heme biosynthesis in methanosarcina barkeri via a pathway involving two methylation reactions.the methanogenic archaeon methanosarcina barkeri synthesizes protoheme via precorrin-2, which is formed from uroporphyrinogen iii in two consecutive methylation reactions utilizing s-adenosyl-l-methionine. the existence of this pathway, previously exclusively found in the sulfate-reducing delta-proteobacterium desulfovibrio vulgaris, was demonstrated for m. barkeri via the incorporation of two methyl groups from methionine into protoheme.200617028275
correlation of mrna expression and protein abundance affected by multiple sequence features related to translational efficiency in desulfovibrio vulgaris: a quantitative analysis.the modest correlation between mrna expression and protein abundance in large-scale data sets is explained in part by experimental challenges, such as technological limitations, and in part by fundamental biological factors in the transcription and translation processes. among various factors affecting the mrna-protein correlation, the roles of biological factors related to translation are poorly understood. in this study, using experimental mrna expression and protein abundance data collected f ...200617028312
new findings for in-gel digestion accelerated by high-intensity focused ultrasound for protein identification by matrix-assisted laser desorption ionization time-of-flight mass findings in sample treatment based on high-intensity focused ultrasound (hifu) for protein digestion after polyacrylamide gel electrophoresis separation are presented. the following variables were studied: (i) sample volume; (ii) sonotrode diameter; (iii) previous protein denaturation; (iv) cooling; (v) enzyme concentration; and (vi) protein concentration. results showed that positive protein identification could be done after protein separation by gel electrophoresis through peptide mass fi ...200717034802
interaction of desulfovibrio desulfuricans biofilms with stainless steel surface and its impact on bacterial study the influence of some metallic elements of stainless steel 304 (ss 304) on the development and activity of a sulfate-reducing bacterial biofilm, using as comparison a reference nonmetallic material polymethylmethacrylate (pmma).200617040232
a 1,1,1-trichloroethane-degrading anaerobic mixed microbial culture enhances biotransformation of mixtures of chlorinated ethenes and ethanes.1,1,1-trichloroethane (1,1,1-tca) is a common groundwater pollutant as a result of improper disposal and accidental spills. it is often found as a cocontaminant with trichloroethene (tce) and inhibits some tce-degrading microorganisms. 1,1,1-tca removal is therefore required for effective bioremediation of sites contaminated with mixed chlorinated organics. this study characterized ms, a 1,1,1-tca-degrading, anaerobic, mixed microbial culture derived from a 1,1,1-tca-contaminated site in the nor ...200617056695
superoxide reduction by archaeoglobus fulgidus desulfoferrodoxin: comparison with neelaredoxin.superoxide reductases (sors) are non-heme iron-containing enzymes that remove superoxide by reducing it to hydrogen peroxide. the active center of sors consists of a ferrous ion coordinated by four histidines and one cysteine in a square-pyramidal geometry. in the 2fe-sor, a distinct family of sors, there is an additional desulforedoxin-like site that does not appear to be involved in sor activity. our previous studies on recombinant archaeoglobus fulgidus neelaredoxin (1fe-sor) have shown that ...200717066300
redox chemistry of low-ph forms of tetrahemic cytochrome c3.desulfovibrio vulgaris hildenborough cytochrome c(3) contains four hemes in a low-spin state with bis-histidinyl coordination. high-spin forms of cytochrome c(3) can be generated by protonation of the axial ligands in order to probe spin equilibrium (low-spin/high-spin). the spin alterations occurring at acid ph, the associated changes in redox potentials, as well as the reactivity towards external ligands were followed by the conjunction of square wave voltammetry and uv-visible, cd, nmr and ep ...200617084898
analysis of diversity and activity of sulfate-reducing bacterial communities in sulfidogenic bioreactors using 16s rrna and dsrb genes as molecular we describe the diversity and activity of sulfate-reducing bacteria (srb) in sulfidogenic bioreactors by using the simultaneous analysis of pcr products obtained from dna and rna of the 16s rrna and dissimilatory sulfite reductase (dsrab) genes. we subsequently analyzed the amplified gene fragments by using denaturing gradient gel electrophoresis (dgge). we observed fewer bands in the rna-based dgge profiles than in the dna-based profiles, indicating marked differences in the populations pr ...200717098925
spectroelectrochemistry of type ii cytochrome c3 on a glycosylated self-assembled monolayer.a modified silver electrode was prepared by the self-assembly of a thiol-derivatized neoglycoconjugate, forming a 2d surface with maltose functionality. this self-assembled-monolayer-modified electrode was utilized for adsorption and spectroelectrochemical studies of tetraheme-containing type ii cytochrome c3. the glycosylated surface allowed for the determination of the hemes' redox potentials and demonstrated enhanced spectroelectrochemical performance, in comparison to the widely used self-as ...200617106964
evolution of the syntrophic interaction between desulfovibrio vulgaris and methanosarcina barkeri: involvement of an ancient horizontal gene transfer.the sulfate reducing bacteria desulfovibrio vulgaris and the methanogenic archaea methanosarcina barkeri can grow syntrophically on lactate. in this study, a set of three closely located genes, dvu2103, dvu2104, and dvu2108 of d. vulgaris, was found to be up-regulated 2- to 4-fold following the lifestyle shift from syntroph to sulfate reducer; moreover, none of the genes in this gene set were differentially regulated when comparing gene expression from various d. vulgaris pure culture experiment ...200717107661
pathway confirmation and flux analysis of central metabolic pathways in desulfovibrio vulgaris hildenborough using gas chromatography-mass spectrometry and fourier transform-ion cyclotron resonance mass spectrometry.flux distribution in central metabolic pathways of desulfovibrio vulgaris hildenborough was examined using 13c tracer experiments. consistent with the current genome annotation and independent evidence from enzyme activity assays, the isotopomer results from both gas chromatography-mass spectrometry (gc-ms) and fourier transform-ion cyclotron resonance mass spectrometry (ft-icr ms) indicate the lack of an oxidatively functional tricarboxylic acid (tca) cycle and an incomplete pentose phosphate p ...200717114264
x-ray structure of the membrane-bound cytochrome c quinol dehydrogenase nrfh reveals novel haem coordination.oxidation of membrane-bound quinol molecules is a central step in the respiratory electron transport chains used by biological cells to generate atp by oxidative phosphorylation. a novel family of cytochrome c quinol dehydrogenases that play an important role in bacterial respiratory chains was recognised in recent years. here, we describe the first structure of a cytochrome from this family, nrfh from desulfovibrio vulgaris, which forms a stable complex with its electron partner, the cytochrome ...200617139260
