular, anti-inflammatory and antiparasitic effects and have been used for the treatment of hepatitis, rheumatism and diarrhea. herein we report the isolation of its active constituents and the testing of their antimicrobial activity against 27 strains of microorganisms using an agar dilution method and of their antioxidative activity using the dpph and sod assays. the results show that the crude hexane, ...200818463592
molecular structure of endotoxins from gram-negative marine bacteria: an update.marine bacteria are microrganisms that have adapted, through millions of years, to survival in environments often characterized by one or more extreme physical or chemical parameters, namely pressure, temperature and salinity. the main interest in the research on marine bacteria is due to their ability to produce several biologically active molecules, such as antibiotics, toxins and antitoxins, antitumor and antimicrobial agents. nonetheless, lipopolysaccharides (lpss), or their portions, from g ...200718463721
measuring global credibility with application to local sequence alignment.computational biology is replete with high-dimensional (high-d) discrete prediction and inference problems, including sequence alignment, rna structure prediction, phylogenetic inference, motif finding, prediction of pathways, and model selection problems in statistical genetics. even though prediction and inference in these settings are uncertain, little attention has been focused on the development of global measures of uncertainty. regardless of the procedure employed to produce a prediction, ...200818464927
comparison of uranium(vi) removal by shewanella oneidensis mr-1 in flow and batch reactors.to better understand the interactions among metal contaminants, nutrients, and microorganisms in subsurface fracture-flow systems, biofilms of pure culture of shewanella oneidensis mr-1 were grown in six fracture-flow reactors (ffrs) of different geometries. the spatial and temporal distribution of uranium and bacteria were examined using a tracer dye (brilliant blue fcf) and microscopy. the results showed that plugging by bacterial cells was dependent on the geometry of the reactor and that bio ...200818468655
the c-type cytochrome omca localizes to the outer membrane upon heterologous expression in escherichia coli.we have functionally produced the outer membrane cytochrome omca from shewanella oneidensis in escherichia coli. substrate accessibility experiments indicate that omca is surface exposed in an e. coli b strain but not in a k-12 strain. we show that a functional type ii secretion system is required for surface localization.200818487320
redox-reactive membrane vesicles produced by shewanella.this manuscript is dedicated to our friend, mentor, and coauthor dr terry beveridge, who devoted his scientific career to advancing fundamental aspects of microbial ultrastructure using innovative electron microscopic approaches. during his graduate studies with professor robert murray, terry provided some of the first glimpses and structural evaluations of the regular surface arrays (s-layers) of gram-negative bacteria (beveridge & murray, 1974, 1975, 1976a). beginning with his early electron m ...200818498526
direct involvement of type ii secretion system in extracellular translocation of shewanella oneidensis outer membrane cytochromes mtrc and omca.mtrc and omca are cell surface-exposed lipoproteins important for reducing solid metal oxides. deletions of type ii secretion system (t2ss) genes reduced their extracellular release and their accessibility to the proteinase k treatment, demonstrating the direct involvement of t2ss in translocation of mtrc and omca to the bacterial cell surface.200818502849
on the origin and function of an insertion element vpai-1 specific to post-1995 pandemic vibrio parahaemolyticus strains.since 1995, new virulent strains of vibrio parahaemolyticus have emerged and spread throughout the world. these "pandemic" strains have four strain specific genomic islands (gis), which are considered to be potential factors of the pandemicity. we investigated the origin and function of 24 genes in the so-called vpai-1, one of the four gis, by searching homologs in various species in bacteria and archaea. of these 24 genes, two are found only in vibrio vulnificus cmcp6 and shewanella sp. mr-7. t ...200818506094
coupled electrostatic, hydrodynamic, and mechanical properties of bacterial interfaces in aqueous media.the interactions of bacteria with their environment are governed by a complex interplay between biological and physicochemical phenomena. the main challenge is the joint determination of the intertwined interfacial characteristics of bacteria such as mechanical and hydrodynamic softness, interfacial heterogeneity, and electrostatic properties. in this study, we have combined electrokinetics and force spectroscopy to unravel this intricate coupling for two types of shewanella bacterial strains th ...200818512877
