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Sample records for zobellella denitrificans mw1

  1. The 5S ribosomal RNAs of Paracoccus denitrificans and Prochloron

    NASA Technical Reports Server (NTRS)

    Mackay, R. M.; Salgado, D.; Bonen, L.; Doolittle, W. F.; Stackebrandt, E.

    1982-01-01

    The nucleotide sequences of the 5S rRNAs of Paracoccus denitrificans and Prochloron sp. are presented, along with the demonstrated phylogenetic relationships of P. denitrificans with purple nonsulfur bacteria, and of Prochloron with cyanobacteria. Structural findings include the following: (1) helix II in both models is much shorter than in other eubacteria, (2) a base-pair has been deleted from helix IV of P. denitrificans 5S, and (3) Prochloron 5S has the potential to form four base-pairs between residues. Also covered are the differences between pairs of sequences in P. denitrificans, Prochloron, wheat mitochondion, spinach chloroplast, and nine diverse eubacteria. Findings include the observation that Prochloron 5S rRNA is much more similar to the 5S of the cyanobacterium Anacystis nidulans (25 percent difference) than either are to any of the other nine eubacterial 5S rRNAs.

  2. A novel prenyltransferase from Paracoccus denitrificans.

    PubMed Central

    Ishii, K; Sagami, H; Ogura, K

    1986-01-01

    A new polyprenyltransferase catalysing the formation of Z-double bonds was found and partially purified from extracts of Paracoccus denitrificans. The enzyme catalysed a consecutive condensation of isopentenyl diphosphate with EE-farnesyl diphosphate as a primer to produce EE-farnesyl-all-Z-hexaprenyl diphosphate (ZE-mixed nonaprenyl diphosphate) as the final product. Not only EE-farnesyl diphosphate but also neryl diphosphate, ZE-farnesyl diphosphate, ZEE-geranylgeranyl diphosphate and ZZEE-pentaprenyl diphosphate were all accepted as substrates. This polyprenyltransferase required detergent such as Triton X-100 for its catalytic activity. The formation of ZE-mixed undecaprenyl diphosphate, which is well known as the precursor of the bacterial sugar-carrier lipid, was not detected in extracts of this bacterium. PMID:3707524

  3. Carbohydrate Metabolism and Carbon Fixation in Roseobacter denitrificans OCh114

    PubMed Central

    Tang, Kuo-Hsiang; Feng, Xueyang; Tang, Yinjie J.; Blankenship, Robert E.

    2009-01-01

    The Roseobacter clade of aerobic marine proteobacteria, which compose 10–25% of the total marine bacterial community, has been reported to fix CO2, although it has not been determined what pathway is involved. In this study, we report the first metabolic studies on carbohydrate utilization, CO2 assimilation, and amino acid biosynthesis in the phototrophic Roseobacter clade bacterium Roseobacter denitrificans OCh114. We develop a new minimal medium containing defined carbon source(s), in which the requirements of yeast extract reported previously for the growth of R. denitrificans can be replaced by vitamin B12 (cyanocobalamin). Tracer experiments were carried out in R. denitrificans grown in a newly developed minimal medium containing isotopically labeled pyruvate, glucose or bicarbonate as a single carbon source or in combination. Through measurements of 13C-isotopomer labeling patterns in protein-derived amino acids, gene expression profiles, and enzymatic activity assays, we report that: (1) R. denitrificans uses the anaplerotic pathways mainly via the malic enzyme to fix 10–15% of protein carbon from CO2; (2) R. denitrificans employs the Entner-Doudoroff (ED) pathway for carbohydrate metabolism and the non-oxidative pentose phosphate pathway for the biosynthesis of histidine, ATP, and coenzymes; (3) the Embden-Meyerhof-Parnas (EMP, glycolysis) pathway is not active and the enzymatic activity of 6-phosphofructokinase (PFK) cannot be detected in R. denitrificans; and (4) isoleucine can be synthesized from both threonine-dependent (20% total flux) and citramalate-dependent (80% total flux) pathways using pyruvate as the sole carbon source. PMID:19794911

  4. Halobacterium denitrificans sp. nov. - An extremely halophilic denitrifying bacterium

    NASA Technical Reports Server (NTRS)

    Tomlinson, G. A.; Jahnke, L. L.; Hochstein, L. I.

    1986-01-01

    Halobacterium denitrificans was one of several carbohydrate-utilizing, denitrifying, extremely halophilic bacteria isolated by anaerobic enrichment in the presence of nitrate. Anaerobic growth took place only when nitrate (or nitrite) was present and was accompanied by the production of dinitrogen. In the presence of high concentrations of nitrate (i.e., 0.5 percent), nitrous oxide and nitrite were also detected. When grown aerobically in a mineral-salts medium containing 0.005 percent yeast extract, H. denitrificans utilized a variety of carbohydrates as sources of carbon and energy. In every case, carbohydrate utilization was accompanied by acid production.

  5. Halobacterium denitrificans sp. nov., an extremely halophilic denitrifying bacterium

    NASA Technical Reports Server (NTRS)

    Tomlinson, G. A.; Jahnke, L. L.; Hochstein, L. I.

    1986-01-01

    Halobacterium denitrificans was one of several carbohydrate-utilizing, denitrifying, extremely halophilic bacteria isolated by anaerobic enrichment in the presence of nitrate. Anaerobic growth took place only when nitrate (or nitrite) was present and was accompanied by the production of dinitrogen. In the presence of high concentrations of nitrate (i.e., 0.5 percent), nitrous oxide and nitrite were also detected. When grown aerobically in a mineral-salts medium containing 0.005 percent yeast extract, H. denitrificans utilized a variety of carbohydrates as sources of carbon and energy. In every case, carbohydrate utilization was accompanied by acid production.

  6. Genetic manipulation of the obligate chemolithoautotrophic bacterium Thiobacillus denitrificans

    SciT

    Beller, H.R.; Legler, T.C.; Kane, S.R.

    2011-07-15

    Chemolithoautotrophic bacteria can be of industrial and environmental importance, but they present a challenge for systems biology studies, as their central metabolism deviates from that of model organisms and there is a much less extensive experimental basis for their gene annotation than for typical organoheterotrophs. For microbes with sequenced genomes but unconventional metabolism, the ability to create knockout mutations can be a powerful tool for functional genomics and thereby render an organism more amenable to systems biology approaches. In this chapter, we describe a genetic system for Thiobacillus denitrificans, with which insertion mutations can be introduced by homologous recombination andmore » complemented in trans. Insertion mutations are generated by in vitro transposition, the mutated genes are amplified by the PCR, and the amplicons are introduced into T. denitrificans by electroporation. Use of a complementation vector, pTL2, based on the IncP plasmid pRR10 is also addressed.« less

  7. Exploring the Denitrification Proteome of Paracoccus denitrificans PD1222

    PubMed Central

    Olaya-Abril, Alfonso; Hidalgo-Carrillo, Jesús; Luque-Almagro, Víctor M.; Fuentes-Almagro, Carlos; Urbano, Francisco J.; Moreno-Vivián, Conrado; Richardson, David J.; Roldán, María D.

    2018-01-01

    Denitrification is a respiratory process that produces nitrous oxide as an intermediate, which may escape to the atmosphere before its reduction to dinitrogen through the nitrous oxide reductase NosZ. In this work, the denitrification process carried out by Paracoccus denitrificans PD1222 has been explored through a quantitative proteomic analysis. Under anaerobic conditions, with nitrate as sole nitrogen source, the synthesis of all the enzymes involved in denitrification, the respiratory nitrate, nitrite, nitric oxide, and nitrous oxide reductases, was increased. However, the periplasmic and assimilatory nitrate reductases decreased. Synthesis of transporters for alcohols, D-methionine, sulfate and copper, most of the enzymes involved in the tricarboxylic acid cycle, and proteins involved in other metabolic processes like lysine catabolism, fatty acids degradation and acetyl-CoA synthesis, was increased during denitrification in P. denitrificans PD1222. As consequence, an enhanced production of the central metabolite acetyl-CoA was observed. After establishing the key features of the denitrification proteome, its changes by the influence of a competitive electron acceptor, oxygen, or competitive nitrogen source, ammonium, were evaluated. PMID:29896187

  8. Exploring the Denitrification Proteome of Paracoccus denitrificans PD1222.

    PubMed

    Olaya-Abril, Alfonso; Hidalgo-Carrillo, Jesús; Luque-Almagro, Víctor M; Fuentes-Almagro, Carlos; Urbano, Francisco J; Moreno-Vivián, Conrado; Richardson, David J; Roldán, María D

    2018-01-01

    Denitrification is a respiratory process that produces nitrous oxide as an intermediate, which may escape to the atmosphere before its reduction to dinitrogen through the nitrous oxide reductase NosZ. In this work, the denitrification process carried out by Paracoccus denitrificans PD1222 has been explored through a quantitative proteomic analysis. Under anaerobic conditions, with nitrate as sole nitrogen source, the synthesis of all the enzymes involved in denitrification, the respiratory nitrate, nitrite, nitric oxide, and nitrous oxide reductases, was increased. However, the periplasmic and assimilatory nitrate reductases decreased. Synthesis of transporters for alcohols, D-methionine, sulfate and copper, most of the enzymes involved in the tricarboxylic acid cycle, and proteins involved in other metabolic processes like lysine catabolism, fatty acids degradation and acetyl-CoA synthesis, was increased during denitrification in P. denitrificans PD1222. As consequence, an enhanced production of the central metabolite acetyl-CoA was observed. After establishing the key features of the denitrification proteome, its changes by the influence of a competitive electron acceptor, oxygen, or competitive nitrogen source, ammonium, were evaluated.

  9. Genome sequences of Alicycliphilus denitrificans strain BC and K601(T)

    SciT

    Oosterkamp, Margreet J.; Veuskens, Teun; Plugge, Caroline M.

    2011-01-01

    Alicycliphilus denitrificans strain BC and A. denitrificans strain K601T degrade cyclic hydrocarbons. These strains have been isolated from a mixture of wastewater treatment plant material and benzene-polluted soil and from a wastewater treatment plant, respectively, suggesting their role in bioremediation of soil and water. Although the strains are phylogenetically closely related, there are some clear physiological differences. The hydrocarbon cyclohexanol, for example, can be degraded by strain K601T but not by strain BC. Furthermore, both strains can use nitrate and oxygen as an electron acceptor, but only strain BC can use chlorate as electron acceptor. To better understand the nitratemore » and chlorate reduction mechanisms coupled to the oxidation of cyclic compounds, the genomes of A. denitrificans strains BC and K601T were sequenced. Here, we report the complete genome sequences of A. denitrificans strains BC and K601T.« less

  10. Extension of Gutenberg-Richter distribution to Mw -1.3, no lower limit in sight

    Boettcher, M.S.; McGarr, A.; Johnston, M.

    2009-01-01

    [1] With twelve years of seismic data from TauTona Gold Mine, South Africa, we show that mining-induced earthquakes follow the Gutenberg-Richter relation with no scale break down to the completeness level of the catalog, at moment magnitude Mw -1.3. Events recorded during relatively quiet hours in 2006 indicate that catalog detection limitations, not earthquake source physics, controlled the previously reported minimum magnitude in this mine. Within the Natural Earthquake Laboratory in South African Mines (NELSAM) experiment's dense seismic array, earthquakes that exhibit shear failure at magnitudes as small as Mw -3.9 are observed, but we find no evidence that Mw -3.9 represents the minimum magnitude. In contrast to previous work, our results imply small nucleation zones and that earthquake processes in the mine can readily be scaled to those in either laboratory experiments or natural faults.

  11. An improved medium for the anaerobic growth of Paracoccus denitrificans Pd1222

    PubMed Central

    Hahnke, Stefanie M.; Moosmann, Philipp; Erb, Tobias J.; Strous, Marc

    2014-01-01

    Paracoccus denitrificans is a well studied model organism with respect to its aerobic and anaerobic respiratory enzymes. However, until now, the growth medium for this organism has not been optimized for anaerobic growth. In particular, the requirements of P. denitrificans for trace elements (TEs) are not well known. In the present study we aimed to improve growth rates of P. denitrificans Pd1222 on a defined medium under anoxic conditions. We designed media containing different combinations of TEs at various concentrations, and tested their performance against previously reported media. Our results suggest that growth rate and yield depend on the availability and concentration of TEs in the medium. A chelated TE solution was more suitable than an acidified TE solution. Highest growth rates were achieved with medium comprising the TEs iron, manganese, molybdenum, copper and zinc ranging from 0.1 to 9 μM. On this medium, P. denitrificans Pd1222 grew with a generation time of 4.4 h under anoxic conditions and 2.8 h under oxic conditions. Diauxic growth was clearly shown with respect to nitrate and nitrite reduction under anoxic conditions. PMID:24550891

  12. An improved medium for the anaerobic growth of Paracoccus denitrificans Pd1222.

    PubMed

    Hahnke, Stefanie M; Moosmann, Philipp; Erb, Tobias J; Strous, Marc

    2014-01-01

    Paracoccus denitrificans is a well studied model organism with respect to its aerobic and anaerobic respiratory enzymes. However, until now, the growth medium for this organism has not been optimized for anaerobic growth. In particular, the requirements of P. denitrificans for trace elements (TEs) are not well known. In the present study we aimed to improve growth rates of P. denitrificans Pd1222 on a defined medium under anoxic conditions. We designed media containing different combinations of TEs at various concentrations, and tested their performance against previously reported media. Our results suggest that growth rate and yield depend on the availability and concentration of TEs in the medium. A chelated TE solution was more suitable than an acidified TE solution. Highest growth rates were achieved with medium comprising the TEs iron, manganese, molybdenum, copper and zinc ranging from 0.1 to 9 μM. On this medium, P. denitrificans Pd1222 grew with a generation time of 4.4 h under anoxic conditions and 2.8 h under oxic conditions. Diauxic growth was clearly shown with respect to nitrate and nitrite reduction under anoxic conditions.

  13. Structural degradation of Thar lignite using MW1 fungal isolate: optimization studies

    Haider, Rizwan; Ghauri, Muhammad A.; Jones, Elizabeth J.; Orem, William H.; SanFilipo, John R.

    2015-01-01

    Biological degradation of low-rank coals, particularly degradation mediated by fungi, can play an important role in helping us to utilize neglected lignite resources for both fuel and non-fuel applications. Fungal degradation of low-rank coals has already been investigated for the extraction of soil-conditioning agents and the substrates, which could be subjected to subsequent processing for the generation of alternative fuel options, like methane. However, to achieve an efficient degradation process, the fungal isolates must originate from an appropriate coal environment and the degradation process must be optimized. With this in mind, a representative sample from the Thar coalfield (the largest lignite resource of Pakistan) was treated with a fungal strain, MW1, which was previously isolated from a drilled core coal sample. The treatment caused the liberation of organic fractions from the structural matrix of coal. Fungal degradation was optimized, and it showed significant release of organics, with 0.1% glucose concentration and 1% coal loading ratio after an incubation time of 7 days. Analytical investigations revealed the release of complex organic moieties, pertaining to polyaromatic hydrocarbons, and it also helped in predicting structural units present within structure of coal. Such isolates, with enhanced degradation capabilities, can definitely help in exploiting the chemical-feedstock-status of coal.

  14. Pseudovibrio denitrificans strain Z143-1, a heptylprodigiosin-producing bacterium isolated from a Philippine tunicate.

    PubMed

    Sertan-de Guzman, Alice A; Predicala, Rey Z; Bernardo, Evelyn B; Neilan, Brett A; Elardo, Sheila P; Mangalindan, Gina C; Tasdemir, Deniz; Ireland, Chris M; Barraquio, Wilfredo L; Concepcion, Gisela P

    2007-12-01

    Microbial isolate Z143-1 found to be associated with an unidentified tunicate was characterized due to its significant antimicrobial activity. Z143-1 is similar to Pseudovibrio ascidiaceicola and Pseudovibrio denitrificans in morphological, physiological and biochemical characteristics, except for its ability to ferment glucose and produce a characteristic red pigment. Fatty acid methyl ester analysis revealed a predominance of the fatty acid 18:1 omega7c at 80.55%, at levels slightly lower than the Pseudovibrio denitrificans type strain DN34(T) (87.7%). The mol% G+C of Z143-1 is 54.02, relatively higher than the Pseudovibrio denitrificans type strain DN34(T) and Pseudovibrio ascidiaceicola with mol% G+C of 51.7 and 51.4, respectively. However, phylogenetic analysis of the 16S rRNA gene sequence of Z143-1 showed 100% similarity with the Pseudovibrio denitrificans type strain DN34(T). In this study, the bacterium Z143-1 is reported as a new strain of Pseudovibrio denitrificans. While there is no report of a secondary metabolite for Pseudovibrio denitrificans, Z143-1 produces the red pigment heptylprodigiosin, also known as 16-methyl-15-heptyl-prodiginine, which shows anti-Staphylococcus aureus activity.

  15. The Genome Sequence of the Obligately Chemolithoautotrophic, Facultatively Anaerobic Bacterium Thiobacillus denitrificans

    PubMed Central

    Beller, Harry R.; Chain, Patrick S. G.; Letain, Tracy E.; Chakicherla, Anu; Larimer, Frank W.; Richardson, Paul M.; Coleman, Matthew A.; Wood, Ann P.; Kelly, Donovan P.

    2006-01-01

    The complete genome sequence of Thiobacillus denitrificans ATCC 25259 is the first to become available for an obligately chemolithoautotrophic, sulfur-compound-oxidizing, β-proteobacterium. Analysis of the 2,909,809-bp genome will facilitate our molecular and biochemical understanding of the unusual metabolic repertoire of this bacterium, including its ability to couple denitrification to sulfur-compound oxidation, to catalyze anaerobic, nitrate-dependent oxidation of Fe(II) and U(IV), and to oxidize mineral electron donors. Notable genomic features include (i) genes encoding c-type cytochromes totaling 1 to 2 percent of the genome, which is a proportion greater than for almost all bacterial and archaeal species sequenced to date, (ii) genes encoding two [NiFe]hydrogenases, which is particularly significant because no information on hydrogenases has previously been reported for T. denitrificans and hydrogen oxidation appears to be critical for anaerobic U(IV) oxidation by this species, (iii) a diverse complement of more than 50 genes associated with sulfur-compound oxidation (including sox genes, dsr genes, and genes associated with the AMP-dependent oxidation of sulfite to sulfate), some of which occur in multiple (up to eight) copies, (iv) a relatively large number of genes associated with inorganic ion transport and heavy metal resistance, and (v) a paucity of genes encoding organic-compound transporters, commensurate with obligate chemolithoautotrophy. Ultimately, the genome sequence of T. denitrificans will enable elucidation of the mechanisms of aerobic and anaerobic sulfur-compound oxidation by β-proteobacteria and will help reveal the molecular basis of this organism's role in major biogeochemical cycles (i.e., those involving sulfur, nitrogen, and carbon) and groundwater restoration. PMID:16452431

  16. Structure and function of the tetraheme cytochrome associated to the reaction center of Roseobacter denitrificans.

    PubMed

    Garcia, D; Richaud, P; Breton, J; Verméglio, A

    1994-01-01

    We have characterized the tetrahemic RC bound cytochrome isolated from the quasi-photosynthetic bacterium Roseobacter denitrificans in terms of absorption spectrum, redox property and orientation with respect to the membrane plane. The heme, designated H1, which possesses the highest redox midpoint potential (+290 mV), absorbs at 555 nm. Its plane makes an angle of 40 degrees with the membrane plane. The second high potential heme, H2 (+240 mV), peaks at 554 nm and makes a tilt of 55 degrees with the membrane. The two low potential hemes, L1 and L2, present a similar and rather high redox midpoint potential (+90 mV). They absorb at 553 nm and 550 nm. One of these hemes is oriented at 40 degrees while the other makes an angle of 90 degrees with the membrane plane. The soluble cytochrome c551 completes the cyclic electron transfer between the RC and the bc1 complex. Both the oxidation and the re-reduction of cytochrome c551 are diffusible processes. Under semi-aerobic conditions, one of the low potential hemes is photo-oxidized under illumination but only extremely slowly re-reduced. This explains the requirement of high aerobic conditions for growth of Roseobacter denitrificans cells in the light.

  17. Isolation and algicidal characterization of Bowmanella denitrificans S088 against Chlorella vulgaris.

    PubMed

    Jiang, Xiao; Ren, Chunhua; Hu, Chaoqun; Zhao, Zhe

    2014-02-01

    One strain of algicidal bacterium, named as S088, was isolated from the intestine of healthy sea cucumbers (Stichopus horrens) in the South China Sea. Based on the analysis of its biochemical characteristics and 16S rDNA gene sequence, S088 was identified as Bowmanella denitrificans. Importantly, the algicidal activity of S088 on Chlorella vulgaris was characterized in this study. The initial densities of bacterial and algal cell showed strong influence on the removal rates of chlorophyll a. When the strain S088 was cultured under a complete darkness condition at 30 °C, its algicidal activity reached the highest level. Furthermore, it was found that the filtered supernatant from bacterial cultures had full algicidal activity, suggesting that the secreted compounds from S088 are involved in the observed algicidal action of S088. Moreover, the algicidal compounds were heat tolerant and had no cytotoxicity against fish cells, indicating that S088 would have a promising application as a safe probiotics for S. horrens. Finally, this is the first report about the algicidal activities in B. denitrificans.

  18. Proteomic analysis of nitrate-dependent acetone degradation by Alicycliphilus denitrificans strain BC.

    PubMed

    Oosterkamp, Margreet J; Boeren, Sjef; Atashgahi, Siavash; Plugge, Caroline M; Schaap, Peter J; Stams, Alfons J M

    2015-06-01

    Alicycliphilus denitrificans strain BC grows anaerobically on acetone with nitrate as electron acceptor. Comparative proteomics of cultures of A. denitrificans strain BC grown on either acetone or acetate with nitrate was performed to study the enzymes involved in the acetone degradation pathway. In the proposed acetone degradation pathway, an acetone carboxylase converts acetone to acetoacetate, an AMP-dependent synthetase/ligase converts acetoacetate to acetoacetyl-CoA, and an acetyl-CoA acetyltransferase cleaves acetoacetyl-CoA to two acetyl-CoA. We also found a putative aldehyde dehydrogenase associated with acetone degradation. This enzyme functioned as a β-hydroxybutyrate dehydrogenase catalyzing the conversion of surplus acetoacetate to β-hydroxybutyrate that may be converted to the energy and carbon storage compound, poly-β-hydroxybutyrate. Accordingly, we confirmed the formation of poly-β-hydroxybutyrate in acetone-grown cells of strain BC. Our findings provide insight in nitrate-dependent acetone degradation that is activated by carboxylation of acetone. This will aid studies of similar pathways found in other microorganisms degrading acetone with nitrate or sulfate as electron acceptor. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  19. Achromobactor denitrificans SP1 produces pharmaceutically active 25C prodigiosin upon utilizing hazardous di(2-ethylhexyl)phthalate

    Achromobacter denitrificans SP1 isolated from soil sludge heavily contaminated with plastic waste produced a novel pharmaceutically-active 25C prodigiosin analog during growth in a simple mineral salt medium supplemented with hazardous di(2-ethylhexyl)phthalate (DEHP) blended PVC plastics (in situ) ...

  20. Genome Sequence of a Heterotrophic Nitrifier and Aerobic Denitrifier, Paracoccus denitrificans Strain ISTOD1, Isolated from Wastewater.

    PubMed

    Medhi, Kristina; Mishra, Arti; Thakur, Indu Shekhar

    2018-04-12

    We report here the draft genome sequence of Paracoccus denitrificans strain ISTOD1 of 4.9 Mb, isolated from wastewater. It has been identified as a heterotrophic nitrifying and aerobic denitrifying bacterium. Genomic analysis revealed genes related to nitrogen and phosphorus removal, showing that the strain holds potential for bioremediation and biorefinery uses. Copyright © 2018 Medhi et al.

  1. Genome Sequence of a Heterotrophic Nitrifier and Aerobic Denitrifier, Paracoccus denitrificans Strain ISTOD1, Isolated from Wastewater

    PubMed Central

    Medhi, Kristina; Mishra, Arti

    2018-01-01

    ABSTRACT We report here the draft genome sequence of Paracoccus denitrificans strain ISTOD1 of 4.9 Mb, isolated from wastewater. It has been identified as a heterotrophic nitrifying and aerobic denitrifying bacterium. Genomic analysis revealed genes related to nitrogen and phosphorus removal, showing that the strain holds potential for bioremediation and biorefinery uses. PMID:29650568

  2. Poly(3-hydroxybutyrate) hyperproduction by a global nitrogen regulator NtrB mutant strain of Paracoccus denitrificans PD1222

    PubMed Central

    Olaya-Abril, Alfonso; Luque-Almagro, Víctor M; Manso, Isabel; Gates, Andrew J; Moreno-Vivián, Conrado; Richardson, David J

    2017-01-01

    Abstract Paracoccus denitrificans PD1222 accumulates short-length polyhydroxyalkanoates, poly(3-hydroxybutyrate), under nitrogen-deficient conditions. Polyhydroxybutyrate metabolism requires the 3-ketoacyl-CoA thiolase PhaA, the acetoacetyl-CoA dehydrogenase/reductase PhaB and the synthase PhaC for polymerization. Additionally, P. denitrificans PD1222 grows aerobically with nitrate as sole nitrogen source. Nitrate assimilation is controlled negatively by ammonium through the two-component NtrBC system. NtrB is a sensor kinase that autophosphorylates a histidine residue under low-nitrogen concentrations and, in turn, transfers a phosphoryl group to an aspartate residue of the response regulator NtrC protein, which acts as a transcriptional activator of the P. denitrificans PD1222 nasABGHC genes. The P. denitrificans PD1222 NtrB mutant was unable to use nitrate efficiently as nitrogen source when compared to the wild-type strain, and it also overproduced poly(3-hydroxybutyrate). Acetyl-CoA concentration in the P. denitrificans PD1222 NtrB mutant strain was higher than in the wild-type strain. The expression of the phaC gene was also increased in the NtrB mutant when compared to the wild-type strain. These results suggest that accumulation of poly(3-hydroxybutyrate) in the NtrB mutant strain of PD1222 responds to the high levels of acetyl-CoA that accumulate in the cytoplasm as consequence of its inability to efficiently use nitrate as nitrogen source. PMID:29228177

  3. Paracoccus denitrificans possesses two BioR homologs having a role in regulation of biotin metabolism.

    PubMed

    Feng, Youjun; Kumar, Ritesh; Ravcheev, Dmitry A; Zhang, Huimin

    2015-08-01

    Recently, we determined that BioR, the GntR family of transcription factor, acts as a repressor for biotin metabolism exclusively distributed in certain species of α-proteobacteria, including the zoonotic agent Brucella melitensis and the plant pathogen Agrobacterium tumefaciens. However, the scenario is unusual in Paracoccus denitrificans, another closely related member of the same phylum α-proteobacteria featuring with denitrification. Not only does it encode two BioR homologs Pden_1431 and Pden_2922 (designated as BioR1 and BioR2, respectively), but also has six predictive BioR-recognizable sites (the two bioR homolog each has one site, whereas the two bio operons (bioBFDAGC and bioYB) each contains two tandem BioR boxes). It raised the possibility that unexpected complexity is present in BioR-mediated biotin regulation. Here we report that this is the case. The identity of the purified BioR proteins (BioR1 and BioR2) was confirmed with LC-QToF-MS. Phylogenetic analyses combined with GC percentage raised a possibility that the bioR2 gene might be acquired by horizontal gene transfer. Gel shift assays revealed that the predicted BioR-binding sites are functional for the two BioR homologs, in much similarity to the scenario seen with the BioR site of A. tumefaciens bioBFDAZ. Using the A. tumefaciens reporter system carrying a plasmid-borne LacZ fusion, we revealed that the two homologs of P. denitrificans BioR are functional repressors for biotin metabolism. As anticipated, not only does the addition of exogenous biotin stimulate efficiently the expression of bioYB operon encoding biotin transport/uptake system BioY, but also inhibits the transcription of the bioBFDAGC operon resembling the de novo biotin synthetic pathway. EMSA-based screening failed to demonstrate that the biotin-related metabolite is involved in BioR-DNA interplay, which is consistent with our former observation with Brucella BioR. Our finding defined a complex regulatory network for biotin

  4. Paracoccus denitrificans possesses two BioR homologs having a role in regulation of biotin metabolism

    PubMed Central

    Feng, Youjun; Kumar, Ritesh; Ravcheev, Dmitry A; Zhang, Huimin

    2015-01-01

    Recently, we determined that BioR, the GntR family of transcription factor, acts as a repressor for biotin metabolism exclusively distributed in certain species of α-proteobacteria, including the zoonotic agent Brucella melitensis and the plant pathogen Agrobacterium tumefaciens. However, the scenario is unusual in Paracoccus denitrificans, another closely related member of the same phylum α-proteobacteria featuring with denitrification. Not only does it encode two BioR homologs Pden_1431 and Pden_2922 (designated as BioR1 and BioR2, respectively), but also has six predictive BioR-recognizable sites (the two bioR homolog each has one site, whereas the two bio operons (bioBFDAGC and bioYB) each contains two tandem BioR boxes). It raised the possibility that unexpected complexity is present in BioR-mediated biotin regulation. Here we report that this is the case. The identity of the purified BioR proteins (BioR1 and BioR2) was confirmed with LC-QToF-MS. Phylogenetic analyses combined with GC percentage raised a possibility that the bioR2 gene might be acquired by horizontal gene transfer. Gel shift assays revealed that the predicted BioR-binding sites are functional for the two BioR homologs, in much similarity to the scenario seen with the BioR site of A. tumefaciens bioBFDAZ. Using the A. tumefaciens reporter system carrying a plasmid-borne LacZ fusion, we revealed that the two homologs of P. denitrificans BioR are functional repressors for biotin metabolism. As anticipated, not only does the addition of exogenous biotin stimulate efficiently the expression of bioYB operon encoding biotin transport/uptake system BioY, but also inhibits the transcription of the bioBFDAGC operon resembling the de novo biotin synthetic pathway. EMSA-based screening failed to demonstrate that the biotin-related metabolite is involved in BioR-DNA interplay, which is consistent with our former observation with Brucella BioR. Our finding defined a complex regulatory network for biotin

  5. Biotransformation of 4-chloro-2-nitrophenol into 5-chloro-2-methylbenzoxazole by a marine Bacillus sp. strain MW-1.

    PubMed

    Arora, Pankaj Kumar; Jain, Rakesh Kumar

    2012-04-01

    Decolourization, detoxification and biotransformation of 4-chloro-2-nitrophenol (4C2NP) by Bacillus sp. strain MW-1 were studied. This strain decolorized 4C2NP only in the presence of an additional carbon source. On the basis of thin layer chromatography (TLC), high performance liquid chromatography (HPLC) and gas chromatography-mass spectrometry (GC-MS), 4-chloro-2-aminophenol, 4-chloro-2-acetaminophenol and 5-chloro-2-methylbenzoxazole were identified as metabolites. Resting cells depleted 4C2NP with stoichiometric formation of 5-chloro-2-methyl benzoxazole. This is the first report of the formation of 5-chloro-2-methylbenzoxazole from 4C2NP by any bacterial strain.

  6. Molecular origins and consequences of High-800 LH2 in Roseobacter denitrificans.

    PubMed

    Duquesne, Katia; Blanchard, Cecile; Sturgis, James N

    2011-08-09

    Roseobacter denitrificans is a marine bacterium capable of using a wide variety of different metabolic schemes and in particular is an anoxygenic aerobic photosynthetic bacterium. In the work reported here we use a deletion mutant that we have constructed to investigate the structural origin of the unusual High-800 light-harvesting complex absorption in this bacterium. We suggest that the structure is essentially unaltered when compared to the usual nonameric complexes but that a change in the environment of the C(13:1) carbonyl group is responsible for the change in spectrum. We tentatively relate this change to the presence of a serine residue in the α-polypeptide. Surprisingly, the low spectral overlap between the peripheral and core light-harvesting systems appears not to compromise energy collection efficiency too severely. We suggest that this may be at the expense of maintaining a low antenna size. © 2011 American Chemical Society

  7. Nitric Oxide Is a Signal for NNR-Mediated Transcription Activation in Paracoccus denitrificans

    PubMed Central

    Van Spanning, Rob J. M.; Houben, Edith; Reijnders, Willem N. M.; Spiro, Stephen; Westerhoff, Hans V.; Saunders, Neil

    1999-01-01

    By using the ′lacZ gene, the activities of the nirI, nirS, and norC promoters were assayed in the wild type and in NNR-deficient mutants of Paracoccus denitrificans grown under various growth conditions. In addition, induction profiles of the three promoters in response to the presence of various nitrogenous oxides were determined. Transcription from the three promoters required the absence of oxygen and the presence both of the transcriptional activator NNR and of nitric oxide. The activity of the nnr promoter itself was halved after the cells had been switched from aerobic respiration to denitrification. This response was apparently not a result of autoregulation or of regulation by FnrP, since the nnr promoter was as active in the wild-type strain as it was in NNR- or FnrP-deficient mutants. PMID:10383987

  8. Purification and properties of a dissimilatory nitrate reductase from Haloferax denitrificans

    NASA Technical Reports Server (NTRS)

    Hochstein, L. I.; Lang, F.

    1991-01-01

    A membrane-bound nitrate reductase (nitrite:(acceptor) oxidoreductase, EC 1.7.99.4) from the extremely halophilic bacterium Haloferax denitrificans was solubilized by incubating membranes in buffer lacking NaCl and purified by DEAE, hydroxylapatite, and Sepharose 6B gel filtration chromatography. The purified nitrate reductase reduced chlorate and was inhibited by azide and cyanide. Preincubating the enzyme with cyanide increased the extent of inhibition which in turn was intensified when dithionite was present. Although cyanide was a noncompetitive inhibitor with respect to nitrate, nitrate protected against inhibition. The enzyme, as isolated, was composed of two subunits (Mr 116,000 and 60,000) and behaved as a dimer during gel filtration (Mr 380,000). Unlike other halobacterial enzymes, this nitrate reductase was most active, as well as stable, in the absence of salt.

  9. Impact of biogenic substrates on sulfamethoxazole biodegradation kinetics by Achromobacter denitrificans strain PR1.

    PubMed

    Nguyen, P Y; Carvalho, Gilda; Reis, A C; Nunes, O C; Reis, M A M; Oehmen, A

    2017-06-01

    Pure cultures have been found to degrade pharmaceutical compounds. However, these cultures are rarely characterized kinetically at environmentally relevant concentrations. This study investigated the kinetics of sulfamethoxazole (SMX) degradation by Achromobacter denitrificans strain PR1 at a wide range of concentrations, from ng/L to mg/L, to assess the feasibility of using it for bioaugmentation purposes. Complete removal of SMX occurred for all concentrations tested, i.e., 150 mg/L, 500 µg/L, 20 µg/L, and 600 ng/L. The reaction rate coefficients (k bio ) for the strain at the ng/L SMX range were: 63.4 ± 8.6, 570.1 ± 15.1 and 414.9 ± 124.2 L/g[Formula: see text]·day), for tests fed without a supplemental carbon source, with acetate, and with succinate, respectively. These results were significantly higher than the value reported for non-augmented activated sludge (0.41 L/(g [Formula: see text]·day) with hundreds of ng/L of SMX. The simultaneous consumption of an additional carbon source and SMX suggested that the energetic efficiency of the cells, boosted by the presence of biogenic substrates, was important in increasing the SMX degradation rate. The accumulation of 3-amino-5-methylisoxazole was observed as the only metabolite, which was found to be non-toxic. SMX inhibited the Vibrio fischeri luminescence after 5 min of contact, with EC 50 values of about 53 mg/L. However, this study suggested that the strain PR1 still can degrade SMX up to 150 mg/L. The results of this work demonstrated that SMX degradation kinetics by A. denitrificans PR1 compares favorably with activated sludge and the strain is a potentially interesting organism for bioaugmentation for SMX removal from polluted waters.

  10. Transcriptional and translational adaptation to aerobic nitrate anabolism in the denitrifier Paracoccus denitrificans

    PubMed Central

    Luque-Almagro, Victor M.; Manso, Isabel; Sullivan, Matthew J.; Rowley, Gary; Ferguson, Stuart J.; Moreno-Vivián, Conrado; Richardson, David J.; Gates, Andrew J.

    2017-01-01

    Transcriptional adaptation to nitrate-dependent anabolism by Paracoccus denitrificans PD1222 was studied. A total of 74 genes were induced in cells grown with nitrate as N-source compared with ammonium, including nasTSABGHC and ntrBC genes. The nasT and nasS genes were cotranscribed, although nasT was more strongly induced by nitrate than nasS. The nasABGHC genes constituted a transcriptional unit, which is preceded by a non-coding region containing hairpin structures involved in transcription termination. The nasTS and nasABGHC transcripts were detected at similar levels with nitrate or glutamate as N-source, but nasABGHC transcript was undetectable in ammonium-grown cells. The nitrite reductase NasG subunit was detected by two-dimensional polyacrylamide gel electrophoresis in cytoplasmic fractions from nitrate-grown cells, but it was not observed when either ammonium or glutamate was used as the N-source. The nasT mutant lacked both nasABGHC transcript and nicotinamide adenine dinucleotide (NADH)-dependent nitrate reductase activity. On the contrary, the nasS mutant showed similar levels of the nasABGHC transcript to the wild-type strain and displayed NasG protein and NADH–nitrate reductase activity with all N-sources tested, except with ammonium. Ammonium repression of nasABGHC was dependent on the Ntr system. The ntrBC and ntrYX genes were expressed at low levels regardless of the nitrogen source supporting growth. Mutational analysis of the ntrBCYX genes indicated that while ntrBC genes are required for nitrate assimilation, ntrYX genes can only partially restore growth on nitrate in the absence of ntrBC genes. The existence of a regulation mechanism for nitrate assimilation in P. denitrificans, by which nitrate induction operates at both transcriptional and translational levels, is proposed. PMID:28385879

  11. Modulation of protein function in membrane mimetics: Characterization of P. denitrificans cNOR in nanodiscs or liposomes.

