Publications

evaluation of the effects of various culture conditions on cr(vi) reduction by shewanella oneidensis mr-1 in a novel high-throughput mini-bioreactor.	the growth and cr(vi) reduction by shewanella oneidensis mr-1 was examined using a mini-bioreactor system that independently monitors and controls ph, dissolved oxygen (do), and temperature for each of its 24, 10-ml reactors. independent monitoring and control of each reactor in the cassette allows the exploration of a matrix of environmental conditions known to influence s. oneidensis chromium reduction. s. oneidensis mr-1 grew in minimal medium without amino acid or vitamin supplementation und ...	2006	16732598
c-type cytochrome-dependent formation of u(iv) nanoparticles by shewanella oneidensis.	modern approaches for bioremediation of radionuclide contaminated environments are based on the ability of microorganisms to effectively catalyze changes in the oxidation states of metals that in turn influence their solubility. although microbial metal reduction has been identified as an effective means for immobilizing highly-soluble uranium(vi) complexes in situ, the biomolecular mechanisms of u(vi) reduction are not well understood. here, we show that c-type cytochromes of a dissimilatory me ...	2006	16875436
a rapid mutant screening technique for detection of technetium [tc(vii)] reduction-deficient mutants of shewanella oneidensis mr-1.	microbial metal reduction forms the basis of alternate bioremediation strategies for reductive precipitation and immobilization of toxic metals such as the radionuclide technetium [tc(vii)]. a rapid mutant screening technique was developed to identify shewanella oneidensis mr-1 respiratory mutants unable to reduce tc(vii) as anaerobic electron acceptor. the tc(vii) reduction-deficient (tcr) mutant screening technique was based on the observation that wild-type s. oneidensis produced a black tc(i ...	2006	16734791
[shewanella genus bacteria isolated from the black sea water and molluscs].	six (6) strains of bacteria isolated from the black sea water and mollusks mytilaster lineatus have been assigned to shewanella genus on the basis of phenotypical and molecular-genetic study. partial sequence of 16s rrna gene revealed 100% similarity of three of these strains to s. baltica, although they had some phenotypical differences. three more strains were genetically related to s. colwelliana and s. affinis (99-100% of 16s rrna sequences similarity), but they differed from these species a ...	2006	16786624
amino acid substitutions in malate dehydrogenases of piezophilic bacteria isolated from intestinal contents of deep-sea fishes retrieved from the abyssal zone.	to examine the occurrence in other deep-sea bacteria of two amino acid substitutions (ala-180 and his-229) in malate dehydrogenase (mdh) found previously in the deep-sea piezophilic moritella sp. strain 2d2, we cloned and sequenced mdh genes of deep-sea piezophilic moritella and shewanella strains isolated from intestinal contents of deep-sea fishes, as well as other moritella species from deep-sea water and sediments: m. marina, m. japonica, and m. yayanosii. the piezophilic moritella strains h ...	2006	16598154
isolation of a high-affinity functional protein complex between omca and mtrc: two outer membrane decaheme c-type cytochromes of shewanella oneidensis mr-1.	shewanella oneidensis mr-1 is a facultatively anaerobic bacterium capable of using soluble and insoluble forms of manganese [mn(iii/iv)] and iron [fe(iii)] as terminal electron acceptors during anaerobic respiration. to assess the structural association of two outer membrane-associated c-type decaheme cytochromes (i.e., omca [so1779] and mtrc [so1778]) and their ability to reduce soluble fe(iii)-nitrilotriacetic acid (nta), we expressed these proteins with a c-terminal tag in wild-type s. oneide ...	2006	16788180
differential recovery of biotinylated microbial proteins using monomeric or polymeric avidin.		2006	16708758
mechanism of a soluble fumarate reductase from shewanella frigidimarina: a theoretical study.	the mechanism of a unique fumarate reductase is explored using the hybrid density functional b3lyp method. the calculations show a two-step mechanism, initiated with a hydride transfer from fad (flavin adenine dinucleotide) to fumarate, followed by a proton shift from arg402. the rate-limiting process is assigned to the hydride transfer, and the energetics are consistent with experimental data. it is shown that the enzyme is essential to correctly position the substrate in the active site, stabi ...	2006	16722766
concentrations and tracking of listeria monocytogenes strains in a seafood-processing environment using a most-probable-number enrichment procedure and randomly amplified polymorphic dna analysis.	concentrations of environmental microflora and listeria monocytogenes were monitored at multiple environmental locations within a seafood-processing facility over the course of 6 months. concentrations of l. monocytogenes were determined using a most-probable-number (mpn) enrichment procedure. two floor drains had persistent low concentrations of l. monocytogenes (0.03 to >1,100 mpn/cm2). in comparison, concentrations of the other organisms in the drain were much higher (heterotrophic plate coun ...	2006	16541676
using size exclusion chromatography-rplc and rplc-cief as two-dimensional separation strategies for protein profiling.	bottom-up proteomics (analyzing peptides that result from protein digestion) has demonstrated capability for broad proteome coverage and good throughput. however, due to incomplete sequence coverage, this approach is not ideally suited to the study of modified proteins. the modification complement of a protein can best be elucidated by analyzing the intact protein. 2-de, typically coupled with the analysis of peptides that result from in-gel digestion, is the most frequently applied protein sepa ...	2006	16732621
[phylogenetic diversity and cold-adaptive hydrolytic enzymes of culturable psychrophilic bacteria associated with sea ice from high latitude ocean, artic].	the phylogenetic diversity of culturable psychrophilic bacteria associated with sea ice from high latitude sea (77 degrees 30'n - 81 degrees 12'n), canadian basin and greenland sea arctic, was investigated. a total of 37 psychrophilic strains were isolated using three different methods of ( i ) spread plate method: 100 microl of each dilution ice-melt sample was spreaded onto the surface of marine 2216 agar (difco laboratories, detroit, mi) and incubated for 2 to 6 weeks at 4 degrees c; ( ii ) b ...	2006	16736573
larval settlement of the common australian sea urchin heliocidaris erythrogramma in response to bacteria from the surface of coralline algae.	bacterial biofilms are increasingly seen as important for the successful settlement of marine invertebrate larvae. here we tested the effects of biofilms on settlement of the sea urchin heliocidaris erythrogramma. larvae settled on many surfaces including various algal species, rocks, sand and shells. settlement was reduced by autoclaving rocks and algae, and by treatment of algae with antibiotics. these results, and molecular and culture-based analyses, suggested that the bacterial community on ...	2006	16794830
