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desulfovibrio piezophilus, sp. nov., a novel piezophilic sulfate-reducing bacteriumisolated from wood falls in mediterranean sea.a novel sulfate-reducing bacterium designated c1tlv30t was isolated from wood falls at a depth of 1,693m in the mediterranean sea. cells were motile vibrios (2-4 x 0.5 µm). strain c1tlv30t grew at temperatures between 15 and 45 °c (optimum 30°c), and at ph between 5.4 and 8.6 (optimum 7.3). it required nacl for growth (optimum at 25 g/l nacl) and tolerated it up to 80 g/l. strain c1tlv30 t used as energy sources: lactate, fumarate, formate, malate, pyruvate and ethanol. the end-products from lac ...201021169465
structure of a crispr-associated protein cas2 from desulfovibrio vulgaris.crisprs (clustered regularly interspaced short palindromic repeats) provide bacteria and archaea with rna-guided acquired immunity to invasive dnas. crispr-associated (cas) proteins carry out the immune effector functions. cas2 is a universal component of the crispr system. here, a 1.35 å resolution crystal structure of cas2 from the bacterium desulfovibrio vulgaris (dvucas2) is reported. dvucas2 is a homodimer, with each protomer consisting of an n-terminal βαββαβ ferredoxin fold (amino acids 1 ...201021139194
self-consistent 3j coupling analysis for the joint calibration of karplus coefficients and evaluation of torsion angles.the concept of self-consistent j coupling evaluation exploits redundant structure information inherent in large sets of 3j coupling constants. application to the protein desulfovibrio vulgaris flavodoxin demonstrates the simultaneous refinement of torsion-angle values and related karplus coefficients. the experimental basis includes quantitative coupling constants related to the polypeptide backbone φ torsion originating from a variety of heteronuclear 2d and 3d nmr correlation experiments, tota ...199921136331
a role for microbial palladium nanoparticles in extracellular electron transfer. 201121132820
abundance and diversity of biofilms in natural and artificial aquifers of the äspö hard rock laboratory, sweden.six cores were drilled and retrieved from 186-m depth in the äspö hard rock laboratory (hrl) tunnel to investigate whether indigenous biofilms develop on fracture surfaces in groundwater-conducting aquifers in granitic rock. a clone library was constructed from fracture surface material (fsm), for community composition analysis. quantitative polymerase chain reaction (qpcr) was applied to quantify gene copies using the 16s rrna gene for domain bacteria and the adenosine-phosphosulfate reductase ...201021132427
microbial communities and electrochemical performance of titanium-based anodic electrodes in a microbial fuel cell.four types of titanium (ti)-based electrodes were tested in the same microbial fuel cell (mfc) anodic compartment. their electrochemical performances and the dominant microbial communities of the electrode biofilms were compared. the electrodes were identical in shape, macroscopic surface area, and core material but differed in either surface coating (pt- or ta-coated metal composites) or surface texture (smooth or rough). the mfc was inoculated with electrochemically active, neutrophilic microo ...201021131513
correlation of bacterial communities supported by different organic materials with sulfate reduction in metal-rich landfill leachate.several different organic materials, typical of those used in passive treatment systems for mine influenced water, were tested for their ability to support sulfate-reducing bacteria and sulfate reduction in an anaerobic biological reactor (abr). the quantity of sulfate-reducing bacteria (srb) in each organic material, as determined using quantitative polymerase chain reaction (q-pcr) of the dissimilatory sulfite reductase (dsr) gene, correlated with the initial c/n ratio of each material. potent ...201021131018
environments that induce synthetic microbial ecosystems.interactions between microbial species are sometimes mediated by the exchange of small molecules, secreted by one species and metabolized by another. both one-way (commensal) and two-way (mutualistic) interactions may contribute to complex networks of interdependencies. understanding these interactions constitutes an open challenge in microbial ecology, with applications ranging from the human microbiome to environmental sustainability. in parallel to natural communities, it is possible to explo ...201021124952
desulfovibrio desulfuricans pglb homolog possesses oligosaccharyltransferase activity with relaxed glycan specificity and distinct protein acceptor sequence requirements.oligosaccharyltransferases (otases) are responsible for the transfer of carbohydrates from lipid carriers to acceptor proteins and are present in all domains of life. in bacteria, the most studied member of this family is pglb from campylobacter jejuni (pglb(cj)). this enzyme is functional in escherichia coli and, contrary to its eukaryotic counterparts, has the ability to transfer a variety of oligo- and polysaccharides to protein carriers in vivo. phylogenetic analysis revealed that in the del ...201021098514
structural insights into the enzyme catalysis from comparison of three forms of dissimilatory sulphite reductase from desulfovibrio gigas.the crystal structures of two active forms of dissimilatory sulphite reductase (dsr) from desulfovibrio gigas, dsr-i and dsr-ii, are compared at 1.76 and 2.05 å resolution respectively. the dimeric α2β2γ2 structure of dsr-i contains eight [4fe-4s] clusters, two saddle-shaped sirohaems and two flat sirohydrochlorins. in dsr-ii, the [4fe-4s] cluster associated with the sirohaem in dsr-i is replaced by a [3fe-4s] cluster. electron paramagnetic resonance (epr) of the active dsr-i and dsr-ii confirm ...201021059110
characterization of microbial community structure and population dynamics of tetrachloroethene-dechlorinating tidal mudflat communities.tetrachloroethene (pce) and trichloroethene (tce) are common groundwater contaminants that also impact tidal flats, especially near urban and industrial areas. however, very little is known about dechlorinating microbial communities in tidal flats. titanium pyrosequencing, 16s rrna gene clone libraries, and dechlorinator-targeted quantitative real-time pcr (qpcr) characterized reductive dechlorinating activities and populations in tidal flat sediments collected from south korea's central west co ...201021053056
purification, crystallization and preliminary x-ray analysis of the dissimilatory sulfite reductase from desulfovibrio vulgaris miyazaki f.dissimilatory sulfite reductase (dsr) plays an important role in sulfate respiration in many sulfate-reducing bacteria. dsr from desulfovibrio vulgaris miyazaki f has been purified and crystallized at 277 k using the sitting-drop vapour-diffusion method with peg 3350 and potassium thiocyanate as precipitants. a data set was collected to 3.7 å resolution from a single crystal at 100 k using synchrotron radiation. the dsr crystal belonged to space group p4(1)2(1)2, with unit-cell parameters a = b ...201021045297