    PubMed

    Ter Beek, Josy; Kahle, Maximilian; Ädelroth, Pia

    2017-10-01

    For detailed functional characterization, membrane proteins are usually studied in detergent. However, it is becoming clear that detergent micelles are often poor mimics of the lipid environment in which these proteins function. In this work we compared the catalytic properties of the membrane-embedded cytochrome c-dependent nitric oxide reductase (cNOR) from Paracoccus (P.) denitrificans in detergent, lipid/protein nanodiscs, and proteoliposomes. We used two different lipid mixtures, an extract of soybean lipids and a defined mix of synthetic lipids mimicking the original P. denitrificans membrane. We show that the catalytic activity of detergent-solubilized cNOR increased threefold upon reconstitution from detergent into proteoliposomes with the P. denitrificans lipid mixture, and above two-fold when soybean lipids were used. In contrast, there was only a small activity increase in nanodiscs. We further show that binding of the gaseous ligands CO and O 2 are affected differently by reconstitution. In proteoliposomes the turnover rates are affected much more than in nanodiscs, but CO-binding is more significantly accelerated in liposomes with soybean lipids, while O 2 -binding is faster with the P. denitrificans lipid mix. We also investigated proton-coupled electron transfer during the reaction between fully reduced cNOR and O 2 , and found that the pK a of the internal proton donor was increased in proteoliposomes but not in nanodiscs. Taking our results together, the liposome-reconstituted enzyme shows significant differences to detergent-solubilized protein. Nanodiscs show much more subtle effects, presumably because of their much lower lipid to protein ratio. Which of these two membrane-mimetic systems best mimics the native membrane is discussed. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. Steroidobacter denitrificans gen. nov., sp. nov., a steroidal hormone-degrading gammaproteobacterium.

    PubMed

    Fahrbach, Michael; Kuever, Jan; Remesch, Markko; Huber, Birgit E; Kämpfer, Peter; Dott, Wolfgang; Hollender, Juliane

    2008-09-01

    divergence and different phenotypic properties from previously described gammaproteobacteria in combination with chemotaxonomic data, strain FS(T) is considered to represent a new genus and species, for which the name Steroidobacter denitrificans gen. nov., sp. nov. is proposed. The type strain of Steroidobacter denitrificans is FS(T) (=DSM 18526(T) =JCM 14622(T)).

  13. A pathway for protons in nitric oxide reductase from Paracoccus denitrificans.

    PubMed

    Reimann, Joachim; Flock, Ulrika; Lepp, Håkan; Honigmann, Alf; Adelroth, Pia

    2007-05-01

    Nitric oxide reductase (NOR) from P. denitrificans is a membrane-bound protein complex that catalyses the reduction of NO to N(2)O (2NO+2e(-)+2H(+)-->N(2)O+H(2)O) as part of the denitrification process. Even though NO reduction is a highly exergonic reaction, and NOR belongs to the superfamily of O(2)-reducing, proton-pumping heme-copper oxidases (HCuOs), previous measurements have indicated that the reaction catalyzed by NOR is non-electrogenic, i.e. not contributing to the proton electrochemical gradient. Since electrons are provided by donors in the periplasm, this non-electrogenicity implies that the substrate protons are also taken up from the periplasm. Here, using direct measurements in liposome-reconstituted NOR during reduction of both NO and the alternative substrate O(2), we demonstrate that protons are indeed consumed from the 'outside'. First, multiple turnover reduction of O(2) resulted in an increase in pH on the outside of the NOR-vesicles. Second, comparison of electrical potential generation in NOR-liposomes during oxidation of the reduced enzyme by either NO or O(2) shows that the proton transfer signals are very similar for the two substrates proving the usefulness of O(2) as a model substrate for these studies. Last, optical measurements during single-turnover oxidation by O(2) show electron transfer coupled to proton uptake from outside the NOR-liposomes with a tau=15 ms, similar to results obtained for net proton uptake in solubilised NOR [U. Flock, N.J. Watmough, P. Adelroth, Electron/proton coupling in bacterial nitric oxide reductase during reduction of oxygen, Biochemistry 44 (2005) 10711-10719]. NOR must thus contain a proton transfer pathway leading from the periplasmic surface into the active site. Using homology modeling with the structures of HCuOs as templates, we constructed a 3D model of the NorB catalytic subunit from P. denitrificans in order to search for such a pathway. A plausible pathway, consisting of conserved protonatable

  14. Transcriptional and translational adaptation to aerobic nitrate anabolism in the denitrifier Paracoccus denitrificans.

    PubMed

    Luque-Almagro, Victor M; Manso, Isabel; Sullivan, Matthew J; Rowley, Gary; Ferguson, Stuart J; Moreno-Vivián, Conrado; Richardson, David J; Gates, Andrew J; Roldán, M Dolores

    2017-05-10

    Transcriptional adaptation to nitrate-dependent anabolism by Paracoccus denitrificans PD1222 was studied. A total of 74 genes were induced in cells grown with nitrate as N-source compared with ammonium, including nasTSABGHC and ntrBC genes. The nasT and nasS genes were cotranscribed, although nasT was more strongly induced by nitrate than nasS The nasABGHC genes constituted a transcriptional unit, which is preceded by a non-coding region containing hairpin structures involved in transcription termination. The nasTS and nasABGHC transcripts were detected at similar levels with nitrate or glutamate as N-source, but nasABGHC transcript was undetectable in ammonium-grown cells. The nitrite reductase NasG subunit was detected by two-dimensional polyacrylamide gel electrophoresis in cytoplasmic fractions from nitrate-grown cells, but it was not observed when either ammonium or glutamate was used as the N-source. The nasT mutant lacked both nasABGHC transcript and nicotinamide adenine dinucleotide (NADH)-dependent nitrate reductase activity. On the contrary, the nasS mutant showed similar levels of the nasABGHC transcript to the wild-type strain and displayed NasG protein and NADH-nitrate reductase activity with all N-sources tested, except with ammonium. Ammonium repression of nasABGHC was dependent on the Ntr system. The ntrBC and ntrYX genes were expressed at low levels regardless of the nitrogen source supporting growth. Mutational analysis of the ntrBCYX genes indicated that while ntrBC genes are required for nitrate assimilation, ntrYX genes can only partially restore growth on nitrate in the absence of ntrBC genes. The existence of a regulation mechanism for nitrate assimilation in P. denitrificans , by which nitrate induction operates at both transcriptional and translational levels, is proposed. © 2017 The Author(s).

  15. Investigating the Proton Donor in the NO Reductase from Paracoccus denitrificans

    PubMed Central

    ter Beek, Josy; Krause, Nils; Ädelroth, Pia

    2016-01-01

    Variant nomenclature: the variants were made in the NorB subunit if not indicated by the superscript c, which are variants in the NorC subunit (e.g. E122A = exchange of Glu-122 in NorB for an Ala, E71cD; exchange of Glu-71 in NorC for an Asp). Bacterial NO reductases (NORs) are integral membrane proteins from the heme-copper oxidase superfamily. Most heme-copper oxidases are proton-pumping enzymes that reduce O2 as the last step in the respiratory chain. With electrons from cytochrome c, NO reductase (cNOR) from Paracoccus (P.) denitrificans reduces NO to N2O via the following reaction: 2NO+2e-+2H+→N2O+H2O. Although this reaction is as exergonic as O2-reduction, cNOR does not contribute to the electrochemical gradient over the membrane. This means that cNOR does not pump protons and that the protons needed for the reaction are taken from the periplasmic side of the membrane (since the electrons are donated from this side). We previously showed that the P. denitrificans cNOR uses a single defined proton pathway with residues Glu-58 and Lys-54 from the NorC subunit at the entrance. Here we further strengthened the evidence in support of this pathway. Our further aim was to define the continuation of the pathway and the immediate proton donor for the active site. To this end, we investigated the region around the calcium-binding site and both propionates of heme b3 by site directed mutagenesis. Changing single amino acids in these areas often had severe effects on cNOR function, with many variants having a perturbed active site, making detailed analysis of proton transfer properties difficult. Our data does however indicate that the calcium ligation sphere and the region around the heme b3 propionates are important for proton transfer and presumably contain the proton donor. The possible evolutionary link between the area for the immediate donor in cNOR and the proton loading site (PLS) for pumped protons in oxygen-reducing heme-copper oxidases is discussed. PMID

  16. Investigating the Proton Donor in the NO Reductase from Paracoccus denitrificans.

    PubMed

    ter Beek, Josy; Krause, Nils; Ädelroth, Pia

    2016-01-01

    Variant nomenclature: the variants were made in the NorB subunit if not indicated by the superscript c, which are variants in the NorC subunit (e.g. E122A = exchange of Glu-122 in NorB for an Ala, E71cD; exchange of Glu-71 in NorC for an Asp). Bacterial NO reductases (NORs) are integral membrane proteins from the heme-copper oxidase superfamily. Most heme-copper oxidases are proton-pumping enzymes that reduce O2 as the last step in the respiratory chain. With electrons from cytochrome c, NO reductase (cNOR) from Paracoccus (P.) denitrificans reduces NO to N2O via the following reaction: 2NO+2e-+2H+→N2O+H2O. Although this reaction is as exergonic as O2-reduction, cNOR does not contribute to the electrochemical gradient over the membrane. This means that cNOR does not pump protons and that the protons needed for the reaction are taken from the periplasmic side of the membrane (since the electrons are donated from this side). We previously showed that the P. denitrificans cNOR uses a single defined proton pathway with residues Glu-58 and Lys-54 from the NorC subunit at the entrance. Here we further strengthened the evidence in support of this pathway. Our further aim was to define the continuation of the pathway and the immediate proton donor for the active site. To this end, we investigated the region around the calcium-binding site and both propionates of heme b3 by site directed mutagenesis. Changing single amino acids in these areas often had severe effects on cNOR function, with many variants having a perturbed active site, making detailed analysis of proton transfer properties difficult. Our data does however indicate that the calcium ligation sphere and the region around the heme b3 propionates are important for proton transfer and presumably contain the proton donor. The possible evolutionary link between the area for the immediate donor in cNOR and the proton loading site (PLS) for pumped protons in oxygen-reducing heme-copper oxidases is discussed.

  17. Phospholipid Fatty Acids as Physiological Indicators of Paracoccus denitrificans Encapsulated in Silica Sol-Gel Hydrogels

    PubMed Central

    Trögl, Josef; Jirková, Ivana; Kuráň, Pavel; Akhmetshina, Elmira; Brovdyová, Tat′jána; Sirotkin, Alexander; Kirilina, Tatiana

    2015-01-01

    The phospholipid fatty acid (PLFA) content was determined in samples of Paracoccus denitrificans encapsulated in silica hydrogel films prepared from prepolymerized tetramethoxysilane (TMOS). Immediately after encapsulation the total PLFA concentration was linearly proportional to the optical density (600 nm) of the input microbial suspension (R2 = 0.99). After 7 days this relationship remained linear, but with significantly decreased slope, indicating a higher extinction of bacteria in suspensions of input concentration 108 cells/mL and higher. trans-Fatty acids, indicators of cytoplasmatic membrane disturbances, were below the detection limit. The cy/pre ratio (i.e., ratio of cyclopropylated fatty acids (cy17:0 + cy19:0) to their metabolic precursors (16:1ω7 + 18:1ω7)), an indicator of the transition of the culture to a stationary growth-phase, decreased depending on co-immobilization of nutrients in the order phosphate buffer > mineral medium > Luria Broth rich medium. The ratio, too, was logarithmically proportional to cell concentration. These results confirm the applicability of total PLFA as an indicator for the determination of living biomass and cy/pre ratio for determination of nutrient limitation of microorganisms encapsulated in sol-gel matrices. This may be of interest for monitoring of sol-gel encapsulated bacteria proposed as optical recognition elements in biosensor construction, as well as other biotechnological applications. PMID:25690547

  18. Paracoccus denitrificans for the effluent recycling during continuous denitrification of liquid food.

    PubMed

    Tippkötter, Nils; Roikaew, Wipa; Ulber, Roland; Hoffmann, Alexander; Denzler, Hans-Jörg; Buchholz, Heinrich

    2010-01-01

    Nitrate is an undesirable component of several foods. A typical case of contamination with high nitrate contents is whey concentrate, containing nitrate in concentrations up to 25 l. The microbiological removal of nitrate by Paracoccus denitrificans under formation of harmless nitrogen in combination with a cell retention reactor is described here. Focus lies on the resource-conserving design of a microbal denitrification process. Two methods are compared. The application of polyvinyl alcohol-immobilized cells, which can be applied several times in whey feed, is compared with the implementation of a two step denitrification system. First, the whey concentrate's nitrate is removed by ion exchange and subsequently the eluent regenerated by microorganisms under their retention by crossflow filtration. Nitrite and nitrate concentrations were determined by reflectometric color measurement with a commercially available Reflectoquant device. Correction factors for these media had to be determined. During the pilot development, bioreactors from 4 to 250 mg x L(-1) and crossflow units with membrane areas from 0.02 to 0.80 m(2) were examined. Based on the results of the pilot plants, a scaling for the exemplary process of denitrifying 1,000 tons per day is discussed. Copyright 2010 American Institute of Chemical Engineers

  19. Genome Analysis and Physiological Comparison of Alicycliphilus denitrificans Strains BC and K601T

    PubMed Central

    Talarico Saia, Flávia; Weelink, Sander A. B.; Goodwin, Lynne A.; Daligault, Hajnalka E.; Bruce, David C.; Detter, John C.; Tapia, Roxanne; Han, Cliff S.; Land, Miriam L.; Hauser, Loren J.; Langenhoff, Alette A. M.; Gerritse, Jan; van Berkel, Willem J. H.; Pieper, Dietmar H.; Junca, Howard; Smidt, Hauke; Schraa, Gosse; Davids, Mark; Schaap, Peter J.; Plugge, Caroline M.; Stams, Alfons J. M.

    2013-01-01

    The genomes of the Betaproteobacteria Alicycliphilus denitrificans strains BC and K601T have been sequenced to get insight into the physiology of the two strains. Strain BC degrades benzene with chlorate as electron acceptor. The cyclohexanol-degrading denitrifying strain K601T is not able to use chlorate as electron acceptor, while strain BC cannot degrade cyclohexanol. The 16S rRNA sequences of strains BC and K601T are identical and the fatty acid methyl ester patterns of the strains are similar. Basic Local Alignment Search Tool (BLAST) analysis of predicted open reading frames of both strains showed most hits with Acidovorax sp. JS42, a bacterium that degrades nitro-aromatics. The genomes include strain-specific plasmids (pAlide201 in strain K601T and pAlide01 and pAlide02 in strain BC). Key genes of chlorate reduction in strain BC were located on a 120 kb megaplasmid (pAlide01), which was absent in strain K601T. Genes involved in cyclohexanol degradation were only found in strain K601T. Benzene and toluene are degraded via oxygenase-mediated pathways in both strains. Genes involved in the meta-cleavage pathway of catechol are present in the genomes of both strains. Strain BC also contains all genes of the ortho-cleavage pathway. The large number of mono- and dioxygenase genes in the genomes suggests that the two strains have a broader substrate range than known thus far. PMID:23825601

  20. Genome-enabled studies of anaerobic, nitrate-dependent iron oxidation in the chemolithoautotrophic bacterium Thiobacillus denitrificans

    PubMed Central

    Beller, Harry R.; Zhou, Peng; Legler, Tina C.; Chakicherla, Anu; Kane, Staci; Letain, Tracy E.; A. O’Day, Peggy

    2013-01-01

    Thiobacillus denitrificans is a chemolithoautotrophic bacterium capable of anaerobic, nitrate-dependent U(IV) and Fe(II) oxidation, both of which can strongly influence the long-term efficacy of in situ reductive immobilization of uranium in contaminated aquifers. We previously identified two c-type cytochromes involved in nitrate-dependent U(IV) oxidation in T. denitrificans and hypothesized that c-type cytochromes would also catalyze Fe(II) oxidation, as they have been found to play this role in anaerobic phototrophic Fe(II)-oxidizing bacteria. Here we report on efforts to identify genes associated with nitrate-dependent Fe(II) oxidation, namely (a) whole-genome transcriptional studies [using FeCO3, Fe2+, and U(IV) oxides as electron donors under denitrifying conditions], (b) Fe(II) oxidation assays performed with knockout mutants targeting primarily highly expressed or upregulated c-type cytochromes, and (c) random transposon-mutagenesis studies with screening for Fe(II) oxidation. Assays of mutants for 26 target genes, most of which were c-type cytochromes, indicated that none of the mutants tested were significantly defective in nitrate-dependent Fe(II) oxidation. The non-defective mutants included the c1-cytochrome subunit of the cytochrome bc1 complex (complex III), which has relevance to a previously proposed role for this complex in nitrate-dependent Fe(II) oxidation and to current concepts of reverse electron transfer. A transposon mutant with a disrupted gene associated with NADH:ubiquinone oxidoreductase (complex I) was ~35% defective relative to the wild-type strain; this strain was similarly defective in nitrate reduction with thiosulfate as the electron donor. Overall, our results indicate that nitrate-dependent Fe(II) oxidation in T. denitrificans is not catalyzed by the same c-type cytochromes involved in U(IV) oxidation, nor have other c-type cytochromes yet been implicated in the process. PMID:24065960

  1. Respiratory Complex I in Bos taurus and Paracoccus denitrificans Pumps Four Protons across the Membrane for Every NADH Oxidized.

    PubMed

    Jones, Andrew J Y; Blaza, James N; Varghese, Febin; Hirst, Judy

    2017-03-24

    Respiratory complex I couples electron transfer between NADH and ubiquinone to proton translocation across an energy-transducing membrane to support the proton-motive force that drives ATP synthesis. The proton-pumping stoichiometry of complex I ( i.e. the number of protons pumped for each two electrons transferred) underpins all mechanistic proposals. However, it remains controversial and has not been determined for any of the bacterial enzymes that are exploited as model systems for the mammalian enzyme. Here, we describe a simple method for determining the proton-pumping stoichiometry of complex I in inverted membrane vesicles under steady-state ADP-phosphorylating conditions. Our method exploits the rate of ATP synthesis, driven by oxidation of NADH or succinate with different sections of the respiratory chain engaged in catalysis as a proxy for the rate of proton translocation and determines the stoichiometry of complex I by reference to the known stoichiometries of complexes III and IV. Using vesicles prepared from mammalian mitochondria (from Bos taurus ) and from the bacterium Paracoccus denitrificans , we show that four protons are pumped for every two electrons transferred in both cases. By confirming the four-proton stoichiometry for mammalian complex I and, for the first time, demonstrating the same value for a bacterial complex, we establish the utility of P. denitrificans complex I as a model system for the mammalian enzyme. P. denitrificans is the first system described in which mutagenesis in any complex I core subunit may be combined with quantitative proton-pumping measurements for mechanistic studies. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  2. Construction of a Specialized Cloning Strain of E. Coli for the Nitrate Reductase Genes of Haloferax Denitrificans

    NASA Technical Reports Server (NTRS)

    Johnson, Emmett

    1999-01-01

    This is the final report on Joint Research Interchange (NCC2-5011) "Construction of a Specialized Cloning Strain of E.. coli for the Nitrate Reductase Genes of Haloferax denitrificans." Originally the award was 11/l/93-10/31/95, but there were no-cost extensions made, because of a year Sabbatical at the Pasteur Institute in Paris and other leaves of 3 months each at the Pasteur Institute, during which work could not be done on this project, which extended the closing date to 10/30/98.

  3. Rhodanobacter denitrificans sp. nov., isolated from nitrate-rich zones of a contaminated aquifer.

    PubMed

    Prakash, Om; Green, Stefan J; Jasrotia, Puja; Overholt, Will A; Canion, Andy; Watson, David B; Brooks, Scott C; Kostka, Joel E

    2012-10-01

    Bacterial strains 2APBS1(T) and 116-2 were isolated from the subsurface of a nuclear legacy waste site where the sediments are co-contaminated with large amounts of acids, nitrate, metal radionuclides and other heavy metals. A combination of physiological and genetic assays indicated that these strains represent the first member of the genus Rhodanobacter shown to be capable of complete denitrification. Cells of strain 2APBS1(T) and 116-2 were Gram-negative, non-spore-forming rods, 3-5 µm long and 0.25-0.5 µm in diameter. The isolates were facultative anaerobes, and had temperature and pH optima for growth of 30 °C and pH 6.5; they were able to tolerate up to 2.0 % NaCl, although growth improved in its absence. Strains 2APBS1(T) and 116-2 contained fatty acid and quinone (ubiquinone-8; 100 %) profiles that are characteristic features of the genus Rhodanobacter. Although strains 2APBS1(T) and 116-2 shared high 16S rRNA gene sequence similarity with Rhodanobacter thiooxydans LCS2(T) (>99 %), levels of DNA-DNA relatedness between these strains were substantially below the 70 % threshold used to designate novel species. Thus, based on genotypic, phylogenetic, chemotaxonomic and physiological differences, strains 2APBS1(T) and 116-2 are considered to represent a single novel species of the genus Rhodanobacter, for which the name Rhodanobacter denitrificans sp. nov. is proposed. The type strain is 2APBS1(T) ( = DSM 23569(T) = JCM 17641(T)).

  4. Genome analysis and physiological comparison of Alicycliphilus denitrificans strains BC and K601T

    SciT

    Oosterkamp, Margreet J.; Veuskens, Teun; Saia, Flavia Talarico

    2013-01-01

    The genomes of the Betaproteobacteria Alicycliphilus denitrificans strains BC and K601T have been sequenced to get insight into the physiology of the two strains. Strain BC degrades benzene with chlorate as electron acceptor. The cyclohexanol-degrading denitrifying strain K601T is not able to use chlorate as electron acceptor, while strain BC cannot degrade cyclohexanol. The 16S rRNA sequences of strains BC and K601T are identical and the fatty acid methyl ester patterns of the strains are similar. Basic Local Alignment Search Tool (BLAST) analysis of predicted open reading frames of both strains showed most hits with Acidovorax sp. JS42, a bacteriummore » that degrades nitro-aromatics. The genomes include strain-specific plasmids (pAlide201 in strain K601T and pAlide01 and pAlide02 in strain BC). Key genes of chlorate reduction in strain BC were located on a 120 kb megaplasmid (pAlide01), which was absent in strain K601T. Genes involved in cyclohexanol degradation were only found in strain K601T. Benzene and toluene are degraded via oxygenase-mediated pathways in both strains. Genes involved in the meta-cleavage pathway of catechol are present in the genomes of both strains. Strain BC also contains all genes of the ortho-cleavage pathway. The large number of mono- and dioxygenase genes in the genomes suggests that the two strains have a broader substrate range than known thus far.« less

  5. The nitric-oxide reductase from Paracoccus denitrificans uses a single specific proton pathway.

    PubMed

    ter Beek, Josy; Krause, Nils; Reimann, Joachim; Lachmann, Peter; Ädelroth, Pia

    2013-10-18

    The NO reductase from Paracoccus denitrificans reduces NO to N2O (2NO + 2H(+) + 2e(-) → N2O + H2O) with electrons donated by periplasmic cytochrome c (cytochrome c-dependent NO reductase; cNOR). cNORs are members of the heme-copper oxidase superfamily of integral membrane proteins, comprising the O2-reducing, proton-pumping respiratory enzymes. In contrast, although NO reduction is as exergonic as O2 reduction, there are no protons pumped in cNOR, and in addition, protons needed for NO reduction are derived from the periplasmic solution (no contribution to the electrochemical gradient is made). cNOR thus only needs to transport protons from the periplasm into the active site without the requirement to control the timing of opening and closing (gating) of proton pathways as is needed in a proton pump. Based on the crystal structure of a closely related cNOR and molecular dynamics simulations, several proton transfer pathways were suggested, and in principle, these could all be functional. In this work, we show that residues in one of the suggested pathways (denoted pathway 1) are sensitive to site-directed mutation, whereas residues in the other proposed pathways (pathways 2 and 3) could be exchanged without severe effects on turnover activity with either NO or O2. We further show that electron transfer during single-turnover reduction of O2 is limited by proton transfer and can thus be used to study alterations in proton transfer rates. The exchange of residues along pathway 1 showed specific slowing of this proton-coupled electron transfer as well as changes in its pH dependence. Our results indicate that only pathway 1 is used to transfer protons in cNOR.

  6. Industrial vitamin B12 production by Pseudomonas denitrificans using maltose syrup and corn steep liquor as the cost-effective fermentation substrates.

    PubMed

    Xia, Wei; Chen, Wei; Peng, Wei-Fu; Li, Kun-Tai

    2015-06-01

    The aerobic Pseudomonas denitrificans is widely used for industrial and commercial vitamin B12 fermentation, due to its higher productivity compared to the anaerobic vitamin B12-producing microorganisms. This paper aimed to develop a cost-effective fermentation medium for industrial vitamin B12 production by P. denitrificans in 120,000-l fermenter. It was found that maltose syrup (a low-cost syrup from corn starch by means of enzymatic or acid hydrolysis) and corn steep liquor (CSL, a by-product of starch industry) were greatly applicable to vitamin B12 production by P. denitrificans. Under the optimal fermentation medium performed by response surface methodology, 198.27 ± 4.60 mg/l of vitamin B12 yield was obtained in 120,000-l fermenter, which was close to the fermentation with the refined sucrose (198.80 mg/l) and was obviously higher than that obtained under beet molasses utilization (181.75 mg/l). Therefore, maltose syrups and CSL were the efficient and economical substrates for industrial vitamin B12 fermentation by P. denitrificans.

  7. Draft Genome Sequence of Bowmanella denitrificans JL63, a Bacterium Isolated from Whiteleg Shrimp (Litopenaeus vannamei) That Can Inhibit the Growth of Vibrio parahaemolyticus

    PubMed Central

    LaPorte, Jason P.; Spinard, Edward J.; Gomez-Chiarri, Marta; Rowley, David C.; Mekalanos, John J.

    2018-01-01

    ABSTRACT Bowmanella denitrificans strain JL63 was isolated from a whiteleg shrimp (Litopenaeus vannamei) and was determined to have antibacterial activity against an acute hepatopancreatic necrosis disease (AHPND) strain of Vibrio parahaemolyticus. Here, we report the draft genome sequence of this strain and identify genes that are potentially involved in its antibacterial activity. PMID:29622614

  8. Efficient simultaneous adsorption-biodegradation of high-concentrated N,N-dimethylformamide from water by Paracoccus denitrificans-graphene oxide microcomposites

    NASA Astrophysics Data System (ADS)

    Zheng, Yuan; Chen, Dongyun; Li, Najun; Xu, Qingfeng; Li, Hua; He, Jinghui; Lu, Jianmei

    2016-02-01

    Water contamination becomes one of the most pervasive environmental issues all over the world in recent years. In this paper, the functionalization of graphene oxide (GO) with copolymers containing methacrylic acid (MAA) and butyl methacrylate (BMA) was investigated to prepare a new microcomposite material (PGO) via free radical solution polymerization. PGO was used for the adsorption of N,N-dimethylformamide (DMF) from aqueous solution by utilizing the characteristics of ultralarge surface and the Van der Waals force between DMF molecules and polymers on the surface of PGO. Besides, PGO was used not only a high-capable adsorbent but also a carrier for the immobilization of Paracoccus denitrificans cells in the treatment of high-concentrated DMF. Bacterial cells could immobilized on the PGO (PGO@P. denitrificans) stably by covalent coupling process after acclimatization and high-concentrated DMF (2000 mg/L) could be removed completely and relatively rapidly from aqueous solutions by the simultaneous adsorption-biodegradation (SAB) process of PGO@P. denitrificans. Furthermore, the excellent recycle performance of PGO@P. denitrificans made the whole process more economical and practical.

  9. Genome-Enabled Studies of Anaerobic, Nitrate-Dependent Iron Oxidation in the Chemolithoautotrophic Bacterium Thiobacillus denitrificans

    NASA Astrophysics Data System (ADS)

    Beller, H. R.; Zhou, P.; Legler, T. C.; Chakicherla, A.; O'Day, P. A.

    2013-12-01

    Thiobacillus denitrificans is a chemolithoautotrophic bacterium capable of anaerobic, nitrate-dependent U(IV) and Fe(II) oxidation, both of which can strongly influence the long-term efficacy of in situ reductive immobilization of uranium in contaminated aquifers. We previously identified two c-type cytochromes involved in nitrate-dependent U(IV) oxidation in T. denitrificans and hypothesized that c-type cytochromes would also catalyze Fe(II) oxidation, as they have been found to play this role in anaerobic phototrophic Fe(II)-oxidizing bacteria. Here we report on efforts to identify genes associated with nitrate-dependent Fe(II) oxidation, namely (a) whole-genome transcriptional studies [using FeCO3, Fe2+, and U(IV) oxides as electron donors under denitrifying conditions], (b) Fe(II) oxidation assays performed with knockout mutants targeting primarily highly expressed or upregulated c-type cytochromes, and (c) random transposon-mutagenesis studies with screening for Fe(II) oxidation. Assays of mutants for 26 target genes, most of which were c-type cytochromes, indicated that none of the mutants tested were significantly defective in nitrate-dependent Fe(II) oxidation. The non-defective mutants included the c1-cytochrome subunit of the cytochrome bc1 complex (complex III), which has relevance to a previously proposed role for this complex in nitrate-dependent Fe(II) oxidation and to current concepts of reverse electron transfer. Of the transposon mutants defective in Fe(II) oxidation, one mutant with a disrupted gene associated with NADH:ubiquinone oxidoreductase (complex I) was ~35% defective relative to the wild-type strain; this strain was similarly defective in nitrate reduction with thiosulfate as the electron donor. Overall, our results indicate that nitrate-dependent Fe(II) oxidation in T. denitrificans is not catalyzed by the same c-type cytochromes involved in U(IV) oxidation, nor have other c-type cytochromes yet been implicated in the process.

  10. Electrochemistry suggests proton access from the exit site to the binuclear center in Paracoccus denitrificans cytochrome c oxidase pathway variants.

    PubMed

    Meyer, Thomas; Melin, Frédéric; Richter, Oliver-M H; Ludwig, Bernd; Kannt, Aimo; Müller, Hanne; Michel, Hartmut; Hellwig, Petra

    2015-02-27

    Two different pathways through which protons access cytochrome c oxidase operate during oxygen reduction from the mitochondrial matrix, or the bacterial cytoplasm. Here, we use electrocatalytic current measurements to follow oxygen reduction coupled to proton uptake in cytochrome c oxidase isolated from Paracoccus denitrificans. Wild type enzyme and site-specific variants with defects in both proton uptake pathways (K354M, D124N and K354M/D124N) were immobilized on gold nanoparticles, and oxygen reduction was probed electrochemically in the presence of varying concentrations of Zn(2+) ions, which are known to inhibit both the entry and the exit proton pathways in the enzyme. Our data suggest that under these conditions substrate protons gain access to the oxygen reduction site via the exit pathway. Copyright © 2015 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  11. The NosX and NirX Proteins of Paracoccus denitrificans Are Functional Homologues: Their Role in Maturation of Nitrous Oxide Reductase

    PubMed Central

    Saunders, Neil F. W.; Hornberg, Jorrit J.; Reijnders, Willem N. M.; Westerhoff, Hans V.; de Vries, Simon; van Spanning, Rob J. M.

    2000-01-01

    The nos (nitrous oxide reductase) operon of Paracoccus denitrificans contains a nosX gene homologous to those found in the nos operons of other denitrifiers. NosX is also homologous to NirX, which is so far unique to P. denitrificans. Single mutations of these genes did not result in any apparent phenotype, but a double nosX nirX mutant was unable to reduce nitrous oxide. Promoter-lacZ assays and immunoblotting against nitrous oxide reductase showed that the defect was not due to failure of expression of nosZ, the structural gene for nitrous oxide reductase. Electron paramagnetic resonance spectroscopy showed that nitrous oxide reductase in cells of the double mutant lacked the CuA center. A twin-arginine motif in both NosX and NirX suggests that the NosX proteins are exported to the periplasm via the TAT translocon. PMID:10960107

  12. Structure of a catalytic dimer of the α- and β-subunits of the F-ATPase from Paracoccus denitrificans at 2.3 Å resolution

    SciT

    Morales-Ríos, Edgar; Montgomery, Martin G.; Leslie, Andrew G. W.

    2015-09-23

    The structure of the αβ heterodimer of the F-ATPase from the α-proteobacterium P. denitrificans has been determined at 2.3 Å resolution. It corresponds to the ‘open’ or ‘empty’ catalytic interface found in other F-ATPases. The structures of F-ATPases have predominantly been determined from mitochondrial enzymes, and those of the enzymes in eubacteria have been less studied. Paracoccus denitrificans is a member of the α-proteobacteria and is related to the extinct protomitochondrion that became engulfed by the ancestor of eukaryotic cells. The P. denitrificans F-ATPase is an example of a eubacterial F-ATPase that can carry out ATP synthesis only, whereas manymore » others can catalyse both the synthesis and the hydrolysis of ATP. Inhibition of the ATP hydrolytic activity of the P. denitrificans F-ATPase involves the ζ inhibitor protein, an α-helical protein that binds to the catalytic F{sub 1} domain of the enzyme. This domain is a complex of three α-subunits and three β-subunits, and one copy of each of the γ-, δ- and ∊-subunits. Attempts to crystallize the F{sub 1}–ζ inhibitor complex yielded crystals of a subcomplex of the catalytic domain containing the α- and β-subunits only. Its structure was determined to 2.3 Å resolution and consists of a heterodimer of one α-subunit and one β-subunit. It has no bound nucleotides, and it corresponds to the ‘open’ or ‘empty’ catalytic interface found in other F-ATPases. The main significance of this structure is that it aids in the determination of the structure of the intact membrane-bound F-ATPase, which has been crystallized.« less

  13. Structure of the two-domain hexameric APS kinase from Thiobacillus denitrificans: structural basis for the absence of ATP sulfurylase activity

    SciT

    Gay, Sean C.; Segel, Irwin H.; Fisher, Andrew J., E-mail: fisher@chem.ucdavis.edu

    2009-10-01

    APS kinase from Thiobacillus denitrificans contains an inactive N-terminal ATP sulfurylase domain. The structure presented unveils the first hexameric assembly for an APS kinase, and reveals that structural changes in the N-terminal domain disrupt the ATP sulfurylase active site thus prohibiting activity. The Tbd-0210 gene of the chemolithotrophic bacterium Thiobacillus denitrificans is annotated to encode a 60.5 kDa bifunctional enzyme with ATP sulfurylase and APS kinase activity. This putative bifunctional enzyme was cloned, expressed and structurally characterized. The 2.95 Å resolution X-ray crystal structure reported here revealed a hexameric assembly with D{sub 3} symmetry. Each subunit contains a large N-terminalmore » sulfurylase-like domain and a C-terminal APS kinase domain reminiscent of the two-domain fungal ATP sulfurylases of Penicillium chrysogenum and Saccharomyces cerevisiae, which also exhibit a hexameric assembly. However, the T. denitrificans enzyme exhibits numerous structural and sequence differences in the N-terminal domain that render it inactive with respect to ATP sulfurylase activity. Surprisingly, the C-terminal domain does indeed display APS kinase activity, indicating that this gene product is a true APS kinase. Therefore, these results provide the first structural insights into a unique hexameric APS kinase that contains a nonfunctional ATP sulfurylase-like domain of unknown function.« less

  14. Achromobacter denitrificans SP1 produces pharmaceutically active 25C prodigiosin upon utilizing hazardous di(2-ethylhexyl)phthalate.

    PubMed

    Pradeep, S; Sarath Josh, M K; Balachandran, S; Sudha Devi, R; Sadasivam, R; Thirugnanam, P E; Doble, Mukesh; Anderson, Robin C; Benjamin, Sailas

    2014-11-01

    This first report describes the purification and identification of an orange-red pigment produced by Achromobacter denitrificans strain SP1 (isolated from sewage sludge heavily contaminated with plastics) during its growth in a simple basal salt medium supplemented with the hazardous di(2-ethylhexyl)phthalate (DEHP) blended in PVC blood bag (in situ) or free DEHP (ex situ) as carbon source. The cell-bound pigment was elucidated, characterized at molecular level, and described as an unusual 25C prodigiosin analog for the first time. At laboratory conditions (in flasks), the dry cell mass was 75.2mg/g blood bag, which upon extraction yielded 7.1mg prodigiosin; at this stage the pH of the medium was dropped from 7.2 to 3.5. Considering its pharmaceutical importance, taking 10 known prodigiosins as controls, this 25C prodigiosin was subjected to molecular docking studies, showed comparable and promising binding efficiencies with the crucial molecular human targets like cycloxygenase-2, ZAP-70 kinase and Jak-3 kinase. Copyright © 2014 Elsevier Ltd. All rights reserved.

  15. Biosynthesis of poly-3-hydroxybutyrate (PHB) from glycerol by Paracoccus denitrificans in a batch bioreactor: effect of process variables.

    PubMed

    Kalaiyezhini, D; Ramachandran, K B

    2015-01-01

    In this study, the kinetics of poly-3-hydroxybutyrate (PHB) biosynthesis from glycerol by Paracoccus denitrificans DSMZ 413 were explored in a batch bioreactor. Effects of inorganic and organic nitrogen source, carbon to nitrogen ratio, and other process variables such as pH, aeration, and initial glycerol concentration on PHB production were investigated in a 2.5-L bioreactor. Yeast extract was found to be the best nitrogen source compared to several organic nitrogen sources tested. At pH 6, specific growth rate, product formation rate, and accumulation of PHB within the cell were maximum. Specific growth rate increased with increase in oxygen transfer rate, but moderate oxygen transfer rate promoted PHB production. High glycerol concentration inhibited specific product formation rate but not growth. High initial carbon/nitrogen (C/N) ratio favored PHB accumulation and its productivity. At a C/N ratio of 21.4 (mol mol(-1)), 10.7 g L(-1) of PHB corresponding to 72% of cell dry weight was attained.

  16. Achromobacter denitrificans Strain YD35 Pyruvate Dehydrogenase Controls NADH Production To Allow Tolerance to Extremely High Nitrite Levels

    PubMed Central

    Doi, Yuki; Shimizu, Motoyuki; Fujita, Tomoya; Nakamura, Akira; Takizawa, Noboru

    2014-01-01

    We identified the extremely nitrite-tolerant bacterium Achromobacter denitrificans YD35 that can grow in complex medium containing 100 mM nitrite (NO2−) under aerobic conditions. Nitrite induced global proteomic changes and upregulated tricarboxylate (TCA) cycle enzymes as well as antioxidant proteins in YD35. Transposon mutagenesis generated NO2−-hypersensitive mutants of YD35 that had mutations at genes for aconitate hydratase and α-ketoglutarate dehydrogenase in the TCA cycle and a pyruvate dehydrogenase (Pdh) E1 component, indicating the importance of TCA cycle metabolism to NO2− tolerance. A mutant in which the pdh gene cluster was disrupted (Δpdh mutant) could not grow in the presence of 100 mM NO2−. Nitrite decreased the cellular NADH/NAD+ ratio and the cellular ATP level. These defects were more severe in the Δpdh mutant, indicating that Pdh contributes to upregulating cellular NADH and ATP and NO2−-tolerant growth. Exogenous acetate, which generates acetyl coenzyme A and then is metabolized by the TCA cycle, compensated for these defects caused by disruption of the pdh gene cluster and those caused by NO2−. These findings demonstrate a link between NO2− tolerance and pyruvate/acetate metabolism through the TCA cycle. The TCA cycle mechanism in YD35 enhances NADH production, and we consider that this contributes to a novel NO2−-tolerating mechanism in this strain. PMID:24413603

  17. Transcriptional regulation, metal binding properties and structure of Pden1597, an unusual zinc transport protein from Paracoccus denitrificans

    DOE PAGES

    Handali, Melody; Neupane, Durga P.; Roychowdhury, Hridindu; ...

