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overcoming the anaerobic hurdle in phenotypic microarrays: generation and visualization of growth curve data for desulfovibrio vulgaris hildenborough.growing anaerobic microorganisms in phenotypic microarrays (pm) and 96-well microtiter plates is an emerging technology that allows high throughput survey of the growth and physiology and/or phenotype of cultivable microorganisms. for non-model bacteria, a method for phenotypic analysis is invaluable, not only to serve as a starting point for further evaluation, but also to provide a broad understanding of the physiology of an uncharacterized wild-type organism or the physiology/phenotype of a n ...200918996155
comparative fe and zn k-edge x-ray absorption spectroscopic study of the ferroxidase centres of human h-chain ferritin and bacterioferritin from desulfovibrio desulfuricans.iron uptake by the ubiquitous iron-storage protein ferritin involves the oxidation of two fe(ii) ions located at the highly conserved dinuclear "ferroxidase centre" in individual subunits. we have measured x-ray absorption spectra of four mutants (k86q, k86q/e27d, k86q/e107d, and k86q/e27d/e107d, involving variations of glu to asp on either or both sides of the dinuclear ferroxidase site) of recombinant human h-chain ferritin (rhuhf) in their complexes with reactive fe(ii) and redox-inactive zn( ...200918766385
spin distribution of the h-cluster in the h(ox)-co state of the [fefe] hydrogenase from desulfovibrio desulfuricans: hyscore and endor study of (14)n and (13)c nuclear interactions.hydrogenases are enzymes which catalyze the reversible cleavage of molecular hydrogen into protons and electrons. in [fefe] hydrogenases the active center is a 6fe6s cluster, referred to as the "h-cluster." it consists of the redox-active binuclear subcluster ([2fe](h)) coordinated by cn(-) and co ligands and the cubane-like [4fe-4s](h) subcluster which is connected to the protein via cys ligands. one of these cys ligands bridges to the [2fe](h) subcluster. the co-inhibited form of [fefe] hydrog ...200919011912
residue mutations in [fe-fe]-hydrogenase impedes o(2) binding: a qm/mm investigation.[fe-fe]-hydrogenases are enzymes that reversibly catalyze the reaction of protons and electrons to molecular hydrogen, which occurs in anaerobic media. in living systems, [fe-fe]-hydrogenases are mostly used for h(2) production. the [fe-fe]-hydrogenase h-cluster is the active site, which contains two iron atoms. the latest theoretical investigations1,2 advocate that the structure of di-iron air inhibited species are either fe(p) (ii)-fe(d) (ii)-o-h(-), or fe(p) (ii)-fe(d) (ii)-o-o-h, thus o(2) h ...200920485511
the crystal structure of desulfovibrio vulgaris dissimilatory sulfite reductase bound to dsrc provides novel insights into the mechanism of sulfate respiration.sulfate reduction is one of the earliest types of energy metabolism used by ancestral organisms to sustain life. despite extensive studies, many questions remain about the way respiratory sulfate reduction is associated with energy conservation. a crucial enzyme in this process is the dissimilatory sulfite reductase (dsir), which contains a unique siroheme-[4fe4s] coupled cofactor. here, we report the structure of desulfoviridin from desulfovibrio vulgaris, in which the dsir dsrab (sulfite reduc ...200818829451
the solution structure of a tetraheme cytochrome from shewanella frigidimarina reveals a novel family structural motif.the bacteria belonging to the genus shewanella are facultative anaerobes that utilize a variety of terminal electron acceptors which includes soluble and insoluble metal oxides. the tetraheme c-type cytochrome isolated during anaerobic growth of shewanella frigidimarina ncimb400 ( sfc) contains 86 residues and is involved in the fe(iii) reduction pathways. although the functional properties of sfc redox centers are quite well described, no structures are available for this protein. in this work, ...200818950243
qm/mm-pbsa method to estimate free energies for reactions in proteins.we have developed a method to estimate free energies of reactions in proteins, called qm/mm-pbsa. it estimates the internal energy of the reactive site by quantum mechanical (qm) calculations, whereas bonded, electrostatic, and van der waals interactions with the surrounding protein are calculated at the molecular mechanics (mm) level. the electrostatic part of the solvation energy of the reactant and the product is estimated by solving the poisson-boltzmann (pb) equation, and the nonpolar part ...200818781715
effect of hofmeister ions on protein thermal stability: roles of ion hydration and peptide groups?we have systematically explored the hofmeister effects of cations and anions (0.3-1.75 m range) for acidic desulfovibrio desulfuricans apoflavodoxin (net charge -19, ph 7) and basic horse heart cytochrome c (net charge +17, ph 4.5). the hofmeister effect of the ions on protein thermal stability was assessed by the parameter dt trs/d[ion] (t trs; thermal midpoint). we show that dt trs/d[ion] correlates with ion partition coefficients between surface and bulk water and ion surface tension effects: ...200818782555
purification, crystallization and preliminary x-ray analysis of adenylylsulfate reductase from desulfovibrio vulgaris miyazaki f.sulfur in its various oxidation states is used for energy conservation in many microorganisms. adenylylsulfate reductase is a key enzyme in the sulfur-reduction pathway of sulfate-reducing bacteria. the adenylylsulfate reductase from desulfovibrio vulgaris miyazaki f has been purified and crystallized at 277 k using the vapour-diffusion method with ammonium sulfate as the precipitating agent. a data set was collected to 1.7 a resolution from a single crystal at 100 k using synchrotron radiation. ...200818997328
simultaneous analysis of ultrafast fluorescence decays of fmn binding protein and its mutated proteins by molecular dynamic simulation and electron transfer theory.ultrafast fluorescence decays of fmn binding proteins (fbp) from desulfovibrio vulgaris (miyazaki f) were analyzed with an electron transfer (et) theory by kakitani and mataga (km theory). time-dependent distances among isoalloxazine (iso) and trp-32, tyr-35, and trp-106 in wild-type fbp (wt), among iso and tyr-32, tyr-35, and trp-106 in w32y (trp-32 was replaced by tyr-32), and among iso and tyr-35 and trp-106 in w32a (trp-32 was replaced by ala-32) were determined by molecular dynamic simulati ...200818800855
activated carbon cloth as anode for sulfate removal in a microbial fuel cell.by employing the sulfate-reducing bacterium desulfovibrio desulfuricans we demonstrate the possibility of electricity generation in a microbialfuel cell (mfc) with concomitant sulfate removal. this approach is based on an in situ anodic oxidative depletion of sulfide produced by d. desulfuricans. three different electrode materials, graphite foil (gf), carbon fiber veil (cfv), and high surface area activated carbon cloth (acc), were evaluated for sulfide electrochemical oxidation. in comparison ...200818678035
experimental approaches to kinetics of gas diffusion in hydrogenase.hydrogenases, which catalyze h(2) to h(+) conversion as part of the bioenergetic metabolism of many microorganisms, are among the metalloenzymes for which a gas-substrate tunnel has been described by using crystallography and molecular dynamics. however, the correlation between protein structure and gas-diffusion kinetics is unexplored. here, we introduce two quantitative methods for probing the rates of diffusion within hydrogenases. one uses protein film voltammetry to resolve the kinetics of ...200818685111
