Publications
| Title | Abstract | Year Filter | PMID(sorted descending) Filter |
|---|
| shewanella pacifica sp. nov., a polyunsaturated fatty acid-producing bacterium isolated from sea water. | six marine bacterial strains, kmm 3597t, kmm 3775, kmm 3590, kmm 3772, kmm 3605 and kmm 3601, that produce polyunsaturated fatty acids were isolated from sea water samples collected from different locations and depths in chazhma bay (sea of japan, pacific ocean) and characterized to clarify their taxonomic position. the dna g+c contents of these strains were 39.5-40.3 mol%. the level of dna hybridization between these strains was conspecific (83-96%), indicating that they represent a single geno ... | 2004 | 15280273 |
| correlated atomic force microscopy and fluorescence lifetime imaging of live bacterial cells. | we report on imaging living bacterial cells by using a correlated tapping-mode atomic force microscopy (afm) and confocal fluorescence lifetime imaging microscopy (flim). for optimal imaging of gram-negative shewanella oneidensis mr-1 cells, we explored different methods of bacterial sample preparation, such as spreading the cells on poly-l-lysine coated surfaces or agarose gel coated surfaces. we have found that the agarose gel containing 99% ammonium acetate buffer can provide sufficient local ... | 2004 | 15261059 |
| differential pressure resistance in the activity of rna polymerase isolated from shewanella violacea and escherichia coli. | rna polymerase was purified from the piezophile shewanella violacea dss12, and the transcriptional activity after pressure treatment was compared with that of the mesophile escherichia coli. application of pressure at 100 mpa for 30 min reduced the e. coli rna polymerase activity to 60% of the activity at atmospheric pressure, whereas the s. violacea rna polymerase maintained full activity, indicating that the s. violacea rna polymerase is more stable than its e. coli counterpart. this result wa ... | 2004 | 15241657 |
| genes regulated by torr, the trimethylamine oxide response regulator of shewanella oneidensis. | the torecad operon encoding the trimethylamine oxide (tmao) respiratory system of shewanella oneidensis is positively controlled by the tors/torr two-component system when tmao is available. activation of the tor operon occurs upon binding of the phosphorylated response regulator torr to a single operator site containing the direct repeat nucleotide sequence ttcatan4ttcata. here we show that the replacement of any nucleotide of one ttcata hexamer prevented torr binding in vitro, meaning that tor ... | 2004 | 15231782 |
| [bacteremia in an obese patient with cellulitis and chronic ulceration in the lower extremity]. | 2004 | 15228905 | |
| the outer membrane protein omp35 affects the reduction of fe(iii), nitrate, and fumarate by shewanella oneidensis mr-1. | shewanella oneidensis mr-1 uses several electron acceptors to support anaerobic respiration including insoluble species such as iron(iii) and manganese(iv) oxides, and soluble species such as nitrate, fumarate, dimethylsulfoxide and many others. mr-1 has complex branched electron transport chains that include components in the cytoplasmic membrane, periplasm, and outer membrane (om). previous studies have implicated a role for anaerobically upregulated om electron transport components in the use ... | 2004 | 15212692 |
| structure of an acidic o-specific polysaccharide from marine bacterium shewanella fidelis kmm 3582t containing nepsilon-[(s)-1-carboxyethyl]-nalpha-(d-galacturonoyl)-l-lysine. | the o-specific polysaccharide was isolated by mild acid degradation of the lipopolysaccharide of the marine bacterium shewanella fidelis type strain kmm 3582t and studied by sugar analysis along with 1h and 13c nmr spectroscopy including one-dimensional noe in difference mode and two-dimensional experiments. the polysaccharide was found to consist of linear tetrasaccharide repeating units containing nepsilon-[(s)-1-carboxyethyl]-nalpha-(d-galacturonoyl)-l-lysine and having the following structur ... | 2004 | 15183741 |
| new method for rapid and sensitive quantification of sulphide-producing bacteria in fish from arctic and temperate waters. | the offensive, fishy, rotten h2s-off-odours in spoiled, aerobically and cold stored fish from arctic and temperate waters are generally caused by sulphide-producing bacteria (spb), mainly shewanella putrefaciens. in the present work, a new, rapid, simple and accurate method for estimation of the spb content in fish from these areas is described. the quantification is based on the formation rate of iron sulphide during growth of spbs incubated at 30 degrees c in a liquid growth medium containing ... | 2004 | 15163589 |
| probing domain mobility in a flavocytochrome. | the crystal structures of various different members of the family of fumarate reductases and succinate dehydrogenases have allowed the identification of a mobile clamp (or capping) domain [e.g., taylor, p., pealing, s. l., reid, g. a., chapman, s. k., and walkinshaw, m. d. (1999) nat. struct. biol. 6, 1108-1112], which has been proposed to be involved in regulating accessibility of the active site to substrate. to investigate this, we have constructed the a251c:s430c double mutant form of the so ... | 2004 | 15109257 |
| identification of 42 possible cytochrome c genes in the shewanella oneidensis genome and characterization of six soluble cytochromes. | through pattern matching of the cytochrome c heme-binding site (cxxch) against the genome sequence of shewanella oneidensis mr-1, we identified 42 possible cytochrome c genes (27 of which should be soluble) out of a total of 4758. however, we found only six soluble cytochromes c in extracts of s. oneidensis grown under several different conditions: (1) a small tetraheme cytochrome c, (2) a tetraheme flavocytochrome c-fumarate reductase, (3) a diheme cytochrome c4, (4) a monoheme cytochrome c5, ( ... | 2004 | 15107237 |
| genetic and biochemical characterization of a chromosome-encoded carbapenem-hydrolyzing ambler class d beta-lactamase from shewanella algae. | a chromosome-encoded beta-lactamase gene from shewanella algae clinical isolate kb-1 was cloned and expressed in escherichia coli. it encoded the ambler class d enzyme oxa-55, sharing less than 55% identity with any other oxacillinases. although conferring a narrow-spectrum beta-lactam resistance phenotype, oxa-55 had carbapenem-hydrolyzing activity that mirrored the reduced susceptibility to imipenem observed in s. algae kb-1. very similar oxacillinases were found in other s. algae isolates. | 2004 | 15105119 |
| biosynthesis and dietary uptake of polyunsaturated fatty acids by piezophilic bacteria. | the biochemistry of piezophilic bacteria is unique in that piezophiles produce polyunsaturated fatty acids (pufas). a pertinent question is if piezophilic bacteria synthesize pufa de novo, through dietary uptake, or both. this study was undertaken to examine the biosynthesis and cellular uptake of pufas by piezophilic bacteria. a moderately piezophilic (shewanella violacea dss12) and two hyperpiezophilic bacteria (s. benthica db21mt-2 and moritella yayanosii db21mt-5) were grown under 50 mpa (me ... | 2004 | 15081997 |