    2015-03-18

    Here, ATP-binding cassette (ABC) transporters of the cluster 9 family are ubiquitous among bacteria and essential for acquiring Zn 2+ and Mn 2+ from the environment or, in the case of pathogens, from the host. These rely on a substrate-binding protein (SBP) to coordinate the relevant metal with high affinity and specificity and subsequently release it to a membrane permease for translocation into the cytoplasm. Although a number of cluster 9 SBP structures have been determined, the structural attributes conferring Zn 2+ or Mn 2+ specificity remain ambiguous. Here we describe the gene expression profile, in vitro metal binding properties,more » and crystal structure of a new cluster 9 SBP from Paracoccus denitrificans we have called AztC. Although all of our results strongly indicate Zn 2+ over Mn 2+ specificity, the Zn 2+ ion is coordinated by a conserved Asp residue only observed to date as a metal ligand in Mn 2+-specific SBPs. The unusual sequence properties of this protein are shared among close homologues, including members from the human pathogens Klebsiella pneumonia and Enterobacter aerogenes, and would seem to suggest a subclass of Zn 2+-specific transporters among the cluster 9 family. In any case, the unusual coordination environment of AztC expands the already considerable range of those available to Zn 2+-specific SBPs and highlights the presence of a His-rich loop as the most reliable indicator of Zn 2+ specificity.« less

  18. Transcriptional Regulation, Metal Binding Properties and Structure of Pden1597, an Unusual Zinc Transport Protein from Paracoccus denitrificans*

    PubMed Central

    Handali, Melody; Neupane, Durga P.; Roychowdhury, Hridindu; Yukl, Erik T.

    2015-01-01

    ATP-binding cassette (ABC) transporters of the cluster 9 family are ubiquitous among bacteria and essential for acquiring Zn2+ and Mn2+ from the environment or, in the case of pathogens, from the host. These rely on a substrate-binding protein (SBP) to coordinate the relevant metal with high affinity and specificity and subsequently release it to a membrane permease for translocation into the cytoplasm. Although a number of cluster 9 SBP structures have been determined, the structural attributes conferring Zn2+ or Mn2+ specificity remain ambiguous. Here we describe the gene expression profile, in vitro metal binding properties, and crystal structure of a new cluster 9 SBP from Paracoccus denitrificans we have called AztC. Although all of our results strongly indicate Zn2+ over Mn2+ specificity, the Zn2+ ion is coordinated by a conserved Asp residue only observed to date as a metal ligand in Mn2+-specific SBPs. The unusual sequence properties of this protein are shared among close homologues, including members from the human pathogens Klebsiella pneumonia and Enterobacter aerogenes, and would seem to suggest a subclass of Zn2+-specific transporters among the cluster 9 family. In any case, the unusual coordination environment of AztC expands the already considerable range of those available to Zn2+-specific SBPs and highlights the presence of a His-rich loop as the most reliable indicator of Zn2+ specificity. PMID:25787075

  19. alphaT244M mutation affects the redox, kinetic, and in vitro folding properties of Paracoccus denitrificans electron transfer flavoprotein.

    PubMed

    Griffin, K J; Dwyer, T M; Manning, M C; Meyer, J D; Carpenter, J F; Frerman, F E

    1997-04-08

    Threonine 244 in the alpha subunit of Paracoccus denitrificans transfer flavoprotein (ETF) lies seven residues to the amino terminus of a proposed dinucleotide binding motif for the ADP moiety of the FAD prosthetic group. This residue is highly conserved in the alpha subunits of all known ETFs, and the most frequent pathogenic mutation in human ETF encodes a methionine substitution at the corresponding position, alphaT266. The X-ray crystal structures of human and P. denitrificans ETFs are very similar. The hydroxyl hydrogen and a backbone amide hydrogen of alphaT266 are hydrogen bonded to N(5) and C(4)O of the flavin, respectively, and the corresponding alphaT244 has the same structural role in P. denitrificans ETF. We substituted a methionine for T244 in the alpha subunit of P. denitrificans ETF and expressed the mutant ETF in Escherichia coli. The mutant protein was purified, characterized, and compared with wild type P. denitrificans ETF. The mutation has no significant effect on the global structure of the protein as inferred from visible and near-ultraviolet absorption and circular dichroism spectra, far-ultraviolet circular dichroism spectra, and infrared spectra in 1H2O and 2H2O. Intrinsic fluorescence due to tryptophan of the mutant protein is 60% greater than that of the wild type ETF. This increased tryptophan fluorescence is probably due to a change in the environment of the nearby W239. Tyrosine fluorescence is unchanged in the mutant protein, although two tyrosine residues are close to the site of the mutation. These results indicate that a change in structure is minor and localized. Kinetic constants of the reductive half-reaction of ETF with porcine medium chain acyl-CoA dehydrogenase are unaltered when alphaT244M ETF serves as the substrate; however, the mutant ETF fails to exhibit saturation kinetics when the semiquinone form of the protein is used as the substrate in the disproportionation reaction catalyzed by P. denitrificans electron transfer

  20. Unidirectional regulation of the F1FO-ATP synthase nanomotor by the ζ pawl-ratchet inhibitor protein of Paracoccus denitrificans and related α-proteobacteria.

    PubMed

    Zarco-Zavala, Mariel; Mendoza-Hoffmann, Francisco; García-Trejo, José J

    2018-06-07

    The ATP synthase is a reversible nanomotor that gyrates its central rotor clockwise (CW) to synthesize ATP and in counter clockwise (CCW) direction to hydrolyse it. In bacteria and mitochondria, two natural inhibitor proteins, namely the ε and IF 1 subunits, prevent the wasteful CCW F 1 F O -ATPase activity by blocking γ rotation at the α DP /β DP /γ interface of the F 1 portion. In Paracoccus denitrificans and related α-proteobacteria, we discovered a different natural F 1 -ATPase inhibitor named ζ. Here we revise the functional and structural data showing that this novel ζ subunit, although being different to ε and IF 1 , it also binds to the α DP /β DP /γ interface of the F 1 of P. denitrificans. ζ shifts its N-terminal inhibitory domain from an intrinsically disordered protein region (IDPr) to an α-helix when inserted in the α DP /β DP /γ interface. We showed for the first time the key role of a natural ATP synthase inhibitor by the distinctive phenotype of a Δζ knockout mutant in P. denitrificans. ζ blocks exclusively the CCW F 1 F O -ATPase rotation without affecting the CW-F 1 F O -ATP synthase turnover, confirming that ζ is important for respiratory bacterial growth by working as an unidirectional pawl-ratchet PdF 1 F O -ATPase inhibitor, thus preventing the wasteful consumption of cellular ATP. In summary, ζ is an useful model that mimics mitochondrial IF 1 but in α-proteobacteria. The structural, functional, and endosymbiotic evolutionary implications of this ζ inhibitor are discussed to shed light on the natural control mechanisms of the three natural inhibitor proteins (ε, ζ, and IF 1 ) of this unique ATP synthase nanomotor, essential for life. Copyright © 2018. Published by Elsevier B.V.

  1. The location of dissimilatory nitrite reductase and the control of dissimilatory nitrate reductase by oxygen in Paracoccus denitrificans.

    PubMed Central

    Alefounder, P R; Ferguson, S J

    1980-01-01

    1. A method is described for preparing spheroplasts from Paracoccus denitrificans that are substantially depleted of dissimilatory nitrate reductase (cytochrome cd) activity. Treatment of cells with lysozyme + EDTA together with a mild osmotic shock, followed by centrifugation, yielded a pellet of spheroplasts and a supernatant that contained d-type cytochrome. The spheroplasts were judged to have retained an intact plasma membrane on the basis that less than 1% of the activity of a cytoplasmic marker protein, malate dehydrogenase, was released from the spheroplasts. In addition to a low activity towards added nitrite, the suspension of spheroplasts accumulated the nitrite that was produced by respiratory chain-linked reduction of nitrate. It is concluded that nitrate reduction occurs at the periplasmic side of the plasma membrane irrespective of whether nitrite is generated by nitrate reduction or is added exogenously. 2. Further evidence for the integrity of the spheroplasts was that nitrate reduction was inhibited by O2, and that chlorate was reduced at a markedly lower rate than nitrate. These data are taken as evidence for an intact plasma membrane because it was shown that cells acquire the capability to reduce nitrate under aerobic conditions after addition of low amounts of Triton X-100 which, with the same titre, also overcame the permeability barrier to chlorate reduction by intact cells. The close relationship between the appearance of chlorate reduction and the loss of the inhibitory effect of O2 on nitrate reduction also suggests that the later feature of nitrate respiration is due to a control on the accessibility of nitrate to its reductase rather than on the flow of electrons to nitrate reductase. PMID:7197918

  2. Paracoccus denitrificans PD1222 Utilizes Hypotaurine via Transamination Followed by Spontaneous Desulfination To Yield Acetaldehyde and, Finally, Acetate for Growth

    PubMed Central

    Felux, Ann-Katrin; Denger, Karin; Weiss, Michael; Cook, Alasdair M.

    2013-01-01

    Hypotaurine (HT; 2-aminoethane-sulfinate) is known to be utilized by bacteria as a sole source of carbon, nitrogen, and energy for growth, as is taurine (2-aminoethane-sulfonate); however, the corresponding HT degradation pathway has remained undefined. Genome-sequenced Paracoccus denitrificans PD1222 utilized HT (and taurine) quantitatively for heterotrophic growth and released the HT sulfur as sulfite (and sulfate) and HT nitrogen as ammonium. Enzyme assays with cell extracts suggested that an HT-inducible HT:pyruvate aminotransferase (Hpa) catalyzes the deamination of HT in an initial reaction step. Partial purification of the Hpa activity and peptide fingerprinting-mass spectrometry (PF-MS) identified the Hpa candidate gene; it encoded an archetypal taurine:pyruvate aminotransferase (Tpa). The same gene product was identified via differential PAGE and PF-MS, as was the gene of a strongly HT-inducible aldehyde dehydrogenase (Adh). Both genes were overexpressed in Escherichia coli. The overexpressed, purified Hpa/Tpa showed HT:pyruvate-aminotransferase activity. Alanine, acetaldehyde, and sulfite were identified as the reaction products but not sulfinoacetaldehyde; the reaction of Hpa/Tpa with taurine yielded sulfoacetaldehyde, which is stable. The overexpressed, purified Adh oxidized the acetaldehyde generated during the Hpa reaction to acetate in an NAD+-dependent reaction. Based on these results, the following degradation pathway for HT in strain PD1222 can be depicted. The identified aminotransferase converts HT to sulfinoacetaldehyde, which desulfinates spontaneously to acetaldehyde and sulfite; the inducible aldehyde dehydrogenase oxidizes acetaldehyde to yield acetate, which is metabolized, and sulfite, which is excreted. PMID:23603744

  3. Modification of surface and enzymatic properties of Achromobacter denitrificans and Stenotrophomonas maltophilia in association with diesel oil biodegradation enhanced with alkyl polyglucosides.

    PubMed

    Sałek, Karina; Zgoła-Grześkowiak, Agnieszka; Kaczorek, Ewa

    2013-11-01

    The article concerns the influence of selected alkyl polyglucosides on biodegradation, cell surface and enzymatic properties of Stenotrophomonas maltophilia and Achromobacter denitrificans. The biodegradation of diesel oil depends on several factors including type and the amount of surfactant as well as bacterial genera used in the process. Nevertheless, a careful selection of these variables must be made as some bacterial strains prefer to use surfactants as their carbon source. This leads to the lowered biodegradation of diesel oil as can be observed for the tested S. maltophilia strain. Alkyl polyglucosides influenced the cell surface properties of both of the tested strains in slightly different ways. Especially for A. denitrificans, for which the hydrophobicity increased with concentration of both--Lutensol GD 70 and Glucopon 215 in diesel oil-surfactant systems. Moreover, judging by the efficiency of biodegradation, the most effective process was observed in the presence of Lutensol GD 70 (240 and 360 mg L(-1)) with biodegradation rising from 32% (without surfactant) to 68%. No such relation was observed for S. maltophilia. Copyright © 2013 Elsevier B.V. All rights reserved.

  4. omega-Amino acid:pyruvate transaminase from Alcaligenes denitrificans Y2k-2: a new catalyst for kinetic resolution of beta-amino acids and amines.

    PubMed

    Yun, Hyungdon; Lim, Seongyop; Cho, Byung-Kwan; Kim, Byung-Gee

    2004-04-01

    Alcaligenes denitrificans Y2k-2 was obtained by selective enrichment followed by screening from soil samples, which showed omega-amino acid:pyruvate transaminase activity, to kinetically resolve aliphatic beta-amino acid, and the corresponding structural gene (aptA) was cloned. The gene was functionally expressed in Escherichia coli BL21 by using an isopropyl-beta-D-thiogalactopyranoside (IPTG)-inducible pET expression system (9.6 U/mg), and the recombinant AptA was purified to show a specific activity of 77.2 U/mg for L-beta-amino-n-butyric acid (L-beta-ABA). The enzyme converts various beta-amino acids and amines to the corresponding beta-keto acids and ketones by using pyruvate as an amine acceptor. The apparent K(m) and V(max) for L-beta-ABA were 56 mM and 500 U/mg, respectively, in the presence of 10 mM pyruvate. In the presence of 10 mM L-beta-ABA, the apparent K(m) and V(max) for pyruvate were 11 mM and 370 U/mg, respectively. The enzyme exhibits high stereoselectivity (E > 80) in the kinetic resolution of 50 mM D,L-beta-ABA, producing optically pure D-beta-ABA (99% enantiomeric excess) with 53% conversion.

  5. ω-Amino Acid:Pyruvate Transaminase from Alcaligenes denitrificans Y2k-2: a New Catalyst for Kinetic Resolution of β-Amino Acids and Amines

    PubMed Central

    Yun, Hyungdon; Lim, Seongyop; Cho, Byung-Kwan; Kim, Byung-Gee

    2004-01-01

    Alcaligenes denitrificans Y2k-2 was obtained by selective enrichment followed by screening from soil samples, which showed ω-amino acid:pyruvate transaminase activity, to kinetically resolve aliphatic β-amino acid, and the corresponding structural gene (aptA) was cloned. The gene was functionally expressed in Escherichia coli BL21 by using an isopropyl-β-d-thiogalactopyranoside (IPTG)-inducible pET expression system (9.6 U/mg), and the recombinant AptA was purified to show a specific activity of 77.2 U/mg for l-β-amino-n-butyric acid (l-β-ABA). The enzyme converts various β-amino acids and amines to the corresponding β-keto acids and ketones by using pyruvate as an amine acceptor. The apparent Km and Vmax for l-β-ABA were 56 mM and 500 U/mg, respectively, in the presence of 10 mM pyruvate. In the presence of 10 mM l-β-ABA, the apparent Km and Vmax for pyruvate were 11 mM and 370 U/mg, respectively. The enzyme exhibits high stereoselectivity (E > 80) in the kinetic resolution of 50 mM d,l-β-ABA, producing optically pure d-β-ABA (99% enantiomeric excess) with 53% conversion. PMID:15066855

  6. The Structure of RdDddP from Roseobacter denitrificans Reveals That DMSP Lyases in the DddP-Family Are Metalloenzymes

    PubMed Central

    Hehemann, Jan-Hendrik; Law, Adrienne; Redecke, Lars; Boraston, Alisdair B.

    2014-01-01

    Marine microbes degrade dimethylsulfoniopropionate (DMSP), which is produced in large quantities by marine algae and plants, with DMSP lyases into acrylate and the gas dimethyl sulfide (DMS). Approximately 10% of the DMS vents from the sea into the atmosphere and this emission returns sulfur, which arrives in the sea through rivers and runoff, back to terrestrial systems via clouds and rain. Despite their key role in this sulfur cycle DMSP lyases are poorly understood at the molecular level. Here we report the first X-ray crystal structure of the putative DMSP lyase RdDddP from Roseobacter denitrificans, which belongs to the abundant DddP family. This structure, determined to 2.15 Å resolution, shows that RdDddP is a homodimeric metalloprotein with a binuclear center of two metal ions located 2.7 Å apart in the active site of the enzyme. Consistent with the crystallographic data, inductively coupled plasma mass spectrometry (ICP-MS) and total reflection X-ray fluorescence (TRXF) revealed the bound metal species to be primarily iron. A 3D structure guided analysis of environmental DddP lyase sequences elucidated the critical residues for metal binding are invariant, suggesting all proteins in the DddP family are metalloenzymes. PMID:25054772

  7. Transcriptional and metabolic regulation of denitrification in Paracoccus denitrificans allows low but significant activity of nitrous oxide reductase under oxic conditions.

    PubMed

    Qu, Zhi; Bakken, Lars R; Molstad, Lars; Frostegård, Åsa; Bergaust, Linda L

    2016-09-01

    Oxygen is known to repress denitrification at the transcriptional and metabolic levels. It has been a common notion that nitrous oxide reductase (N2 OR) is the most sensitive enzyme among the four N-oxide reductases involved in denitrification, potentially leading to increased N2 O production under suboxic or fluctuating oxygen conditions. We present detailed gas kinetics and transcription patterns from batch culture experiments with Paracoccus denitrificans, allowing in vivo estimation of e(-) -flow to O2 and N2 O under various O2 regimes. Transcription of nosZ took place concomitantly with that of narG under suboxic conditions, whereas transcription of nirS and norB was inhibited until O2 levels approached 0 μM in the liquid. Catalytically functional N2 OR was synthesized and active in aerobically raised cells transferred to vials with 7 vol% O2 in headspace, but N2 O reduction rates were 10 times higher when anaerobic pre-cultures were subjected to the same conditions. Upon oxygen exposure, there was an incomplete and transient inactivation of N2 OR that could be ascribed to its lower ability to compete for electrons compared with terminal oxidases. The demonstrated reduction of N2 O at high O2 partial pressure and low N2 O concentrations by a bacterium not known as a typical aerobic denitrifier may provide one clue to the understanding of why some soils appear to act as sinks rather than sources for atmospheric N2 O. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

  8. Emendation of genus Achromobacter and Achromobacter xylosoxidans (Yabuuchi and Yano) and proposal of Achromobacter ruhlandii (Packer and Vishniac) comb. nov., Achromobacter piechaudii (Kiredjian et al.) comb. nov., and Achromobacter xylosoxidans subsp. denitrificans (Rüger and Tan) comb. nov.

    PubMed

    Yabuuchi, E; Kawamura, Y; Kosako, Y; Ezaki, T

    1998-01-01

    Based on the results of GC content determination and 16S rRNA sequence analysis among the type strains of Achromobacter xylosoxidans, 4 Alcaligenes species, 5 Bordetella species, and 12 species of 4 other genera, the separation of genus Achromobacter Yabuuchi and Yano 1981, with the type species Achromobacter xylosoxidans, is confirmed. Alcaligenes ruhlandii (Packer and Vishniac) Aragno and Schlegel 1992 is a distinct species and not a senior synonym of Achromobacter xylosoxidans. Alcaligenes ruhlandii and Alcaligenes piechaudii Kiredjian et al 1986 are transferred to genus Achromobacter. Thus 2 new combinations, Achromobacter ruhlandii (Packer and Vishniac) and Achromobacter piechaudii (Kiredjian et al) are proposed; their type strains are ATCC 15749 and ATCC 43552, respectively. Alcaligenes denitrificans Rüger and Tan 1983 is also transferred to genus Achromobacter and ranked down to the subspecies of Achromobacter xylosoxidans. Thus a new subspecies name, Achromobacter xylosoxidans subsp. denitrificans (Rüger and Tan) is proposed. The type strain of the subspecies is ATCC 15173. This proposal automatically creates type subspecies, Achromobacter xylosoxidans subsp. xylosoxidans, with type strain ATCC 27061. An emended description of genus Achromobacter and of type species Achromobacter xylosoxidans are given.

  9. The insertion of the non-heme FeB cofactor into nitric oxide reductase from P. denitrificans depends on NorQ and NorD accessory proteins.

    PubMed

    Kahle, Maximilian; Ter Beek, Josy; Hosler, Jonathan P; Ädelroth, Pia

    2018-06-03

    Bacterial NO reductases (NOR) catalyze the reduction of NO into N 2 O, either as a step in denitrification or as a detoxification mechanism. cNOR from Paracoccus (P.) denitrificans is expressed from the norCBQDEF operon, but only the NorB and NorC proteins are found in the purified NOR complex. Here, we established a new purification method for the P. denitrificans cNOR via a His-tag using heterologous expression in E. coli. The His-tagged enzyme is both structurally and functionally very similar to non-tagged cNOR. We were also able to express and purify cNOR from the structural genes norCB only, in absence of the accessory genes norQDEF. The produced protein is a stable NorCB complex containing all hemes and it can bind gaseous ligands (CO) to heme b 3 , but it is catalytically inactive. We show that this deficient cNOR lacks the non-heme iron cofactor Fe B . Mutational analysis of the nor gene cluster revealed that it is the norQ and norD genes that are essential to form functional cNOR. NorQ belongs to the family of MoxR P-loop AAA+ ATPases, which are in general considered to facilitate enzyme activation processes often involving metal insertion. Our data indicates that NorQ and NorD work together in order to facilitate non-heme Fe insertion. This is noteworthy since in many cases Fe cofactor binding occurs spontaneously. We further suggest a model for NorQ/D-facilitated metal insertion into cNOR. Copyright © 2018 Elsevier B.V. All rights reserved.

  10. Photo-Initiated Electron Transfer Within the P. denitrificans Cytochrome bc1 Complex: The mobility of the Iron Sulfur Protein is modulated by the occupant of the Qo site†

    PubMed Central

    Havens, Jeffrey; Castellani, Michela; Kleinschroth, Thomas; Ludwig, Bernd; Durham, Bill; Millett, Francis

    2011-01-01

    Domain rotation of the Rieske iron-sulfur protein (ISP) between the cytochrome (cyt) b and cyt c1 redox centers plays a key role in the mechanism of the cyt bc1 complex. Electron transfer within the cyt bc1 complex of P. denitrificans was studied using a ruthenium dimer to rapidly photo-oxidize cyt c1 within 1 μs and initiate the reaction. In the absence of any added quinol or inhibitor of the bc1 complex at pH 8.0, electron transfer from reduced ISP to cyt c1 was biphasic with rate constants of k1f = 6300 ± 3000 s−1 and k1s = 640 ± 300 s−1 and amplitudes of 10 ± 3% and 16 ± 4 % of the total amount of cyt c1 photooxidized. Upon addition of any of the Pm type inhibitors MOA-stilbene, myxothiazol, or azoxystrobin to cyt bc1 in the absence of quinol, the total amplitude increased 2-fold, consistent with a decrease in redox potential of the ISP. In addition, the relative amplitude of the fast phase increased significantly, consistent with a change in the dynamics of the ISP domain rotation. In contrast, addition of the Pf type inhibitors JG-144 and famoxadone decreased the rate constant k1f by 5 to 10-fold, and increased the amplitude over 2-fold. Addition of quinol substrate in the absence of inhibitors led to a two-fold increase in the amplitude of the k1f phase. The effect of QH2 on the kinetics of electron transfer from reduced ISP to cyt c1 was thus similar to that of the Pm inhibitors and very different from that of the Pf inhibitors. The current results indicate that the species occupying the Qo site has a significant conformational influence on the dynamics of the ISP domain rotation. PMID:22026826

  11. Noviherbaspirillum denitrificans sp. nov., a denitrifying bacterium isolated from rice paddy soil and Noviherbaspirillum autotrophicum sp. nov., a denitrifying, facultatively autotrophic bacterium isolated from rice paddy soil and proposal to reclassify Herbaspirillum massiliense as Noviherbaspirillum massiliense comb. nov.

    PubMed

    Ishii, Satoshi; Ashida, Naoaki; Ohno, Hiroki; Segawa, Takahiro; Yabe, Shuhei; Otsuka, Shigeto; Yokota, Akira; Senoo, Keishi

    2017-06-01

    Thirty-nine denitrifying bacterial strains closely related to one another, represented by strains TSA40T and TSA66T, were isolated from rice paddy soils. Strains TSA40T and TSA66T were Gram-stain-negative, slightly curved rod-shaped, and motile by means of polar flagella. They were able to reduce nitrate, nitrite and nitrous oxide, but unable to fix atmospheric N2. While strain TSA66T was able to grow autotrophically by H2-dependent denitrification, strain TSA40T could not. Phylogenetic analysis suggested that they belong to the family Oxalobacteraceae, the order Burkholderiales in the class Betaproteobacteria. Major components in the fatty acids (C16 : 0, C17 : 0 cyclo, C18 : 1ω7c and summed feature 3) and quinone (Q-8) also supported the affiliation of strains TSA40T and TSA66T to the family Oxalobacteraceae. Based on 16S rRNA gene sequence comparisons, strains TSA40T and TSA66T showed the greatest degree of similarity to Herbaspirillum massiliense JC206T, Noviherbaspirillum malthae CC-AFH3T, Noviherbaspirillum humi U15T, Herbaspirillum seropedicae Z67T and Paucimonas lemoignei LMG 2207T, and lower similarities to the members of other genera. Average nucleotide identity values between the genomes of strain TSA40T, TSA66T and H. massiliense JC206T were 75-77 %, which was lower than the threshold value for species discrimination (95-96 %). Based on the 16S rRNA gene sequence analysis in combination with physiological, chemotaxonomic and genomic properties, strains TSA40T (=JCM 17722T=ATCC TSD-69T) and TSA66T (=JCM 17723T=DSM 25787T) are the type strains of two novel species within the genus Noviherbaspirillum, for which the names Noviherbaspirillum denitrificans sp. nov. and Noviherbaspirillum autotrophicum sp. nov. are proposed, respectively. We also propose the reclassification of Herbaspirillum massiliense as Noviherbaspirillum massiliense comb. nov.

  12. Extension of Gutenberg-Richter distribution to MW -1.3, no lower limit in sight

    NASA Astrophysics Data System (ADS)

    Boettcher, Margaret S.; McGarr, A.; Johnston, Malcolm

    2009-05-01

    With twelve years of seismic data from TauTona Gold Mine, South Africa, we show that mining-induced earthquakes follow the Gutenberg-Richter relation with no scale break down to the completeness level of the catalog, at moment magnitude M W -1.3. Events recorded during relatively quiet hours in 2006 indicate that catalog detection limitations, not earthquake source physics, controlled the previously reported minimum magnitude in this mine. Within the Natural Earthquake Laboratory in South African Mines (NELSAM) experiment's dense seismic array, earthquakes that exhibit shear failure at magnitudes as small as M W -3.9 are observed, but we find no evidence that M W -3.9 represents the minimum magnitude. In contrast to previous work, our results imply small nucleation zones and that earthquake processes in the mine can readily be scaled to those in either laboratory experiments or natural faults.

  13. 55-mW, 1.2-V, 12-bit, 100-MSPS Pipeline ADCs for Wireless Receivers

    NASA Astrophysics Data System (ADS)

    Ito, Tomohiko; Kurose, Daisuke; Ueno, Takeshi; Yamaji, Takafumi; Itakura, Tetsuro

    For wireless receivers, low-power 1.2-V 12-bit 100-MSPS pipeline ADCs are fabricated in 90-nm CMOS technology. To achieve low-power dissipation at 1.2V without the degradation of SNR, the configuration of 2.5bit/stage is employed with an I/Q amplifier sharing technique. Furthermore, single-stage pseudo-differential amplifiers are used in a Sample-and-Hold (S/H) circuit and a 1st Multiplying Digital-to-Analog Converter (MDAC). The pseudo-differential amplifier with two-gain-stage transimpedance gain-boosting amplifiers realizes high DC gain of more than 90dB with low power. The measured SNR of the 100-MSPS ADC is 66.7dB at 1.2-V supply. Under that condition, each ADC dissipates only 55mW.

  14. Structural and Biochemical Characterization of a Bifunctional Ketoisomerase/N-acetyltransferase from Shewanella denitrificans

    PubMed Central

    Chantigian, Daniel P.; Thoden, James B.; Holden, Hazel M.

    2014-01-01

    Unusual N-acetylated sugars have been observed on the O-antigens of some Gram-negative bacteria and on the S-layers of both Gram-positive and Gram-negative bacteria. One such sugar is 3-acetamido-3,6-dideoxy-α-d-galactose or Fuc3NAc. The pathway for its production requires five enzymes with the first step involving the attachment of dTMP to glucose-1-phosphate. Here we report a structural and biochemical characterization of a bifunctional enzyme from Shewanella denitificans thought to be involved in the biosynthesis of dTDP-Fuc3NAc. On the basis of a bioinformatics analysis, the enzyme, hereafter referred to as FdtD, has been postulated to catalyze the third and fifth steps in the pathway, namely a 3,4-keto isomerization and an N-acetyltransferase reaction. For the X-ray analysis reported here, the enzyme was crystallized in the presence of dTDP and CoA. The crystal structure shows that FdtD adopts a hexameric quaternary structure with 322 symmetry. Each subunit of the hexamer folds into two distinct domains connected by a flexible loop. The N-terminal domain adopts a left-handed β-helix motif and is responsible for the N-acetylation reaction. The C-terminal domain folds into an antiparallel flattened β-barrel that harbors the active site responsible for the isomerization reaction. Biochemical assays verify the two proposed catalytic activities of the enzyme and reveal that the 3,4-keto isomerization event leads to inversion of configuration about the hexose C-4' carbon. PMID:24128043

  15. Adenosine Monophosphate Binding Stabilizes the KTN Domain of the Shewanella denitrificans Kef Potassium Efflux System.

    PubMed

    Pliotas, Christos; Grayer, Samuel C; Ekkerman, Silvia; Chan, Anthony K N; Healy, Jess; Marius, Phedra; Bartlett, Wendy; Khan, Amjad; Cortopassi, Wilian A; Chandler, Shane A; Rasmussen, Tim; Benesch, Justin L P; Paton, Robert S; Claridge, Timothy D W; Miller, Samantha; Booth, Ian R; Naismith, James H; Conway, Stuart J

    2017-08-15

    Ligand binding is one of the most fundamental properties of proteins. Ligand functions fall into three basic types: substrates, regulatory molecules, and cofactors essential to protein stability, reactivity, or enzyme-substrate complex formation. The regulation of potassium ion movement in bacteria is predominantly under the control of regulatory ligands that gate the relevant channels and transporters, which possess subunits or domains that contain Rossmann folds (RFs). Here we demonstrate that adenosine monophosphate (AMP) is bound to both RFs of the dimeric bacterial Kef potassium efflux system (Kef), where it plays a structural role. We conclude that AMP binds with high affinity, ensuring that the site is fully occupied at all times in the cell. Loss of the ability to bind AMP, we demonstrate, causes protein, and likely dimer, instability and consequent loss of function. Kef system function is regulated via the reversible binding of comparatively low-affinity glutathione-based ligands at the interface between the dimer subunits. We propose this interfacial binding site is itself stabilized, at least in part, by AMP binding.

  16. TSCA Environmental Release Application (TERA) for Alcaligenes xylosoxidans subspecies denitrificans strain AL6.1

    EPA Pesticide Factsheets

    TERA submitted by University of California, Riverside and given the tracking designation of R-03-0001. The microorganism has been modified to carry a coding sequence of DsRed for expressing a red fluorescent protein.

  17. Adenosine Monophosphate Binding Stabilizes the KTN Domain of the Shewanella denitrificans Kef Potassium Efflux System

    PubMed Central

    2017-01-01

    Ligand binding is one of the most fundamental properties of proteins. Ligand functions fall into three basic types: substrates, regulatory molecules, and cofactors essential to protein stability, reactivity, or enzyme–substrate complex formation. The regulation of potassium ion movement in bacteria is predominantly under the control of regulatory ligands that gate the relevant channels and transporters, which possess subunits or domains that contain Rossmann folds (RFs). Here we demonstrate that adenosine monophosphate (AMP) is bound to both RFs of the dimeric bacterial Kef potassium efflux system (Kef), where it plays a structural role. We conclude that AMP binds with high affinity, ensuring that the site is fully occupied at all times in the cell. Loss of the ability to bind AMP, we demonstrate, causes protein, and likely dimer, instability and consequent loss of function. Kef system function is regulated via the reversible binding of comparatively low-affinity glutathione-based ligands at the interface between the dimer subunits. We propose this interfacial binding site is itself stabilized, at least in part, by AMP binding. PMID:28656748

  18. Energy coupling to nitrate uptake into the denitrifying cells of Paracoccus denitrificans.

    PubMed

    Kucera, Igor

    2005-09-05

    This study deals with the effects of the agents that dissipate the individual components of the proton motive force (short-chain fatty acids, nigericin, and valinomycin) upon the methyl viologen-coupled nitrate reductase activity in intact cells. Substitution of butyrate or acetate for chloride in Tris-buffered assay media resulted in a marked inhibition at pH 7. In a Tris--chloride buffer of neutral pH, the reaction was almost fully inhibitable by nigericin. Alkalinisation increased the IC(50) value for nigericin and decreased the maximal inhibition attained. Both types of inhibitions could be reversed by the permeabilisation of cells or by the addition of nitrite, and that caused by nigericin disappeared at high extracellular concentrations of potassium. These data indicate that nitrate transport step relies heavily on the pH gradient at neutral pH. Since the affinity of cells for nitrate was strongly diminished by imposing an inside-positive potassium (or lithium) diffusion potential at alkaline external pH, a potential dependent step may be of significance in the transporter cycle under these conditions. Experiments with sodium-depleted media provided no hints for Na(+) as a possible H(+) substitute.

  19. TSCA Environmental Release Application (TERA) for Alcaligenes xylosoxidans subspecies denitrificans strain AL6.1, R05-01

    EPA Pesticide Factsheets

    TERA submitted by the University of California, Riverside. The microorganism will be tested to determine its biology and behavior in vineyard ecosystems as part of a research program to prevent or cure Pierce's disease in grapes.

  20. Catalysis by Methylamine Dehydrogenase and Electron Transfer to Amicyanin and Cytochrome C(551I) from Paracoccus Denitrificans.

    NASA Astrophysics Data System (ADS)

    Brooks, Harold Burns

    1995-01-01

    The quinoprotein methylamine dehydrogenase (MADH), a type I copper protein, amicyanin, and cytochrome c _{55li} form a physiologic ternary complex (Chen et al. (1994) Science 264, 86-90) in which electrons are transferred from tryptophan tryptophylquinone to copper to heme. The reduction of MADH by rm H_3- and rm D_3 -methylamine, the reoxidation of MADH by amicyanin, and the reduction of cytochrome c_{55li } by reduced amicyanin in the presence of MADH have been studied by stopped-flow spectroscopy. When rm CD_3NH_2 was used as a substrate for MADH a deuterium kinetic isotope effect of 17.2 was measured for the hydrogen abstraction step. The maximum deuterium kinetic isotope effect that was measured in steady-state kinetic experiments was 3.0. The temperature dependencies of the rate constants for the reaction of methylamine with MADH were also determined. An iminosemiquinone intermediate for the oxidation of substrate-reduced MADH by amicyanin was detected using stopped-flow spectroscopy, and the presence of the substrate derived nitrogen was confirmed by electron spin echo envelope modulation (ESEEM) spectroscopy. Marcus theory, which was used to analyze the electron transfer reaction between the dithionite-generated redox forms of MADH and amicyanin, gave values of 218 kJ rm mol^{ -1} (2.3 eV) for the reorganizational energy (lambda ) and 11.6 rm cm^{-1} for the coupling rm (H_{AB}). In contrast, the oxidation of substrate-reduced MADH by amicyanin was a gated electron transfer reaction with values for DeltaH* of 76 kJ rm mol^ {-1} and DeltaS* of -41 J rm mol^{ -1} ^circ K^ {-1}. These studies are consistent with the formation of transient unstable intermediates preceeding electron transfer between MADH and amicyanin. Preliminary investigations of the ternary complex of MADH, amicyanin, and cytochrome c_{55li } suggest two distinct cytochrome c _{55li} binding sites on amicyanin. This conclusion is supported by the biphasic nature of the stopped -flow trace, the inhibition of the rm k^ {fast}_{obs} by MADH, and the ionic strength dependence of the two phases. The slow phase had a rate of 3.1 rm s^ {-1} which is consistent with electron transfer between amicyanin and cytochrome c_ {55li} within the ternary complex. The fast phase does not exhibit saturation behavior, must have an electron transfer rate greater than 1000 rm s^{-1}, and likely involves a complex of amicyanin and cytochrome c_{55li } near the hydrophobic patch of amicyanin.

  1. The Role of Hydrogen for Sulfurimonas denitrificans’ Metabolism

    PubMed Central

    Han, Yuchen; Perner, Mirjam

    2014-01-01

    Sulfurimonas denitrificans was originally isolated from coastal marine sediments. It can grow with thiosulfate and nitrate or sulfide and oxygen. Recently sequencing of its genome revealed that it encodes periplasmic and cytoplasmic [NiFe]-hydrogenases but the role of hydrogen for its metabolism has remained unknown. We show the first experimental evidence that S. denitrificans can indeed express a functional hydrogen uptake active hydrogenase and can grow on hydrogen. In fact, under the provided conditions it grew faster and denser on hydrogen than on thiosulfate alone and even grew with hydrogen in the absence of reduced sulfur compounds. In our experiments, at the time points tested, the hydrogen uptake activity appeared to be related to the periplasmic hydrogenase and not to the cytoplasmic hydrogenase. Our data suggest that under the provided conditions S. denitrificans can grow more efficiently with hydrogen than with thiosulfate. PMID:25170905

  2. Prediction and Biochemical Demonstration of a Catabolic Pathway for the Osmoprotectant Proline Betaine

    PubMed Central

    Kumar, Ritesh; Zhao, Suwen; Vetting, Matthew W.; Wood, B. McKay; Sakai, Ayano; Cho, Kyuil; Solbiati, José; Almo, Steven C.; Sweedler, Jonathan V.; Jacobson, Matthew P.; Gerlt, John A.; Cronan, John E.

