Publications

redox and ph microenvironments within shewanella oneidensis mr-1 biofilms reveal electron transfer mechanism.	the goal of this research was to quantify the variations in redox potential and ph in shewanella oneidensis mr-1 biofilms respiring on electrodes. we grew s. oneidensis mr-1 on a graphite electrode, which was used to accept electrons for microbial respiration. we modified well-known redox and ph microelectrodes with a built-in reference electrode so that they could operate near polarized surfaces and quantified the redox potential and ph profiles in these biofilms. in addition, we used a ferri / ...	2011	21648431
monodispersed biocompatible silver sulfide nanoparticles: facile extracellular biosynthesis using the γ-proteobacterium, shewanella oneidensis.	interest in engineered metal and semiconductor nanocrystallites continues to grow due to their unique size- and shape-dependent optoelectronic, physicochemical and biological properties. therefore identifying novel non-hazardous nanoparticle synthesis routes that address hydrophilicity, size and shape control and production costs has become a priority. in the present article we report for the first time on the efficient generation of extracellular silver sulfide (ag(2)s) nanoparticles by the met ...	2011	21798382
cold adaptation of the mononuclear molybdoenzyme periplasmic nitrate reductase from the antarctic bacterium shewanella gelidimarina.	the reduction of nitrate to nitrite is catalysed in bacteria by periplasmic nitrate reductase (nap) which describes a system of variable protein subunits encoded by the nap operon. nitrate reduction occurs in the napa subunit, which contains a bis-molybdopterin guanine dinucleotide (mo-mgd) cofactor and one [4fe-4s] iron-sulfur cluster. the activity of periplasmic nitrate reductase (nap) isolated as native protein from the cold-adapted (psychrophilic) antarctic bacterium shewanella gelidimarina ...	2011	22005463
a novel low-temperature-active β-glucosidase from symbiotic serratia sp. tn49 reveals four essential positions for substrate accommodation.	a 2,373-bp full-length gene (bgla49) encoding a 790-residue polypeptide (bgla49) with a calculated mass of 87.8 kda was cloned from serratia sp. tn49, a symbiotic bacterium isolated from the gut of longhorned beetle (batocera horsfieldi) larvae. the deduced amino acid sequence of bgla49 showed the highest identities of 80.1% with a conceptually translated protein from pantoea sp. at-9b (eew02556), 38.3% with the identified glycoside hydrolase (gh) family 3 β-glucosidase from clostridium stercora ...	2011	21559826
deciphering the electron transport pathway for graphene oxide reduction by shewanella oneidensis mr-1.	we determined that graphene oxide reduction by shewanella oneidensis mr-1 requires the mtr respiratory pathway by analyzing a range of mutants lacking these proteins. electron-shuttling compounds accelerated graphene oxide reduction rate by 3 to 5 fold. these results may help facilitate the use of bacteria for large-scale graphene production.	2011	21602337
draft genome sequence of shewanella sp. strain hn-41, which produces arsenic-sulfide nanotubes.	the dissimilatory metal reducing bacterium shewanella sp. strain hn-41 was first reported to produce novel photoactive as-s nanotubes via reduction of as(v) and s(2)o(3)(2-) under anaerobic conditions. here we report the draft genome sequence and annotation of strain hn-41.	2011	21868804
so2907, a putative tonb-dependent receptor, is involved in dissimilatory iron reduction by shewanella oneidensis mr-1.	shewanella oneidensis strain mr-1 utilizes soluble and insoluble ferric ions as terminal electron acceptors during anaerobic respiration. the components of respiratory metabolism are localized in the membrane fractions which include the outer membrane and cytoplasmic membrane. many of the biological components that interact with the various iron forms are proposed to be localized in these membrane fractions. to identify the iron-binding proteins acting either as an iron transporter or as a termi ...	2011	21813652
a survey of culturable aerobic and anaerobic marine bacteria in de novo biofilm formation on natural substrates in st. andrews bay, scotland.	this study reports a novel study of marine biofilm formation comprising aerobic and anaerobic bacteria. samples of quartz and feldspar, minerals commonly found on the earth, were suspended 5 m deep in the north sea off the east coast of st. andrews, scotland for 5 weeks. the assemblage of organisms attached to these stones was cultivated under aerobic and anaerobic conditions in the laboratory. bacteria isolated on marine agar 2216 were all gram-negative and identified to genus level by sequenci ...	2011	21638112
anaerobic biodecolorization mechanism of methyl orange by shewanella oneidensis mr-1.	in this work, we investigated the anaerobic decolorization of methyl orange (mo), a typical azo dye, by shewanella oneidensis mr-1, which can use various organic and inorganic substances as its electron acceptor in natural and engineered environments. s. oneidensis mr-1 was found to be able to obtain energy for growth through anaerobic respiration accompanied with dissimilatory azo-reduction of mo. chemical analysis shows that mo reduction occurred via the cleavage of azo bond. block of mtr resp ...	2011	21808969
bacterial formation of extracellular u(vi) nanowires.	shewanella oneidensis mr-1 rapidly accumulates long, extracellular, u(vi) nanowires composed of polycrystalline chains of discrete meta-schoepite (uo(3)-à2h(2)o) nanocrystallites. the production of uranium(vi) nanowires could provide a novel strategy for remediation of uranium contamination in sediments and aquifers, as well as the recovery of uranium in manufacturing processes.	2011	21681306
Solution and microbial controls on the formation of reduced U(IV) species.	Reduction of U(VI) to U(IV) as the result of direct or indirect microbial activity is currently being explored for in situ remediation of subsurface U plumes, under the assumption that U(IV) solubility is controlled by the low-solubility mineral uraninite (U(IV)-dioxide). However, recent characterizations of U in sediments from biostimulated field sites, as well as laboratory U(VI) bioreduction studies, report on the formation of U(IV) species that lack the U-O(2)-U coordination of uraninite, su ...	2011	21846108
control of proteobacterial central carbon metabolism by the hexr transcriptional regulator: a case study in shewanella oneidensis.	bacteria exploit multiple mechanisms for controlling central carbon metabolism (ccm). thus, a bioinformatic analysis together with some experimental data implicated the hexr transcriptional factor as a global ccm regulator in some lineages of gammaproteobacteria operating as a functional replacement of the cra regulator characteristic of enterobacteriales. in this study, we combined a large scale comparative genomic reconstruction of hexr-controlled regulons in 87 species of proteobacteria with ...	2011	21849503
mapping the iron binding site(s) on the small tetraheme cytochrome of shewanella oneidensis mr-1.	in the model microbe shewanella oneidensis, multi-heme proteins are utilized for respiratory metabolism where metals serve as the terminal electron acceptor. among those is the periplasm-localized small tetraheme cytochrome (stc). stc has been extensively characterized structurally and electrochemically to which electron flow in and out of the protein has been modeled. however, until the present work, no kinetic studies have been performed to probe the route of electron flow or to determine the ...	2011	21682327
