Publications
| Title | Abstract | Year Filter | PMID(sorted ascending) Filter |
|---|
| characterization of purified c-type heme-containing peptides and identification of c-type heme-attachment sites in shewanella oneidenis cytochromes using mass spectrometry. | we describe methods for mass spectrometric identification of heme-containing peptides from c-type cytochromes that contain the cxxch (x=any amino acid) sequence motif. the heme fragment ion yielded the most abundant ms/ms peak for standard heme-containing peptides with one amino acid difference for both 2+ and 3+ peptide charge states; both sequence and charge affect the extent of heme loss. application to shewanella oneidenis demonstrated the utility of this approach for identifying c-type heme ... | 2005 | 15952731 |
| genome-assisted analysis of dissimilatory metal-reducing bacteria. | the availability of whole genome sequences for shewanella oneidensis and geobacter sulfurreducens has provided numerous new biological insights into the function of these model dissimilatory metal-reducing bacteria. many of these findings, including the identification of a high number of c-type cytochromes in both organisms, have resulted from comparative genomic analyses, and several have been experimentally confirmed. these genome sequences have also aided the identification of genes important ... | 2005 | 15961027 |
| nitrate reduction by desulfovibrio desulfuricans: a periplasmic nitrate reductase system that lacks napb, but includes a unique tetraheme c-type cytochrome, napm. | many sulphate reducing bacteria can also reduce nitrite, but relatively few isolates are known to reduce nitrate. although nitrate reductase genes are absent from desulfovibrio vulgaris strain hildenborough, for which the complete genome sequence has been reported, a single subunit periplasmic nitrate reductase, napa, was purified from desulfovibrio desulfuricans strain 27774, and the structural gene was cloned and sequenced. chromosome walking methods have now been used to determine the complet ... | 2005 | 15972253 |
| influence of sediment bioreduction and reoxidation on uranium sorption. | the influence of sediment bioreduction and reoxidation on u(vi) sorption was studied using fe(ii) oxide-containing saprolite from the u.s. department of energy (doe) oak ridge site. bioreduced sediments were generated by anoxic incubation with a metal-reducing bacterium, shewanella putrefaciens strain cn32, supplied with lactate as an electron donor. the reduced sediments were subsequently reoxidized by air contact. u(vi) sorption was studied in nano3-hco3 electrolytes that were both closed and ... | 2005 | 15984791 |
| [characterization and influence factors of fe(iii) reduction of shewanella cinica d14t]. | this is the first time to described the dissimilatory fe(iii) reducing characteristics of shewanella cinica d14t. the effects of o2, light, temperature and ph on dissimilatory fe(iii) reduction were examined. the results suggested that the rate of fe(iii) reduction decreased with increasing fe(iii) concentration. fe(iii) reduction was partially inhibited by the presence of either o2 or light. the optimum temperature for fe(iii) reduction is 37 degrees c. at ph 6.0-10.0, strain d14t can reduce fe ... | 2005 | 15989248 |
| ['in vitro' activity of different antimicrobial agents on gram-negative nonfermentative bacilli, excluding pseudomonas aeruginosa and acinetobacter spp]. | gram-negative nonfermentative bacilli (nfb) are widely spread in the environment. besides of difficulties for identification, they often have a marked multiresistance to antimicrobial agents, including those active against pseudomonas aeruginosa. the objective of this study was to evaluate the 'in vitro' activity of different antimicrobial agents on 177 gram-negative nonfermentative bacilli isolates (excluding pseudomonas aeruginosa and acinetobacter spp.) isolated from clinical specimens. minim ... | 2005 | 15991478 |
| chemotactic responses to metals and anaerobic electron acceptors in shewanella oneidensis mr-1. | although a previous study indicated that the dissimilatory metal-reducing bacterium shewanella oneidensis mr-1 lacks chemotactic responses to metals that can be used as anaerobic electron acceptors, new results show that this bacterium responds to both mn(iii) and fe(iii). cells were also shown to respond to another unusual electron acceptor, the humic acid analog anthraquinone-2,6-disulfonate. these results indicate that s. oneidensis is capable of moving towards a number of unusual anaerobic e ... | 2005 | 15995227 |
| degradation of crude oil by an arctic microbial consortium. | the ability of a psychrotolerant microbial consortium to degrade crude oil at low temperatures was investigated. the enriched arctic microbial community was also tested for its ability to utilize various hydrocarbons, such as long-chain alkanes (n-c24 to n-c34), pristane, (methyl-)naphthalenes, and xylenes, as sole carbon and energy sources. except for o-xylene and methylnaphthalenes, all tested compounds were metabolized under conditions that are typical for contaminated marine liquid sites, na ... | 2005 | 15999222 |
| development of a simple and rapid fluorogenic procedure for identification of vibrionaceae family members. | we describe a simple colony overlay procedure for peptidases (copp) for the rapid fluorogenic detection and quantification of vibrionaceae from seawater, shellfish, sewage, and clinical samples. the assay detects phosphoglucose isomerase with a lysyl aminopeptidase activity that is produced by vibrionaceae family members. overnight cultures are overlaid for 10 min with membranes containing a synthetic substrate, and the membranes are examined for fluorescent foci under uv illumination. fluoresce ... | 2005 | 16000757 |