simultaneous determination of mercury methylation and demethylation capacities of various sulfate-reducing bacteria using species-specific isotopic tracers.the use of species-specific isotopic tracers for inorganic and methyl mercury has allowed the simultaneous determination of the methylation and demethylation potentials of pure culture of isolated sulfate-reducing (sr) bacterial strains using low hg species concentration levels (7 µg/l (199)hg(ii), 1 µg/l me(201)hg). a major advantage of the method reported here is that it can be used to follow simultaneously both the degradation of the species added but also the formation of their degradation p ...201121038431
bacterial colonization of colonic crypt mucous gel and disease activity in ulcerative colitis.to optimize total bacterial 16s rrna quantification in microdissected colonic crypts in healthy controls and patients with ulcerative colitis (uc) and to characterize the findings with disease activity.201021037444
chemical composition of desulfovibrio desulfuricans lipid a.lipopolysaccharides also called endotoxins are an integral component of the outer membrane of gram-negative bacteria. when released from the bacterial surface, they interact with a host immune system, triggering excessive inflammatory response. lipid a is the biologically most active part of endotoxin, and its activity is modulated by the quantity, quality and arrangement of its fatty acids. desulfovibrio desulfuricans is sulfate-reducing, gram-negative bacterium that is supposed to be opportuni ...201020978743
artefacts induced on c-type haem proteins by electrode surfaces.in this work it is demonstrated that the characterization of c-type haem containing proteins by electrochemical techniques needs to be cautiously performed when using pyrolytic graphite electrodes. an altered form of the cytochromes, which has a redox potential 300 mv lower than that of the native state and displays peroxidatic activity, can be induced by interaction with the pyrolytic graphite electrode. proper control experiments need to be performed, as altered conformations of the enzymes co ...201020963615
mercury methylation in sphagnum moss mats and its association with sulfate-reducing bacteria in an acidic adirondack forest lake wetland.processes leading to the bioaccumulation of methylmercury (mehg) in northern wetlands are largely unknown. we have studied various ecological niches within a remote, acidic forested lake ecosystem in the southwestern adirondacks, ny, to discover that mats comprised of sphagnum moss were a hot spot for mercury (hg) and mehg accumulation (190.5 and 18.6 ng g⁻¹ dw, respectively). furthermore, significantly higher potential methylation rates were measured in sphagnum mats as compared with other site ...201020955196
desulfovibrio bacterial species are increased in ulcerative colitis.debate persists regarding the role of desulfovibrio subspecies in ulcerative colitis. combined microscopic and molecular techniques enable this issue to be investigated by allowing precise enumeration of specific bacterial species within the colonic mucous gel. the aim of this study was to combine laser capture microdissection and quantitative polymerase chain reaction to determine desulfovibrio copy number in crypt-associated mucous gel in health and in acute and chronic ulcerative colitis.201020940602
visual proteomics.visual proteomics attempts to generate molecular atlases by providing the position and angular orientation of protein complexes inside of cells. this is accomplished by template matching (pattern recognition), a cross-correlation-based process that matches the structure of a specific protein complex to the densities of the whole volume or subvolume of a cell, that is typically acquired by cryoelectron tomography. thereby, a search is performed that scans the entire volume for structural template ...201020888477
redox linked conformational changes in cytochrome c3 from desulfovibrio desulfuricans atcc 27774.cytochrome c3 from desulfovibrio desulfuricans atcc 27774 appears to be capable of receiving two protons and two electrons from hydrogenase for transport to the membrane, and converting electronic energy into proton motive force. detailed studies of the mechanism require control both of the redox state and of the protonation state of the protein; hence, structure determination of the protein in solution by nmr is the preferred method. this work compares the structures of the protonated protein i ...201020886839
association of symptoms with gastrointestinal microbiota in irritable bowel syndrome.to investigate the correlations between self-reported symptoms of irritable bowel syndrome (ibs) and the gastrointestinal (gi) microbiota composition.201020857523
a nickel(ii)-sulfur-based radical-ligand complex as a functional model of hydrogenase. 201020853299
formate-driven growth coupled with h(2) production.although a common reaction in anaerobic environments, the conversion of formate and water to bicarbonate and h(2) (with a change in gibbs free energy of δg° = +1.3 kj mol(-1)) has not been considered energetic enough to support growth of microorganisms. recently, experimental evidence for growth on formate was reported for syntrophic communities of moorella sp. strain amp and a hydrogen-consuming methanothermobacter species and of desulfovibrio sp. strain g11 and methanobrevibacter arboriphilus ...201020844539
geochip-based functional gene analysis of anodophilic communities in microbial electrolysis cells under different operational modes.a microbial electrolysis cell (mec) is a bioelectrochemical system that can produce hydrogen from acetate at high hydrogen recoveries, but the composition and structure of the microbial communities in this system have not been extensively studied. we used a high throughput metagenomics technology (geochip) to examine the microbial community functional structure in mecs initially operated under different conditions. we found that startup conditions had little or no effect on reactor performance i ...201020831218
crystal structure of the zinc-, cobalt-, and iron-containing adenylate kinase from desulfovibrio gigas: a novel metal-containing adenylate kinase from gram-negative bacteria.adenylate kinases (ak) from gram-negative bacteria are generally devoid of metal ions in their lid domain. however, three metal ions, zinc, cobalt, and iron, have been found in ak from gram-negative bacteria. crystal structures of substrate-free ak from desulfovibrio gigas with three different metal ions (zn(2+), zn-ak; co(2+), co-ak; and fe(2+), fe-ak) bound in its lid domain have been determined by x-ray crystallography to resolutions 1.8, 2.0, and 3.0 å, respectively. the zinc and iron forms ...201120821240
desulfovibrio legallis sp. nov.: a moderately halophilic, sulfate-reducing bacterium isolated from a wastewater digestor in tunisia.a new moderately halophilic sulfate-reducing bacterium (strain h₁(t) ) was enriched and isolated from a wastewater digestor in tunisia. cells were curved, motile rods (2-3 x 0.5 μm). strain h₁(t) grew at temperatures between 22 and 43°c (optimum 35°c), and at ph between 5.0 and 9.2 (optimum 7.3-7.5). strain h₁(t) required salt for growth (1-45 g of nacl/l), with an optimum at 20-30 g/l. sulfate, sulfite, thiosulfate, and elemental sulfur were used as terminal electron acceptors but not nitrate a ...201120814681