    2014-01-01

    ABSTRACT Through the use of genetic, enzymatic, metabolomic, and structural analyses, we have discovered the catabolic pathway for proline betaine, an osmoprotectant, in Paracoccus denitrificans and Rhodobacter sphaeroides. Genetic and enzymatic analyses showed that several of the key enzymes of the hydroxyproline betaine degradation pathway also function in proline betaine degradation. Metabolomic analyses detected each of the metabolic intermediates of the pathway. The proline betaine catabolic pathway was repressed by osmotic stress and cold stress, and a regulatory transcription factor was identified. We also report crystal structure complexes of the P. denitrificans HpbD hydroxyproline betaine epimerase/proline betaine racemase with l-proline betaine and cis-hydroxyproline betaine. PMID:24520058

  3. Sulfide and ammonium oxidation, acetate mineralization by denitrification in a multipurpose UASB reactor.

    PubMed

    Beristain-Cardoso, Ricardo; Gómez, Jorge; Méndez-Pampín, Ramón

    2011-02-01

    The physiological and kinetic behavior of a denitrifying granular sludge exposed to different sulfide loading rates (55-295 mg/L d) were evaluated in a UASB reactor fed with acetate, ammonium and nitrate. At any sulfide loading rates, the consumption efficiencies of sulfide, acetate and ammonium were above 95%, while nitrate consumption efficiencies were around 62-72%. At the highest sulfide loading rate the ammonium was used as electron donor for N(2) production. The increase of sulfide loading rate also affected the fate of sulfide oxidation, since elemental sulfur was the main end product instead of sulfate. However, the lithotrophic denitrifying kinetic was not affected. FISH oligonucleotide probes for Thiobacillus denitrificans, Thiomiscropira denitrificans, genus Paracoccus and Pseudomonas spp. were used to follow the microbial ecology. The results of this work have shown that four pollutants could simultaneously be removed, namely, sulfide, ammonium, acetate and nitrate under well defined denitrifying conditions. Copyright © 2010 Elsevier Ltd. All rights reserved.

  4. A preliminary cost analysis of the biotreatment of refinery spent-sulfidic caustic.

    PubMed

    Sublette, K L

    1997-01-01

    Caustics are used in petroleum refining to remove hydrogen sulfide from various hydrocarbon streams. Spent-sulfidic caustics from three refineries have been successfully biotreated on the bench and pilot scale, resulting in neutralization and removal of active Sulfides. Sulfides were completely oxidized to sulfate by Thiobacillus denitrificans strain F. Microbial oxidation of sulfide produced acid, which at least partially neutralized the caustic. A commercial-scale treatment system has been designed that features a bioreactor with a suspended culture of flocculated T. denitrificans, a settler and acid and nutrient storage and delivery systems. A cost analysis has been performed for nine cases representing a range of spent caustic sulfide and hydroxide concentrations at a base treatment rate of 10 gpm. This analysis shows that refinery spent-sulfidic caustic can be biotreated for 4-8.3 cent/gal.

  5. Oxidation/Biodegradation of Solid Propellants Used in Legacy Chemical Rounds

    DTIC Science & Technology

    2007-08-01

    Bioreactor Sample Source Sample Number Similarity Index Genus Species ICB M28-1 Sample 1A 0.771 Kluyvera cryocrescenes 0.704 Enterobacter cloacae...0.678 Photorhabdus luminencent 0.676 Entrobacter aerogenes Sample 1B 0.901 Alcaligenes faecalis Sample 2 0.894 Pseudomonas stutzeri 0.807 Pseudomonas...et. al. 13 has also described the role of Enterobacter cloacae NADH in the degradation of nitro aromatic compounds. Paracoccus denitrificans, commonly

  6. Electron transfer flavoprotein domain II orientation monitored using double electron-electron resonance between an enzymatically reduced, native FAD cofactor, and spin labels.

    PubMed

    Swanson, Michael A; Kathirvelu, Velavan; Majtan, Tomas; Frerman, Frank E; Eaton, Gareth R; Eaton, Sandra S

    2011-03-01

    Human electron transfer flavoprotein (ETF) is a soluble mitochondrial heterodimeric flavoprotein that links fatty acid β-oxidation to the main respiratory chain. The crystal structure of human ETF bound to medium chain acyl-CoA dehydrogenase indicates that the flavin adenine dinucleotide (FAD) domain (αII) is mobile, which permits more rapid electron transfer with donors and acceptors by providing closer access to the flavin and allows ETF to accept electrons from at least 10 different flavoprotein dehydrogenases. Sequence homology is high and low-angle X-ray scattering is identical for Paracoccus denitrificans (P. denitrificans) and human ETF. To characterize the orientations of the αII domain of P. denitrificans ETF, distances between enzymatically reduced FAD and spin labels in the three structural domains were measured by double electron-electron resonance (DEER) at X- and Q-bands. An FAD to spin label distance of 2.8 ± 0.15 nm for the label in the FAD-containing αII domain (A210C) agreed with estimates from the crystal structure (3.0 nm), molecular dynamics simulations (2.7 nm), and rotamer library analysis (2.8 nm). Distances between the reduced FAD and labels in αI (A43C) were between 4.0 and 4.5 ± 0.35 nm and for βIII (A111C) the distance was 4.3 ± 0.15 nm. These values were intermediate between estimates from the crystal structure of P. denitrificans ETF and a homology model based on substrate-bound human ETF. These distances suggest that the αII domain adopts orientations in solution that are intermediate between those which are observed in the crystal structures of free ETF (closed) and ETF bound to a dehydrogenase (open). Copyright © 2011 The Protein Society.

  7. Electron transfer flavoprotein domain II orientation monitored using double electron-electron resonance between an enzymatically reduced, native FAD cofactor, and spin labels

    PubMed Central

    Swanson, Michael A; Kathirvelu, Velavan; Majtan, Tomas; Frerman, Frank E; Eaton, Gareth R; Eaton, Sandra S

    2011-01-01

    Human electron transfer flavoprotein (ETF) is a soluble mitochondrial heterodimeric flavoprotein that links fatty acid β-oxidation to the main respiratory chain. The crystal structure of human ETF bound to medium chain acyl-CoA dehydrogenase indicates that the flavin adenine dinucleotide (FAD) domain (αII) is mobile, which permits more rapid electron transfer with donors and acceptors by providing closer access to the flavin and allows ETF to accept electrons from at least 10 different flavoprotein dehydrogenases. Sequence homology is high and low-angle X-ray scattering is identical for Paracoccus denitrificans (P. denitrificans) and human ETF. To characterize the orientations of the αII domain of P. denitrificans ETF, distances between enzymatically reduced FAD and spin labels in the three structural domains were measured by double electron-electron resonance (DEER) at X- and Q-bands. An FAD to spin label distance of 2.8 ± 0.15 nm for the label in the FAD-containing αII domain (A210C) agreed with estimates from the crystal structure (3.0 nm), molecular dynamics simulations (2.7 nm), and rotamer library analysis (2.8 nm). Distances between the reduced FAD and labels in αI (A43C) were between 4.0 and 4.5 ± 0.35 nm and for βIII (A111C) the distance was 4.3 ± 0.15 nm. These values were intermediate between estimates from the crystal structure of P. denitrificans ETF and a homology model based on substrate-bound human ETF. These distances suggest that the αII domain adopts orientations in solution that are intermediate between those which are observed in the crystal structures of free ETF (closed) and ETF bound to a dehydrogenase (open). PMID:21308847

  8. Phylogenetic origins of the plant mitochondrion based on a comparative analysis of 5S ribosomal RNA sequences

    NASA Technical Reports Server (NTRS)

    Villanueva, E.; Delihas, N.; Luehrsen, K. R.; Fox, G. E.; Gibson, J.

    1985-01-01

    The complete nucleotide sequences of 5S ribosomal RNAs from Rhodocyclus gelatinosa, Rhodobacter sphaeroides, and Pseudomonas cepacia were determined. Comparisons of these 5S RNA sequences show that rather than being phylogenetically related to one another, the two photosynthetic bacterial 5S RNAs share more sequence and signature homology with the RNAs of two nonphotosynthetic strains. Rhodobacter sphaeroides is specifically related to Paracoccus denitrificans and Rc. gelatinosa is related to Ps. cepacia. These results support earlier 16S ribosomal RNA studies and add two important groups to the 5S RNA data base. Unique 5S RNA structural features previously found in P. denitrificans are present also in the 5S RNA of Rb. sphaeroides; these provide the basis for subdivisional signatures. The immediate consequence of obtaining these new sequences is that it is possible to clarify the phylogenetic origins of the plant mitochondrion. In particular, a close phylogenetic relationship is found between the plant mitochondria and members of the alpha subdivision of the purple photosynthetic bacteria, namely, Rb. sphaeroides, P. denitrificans, and Rhodospirillum rubrum.

  9. Enhanced fatty acid production in engineered chemolithoautotrophic bacteria using reduced sulfur compounds as energy sources

    DOE PAGES

    Beller, Harry R.; Zhou, Peng; Jewell, Talia N. M.; ...

    2016-07-05

    Chemolithoautotrophic bacteria that oxidize reduced sulfur compounds, such as H 2 S, while fixing CO 2 are an untapped source of renewable bioproducts from sulfide-laden waste, such as municipal wastewater. In this study, we report engineering of the chemolithoautotrophic bacterium Thiobacillus denitrificans to produce up to 52-fold more fatty acids than the wild-type strain when grown with thiosulfate and CO 2 . A modified thioesterase gene from E. coli ('tesA) was integrated into the T. denitrificans chromosome under the control of P kan or one of two native T. denitrificans promoters. The relative strength of the two native promoters asmore » assessed by fatty acid production in engineered strains was very similar to that assessed by expression of the cognate genes in the wild-type strain. This proof-of-principle study suggests that engineering sulfide-oxidizing chemolithoautotrophic bacteria to overproduce fatty acid-derived products merits consideration as a technology that could simultaneously produce renewable fuels/chemicals as well as cost-effectively remediate sulfide-contaminated wastewater.« less

  10. DEER distance measurement between a spin label and a native FAD semiquinone in electron transfer flavoprotein.

    PubMed

    Swanson, Michael A; Kathirvelu, Velavan; Majtan, Tomas; Frerman, Frank E; Eaton, Gareth R; Eaton, Sandra S

    2009-11-11

    The human mitochondrial electron transfer flavoprotein (ETF) accepts electrons from at least 10 different flavoprotein dehydrogenases and transfers electrons to a single electron acceptor in the inner membrane. Paracoccus denitrificans ETF has the identical function, shares the same three-dimensional structure and functional domains, and exhibits the same conformational mobility. It has been proposed that the mobility of the alphaII domain permits the promiscuous behavior of ETF with respect to a variety of redox partners. Double electron-electron resonance (DEER) measurements between a spin label and an enzymatically reduced flavin adenine dinucleotide (FAD) cofactor in P. denitrificans ETF gave two distributions of distances: a major component centered at 4.2 +/- 0.1 nm and a minor component centered at 5.1 +/- 0.2 nm. Both components had widths of approximately 0.3 nm. A distance of 4.1 nm was calculated using the crystal structure of P. denitrificans ETF, which agrees with the major component obtained from the DEER measurement. The observation of a second distribution suggests that ETF, in the absence of substrate, adopts some conformations that are intermediate between the predominant free and substrate-bound states.

  11. DEER Distance Measurement Between a Spin Label and a Native FAD Semiquinone in Electron Transfer Flavoprotein

    PubMed Central

    Swanson, Michael A.; Kathirvelu, Velavan; Majtan, Tomas; Frerman, Frank E.; Eaton, Gareth R.; Eaton, Sandra S.

    2009-01-01

    The human mitochondrial electron transfer flavoprotein (ETF) accepts electrons from at least 10 different flavoprotein dehydrogenases and transfers electrons to a single electron acceptor in the inner membrane. Paracoccus denitrificans ETF has the identical function, shares the same three dimensional structure and functional domains, and exhibits the same conformational mobility. It has been proposed that the mobility of the αII domain permits the promiscuous behavior of ETF with respect to a variety of redox partners. Double electron-electron resonance (DEER) measurements between a spin label and an enzymatically reduced flavin adenine dinucleotide (FAD) cofactor in P. denitrificans ETF gave two distributions of distances: a major component centered at 4.2 ± 0.1 nm and a minor component centered at 5.1 ± 0.2 nm. Both components had widths of approximately 0.3 nm. A distance of 4.1 nm was calculated using the crystal structure of P. denitrificans ETF, which agrees with the major component obtained from the DEER measurement. The observation of a second distribution suggests that ETF, in the absence of substrate, adopts some conformations that are intermediate between the predominant free and substrate-bound states. PMID:19886689

  12. EVELOPMENT OF AN ENVIRONMENTALLY BENIGN MICROBIAL INHIBITOR TO CONTROL INTERNAL PIPELINE CORROSION

    SciT

    Bill W. Bogan; Wendy R. Sullivan; Kristine M. H. Cruz

    2004-04-30

    The overall program objective is to develop and evaluate environmentally benign agents or products that are effective in the prevention, inhibition, and mitigation of microbially influenced corrosion (MIC) in the internal surfaces of metallic natural gas pipelines. The goal is to develop one or more environmentally benign (a.k.a. ''green'') products that can be applied to maintain the structure and dependability of the natural gas infrastructure. Previous testing of pepper extracts resulted in preliminary data indicating that some pepper extracts inhibit the growth of some corrosion-associated microorganisms. This quarter additional tests were performed to more specifically investigate the ability of threemore » pepper extracts to inhibit the growth, and to influence the metal corrosion caused by two microbial species: Desulfovibrio vulgaris, and Comomonas denitrificans. All three pepper extracts rapidly killed Desulfovibrio vulgaris, but did not appear to inhibit Comomonas denitrificans. While corrosion rates were at control levels in experiments with Desulfovibrio vulgaris that received pepper extract, corrosion rates were increased in the presence of Comomonas denitrificans plus pepper extract. Further testing with a wider range of pure bacterial cultures, and more importantly, with mixed bacterial cultures should be performed to determine the potential effectiveness of pepper extracts to inhibit MIC.« less

  13. SciT

    Sublette, K.L.

    With the continual increase in the utilization of high sulfur and high nitrogen containing fossil fuels, the release of airborne pollutants into the environment has become a critical problem. The fuel sulfur is converted to SO{sub 2} during combustion. Fuel nitrogen and a fraction of the nitrogen from the combustion air are converted to nitric oxide and nitrogen dioxide, NO{sub x}. For the past five years Combustion Engineering (now Asea Brown Boveri or ABB) and, since 1986, the University of Tulsa (TU) have been investigating the oxidation of H{sub 2}S by the facultatively anaerobic and autotrophic bacterium Thiobacillus denitrificans andmore » have developed a process, concept for the microbial removal of H{sub 2}S from a gas stream the simultaneous removal of SO{sub 2} and NO by D. desulfuricans and T. denitrificans co-cultures and cultures-in-series was demonstrated. These systems could not be sustained due to NO inhibition of D. desulfuricans. However, a preliminary economic analysis has shown that microbial reduction of SO{sub 2} to H{sub 2}S with subsequent conversion to elemental sulfur by the Claus process is both technically and economically feasible if a less expensive carbon and/or energy source can be found. It has also been demonstrated that T. denitrificans can be grown anaerobically on NO(g) as a terminal electron acceptor with reduction to elemental nitrogen. Microbial reduction of NO{sub x} is a viable process concept for the disposal of concentrated streams of NO{sub x} as may be produced by certain regenerable processes for the removal of SO{sub 2} and NO{sub x} from flue gas.« less

  14. Independent Research Program Annual Report FY88

    DTIC Science & Technology

    1989-04-01

    thermal degradation of the sample with some separation of pyrolysates (Figure 4 ). It The run-to-run reproducibility of the method was anticipated that the... DEGRADATION BY Alcaligenes denrif(icans T-I S-.- 4 -,.- T.2 260 S60 0 0 tO is 20 20 TIME (DAYS) 0 4 ,.FIGURE 5. REDUCTION OF CR IN SAM MEDIA OVER A 23 DAY...CA FIGURE 4 . EXAMPLE Or A CHPOMAIOGRAM FIGURE 7. REDUCTION OF THE TOXICITY Ofý P DEMONSTRATING THE DEGRADATION OF CR CR SOLUTION BY A. DENITRIFICANS

  15. Achromobacter species endocarditis: A case report and literature review

    PubMed Central

    Derber, Catherine; Elam, Kara; Forbes, Betty A; Bearman, Gonzalo

    2011-01-01

    Endocarditis due to Achromobacter species is a rare, yet serious, endovascular infection. Achromobacter species infective endocarditis is associated with underlying immunodeficiencies or prosthetic heart valves and devices. A case of prosthetic pulmonary valve endocarditis secondary to Achromobacter xylosoxidans subspecies denitrificans is described in the present report. This life-threatening infection was successfully treated with combined valve replacement and prolonged antibiotic therapy. A Medline/PubMed literature review of Achromobacter endocarditis was also performed. Achromobacter species are an uncommon, yet important, cause of nosocomial endocarditis. Given the significant associated morbidity and mortality, along with a high degree of intrinsic antibiotic resistance, Achromobacter species infective endocarditis remains a clinical treatment challenge. PMID:22942890

  16. Nitrous Oxide Abatement Coupled with Biopolymer Production As a Model GHG Biorefinery for Cost-Effective Climate Change Mitigation.

    PubMed

    Frutos, Osvaldo D; Cortes, Irene; Cantera, Sara; Arnaiz, Esther; Lebrero, Raquel; Muñoz, Raúl

    2017-06-06

    N 2 O represents ∼6% of the global greenhouse gas emission inventory and the most important O 3 -depleting substance emitted in this 21st century. Despite its environmental relevance, little attention has been given to cost-effective and environmentally friendly N 2 O abatement methods. Here we examined, the potential of a bubble column (BCR) and an internal loop airlift (ALR) bioreactors of 2.3 L for the abatement of N 2 O from a nitric acid plant emission. The process was based on the biological reduction of N 2 O by Paracoccus denitrificans using methanol as a carbon/electron source. Two nitrogen limiting strategies were also tested for the coproduction of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) coupled with N 2 O reduction. High N 2 O removal efficiencies (REs) (≈87%) together with a low PHBV cell accumulation were observed in both bioreactors in excess of nitrogen. However, PHBV contents of 38-64% were recorded under N limiting conditions along with N 2 O-REs of ≈57% and ≈84% in the ALR and BCR, respectively. Fluorescence in situ hybridization analyses showed that P. denitrificans was dominant (>50%) after 6 months of experimentation. The successful abatement of N 2 O concomitant with PHBV accumulation confirmed the potential of integrating biorefinery concepts into biological gas treatment for a cost-effective GHG mitigation.

  17. Structure of nitrogen-converting communities induced by hydraulic retention time and COD/N ratio in constantly aerated granular sludge reactors treating digester supernatant.

    PubMed

    Cydzik-Kwiatkowska, Agnieszka; Rusanowska, Paulina; Zielińska, Magdalena; Bernat, Katarzyna; Wojnowska-Baryła, Irena

    2014-02-01

    This study investigated how hydraulic retention time (HRT) and COD/N ratio affect nitrogen-converting consortia in constantly aerated granules treating high-ammonium digester supernatant. Three HRTs (10, 13, 19 h) were tested at COD/N ratios of 4.5 and 2.3. Denaturing gradient gel electrophoresis and relative real-time PCR were used to characterize the microbial communities. When changes in HRT and COD/N increased nitrogen loading, the ratio of the relative abundance of aerobic to anaerobic ammonium-oxidizers decreased. The COD/N ratio determined the species composition of the denitrifiers; however, Thiobacillus denitrificans, Pseudomonas denitrificans and Azoarcus sp. showed a high tolerance to the environmental conditions and occurred in the granules from all reactors. Denitrifier genera that support granule formation were identified, such as Pseudomonas, Shinella, and Flavobacterium. In aerated granules, nirK-possessing bacteria were more diverse than nirS-possessing bacteria. At a low COD/N ratio, N2O-reducer diversity increased because of the presence of bacteria known as aerobic denitrifiers. Copyright © 2013 Elsevier Ltd. All rights reserved.

  18. Substrate binding site for nitrate reductase of Escherichia coli is on the inner aspect of the membrane.

    PubMed Central

    Kristjansson, J K; Hollocher, T C

    1979-01-01

    Escherichia coli grown anaerobically on nitrate exhibited the same transport barrier to reduction of chlorate, relative to nitrate, as that exhibited by Paracoccus denitrificans. This establishes that the nitrate binding site of nitrate reductase (EC 1.7.99.4) in E. coli must also lie on the cell side of the nitrate transporter which is associated with the plasma membrane. Because nitrate reductase is membrane bound, the nitrate binding site is thus located on the inner aspect of the membrane. Nitrate pulse studies on E. coli in the absence of valinomycin showed a small transient alkalinization (leads to H+/NO3- congruent to --0.07) which did not occur with oxygen pulses. By analogy with P. denitrificans, the alkaline transient is interpreted to arise from proton-linked nitrate uptake which is closely followed by nitrite efflux. The result is consistent with internal reduction of nitrate, whereas external reduction would be expected to give leads to H+/NO3-ratios approaching --2. PMID:374343

  19. Integrated multi-omics analyses reveal the biochemical mechanisms and phylogenetic relevance of anaerobic androgen biodegradation in the environment

    PubMed Central

    Yang, Fu-Chun; Chen, Yi-Lung; Tang, Sen-Lin; Yu, Chang-Ping; Wang, Po-Hsiang; Ismail, Wael; Wang, Chia-Hsiang; Ding, Jiun-Yan; Yang, Cheng-Yu; Yang, Chia-Ying; Chiang, Yin-Ru

    2016-01-01

    Steroid hormones, such as androgens, are common surface-water contaminants. However, literature on the ecophysiological relevance of steroid-degrading organisms in the environment, particularly in anoxic ecosystems, is extremely limited. We previously reported that Steroidobacter denitrificans anaerobically degrades androgens through the 2,3-seco pathway. In this study, the genome of Sdo. denitrificans was completely sequenced. Transcriptomic data revealed gene clusters that were distinctly expressed during anaerobic growth on testosterone. We isolated and characterized the bifunctional 1-testosterone hydratase/dehydrogenase, which is essential for anaerobic degradation of steroid A-ring. Because of apparent substrate preference of this molybdoenzyme, corresponding genes, along with the signature metabolites of the 2,3-seco pathway, were used as biomarkers to investigate androgen biodegradation in the largest sewage treatment plant in Taipei, Taiwan. Androgen metabolite analysis indicated that denitrifying bacteria in anoxic sewage use the 2,3-seco pathway to degrade androgens. Metagenomic analysis and PCR-based functional assays showed androgen degradation in anoxic sewage by Thauera spp. through the action of 1-testosterone hydratase/dehydrogenase. Our integrative ‘omics' approach can be used for culture-independent investigations of the microbial degradation of structurally complex compounds where isotope-labeled substrates are not easily available. PMID:26872041

  20. Biodegradation of Para Amino Acetanilide by Halomonas sp. TBZ3.

    PubMed

    Hajizadeh, Nader; Sefidi Heris, Youssof; Zununi Vahed, Sepideh; Vallipour, Javad; Hejazi, Mohammad Amin; Golabi, Sayyed Mahdi; Asadpour-Zeynali, Karim; Hejazi, Mohammad Saeid

    2015-09-01

    Aromatic compounds are known as a group of highly persistent environmental pollutants. Halomonas sp. TBZ3 was isolated from the highly salty Urmia Lake of Iran. In this study, characterization of a new Halomonas isolate called Halomonas sp. TBZ3 and its employment for biodegradation of para-amino acetanilide (PAA), as an aromatic environmental pollutant, is described. This study aimed to characterize the TBZ3 isolate and to elucidate its ability as a biodegradative agent that decomposes PAA. Primarily, DNA-DNA hybridization between TBZ3, Halomonas denitrificans DSM18045T and Halomonas saccharevitans LMG 23976T was carried out. Para-amino acetanilide biodegradation was assessed using spectrophotometry and confirmed by gas chromatography-mass spectroscopy (GC-MS). Parameters effective on biodegradation of PAA were optimized by the Response Surface Methodology (RSM). The DNA-DNA hybridization experiments between isolate TBZ3, H. denitrificans and H. saccharevitans revealed relatedness levels of 57% and 65%, respectively. According to GC-MS results, TBZ3 degrades PAA to benzene, hexyl butanoate, 3-methyl-1-heptanol and hexyl hexanoate. Temperature 32.92°C, pH 6.76, and salinity 14% are the optimum conditions for biodegradation with a confidence level of 95% (at level α = 0.05). According to our results, Halomonas sp. TBZ3 could be considered as a biological agent for bioremediation of PAA and possibly other similar aromatic compounds.

  1. Biodegradation of Para Amino Acetanilide by Halomonas sp. TBZ3

    PubMed Central

    Hajizadeh, Nader; Sefidi Heris, Youssof; Zununi Vahed, Sepideh; Vallipour, Javad; Hejazi, Mohammad Amin; Golabi, Sayyed Mahdi; Asadpour-Zeynali, Karim; Hejazi, Mohammad Saeid

    2015-01-01

    Background: Aromatic compounds are known as a group of highly persistent environmental pollutants. Halomonas sp. TBZ3 was isolated from the highly salty Urmia Lake of Iran. In this study, characterization of a new Halomonas isolate called Halomonas sp. TBZ3 and its employment for biodegradation of para-amino acetanilide (PAA), as an aromatic environmental pollutant, is described. Objectives: This study aimed to characterize the TBZ3 isolate and to elucidate its ability as a biodegradative agent that decomposes PAA. Materials and Methods: Primarily, DNA-DNA hybridization between TBZ3, Halomonas denitrificans DSM18045T and Halomonas saccharevitans LMG 23976T was carried out. Para-amino acetanilide biodegradation was assessed using spectrophotometry and confirmed by gas chromatography-mass spectroscopy (GC-MS). Parameters effective on biodegradation of PAA were optimized by the Response Surface Methodology (RSM). Results: The DNA-DNA hybridization experiments between isolate TBZ3, H. denitrificans and H. saccharevitans revealed relatedness levels of 57% and 65%, respectively. According to GC-MS results, TBZ3 degrades PAA to benzene, hexyl butanoate, 3-methyl-1-heptanol and hexyl hexanoate. Temperature 32.92°C, pH 6.76, and salinity 14% are the optimum conditions for biodegradation with a confidence level of 95% (at level α = 0.05). Conclusions: According to our results, Halomonas sp. TBZ3 could be considered as a biological agent for bioremediation of PAA and possibly other similar aromatic compounds. PMID:26495103

  2. Characteristics of nitrogen removal and microbial distribution by application of spent sulfidic caustic in pilot scale wastewater treatment plant.

    PubMed

    Park, S; Lee, J; Park, J; Byun, I; Park, T; Lee, T

    2010-01-01

    Since spent sulfidic caustic (SSC) produced from petrochemical industry contains a high concentration of alkalinity and sulfide, it was expected that SSC could be used as an electron donor for autotrophic denitrification. To investigate the nitrogen removal performance, a pilot scale Bardenpho process was operated. The total nitrogen removal efficiency increased as SSC dosage increased, and the highest efficiency was observed as 77.5% when SSC was injected into both anoxic tank (1) and (2). FISH analysis was also performed to shed light on the effect of SSC dosage on the distribution ratio of nitrifying bacteria and Thiobacillus denitrificans. FISH results indicated that the relative distribution ratio of ammonia-oxidizing bacteria, Nitrobacter spp., Nitrospira genus and Thiobacillus denitrificans to eubacteria varied little with the pH of the tanks, and SSC injection did not give harmful effect on nitrification efficiency. These results show that SSC can be applied as an electron donor of autotrophic denitrification to biological nitrogen removal process effectively, without any inhibitory effects to nitrifying bacteria and sulfur-utilizing denitrifying bacteria.

  3. Inhibition of existing denitrification enzyme activity by chloramphenicol

    Brooks, M.H.; Smith, R.L.; Macalady, D.L.

    1992-01-01

    Chloramphenicol completely inhibited the activity of existing denitrification enzymes in acetylene-block incubations with (i) sediments from a nitrate-contaminated aquifer and (ii) a continuous culture of denitrifying groundwater bacteria. Control flasks with no antibiotic produced significant amounts of nitrous oxide in the same time period. Amendment with chloramphenicol after nitrous oxide production had begun resulted in a significant decrease in the rate of nitrous oxide production. Chloramphenicol also decreased (>50%) the activity of existing denitrification enzymes in pure cultures of Pseudomonas denitrificans that were harvested during log- phase growth and maintained for 2 weeks in a starvation medium lacking electron donor. Short-term time courses of nitrate consumption and nitrous oxide production in the presence of acetylene with P. denitrificans undergoing carbon starvation were performed under optimal conditions designed to mimic denitrification enzyme activity assays used with soils. Time courses were linear for both chloramphenicol and control flasks, and rate estimates for the two treatments were significantly different at the 95% confidence level. Complete or partial inhibition of existing enzyme activity is not consistent with the current understanding of the mode of action of chloramphenicol or current practice, in which the compound is frequently employed to inhibit de novo protein synthesis during the course of microbial activity assays. The results of this study demonstrate that chloramphenicol amendment can inhibit the activity of existing denitrification enzymes and suggest that caution is needed in the design and interpretation of denitrification activity assays in which chloramphenicol is used to prevent new protein synthesis.

  4. Alternative Fuels Data Center: Nevada Transportation Data for Alternative

    . Gasoline Diesel Natural Gas Electricity Transportation Fuel Consumption Source: State Energy Data System Renewable Power Plant Capacity (nameplate, MW) 1,684 Source: BioFuels Atlas from the National Renewable Source: Average prices per gasoline gallon equivalent (GGE) for the West Coast PADD from the Alternative

  5. Alternative Fuels Data Center: Rhode Island Transportation Data for

    (million cubic feet) 94,453 Conventional Power Plants 10 Generating Capacity (nameplate, MW) 1,991 Oil Refineries 0 Oil Refinery Capacity (bbl/day) 0 Renewable Power Plants 2 Renewable Power Plant Capacity More Rhode Island Videos on YouTube Video thumbnail for Cooking Oil Powers Biodiesel Vehicles in Rhode

  6. Neutron and Atomic Resolution X-ray Structures of a Lytic Polysaccharide Monooxygenase Reveal Copper-Mediated Dioxygen Binding and Evidence for N-Terminal Deprotonation

    SciT

    Bacik, John-Paul; Mekasha, Sophanit; Forsberg, Zarah

    A 1.1 Å resolution, room-temperature X-ray structure and a 2.1 Å resolution neutron structure of a chitin-degrading lytic polysaccharide monooxygenase domain from the bacterium Jonesia denitrificans (JdLPMO10A) show a putative dioxygen species equatorially bound to the active site copper. We found that both structures show an elongated density for the dioxygen, most consistent with a Cu(II)-bound peroxide. The coordination environment is consistent with Cu(II). Furthermore, in the neutron and X-ray structures, difference maps reveal the N-terminal amino group, involved in copper coordination, is present as a mixed ND 2 and ND –, suggesting a role for the copper ion inmore » shifting the pK a of the amino terminus.« less

  7. Electricity from methane by reversing methanogenesis

    NASA Astrophysics Data System (ADS)

    McAnulty, Michael J.; G. Poosarla, Venkata; Kim, Kyoung-Yeol; Jasso-Chávez, Ricardo; Logan, Bruce E.; Wood, Thomas K.

    2017-05-01

    Given our vast methane reserves and the difficulty in transporting methane without substantial leaks, the conversion of methane directly into electricity would be beneficial. Microbial fuel cells harness electrical power from a wide variety of substrates through biological means; however, the greenhouse gas methane has not been used with much success previously as a substrate in microbial fuel cells to generate electrical current. Here we construct a synthetic consortium consisting of: (i) an engineered archaeal strain to produce methyl-coenzyme M reductase from unculturable anaerobic methanotrophs for capturing methane and secreting acetate; (ii) micro-organisms from methane-acclimated sludge (including Paracoccus denitrificans) to facilitate electron transfer by providing electron shuttles (confirmed by replacing the sludge with humic acids), and (iii) Geobacter sulfurreducens to produce electrons from acetate, to create a microbial fuel cell that converts methane directly into significant electrical current. Notably, this methane microbial fuel cell operates at high Coulombic efficiency.

  8. Electricity from methane by reversing methanogenesis

    PubMed Central

    McAnulty, Michael J.; G. Poosarla, Venkata; Kim, Kyoung-Yeol; Jasso-Chávez, Ricardo; Logan, Bruce E.; Wood, Thomas K.

    2017-01-01

    Given our vast methane reserves and the difficulty in transporting methane without substantial leaks, the conversion of methane directly into electricity would be beneficial. Microbial fuel cells harness electrical power from a wide variety of substrates through biological means; however, the greenhouse gas methane has not been used with much success previously as a substrate in microbial fuel cells to generate electrical current. Here we construct a synthetic consortium consisting of: (i) an engineered archaeal strain to produce methyl-coenzyme M reductase from unculturable anaerobic methanotrophs for capturing methane and secreting acetate; (ii) micro-organisms from methane-acclimated sludge (including Paracoccus denitrificans) to facilitate electron transfer by providing electron shuttles (confirmed by replacing the sludge with humic acids), and (iii) Geobacter sulfurreducens to produce electrons from acetate, to create a microbial fuel cell that converts methane directly into significant electrical current. Notably, this methane microbial fuel cell operates at high Coulombic efficiency. PMID:28513579

  9. Structure-based analysis of CysZ-mediated cellular uptake of sulfate

    PubMed Central

    Assur Sanghai, Zahra; Liu, Qun; Clarke, Oliver B; Belcher-Dufrisne, Meagan; Wiriyasermkul, Pattama; Giese, M Hunter; Leal-Pinto, Edgar; Kloss, Brian; Tabuso, Shantelle; Love, James; Punta, Marco; Banerjee, Surajit; Rajashankar, Kanagalaghatta R; Rost, Burkhard; Logothetis, Diomedes; Quick, Matthias; Hendrickson, Wayne A

    2018-01-01

    Sulfur, most abundantly found in the environment as sulfate (SO42-), is an essential element in metabolites required by all living cells, including amino acids, co-factors and vitamins. However, current understanding of the cellular delivery of SO42- at the molecular level is limited. CysZ has been described as a SO42- permease, but its sequence family is without known structural precedent. Based on crystallographic structure information, SO42- binding and flux experiments, we provide insight into the molecular mechanism of CysZ-mediated translocation of SO42- across membranes. CysZ structures from three different bacterial species display a hitherto unknown fold and have subunits organized with inverted transmembrane topology. CysZ from Pseudomonas denitrificans assembles as a trimer of antiparallel dimers and the CysZ structures from two other species recapitulate dimers from this assembly. Mutational studies highlight the functional relevance of conserved CysZ residues. PMID:29792261

  10. Low-temperature kinetic measurements of microsecond freeze-hyperquench (MHQ) cytochrome oxidase monitored by UV-visible spectroscopy with a newly designed cuvette.

    PubMed

    Wiertz, F G M; de Vries, S

    2006-02-01

    A special cuvette was designed to measure optical changes of MHQ (microsecond freeze-hyperquench) powder samples at temperatures below approx. 250 K. Reduced cytochrome c oxidase from Paracoccus denitrificans was reacted with O(2) for 100 micros, frozen as a powder and transferred to the cuvette. Subsequently, cytochrome oxidase was allowed to react further following stepwise increments of the temperature from 100 K up to 250 K while recording spectra between 300 and 700 nm. The temperature was raised only when no further changes in the spectra could be detected. The experiment yielded spectra of the A, P(M), F and O intermediate states. This demonstrated that the catalytic cycle of cytochrome oxidase at low temperature is similar to that at room temperature and so verifies the suitability of this method for the study of enzymes with high catalytic-centre activity.

  11. Final Report: Molecular mechanisms and kinetics of microbial anaerobic nitrate-dependent U(IV) and Fe(II) oxidation

    SciT

    O'Day, Peggy A.; Asta, Maria P.; Kanematsu, Masakazu

    2015-02-27

    In this project, we combined molecular genetic, spectroscopic, and microscopic techniques with kinetic and reactive transport studies to describe and quantify biotic and abiotic mechanisms underlying anaerobic, nitrate-dependent U(IV) and Fe(II) oxidation, which influences the long-term efficacy of in situ reductive immobilization of uranium at DOE sites. In these studies, Thiobacillus denitrificans, an autotrophic bacterium that catalyzes anaerobic U(IV) and Fe(II) oxidation, was used to examine coupled oxidation-reduction processes under either biotic (enzymatic) or abiotic conditions in batch and column experiments with biogenically produced UIVO2(s). Synthesis and quantitative analysis of coupled chemical and transport processes were done with the reactivemore » transport modeling code Crunchflow. Research focused on identifying the primary redox proteins that catalyze metal oxidation, environmental factors that influence protein expression, and molecular-scale geochemical factors that control the rates of biotic and abiotic oxidation.« less

  12. Presence of a new cytochrome b - like pigment with a peak at 567 nm in various aerobic bacteria.

    PubMed

    Jacobs, N J; O'Hara, J; Gray, C T

    1983-09-01

    Several physiological groups of bacteria were examined for the presence of a cytochrome b - like pigment which is demonstrable in dithionite-reduced minus substrate-reduced difference spectra. This pigment is characterized by an unusually high alpha band at 567 nm, a low concentration relative to conventional cytochromes, and an inability to be fully reduced by endogenous substrates or NADH. Previous studies with one denitrifying and nondenitrifying species of the genus Pseudomonas, in Paracoccus denitrificans, in Alcaligenes faecalis, in Azotobacter vinelandii, in Branhamella catarrhalis, and in Neisseria lactamicus. In all these organisms, the peak of the 567-nm pigment is accompanied by a peak of about equal height at approximately 559 nm, which exhibits similar properties to the 567-nm pigment. The 567-nm pigment was not demonstrable by this technique in Gluconobacter oxydans subspecies suboxydans, Bacillus subtilis, Bacillus licheniformis, Aeromonas hydrophilia, Escherichia coli, a Klebsiella species, Moraxella osloensis, Aquaspirillum itersonii, Micrococcus lysodeikticus, Micrococcus luteus, Agrobacterium tumefaciens, or Rhizobium meliloti.

  13. Sequence conservation from human to prokaryotes of Surf1, a protein involved in cytochrome c oxidase assembly, deficient in Leigh syndrome.