characterisation of the microbiota of atlantic mackerel (scomber scombrus).	in this study the microbiota of atlantic mackerel (scomber scombrus) collected by a commercial purse seiner was examined. fish were collected directly from the purse seine and from the refrigerated sea water (rsw) transport tank after loading. the culturable microbiota and specific spoilage bacteria (ssb) were quantified on iron agar lyngby (ial) and identified using commercially available biochemical api® kits on pure cultured isolates. these kits showed to be sub-optimal in characterising the ...	2011	21914558
nile red detection of bacterial hydrocarbons and ketones in a high-throughput format.	a method for use in high-throughput screening of bacteria for the production of long-chain hydrocarbons and ketones by monitoring fluorescent light emission in the presence of nile red is described. nile red has previously been used to screen for polyhydroxybutyrate (phb) and fatty acid esters, but this is the first report of screening for recombinant bacteria making hydrocarbons or ketones. the microtiter plate assay was evaluated using wild-type and recombinant strains of shewanella oneidensis ...	2011	21712420
highly sensitive detection of proteins and bacteria in aqueous solution using surface-enhanced raman scattering and optical fibers.	we report the detection of the proteins lysozyme and cytochrome c as well as the live bacterial cells of shewanella oneidensis mr-1 in aqueous solutions with sensitivities order(s) of magnitude higher than those previously reported. two highly sensitive surface-enhanced raman scattering (sers)-based biosensors using optical fibers have been employed for such label-free macromolecule detections. the first sensor is based on a tip-coated multimode fiber (tcmmf) with a double-substrate "sandwich" s ...	2011	21692506
shewanella arctica sp. nov., an iron-reducing bacterium isolated from arctic marine sediment.	two dissimilatory iron reducing bacteria (ir12t and ir26), which could couple lactate oxidation to iron reduction for energy conservation, were isolated from arctic marine sediment. two isolates were gram-staining-negative, catalase- and oxidase-positive and facultative anaerobic bacteria. cells of the isolates were rod-shaped and motile by means of a polar flagellum. the isolates grew in the presence of 0.5-3.5% (w/v) nacl with the absolute requirement of sodium ion. the isolates were psychroto ...	2011	21724958
solution-based structural analysis of the decaheme cytochrome, mtra, by small-angle x-ray scattering and analytical ultracentrifugation.	the potential exploitation of metal-reducing bacteria as a means for environmental cleanup or alternative fuel is an exciting prospect; however, the cellular processes that would allow for these applications need to be better understood. mtra is a periplasmic decaheme c-type cytochrome from shewanella oneidensis involved in the reduction of extracellular iron oxides and therefore is a critical element in shewanella ability to engage in extracellular charge transfer. as a relatively small 333-res ...	2011	21838277
identification of c-type heme-containing peptides using nonactivated immobilized metal affinity chromatography resin enrichment and higher-energy collisional dissociation.	the c-type cytochromes play essential roles in many biological activities of both prokaryotic and eukaryotic cells, including electron transfer, enzyme catalysis, and induction of apoptosis. we report a novel enrichment strategy for identifying c-type heme-containing peptides that uses nonactivated imac resin. the strategy demonstrated at least 7-fold enrichment for heme-containing peptides digested from a cytochrome c protein standard, and quantitative linear performance was also assessed for h ...	2011	21740036
characterization of microbial communities during anode biofilm reformation in a two-chambered microbial electrolysis cell (mec).	geochip (ii) and single strand conformation polymorphism (sscp) were used to characterize anode microbial communities of a microbial electrolysis cell (mec). biofilm communities, enriched in a two-chamber mec (r1, 0.6v applied) having a coulombic efficiency (ce) of 35±4% and a hydrogen yield [formula: see text] of 31±3%, were used as the inoculum for a new reactor (r2). after three months r2 achieved stable performance with ce=38±4% and [formula: see text] few changes in the predominant populati ...	2011	21939699
comparative genomic reconstruction of transcriptional networks controlling central metabolism in the shewanella genus.	genome-scale prediction of gene regulation and reconstruction of transcriptional regulatory networks in bacteria is one of the critical tasks of modern genomics. the shewanella genus is comprised of metabolically versatile gamma-proteobacteria, whose lifestyles and natural environments are substantially different from escherichia coli and other model bacterial species. the comparative genomics approaches and computational identification of regulatory sites are useful for the in silico reconstruc ...	2011	21810205
roles of two shewanella oneidensis mr-1 extracellular endonucleases.	the dissimilatory iron-reducing bacterium shewanella oneidensis mr-1 is capable of using extracellular dna (edna) as the sole source of carbon, phosphorus, and nitrogen. in addition, we recently demonstrated that s. oneidensis mr-1 requires edna as a structural component during all stages of biofilm formation. in this study, we characterize the roles of two shewanella extracellular endonucleases, exes and exem. while exes is likely secreted into the medium, exem is predicted to remain associated ...	2011	21705528
shewanella upenei sp. nov., a lipolytic bacterium isolated from bensasi goatfish upeneus bensasi.	a gram-staining-negative, motile, non-spore-forming and rod-shaped bacterial strain, 20-23r(t), was isolated from intestine of bensasi goatfish, upeneus bensasi, and its taxonomic position was investigated by using a polyphasic study. phylogenetic analyses based on 16s rrna gene sequences revealed that strain 20-23r(t) belonged to the genus shewanella. strain 20-23r(t) exhibited 16s rrna gene sequence similarity values of 99.5, 99.2, and 97.5% to shewanella algae atcc 51192(t), shewanella haliot ...	2011	21717322
microbiological analysis of the mummy of st. marcian.	the paper provides the results of the microbiological analysis of samples taken from the mummified remains of st. marcian. microorganisms found belong to bacteria and fungi of the genera aspergillus, bacillus, penicillium, sarcina, and shewanella which are all apart of the common air, soil, and human microbial flora and therefore present no health hazard.	2011	22053579
genome-wide protein localization prediction strategies for gram negative bacteria.	genome-wide prediction of protein subcellular localization is an important type of evidence used for inferring protein function. while a variety of computational tools have been developed for this purpose, errors in the gene models and use of protein sorting signals that are not recognized by the more commonly accepted tools can diminish the accuracy of their output.	2011	21810203