strategic roles of axial histidines in structure formation and redox regulation of tetraheme cytochrome c3.tetraheme cytochrome c 3 (cyt c 3) exhibits extremely low reduction potentials and unique properties. since axial ligands should be the most important factors for this protein, every axial histidine of desulfovibrio vulgaris miyazaki f cyt c 3 was replaced with methionine, one by one. on mutation at the fifth ligand, the relevant heme could not be linked to the polypeptide, revealing the essential role of the fifth histidine in heme linking. the fifth histidine is the key residue in the structur ...200818702516
ftir spectroelectrochemical characterization of the ni-fe-se hydrogenase from desulfovibrio vulgaris hildenborough.for the first time a complete characterization by infrared spectroscopy of a ni-fe-se hydrogenase in its different redox states is reported. the ni-fe-se hydrogenase was isolated from desulfovibrio vulgaris hildenborough. two different electron paramagnetic resonance silent and air-stable redox states that are not in equilibrium were detected. upon reduction of these states the catalytically active states ni-r and ni-c appear immediately. these states are in redox equilibrium and their formal re ...200818704522
purification, crystallization and preliminary crystallographic analysis of a dissimilatory dsrab sulfite reductase in complex with dsrc.dissimilatory sulfite reductase (dsir, dsrab) is a key protein in dissimilatory sulfur metabolism, one of the earliest types of energy metabolism to be traced on earth. dsirs are large oligomeric proteins around 200kda forming an alpha(2)beta(2) arrangement and including a unique siroheme-[4fe-4s] coupled cofactor. here, we report the purification, crystallization and preliminary x-ray diffraction analysis of dsir isolated from desulfovibrio vulgaris hildenborough, also known as desulfoviridin. ...200818706503
isolation and characterization of porins from desulfovibrio piger and bilophila wadsworthia: structure and gene sequencing.the outer membrane proteins of desulfovibrio piger and bilophila wadsworthia (omp-dp and omp-bw, respectively) and the genes encoding them (omp-dp and omp-bw) were isolated and characterized. native omp-dp and omp-bw form a trimeric structure of approximately 120 kda. these proteins disaggregated into monomers with a molecular weight of approximately 53 kda after heating at 95 degrees c for 10 min. the pore-forming abilities of these oligomeric proteins demonstrated that they form small nonspeci ...200818709355
the haem-copper oxygen reductase of desulfovibrio vulgaris contains a dihaem cytochrome c in subunit ii.the genome of the sulphate reducing bacterium desulfovibrio vulgaris hildenborough, still considered a strict anaerobe, encodes two oxygen reductases of the bd and haem-copper types. the haem-copper oxygen reductase deduced amino acid sequence reveals that it is a type a2 enzyme, which in its subunit ii contains two c-type haem binding motifs. we have characterized the cytochrome c domain of subunit ii and confirmed the binding of two haem groups, both with met-his iron coordination. hence, this ...200818930018
crystallization and preliminary x-ray crystallographic study of flavoredoxin from desulfovibrio vulgaris miyazaki f.flavoredoxin from desulfovibrio vulgaris miyazaki f has been overexpressed, purified and crystallized using the sitting-drop vapour-diffusion method with 10%(w/v) peg 8000, 0.2 m zinc acetate and 100 mm mes ph 6.0. the diffraction pattern of the crystal extended to 1.05 a resolution under cryogenic conditions. the space group was determined to be p3(1)21, with unit-cell parameters a = b = 53.35, c = 116.22 a. phase determination was carried out by the sad method using methylmercuric chloride.200818765921
development and comparison of sybr green quantitative real-time pcr assays for detection and enumeration of sulfate-reducing bacteria in stored swine manure.to develop and evaluate primer sets targeted to the dissimilatory sulfite reductase gene (dsra) for use in quantitative real-time pcr detection of sulfate-reducing bacteria (srb) in stored swine manure.200819120660
bacteremia caused by desulfovibrio fairfieldensis.desulfovibrio species are anaerobic gram-negative, pleomorphic bacilli rarely causing infection in humans. in the present report, we describe a case of bacteremia caused by desulfovibrio fairfieldensis. the patient, for whom biapenem was administered, rapidly improved without any sequelae. as far as we know, this is the first case report of infection by desulfovibrio species in japan.200818936890
membrane tetraheme cytochrome c(m552) of the ammonia-oxidizing nitrosomonas europaea: a ubiquinone reductase.cytochrome c(m552) (cyt c(m552)) from the ammonia-oxidizing nitrosomonas europaea is encoded by the cycb gene, which is preceded in a gene cluster by three genes encoding proteins involved in the oxidation of hydroxylamine: hao, hydroxylamine oxidoreductase; orf2, a putative membrane protein; cyca, cyt c(554). by amino acid sequence alignment of the core tetraheme domain, cyt c(m552) belongs to the napc/torc family of tetra- or pentaheme cytochrome c species involved in electron transport from m ...200818505274
syntrophic growth on formate: a new microbial niche in anoxic environments.anaerobic syntrophic associations of fermentative bacteria and methanogenic archaea operate at the thermodynamic limits of life. the interspecies transfer of electrons from formate or hydrogen as a substrate for the methanogens is key. contrary requirements of syntrophs and methanogens for growth-sustaining product and substrate concentrations keep the formate and hydrogen concentrations low and within a narrow range. since formate is a direct substrate for methanogens, a niche for microorganism ...200818708519
exopolysaccharides produced by intestinal bifidobacterium strains act as fermentable substrates for human intestinal bacteria.eleven exopolysaccharides (eps) isolated from different human intestinal bifidobacterium strains were tested in fecal slurry batch cultures and compared with glucose and the prebiotic inulin for their abilities to act as fermentable substrates for intestinal bacteria. during incubation, the increases in levels of short-chain fatty acids (scfa) were considerably more pronounced in cultures with eps, glucose, and inulin than in controls without carbohydrates added, indicating that the substrates a ...200818539803
formation of magnetite by bacteria and its application.magnetic particles offer high technological potential since they can be conveniently collected with an external magnetic field. magnetotactic bacteria synthesize bacterial magnetic particles (bacmps) with well-controlled size and morphology. bacmps are individually covered with thin organic membrane, which confers high and even dispersion in aqueous solutions compared with artificial magnetites, making them ideal biotechnological materials. recent molecular studies including genome sequence, mut ...200818559314
structural and functional relationships in the hybrid cluster protein family: structure of the anaerobically purified hybrid cluster protein from desulfovibrio vulgaris at 1.35 a resolution.the hybrid cluster protein (hcp) from the sulfate-reducing bacterium desulfovibrio vulgaris strain hildenborough has been isolated and crystallized anaerobically. the phase problem was solved for a p2(1)2(1)2(1) crystal form using multiple-wavelength anomalous diffraction data collected in the vicinity of the fe k absorption edge. although the overall protein structure is essentially the same as that previously obtained, it shows that the nature of the hybrid cluster has particular differences w ...200818560155