| biogeochemical influence on transport of chromium in manganese sediments: experimental and modeling approaches. | hexavalent chromium (cr(vi)) was reduced to immobile and nontoxic cr(iii) by a dissimilatory metal reducing bacteria, shewanella alga simidu (bry-mt) atcc 55627. a series of kinetic batch and dynamic column experiments were conducted to provide an understanding of cr(vi) reduction by the facultative anaerobe bry-mt. reduction of cr(vi) was rapid (within 1 h) in columns packed with quartz sand and bacteria, whereas cr(vi) reduction by bry-mt was delayed (57 h) in the presence of beta-mno2-coated ... | 2004 | 15068867 |
| isolation of extremophiles with the detection and retrieval of shewanella strains in deep-sea sediments from the west pacific. | tests to detect the presence of piezophilic shewanella strains in the deep-sea sediments of the west, mid- and east pacific at different depths were done by amplification of previously identified pressure-regulated operons (orf1,2 and orf3). the operon fragments were detected in all the deep-sea sediment samples, indicating the broad presence of piezophilic deep-sea shewanella species or related species in the deep-sea sediments across the pacific. extremophiles were isolated from the deep-sea s ... | 2004 | 15064982 |
| characterisation of a tetrasaccharide released on mild acid hydrolysis of lps from two rough strains of shewanella species representing different dna homology groups. | a reducing tetrasaccharide of the following structure was released by mild acid hydrolysis of r-type lps from shewanella putrefaciens strains ncimb 10472 and 10473. the same tetrasaccharide containing acetal-linked open-chain galnac is present in the core region of lps from s. oneidensis strain mr-1 and may be characteristic of genomic groups ii and iii of s. putrefaciens and related strains. (1s)-d-galanac-(1-->4,6)-alpha-d-galp-(1-->6)-alpha-d-galp-(1-->3)-d-gal. | 2004 | 15063209 |
| from hyperthermophiles to psychrophiles: the structural basis of temperature stability of the amino acid dehydrogenases. | the determination and comparison of the structures of a number of glutamate dehydrogenases that span the spectrum of thermal stability from mesophiles to hyperthermophiles have revealed that the formation of extended ion-pair networks is a major stabilizing feature in the adaptation of the organism to life at 100 degrees c. analysis of the structures of other hyperthermophilic proteins has shown that ion-pair networks also play roles in their stabilization, including the phosphoglucose isomerase ... | 2004 | 15046585 |
| [investigation of the bacteria in the seawater of xisha in the south china sea and their antibiotic sensitivity profile]. | to investigate the distribution and antibiotic sensitivity of the bacteria in the seawater of xisha in the south china sea. | 2004 | 15041561 |
| shewanella putrefaciens isolated in a case of ventilator-associated pneumonia. | we report the isolation of the aquatic gram-negative bacterium shewanella putrefaciens from the bronchoalveolar lavage in a case of ventilator-associated pneumonia. to our knowledge, this species has never been isolated from the lower respiratory tract before as a potential pathogen. | 2004 | 15031580 |
| possible involvement of an fkbp family member protein from a psychrotrophic bacterium shewanella sp. sib1 in cold-adaptation. | a psychrotrophic bacterium shewanella sp. strain sib1 was grown at 4 and 20 degrees c, and total soluble proteins extracted from the cells were analyzed by two-dimensional polyacrylamide gel electrophoresis. comparison of these patterns showed that the cellular content of a protein with a molecular mass of 28 kda and an isoelectric point of four greatly increased at 4 degrees c compared to that at 20 degrees c. determination of the n-terminal amino acid sequence, followed by the cloning and sequ ... | 2004 | 15030488 |
| identification of a novel steroid inducible gene associated with the beta hsd locus of comamonas testosteroni. | comamonas testosteroni is a soil bacterium, which can use a variety of steroids as carbon and energy source. even if it can be estimated that the complete degradation of the steroid nucleus requires more than 20 enzymatic reactions, the complete molecular characterization of the genes encoding these steroid degradative enzymes as well as the genetic organization of them remain to be elucidated. we have previously reported the cloning and nucleotide sequence of two steroid-inducible genes, beta h ... | 2004 | 15026087 |
| shewanella gaetbuli sp. nov., a slight halophile isolated from a tidal flat in korea. | a gram-negative, motile, non-spore-forming, rod-shaped strain, tf-27(t) (=kccm 41648(t)=jcm 11814(t)), was isolated from a tidal flat in korea. this organism grew well at 25-35 degrees c, with optimum growth at 30 degrees c. strain tf-27(t) grew optimally in the presence of 2 % nacl; it did not grow without nacl or in the presence of >8 % nacl. strain tf-27(t) simultaneously contained both menaquinones and ubiquinones as isoprenoid quinones. the predominant menaquinone was mk-7 and the predomina ... | 2004 | 15023965 |
| the structure of the core region of the lipopolysaccharide from shewanella algae bry, containing 8-amino-3,8-dideoxy-d-manno-oct-2-ulosonic acid. | the structure of the carbohydrate backbone of the lipid a-core region of the lps from shewanella algae strain bry was analysed. the lps was n,o-deacylated to give three products, which were isolated and studied by chemical methods, nmr and mass spectrometry: [carbohydrate structures: see text]. all monosaccharides except l-rhamnose had the d-configuration. this lps presents a second example (after s. oneidensis) of the structure with a novel linking unit between the core and lipid a moieties, 8- ... | 2004 | 15013415 |
| dissociation behavior of doubly-charged tryptic peptides: correlation of gas-phase cleavage abundance with ramachandran plots. | analysis of fragmentation patterns from 5654 unique doubly charged tryptic peptides is obtained. great variability of average relative abundance of bond cleavage is found between different amino acid combinations. there exist similarities as well as differences between b and y ions. strong enhancement or suppression of cleavage gives insight into possible chemical interactions at reactive conformations formed by preferred phi-psi angles. | 2004 | 15012117 |
| direct observation of microbial inhibition of calcite dissolution. | vertical scanning interferometry (vsi) provides a method for quantification of surface topography at the angstrom to nanometer level. time-dependent vsi measurements can be used to study the surface-normal retreat across crystal and other solid surfaces during dissolution or corrosion processes. therefore, vsi can be used to directly and nondestructively measure mineral dissolution rates with high precision. we have used this method to compare the abiotic dissolution behavior of a representative ... | 2004 | 15006787 |
| vanadium(v) reduction by shewanella oneidensis mr-1 requires menaquinone and cytochromes from the cytoplasmic and outer membranes. | the metal-reducing bacterium shewanella oneidensis mr-1 displays remarkable anaerobic respiratory plasticity, which is reflected in the extensive number of electron transport components encoded in its genome. in these studies, several cell components required for the reduction of vanadium(v) were determined. v(v) reduction is mediated by an electron transport chain which includes cytoplasmic membrane components (menaquinone and the tetraheme cytochrome cyma) and the outer membrane (om) cytochrom ... | 2004 | 15006760 |