Effects of disinfectant and biofilm on the corrosion of cast iron pipes in a reclaimed water distribution system.	The effects of disinfection and biofilm on the corrosion of cast iron pipe in a model reclaimed water distribution system were studied using annular reactors (ARs). The corrosion scales formed under different conditions were characterized by X-ray diffraction (XRD), energy dispersive spectroscopy (EDS), and scanning electron microscopy (SEM), while the bacterial characteristics of biofilm on the surface were determined using several molecular methods. The corrosion scales from the ARs with chlor ...	2011	22209261
transient storage of electrical charge in biofilms of shewanella oneidensis mr-1 growing in a microbial fuel cell.	current output of microbial fuel cells (mfcs) depends on a number of engineering variables mainly related to the design of the fuel cell reactor and the materials used. in most cases the engineering of mfcs relies on the premise that for a constant biomass, current output correlates well with the metabolic activity of the cells. in this study we analyze to what extent, mfc output is also affected by the mode of operation, emphasizing how discontinuous operation can affect temporal patterns of cu ...	2011	21981730
conductive artificial biofilm dramatically enhances bioelectricity production in shewanella-inoculated microbial fuel cells.	a new strategy of electrogen immobilization was developed to construct a conductive artificial biofilm (cab) on an anode of a microbial fuel cell (mfc). the mfcs equipped with an optimized cab exhibited an eleven fold increase in power output compared with natural biofilms.	2011	22048750
cu-doped tio(2) nanoparticles enhance survival of shewanella oneidensis mr-1 under ultraviolet light (uv) exposure.	it has been shown that photocatalytic tio(2) nanoparticles (nps) can be used as an efficient anti-microbial agent under uv light due to generation of reactive oxygen species (ros), while shewanella oneidensis mr-1 is a metal-reducing bacterium highly susceptible to uv radiation. interestingly, we found that the presence of cu-doped tio(2) nps in the cultural medium dramatically increased the survival rates (based on colony-forming unit) of strain mr-1 by over 10,000-fold (incubation without shak ...	2011	21855961
selection of shewanella oneidensis mr-1 gene-knockout mutants that adapt to an electrode-respiring condition.	mutants of shewanella oneidensis mr-1 that adapted to an electrode-respiring condition were selected from a random transposon-insertion mutant library to obtain active current-generating mutants and identify relevant cellular components. the mutants were selected in the presence of an electrode (poised at +0.2 v vs. an ag/agcl reference electrode) as the sole electron acceptor, and they were isolated on agar plates. transposon-insertion sites in the isolated mutants were identified by inverse pc ...	2011	22056453
identification and characterization of alkaline serine protease from goat skin surface metagenome.	abstract: metagenomic dna isolated from goat skin surface was used to construct plasmid dna library in escherichia coli dh10b. recombinant clones were screened for functional protease activity on skim milk agar plates. upon screening 70,000 clones, a clone carrying recombinant plasmid psp1 exhibited protease activity. in vitro transposon mutagenesis and sequencing of the insert dna in this clone revealed an orf of 1890 bp encoding a protein with 630 amino acids which showed significant sequence ...	2011	21906326
thermal stability of cytochrome c₅ of pressure-sensitive shewanella livingstonensis.	cytochrome c₅ of pressure-sensitive shewanella livingstonensis (sl cytc₅) exhibits lower thermal stability than a highly homologous counterpart of pressure-tolerant shewanella violacea. this stability difference is due to an enthalpic effect that can be attributed to the amino acid residue at position 50 (leu or lys). these cytc₅ proteins are appropriate materials for understanding the protein stability mechanism.	2011	21897014
towards a structural understanding of drug and peptide transport within the proton-dependent oligopeptide transporter (pot) family.	one of the principal aims of modern drug design is the targeted delivery of drugs within the body, such as to the central nervous system, combined with their exclusion from the liver and kidneys, which break down foreign molecules and subsequently eliminate them. many of the commonly prescribed drugs are transported into cells and across the plasma membrane via endogenous membrane transporters, whose principal roles are the uptake of essential nutrients for metabolism. in many cases, such drug t ...	2011	21936814
bacterial community associated with the intestinal tract of p. monodon in commercial farms.	the potentially important roles of intestinal bacteria on immune response, disease resistance, and nutrition for the black tiger shrimp penaeus monodon have been increasingly investigated. however, so far, little is known about the intestinal bacterial community of the shrimp in the commercial aquaculture settings. in this study, the intestinal bacterial communities of juvenile p. monodon (70 individuals) from eight commercial farms in thailand were examined using 16s rdna pcr-dgge, and seven 16 ...	2011	21915632
targeted protein degradation of outer membrane decaheme cytochrome mtrc metal reductase in shewanella oneidensis mr-1 measured using biarsenical probe crash-edt(2).	development of efficient microbial biofuel cells requires an ability to exploit interfacial electron transfer reactions to external electron acceptors, such as metal oxides; such reactions occur in the facultative anaerobic gram-negative bacterium shewanella oneidensis mr-1 through the catalytic activity of the outer membrane decaheme c-type cytochrome mtrc. central to the utility of this pathway to synthetic biology is an understanding of cellular mechanisms that maintain optimal mtrc function, ...	2011	21999518
enhanced performance and mechanism study of microbial electrolysis cells using fe nanoparticle-decorated anodes.	anode properties are critical for the performance of microbial electrolysis cells (mecs). in the present study, fe nanoparticle-modified graphite disks were used as anodes to investigate the effects of nanoparticles on the performance of shewanella oneidensis mr-1 in mecs. results demonstrated that the average current densities produced with fe nanoparticle-decorated anodes up to 5.89-fold higher than plain graphite anodes. whole genome microarray analysis of the gene expression showed that gene ...	2011	22080340
Zinc oxide and indium tin oxide thin films for the growth and characterization of Shewanella loihica PV-4 electroactive biofilms.		2011	21921690
glygly-cterm and rhombosortase: a c-terminal protein processing signal in a many-to-one pairing with a rhomboid family intramembrane serine protease.	the rhomboid family of serine proteases occurs in all domains of life. its members contain at least six hydrophobic membrane-spanning helices, with an active site serine located deep within the hydrophobic interior of the plasma membrane. the model member glpg from escherichia coli is heavily studied through engineered mutant forms, varied model substrates, and multiple x-ray crystal studies, yet its relationship to endogenous substrates is not well understood. here we describe an apparent membr ...	2011	22194940