[taxonomic position of certain representatives of sulphate-reducing corrosive microbial community].sulfate-reducing bacteria and their heterotrophic satellites have been isolated from the biofilm formed on steel by sulfidogenic corrosive microbial community. bacteria were characterized according to phenotypical features and investigated by the methods of molecular-genetic analysis. in accordance with the phenotypical features the studied strain of sulfate-reducing bacteria were related to desulfovibrio genus, gram-positive strains of heterotrophic satellites were related to bacillus genus, b. ...201020812503
towards an integrated system for bio-energy: hydrogen production by escherichia coli and use of palladium-coated waste cells for electricity generation in a fuel cell.escherichia coli strains mc4100 (parent) and a mutant strain derived from this (ic007) were evaluated for their ability to produce h(2) and organic acids (oas) via fermentation. following growth, each strain was coated with pd(0) via bioreduction of pd(ii). dried, sintered pd-biomaterials ('bio-pd') were tested as anodes in a proton exchange membrane (pem) fuel cell for their ability to generate electricity from h(2). both strains produced hydrogen and oas but 'palladised' cells of strain ic007 ...201020809286
biorefining of precious metals from wastes: an answer to manufacturing of cheap nanocatalysts for fuel cells and power generation via an integrated biorefinery?bio-manufacturing of nano-scale palladium was achieved via enzymatically-mediated deposition of pd from solution using desulfovibrio desulfuricans, escherichia coli and cupriavidus metallidurans. dried 'bio-pd' materials were sintered, applied onto carbon papers and tested as anodes in a proton exchange membrane (pem) fuel cell for power production. at a pd(0) loading of 25% by mass the fuel cell power using bio-pd( d. desulfuricans ) (positive control) and bio-pd( e. coli ) (negative control) w ...201020734111
significant association between sulfate-reducing bacteria and uranium-reducing microbial communities as revealed by a combined massively parallel sequencing-indicator species approach.massively parallel sequencing has provided a more affordable and high-throughput method to study microbial communities, although it has mostly been used in an exploratory fashion. we combined pyrosequencing with a strict indicator species statistical analysis to test if bacteria specifically responded to ethanol injection that successfully promoted dissimilatory uranium(vi) reduction in the subsurface of a uranium contamination plume at the oak ridge field research center in tennessee. remediati ...201020729318
dsrj, an essential part of the dsrmkjop transmembrane complex in the purple sulfur bacterium allochromatium vinosum, is an unusual triheme cytochrome c.the dsrmkjop transmembrane complex has a most important function in dissimilatory sulfur metabolism, not only in many sulfur-oxidizing organisms but also in sulfate-reducing prokaryotes. here, we focused on an individual component of this complex, the triheme cytochrome c dsrj from the purple sulfur bacterium allochromatium vinosum. in a. vinosum, the signal peptide of dsrj is not cleaved off but serves as a membrane anchor. sequence analysis suggested the presence of three heme c species with b ...201020726534
polymicrobial bloodstream infection with eggerthella lenta and desulfovibrio desulfuricans.the advancement in culture identification methods has made possible the culture and identification of slow-growing anaerobic bacteria in clinical samples. here, we describe a case of polymicrobial bloodstream infection (bsi) caused by eggerthella lenta and desulfovibrio desulfuricans, identified by api 20a and vitek 2 systems and by 16s rrna sequencing.201020720029
silage supports sulfate reduction in the treatment of metals- and sulfate-containing waste waters.silage was used as source of carbon and electrons for enrichment of silage-degrading and sulfate reducing bacteria (srb) from boreal, acidic, metals-containing peat-bog samples and to support their use in batch and semi-batch systems in treatment of synthetic waste water. sulfidogenic silage utilization resulted in a rapid decrease in lactate concentrations; concentrations of acetate, butyrate and propionate increased concomitantly. synthetic waste water consisting of mn, mg and fe (ii) ions inh ...201020708212
alternative e.cosy techniques for the measurement of 3j(c (i) (') (-1),c (i) (beta) ) and (3) j(h (i) (n) ,c (i) (beta) ) coupling constants in proteins.experiments are proposed for the measurement of the vicinal coupling constants between beta-carbons and either amide protons of the same or carbonyl carbons of the preceding amino acid residue in 13c/15n-labeled proteins. both couplings depend on the backbone torsional angle phi. the three-dimensional pulse sequences give rise to e.cosy-like multiplet patterns in which heteronuclear one-bond couplings separate the doublet components corresponding to the two spin states of the respective passive ...199920700819
response of desulfovibrio vulgaris hildenborough to hydrogen peroxide: enzymatic and transcriptional analyses.we studied the effect of hydrogen peroxide (h(2)o(2)) stress on the anaerobic sulfate-reducing bacterium desulfovibrio vulgaris hildenborough. in a lactate/sulfate medium, growth was affected from 0.1 mm h(2)o(2) and totally inhibited at 0.7 mm. surprisingly, transcript analyses revealed that the perr regulon exhibited opposite regulation in the presence of 0.1 and 0.3 mm h(2)o(2). the variations in peroxidase- and superoxide dismutase-specific activities in the cell-free extracts of h(2)o(2)-st ...201020695895
measuring the cytochrome c nitrite reductase activity-practical considerations on the enzyme assays.the cytochrome c nitrite reductase (ccnir) from desulfovibrio desulfuricans atcc 27774 is able to reduce nitrite to ammonia in a six-electron transfer reaction. although extensively characterized from the spectroscopic and structural points-of-view, some of its kinetic aspects are still under explored. in this work the kinetic behaviour of ccnir has been evaluated in a systematic manner using two different spectrophotometric assays carried out in the presence of different redox mediators and a d ...201020689707
the crystal structure of the [nife] hydrogenase from the photosynthetic bacterium allochromatium vinosum: characterization of the oxidized enzyme (ni-a state).the crystal structure of the membrane-associated [nife] hydrogenase from allochromatium vinosum has been determined to 2.1 å resolution. electron paramagnetic resonance (epr) and fourier transform infrared spectroscopy on dissolved crystals showed that it is present in the ni-a state (>90%). the structure of the a. vinosum [nife] hydrogenase shows significant similarities with [nife] hydrogenase structures derived from desulfovibrio species. the amino acid sequence identity is ∼ 50%. the bimetal ...201020673834
interaction of the active site of the ni-fe-se hydrogenase from desulfovibrio vulgaris hildenborough with carbon monoxide and oxygen inhibitors.the study of ni-fe-se hydrogenases is interesting from the basic research point of view because their active site is a clear example of how nature regulates the catalytic function of an enzyme by the change of a single residue, in this case a cysteine, which is replaced by a selenocysteine. most hydrogenases are inhibited by co and o(2). in this work we studied these inhibition processes for the ni-fe-se hydrogenase from desulfovibrio vulgaris hildenborough by combining catalytic activity measur ...201020669037