enhancement of polyunsaturated fatty acid production by tn5 transposon in shewanella baltica.	transposon tn5 mutagenesis was used to generate random mutations in shewanella baltica mac1, a polyunsaturated fatty acid (pufa)-producing bacterium. three mutants produced 3-5 times more eicosapentaenoic acid (epa 20:5 n-3) compared to the wild type at 10 degrees c. one of the mutants produced 0.3 mg epa g(-1) when grown at high temperature (30 degrees c). moreover, 2 mg docosahexaenoic acid (dha 22:6 n-3) g(-1) was produced by s. baltica mutants at 4 degrees c. sequencing of insertion mutation ...	2006	16799757
genomic analysis of carbon source metabolism of shewanella oneidensis mr-1: predictions versus experiments.	genomic sequences have been used to find the genetic foundation for carbon source metabolism in shewanella oneidensis mr-1. annotated s. oneidensis mr-1 gene products were examined for their sequence similarity to enzymes participating in pathways for utilization of carbon and energy as described in the biocyc database (http://www.biocyc.org/) or in the primary literature. a picture emerges that relegates five- and six-carbon sugars to minor roles as carbon sources, whereas multiple pathways for ...	2006	16788168
microbial selenate sorption and reduction in nutrient limited systems.	in this study, batch sorption experiments and x-ray adsorption spectroscopy (xas) were utilized to investigate selenate sorption onto shewanella putrefaciens 200r. selenate sorption was studied as a function of ph (ranging from 3 to 7), ionic strength (ranging from 0.1 to 0.001 m), and initial selenate concentration (ranging from 10 to 5000 microm) in the absence of external electron donors. the results show that the extent of selenate sorption is strongly dependent on ph and ionic strength, wit ...	2006	16830542
influence of sediment components on the immobilization of zn during microbial fe-(hydr)oxide reduction.	the fate of zn and other sorbed heavy metals during microbial reduction of iron oxides is different when comparing synthetic fe-(hydr)oxides and natural sediments undergoing a similar degree of iron reduction. batch experiments with the iron-reducing organism shewanella putrefaciens were conducted to examine the effects of an aqueous complexant (nitrilotriacetic acid or nta), two solid-phase complexants (kaolinite and montmorillonite), an electron carrier (anthraquinone disulfonic acid or aqds), ...	2006	16830547
crystallographic studies of the binding of ligands to the dicarboxylate site of complex ii, and the identity of the ligand in the "oxaloacetate-inhibited" state.	mitochondrial complex ii (succinate:ubiquinone oxidoreductase) is purified in a partially inactivated state, which can be activated by removal of tightly bound oxaloacetate (e.b. kearney, et al., biochem. biophys. res. commun. 49 1115-1121). we crystallized complex ii in the presence of oxaloacetate or with the endogenous inhibitor bound. the structure showed a ligand essentially identical to the "malate-like intermediate" found in shewanella flavocytochrome c crystallized with fumarate (p. tayl ...	2006	16935256
shewanella surugensis sp. nov., shewanella kaireitica sp. nov. and shewanella abyssi sp. nov., isolated from deep-sea sediments of suruga bay, japan.	six strains representing three novel species were isolated from deep-sea sediment in suruga bay, japan, at a depth of 2406-2409 m. on the basis of 16s rrna gene sequence analysis, the isolated strains, c931(t), c941(t), d943, c952, d954 and c959(t), are closely affiliated with members of the genus shewanella. the hybridization values for dna-dna relatedness between these strains and shewanella reference strains were significantly lower than that which is accepted as the phylogenetic definition o ...	2006	16825637
biogenic amine formation and microbial spoilage in chilled garfish (belone belone belone)--effect of modified atmosphere packaging and previous frozen storage.	to evaluate biogenic amine formation and microbial spoilage in fresh and thawed chilled garfish.	2006	16834594
spatiometabolic stratification of shewanella oneidensis biofilms.	biofilms, or surface-attached microbial communities, are both ubiquitous and resilient in the environment. although much is known about how biofilms form, develop, and detach, very little is understood about how these events are related to metabolism and its dynamics. it is commonly thought that large subpopulations of cells within biofilms are not actively producing proteins or generating energy and are therefore dead. an alternative hypothesis is that within the growth-inactive domains of biof ...	2006	16936048
toward a more robust assessment of intraspecies diversity, using fewer genetic markers.	phylogenetic sequence analysis of single or multiple genes has dominated the study and census of the genetic diversity among closely related bacteria. it remains unclear, however, how the results based on a few genes in the genome correlate with whole-genome-based relatedness and what genes (if any) best reflect whole-genome-level relatedness and hence should be preferentially used to economize on cost and to improve accuracy. we show here that phylogenies of closely related organisms based on t ...	2006	16980418
atr-ftir spectroscopy reveals bond formation during bacterial adhesion to iron oxide.	the contribution of various bacterial surface functional groups to adhesion at hematite and znse surfaces was examined using attenuated total reflectance (atr) fourier transform infrared (ftir) spectroscopy. when live shewanella oneidensis, pseudomonas aeruginosa, and bacillus subtilis cells were introduced to a horizontal hematite (alpha-fe(2)o(3))-coated internal reflection element (ire), ftir peaks emerged corresponding to bacterial phosphate group binding. these ir peaks were not observed wh ...	2006	16981768
electronic coupling between heme electron-transfer centers and its decay with distance depends strongly on relative orientation.	a method for calculating the electron-transfer matrix element v(rp) using density functional theory kohn-sham orbitals is presented and applied to heme dimers of varying relative orientation. the electronic coupling decays with increased iron separation according to v(rp) = v(0)(rp)exp(-beta r/2) with a distance dependence parameter beta approximately 2 a(-1) for hemes with parallel porphyrins and either 1.1 or 4.0 a(-1) when the porphyrin planes are perpendicular, depending on the alignment of ...	2006	16884282
biological control of the size and reactivity of catalytic pd(0) produced by shewanella oneidensis.	the interaction between shewanella oneidensis mr-1 and the soluble metal pd(ii) during the reductive precipitation of pd(0) determined the size and properties of the precipitated pd(0) nanoparticles. assessment of cell viability indicated that the bioreduction of pd(ii) was a detoxification mechanism depending on the pd(ii) concentration and on the presence and properties of the electron donor. the addition of h(2) in the headspace allowed s. oneidensis to resist the toxic effects of pd(ii). int ...	2006	17033880
mercury methylation by dissimilatory iron-reducing bacteria.	the hg-methylating ability of dissimilatory iron-reducing bacteria in the genera geobacter, desulfuromonas, and shewanella was examined. all of the geobacter and desulfuromonas strains tested methylated mercury while reducing fe(iii), nitrate, or fumarate. in contrast, none of the shewanella strains produced methylmercury at higher levels than abiotic controls under similar culture conditions. geobacter and desulfuromonas are closely related to known hg-methylating sulfate-reducing bacteria with ...	2006	17056699