comparative architecture of octahedral protein cages. i. indexed enclosing forms.the architectural elements of four protein cages (bacterio ferritin, human mitochondrial ferritin, sulfur oxygenase reductase and small heat-shock protein) are compared top-to-bottom. the starting points are polyhedra with octahedral symmetry 432 enclosing the cage and delimiting the central cavity, respectively, which have vertices at points of a species-dependent cubic form lattice. the approach is extended from the whole cage to axial-symmetric clusters down to polyhedral forms of single mono ...200818560166
purification, crystallization and preliminary x-ray diffraction analysis of adenosine triphosphate sulfurylase (atps) from the sulfate-reducing bacterium desulfovibrio desulfuricans atcc 27774.native zinc/cobalt-containing atp sulfurylase (atps; ec 2.7.7.4; mgatp:sulfate adenylyltransferase) from desulfovibrio desulfuricans atcc 27774 was purified to homogeneity and crystallized. the orthorhombic crystals diffracted to beyond 2.5 a resolution and the x-ray data collected should allow the determination of the structure of the zinc-bound form of this atps. although previous biochemical studies of this protein indicated the presence of a homotrimer in solution, a dimer was found in the a ...200818607083
manufacture of stable palladium and gold nanoparticles on native and genetically engineered flagella scaffolds.the use of bacterial flagella as templates for the immobilization of pd and au nanoparticles is described. complete coverage of d. desulfuricans flagellar filaments by pd(0) nanoparticles was obtained via the h(2)-mediated reduction of pd(nh3)4]cl2 but similar results were not obtained using haucl4. the introduction of additional cysteine-derived thiol residues in the e. coli flic protein increased au(iii) sorption and reduction onto the surface of the flagellar filament and resulted in the prod ...200818819156
comparative architecture of octahedral protein cages. ii. interplay between structural elements.in paper i [janner (2008). acta cryst. a64, 494-502], the enclosing forms of the monomers of four octahedral holoenzymes (bacterio and mitochondrial ferritins, small heat-shock protein and sulfur oxygenase reductase) were derived, with vertices at points of a cubic lattice and indexed accordingly. the correspondence between vertices and neighboring residues allows a sequential ordering of the vertices within the polyline defined by the c(alpha) atoms of the primary structure. the alignment of th ...200818560167
desulfovibrio vulgaris hildenborough hyde and hydg interact with the hyda subunit of the [fefe] hydrogenase.hyde, hydf, and hydg participate in the synthesis of the complex di-iron center of [fefe] hydrogenases. the hyde, hydf, hydg, hyda, and hydb genes of desulfovibrio vulgaris hildenborough were cloned and his-tag pull-down assays were used to study the potential interaction between hyde, hydf, and hydg with the hyda and hydb protein subunits of the d. vulgaris [fefe] hydrogenase. interaction of hyde and hydg with hyda was demonstrated. hydf did not interact with hyda, and none of the accessory pro ...200818563582
desulfovibrio marinisediminis sp. nov., a novel sulfate-reducing bacterium isolated from coastal marine sediment via enrichment with casamino acids.to obtain amino acid-utilizing sulfate reducers, enrichment culture was carried out with a medium containing casamino acids and sulfate and inoculated with coastal marine sediment from the eutrophic tokyo bay, japan. a sulfate reducer, designated strain c/l2(t), was isolated from the sulfide-producing enrichment culture after further enrichment with lactate and sulfate by means of the agar shake dilution method. cells of strain c/l2(t) were vibrio-shaped, gram-negative, motile rods (0.7-1.0 mum ...200818842870
comparison of microbial community composition and activity in sulfate-reducing batch systems remediating mine drainage.five microbial inocula were evaluated in batch tests for the ability to remediate mine drainage (md). dairy manure (dm), anaerobic digester sludge, substrate from the luttrell (lutr) and peerless jenny king (pjk) sulfate-reducing permeable reactive zones (sr-przs) and material from an md-treatment column that had been inoculated with material from a previous md-treatment column were compared in terms of sulfate and metal removal and ph neutralization. the microbial communities were characterized ...200818512260
polysulfide reduction using sulfate-reducing bacteria in a photocatalytic hydrogen generation system.a hydrogen generation process using photocatalytic reactions has been proposed. in this process, hydrogen sulfide is a source of hydrogen and is turned into polysulfide. in order to establish the cyclic operation of a photocatalytic hydrogen generation system, it is necessary to convert polysulfide back into hydrogen sulfide with a small energy input. this paper proposes the use of sulfate-reducing bacteria (srb) for the regeneration of hydrogen sulfide. batch cultivation of natural source srb s ...200818929995
biocatalysts for fuel cells: efficient hydrogenase orientation for h2 oxidation at electrodes modified with carbon nanotubes.we report the modification of gold and graphite electrodes with commercially available carbon nanotubes for immobilization of desulfovibrio fructosovorans [nife] hydrogenase, for hydrogen evolution or consumption. multiwalled carbon nanotubes, single-walled carbon nanotubes (swcns), and amine-modified and carboxyl-functionalized swcns were used and compared throughout. two separate methods were performed: covalent attachment of oriented hydrogenase by controlled architecture of carbon nanotubes ...200818592277
quinol oxidation by c-type cytochromes: structural characterization of the menaquinol binding site of nrfha.membrane-bound cytochrome c quinol dehydrogenases play a crucial role in bacterial respiration by oxidizing menaquinol and transferring electrons to various periplasmic oxidoreductases. in this work, the menaquinol oxidation site of nrfh was characterized by the determination of the x-ray structure of desulfovibrio vulgaris nrfha nitrite reductase complex bound to 2-heptyl-4-hydroxyquinoline-n-oxide, which is shown to act as a competitive inhibitor of nrfh quinol oxidation activity. the structur ...200818597779
biogeochemical processes in ethanol stimulated uranium-contaminated subsurface sediments.a laboratory incubation experiment was conducted with uranium-contaminated subsurface sediment to assess the geochemical and microbial community response to ethanol amendment. a classical sequence of terminal electron-accepting processes (teaps) was observed in ethanol-amended slurries, with no3- reduction, fe(iii) reduction, so4(2-) reduction, and ch4 production proceeding in sequence until all of the added 13c-ethanol (9 mm) was consumed. approximately 60% of the u(vi) content of the sediment ...200818605559
real-time polymerase chain reaction quantification of specific butyrate-producing bacteria, desulfovibrio and enterococcus faecalis in the feces of patients with colorectal cancer.bacterial metabolites produced in the bowel are potentially related to the genesis of colorectal cancer. butyrate is protective against cancer, whereas hydrogen sulfide and oxygen free radicals can be toxic to the epithelium. the present study was designed to quantitate eubacterium rectale, faecalibacterium prausnitzii (both butyrate-producing bacteria), desulfovibrio (sulfate-reducing bacteria), and enterococcus faecalis (that produces extracellular superoxide) in the feces of patients with col ...200818624900
