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raman chemical imaging of chromate reduction sites in a single bacterium using intracellularly grown gold nanoislands.imaging live molecular events within micro-organisms at single-cell resolution would deliver valuable mechanistic information much needed in understanding key biological processes. we present a surface-enhanced raman (sers) chemical imaging strategy as a first step toward exploring the intracellular bioreduction pockets of toxic chromate in shewanella. in order to achieve this, we take advantage of an innate reductive mechanism in bacteria of reducing gold ions into intracellular gold nanoisland ...201121634405
a survey of culturable aerobic and anaerobic marine bacteria in de novo biofilm formation on natural substrates in st. andrews bay, scotland.this study reports a novel study of marine biofilm formation comprising aerobic and anaerobic bacteria. samples of quartz and feldspar, minerals commonly found on the earth, were suspended 5 m deep in the north sea off the east coast of st. andrews, scotland for 5 weeks. the assemblage of organisms attached to these stones was cultivated under aerobic and anaerobic conditions in the laboratory. bacteria isolated on marine agar 2216 were all gram-negative and identified to genus level by sequenci ...201121638112
large scale comparative phenotypic and genomic analyses reveal ecological preferences of shewanella species and identify metabolic pathways conserved at genus level.the use of comparative genomics among different microbiological species has increased substantially as sequence technologies become more affordable. however, efforts to fully link a genotype to its phenotype remain limited to the development of one mutant at the time. in this study, we provide a high throughput alternative to this limiting step by coupling comparative genomics to phenotype arrays for five sequenced shewanella strains. positive phenotypes were obtained for 441 nutrients (c, n, p, ...201121642407
seafood quality analysis: molecular identification of dominant microbiota after ice storage on several general growth media.this study points out the limitations of several general growth media frequently used in seafood research by a systematic identification of the microorganisms on fish samples during ice storage unable to grow on those media. aerobic psychrotrophic count (apc), replication on various general media and total cultivable microbial community denaturing gradient gel electrophoresis (dgge) analysis revealed that many potential spoilage microorganisms were overlooked. those microorganisms overlooked by ...201121645815
redox and ph microenvironments within shewanella oneidensis mr-1 biofilms reveal electron transfer mechanism.the goal of this research was to quantify the variations in redox potential and ph in shewanella oneidensis mr-1 biofilms respiring on electrodes. we grew s. oneidensis mr-1 on a graphite electrode, which was used to accept electrons for microbial respiration. we modified well-known redox and ph microelectrodes with a built-in reference electrode so that they could operate near polarized surfaces and quantified the redox potential and ph profiles in these biofilms. in addition, we used a ferri / ...201121648431
competitive microbially and mn oxide mediated redox processes controlling arsenic speciation and partitioning.the speciation and partitioning of arsenic (as) in surface and subsurface environments are controlled, in part, by redox processes. within soils and sediments, redox gradients resulting from mass transfer limitations lead to competitive reduction-oxidation reactions that drive the fate of as. accordingly, the objective of this study was to determine the fate and redox cycling of as at the interface of birnessite (a strong oxidant in soil with a nominal formula of mno(x), where x ≈ 2) and dissimi ...201121648436
identification and characterization of undahrcr-6, an outer membrane endecaheme c-type cytochrome of shewanella sp. strain hrcr-6.unda(hrcr-6) was identified from the metal-reducing bacterium shewanella sp. strain hrcr-6. both in vivo and in vitro characterization results indicate that unda(hrcr-6) is an outer membrane endecaheme c-type cytochrome and probably has a key functional role in the extracellular reduction of iron [fe(iii)] oxides and uranium [u(vi)] by shewanella sp. hrcr-6.201121652739
diversity of protease-producing marine bacteria from sub-antarctic environments.from seawater and the intestines of benthonic organisms collected from the beagle channel, argentina, 230 marine bacteria were isolated. cultivable bacteria were characterized and classified as psychrotolerant, whereas few isolates were psychrophiles. these isolates were capable of producing proteases at 4 and 15 °c under neutral (ph 7.0), alkaline (ph 10.0) and acidic (ph 4.5) conditions on different media, revealing 62, 33 and 22% producers at cold and 84, 47 and 33% producers at low temperatu ...201121656810
fatty acid and hydrocarbon composition in tropical marine shewanella amazonensis strain sb2b(t).shewanella amazonensis strain sb2b(t) is an isolate from shallow-water marine sediments derived from the amazon river delta. this bacterium contained a long-chain polyunsaturated hydrocarbon, all-cis -3,6,9,12,16,19,22,25,28 hentriacontanonaene (c31:9), constituting 1-2% of the total fatty acid methyl ester and hydrocarbon fraction, which was produced dependently of decreased growth temperature. analysis of its cellular fatty acid composition demonstrated that isopentadecanoic acid was the major ...201121656813
the luxs mutation causes loosely-bound biofilms in shewanella oneidensis.abstract:201121663678
so2907, a putative tonb-dependent receptor, is involved in dissimilatory iron reduction by shewanella oneidensis mr-1.shewanella oneidensis strain mr-1 utilizes soluble and insoluble ferric ions as terminal electron acceptors during anaerobic respiration. the components of respiratory metabolism are localized in the membrane fractions which include the outer membrane and cytoplasmic membrane. many of the biological components that interact with the various iron forms are proposed to be localized in these membrane fractions. to identify the iron-binding proteins acting either as an iron transporter or as a termi ...201121813652
observation of in vivo cytochrome-based electron-transport dynamics using time-resolved evanescent wave electroabsorption spectroscopy. 201121812075
anaerobic biodecolorization mechanism of methyl orange by shewanella oneidensis mr-1.in this work, we investigated the anaerobic decolorization of methyl orange (mo), a typical azo dye, by shewanella oneidensis mr-1, which can use various organic and inorganic substances as its electron acceptor in natural and engineered environments. s. oneidensis mr-1 was found to be able to obtain energy for growth through anaerobic respiration accompanied with dissimilatory azo-reduction of mo. chemical analysis shows that mo reduction occurred via the cleavage of azo bond. block of mtr resp ...201121808969