combined strategy for the precipitation of heavy metals and biodegradation of petroleum in industrial wastewaters.the precipitation of chromium(iii), copper(ii), manganese(ii) and zinc(ii) by biogenic hydrogen sulfide generated by sulfate-reducing bacteria, desulfovibrio sp., and the degradation of total petroleum hydrocarbons (tph) in the presence of heavy metal by pseudomonas aeruginosa at18 have been carried out. an anaerobic stirred tank reactor was used to generate hydrogen sulfide with desulfovibrio sp. culture and the precipitation of more than 95% of each metal was achieved in 24 h (metal solutions ...201020667656
the role of desulfovibrio desulfuricans lipopolysaccharides in modulation of periodontal inflammation through stimulation of human gingival fibroblasts.objective: periodontitis is a destructive disease which is likely to be the result of the activities of different microbial complexes. recently, sulphate-reducing bacteria (srb) have been detected in the oral cavity, and they have been found to be common inhabitants of sites showing periodontal destruction. the aim of study was to evaluate the influence of endotoxins of desulfovibrio desulfuricans bacteria on human gingival fibroblast hgf-1 line. methods: the immunological response of gingival f ...201020627263
pyrosequencing study of fecal microflora of autistic and control children.there is evidence of genetic predisposition to autism, but the percent of autistic subjects with this background is unknown. it is clear that other factors, such as environmental influences, may play a role in this disease. in the present study, we have examined the fecal microbial flora of 33 subjects with various severities of autism with gastrointestinal symptoms, 7 siblings not showing autistic symptoms (sibling controls) and eight non-sibling control subjects, using the bacterial tag encode ...201020603222
the role of desulfovibrio desulfuricans lipopolysaccharides in modulation of periodontal inflammation through stimulation of human gingival fibroblasts.periodontitis is a destructive disease which is likely to be the result of the activities of different microbial complexes. recently, sulphate-reducing bacteria (srb) have been detected in the oral cavity, and they have been found to be common inhabitants of sites showing periodontal destruction. the aim of study was to evaluate the influence of endotoxins of desulfovibrio desulfuricans bacteria on human gingival fibroblast hgf-1 line.201020593542
effect of the deletion of qmoabc and the promoter-distal gene encoding a hypothetical protein on sulfate reduction in desulfovibrio vulgaris hildenborough.the pathway of electrons required for the reduction of sulfate in sulfate-reducing bacteria (srb) is not yet fully characterized. in order to determine the role of a transmembrane protein complex suggested to be involved in this process, a deletion in desulfovibrio vulgaris hildenborough was created by marker exchange mutagenesis that eliminated four genes putatively encoding the qmoabc complex and a hypothetical protein (dvu0851). the qmo (quinone-interacting membrane-bound oxidoreductase) comp ...201020581180
global transcriptomics analysis of the desulfovibrio vulgaris change from syntrophic growth with methanosarcina barkeri to sulfidogenic metabolism.desulfovibrio vulgaris is a metabolically flexible micro-organism. it can use sulfate as an electron acceptor to catabolize a variety of substrates, or in the absence of sulfate can utilize organic acids and alcohols by forming a syntrophic association with a hydrogen-scavenging partner to relieve inhibition by hydrogen. these alternative metabolic types increase the chance of survival for d. vulgaris in environments where one of the potential external electron acceptors becomes depleted. in thi ...201020576691
helicobacter pylori apo-fur regulation appears unconserved across species.the ferric uptake regulator (fur) is a transcriptional regulator that is conserved across a broad number of bacterial species and has been shown to regulate expression of iron uptake and storage genes. additionally, fur has been shown to be an important colonization factor of the gastric pathogen helicobacter pylori. in h. pylori, fur-dependent regulation appears to be unique in that fur is able to act as a transcriptional repressor when bound to iron as well as in its iron free (apo) form. to d ...201020571957
desulfovibrio magneticus rs-1 contains an iron- and phosphorus-rich organelle distinct from its bullet-shaped magnetosomes.intracellular magnetite crystal formation by magnetotactic bacteria has emerged as a powerful model for investigating the cellular and molecular mechanisms of biomineralization, a process common to all branches of life. although magnetotactic bacteria are phylogenetically diverse and their crystals morphologically diverse, studies to date have focused on a few, closely related species with similar crystal habits. here, we investigate the process of magnetite biomineralization in desulfovibrio ma ...201020566879
desulfovibrio spp. survive within kb cells and modulate inflammatory responses.desulfovibrio are sulfate-reducing anaerobic gram-negative rods that have been proposed as potential periodontopathogens. we investigated the capacity of desulfovibrio to invade epithelial cells and induce cytokine secretion from these cells. desulfovibrio strains were co-cultured with kb cells and counts of intracellular bacteria evaluated up to 3 days after infection. desulfovibrio desulfuricans and desulfovibrio fairfieldensis were able to survive within epithelial cells. intracytoplasmic loc ...201020536750
endophytic bacterial diversity in roots of phragmites australis in constructed beijing cuihu wetland (china).the community structure and diversity of endophytic bacteria in reed (phragmites australis) roots growing in the beijing cuihu wetland, china was investigated using the 16s rrna library technique. primers 799f and 1492r were used to amplify the specific bacterial 16s rrna fragments successfully and construct the clone library. in total, 166 individual sequences were verified by colony pcr and used to assess the diversity of endophytic bacteria in reed roots. phylogenetic analysis revealed that 7 ...201020528944
effect of dechlorination and sulfate reduction on the microbial community structure in denitrifying membrane-biofilm reactors.recent studies showed that the chlorinated solvents trichloroethene (tce), 1,1,1-trichloroethane (tca), and chloroform (cf) were reductively dehalogenated in a h(2)-based membrane biofilm reactor (mbfr) under denitrifying conditions. here, we describe a detailed phylogenetic characterization of mbfr biofilm communities having distinctly different metabolic functions with respect to electron-acceptor reduction. using massively parallel pyrosequencing of the v6 region of the 16s rrna gene, we dete ...201020524654
the qrc membrane complex, related to the alternative complex iii, is a menaquinone reductase involved in sulfate respiration.biological sulfate reduction is a process with high environmental significance due to its major contribution to the carbon and sulfur cycles in anaerobic environments. however, the respiratory chain of sulfate-reducing bacteria is still poorly understood. here we describe a new respiratory complex that was isolated as a major protein present in the membranes of desulfovibrio vulgaris hildenborough. the complex, which was named qrc, is the first representative of a new family of redox complexes. ...201020498375