correlating epr and x-ray structural analysis of arsenite-inhibited forms of aldehyde oxidoreductase.two arsenite-inhibited forms of each of the aldehyde oxidoreductases from desulfovibrio gigas and desulfovibrio desulfuricans have been studied by x-ray crystallography and electron paramagnetic resonance (epr) spectroscopy. the molybdenum site of these enzymes shows a distorted square-pyramidal geometry in which two ligands, a hydroxyl/water molecule (the catalytic labile site) and a sulfido ligand, have been shown to be essential for catalysis. arsenite addition to active as-prepared enzyme or ...200717139522
application of cell-free translation systems to studies of cofactor binding develop applications of in vitro cell-free translation systems for production and characterization of cofactor binding proteins, we investigate the production of apo- or holo-forms of flavin mono nucleotide (fmn)-binding protein from desulfovibrio vulgaris (miyazaki f) and purified them. the redox potential analysis and measurements of uv-, visible, and fluorescent spectra of reconstructed holo-protein showed that the fmn correctly bound to the fmn binding site. on the other hand, contrary to ...200417150519
isolation of sulfate-reducing bacteria from tunisian marine sediments and description of desulfovibrio bizertensis sp. nov.several strains of sulfate-reducing bacteria were isolated from marine sediments recovered near tunis, korbous and bizerte, tunisia. they all showed characteristics consistent with members of the genus desulfovibrio. one of these strains, designated mb3(t), was characterized further. cells of strain mb3(t) were slender, curved, vibrio-shaped, motile, gram-negative, non-spore-forming rods. they were positive for desulfoviridin as bisulfite reductase. strain mb3(t) grew at temperatures of 15-45 de ...200617158997
phytic acid modulates in vitro il-8 and il-6 release from colonic epithelial cells stimulated with lps and il-1beta.phytic acid (pa), a major fiber-associated component of wheat bran and legumes, is physiologically present in the human large gut. the aim of this study was to examine the role of pa in immunologic function of intestinal epithelial cells by analyzing its effect on interleukin (il)-8 and il-6 secretion by colonocytes and its role in the response of these cells to bacterial lipopolysaccharides (lps) and il-1beta. the human colon cell line caco-2 was exposed to lps isolated from two strains of desu ...200717160716
direct force measurement of bacteria adhesion on metal in aqueous media.the adhesion of bacteria on metal surfaces in aqueous media and the development of biofilm and resultant biofouling are important phenomena in both the natural environment and engineering systems. this work reports on the use of a force microscopy technique to measure bacterial metal adhesion by two anaerobic sulphate-reducing bacteria (desulfovibrio desulfuricans and a local marine isolate) and an aerobe (pseudomonas sp.). using a modified bacteria tip, the atomic force microscope was able to q ...200617163038
process of maturation of tetraheme cytochrome c3 in a shewanella expression system.the process of maturation of multiheme proteins is not yet well known, while that of monoheme ones has been relatively well investigated. two kinds of partly unfolded tetraheme cytochrome c3 were obtained on overexpression in shewanella oneidensis tsp-c. these proteins were characterized by circular dichroism and nuclear magnetic resonance spectroscopy. it turned out that the tetraheme architecture, and the fifth and sixth ligand coordination are almost mature, while some parts of the polypeptid ...200717167041
electrochemical investigations of the interconversions between catalytic and inhibited states of the [fefe]-hydrogenase from desulfovibrio desulfuricans.studies of the catalytic properties of the [fefe]-hydrogenase from desulfovibrio desulfuricans by protein film voltammetry, under a h2 atmosphere, reveal and establish a variety of interesting properties not observed or measured quantitatively with other techniques. the catalytic bias (inherent ability to oxidize hydrogen vs reduce protons) is quantified over a wide ph range: the enzyme is proficient at both h2 oxidation (from ph > 6) and h2 production (ph < 6). hydrogen production is inhibited ...200617177431
environment. spain's prestige oil spill resurfaces. 200617185574
a needle in a haystack: the active site of the membrane-bound complex cytochrome c nitrite reductase.cytochrome c nitrite reductase is a multicenter enzyme that uses a five-coordinated heme to perform the six-electron reduction of nitrite to ammonium. in the sulfate reducing bacterium desulfovibrio desulfuricans atcc 27774, the enzyme is purified as a nrfa2nrfh complex that houses 14 hemes. the number of closely-spaced hemes in this enzyme and the magnetic interactions between them make it very difficult to study the active site by using traditional spectroscopic approaches such as epr or uv-vi ...200717207484
the bacterial metallome: composition and stability with specific reference to the anaerobic bacterium desulfovibrio bacteria, the intracellular metal content or metallome reflects the metabolic requirements of the cell. when comparing the composition of metals in phytoplankton and bacteria that make up the macronutrients and the trace elements, we have determined that the content of trace elements in both of these microorganisms is markedly similar. the trace metals consisting of transition metals plus zinc are present in a stoichometric molar formula that we have calculated to be as follows: fe(1)mn(0.3)z ...200717216357
molecular characterisation of the gut microflora of healthy and inflammatory bowel disease cats using fluorescence in situ hybridisation with special reference to desulfovibrio spp.inflammatory bowel disease (ibd) is a common cause of chronic large bowel diarrhoea in cats. although the aetiology of ibd is unknown, an immune-mediated response to a luminal antigen is thought to be involved. as knowledge concerning the colonic microflora of cats is limited and requires further investigation, the purpose of this study was to determine the presence of specific bacterial groups in normal and ibd cats, and the potential role they play in the health of the host. total bacterial po ...200717217390
preparation, structures and electrochemical property of phosphine substituted diiron azadithiolates relevant to the active site of fe-only hydrogenases.mono- and di-phosphine diiron azadithiolate complexes [{(mu-sch(2))(2)n(4-no(2)c(6)h(4))}fe(2)(co)(5)(pme(3))] (2), [{(mu-sch(2))(2)n(4-no(2)c(6)h(4))}{fe(co)(2)l}(2)] (3, l=pme(3); 4, pme(2)ph) and the mu-hydride diiron complex [3(fehfe)](+)[pf(6)](-) were prepared as biomimetic models of the active site of fe-only hydrogenases. the complexes 2-4 and [3(fehfe)](+)[pf(6)](-) were characterized by ir, (31)p, (1)h and (13)c nmr spectra and their molecular structures were determined by single cryst ...200717222911