| empirical establishment of oligonucleotide probe design criteria. | criteria for the design of gene-specific and group-specific oligonucleotide probes were established experimentally via an oligonucleotide array that contained perfect match (pm) and mismatch probes (50-mers and 70-mers) based upon four genes. the effects of probe-target identity, continuous stretch, mismatch position, and hybridization free energy on specificity were tested. little hybridization was observed at a probe-target identity of < or =85% for both 50-mer and 70-mer probes. pm signal int ... | 2005 | 16000786 |
| shewanella sediminis sp. nov., a novel na+-requiring and hexahydro-1,3,5-trinitro-1,3,5-triazine-degrading bacterium from marine sediment. | previously, a psychrophilic rod-shaped marine bacterium (strain haw-eb3(t)) isolated from halifax harbour sediment was noted for its ability to degrade hexahydro-1,3,5-trinitro-1,3,5-triazine (rdx). in the present study phenotypic, chemotaxonomic and genotypic characterization showed that strain haw-eb3(t) represents a novel species of shewanella. strain haw-eb3(t) contained lysine decarboxylase, which is absent in other known shewanella species, and distinguished itself from most other species ... | 2005 | 16014474 |
| emergence of plasmid-mediated resistance to quinolones in enterobacteriaceae. | although quinolone resistance results mostly from chromosomal mutations in enterobacteriaceae, it may also be mediated by plasmid-encoded qnr determinants. qnr proteins protect dna from quinolone binding and compromise the efficacy of quinolones such as nalidixic acid. qnr proteins (qnra-like, qnrb and qnrs) have been identified worldwide with a quite high prevalence among asian isolates with a frequent association with clavulanic acid inhibited expanded-spectrum beta-lactamases and plasmid-medi ... | 2005 | 16020539 |
| genome-wide examination of the natural solar radiation response in shewanella oneidensis mr-1. | we previously reported that shewanella oneidensis mr-1 is extremely sensitive to natural solar radiation (nsr). here we analyzed the global transcriptional profile of mr-1 during a 1-h recovering period after exposure to ambient solar light at a dose that yields about 20% survival rate on a luria-bertani (lb) plate. we observed the induction of dna damage-repair genes, the sos response as well as detoxification strategies that we previously observed in mr-1 following artificial uv-a irradiation. ... | 2005 | 16022560 |
| effects of a strong static magnetic field on bacterium shewanella oneidensis: an assessment by using whole genome microarray. | the effect of a strong static 14.1 t magnetic field on log phase cells of bacterial strain shewanella oneidensis mr-1 was evaluated by using whole genome microarray of this bacterium. although differences were not observed between the treatment and control by measuring the optical density (od), colony forming unit (cfu), as well as post-exposure growth of cells, transcriptional expression levels of 65 genes were altered according to our microarray data. among these genes, 21 were upregulated whi ... | 2005 | 16037957 |
| global detection and characterization of hypothetical proteins in shewanella oneidensis mr-1 using lc-ms based proteomics. | the availability of whole genome sequences has enabled the application of powerful tools for assaying global expression patterns in environmentally relevant bacteria such as shewanella oneidensis mr-1. a large number of genes in prokaryote genomes, including mr-1, have been annotated as hypothetical, indicating that no similar protein has yet been identified in other organisms. using high-sensitivity ms coupled with accurate mass and time (amt) tag methodology, 1078 tryptic peptides were collect ... | 2005 | 16038018 |
| cloning and characterization of the rpoe gene encoding an rna polymerase sigmae factor from the deep-sea piezophilic shewanella violacea strain dss12. | the rpoe gene encoding an rna polymerase sigmae subunit was isolated from a gamma-phage library of the deep-sea piezophilic and psychrophilic bacterium shewanella violacea strain dss12. structual analysis showed that the gene organization of the fragment containing s. violacearpoe was the l-aspartate oxidase-coding gene, rpoe, rsea, rseb and rsec in that order, the same as in the case of photobacterium profundum ss9 and escherichia coli k-12. the cloned gene, 576 bp in length, was found to encod ... | 2005 | 16040350 |
| protein-dna interactions under high-pressure conditions, studied by capillary narrow-tube electrophoresis. | the method of electrophoretic mobility shift assay under high-pressure conditions was improved using a high-pressure electrophoresis apparatus with capillary narrow-tube gel. it was found that the protein-dna complex in the gel was stained as a high-resolution spot with ethidium bromide. using this method, it was found that the behavior under high-pressure conditions of the protein-dna complex composed of ntrc protein and its target promoter dna is important for the pressure-regulated transcript ... | 2005 | 16041150 |
| estimating the dual-enzyme kinetic parameters for cr (vi) reduction by shewanella oneidensis mr-1 from soil column experiments. | hexavalent chromium (cr (vi)) contamination of soil and groundwater is considered a major environmental concern. bioreduction of cr (vi) to trivalent chromium (cr (iii)) can be considered an effective technology in remediating cr (vi) contaminated sites. among the cr (vi) reducing bacteria, shewanella oneidensis mr-1 (mr-1) is relatively effective. reduction of cr (vi) by mr-1 is defined by the dual-enzyme kinetic model. the feasibility of bioreduction of cr (vi) is usually evaluated by performi ... | 2005 | 16045962 |