The Response of Shewanella oneidensis MR-1 to Cr(III) Toxicity Differs from that to Cr(VI).	Chromium is a contaminant of concern that is found in drinking water in its soluble, hexavalent form [Cr(VI)] and that is known to be toxic to eukaryotes and prokaryotes. Trivalent chromium [Cr(III)] is thought to be largely harmless due to its low solubility and inability to enter cells. Previous work has suggested that Cr(III) may also be toxic to microorganisms but the mechanism remained elusive. In this work, we probe the toxicity of Cr(III) to Shewanella oneidensis MR-1, a bacterium able to ...	2011	22125549
Effects of specific egg yolk antibody (IgY) on the quality and shelf life of refrigerated Paralichthys olivaceus.	BACKGROUND: The spoilage of fishery food has been attributed to limited types of microorganisms called specific spoilage organisms (SSO). Unlike traditional food-preserving techniques which usually exploit broad-spectrum antimicrobial agents, here, based on the specific antimicrobial activity of egg yolk antibodies (IgY) against two SSO in refrigerated fish (Shewanella putrefaciens and Pseudomonas fluorescens), a novel strategy for fish preservation was suggested and evaluated. RESULTS: During s ...	2011	22052727
High frequency of glucose-utilizing mutants in Shewanella oneidensis MR-1.	Shewanella oneidensis MR-1 has conventionally been considered unable to use glucose as a carbon substrate for growth. The genome sequence of S. oneidensis MR-1 however suggests the ability to use glucose. Here, we demonstrate that during initial glucose exposure, S. oneidensis MR-1 quickly and frequently gains the ability to utilize glucose as a sole carbon source, in contrast to wild-type S. oneidensis, which cannot immediately use glucose as a sole carbon substrate. High-performance liquid chr ...	2011	22092702
Detection of biological uranium reduction using magnetic resonance.	The conversion of soluble uranyl ions (UO?22+) by bacterial reduction to sparingly soluble uraninite (UO(2(s)) ) is being studied as a way of immobilizing subsurface uranium contamination. Under anaerobic conditions, several known types of bacteria including iron and sulfate reducing bacteria have been shown to reduce U (VI) to U (IV). Experiments using a suspension of uraninite (UO(2(s)) ) particles produced by Shewanella putrefaciens CN32 bacteria show a dependence of both longitudinal (T(1) ) ...	2011	22095467
FK506-Binding Protein 22 from a Psychrophilic Bacterium, a Cold Shock-Inducible Peptidyl Prolyl Isomerase with the Ability to Assist in Protein Folding.	Adaptation of microorganisms to low temperatures remains to be fully elucidated. It has been previously reported that peptidyl prolyl cis-trans isomerases (PPIases) are involved in cold adaptation of various microorganisms whether they are hyperthermophiles, mesophiles or phsycrophiles. The rate of cis-trans isomerization at low temperatures is much slower than that at higher temperatures and may cause problems in protein folding. However, the mechanisms by which PPIases are involved in cold ada ...	2011	21954357
biosupported bimetallic pd-au nanocatalysts for dechlorination of environmental contaminants.	biologically produced monometallic palladium nanoparticles (bio-pd) have been shown to catalyze the dehalogenation of environmental contaminants, but fail to efficiently catalyze the degradation of other important recalcitrant halogenated compounds. this study represents the first report of biologically produced bimetallic pd/au nanoparticle catalysts. the obtained catalysts were tested for the dechlorination of diclofenac and trichlorethylene. when aqueous bivalent pd(ii) and trivalent au(iii) ...	2011	21877727
Shewanella putrefaciens, a rare cause of splenic abscess.	Splenic abscess is uncommon and is still associated with significant morbidity and mortality. Gram-negative bacilli are the most commonly isolated organisms, followed by Gram-positive cocci. However, the predominant organisms found depend on the geographic location. Shewanella putrefaciens is a Gram-negative non-fermentative oxidative bacillus found in the environment. Infection usually manifests with a number of clinical syndromes, most commonly as skin or soft tissue infections, typically in p ...	2011	22154677
Shuttling happens: soluble flavin mediators of extracellular electron transfer in Shewanella.	The genus Shewanella contains Gram negative ?-proteobacteria capable of reducing a wide range of substrates, including insoluble metals and carbon electrodes. The utilization of insoluble respiratory substrates by bacteria requires a strategy that is quite different from a traditional respiratory strategy because the cell cannot take up the substrate. Electrons generated by cellular metabolism instead must be transported outside the cell, and perhaps beyond, in order to reduce an insoluble subst ...	2011	22072194
construction and elementary mode analysis of a metabolic model for shewanella oneidensis mr-1.	a stoichiometric model describing the central metabolism of shewanella oneidensis mr-1 wild-type and derivative strains was developed and used in elementary mode analysis (ema). shewanella oneidensis mr-1 can anaerobically respire a diverse pool of electron acceptors, and may be applied in several biotechnology settings, including bioremediation of toxic metals, electricity generation in microbial fuel cells, and whole-cell biocatalysis. the metabolic model presented here was adapted and verifie ...	2011	22024451
dissimilatory reduction of extracellular electron acceptors in anaerobic respiration.	an extension of the respiratory chain to the cell surface is necessary to reduce extracellular electron acceptors like ferric iron or manganese oxides. in the last years more and more compounds were revealed to be reduced at the surface of the outer membrane of gram-negative bacteria and the list does not seem to have an end so far. shewanella as well as geobacter strains are model organisms to discover the biochemistry that enables the dissimilatory reduction of extracellular electron acceptors ...	2011	22179232
the metj regulon in gammaproteobacteria determined by comparative genomics methods.	whole-genome sequencing of bacteria has proceeded at an exponential pace but annotation validation has lagged behind. for instance, the metj regulon, which controls methionine biosynthesis and transport, has been studied almost exclusively in e. coli and salmonella, but homologs of metj exist in a variety of other species. these include some that are pathogenic (e.g. yersinia) and some that are important for environmental remediation (e.g. shewanella) but many of which have not been extensively ...	2011	22082356
specificity of motor components in the dual flagellar system of shewanella putrefaciens cn-32.	bacterial flagellar motors are intricate nanomachines in which the stator units and rotor component flim may be dynamically exchanged during function. similar to other bacterial species, the gammaproteobacterium shewanella putrefaciens cn-32 possesses a complete secondary flagellar system along with a corresponding stator unit. expression of the secondary system occurs during planktonic growth in complex media and leads to the formation of a subpopulation with one or more additional flagella at ...	2011	22151089
