Publications

anaerobic ammonium oxidation mediated by mn-oxides: from sediment to strain level.	nitrite and (29)n(2) productions in slurry incubations of anaerobically sediment after (15)no(3) or (15)nh(4) labelling in the presence of mn-oxides suggested that anaerobic mn-oxides mediated nitrification coupled with denitrification in muddy intertidal sediments of arcachon bay (sw atlantic french coast). from this sediment, bacterial strains were isolated and physiologically characterized in terms of mn-oxides and nitrate reduction as well as potential anaerobic nitrification. one of the iso ...	2011	21288484
extracellular reduction of hexavalent chromium by cytochromes mtrc and omca of shewanella oneidensis mr-1.	to characterize the roles of cytochromes mtrc and omca of shewanella oneidensis mr-1 in cr(vi) reduction, the impacts of deleting mtrc and/or omca genes on cr(vi) reduction and cellular locations of reduced cr(iii) precipitates were investigated. compared to wild type (wt), deletion of mtrc decreased initial rate of cr(vi) reduction by 43.5%, while deletion of omca or both mtrc and omca lowered the rates by 53.4% and 68.9%, respectively. in wt cells, cr(iii) precipitates were detected by transmi ...	2011	21498755
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
heterologous expression, purification, and characterization of an α-mannosidase belonging to glycoside hydrolase family 99 of shewanella amazonensis.	shewanella amazonensis α-mannosidase (sama99), a member of glycoside hydrolase family 99, was expressed in escherichia coli. the purified sama99 hydrolyzed pyridylamino (pa)-sugars, glc(1)man(9)glcnac(2)-pa, and glc(3)man(9)glcnac(2)-pa, and the product was probably a pyridylamino-decasaccharide in both cases. the mode of action of sama99 was found to be essentially identical to that of rat endo-α-1,2-mannosidase, but the specificity of sama99 was low.	2011	21512220
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
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
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
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
multidrug resistance in hydrocarbon-tolerant gram-positive and gram-negative bacteria.	new gram-positive and gram-negative bacteria were isolated from poeni oily sludge, using enrichment procedures. the six gram-positive strains belong to bacillus, lysinibacillus and rhodococcus genera. the eight gram-negative strains belong to shewanella, aeromonas, pseudomonas and klebsiella genera. isolated bacterial strains were tolerant to saturated (i.e., n-hexane, n-heptane, n-decane, n-pentadecane, n-hexadecane, cyclohexane), monoaromatic (i.e., benzene, toluene, styrene, xylene isomers, e ...	2011	21478643
[shewanella algae bacteremia after contact with seawater in an immunocompromised patient.]		2011	21543067
gapped spectral dictionaries and their applications for database searches of tandem mass spectra.	generating all plausible de novo interpretations of a peptide tandem mass (ms/ms) spectrum (spectral dictionary) and quickly matching them against the database represent a recently emerged alternative approach to peptide identification. however, the sizes of the spectral dictionaries quickly grow with the peptide length making their generation impractical for long peptides. we introduce gapped spectral dictionaries (all plausible de novo interpretations with gaps) that can be easily generated fo ...	2011	21444829
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
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
impacts of shewanella putrefaciens strain cn-32 cells and extracellular polymeric substances on the sorption of as(v) and as(iii) on fe(iii)-(hydr)oxides.	we investigated the effects of shewanella putrefaciens cells and extracellular polymeric substances on the sorption of as(iii) and as(v) to goethite, ferrihydrite, and hematite at ph 7.0. adsorption of as(iii) and as(v) at solution concentrations between 0.001 and 20 µm decreased by 10 to 45% in the presence of 0.3 g l(-1) eps, with as(iii) being affected more strongly than as(v). also, inactivated shewanella cells induced desorption of as(v) from the fe(iii)-(hydr)oxide mineral surfaces. atr-ft ...	2011	21375285
miniaturizing microbial fuel cells.	microbial fuel cells (mfcs) represent an emerging technology for electricity generation from renewable biomass. given the demand for a better understanding of the bio/inorganic interface that plays a key role in mfc energy production, small-scale mfcs are receiving considerable attention owing to their intrinsic advantages in both fundamental studies and applications as high-throughput platforms. here, we present a brief review centered on the development of miniature mfcs at the milliliter to m ...	2011	21075467