| origin of plasmid-mediated quinolone resistance determinant qnra. | plasmid-mediated resistance to quinolones is increasingly reported in studies of enterobacteriaceae. using a pcr-based strategy, a series of gram-negative species were screened for qnra-like genes. shewanella algae, an environmental species from marine and fresh water, was identified as its reservoir. this is a one of the very few examples of progenitor identification of an acquired antibiotic resistance gene. | 2005 | 16048974 |
| chemical characterization of exopolysaccharides from antarctic marine bacteria. | exopolysaccharides (eps) may have an important role in the antarctic marine environment, possibly acting as ligands for trace metal nutrients such as iron or providing cryoprotection for growth at low temperature and high salinity. ten bacterial strains, isolated from southern ocean particulate material or from sea ice, were characterized. whole cell fatty acid profiles and 16s rrna gene sequences showed that the isolates included representatives of the genera pseudoalteromonas, shewanella, pola ... | 2005 | 16052372 |
| preparation of 20-microm-i.d. silica-based monolithic columns and their performance for proteomics analyses. | we describe the preparation and performance of high-efficiency 70 cm x 20 microm i.d. silica-based monolithic capillary lc columns. the monolithic columns at a mobile-phase pressure of 5000 psi provide flow rates of approximately 40 nl/min at a linear velocity of approximately 0.24 cm/s. the columns provide a separation peak capacity of approximately 420 in conjunction with both on-line coupling with microsolid-phase extraction and nanoelectrospray ionization-mass spectrometry. performance was e ... | 2005 | 16053318 |
| shewanella oneidensis mr-1 uses overlapping pathways for iron reduction at a distance and by direct contact under conditions relevant for biofilms. | we developed a new method to measure iron reduction at a distance based on depositing fe(iii) (hydr)oxide within nanoporous glass beads. in this "fe-bead" system, shewanella oneidensis reduces at least 86.5% of the iron in the absence of direct contact. biofilm formation accompanies fe-bead reduction and is observable both macro- and microscopically. fe-bead reduction is catalyzed by live cells adapted to anaerobic conditions, and maximal reduction rates require sustained protein synthesis. the ... | 2005 | 16085832 |
| biological control of hog waste odor through stimulated microbial fe(iii) reduction. | odor control and disposal of swine waste have inhibited expansion of swine production facilities throughout the united states. swine waste odor is associated primarily with high concentrations of volatile fatty acids (vfas). here, we demonstrate that stimulated fe(iii) reduction in hog manure can rapidly remove the malodorous compounds and enhance methane production by 200%. as part of these studies, we enumerated the indigenous fe(iii)-reducing population in swine waste and identified members o ... | 2005 | 16085869 |
| identification of genes involved in cytochrome c biogenesis in shewanella oneidensis, using a modified mariner transposon. | a modified mariner transposon, minihimar rb1, was generated to mutagenize cells of the metal-reducing bacterium shewanella oneidensis. the use of this transposon led to the isolation of stable mutants and allowed rapid identification of disrupted genes. fifty-eight mutants, including bg104 and bg148 with transposon insertions in the cytochrome c maturation genes ccmc and ccmf1, respectively, were analyzed. both mutants were deficient in anaerobic respiration and cytochrome c production. | 2005 | 16085900 |
| cultivation of microorganisms in the cultural medium made from squid internal organs and accumulation of polyunsaturated fatty acids in the cells. | the disposal and more efficient utilization of marine wastes is becoming increasingly serious. a culture media for microorganisms has been prepared from squid internal organs that are rich in polyunsaturated fatty acids (pufas). both freshwater and marine bacteria grew well in this medium and some bacteria accumulated pufas in their lipids, suggesting uptake of exogenous pufas. higher pufa accumulations were observed in escherichia coli mutant cells defective either in unsaturated fatty acid bio ... | 2005 | 16091889 |
| 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 |
| 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 |
| use of microarrays with different probe sizes for monitoring gene expression. | microarrays with oligonucleotides of different lengths were used to monitor gene expression at a whole-genome level. to determine what length of oligonucleotide is a better alternative to pcr-generated probes, the performance of oligonucleotide probes was systematically compared to that of their pcr-generated counterparts for 96 genes from shewanella oneidensis mr-1 in terms of overall signal intensity, numbers of genes detected, specificity, sensitivity, and differential gene expression under e ... | 2005 | 16151099 |
| inhibition of no3- and no2- reduction by microbial fe(iii) reduction: evidence of a reaction between no2- and cell surface-bound fe2+. | a recent study (d. c. cooper, f. w. picardal, a. schimmelmann, and a. j. coby, appl. environ. microbiol. 69:3517-3525, 2003) has shown that no(3)(-) and no(2)(-) (no(x)(-)) reduction by shewanella putrefaciens 200 is inhibited in the presence of goethite. the hypothetical mechanism offered to explain this finding involved the formation of a fe(iii) (hydr)oxide coating on the cell via the surface-catalyzed, abiotic reaction between fe(2+) and no(2)(-). this coating could then inhibit reduction of ... | 2005 | 16151113 |
| selenite and tellurite reduction by shewanella oneidensis. | shewanella oneidensis mr-1 reduces selenite and tellurite preferentially under anaerobic conditions. the se(0) and te(0) deposits are located extracellularly and intracellularly, respectively. this difference in localization and the distinct effect of some inhibitors and electron acceptors on these reduction processes are taken as evidence of two independent pathways. | 2005 | 16151159 |