monodispersed biocompatible silver sulfide nanoparticles: facile extracellular biosynthesis using the γ-proteobacterium, shewanella oneidensis.interest in engineered metal and semiconductor nanocrystallites continues to grow due to their unique size- and shape-dependent optoelectronic, physicochemical and biological properties. therefore identifying novel non-hazardous nanoparticle synthesis routes that address hydrophilicity, size and shape control and production costs has become a priority. in the present article we report for the first time on the efficient generation of extracellular silver sulfide (ag(2)s) nanoparticles by the met ...201121798382
soft tissue infections caused by marine bacterial pathogens: epidemiology, diagnosis, and management.skin and soft tissue infections (sstis) are one of the most common infection syndromes and may be caused by a large number of microorganisms. some principles of aquatic injuries are different than those of land-based trauma. wounds sustained in marine environment are exposed to a milieu of bacteria rarely encountered in different settings. these include vibrio spp., aeromonas spp., shewanella spp., erysipelothrix rhusiopathiae, mycobacterium marinum, streptococcus iniae, and other microbes. fail ...201121785929
shewasin a, an active pepsin homologue from the bacterium shewanella amazonensis.the view has been widely held that pepsin-like aspartic proteinases are found only in eukaryotes and not in bacteria. however, a recent bioinformatics search (rawlings, n.d. & bateman, a. [2009] bmc genomics 10, 437) revealed that in 7 out of ~1,000 completely-sequenced bacterial genomes, genes were present encoding polypeptides that displayed the requisite hallmark sequence motifs of pepsin-like aspartic proteinases. the implications of this theoretical observation prompted us to generate bioch ...201121749650
origin of oxa-181, an emerging carbapenem-hydrolyzing oxacillinase, as a chromosomal gene in shewanella xiamenensis.plasmid-mediated carbapenem-hydrolyzing ß-lactamases is becoming emerging threats in enterobacteriaceae. in particular, the carbapenem-hydrolyzing class d ß-lactamase oxa-48 and its derivative oxa-181 are increasingly worldwide reported. using a pcr-based strategy, environmental samples were screened for bla(oxa-48)-like genes. shewanella xiamenensis, an environmental species from marine and fresh water, was identified as the progenitor of the bla(oxa-181) gene. this work identifies the reservoi ...201121746953
influence of the diet on the microbial diversity of faecal and gastrointestinal contents in gilthead sea bream (sparus aurata) and intestinal contents in goldfish (carassius auratus).fish intestinal microbiota changes with the diet and this effect is of particular interest considering the increasing substitution of fish meal by plant protein sources. the objective of this work was to study the effects of partial substitution of fish meal with lupin and rapeseed meals on gut microbiota of the gilthead sea bream (sparus aurata) and in goldfish (carassius auratus). faecal, gastrointestinal and intestinal contents were characterized using culture-based and molecular methods. vib ...201121692817
purification and characterization of the [nife]-hydrogenase of shewanella oneidensis mr-1.shewanella oneidensis mr-1 possesses a periplasmic [nife]-hydrogenase (mr-1 [nife]-h(2)ase) that has been implicated in h(2) production and oxidation as well as technetium [tc(vii)] reduction. to characterize the roles of mr-1 [nife]-h(2)ase in these proposed reactions, the genes encoding both subunits of mr-1 [nife]-h(2)ase were cloned and then expressed in an mr-1 mutant without hyab and hyda genes. expression of recombinant mr-1 [nife]-h(2)ase in trans restored the mutant's ability to produce ...201121724888
identification of c-type heme-containing peptides using nonactivated immobilized metal affinity chromatography resin enrichment and higher-energy collisional dissociation.the c-type cytochromes play essential roles in many biological activities of both prokaryotic and eukaryotic cells, including electron transfer, enzyme catalysis, and induction of apoptosis. we report a novel enrichment strategy for identifying c-type heme-containing peptides that uses nonactivated imac resin. the strategy demonstrated at least 7-fold enrichment for heme-containing peptides digested from a cytochrome c protein standard, and quantitative linear performance was also assessed for h ...201121740036
identification and analysis of the shewanella oneidensis major oxygen-independent coproporphyrinogen iii oxidase gene.shewanella oneidenesis mr-1 is a facultative anaerobe that can use a large number of electron acceptors including metal oxides. during anaerobic respiration, s. oneidensis mr-1 synthesizes a large number of c cytochromes that give the organism its characteristic orange color. using a modified mariner transposon, a number of s. oneidensis mutants deficient in anaerobic respiration were generated. one mutant, bg163, exhibited reduced pigmentation and was deficient in c cytochromes normally synthes ...201121726654
crystal structure of n-domain of fkbp22 from shewanella sp. sib1: dimer dissociation by disruption of val-leu knot.fk506-binding protein 22 (fkbp22) from the psychrotophic bacterium shewanella sp. sib1 (sib1 fkbp22) is a homodimeric protein with peptidyl prolyl cis-trans isomerase (ppiase) activity. each monomer consists of the n-terminal domain responsible for dimerization and c-terminal catalytic domain. to reveal interactions at the dimer interface of sib1 fkbp22, the crystal structure of the n-domain of sib1 fkbp22 (sn-fkbp22, residues 1-68) was determined at 1.9 +à resolution. sn-fkbp22 forms a dimer, i ...201121837652
mapping the iron binding site(s) on the small tetraheme cytochrome of shewanella oneidensis mr-1.in the model microbe shewanella oneidensis, multi-heme proteins are utilized for respiratory metabolism where metals serve as the terminal electron acceptor. among those is the periplasm-localized small tetraheme cytochrome (stc). stc has been extensively characterized structurally and electrochemically to which electron flow in and out of the protein has been modeled. however, until the present work, no kinetic studies have been performed to probe the route of electron flow or to determine the ...201121682327
nile red detection of bacterial hydrocarbons and ketones in a high-throughput format.a method for use in high-throughput screening of bacteria for the production of long-chain hydrocarbons and ketones by monitoring fluorescent light emission in the presence of nile red is described. nile red has previously been used to screen for polyhydroxybutyrate (phb) and fatty acid esters, but this is the first report of screening for recombinant bacteria making hydrocarbons or ketones. the microtiter plate assay was evaluated using wild-type and recombinant strains of shewanella oneidensis ...201121712420
highly sensitive detection of proteins and bacteria in aqueous solution using surface-enhanced raman scattering and optical fibers.we report the detection of the proteins lysozyme and cytochrome c as well as the live bacterial cells of shewanella oneidensis mr-1 in aqueous solutions with sensitivities order(s) of magnitude higher than those previously reported. two highly sensitive surface-enhanced raman scattering (sers)-based biosensors using optical fibers have been employed for such label-free macromolecule detections. the first sensor is based on a tip-coated multimode fiber (tcmmf) with a double-substrate "sandwich" s ...201121692506