manganese sulfide formation via concomitant microbial manganese oxide and thiosulfate reduction.	the dissimilatory metal-reducing bacterium, shewanella oneidensis mr-1 produced γ-mns (rambergite) nanoparticles during the concurrent reduction of mno₂ and thiosulfate coupled to h₂ oxidation. to investigate effect of direct microbial reduction of mno₂ on mns formation, two mr-1 mutants defective in outer membrane c-type cytochromes (δmtrc/δomca and δmtrc/δomca/δmtrf) were also used and it was determined that direct reduction of mno₂ was dominant relative to chemical reduction by biogenic sulfi ...	2011	21951417
lactate oxidation coupled to iron or electrode reduction by geobacter sulfurreducens pca.	geobacter sulfurreducens pca completely oxidized lactate and reduced iron or an electrode, producing pyruvate and acetate intermediates. compared to the current produced by shewanella oneidensis mr-1, g. sulfurreducens pca produced 10-times-higher current levels in lactate-fed microbial electrolysis cells. the kinetic and comparative analyses reported here suggest a prominent role of g. sulfurreducens strains in metal- and electrode-reducing communities supplied with lactate.	2011	22003020
Optimal method for efficiently removing extracellular nanofilaments from Shewanella oneidensis MR-1.	The identification, production, and potential electron conductivity of bacterial extracellular nanofilaments is an area of great study, specifically in Shewanella oneidensis MR-1. While some studies focus on nanofilaments attached to the cellular body, many studies require the removal of these nanofilaments for downstream applications. The removal of nanofilaments from S. oneidensis MR-1 for further study requires not only that the nanofilaments be detached, but also for the cell bodies to remai ...	2011	21963962
The acid-tolerant L-arabinose isomerase from the mesophilic Shewanella sp. ANA-3 is highly active at low temperatures.	ABSTRACT:	2011	22074172
Improving liquid chromatography-mass spectrometry sensitivity using a subambient pressure ionization with nanoelectrospray (SPIN) interface.	In this work, the subambient pressure ionization with nanoelectrospray (SPIN) ion source and interface, which operates at ~15-30 Torr, is demonstrated to be compatible with gradient reversed-phase liquid chromatography-MS applications, exemplified here with the analysis of complex samples (a protein tryptic digest and a whole cell lysate). A low liquid chromatographic flow rate (100-400 nL/min) allowed stable electrospray to be established while avoiding electrical breakdown. Efforts to increase ...	2011	21953185
Stress responses of shewanella.	The shewanellae are ubiquitous in aquatic and sedimentary systems that are chemically stratified on a permanent or seasonal basis. In addition to their ability to utilize a diverse array of terminal electron acceptors, the microorganisms have evolved both common and unique responding mechanisms to cope with various stresses. This paper focuses on the response and adaptive mechanism of the shewanellae, largely based on transcriptional data.	2011	21912550
the structural diversity of carbohydrate antigens of selected gram-negative marine bacteria.	marine microorganisms have evolved for millions of years to survive in the environments characterized by one or more extreme physical or chemical parameters, e.g., high pressure, low temperature or high salinity. marine bacteria have the ability to produce a range of biologically active molecules, such as antibiotics, toxins and antitoxins, antitumor and antimicrobial agents, and as a result, they have been a topic of research interest for many years. among these biologically active molecules, t ...	2011	22073003
Functional assessment of EnvZ/OmpR two-component system in Shewanella oneidensis.	EnvZ and OmpR constitute the bacterial two-component signal transduction system known to mediate osmotic stress response in a number of gram-negative bacteria. In an effort to understand the mechanism through which Shewanella oneidensis senses and responds to environmental osmolarity changes, structure of the ompR-envZ operon was determined with Northern blotting assay and roles of the EnvZ/OmpR two-component system in response to various stresses were investigated with mutational analysis, quan ...	2011	21886811
prediction of biological functions of shewanella-like protein phosphatases (shelphs) across different domains of life.	ppp protein phosphatases are an important enzyme family involved in a variety of aspects of cellular signalling and metabolism. ppps are ubiquitous in eukaryotes, and are also present in many bacteria. canonical eukaryotic ppp phosphotases are represented by five major subfamilies (pp1, pp2a, calcineurin, pp5 and ppef/pp7). we previously reported that three "bacterial-like" ppp groups span the prokaryote-eukaryote boundary, including "shewanella-like" phosphatases (shelphs), which are in the foc ...	2011	21960277
microbial carbon capture cell using cyanobacteria for simultaneous power generation, carbon dioxide sequestration and wastewater treatment.	microbial carbon capture cells (mccs) were constructed with cyanobacteria growing in a photo biocathode in dual-chambered flat plate mediator-less mfcs separated by an anion exchange membrane from the anode compartment containing shewanella putrefaciens. the performance of the mcc with anabaena sparged with co(2)-air mixture was compared with that of a conventional cathode sparged with air only. the power densities achieved were 57.8mw/m(2) for anabaena sparged with a co(2)-air mixture, 39.2mw/m ...	2011	22221988
Fabrication of macroporous chitosan scaffolds doped with carbon nanotubes and their characterization in microbial fuel cell operation.	Chitosan (CHIT) scaffolds doped with multi-walled carbon nanotubes (CNT) were fabricated and evaluated for their utility as a microbial fuel cell (MFC) anodic material. High resolution microscopy verified the ability of Shewanella oneidensis MR-1 to directly colonize CHIT-CNT scaffolds. Cross-linking agents 1-ethyl-3-[3-dimethylaminopropyl] carbodimide hydrochloride (EDC), glutaraldehyde and glyoxal were independently studied for their ability to strengthen the CHIT-CNT matrix without disrupting ...	2011	22113017
evidence-based annotation of gene function in shewanella oneidensis mr-1 using genome-wide fitness profiling across 121 conditions.	most genes in bacteria are experimentally uncharacterized and cannot be annotated with a specific function. given the great diversity of bacteria and the ease of genome sequencing, high-throughput approaches to identify gene function experimentally are needed. here, we use pools of tagged transposon mutants in the metal-reducing bacterium shewanella oneidensis mr-1 to probe the mutant fitness of 3,355 genes in 121 diverse conditions including different growth substrates, alternative electron acc ...	2011	22125499
analysis of the bara/uvry two-component system in shewanella oneidensis mr-1.	the bara/uvry two-component system is well conserved in species of the γ-proteobacteria and regulates numerous processes predominantly by controlling the expression of a subset of noncoding small rnas. in this study, we identified and characterized the bara/uvry two-component system in the gammaproteobacterium shewanella oneidensis mr-1. functional interaction of sensor kinase bara and the cognate response regulator uvry was indicated by in vitro phosphotransfer studies. the expression of two pr ...	2011	21931597