competitive reduction of pertechnetate (99tco4-) by dissimilatory metal reducing bacteria and biogenic fe(ii).	the fate of pertechnetate ((99)tc(vii)o(4)(-)) during bioreduction was investigated in the presence of 2-line ferrihydrite (fh) and various dissimilatory metal reducing bacteria (dmrb) (geobacter, anaeromyxobacter, shewanella) in comparison with tco(4)(-) bioreduction in the absence of fh. in the presence of fh, tc was present primarily as a fine-grained tc(iv)/fe precipitate that was distinct from the tc(iv)o(2)·nh(2)o solids produced by direct biological tc(vii) reduction. aqueous tc concentra ...	2011	21210705
pressurized pepsin digestion in proteomics: an automatable alternative to trypsin for integrated top-down bottom-up proteomics.	integrated top-down bottom-up proteomics combined with on-line digestion has great potential to improve the characterization of protein isoforms in biological systems and is amendable to high throughput proteomics experiments. bottom-up proteomics ultimately provides the peptide sequences derived from the tandem ms analyses of peptides after the proteome has been digested. top-down proteomics conversely entails the ms analyses of intact proteins for more effective characterization of genetic var ...	2011	20627868
The spoilage of air-packaged broiler meat during storage at normal and fluctuating storage temperatures.	Bacterial diversity and the major flora present on air-packaged broiler meat during storage at normal (4°C) and fluctuating storage temperatures (0-4°C and 4-10°C) were investigated using culture-dependent and culture-independent approaches. Culture-dependent analysis revealed that the growth of microflora was retarded when broiler meat was stored at lower temperatures (0-4°C). Denaturing gradient gel electrophoresis profiles showed that Staphylococcus spp., Pseudomonas spp., Acinetobacter spp., ...	2012	22184446
Bacterial infections of Chinook salmon, Oncorhynchus tshawytscha (Walbaum), returning to gamete collecting weirs in Michigan.	Herein, we describe the prevalence of bacterial infections in Chinook salmon, Oncorhynchus tshawytscha (Walbaum), returning to spawn in two tributaries within the Lake Michigan watershed. Ten bacterial genera, including Renibacterium, Aeromonas, Carnobacterium, Serratia, Proteus, Pseudomonas, Hafnia, Salmonella, Shewanella and Morganella, were detected in the kidneys of Chinook salmon (n = 480) using culture, serological and molecular analyses. Among these, Aeromonas salmonicida was detected at ...	2012	22168454
Aggrandizing power output from Shewanella oneidensis MR-1 microbial fuel cells using calcium chloride.	There are several interconnected metabolic pathways in bacteria essential for the conversion of carbon electron sources directly into electrical currents using microbial fuel cells (MFCs). This study establishes a direct exogenous method to increase power output from a Shewanella oneidensis MR-1 containing MFC by adding calcium chloride to the culture medium. The current output from each CaCl(2) concentration tested revealed that the addition of CaCl(2) to 1400µM increased the current density by ...	2012	22154401
role of polar and nonpolar residues at the active site for ppiase activity of fkbp22 from shewanella sp. sib1.	fkbp22 from the psychotropic bacterium shewanella sp. sib1 is a homodimeric protein with peptidyl prolyl cis-trans isomerase (ppiase) activity. according to a tertiary model, several nonpolar residues including trp157 and phe197 form a substrate-binding cavity, and asp137 and arg142, which form a salt bridge, are located at the edge of this cavity. to analyze the role of these residues, nine single (d137a, r142a, w157a/f/y, f197a/l/y/w) and one double (d137a/r142a) mutant proteins of sib1 fkbp22 ...	2012	22244380
transcriptome analysis of pellicle formation of shewanella oneidensis.	although the pellicle is one of the major growth modes of microorganisms, the metabolic features of pellicle cells and the determinative factors for pellicle formation are largely unknown. in recent years, biofilm development of shewanella oneidensis, an important model organism for bioremediation studies, has been extensively studied. in this paper, a transcriptional profiling of pellicle cells relative to planktonic cells indicated that cells in pellicles were more metabolically active than th ...	2012	22228442
involvement of cytochrome c cyma in the anaerobic metabolism of rdx by shewanella oneidensis mr-1.	hexahydro-1,3,5-trinitro-1,3,5-triazine (rdx) is a cyclic nitramine explosive commonly used for military applications that is responsible for severe soil and groundwater contamination. in this study, shewanella oneidensis mr-1 was shown to efficiently degrade rdx anaerobically (3.5 µmol·h(-1)·(g protein)(-1)) via two initial routes: (1) sequential n-no(2) reductions to the corresponding nitroso (n-no) derivatives (94% of initial rdx degradation) and (2) denitration followed by ring cleavage. t ...	2012	22260206