| oxidative remobilization of biogenic uranium(iv) precipitates: effects of iron(ii) and ph. | the oxidative remobilization of uranium from biogenic u(iv) precipitates was investigated in bioreduced sediment suspensions in contact with atmospheric o2 with an emphasis on the influence of fe(ii) and ph on the rate and extent of u release from the solid to the aqueous phase. the sediment was collected from the u.s. department of energy field research center (frc) site at oak ridge, tennessee. biogenic u(iv) precipitates and bioreduced sediment were generated through anaerobic incubation with ... | 2005 | 16151228 |
| 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 |
| evaluation of ochrobactrum intermedium bacteremia in a patient with bladder cancer. | it is generally believed that ochrobactrum anthropi is the only pathogenic species in the genus ochrobactrum. we report a case of presumptive ochrobactrum intermedium bacteremia in a patient with bladder cancer. identification of a rare species using rapid commercial panel could lead to an erroneous result as this clinical isolate was initially reported to be shewanella putrefaciens. the patient was successfully treated with imipenem and ciprofloxacin. | 2005 | 16168615 |
| global transcriptome analysis of shewanella oneidensis mr-1 exposed to different terminal electron acceptors. | to gain insight into the complex structure of the energy-generating networks in the dissimilatory metal reducer shewanella oneidensis mr-1, global mrna patterns were examined in cells exposed to a wide range of metal and non-metal electron acceptors. gene expression patterns were similar irrespective of which metal ion was used as electron acceptor, with 60% of the differentially expressed genes showing similar induction or repression relative to fumarate-respiring conditions. several groups of ... | 2005 | 16199584 |
| first case of osteomyelitis due to shewanella algae. | shewanella spp. are infrequently recovered from clinical specimens. we report here on the first case of osteomyelitis due to shewanella algae. this bacterium, at first misidentified by phenotypic tests as shewanella putrefaciens, was subsequently identified correctly as s. algae by 16s rrna gene sequence analysis. | 2005 | 16208026 |
| [exposure assessment to harmful agents in workplaces in sewage plant workers]. | the purpose of the study was to evaluate exposure to biological and chemical agents in a sewage treatment plant. | 2005 | 16218135 |
| microbial dimethylsulfoxide and trimethylamine-n-oxide respiration. | over the last two decades, the biochemistry and genetics of dimethylsulfoxide (dmso) and trimethylamine-n-oxide (tmao) respiration has been characterised, particularly in escherichia coli marine bacteria of the genus shewanella and the purple phototrophic bacteria, rhodobacter sphaeroides and r. capsulatus. all of the enzymes (or catalytic subunits) involved the final step in dmso and tmao respiration contain a pterin molybdenum cofactor and are members of the dmso reductase family of molybdoenz ... | 2005 | 16221580 |
| binding analysis of a psychrotrophic fkbp22 to a folding intermediate of protein using surface plasmon resonance. | sib1 fkbp22 is a homodimer, with each subunit consisting of the c-terminal catalytic domain and n-terminal dimerization domain. this protein exhibits peptidyl prolyl cis-trans isomerase activity for both peptide and protein substrates. however, truncation of the n-terminal domain greatly reduces the activity only for a protein substrate. using surface plasmon resonance, we showed that sib1 fkbp22 loses the binding ability to a folding intermediate of protein upon truncation of the n-terminal dom ... | 2005 | 16223489 |
| expression dynamics of arsenic respiration and detoxification in shewanella sp. strain ana-3. | because arsenate [as(v)] reduction by bacteria can significantly enhance arsenic mobility in the environment, it is important to be able to predict when this activity will occur. currently, two bacterial systems are known that specifically reduce as(v), namely, a respiratory system (encoded by the arr genes) and a detoxification system (encoded by the ars genes). here we analyze the conditions under which these two systems are expressed in shewanella sp. strain ana-3. the ars system is expressed ... | 2005 | 16237022 |
| shelf-life extension of refrigerated mediterranean mullet (mullus surmuletus) using modified atmosphere packaging. | the present work evaluated the quality and freshness characteristics and the effect of modified atmosphere packaging (map) on the shelf-life extension of refrigerated mediterranean mullet using microbiological, biochemical, and sensory analyses. fresh open sea red mullet (mullus surmuletus) were packaged in four different atmospheres: m1, 10%/20%/70% (o2/ co2/n2); m2, 10%/40%/50% (o2/co2/n2); m3, 10%/60%/30% (o2/co2/n2); identical fish samples were packaged in air. all fish were kept under refri ... | 2005 | 16245730 |
| identification of shewanella baltica as the most important h2s-producing species during iced storage of danish marine fish. | shewanella putrefaciens has been considered the main spoilage bacteria of low-temperature stored marine seafood. however, psychrotropic shewanella have been reclassified during recent years, and the purpose of the present study was to determine whether any of the new shewanella species are important in fish spoilage. more than 500 h2s-producing strains were isolated from iced stored marine fish (cod, plaice, and flounder) caught in the baltic sea during winter or summer time. all strains were id ... | 2005 | 16269698 |