[the effects of the humic substances on azoreduction by shewanella spp].	under anaerobic conditions, shewanella cinicad14(t), shewanella baltica and shewane-lla putrefaciens are capable of high-rate azoreduction and humus reduction. the results indicated that at low concentration ( <2 mmol/l) aqs was a accelerator for bacterial azoreduction. however, when the concentration of aqs was more than 5 mmol/l a strong inhibition was occurred. on the other hand, the concentration of aqds as high as 12 mmol/l the inhibition of azoreduction was still not exhibited, but the eff ...	2006	17037061
simultaneous microbial reduction of iron(iii) and arsenic(v) in suspensions of hydrous ferric oxide.	bacterial reduction of arsenic(v) and iron(iii) oxides influences the redox cycling and partitioning of arsenic (as) between solid and aqueous phases in sediment-porewater systems. two types of anaerobic bacterial incubations were designed to probe the relative order of as(v) and fe(iii) oxide reduction and to measure the effect of adsorbed as species on the rate of iron reduction, using hydrous ferric oxide (hfo) as the iron substrate. in one set of experiments, hfo was pre-equilibrated with as ...	2006	17051784
high-affinity binding and direct electron transfer to solid metals by the shewanella oneidensis mr-1 outer membrane c-type cytochrome omca.	the purified outer membrane bacterial protein omca binds densely to the surface of hematite (fe2o3), permitting direct electron transfer to this solid mineral to reduce fe (iii) with an electron flux of about 1013 electrons /cm2/s. in the presence of hematite, there is a substantial increase in the amplitude of internal protein motions that correlate with metal reduction. binding is highly favorable, with a partition coefficient of approximately 2 x 105 (deltago' = -28 kj/mol), where approximate ...	2006	17061851
the bacterial species definition in the genomic era.	the bacterial species definition, despite its eminent practical significance for identification, diagnosis, quarantine and diversity surveys, remains a very difficult issue to advance. genomics now offers novel insights into intra-species diversity and the potential for emergence of a more soundly based system. although we share the excitement, we argue that it is premature for a universal change to the definition because current knowledge is based on too few phylogenetic groups and too few samp ...	2006	17062412
a novel ice in the genome of shewanella putrefaciens w3-18-1: comparison with the sxt/r391 ice-like elements.	a novel r391-like ice (integrating conjugative element) has been detected in the 4.2 mb genome of shewanella putrefaciens w3-18-1 located on three different contigs. assembly of the ice encoding contigs based on similarity with r391 revealed a mosaic element of plasmid, phage and transposon-like sequences typical of sxt/r391 ice-like elements. the element, which is 110 057 bp in length, was highly similar to r391 sequences, with most related orfs showing >96% amino acid sequence identity. the el ...	2006	17020552
biological reduction of nanoengineered iron(iii) oxide sculptured thin films.	sculptured thin films (stfs) are assemblies of nominally identical, parallel nanowires with tailored shapes such as chevrons and spirals. a series of iron(lll) stfs were produced with varied crystallinity (from hematite toferrihydrite) and nanowire shapes (slanted columnar, clockwise helical, and counterclockwise helical). when the dissimilatory metal-reducing bacterium shewanella putrefaciens cn32 was used to measure their bioreducibility, it was found that bioreduction was controlled primarily ...	2006	16999129
reactive azo dye reduction by shewanella strain j18 143.	a bacterial isolate designated strain j18 143, originally isolated from soil contaminated with textile wastewater, was shown to reduce intensely coloured solutions of the reactive azo dye, remazol black b to colourless solutions. phylogenetic placement based on 16s rrna gene sequence homology identified the bacterium as a shewanella species. based on results from analyses of the end products of dye decoloration of remazol black b and the simpler molecule, acid orange 7, using capillary electroph ...	2006	16804943
global molecular and morphological effects of 24-hour chromium(vi) exposure on shewanella oneidensis mr-1.	the biological impact of 24-h ("chronic") chromium(vi) [cr(vi) or chromate] exposure on shewanella oneidensis mr-1 was assessed by analyzing cellular morphology as well as genome-wide differential gene and protein expression profiles. cells challenged aerobically with an initial chromate concentration of 0.3 mm in complex growth medium were compared to untreated control cells grown in the absence of chromate. at the 24-h time point at which cells were harvested for transcriptome and proteome ana ...	2006	16957260
comparative genomics and experimental characterization of n-acetylglucosamine utilization pathway of shewanella oneidensis.	we used a comparative genomics approach implemented in the seed annotation environment to reconstruct the chitin and glcnac utilization subsystem and regulatory network in most proteobacteria, including 11 species of shewanella with completely sequenced genomes. comparative analysis of candidate regulatory sites allowed us to characterize three different glcnac-specific regulons, nagc, nagr, and nagq, in various proteobacteria and to tentatively assign a number of novel genes with specific funct ...	2006	16857666
physiological changes induced in four bacterial strains following oxidative stress.	in order to study the behaviour and resistance of bacteria under extreme conditions, physiological changes associated with oxidative stress were monitored using flow cytometry. the study was conducted to assess the maintenance of membrane integrity and potential as well as the esterase activity, the intracellular ph and the production of superoxide anions in four bacterial strains (ralstonia metallidurans, escherichia coli, shewanella oneidensis and deinococcus radiodurans). the strains were cho ...	2006	17022450
electrically conductive bacterial nanowires produced by shewanella oneidensis strain mr-1 and other microorganisms.	shewanella oneidensis mr-1 produced electrically conductive pilus-like appendages called bacterial nanowires in direct response to electron-acceptor limitation. mutants deficient in genes for c-type decaheme cytochromes mtrc and omca, and those that lacked a functional type ii secretion pathway displayed nanowires that were poorly conductive. these mutants were also deficient in their ability to reduce hydrous ferric oxide and in their ability to generate current in a microbial fuel cell. nanowi ...	2006	16849424
ligand-induced conformational changes in the capping subdomain of a bacterial old yellow enzyme homologue and conserved sequence fingerprints provide new insights into substrate binding.	we have recently reported that shewanella oneidensis, a gram-negative gamma-proteobacterium with a rich arsenal of redox proteins, possesses four old yellow enzyme (oye) homologues. here, we report a series of high resolution crystal structures for one of these oyes, shewanella yellow enzyme 1 (sye1), in its oxidized form at 1.4a resolution, which binds a molecule of peg 400 in the active site, and in its nadh-reduced and p-hydroxybenzaldehyde- and p-hydroxyacetophenone-bound forms at 1.7a resol ...	2006	16857682