direct electrochemical study of the multiple redox centers of hydrogenase from desulfovibrio gigas.direct electrochemical response was first time observed for the redox centers of desulfovibrio gigas [nife]-hase, in non-turnover conditions, by cyclic voltammetry, in solution at glassy carbon electrode. the activation of the enzyme was achieved by reduction with h(2) and by electrochemical control and electrocatalytic activity was observed. the inactivation of the [nife]-hase was also attained through potential control. all electrochemical data was obtained in the absence of enzyme inhibitors. ...200818632311
proton pathways in a [nife]-hydrogenase: a theoretical study.we present here a theoretical study to investigate possible proton pathways in the [nife]-hydrogenase from desulfovibrio gigas. the approach used in this study consists of a combination of poisson-boltzmann and monte carlo simulations together with a distance-based network analysis to find possible groups involved in the proton transfer. results obtained at different ph values show a reasonable number of proton active residues distributed by the protein interior and surface, with a concentration ...200817847093
crystallization and preliminary x-ray analysis of a class ii release factor rf3 from a sulfate-reducing bacterium.class ii release factor 3 (rf3) from the sulfate-reducing bacterium desulfovibrio vulgaris miyazaki f, which promotes rapid dissociation of a class i release factor, has been overexpressed, purified and crystallized in complex with gdp at 293 k using the sitting-drop vapour-diffusion method. a data set was collected to 1.8 a resolution from a single crystal at 100 k using synchrotron radiation. the crystal belongs to space group p1, with unit-cell parameters a = 47.39, b = 82.80, c = 148.29 a, a ...200818607091
a qm/mm study of proton transport pathways in a [nife] hydrogenase.a theoretical qm/mm study of the [nife] hydrogenase from desulfovibrio fructosovorans has been performed to investigate possible routes of proton transfer between the active site and the protein surface. we obtained the minimum energy paths, with a modified version of the nudged elastic band method, for a set of proposed pathways. the calculations were carried out for the crystallographic structure and for several structures of the protein obtained from a molecular dynamics simulation. the resul ...200818412257
post-translational modifications of desulfovibrio vulgaris hildenborough sulfate reduction pathway proteins.recent developments in shotgun proteomics have enabled high-throughput studies of a variety of microorganisms at a proteome level and provide experimental validation for predicted open reading frames in the corresponding genome. more importantly, advances in mass spectrometric data analysis now allow mining of large proteomics data sets for the presence of post-translational modifications (ptms). although ptms are a critical aspect of cellular activity, such information eludes cell-wide studies ...200818416566
microbial community analysis of two field-scale sulfate-reducing bioreactors treating mine drainage.the microbial communities of two field-scale pilot sulfate-reducing bioreactors treating acid mine drainage (amd), luttrell and peerless jenny king (pjk), were compared using biomolecular tools and multivariate statistical analyses. the two bioreactors were well suited for this study because their geographic locations and substrate compositions were similar while the characteristics of influent amd, configuration and degree of exposure to oxygen were distinct. the two bioreactor communities were ...200818430021
application of molecular techniques to evaluate the methanogenic archaea and anaerobic bacteria in the presence of oxygen with different cod:sulfate ratios in a uasb reactor.in this paper, the microbial characteristics of the granular sludge in the presence of oxygen (3.0+/-0.7 mg o2 l(-1)) were analyzed using molecular biology techniques. the granules were provided by an upflow anaerobic sludge blanket (uasb) operated over 469 days and fed with synthetic substrate. ethanol and sulfate were added to obtain different cod/so4(2-) ratios (3.0, 2.0, and 1.6). the results of fluorescent in situ hybridization (fish) analyses showed that archaeal cells, detected by the arc ...200818634895
molecular characterization of bacterial communities mineralizing benzene under sulfate-reducing conditions.the microbial communities of in situ reactor columns degrading benzene with sulfate as an electron acceptor were analyzed based on clone libraries and terminal restriction fragment length polymorphism fingerprinting of pcr-amplified 16s rrna genes. the columns were filled with either lava granules or sand particles and percolated with groundwater from a benzene-contaminated aquifer. the predominant organisms colonizing the lava granules were related to magnetobacterium sp., followed by a phyloty ...200818637040
microbial communities in contaminated sediments, associated with bioremediation of uranium to submicromolar levels.microbial enumeration, 16s rrna gene clone libraries, and chemical analysis were used to evaluate the in situ biological reduction and immobilization of uranium(vi) in a long-term experiment (more than 2 years) conducted at a highly uranium-contaminated site (up to 60 mg/liter and 800 mg/kg solids) of the u.s. department of energy in oak ridge, tn. bioreduction was achieved by conditioning groundwater above ground and then stimulating growth of denitrifying, fe(iii)-reducing, and sulfate-reducin ...200818456853
quantification of desulfovibrio vulgaris dissimilatory sulfite reductase gene expression during electron donor- and electron acceptor-limited growth.previous studies have suggested that levels of transcripts for dsra, a gene encoding a subunit of the dissimilatory sulfite reductase, are not directly related to the rates of sulfate reduction in sediments under all conditions. this phenomenon was further investigated with chemostat-grown desulfovibrio vulgaris. under sulfate-limiting conditions, dsra transcript levels increased as the bulk rates of sulfate reduction in the chemostat increased, but transcript levels were similar at all sulfate ...200818658285
two distinct roles for two functional cobaltochelatases (cbik) in desulfovibrio vulgaris hildenborough.the sulfate-reducing bacterium desulfovibrio vulgaris hildenborough possesses a large number of porphyrin-containing proteins whose biosynthesis is poorly characterized. in this work, we have studied two putative cbik cobaltochelatases present in the genome of d. vulgaris. the assays revealed that both enzymes insert cobalt and iron into sirohydrochlorin, with specific activities with iron lower than that measured with cobalt. nevertheless, the two d. vulgaris chelatases complement an e. coli cy ...200818457416
presence and expression of terminal oxygen reductases in strictly anaerobic sulfate-reducing bacteria isolated from salt-marsh sediments.in the anaerobic sulfate-reducing bacterium desulfovibrio vulgaris hildenborough genes were found encoding membrane terminal oxygen reductases of two types: a cytochrome c oxidase and a cytochrome bd oxidase, both enzymes are terminal oxidases typical of facultative or aerobic microorganisms (heidelberg jf, et al., the genome sequence of the anaerobic, sulfate-reducing bacterium d. vulgaris hildenborough. nat biotechnol 2004; 22: 554-9). to apprehend the presence of both oxidases in other sulfat ...200818457966
bioaccumulation of palladium by desulfovibrio fructosivorans wild-type and hydrogenase-deficient strains.wild-type desulfovibrio fructosivorans and three hydrogenase-negative mutants reduced pd(ii) to pd(0). the location of pd(0) nanoparticles on the cytoplasmic membrane of the mutant retaining only cytoplasmic membrane-bound hydrogenase was strong evidence for the role of hydrogenases in pd(0) deposition. hydrogenase activity was retained at acidic ph, shown previously to favor pd(0) deposition.200818689514