establishment and metabolic analysis of a model microbial community for understanding trophic and electron accepting interactions of subsurface anaerobic environments.communities of microorganisms control the rates of key biogeochemical cycles, and are important for biotechnology, bioremediation, and industrial microbiological processes. for this reason, we constructed a model microbial community comprised of three species dependent on trophic interactions. the three species microbial community was comprised of clostridium cellulolyticum, desulfovibrio vulgaris hildenborough, and geobacter sulfurreducens and was grown under continuous culture conditions. cell ...201020497531
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
hydrogen peroxide-induced oxidative stress responses in desulfovibrio vulgaris hildenborough.to understand how sulphate-reducing bacteria respond to oxidative stresses, the responses of desulfovibrio vulgaris hildenborough to h(2)o(2)-induced stresses were investigated with transcriptomic, proteomic and genetic approaches. h(2)o(2) and induced chemical species (e.g. polysulfide, ros) and redox potential shift increased the expressions of the genes involved in detoxification, thioredoxin-dependent reduction system, protein and dna repair, and decreased those involved in sulfate reduction ...201020482586
temperature and nutrient induced responses of lake fryxell sulfate-reducing prokaryotes and description of desulfovibrio lacusfryxellense, sp. nov., a pervasive, cold-active, sulfate-reducing bacterium from lake fryxell, antarctica.the effects of temperature and carbon substrate availability on the stimulation of sulfate reduction by indigenous populations of sulfate-reducing prokaryotes (srp) in permanently ice-covered lake fryxell, antarctica were investigated. psychrophilic and halotolerant, lactate-degrading srp showed significant metabolic activity throughout all sampled depths of the water column, suggesting that such organisms, possibly of marine origin, may be key contributors to carbon and sulfur cycling in lake f ...201020473538
diversity of dissimilatory sulfite reductase genes (dsrab) in a salt marsh impacted by long-term acid mine drainage.sulfate-reducing bacteria (srb) play a major role in the coupled biogeochemical cycling of sulfur and chalcophilic metal(loid)s. by implication, they can exert a strong influence on the speciation and mobility of multiple metal(loid) contaminants. in this study, we combined dsrab gene sequencing and sulfur isotopic profiling to identify the phylogeny and distribution of srb and to assess their metabolic activity in salt marsh sediments exposed to acid mine drainage (amd) for over 100 years. reco ...201020472728
c-type cytochrome biogenesis can occur via a natural ccm system lacking ccmh, ccmg, and the heme-binding histidine of ccme.the ccm cytochrome c maturation system i catalyzes covalent attachment of heme to apocytochromes c in many bacterial species and some mitochondria. a covalent, but transient, bond between heme and a conserved histidine in ccme along with an interaction between ccmh and the apocytochrome have been previously indicated as core aspects of the ccm system. here, we show that in the ccm system from desulfovibrio desulfuricans, no ccmh is required, and the holo-ccme covalent bond occurs via a cysteine ...201020466730
ftir study on the light sensitivity of the [nife] hydrogenase from desulfovibrio vulgaris miyazaki f: ni-c to ni-l photoconversion, kinetics of proton rebinding and h/d isotope effect.the light-induced ni-c to ni-l transition results in the dissociation of a hydrogenic species, originating from the dihydrogen splitting at the active site. back conversion in the dark to form ni-c was investigated by studying the rebinding kinetics of this ligand in protonated (h(2)/h(2)o) and deuterated (d(2)/d(2)o) samples using time resolved ftir spectroscopy.200920449009
impact of elevated nitrate on sulfate-reducing bacteria: a comparative study of desulfovibrio vulgaris.sulfate-reducing bacteria have been extensively studied for their potential in heavy-metal bioremediation. however, the occurrence of elevated nitrate in contaminated environments has been shown to inhibit sulfate reduction activity. although the inhibition has been suggested to result from the competition with nitrate-reducing bacteria, the possibility of direct inhibition of sulfate reducers by elevated nitrate needs to be explored. using desulfovibrio vulgaris as a model sulfate-reducing bact ...201020445634
effects of biocides on gene expression in the sulfate-reducing bacterium desulfovibrio vulgaris hildenborough.although sulfate-reducing bacteria (srb), such as desulfovibrio vulgaris hildenborough (dvh) are often eradicated in oil and gas operations with biocides, such as glutaraldehyde (glut), tetrakis (hydroxymethyl) phosphonium sulfate (thps), and benzalkonium chloride (bac), their response to these agents is not well known. whole genome microarrays of d. vulgaris treated with biocides well below the minimum inhibitory concentration showed that 256, 96, and 198 genes were responsive to glut, thps, an ...201020437234
effects of the disappearance of one charge on ultrafast fluorescence dynamics of the fmn binding protein.crystal structures of e13t (glu13 was replaced by thr13) and e13q (glu13 was replaced by gln13) fmn binding proteins (fmn-bp) from desulfovibrio vulgaris, strain miyazaki f, were determined by the x-ray diffraction method. geometrical factors related to photoinduced electron transfer from trp32, tyr35, and trp106 to the excited isoalloxazine (iso*) were compared among the three forms of fmn-bp. the rate of et is considered to be fastest from trp32 to iso* in fmn-bp and then from tyr35 and trp106 ...201020397678
1h, 13c and 15n backbone and side-chain chemical shift assignments for oxidized and reduced desulfothioredoxin.based on sequence homology, desulfothioredoxin (dtrx) from desulfovibrio vulgaris hildenborough has been identified as a new member of the thioredoxin superfamily. desulfothioredoxin (104 amino acids) contains a particular active site consensus sequence, cphc probably correlated to the anaerobic metabolism of these bacteria. we report the full 1h, 13c and 15n resonance assignments of the reduced and the oxidized form of desulfothioredoxin (dtrx). 2d and 3d heteronuclear nmr experiments were perf ...201020390383
rubredoxin mutant a51c unfolding dynamics: a förster resonance energy transfer study.the unfolding dynamics of the rubredoxin mutant a51c (rda51c) from desulfovibrio vulgaris (dvrd) was studied on the temperature range from 25 degrees c to 90 degrees c and by incubation at 90 degrees c. by förster resonance energy transfer (fret) the donor (d; trp37) to acceptor (a; 1,5-iaedans) distance distribution was probed at several temperatures between 25 degrees c and 90 degrees c, and incubation times at 90 degrees c. from 25 degrees c to 50 degrees c the half-width distributions values ...201020381231
substrate binding to a nitrite reductase induces a spin transition.the multiheme enzyme nitrite reductase catalyzes a 6-electron reduction of nitrite to ammonia. the reaction is initiated by substrate binding to the free axial position of the high spin penta-coordinated heme active site. the spin configuration of the resulting complex is crucial for discrimination between the heterolytic vs homolytic character of the cleavage of the n-o bond and, therefore, subsequent steps of the catalytic cycle. here, we report the first experimental evidence, based on resona ...201020369861