| a method adapting microarray technology for signature-tagged mutagenesis of desulfovibrio desulfuricans g20 and shewanella oneidensis mr-1 in anaerobic sediment survival experiments. | signature-tagged mutagenesis (stm) is a powerful technique that can be used to identify genes expressed by bacteria during exposure to conditions in their natural environments. to date, there have been no reports of studies in which this approach was used to study organisms of environmental, rather than pathogenic, significance. we used a mini-tn10 transposon-bearing plasmid, pbsl180, that efficiently and randomly mutagenized desulfovibrio desulfuricans g20 in addition to shewanella oneidensis m ... | 2005 | 16269742 |
| global transcriptional profiling of shewanella oneidensis mr-1 during cr(vi) and u(vi) reduction. | whole-genome dna microarrays were used to examine the gene expression profile of shewanella oneidensis mr-1 during u(vi) and cr(vi) reduction. the same control, cells pregrown with nitrate and incubated with no electron acceptor, was used for the two time points considered and for both metals. u(vi)-reducing conditions resulted in the upregulation (> or = 3-fold) of 121 genes, while 83 genes were upregulated under cr(vi)-reducing conditions. a large fraction of the genes upregulated [34% for u(v ... | 2005 | 16269787 |
| shewanella pneumatophori sp. nov., an eicosapentaenoic acid-producing marine bacterium isolated from the intestines of pacific mackerel (pneumatophorus japonicus). | an eicosapentaenoic acid-producing bacterium, previously described as shewanella sp. strain scrc-2738, was classified by phenotypic characterization, chemotaxonomic analysis, 16s rrna gene sequence analysis and dna-dna hybridization. the isolate was gram-negative, rod-shaped and motile by using polar flagella. the strain grew at 4-32 degrees c; the optimum growth temperature was 27 degrees c. nacl was required for growth. the major isoprenoid quinones were ubiquinone-7 and ubiquinone-8 and its d ... | 2005 | 16280496 |
| 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 |
| biogenic amine index for freshness evaluation in iced mediterranean hake (merluccius merluccius). | biogenic amine accumulation was studied during the ice storage of mediterranean hake. sensory analysis and counts of shewanella, pseudomonas, enterobacteria, psychrotrophic, and mesophilic bacteria provided complementary information on hake spoilage. putrescine and cadaverine were the main amines accumulated, whereas histamine and tyramine were minor amines but had qualitative interest from the hygienic point of view. although all biogenic amines were less abundant than in pelagic fish, they may ... | 2005 | 16300084 |
| large-scale mulc-ms/ms for silver- and coomassie blue-stained polyacrylamide gels. | 2-de combined with lc-ms/ms has become a routine, reliable protein separation and identification technology for proteome analysis. the demand for large-scale protein identifications after 2-de separation requires a sensitive and high-throughput lc-ms/ms method. in this report, a simple, splitless, fully automated capillary lc-ms/ms system was described for the large-scale identification of proteins from gels stained with either silver or cbb. the gel samples were digested and peptides were extra ... | 2005 | 16315175 |
| influence of crude oil on changes of bacterial communities in arctic sea-ice. | the danger of a petroleum hydrocarbon spillage in the polar, ice-covered regions is increasing due to oil exploration in arctic offshore areas and a growing interest in using the northern sea route (nsr) as an alternative transportation route for arctic oil and gas. however, little is known about the potential impact of accidental oil spills on this environment. we investigated the impact of crude oil on microbial community composition in six different arctic sea-ice samples incubated with crude ... | 2004 | 16329935 |
| improving solubility of shewanella oneidensis mr-1 and clostridium thermocellum jw-20 proteins expressed into esherichia coli. | low solubility of proteins overexpressed in e. coli is a frequent problem in high-throughput structural genomics. to improve solubility of proteins from mesophilic shewanella oneidensis mr-1 and thermophilic clostridium thermocellum jw20, an approach was attempted that included a fusion of the target protein to a maltose-binding protein (mbp) and a decrease of induction temperature. the mbp was selected as the most efficient solubilizing carrier when compared to a glutathione s-transferase and a ... | 2005 | 16335938 |
| sustained and complete hexahydro-1,3,5-trinitro-1,3,5-triazine (rdx) degradation in zero-valent iron simulated barriers under different microbial conditions. | flow-through columns packed with "aged" zero-valent iron (zvi) between layers of soil and sand were constructed to mimic a one-dimensional permeable reactive iron barrier (prb). the columns were continuously fed rdx (hexahydro-1,3,5-trinitro-1,3,5-triazine, ca. 18 mg l(-1)) for over one year. two columns were bioaugmented with dissimilatory iron reducing bacteria (dirb) shewanella algae bry or geobacter metallireducens gs-15 to investigate their potential to enhance the reactivity of aged iron b ... | 2005 | 16342534 |
| regulation of dissimilatory fe(iii) reduction activity in shewanella putrefaciens. | under anaerobic conditions, shewanella putrefaciens is capable of respiratory-chain-linked, high-rate dissimilatory iron reduction via both a constitutive and inducible fe(iii)-reducing system. in the presence of low levels of dissolved oxygen, however, iron reduction by this microorganism is extremely slow. fe(ii)-trapping experiments in which fe(iii) and o(2) were presented simultaneously to batch cultures of s. putrefaciens indicated that autoxidation of fe(ii) was not responsible for the abs ... | 1990 | 16348289 |