automated gain control ion funnel trap for orthogonal time-of-flight mass spectrometry.time-of-flight mass spectrometry (tof ms) is increasingly used in proteomics research. herein, we report on the development and characterization of a tof ms instrument with improved sensitivity equipped with an electrodynamic ion funnel trap (ift) that employs an automated gain control (agc) capability. the ift-tof ms was coupled to a reversed-phase capillary liquid chromatography (rplc) separation and evaluated in experiments with complex proteolytic digests. when applied to a global tryptic di ...200818512944
insights and inferences about integron evolution from genomic data.integrons are mechanisms that facilitate horizontal gene transfer, allowing bacteria to integrate and express foreign dna. these are important in the exchange of antibiotic resistance determinants, but can also transfer a diverse suite of genes unrelated to pathogenicity. here, we provide a systematic analysis of the distribution and diversity of integron inti genes and integron-containing bacteria.200818513439
a plasmid-borne shewanella algae gene, qnra3, and its possible transfer in vivo between kluyvera ascorbata and klebsiella pneumoniae.the plasmid-borne quinolone resistance gene qnra1 is prevalent in multidrug-resistant enterobacteriaceae. a chromosomally encoded homologue in shewanella algae, qnra3, has been described. we isolated two qnra3-positive strains, one of klebsiella pneumoniae (he96) and one of kluyvera ascorbata (kas96), from the feces of an immunocompromised outpatient. the qnra3 allele was identical to that of s. algae except for 5 nucleotides and differed from qnra1 by 29 nucleotides affecting three amino acids. ...200818515416
[electricity from microorganisms].over the last ten years, the recently discovered process of direct electron transfer from anaerobically grown microorganisms to an electrode of a fuel cell has been the object of intense study. the microorganisms responsible for such electron transport were termed electrogenic; the devices using them to generate electric current, microbial fuel cells (mfcs). the review discussed the molecular mechanisms of electron transfer to the environment in the case of the two best studied microorganisms, s ...200818522314
expression of chromate resistance genes from shewanella sp. strain ana-3 in escherichia coli.the plasmidic chromate resistance genes chrbac from shewanella sp. strain ana-3 were transferred to escherichia coli. expression of chra alone, on a high- or low-copy number plasmid, conferred increased chromate resistance. in contrast, expression of the complete operon chrbac on a high-copy number plasmid did not result in a significant increase in resistance, although expression on a low-copy number plasmid made the cells up to 10-fold more resistant to chromate. the chra gene also conferred i ...200818537831
expression, purification, crystallization and structure determination of two glutathione s-transferase-like proteins from shewanella oneidensis.genome analysis of shewanella oneidensis, a gram-negative bacterium with an unusual repertoire of respiratory and redox capabilities, revealed the presence of six glutathione s-transferase-like genes (sogst1-sogst6). glutathione s-transferases (gsts; ec 2.5.1.18) are found in all kingdoms of life and are involved in phase ii detoxification processes by catalyzing the nucleophilic attack of reduced glutathione on diverse electrophilic substrates, thereby decreasing their reactivity. structure-fun ...200818540073
desorption and dissolution of heavy metals from contaminated soil using shewanella sp. (hn-41) amended with various carbon sources and synthetic soil organic matters.heavy metals in soil are considered a major environmental problem facing many countries around the world. contamination of heavy metals occurs in soil due to both anthropogenic and natural causes. during the last two decades, extensive attention has been paid to the management and control of soil contamination. decontamination of heavy metals in the soil has been a challenge for a long time. microbial solubilization is one of promising process for remediation of heavy metals from contaminated si ...200918541365
identification of diverse carbon utilization pathways in shewanella oneidensis mr-1 via expression profiling.to identify pathways of carbon utilization in the metal-reducing marine bacterium shewanella oneidensis mr-1, we assayed the expression of cells grown with various carbon sources using a high-density oligonucleotide affymetrix microarray. our expression profiles reveal genes and regulatory mechanisms which govern the sensing, import, and utilization of the nucleoside inosine, the chitin monomer n-acetylglucosamine, and a casein-derived mixture of amino acids. our analysis suggests a prominent ro ...200718546496
in vitro evolution of a peptide with a hematite binding motif that may constitute a natural metal-oxide binding archetype.phage-display technology was used to evolve peptides that selectively bind to the metal-oxide hematite (fe2o3) from a library of approximately 3 billion different polypeptides. the sequences of these peptides contained the highly conserved amino acid motif, ser/thr-hydrophobic/aromatic-ser/thr-pro-ser/thr. to better understand the nature of the peptide-metal oxide binding demonstrated by these experiments, molecular dynamics simulations were carried out for ser-pro-ser at a hematite surface. the ...200818546729