shewanella arctica sp. nov., an iron-reducing bacterium isolated from arctic marine sediment.two dissimilatory iron reducing bacteria (ir12t and ir26), which could couple lactate oxidation to iron reduction for energy conservation, were isolated from arctic marine sediment. two isolates were gram-staining-negative, catalase- and oxidase-positive and facultative anaerobic bacteria. cells of the isolates were rod-shaped and motile by means of a polar flagellum. the isolates grew in the presence of 0.5-3.5% (w/v) nacl with the absolute requirement of sodium ion. the isolates were psychroto ...201121724958
influence of arsenate adsorption to ferrihydrite, goethite, and boehmite on the kinetics of arsenate reduction by shewanella putrefaciens strain cn-32.the kinetics of as(v) reduction by shewanella putrefaciens strain cn-32 was investigated in suspensions of 0.2, 2, or 20 g l(-1) ferrihydrite, goethite, or boehmite at low as (10 ++m) and lactate (25 ++m) concentrations. experimental data were compared with model predictions based on independently determined sorption isotherms and rates of as(v) desorption, as(iii) adsorption, and microbial reduction of dissolved as(v), respectively. the low lactate concentration was chosen to prevent significan ...201121819067
solution-based structural analysis of the decaheme cytochrome, mtra, by small-angle x-ray scattering and analytical ultracentrifugation.the potential exploitation of metal-reducing bacteria as a means for environmental cleanup or alternative fuel is an exciting prospect; however, the cellular processes that would allow for these applications need to be better understood. mtra is a periplasmic decaheme c-type cytochrome from shewanella oneidensis involved in the reduction of extracellular iron oxides and therefore is a critical element in shewanella ability to engage in extracellular charge transfer. as a relatively small 333-res ...201121838277
comparative genomic reconstruction of transcriptional networks controlling central metabolism in the shewanella genus.genome-scale prediction of gene regulation and reconstruction of transcriptional regulatory networks in bacteria is one of the critical tasks of modern genomics. the shewanella genus is comprised of metabolically versatile gamma-proteobacteria, whose lifestyles and natural environments are substantially different from escherichia coli and other model bacterial species. the comparative genomics approaches and computational identification of regulatory sites are useful for the in silico reconstruc ...201121810205
roles of two shewanella oneidensis mr-1 extracellular endonucleases.the dissimilatory iron-reducing bacterium shewanella oneidensis mr-1 is capable of using extracellular dna (edna) as the sole source of carbon, phosphorus, and nitrogen. in addition, we recently demonstrated that s. oneidensis mr-1 requires edna as a structural component during all stages of biofilm formation. in this study, we characterize the roles of two shewanella extracellular endonucleases, exes and exem. while exes is likely secreted into the medium, exem is predicted to remain associated ...201121705528
bacterial formation of extracellular u(vi) nanowires.shewanella oneidensis mr-1 rapidly accumulates long, extracellular, u(vi) nanowires composed of polycrystalline chains of discrete meta-schoepite (uo(3)-à2h(2)o) nanocrystallites. the production of uranium(vi) nanowires could provide a novel strategy for remediation of uranium contamination in sediments and aquifers, as well as the recovery of uranium in manufacturing processes.201121681306
shewanella upenei sp. nov., a lipolytic bacterium isolated from bensasi goatfish upeneus bensasi.a gram-staining-negative, motile, non-spore-forming and rod-shaped bacterial strain, 20-23r(t), was isolated from intestine of bensasi goatfish, upeneus bensasi, and its taxonomic position was investigated by using a polyphasic study. phylogenetic analyses based on 16s rrna gene sequences revealed that strain 20-23r(t) belonged to the genus shewanella. strain 20-23r(t) exhibited 16s rrna gene sequence similarity values of 99.5, 99.2, and 97.5% to shewanella algae atcc 51192(t), shewanella haliot ...201121717322
genetic and molecular characterization of flagellar assembly in shewanella oneidensis.shewanella oneidensis is a highly motile organism by virtue of a polar flagellum. unlike most flagellated bacteria, it contains only one major chromosome segment encoding the components of the flagellum with the exception of the motor proteins. in this region, three genes encode flagellinsaccording to the original genome annotation. however, we find that only flaa and flab encode functional filament subunits. although these two genesare under the control of different promoters, they are actively ...201121731763
crystal structure of the complex between 4-hydroxybutyrate coa-transferase from clostridium aminobutyricum and coa.clostridium aminobutyricum ferments 4-aminobutyrate (+¦-aminobutyrate, gaba) to ammonia, acetate and butyrate via 4-hydroxybutyrate that is activated to the coa-thioester catalyzed by 4-hydroxybutyrate coa-transferase. then, 4-hydroxybutyryl-coa is dehydrated to crotonyl-coa, which disproportionates to butyryl-coa and acetyl-coa. cocrystallization of the coa-transferase with the alternate substrate butyryl-coa yielded crystals with non-covalently bound coa and two water molecules at the active s ...201121833509
genome-wide protein localization prediction strategies for gram negative bacteria.genome-wide prediction of protein subcellular localization is an important type of evidence used for inferring protein function. while a variety of computational tools have been developed for this purpose, errors in the gene models and use of protein sorting signals that are not recognized by the more commonly accepted tools can diminish the accuracy of their output.201121810203
investigation of the electron transport chain to and the catalytic activity of the diheme cytochrome c peroxidase ccpa of shewanella oneidensis.bacterial diheme c-type cytochrome peroxidases (bccps) catalyze the periplasmic reduction of hydrogen peroxide to water. the gammaproteobacterium shewanella oneidensis produces the peroxidase ccpa under a number of anaerobic conditions, including dissimilatory iron-reducing conditions. we wanted to understand the function of this protein in the organism and its putative connection to the electron transport chain to ferric iron. ccpa was isolated and tested for peroxidase activity, and its struct ...201121742904
biological characterization of two marine bdellovibrio-and-like organisms isolated from daya bay of shenzhen, china and their application in the elimination of vibrio parahaemolyticus in oyster.bdellovibrio-and-like organisms (balos) are a group of highly motile delta-proteobacteria that prey on other gram-negative bacteria. however, nothing is known of the application potential of marine balos in safeguarding seafood safety. here, biological characterization of two marine balos strains and their application in the elimination of vibrio parahaemolyticus in oyster (crassostrea ariakensis) at the laboratory scale were investigated. balos strains bdh12 and bdhsh06 were isolated from sedim ...201121899909