    PubMed

    Poyau, A; Buchet, K; Godinot, C

    1999-12-03

    The human SURF1 gene encoding a protein involved in cytochrome c oxidase (COX) assembly, is mutated in most patients presenting Leigh syndrome associated with COX deficiency. Proteins homologous to the human Surf1 have been identified in nine eukaryotes and six prokaryotes using database alignment tools, structure prediction and/or cDNA sequencing. Their sequence comparison revealed a remarkable Surf1 conservation during evolution and put forward at least four highly conserved domains that should be essential for Surf1 function. In Paracoccus denitrificans, the Surf1 homologue is found in the quinol oxidase operon, suggesting that Surf1 is associated with a primitive quinol oxidase which belongs to the same superfamily as cytochrome oxidase.

  14. Neutron and Atomic Resolution X-ray Structures of a Lytic Polysaccharide Monooxygenase Reveal Copper-Mediated Dioxygen Binding and Evidence for N-Terminal Deprotonation

    DOE PAGES

    Bacik, John-Paul; Mekasha, Sophanit; Forsberg, Zarah; ...

    2017-05-08

    A 1.1 Å resolution, room-temperature X-ray structure and a 2.1 Å resolution neutron structure of a chitin-degrading lytic polysaccharide monooxygenase domain from the bacterium Jonesia denitrificans (JdLPMO10A) show a putative dioxygen species equatorially bound to the active site copper. We found that both structures show an elongated density for the dioxygen, most consistent with a Cu(II)-bound peroxide. The coordination environment is consistent with Cu(II). Furthermore, in the neutron and X-ray structures, difference maps reveal the N-terminal amino group, involved in copper coordination, is present as a mixed ND 2 and ND –, suggesting a role for the copper ion inmore » shifting the pK a of the amino terminus.« less

  15. Microbial oxidation of mixtures of methylmercaptan and hydrogen sulfide.

    PubMed

    Subramaniyan, A; Kolhatkar, R; Sublette, K L; Beitle, R

    1998-01-01

    Refinery spent-sulfidic caustic, containing only inorganic sulfides, has previously been shown to be amenable to biotreatment with Thiobacillus denitrificans strain F with complete oxidation of sulfides to sulfate. However, many spent caustics contain mercaptans that cannot be metabolized by this strict autotroph. An aerobic enrichment culture was developed from mixed Thiobacilli and activated sludge that was capable of simultaneous oxidation of inorganic sulfide and mercaptans using hydrogen sulfide (H2S) and methylmercaptan (MeSH) gas feeds used to simulate the inorganic and organic sulfur of a spent-sulfidic caustic. The enrichment culture was also capable of biotreatment of an actual mercaptan-containing, spent-sulfidic caustic but at lower rates than predicted by operation on MeSH and H2S fed to the culture in the gas phase, indicating that the caustic contained other inhibitory components.

  16. A modified culture-based study of bacterial community composition in a tannery wastewater treatment plant.

    PubMed

    Desta, Adey F; Dalhammer, Gunnel; Kittuva, Gunatrana R

    2010-01-01

    Though culture-independent methods have been used in preference to traditional isolation techniques for characterization of microbial community of wastewater treatment plants, it is difficult to widely apply this approach in resource-poor countries. The present study aimed to develop a test to identify the culturable portion of bacterial community in a high-strength wastewater. Wastewater samples were collected from nitrification-denitrification and settling tanks of the treatment plant of Elmo Leather AB tannery located in Borås, Sweden. After cultivating on nutrient agar with the optimal dilution (10⁻²), phenotypic and biochemical identification of the bacteria were done with colony morphology, Gram reaction, growth on MacConkey, phenylethanol media, triple sugar Iron agar slants, catalase and oxidase tests. Biochemical grouping of the isolates was done based on their test results for MacConkey, phenylethanol media, triple sugar Iron agar and oxidase test reaction. From the biochemical groups, isolates were randomly selected for API test and 16SrRNA gene sequencing. The isolates from the denitrification, nitrification tank were identified to be Paracoccus denitrificans (67%), Azoarcus spp (3%) and Spingomonas wittichii (1%). From the settling tank, Paracoccus denitrificans (22%), Corynebacterium freneyi (20%) and Bacillus cereus (1%) were identified. The grouping based on biochemical test results as well as the identification based on sequencing has shown coherence except for discrepancies with the API test. The preliminary implications of the grouping based on culture-based characteristics and its potential application for resource-limited environmental microbial studies is discussed.

  17. GeoChip-based analysis of the microbial community functional structures in simultaneous desulfurization and denitrification process.

    PubMed

    Yu, Hao; Chen, Chuan; Ma, Jincai; Liu, Wenzong; Zhou, Jizhong; Lee, Duu-Jong; Ren, Nanqi; Wang, Aijie

    2014-07-01

    The elemental sulfur (S°) recovery was evaluated in the presence of nitrate in two development models of simultaneous desulfurization and denitrification (SDD) process. At the loading rates of 0.9 kg S/(m³·day) for sulfide and 0.4 kg N/(m³·day) for nitrate, S° conversion rate was 91.1% in denitrifying sulfide removal (DSR) model which was higher than in integrated simultaneous desulfurization and denitrification (ISDD) model (25.6%). A comprehensive analysis of functional diversity, structure and metabolic potential of microbial communities was examined in two models by using functional gene array (GeoChip 2.0). GeoChip data indicated that diversity indices, community structure, and abundance of functional genes were distinct between two models. Diversity indices (Simpson's diversity index (1/D) and Shannon-Weaver index (H')) of all detected genes showed that with elevated influent loading rate, the functional diversity decreased in ISDD model but increased in DSR model. In contrast to ISDD model, the overall abundance of dsr genes was lower in DSR model, while some functional genes targeting from nitrate-reducing sulfide-oxidizing bacteria (NR-SOB), such as Thiobacillus denitrificans, Sulfurimonas denitrificans, and Paracoccus pantotrophus were more abundant in DSR model which were highly associated with the change of S(0) conversion rate obtained in two models. The results obtained in this study provide additional insights into the microbial metabolic mechanisms involved in ISDD and DSR models, which in turn will improve the overall performance of SDD process. Copyright © 2014. Published by Elsevier B.V.

  18. Planktonic and biofilm-grown nitrogen-cycling bacteria exhibit different susceptibilities to copper nanoparticles.

    PubMed

    Reyes, Vincent C; Opot, Stephen O; Mahendra, Shaily

    2015-04-01

    Proper characterization of nanoparticle (NP) interactions with environmentally relevant bacteria under representative conditions is necessary to enable their sustainable manufacture, use, and disposal. Previous nanotoxicology research based on planktonic growth has not adequately explored biofilms, which serve as the predominant mode of bacterial growth in natural and engineered environments. Copper nanoparticle (Cu-NP) impacts on biofilms were compared with respective planktonic cultures of the ammonium-oxidizing Nitrosomonas europaea, nitrogen-fixing Azotobacter vinelandii, and denitrifying Paracoccus denitrificans using a suite of independent toxicity diagnostics. Median inhibitory concentration (IC50) values derived from adenosine triphosphate (ATP) for Cu-NPs were lower in N. europaea biofilms (19.6 ± 15.3 mg/L) than in planktonic cells (49.0 ± 8.0 mg/L). However, in absorbance-based growth assays, compared with unexposed controls, N. europaea growth rates in biofilms were twice as resilient to inhibition than those in planktonic cultures. Similarly, relative to unexposed controls, growth rates and yields of P. denitrificans in biofilms exposed to Cu-NPs were 40-fold to 50-fold less inhibited than those in planktonic cells. Physiological evaluation of ammonium oxidation and nitrate reduction suggested that biofilms were also less inhibited by Cu-NPs than planktonic cells. Furthermore, functional gene expression for ammonium oxidation (amoA) and nitrite reduction (nirK) showed lower inhibition by NPs in biofilms relative to planktonic-grown cells. These results suggest that biofilms mitigate NP impacts, and that nitrogen-cycling bacteria in wastewater, wetlands, and soils might be more resilient to NPs than planktonic-based assessments suggest. © 2014 SETAC.

  19. Formation of Polyhydroxyalkanoate in Aerobic Anoxygenic Phototrophic Bacteria and Its Relationship to Carbon Source and Light Availability▿

    PubMed Central

    Xiao, Na; Jiao, Nianzhi

    2011-01-01

    Aerobic anoxygenic phototrophic bacteria (AAPB) are unique players in carbon cycling in the ocean. Cellular carbon storage is an important mechanism regulating the nutrition status of AAPB but is not yet well understood. In this paper, six AAPB species (Dinoroseobacter sp. JL1447, Roseobacter denitrificans OCh 114, Roseobacter litoralis OCh 149, Dinoroseobacter shibae DFL 12T, Labrenzia alexandrii DFL 11T, and Erythrobacter longus DSMZ 6997) were examined, and all of them demonstrated the ability to form the carbon polymer polyhydroxyalkanoate (PHA) in the cell. The PHA in Dinoroseobacter sp. JL1447 was identified as poly-beta-hydroxybutyrate (PHB) according to evidence from Fourier transform infrared spectroscopy, differential scanning calorimetry, and 1H nuclear magnetic resonance spectroscopy examinations. Carbon sources turned out to be critical for PHA production in AAPB. Among the eight media tested with Dinoroseobacter sp. JL1447, sodium acetate, giving a PHA production rate of 72%, was the most productive carbon source, followed by glucose, with a 68% PHA production rate. Such PHA production rates are among the highest recorded for all bacteria. The C/N ratio of substrates was verified by the experiments as another key factor in PHA production. In the case of R. denitrificans OCh 114, PHA was not detected when the organism was cultured at C/N ratios of <2 but became apparent at C/N ratios of >3. Light is also important for the formation of PHA in AAPB. In the case of Dinoroseobacter sp. JL1447, up to a one-quarter increase in PHB production was observed when the culture underwent growth in a light-dark cycle compared to growth completely in the dark. PMID:21908634

  20. Potential Role of Nitrite for Abiotic Fe(II) Oxidation and Cell Encrustation during Nitrate Reduction by Denitrifying Bacteria

    PubMed Central

    Klueglein, Nicole; Zeitvogel, Fabian; Stierhof, York-Dieter; Floetenmeyer, Matthias; Konhauser, Kurt O.; Obst, Martin

    2014-01-01

    Microorganisms have been observed to oxidize Fe(II) at neutral pH under anoxic and microoxic conditions. While most of the mixotrophic nitrate-reducing Fe(II)-oxidizing bacteria become encrusted with Fe(III)-rich minerals, photoautotrophic and microaerophilic Fe(II) oxidizers avoid cell encrustation. The Fe(II) oxidation mechanisms and the reasons for encrustation remain largely unresolved. Here we used cultivation-based methods and electron microscopy to compare two previously described nitrate-reducing Fe(II) oxidizers ( Acidovorax sp. strain BoFeN1 and Pseudogulbenkiania sp. strain 2002) and two heterotrophic nitrate reducers (Paracoccus denitrificans ATCC 19367 and P. denitrificans Pd 1222). All four strains oxidized ∼8 mM Fe(II) within 5 days in the presence of 5 mM acetate and accumulated nitrite (maximum concentrations of 0.8 to 1.0 mM) in the culture media. Iron(III) minerals, mainly goethite, formed and precipitated extracellularly in close proximity to the cell surface. Interestingly, mineral formation was also observed within the periplasm and cytoplasm; intracellular mineralization is expected to be physiologically disadvantageous, yet acetate consumption continued to be observed even at an advanced stage of Fe(II) oxidation. Extracellular polymeric substances (EPS) were detected by lectin staining with fluorescence microscopy, particularly in the presence of Fe(II), suggesting that EPS production is a response to Fe(II) toxicity or a strategy to decrease encrustation. Based on the data presented here, we propose a nitrite-driven, indirect mechanism of cell encrustation whereby nitrite forms during heterotrophic denitrification and abiotically oxidizes Fe(II). This work adds to the known assemblage of Fe(II)-oxidizing bacteria in nature and complicates our ability to delineate microbial Fe(II) oxidation in ancient microbes preserved as fossils in the geological record. PMID:24271182

  1. The Complete Genome Sequence and Analysis of the Epsilonproteobacterium Arcobacter butzleri

    PubMed Central

    Miller, William G.; Parker, Craig T.; Rubenfield, Marc; Mendz, George L.; Wösten, Marc M. S. M.; Ussery, David W.; Stolz, John F.; Binnewies, Tim T.; Hallin, Peter F.; Wang, Guilin; Malek, Joel A.; Rogosin, Andrea; Stanker, Larry H.; Mandrell, Robert E.

    2007-01-01

    Background Arcobacter butzleri is a member of the epsilon subdivision of the Proteobacteria and a close taxonomic relative of established pathogens, such as Campylobacter jejuni and Helicobacter pylori. Here we present the complete genome sequence of the human clinical isolate, A. butzleri strain RM4018. Methodology/Principal Findings Arcobacter butzleri is a member of the Campylobacteraceae, but the majority of its proteome is most similar to those of Sulfuromonas denitrificans and Wolinella succinogenes, both members of the Helicobacteraceae, and those of the deep-sea vent Epsilonproteobacteria Sulfurovum and Nitratiruptor. In addition, many of the genes and pathways described here, e.g. those involved in signal transduction and sulfur metabolism, have been identified previously within the epsilon subdivision only in S. denitrificans, W. succinogenes, Sulfurovum, and/or Nitratiruptor, or are unique to the subdivision. In addition, the analyses indicated also that a substantial proportion of the A. butzleri genome is devoted to growth and survival under diverse environmental conditions, with a large number of respiration-associated proteins, signal transduction and chemotaxis proteins and proteins involved in DNA repair and adaptation. To investigate the genomic diversity of A. butzleri strains, we constructed an A. butzleri DNA microarray comprising 2238 genes from strain RM4018. Comparative genomic indexing analysis of 12 additional A. butzleri strains identified both the core genes of A. butzleri and intraspecies hypervariable regions, where <70% of the genes were present in at least two strains. Conclusion/Significance The presence of pathways and loci associated often with non-host-associated organisms, as well as genes associated with virulence, suggests that A. butzleri is a free-living, water-borne organism that might be classified rightfully as an emerging pathogen. The genome sequence and analyses presented in this study are an important first step in

  2. Isotopomeric characterization of nitrous oxide produced by reaction of enzymes extracted from nitrifying and denitrifying bacteria

    NASA Astrophysics Data System (ADS)

    Yamazaki, T.; Hozuki, T.; Arai, K.; Toyoda, S.; Koba, K.; Fujiwara, T.; Yoshida, N.

    2014-05-01

    Nitrous oxide (N2O) is a potent greenhouse gas and produced in denitrification and nitrification by various microorganisms. Site preference (SP) of 15N in N2O, which is defined as the difference in the natural abundance of isotopomers 14N15NO and 15N14NO relative to 14N14NO, has been reported to be a useful tool to quantitatively distinguish N2O production pathways. To determine representative SP values for each microbial process, we firstly measured SP of N2O produced in the enzyme reaction of hydroxylamine oxidoreductase (HAO) purified from two species of ammonia oxidizing bacteria (AOB), Nitrosomonas europaea and Nitrosococcus oceani, and that of nitric oxide reductase (NOR) from Paracoccus denitrificans. The SP value for NOR reaction (-5.9 ± 2.1‰) showed nearly the same value as that reported for N2O produced by P. denitrificans in pure culture. In contrast, SP value for HAO reaction (36.3 ± 2.3‰) was a little higher than the values reported for N2O produced by AOB in aerobic pure culture. Using the SP values obtained by HAO and NOR reactions, we calculated relative contribution of the nitrite (NO2-) reduction (which is followed by NO reduction) to N2O production by N. oceani incubated under different O2 availability. Our calculations revealed that previous in vivo studies might have underestimated the SP value for the NH2OH oxidation pathway possibly due to a small contribution of NO2- reduction pathway. Further evaluation of isotopomer signatures of N2O using common enzymes of other processes related to N2O would improve the isotopomer analysis of N2O in various environments.

  3. Isotopomeric characterization of nitrous oxide produced by reaction of enzymes extracted from nitrifying and denitrifying bacteria

    NASA Astrophysics Data System (ADS)

    Yamazaki, T.; Hozuki, T.; Arai, K.; Toyoda, S.; Koba, K.; Fujiwara, T.; Yoshida, N.

    2013-10-01

    Nitrous oxide (N2O) is a potent greenhouse gas and produced in denitrification and nitrification in environmental nitrogen cycle by various microorganism. Site preference (SP) of 15N in N2O, which is defined as the difference in the natural abundance of isotopomers 14N15NO and 15N14NO relative to 14N14NO, has been reported to be a useful tool to quantitatively distinguish N2O production pathway. To determine representative SP value for each microbial process, we firstly measured SP of N2O produced in the enzyme reaction of hydroxylamine oxidoreductase (HAO) purified from two species of ammonia oxidizing bacteria (AOB), Nitrosomonas europaea and Nitrosococcus oceani, and that of nitric oxide reductase (NOR) from Paracoccus denitrificans, respectively. The SP value for NOR reaction (-5.9 ± 2.1‰) showed nearly the same value as that reported for N2O produced by P. denitrificans in pure culture. In contrast, SP value for HAO reaction (36.3 ± 2.3‰) was a little higher than the values reported for N2O produced by AOB in aerobic pure culture. Using the SP values obtained by HAO and NOR reactions, we calculated relative contribution of the nitrite (NO2-) reduction (which is followed by NO reduction) to N2O production by N. oceani incubated under different O2 availability. Our calculations revealed that previous in vivo studies might have underestimated the SP value for NH2OH oxidation pathway possibly due to a small contribution of NO2- reduction pathway. Further evaluation of isotopomer signatures of N2O using common enzymes of other processes related to N2O would improve the isotopomer analysis of N2O in various environments.

  4. Nitrate-Dependent Degradation of Acetone by Alicycliphilus and Paracoccus Strains and Comparison of Acetone Carboxylase Enzymes ▿

    PubMed Central

    Dullius, Carlos Henrique; Chen, Ching-Yuan; Schink, Bernhard

    2011-01-01

    A novel acetone-degrading, nitrate-reducing bacterium, strain KN Bun08, was isolated from an enrichment culture with butanone and nitrate as the sole sources of carbon and energy. The cells were motile short rods, 0.5 to 1 by 1 to 2 μm in size, which gave Gram-positive staining results in the exponential growth phase and Gram-negative staining results in the stationary-growth phase. Based on 16S rRNA gene sequence analysis, the isolate was assigned to the genus Alicycliphilus. Besides butanone and acetone, the strain used numerous fatty acids as substrates. An ATP-dependent acetone-carboxylating enzyme was enriched from cell extracts of this bacterium and of Alicycliphilus denitrificans K601T by two subsequent DEAE Sepharose column procedures. For comparison, acetone carboxylases were enriched from two additional nitrate-reducing bacterial species, Paracoccus denitrificans and P. pantotrophus. The products of the carboxylase reaction were acetoacetate and AMP rather than ADP. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis of cell extracts and of the various enzyme preparations revealed bands corresponding to molecular masses of 85, 78, and 20 kDa, suggesting similarities to the acetone carboxylase enzymes described in detail for the aerobic bacterium Xanthobacter autotrophicus strain Py2 (85.3, 78.3, and 19.6 kDa) and the phototrophic bacterium Rhodobacter capsulatus. Protein bands were excised and compared by mass spectrometry with those of acetone carboxylases of aerobic bacteria. The results document the finding that the nitrate-reducing bacteria studied here use acetone-carboxylating enzymes similar to those of aerobic and phototrophic bacteria. PMID:21841031

  5. An additional simple denitrification bioreactor using packed gel envelopes applicable to industrial wastewater treatment.

    PubMed

    Morita, Masahiko; Uemoto, Hiroaki; Watanabe, Atsushi

    2007-08-15

    A simple denitrification bioreactor for nitrate-containing wastewater without organic compounds was developed. This bioreactor consisted of packed gel envelopes in a single tank. Each envelope comprised two plates of gels containing Paracoccus denitrificans cells with an internal space between the plates. As an electron donor for denitrification, ethanol was injected into the internal space and not directly into the wastewater. P. denitrificans cells in the gel reduced nitrate to nitrogen gas by using the injected ethanol. Nitrate-containing desulfurization wastewater derived from a coal-fired thermal power plant was continuously treated with 20 packed gel envelopes (size, 1,000 x 900 x 12 mm; surface area, 1.44 m(2)) in a reactor tank (volume 1.5 m(3)). When the total nitrogen concentration in the inflow was around 150 mg-N x L(-1), the envelopes removed approximately 60-80% of the total nitrogen, and the maximum nitrogen removal rate was 5.0 g-N x day(-1) per square meter of the gel surface. This value corresponded to the volumetric nitrogen removal performance of 0.109 kg-N x m(-3) x day(-1). In each envelope, a high utilization efficiency of the electron donor was attained, although more than the double amount of the electron donor was empirically injected in the present activated sludge system to achieve denitrification when compared with the theoretical value. The bioreactor using the envelopes would be extremely effective as an additional denitrification system because these envelopes can be easily installed in the vacant spaces of preinstalled water treatment systems, without requiring additional facilities for removing surplus ethanol and sludge. (c) 2007 Wiley Periodicals, Inc.

  6. Bioreactor performance and functional gene analysis of microbial community in a limited-oxygen fed bioreactor for co-reduction of sulfate and nitrate with high organic input.

    PubMed

    Xu, Xi-jun; Chen, Chuan; Wang, Ai-jie; Yu, Hao; Zhou, Xu; Guo, Hong-liang; Yuan, Ye; Lee, Duu-jong; Zhou, Jizhong; Ren, Nan-qi

    2014-08-15

    Limited-oxygen mediated synergistic relationships between sulfate-reducing bacteria (SRB), nitrate-reducing bacteria (NRB) and sulfide-oxidizing bacteria (SOB, including nitrate-reducing, sulfide-oxidizing bacteria NR-SOB) were predicted to simultaneously remove contaminants of nitrate, sulfate and high COD, and eliminate sulfide generation. A lab-scale experiment was conducted to examine the impact of limited oxygen on these oxy-anions degradation, sulfide oxidation and associated microbial functional responses. In all scenarios tested, the reduction of both nitrate and sulfate was almost complete. When limited-oxygen was fed into bioreactors, S(0) formation was significantly improved up to ∼ 70%. GeoChip 4.0, a functional gene microarray, was used to determine the microbial gene diversity and functional potential for nitrate and sulfate reduction, and sulfide oxidation. The diversity of the microbial community in bioreactors was increased with the feeding of limited oxygen. Whereas the intensities of the functional genes involved in sulfate reduction did not show a significant difference, the abundance of the detected denitrification genes decreased in limited oxygen samples. More importantly, sulfide-oxidizing bacteria may alter their populations/genes in response to limited oxygen potentially to function more effectively in sulfide oxidation, especially to elemental sulfur. The genes fccA/fccB from nitrate-reducing, sulfide-oxidizing bacteria (NR-SOB), such as Paracoccus denitrificans, Thiobacillus denitrificans, Beggiatoa sp., Thiomicrospira sp., and Thioalkalivibrio sp., were more abundant under limited-oxygen condition. Copyright © 2014 Elsevier B.V. All rights reserved.

  7. Metatranscriptome Analysis of Aquifer Samples Reveals Unexpected Metabolic Lifestyles Relevant to Active Biogeochemical Cycling

    NASA Astrophysics Data System (ADS)

    Beller, H. R.; Jewell, T. N. M.; Karaoz, U.; Banfield, J. F.; Brodie, E.; Williams, K. H.

    2015-12-01

    Modern molecular ecology techniques are revealing the metabolic potential of uncultivated microorganisms, but there is still much to be learned about the actual biogeochemical roles of microbes that have cultivated relatives. Here, we present metatranscriptomic and metagenomic data from a field study that provides evidence of coupled redox processes that have not been documented in cultivated relatives and, indeed, represent strains with metabolic traits that are novel with respect to closely related isolates. The data come from omics analysis of groundwater samples collected during an experiment in which nitrate (a native electron acceptor) was injected into a perennially suboxic aquifer in Rifle (CO). Transcriptional data indicated that just two groups of chemolithoautotrophic bacteria accounted for a very large portion (~80%) of overall community gene expression: (1) members of the Fe(II)-oxidizing Gallionellaceae family and (2) strains of the S-oxidizing species, Sulfurimonas denitrificans. Metabolic lifestyles for Gallionellaceae strains that were novel compared to cultivated representatives included nitrate-dependent Fe(II) oxidation and S oxidation. Evidence for these metabolisms included highly correlated temporal expression in binned data of nitrate reductase (e.g., narGHI) genes (which have never been reported in Gallionellaceae genomes) and Fe(II) oxidation genes (e.g., mtoA) or S oxidation genes (e.g., dsrE, aprA). Of the two most active strains of S. denitrificans, only one showed strong expression of S oxidation genes, whereas the other was apparently using an unexpected (as-yet unidentified) primary electron donor. Transcriptional data added considerable interpretive value to this study, as (1) metagenomic data would not have highlighted these organisms, which had a disproportionately large role in community metabolism relative to their populations, and (2) co-expression of coupled pathway genes could not be predicted based solely on metagenomic data.

  8. Technological aspects of the microbial treatment of sulfide-rich wastewaters: a case study.

    PubMed

    Sublette, K L; Kolhatkar, R; Raterman, K

    1998-01-01

    Thiobacillus denitrificans has been shown to be an effective biocatalyst for the treatment of a variety of sulfide-laden waste streams including sour water, sour gases, and refinery spent-sulfidic caustics. The term 'sour' originated in the petroleum industry to describe a waste contaminated with hydrogen sulfide or salts of sulfide and bisulfide. The microbial treatment of sour waste streams resulting from the production or refining of natural gas and crude oil have been investigated in this laboratory for many years. The application of this technology to the treatment of sour wastes on a commercially useful scale has presented several technical barriers including substrate inhibition (sulfide), product inhibition (sulfate), the need for septic operation, biomass recycle and recovery, mixed waste issues, and the need for large-scale cultivation of the organism for process startup. The removal of these barriers through process improvements are discussed in terms of a case study of the full-scale treatment of sulfide-rich wastewater. The ability of T. denitrificans to deodorize and detoxify an oil-field produced water containing sulfides was evaluated under full-scale field conditions at Amoco Production Co. Salt Creek Field in Midwest, WY. More than 800 m3/d of produced water containing 100 mg/L sulfide and total dissolved solids of 4800 mg/L were successfully biotreated in an earthen pit (3000 m3) over a six-month period. Complete removal of sulfides and elimination of associated odors were observed. The system could be upset by severe hydraulic disturbances; however, the system recovered rapidly when normal influent flow rates were restored.

  9. Demonstration that CobG, the monooxygenase associated with the ring contraction process of the aerobic cobalamin (vitamin B12) biosynthetic pathway, contains an Fe-S center and a mononuclear non-heme iron center.

    PubMed

    Schroeder, Susanne; Lawrence, Andrew D; Biedendieck, Rebekka; Rose, Ruth-Sarah; Deery, Evelyne; Graham, Ross M; McLean, Kirsty J; Munro, Andrew W; Rigby, Stephen E J; Warren, Martin J

    2009-02-20

    The ring contraction process that occurs during cobalamin (vitamin B(12)) biosynthesis is mediated via the action of two enzymes, CobG and CobJ. The first of these generates a tertiary alcohol at the C-20 position of precorrin-3A by functioning as a monooxygenase, a reaction that also forms a gamma lactone with the acetic acid side chain on ring A. The product, precorrin-3B, is then acted upon by CobJ, which methylates at the C-17 position and promotes ring contraction of the macrocycle by catalyzing a masked pinacol rearrangement. Here, we report the characterization of CobG enzymes from Pseudomonas denitrificans and Brucella melitensis. We show that both contain a [4Fe-4S] center as well as a mononuclear non-heme iron. Although both enzymes are active in vivo, the P. denitrificans enzyme was found to be inactive in vitro. Further analysis of this enzyme revealed that the mononuclear non-heme iron was not reducible, and it was concluded that it is rapidly inactivated once it is released from the bacterial cell. In contrast, the B. melitensis enzyme was found to be fully active in vitro and the mononuclear non-heme iron was reducible by dithionite. The reduced mononuclear non-heme was able to react with the oxygen analogue NO, but only in the presence of the substrate precorrin-3A. The cysteine residues responsible for binding the Fe-S center were identified by site-directed mutagenesis. A mechanism for CobG is presented.

  10. AC Coupled Interconnect for Low Power Spaceborne Electronics

    DTIC Science & Technology

    2012-01-18

    Apad = 175x175µm2 (200µm pitch and 25µm spacing on package), CC,row,min = 500fF (from preliminary simulation with TRX in 0.13µm standard CMOS and 80cm...the TRX performance with state-of-the-art designs. It is demonstrated that the TRX , benefitting from the CT-FSE scheme combined with use of the...8.9Gb/s TX Power 5.2mW 6.5mW 7.6mW 4.9mW - 11.6mW RX Power 1.1mW 1.1mW 1.1mW 8mW 10.9mW 5.4mW TRX Total Area .007mm 2 .307mm 2 .054mm 2 .023mm 2

  11. Low-Absorption Liquid Crystals for Infrared Beam Steering

    DTIC Science & Technology

    2015-09-30

    liquid crystals for infrared laser beam steering applications. To suppress the optical loss in MW1R and LW1R, we have investigated following...dielectric anisotropy, and low optical loss nematic liquid crystals for infrared laser beam steering applications. To suppress the optical loss in MWIR and...modulators. 1. Objective The main objective of this program is to develop low-loss liquid crystals for electronic laser beam steering in the infrared

  12. Alteration of Multiple Cell Membrane Functions in L-6 Myoblasts by T-2 Toxin: An Important Mechanism of Action.

    DTIC Science & Technology

    1986-06-04

    menbrane functions. All are in a range that would in turn be expected to alter other cell functions. Intracellular LEH was reduced 10 min after T-2... Plasma amino F-id changes in guinea pigs injected with T-2 rnycotoxin. Fed. Proc. 42, 625. 20 1111" ll p J IIIý f%𔃻 11 IC IA 114 WEAVER, G.A., MW1•Z, H.J

  13. Alternative Fuels Data Center: Arkansas Transportation Data for Alternative

    Diesel Natural Gas Electricity Transportation Fuel Consumption Source: State Energy Data System based on Renewable Power Plant Capacity (nameplate, MW) 1,349 Source: BioFuels Atlas from the National Renewable $2.50/gallon $2.50/GGE Diesel $2.61/gallon $2.35/GGE $2.96/gallon $2.66/GGE Source: Average prices per

  14. The kinetics of the oxidation of cytochrome c by Paracoccus cytochrome c peroxidase.

    PubMed

    Gilmour, R; Goodhew, C F; Pettigrew, G W; Prazeres, S; Moura, J J; Moura, I

    1994-06-15

    In work that is complementary to our investigation of the spectroscopic features of the cytochrome c peroxidase from Paracoccus denitrificans [Gilmour, Goodhew, Pettigrew, Prazeres, Moura and Moura (1993) Biochem. J. 294, 745-752], we have studied the kinetics of oxidation of cytochrome c by this enzyme. The enzyme, as isolated, is in the fully oxidized form and is relatively inactive. Reduction of the high-potential haem at pH 6 with ascorbate results in partial activation of the enzyme. Full activation is achieved by addition of 1 mM CaCl2. Enzyme activation is associated with formation of a high-spin state at the oxidized low-potential haem. EGTA treatment of the oxidized enzyme prevents activation after reduction with ascorbate, while treatment with EGTA of the reduced, partially activated, form abolishes the activity. We conclude that the active enzyme is a mixed-valence form with the low-potential haem in a high-spin state that is stabilized by Ca2+. Dilution of the enzyme results in a progressive loss of activity, the extent of which depends on the degree of dilution. Most of the activity lost upon dilution can be recovered after reconcentration. The M(r) of the enzyme on molecular-exclusion chromatography is concentration-dependent, with a shift to lower values at lower concentrations. Values of M(r) obtained are intermediate between those of a monomer (39,565) and a dimer. We propose that the active form of the enzyme is a dimer which dissociates at high dilution to give inactive monomers. From the activity of the enzyme at different dilutions, a KD of 0.8 microM can be calculated for the monomerdimer equilibrium. The cytochrome c peroxidase oxidizes horse ferrocytochrome c with first-order kinetics, even at high ferrocytochrome c concentrations. The maximal catalytic-centre activity ('turnover number') under the assay conditions used is 62,000 min-1, with a half-saturating ferrocytochrome c concentration of 3.3 microM. The corresponding values for the

  15. A field demonstration of the microbial treatment of sour produced water

    SciT

    Sublette, K.L.; Morse, D.; Raterman, K.

    1995-12-31

    The potential for detoxification and deodorization of sulfide-laden water (sour water) by microbial treatment was evaluated at a petroleum production site under field conditions. A sulfide-tolerant strain of the chemautotroph and facultative anaerobe, Thiobacillus denitrificans, was introduced into an oil-skimming pit of the Amoco Production Company LACT 10 Unit of the Salt Creek Field, Wyoming. Field-produced water enters this pit from the oil/water separation treatment train at an average flowrate of 5,000 bbl/D (795 m{sup 3}/D) with a potential maximum of 98,000 bbl/D (15,580 m{sup 3}/D). Water conditions at the pit inlet are 4,800 mg/l TDS, 100 mg/l sulfide, pHmore » 7.8, and 107{degrees}F. To this water an aqueous solution of ammonium nitrate and diphosphorous pentoxide was added to provide required nutrients for the bacteria. The first 20% of the pit was aerated to a maximum depth of 5 ft (1.5 m) to facilitate the aerobic oxidation of sulfide. No provisions for pH control or biomass recovery and recycle were made. Pilot operations were initiated in October 1992 with the inoculation of the 19,000 bbl (3,020 m{sup 3}) pit with 40 lb (18.1 kg) of dry weight biomass. After a brief acclimation period, a nearly constant mass flux of 175 lb/D (80 kg/D) sulfide was established to the pit. Bio-oxidation of sulfide to elemental sulfur and sulfate was immediate and complete. Subsequent pilot operations focused upon process optimization and process sensitivity to system upsets. The process appeared most sensitive to large variations in sulfide loading due to maximum water discharge events. However, recoveries from such events could be accomplished within hours. This paper details all pertinent aspects of pilot operation, performance, and economics. Based on this body of evidence, it is suggested that the oxidation of inorganic sulfides by T denitrificans represents a viable concept for the treatment of sour water coproduced with oil and gas.« less

  16. Microbial control of hydrogen sulfide production

    SciT

    Montgomery, A.D.; Bhupathiraju, V.K.; Wofford, N.

    1995-12-31

    A sulfide-resistant strain of Thiobacillus denitrificans, strain F, prevented the accumulation of sulfide by Desulfovibrio desulfuricans when both organisms were grown in liquid medium. The wild-type strain of T. denitrificans did not prevent the accumulation of sulfide produced by D. desulfuricans. Strain F also prevented the accumulation of sulfide by a mixed population of sulfate-reducing bacteria enriched from an oil field brine. Fermentation balances showed that strain F stoichiometrically oxidized the sulfide produced by D. desulfuricans and the oil field brine enrichment to sulfate. The ability of a strain F to control sulfide production in an experimental system of coresmore » and formation water from the Redfield, Iowa, natural gas storage facility was also investigated. A stable, sulfide-producing biofilm was established in two separate core systems, one of which was inoculated with strain F while the other core system (control) was treated in an identical manner, but was not inoculated with strain F. When formation water with 10 mM acetate and 5 mM nitrate was injected into both core systems, the effluent sulfide concentrations in the control core system ranged from 200 to 460 {mu}M. In the test core system inoculated with strain F, the effluent sulfide concentrations were lower, ranging from 70 to 110 {mu}M. In order to determine whether strain F could control sulfide production under optimal conditions for sulfate-reducing bacteria, the electron donor was changed to lactate and inorganic nutrients (nitrogen and phosphate sources) were added to the formation water. When nutrient-supplemented formation water with 3.1 mM lactate and 10 mM nitrate was used, the effluent sulfide concentrations of the control core system initially increased to about 3,800 {mu}M, and then decreased to about 1,100 {mu}M after 5 weeks. However, in the test core system inoculated with strain F, the effluent sulfide concentrations were much lower, 160 to 330 {mu}M.« less

  17. Effect of CO2 on NADH production of denitrifying microbes via inhibiting carbon source transport and its metabolism.

    PubMed

    Wan, Rui; Chen, Yinguang; Zheng, Xiong; Su, Yinglong; Huang, Haining

    2018-06-15

    The potential effect of CO 2 on environmental microbes has drawn much attention recently. As an important section of the nitrogen cycle, biological denitrification requires electron donor to reduce nitrogen oxide. Nicotinamide adenine dinucleotide (NADH), which is formed during carbon source metabolism, is a widely reported electron donor for denitrification. Here we studied the effect of CO 2 on NADH production and carbon source utilization in the denitrifying microbe Paracoccus denitrificans. We observed that NADH level was decreased by 45.5% with the increase of CO 2 concentration from 0 to 30,000ppm, which was attributed to the significantly decreased utilization of carbon source (i.e., acetate). Further study showed that CO 2 inhibited carbon source utilization because of multiple negative influences: (1) suppressing the growth and viability of denitrifier cells, (2) weakening the driving force for carbon source transport by decreasing bacterial membrane potential, and (3) downregulating the expression of genes encoding key enzymes involved in intracellular carbon metabolism, such as citrate synthase, aconitate hydratase, isocitrate dehydrogenase, succinate dehydrogenase, and fumarate reductase. This study suggests that the inhibitory effect of CO 2 on NADH production in denitrifiers might deteriorate the denitrification performance in an elevated CO 2 climate scenario. Copyright © 2018 Elsevier B.V. All rights reserved.

  18. Neutron and high-resolution room-temperature X-ray data collection from crystallized lytic polysaccharide monooxygenase

    SciT

    Bacik, John -Paul; Mekasha, Sophanit; Forsberg, Zarah

    Bacteria and fungi express lytic polysaccharide monooxgyenase (LPMO) enzymes that act in conjunction with canonical hydrolytic sugar-processing enzymes to rapidly convert polysaccharides such as chitin, cellulose and starch to single monosaccharide products. In order to gain a better understanding of the structure and oxidative mechanism of these enzymes, large crystals (1–3 mm 3) of a chitin-processing LPMO from the Gram-positive soil bacterium Jonesia denitrificans were grown and screened for their ability to diffract neutrons. In addition to the collection of neutron diffraction data, which were processed to 2.1 Å resolution, a high-resolution room-temperature X-ray diffraction data set was collected andmore » processed to 1.1 Å resolution in space group P2 12 12 1. To our knowledge, this work marks the first successful neutron crystallographic experiment on an LPMO. As a result, joint X-ray/neutron refinement of the resulting data will reveal new details of the structure and mechanism of this recently discovered class of enzymes.« less

  19. Neutron and high-resolution room-temperature X-ray data collection from crystallized lytic polysaccharide monooxygenase

    DOE PAGES

    Bacik, John -Paul; Mekasha, Sophanit; Forsberg, Zarah; ...