a phosphopantetheinyl transferase gene essential for biosynthesis of n-3 polyunsaturated fatty acids from moritella marina strain mp-1.	a phosphopantetheinyl transferase (pptase) gene (pfae), cloned from the docosahexaenoic acid (dha)-producing bacterium moritella marina strain mp-1, has an open reading frame of 861 bp encoding a 287-amino acid protein. when the pfae gene was expressed with pfaa-d, which are four out of five essential genes for biosynthesis of eicosapentaenoic acid (epa) derived from shewanella pneumatophori scrc-2738 in escherichia coli, the recombinant produced 12% epa of total fatty acids. this suggests that ...	2006	16859689
mediating electron transfer from bacteria to a gold electrode via a self-assembled monolayer.	numerous bacterial genera are known to respire anaerobically using macroscopic electrodes as electron acceptors. typically, inexpensive graphite electrodes, which are readily colonized, are used to monitor electrogenic bacterial metabolism for microbial fuel cell and bioelectronics studies. we compare current production by electrogenic bacteria on gold electrodes coated with various alkanethiol self-assembled monolayers to current production on glassy carbon electrodes. current production is cor ...	2006	17073464
influence of storage temperature on microbial spoilage characteristics of haddock fillets (melanogrammus aeglefinus) evaluated by multivariate quality prediction.	the proliferation of specific spoilage organisms (sso) and quality changes were evaluated in haddock fillets stored in styrofoam boxes at 0, 7 and 15 degrees c and under temperature fluctuations. a rapid electronic nose technique was used to monitor different classes of compounds, representing microbial metabolites that were characteristic for the onset of spoilage odors. photobacterium phosphoreum predominated among the spoilage bacteria and high levels of tvb-n were observed at sensory rejecti ...	2006	16889858
shewanella loihica sp. nov., isolated from iron-rich microbial mats in the pacific ocean.	a novel marine bacterial strain, pv-4(t), isolated from a microbial mat located at a hydrothermal vent of loihi seamount in the pacific ocean, has been characterized. this micro-organism is orangey in colour, gram-negative, polarly flagellated, facultatively anaerobic and psychrotolerant (temperature range, 0-42 degrees c). no growth was observed with nitrate, nitrite, dmso or thiosulfate as the electron acceptor and lactate as the electron donor. the major fatty acid detected in strain pv-4(t) ...	2006	16902030
nhad type sodium/proton-antiporter of halomonas elongata: a salt stress response mechanism in marine habitats?	sodium/proton-antiporters (nha) are known to play an important role in ph- and na+-homeostasis. in microorganisms several types with different capacity, affinity and selectivity for na+ and li+ exist. the homeostasis system of e. coli, nhaa and nhab, is well researched, but the function of other types of na+/h+-antiporters like nhad is yet to be fully understood. since several antiporters play an important role at various points in the physiology of higher organisms, one can speculate that the m ...	2006	16872527
isolation and identification of shewanella alga and its pathogenic effects on post-larvae of abalone haliotis diversicolor supertexta.		2006	16911538
ultra-sensitive and quantitative characterization of proteomes.	electrospray ionization mass spectrometry combined with high efficiency capillary liquid chromatography provides high sensitivity and broad dynamic range measurements for the characterization of biological macromolecules in complex matrices, and is an increasingly powerful analytical tool for systems biology research.	2006	16880940
tale of two metal reducers: comparative proteome analysis of geobacter sulferreducens pca and shewanella oneidensis mr-1.	geobacter sulfurreducens and s. oneidensis are the subjects of intense research efforts due to their potential applications to bioremediation. the characterization of their proteomes, being done in parallel with the analysis of their genome sequences, transcriptomes, and metabolomes, is providing valuable insights to both their similarities and their differences. a primary target of interest in the proteomes of both of these metal-reducing microbes is the characterization of their c-type cytochr ...	2006	16929676
amt tag approach to proteomic characterization of deinococcus radiodurans and shewanella oneidensis.		2006	16929677
graphical estimation of the dual-enzyme kinetic parameters for cr(vi) reduction.	chromium(vi) (cr(vi)) contamination of soil and groundwater is a major environmental concern. bioreduction of cr(vi) by shewanella oneidensis mr-1 (mr-1) can be considered a feasible option to reduce the toxic and mobile cr(vi) to the less toxic and less mobile chromium(iii) (cr(iii)). the reaction rate expression for cr(vi) reduction is nonlinear and the rate constants are evaluated by employing nonlinear optimization techniques. the outcome of the optimization techniques, in general, depends o ...	2006	16140357
differential label-free quantitative proteomic analysis of shewanella oneidensis cultured under aerobic and suboxic conditions by accurate mass and time tag approach.	we describe the application of lc-ms without the use of stable isotope labeling for differential quantitative proteomic analysis of whole cell lysates of shewanella oneidensis mr-1 cultured under aerobic and suboxic conditions. lc-ms/ms was used to initially identify peptide sequences, and lc-fticr was used to confirm these identifications as well as measure relative peptide abundances. 2343 peptides covering 668 proteins were identified with high confidence and quantified. among these proteins, ...	2006	16401633
transcriptome profiling of shewanella oneidensis gene expression following exposure to acidic and alkaline ph.	the molecular response of shewanella oneidensis mr-1 to variations in extracellular ph was investigated based on genomewide gene expression profiling. microarray analysis revealed that cells elicited both general and specific transcriptome responses when challenged with environmental acid (ph 4) or base (ph 10) conditions over a 60-min period. global responses included the differential expression of genes functionally linked to amino acid metabolism, transcriptional regulation and signal transdu ...	2006	16452448
shewanella halifaxensis sp. nov., a novel obligately respiratory and denitrifying psychrophile.	indigenous bacteria found in the sediment of the emerald basin (depth of 215 m, atlantic ocean) located offshore of halifax harbour (nova scotia, canada) were previously found to be able to degrade the explosive compound hexahydro-1,3,5-trinitro-1,3,5-triazine (rdx). in the present study, a novel obligately respiratory, denitrifying and rdx-mineralizing bacterium, designated strain haw-eb4(t), was isolated from the marine sediment. this bacterium utilized peptone, yeast extract, casamino acids, ...	2006	16403888
design of shewanella-specific 16s rrna primers and application to analysis of shewanella in a minerotrophic wetland.	in this study, an existing probe was used as a polymerase chain reaction (pcr) primer to study iron-reducing members of the genus shewanella in a minerotrophic wetland where iron reduction had previously been implicated. the probe was found to be non-specific and a new set of pcr primers were developed that were specific for shewanella. these primers were used to analyse the wetland iron-reducing communities by characterizing 16s rrna genes amplified from dna extracted from peat. polymerase chai ...	2006	16478449