the o2-scavenging flavodiiron protein in the human parasite giardia intestinalis.the flavodiiron proteins (fdp) are widespread among strict or facultative anaerobic prokaryotes, where they are involved in the response to nitrosative and/or oxidative stress. unexpectedly, fdps were fairly recently identified in a restricted group of microaerobic protozoa, including giardia intestinalis, the causative agent of the human infectious disease giardiasis. the fdp from giardia was expressed, purified, and extensively characterized by x-ray crystallography, stopped-flow spectroscopy, ...200818077462
evaluation of the sulfate-reducing bacterial population associated with stored swine slurry.hydrogen sulfide, produced by sulfate-reducing bacteria (srb), is one of the most potent malodors emitted from anaerobic swine waste storage systems. however, little is known about the prevalence and diversity of srb in those systems. the goals of this study were to evaluate the srb population in swine manure storage systems and to develop quantitative, real-time pcr (qrt-pcr) assays to target four of the srb groups. dissimilatory sulfite reductase (dsr) gene sequences were obtained from swine s ...200818457964
disulfide bond-dependent mechanism of protection against oxidative stress in pyruvate-ferredoxin oxidoreductase of anaerobic desulfovibrio bacteria.oxidative decarboxylation of pyruvate forming acetyl-coenzyme a is a crucial step in many metabolic pathways. in most anaerobes, this reaction is carried out by pyruvate-ferredoxin oxidoreductase (pfor), an enzyme normally oxygen sensitive except in desulfovibrio africanus (da), where it shows an abnormally high oxygen stability. using site-directed mutagenesis, we have specified a disulfide bond-dependent protective mechanism against oxidative conditions in da pfor. our data demonstrated that t ...200818161989
dehalorespiration with polychlorinated biphenyls by an anaerobic ultramicrobacterium.anaerobic microbial dechlorination is an important step in the detoxification and elimination of polychlorinated biphenyls (pcbs), but a microorganism capable of coupling its growth to pcb dechlorination has not been isolated. here we describe the isolation from sediment of an ultramicrobacterium, strain df-1, which is capable of dechlorinating pcbs containing double-flanked chlorines added as single congeners or as aroclor 1260 in contaminated soil. the isolate requires desulfovibrio spp. in co ...200818223104
protein thermal stabilization by charged compatible solutes: computational studies in rubredoxin from desulfovibrio gigas.molecular dynamics simulation studies of rubredoxin from desulfovibrio gigas (rdg) were used to characterize the molecular mechanism of thermal stabilization by the compatible solute (cs) diglycerol-phospate (dgp). dgp is a negatively charged cs that accumulates under salt stress in archaeoglobus fulgidus. experimental results show that a 100 mm dgp solution exerts a strong protection effect in the half-life of rdg at 363 k (lamosa et al., appl environ microbiol 2000;66:1974-1979). rdg was simul ...200818247348
electron-electron double resonance-detected nmr to measure metal hyperfine interactions: 61ni in the ni-b state of the [nife] hydrogenase of desulfovibrio vulgaris miyazaki f. 200818251542
desulfovibrio carbinoliphilus sp. nov., a benzyl alcohol-oxidizing, sulfate-reducing bacterium isolated from a gas condensate-contaminated aquifer.phenotypic and phylogenetic studies were performed on a novel sulfate-reducing bacterium, strain d41(t), isolated as part of a methanogenic syntrophic culture from a gas condensate-contaminated aquifer undergoing intrinsic bioremediation. the bacterium was a gram-negative, non-spore-forming, curved rod, motile by a single polar flagellum, which oxidized several alcohols incompletely, including methanol, ethanol, 1-propanol, 2-propanol, 1-butanol, 2-butanol, 3-methyl-1-butanol (isoamyl alcohol), ...200818523171
methanogenesis versus electrogenesis: morphological and phylogenetic comparisons of microbial communities.two h-type microbial fuel cells were prepared. the anaerobic chambers were inoculated with rice paddy field soil and fed cellulose as an energy source. in one reactor, the anode and cathode were connected with a wire (closed circuit, cc), while they were not connected in the other reactor (open circuit, oc). the oc reactor actively produced methane. in the cc reactor, however, an electric current of 0.2 to 0.3 ma was constantly generated, and methane production was almost completely suppressed. ...200818256466
hexavalent chromium reduction in desulfovibrio vulgaris hildenborough causes transitory inhibition of sulfate reduction and cell growth.desulfovibrio vulgaris hildenborough is a well-studied sulfate reducer that can reduce heavy metals and radionuclides [e.g., cr(vi) and u(vi)]. cultures grown in a defined medium had a lag period of approximately 30 h when exposed to 0.05 mm cr(vi). substrate analyses revealed that although cr(vi) was reduced within the first 5 h, growth was not observed for an additional 20 h. the growth lag could be explained by a decline in cell viability; however, during this time small amounts of lactate we ...200818265973
selectivity of thiolate ligand and preference of substrate in model reactions of dissimilatory nitrate reductase.complexes analogous to the active site of dissimilatory nitrate reductase from desulfovibrio desulfuricans are synthesized. the hexacoordinated complexes [pph 4][mo (iv)(pph 3)(sr)(mnt) 2] (r = -ch 2ch 3 ( 1), -ch 2ph ( 2)) released pph 3 in solution to generate the active model cofactor, {mo (iv)(sr)(mnt) 2} (1-), ready with a site for nitrate binding. kinetics for nitrate reduction by the complexes 1 and 2 followed michaelis-menten saturation kinetics with a faster rate in the case of 1 ( v ma ...200818335980
enhancement of biogenic sulfide production in a packed-bed bioreactor via critical inoculum design and carrier material selection.sulfate reducing bacteria (srb) are commonly used in environmental bioprocesses for the treatment of acid mine drainage and sulfate wastewaters. biogenic h(2)s is also a potential source of h(2) fuel with the recent development of h(2)s splitting technologies. in this study, a sulfate reducing packed bed bioreactor (pbr) capable of rapidly achieving high volumetric productivities was developed using a novel method of rational inoculum design and the selection of improved biomass carrier material ...200818350591
redox potential difference between desulfovibrio vulgaris and clostridium beijerinckii flavodoxins.the redox potential of the flavin mononucleotide (fmn) hydroquinones for one-electron reduction in the desulfovibrio vulgaris ( d. vulgaris) flavodoxin ( e sq/hq for fmnh (*)/fmnh (-)) was calculated using the crystal structure of the relevant hydroquinone form and compared to the results of the clostridium beijerinckii ( c. beijerinckii) flavodoxin. in d. vulgaris and c. beijerinckii flavodoxins, the protein side chain causes significant downshifts of 170 and 240 mv in e sq/hq, respectively. in ...200818355044
integrative analyses of posttranscriptional regulation in the yeast saccharomyces cerevisiae using transcriptomic and proteomic data.correlation between mrna and protein expression is typically modest due to substantial posttranscriptional regulation. using large-scale transcriptomic and proteomic data of the yeast saccharomyces cerevisiae, we quantitatively examined the effects of several posttranscriptional biological properties on the correlation between mrna and protein expression levels (mrna-protein correlation) on a genomewide scale. the two classes of properties investigated are (1) stability of mrna and protein molec ...200818363056