| isolation and characterization of integron-containing bacteria without antibiotic selection. | the emergence of antibiotic resistance among pathogenic and commensal bacteria has become a serious problem worldwide. the use and overuse of antibiotics in a number of settings are contributing to the development of antibiotic-resistant microorganisms. the class 1 and 2 integrase genes (inti1 and inti2, respectively) were identified in mixed bacterial cultures enriched from bovine feces by growth in buffered peptone water (bpw) followed by integrase-specific pcr. integrase-positive bacterial co ... | 2004 | 14982773 |
| specification of amino acid residues essential for the catalytic reaction of cold-active protein-tyrosine phosphatase of a psychrophile, shewanella sp. | protein-tyrosine phosphatase [ec 3.1.3.48] from a psychrophile, shewanella sp. shows high activity at low temperatures and has the conserved amino acid sequence of protein-ser/thr-phosphatases. site-directed mutagenesis with the conserved amino acid residues indicated that his148 could be important as a general acid catalyst and asp115 assists the protonation with his148 of the leaving group of a substrate, and that asp76 and asp112 were involved in binding to magnesium ions. | 2004 | 14981312 |
| a new isolation method for labyrinthulids using a bacterium, psychrobacter phenylpyruvicus. | a new isolation method for labyrinthulids, marine microbes with spindle-shaped vegetative cells and gliding movement, is presented. the method for isolating labyrinthulids has been found to be more difficult and less reproducible than that for thraustochytrids, classified in the same order. so far serum seawater agar fortified with antibiotics has been proposed to be the best for isolation of labyrinthulids. the method presented here involves placing plant samples on an agar medium on which a ma ... | 2001 | 14961392 |
| phenazines and other redox-active antibiotics promote microbial mineral reduction. | natural products with important therapeutic properties are known to be produced by a variety of soil bacteria, yet the ecological function of these compounds is not well understood. here we show that phenazines and other redox-active antibiotics can promote microbial mineral reduction. pseudomonas chlororaphis pcl1391, a root isolate that produces phenazine-1-carboxamide (pcn), is able to reductively dissolve poorly crystalline iron and manganese oxides, whereas a strain carrying a mutation in o ... | 2004 | 14766572 |
| role of microbes in the smectite-to-illite reaction. | temperature, pressure, and time have been thought to control the smectite-to-illite (s-i) reaction, an important diagenetic process used for petroleum exploration. we demonstrated that microorganisms can promote the s-i reaction by dissolving smectite through reduction of structural fe(iii) at room temperature and 1 atmosphere within 14 days. this reaction typically requires conditions of 300 degrees to 350 degrees c, 100 megapascals, and 4 to 5 months in the absence of microbial activity. these ... | 2004 | 14764877 |
| toxic effects of chromium(vi) on anaerobic and aerobic growth of shewanella oneidensis mr-1. | cr(vi) was added to early- and mid-log-phase shewanella oneidensis (s. oneidensis) mr-1 cultures to study the physiological state-dependent toxicity of cr(vi). cr(vi) reduction and culture growth were measured during and after cr(vi) reduction. inhibition of growth was observed when cr(vi) was added to cultures of mr-1 growing aerobically or anaerobically with fumarate as the terminal electron acceptor. under anaerobic conditions, there was immediate cessation of growth upon addition of cr(vi) i ... | 2004 | 14763828 |
| inhibition of biological reductive dissolution of hematite by ferrous iron. | bacterial dissimilatory iron reduction is self-inhibited by the production of ferrous [fe(ii)] iron resulting in diminished iron reduction as fe(ii) accumulates. experiments were conducted to investigate the mechanisms of fe(ii) inhibition employing the dissimilatory metal-reducing bacterium shewanella putrefaciens strain cn32 under nongrowth conditions in a system designed to minimize precipitation of ferrous iron minerals. after an initial period (ca. 1 day) of relatively rapid iron reduction, ... | 2004 | 14740735 |
| putrescine, cadaverine, and indole production by bacteria isolated from wild and aquacultured penaeid shrimp stored at 0, 12, 24, and 36 degrees c. | putrescine, cadaverine, and indole production capabilities of bacteria isolated from wild domestic and aquacultured ni-caraguan penaeid shrimp in progressive decomposition states were evaluated. the numbers and types of microorganisms responsible for the production of putrescine, cadaverine, and indole in wild and aquacultured shrimp increased with increasing decomposition temperature and time. throughout the storage experiments, mean aerobic plate counts (log/g) ranged from 4.5 to 9.7 and 4.5 t ... | 2004 | 14717362 |
| hierarchical scaffolding with bambus. | the output of a genome assembler generally comprises a collection of contiguous dna sequences (contigs) whose relative placement along the genome is not defined. a procedure called scaffolding is commonly used to order and orient these contigs using paired read information. this ordering of contigs is an essential step when finishing and analyzing the data from a whole-genome shotgun project. most recent assemblers include a scaffolding module; however, users have little control over the scaffol ... | 2004 | 14707177 |
| the acnd genes of shewenella oneidensis and vibrio cholerae encode a new fe/s-dependent 2-methylcitrate dehydratase enzyme that requires prpf function in vivo. | the propionate utilization operons of several bacteria differ from each other in the occurrence of two genes, acnd and prpf, in place of or in addition to the prpd gene encoding an fe/s-independent 2-methylcitrate dehydratase enzyme. we cloned the acnd and prpf genes from two organisms, shewanella oneidensis and vibrio cholerae, and found that, together, the acnd and prpf proteins restored the ability of a prpd mutant strain of salmonella enterica to grow on propionate as a source of carbon and ... | 2004 | 14702315 |
| chromosome-encoded ambler class d beta-lactamase of shewanella oneidensis as a progenitor of carbapenem-hydrolyzing oxacillinase. | a chromosome-encoded beta-lactamase gene from a shewanella oneidensis reference strain was cloned and expressed in escherichia coli. it encoded a carbapenem-hydrolyzing ambler class d beta-lactamase, oxa-54, that shared 92% amino acid identity with the plasmid-encoded carbapenem-hydrolyzing oxacillinase oxa-48 from klebsiella pneumoniae. this work suggests that shewanella spp. may produce the progenitor of oxacillinases compromising the efficacy of imipenem in clinically relevant gram-negative p ... | 2004 | 14693565 |
| gelbank: a database of annotated two-dimensional gel electrophoresis patterns of biological systems with completed genomes. | gelbank is a publicly available database of two-dimensional gel electrophoresis (2de) gel patterns of proteomes from organisms with known genome information (available at http://gelbank.anl.gov and ftp://bioinformatics.anl.gov/gelbank/). currently it includes 131 completed, mostly microbial proteomes available from the national center for biotechnology information. a web interface allows the upload of 2d gel patterns and their annotation for registered users. the images are organized by species, ... | 2004 | 14681486 |
| phylogenetic analysis and in situ identification of the intestinal microbial community of rainbow trout (oncorhynchus mykiss, walbaum). | to identify the dominant culturable and nonculturable microbiota of rainbow trout intestine. | 2004 | 14678165 |