improved pulse sequences for sequence specific assignment of aromatic proton resonances in proteins.aromatic proton resonances of proteins are notoriously difficult to assign. through-bond correlation experiments are preferable over experiments that rely on through-space interactions because they permit aromatic chemical shift assignments to be established independently of the structure determination process. known experimental schemes involving a magnetization transfer across the cbeta-cgamma bond in aromatic side chains either suffer from low efficiency for the relay beyond the cdelta positi ...200717237975
the anaerobe desulfovibrio desulfuricans atcc 27774 grows at nearly atmospheric oxygen levels.sulfate reducing bacteria of the desulfovibrio genus are considered anaerobes, in spite of the fact that they are frequently isolated close to oxic habitats. however, until now, growth in the presence of high concentrations of oxygen was not reported for members of this genus. this work shows for the first time that the sulfate reducing bacterium desulfovibrio desulfuricans atcc 27774 is able to grow in the presence of nearly atmospheric oxygen levels. in addition, the activity and expression pr ...200717239374
determination of the role of the carboxyl-terminal leucine-122 in fmn-binding protein by mutational and structural analysis.mutants of flavin mononucleotide-binding protein (fmn-bp) were made by site-directed mutagenesis to investigate the role of carboxyl-terminal leu122 of the pairing subunit in controlling redox potentials, binding the prosthetic group, and forming the tertiary and quaternary structure. we compared the oxidation-reduction potentials, fmn-binding properties, and higher structures of wild-type fmn-bp and four mutant proteins (l122y, l122e, l122k and l122-deleted). we found that the redox potentials ...200717261542
sonoreactor-based technology for fast high-throughput proteolytic digestion of (120 s) and high-throughput (more than six samples at once) in-gel trypsin digestion of proteins using sonoreactor technology has been achieved. successful protein identification was done by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, maldi-tof-ms. specific identification of the adenylylsulphate reductase alfa subunit from a complex protein mixture from desulfovibrio desulfuricans atcc 27774 was done as a proof of the methodology. the new sample treatment i ...200717269750
plasticity of the domain structure in flgj, a bacterial protein involved in flagellar rod formation.bacterial flagellar rod structure is built across the peptidoglycan (pg) layer. a salmonella enterica flagellar protein flgj is believed to consist of two functional domains, the n-terminal half acting as a scaffold or cap essential for rod assembly and the c-terminal half acting as a pg hydrolase (pgase) that makes a hole in the pg layer to facilitate rod penetration. in this study, molecular data analyses were conducted on flgj data sets sampled from a variety of bacterial species, and three t ...200617283383
from bio-mineralisation to fuel cells: biomanufacture of pt and pd nanocrystals for fuel cell electrode catalyst.biosynthesis of nano-scale platinum and palladium was achieved via enzymatically-mediated deposition of metal ions from solution. the bio-accumulated pt(0) and pd(0) crystals were dried, applied onto carbon paper and tested as anodes in a polymer electrolyte membrane (pem) fuel cell for power production. up to 100% and 81% of the maximum power generation was achieved by the bio-pt and bio-pd catalysts, respectively, compared to commercial fuel cell grade pt catalyst. hence, biomineralisation cou ...200717295088
analysis of amino acid isotopomers using ft-icr ms.fluxes through known metabolic pathways and the presence of novel metabolic reactions are often determined by feeding isotopically labeled substrate to an organism and then determining the isotopomer distribution in amino acids in proteins. however, commonly used techniques to measure the isotopomer distributions require derivatization prior to analysis (gas chromatography/mass spectrometry (gc/ms)) or large sample sizes (nuclear magnetic resonance (nmr) spectroscopy). here, we demonstrate the u ...200717305312
oil field souring control by nitrate-reducing sulfurospirillum spp. that outcompete sulfate-reducing bacteria for organic electron donors.nitrate injection into oil reservoirs can prevent and remediate souring, the production of hydrogen sulfide by sulfate-reducing bacteria (srb). nitrate stimulates nitrate-reducing, sulfide-oxidizing bacteria (nr-sob) and heterotrophic nitrate-reducing bacteria (hnrb) that compete with srb for degradable oil organics. up-flow, packed-bed bioreactors inoculated with water produced from an oil field and injected with lactate, sulfate, and nitrate served as sources for isolating several nrb, includi ...200717308184
functional properties of type i and type ii cytochromes c3 from desulfovibrio africanus.type i cytochrome c(3) is a key protein in the bioenergetic metabolism of desulfovibrio spp., mediating electron transfer between periplasmic hydrogenase and multihaem cytochromes associated with membrane bound complexes, such as type ii cytochrome c(3). this work presents the nmr assignment of the haem substituents in type i cytochrome c(3) isolated from desulfovibrio africanus and the thermodynamic and kinetic characterisation of type i and type ii cytochromes c(3) belonging to the same organi ...200717316553
force measurements of bacterial adhesion on metals using a cell probe atomic force microscope.the adhesion of microbial cells to metal surfaces in aqueous media is an important phenomenon in both the natural environment and engineering systems. the adhesion of two anaerobic sulfate-reducing bacteria (desulfovibrio desulfuricans and a local marine isolate) and an aerobe (pseudomonas sp.) to four polished metal surfaces (i.e., stainless steel 316, mild steel, aluminum, and copper) was examined using a force spectroscopy technique with an atomic force microscope (afm). using a modified bact ...200717321534
experimental evaluation and mathematical modeling of microbially enhanced tetrachloroethene (pce) dissolution.experiments to assess metabolic reductive dechlorination (chlororespiration) at high concentration levels consistent with the presence of free-phase tetrachloroethene (pce) were performed using three pce-to-cis-1,2-dichloroethene (cis-dce) dechlorinating pure cultures (sulfurospirillum multivorans, desulfuromonas michiganensis strain bb1, and geobacter lovleyi strain sz) and desulfitobacterium sp. strain viet1, a pce-to-trichloroethene (tce) dechlorinating isolate. despite recent evidence sugges ...200717328210