beta-propeller phytases in the aquatic environment.	phytate, which is one of the dominant organic phosphorus compounds in nature, is very stable in soils. although a substantial amount of phytate is carried from terrestrial to aquatic systems, it is a minor component of organic phosphorus in coastal sediments. the ephemeral nature of phytate implies the rapid hydrolysis of phytate under aquatic conditions. among the four classes of known phytases that have been identified in terrestrial organisms, only beta-propeller phytase-like sequences have b ...	2006	16402222
shewanella hafniensis sp. nov. and shewanella morhuae sp. nov., isolated from marine fish of the baltic sea.	two novel species belonging to the genus shewanella are described on the basis of their phenotypic characteristics, phylogenetic analyses of 16s rrna and gyrb gene sequences and levels of dna-dna hybridization. a total of 47 strains belonging to two novel gram-negative, psychrotolerant, h2s-producing bacterial species were isolated from marine fish (cod and flounder) caught from the baltic sea off denmark. the phenotypic characteristics of strains belonging to group 1 (14 strains) indicated that ...	2006	16403893
automated purification of recombinant proteins: combining high-throughput with high yield.	protein crystallography, mapping protein interactions, and other functional genomic approaches require purifying many different proteins, each of sufficient yield and homogeneity, for subsequent high-throughput applications. to fill this requirement efficiently, there is a need to develop robust, automated, high-throughput protein expression, and purification processes. we developed and compared two alternative workflows for automated purification of recombinant proteins based on expression of b ...	2006	16406573
probing surface structures of shewanella spp. by microelectrophoresis.	long-range electrostatic forces substantially influence bacterial interactions and bacterial adhesion during the preliminary steps of biofilm formation. the strength of these forces depends strongly on the structure of the bacterium surfaces investigated. the latter may be addressed from appropriate analysis of electrophoretic mobility measurements. due to the permeable character of the bacterium wall and/or surrounding polymer layer, bacteria may be regarded as paradigms of soft bioparticles. t ...	2006	16415062
confirmation of the expression of a large set of conserved hypothetical proteins in shewanella oneidensis mr-1.	high-throughput "omic" technologies have allowed for a relatively rapid, yet comprehensive analysis of the global expression patterns within an organism in response to perturbations. in the current study, 9503 different tryptic peptides were identified with high confidence from capillary liquid chromatography-mass spectrometry analysis of 26 chemostat cultures of shewanella oneidensis mr-1 under various conditions. using at least one distinctive and a total of two total peptide identifications p ...	2006	16417935
genomic comparisons among gamma-proteobacteria.	predicted highly expressed (phx) genes are compared for 16 gamma-proteobacteria and their similarities and differences are interpreted with respect to known or predicted physiological characteristics of the organisms. predicted highly expressed genes often reflect the organism's predominant lifestyle, habitat, nutrition sources and metabolic propensities. this technique allows to predict principal metabolic activities of the microorganisms operating in their natural habitats. among our findings ...	2006	16423015
reduction of prussian blue by the two iron-reducing microorganisms geobacter metallireducens and shewanella alga.	cyanide or cyanide-metal complexes are frequent contaminants of soil or aquifers at industrial sites, which can be released from such sites by outgassing or transport with the groundwater. they form very stable complexes with iron, which may occur in the subsurface as an insoluble blue mineral, the so-called prussian blue (fe(4)[fe(cn)(6)](3)). in this study, we show that the insoluble and colloidal fe(iii)-cyanide complex prussian blue can be reduced and utilized as electron acceptor by the dis ...	2006	16423022
transcriptome analysis applied to survival of shewanella oneidensis mr-1 exposed to ionizing radiation.	the ionizing radiation (ir) dose that yields 20% survival (d20) of shewanella oneidensis mr-1 is lower by factors of 20 and 200 than those for escherichia coli and deinococcus radiodurans, respectively. transcriptome analysis was used to identify the genes of mr-1 responding to 40 gy (d20). we observed the induction of 170 genes and repression of 87 genes in mr-1 during a 1-h recovery period after irradiation. the genomic response of mr-1 to ir is very similar to its response to uv radiation (25 ...	2006	16428429
cellular response of shewanella oneidensis to strontium stress.	the physiology and transcriptome dynamics of the metal ion-reducing bacterium shewanella oneidensis strain mr-1 in response to nonradioactive strontium (sr) exposure were investigated. studies indicated that mr-1 was able to grow aerobically in complex medium in the presence of 180 mm srcl2 but showed severe growth inhibition at levels above that concentration. temporal gene expression profiles were generated from aerobically grown, mid-exponential-phase mr-1 cells shocked with 180 mm srcl2 and ...	2006	16391131
fumarate reductase: structural and mechanistic insights from the catalytic reduction of 2-methylfumarate.	the soluble fumarate reductase (fr) from shewanella frigidimarina can catalyse the reduction of 2-methylfumarate with a k(cat) of 9.0 s(-1) and a k(m) of 32 microm. this produces the chiral molecule 2-methylsuccinate. here, we present the structure of fr to a resolution of 1.5 a with 2-methylfumarate bound at the active site. the mode of binding of 2-methylfumarate allows us to predict the stereochemistry of the product as (s)-2-methylsuccinate. to test this prediction we have analysed the produ ...	2006	16497301
control of formation and cellular detachment from shewanella oneidensis mr-1 biofilms by cyclic di-gmp.	stability and resilience against environmental perturbations are critical properties of medical and environmental biofilms and pose important targets for their control. biofilm stability is determined by two mutually exclusive processes: attachment of cells to and detachment from the biofilm matrix. using shewanella oneidensis mr-1, an environmentally versatile, fe(iii) and mn(iv) mineral-reducing microorganism, we identified mxdabcd as a new set of genes essential for formation of a three-dimen ...	2006	16547056
rapid identification of marine bioluminescent bacteria by amplified 16s ribosomal rna gene restriction analysis.	to rapidly identify natural isolates of marine bioluminescent bacteria, we developed amplified ribosomal dna restriction analysis (ardra) methods. ardra, which is based on the restriction patterns of 16s rrna gene digested with five enzymes (ecori, ddei, hhai, hinfi, rsai), clearly distinguished the 14 species of marine bioluminescent bacteria currently known, which belong to the genera vibrio, photobacterium, and shewanella. when we applied ardra to 129 natural isolates from two cruises in saga ...	2006	16499620