[performance of a combined bio-chemical sulfidogenic system and microbial characteristics in the presence of h2].to study and evaluate the performance of the continuously-operated autohydrogenotrophic sulfate reduction technique enhanced with electrochemical method and to improve the sulfate removal efficiency, a combined bio-electrical sulfidogenic system was developed with a three-dimensional bio-cathode. sulfate reduction rate was elevated markedly owing to h2 mass transfer enhancement, biomass augmentation and electrical field stimulation. indeed, when a current of 0.50 ma was applied to the system, th ...201020358831
inorganic-organic hybrid coatings on stainless steel by layer-by-layer deposition and surface-initiated atom-transfer-radical polymerization for combating biocorrosion.to improve the biocorrosion resistance of stainless steel (ss) and to confer the bactericidal function on its surface for inhibiting bacterial adhesion and biofilm formation, well-defined inorganic-organic hybrid coatings, consisting of the inner compact titanium oxide multilayers and outer dense poly(vinyl-n-hexylpyridinium) brushes, were successfully developed. nanostructured titanium oxide multilayer coatings were first built up on the ss substrates via the layer-by-layer sol-gel deposition p ...200920355986
microbially induced separation of quartz from hematite using sulfate reducing bacteria.cells and metabolic products of desulfovibrio desulfuricans were successfully used to separate quartz from hematite through environmentally benign microbially induced flotation. bacterial metabolic products such as extracellular proteins and polysaccharides were isolated from both unadapted and mineral-adapted bacterial metabolite and their basic characteristics were studied in order to get insight into the changes brought about on bioreagents during adaptation. interaction between bacterial cel ...201020347277
journal club. an evolutionary biologist marvels at how species evolve to help each other out. 201020336096
effect of uranium (vi) on two sulphate-reducing bacteria cultures from a uranium mine site.this work was conducted to assess the impact of uranium (vi) on sulphate-reducing bacteria (srb) communities obtained from environmental samples collected on the portuguese uranium mining area of urgeiriça. culture u was obtained from a sediment, while culture w was obtained from sludge from the wetland of that mine. temperature gradient gel electrophoresis (tgge) was used to monitor community changes under uranium stress conditions. tgge profiles of dsrb gene fragment demonstrated that the init ...201020334901
sulfate reduction at ph 4.0 for treatment of process and wastewaters.acidic industrial process and wastewaters often contain high sulfate and metal concentrations and their direct biological treatment is thus far not possible as biological processes at ph < 5 have been neglected. sulfate-reducing bacteria convert sulfate to sulfide that can subsequently be used to recover metals as metal-sulfides precipitate. this study reports on high-rate sulfate reduction with a mixed microbial community at ph 4.0 and 4.5 with hydrogen and/or formate as electron donors. the ma ...201020306533
oil phytoremediation potential of hypersaline coasts of the arabian gulf using rhizosphere technology.the rhizosphere and phyllosphere of the halophyte halonemum strobilaceum naturally inhabiting hypersaline coastal areas of the arabian gulf harbor up to 8.1 x 10(4)g(-1) and 3 x 10(2)g(-1), respectively, of extremely halophilic oil-utilizing microorganisms. such organisms were 14- to 38-fold more frequent in the rhizosphere than in the plant-free soil. frequent genera in the rhizosphere were affiliated to the archaea halobacterium sp. and halococcus sp., the firmicute brevibacillus borstenlensis ...201020303746
functionally relevant interplay between the fe(4)s(4) cluster and cn(-) ligands in the active site of [fefe]-hydrogenases.[fefe]-hydrogenases are highly efficient h(2)-evolving metalloenzymes that include cyanides and carbonyls in the active site. the latter is an fe(6)s(6) cluster (the so-called h-cluster) that can be subdivided into a binuclear portion carrying the co and cn(-) groups and a tetranuclear subcluster. the fundamental role of cyanide ligands in increasing the basicity of the h-cluster has been highlighted previously. here a more subtle but crucial role played by the two cn(-) ligands in the active si ...201020302340
intermediates in the catalytic cycle of [nife] hydrogenase: functional spectroscopy of the active site.the [nife] hydrogenase from the anaerobic sulphate reducing bacterium desulfovibrio vulgaris miyazaki f is an excellent model for constructing a mechanism for the function of the so-called 'oxygen-sensitive' hydrogenases. the present review focuses on spectroscopic investigations of the active site intermediates playing a role in the activation/deactivation and catalytic cycle of this enzyme as well as in the inhibition by carbon monoxide or molecular oxygen and the light-sensitivity of the hydr ...201020301175
microbial equol production attenuates colonic methanogenesis and sulphidogenesis in vitro.hydrogen gas produced during colonic fermentation is excreted in breath and flatus, or removed by hydrogen-consuming bacteria such as methanogens and sulphate-reducing bacteria. however, recent research has shown that h2 is also consumed by equol-producing bacteria during the reduction of daidzein into equol. in this study, the interactions between methanogens, sulphate-reducing, and equol-producing bacteria were investigated under in vitro simulated intestinal conditions. in the presence of dai ...201020298796
responses of microbial community functional structures to pilot-scale uranium in situ bioremediation.a pilot-scale field test system with an inner loop nested within an outer loop was constructed for in situ u(vi) bioremediation at a us department of energy site, oak ridge, tn. the outer loop was used for hydrological protection of the inner loop where ethanol was injected for biostimulation of microorganisms for u(vi) reduction/immobilization. after 2 years of biostimulation with ethanol, u(vi) levels were reduced to below drinking water standard (<30 microg l(-1)) in the inner loop monitoring ...201020237512
concerto catalysis--harmonising [nife]hydrogenase and niru model catalysts.this communication reports the successful merging of the chemical properties of a natural [nife]hydrogenase (desulfovibrio vulgaris miyazaki f) and our previously reported [niru] hydrogenase-mimic. the catalytic activity of both the natural enzyme and the mimic is almost identical, with the exception of working ph ranges, and this allows us to use them simultaneously in the same reaction flask. in such a manner, isotope exchange between d(2) and h(2)o could be conducted over an extended ph range ...201020221530