alkane biodegradation and dynamics of phylogenetic subgroups of sulfate-reducing bacteria in an anoxic coastal marine sediment artificially contaminated with oil.for 503 days, unoiled control and artificially oiled sediments were incubated in situ at 20m water depth in a mediterranean coastal area. degradation of the aliphatic fraction of the oil added was followed by gc-ms. at the same time, terminal restriction fragment length polymorphism (t-rflp) of 16s rrna encoding genes was used to detect dynamics in the sulfate-reducing bacteria (srb) community in response to the oil contamination. specific polymerase chain reaction (pcr) primer sets for five gen ...200717337033
influence of vitamin b12 and cocultures on the growth of dehalococcoides isolates in defined medium.bacteria belonging to the genus dehalococcoides play a key role in the complete detoxification of chloroethenes as these organisms are the only microbes known to be capable of dechlorination beyond dichloroethenes to vinyl chloride (vc) and ethene. however, dehalococcoides strains usually grow slowly with a doubling time of 1 to 2 days and have complex nutritional requirements. here we describe the growth of dehalococcoides ethenogenes 195 in a defined mineral salts medium, improved growth of st ...200717337553
regulation of arsenate resistance in desulfovibrio desulfuricans g20 by an arsrbcc operon and an arsc gene.desulfovibrio desulfuricans g20 grows and reduces 20 mm arsenate to arsenite in lactate-sulfate media. sequence analysis and experimental data show that d. desulfuricans g20 has one copy of arsc and a complete arsrbcc operon in different locations within the genome. two mutants of strain g20 with defects in arsenate resistance were generated by nitrosoguanidine mutagenesis. the arsrbcc operons were intact in both mutant strains, but each mutant had one point mutation in the single arsc gene. mut ...200717337573
molecular characterization of sheep ruminal enrichments that detoxify pyrrolizidine alkaloids by denaturing gradient gel electrophoresis and enrichment of strictly anaerobic bacteria from ovine rumen fluid, which has previously been named l4m2, is known to detoxify animal hepatotoxins from the pyrrolizidine alkaloid family. these toxins are present in the tansy ragwort plant (senecio jacobaea). these plants have been described in livestock animals' range forages in regions of the world such as the northwest united states and south africa. the bacterial enrichment was characterized by molecular cloning techniques and by the molecul ...200717345134
detection of structural changes in a cofactor binding protein by using a wheat germ cell-free protein synthesis system coupled with unnatural amino acid probing.a cell-free protein synthesis system is a powerful tool with which unnatural amino acids can be introduced into polypeptide chains. here, the authors describe unnatural amino acid probing in a wheat germ cell-free translation system as a method for detecting the structural changes that occur in a cofactor binding protein on a conversion of the protein from an apo-form to a holo-form. the authors selected the fmn-binding protein from desulfovibrio vulgaris as a model protein. the apo-form of the ...200717348022
quantification of sulfate-reducing bacteria in industrial wastewater, by real-time polymerase chain reaction (pcr) using dsra and apsa genes.real-time polymerase chain reaction (pcr) is considered a highly sensitive method for the quantification of microbial organisms in environmental samples. this study was conducted to evaluate real-time pcr with sybrgreen detection as a quantification method for sulfate-reducing bacteria (srb) in industrial wastewater produced by several chemical industries. we designed four sets of primers and developed standard curves based on genomic dna of desulfovibrio vulgaris from pure culture and on plasmi ...200717351812
metabolic modeling of a mutualistic microbial community.the rate of production of methane in many environments depends upon mutualistic interactions between sulfate-reducing bacteria and methanogens. to enhance our understanding of these relationships, we took advantage of the fully sequenced genomes of desulfovibrio vulgaris and methanococcus maripaludis to produce and analyze the first multispecies stoichiometric metabolic model. model results were compared to data on growth of the co-culture on lactate in the absence of sulfate. the model accurate ...200717353934
nitrogen fixation by reductively dechlorinating bacteria.significant advances in the ecology, physiology and genetics of reductively dechlorinating bacteria have revealed their important environmental roles in bioremediation and in the global chlorine cycle. n2 fixation has been widely observed in symbiotic, associative and free-living bacteria. here we show physiological and molecular evidence that reductively dechlorinating bacteria are capable of fixing atmospheric nitrogen. furthermore, n2 fixation in some of these dechlorinating bacteria stimulat ...200717359278
functional roles of the heme architecture and its environment in tetraheme cytochrome c.cytochromes are involved in a wide variety of redox reactions in living systems. some of them contain multiple hemes such as desulfovibrio cytochrome c3 and shewanella small tetraheme cytochrome c. the significance of c-type tetraheme architectures was discussed. a cyclic heme architecture and its environment regulate the extremely low redox potentials of cytochrome c3 in addition to bis-imidazole coordination and heme exposure. each heme in cytochrome c3 plays a different role in the electron t ...200717370988
abundance and diversity of octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (hmx)-metabolizing bacteria in uxo-contaminated marine sediments.octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (hmx) is a toxic explosive known to be resistant to biodegradation. in this study, we found that sediment collected from two unexploded ordnance (uxo) disposal sites (uxo-3, uxo-5) and one nearby reference site (midref) in hawaii contained anaerobic bacteria capable of removing hmx. two groups of hmx-removing bacteria were found in uxo-5: group i contained aerotolerant anaerobes and microaerophiles, and group ii contained facultative anaerobes. in ...200717381523
[sulfate-reducing bacteria in reservoirs of the yavoriv sulfur field].fifteen cultures of bacteria which perform dissimilation sulfate reduction have been isolated from the reservoirs of the yavoriv sulfur deposit. electron-microscopic investigations have shown that the cells of all cultures are of vibroid, spiral and bacillary form. they form no spores. they grow in the medium with sulfates and lactates and do not use propionate and acetate. in the medium with lactate all the cultures accumulated acetate in the medium. cells of all the studied bacteria contain de ...200617388124
octomeric pyruvate-ferredoxin oxidoreductase from desulfovibrio vulgaris.pyruvate-ferredoxin oxidoreductatse (pfor) carries out the central step in oxidative decarboxylation of pyruvate to acetyl-coa. we have purified this enzyme from desulfovibrio vulgaris hildenborough (dvh) as part of a systematic characterization of as many multiprotein complexes as possible for this organism, and the three-dimensional structure of this enzyme has been determined by a combination of electron microscopy (em), single particle image analysis, homology modeling and computational mole ...200717400475