| interactions between shewanella colwelliana, oyster larvae, and hydrophobic organophosphate pesticides. | shewanella colwelliana (strain d) is a periphytic estuarine bacterium that forms biofilms beneficial to oyster set. our study examined whether these and other films concentrated two hydrophobic, organophosphate pesticides, abate and malathion, that are detected in chesapeake bay oyster waters. both biofilms and purified exopolysaccharide of s. colwelliana did not adsorb more of the abate or malathion than could be accounted for by adsorption to control surfaces. similar results were obtained by ... | 1990 | 16348382 |
| hyphomonas spp., shewanella spp., and other marine bacteria lack heterogeneous (ladderlike) lipopolysaccharides. | the lipopolysaccharides (lps) of 19 marine bacteria were examined for size heterogeneities by using sodium dodecyl sulfate-polyacrylamide gel electrophoresis in conjunction with an lps-specific silver staining method. fifteen marine bacteria had an r-type lps instead of the ladderlike lps array characteristic of most bacteria. in addition, three marine bacteria also had a single large lps molecule. without constraints (e.g., surface masking), r-type lps, a more hydrophobic molecule, predominates ... | 1991 | 16348529 |
| siderophore-mediated iron sequestering by shewanella putrefaciens. | the iron-sequestering abilities of 51 strains of shewanella putrefaciens isolated from different sources (fish, water, and warm-blooded animals) were assessed. thirty strains (60%) produced siderophores in heat-sterilized fish juice as determined by the chrome-azurol-s assay. all cultures were negative for the catechol-type siderophore, whereas 24 of the 30 siderophore-producing strains tested positive in the csáky test, indicating the production of siderophores of the hydroxamate type. sideroph ... | 1994 | 16349298 |
| 3-nitropropionic acid is a suicide inhibitor of mitochondrial respiration that, upon oxidation by complex ii, forms a covalent adduct with a catalytic base arginine in the active site of the enzyme. | we report three new structures of mitochondrial respiratory complex ii (succinate ubiquinone oxidoreductase, e.c. 1.3.5.1) at up to 2.1 a resolution, with various inhibitors. the structures define the conformation of the bound inhibitors and suggest the residues involved in substrate binding and catalysis at the dicarboxylate site. in particular they support the role of arg(297) as a general base catalyst accepting a proton in the dehydrogenation of succinate. the dicarboxylate ligand in oxaloac ... | 2006 | 16371358 |
| 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 |
| [unsaturated organic acids as terminal electron acceptors for reductase chains of anaerobic bacteria]. | this paper summarizes the current knowledge of unsaturated organic acids in their role as terminal electron acceptors of anaerobic bacteria. the mechanisms and enzyme systems involved in the reduction of fumarate by escherichia coli, wolinella succinogenes, and some species of the genus shewanella are considered. particular attention is given to reduction of the double bond of the unnatural compound methacrylate by the sigma-proteobacterium geobacter sulfurreducens am-1. soluble periplasmic flav ... | 2005 | 16400981 |
| [lipid composition of novel shewanella species isolated from far eastern seas]. | a comparative study of the lipid composition of 26 strains (including type strains) of marine gammaproteobacteria belonging to the genera shewanella, alteromonas, pseudoalteromonas, marinobacterium, microbulbifer, and marinobacter was carried out. the bacteria exhibited genus-specific profiles of ubiquinones, phospholipids, and fatty acids, which can serve as reliable chemotaxonomic markers for tentative identification of new isolates. the studied species of the genus shewanella were distinguish ... | 2005 | 16400986 |
| 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 |
| 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 |
| randomized sequence databases for tandem mass spectrometry peptide and protein identification. | tandem mass spectrometry (ms/ms) combined with database searching is currently the most widely used method for high-throughput peptide and protein identification. many different algorithms, scoring criteria, and statistical models have been used to identify peptides and proteins in complex biological samples, and many studies, including our own, describe the accuracy of these identifications, using at best generic terms such as "high confidence." false positive identification rates for these cri ... | 2005 | 16402894 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| molecular dynamics of the shewanella oneidensis response to chromate stress. | temporal genomic profiling and whole-cell proteomic analyses were performed to characterize the dynamic molecular response of the metal-reducing bacterium shewanella oneidensis mr-1 to an acute chromate shock. the complex dynamics of cellular processes demand the integration of methodologies that describe biological systems at the levels of regulation, gene and protein expression, and metabolite production. genomic microarray analysis of the transcriptome dynamics of midexponential phase cells s ... | 2006 | 16524964 |
| a novel phosphorimager-based technique for monitoring the microbial reduction of technetium. | a novel phosphorimager-based technique which can be used to quantify low concentrations of radionuclides is described. the technique offers several benefits, combining very high sensitivity with containment of the radioisotope in the solid state, thus minimizing disposal procedures. in this study, it was used in conjunction with paper chromatography to quantify different oxidation states of (sup99)tc in solution. the technique was used to evaluate the potential of anaerobic cultures of shewanell ... | 1996 | 16535242 |