an efficient non-mediated amperometric biosensor for nitrite determination.in this paper we propose the construction of a new non-mediated electrochemical biosensor for nitrite determination in complex samples. the device is based on the stable and selective cytochrome c nitrite reductase (ccnir) from desulfovibrio desulfuricans, which has both high turnover and heterogeneous electron transfer rates. in opposition to previous efforts making use of several redox mediators, in this work we exploited the capacity of ccnir to display a direct electrochemical response when ...201020188536
comparison of the membrane-bound [nife] hydrogenases from r. eutropha h16 and d. vulgaris miyazaki f in the oxidized ready state by pulsed epr.the geometric and electronic structures of the active sites in the oxidized ni(r)-b state of the [nife] hydrogenases from ralstonia eutropha h16 and desulfovibrio vulgaris miyazaki f were investigated in pulsed epr and endor experiments at two different microwave frequencies (x- and q-band). two hyperfine-couplings were clearly resolved in the frozen solution spectra arising from the beta-protons of the nickel-coordinating cysteine residues cys549 and cys586 from the desulfovibrio vulgaris and r ...201020165762
the molecular determinants of the increased reduction potential of the rubredoxin domain of rubrerythrin relative to rubredoxin.based on the crystal structures, three possible sequence determinants have been suggested as the cause of a 285 mv increase in reduction potential of the rubredoxin domain of rubrerythrin over rubredoxin by modulating the polar environment around the redox site. here, electrostatic calculations of crystal structures of rubredoxin and rubrerythrin and molecular dynamics simulations of rubredoxin wild-type and mutants are used to elucidate the contributions to the increased reduction potential. as ...201020159152
first isolation of desulfovibrio from the human vaginal flora.four desulfovibrio species, including 2 subtypes of 1 species, namely, desulfovibrio piger, desulfovibrio desulfuricans mb subtype and essex 6 subtype, desulfovibrio fairfieldensis, and desulfovibrio vulgaris, have been isolated from the human oral and intestinal flora, but not previously from the vaginal flora. they are opportunistic pathogens and have been considered as possible environmental and etiologic agents involved in ulcerative colitis and chronic periodontitis. we isolated desulfovibr ...201020159048
rapid evolution of stability and productivity at the origin of a microbial mutualism.mutualistic interactions are taxonomically and functionally diverse. despite their ubiquity, however, the basic ecological and evolutionary processes underlying their origin and maintenance are poorly understood. a major reason for this is the lack of an experimentally tractable model system. we examine the evolution of an experimentally imposed obligate mutualism between sulfate-reducing and methanogenic microorganisms that have no known history of previous interaction. twenty-four independent ...201020133857
a multichannel gel electrophoresis and continuous fraction collection apparatus for high-throughput protein separation and characterization.to facilitate a direct interface between protein separation by page and protein identification by mass spectrometry, we developed a multichannel system that continuously collects fractions as protein bands migrate off the bottom of gel electrophoresis columns. the device was constructed using several short linear gel columns, each of a different percent acrylamide, to achieve a separation power similar to that of a long gradient gel. a "counter free-flow" elution technique then allows continuous ...201020119951
comparison of the anaerobic microbiota of deep-water geodia spp. and sandy sediments in the straits of florida.marine sediments and sponges may show steep variations in redox potential, providing niches for both aerobic and anaerobic microorganisms. geodia spp. and sediment specimens from the straits of florida were fixed using paraformaldehyde and 95% ethanol (v/v) for fluorescence in situ hybridization (fish). in addition, homogenates of sponge and sediment samples were incubated anaerobically on various cysteine supplemented agars. fish analysis showed a prominent similarity of microbiota in sediments ...201020090787
the toxicity of lead to desulfovibrio desulfuricans g20 in the presence of goethite and quartz.an aqueous mixture of goethite, quartz, and lead chloride (pbcl(2)) was treated with the sulfate-reducing bacterium, desulfovibrio desulfuricans g20 (d. desulfuricans g20), in a medium specifically designed to assess metal toxicity. in the presence of 26 mum of soluble pb, together with the goethite and quartz, d. desulfuricans g20 grew after a lag time of 5 days compared to 2 days in pb-, goethite-, and quartz-free treatments. in the absence of goethite and quartz, however, with 26 microm solub ...201020082378
biodiversity analysis by polyphasic study of marine bacteria associated with biocorrosion phenomena.a polyphasic approach was used to study the biodiversity bacteria associated with biocorrosion processes, in particular sulfate-reducing bacteria (srb) and thiosulfate-reducing bacteria (trb) which are described to be particularly aggressive towards metallic materials, notably via hydrogen sulfide release.201020059620
development of a common oligonucleotide reference standard for microarray data normalization and comparison across different microbial communities.high-density functional gene arrays have become a powerful tool for environmental microbial detection and characterization. however, microarray data normalization and comparison for this type of microarray remain a challenge in environmental microbiology studies because some commonly used normalization methods (e.g., genomic dna) for the study of pure cultures are not applicable. in this study, we developed a common oligonucleotide reference standard (cors) method to address this problem. a uniq ...201020038701
global transcriptional, physiological, and metabolite analyses of the responses of desulfovibrio vulgaris hildenborough to salt adaptation.the response of desulfovibrio vulgaris hildenborough to salt adaptation (long-term nacl exposure) was examined by performing physiological, global transcriptional, and metabolite analyses. salt adaptation was reflected by increased expression of genes involved in amino acid biosynthesis and transport, electron transfer, hydrogen oxidation, and general stress responses (e.g., heat shock proteins, phage shock proteins, and oxidative stress response proteins). the expression of genes involved in ca ...201020038696
smoking and other personal characteristics as potential predictors for fecal bacteria populations in humans.intestinal microbes have been postulated to play an important role in the development of colorectal cancer. recently developed methods for preserving and delivering fecal samples at ambient temperature to the laboratory for molecular analysis of bacterial constituents were used to test associations of bacterial populations with epidemiologic risk factors for colorectal cancer.201020037488
the three-dimensional structure of [nifese] hydrogenase from desulfovibrio vulgaris hildenborough: a hydrogenase without a bridging ligand in the active site in its oxidised, "as-isolated" state.hydrogen is a good energy vector, and its production from renewable sources is a requirement for its widespread use. [nifese] hydrogenases (hases) are attractive candidates for the biological production of hydrogen because they are capable of high production rates even in the presence of moderate amounts of o(2), lessening the requirements for anaerobic conditions. the three-dimensional structure of the [nifese] hase from desulfovibrio vulgaris hildenborough has been determined in its oxidised " ...201020026074