dehalogenation of polychlorinated biphenyls and polybrominated diphenyl ethers using a hybrid bioinorganic catalyst.the environmentally prevalent polybrominated diphenyl ether (pbde) #47 and polychlorinated biphenyls (pcbs) #28 and #118 were challenged for 24 hours with a novel biomass-supported pd catalyst (bio-pd(0)). analysis of the products via gc-ms revealed the bio-pd(0) to cause the challenged compounds to undergo stepwise dehalogenation with preferential loss of the least sterically hindered halogen atom. a mass balance for pcb #28 showed that it is degraded to three dichlorobiphenyls (33.9%), two mon ...200717410306
hydrogen sulfide production from elemental sulfur by desulfovibrio desulfuricans in an anaerobic bioreactor.feasibility of elemental sulfur reduction by desulfovibrio desulfuricans in anaerobic conditions in a stirred reactor was studied. hydrogen was used as energy source, whereas the carbonated species were bicarbonate and yeast extract. attention was paid to reactor engineering aspects, biofilm formation on the sulfur surface, hydrogen sulfide formation rate and kinetics limitations of the sulfur reduction. d. desulfuricans formed stable biofilms on the sulfur surface. it was found that active sulf ...200717421040
co-existence of physiologically similar sulfate-reducing bacteria in a full-scale sulfidogenic bioreactor fed with a single organic electron donor.a combination of culture-dependent and independent methods was used to study the co-existence of different sulfate-reducing bacteria (srb) in an upflow anaerobic sludge bed reactor treating sulfate-rich wastewater. the wastewater was fed with ethanol as an external electron donor. twenty six strains of srb were randomly picked and isolated from the highest serial dilution that showed growth (i.e. 10(8)). repetitive enterobacterial palindromic polymerase chain reaction and whole cell protein prof ...200717440719
development and assessment of whole-genome oligonucleotide microarrays to analyze an anaerobic microbial community and its responses to oxidative stress.the application of dna microarray technology to investigate multiple-species microbial communities presents great challenges. in this study, we reported the design and quality assessment of four whole genome oligonucleotide microarrays for two syntroph bacteria, desulfovibrio vulgaris and syntrophobacter fumaroxidans, and two archaeal methanogens, methanosarcina barkeri, and methanospirillum hungatei, and their application to analyze global gene expression in a four-species microbial community i ...200717498652
superoxide radical sensing using a cytochrome c3 immobilized conducting polymer electrode.a biosensor based on cytochrome c3 (cyt c3) has been introduced to detect and quantify superoxide radical (o2*-). cyt c3, isolated from the sulfate-reducing bacterium (desulfovibrio vulgaris miyazaki f. strain), and its mutant were immobilized onto a conducting polymer coated electrodes by the covalent bonding with carbodiimide chemistry. the immobilization of cyt c3 was investigated with quartz crystal microbalance, electrochemical impedance spectroscopy, and cyclic voltammetric studies. the cv ...200717507210
prophage-like gene transfer agents-novel mechanisms of gene exchange for methanococcus, desulfovibrio, brachyspira, and rhodobacter species.gene transfer agents (gtas) are novel mechanisms for bacterial gene transfer. they resemble small, tailed bacteriophages in ultrastructure and act like generalized transducing prophages. in contrast to functional prophages, gtas package random fragments of bacterial genomes and incomplete copies of their own genomes. the packaged dna content is characteristic of the gta and ranges in size from 4.4 to 13.6kb. gtas have been reported in species of brachyspira, methanococcus, desulfovibrio, and rho ...200717513139
crystal structure of the 16 heme cytochrome from desulfovibrio gigas: a glycosylated protein in a sulphate-reducing bacterium.sulphate-reducing bacteria have a wide variety of periplasmic cytochromes involved in electron transfer from the periplasm to the cytoplasm. hmca is a high molecular mass cytochrome of 550 amino acid residues that harbours 16 c-type heme groups. we report the crystal structure of hmca isolated from the periplasm of desulfovibrio gigas. crystals were grown using polyethylene glycol 8k and zinc acetate, and diffracted beyond 2.1 a resolution. a multiple-wavelength anomalous dispersion experiment a ...200717531266
cell-wide responses to low-oxygen exposure in desulfovibrio vulgaris hildenborough.the responses of the anaerobic, sulfate-reducing organism desulfovibrio vulgaris hildenborough to low-oxygen exposure (0.1% o(2)) were monitored via transcriptomics and proteomics. exposure to 0.1% o(2) caused a decrease in the growth rate without affecting viability. concerted upregulation of the predicted peroxide stress response regulon (perr) genes was observed in response to the 0.1% o(2) exposure. several of the candidates also showed increases in protein abundance. among the remaining sma ...200717545284
assessing the role of the active-site cysteine ligand in the superoxide reductase from desulfoarculus baarsii.superoxide reductase is a novel class of non-heme iron proteins that catalyzes the one-electron reduction of o(2)(.) to h(2)o(2), providing an antioxidant defense in some bacteria. its active site consists of an unusual non-heme fe(2+) center in a [his(4) cys(1)] square pyramidal pentacoordination. in this class of enzyme, the cysteine axial ligand has been hypothesized to be an essential feature in the reactivity of the enzyme. previous fourier transform infrared spectroscopy studies on the enz ...200717545670
a dual-electrochemical cell to study the biocorrosion of stainless steel.the presence of microorganisms on metal surfaces can alter the local physical/chemical conditions and lead to microbiologically influenced corrosion (mic). the goal of the present work was to study the effect of a mixed aerobic-anaerobic biofilm on the behaviour of stainless steel (316 l) in underground conditions. rather than testing different bacteria or consortia, investigations were based on the mechanisms of mic. mixed biofilms were simulated by the addition of glucose oxidase to reproduce ...200717547022
desulfovibrio fairfieldensis bacteremia associated with choledocholithiasis and endoscopic retrograde cholangiopancreatography.desulfovibrio fairfieldensis is a gram-negative, curved, motile, anaerobic bacillus. d. fairfieldensis has been isolated only from human specimens and is considered a normal resident of the human gastrointestinal tract. we report the second case of desulfovibrio bacteremia associated with choledocholithiasis and review the other reported cases of d. fairfieldensis bacteremia.200717567792