removal of methylmercury and tributyltin (tbt) using marine microorganisms.	two marine species of bacteria were isolated that are capable of degrading organometallic contaminants: pseudomonas balearica, which decomposes methylmercury; and shewanella putrefaciens, which decomposes tributyltin. p. balearica decomposed 97% of methylmercury (20.0 μg/l) into inorganic mercury after 3 h, while s. putrefaciens decomposed 88% of tributyltin (55.3 μg sn/l) in real wastewater after 36 h. these data indicate that the two bacteria efficiently decomposed the targeted substances and ...	2012	22212416
shewanella algae bacteremia in a preterm newborn.		2012	22217974
identification of bacterial microflora in the midgut of the larvae and adult of wild caught anopheles stephensi: a step toward finding suitable paratransgenesis candidates.	to describe the midgut microbial diversity and to find the candidate bacteria for the genetic manipulation for the generation of paratransgenic anopheline mosquitoes refractory to transmission of malaria, the microbiota of wild larvae and adult anopheles stephensi mosquito midgut from southern iran was studied using a conventional cell-free culture technique and analysis of a 16s ribosomal rna (rrna) gene sequence library. forty species in 12 genera including seven gram-negative myroides, chryse ...	2012	22074685
A biogeochemical framework for bioremediation of plutonium(V) in the subsurface environment.	Accidental release of plutonium (Pu) from storage facilities in the subsurface environment is a concern for the safety of human beings and the environment. Given the complexity of the subsurface environment and multivalent state of Pu, we developed a quantitative biogeochemical framework for bioremediation of Pu(V)O(2) (+) in the subsurface environment. We implemented the framework in the biogeochemical model CCBATCH by expanding its chemical equilibrium for aqueou ...	2012	22209805
adenylylation control by intra- or intermolecular active-site obstruction in fic proteins.	fic proteins that are defined by the ubiquitous fic (filamentation induced by cyclic amp) domain are known to catalyse adenylylation (also called ampylation); that is, the transfer of amp onto a target protein. in mammalian cells, adenylylation of small gtpases through fic proteins injected by pathogenic bacteria can cause collapse of the actin cytoskeleton and cell death. it is unknown how this potentially deleterious adenylylation activity is regulated in the widespread fic proteins that are f ...	2012	22266942
coastal seawater bacteria harbor a large reservoir of plasmid-mediated quinolone resistance determinants in jiaozhou bay, china.	diversity and prevalence of plasmid-mediated quinolone resistance determinants were investigated in environmental bacteria isolated from surface seawater of jiaozhou bay, china. five qnr gene alleles were identified in 34 isolates by pcr amplification, including qnra3 gene in a shewanella algae isolate, qnrb9 gene in a citrobacter freundii isolate, qnrd gene in 22 proteus vulgaris isolates, qnrs1 gene in 1 enterobacter sp. and 4 klebsiella spp. isolates, and qnrs2 gene in 1 pseudomonas sp. and 4 ...	2012	22252223
Roles of siderophore in manganese-oxide reduction by Shewanella oneidensis MR-1.	Dissimilatory metal-reducing bacteria (DMRB), such as Shewanella oneidensis MR-1, are of great interest for their importance in the biogeochemical cycling of metals and utility in biotechnological processes, such as bioremediation and microbial fuel cells. To identify genes necessary for metal reduction, this study constructed a random transposon-insertion mutant library of MR-1 and screened it for isolating mutants that were deficient in metal reduction. Examination of approximately 5000 mutant ...	2012	22092340
E622, a miniature, virulence-associated mobile element.	Miniature inverted terminal repeat elements (MITEs) are nonautonomous mobile elements that have a significant impact on bacterial evolution. Here we characterize E622, a 611-bp virulence-associated MITE from Pseudomonas syringae, which contains no coding region but has almost perfect 168-bp inverted repeats. Using an antibiotic coupling assay, we show that E622 is transposable and can mobilize an antibiotic resistance gene contained between its borders. Its predicted parent element, designated T ...	2012	22081398
Comparative bioelectricity production from various wastewaters in microbial fuel cells using mixed cultures and a pure strain of Shewanella oneidensis.	Current and power density from four wastewaters, agriculture (AWW), domestic (DWW), paper (PWW), and food/dairy (FDWW), were comparatively evaluated in combination with three inocula: wastewater endogenous microbes (MFC1), Shewanella oneidensis MR-1 (MFC2), and wastewater endogenous microbes with MR-1 (MFC3) in single chamber microbial fuel cells (MFC). Using AWW (0.011mA/cm(2); 0.0013mW/cm(2)) and DWW (0.017mA/cm(2); 0.0036mW/cm(2)), MFC2 was the best candidate providing the maximum current, wh ...	2012	22123299