| structures of polysaccharides and oligosaccharides of some gram-negative marine proteobacteria. | the chemical structures of polysaccharides and lps core oligosaccharides, isolated from various gram-negative marine bacteria from the genera pseudoalteromonas and shewanella belonging to the alteromonadaceae family and gamma-subclass of proteobacteria, are reviewed. the polysaccharides are distinguished by the acidic character (e.g., due to the presence of hexuronic and aldulosonic acids and their derivatives) and the occurrence of unusual sugars, including n-acyl derivatives of 6-deoxyamino su ... | 2003 | 14670708 |
| pore exclusion chromatography-inductively coupled plasma-mass spectrometry for monitoring elements in bacteria: a study on microbial removal of uranium from aqueous solution. | the interstitial spaces between spherical particles in a packed column can act as a sieve that passes microorganisms below a certain size. if the bed is a perfusion-type material (containing a binary distribution of large and small pores), colloidal-size microorganisms are subject only to pore exclusion, while all molecules are subject to size exclusion among the various pores. thus, microorganisms elute first, followed by macromolecules, and then small molecules. coupling this separation method ... | 2003 | 14670051 |
| characterizing gene sets with funcassociate. | summary: funcassociate is a web-based tool to help researchers use gene ontology attributes to characterize large sets of genes derived from experiment. distinguishing features of funcassociate include the ability to handle ranked input lists, and a monte carlo simulation approach that is more appropriate to determine significance than other methods, such as bonferroni or idák p-value correction. funcassociate currently supports 10 organisms (vibrio cholerae, shewanella oneidensis, saccharomyces ... | 2003 | 14668247 |
| bacterial synergism or antagonism in a gel cassette system. | the growth and the metabolic activity of shewanella putrfaciens, brochothrix thermosphacta, and pseudomonas sp., when cultured individually or in all possible combinations in gel cassettes system supplemented with 0.1% glucose at 5 degrees c, were investigated. the overall outcome was that the coexistence of the above-mentioned microorganisms affected not only each growth rate but also their type of metabolic end products compared to the control cultures. these effects were varied and depended o ... | 2003 | 14660367 |
| cell density related h2 consumption in relation to anoxic fe(0) corrosion and precipitation of corrosion products by shewanella oneidensis mr-1. | in the absence of oxygen, a protective h2 film is formed around an fe(0) surface, inhibiting the electron flow from this surface. our study of anoxic corrosion of fe(0) beads revealed that, in the presence of shewanella oneidensis mr-1, h2 removal and precipitation of fe mineral particles on the cell surface are determining processes for corrosion. these two biologically mediated processes were governed by cell density. h2 removal by shewanella oneidensis was detected at cell concentrations of 1 ... | 2003 | 14641597 |
| shewanella sp. ga-22, a psychrophilic hydrocarbonoclastic antarctic bacterium producing polyunsaturated fatty acids. | the effects of different growth media and temperature on production of polyunsaturated fatty acids (pufa) by shewanella sp. ga-22 were investigated. the attempts to characterize the ga-22 genes, homologous to those of pufa biosynthesis gene cluster, was performed. | 2003 | 14633042 |
| integration of electrokinetic-based multidimensional separation/concentration platform with electrospray ionization-fourier transform ion cyclotron resonance-mass spectrometry for proteome analysis of shewanella oneidensis. | this work focuses on the development of a multidimensional electrokinetic-based separation/concentration platform coupled with electrospray ionization-fourier transform ion cyclotron resonance mass spectrometry (esi-fticr-ms) for achieving the high resolution and ultrasensitive analysis of complex protein/peptide mixtures. a microdialysis junction is employed as the interface for on-line combination of capillary isoelectric focusing (cief) with transient capillary isotachophoresis/zone electroph ... | 2003 | 14632047 |
| histidine 61: an important heme ligand in the soluble fumarate reductase from shewanella frigidimarina. | an examination of the x-ray structure of the soluble fumarate reductase from shewanella frigidimarina [taylor, p., pealing, s. l., reid, g. a., chapman, s. k., and walkinshaw, m. d. (1999) nat. struct. biol. 6, 1108-1112] shows the presence of four, bis-his-ligated, c-type hemes and one flavin adenine dinucleotide, fad. the heme groups provide a "molecular wire" for the delivery of electrons to the fad. heme iv is closest to the fad (7.4 a from heme methyl to fad c7), and his61, a ligand to heme ... | 2003 | 14609326 |
| diversity and structure of bacterial communities in arctic versus antarctic pack ice. | a comprehensive assessment of bacterial diversity and community composition in arctic and antarctic pack ice was conducted through cultivation and cultivation-independent molecular techniques. we sequenced 16s rrna genes from 115 and 87 pure cultures of bacteria isolated from arctic and antarctic pack ice, respectively. most of the 33 arctic phylotypes were >97% identical to previously described antarctic species or to our own antarctic isolates. at both poles, the alpha- and gamma-proteobacteri ... | 2003 | 14602620 |
| proteomics of the dissimilatory iron-reducing bacterium shewanella oneidensis mr-1, using a matrix-assisted laser desorption/ionization-tandem-time of flight mass spectrometer. | shewanella oneidensis mr-1 is a gram-negative facultative aerobic bacterium living at oxic-anoxic interfaces in nature. the plasticity of terminal electron-acceptors used under anaerobic conditions is huge, but the adaptation to these different environmental conditions remains unclear. in this work, we used a proteomic approach to study the protein content when the organism is grown under anaerobic respiration conditions on insoluble ferric oxide. by analysis of two-dimensional gel patterns of s ... | 2003 | 14595823 |
| [search for alternative secondary structures of rna, regulating expression of bacterial genes]. | expression of many bacterial genes is regulated by formation of alternative secondary rna structure within the leader mrna sequence. our algorithm designed to search for these structures (basing on analysis of one nucleotide sequence) was applied to analyze operons of amino acid biosynthesis in alpha- and gamma-proteobacteria. the attenuators of these operons are predicted for genomes of some poorly known gamma-proteobacteria including shewanella putrefaciens, attenuators of the tryptophan opero ... | 2003 | 14593920 |
| phospholipid fa of piezophilic bacteria from the deep sea. | phospholipid fa (plfa) profiles were determined on four piezophilic bacteria from the deep sea: moritella japonica dsk1, shewanella violacea dss12, s. benthica db6705, and s. benthica db21mt-2. the total concentrations of plfa were higher in strains grown at low pressure (dsk1, 10 mpa, 27.0 mg/g dry wt cells; dss12, 50 mpa, 24.0 mg/g), and lower in strains grown at high pressure (db6705, 85 mpa, 1.9 mg/g; db21mt-2, 100 mpa, 3.0 mg/g). the piezophilic bacteria were characterized by a high abundan ... | 2003 | 14577669 |