comparative transcriptome analysis of desulfovibrio vulgaris grown in planktonic culture and mature biofilm on a steel surface.biofilm build-up of sulphate-reducing bacteria (srb) on metal surfaces may lead to severe corrosion of iron. to understand the processes at molecular level, in this study, a whole-genome oligonucleotide microarray was used to examine differential expression patterns between planktonic populations and mature biofilm of desulfovibrio vulgaris on a steel surface. statistical analysis revealed that 472 genes were differentially expressed (1.5-fold or more with a q value less than 0.025) by comparing ...200717571259
epr characterization of the molybdenum(v) forms of formate dehydrogenase from desulfovibrio desulfuricans atcc 27774 upon formate reduction.the epr characterization of the molybdenum(v) forms obtained on formate reduction of both as-prepared and inhibited formate dehydrogenase from desulfovibrio desulfuricans atcc 27774, an enzyme that catalyzes the oxidation of formate to co(2), is reported. the mo(v) epr signal of the as-prepared formate-reduced enzyme is rhombic (g(max)=2.012, g(mid)=1.996, g(min)=1.985) and shows hyperfine coupling with two nuclear species with i=1/2. one of them gives an anisotropic splitting and is not solvent ...200717574676
diversity of substrate utilization and growth characteristics of sulfate-reducing bacteria isolated from estuarine sediment in japan.two different isolation methods, the dilution colony-counting method (colony-isolation) and enrichment culture, were used to isolate sulfate-reducing bacteria (srbs) from estuarine sediment in japan. lactate was used as an electron donor for colony-isolation, and lactate or propionate was used for enrichment culture. all isolates were classified into six different phylogenetic groups according to the 16s rrna gene-based analysis. the closest relatives of the colony-isolates (12 strains) were spe ...200717575452
redox-linked conformational changes of a multiheme cytochrome from geobacter sulfurreducens.multiheme c-type cytochromes from members of the desulfovibrionacea and geobactereacea families play crucial roles in the bioenergetics of these microorganisms. thermodynamic studies using nmr and visible spectroscopic techniques on tetraheme cytochromes c(3) isolated from desulfovibrio spp. and more recently on a triheme cytochrome from geobacter sulfurreducens showed that the properties of each redox centre are modulated by the neighbouring redox centres enabling these proteins to perform ener ...200717583674
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
the [nifese] hydrogenase from desulfovibrio vulgaris hildenborough is a bacterial lipoprotein lacking a typical lipoprotein signal peptide.desulfovibrio vulgaris hildenborough has a membrane-bound [nifese] hydrogenase whose mode of membrane association was unknown since it is constituted by two hydrophilic subunits. this work shows that this hydrogenase is a bacterial lipoprotein bound to the membrane by lipidic groups found at the n-terminus of the large subunit, which is unusual since it is missing the typical lipoprotein signal peptide. nevertheless, the large subunit has a conserved four residue lipobox and its synthesis is sen ...200717601576
function of periplasmic hydrogenases in the sulfate-reducing bacterium desulfovibrio vulgaris hildenborough.the sulfate-reducing bacterium desulfovibrio vulgaris hildenborough possesses four periplasmic hydrogenases to facilitate the oxidation of molecular hydrogen. these include an [fe] hydrogenase, an [nifese] hydrogenase, and two [nife] hydrogenases encoded by the hyd, hys, hyn1, and hyn2 genes, respectively. in order to understand their cellular functions, we have compared the growth rates of existing (hyd and hyn1) and newly constructed (hys and hyn-1 hyd) mutants to those of the wild type in def ...200717601789
advantages of using microbial technology over traditional chemical technology in removal of black crusts from stone surfaces of historical monuments.this study compares two cleaning methods, one involving an ammonium carbonate-edta mixture and the other involving the sulfate-reducing bacterium desulfovibrio vulgaris subsp. vulgaris atcc 29579, for the removal of black crust (containing gypsum) on marble of the milan cathedral (italy). in contrast to the chemical cleaning method, the biological procedure resulted in more homogeneous removal of the surface deposits and preserved the patina noble under the black crust. whereas both of the treat ...200717601804
a qm/mm investigation of the activation and catalytic mechanism of fe-only hydrogenases.fe-only hydrogenases are enzymes that catalyze dihydrogen production or oxidation, due to the presence of an unusual fe(6)s(6) cluster (the so-called h-cluster) in their active site, which is composed of a fe(2)s(2) subsite, directly involved in catalysis, and a classical fe(4)s(4) cubane cluster. here, we present a hybrid quantum mechanical and molecular mechanical (qm/mm) investigation of the fe-only hydrogenase from desulfovibrio desulfuricans, in order to unravel key issues regarding the act ...200717602468
proteome analysis of desulfovibrio desulfuricans g20 mutants using the accurate mass and time (amt) tag approach.abundance values obtained from direct lc-ms analyses were used to compare the proteomes of six transposon-insertion mutants of desulfovibrio desulfuricans g20, the lab strain (g20lab) and a sediment-adapted strain (g20sediment). three mutations were in signal transduction histidine kinases, and three mutations were in other regulatory proteins. the high-throughput accurate mass and time (amt) tag proteomic approach was utilized to analyze the proteomes. a total of 1318 proteins was identified wi ...200717602684
comparison between ultrafast fluorescence dynamics of fmn binding protein from desulfovibrio vulgaris, strain miyazaki, in solution vs crystal phases.ultrafast fluorescence dynamics of fmn binding protein (fbp) from desulfobivrio vulgaris, strain miyaxaki f, were compared in solution and crystal phases. fluorescence lifetimes of fbp were 167 fs (96%) and 1.5 ps (4%) in solution (tau(av) = 220 fs), and 730 fs (60%) and longer than 10 ps (40%) in crystals (tau(av) = 4.44 ps). the quenching of the fluorescence of flavin in the protein was considered to be due to photoinduced electron transfer (et) from trp or tyr to the excited isoalloxazine (is ...200717608527
analysis of a ferric uptake regulator (fur) mutant of desulfovibrio vulgaris hildenborough.previous experiments examining the transcriptional profile of the anaerobe desulfovibrio vulgaris demonstrated up-regulation of the fur regulon in response to various environmental stressors. to test the involvement of fur in the growth response and transcriptional regulation of d. vulgaris, a targeted mutagenesis procedure was used for deleting the fur gene. growth of the resulting deltafur mutant (jw707) was not affected by iron availability, but the mutant did exhibit increased sensitivity to ...200717630305