    2015-01-01

    Bacteria and fungi express lytic polysaccharide monooxgyenase (LPMO) enzymes that act in conjunction with canonical hydrolytic sugar-processing enzymes to rapidly convert polysaccharides such as chitin, cellulose and starch to single monosaccharide products. In order to gain a better understanding of the structure and oxidative mechanism of these enzymes, large crystals (1–3 mm 3) of a chitin-processing LPMO from the Gram-positive soil bacterium Jonesia denitrificans were grown and screened for their ability to diffract neutrons. In addition to the collection of neutron diffraction data, which were processed to 2.1 Å resolution, a high-resolution room-temperature X-ray diffraction data set was collected andmore » processed to 1.1 Å resolution in space group P2 12 12 1. To our knowledge, this work marks the first successful neutron crystallographic experiment on an LPMO. As a result, joint X-ray/neutron refinement of the resulting data will reveal new details of the structure and mechanism of this recently discovered class of enzymes.« less

  20. Nonspecific Bacterial Flora Isolated from the Body Surface and Inside Ixodes ricinus Ticks.

    PubMed

    Okła, Hubert; Sosnowska, Malwina; Jasik, Krzysztof P; Słodki, Jan; Wojtyczka, Robert D

    2012-09-28

    Ixodes ricinus and other representatives of the order Ixodida are vectors of typical pathogens: Borrelia burgdorferi sensu lato, Anaplasma phagocytophilium, Babesia spp., a tick-borne encephalitis virus, and other microorganisms which are important from a medical and veterinary point of view. The presented study focuses on the verification of nonspecific bacterial flora of I. ricinus. We analyzed ticks collected in a forest region in Silesia, an industrial district in Poland. Methods of classical microbiology and biochemical assays (API 20 NE test, API Staph test and MICRONAUT System) were used for isolation and identification of microorganisms living on the body surface of I. ricinus and inside ticks. The results show the presence of various bacteria on the surface and inside ticks' bodies. During the study, we isolated Acinetobacter lwoffi, Pseudomonas fluorescens, Aeromonas hydrophila, Achromobacter denitrificans, Alcaligenes faecalis, Stenotrophomonas maltophilia, Pseudomonas oryzihabitans, Micrococcus spp., Kocuria varians, Staphylococcus lentus, Kocuria kristinae, Streptococcus pneumoniae, Rhizobium radiobacter, Staphylococcus xylosus. Majority of the isolated species are non-pathogenic environmental microorganisms, but some of the isolated bacterial strains could cause severe infections.

  1. Nitrate promotes biological oxidation of sulfide in wastewaters: experiment at plant-scale.

    PubMed

    García de Lomas, Juan; Corzo, Alfonso; Gonzalez, Juan M; Andrades, Jose A; Iglesias, Emilio; Montero, María José

    2006-03-05

    Biogenic production of sulfide in wastewater treatment plants involves odors, toxicity and corrosion problems. The production of sulfide is a consequence of bacterial activity, mainly sulfate-reducing bacteria (SRB). To prevent this production, the efficiency of nitrate addition to wastewater was tested at plant-scale by dosing concentrated calcium nitrate (Nutriox) in the works inlet. Nutriox dosing resulted in a sharp decrease of sulfide, both in the air and in the bulk water, reaching maximum decreases of 98.7% and 94.7%, respectively. Quantitative molecular microbiology techniques indicated that the involved mechanism is the development of the nitrate-reducing, sulfide-oxidizing bacterium Thiomicrospira denitrificans instead of the direct inhibition of the SRB community. Denitrification rate in primary sedimentation tanks was enhanced by nitrate, being this almost completely consumed. No significant increase of inorganic nitrogen was found in the discharged effluent, thus reducing potential environmental hazards to receiving waters. This study demonstrates the effectiveness of nitrate addition in controlling sulfide generation at plant-scale, provides the mechanism and supports the environmental adequacy of this strategy.

  2. Structure-based analysis of CysZ-mediated cellular uptake of sulfate

    SciT

    Assur Sanghai, Zahra; Liu, Qun; Clarke, Oliver B.

    Sulfur, most abundantly found in the environment as sulfate (SO42-), is an essential element in metabolites required by all living cells, including amino acids, co-factors and vitamins. However, current understanding of the cellular delivery of SO42- at the molecular level is limited. CysZ has been described as a SO42- permease, but its sequence family is without known structural precedent. Based on crystallographic structure information, SO42- binding and flux experiments, we provide insight into the molecular mechanism of CysZ-mediated translocation of SO42- across membranes. CysZ structures from three different bacterial species display a hitherto unknown fold and have subunits organized withmore » inverted transmembrane topology. CysZ from Pseudomonas denitrificans assembles as a trimer of antiparallel dimers and the CysZ structures from two other species recapitulate dimers from this assembly. Mutational studies highlight the functional relevance of conserved CysZ residues.« less

  3. Ligand-Enhanced Abiotic Iron Oxidation and the Effects of Chemical versus Biological Iron Cycling in Anoxic Environments

    PubMed Central

    2013-01-01

    This study introduces a newly isolated, genetically tractable bacterium (Pseudogulbenkiania sp. strain MAI-1) and explores the extent to which its nitrate-dependent iron-oxidation activity is directly biologically catalyzed. Specifically, we focused on the role of iron chelating ligands in promoting chemical oxidation of Fe(II) by nitrite under anoxic conditions. Strong organic ligands such as nitrilotriacetate and citrate can substantially enhance chemical oxidation of Fe(II) by nitrite at circumneutral pH. We show that strain MAI-1 exhibits unambiguous biological Fe(II) oxidation despite a significant contribution (∼30–35%) from ligand-enhanced chemical oxidation. Our work with the model denitrifying strain Paracoccus denitrificans further shows that ligand-enhanced chemical oxidation of Fe(II) by microbially produced nitrite can be an important general side effect of biological denitrification. Our assessment of reaction rates derived from literature reports of anaerobic Fe(II) oxidation, both chemical and biological, highlights the potential competition and likely co-occurrence of chemical Fe(II) oxidation (mediated by microbial production of nitrite) and truly biological Fe(II) oxidation. PMID:23402562

  4. Diversity of microbes and potential exoelectrogenic bacteria on anode surface in microbial fuel cells.

    PubMed

    Sun, Yujiao; Zuo, Jiane; Cui, Longtao; Deng, Qian; Dang, Yan

    2010-02-01

    Single-chamber microbial fuel cells (MFCs), inoculated with anaerobic sludge and continuously run with two kinds of organic wastewater influents, were systemically investigated. The diversity of microbes, determined by 16S rDNA analysis, was analyzed on three anodes under different conditions. One anode was in a closed circuit in synthetic wastewater containing glucose. The other two anodes, in open or closed circuits, were fed effluent from an anaerobic reactor treating starch wastewater. The chemical oxygen demand (COD) removal efficiency was about 70%, and the exported voltages were about 450 mV. The 16S rDNA molecular clones of microbes on anode surfaces showed significant changes in Eubacterial structure under different conditions. gamma-Proteobacteria and the high G+C gram-positive groups were predominant in the synthetic wastewater, while epsilon-Proteobacteria predominated in the anaerobic reactor effluent. Known exoelectrogenic bacterial species composition also changed greatly depending on substrate. On the artificial substrate, 28% of the bacterial sequences were affiliated with Aeromonas, Pseudomonas, Geobacter, and Desulfobulbus. On the anaerobic effluent, only 6% were affiliated with Geobacter or Clostridium. Because only a few exoelectrogenic bacteria from MFCs have been directly isolated and studied, we compared the community structures of two bacterial anodes, in open and closed circuits, under the same substrate of anaerobic effluent in order to identify additional exoelectrogenic bacterial strains. Alcaligenes monasteriensis, Comamonas denitrificans, and Dechloromonas sp. were found to be potential exoelectrogenic bacteria worthy of further research.

  5. SciT

    Handali, Melody; Neupane, Durga P.; Roychowdhury, Hridindu

    Here, ATP-binding cassette (ABC) transporters of the cluster 9 family are ubiquitous among bacteria and essential for acquiring Zn 2+ and Mn 2+ from the environment or, in the case of pathogens, from the host. These rely on a substrate-binding protein (SBP) to coordinate the relevant metal with high affinity and specificity and subsequently release it to a membrane permease for translocation into the cytoplasm. Although a number of cluster 9 SBP structures have been determined, the structural attributes conferring Zn 2+ or Mn 2+ specificity remain ambiguous. Here we describe the gene expression profile, in vitro metal binding properties,more » and crystal structure of a new cluster 9 SBP from Paracoccus denitrificans we have called AztC. Although all of our results strongly indicate Zn 2+ over Mn 2+ specificity, the Zn 2+ ion is coordinated by a conserved Asp residue only observed to date as a metal ligand in Mn 2+-specific SBPs. The unusual sequence properties of this protein are shared among close homologues, including members from the human pathogens Klebsiella pneumonia and Enterobacter aerogenes, and would seem to suggest a subclass of Zn 2+-specific transporters among the cluster 9 family. In any case, the unusual coordination environment of AztC expands the already considerable range of those available to Zn 2+-specific SBPs and highlights the presence of a His-rich loop as the most reliable indicator of Zn 2+ specificity.« less

  6. Interaction of rhizosphere bacteria, fertilizer, and vesicular-arbuscular mycorrhizal fungi with sea oats.

    PubMed

    Will, M E; Sylvia, D M

    1990-07-01

    Plants must be established quickly on replenished beaches in order to stabilize the sand and begin the dune-building process. The objective of this research was to determine whether inoculation of sea oats (Uniola paniculata L.) with bacteria (indigenous rhizosphere bacteria and N(2) fixers) alone or in combination with vesicular-arbuscular mycorrhizal fungi would enhance plant growth in beach sand. At two fertilizer-N levels, Klebsiella pneumoniae and two Azospirillum spp. did not provide the plants with fixed atmospheric N; however, K. pneumoniae increased root and shoot growth. When a sparingly soluble P source (CaHPO(4)) was added to two sands, K. pneumoniae increased plant growth in sand with a high P content. The phosphorus content of shoots was not affected by bacterial inoculation, indicating that a mechanism other than bacterially enhanced P availability to plants was responsible for the growth increases. When sea oats were inoculated with either K. pneumoniae or Acaligenes denitrificans and a mixed Glomus inoculum, there was no consistent evidence of a synergistic effect on plant growth. Nonetheless, bacterial inoculation increased root colonization by vesicular-arbuscular mycorrhizal fungi when the fungal inoculum consisted of colonized roots but had no effect on colonization when the inoculum consisted of spores alone. K. pneumoniae was found to increase spore germination and hyphal growth of Glomus deserticola compared with the control. The use of bacterial inoculants to enhance establishment of pioneer dune plants warrants further study.

  7. Structure and Evolution of Chlorate Reduction Composite Transposons

    PubMed Central

    Clark, Iain C.; Melnyk, Ryan A.; Engelbrektson, Anna; Coates, John D.

    2013-01-01

    ABSTRACT The genes for chlorate reduction in six bacterial strains were analyzed in order to gain insight into the metabolism. A newly isolated chlorate-reducing bacterium (Shewanella algae ACDC) and three previously isolated strains (Ideonella dechloratans, Pseudomonas sp. strain PK, and Dechloromarinus chlorophilus NSS) were genome sequenced and compared to published sequences (Alicycliphilus denitrificans BC plasmid pALIDE01 and Pseudomonas chloritidismutans AW-1). De novo assembly of genomes failed to join regions adjacent to genes involved in chlorate reduction, suggesting the presence of repeat regions. Using a bioinformatics approach and finishing PCRs to connect fragmented contigs, we discovered that chlorate reduction genes are flanked by insertion sequences, forming composite transposons in all four newly sequenced strains. These insertion sequences delineate regions with the potential to move horizontally and define a set of genes that may be important for chlorate reduction. In addition to core metabolic components, we have highlighted several such genes through comparative analysis and visualization. Phylogenetic analysis places chlorate reductase within a functionally diverse clade of type II dimethyl sulfoxide (DMSO) reductases, part of a larger family of enzymes with reactivity toward chlorate. Nucleotide-level forensics of regions surrounding chlorite dismutase (cld), as well as its phylogenetic clustering in a betaproteobacterial Cld clade, indicate that cld has been mobilized at least once from a perchlorate reducer to build chlorate respiration. PMID:23919996

  8. Alteration of intracellular protein expressions as a key mechanism of the deterioration of bacterial denitrification caused by copper oxide nanoparticles.

    PubMed

    Su, Yinglong; Zheng, Xiong; Chen, Yinguang; Li, Mu; Liu, Kun

    2015-10-28

    The increasing production and utilization of copper oxide nanoparticles (CuO NPs) result in the releases into the environment. However, the influence of CuO NPs on bacterial denitrification, one of the most important pathways to transform nitrate to dinitrogen in environment, has seldom been studied. Here we reported that CuO NPs caused a significant alteration of key protein expressions of a model denitrifier, Paracoccus denitrificans, leading to severe inhibition to denitrification. Total nitrogen removal efficiency was decreased from 98.3% to 62.1% with the increase of CuO NPs from 0.05 to 0.25 mg/L. Cellular morphology and integrity studies indicated that nanoparticles entered the cells. The proteomic bioinformatics analysis showed that CuO NPs caused regulation of proteins involved in nitrogen metabolism, electron transfer and substance transport. The down-regulation of GtsB protein (responsible for glucose transport) decreased the production of NADH (electron donor for denitrification). Also, the expressions of key electron-transfer proteins (including NADH dehydrogenase and cytochrome) were suppressed by CuO NPs, which adversely affected electrons transfer for denitrification. Further investigation revealed that CuO NPs significantly inhibited the expressions and catalytic activities of nitrate reductase and nitrite reductase. These results provided a fundamental understanding of the negative influences of CuO NPs on bacterial denitrification.

  9. Alteration of intracellular protein expressions as a key mechanism of the deterioration of bacterial denitrification caused by copper oxide nanoparticles

    PubMed Central

    Su, Yinglong; Zheng, Xiong; Chen, Yinguang; Li, Mu; Liu, Kun

    2015-01-01

    The increasing production and utilization of copper oxide nanoparticles (CuO NPs) result in the releases into the environment. However, the influence of CuO NPs on bacterial denitrification, one of the most important pathways to transform nitrate to dinitrogen in environment, has seldom been studied. Here we reported that CuO NPs caused a significant alteration of key protein expressions of a model denitrifier, Paracoccus denitrificans, leading to severe inhibition to denitrification. Total nitrogen removal efficiency was decreased from 98.3% to 62.1% with the increase of CuO NPs from 0.05 to 0.25 mg/L. Cellular morphology and integrity studies indicated that nanoparticles entered the cells. The proteomic bioinformatics analysis showed that CuO NPs caused regulation of proteins involved in nitrogen metabolism, electron transfer and substance transport. The down-regulation of GtsB protein (responsible for glucose transport) decreased the production of NADH (electron donor for denitrification). Also, the expressions of key electron-transfer proteins (including NADH dehydrogenase and cytochrome) were suppressed by CuO NPs, which adversely affected electrons transfer for denitrification. Further investigation revealed that CuO NPs significantly inhibited the expressions and catalytic activities of nitrate reductase and nitrite reductase. These results provided a fundamental understanding of the negative influences of CuO NPs on bacterial denitrification. PMID:26508362

  10. Redox-dependent open and closed forms of the active site of the bacterial respiratory nitric-oxide reductase revealed by cyanide binding studies.

    PubMed

    Grönberg, Karin L C; Watmough, Nicholas J; Thomson, Andrew J; Richardson, David J; Field, Sarah J

    2004-04-23

    The bacterial respiratory nitric-oxide reductase (NOR) catalyzes the respiratory detoxification of nitric oxide in bacteria and Archaea. It is a member of the well known super-family of heme-copper oxidases but has a [heme Fe-non-heme Fe] active site rather than the [heme Fe-Cu(B)] active site normally associated with oxygen reduction. Paracoccus denitrificans NOR is spectrally characterized by a ligand-to-metal charge transfer absorption band at 595 nm, which arises from the high spin ferric heme iron of a micro-oxo-bridged [heme Fe(III)-O-Fe(III)] active site. On reduction of the nonheme iron, the micro-oxo bridge is broken, and the ferric heme iron is hydroxylated or hydrated, depending on the pH. At present, the catalytic cycle of NOR is a matter of much debate, and it is not known to which redox state(s) of the enzyme nitric oxide can bind. This study has used cyanide to probe the nature of the active site in a number of different redox states. Our observations suggest that the micro-oxo-bridged [heme Fe(III)-O-Fe(III)] active site represents a closed or resting state of NOR that can be opened by reduction of the non-heme iron.

  11. Structure-based analysis of CysZ-mediated cellular uptake of sulfate

    SciT

    Assur Sanghai, Zahra; Liu, Qun; Clarke, Oliver B.

    Sulfur, most abundantly found in the environment as sulfate (SO 4 2-), is an essential element in metabolites required by all living cells, including amino acids, co-factors and vitamins. However, current understanding of the cellular delivery of SO 4 2- at the molecular level is limited. CysZ has been described as a SO 4 2- permease, but its sequence family is without known structural precedent. Based on crystallographic structure information, SO 4 2- binding and flux experiments, we provide insight into the molecular mechanism of CysZ-mediated translocation of SO 4 2- across membranes. CysZ structures from three different bacterial speciesmore » display a hitherto unknown fold and have subunits organized with inverted transmembrane topology. CysZ from Pseudomonas denitrificans assembles as a trimer of antiparallel dimers and the CysZ structures from two other species recapitulate dimers from this assembly. In conclusion, mutational studies highlight the functional relevance of conserved CysZ residues.« less

  12. Genetic tools for the investigation of Roseobacter clade bacteria

    PubMed Central

    2009-01-01

    Background The Roseobacter clade represents one of the most abundant, metabolically versatile and ecologically important bacterial groups found in marine habitats. A detailed molecular investigation of the regulatory and metabolic networks of these organisms is currently limited for many strains by missing suitable genetic tools. Results Conjugation and electroporation methods for the efficient and stable genetic transformation of selected Roseobacter clade bacteria including Dinoroseobacter shibae, Oceanibulbus indolifex, Phaeobacter gallaeciensis, Phaeobacter inhibens, Roseobacter denitrificans and Roseobacter litoralis were tested. For this purpose an antibiotic resistance screening was performed and suitable genetic markers were selected. Based on these transformation protocols stably maintained plasmids were identified. A plasmid encoded oxygen-independent fluorescent system was established using the flavin mononucleotide-based fluorescent protein FbFP. Finally, a chromosomal gene knockout strategy was successfully employed for the inactivation of the anaerobic metabolism regulatory gene dnr from D. shibae DFL12T. Conclusion A genetic toolbox for members of the Roseobacter clade was established. This provides a solid methodical basis for the detailed elucidation of gene regulatory and metabolic networks underlying the ecological success of this group of marine bacteria. PMID:20021642

  13. STRUCTURE AND FUNCTION OF SUBSURFACE MICROBIAL COMMUNITIES AFFECTING RADIONUCLIDE TRANSPORT AND BIOIMMOBILIZATION

    SciT

    Joel E. Kostka; Lee Kerkhof; Kuk-Jeong Chin

    2011-06-15

    are new to science all show high sequence identity to sequences retrieved from ORFRC subsurface. (2) Based on physiological and phylogenetic characterization, two new species of subsurface bacteria were described: the metal-reducer Geobacter daltonii, and the denitrifier Rhodanobacter denitrificans. (3) Strains isolated from the ORFRC show that Rhodanobacter species are well adapted to the contaminated subsurface. Strains 2APBS1 and 116-2 grow at high salt (3% NaCl), low pH (3.5) and tolerate high concentrations of nitrate (400mM) and nitrite (100mM). Strain 2APBS1 was demonstrated to grow at in situ acidic pHs down to 2.5. (4) R. denitrificans strain 2APBS1 is the first described Rhodanobacter species shown to denitrify. Nitrate is almost entirely converted to N2O, which may account for the large accumulation of N2O in the ORFRC subsurface. (5) G. daltonii, isolated from uranium- and hydrocarbon-contaminated subsurface sediments of the ORFRC, is the first organism from the subsurface clade of the genus Geobacter that is capable of growth on aromatic hydrocarbons. (6) High quality draft genome sequences and a complete eco-physiological description are completed for R. denitrificans strain 2APBS1 and G. daltonii strain FRC-32. (7) Given their demonstrated relevance to DOE remediation efforts and the availability of detailed genotypic/phenotypic characterization, Rhodanobacter denitrificans strain 2APBS1 and Geobacter daltonii strain FRC-32 represent ideal model organisms to provide a predictive understanding of subsurface microbial activity through metabolic modeling. Tasks II and III-Diversity and distribution of active anaerobes and Mechanisms linking electron transport and the fate of radionuclides: (1) Our study showed that members of genus Rhodanobacter and Geobacter are abundant and active in the uranium and nitrate contaminated subsurface. In the contaminant source zone of the Oak Ridge site, Rhodanobacter spp. are the predominant, active organisms detected

  14. Metatranscriptomic evidence of pervasive and diverse chemolithoautotrophy relevant to C, S, N and Fe cycling in a shallow alluvial aquifer

    PubMed Central

    Jewell, Talia N M; Karaoz, Ulas; Brodie, Eoin L; Williams, Kenneth H; Beller, Harry R

    2016-01-01

    Groundwater ecosystems are conventionally thought to be fueled by surface-derived allochthonous organic matter and dominated by heterotrophic microbes living under often-oligotrophic conditions. However, in a 2-month study of nitrate amendment to a perennially suboxic aquifer in Rifle (CO), strain-resolved metatranscriptomic analysis revealed pervasive and diverse chemolithoautotrophic bacterial activity relevant to C, S, N and Fe cycling. Before nitrate injection, anaerobic ammonia-oxidizing (anammox) bacteria accounted for 16% of overall microbial community gene expression, whereas during the nitrate injection, two other groups of chemolithoautotrophic bacteria collectively accounted for 80% of the metatranscriptome: (1) members of the Fe(II)-oxidizing Gallionellaceae family and (2) strains of the S-oxidizing species, Sulfurimonas denitrificans. Notably, the proportion of the metatranscriptome accounted for by these three groups was considerably greater than the proportion of the metagenome coverage that they represented. Transcriptional analysis revealed some unexpected metabolic couplings, in particular, putative nitrate-dependent Fe(II) and S oxidation among nominally microaerophilic Gallionellaceae strains, including expression of periplasmic (NapAB) and membrane-bound (NarGHI) nitrate reductases. The three most active groups of chemolithoautotrophic bacteria in this study had overlapping metabolisms that allowed them to occupy different yet related metabolic niches throughout the study. Overall, these results highlight the important role that chemolithoautotrophy can have in aquifer biogeochemical cycling, a finding that has broad implications for understanding terrestrial carbon cycling and is supported by recent studies of geochemically diverse aquifers. PMID:26943628

  15. Low-Toxicity Diindol-3-ylmethanes as Potent Antifouling Compounds.

    PubMed

    Wang, Kai-Ling; Xu, Ying; Lu, Liang; Li, Yongxin; Han, Zhuang; Zhang, Jun; Shao, Chang-Lun; Wang, Chang-Yun; Qian, Pei-Yuan

    2015-10-01

    In the present study, eight natural products that belonged to di(1H-indol-3-yl)methane (DIM) family were isolated from Pseudovibrio denitrificans UST4-50 and tested for their antifouling activity against larval settlement (including both attachment and metamorphosis) of the barnacle Balanus (=Amphibalanus) amphitrite and the bryozoan Bugula neritina. All diindol-3-ylmethanes (DIMs) showed moderate to strong inhibitory effects against larval settlement of B. amphitrite with EC50 values ranging from 18.57 to 1.86 μM and could be considered as low-toxicity antifouling compounds since their LC50/EC50 ratios were larger than 15. Furthermore, the DIM- and 4-(di(1H-indol-3-yl)methyl)phenol (DIM-Ph-4-OH)-treated larvae completed normal settlement when they were transferred to clean seawater after being exposed to those compounds for 24 h. DIM also showed comparable antifouling performance to the commercial antifouling biocide Sea-Nine 211(™) in the field test over a period of 5 months, which further confirmed that DIMs can be considered as promising candidates of environmentally friendly antifouling compounds.

  16. Characterization of the bacterial community in a biotrickling filter treating high loads of H(2)S by molecular biology tools.

    PubMed

    Maestre, Juan P; Rovira, Roger; Gamisans, Xavier; Kinney, Kerry A; Kirisits, Mary Jo; Lafuente, Javier; Gabriel, David

    2009-01-01

    The diversity and spatial distribution of bacteria in a lab-scale biotrickling filter treating high loads of hydrogen sulfide (H(2)S) were investigated. Diversity and community structure were studied by terminal-restriction fragment length polymorphism (T-RFLP). A 16S rRNA gene clone library was established. Near Full-length 16S rRNA gene sequences were obtained, and clones were clustered into 24 operational taxonomic units (OTUs). Nearly 74% and 26% of the clones were affiliated with the phyla Proteobacteria and Bacteroidetes, respectively. Beta-, epsilon- and gamma-proteobacteria accounted for 15, 9 and 48%, respectively. Around 45% of the sequences retrieved were affiliated to bacteria of the sulfur cycle including Thiothrix spp., Thiobacillus spp. and Sulfurimonas denitrificans. Sequences related to Thiothrix lacustris accounted for a 38%. Rarefaction curve demonstrated that clone library constructed can be sufficient to describe the vast majority of the bacterial diversity of this reactor operating under strict conditions (2,000 ppm(v) of H(2)S). A spatial distribution of bacteria was found along the length of the reactor by means of the T-RFLP technique. Although aerobic species were predominant along the reactor, facultative anaerobes had a major relative abundance in the inlet part of the reactor, where the sulfide to oxygen ratio is higher.

  17. Compared microbiology of granular sludge under autotrophic, mixotrophic and heterotrophic denitrification conditions.

    PubMed

    Fernández, N; Sierra-Alvarez, R; Amils, R; Field, J A; Sanz, J L

    2009-01-01

    Water contamination by nitrate is a wideworld extended phenomena. Biological autotrophic denitrification has a real potential to face this problem and presents less drawbacks than the most extended heterotrophic denitrification. Three bench-scale UASB reactors were operated under autotrophic (R1, H2S as electron donor), mixotrophic (R2, H2S plus p-cresol as electron donors) and heterotrophic (R3, p-cresol as electron donor) conditions using nitrate as terminal electron acceptor. 16S rDNA genetic libraries were built up to compare their microbial biodiversity. Six different bacteria phyla and three archaeal classes were observed. Proteobacteria was the main phyla in all reactors standing out the presence of denitrifiers. Microorganisms similar to Thiobacillus denitrificans and Acidovorax sp. performed the autotrophic denitification. These OTUs were displaced by chemoheterotrophic denitrifiers, especially by Limnobacter-like and Ottowia-like OTUs. Other phyla were Bacteroidetes, Chloroflexi, Firmicutes and Actinobacteria that--as well as Archaea members--were implicated in the degradation of organic matter, as substrate added as coming from endogenous sludge decay under autotrophic conditions. Archaea diversity remained low in all the reactors being Methanosaeta concilii the most abundant one.

  18. Shifts in microbial community composition and function in the acidification of a lead/zinc mine tailings.

    PubMed

    Chen, Lin-Xing; Li, Jin-Tian; Chen, Ya-Ting; Huang, Li-Nan; Hua, Zheng-Shuang; Hu, Min; Shu, Wen-Sheng

    2013-09-01

    In an attempt to link the microbial community composition and function in mine tailings to the generation of acid mine drainage, we simultaneously explored the geochemistry and microbiology of six tailings collected from a lead/zinc mine, i.e. primary tailings (T1), slightly acidic tailings (T2), extremely acidic tailings (T3, T4 and T5) and orange-coloured oxidized tailings (T6). Geochemical results showed that the six tailings (from T1 to T6) likely represented sequential stages of the acidification process of the mine tailings. 16S rRNA pyrosequencing revealed a contrasting microbial composition between the six tailings: Proteobacteria-related sequences dominated T1-T3 with relative abundance ranging from 56 to 93%, whereas Ferroplasma-related sequences dominated T4-T6 with relative abundance ranging from 28 to 58%. Furthermore, metagenomic analysis of the microbial communities of T2 and T6 indicated that the genes encoding key enzymes for microbial carbon fixation, nitrogen fixation and sulfur oxidation in T2 were largely from Thiobacillus and Acidithiobacillus, Methylococcus capsulatus, and Thiobacillus denitrificans respectively; while those in T6 were mostly identified in Acidithiobacillus and Leptospirillum, Acidithiobacillus and Leptospirillum, and Acidithiobacillus respectively. The microbial communities in T2 and T6 harboured more genes suggesting diverse metabolic capacities for sulfur oxidation/heavy metal detoxification and tolerating low pH respectively. © 2013 John Wiley & Sons Ltd and Society for Applied Microbiology.

  19. Short-term microbial effects of a large-scale mine-tailing storage facility collapse on the local natural environment

    PubMed Central

    Baldwin, Susan A.; Taylor, Jon; Gurr, David B.; Denesiuk, Daniel R.; Van Hamme, Jonathan D.; Fraser, Lauchlan H.

    2018-01-01

    We investigated the impacts of the Mount Polley tailings impoundment failure on chemical, physical, and microbial properties of substrates within the affected watershed, comprised of 70 hectares of riparian wetlands and 40 km of stream and lake shore. We established a biomonitoring network in October of 2014, two months following the disturbance, and evaluated riparian and wetland substrates for microbial community composition and function via 16S and full metagenome sequencing. A total of 234 samples were collected from substrates at 3 depths and 1,650,752 sequences were recorded in a geodatabase framework. These data revealed a wealth of information regarding watershed-scale distribution of microbial community members, as well as community composition, structure, and response to disturbance. Substrates associated with the impact zone were distinct chemically as indicated by elevated pH, nitrate, and sulphate. The microbial community exhibited elevated metabolic capacity for selenate and sulfate reduction and an abundance of chemolithoautotrophs in the Thiobacillus thiophilus/T. denitrificans/T. thioparus clade that may contribute to nitrate attenuation within the affected watershed. The most impacted area (a 6 km stream connecting two lakes) exhibited 30% lower microbial diversity relative to the remaining sites. The tailings impoundment failure at Mount Polley Mine has provided a unique opportunity to evaluate functional and compositional diversity soon after a major catastrophic disturbance to assess metabolic potential for ecosystem recovery. PMID:29694379

  20. Copper control of bacterial nitrous oxide emission and its impact on vitamin B12-dependent metabolism

    PubMed Central

    Sullivan, Matthew J.; Gates, Andrew J.; Appia-Ayme, Corinne; Rowley, Gary; Richardson, David J.

    2013-01-01

    Global agricultural emissions of the greenhouse gas nitrous oxide (N2O) have increased by around 20% over the last 100 y, but regulation of these emissions and their impact on bacterial cellular metabolism are poorly understood. Denitrifying bacteria convert nitrate in soils to inert di-nitrogen gas (N2) via N2O and the biochemistry of this process has been studied extensively in Paracoccus denitrificans. Here we demonstrate that expression of the gene encoding the nitrous oxide reductase (NosZ), which converts N2O to N2, is regulated in response to the extracellular copper concentration. We show that elevated levels of N2O released as a consequence of decreased cellular NosZ activity lead to the bacterium switching from vitamin B12-dependent to vitamin B12-independent biosynthetic pathways, through the transcriptional modulation of genes controlled by vitamin B12 riboswitches. This inhibitory effect of N2O can be rescued by addition of exogenous vitamin B12. PMID:24248380

  1. Identifying and Quantifying the Intermediate Processes during Nitrate-Dependent Iron(II) Oxidation.

    PubMed

    Jamieson, James; Prommer, Henning; Kaksonen, Anna H; Sun, Jing; Siade, Adam J; Yusov, Anna; Bostick, Benjamin

    2018-05-15

    Microbially driven nitrate-dependent iron (Fe) oxidation (NDFO) in subsurface environments has been intensively studied. However, the extent to which Fe(II) oxidation is biologically catalyzed remains unclear because no neutrophilic iron-oxidizing and nitrate reducing autotroph has been isolated to confirm the existence of an enzymatic pathway. While mixotrophic NDFO bacteria have been isolated, understanding the process is complicated by simultaneous abiotic oxidation due to nitrite produced during denitrification. In this study, the relative contributions of biotic and abiotic processes during NDFO were quantified through the compilation and model-based interpretation of previously published experimental data. The kinetics of chemical denitrification by Fe(II) (chemodenitrification) were assessed, and compelling evidence was found for the importance of organic ligands, specifically exopolymeric substances secreted by bacteria, in enhancing abiotic oxidation of Fe(II). However, nitrite alone could not explain the observed magnitude of Fe(II) oxidation, with 60-75% of overall Fe(II) oxidation attributed to an enzymatic pathway for investigated strains: Acidovorax ( A.) strain BoFeN1, 2AN, A. ebreus strain TPSY, Paracoccus denitrificans Pd 1222, and Pseudogulbenkiania sp. strain 2002. By rigorously quantifying the intermediate processes, this study eliminated the potential for abiotic Fe(II) oxidation to be exclusively responsible for NDFO and verified the key contribution from an additional, biological Fe(II) oxidation process catalyzed by NDFO bacteria.

  2. Operational and biological analyses of branched water-adjustment and combined treatment of wastewater from a chemical industrial park.

    PubMed

    Xu, Ming; Cao, Jiashun; Li, Chao; Tu, Yong; Wu, Haisuo; Liu, Weijing

    2018-01-01

    The combined biological processes of branched water-adjustment, chemical precipitation, hydrolysis acidification, secondary sedimentation, Anoxic/Oxic and activated carbon treatment were used for chemical industrial wastewater treatment in the Taihu Lake Basin. Full-scale treatment resulted in effluent chemical oxygen demand, total nitrogen, NH 3 -N and total phosphorus of 35.1, 5.20, 3.10 and 0.15 mg/L, respectively, with a total removal efficiency of 91.1%, 67.1%, 70.5% and 89.3%, respectively. In this process, short-circuited organic carbon from brewery wastewater was beneficial for denitrification and second-sulfate reduction. The concentration of effluent fluoride was 6.22 mg/L, which also met the primary standard. Gas Chromatography-Mass Spectrometry analysis revealed that many types of refractory compounds were present in the inflow. Microbial community analysis performed in the summer by PCR-denaturing gradient gel electrophoresis and MiSeq demonstrated that certain special functional bacteria, such as denitrificans, phosphorus-accumulating bacteria, sulfate- and perhafnate-reducing bacteria, aromatic compound-degrading bacteria and organic fluoride-degrading bacteria, present in the bio-tanks were responsible for the acceptable specific biological pollutant reduction achieved.

  3. Structures and physiological roles of 13 integral lipids of bovine heart cytochrome c oxidase

    PubMed Central

    Shinzawa-Itoh, Kyoko; Aoyama, Hiroshi; Muramoto, Kazumasa; Terada, Hirohito; Kurauchi, Tsuyoshi; Tadehara, Yoshiki; Yamasaki, Akiko; Sugimura, Takashi; Kurono, Sadamu; Tsujimoto, Kazuo; Mizushima, Tsunehiro; Yamashita, Eiki; Tsukihara, Tomitake; Yoshikawa, Shinya

    2007-01-01

    All 13 lipids, including two cardiolipins, one phosphatidylcholine, three phosphatidylethanolamines, four phosphatidylglycerols and three triglycerides, were identified in a crystalline bovine heart cytochrome c oxidase (CcO) preparation. The chain lengths and unsaturated bond positions of the fatty acid moieties determined by mass spectrometry suggest that each lipid head group identifies its specific binding site within CcOs. The X-ray structure demonstrates that the flexibility of the fatty acid tails facilitates their effective space-filling functions and that the four phospholipids stabilize the CcO dimer. Binding of dicyclohexylcarbodiimide to the O2 transfer pathway of CcO causes two palmitate tails of phosphatidylglycerols to block the pathway, suggesting that the palmitates control the O2 transfer process.The phosphatidylglycerol with vaccenate (cis-Δ11-octadecenoate) was found in CcOs of bovine and Paracoccus denitrificans, the ancestor of mitochondrion, indicating that the vaccenate is conserved in bovine CcO in spite of the abundance of oleate (cis-Δ9-octadecenoate). The X-ray structure indicates that the protein moiety selects cis-vaccenate near the O2 transfer pathway against trans-vaccenate. These results suggest that vaccenate plays a critical role in the O2 transfer mechanism. PMID:17332748

  4. Perchlorate and halophilic prokaryotes: implications for possible halophilic life on Mars.

    PubMed

    Oren, Aharon; Elevi Bardavid, Rahel; Mana, Lily

    2014-01-01

    In view of the finding of perchlorate among the salts detected by the Phoenix Lander on Mars, we investigated the relationships of halophilic heterotrophic microorganisms (archaea of the family Halobacteriaceae and the bacterium Halomonas elongata) toward perchlorate. All strains tested grew well in NaCl-based media containing 0.4 M perchlorate, but at the highest perchlorate concentrations, tested cells were swollen or distorted. Some species (Haloferax mediterranei, Haloferax denitrificans, Haloferax gibbonsii, Haloarcula marismortui, Haloarcula vallismortis) could use perchlorate as an electron acceptor for anaerobic growth. Although perchlorate is highly oxidizing, its presence at a concentration of 0.2 M for up to 2 weeks did not negatively affect the ability of a yeast extract-based medium to support growth of the archaeon Halobacterium salinarum. These findings show that presence of perchlorate among the salts on Mars does not preclude the possibility of halophilic life. If indeed the liquid brines that may exist on Mars are inhabited by salt-requiring or salt-tolerant microorganisms similar to the halophiles on Earth, presence of perchlorate may even be stimulatory when it can serve as an electron acceptor for respiratory activity in the anaerobic Martian environment.