| purification and characterization of an antibacterial protein in the skin secretion of rockfish sebastes schlegeli. | an antibacterial protein in the skin secretion of rockfish (sebastes schlegeli) was purified by lectin affinity chromatography on con a-sepharose and gel filtration on tskgel g3000sw. the antibacterial protein featured the high molecular mass and selective action against gram-negative bacteria. the molecular mass of the protein was estimated to be approximately 150 kda in gel filtration and approximately 75 kda by sds-page, suggesting that it is dimeric. the antibacterial principle was an acidic ... | 2003 | 14522599 |
| reconstitution and characterization of ntrc protein in a deep-sea piezophilic bacterium, shewanella violacea strain dss12. | ntrc protein of piezophilic shewanella violacea was overexpressed and purified, to confirm the protein-dna interaction. an electrophoretic mobility shift assay demonstrated that the ntrc recognizes the sequence for ntrc binding within the region upstream of the glna operon. western blot analysis also showed that the ntrc is expressed at a higher level under high-pressure conditions than under atmospheric pressure conditions. | 2003 | 14519985 |
| a computational study of shewanella oneidensis mr-1: structural prediction and functional inference of hypothetical proteins. | the genomes of many organisms have been sequenced in the last 5 years. typically about 30% of predicted genes from a newly sequenced genome cannot be given functional assignments using sequence comparison methods. in these situations three-dimensional structural predictions combined with a suite of computational tools can suggest possible functions for these hypothetical proteins. suggesting functions may allow better interpretation of experimental data (e.g., microarray data and mass spectrosco ... | 2003 | 14506847 |
| reannotation of shewanella oneidensis genome. | as more and more complete bacterial genome sequences become available, the genome annotation of previously sequenced genomes may become quickly outdated. this is primarily due to the discovery and functional characterization of new genes. we have reannotated the recently published genome of shewanella oneidensis with the following results: 51 new genes have been identified, and functional annotation has been added to the 97 genes, including 15 new and 82 existing ones with previously unassigned ... | 2003 | 14506846 |
| the structure of the rough-type lipopolysaccharide from shewanella oneidensis mr-1, containing 8-amino-8-deoxy-kdo and an open-chain form of 2-acetamido-2-deoxy-d-galactose. | the lps from shewanella oneidensis strain mr-1 was analysed by chemical methods and by nmr spectroscopy and mass spectrometry. the lps contained no polysaccharide o-chain, and its carbohydrate backbone had the following structure: (1s)-galnaco-(1-->4,6)-alpha-gal-(1-->6)-alpha-gal-(1-->3)-alpha-gal-(1-p-3)-alpha-ddhep-(1-->5)-alpha-8-aminokdo4r-(2-->6)-beta-glcn4p-(1-->6)-alpha-glcn1p, where r is p or etnpp. there are several novel aspects to this lps. it contains a novel linking unit between th ... | 2003 | 14499575 |
| shewanella waksmanii sp. nov., isolated from a sipuncula (phascolosoma japonicum). | two marine bacterial strains, kmm 3823(t) and kmm 3836, isolated from a sipuncula (phascolosoma japonicum), a common inhabitant of troitsa bay in the gulf of peter the great (sea of japan), were studied. comparative 16s rrna gene sequence-based phylogenetic analysis placed these bacteria into a separate branch of the 'gammaproteobacteria' within members of the genus shewanella: kmm 3823(t) showed the highest similarity (96.6 %) with shewanella fidelis. the dna g+c contents of the two strains stu ... | 2003 | 13130035 |
| ochrobactrum anthropi misidentified as shewanella putrefaciens. | 2003 | 12958302 | |
| specific surface chemical interactions between hydrous ferric oxide and iron-reducing bacteria determined using pk(a) spectra. | a modified regularized least squares pk(a) spectrum approach is applied to determine disassociation constants and proton binding site concentrations on bacteria, hydrous ferric oxide (hfo), and bacteria/hfo composite surfaces. this involves fitting experimental acid-base titration data to a continuous binding site model for a chemically heterogeneous surface with a variety of reactive groups yielding a pk(a) spectrum. the modified parameter fitting method optimizes simultaneously for both smooth ... | 2003 | 12957582 |
| genetic identification of a respiratory arsenate reductase. | for more than a decade, it has been recognized that arsenate [h2aso41-; as(v)] can be used by microorganisms as a terminal electron acceptor in anaerobic respiration. given the toxicity of arsenic, the mechanistic basis of this process is intriguing, as is its evolutionary origin. here we show that a two-gene cluster (arrab; arsenate respiratory reduction) in the bacterium shewanella sp. strain ana-3 specifically confers respiratory as(v) reductase activity. mutants with in-frame deletions of ei ... | 2003 | 12939408 |
| predictive modelling of growth and enzyme production and activity by a cocktail of pseudomonas spp., shewanella putrefaciens and acinetobacter sp. | the possibility was examined of developing a predictive model that combined microbial growth (increase in cellular number) with extracellular lipolytic and proteolytic enzyme activity of a cocktail of four strains of pseudomonas spp. and one strain each of acinetobacter sp. and shewanella putrefaciens. environmental conditions within the following matrix of conditions were examined: temperature 2-20 degrees c, ph value 4.0-7.5 and water activity (a(w)) 0.95-0.995 and a model was constructed, whi ... | 2003 | 12915038 |
| a derivative of the menaquinone precursor 1,4-dihydroxy-2-naphthoate is involved in the reductive transformation of carbon tetrachloride by aerobically grown shewanella oneidensis mr-1. | transformation of carbon tetrachloride (ct) by shewanella oneidensis mr-1 has been proposed to involve the anaerobic respiratory-chain component menaquinone. to investigate this hypothesis a series of menaquinone mutants were constructed. the menf mutant is blocked at the start of the menaquinone biosynthetic pathway. the menb, mena and meng mutants are all blocked towards the end of the pathway, being unable to produce 1,4-dihydroxy-2-naphthoic acid (dhna), demethyl-menaquinone and menaquinone, ... | 2004 | 12908086 |
| cell surface exposure of the outer membrane cytochromes of shewanella oneidensis mr-1. | to determine if the outer membrane (om) cytochromes of the metal-reducing bacterium shewanella oneidensis mr-1 are exposed on the cell surface. | 2003 | 12904229 |
| curvularia haloperoxidase: antimicrobial activity and potential application as a surface disinfectant. | a presumed antimicrobial enzyme system, the curvularia haloperoxidase system, was examined with the aim of evaluating its potential as a sanitizing agent. in the presence of hydrogen peroxide, curvularia haloperoxidase facilitates the oxidation of halides, such as chloride, bromide, and iodide, to antimicrobial compounds. the curvularia haloperoxidase system caused several-log-unit reductions in counts of bacteria (pseudomonas spp., escherichia coli, serratia marcescens, aeromonas salmonicida, s ... | 2003 | 12902249 |