a pcr marker for detection in surface waters of faecal pollution derived from ducks.detection of the faecal pollution contribution from wildfowl is an important adjunct in determining the sources of faecal pollution in waterways. this is particularly true, where human waste and other animal faecal sources have been eliminated as the pollution source. a polymerase chain reaction (pcr) marker was developed as a duck-specific marker of faecal pollution. the semi-nested primer system targeted an unknown bacterium (e2) isolated from mallard ducks. e2 had the closest 16s rrna sequenc ...200717631940
characterization of black band disease in red sea stony corals.microbial communities associated with black band disease (bbd) in massive stony corals from the northern red sea (eilat) were examined for the first time using molecular tools and microscopy. a high microbial diversity was revealed in the affected tissue in comparison with the healthy area of the same colony. microscopy revealed the penetration of cyanobacteria into the coral mesoglea and adjacent tissues. cyanobacterial sequences from red sea bbd-affected corals formed a cluster with sequences ...200717635545
[clinical significance of sulfate-reducing bacteria for ulcerative colitis].ulcerative colitis(uc) is colon localized disease. broad epithelial cell damage, crypt abscesses and accumulation of neutrophils are recognized for uc. although the cause of uc is indistinct at this time, there is a growing consensus that abnormal intestinal microflora would be related with uc. there have been several evidences that excessive production of hydrogen sulfide by bacteria in colon would be associated with uc. sulfate reducing bacteria are able to utilize sulfate as an electron recep ...200717642254
on the predictability of protein database search complexity and its relevance to optimization of distributed searches.we discuss several aspects related to load balancing of database search jobs in a distributed computing environment, such as linux cluster. load balancing is a technique for making the most of multiple computational resources, which is particularly relevant in environments in which the usage of such resources is very high. the particular case of the sequest program is considered here, but the general methodology should apply to any similar database search program. we show how the runtimes for se ...200717663575
[effect of corrosion inhibitor on the producing of exopolymer complex by sulphate-reducing bacteria].it is established that the specific productivity of exopolymer complex (epm) synthesized by the cells of sulphate-reducing bacteria in a biofilm was 1.5 times higher than in plankton. a sharp increase of the specific productivity of epm in the biofilm is observed when corrosion inhibitor is introduced in the environment. the inhibitor concentration being 1.0 g/l, the biofilm cells produced almost 18 times more of epm than the bacteria cells in plankton. it is shown that the film exopolymers incl ...200717682530
improving sample treatment for in-solution protein identification by peptide mass fingerprint using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.three ultrasonic energy sources were studied to speed up the sample treatment for in-solution protein identification by peptide mass fingerprint using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. protein reduction, alkylation, and enzymatic digestion steps were done in 15 min. nine proteins, including zinc resistance-associated protein precursor from desulfovibrio desulfuricans strain g20 and split-soret cytochrome c from d. desulfuricans atcc27774 were successfu ...200717683131
thermodynamic and kinetic characterisation of individual haems in multicentre cytochromes c3.the characterisation of individual centres in multihaem proteins is difficult due to the similarities in the redox and spectroscopic properties of the centres. nmr has been used successfully to distinguish redox centres and allow the determination of the microscopic thermodynamic parameters in several multihaem cytochromes c(3) isolated from different sulphate-reducing bacteria. in this article we show that it is also possible to discriminate the kinetic properties of individual centres in multi ...200717692816
analyses of the vrl gene cluster in desulfococcus multivorans: homologous to the virulence-associated locus of the ovine footrot pathogen dichelobacter nodosus strain a198.major parts of the virulence-associated vrl locus known from the gammaproteobacterium dichelobacter nodosus, the causative agent of ovine footrot, were analyzed in the genome of the sulfate-reducing deltaproteobacterium desulfococcus multivorans. in the genome of d. multivorans 13 of the 19 vrl genes described for d. nodosus are present and highly conserved with respect to gene sequence and order. the vrl locus and its flanking regions suggest a bacteriophage-mediated transfer into the genome of ...200717693723
identification of genes that confer sediment fitness to desulfovibrio desulfuricans g20.signature-tagged mutants of desulfovibrio desulfuricans g20 were screened, and 97 genes crucial for sediment fitness were identified. these genes belong to functional categories including signal transduction, binding and transport, insertion elements, and others. mutants with mutations in genes encoding proteins involved in amino acid biosynthesis, hydrogenase activity, and dna repair were further characterized.200717704273
crystal structures of hydrogenase maturation protein hype in the apo and atp-bound forms.the hydrogenase maturation protein hype serves an essential function in the biosynthesis of the nitrile group, which is subsequently coordinated to fe as cn(-) ligands in [ni-fe] hydrogenase. here, we present the crystal structures of hype from desulfovibrio vulgaris hildenborough in the presence and in the absence of atp at a resolution of 2.0 a and 2.6 a, respectively. comparison of the apo structure with the atp-bound structure reveals that binding atp causes an induced-fit movement of the n- ...200717706667
molecular determinants for fmn-binding in desulfovibrio gigas flavoredoxin.flavoredoxin participates in desulfovibrio gigas thiosulfate reduction pathway. its 3-dimensional model was generated allowing the oxidized riboflavin-5'-phosphate (fmn) site to be predicted. residues likely to be involved in fmn-binding were identified (n29, w35, t56, k92, h131 and f164) and mutated to alanine. fluorescence titration with apoprotein showed that fmn is strongly bound in the wild-type protein. comparison of k(d) values for mutants suggests that interactions with the phosphate gro ...200717719581
ultrasonic assisted protein enzymatic digestion for fast protein identification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. sonoreactor versus ultrasonic probe.two different ultrasonic energy sources, the sonoreactor and the ultrasonic probe, are compared for enzymatic digestion of proteins for protein identification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (maldi-tof-ms) using the peptide mass fingerprint (pmf) procedure. variables such as (i) trypsin/protein ratio; (ii) sonication time; (iii) ultrasound amplitude; and (iv) protein concentration are studied and compared. as a general rule, the trypsin/protein rat ...200717719595