| genotyping of heterotrophic bacteria from the central baltic sea by use of low-molecular-weight rna profiles. | the gotland deep, an anoxic basin, was investigated for its heterotrophic microflora as a station representative of the central baltic sea and as an example of a brackish water environment. one hundred twenty-three bacterial strains were isolated along the water column by use of four different cultivation procedures. high-resolution electrophoresis of the low-molecular-weight (lmw) rna (5s rrna and trna) was used for analysis of the taxonomic position of the strains. the banding pattern of the l ... | 1996 | 16535296 |
| deflocculation of activated sludge by the dissimilatory fe(iii)-reducing bacterium shewanella alga bry. | the influence of microbial fe(iii) reduction on the deflocculation of autoclaved activated sludge was investigated. fe(iii) flocculated activated sludge better than fe(ii). decreasing concentrations of fe(iii) caused an increase in sludge bulk water turbidity, while bulk water turbidity remained relatively constant over a range of fe(ii) concentrations. cells of the dissimilatory metal-reducing bacterium shewanella alga bry coupled the oxidation of h(inf2) to the reduction of fe(iii) bound in sl ... | 1996 | 16535299 |
| a pressurized chemostat for the study of marine barophilic and oligotrophic bacteria. | a continuous culture system that allows bacteria to be grown in steady-state populations under pressures of up to 700 atm (71 mpa) was constructed and tested. with readily available or slightly modified high-pressure chromatography equipment, a continuous flow of sterile medium is pressurized and passed through a 500-ml nylon-coated titanium reactor at flow rates of 0.01 to 10 ml min(sup-1). the pressure in the reactor is controlled by a backpressure regulator with greater than 1% accuracy. in t ... | 1996 | 16535311 |
| clustering of marine bacteria in seawater enrichments. | seawater enrichments of marine bacteria clustered in 20- to 50-(mu)m-wide bands near air-water interfaces. the cells within the band travelled at up to 212 (mu)m s(sup-1) and at an average speed of 163 (mu)m s(sup-1). mean cell speeds peaked mid-run at 187 (mu)m s(sup-1). at the end of the run, bacteria reversed direction rather than randomly reorienting. the duration of the stops during reversal was estimated at 18 ms, six to seven times shorter than that found in enteric bacteria. cells hundre ... | 1996 | 16535420 |
| evolutionary relationships of cultivated psychrophilic and barophilic deep-sea bacteria. | evolutionary relationships of cultivated barophilic bacteria were determined. all psychrophilic and barophilic isolates were affiliated with one of five genera of the gamma subdivision of the class proteobacteria ((gamma)-proteobacteria): shewanella, photobacterium, colwellia, moritella, and a new group containing strain cnpt3. the data indicate that the barophilic phenotype has evolved independently in different (gamma)-proteobacteria genera. | 1997 | 16535621 |
| role of hydrophobicity in adhesion of the dissimilatory fe(iii)-reducing bacterium shewanella alga to amorphous fe(iii) oxide. | the mechanisms by which the dissimilatory fe(iii)-reducing bacterium shewanella alga adheres to amorphous fe(iii) oxide were examined through comparative analysis of s. alga bry and an adhesion-deficient strain of this species, s. alga rad20. approximately 100% of s. alga bry cells typically adhered to amorphous fe(iii) oxide, while less than 50% of s. alga rad20 cells adhered. bulk chemical analysis, isoelectric point analysis, and cell surface analysis by time-of-flight secondary-ion mass spec ... | 1997 | 16535706 |
| reduction of hexavalent uranium from organic complexes by sulfate- and iron-reducing bacteria. | the influence of organic-hexavalent-uranium [u(vi)] complexation on u(vi) reduction by a sulfate-reducing bacterium (desulfovibrio desulfuricans) and an iron-reducing bacterium (shewanella alga) was evaluated. four aliphatic ligands (acetate, malonate, oxalate, and citrate) and an aromatic ligand (tiron [4,5-dihydroxy-1,3-benzene disulfonic acid]) were used to study complexed-uranium bioavailability. the trends in uranium reduction varied with the nature and the amount of u(vi)-organic complex f ... | 1997 | 16535729 |
| extracellular respiration of dimethyl sulfoxide by shewanella oneidensis strain mr-1. | shewanella species are renowned for their respiratory versatility, including their ability to respire poorly soluble substrates by using enzymatic machinery that is localized to the outside of the cell. the ability to engage in "extracellular respiration" to date has focused primarily on respiration of minerals. here, we identify two gene clusters in shewanella oneidensis strain mr-1 that each contain homologs of genes required for metal reduction and genes that are predicted to encode dimethyl ... | 2006 | 16537430 |
| 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 |
| 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 |
| reduction of soluble and insoluble iron forms by membrane fractions of shewanella oneidensis grown under aerobic and anaerobic conditions. | the effect of iron substrates and growth conditions on in vitro dissimilatory iron reduction by membrane fractions of shewanella oneidensis mr-1 was characterized. membrane fractions were separated by sucrose density gradients from cultures grown with o(2), fumarate, and aqueous ferric citrate as the terminal electron acceptor. marker enzyme assays and two-dimensional gel electrophoresis demonstrated the high degree of separation between the outer and cytosolic membrane. protein expression patte ... | 2006 | 16597999 |
| 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 |