| the tetraheme cytochrome cyma is required for anaerobic respiration with dimethyl sulfoxide and nitrite in shewanella oneidensis. | the tetraheme c-type cytochrome, cyma, from shewanella oneidensis mr-1 has previously been shown to be required for respiration with fe(iii), nitrate, and fumarate [myers, c. r., and myers, j. m. (1997) j. bacteriol. 179, 1143-1152]. it is located in the cytoplasmic membrane where the bulk of the protein is exposed to the periplasm, enabling it to transfer electrons to a series of redox partners. we have expressed and purified a soluble derivative of cyma (cyma(sol)) that lacks the n-terminal me ... | 2003 | 12899636 |
| cometabolism of cr(vi) by shewanella oneidensis mr-1 produces cell-associated reduced chromium and inhibits growth. | microbial reduction is a promising strategy for chromium remediation, but the effects of competing electron acceptors are still poorly understood. we investigated chromate (cr(vi)) reduction in batch cultures of shewanella oneidensis mr-1 under aerobic and denitrifying conditions and in the absence of an additional electron acceptor. growth and cr(vi) removal patterns suggested a cometabolic reduction; in the absence of nitrate or oxygen, mr-1 reduced cr(vi), but without any increase in viable c ... | 2003 | 12889027 |
| modeling chromate reduction in shewanella oneidensis mr-1: development of a novel dual-enzyme kinetic model. | chromate (cr(vi)) reduction tests were performed with nitrate- and fumarate-grown stationary phase cultures of shewanella oneidensis mr-1 (henceforth referred to as mr-1) and disappearance of cr(vi) was monitored over time. a rapid initial decrease in cr(vi) concentration was observed, which was followed by a slower, steady decrease. these observations appear to be consistent with our previous results indicating that cr(vi) reduction in mr-1 involves at least two mechanisms (viamajala et al., 20 ... | 2003 | 12889019 |
| influence of electron donor/acceptor concentrations on hydrous ferric oxide (hfo) bioreduction. | dissimilatory metal-reducing bacteria (dmrb) facilitate the reduction of fe and mn oxides in anoxic soils and sediments and play an important role in the cycling of these metals and other elements such as carbon in aqueous environments. previous studies investigating the reduction of fe(iii) oxides by dmrb focused on reactions under constant initial electron donor (lactate) and electron acceptor (fe oxide) concentrations. because the concentrations of these reactants can vary greatly in the envi ... | 2003 | 12877465 |
| identification of the gene encoding the sole physiological fumarate reductase in shewanella oneidensis mr-1. | shewanella oneidensis mr-1 is a gram-negative, nonfermentative rod with a complex electron transport system which facilitates its ability to use a variety of terminal electron acceptors, including fumarate, for anaerobic respiration. cmtn-3, a mutant isolated by transposon (tnphoa) mutagenesis, can no longer use fumarate as an electron acceptor; it lacks fumarate reductase activity as well as a 65-kda soluble tetraheme flavocytochrome c. the sequence of the tnphoa-flanking genomic dna of cmtn-3 ... | 2003 | 12872312 |
| characterization of transcriptional regulation of shewanella frigidimarina fe(iii)-induced flavocytochrome c reveals a novel iron-responsive gene regulation system. | the bacterium shewanella frigidimarina can grow anaerobically by utilizing fe(iii) as a respiratory electron acceptor. this results in the synthesis of a number of periplasmic c-type cytochromes, which are absent when the organism is grown in the absence of added fe(iii). one cytochrome, ifca, is synthesized when fe(iii) is present as the sole respiratory electron acceptor or when it is present in combination with oxygen, fumarate, or nitrate. the ifca gene was thus selected for a study of iron- ... | 2003 | 12867466 |
| occurrence and diversity of mesophilic shewanella strains isolated from the north-west pacific ocean. | although bacteria of the genus shewanella belong to one of the readily cultivable groups of "gammaproteobacteria", little is known about the occurrence and abundance of these microorganisms in the marine ecosystem. studies revealed that of 654 isolates obtained from marine invertebrates (ophiuroid amphiopholis kochii, sipuncula phascolosoma japonicum, and holothurian apostichopus japonicus, cucumaria japonica), seawater and sediments of the north-west pacific ocean (i.e. the sea of japan and itu ... | 2003 | 12866857 |
| molecular phylogenetic exploration of bacterial diversity in a bakreshwar (india) hot spring and culture of shewanella-related thermophiles. | the bacterial diversity of a hot spring in bakreshwar, india, was investigated by a culture-independent approach. 16s ribosomal dna clones derived from the sediment samples were found to be associated with gamma-proteobacteria, cyanobacteria, and green nonsulfur and low-gc gram-positive bacteria. the first of the above phylotypes cobranches with shewanella, a well-known iron reducer. this phylogenetic correlation has been exploited to develop culture conditions for thermophilic iron-reducing mic ... | 2003 | 12839826 |
| microbial ferric iron reductases. | almost all organisms require iron for enzymes involved in essential cellular reactions. aerobic microbes living at neutral or alkaline ph encounter poor iron availability due to the insolubility of ferric iron. assimilatory ferric reductases are essential components of the iron assimilatory pathway that generate the more soluble ferrous iron, which is then incorporated into cellular proteins. dissimilatory ferric reductases are essential terminal reductases of the iron respiratory pathway in iro ... | 2003 | 12829278 |
| isolation and characterization of marine psychrophilic phage-host systems from arctic sea ice. | phage-host systems from extreme cold environments have rarely been surveyed. this study is concerned with the isolation and characterization of three different phage-host systems from arctic sea ice and melt pond samples collected north-west of svalbard (arctic). on the basis of 16s rdna sequences, the three bacterial phage hosts exhibited the greatest similarity to the species shewanella frigidimarina (96.0%), flavobacterium hibernum (94.0%), and colwellia psychrerythraea (98.4%), respectively. ... | 2003 | 12820036 |
| overlapping role of the outer membrane cytochromes of shewanella oneidensis mr-1 in the reduction of manganese(iv) oxide. | to determine if the outer membrane (om) cytochromes omca and omcb of the metal-reducing bacterium shewanella oneidensis mr-1 have distinct or overlapping roles in the reduction of insoluble manganese(iv) oxide. | 2003 | 12803550 |
| microbial reduction and precipitation of vanadium by shewanella oneidensis. | shewanella oneidensis couples anaerobic oxidation of lactate, formate, and pyruvate to the reduction of vanadium pentoxide (v(v)). the bacterium reduces v(v) (vanadate ion) to v(iv) (vanadyl ion) in an anaerobic atmosphere. the resulting vanadyl ion precipitates as a v(iv)-containing solid. | 2003 | 12788772 |
| chemical and biological interactions during nitrate and goethite reduction by shewanella putrefaciens 200. | although previous research has demonstrated that no(3)(-) inhibits microbial fe(iii) reduction in laboratory cultures and natural sediments, the mechanisms of this inhibition have not been fully studied in an environmentally relevant medium that utilizes solid-phase, iron oxide minerals as a fe(iii) source. to study the dynamics of fe and no(3)(-) biogeochemistry when ferric (hydr)oxides are used as the fe(iii) source, shewanella putrefaciens 200 was incubated under anoxic conditions in a low-io ... | 2003 | 12788758 |