gene expression by the sulfate-reducing bacterium desulfovibrio vulgaris hildenborough grown on an iron electrode under cathodic protection conditions.the genome sequence of the sulfate-reducing bacterium desulfovibrio vulgaris hildenborough was reanalyzed to design unique 70-mer oligonucleotide probes against 2,824 probable protein-coding regions. these included three genes not previously annotated, including one that encodes a c-type cytochrome. using microarrays printed with these 70-mer probes, we analyzed the gene expression profile of wild-type d. vulgaris grown on cathodic hydrogen, generated at an iron electrode surface with an imposed ...200818310429
mercury biomethylation assessment in the estuary of bilbao (north of spain).the relationship between the microbial methylation of mercury and the microbial activities in sediments and water collected from the estuary of bilbao (north of spain) was studied in three different sampling points and in two different seasons. three different cultures were prepared with a sediment slurry to distinguish between biotic and abiotic methylation pathways and the variations of the methylmercury concentration and the variations of the population of total number of bacteria (tdc), anae ...200818313183
periplasmic nitrate reductase revisited: a sulfur atom completes the sixth coordination of the catalytic molybdenum.nitrate reductase from desulfovibrio desulfuricans atcc 27774 (ddnapa) is a monomeric protein of 80 kda harboring a bis(molybdopterin guanine dinucleotide) active site and a [4fe-4s] cluster. previous electron paramagnetic resonance (epr) studies in both catalytic and inhibiting conditions showed that the molybdenum center has high coordination flexibility when reacted with reducing agents, substrates or inhibitors. as-prepared ddnapa samples, as well as those reacted with substrates and inhibit ...200818327621
a new type of metal-binding site in cobalt- and zinc-containing adenylate kinases isolated from sulfate-reducers desulfovibrio gigas and desulfovibrio desulfuricans atcc 27774.adenylate kinase (ak) mediates the reversible transfer of phosphate groups between the adenylate nucleotides and contributes to the maintenance of their constant cellular level, necessary for energy metabolism and nucleic acid synthesis. the ak were purified from crude extracts of two sulfate-reducing bacteria (srb), desulfovibrio (d.) gigas ncib 9332 and desulfovibrio desulfuricans atcc 27774, and biochemically and spectroscopically characterised in the native and fully cobalt- or zinc-substitu ...200818328566
contributions of fermentative acidogenic bacteria and sulfate-reducing bacteria to lactate degradation and sulfate reduction.the roles of fermentative acidogenic bacteria and sulfate-reducing bacteria (srb) in lactate degradation and sulfate reduction in a sulfidogenic bioreactor were investigated by traditional chemical monitoring and culture-independent methods. a continuously stirred tank reactor fed with synthetic wastewater containing lactate and so(2-)(4) at 35 degrees c, 10h of hydraulic retention time was used. the results showed that sulfate removal efficiency reached 99%, and sulfide and acetate were the mai ...200818331751
role of cations in stability of acidic protein desulfovibrio desulfuricans apoflavodoxin.apoflavodoxin from the sulfate reducing bacteria desulfovibrio desulfuricans is a small, acidic protein with a net charge of -19 at neutral ph. here, we show that monovalent cations in biologically relevant amounts have dramatic effects on apoflavodoxin stability. the effect is largest for gdm(+) and decreases as a function of increased cation charge density (gdm(+)>nh(4)(+)k(+) approximately cs(+) approximately na(+)>li(+)). a linear correlation of stabilizing effects with cation hydration prop ...200818342618
cobalt limitation of growth and mercury methylation in sulfate-reducing bacteria.sulfate-reducing bacteria (srb) have been identified as the primary organisms responsible for monomethylmercury (mehg) production in aquatic environments, but little is known of the physiologyand biochemistry of mercury(hg) methylation. corrinoid compounds have been implicated in enzymatic hg methylation, although recent experiments with a vitamin b12 inhibitor indicated that incomplete-oxidizing srb likely do not use a corrinoid-enzyme for hg methylation, whereas experiments with complete-oxidi ...200818350881
ferric iron reduction by desulfovibrio vulgaris hildenborough wild type and energy metabolism mutants.desulfovibrio vulgaris hildenborough wild type and its hyn1, hyd and hmc mutants, lacking genes for periplasmic [nife] hydrogenase-1, periplasmic [fefe] hydrogenase or the transmembrane high molecular weight cytochrome (hmc) complex, respectively, were able to reduce fe(iii) chelated with nitrilotriacetic acid (nta), but not insoluble ferric oxide, with lactate as the electron donor. the rate and extent of fe(iii)-nta reduction followed the order hyn = wt > hmc >> hyd, suggesting that reduction ...200817588123
growth and cometabolic reduction kinetics of a uranium- and sulfate-reducing desulfovibrio/clostridia mixed culture: temperature effects.bioremediation of contaminated soils and aquifers is subject to spatial and temporal temperature changes that can alter the kinetics of key microbial processes. this study quantifies temperature effects on the kinetics of an ethanol-fed sulfate-reducing mixed culture derived from a uranium-contaminated aquifer subject to seasonal temperature fluctuations. the mixed culture contains desulfovibrio sp. and a clostridia-like organism. rates of growth, ethanol utilization, decay, and uranium reductio ...200817929318
a sulfate-reducing bacterium with unusual growing capacity in moderately acidic conditions.the use of sulfate-reducing bacteria (srb) is a cost-effective route to treat sulfate- contaminated waters and precipitate metals. the isolation and characterization of a srb strain from an amd in a brazilian tropical region site was carried out. with a moderately acidic ph (5.5), the c.1 strain began its growth and with continued growth, modified the ph accordingly. the strain under these conditions reduced sulfate at the same rate as an experiment performed using an initial ph of 7.0. the dsrb ...200818040868
integrated bacterial process for the treatment of a spent nickel catalyst.integrated biological processes involving the dissolution and subsequent precipitation have been used for the treatment of the spent material from the hydrogenation of vegetable oil containing a high-level of nickel. our results show that nickel was successfully leached using acidithiobacillus thiooxidans. the percentages of nickel leached using a. thiooxidans were higher than those obtained with dilute sulphuric acid solutions. due to the physical characteristics of the residue, the best result ...200818079054
secondary structures and functional requirements for thim riboswitches from desulfovibrio vulgaris, erwinia carotovora and rhodobacter spheroides.abstract bacterial thim riboswitches contain aptamer domains that bind the metabolite thiamine pyrophosphate (tpp). binding of tpp to the aptamer domain induces structural rearrangements that are relayed to the expression domain, thereby interfering with gene expression. here, we report identification of three putative thim riboswitches from different bacteria and analysis of their secondary structures. chemical probing revealed that the riboswitches share similar secondary structures in their a ...200818163882