effect of heat-inactivated fish and non-fish derived probiotics on the innate immune parameters of a teleost fish (sparus aurata l.).	the in vitro effects of four heat-inactivated bacterial species on the cellular innate immune responses of the gilthead seabream (sparus aurata l.) were investigated. head-kidney leucocytes were isolated and incubated for 30 min with two bacteria isolated from seabream skin (pdp11 and 51m6; members of the vibrionaceae and in the genus shewanella) and two bacteria used as probiotics in humans and cattle (lactobacillus delbrüeckii subsp. lactis and bacillus subtilis) at 5 x 10(5), 5 x 10(6) or 5 x ...	2006	16516307
identification of genes regulated by changing salinity in the deep-sea bacterium shewanella sp. wp3 using rna arbitrarily primed pcr.	the differential gene transcription of a deep-sea bacterium shewanella sp. wp3 in response to changing salinity was analyzed by rna fingerprinting using arbitrarily primed pcr (rap-pcr). ninety primer sets were used to scan two different rna pools derived from cultures of 1% and 7% nacl concentrations. forty-three putative differential-expressed fragments were identified, cloned, and sequenced. six out of the 43 fragments were confirmed to be truly differentially transcribed in terms of changing ...	2006	16133656
decolorization of anthraquinone dye by shewanella decolorationis s12.	a new species of genus shewanella, shewanella decolorationis s12, from activated sludge of a textile-printing wastewater treatment plant, can decolorize reactive brilliant blue k-gr, one kind of anthraquinone dye, with flocculation first. although s. decolorationis displayed good growth in an aerobic condition, color removal was the best in an anaerobic condition. for color removal, the most suitable ph values and temperatures were ph 6.0-8.0 and 30-37 degrees c under anaerobic culture. more tha ...	2006	16160829
treatment failure due to emergence of resistance to carbapenem during therapy for shewanella algae bacteremia.	we describe a case of bacteremia due to imipenem-susceptible shewanella algae. despite treatment with imipenem, the patient developed a spinal epidural abscess, from which imipenem-resistant s. algae was isolated. the development of resistance should be monitored when s. algae infection is treated with imipenem, even though the strain is initially susceptible to imipenem.	2006	16517923
agga is required for aggregation and increased biofilm formation of a hyper-aggregating mutant of shewanella oneidensis mr-1.	shewanella oneidensis coag, a hyper-aggregating mutant of mr-1, was isolated from a rifampicin-challenged culture. compared to the wild-type, coag exhibited increased biofilm formation on glass carrier material. the role of surface-located proteins in the process of coag auto-aggregation was confirmed by different proteolytic treatments of the aggregates. all of the tested proteolytic enzymes resulted in deflocculation within 3 h of incubation. in order to examine the altered expression of outer ...	2006	16514152
comparative characterization and expression analysis of the four old yellow enzyme homologues from shewanella oneidensis indicate differences in physiological function.	shewanella oneidensis contains four genes that encode proteins that have high sequence identity with yeast oye (old yellow enzyme, an nadph oxidoreductase), the well-studied archetype of the oye protein family. the present paper describes the first comparative study of oyes that are present in a single bacterial species, performed to gain insight into their biochemical properties and physiological importance. the four proteins [named sye1-sye4 (shewanella yellow enzyme 1-4)] were expressed as gl ...	2006	16293111
genes that enhance the ecological fitness of shewanella oneidensis mr-1 in sediments reveal the value of antibiotic resistance.	environmental bacteria persist in various habitats, yet little is known about the genes that contribute to growth and survival in their respective ecological niches. signature-tagged mutagenesis (stm) of shewanella oneidensis mr-1 coupled with a screen involving incubations of mutant strains in anoxic aquifer sediments allowed us to identify 47 genes that enhance fitness in sediments. gene functions inferred from annotations provide us with insight into physiological and ecological processes tha ...	2007	17114320
a kinetic model describing shewanella oneidensis mr-1 growth, substrate consumption, and product secretion.	aerobic growth of shewanella oneidensis mr-1 in minimal lactate medium was studied in batch cultivation. acetate production was observed in the middle of the exponential growth phase and was enhanced when the dissolved oxygen (do) concentration was low. once the lactate was nearly exhausted, s. oneidensis mr-1 used the acetate produced during growth on lactate with a similar biomass yield as lactate. a two-substrate monod model, with competitive and uncompetitive substrate inhibition, was devise ...	2007	16865732
respiratory nitrate ammonification by shewanella oneidensis mr-1.	anaerobic cultures of shewanella oneidensis mr-1 grown with nitrate as the sole electron acceptor exhibited sequential reduction of nitrate to nitrite and then to ammonium. little dinitrogen and nitrous oxide were detected, and no growth occurred on nitrous oxide. a mutant with the napa gene encoding periplasmic nitrate reductase deleted could not respire or assimilate nitrate and did not express nitrate reductase activity, confirming that the napa enzyme is the sole nitrate reductase. hence, s. ...	2007	17098906
microarray-based analysis of microbial community rnas by whole-community rna amplification.	a new approach, termed whole-community rna amplification (wcra), was developed to provide sufficient amounts of mrnas from environmental samples for microarray analysis. this method employs fusion primers (six to nine random nucleotides with an attached t7 promoter) for the first-strand synthesis. the shortest primer (t7n6s) gave the best results in terms of the yield and representativeness of amplification. about 1,200- to 1,800-fold amplification was obtained with amounts of the rna templates ...	2007	17098911
respiration and growth of shewanella decolorationis s12 with an azo compound as the sole electron acceptor.	the ability of shewanella decolorationis s12 to obtain energy for growth by coupling the oxidation of various electron donors to dissimilatory azoreduction was investigated. this microorganism can reduce a variety of azo dyes by use of formate, lactate, pyruvate, or h(2) as the electron donor. furthermore, strain s12 grew to a maximal density of 3.0 x 10(7) cells per ml after compete reduction of 2.0 mm amaranth in a defined medium. this was accompanied by a stoichiometric consumption of 4.0 mm ...	2007	17085710
process of maturation of tetraheme cytochrome c3 in a shewanella expression system.	the process of maturation of multiheme proteins is not yet well known, while that of monoheme ones has been relatively well investigated. two kinds of partly unfolded tetraheme cytochrome c3 were obtained on overexpression in shewanella oneidensis tsp-c. these proteins were characterized by circular dichroism and nuclear magnetic resonance spectroscopy. it turned out that the tetraheme architecture, and the fifth and sixth ligand coordination are almost mature, while some parts of the polypeptid ...	2007	17167041
lateral transfer of the lux gene cluster.	the lux operon is an uncommon gene cluster. to find the pathway through which the operon has been transferred, we sequenced the operon and both flanking regions in four typical luminous species. in vibrio cholerae ncimb 41, a five-gene cluster, most genes of which were highly similar to orthologues present in gram-positive bacteria, along with the lux operon, is inserted between vc1560 and vc1563, on chromosome 1. because this entire five-gene cluster is present in photorhabdus luminescens tt01, ...	2007	17169972