phylogenetic distribution and evolutionary history of bacterial dead-box proteins.dead-box proteins are found in all domains of life and participate in almost all cellular processes that involve rna. the presence of dead and helicase_c conserved domains distinguish these proteins. dead-box proteins exhibit rna-dependent atpase activity in vitro, and several also show rna helicase activity. in this study, we analyzed the distribution and architecture of dead-box proteins among bacterial genomes to gain insight into the evolutionary pathways that have shaped their history. we i ...201121437710
gapped spectral dictionaries and their applications for database searches of tandem mass spectra.generating all plausible de novo interpretations of a peptide tandem mass (ms/ms) spectrum (spectral dictionary) and quickly matching them against the database represent a recently emerged alternative approach to peptide identification. however, the sizes of the spectral dictionaries quickly grow with the peptide length making their generation impractical for long peptides. we introduce gapped spectral dictionaries (all plausible de novo interpretations with gaps) that can be easily generated fo ...201121444829
fnr (etra) acts as a fine-tuning regulator of anaerobic metabolism in shewanella oneidensis mr-1.etra in shewanella oneidensis mr-1, a model organism for study of adaptation to varied redox niches, shares 73.6% and 50.8% amino acid sequence identity with the oxygen-sensing regulators fnr in e. coli and anr in pseudomonas aeruginosa, respectively; however, its regulatory role of anaerobic metabolism in shewanella spp. is complex and not well understood.201121450087
selection of bacteria capable of dissimilatory reduction of fe(iii) from a long-term continuous culture on molasses and their use in a microbial fuel cell.ferric ion-respiring microorganisms (frms) are a group of prokaryotes that use fe(iii) as well as other metals as terminal electron acceptors in the process of anaerobic respiration. special attention is paid to a biotechnological significance of frms because of their potential role in electricity production in microbial fuel cells (mfcs) where the terminal acceptor of the electrons during anaerobic respiration is not a ferric ion but the anode. one of the best known frms is the shewanellaceae f ...201121464603
a rapid fingerprinting approach to distinguish between closely related strains of shewanella.one of the big operational problems facing laboratories today is the ability to rapidly distinguish between strains of bacteria that, while physiologically distinct, are nearly impossible to separate based on 16s rrna gene sequence differences. here we demonstrate that its-dgge provides a convenient approach to distinguishing between closely related strains of shewanella, some of which were impossible to separate and identify by 16 rrna gene sequence alone. examined shewanella genomes contain 8- ...201121477623
multidrug resistance in hydrocarbon-tolerant gram-positive and gram-negative bacteria.new gram-positive and gram-negative bacteria were isolated from poeni oily sludge, using enrichment procedures. the six gram-positive strains belong to bacillus, lysinibacillus and rhodococcus genera. the eight gram-negative strains belong to shewanella, aeromonas, pseudomonas and klebsiella genera. isolated bacterial strains were tolerant to saturated (i.e., n-hexane, n-heptane, n-decane, n-pentadecane, n-hexadecane, cyclohexane), monoaromatic (i.e., benzene, toluene, styrene, xylene isomers, e ...201121478643
how does organic matter constrain the nature, size and availability of fe nanoparticles for biological reduction?few studies have so far examined the kinetics and extent of the formation of fe-colloids in the presence of natural organic ligands. the present study used an experimental approach to investigate the rate and amount of colloidal fe formed in presence of humic substances, by gradually oxidizing fe(ii) at ph 6.5 with or without humic substances (hs) (in this case, humic acid - ha and fulvic acid - fa). without hs, micronic aggregates (0.1-1μm diameter) of nano-lepidocrocite is obtained, whereas, i ...201121482426
effect of uranium(vi) speciation on simultaneous microbial reduction of uranium(vi) and iron(iii).uranium is a pollutant of concern to both human and ecosystem health. uranium's redox state often dictates whether it will reside in the aqueous or solid phase and thus plays an integral role in the mobility of uranium within the environment. in anaerobic environments, the more oxidized and mobile form of uranium (uo2(2+) and associated species) may be reduced, directly or indirectly, by microorganisms to u(iv) with subsequent precipitation of uo. however, various factors within soils and sedime ...201121488497
impact of a static magnetic field on the electricity production of shewanella-inoculated microbial fuel cells.the electricity production of shewanella-inoculated microbial fuel cells (mfcs) under magnetic field (mf) exposure was investigated in different reactor systems. the persistency of the mf effect and the influences of mf intensity and direction on mfc performance were also studied. application of a 100-mt static mf to the mfcs improved electricity production considerably, with an increase in the maximum voltage by 20-27% in both single- and two-chamber mfcs, while a more conspicuous improvement i ...201121493055
microbial electricity generation via microfluidic flow control.next generation battery technology is rapidly evolving to meet the demand for higher power densities and smaller footprints through novel catalysts and battery architecture. we present a µ-scale, biological fuel cell which utilizes microbial electricity generation enabled by microfluidic flow control to produce power. the new fuel cell, the smallest of its kind, with a total volume of 0.3 µl, produces scalable and controllable electrical energy from organic matter which is sustained through micr ...201121495007
extracellular reduction of hexavalent chromium by cytochromes mtrc and omca of shewanella oneidensis mr-1.to characterize the roles of cytochromes mtrc and omca of shewanella oneidensis mr-1 in cr(vi) reduction, the impacts of deleting mtrc and/or omca genes on cr(vi) reduction and cellular locations of reduced cr(iii) precipitates were investigated. compared to wild type (wt), deletion of mtrc decreased initial rate of cr(vi) reduction by 43.5%, while deletion of omca or both mtrc and omca lowered the rates by 53.4% and 68.9%, respectively. in wt cells, cr(iii) precipitates were detected by transmi ...201121498755
decolorization of azo dyes by shewanella oneidensis mr-1 in the presence of humic acids.the effects of humic acid (ha) on azo dye decolorization by shewanella oneidensis mr-1 were studied. it was found that ha species isolated from different sources could all accelerate the decolorization of acid red 27 (ar27). anoxic and anaerobic conditions were required for the enhancement of azo dye decolorization by ha. in the presence of 50 mg doc l(-1) aldrich ha, 15-29% increases in decolorization efficiencies of azo dyes with different structures were achieved in 11 h. the enhancing effect ...201121509566