eicosapentaenoic acid plays a role in stabilizing dynamic membrane structure in the deep-sea piezophile shewanella violacea: a study employing high-pressure time-resolved fluorescence anisotropy measurement.	shewanella violacea dss12 is a psychrophilic piezophile that optimally grows at 30mpa. it contains a substantial amount of eicosapentaenoic acid (epa) in the membrane. despite evidence linking increased fatty acid unsaturation and bacterial growth under high pressure, little is known of how the physicochemical properties of the membrane are modulated by unsaturated fatty acids in vivo. by means of the newly developed system performing time-resolved fluorescence anisotropy measurement under high ...	2011	22037146
resin-based investigation of acyl carrier protein interaction networks in escherichia coli.	protein-protein interactions play an integral role in metabolic regulation. elucidation of these networks is complicated by the changing identity of the proteins themselves. here we demonstrate a resin-based technique that leverages the unique tools for acyl carrier protein (acp) modification with non-hydrolyzable linkages. acps from escherichia coli and shewanella oneidensis mr-1 are bound to affigel-15 with varying acyl groups attached and introduced to proteomic samples. isolation of these bi ...	2011	22104437
culture-based and denaturing gradient gel electrophoresis analysis of the bacterial community structure from the intestinal tracts of earthworms(eisenia fetida).	the bacterial communities in the intestinal tracts of earthworm were investigated by culture-dependent and - independent approaches. in total, 72 and 55 pure cultures were isolated from the intestinal tracts of earthworms under aerobic and anaerobic conditions, respectively. aerobic bacteria were classified as aeromonas (40%), bacillus (37%), photobacterium (10%), pseudomonas (7%), and shewanella (6%). anaerobic bacteria were classified as aeromonas (52%), bacillus (27%), shewanella (12%), paeni ...	2011	21952364
investigation of the electron transport chain to and the catalytic activity of the diheme cytochrome c peroxidase ccpa of shewanella oneidensis.	bacterial diheme c-type cytochrome peroxidases (bccps) catalyze the periplasmic reduction of hydrogen peroxide to water. the gammaproteobacterium shewanella oneidensis produces the peroxidase ccpa under a number of anaerobic conditions, including dissimilatory iron-reducing conditions. we wanted to understand the function of this protein in the organism and its putative connection to the electron transport chain to ferric iron. ccpa was isolated and tested for peroxidase activity, and its struct ...	2011	21742904
Two Ancient Bacterial-like PPP Family Phosphatases from Arabidopsis Are Highly Conserved Plant Proteins That Possess Unique Properties.	Protein phosphorylation, catalyzed by the opposing actions of protein kinases and phosphatases, is a cornerstone of cellular signaling and regulation. Since their discovery, protein phosphatases have emerged as highly regulated enzymes with specificity that rivals their counteracting kinase partners. However, despite years of focused characterization in mammalian and yeast systems, many protein phosphatases in plants remain poorly or incompletely characterized. Here, we describe a bioinformatic, ...	2011	21976480
Shewanella dokdonensis sp. nov., isolated from the Dong-do coast sea water at Dokdo island, Korea.	The strain designated as UDC329(T) was obtained from a sea water sample collected off the coast at Dong-do, Dokdo Island, Korea. This strain is Gram-negative, motile, facultative anaerobic non-spore forming, rod-shaped isolate forming dark orange-yellow coloured colonies. This organism grew optimally at 25-30 °C in the presence of 1% NaCl, and at pH 7. The organism grew in the absence of NaCl but did not grow in the presence in NaCl of >7%. Strain UDC329(T) contained both menaquinones and ubiqui ...	2011	21890724
Structure of the O-Specific polysaccharide from Shewanella japonica KMM 3601 containing 5,7-Diacetamido-3,5,7,9-tetradeoxy-D-glycero-D-talo-non-2-ulosonic acid.	Structure of the O-specific polysaccharide chain of the lipopolysaccharide (LPS) of Shewanella japonica KMM 3601 was elucidated. The initial and O-deacylated LPS as well as a trisaccharide representing the O-deacetylated repeating unit of the O-specific polysaccharide were studied by sugar analysis along with 1H and 13C NMR spectroscopy. The polysaccharide was found to contain a rare higher sugar, 5,7-diacetamido-3,5,7,9-tetradeoxy-D-glycero-D-talo-non-2-ulosonic acid (a derivative of 4-epilegio ...	2011	21999540
identification of novel sweet protein for nutritional applications.	the prevalence of obesity and diabetes has increased exponentially in recent years around the globe, especially in india. sweet proteins have the potential to substitute the sugars, by acting as natural, good and low calorie sweeteners. they also do not trigger a demand for insulin in diabetic patients unlike sucrose. in humans, the sweet taste perception is mainly due to taste-specific g protein-coupled heterodimeric receptors t1r2-t1r3. these receptors recognize diverse natural and synthetic s ...	2011	22125379
Identification of nicotinamide mononucleotide deamidase of the bacterial pyridine nucleotide cycle reveals a novel broadly conserved amidohydrolase family.	The pyridine nucleotide cycle is a network of salvage and recycling routes maintaining homeostasis of NAD(P) cofactor pool in the cell. Nicotinamide mononucleotide (NMN) deamidase (EC 3.5.1.42), one of the key enzymes of the bacterial pyridine nucleotide cycle, was originally described in Enterobacteria, but the corresponding gene eluded identification for over 30 years. A genomics-based reconstruction of NAD metabolism across hundreds of bacterial species suggested that NMN deamidase reaction i ...	2011	21953451
pyruvate and lactate metabolism by shewanella oneidensis mr-1 under fermentation, oxygen limitation, and fumarate respiration conditions.	shewanella oneidensis mr-1 is a facultative anaerobe that derives energy by coupling organic matter oxidation to the reduction of a wide range of electron acceptors. here, we quantitatively assessed the lactate and pyruvate metabolism of mr-1 under three distinct conditions: electron acceptor-limited growth on lactate with o(2), lactate with fumarate, and pyruvate fermentation. the latter does not support growth but provides energy for cell survival. using physiological and genetic approaches co ...	2011	21965410
crystal structure of the complex between 4-hydroxybutyrate coa-transferase from clostridium aminobutyricum and coa.	clostridium aminobutyricum ferments 4-aminobutyrate (+¦-aminobutyrate, gaba) to ammonia, acetate and butyrate via 4-hydroxybutyrate that is activated to the coa-thioester catalyzed by 4-hydroxybutyrate coa-transferase. then, 4-hydroxybutyryl-coa is dehydrated to crotonyl-coa, which disproportionates to butyryl-coa and acetyl-coa. cocrystallization of the coa-transferase with the alternate substrate butyryl-coa yielded crystals with non-covalently bound coa and two water molecules at the active s ...	2011	21833509
dehalogenation of trichloroethylene in microbial electrolysis cells with biogenic palladium nanoparticles.		2011	21539223