  5. Evaluation of pyrrolidonyl arylamidase for the identification of nonfermenting Gram-negative rods.

    PubMed

    Bombicino, Karina A; Almuzara, Marisa N; Famiglietti, Angela M R; Vay, Carlos

    2007-01-01

    To evaluate the activity of pyrrolidonyl arylamidase (PYR) for the differentiation and identification of nonfermenting gram negative rods (NFGNR), 293 isolates were tested. A 24 h culture of each test organism was prepared. From this a 108-109 cfu/mL suspension was added to 0.25 mL of sterile physiologic solution. A PYR disk was then added and the test was incubated for 30 minutes at 35-37 degrees C, at environmental atmosphere. Reading was done by adding 1 drop of cinnamaldehyde reagent. Strains of Acinetobacter baumannii, Acinetobacter haemolyticus, Alcaligenes faecalis, Bergeyella zoohelcum, Bordetella bronchiseptica, Bordetella hinzii, Brevundimonas diminuta, Brevundimonas vesicularis, Brucella ovis, Brucella spp., Brucella suis, Burkholderia cepacia complex, Moraxella catarrhalis, Moraxella lacunata, Moraxella nonliquefaciens, Moraxella osloensis, Oligella ureolytica, Pseudomonas alcaligenes, Pseudomonas mendocina, Pseudomonas pseudoalcaligenes, Pseudomonas putida, Pseudomonas stutzeri, Pseudomonas Vb3, Psychrobacter phenylpyruvicus, and Stenotrophomonas maltophilia were PYR negative. On the other hand Achromobacter piechaudii, Achromobacter denitrificans, Achromobacter xylosoxidans, Burkholderia gladioli, Chryseobacterium gleum-indologenes, Comamonas testosroni, Cupriavidus pauculus, Delftia acidovorans, Elizabethkingia meningoseptica, Myroides spp., Ochrobactrum anthropi, Pseudomonas oryzihabitans, Ralstonia pickettii, Rhizobium radiobacter, Shewanella spp., Sphingobacterium multivorum, Sphingobacterium spiritivorum, and Weeksella virosa were PYR positive. Finally, Acinetobacter lwoffii, Pseudomonas aeruginosa, Pseudomonas fluorescens, Roseomonas spp., and Sphingomonas paucimobilis-parapaucimobilis were PYR variable. PYR testing should be considered as a useful tool to facilitate the identification of NFGNR.

  6. Metatranscriptomic evidence of pervasive and diverse chemolithoautotrophy relevant to C, S, N and Fe cycling in a shallow alluvial aquifer

    DOE PAGES

    Jewell, Talia N. M.; Karaoz, Ulas; Brodie, Eoin L.; ...

    2016-03-04

    Groundwater ecosystems are conventionally thought to be fueled by surface-derived allochthonous organic matter and dominated by heterotrophic microbes living under often-oligotrophic conditions. However, in a 2-month study of nitrate amendment to a perennially suboxic aquifer in Rifle (CO), strain-resolved metatranscriptomic analysis revealed pervasive and diverse chemolithoautotrophic bacterial activity relevant to C, S, N and Fe cycling. Before nitrate injection, anaerobic ammonia-oxidizing (anammox) bacteria accounted for 16% of overall microbial community gene expression, whereas during the nitrate injection, two other groups of chemolithoautotrophic bacteria collectively accounted for 80% of the metatranscriptome: (1) members of the Fe(II)-oxidizing Gallionellaceae family and (2) strainsmore » of the S-oxidizing species, Sulfurimonas denitrificans. Notably, the proportion of the metatranscriptome accounted for by these three groups was considerably greater than the proportion of the metagenome coverage that they represented. Transcriptional analysis revealed some unexpected metabolic couplings, in particular, putative nitrate-dependent Fe(II) and S oxidation among nominally microaerophilic Gallionellaceae strains, including expression of periplasmic (NapAB) and membrane-bound (NarGHI) nitrate reductases. The three most active groups of chemolithoautotrophic bacteria in this study had overlapping metabolisms that allowed them to occupy different yet related metabolic niches throughout the study. Overall, these results highlight the important role that chemolithoautotrophy can have in aquifer biogeochemical cycling, a finding that has broad implications for understanding terrestrial carbon cycling and is supported by recent studies of geochemically diverse aquifers.« less

  7. Structure-based analysis of CysZ-mediated cellular uptake of sulfate

    DOE PAGES

    Assur Sanghai, Zahra; Liu, Qun; Clarke, Oliver B.; ...

    2018-05-24

    Sulfur, most abundantly found in the environment as sulfate (SO 4 2-), is an essential element in metabolites required by all living cells, including amino acids, co-factors and vitamins. However, current understanding of the cellular delivery of SO 4 2- at the molecular level is limited. CysZ has been described as a SO 4 2- permease, but its sequence family is without known structural precedent. Based on crystallographic structure information, SO 4 2- binding and flux experiments, we provide insight into the molecular mechanism of CysZ-mediated translocation of SO 4 2- across membranes. CysZ structures from three different bacterial speciesmore » display a hitherto unknown fold and have subunits organized with inverted transmembrane topology. CysZ from Pseudomonas denitrificans assembles as a trimer of antiparallel dimers and the CysZ structures from two other species recapitulate dimers from this assembly. In conclusion, mutational studies highlight the functional relevance of conserved CysZ residues.« less

  8. The role of microbial biofilms in deterioration of space station candidate materials.

    PubMed

    Gu, J D; Roman, M; Esselman, T; Mitchell, R

    1998-01-01

    Formation of microbial biofilms on surfaces of a wide range of materials being considered as candidates for use on the International Space Station was investigated. The materials included a fibre-reinforced polymeric composite, an adhesive sealant, a polyimide insulation foam, teflon cable insulation, titanium, and an aliphatic polyurethane coating. They were exposed to a natural mixed population of bacteria under controlled conditions of temperature and relative humidity (RH). Biofilms formed on the surfaces of the materials at a wide range of temperatures and RHs. The biofilm population was dominated by Pseudomonas aeruginosa, Ochrobactrum anthropi, Alcaligenes denitrificans, Xanthomonas maltophila, and Vibrio harveyi. The biocide, diiodomethyl-p-tolyl sulfone, impregnated in the polyurethane coating, was ineffective against microbial colonization and growth. Degradation of the polyurethane coatings was monitored with electrochemical impedance spectroscopy (EIS). The impedance spectra indicated that microbial degradation of the coating occurred in several stages. The initial decreases in impedance were due to the transport of water and solutes into the polymeric matrices. Further decreases were a result of polymer degradation by microorganisms. Our data showed that these candidate materials for space application are susceptible to biofilm formation and subsequent degradation. Our study suggests that candidate materials for use in space missions need to be carefully evaluated for their susceptibility to microbial biofilm formation and biodegradation.

  9. Molybdoenzyme That Catalyzes the Anaerobic Hydroxylation of a Tertiary Carbon Atom in the Side Chain of Cholesterol*

    PubMed Central

    Dermer, Juri; Fuchs, Georg

    2012-01-01

    Cholesterol is a ubiquitous hydrocarbon compound that can serve as substrate for microbial growth. This steroid and related cyclic compounds are recalcitrant due to their low solubility in water, complex ring structure, the presence of quaternary carbon atoms, and the low number of functional groups. Aerobic metabolism therefore makes use of reactive molecular oxygen as co-substrate of oxygenases to hydroxylate and cleave the sterane ring system. Consequently, anaerobic metabolism must substitute oxygenase-catalyzed steps by O2-independent hydroxylases. Here we show that one of the initial reactions of anaerobic cholesterol metabolism in the β-proteobacterium Sterolibacterium denitrificans is catalyzed by an unprecedented enzyme that hydroxylates the tertiary C25 atom of the side chain without molecular oxygen forming a tertiary alcohol. This steroid C25 dehydrogenase belongs to the dimethyl sulfoxide dehydrogenase molybdoenzyme family, the closest relative being ethylbenzene dehydrogenase. It is a heterotrimer, which is probably located at the periplasmic side of the membrane and contains one molybdenum cofactor, five [Fe-S] clusters, and one heme b. The draft genome of the organism contains several genes coding for related enzymes that probably replace oxygenases in steroid metabolism. PMID:22942275

  10. Cytochrome c Oxidase Biogenesis and Metallochaperone Interactions: Steps in the Assembly Pathway of a Bacterial Complex

    PubMed Central

    Ludwig, Bernd

    2017-01-01

    Biogenesis of mitochondrial cytochrome c oxidase (COX) is a complex process involving the coordinate expression and assembly of numerous subunits (SU) of dual genetic origin. Moreover, several auxiliary factors are required to recruit and insert the redox-active metal compounds, which in most cases are buried in their protein scaffold deep inside the membrane. Here we used a combination of gel electrophoresis and pull-down assay techniques in conjunction with immunostaining as well as complexome profiling to identify and analyze the composition of assembly intermediates in solubilized membranes of the bacterium Paracoccus denitrificans. Our results show that the central SUI passes through at least three intermediate complexes with distinct subunit and cofactor composition before formation of the holoenzyme and its subsequent integration into supercomplexes. We propose a model for COX biogenesis in which maturation of newly translated COX SUI is initially assisted by CtaG, a chaperone implicated in CuB site metallation, followed by the interaction with the heme chaperone Surf1c to populate the redox-active metal-heme centers in SUI. Only then the remaining smaller subunits are recruited to form the mature enzyme which ultimately associates with respiratory complexes I and III into supercomplexes. PMID:28107462

  11. Microbial interspecies electron transfer via electric currents through conductive minerals

    PubMed Central

    Kato, Souichiro; Hashimoto, Kazuhito; Watanabe, Kazuya

    2012-01-01

    In anaerobic biota, reducing equivalents (electrons) are transferred between different species of microbes [interspecies electron transfer (IET)], establishing the basis of cooperative behaviors and community functions. IET mechanisms described so far are based on diffusion of redox chemical species and/or direct contact in cell aggregates. Here, we show another possibility that IET also occurs via electric currents through natural conductive minerals. Our investigation revealed that electrically conductive magnetite nanoparticles facilitated IET from Geobacter sulfurreducens to Thiobacillus denitrificans, accomplishing acetate oxidation coupled to nitrate reduction. This two-species cooperative catabolism also occurred, albeit one order of magnitude slower, in the presence of Fe ions that worked as diffusive redox species. Semiconductive and insulating iron-oxide nanoparticles did not accelerate the cooperative catabolism. Our results suggest that microbes use conductive mineral particles as conduits of electrons, resulting in efficient IET and cooperative catabolism. Furthermore, such natural mineral conduits are considered to provide ecological advantages for users, because their investments in IET can be reduced. Given that conductive minerals are ubiquitously and abundantly present in nature, electric interactions between microbes and conductive minerals may contribute greatly to the coupling of biogeochemical reactions. PMID:22665802

  12. Autotrophic, hydrogen-oxidizing, denitrifying bacteria in groundwater, potential agents for bioremediation of nitrate contamination

    Smith, R.L.; Ceazan, M.L.; Brooks, M.H.

    1994-01-01

    Addition of hydrogen or formate significantly enhanced the rate of consumption of nitrate in slurried core samples obtained from an active zone of denitrification in a nitrate-contaminated sand and gravel aquifer (Cape Cod, Mass.). Hydrogen uptake by the core material was immediate and rapid, with an apparent K(m) of 0.45 to 0.60 ??M and a V(max) of 18.7 nmol cm-3 h-1 at 30??C. Nine strains of hydrogen-oxidizing denitrifying bacteria were subsequently isolated from the aquifer. Eight of the strains grew autotrophically on hydrogen with either oxygen or nitrate as the electron acceptor. One strain grew mixotrophically. All of the isolates were capable of heterotrophic growth, but none were similar to Paracoccus denitrificans, a well-characterized hydrogen-oxidizing denitrifier. The kinetics for hydrogen uptake during denitrification were determined for each isolate with substrate depletion progress curves; the K(m)s ranged from 0.30 to 3.32 ??M, with V(max)s of 1.85 to 13.29 fmol cell-1 h-1. Because these organisms appear to be common constituents of the in situ population of the aquifer, produce innocuous end products, and could be manipulated to sequentially consume oxygen and then nitrate when both were present, these results suggest that these organisms may have significant potential for in situ bioremediation of nitrate contamination in groundwater.

  13. A novel in situ permeation system and its utility in cancer tissue ablation

    PubMed Central

    WATANABE, MASAMI

    2015-01-01

    Focal ablation therapy is an emerging treatment modality for localized cancer lesions. It is an attractive strategy for inhibiting tumor progression and preventing morbidity associated with open surgery. As for intratissue drug delivery systems for use in local therapy, the convection-enhanced delivery (CED) of liquid drugs has been utilized, particularly for the treatment of malignant brain tumors. Although the conventional CED system is useful for providing drug/vehicle-based local therapy, there are several reported disadvantages in terms of the ability to control the extent of drug diffusion. We herein developed and validated a novel in situ permeation (ISP)-MW-1 system for achieving intratissue drug diffusion. The ISP system includes a perfusion catheter connected to an injector and aspirator, which enables intratissue perfusion of the solute diluted in the vehicle in the tip-inserted cavity. We subsequently evaluated the utility of the ISP-MW-1 system for in situ permeation in a subcutaneous tumor model in hamsters. Dehydrated ethanol, saline and 50% acetic acid were evaluated as the vehicle, and methylene blue was used as a dissolved substance for evaluating the diffusion of the agent. As a result, almost all of the tumor tissue within the capsule (tumor size: ~3 cm) was permeated with the dehydrated ethanol and 50% acetic acid and partially with the saline. We further demonstrated that ISP treatment with 50% acetic acid completely ablated the subcutaneous tumors in all of the treated hamsters (n=3). Therefore, the ISP-MW-1 system is a promising approach for controlling the intratissue diffusion of therapeutic agents and for providing local ablation therapy for cancer lesions. We believe that this system may be applicable to a broad range of medicinal and industrial fields, such as regenerative medicine, drug delivery systems, biochemistry and material technologies as well as cancer therapy. PMID:26134633

  14. Validation of the Compassion Fatigue Short Scale among Chinese medical workers and firefighters: a cross-sectional study

    PubMed Central

    Sun, Binghai; Hu, Mengna; Yu, Shitian; Jiang, Yiru; Lou, Baona

    2016-01-01

    Objectives To examine the psychometric properties of the Chinese version of the C-Compassion Fatigue (CF)-Short Scale among 4 independent samples of Chinese emergency workers (medical workers and firefighters). Design Cross-sectional. Setting 6 hospitals in Zhejiang Province and 12 fire stations in Shanghai. Participants Emergency workers (medical and firefighters) were consecutively recruited and divided into 4 groups: the MW1 group (medical workers, n=167), the FF1 group (firefighters, n=157), the MW2 group (medical workers, n=265) and the FF2 group (firefighters, n=231). Interventions All patients completed the C-CF-Short Scale to identify factors associated with compassion fatigue. The MW1 and FF1 groups were used for the exploratory analyses. The MW2 and FF2 groups were used for the confirmatory factor analyses. Primary and secondary outcome measures Factor loading, correlations with previously validated questionnaires (the Ego-Resiliency Scale, the Social Support Questionnaire and the Job Pressure Scale) and Cronbach's α coefficient were tested for each factor. Results The C-CF-Short Scale demonstrated excellent construct validity and good internal consistency. Specifically, the results of exploratory factor analyses in the MW1 and FF1 groups showed that secondary trauma and job burnout were associated with compassion fatigue in these emergency workers. The confirmatory factor analyses in the MW2 and FF2 groups indicated that all the fit indices of the 2-factor model were satisfactory. Finally, the Cronbach's α coefficient of each factor was excellent. Conclusions The findings suggest that the C-CF-Short Scale has good psychometric properties and can be applied to study Chinese emergency workers. PMID:27363817

  15. Very Low Cost Expendable Harassment System Design Study. Volume 3

    DTIC Science & Technology

    1975-12-01

    Vst = W = wf. w = g a, = a O. 3D LO * n ■ 0 = thrust horsepower anailable (hp) thrust horsepower required (hp) airspeed (mph) stall...A-113 ^rr-r-^rfr^r- "- -—’^’ iääaääiäitämäiA Hi^l^Wt^MjMW^1^-^^^ APPENDIX A-6-2 DESIGN OUTPUT VST SL VST 3K WEIGHT VST (S=17,0... angular velocity change of rolling moment from a change in yaw angular velocity change of rolling moment from a change in sideslip angle change of

  16. Asymmetric Multilevel Outphasing (AMO): A New Architecture for All-Silicon mm-Wave Transmitter ICs

    DTIC Science & Technology

    2015-06-12

    power-amplifiers for mobile basestation infrastructure and handsets. NanoSemi Inc. designs linearization solutions for analog front-ends such as...ward flexible, multi-standard radio chips, increases the need for high-precision, high-throughput and energy-efficient backend processing. The desire...peak PAE is affected by less than 1% (46 mW/(46 mW 1.8 W/0.4)) by this 64-QAM capable AMO SCS backend . 378 IEEE JOURNAL OF SOLID-STATE CIRCUITS, VOL. 48

  17. LASER APPLICATIONS AND OTHER TOPICS IN QUANTUM ELECTRONICS: Laser microphotoacoustic sensor of ammonia traces in the atmosphere

    NASA Astrophysics Data System (ADS)

    Serebryakov, D. V.; Morozov, I. V.; Kosterev, A. A.; Letokhov, V. S.

    2010-02-01

    A microphotoacoustic highly selective sensor of ammonia is built. Main attention is paid to the operation mechanism of the acoustic sensor based on a quartz tuning fork. The optimal dimensions and configuration of the acoustic resonator are determined, which made it possible to increase the sensor sensitivity by two—three times compared to the sensitivity of the existing devices. The detector sensitivity for ammonia was 60ppb (0.05 mg m-3) for the measurement time of 10s and a 25-mW, 1.53-μm laser beam in the acoustic resonator.

  18. Efficient telecom to visible wavelength conversion in doubly resonant gallium phosphide microdisks

    NASA Astrophysics Data System (ADS)

    Lake, David P.; Mitchell, Matthew; Jayakumar, Harishankar; dos Santos, Laís Fujii; Curic, Davor; Barclay, Paul E.

    2016-01-01

    Resonant second harmonic generation between 1550 nm and 775 nm with normalized outside efficiency > 3.8 × 10 - 4 mW - 1 is demonstrated in a gallium phosphide microdisk supporting high-Q modes at visible ( Q ˜ 10 4 ) and infrared ( Q ˜ 10 5 ) wavelengths. The double resonance condition is satisfied for a specific pump power through intracavity photothermal temperature tuning using ˜ 360 μ W of 1550 nm light input to a fiber taper and coupled to a microdisk resonance. Power dependent efficiency consistent with a simple model for thermal tuning of the double resonance condition is observed.

  19. Packaged, High-Power, Narrow-Linewidth Slab-Coupled Optical Waveguide External Cavity Laser (SCOWECL)

    DTIC Science & Technology

    2010-12-01

    1946. [21 Y. Li and P. Herczfe1d, "Coherent PM Optical Link Employing ACP-PPLL," 1. Light\\\\"{l\\’e TechI /O!., vol. 27 . pp. 1086-1094, 2009. [31 C...Lightli"rn·e TechI /O!. , vol. 22, pp. 57- 62.2004. [4] G. A. finll, C. E. Holton, G. Hull-Allen, ::md W. W. l\\·lorey. ඄ mW 1.5 )1111 si ngle

  20. Fungal degradation of coal as a pretreatment for methane production

    Haider, Rizwan; Ghauri, Muhammad A.; SanFilipo, John R.; Jones, Elizabeth J.; Orem, William H.; Tatu, Calin A.; Akhtar, Kalsoom; Akhtar, Nasrin

    2013-01-01

    Coal conversion technologies can help in taking advantage of huge low rank coal reserves by converting those into alternative fuels like methane. In this regard, fungal degradation of coal can serve as a pretreatment step in order to make coal a suitable substrate for biological beneficiation. A fungal isolate MW1, identified as Penicillium chrysogenum on the basis of fungal ITS sequences, was isolated from a core sample of coal, taken from a well drilled by the US. Geological Survey in Montana, USA. The low rank coal samples, from major coal fields of Pakistan, were treated with MW1 for 7 days in the presence of 0.1% ammonium sulfate as nitrogen source and 0.1% glucose as a supplemental carbon source. Liquid extracts were analyzed through Excitation–Emission Matrix Spectroscopy (EEMS) to obtain qualitative estimates of solubilized coal; these analyses indicated the release of complex organic functionalities. In addition, GC–MS analysis of these extracts confirmed the presence of single ring aromatics, polyaromatic hydrocarbons (PAHs), aromatic nitrogen compounds and aliphatics. Subsequently, the released organics were subjected to a bioassay for the generation of methane which conferred the potential application of fungal degradation as pretreatment. Additionally, fungal-mediated degradation was also prospected for extracting some other chemical entities like humic acids from brown coals with high huminite content especially from Thar, the largest lignite reserve of Pakistan.

  1. Effect of polymerization method and fabrication method on occlusal vertical dimension and occlusal contacts of complete-arch prosthesis.

    PubMed

    Lima, Ana Paula Barbosa; Vitti, Rafael Pino; Amaral, Marina; Neves, Ana Christina Claro; da Silva Concilio, Lais Regiane

    2018-04-01

    This study evaluated the dimensional stability of a complete-arch prosthesis processed by conventional method in water bath or microwave energy and polymerized by two different curing cycles. Forty maxillary complete-arch prostheses were randomly divided into four groups (n = 10): MW1 - acrylic resin cured by one microwave cycle; MW2 - acrylic resin cured by two microwave cycles: WB1 - conventional acrylic resin polymerized using one curing cycle in a water bath; WB2 - conventional acrylic resin polymerized using two curing cycles in a water bath. For evaluation of dimensional stability, occlusal vertical dimension (OVD) and area of contact points were measured in two different measurement times: before and after the polymerization method. A digital caliper was used for OVD measurement. Occlusal contact registration strips were used between maxillary and mandibular dentures to measure the contact points. The images were measured using the software IpWin32, and the differences before and after the polymerization methods were calculated. The data were statistically analyzed using the one-way ANOVA and Tukey test (α = .05). he results demonstrated significant statistical differences for OVD between different measurement times for all groups. MW1 presented the highest OVD values, while WB2 had the lowest OVD values ( P <.05). No statistical differences were found for area of contact points among the groups ( P =.7150). The conventional acrylic resin polymerized using two curing cycles in a water bath led to less difference in OVD of complete-arch prosthesis.

  2. Macro-hydrogels versus nanoparticles by the controlled assembly of polysaccharides.

    PubMed

    Costalat, M; Alcouffe, P; David, L; Delair, T

    2015-12-10

    The controlled assembly of oppositely charged chitosan (CS, Mw ∼ 33 × 10(3) to 600 × 10(3)g mol(-1)) and dextran sulfate (DS, Mw = 1.3 × 10(6)g mol(-1)) or heparin (HP, Mw = 1.8 × 10(4)g mol(-1)) led either to nanoparticles or macro-hydrogels, at room temperature. The control over the electrostatic attractive interactions was achieved using 2 mol L(-1) NaCl in the polyion solutions and subsequent dialysis to let the assembly occur. Macrohydrogels formed with an excess of polyanion. In the presence of an excess of polycation, colloidal gels were exclusively obtained. At salt concentrations lower than 1 mol L(-1), the spontaneous gelation provided macro-hydrogels, whatever the polyion in excess. Rheology measurements showed a similar elastic behaviour for CS-DS and CS-HP hydrogels, though CS-HP hydrogels appeared less cohesive. SAXS experiments revealed an aggregate morphology with internal and surface structure depending on the degree of acetylation (DA) of chitosan. Copyright © 2015 Elsevier Ltd. All rights reserved.

  3. Correction methods of medicinal properties of mineral waters in Pyatigorsk resort

    NASA Astrophysics Data System (ADS)

    Reps, Valentina; Potapov, Evgeniy; Abramtsova, Anna; Kotova, Margarita

    2016-04-01

    Mineral Water (MW) of Pyatigorsk deposit (PD) is united in five genetic groups (operational stocks of 2809,8 m3/day): carbonic and hydrosulphuric, carbonic, carbonic chloride-hydrocarbonate sodium (salt and alkaline), radonic low carbonate, nitrogen-carbonic terms. A variety of MW types is explained by peculiarities of geological structure and hydrogeological conditions of PD. Here on the sites of the development of deep semi-ring splits there are overflows and a mixture of various complexes. Unloading of deep water strikes happens not only on the earth surface in the form of springs but also at the depth in its edging crumbling rocks of Palaeocene and quarternary deposits. As a result of mixture processes of water and its subsequent metamorphization, various types of mineral water of this deposit are formed. Pyatigorsk resort is in a special protected ecologo-resort region which mode allows to keep stability of structure and ecological purity of MW. Nevertheless, MW variability, compositional differences and MW mineralization determining the level of its biological effect demand studying of action mechanisms of both natural MW, and possibility of its modification for range expansion of rehabilitation action. There have been examined biological effects of the course drinking reception In experiment on 80 rats males of the Wistar line biological effects of the course drinking reception of two MW types: "Krasnoarmeyskaya new" (MW1) of sulphate-hydrocarbonate-chloride calcium-sodium structure with the raised contents of iron (3-5 mg/dm3), mineralization of 5,0-5,2 g/dm3, CO2 of 1,3-2,2 g/dm3, daily flow of 10-86 m3/day, temperature from 14 to 370C on the mouth of the well and spring №2 (MW2) low sulphate, low carbonate sulphate-hydrocarbonate-chloride calcium-sodium, mineralization of 5,0 g/l, CO2 of 0,7 g/dm3, H2 of S 0,01 g/dm3. There has been shown an ability of the drinking course MW1 to influence on endocrine and metabolic continium - cortisol level increased

  4. Groundwater geochemical and selected volatile organic compound data, Operable Unit 1, Naval Undersea Warfare Center, Division Keyport, Washington, June 2009

    Huffman, R.L.; Dinicola, R.S.

    2011-01-01

    than chlorinated VOC concentrations measured in previous years. In 2009, concentrations of reductive dechlorination byproducts ethane and ethene were less than those measured in 2008 at most northern plantation wells and piezometers. For the upper aquifer beneath the southern phytoremediation plantation, chlorinated VOC concentrations in 2009 at the piezometers were extremely high and continued to vary considerably over space and between years. At piezometer P1-9, the total chlorinated VOC concentration increased from 25,000 micrograms per liter in 2008 to more than 172,000 micrograms per liter in 2009. At piezometer P1-7 in 2009, the concentrations of trichloroethene and cis-1,2-dichloroethene (cis-DCE) were the highest to date. The reductive dechlorination byproducts ethane and ethene were detected at all wells and piezometers in the southern plantation with the exception of piezometer P1-8, although the measured concentrations were not consistently high. For the intermediate aquifer, concentrations of redox sensitive constituents and VOCs in 2009 at wells MW1-25, MW1-28, and MW1-39 were consistent with concentrations measured in previous years. Concentrations of the reductive dechlorination byproducts ethane and ethene at wells MW1-25 and MW1-28 were equal to or greater than previously measured concentrations.

  5. Final report : groundwater monitoring at Morrill, Kansas, in September 2005 and March 2006, with expansion of the monitoring network in January 2006.

    SciT

    LaFreniere, L. M.; Environmental Science Division

    2007-06-30

    This document reports the results of groundwater monitoring in September 2005 and March 2006 at the grain storage facility formerly operated at Morrill, Kansas, by the Commodity Credit Corporation of the U.S. Department of Agriculture (CCC/USDA). These activities were the first and second twice yearly sampling events of the two-year monitoring program approved by the CCC/USDA and Kansas Department of Health and Environment (KDHE) project managers. The monitoring network sampled in September 2005 consisted of 9 monitoring wells (MW1S-MW5S and MW1D [installed in the mid 1990s] and MW6S-MW8S [installed in 2004]), plus 3 private wells (Isch, Rillinger, and Stone). Themore » groundwater samples collected in this first event were analyzed for volatile organic compounds (VOCs), dissolved hydrogen, and additional groundwater parameters to aid in evaluating the potential for reductive dechlorination processes. After the monitoring in September 2005, Argonne recommended expansion of the initial monitoring network. Previous sampling (August 2004) had already suggested that the initial network was inadequate to delineate the extent of the carbon tetrachloride plume. With the approval of the CCC/USDA and KDHE project managers, the monitoring network was expanded in January 2006 through the installation of 3 additional monitoring wells (MW9S-MW11S). Details of the monitoring well installations are reported in this document. The expanded monitoring network of 12 monitoring wells (MW1S-MW11S and MW1D) and 3 private wells (Isch, Rillinger, and Stone) was sampled in March 2006, the second monitoring event in the planned two-year program. Results of analyses for VOCs showed minor increases or decreases in contaminant levels at various locations but indicated that the leading edge of the contaminant plume is approaching the intermittent stream leading to Terrapin Creek. The groundwater samples collected in March 2006 were also analyzed for additional groundwater parameters to aid in

  6. Comparison of the MBBR denitrification carriers for advanced nitrogen removal of wastewater treatment plant effluent.

    PubMed

    Yuan, Quan; Wang, Haiyan; Hang, Qianyu; Deng, Yangfan; Liu, Kai; Li, Chunmei; Zheng, Shengzhi

    2015-09-01

    The moving bed biofilm reactors (MBBRs) were used to remove the residual NO3(-)-N of wastewater treatment plant (WWTP) effluent, and the MBBR carriers for denitrification were compared. The results showed that high denitrification efficiency can be achieved with polyethylene, polypropylene, polyurethane foam, and haydite carriers under following conditions: 7.2 to 8.0 pH, 24 to 26 °C temperature, 12 h hydraulic retention time (HRT), and 25.5 mg L(-1) external methanol dosage, while the WWTP effluent total nitrogen (TN) was between 2.6 and 15.4 mg L(-1) and NO3(-)-N was between 0.2 and 12.6 mg L(-1). The MBBR filled with polyethylene carriers had higher TN and NO3(-)-N removal rate (44.9 ± 19.1 and 83.4 ± 13.0%, respectively) than those with other carriers. The minimum effluent TN and NO3(-)-N of polyethylene MBBR were 1.6 and 0.1 mg L(-1), respectively, and the maximum denitrification rate reached 23.0 g m(-2) day(-1). When chemical oxygen demand (COD)/TN ratio dropped from 6 to 4, the NO3(-)- N and TN removal efficiency decreased significantly in all reactors except for that filled with polyethylene, which indicated that the polyethylene MBBR can resist influent fluctuation much better. The three-dimensional excitation-emission matrix analysis showed that all the influent and effluent of MBBRs contain soluble microbial products (SMPs)-like organics and biochemical oxygen demand (BOD), which can be removed better by MBBRs filled with haydite and polyethylene carriers. The nitrous oxide reductase (nosZ)-based terminal restriction fragment length polymorphism (T-RFLP) analysis suggested that the dominant bacteria in polyethylene MBBR are the key denitrificans.

  7. Characterization of Microbial Communities in Gas Industry Pipelines

    PubMed Central

    Zhu, Xiang Y.; Lubeck, John; Kilbane, John J.

    2003-01-01

    Culture-independent techniques, denaturing gradient gel electrophoresis (DGGE) analysis, and random cloning of 16S rRNA gene sequences amplified from community DNA were used to determine the diversity of microbial communities in gas industry pipelines. Samples obtained from natural gas pipelines were used directly for DNA extraction, inoculated into sulfate-reducing bacterium medium, or used to inoculate a reactor that simulated a natural gas pipeline environment. The variable V2-V3 (average size, 384 bp) and V3-V6 (average size, 648 bp) regions of bacterial and archaeal 16S rRNA genes, respectively, were amplified from genomic DNA isolated from nine natural gas pipeline samples and analyzed. A total of 106 bacterial 16S rDNA sequences were derived from DGGE bands, and these formed three major clusters: beta and gamma subdivisions of Proteobacteria and gram-positive bacteria. The most frequently encountered bacterial species was Comamonas denitrificans, which was not previously reported to be associated with microbial communities found in gas pipelines or with microbially influenced corrosion. The 31 archaeal 16S rDNA sequences obtained in this study were all related to those of methanogens and phylogenetically fall into three clusters: order I, Methanobacteriales; order III, Methanomicrobiales; and order IV, Methanosarcinales. Further microbial ecology studies are needed to better understand the relationship among bacterial and archaeal groups and the involvement of these groups in the process of microbially influenced corrosion in order to develop improved ways of monitoring and controlling microbially influenced corrosion. PMID:12957923

  8. Permanent draft genome of Thiobacillus thioparus DSM 505T, an obligately chemolithoautotrophic member of the Betaproteobacteria

    DOE PAGES

    Hutt, Lee P.; Huntemann, Marcel; Clum, Alicia; ...

    2017-01-19

    Thiobacillus thioparus DSM 505 T is one of first two isolated strains of inorganic sulfur-oxidising Bacteria. The original strain of T. thioparus was lost almost 100 years ago and the working type strain is Culture C T (=DSM 505 T = ATCC 8158 T ) isolated by Starkey in 1934 from agricultural soil at Rutgers University, New Jersey, USA. It is an obligate chemolithoautotroph that conserves energy from the oxidation of reduced inorganic sulfur compounds using the Kelly-Trudinger pathway and uses it to fix carbon dioxide It is not capable of heterotrophic or mixotrophic growth. The strain has a genomemore » size of 3,201,518 bp. Here we report the genome sequence, annotation and characteristics. The genome contains 3,135 protein coding and 62 RNA coding genes. Genes encoding the transaldolase variant of the Calvin-Benson-Bassham cycle were also identified and an operon encoding carboxysomes, along with Smith's biosynthetic horseshoe in lieu of Krebs' cycle sensu stricto. Terminal oxidases were identified, viz. cytochrome c oxidase (cbb3, EC 1.9.3.1) and ubiquinol oxidase (bd, EC 1.10.3.10). There is a partial sox operon of the Kelly-Friedrich pathway of inorganic sulfur-oxidation that contains soxXYZAB genes but lacking soxCDEF, there is also a lack of the DUF302 gene previously noted in the sox operon of other members of the 'Proteobacteria' that can use trithionate as an energy source. In spite of apparently not growing anaerobically with denitrification, the nar, nir, nor and nos operons encoding enzymes of denitrification are found in the T. thioparus genome, in the same arrangements as in the true denitrifier T. denitrificans.« less

  9. Permanent draft genome of Thermithiobacillus tepidarius DSM 3134 T, a moderately thermophilic, obligately chemolithoautotrophic member of the Acidithiobacillia

    DOE PAGES

    Boden, Rich; Hutt, Lee P.; Huntemann, Marcel; ...

    2016-09-26

    Thermithiobacillus tepidarius DSM 3134 T was originally isolated (1983) from the waters of a sulfidic spring entering the Roman Baths (Temple of Sulis-Minerva) at Bath, United Kingdom and is an obligate chemolithoautotroph growing at the expense of reduced sulfur species. This strain has a genome size of 2,958,498 bp. Here we report the genome sequence, annotation and characteristics. The genome comprises 2,902 protein coding and 66 RNA coding genes. Genes responsible for the transaldolase variant of the Calvin-Benson-Bassham cycle were identified along with a biosynthetic horseshoe in lieu of Krebs' cycle sensu stricto. Terminal oxidases were identified, viz. cytochrome cmore » oxidase (cbb 3 , EC 1.9.3.1) and ubiquinol oxidase (bd, EC 1.10.3.10). Metalloresistance genes involved in pathways of arsenic and cadmium resistance were found. Evidence of horizontal gene transfer accounting for 5.9 % of the protein-coding genes was found, including transfer from Thiobacillus spp. and Methylococcus capsulatus Bath, isolated from the same spring. A sox gene cluster was found, similar in structure to those from other Acidithiobacillia - by comparison with Thiobacillus thioparus and Paracoccus denitrificans, an additional gene between soxA and soxB was found, annotated as a DUF302-family protein of unknown function. As the Kelly-Friedrich pathway of thiosulfate oxidation (encoded by sox) is not used in Thermithiobacillus spp., the role of the operon (if any) in this species remains unknown. We speculate that DUF302 and sox genes may have a role in periplasmic trithionate oxidation.« less

  10. Permanent draft genome of Thermithiobacillus tepidarius DSM 3134 T, a moderately thermophilic, obligately chemolithoautotrophic member of the Acidithiobacillia

    SciT

    Boden, Rich; Hutt, Lee P.; Huntemann, Marcel

    Thermithiobacillus tepidarius DSM 3134 T was originally isolated (1983) from the waters of a sulfidic spring entering the Roman Baths (Temple of Sulis-Minerva) at Bath, United Kingdom and is an obligate chemolithoautotroph growing at the expense of reduced sulfur species. This strain has a genome size of 2,958,498 bp. Here we report the genome sequence, annotation and characteristics. The genome comprises 2,902 protein coding and 66 RNA coding genes. Genes responsible for the transaldolase variant of the Calvin-Benson-Bassham cycle were identified along with a biosynthetic horseshoe in lieu of Krebs' cycle sensu stricto. Terminal oxidases were identified, viz. cytochrome cmore » oxidase (cbb 3 , EC 1.9.3.1) and ubiquinol oxidase (bd, EC 1.10.3.10). Metalloresistance genes involved in pathways of arsenic and cadmium resistance were found. Evidence of horizontal gene transfer accounting for 5.9 % of the protein-coding genes was found, including transfer from Thiobacillus spp. and Methylococcus capsulatus Bath, isolated from the same spring. A sox gene cluster was found, similar in structure to those from other Acidithiobacillia - by comparison with Thiobacillus thioparus and Paracoccus denitrificans, an additional gene between soxA and soxB was found, annotated as a DUF302-family protein of unknown function. As the Kelly-Friedrich pathway of thiosulfate oxidation (encoded by sox) is not used in Thermithiobacillus spp., the role of the operon (if any) in this species remains unknown. We speculate that DUF302 and sox genes may have a role in periplasmic trithionate oxidation.« less

  11. Sulfurirhabdus autotrophica gen. nov., sp. nov., isolated from a freshwater lake.

    PubMed

    Watanabe, Tomohiro; Kojima, Hisaya; Shinohara, Arisa; Fukui, Manabu

    2016-01-01

    A novel sulfur-oxidizing bacterium, designated strain BiS0T, was isolated from a sediment sample collected from a freshwater lake in Japan. The cells were rod-shaped, 1.4-4.6 × 0.4-0.7 μm and Gram-stain-negative. The G+C content of the genomic DNA was around 44 mol%. The isolate possessed summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C10 : 0 3-OH as major cellular fatty acids. Strain BiS0T grew by carbon dioxide fixation and oxidation of inorganic sulfur compounds with oxygen as the electron acceptor. Growth was observed over a temperature range of 0-32 °C (optimum, 15-22 °C), an NaCl concentration range of 0-546.4 mM (optimum 0-66.7 mM) and a pH range of 5.2-8.1 (optimum 6.1-6.3). Phylogenetic analysis, based on 16S rRNA gene sequences, indicated that strain BiS0T belongs to the family Sulfuricellaceae in the class Betaproteobacteria. The closest cultured relatives were Sulfuricella denitrificans skB26T and Sulfuricella sp. T08, with 16S rRNA gene sequence similarities of 96.3 %. On the basis of the data obtained in this study, strain BiS0T represents a novel species of a novel genus, for which the name Sulfurirhabdus autotrophica gen. nov., sp. nov. is proposed. The type strain is BiS0T ( = NBRC 110941T = DSM 100309T).