[laser tweezers raman spectroscopy analysis of cold-adapted aromatic hydrocarbons-degradating strains isolated from antarctic sea].laser tweezers raman spectroscopy can help with observing and studying individual cells or organelles in a natural state for a relatively long period. in the present experiment, laser tweezers raman spectroscopy (ltrs) was used as a tool to report physiological metabolism such as cells growth and nucleic acid, proteins, lipid and glucose of a single active cold-adapted aromatic hydrocarbons-degradating strains isolated from antarctic sea. after the raman spectrum was collected and analyzed, the ...201121510394
heterologous expression, purification, and characterization of an α-mannosidase belonging to glycoside hydrolase family 99 of shewanella amazonensis.shewanella amazonensis α-mannosidase (sama99), a member of glycoside hydrolase family 99, was expressed in escherichia coli. the purified sama99 hydrolyzed pyridylamino (pa)-sugars, glc(1)man(9)glcnac(2)-pa, and glc(3)man(9)glcnac(2)-pa, and the product was probably a pyridylamino-decasaccharide in both cases. the mode of action of sama99 was found to be essentially identical to that of rat endo-α-1,2-mannosidase, but the specificity of sama99 was low.201121512220
favourable effects of eicosapentaenoic acid on the late step of the cell division in a piezophilic bacterium, shewanella violacea dss12, at high-hydrostatic pressures.shewanella violacea dss12, a deep-sea bacterium, produces eicosapentaenoic acid (epa) as a component of membrane phospholipids. although various isolates from the deep sea, such as photobacterium profundum ss9, colwellia psychrerythraea 34h and various shewanella strains, produce epa- or docosahexaenoic acid-containing phospholipids, the physiological role of these polyunsaturated fatty acids remains unclear. in this article, we illustrate the physiological importance of epa for high-pressure ad ...201121518217
microbial growth at hyperaccelerations up to 403,627 x g.it is well known that prokaryotic life can withstand extremes of temperature, ph, pressure, and radiation. little is known about the proliferation of prokaryotic life under conditions of hyperacceleration attributable to extreme gravity, however. we found that living organisms can be surprisingly proliferative during hyperacceleration. in tests reported here, a variety of microorganisms, including gram-negative escherichia coli, paracoccus denitrificans, and shewanella amazonensis; gram-positive ...201121518884
a novel conico-cylindrical flask aids easy identification of critical process parameters for cultivation of marine bacteria.a polymethylmethacrylate (pmma) conico-cylindrical flask (ccf) with an inner arrangement consisting of eight equidistantly spaced rectangular strips mounted radially on a circular disk to provide additional surface area for microbial attachment and ports to allow air supply was employed for melanin production by shewanella colwelliana and antibiotic production by pseudoalteromonas rubra. the design allowed comparison of production between (1) ccf with hydrophobic surface (pmma-ccf), (2) ccf with ...201121210106
competitive reduction of pertechnetate (99tco4-) by dissimilatory metal reducing bacteria and biogenic fe(ii).the fate of pertechnetate ((99)tc(vii)o(4)(-)) during bioreduction was investigated in the presence of 2-line ferrihydrite (fh) and various dissimilatory metal reducing bacteria (dmrb) (geobacter, anaeromyxobacter, shewanella) in comparison with tco(4)(-) bioreduction in the absence of fh. in the presence of fh, tc was present primarily as a fine-grained tc(iv)/fe precipitate that was distinct from the tc(iv)o(2)·nh(2)o solids produced by direct biological tc(vii) reduction. aqueous tc concentra ...201121210705
integrative analysis of transcriptomic and proteomic data of shewanella oneidensis: missing value imputation using temporal datasets.despite significant improvements in recent years, proteomic datasets currently available still suffer from large number of missing values. integrative analyses based upon incomplete proteomic and transcriptomic datasets could seriously bias the biological interpretation. in this study, we applied a non-linear data-driven stochastic gradient boosted trees (gbt) model to impute missing proteomic values using a temporal transcriptomic and proteomic dataset of shewanella oneidensis. in this dataset, ...201121212895
mercury reduction and complexation by natural organic matter in anoxic environments.mercuric hg(ii) species form complexes with natural dissolved organic matter (dom) such as humic acid (ha), and this binding is known to affect the chemical and biological transformation and cycling of mercury in aquatic environments. dissolved elemental mercury, hg(0), is also widely observed in sediments and water. however, reactions between hg(0) and dom have rarely been studied in anoxic environments. here, under anoxic dark conditions we show strong interactions between reduced ha and hg(0) ...201121220311
air-cathode microbial fuel cell array: a device for identifying and characterizing electrochemically active microbes.microbial fuel cells (mfcs) have generated excitement in environmental and bioenergy communities due to their potential for coupling wastewater treatment with energy generation and powering diverse devices. the pursuit of strategies such as improving microbial cultivation practices and optimizing mfc devices has increased power generating capacities of mfcs. however, surprisingly few microbial species with electrochemical activity in mfcs have been identified because current devices do not suppo ...201120655725
the utility of shewanella japonica for microbial fuel cells.shewanella-containing microbial fuel cells (mfcs) typically use the fresh water wild-type strain shewanella oneidensis mr-1 due to its metabolic diversity and facultative oxidant tolerance. however, s. oneidensis mr-1 is not capable of metabolizing polysaccharides for extracellular electron transfer. the applicability of shewanella japonica (an agar-lytic shewanella strain) for power applications was analyzed using a diverse array of carbon sources for current generation from mfcs, cellular phys ...201120663660
indirect modulation of the intracellular c-di-gmp level in shewanella oneidensis mr-1 by mxda.the ggdef domain protein mxda, which is important for biofilm formation in shewanella oneidensis mr-1, was hypothesized to possess diguanylate cyclase activity. here, we demonstrate that while mxda controls the cellular level of c-di-gmp in s. oneidensis, it modulates the c-di-gmp pool indirectly.201121278272
in vivo participation of artificial porphyrins in electron-transport chains: electrochemical and spectroscopic analyses of microbial metabolism.the effects of artificial porphyrins on the electron-transport chains of living microbes were investigated. the participation of porphyrins in the microbial electron-transport chains was demonstrated by spectroscopic and current-generation measurements. large enhancement of the microbial current generation was accomplished by adding a cationic water-soluble manganese porphyrin as an electron mediator.201121280587
anaerobic ammonium oxidation mediated by mn-oxides: from sediment to strain level.nitrite and (29)n(2) productions in slurry incubations of anaerobically sediment after (15)no(3) or (15)nh(4) labelling in the presence of mn-oxides suggested that anaerobic mn-oxides mediated nitrification coupled with denitrification in muddy intertidal sediments of arcachon bay (sw atlantic french coast). from this sediment, bacterial strains were isolated and physiologically characterized in terms of mn-oxides and nitrate reduction as well as potential anaerobic nitrification. one of the iso ...201121288484