surface-enhanced raman imaging of intracellular bioreduction of chromate in shewanella oneidensis.	this proposed research aims to use novel nanoparticle sensors and spectroscopic tools constituting surface-enhanced raman spectroscopy (sers) and fluorescence lifetime imaging (flim) to study intracellular chemical activities within single bioremediating microorganism. the grand challenge is to develop a mechanistic understanding of chromate reduction and localization by the remediating bacterium shewanella oneidensis mr-1 by chemical and lifetime imaging. mr-1 has attracted wide interest from t ...	2011	21364911
nosocomial peripancreatic infection associated with shewanella xiamenesis.	shewanella xiamenesis, a newly-established species originally from sea sediments, was repeatedly recovered from peripancreatic drainages in a patient and was the probable pathogen of hospital-acquired peripancreatic infection. commercially-available system misidentified it as shewanella putrefaciens, suggesting some previous reported cases with s. putrefaciens infection might be caused by other shewanella species. precise species identification of shewanella species usually requires gyrb sequenc ...	2011	21546561
a site-saturated mutagenesis study of pentaerythritol tetranitrate reductase reveals that residues 181 and 184 influence ligand binding, stereochemistry and reactivity.	we have conducted a site-specific saturation mutagenesis study of h181 and h184 of flavoprotein pentaerythritol tetranitrate reductase (petn reductase) to probe the role of these residues in substrate binding and catalysis with a variety of a,ß-unsaturated alkenes. single mutations at these residues were sufficient to dramatically increase the enantiopurity of products formed by reduction of 2-phenyl-1-nitropropene. in addition, many mutants exhibited a switch in reactivity to predominantly cata ...	2011	21374779
composition and variability of biofouling organisms in seawater reverse osmosis desalination plants.	seawater reverse osmosis (swro) membrane biofouling remains a common challenge in desalination industry. however, the marine bacterial community that causes membrane fouling is poorly understood. microbial communities at different stage of treatment processes (intake, cartridge filtration and swro) of a desalination pilot plant were examined by both culture-based and culture-independent approaches. bacterial isolates were identified to match genus shewanella, alteromonas, vibrio and cellulophaga ...	2011	21551282
partial functional replacement of cyma by sircd in shewanella oneidensis mr-1.	the gammaproteobacterium shewanella oneidensis mr-1 utilizes a complex electron transfer network composed primarily of c-type cytochromes to respire under anoxic conditions a variety of compounds, including fumarate, nitrate, and dimethyl sulfoxide (dmso), in addition to the minerals fe(iii) and mn(iv). central to several respiratory pathways is cyma, a cytoplasmic membrane-bound tetraheme c-type cytochrome that functions as the major hydroquinone dehydrogenase. to investigate functional redunda ...	2011	21378180
sers spectroscopy and sers imaging of shewanella oneidensis using silver nanoparticles and nanowires.	facile and reproducible sers signals from shewanella oneidensis were obtained utilizing silver nanoparticles (agnps) and silver nanowires (agnws). additionally, sers images identify the distribution of sers hot-spots. one important observation is the synergistically enhanced sers signal when agnps and agnws are used in conjunction, due to constructively enhanced electromagnetic field.	2011	21380475
the chemical-in-++well: a high-throughput technique for identifying solutes eliciting a chemotactic response in motile bacteria.	bacteria, and in particular marine bacteria, can be found in environments that are poor in nutrients. to survive, they are able to move toward more favorable niches by a mechanism called chemotaxis, whose first step consists in the detection of substrates by chemoreceptors. we developed a chemotactic assay enabling rapid testing of several hundred different solutes and we identified several molecules eliciting a chemotactic response from two aquatic shewanella species. we propose that this assay ...	2011	21392571
genome-level homology and phylogeny of shewanella (gammaproteobacteria: lteromonadales: shewanellaceae).	abstract:	2011	21569439
microbes enhance mobility of arsenic in pleistocene aquifer sand from bangladesh.	dissimilatory metal-reducing bacteria can mobilize as, but few studies have studied such processes in deeper orange-colored pleistocene sands containing 1-2 mg kg(-1) as that are associated with low-as groundwater in bangladesh. to address this gap, anaerobic incubations were conducted in replicate over 90 days using natural orange sands initially containing 0.14 mg kg(-1) of 1 m phosphate-extractable as (24 h), >99% as as(v), and 0.8 g kg(-1) of 1.2 m hcl-leachable fe (1 h at 80 °c), 95% as fe( ...	2011	21405115
energy-dependent stability of shewanella oneidensis mr-1 biofilms.	stability and resistance to dissolution are key features of microbial biofilms. how these macroscopic properties are determined by the physiological state of individual biofilm cells in their local physical-chemical and cellular environment is largely unknown. in order to obtain molecular and energetic insight into biofilm stability, we investigated whether maintenance of biofilm stability is an energy-dependent process and whether transcription and/or translation are required for biofilm dissol ...	2011	21572002
analysis of in situ manganese(ii) oxidation in the columbia river and offshore plume: linking aurantimonas and the associated microbial community to an active biogeochemical cycle.	the columbia river is a major source of dissolved nutrients and trace metals for the west coast of north america. a large proportion of these nutrients are sourced from the columbia river estuary, where coastal and terrestrial waters mix and resuspend particulate matter within the water column. as estuarine water is discharged off the coast, it transports the particulate matter, dissolved nutrients and microorganisms forming nutrient-rich and metabolically dynamic plumes. in this study, bacteria ...	2011	21418498
a microfluidic microbial fuel cell fabricated by soft lithography.	here we report a new microfluidic microbial fuel cell (mfc) platform built by soft-lithography techniques. the mfc design includes a unique sub-5 µl polydimethylsiloxane soft chamber featuring carbon cloth electrodes and microfluidic delivery of electrolytes. bioelectricity was generated using shewanella oneidensis mr-1 cultivated on either complex organic substrates or lactate-based minimal medium. these micro-mfcs exhibited fast start-ups, reproducible current generation, and enhanced power de ...	2011	21421307
extracellular polymeric substances from shewanella sp. hrcr-1 biofilms: characterization by infrared spectroscopy and proteomics.	the composition of extracellular polymeric substances (eps) from shewanella sp. hrcr-1 biofilms was investigated using infrared spectroscopy and proteomics to provide insight into potential ecophysiological functions and redox activity of the eps. both bound and loosely associated eps were extracted from shewanella sp. hrcr-1 biofilms prepared using a hollow-fibre membrane biofilm reactor. fourier transform infrared spectra revealed the presence of proteins, polysaccharides, nucleic acids, membr ...	2011	21251176