culturable and vbnc vibrio cholerae: interactions with chironomid egg masses and their bacterial population.	vibrio cholerae, the etiologic agent of cholera, is autochthonous to various aquatic environments. recently, it was found that chironomid (nonbiting midges) egg masses serve as a reservoir for the cholera bacterium and that flying chironomid adults are possible windborne carriers of v. cholerae non-o1 non-o139. chironomids are the most widely distributed insect in freshwater. females deposit egg masses at the water's edge, and each egg mass contains eggs embedded in a gelatinous matrix. hemagglu ...	2007	17186156
effects of electron donors and acceptors on anaerobic reduction of azo dyes by shewanella decolorationis s12.	shewanella decolorationis s12 was able to reduce various azo dyes in a defined medium with formate, lactate, and pyruvate or h(2) as electron donors under anaerobic conditions. purified membranous, periplasmic, and cytoplasmic fractions from strain s12 analyzed, respectively, only membranous fraction was capable of reducing azo dye in the presence of electron donor, indicating that the enzyme system for anaerobic azoreduction was located on cellular membrane. respiratory inhibitor cu(2+), dicuma ...	2007	17043816
hydrogen metabolism in shewanella oneidensis mr-1.	shewanella oneidensis mr-1 is a facultative sediment microorganism which uses diverse compounds, such as oxygen and fumarate, as well as insoluble fe(iii) and mn(iv) as electron acceptors. the electron donor spectrum is more limited and includes metabolic end products of primary fermenting bacteria, such as lactate, formate, and hydrogen. while the utilization of hydrogen as an electron donor has been described previously, we report here the formation of hydrogen from pyruvate under anaerobic, s ...	2007	17189435
predicting gene expression level from codon usage bias.	the "expression measure" of a gene, e(g), is a statistic devised to predict the level of gene expression from codon usage bias. e(g) has been used extensively to analyze prokaryotic genome sequences. we discuss 2 problems with this approach. first, the formulation of e(g) is such that genes with the strongest selected codon usage bias are not likely to have the highest predicted expression levels; indeed the correlation between e(g) and expression level is weak among moderate to highly expressed ...	2007	17038449
a conserved histidine in cytochrome c maturation permease ccmb of shewanella putrefaciens is required for anaerobic growth below a threshold standard redox potential.	shewanella putrefaciens strain 200 respires a wide range of compounds as terminal electron acceptor. the respiratory versatility of shewanella is attributed in part to a set of c-type cytochromes with widely varying midpoint redox potentials (e'(0)). a point mutant of s. putrefaciens, originally designated urr14 and here renamed ccmb1, was found to grow at wild-type rates on electron acceptors with high e'0 [o2, no3-, fe(iii) citrate, mno2, and mn(iii) pyrophosphate] yet was severely impaired fo ...	2007	17142390
biocatalytic dechlorination of lindane by nano-scale particles of pd(0) deposited on shewanella oneidensis.	a new approach for the removal of the pesticide lindane (gamma-hexachlorocyclohexane or gamma-hch) makes use of catalytic reduction of hch to benzene over a metal catalyst, namely pd(0). since specific surface area plays an important role in reactivity of catalysts, this study investigated the use of biopd(0), i.e. nano-scale pd(0) particles precipitated on the biomass of shewanella oneidensis, for the removal of lindane. it was demonstrated that biopd(0) has catalytic activity towards dechlorin ...	2007	16797673
optimization of the biological component of a bioelectrochemical cell.	the efficiency of electron transduction by shewanella oneidensis mr-1 was investigated both in batch culture and in a dual-chambered electrochemical cell. aerobically grown bacteria were inoculated into an insoluble feooh suspension in an anaerobic environment. as the bacteria reduced fe(iii) to fe(ii) there was a visible color change from red to bluish black; this simple color change assay proved to be a robust method for determining the electrochemical activity of s. oneidensis mr-1. in an eff ...	2007	16713750
evaluation of pyrrolidonyl arylamidase for the identification of nonfermenting gram-negative rods.	to evaluate the activity of pyrrolidonyl arylamidase (pyr) for the differentiation and identification of nonfermenting gram negative rods (nfgnr), 293 isolates were tested. a 24 h culture of each test organism was prepared. from this a 108-109 cfu/ml suspension was added to 0.25 ml of sterile physiologic solution. a pyr disk was then added and the test was incubated for 30 minutes at 35-37 degrees c, at environmental atmosphere. reading was done by adding 1 drop of cinnamaldehyde reagent. strain ...	2007	16822636
toxicity of cr(lll) to shewanella sp. strain mr-4 during cr(vi) reduction.	bioremediation of chromium through the reduction of hexavalent chromium (as the chromate ion, cro42-) is based on the notion that the product, trivalent chromium (cr(iii)), is less toxic than chromate. in this study, we show that soluble cr(iii), present at ph 6-8 as the cr3+ ion and/or hydroxyl complexes (henceforth referred to as uncomplexed cr(iii)), can be found transiently in significant concentrations and has a deleterious effect on shewanella sp. mr-4. however, cr(lll) complexed to an org ...	2007	17265950
microspe-nanolc-esi-ms/ms using 10-microm-i.d. silica-based monolithic columns for proteomics.	silica-based monolithic capillary columns (25 cm x 10 microm i.d.) with integrated nanoesi emitters have been developed to provide high-quality and robust microspe-nanolc-esi-ms analyses. the integrated nanoesi emitter adds no dead volume to the lc separation, allowing stable electrospray operation at flow rates of approximately 10 nl/min. in an initial application with a linear ion trap ms, we identified 5510 unique peptides that covered 1443 distinct shewanella oneidensis proteins from a 300-n ...	2007	17222018
reduction and partial degradation mechanisms of naphthylaminesulfonic azo dye amaranth by shewanella decolorationis s12.	reduction and biodegradation mechanisms of naphthylaminesulfonic azo dye amaranth using a newly isolated shewanella decolorationis strain s12 were investigated. under anaerobic conditions, amaranth was reduced by strain s12, and a stoichiometric amount of two reduction products rp-1 and rp-2 were generated. uv/visible spectrophotometric and high performance liquid chromatography (hplc) analysis indicated that rp-1 and rp-2 were 1-aminenaphthylene -4-sulfonic acid and 1-aminenaphthylene-2-hydroxy ...	2007	17260140
shewanella spp. infection following treatment for upper gastrointestinal bleeding.	shewanella spp. are an uncommon cause of human infection, with exposure to water being the commonest source. we report a patient with a malignancy and upper gastrointestinal bleeding who underwent a gastric lavage followed by an endoscopy as part of her investigations. she subsequently developed shewanella spp. bacteraemia without any clinical source of infection.	2007	17454904