towards electrosynthesis in shewanella: energetics of reversing the mtr pathway for reductive metabolism.bioelectrochemical systems rely on microorganisms to link complex oxidation/reduction reactions to electrodes. for example, in shewanella oneidensis strain mr-1, an electron transfer conduit consisting of cytochromes and structural proteins, known as the mtr respiratory pathway, catalyzes electron flow from cytoplasmic oxidative reactions to electrodes. reversing this electron flow to drive microbial reductive metabolism offers a possible route for electrosynthesis of high value fuels and chemic ...201121311751
evidence for the role of horizontal transfer in generating pvt1, a large mosaic conjugative plasmid from the clam pathogen, vibrio tapetis.the marine bacterium vibrio tapetis is the causative agent of the brown ring disease, which affects the clam ruditapes philippinarum and causes heavy economic losses in north of europe and in eastern asia. further characterization of v. tapetis isolates showed that all the investigated strains harbored at least one large plasmid. we determined the sequence of the 82,266 bp plasmid pvt1 from the cect4600(t) reference strain and analyzed its genetic content. pvt1 is a mosaic plasmid closely relate ...201121326607
tools for resolving complexity in the electron transfer networks of multiheme cytochromes c.examining electron transfer between two proteins with identical spectroscopic signatures is a challenging task. it is supposed that several multiheme cytochromes in shewanella oneidensis form a molecular "wire" through which electrons are transported across the cellular space and a direct study of this transient protein-protein interaction has not yet been reported. in this study, we present variations on catalytic protein film voltammetry and an anaerobic affinity chromatography assay to demons ...201121327265
feedback stabilization involving redox states of c-type cytochromes in living bacteria.the formal potential of c-type cytochromes expressed in the bacterial outer membrane was dependent on their redox state functioning in mediating extracellular electron transfer. its negative (positive) shifting accompanying with the oxidization (reduction) of c-type cytochromes can serve to stabilize the redox states in a feedback manner.201121331401
pulsed multiple reaction monitoring approach to enhancing sensitivity of a tandem quadrupole mass spectrometer.liquid chromatography (lc)-triple quadrupole mass spectrometers operating in a multiple reaction monitoring (mrm) mode are increasingly used for quantitative analysis of low-abundance analytes in highly complex biochemical matrixes. after development and selection of optimum mrm transitions, sensitivity and data quality limitations are largely related to mass spectral peak interferences from sample or matrix constituents and statistical limitations at low number of ions reaching the detector. he ...201121344863
reproducibility and quantitation of amplicon sequencing-based detection.to determine the reproducibility and quantitation of the amplicon sequencing-based detection approach for analyzing microbial community structure, a total of 24 microbial communities from a long-term global change experimental site were examined. genomic dna obtained from each community was used to amplify 16s rrna genes with two or three barcode tags as technical replicates in the presence of a small quantity (0.1% wt/wt) of genomic dna from shewanella oneidensis mr-1 as the control. the techni ...201121346791
the octahaem sira catalyses dissimilatory sulfite reduction in shewanella oneidensis mr-1.shewanella oneidensis mr-1 is a metal reducer that uses a large number of electron acceptors including thiosulfate, polysulfide and sulfite. the enzyme required for thiosulfate and polysulfide respiration has been recently identified, but the mechanisms of sulfite reduction remained unexplored. analysis of mr-1 cultures grown anaerobically with sulfite suggested that the dissimilatory sulfite reductase catalyses six-electron reduction of sulfite to sulfide. reduction of sulfite required menaquin ...201121199252
unprecedented levels of horizontal gene transfer among spatially co-occurring shewanella bacteria from the baltic sea.high-throughput sequencing studies during the last decade have uncovered that bacterial genomes are very diverse and dynamic, resulting primarily from the frequent and promiscuous horizontal gene exchange that characterizes the bacterial domain of life. however, a robust understanding of the rates of genetic exchange for most bacterial species under natural conditions and the influence of the ecological settings on the rates remain elusive, severely limiting our view of the microbial world. here ...201120596068
electricity generation of single-chamber microbial fuel cells at low temperatures.practical applications of microbial fuel cells (mfcs) for wastewater treatment will require operation of these systems over a wide range of wastewater temperatures. mfcs at room or higher temperatures (20-35°c) are relatively well studied compared those at lower temperatures. mfc performance was examined here over a temperature range of 4-30°c in terms of startup time needed for reproducible power cycles, and performance. mfcs initially operated at 15°c or higher all attained a reproducible cycl ...201120627513
pressurized pepsin digestion in proteomics: an automatable alternative to trypsin for integrated top-down bottom-up proteomics.integrated top-down bottom-up proteomics combined with on-line digestion has great potential to improve the characterization of protein isoforms in biological systems and is amendable to high throughput proteomics experiments. bottom-up proteomics ultimately provides the peptide sequences derived from the tandem ms analyses of peptides after the proteome has been digested. top-down proteomics conversely entails the ms analyses of intact proteins for more effective characterization of genetic var ...201120627868
miniaturizing microbial fuel cells.microbial fuel cells (mfcs) represent an emerging technology for electricity generation from renewable biomass. given the demand for a better understanding of the bio/inorganic interface that plays a key role in mfc energy production, small-scale mfcs are receiving considerable attention owing to their intrinsic advantages in both fundamental studies and applications as high-throughput platforms. here, we present a brief review centered on the development of miniature mfcs at the milliliter to m ...201121075467
nanoparticle decorated anodes for enhanced current generation in microbial electrochemical cells.the development of highly efficient anode materials is critical for enhancing the current output of microbial electrochemical cells. in this study, au and pd nanoparticle decorated graphite anodes were developed and evaluated in a newly designed multi-anode microbial electrolysis cell (mec). the anodes decorated with au nanoparticles produced current densities up to 20-fold higher than plain graphite anodes by shewanella oneidensis mr-1, while those of pd-decorated anodes with similar morphologi ...201120542420