saccharides cross-reactive with bacillus anthracis spore glycoprotein as an anthrax vaccine component.bacillus anthracis is a spore-forming bacterium that causes anthrax in humans and in other mammals. the glycoprotein bcla (bacillus collagen-like protein of anthracis) is a major constituent of the exosporium, the outermost surface of b. anthracis spores. the glycosyl part of bcla is an oligosaccharide composed of 2-o-methyl-4-(3-hydroxy-3-methylbutanamido)-4,6-dideoxy-d-glucose, referred to as anthrose, and three rhamnose residues. a structure similar to anthrose, 4-(3-hydroxy-3-methylbutanamid ...200818562275
shewanella soft tissue infection: case report and literature review.to better understand the clinical characteristics of soft tissue infections caused by shewanella in humans.200818565779
structure of so2946 orphan from shewanella oneidensis shows "jelly-roll" fold with carbohydrate-binding module.the crystal structure of the uncharacterized protein so2946 from shewanella oneidensis mr-1 was determined with single-wavelength anomalous diffraction (sad) and refined to 2.0 a resolution. the so2946 protein consists of a short helical n-terminal domain and a large c-terminal domain with the "jelly-roll" topology. the protein assembles into a propeller consisting of three c-terminal blades arranged around a central core formed by the n-terminal domains. the function of so2946 could not be infe ...200818566914
toxin-screening and identification of bacteria isolated from highly toxic marine gastropod nassarius semiplicatus.bacteria isolated from a highly toxic sample of gastropod nassarius semiplicatus in lianyungang, jiangsu province in july 2007, were studied to probe into the relationship between bacteria and toxicity of nassariid gastropod. the toxicity of the gastropod sample was 2 x 10(2)mouse unit (mu) per gram of tissue (wet weight). high concentration of tetrodotoxin (ttx) and its analogues (ttxs) were found in the digestive gland and muscle of the gastropod, using high performance liquid chromatography c ...200818573274
electrochemical interrogations of the mtr cytochromes from shewanella: opening a potential window.the multi-heme cytochromes from shewanella oneidensis associated with the dissimilatory metal reduction (dmr) pathway have been investigated using the technique of protein film voltammetry (pfv). using pfv, we have interrogated each of the multi-heme cytochromes (mtra, stc, and solubilized versions of the membrane-bound proteins cyma, omca, and mtrc) under identical conditions for the first time. each cytochrome reveals a broad envelope of voltammetric response, indicative of multiple redox cofa ...200818575901
the effect of an acidic, copper sulfate-based commercial sanitizer on indicator, pathogenic, and spoilage bacteria associated with broiler chicken carcasses when applied at various intervention points during poultry processing.studies were conducted to evaluate 1) the effect of an acidic, copper sulfate-based commercial sanitizer on pathogenic, indicator, and spoilage bacteria in a model scalder system, 2) the effect of this sanitizer on total aerobic bacteria (apc) and escherichia coli counts, and salmonella prevalence on broiler chicken carcasses when applied during scalding or scalding and postpick dipping, and 3) the ability of sanitizer to extend the shelf-life of broiler chicken carcasses. exposure of salmonella ...200818577627
purulent pericarditis with greenish pericardial effusion caused by shewanella algae.we report the first case of purulent pericarditis with greenish pericardial effusion caused by shewanella algae in a patient with gastric and gallbladder cancer. this case expands the reported spectrum of infection caused by s. algae and raises the possibility that s. algae is a causative pathogen for purulent pericarditis.200818579719
biodegradation of crystal violet by a shewanella sp. ntou1.a bacterial isolate, strain ntou1, originally isolated from the cooling system in an oil refinery could decolorize and detoxify crystal violet under anaerobic conditions. the strain was characterized and identified as a member of shewanella decolorationis based on gram staining, morphology characters, biochemical tests, the 16s rrna gene and the gyrase subunit beta gene (gyrb). the optimum ph value and temperature for decolorization of crystal violet by this strain under anaerobic conditions wer ...200818582917
a general system for studying protein-protein interactions in gram-negative bacteria.one of the most promising methods for large-scale studies of protein interactions is isolation of an affinity-tagged protein with its in vivo interaction partners, followed by mass spectrometric identification of the copurified proteins. previous studies have generated affinity-tagged proteins using genetic tools or cloning systems that are specific to a particular organism. to enable protein-protein interaction studies across a wider range of gram-negative bacteria, we have developed a methodol ...200818590317