the electronic structure of the h-cluster in the [fefe]-hydrogenase from desulfovibrio desulfuricans: a q-band 57fe-endor and hyscore study.the active site of the (57)fe-enriched [fefe]-hydrogenase (i.e., the "h-cluster") from desulfovibrio desulfuricans has been examined using advanced pulse epr methods at x- and q-band frequencies. for both the active oxidized state (h(ox)) and the co inhibited form (h(ox)-co) all six (57)fe hyperfine couplings were detected. the analysis shows that the apparent spin density extends over the whole h-cluster. the investigations revealed different hyperfine couplings of all six (57)fe nuclei in the ...200717722921
force-field development and molecular dynamics simulations of ferrocene-peptide conjugates as a scaffold for hydrogenase mimics.the increasing importance of hydrogenase enzymes in the new energy research field has led us to examine the structure and dynamics of potential hydrogenase mimics, based on a ferrocene-peptide scaffold, using molecular dynamics (md) simulations. to enable this md study, a molecular mechanics force field for ferrocene-bearing peptides was developed and implemented in the charmm simulation package, thus extending the usefulness of the package into peptide-bioorganometallic chemistry. using the aut ...200717763506
desulfovibrio marinus sp. nov., a moderately halophilic sulfate-reducing bacterium isolated from marine sediments in tunisia.two novel sulfate-reducing bacterial strains, designated e-2(t) and imp-2, were isolated from geographically distinct locations. strain e-2(t) was recovered from marine sediments near sfax (tunisia), whereas strain imp-2 originated from oilfield production fluids in the gulf of mexico. cells were gram-negative, non-sporulated, motile, vibrio-shaped or sigmoid. they were strictly anaerobic, mesophilic and moderately halophilic. sulfate, sulfite, thiosulfate and elemental sulfur served as electron ...200717766893
inorganic pyrophosphate: energy source for sulfate-reducing bacteria of the genus desulfotomaculum.sulfate-reducing bacteria belonging to the genus desulfotomaculum utilized inorganic pyrophosphate as a source of energy for growth in the presence of fixed carbon (acetate and yeast extract) and sulfate. pyrophosphate does not support the growth of desulfovibrio under the same growth conditions. over a limited range of concentrations, growth is proportional to pyrophosphate, and extracts of bacteria grown on pyrophosphate medium have enzymatic activities similar to extracts prepared from bacter ...198217791517
direct evidence for the cathodic depolarization theory of bacterial corrosion.cathodic depolarization of mild steel by desulfovibrio desulfuricans was demonstrated with benzyl viologen used as an electron acceptor. direct measurement of the cathodic depolarization current indicated a maximum current density of 1 microampere per square centimeter. aluminum alloys were also cathodically depolarized by the organism.196617796779
sulfate-reducing bacteria and pyritic sediments in lacustrine and marine sediments occur in the mcmurdo sound region of antarctica. the black color is due to the presence of iron sulfide, precipitated by sulfate-reducing bacteria (desulfovibrio) in the presence of decaying organic matter of algal origin. viability of sulfate-reducing bacteria in the sediments was demonstrated in the laboratory by culturing in anaerobic liquid media. it is probable that sulfate-reducing bacteria are widely distributed in antarctica.196117818715
[application of "microring an" to "level 1": presumptive identification of anaerobic gram-negative bacilli].commonly isolated anaerobic gram-negative rods (4 genus 64 strains), some other important gram-negative anaerobic species (9 genus 45 strains), and cigar-shaped clostridia (11 strains) were studied on their susceptibility patterns to 6 agents on "microring an". some modifications were made in the methods and interpretation of results. susceptibility patterns to erythromycin, rifampicin, colistin, benzylpenicillin, kanamycin, and vancomycin were following (sensitive [s], intermediate [i], resista ...200617822332
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
reaction of desulfovibrio vulgaris two-iron superoxide reductase with superoxide: insights from stopped-flow spectrophotometry.stopped-flow mixing of the desulfovibrio vulgaris two-iron superoxide reductase (2fe-sor) containing the ferrous active site with superoxide generates a dead time intermediate whose absorption spectrum is identical to that of a putative ferric-hydroperoxo intermediate previously observed by pulse radiolysis. the dead time intermediate is shown to be a product of reaction with superoxide and to be generated at a much higher proportion of active sites than by pulse radiolysis. this intermediate de ...200717854204
influence of bicarbonate, sulfate, and electron donors on biological reduction of uranium and microbial community composition.a microcosm study was performed to investigate the effect of ethanol and acetate on uranium(vi) biological reduction and microbial community changes under various geochemical conditions. each microcosm contained an uranium-contaminated sediment (up to 2.8 g u/kg) suspended in buffer with bicarbonate at concentrations of either 1 or 40 mm and sulfate at either 1.1 or 3.2 mm. ethanol or acetate was used as an electron donor. results indicate that ethanol yielded in significantly higher u(vi) reduc ...200717874092
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 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
dethiosulfatibacter aminovorans gen. nov., sp. nov., a novel thiosulfate-reducing bacterium isolated from coastal marine sediment via sulfate-reducing enrichment with casamino acids.a sulfate-reducing enrichment culture originating from coastal marine sediment of the eutrophic tokyo bay, japan, was successfully established with casamino acids as a substrate. a thiosulfate reducer, strain c/g2(t), was isolated from the enrichment culture after further enrichment with glutamate. cells of strain c/g2(t) were non-motile rods (0.6-0.8 microm x 2.2-4.8 microm) and were found singly or in pairs and sometimes in short chains. spores were not formed. cells of strain c/g2(t) stained ...200717911304
macromolecular crowding increases structural content of folded 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
culture-dependent and -independent characterization of microbial communities associated with a shallow submarine hydrothermal system occurring within a coral reef off taketomi island, japan.microbial communities in a shallow submarine hydrothermal system near taketomi island, japan, were investigated using cultivation-based and molecular techniques. the main hydrothermal activity occurred in a craterlike basin (depth, approximately 23 m) on the coral reef seafloor. the vent fluid (maximum temperature, >52 degrees c) contained 175 microm h2s and gas bubbles mainly composed of ch4 (69%) and n2 (29%). a liquid serial dilution cultivation technique targeting a variety of metabolism typ ...200717921273
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
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