competition and coexistence of sulfate-reducing bacteria, acetogens and methanogens in a lab-scale anaerobic bioreactor as affected by changing substrate to sulfate ratio.the microbial population structure and function of natural anaerobic communities maintained in lab-scale continuously stirred tank reactors at different lactate to sulfate ratios and in the absence of sulfate were analyzed using an integrated approach of molecular techniques and chemical analysis. the population structure, determined by denaturing gradient gel electrophoresis and by the use of oligonucleotide probes, was linked to the functional changes in the reactors. at the influent lactate t ...200818305937
the influence of ionic strength, nutrients and ph on bacterial adhesion to metals.bacteria-metal interactions in aqueous solutions are important in biofilm formation, biofouling and biocorrosion problems in the natural environment and engineered systems. in this study, the adhesion forces of two anaerobes (desulfovibrio desulfuricans and desulfovibrio singaporenus) and an aerobe (pseudomonas sp.) to stainless steel 316 in various aqueous systems were quantified using atomic force microscopy (afm) with a cell probe. results show that the nutrient and ionic strength of the solu ...200818343395
superoxide reduction by nanoarchaeum equitans neelaredoxin, an enzyme lacking the highly conserved glutamate iron ligand.superoxide reductases (sors) are antioxidant enzymes present in many prokaryotes, either anaerobes or microaerophiles, which detoxify superoxide by reducing it to hydrogen peroxide. the reaction mechanism involves the diffusion-limited encounter of superoxide with the reduced iron site and concomitant formation of an fe(3+)-(hydro)peroxo adduct that, upon protonation, leads to the formation of hydrogen peroxide. by the end of this process, a glutamate residue coordinates the ferric ion, acting a ...200817968598
biorecovery of gold by escherichia coli and desulfovibrio desulfuricans.microbial precipitation of gold was achieved using escherichia coli and desulfovibrio desulfuricans provided with h2 as the electron donor. no precipitation was observed using h2 alone or with heat-killed cells. reduction of aqueous auiii ions by both strains was demonstrated at ph 7 using 2 mm haucl4 solution and the concept was successfully applied to recover 100% of the gold from acidic leachate (115 ppm of auiii) obtained from jewelry waste. bioreductive recovery of gold from aqueous solutio ...200817969152
biomass-supported palladium catalysts on desulfovibrio desulfuricans and rhodobacter sphaeroides.a rhodobacter sphaeroides-supported dried, ground palladium catalyst ("rs-pd(0)") was compared with a desulfovibrio desulfuricans-supported catalyst ("dd-pd(0)") and with unsupported palladium metal particles made by reduction under h2 ("chem-pd(0)"). cell surface-located clusters of pd(0) nanoparticles were detected on both d. desulfuricans and r. sphaeroides but the size and location of deposits differed among comparably loaded preparations. these differences may underlie the observation of di ...200817969153
capillary electrophoresis-fourier transform ion cyclotron resonance mass spectrometry for the identification of cationic metabolites via a ph-mediated stacking-transient isotachophoretic method.capillary electrophoresis-mass spectrometry (ce-ms) is still widely regarded as an emerging tool in the field of metabolomics and metabolite profiling. a major reason for this is a reported lack of sensitivity of ce-ms when compared to gas chromatography-mass spectrometry gc/ms and liquid chromatography-mass spectrometry. the problems caused by the lack of sensitivity are exacerbated when ce is coupled to fourier transform ion cyclotron resonance mass spectrometry (ft-icr ms), due to the relativ ...200818384203
desulfovibrio psychrotolerans sp. nov., a psychrotolerant and moderately alkaliphilic sulfate-reducing deltaproteobacterium from the himalayas.a novel sulfate-reducing bacterium (strain js1t) was isolated from lake pangong, a salt-water lake situated in the himalayas of leh district, jammu and kashmir, india. cells of strain js1t are gram-negative, vibriod, motile by means of single polar flagellum, contain desulfoviridin, are catalase-positive and can hydrolyse starch. strain js1t grew optimally at ph 8.5-9.0 and at temperatures ranging from 10 to 50 degrees c (optimum 28-30 degrees c). chemo-organoheterotrophy was the only growth mod ...200818398176
energy metabolism in desulfovibrio vulgaris hildenborough: insights from transcriptome analysis.sulphate-reducing bacteria are important players in the global sulphur and carbon cycles, with considerable economical and ecological impact. however, the process of sulphate respiration is still incompletely understood. several mechanisms of energy conservation have been proposed, but it is unclear how the different strategies contribute to the overall process. in order to obtain a deeper insight into the energy metabolism of sulphate-reducers whole-genome microarrays were used to compare the t ...200818060515
transcriptional response of desulfovibrio vulgaris hildenborough to oxidative stress mimicking environmental conditions.sulfate-reducing bacteria (srb) are anaerobes readily found in oxic-anoxic interfaces. multiple defense pathways against oxidative conditions were identified in these organisms and proposed to be differentially expressed under different concentrations of oxygen, contributing to their ability to survive oxic conditions. in this study, desulfovibrio vulgaris hildenborough cells were exposed to the highest concentration of oxygen that srb are likely to encounter in natural habitats, and the global ...200818060664
diversity of sulfate-reducing bacteria inhabiting the rhizosphere of phragmites australis in lake velencei (hungary) revealed by a combined cultivation-based and molecular approach.the community structure of sulfate-reducing bacteria (srb) associated with reed (phragmites australis) rhizosphere in lake velencei (hungary) was investigated by using cultivation-based and molecular methods. the cultivation methods were restricted to recover lactate-utilizing species with the exclusion of desulfobacter and some desulfobacterium species presumably not being dominant members of the examined community. the most-probable-number (mpn) estimations of lactate-utilizing srb showed that ...200818066486
variants of the tetrahaem cytochrome c quinol dehydrogenase nrfh characterize the menaquinol-binding site, the haem c-binding motifs and the transmembrane segment.members of the napc/nrfh family are multihaem c-type cytochromes that exchange electrons with oxidoreductases situated at the outside of the cytoplasmic membrane or in the periplasmic space of many proteobacteria. they form a group of membrane-bound quinol dehydrogenases that are essential components of several electron transport chains, for example those of periplasmic nitrate respiration and respiratory nitrite ammonification. knowledge of the structure-function relationships of napc/nrfh prot ...200818439144
quantum mechanical study of photoinduced charge transfer in fmn binding protein.ct interactions between iso* and nearby aromatic amino acids in fbp were investigated by a semiempirical mo method. atomic coordinates of lumiflavin as iso, 3-methylindole as trp, and 4-methylphenol as tyr, used for mo calculations, were obtained from crystal, 20 nmr structures and 40 md structures (20 ps time intervals). geometries of iso-trp32, iso-trp106 and iso-tyr35 systems were optimized by the pm3 method. the interaction energies (kcal/mol) of crystal structure were -16.9 in the iso-trp32 ...200819053889