| involvement of cyclic amp (camp) and camp receptor protein in anaerobic respiration of shewanella oneidensis. | shewanella oneidensis is a metal reducer that can use several terminal electron acceptors for anaerobic respiration, including fumarate, nitrate, dimethyl sulfoxide (dmso), trimethylamine n-oxide (tmao), nitrite, and insoluble iron and manganese oxides. two s. oneidensis mutants, sr-558 and sr-559, with tn5 insertions in crp, were isolated and analyzed. both mutants were deficient in fe(iii) and mn(iv) reduction. they were also deficient in anaerobic growth with, and reduction of, nitrate, fumar ... | 2003 | 12775705 |
| inhibition of bacterial u(vi) reduction by calcium. | the rapid kinetics of bacterial u(vi) reduction and low solubility of uraninite (uo2,cr) make this process an attractive option for removing uranium from groundwater. nevertheless, conditions that may promote or inhibit u(vi) reduction are not well-defined. recent descriptions of ca-uo2-co3 complexes indicate that these species may dominate the aqueous speciation of u(vi) in many environments. we monitored the bacterial reduction of u(vi) in bicarbonate-buffered solution in the presence and abse ... | 2003 | 12775057 |
| catalytic efficiency and some structural properties of cold-active protein-tyrosine-phosphatase. | a procedure was established for expression and purification of abundant recombinant cold-active protein-tyrosine-phosphatase (rcptpase), which showed identical enzymatic characteristics to the native enzyme (ncptpase). the purified rcptpase showed high catalytic activity at low temperature and maximal activity at 30 degrees c. rcptpase has a thermodynamic characteristic in that its activation enthalpy was determined to be low, 4.3 kcal/mol, at temperatures below 19.3 degrees c, where the arrheni ... | 2003 | 12761186 |
| analysis of the shewanella oneidensis proteome by two-dimensional gel electrophoresis under nondenaturing conditions. | proteomes are dynamic, i.e., the protein components of living cells change in response to various stimuli. protein changes can involve shifts in the abundance of protein components, in the interactions of protein components, and in the activity of protein components. two-dimensional gel electrophoresis (2-de) coupled with peptide mass spectrometry is useful for the analysis of relative protein abundance, but the denaturing conditions of classical 2-de do not allow analysis of protein interaction ... | 2003 | 12748955 |
| soft tissue infection and bacteremia caused by shewanella putrefaciens. | shewanella putrefaciens is as yet rarely responsible for clinical syndromes in humans. however, a case involving multiple organs in an elderly male under treatment with appropriate steroids confirms that attention should be devoted to unusual pathogens. | 2003 | 12734291 |
| characterization of the shewanella oneidensis mr-1 decaheme cytochrome mtra: expression in escherichia coli confers the ability to reduce soluble fe(iii) chelates. | shewanella oneidensis mr-1 has the metabolic capacity to grow anaerobically using fe(iii) as a terminal electron acceptor. growth under these conditions results in the de novo synthesis of a number of periplasmic c-type cytochromes, many of which are multiheme in nature and are thought to be involved in the fe(iii) respiratory process. to begin a biochemical study of these complex cytochromes, the mtra gene that encodes an approximate 32-kda periplasmic decaheme cytochrome has been heterologousl ... | 2003 | 12732647 |
| sequence versus structure for the direct detection of 16s rrna on planar oligonucleotide microarrays. | a two-probe proximal chaperone detection system consisting of a species-specific capture probe for the microarray and a labeled, proximal chaperone probe for detection was recently described for direct detection of intact rrnas from environmental samples on oligonucleotide arrays. in this study, we investigated the physical spacing and nucleotide mismatch tolerance between capture and proximal chaperone detector probes that are required to achieve species-specific 16s rrna detection for the diss ... | 2003 | 12732571 |
| the ars detoxification system is advantageous but not required for as(v) respiration by the genetically tractable shewanella species strain ana-3. | arsenate [as(v); haso(4)(2-)] respiration by bacteria is poorly understood at the molecular level largely due to a paucity of genetically tractable organisms with this metabolic capability. we report here the isolation of a new as(v)-respiring strain (ana-3) that is phylogenetically related to members of the genus shewanella and that also provides a useful model system with which to explore the molecular basis of as(v) respiration. this gram-negative strain stoichiometrically couples the oxidati ... | 2003 | 12732551 |
| microbiological reduction of chromium(vi) in presence of pyrolusite-coated sand by shewanella alga simidu atcc 55627 in laboratory column experiments. | hexavalent chromium (cr(vi)) was reduced to non-toxic trivalent chromium (cr(iii)) by a dissimilatory metal reducing bacteria, shewanella alga simidu (bry-mt) atcc 55627. a series of dynamic column experiments were conducted to provide an understanding of cr(vi) reduction by the facultative anaerobe bry-mt in the presence of pyrolusite (beta-mno(2)) coated sand and uncoated-quartz sand. all dynamic column experiments were conducted under growth conditions using cr(vi) as the terminal electron ac ... | 2003 | 12729700 |
| dehydrochlorination of 1,1,1-trichloroethane and pentachloroethane by microbially reduced ferruginous smectite. | reduction of structural fe(iii) in smectite clay minerals has been identified as a means to promote dechlorination of polychlorinated ethanes, but its environmental significance has yet to be fully assessed because fe reduction has normally been achieved by agents uncommon in the environment (e.g., dithionite). this study reports the dehydrochlorination of pentachloroethane and 1,1,1-trichloroethane in the presence of ferruginous smectite reduced by two cultures of microorganisms, shewanella one ... | 2003 | 12729213 |
| specificity in the settlement -- modifying response of bacterial biofilms towards zoospores of the marine alga enteromorpha. | previous studies have shown that the rate of settlement of zoospores of the green alga enteromorpha is stimulated by mixed microbial biofilms and that the number of zoospores settling is positively correlated with the number of bacteria in the biofilm. in the present study the specificity of this relationship has been investigated. ninety-nine strains of marine bacteria were isolated from natural biofilms on rocks and the surface of enteromorpha plants. isolates were screened by denaturing gradi ... | 2003 | 12713460 |
| the roles of natural organic matter in chemical and microbial reduction of ferric iron. | although natural organic matter (nom) is known to be redox reactive, the roles and effectiveness of specific functional groups of nom in metal reduction are still a subject of intense investigation. this study entails the investigation of the fe(iii) reduction kinetics and capacity by three fractionated nom subcomponents in the presence or absence of the dissimilatory metal reducing bacterium shewanella putrefaciens cn32. results indicate that nom was able to reduce fe(iii) abiotically; the redu ... | 2003 | 12711432 |