simple menaquinones reduce carbon tetrachloride and iron (iii).cell-free supernatant from shewanella oneidensis mr-1 reduced carbon tetrachloride to chloroform, a suspension of fe(iii) and solid fe(iii) to iron (ii). the putative reducing agent was tentatively identified as menaquinone-1 (mq-1)-a water-soluble menaquinone with a single isoprenoid residue in the side chain. synthetic mq-1 reduced carbon tetrachloride to chloroform and amorphous iron (iii) hydroxide to iron (ii). to test the generality of this result among menaquinones, the reductive activiti ...200918594993
spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases.a key problem in computational proteomics is distinguishing between correct and false peptide identifications. we argue that evaluating the error rates of peptide identifications is not unlike computing generating functions in combinatorics. we show that the generating functions and their derivatives ( spectral energy and spectral probability) represent new features of tandem mass spectra that, similarly to delta-scores, significantly improve peptide identifications. furthermore, the spectral pr ...200818597511
identification and characterization of n-acylhomoserine lactone-acylase from the fish intestinal shewanella sp. strain mib015.n-acylhomoserine lactones (ahls) are used as quorum-sensing signal molecules by many gram-negative bacteria. we have reported that shewanella sp. strain mib015 degrades ahls. in the present study, we cloned the aac gene from mib015 by pcr with specific primers based on the aac gene in shewanella oneidensis strain mr-1, which showed high homology with the known ahl-acylases. escherichia coli expressing aac showed high degrading activity of ahls with long acyl chains. hplc analysis revealed that a ...200818603799
towards environmental systems biology of shewanella.bacteria of the genus shewanella are known for their versatile electron-accepting capacities, which allow them to couple the decomposition of organic matter to the reduction of the various terminal electron acceptors that they encounter in their stratified environments. owing to their diverse metabolic capabilities, shewanellae are important for carbon cycling and have considerable potential for the remediation of contaminated environments and use in microbial fuel cells. systems-level analysis ...200818604222
application of pressurized solvents for ultrafast trypsin hydrolysis in proteomics: proteomics on the fly.a new method for rapid proteolytic digestion of proteins under high pressure that uses pressure cycling technology in the range of 5-35 kpsi was demonstrated for proteomic analysis. successful in-solution digestions of single proteins and complex protein mixtures were achieved in 60 s and then analyzed by reversed phase liquid chromatography-electrospray ionization ion trap-mass spectrometry. method performance in terms of the number of shewanella oneidensis peptides and proteins identified in a ...200818605748
genetic analysis of trimethylamine n-oxide reductases in the light organ symbiont vibrio fischeri es114.trimethylamine n-oxide (tmao) reductases are widespread in bacteria and often function in anaerobic respiration. the regulation and expression of tmao reductase operons have been well studied in model genera such as escherichia, shewanella, and rhodobacter, although tmao reductases are present in many other bacteria, including the marine vibrio species. the genome sequence of vibrio fischeri revealed three putative tmao reductase operons, and a previous report identified tmao reductase activity ...200818606737
use of atomic force microscopy and transmission electron microscopy for correlative studies of bacterial capsules.bacteria can possess an outermost assembly of polysaccharide molecules, a capsule, which is attached to their cell wall. we have used two complementary, high-resolution microscopy techniques, atomic force microscopy (afm) and transmission electron microscopy (tem), to study bacterial capsules of four different gram-negative bacterial strains: escherichia coli k30, pseudomonas aeruginosa frd1, shewanella oneidensis mr-4, and geobacter sulfurreducens pca. tem analysis of bacterial cells using diff ...200818606791
remarkable stabilization of a psychrotrophic rnase hi by a combination of thermostabilizing mutations identified by the suppressor mutation method.ribonuclease hi from the psychrotrophic bacterium shewanella oneidensis mr-1 (so-rnase hi) is much less stable than escherichia coli rnase hi (ec-rnase hi) by 22.4 degrees c in t m and 12.5 kj mol (-1) in delta g(h 2o), despite their high degrees of structural and functional similarity. to examine whether the stability of so-rnase hi increases to a level similar to that of ec-rnase hi via introduction of several mutations, the mutations that stabilize so-rnase hi were identified by the suppresso ...200818616283
the structure of the carbohydrate backbone of the lps from shewanella spp. mr-4.the rough type lipopolysaccharide isolated from shewanella spp. strain mr-4 was analyzed using nmr, mass spectroscopy, and chemical methods. two structural variants have been found, both contained 8-amino-3,8-dideoxy-d-manno-octulosonic acid and lacked l-glycero-d-manno-heptose. a minor variant of the lps contained phosphoramide substituent.200818619581