pulsed multiple reaction monitoring approach to enhancing sensitivity of a tandem quadrupole mass spectrometer.	liquid chromatography (lc)-triple quadrupole mass spectrometers operating in a multiple reaction monitoring (mrm) mode are increasingly used for quantitative analysis of low-abundance analytes in highly complex biochemical matrixes. after development and selection of optimum mrm transitions, sensitivity and data quality limitations are largely related to mass spectral peak interferences from sample or matrix constituents and statistical limitations at low number of ions reaching the detector. he ...	2011	21344863
reproducibility and quantitation of amplicon sequencing-based detection.	to determine the reproducibility and quantitation of the amplicon sequencing-based detection approach for analyzing microbial community structure, a total of 24 microbial communities from a long-term global change experimental site were examined. genomic dna obtained from each community was used to amplify 16s rrna genes with two or three barcode tags as technical replicates in the presence of a small quantity (0.1% wt/wt) of genomic dna from shewanella oneidensis mr-1 as the control. the techni ...	2011	21346791
a novel conico-cylindrical flask aids easy identification of critical process parameters for cultivation of marine bacteria.	a polymethylmethacrylate (pmma) conico-cylindrical flask (ccf) with an inner arrangement consisting of eight equidistantly spaced rectangular strips mounted radially on a circular disk to provide additional surface area for microbial attachment and ports to allow air supply was employed for melanin production by shewanella colwelliana and antibiotic production by pseudoalteromonas rubra. the design allowed comparison of production between (1) ccf with hydrophobic surface (pmma-ccf), (2) ccf with ...	2011	21210106
integrative analysis of transcriptomic and proteomic data of shewanella oneidensis: missing value imputation using temporal datasets.	despite significant improvements in recent years, proteomic datasets currently available still suffer from large number of missing values. integrative analyses based upon incomplete proteomic and transcriptomic datasets could seriously bias the biological interpretation. in this study, we applied a non-linear data-driven stochastic gradient boosted trees (gbt) model to impute missing proteomic values using a temporal transcriptomic and proteomic dataset of shewanella oneidensis. in this dataset, ...	2011	21212895
the octahaem sira catalyses dissimilatory sulfite reduction in shewanella oneidensis mr-1.	shewanella oneidensis mr-1 is a metal reducer that uses a large number of electron acceptors including thiosulfate, polysulfide and sulfite. the enzyme required for thiosulfate and polysulfide respiration has been recently identified, but the mechanisms of sulfite reduction remained unexplored. analysis of mr-1 cultures grown anaerobically with sulfite suggested that the dissimilatory sulfite reductase catalyses six-electron reduction of sulfite to sulfide. reduction of sulfite required menaquin ...	2011	21199252
how does organic matter constrain the nature, size and availability of fe nanoparticles for biological reduction?	few studies have so far examined the kinetics and extent of the formation of fe-colloids in the presence of natural organic ligands. the present study used an experimental approach to investigate the rate and amount of colloidal fe formed in presence of humic substances, by gradually oxidizing fe(ii) at ph 6.5 with or without humic substances (hs) (in this case, humic acid - ha and fulvic acid - fa). without hs, micronic aggregates (0.1-1μm diameter) of nano-lepidocrocite is obtained, whereas, i ...	2011	21482426
selection of bacteria capable of dissimilatory reduction of fe(iii) from a long-term continuous culture on molasses and their use in a microbial fuel cell.	ferric ion-respiring microorganisms (frms) are a group of prokaryotes that use fe(iii) as well as other metals as terminal electron acceptors in the process of anaerobic respiration. special attention is paid to a biotechnological significance of frms because of their potential role in electricity production in microbial fuel cells (mfcs) where the terminal acceptor of the electrons during anaerobic respiration is not a ferric ion but the anode. one of the best known frms is the shewanellaceae f ...	2011	21464603
towards electrosynthesis in shewanella: energetics of reversing the mtr pathway for reductive metabolism.	bioelectrochemical systems rely on microorganisms to link complex oxidation/reduction reactions to electrodes. for example, in shewanella oneidensis strain mr-1, an electron transfer conduit consisting of cytochromes and structural proteins, known as the mtr respiratory pathway, catalyzes electron flow from cytoplasmic oxidative reactions to electrodes. reversing this electron flow to drive microbial reductive metabolism offers a possible route for electrosynthesis of high value fuels and chemic ...	2011	21311751
tools for resolving complexity in the electron transfer networks of multiheme cytochromes c.	examining electron transfer between two proteins with identical spectroscopic signatures is a challenging task. it is supposed that several multiheme cytochromes in shewanella oneidensis form a molecular "wire" through which electrons are transported across the cellular space and a direct study of this transient protein-protein interaction has not yet been reported. in this study, we present variations on catalytic protein film voltammetry and an anaerobic affinity chromatography assay to demons ...	2011	21327265
phylogenetic distribution and evolutionary history of bacterial dead-box proteins.	dead-box proteins are found in all domains of life and participate in almost all cellular processes that involve rna. the presence of dead and helicase_c conserved domains distinguish these proteins. dead-box proteins exhibit rna-dependent atpase activity in vitro, and several also show rna helicase activity. in this study, we analyzed the distribution and architecture of dead-box proteins among bacterial genomes to gain insight into the evolutionary pathways that have shaped their history. we i ...	2011	21437710
feedback stabilization involving redox states of c-type cytochromes in living bacteria.	the formal potential of c-type cytochromes expressed in the bacterial outer membrane was dependent on their redox state functioning in mediating extracellular electron transfer. its negative (positive) shifting accompanying with the oxidization (reduction) of c-type cytochromes can serve to stabilize the redox states in a feedback manner.	2011	21331401
cyclic voltammetric analysis of the electron transfer of shewanella oneidensis mr-1 and nanofilament and cytochrome knock-out mutants.	shewanella is frequently used as a model microorganism for microbial bioelectrochemical systems. in this study, we used cyclic voltammetry (cv) to investigate extracellular electron transfer mechanisms from s. oneidensis mr-1 (wt) and five deletion mutants: membrane bound cytochrome (?mtrc/?omca), transmembrane pili (?pilm-q, ?mshh-q, and ?pilm-q/?mshh-q) and flagella (?flg). we demonstrate that the formal potentials of mediated and direct electron transfer sites of the derived biofilms can be g ...	2011	21402501