| shewanella fidelis sp. nov., isolated from sediments and sea water. | two marine bacterial strains, kmm 3582t and kmm 3589, isolated respectively from sediments of the south china sea and sea water of the sea of japan, have been characterized. comparative 16s rdna sequence-based phylogenetic analysis placed the two strains in a separate branch of the gamma-proteobacteria within the members of the genus shewanella. kmm 3582t showed the highest similarity (97.1 and 97.4%, respectively) to shewanella pealeana and shewanella gelidimarina. the g + c contents of the dna ... | 2003 | 12710629 |
| shewanella marinintestina sp. nov., shewanella schlegeliana sp. nov. and shewanella sairae sp. nov., novel eicosapentaenoic-acid-producing marine bacteria isolated from sea-animal intestines. | three novel shewanella species are described on the basis of phenotypic, chemotaxonomic and phylogenetic studies. a total of six novel halophilic, aerobic organisms with the ability to produce eicosapentaenoic acid (epa) were isolated from various sea animals in japan. cells of all six isolates were gram-negative, rod-shaped and motile by means of polar flagella. they were able to produce large amounts of epa (about 20% of the total fatty acids) and had isoprenoid quinones q-7 and q-8 as major c ... | 2003 | 12710618 |
| detection of fatty acids from intact microorganisms by molecular beam static secondary ion mass spectrometry. | we report the use of a surface analysis approach, static secondary ion mass spectrometry (sims) equipped with a molecular (reo(4)(-)) ion primary beam, to analyze the surface of intact microbial cells. sims spectra of 28 microorganisms were compared to fatty acid profiles determined by gas chromatographic analysis of transesterfied fatty acids extracted from the same organisms. the results indicate that surface bombardment using the molecular primary beam cleaved the ester linkage characteristic ... | 2003 | 12689707 |
| evaluation of preservative systems in a sunscreen formula by linear regression method. | a sunscreen formula with eight different preservative systems was evaluated by linear regression, pharmacopeial, and the ctfa (cosmetic, toiletry and fragrance association) methods. the preparations were tested against staphylococcus aureus, burkholderia cepacia, shewanella putrefaciens, escherichia coli, and bacillus sp. the linear regression method proved to be useful in the selection of the most effective preservative system used in cosmetic formulation. | 2003 | 12688287 |
| phylogenetic analysis of bacterial populations in an anaerobic microbial consortium capable of degrading saturation concentrations of tetrachloroethylene. | an anaerobic microbial consortium able to biodegrade saturation levels of perchloroethylene (pce) in a column containing a source zone of pce was examined phylogenetically to determine microbial community structure and spatial variation in relation to the pce source. the consortium was comprised of at least 34 members with 7 organisms sharing affiliations with known respiratory or cometabolic dechlorinators. seven other organisms had their closest phylogenetic relative detected in other environm ... | 2003 | 12674344 |
| alanine dehydrogenase from the psychrophilic bacterium strain pa-43: overexpression, molecular characterization, and sequence analysis. | the gene encoding alanine dehydrogenase (aladh; ec 1.4.1.1) from the marine psychrophilic bacterium strain pa-43 was cloned, sequenced, and overexpressed in escherichia coli. the primary structure was deduced on the basis of the nucleotide sequence. the enzyme subunit contains 371 amino acid residues, and the sequence is 90% and 77% identical, respectively, to aladhs from shewanella ac10 and vibrio proteolyticus. the half-life of pa-43 aladh at 52 degrees c is 9 min, and it is thus more thermola ... | 2003 | 12664266 |
| integrating 'top-down" and "bottom-up" mass spectrometric approaches for proteomic analysis of shewanella oneidensis. | here we present a comprehensive method for proteome analysis that integrates both intact protein measurement ("top-down") and proteolytic fragment characterization ("bottom-up") mass spectrometric approaches, capitalizing on the unique capabilities of each method. this integrated approach was applied in a preliminary proteomic analysis of shewanella oneidensis, a metal-reducing microbe of potential importance to the field of bioremediation. cellular lysates were examined directly by the "bottom- ... | 2002 | 12645901 |
| electron transfer from shewanella algae bry to hydrous ferric oxide is mediated by cell-associated melanin. | shewanella algae bry uses insoluble mineral oxides as terminal electron acceptors, but the mechanism of electron transfer from cell surface to mineral surface is not well understood. we tested the hypothesis that cell-associated melanin produced by s. algae bry serves as an electron conduit for bacterial-mineral reduction. results from fourier transform infrared spectroscopy and cell surface hydrophobicity assays indicated that extracellular melanin was associated with the cell surface. with h(2 ... | 2003 | 12644234 |
| use of artificial neural networks for the accurate prediction of peptide liquid chromatography elution times in proteome analyses. | the use of artificial neural networks (anns) is described for predicting the reversed-phase liquid chromatography retention times of peptides enzymatically digested from proteome-wide proteins. to enable the accurate comparison of the numerous lc/ms data sets, a genetic algorithm was developed to normalize the peptide retention data into a range (from 0 to 1), improving the peptide elution time reproducibility to approximately 1%. the network developed in this study was based on amino acid resid ... | 2003 | 12641221 |
| characterization of microbial communities from coastal waters using microarrays. | molecular methods, including dna probes, were used to identify and enumerate pathogenic vibrio species in the chesapeake bay; our data indicated that vibrio vulnificus exhibits seasonal fluctuations in number. our work included a characterization of total microbial communities from the bay; development of microarrays that identify and quantify the diversity of those communities; and observation of temporal changes in those communities. to identify members of the microbial community, we amplified ... | 2003 | 12620025 |
| effects of isso2 insertions in structural and regulatory genes of the trimethylamine oxide reductase of shewanella oneidensis. | we have isolated three shewanella oneidensis mutants specifically impaired in trimethylamine oxide (tmao) respiration. the mutations arose from insertions of an isso2 element into tora, torr, and tors, encoding, respectively, the tmao reductase tora, the response regulator torr, and the sensor tors. although tora is not the sole enzyme reducing tmao in s. oneidensis, growth analysis showed that it is the main respiratory tmao reductase. use of a plasmid-borne tore'-lacz fusion confirmed that the ... | 2003 | 12618472 |
| in situ environmental cell-transmission electron microscopy study of microbial reduction of chromium(vi) using electron energy loss spectroscopy. | reduction of cr(vi) by the bacterium, shewanella oneidensis (previously classified shewanella putrefaciens strain mr-1), was studied by absorption spectrophotometry and in situ, environmental cell-transmission electron microscopy (ec-tem) coupled with electron energy loss spectroscopy (eels). bacteria from rinsed cultures were placed directly in the environmental cell of the transmission electron microscope and examined under 100 torr pressure. bright field ec-tem images show two distinct popula ... | 2001 | 12597792 |