quantifying constraints imposed by calcium and iron on bacterial reduction of uranium(vi).	uranium is a redox active contaminant of concern to both human health and ecological preservation. in anaerobic soils and sediments, the more mobile, oxidized form of uranium (uo(2)(2+) and associated species) may be reduced by dissimilatory metal-reducing bacteria. despite rapid reduction in controlled, experimental systems, various factors within soils or sediments may limit biological reduction of u(vi), inclusive of competing electron acceptors and alterations in uranyl speciation. here we e ...	2007	17255623
description of shewanella glacialipiscicola sp. nov. and shewanella algidipiscicola sp. nov., isolated from marine fish of the danish baltic sea, and proposal that shewanella affinis is a later heterotypic synonym of shewanella colwelliana.	two novel species belonging to the genus shewanella are described on the basis of a polyphasic taxonomic approach. a total of 40 strains of gram-negative, psychrotolerant, h2s-producing bacteria were isolated from marine fish (cod and plaice) caught in the baltic sea off denmark. strains belonging to group 1 (seven strains) were a lactate-assimilating variant of shewanella morhuae with a g+c content of 44 mol%. the strains of group 2 (33 strains) utilized lactate, n-acetylglucosamine and malate ...	2007	17267977
proteomic profiling of intact proteins using wax-rplc 2-d separations and fticr mass spectrometry.	we investigated the combination of weak anion exchange (wax) fractionation and on-line reversed-phase liquid chromatography (rplc) separation using a 12 t fticr mass spectrometer for the detection of intact proteins from a shewanella oneidensis mr-1 cell lysate. this work aimed at optimizing intact protein detection for profiling proteins at a level that incorporates their modification state. a total of 715 intact proteins were detected, and the combined results from the wax fractions and the un ...	2007	17269717
metabolic activity and phylogenetic diversity of reed (phragmites australis) periphyton bacterial communities in a hungarian shallow soda lake.	in the present study, the species composition and potential metabolic activities of bacterial communities of reed phragmites australis (cav.) (trin. ex steudel) periphyton from lake velencei were studied by cultivation-based and metabolic fingerprinting methods. serially diluted spring biofilm samples were used to test the community-level physiological profiling (clpp) using biolog microplates, and for plating onto different media. on the basis of their morphological, biochemical, and physiologi ...	2007	17406774
functional roles of the heme architecture and its environment in tetraheme cytochrome c.	cytochromes are involved in a wide variety of redox reactions in living systems. some of them contain multiple hemes such as desulfovibrio cytochrome c3 and shewanella small tetraheme cytochrome c. the significance of c-type tetraheme architectures was discussed. a cyclic heme architecture and its environment regulate the extremely low redox potentials of cytochrome c3 in addition to bis-imidazole coordination and heme exposure. each heme in cytochrome c3 plays a different role in the electron t ...	2007	17370988
the surface physicochemistry and adhesiveness of shewanella are affected by their surface polysaccharides.	shewanella strains have previously been studied with regard to their cell surface ultrastructure and lps composition. they have now been further characterized with respect to their surface physicochemistry and ability to adhere to haematite. the surfaces of the shewanella strains were found to be electronegative and hydrophilic, and these properties could be correlated with lps composition or the presence of capsular polysaccharides. strains expressing rough lps with no capsule were more hydroph ...	2007	17526844
combined spectroscopic and topographic characterization of nanoscale domains and their distributions of a redox protein on bacterial cell surfaces.	redox protein nanoscale domains on the cell surface of a bacterium, shewanella oneidensis mr1, grown in the absence and presence of electron acceptors, is topographically characterized using combined atomic force microscopy (afm) and confocal surface enhanced raman scattering (sers) spectroscopy. the protruding nanoscale domains on the outer membrane of s. oneidensis were observed, as was their disappearance upon exposure to electron acceptors such as oxygen, nitrate, fumarate, and iron nitrilot ...	2007	17241055
dosage-dependent proteome response of shewanella oneidensis mr-1 to acute chromate challenge.	proteome alterations in the metal-reducing bacterium shewanella oneidensis mr-1 in response to different acute dose challenges (0.3, 0.5, or 1 mm) of the toxic metal chromate [cr(vi)] were characterized with multidimensional hplc-ms/ms. proteome measurements were performed and compared on both quadrupole ion traps as well as linear trapping quadrupole mass spectrometers. we have found that the implementation of multidimensional liquid chromatography on-line with the rapid scanning, high throughp ...	2007	17385904
characterisation of the bacterial flora of modified atmosphere packaged farmed atlantic cod (gadus morhua) by pcr-dgge of conserved 16s rrna gene regions.	the present article describes the use of broad-range molecular analyses to characterise the microbial population of farmed atlantic cod (gadus morhua) packaged for the retail market. cod was filleted post rigor, packaged in air or in modified atmosphere (ma) (50% co(2):50% n(2) or 50% co(2):50% o(2)) and stored at 0 degrees c for 11 days. to determine the community profiles of the samples the variable v3-region of the bacterial 16s rrna gene were amplified by pcr, before the pcr products were se ...	2007	17467836
phosphate imposed limitations on biological reduction and alteration of ferrihydrite.	biogeochemical transformation (inclusive of dissolution) of iron (hydr)oxides resulting from dissimilatory reduction has a pronounced impact on the fate and transport of nutrients and contaminants in subsurface environments. despite the reactivity noted for pristine (unreacted) minerals, iron (hydr)oxides within native environments will likely have a different reactivity owing in part to changes in surface composition. accordingly, here we explore the impact of surface modifications induced by p ...	2007	17265943
the three-dimensional crystal structure of the prpf protein of shewanella oneidensis complexed with trans-aconitate: insights into its biological function.	in bacteria, the dehydration of 2-methylcitrate to yield 2-methylaconitate in the 2-methylcitric acid cycle is catalyzed by a cofactor-less (prpd) enzyme or by an aconitase-like (acnd) enzyme. bacteria that use acnd also require the function of the prpf protein, whose function was previously unknown. to gain insights into the function of prpf, the three-dimensional crystal structure of the prpf protein from the bacterium shewanella oneidensis was solved at 2.0 a resolution. the protein fold of p ...	2007	17567742
influence of lipopolysaccharide on the surface proton-binding behavior of shewanella spp.	this study investigates the potentiometric properties of several strains of shewanella spp. and determines whether these properties can be correlated with lipopolysaccharide (lps) type. the lps of eight shewanella strains was characterized using silver-stained sodium dodecyl sulfate-polyacrylamide gel electrophoresis (sds-page) and their potentiometric properties determined using high-resolution acid-base titrations. titrations showed that total ligand concentrations (l(t)) ranged from 0.903 +/- ...	2007	17570012