Solution and microbial controls on the formation of reduced U(IV) species.Reduction of U(VI) to U(IV) as the result of direct or indirect microbial activity is currently being explored for in situ remediation of subsurface U plumes, under the assumption that U(IV) solubility is controlled by the low-solubility mineral uraninite (U(IV)-dioxide). However, recent characterizations of U in sediments from biostimulated field sites, as well as laboratory U(VI) bioreduction studies, report on the formation of U(IV) species that lack the U-O(2)-U coordination of uraninite, su ...201121846108
control of proteobacterial central carbon metabolism by the hexr transcriptional regulator: a case study in shewanella oneidensis.bacteria exploit multiple mechanisms for controlling central carbon metabolism (ccm). thus, a bioinformatic analysis together with some experimental data implicated the hexr transcriptional factor as a global ccm regulator in some lineages of gammaproteobacteria operating as a functional replacement of the cra regulator characteristic of enterobacteriales. in this study, we combined a large scale comparative genomic reconstruction of hexr-controlled regulons in 87 species of proteobacteria with ...201121849503
thermal stability of cytochrome c₅ of pressure-sensitive shewanella livingstonensis.cytochrome c₅ of pressure-sensitive shewanella livingstonensis (sl cytc₅) exhibits lower thermal stability than a highly homologous counterpart of pressure-tolerant shewanella violacea. this stability difference is due to an enthalpic effect that can be attributed to the amino acid residue at position 50 (leu or lys). these cytc₅ proteins are appropriate materials for understanding the protein stability mechanism.201121897014
characterisation of the microbiota of atlantic mackerel (scomber scombrus).in this study the microbiota of atlantic mackerel (scomber scombrus) collected by a commercial purse seiner was examined. fish were collected directly from the purse seine and from the refrigerated sea water (rsw) transport tank after loading. the culturable microbiota and specific spoilage bacteria (ssb) were quantified on iron agar lyngby (ial) and identified using commercially available biochemical api® kits on pure cultured isolates. these kits showed to be sub-optimal in characterising the ...201121914558
enhanced performance and mechanism study of microbial electrolysis cells using fe nanoparticle-decorated anodes.anode properties are critical for the performance of microbial electrolysis cells (mecs). in the present study, fe nanoparticle-modified graphite disks were used as anodes to investigate the effects of nanoparticles on the performance of shewanella oneidensis mr-1 in mecs. results demonstrated that the average current densities produced with fe nanoparticle-decorated anodes up to 5.89-fold higher than plain graphite anodes. whole genome microarray analysis of the gene expression showed that gene ...201122080340
conductive artificial biofilm dramatically enhances bioelectricity production in shewanella-inoculated microbial fuel cells.a new strategy of electrogen immobilization was developed to construct a conductive artificial biofilm (cab) on an anode of a microbial fuel cell (mfc). the mfcs equipped with an optimized cab exhibited an eleven fold increase in power output compared with natural biofilms.201122048750
dissimilatory reduction of extracellular electron acceptors in anaerobic respiration.an extension of the respiratory chain to the cell surface is necessary to reduce extracellular electron acceptors like ferric iron or manganese oxides. in the last years more and more compounds were revealed to be reduced at the surface of the outer membrane of gram-negative bacteria and the list does not seem to have an end so far. shewanella as well as geobacter strains are model organisms to discover the biochemistry that enables the dissimilatory reduction of extracellular electron acceptors ...201122179232
biosupported bimetallic pd-au nanocatalysts for dechlorination of environmental contaminants.biologically produced monometallic palladium nanoparticles (bio-pd) have been shown to catalyze the dehalogenation of environmental contaminants, but fail to efficiently catalyze the degradation of other important recalcitrant halogenated compounds. this study represents the first report of biologically produced bimetallic pd/au nanoparticle catalysts. the obtained catalysts were tested for the dechlorination of diclofenac and trichlorethylene. when aqueous bivalent pd(ii) and trivalent au(iii) ...201121877727
cu-doped tio(2) nanoparticles enhance survival of shewanella oneidensis mr-1 under ultraviolet light (uv) exposure.it has been shown that photocatalytic tio(2) nanoparticles (nps) can be used as an efficient anti-microbial agent under uv light due to generation of reactive oxygen species (ros), while shewanella oneidensis mr-1 is a metal-reducing bacterium highly susceptible to uv radiation. interestingly, we found that the presence of cu-doped tio(2) nps in the cultural medium dramatically increased the survival rates (based on colony-forming unit) of strain mr-1 by over 10,000-fold (incubation without shak ...201121855961
characterization of microbial communities during anode biofilm reformation in a two-chambered microbial electrolysis cell (mec).geochip (ii) and single strand conformation polymorphism (sscp) were used to characterize anode microbial communities of a microbial electrolysis cell (mec). biofilm communities, enriched in a two-chamber mec (r1, 0.6v applied) having a coulombic efficiency (ce) of 35±4% and a hydrogen yield [formula: see text] of 31±3%, were used as the inoculum for a new reactor (r2). after three months r2 achieved stable performance with ce=38±4% and [formula: see text] few changes in the predominant populati ...201121939699
selection of shewanella oneidensis mr-1 gene-knockout mutants that adapt to an electrode-respiring condition.mutants of shewanella oneidensis mr-1 that adapted to an electrode-respiring condition were selected from a random transposon-insertion mutant library to obtain active current-generating mutants and identify relevant cellular components. the mutants were selected in the presence of an electrode (poised at +0.2 v vs. an ag/agcl reference electrode) as the sole electron acceptor, and they were isolated on agar plates. transposon-insertion sites in the isolated mutants were identified by inverse pc ...201122056453
pyruvate and lactate metabolism by shewanella oneidensis mr-1 under fermentation, oxygen limitation, and fumarate respiration conditions.shewanella oneidensis mr-1 is a facultative anaerobe that derives energy by coupling organic matter oxidation to the reduction of a wide range of electron acceptors. here, we quantitatively assessed the lactate and pyruvate metabolism of mr-1 under three distinct conditions: electron acceptor-limited growth on lactate with o(2), lactate with fumarate, and pyruvate fermentation. the latter does not support growth but provides energy for cell survival. using physiological and genetic approaches co ...201121965410