structural and biochemical characterization of flavoredoxin from the archaeon methanosarcina acetivorans.flavoredoxin is a fmn-containing electron transfer protein that functions in the energy-yielding metabolism of desulfovibrio gigas of the bacteria domain. although characterization of this flavoredoxin is the only one reported, a database search revealed homologues widely distributed in both the bacteria and archaea domains that define a novel family. to improve our understanding of this family, a flavoredoxin from methanosarcina acetivorans of the archaea domain was produced in escherichia coli ...200818842001
oligosaccharide-mediated inhibition of the adhesion of pathogenic escherichia coli strains to human gut epithelial cells in vitro.the aim of the study was to investigate the ability of pectic oligosaccharides (pos) to inhibit adhesion of three strains of verotoxigenic escherichia coli, three strains of enteropathogenic e. coli, and one nonclinical strain of desulfovibrio desulfuricans to human intestinal epithelial cell cultures. lactobacillus acidophilus and lactobacillus gasseri were included for comparison. attachment was determined in the human ht29 cell line by viable count of adherent bacteria. pos in buffer at ph 7. ...200819044272
nmr assignment of the apo-form of a desulfovibrio gigas protein containing a novel mo-cu cluster.we report the 98% assignment of the apo-form of an orange protein, containing a novel mo-cu cluster isolated from desulfovibrio gigas. this protein presents a region where backbone amide protons exchange fast with bulk solvent becoming undetectable. these residues were assigned using 13c-detection experiments.200719636833
[microbiological analysis of cryopegs from the varandei peninsula, barents sea].the paper deals with the microbiological characterization of water-saturated horizons in permafrost soils (cryopegs) found on the varandei peninsula (barents sea coast), 4-20 m deep. the total quantity of bacteria in the water of cryopegs was 3.5 x 10(8) cells/ml. the population of cultivated aerobic heterotrophic bacteria was 3-4 x 10(7) cells/ml and the number of anaerobic heterotrophic bacteria varied from 10(2) to 10(5) cells/ml depending on cultivation temperature and salinity. sulfate-redu ...200718069331
mercury methylation by planktonic and biofilm cultures of desulfovibrio desulfuricans.while biofilms are now known to be the predominant form of microbial growth in nature, very little is yet known about their role in environmental mercury (hg) methylation. findings of hg methylation in periphyton communities have indicated the importance of investigating how environmental biofilms affect hg methylation, as periphyton can be the base of the food webs in aquatic ecosystems. chemical speciation influences the microbial uptake and methylation of inorganic hg by planktonic cultures o ...200717969682
molecular crowding enhances native structure and stability of alpha/beta protein flavodoxin.to investigate the consequences of macromolecular crowding on the behavior of a globular protein, we performed a combined experimental and computational study on the 148-residue single-domain alpha/beta protein, desulfovibrio desulfuricans apoflavodoxin. in vitro thermal unfolding experiments, as well as assessment of native and denatured structures, were probed by using far-uv cd in the presence of various amounts of ficoll 70, an inert spherical crowding agent. ficoll 70 has a concentration-de ...200718024596
in situ bioreduction of uranium (vi) to submicromolar levels and reoxidation by dissolved oxygen.groundwater within area 3 of the u.s. department of energy (doe) environmental remediation sciences program (ersp) field research center at oak ridge, tn (orfrc) contains up to 135 microm uranium as u(vi). through a series of experiments at a pilot scale test facility, we explored the lower limits of groundwater u(vi) that can be achieved by in-situ biostimulation and the effects of dissolved oxygen on immobilized uranium. weekly 2 day additions of ethanol over a 2-year period stimulated growth ...200717874778
simplifying sample handling for protein identification by peptide mass fingerprint using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.an ultrasonic bath, an ultrasonic probe and a sonoreactor were used to speed up the kinetics of the reactions involved in each step of the sample handling for in-gel protein identification by peptide mass fingerprint, pmf, using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (maldi-tof-ms). the following steps were successfully accelerated using ultrasonic energy: gel washing, protein reduction, and protein alkylation. as a result, a reduction comprising 80% to 90% ...200717879394
macromolecular crowding increases structural content of folded proteins.here we show that increased amount of secondary structure is acquired in the folded states of two structurally-different proteins (alpha-helical vlse and alpha/beta flavodoxin) in the presence of macromolecular crowding agents. the structural content of flavodoxin and vlse is enhanced by 33% and 70%, respectively, in 400 mg/ml ficoll 70 (ph 7, 20 degrees c) and correlates with higher protein-thermal stability. in the same ficoll range, there are only small effects on the unfolded-state structure ...200717919600
response of desulfovibrio vulgaris to alkaline stress.the response of exponentially growing desulfovibrio vulgaris hildenborough to ph 10 stress was studied using oligonucleotide microarrays and a study set of mutants with genes suggested by microarray data to be involved in the alkaline stress response deleted. the data showed that the response of d. vulgaris to increased ph is generally similar to that of escherichia coli but is apparently controlled by unique regulatory circuits since the alternative sigma factors (sigma s and sigma e) contribut ...200717921288
measuring the ph dependence of hydrogenase activities.the ph dependences of activities of homogenous hydrogenases of thiocapsa roseopersicina and desulfomicrobium baculatum in the reaction of hydrogen uptake in solution in the presence of benzyl viologen and the ph dependences of catalytic currents of hydrogen oxidation by electrodes on which these hydrogenases were immobilized were compared. maximal activities of the hydrogenases from t. roseopersicina and d. baculatum in the reaction hydrogen uptake in solution were observed at ph 9.5 and 8.5, re ...200717922655
biofilm formation in desulfovibrio vulgaris hildenborough is dependent upon protein filaments.desulfovibrio vulgaris hildenborough is a gram-negative sulfate-reducing bacterium (srb), and the physiology of srbs can impact many anaerobic environments including radionuclide waste sites, oil reservoirs and metal pipelines. in an attempt to understand d. vulgaris as a population that can adhere to surfaces, d. vulgaris cultures were grown in a defined medium and analysed for carbohydrate production, motility and biofilm formation. desulfovibrio vulgaris wild-type cells had increasing amounts ...200717922767
inhibition of a u(vi)- and sulfate-reducing consortia by u(vi).the stimulation of microbial u(vi) reduction is currently being investigated as a means to reduce uranium's mobility in groundwater, but little is known about the concentration at which u(vi) might inhibit microbial activity, or the effect of u(vi) on bacterial community structure. we investigated these questions with an ethanol-fed u(vi)- and sulfate-reducing enrichment developed from sediment from the site of an ongoing field biostimulation experiment at area 3 of the oak ridge field research ...200717948804
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