a bacterial ice-binding protein from the vostok ice core.bacterial and yeast isolates recovered from a deep antarctic ice core were screened for proteins with ice-binding activity, an indicator of adaptation to icy environments. a bacterial strain recovered from glacial ice at a depth of 3,519 m, just above the accreted ice from subglacial lake vostok, was found to produce a 54 kda ice-binding protein (genbank eu694412) that is similar to ice-binding proteins previously found in sea ice diatoms, a snow mold, and a sea ice bacterium. the protein has th ...200818622572
identification of a gene cluster that directs putrebactin biosynthesis in shewanella species: pubc catalyzes cyclodimerization of n-hydroxy-n-succinylputrescine.putrebactin is a dihydroxamate iron chelator produced by the metabolically versatile marine bacterium shewanella putrefaciens. it is a macrocyclic dimer of n-hydroxy-n-succinyl-putrescine (hsp) and is structurally related to desferrioxamine e, which is a macrocyclic trimer of n-hydroxy-n-succinyl-cadaverine (hsc). we recently showed that desd, a member of the nis synthetase superfamily, catalyzes the key step in desferrioxamine e biosynthesis: atp-dependent trimerisation and macrocylization of h ...200818630910
outbreak of shewanella algae and shewanella putrefaciens infections caused by a shared measuring cup in a general surgery unit in korea.to control an outbreak of shewanella algae and s. putrefaciens infections by identifying the risk factors for infection and transmission.200818631115
enzyme phylogenies as markers for the oxidation state of the environment: the case of respiratory arsenate reductase and related enzymes.phylogenies of certain bioenergetic enzymes have proved to be useful tools for deducing evolutionary ancestry of bioenergetic pathways and their relationship to geochemical parameters of the environment. our previous phylogenetic analysis of arsenite oxidase, the molybdopterin enzyme responsible for the biological oxidation of arsenite to arsenate, indicated its probable emergence prior to the archaea/bacteria split more than 3 billion years ago, in line with the geochemical fact that arsenite w ...200818631373
application of molecular techniques to evaluate the methanogenic archaea and anaerobic bacteria in the presence of oxygen with different cod:sulfate ratios in a uasb reactor.in this paper, the microbial characteristics of the granular sludge in the presence of oxygen (3.0+/-0.7 mg o2 l(-1)) were analyzed using molecular biology techniques. the granules were provided by an upflow anaerobic sludge blanket (uasb) operated over 469 days and fed with synthetic substrate. ethanol and sulfate were added to obtain different cod/so4(2-) ratios (3.0, 2.0, and 1.6). the results of fluorescent in situ hybridization (fish) analyses showed that archaeal cells, detected by the arc ...200818634895
kinetics of u(vi) reduction by a dissimilatory fe(iii)-reducing bacterium under non-growth conditions.dissimilatory metal-reducing microorganisms may be useful in processes designed for selective removal of uranium from aqueous streams. these bacteria can use u(vi) as an electron acceptor and thereby reduce soluble u(vi) to insoluble u(iv). while significant research has been devoted to demonstrating and describing the mechanism of dissimilatory metal reduction, the reaction kinetics necessary to apply this for remediation processes have not been adequately defined. in this study, pure culture s ...199718636514
the role of group bulkiness in the catalytic activity of psychrophile cold-active protein tyrosine phosphatase.the cold-active protein tyrosine phosphatase found in psychrophilic shewanella species exhibits high catalytic efficiency at low temperatures as well as low thermostability, both of which are characteristics shared by many cold-active enzymes. the structure of cold-active protein tyrosine phosphatase is notable for the presence of three hydrophobic sites (termed the ca, zn-1 and zn-2 sites) behind the loop structures comprising the catalytic region. to identify the structural components responsi ...200818647345
identification of an uptake hydrogenase for hydrogen-dependent dissimilatory azoreduction by shewanella decolorationis s12.shewanella decolorationis s12, a representative dissimilatory azo-reducing bacterium of shewanella genus, can grow by coupling the oxidation of hydrogen to the reduction of azo compounds as the sole electron acceptor, indicating that an uptake hydrogenase is an important component for electron transfer for azoreduction. for searching to the uptake hydrogenase in the genome of s. decolorationis, two operons, hyd and hya, were cloned and sequenced, which encode periplasmically oriented fe-only hyd ...200818651140
a high-throughput percentage-of-binding strategy to measure binding energies in dna-protein interactions: application to genome-scale site discovery.quantifying the binding energy in dna-protein interactions is of critical importance to understand transcriptional regulation. based on a simple computational model, this study describes a high-throughput percentage-of-binding strategy to measure the binding energy in dna-protein interactions between the shewanella oneidensis arca two-component transcription factor protein and a systematic set of mutants in an arca-p (phosphorylated arca) binding site. the binding energies corresponding to each ...200818653527
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