desulfovibrio oceani subsp. oceani sp. nov., subsp. nov. and desulfovibrio oceani subsp. galateae subsp. nov., novel sulfate-reducing bacteria isolated from the oxygen minimum zone off the coast of peru.two deltaproteobacterial sulfate reducers, designated strain i.8.1(t) and i.9.1(t), were isolated from the oxygen minimum zone water column off the coast of peru at 400 and 500 m water depth. the strains were gram-negative, vibrio-shaped and motile. both strains were psychrotolerant, grew optimally at 20 degrees c at ph 7.0-8.0 and at 2.5-3.5% nacl (w/v). the strains grew by utilizing hydrogen/acetate, c(3-4) fatty acids, amino acids and glycerol as electron acceptors for sulfate reduction. fuma ...201020012196
structural biology: molecular coin slots for urea. 200920010678
composition and dynamics of sulfate-reducing bacteria during the waterflooding process in the oil field application.the composition and dynamics of sulfate-reducing bacteria (srb) during the waterflooding process of daqing oilfield were investigated in this study. pcr-dgge analysis indicated that the microbial communities were significantly different in each treatment unit, and the dominant members were mainly close to clostridium sp., thauera sp., hydrogenophaga sp., pseudomonas sp., eubacterium sp. and arcobacter sp. however, the members belonging to srb were relatively few and mainly consisted of desulfovi ...201020005702
antibacterial inorganic-organic hybrid coatings on stainless steel via consecutive surface-initiated atom transfer radical polymerization for biocorrosion prevention.to enhance the corrosion resistance of stainless steel (ss) and to impart its surface with antibacterial functionality for inhibiting biofilm formation and biocorrosion, well-defined inorganic-organic hybrid coatings, consisting of a polysilsesquioxane inner layer and quaternized poly(2-(dimethyamino)ethyl methacrylate) (p(dmaema)) outer blocks, were prepared via successive surface-initiated atom transfer radical polymerization (atrp) of 3-(trimethoxysilyl)propyl methacrylate (tmspma) and 2-(dim ...201020000424
an nmr structural study of nickel-substituted rubredoxin.the ni(ii) and zn(ii) derivatives of desulfovibrio vulgaris rubredoxin (dvrd) have been studied by nmr spectroscopy to probe the structure at the metal centre. the beta ch(2) proton pairs from the cysteines that bind the ni(ii) atom have been identified using 1d nuclear overhauser enhancement (noe) difference spectra and sequence specifically assigned via noe correlations to neighbouring protons and by comparison with the published x-ray crystal structure of a ni(ii) derivative of clostridium pa ...201019997764
relating diffusion along the substrate tunnel and oxygen sensitivity in hydrogenase.in hydrogenases and many other redox enzymes, the buried active site is connected to the solvent by a molecular channel whose structure may determine the enzyme's selectivity with respect to substrate and inhibitors. the role of these channels has been addressed using crystallography and molecular dynamics, but kinetic data are scarce. using protein film voltammetry, we determined and then compared the rates of inhibition by co and o2 in ten nife hydrogenase mutants and two fefe hydrogenases. we ...201019966788
response of the sulfate-reducing community to the re-establishment of estuarine conditions in two contrasting soils: a mesocosm approach.we studied the response of the sulfate-reducing prokaryote (srp) communities to the experimental variation of salinity and tide in an outdoor mesocosm setup. intact soil monoliths were collected at two areas of the haringvliet lagoon (the netherlands): one sampling location consisted of agricultural grassland, drained and fertilized for at least the last century; the other of a freshwater marshland with more recent sea influence. two factors, i.e., "salinity" (freshwater/oligohaline) and "tide" ...201019953240
changes in iron, sulfur, and arsenic speciation associated with bacterial sulfate reduction in ferrihydrite-rich systems.biologically mediated redox processes have been shown to affect the mobility of iron oxide-bound arsenic in reducing aquifers. this work investigates how dissimilatory sulfate reduction and secondary iron reduction affect sulfur, iron, and arsenic speciation. incubation experiments were conducted with as(iii/v)-bearing ferrihydrite in carbonate-buffered artificial groundwater enriched with lactate (10 mm) and sulfate (0.08-10 mm) and inoculated with desulfovibrio vulgaris (atcc 7757, formerly d. ...200919943647
[development of mono- and associative cultures of sulphate-reducing bacteria and formation of exopolymeric complex].differences were found in development of the monoculture of sulphate-reducing bacteria desulfovibrio sp. kyiv-10 and artificial associations of cultures of sulphate reducing bacteria with heterotrophic satellites under development in a form of biofilm or plankton. correlation between exopolymers synthesis in the biofilm and steel corrosion velocity has been found. glucose, galactose, mannose, xylose, rhibose and nonidentified carbohydrates were found in the composition of exopolymers synthesized ...200919938590
inhibition of the [nife] hydrogenase from desulfovibrio vulgaris miyazaki f by carbon monoxide: an ftir and epr spectroscopic study.x-ray crystallographic studies [ogata et al., j. am. chem. soc. 124 (2002) 11628-11635] have shown that carbon monoxide binds to the nickel ion at the active site of the [nife] hydrogenase from desulfovibriovulgaris miyazaki f and inhibits its catalytic function. in the present work spectroscopic aspects of the co inhibition for this bacterial organism are reported for the first time and enable a direct comparison with the existing crystallographic data. the binding affinity of each specific red ...201019925776
structural similarities between biogenic uraninites produced by phylogenetically and metabolically diverse bacteria.while the product of microbial uranium reduction is often reported to be "uo(2)", a comprehensive characterization including stoichiometry and unit cell determination is available for only one shewanella species. here, we compare the products of batch uranyl reduction by a collection of dissimilatory metal- and sulfate-reducing bacteria of the genera shewanella, geobacter, anaeromyxobacter, and desulfovibrio under similar laboratory conditions. our results demonstrate that u(vi) bioreduction by ...200919924959
residue-specific analysis of frustration in the folding landscape of repeat beta/alpha protein apoflavodoxin.flavodoxin adopts the common repeat beta/alpha topology and folds in a complex kinetic reaction with intermediates. to better understand this reaction, we analyzed a set of desulfovibrio desulfuricans apoflavodoxin variants with point mutations in most secondary structure elements by in vitro and in silico methods. by equilibrium unfolding experiments, we first revealed how different secondary structure elements contribute to overall protein resistance to heat and urea. next, using stopped-flow ...201019913555
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