identification and characterization of alkaline serine protease from goat skin surface metagenome.abstract: metagenomic dna isolated from goat skin surface was used to construct plasmid dna library in escherichia coli dh10b. recombinant clones were screened for functional protease activity on skim milk agar plates. upon screening 70,000 clones, a clone carrying recombinant plasmid psp1 exhibited protease activity. in vitro transposon mutagenesis and sequencing of the insert dna in this clone revealed an orf of 1890 bp encoding a protein with 630 amino acids which showed significant sequence ...201121906326
microbiological analysis of the mummy of st. marcian.the paper provides the results of the microbiological analysis of samples taken from the mummified remains of st. marcian. microorganisms found belong to bacteria and fungi of the genera aspergillus, bacillus, penicillium, sarcina, and shewanella which are all apart of the common air, soil, and human microbial flora and therefore present no health hazard.201122053579
towards a structural understanding of drug and peptide transport within the proton-dependent oligopeptide transporter (pot) family.one of the principal aims of modern drug design is the targeted delivery of drugs within the body, such as to the central nervous system, combined with their exclusion from the liver and kidneys, which break down foreign molecules and subsequently eliminate them. many of the commonly prescribed drugs are transported into cells and across the plasma membrane via endogenous membrane transporters, whose principal roles are the uptake of essential nutrients for metabolism. in many cases, such drug t ...201121936814
bacterial community associated with the intestinal tract of p. monodon in commercial farms.the potentially important roles of intestinal bacteria on immune response, disease resistance, and nutrition for the black tiger shrimp penaeus monodon have been increasingly investigated. however, so far, little is known about the intestinal bacterial community of the shrimp in the commercial aquaculture settings. in this study, the intestinal bacterial communities of juvenile p. monodon (70 individuals) from eight commercial farms in thailand were examined using 16s rdna pcr-dgge, and seven 16 ...201121915632
specificity of motor components in the dual flagellar system of shewanella putrefaciens cn-32.bacterial flagellar motors are intricate nanomachines in which the stator units and rotor component flim may be dynamically exchanged during function. similar to other bacterial species, the gammaproteobacterium shewanella putrefaciens cn-32 possesses a complete secondary flagellar system along with a corresponding stator unit. expression of the secondary system occurs during planktonic growth in complex media and leads to the formation of a subpopulation with one or more additional flagella at ...201122151089
Shuttling happens: soluble flavin mediators of extracellular electron transfer in Shewanella.The genus Shewanella contains Gram negative ?-proteobacteria capable of reducing a wide range of substrates, including insoluble metals and carbon electrodes. The utilization of insoluble respiratory substrates by bacteria requires a strategy that is quite different from a traditional respiratory strategy because the cell cannot take up the substrate. Electrons generated by cellular metabolism instead must be transported outside the cell, and perhaps beyond, in order to reduce an insoluble subst ...201122072194
Identification of nicotinamide mononucleotide deamidase of the bacterial pyridine nucleotide cycle reveals a novel broadly conserved amidohydrolase family.The pyridine nucleotide cycle is a network of salvage and recycling routes maintaining homeostasis of NAD(P) cofactor pool in the cell. Nicotinamide mononucleotide (NMN) deamidase (EC 3.5.1.42), one of the key enzymes of the bacterial pyridine nucleotide cycle, was originally described in Enterobacteria, but the corresponding gene eluded identification for over 30 years. A genomics-based reconstruction of NAD metabolism across hundreds of bacterial species suggested that NMN deamidase reaction i ...201121953451
lactate oxidation coupled to iron or electrode reduction by geobacter sulfurreducens pca.geobacter sulfurreducens pca completely oxidized lactate and reduced iron or an electrode, producing pyruvate and acetate intermediates. compared to the current produced by shewanella oneidensis mr-1, g. sulfurreducens pca produced 10-times-higher current levels in lactate-fed microbial electrolysis cells. the kinetic and comparative analyses reported here suggest a prominent role of g. sulfurreducens strains in metal- and electrode-reducing communities supplied with lactate.201122003020
Optimal method for efficiently removing extracellular nanofilaments from Shewanella oneidensis MR-1.The identification, production, and potential electron conductivity of bacterial extracellular nanofilaments is an area of great study, specifically in Shewanella oneidensis MR-1. While some studies focus on nanofilaments attached to the cellular body, many studies require the removal of these nanofilaments for downstream applications. The removal of nanofilaments from S. oneidensis MR-1 for further study requires not only that the nanofilaments be detached, but also for the cell bodies to remai ...201121963962
The acid-tolerant L-arabinose isomerase from the mesophilic Shewanella sp. ANA-3 is highly active at low temperatures.ABSTRACT:201122074172
evidence-based annotation of gene function in shewanella oneidensis mr-1 using genome-wide fitness profiling across 121 conditions.most genes in bacteria are experimentally uncharacterized and cannot be annotated with a specific function. given the great diversity of bacteria and the ease of genome sequencing, high-throughput approaches to identify gene function experimentally are needed. here, we use pools of tagged transposon mutants in the metal-reducing bacterium shewanella oneidensis mr-1 to probe the mutant fitness of 3,355 genes in 121 diverse conditions including different growth substrates, alternative electron acc ...201122125499
the metj regulon in gammaproteobacteria determined by comparative genomics methods.whole-genome sequencing of bacteria has proceeded at an exponential pace but annotation validation has lagged behind. for instance, the metj regulon, which controls methionine biosynthesis and transport, has been studied almost exclusively in e. coli and salmonella, but homologs of metj exist in a variety of other species. these include some that are pathogenic (e.g. yersinia) and some that are important for environmental remediation (e.g. shewanella) but many of which have not been extensively ...201122082356
Improving liquid chromatography-mass spectrometry sensitivity using a subambient pressure ionization with nanoelectrospray (SPIN) interface.In this work, the subambient pressure ionization with nanoelectrospray (SPIN) ion source and interface, which operates at ~15-30 Torr, is demonstrated to be compatible with gradient reversed-phase liquid chromatography-MS applications, exemplified here with the analysis of complex samples (a protein tryptic digest and a whole cell lysate). A low liquid chromatographic flow rate (100-400 nL/min) allowed stable electrospray to be established while avoiding electrical breakdown. Efforts to increase ...201121953185
Zinc oxide and indium tin oxide thin films for the growth and characterization of Shewanella loihica PV-4 electroactive biofilms. 201121921690
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