| 16s rdna-based analysis of dominant bacterial populations associated with early life stages of coho salmon (oncorhynchus kisutch). | in this study, we used a 16s rdna-based approach to determine bacterial populations associated with coho salmon (oncorhynchus kisutch) in its early life stages, highlighting dominant bacteria in the gastrointestinal tract during growth in freshwater. the present article is the first molecular analysis of bacterial communities of coho salmon. cultivability of the salmon gastrointestinal microbiota was estimated by comparison of direct microscopic counts (using acridine orange) with colony counts ... | 2006 | 16598631 |
| knock-out of so1377 gene, which encodes the member of a conserved hypothetical bacterial protein family cog2268, results in alteration of iron metabolism, increased spontaneous mutation and hydrogen peroxide sensitivity in shewanella oneidensis mr-1. | shewanella oneidensis mr-1 is a facultative, gram-negative bacterium capable of coupling the oxidation of organic carbon to a wide range of electron acceptors such as oxygen, nitrate and metals, and has potential for bioremediation of heavy metal contaminated sites. the complete 5-mb genome of s. oneidensis mr-1 was sequenced and standard sequence-comparison methods revealed approximately 42% of the mr-1 genome encodes proteins of unknown function. defining the functions of hypothetical proteins ... | 2006 | 16600046 |
| the repetitive dna elements called crisprs and their associated genes: evidence of horizontal transfer among prokaryotes. | we have found direct dna repeats 21-47 bp in length interspersed with nonrepetitive sequences of similar length, or clustered regularly interspaced short palindromic repeats (crisprs) in a wide range of diverse prokaryotes, including many archaeal and eubacterial species. a number of cas, crispr-associated genes have also been characterized in many of the same organisms. phylogenetic analysis of these cas genes suggests that the crispr loci have been propagated via hgt, horizontal gene transfer. ... | 2006 | 16612537 |
| development of bioconcrete material using an enrichment culture of novel thermophilic anaerobic bacteria. | in the biosphere, bacteria can function as geo-chemical agents, promoting the dispersion, fractionation and/or concentration of materials. microbial mineral precipitation is resulted from metabolic activities of microorganisms. based on this biomineralogy concept, an attempt has been made to develop bioconcrete material incorporating of an enrichment culture of thermophilic and anaerobic bacteria within cement-sand mortar/concrete. the results showed a significant increase in compressive strengt ... | 2006 | 16629379 |
| identification of rnase hii from psychrotrophic bacterium, shewanella sp. sib1 as a high-activity type rnase h. | the gene encoding rnase hii from the psychrotrophic bacterium, shewanella sp. sib1 was cloned, overexpressed in escherichia coli, and the recombinant protein was purified and biochemically characterized. sib1 rnase hii is a monomeric protein with 212 amino acid residues and shows an amino acid sequence identity of 64% to e. coli rnase hii. the enzymatic properties of sib1 rnase hii, such as metal ion preference, ph optimum, and cleavage mode of substrate, were similar to those of e. coli rnase h ... | 2006 | 16650002 |
| metal reduction and iron biomineralization by a psychrotolerant fe(iii)-reducing bacterium, shewanella sp. strain pv-4. | a marine psychrotolerant, dissimilatory fe(iii)-reducing bacterium, shewanella sp. strain pv-4, from the microbial mat at a hydrothermal vent of loihi seamount in the pacific ocean has been further characterized, with emphases on metal reduction and iron biomineralization. the strain is able to reduce metals such as fe(iii), co(iii), cr(vi), mn(iv), and u(vi) as electron acceptors while using lactate, formate, pyruvate, or hydrogen as an electron donor. growth during iron reduction occurred over ... | 2006 | 16672462 |
| more sensitive and quantitative proteomic measurements using very low flow rate porous silica monolithic lc columns with electrospray ionization-mass spectrometry. | the sensitivity of proteomics measurements using liquid chromatography (lc) separations interfaced with electrospray ionization-mass spectrometry (esi-ms) improves approximately inversely with liquid flow rate (for the columns having the same separation efficiency, linear velocity, and porosity), making attractive the use of smaller inner diameter lc columns. we report the development and initial application of 10 microm i.d. silica-based monolithic lc columns providing more sensitive proteomics ... | 2006 | 16674098 |
| a tiny but powerful microbial fuel cell. | 2006 | 16683579 | |
| high power density from a miniature microbial fuel cell using shewanella oneidensis dsp10. | a miniature microbial fuel cell (mini-mfc) is described that demonstrates high output power per device cross-section (2.0 cm2) and volume (1.2 cm3). shewanella oneidensis dsp10 in growth medium with lactate and buffered ferricyanide solutions were used as the anolyte and catholyte, respectively. maximum power densities of 24 and 10 mw/m2 were measured using the true surface areas of reticulated vitreous carbon (rvc) and graphite felt (gf) electrodes without the addition of exogenous mediators in ... | 2006 | 16683602 |
| a proton delivery pathway in the soluble fumarate reductase from shewanella frigidimarina. | the mechanism for fumarate reduction by the soluble fumarate reductase from shewanella frigidimarina involves hydride transfer from fad and proton transfer from the active-site acid, arg-402. it has been proposed that arg-402 forms part of a proton transfer pathway that also involves glu-378 and arg-381 but, unusually, does not involve any bound water molecules. to gain further insight into the importance of this proton pathway we have perturbed it by substituting arg-381 by lysine and methionin ... | 2006 | 16699170 |