  12. HAEM SYNTHASE AND COBALT PORPHYRIN SYNTHASE IN VARIOUS MICRO-ORGANISMS.

    PubMed

    PORRA, R J; ROSS, B D

    1965-03-01

    1. The preparation of a crude extract of Clostridium tetanomorphum containing cobalt porphyrin synthase but little haem-synthase activity is described. 2. The properties of cobalt porphyrin synthase in the clostridial extracts is compared with the properties of a haem synthase present in crude extracts of the yeast Torulopsis utilis. 3. Cobalt porphyrin synthase in extracts of C. tetanomorphum inserts Co(2+) ions into the following dicarboxylic porphyrins in descending order of rate of insertion: meso-, deutero- and proto-porphyrins. Esterification renders meso- and deutero-porphyrins inactive as substrates. Neither the tetracarboxylic (coproporphyrin III) nor the octacarboxylic (uroporphyrin III) compounds are converted into cobalt porphyrins by the extract, but the non-enzymic incorporation of Co(2+) ions into these two porphyrins is rapid. These extracts are unable to insert Mn(2+), Zn(2+), Mg(2+) or Cu(2+) ions into mesoporphyrin. 4. Crude extracts of T. utilis readily insert both Co(2+) and Fe(2+) ions into deutero-, meso, and proto-porphyrins. Unlike the extracts of C. tetanomorphum, these preparations catalyse the insertion of Co(2+) ions into deuteroporphyrin more rapidly than into mesoporphyrin. This parallels the formation of haems by the T. utilis extract. 5. Cobalt porphyrin synthase is present in the particulate fraction of the extracts of C. tetanomorphum but requires a heat-stable factor present in the soluble fraction. This soluble factor can be replaced by GSH. 6. Cobalt porphyrin synthase in the clostridial extract is inhibited by iodoacetamide and to a smaller extent by p-chloromercuribenzoate and N-ethylmaleimide. The haem synthases of T. utilis and Micrococcus denitrificans are also inhibited by various thiol reagents.

  13. Reaction mechanism of sterol hydroxylation by steroid C25 dehydrogenase - Homology model, reactivity and isoenzymatic diversity.

    PubMed

    Rugor, Agnieszka; Wójcik-Augustyn, Anna; Niedzialkowska, Ewa; Mordalski, Stefan; Staroń, Jakub; Bojarski, Andrzej; Szaleniec, Maciej

    2017-08-01

    Steroid C25 dehydrogenase (S25DH) is a molybdenum-containing oxidoreductase isolated from the anaerobic Sterolibacterium denitrificans Chol-1S. S25DH is classified as 'EBDH-like' enzyme (EBDH, ethylbenzene dehydrogenase) and catalyzes the introduction of an OH group to the C25 atom of a sterol aliphatic side-chain. Due to its regioselectivity, S25DH is proposed as a catalyst in production of pharmaceuticals: calcifediol or 25-hydroxycholesterol. The aim of presented research was to obtain structural model of catalytic subunit α and investigate the reaction mechanism of the O 2 -independent tertiary carbon atom activation. Based on homology modeling and theoretical calculations, a S25DH α subunit model was for the first time characterized and compared to other S25DH-like isoforms. The molecular dynamics simulations of the enzyme-substrate complexes revealed two stable binding modes of a substrate, which are stabilized predominantly by van der Waals forces in the hydrophobic substrate channel. However, H-bond interactions involving polar residues with C3=O/C3-OH in the steroid ring appear to be responsible for positioning the substrate. These results may explain the experimental kinetic results which showed that 3-ketosterols are hydroxylated 5-10-fold faster than 3-hydroxysterols. The reaction mechanism was studied using QM:MM and QM-only cluster models. The postulated mechanism involves homolytic CH cleavage by the MoO ligand, giving rise to a radical intermediate with product obtained in an OH rebound process. The hypothesis was supported by kinetic isotopic effect (KIE) experiments involving 25,26,26,26-[ 2 H]-cholesterol (4.5) and the theoretically predicted intrinsic KIE (7.0-7.2). Finally, we have demonstrated that the recombinant S25DH-like isoform catalyzes the same reaction as S25DH. Copyright © 2017 Elsevier Inc. All rights reserved.

  14. An integrated bioremediation process for petroleum hydrocarbons removal and odor mitigation from contaminated marine sediment.

    PubMed

    Zhang, Zhen; Lo, Irene M C; Yan, Dickson Y S

    2015-10-15

    This study developed a novel integrated bioremediation process for the removal of petroleum hydrocarbons and the mitigation of odor induced by reduced sulfur from contaminated marine sediment. The bioremediation process consisted of two phases. In Phase I, acetate was dosed into the sediment as co-substrate to facilitate the sulfate reduction process. Meanwhile, akaganeite (β-FeOOH) was dosed in the surface layer of the sediment to prevent S(2-) release into the overlying seawater. In Phase II, NO3(-) was injected into the sediment as an electron acceptor to facilitate the denitrification process. After 20 weeks of treatment, the sequential integration of the sulfate reduction and denitrification processes led to effective biodegradation of total petroleum hydrocarbons (TPH), in which about 72% of TPH was removed. In Phase I, the release of S(2-) was effectively controlled by the addition of akaganeite. The oxidation of S(2-) by Fe(3+) and the precipitation of S(2-) by Fe(2+) were the main mechanisms for S(2-) removal. In Phase II, the injection of NO3(-) completely inhibited the sulfate reduction process. Most of residual AVS and S(0) were removed within 4 weeks after NO3(-) injection. The 16S rRNA clone library-based analysis revealed a distinct shift of bacterial community structure in the sediment over different treatment phases. The clones affiliated with Desulfobacterales and Desulfuromonadales were the most abundant in Phase I, while the clones related to Thioalkalivibrio sulfidophilus, Thiohalomonas nitratireducens and Sulfurimonas denitrificans predominated in Phase II. Copyright © 2015 Elsevier Ltd. All rights reserved.

  15. Formation of palladium(0) nanoparticles at microbial surfaces.

    PubMed

    Bunge, Michael; Søbjerg, Lina S; Rotaru, Amelia-Elena; Gauthier, Delphine; Lindhardt, Anders T; Hause, Gerd; Finster, Kai; Kingshott, Peter; Skrydstrup, Troels; Meyer, Rikke L

    2010-10-01

    The increasing demand and limited natural resources for industrially important platinum-group metal (PGM) catalysts render the recovery from secondary sources such as industrial waste economically interesting. In the process of palladium (Pd) recovery, microorganisms have revealed a strong potential. Hitherto, bacteria with the property of dissimilatory metal reduction have been in focus, although the biochemical reactions linking enzymatic Pd(II) reduction and Pd(0) deposition have not yet been identified. In this study we investigated Pd(II) reduction with formate as the electron donor in the presence of Gram-negative bacteria with no documented capacity for reducing metals for energy production: Cupriavidus necator, Pseudomonas putida, and Paracoccus denitrificans. Only large and close-packed Pd(0) aggregates were formed in cell-free buffer solutions. Pd(II) reduction in the presence of bacteria resulted in smaller, well-suspended Pd(0) particles that were associated with the cells (called "bioPd(0)" in the following). Nanosize Pd(0) particles (3-30 nm) were only observed in the presence of bacteria, and particles in this size range were located in the periplasmic space. Pd(0) nanoparticles were still deposited on autoclaved cells of C. necator that had no hydrogenase activity, suggesting a hydrogenase-independent formation mechanism. The catalytic properties of Pd(0) and bioPd(0) were determined by the amount of hydrogen released in a reaction with hypophosphite. Generally, bioPd(0) demonstrated a lower level of activity than the Pd(0) control, possibly due to the inaccessibility of the Pd(0) fraction embedded in the cell envelope. Our results demonstrate the suitability of bacterial cells for the recovery of Pd(0), and formation and immobilization of Pd(0) nanoparticles inside the cell envelope. However, procedures to make periplasmic Pd(0) catalytically accessible need to be developed for future nanobiotechnological applications.

  16. MALDI-TOF Mass Spectrometry: A Powerful Tool for Clinical Microbiology at Hôpital Principal de Dakar, Senegal (West Africa)

    PubMed Central

    Lo, Cheikh I.; Fall, Bécaye; Sambe-Ba, Bissoume; Diawara, Silman; Gueye, Mamadou W.; Mediannikov, Oleg; Sokhna, Cheikh; Faye, Ngor; Diemé, Yaya; Wade, Boubacar; Raoult, Didier; Fenollar, Florence

    2015-01-01

    Our team in Europe has developed the routine clinical laboratory identification of microorganisms by matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS). To evaluate the utility of MALDI-TOF MS in tropical Africa in collaboration with local teams, we installed an apparatus in the Hôpital Principal de Dakar (Senegal), performed routine identification of isolates, and confirmed or completed their identification in France. In the case of discordance or a lack of identification, molecular biology was performed. Overall, 153/191 (80.1%) and 174/191 (91.1%) isolates yielded an accurate and concordant identification for the species and genus, respectively, with the 2 different MALDI-TOF MSs in Dakar and Marseille. The 10 most common bacteria, representing 94.2% of all bacteria routinely identified in the laboratory in Dakar (Escherichia coli, Klebsiella pneumoniae, Streptococcus agalactiae, Acinetobacter baumannii, Pseudomonas aeruginosa, Staphylococcus aureus, Staphylococcus haemolyticus, Enterobacter cloacae, Enterococcus faecalis, and Staphylococcus epidermidis) were accurately identified with the MALDI-TOF MS in Dakar. The most frequent misidentification in Dakar was at the species level for Achromobacter xylosoxidans, which was inaccurately identified as Achromobacter denitrificans, and the bacteria absent from the database, such as Exiguobacterium aurientacum or Kytococcus schroeteri, could not be identified. A few difficulties were observed with MALDI-TOF MS for Bacillus sp. or oral streptococci. 16S rRNA sequencing identified a novel bacterium, “Necropsobacter massiliensis.” The robust identification of microorganisms by MALDI-TOF MS in Dakar and Marseille demonstrates that MALDI-TOF MS can be used as a first-line tool in clinical microbiology laboratories in tropical countries. PMID:26716681

  17. A complex regulatory network controls aerobic ethanol oxidation in Pseudomonas aeruginosa: indication of four levels of sensor kinases and response regulators.

    PubMed

    Mern, Demissew S; Ha, Seung-Wook; Khodaverdi, Viola; Gliese, Nicole; Görisch, Helmut

    2010-05-01

    In addition to the known response regulator ErbR (former AgmR) and the two-component regulatory system EraSR (former ExaDE), three additional regulatory proteins have been identified as being involved in controlling transcription of the aerobic ethanol oxidation system in Pseudomonas aeruginosa. Two putative sensor kinases, ErcS and ErcS', and a response regulator, ErdR, were found, all of which show significant similarity to the two-component flhSR system that controls methanol and formaldehyde metabolism in Paracoccus denitrificans. All three identified response regulators, EraR (formerly ExaE), ErbR (formerly AgmR) and ErdR, are members of the luxR family. The three sensor kinases EraS (formerly ExaD), ErcS and ErcS' do not contain a membrane domain. Apparently, they are localized in the cytoplasm and recognize cytoplasmic signals. Inactivation of gene ercS caused an extended lag phase on ethanol. Inactivation of both genes, ercS and ercS', resulted in no growth at all on ethanol, as did inactivation of erdR. Of the three sensor kinases and three response regulators identified thus far, only the EraSR (formerly ExaDE) system forms a corresponding kinase/regulator pair. Using reporter gene constructs of all identified regulatory genes in different mutants allowed the hierarchy of a hypothetical complex regulatory network to be established. Probably, two additional sensor kinases and two additional response regulators, which are hidden among the numerous regulatory genes annotated in the genome of P. aeruginosa, remain to be identified.

  18. Microbiology and potential applications of aerobic methane oxidation coupled to denitrification (AME-D) process: A review.

    PubMed

    Zhu, Jing; Wang, Qian; Yuan, Mengdong; Tan, Giin-Yu Amy; Sun, Faqian; Wang, Cheng; Wu, Weixiang; Lee, Po-Heng

    2016-03-01

    Aerobic methane oxidation coupled to denitrification (AME-D) is an important link between the global methane and nitrogen cycles. This mini-review updates discoveries regarding aerobic methanotrophs and denitrifiers, as a prelude to spotlight the microbial mechanism and the potential applications of AME-D. Until recently, AME-D was thought to be accomplished by a microbial consortium where denitrifying bacteria utilize carbon intermediates, which are excreted by aerobic methanotrophs, as energy and carbon sources. Potential carbon intermediates include methanol, citrate and acetate. This mini-review presents microbial thermodynamic estimations and postulates that methanol is the ideal electron donor for denitrification, and may serve as a trophic link between methanotrophic bacteria and denitrifiers. More excitingly, new discoveries have revealed that AME-D is not only confined to the conventional synergism between methanotrophic bacteria and denitrifiers. Specifically, an obligate aerobic methanotrophic bacterium, Methylomonas denitrificans FJG1, has been demonstrated to couple partial denitrification with methane oxidation, under hypoxia conditions, releasing nitrous oxide as a terminal product. This finding not only substantially advances the understanding of AME-D mechanism, but also implies an important but unknown role of aerobic methanotrophs in global climate change through their influence on both the methane and nitrogen cycles in ecosystems. Hence, further investigation on AME-D microbiology and mechanism is essential to better understand global climate issues and to develop niche biotechnological solutions. This mini-review also presents traditional microbial techniques, such as pure cultivation and stable isotope probing, and powerful microbial techniques, such as (meta-) genomics and (meta-) transcriptomics, for deciphering linked methane oxidation and denitrification. Although AME-D has immense potential for nitrogen removal from wastewater, drinking

  19. Relationship between gaseous N dynamics and the hydraulic state of hierarchically structured soils

    NASA Astrophysics Data System (ADS)

    Schlüter, Steffen; Dörsch, Peter; Vogel, Hans-Jörg

    2017-04-01

    The inherent spatial heterogeneity of soil generates spatially distributed micro-sites with different local N gas (NO, N2O, N2) production and release rates. Moreover, local micro-site conditions and the pathways between them depend on soil moisture which itself is highly dynamic close to the soil surface. These relationships need to be taken into account for a quantitative understanding of soil denitrification and associated N gas dynamics. Soil structure has been recognized as a key factor to understand the high spatial variability of N gas emissions. In particular gaseous N release from soils depends on: i) the total denitrification rate, which is related to the spatial extent and distribution of anaerobic sites and ii) the probability of N2O to escape from the soil without being further reduced to N2. This impact of soil structure is typically ignored in studies with soil slurries or repacked soil. In this project we run well-defined mesocosm experiments on N gas dynamics with hierarchically structured, artificial soils in which the spatial distribution of substrate and denitrifiers is known exactly. Sintered, porous glass pellets are inoculated with strains of Paracoccus denitrificans and/or Agrobacterium tumefaciens and amended with nutrient solution. These pellets are embedded in coarse-grained sand within gas-tight columns under O2/He atmosphere. The pellets are either places in layers or randomly to create different patterns of N gas production sites and diffusion pathways. Denitrification occurs in the anaerobic centers of the porous pellets, while the partially saturated sand matrix controls the diffusive transport of N gases towards the headspace, where all relevant gas concentrations are monitored with gas chromatography. Water saturations are adjusted such that the diffusive pathways are either fully continuous or partially discontinuous. Preliminary results indicate that the water content exert a major control on the magnitude of denitrification

  20. Gradients in microbial methanol uptake: productive coastal upwelling waters to oligotrophic gyres in the Atlantic Ocean

    PubMed Central

    Dixon, Joanna L; Sargeant, Stephanie; Nightingale, Philip D; Colin Murrell, J

    2013-01-01

    Methanol biogeochemistry and its importance as a carbon source in seawater is relatively unexplored. We report the first microbial methanol carbon assimilation rates (k) in productive coastal upwelling waters of up to 0.117±0.002 d−1 (∼10 nmol l−1 d−1). On average, coastal upwelling waters were 11 times greater than open ocean northern temperate (NT) waters, eight times greater than gyre waters and four times greater than equatorial upwelling (EU) waters; suggesting that all upwelling waters upon reaching the surface (⩽20 m), contain a microbial population that uses a relatively high amount of carbon (0.3–10 nmol l−1 d−1), derived from methanol, to support their growth. In open ocean Atlantic regions, microbial uptake of methanol into biomass was significantly lower, ranging between 0.04–0.68 nmol l−1 d−1. Microbes in the Mauritanian coastal upwelling used up to 57% of the total methanol for assimilation of the carbon into cells, compared with an average of 12% in the EU, and 1% in NT and gyre waters. Several methylotrophic bacterial species were identified from open ocean Atlantic waters using PCR amplification of mxaF encoding methanol dehydrogenase, the key enzyme in bacterial methanol oxidation. These included Methylophaga sp., Burkholderiales sp., Methylococcaceae sp., Ancylobacter aquaticus, Paracoccus denitrificans, Methylophilus methylotrophus, Methylobacterium oryzae, Hyphomicrobium sp. and Methylosulfonomonas methylovora. Statistically significant correlations for upwelling waters between methanol uptake into cells and both chlorophyll a concentrations and methanol oxidation rates suggest that remotely sensed chlorophyll a images, in these productive areas, could be used to derive total methanol biological loss rates, a useful tool for atmospheric and marine climatically active gas modellers, and air–sea exchange scientists. PMID:23178665

  1. ENVIROMENTALLY BENIGN MITIGATION OF MICROBIOLOGICALLY INFLUENCED CORROSION (MIC)

    SciT

    J. Robert Paterek; Gemma Husmillo; Amrutha Daram

    The overall program objective is to develop and evaluate environmentally benign agents or products that are effective in the prevention, inhibition, and mitigation of microbially influenced corrosion (MIC) in the internal surfaces of metallic natural gas pipelines. The goal is to develop one or more environmentally benign (a.k.a. ''green'') products that can be applied to maintain the structure and dependability of the natural gas infrastructure. The technical approach for this quarter includes the application of the method of fractionation of the extracts by high performance liquid chromatography (HPLC); determination of antimicrobial activities of the new extracts and fractions using amore » growth inhibition assay, and evaluation of the extracts' ability to inhibit biofilm formation. We initiated the delivery system for these new biocides in the test cell and in mixtures of foam components and biocides/anti-biofilms. A total of 51 fractions collected by HPLC from crude extracts that were obtained from three varieties of Capsicum sp. (Serrano, Habanero, Chile de Arbol) were subjected to growth inhibition tests against two SRB strains, D. vulgaris and D. desulfuricans. Five fractions showed growth inhibition against both strains while seven inhibited D. desulfuricans only. The crude extracts did not show growth inhibition on both strains but were proven to be potent in preventing the formation of biofilm. Growth inhibition tests of the same set of crude extracts against Comamonas denitrificans did not show positive results. The fractions will be subjected to biofilm inhibition and dissociation assay as well. The delivery system to be evaluated first was foam. The ''foam pig'' components of surfactants and water were tested with the biocide addition. The first chemical and physical parameters to be tested were pH and surfactants. Tests using the fractionated pepper extracts are progressing rapidly. Gas chromatographic analysis on a number of fractions is underway

  2. Members of Microvirga and Bradyrhizobium genera are native endosymbiotic bacteria nodulating Lupinus luteus in Northern Tunisian soils.

    PubMed

    Msaddak, Abdelhakim; Rejili, Mokhtar; Durán, David; Rey, Luis; Imperial, Juan; Palacios, Jose Manuel; Ruiz-Argüeso, Tomas; Mars, Mohamed

    2017-06-01

    The genetic diversity of bacterial populations nodulating Lupinus luteus (yellow lupine) in Northern Tunisia was examined. Phylogenetic analyses of 43 isolates based on recA and gyrB partial sequences grouped them in three clusters, two of which belong to genus Bradyrhizobium (41 isolates) and one, remarkably, to Microvirga (2 isolates), a genus never previously described as microsymbiont of this lupine species. Representatives of the three clusters were analysed in-depth by multilocus sequence analysis of five housekeeping genes (rrs, recA, glnII, gyrB and dnaK). Surprisingly, the Bradyrhizobium cluster with the two isolates LluI4 and LluTb2 may constitute a new species defined by a separate position between Bradyrhizobium manausense and B. denitrificans. A nodC-based phylogeny identified only two groups: one formed by Bradyrhizobium strains included in the symbiovar genistearum and the other by the Microvirga strains. Symbiotic behaviour of representative isolates was tested, and among the seven legumes inoculated only a difference was observed i.e. the Bradyrhizobium strains nodulated Ornithopus compressus unlike the two strains of Microvirga. On the basis of these data, we conclude that L. luteus root nodule symbionts in Northern Tunisia are mostly strains within the B. canariense/B. lupini lineages, and the remaining strains belong to two groups not previously identified as L. luteus endosymbionts: one corresponding to a new clade of Bradyrhizobium and the other to the genus Microvirga. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  3. Permanent draft genome of Thiobacillus thioparus DSM 505T, an obligately chemolithoautotrophic member of the Betaproteobacteria

    SciT

    Hutt, Lee P.; Huntemann, Marcel; Clum, Alicia

    Thiobacillus thioparus DSM 505 T is one of first two isolated strains of inorganic sulfur-oxidising Bacteria. The original strain of T. thioparus was lost almost 100 years ago and the working type strain is Culture C T (=DSM 505 T = ATCC 8158 T ) isolated by Starkey in 1934 from agricultural soil at Rutgers University, New Jersey, USA. It is an obligate chemolithoautotroph that conserves energy from the oxidation of reduced inorganic sulfur compounds using the Kelly-Trudinger pathway and uses it to fix carbon dioxide It is not capable of heterotrophic or mixotrophic growth. The strain has a genomemore » size of 3,201,518 bp. Here we report the genome sequence, annotation and characteristics. The genome contains 3,135 protein coding and 62 RNA coding genes. Genes encoding the transaldolase variant of the Calvin-Benson-Bassham cycle were also identified and an operon encoding carboxysomes, along with Smith's biosynthetic horseshoe in lieu of Krebs' cycle sensu stricto. Terminal oxidases were identified, viz. cytochrome c oxidase (cbb3, EC 1.9.3.1) and ubiquinol oxidase (bd, EC 1.10.3.10). There is a partial sox operon of the Kelly-Friedrich pathway of inorganic sulfur-oxidation that contains soxXYZAB genes but lacking soxCDEF, there is also a lack of the DUF302 gene previously noted in the sox operon of other members of the 'Proteobacteria' that can use trithionate as an energy source. In spite of apparently not growing anaerobically with denitrification, the nar, nir, nor and nos operons encoding enzymes of denitrification are found in the T. thioparus genome, in the same arrangements as in the true denitrifier T. denitrificans.« less

  4. Mechanisms of zinc binding to the solute-binding protein AztC and transfer from the metallochaperone AztD.

    PubMed

    Neupane, Durga P; Avalos, Dante; Fullam, Stephanie; Roychowdhury, Hridindu; Yukl, Erik T

    2017-10-20

    Bacteria can acquire the essential metal zinc from extremely zinc-limited environments by using ATP-binding cassette (ABC) transporters. These transporters are critical virulence factors, relying on specific and high-affinity binding of zinc by a periplasmic solute-binding protein (SBP). As such, the mechanisms of zinc binding and release among bacterial SBPs are of considerable interest as antibacterial drug targets. Zinc SBPs are characterized by a flexible loop near the high-affinity zinc-binding site. The function of this structure is not always clear, and its flexibility has thus far prevented structural characterization by X-ray crystallography. Here, we present intact structures for the zinc-specific SBP AztC from the bacterium Paracoccus denitrificans in the zinc-bound and apo-states. A comparison of these structures revealed that zinc loss prompts significant structural rearrangements, mediated by the formation of a sodium-binding site in the apo-structure. We further show that the AztC flexible loop has no impact on zinc-binding affinity, stoichiometry, or protein structure, yet is essential for zinc transfer from the metallochaperone AztD. We also found that 3 His residues in the loop appear to temporarily coordinate zinc and then convey it to the high-affinity binding site. Thus, mutation of any of these residues to Ala abrogated zinc transfer from AztD. Our structural and mechanistic findings conclusively identify a role for the AztC flexible loop in zinc acquisition from the metallochaperone AztD, yielding critical insights into metal binding by AztC from both solution and AztD. These proteins are highly conserved in human pathogens, making this work potentially useful for the development of novel antibiotics. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  5. The link between the microbial ecology, gene expression, and biokinetics of denitrifying polyphosphate-accumulating systems under different electron acceptor combinations.

    PubMed

    Vieira, A; Ribera-Guardia, A; Marques, R; Barreto Crespo, M T; Oehmen, A; Carvalho, G

    2018-06-02

    The emission of the greenhouse gas nitrous oxide (N 2 O) can occur during biological nutrient removal. Denitrifying enhanced biological phosphorus removal (d-EBPR) systems are an efficient means of removing phosphate and nitrogen, performed by denitrifying polyphosphate-accumulating organisms (d-PAOs). The aim of this work was to study the effect of various combinations of electron acceptors, nitrate (NO 3 - ), nitrite (NO 2 - ), and N 2 O, on the denitrification pathway of a d-EBPR system. Batch tests were performed with different electron acceptor combinations, to explore the denitrification pathway. Reverse transcriptase-qPCR (RT-qPCR) and high-throughput sequencing, combined with chemical analysis, were used to study gene expression, microbial diversity, and denitrification kinetics. The potential for N 2 O production was greater than the potential for its reduction in most tests. A strong correlation was observed between the N 2 O reduction rate and the relative gene expression of nitrous oxide reductase per nitrite reductase (nosZ/(nirS + nirK)), suggesting that the expression of denitrifying marker genes is a strong predictor of the N 2 O reduction rate. The d-EBPR community maintained a core population with low variations throughout the study. Furthermore, phylogenetic analyses of the studied marker genes revealed that the organisms actively involved in denitrification were closely related to Thauera sp., Candidatus Accumulibacter phosphatis, and Candidatus Competibacter denitrificans. Moreover, Competibacter-related OTUs seem to be important contributors to the N 2 O reduction capacity of the system, likely scavenging the N 2 O produced by other organisms. Overall, this study contributes to a better understanding of the microbial biochemistry and the genetics involving biological denitrification removal, important to minimize N 2 O emissions in wastewater treatment plants.

  6. Isolation and characterization of a sulfur-oxidizing chemolithotroph growing on crude oil under anaerobic conditions.

    PubMed

    Kodama, Yumiko; Watanabe, Kazuya

    2003-01-01

    Molecular approaches have shown that a group of bacteria (called cluster 1 bacteria) affiliated with the epsilon subclass of the class Proteobacteria constituted major populations in underground crude-oil storage cavities. In order to unveil their physiology and ecological niche, this study isolated bacterial strains (exemplified by strain YK-1) affiliated with the cluster 1 bacteria from an oil storage cavity at Kuji in Iwate, Japan. 16S rRNA gene sequence analysis indicated that its closest relative was Thiomicrospira denitrificans (90% identity). Growth experiments under anaerobic conditions showed that strain YK-1 was a sulfur-oxidizing obligate chemolithotroph utilizing sulfide, elemental sulfur, thiosulfate, and hydrogen as electron donors and nitrate as an electron acceptor. Oxygen also supported its growth only under microaerobic conditions. Strain YK-1 could not grow on nitrite, and nitrite was the final product of nitrate reduction. Neither sugars, organic acids (including acetate), nor hydrocarbons could serve as carbon and energy sources. A typical stoichiometry of its energy metabolism followed an equation: S(2-) + 4NO(3)(-) --> SO(4)(2-) + 4NO(2)(-) (Delta G(0) = -534 kJ mol(-1)). In a difference from other anaerobic sulfur-oxidizing bacteria, this bacterium was sensitive to NaCl; growth in medium containing more than 1% NaCl was negligible. When YK-1 was grown anaerobically in a sulfur-depleted inorganic medium overlaid with crude oil, sulfate was produced, corresponding to its growth. On the contrary, YK-1 could not utilize crude oil as a carbon source. These results suggest that the cluster 1 bacteria yielded energy for growth in oil storage cavities by oxidizing petroleum sulfur compounds. Based on its physiology, ecological interactions with other members of the groundwater community are discussed.

  7. Chaperones of F[subscript 1]-ATPase

    SciT

    Ludlam, Anthony; Brunzelle, Joseph; Pribyl, Thomas

    2009-09-25

    Mitochondrial F{sub 1}-ATPase contains a hexamer of alternating {alpha} and {beta} subunits. The assembly of this structure requires two specialized chaperones, Atp11p and Atp12p, that bind transiently to {beta} and {alpha}. In the absence of Atp11p and Atp12p, the hexamer is not formed, and {alpha} and {beta} precipitate as large insoluble aggregates. An early model for the mechanism of chaperone-mediated F{sub 1} assembly (Wang, Z. G., Sheluho, D., Gatti, D. L., and Ackerman, S. H. (2000) EMBO J. 19, 1486--1493) hypothesized that the chaperones themselves look very much like the {alpha} and {beta} subunits, and proposed an exchange of Atp11pmore » for {alpha} and of Atp12p for {beta}; the driving force for the exchange was expected to be a higher affinity of {alpha} and {beta} for each other than for the respective chaperone partners. One important feature of this model was the prediction that as long as Atp11p is bound to {beta} and Atp12p is bound to {alpha}, the two F{sub 1} subunits cannot interact at either the catalytic site or the noncatalytic site interface. Here we present the structures of Atp11p from Candida glabrata and Atp12p from Paracoccus denitrificans, and we show that some features of the Wang model are correct, namely that binding of the chaperones to {alpha} and {beta} prevents further interactions between these F1 subunits. However, Atp11p and Atp12p do not resemble {alpha} or {beta}, and it is instead the F{sub 1} {gamma} subunit that initiates the release of the chaperones from {alpha} and {beta} and their further assembly into the mature complex.« less

  8. Analysis of a microbial community oxidizing inorganic sulfide and mercaptans.

    PubMed

    Duncan, K E; Sublette, K L; Rider, P A; Stepp, A; Beitle, R R; Conner, J A; Kolhatkar, R

    2001-01-01

    Successful treatment of refinery spent-sulfidic caustic (which results from the addition of sodium hydroxide solutions to petroleum refinery waste streams) was achieved in a bioreactor containing an enrichment culture immobilized in organic polymer beads with embedded powdered activated carbon (Bio-Sep). The aerobic enrichment culture had previously been selected using a gas mixture of hydrogen sulfide and methyl mercaptan (MeSH) as the sole carbon and energy sources. The starting cultures for the enrichment consisted of several different Thiobacilli spp. (T. thioparus, T. denitrificans, T. thiooxidans, and T. neopolitanus), as well as activated sludge from a refinery aerobic wastewater treatment system and sludge from an industrial anaerobic digester. Microscopic examination (light and SEM) of the beads and of microbial growth on the walls of the bioreactor revealed a great diversity of microorganisms. Further characterization was undertaken starting with culturable aerobic heterotrophic microorganisms (sequencing of PCR-amplified DNA coding for 16S rRNA, Gram staining) and by PCR amplification of DNA coding for 16S rRNA extracted directly from the cell mass, followed by the separation of the PCR products by DGGE (denaturing gradient gel electrophoresis). Eight prominent bands from the DGGE gel were sequenced and found to be closest to sequences of uncultured Cytophagales (3 bands), Gram-positive cocci (Micrococcineae), alpha proteobacteria (3 bands), and an unidentified beta proteobacterium. Culturable microbes included several genera of fungi as well as various Gram-positive and Gram-negative heterotrophic bacteria not seen in techniques using direct DNA extraction.

  9. The growth of Steroidobacter agariperforans sp. nov., a novel agar-degrading bacterium isolated from soil, is enhanced by the diffusible metabolites produced by bacteria belonging to Rhizobiales.

    PubMed

    Sakai, Masao; Hosoda, Akifumi; Ogura, Kenjiro; Ikenaga, Makoto

    2014-01-01

    An agar-degrading bacterium was isolated from soil collected in a vegetable cropping field. The growth of this isolate was enhanced by supplying culture supernatants of bacteria belonging to the order Rhizobiales. Phylogenetic analysis based on 16S rRNA gene sequences indicated the novel bacterium, strain KA5-B(T), belonged to the genus Steroidobacter in Gammaproteobacteria, but differed from its closest relative, Steroidobacter denitrificans FS(T), at the species level with 96.5% similarity. Strain KA5-B(T) was strictly aerobic, Gram-negative, non-motile, non-spore forming, and had a straight to slightly curved rod shape. Cytochrome oxidase and catalase activities were positive. The strain grew on media containing culture supernatants in a temperature range of 15-37°C and between pH 4.5 and 9.0, with optimal growth occurring at 30°C and pH 6.0-8.0. No growth occurred at 10 or 42°C or at NaCl concentrations more than 3% (w/v). The main cellular fatty acids were iso-C15:0, C16:1ω7c, and iso-C17:1ω9c. The main quinone was ubiquinone-8 and DNA G+C content was 62.9 mol%. In contrast, strain FS(T) was motile, did not grow on the agar plate, and its dominant cellular fatty acids were C15:0 and C17:1ω8c. Based on its phylogenetic and phenotypic properties, strain KA5-B(T) (JCM 18477(T) = KCTC 32107(T)) represents a novel species in genus Steroidobacter, for which the name Steroidobacter agariperforans sp. nov. is proposed.

  10. Characterizing the proton loading site in cytochrome c oxidase.

    PubMed

    Lu, Jianxun; Gunner, M R

    2014-08-26

    Cytochrome c oxidase (CcO) uses the energy released by reduction of O2 to H2O to drive eight charges from the high pH to low pH side of the membrane, increasing the electrochemical gradient. Four electrons and protons are used for chemistry, while four more protons are pumped. Proton pumping requires that residues on a pathway change proton affinity through the reaction cycle to load and then release protons. The protonation states of all residues in CcO are determined in MultiConformational Continuum Electrostatics simulations with the protonation and redox states of heme a, a3, Cu(B), Y288, and E286 used to define the catalytic cycle. One proton is found to be loaded and released from residues identified as the proton loading site (PLS) on the P-side of the protein in each of the four CcO redox states. Thus, the same proton pumping mechanism can be used each time CcO is reduced. Calculations with structures of Rhodobacter sphaeroides, Paracoccus denitrificans, and bovine CcO derived by crystallography and molecular dynamics show the PLS functions similarly in different CcO species. The PLS is a cluster rather than a single residue, as different structures show 1-4 residues load and release protons. However, the proton affinity of the heme a3 propionic acids primarily determines the number of protons loaded into the PLS; if their proton affinity is too low, less than one proton is loaded.

  11. Characterizing the proton loading site in cytochrome c oxidase

    PubMed Central

    Lu, Jianxun; Gunner, M. R.

    2014-01-01

    Cytochrome c oxidase (CcO) uses the energy released by reduction of O2 to H2O to drive eight charges from the high pH to low pH side of the membrane, increasing the electrochemical gradient. Four electrons and protons are used for chemistry, while four more protons are pumped. Proton pumping requires that residues on a pathway change proton affinity through the reaction cycle to load and then release protons. The protonation states of all residues in CcO are determined in MultiConformational Continuum Electrostatics simulations with the protonation and redox states of heme a, a3, CuB, Y288, and E286 used to define the catalytic cycle. One proton is found to be loaded and released from residues identified as the proton loading site (PLS) on the P-side of the protein in each of the four CcO redox states. Thus, the same proton pumping mechanism can be used each time CcO is reduced. Calculations with structures of Rhodobacter sphaeroides, Paracoccus denitrificans, and bovine CcO derived by crystallography and molecular dynamics show the PLS functions similarly in different CcO species. The PLS is a cluster rather than a single residue, as different structures show 1–4 residues load and release protons. However, the proton affinity of the heme a3 propionic acids primarily determines the number of protons loaded into the PLS; if their proton affinity is too low, less than one proton is loaded. PMID:25114210

  12. Structural characterization of the bacterial proteasome homolog BPH reveals a tetradecameric double-ring complex with unique inner cavity properties.

    PubMed

    Fuchs, Adrian C D; Maldoner, Lorena; Hipp, Katharina; Hartmann, Marcus D; Martin, Jörg

    2018-01-19

    Eukaryotic and archaeal proteasomes are paradigms for self-compartmentalizing proteases. To a large extent, their function requires interplay with hexameric ATPases associated with diverse cellular activities (AAA+) that act as substrate unfoldases. Bacteria have various types of self-compartmentalizing proteases; in addition to the proteasome itself, these include the proteasome homolog HslV, which functions together with the AAA+ HslU; the ClpP protease with its partner AAA+ ClpX; and Anbu, a recently characterized ancestral proteasome variant. Previous bioinformatic analysis has revealed a novel bacterial member of the proteasome family Betaproteobacteria proteasome homolog (BPH). Using cluster analysis, we here affirmed that BPH evolutionarily descends from HslV. Crystal structures of the Thiobacillus denitrificans and Cupriavidus metallidurans BPHs disclosed a homo-oligomeric double-ring architecture in which the active sites face the interior of the cylinder. Using small-angle X-ray scattering (SAXS) and electron microscopy averaging, we found that BPH forms tetradecamers in solution, unlike the dodecamers seen in HslV. Although the highly acidic inner surface of BPH was in striking contrast to the cavity characteristics of the proteasome and HslV, a classical proteasomal reaction mechanism could be inferred from the covalent binding of the proteasome-specific inhibitor epoxomicin to BPH. A ligand-bound structure implied that the elongated BPH inner pore loop may be involved in substrate recognition. The apparent lack of a partner unfoldase and other unique features, such as Ser replacing Thr as the catalytic residue in certain BPH subfamilies, suggest a proteolytic function for BPH distinct from those of known bacterial self-compartmentalizing proteases. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

  13. Structural characterization of the bacterial proteasome homolog BPH reveals a tetradecameric double-ring complex with unique inner cavity properties

    PubMed Central

    Fuchs, Adrian C. D.; Maldoner, Lorena; Hipp, Katharina; Hartmann, Marcus D.; Martin, Jörg

    2018-01-01

    Eukaryotic and archaeal proteasomes are paradigms for self-compartmentalizing proteases. To a large extent, their function requires interplay with hexameric ATPases associated with diverse cellular activities (AAA+) that act as substrate unfoldases. Bacteria have various types of self-compartmentalizing proteases; in addition to the proteasome itself, these include the proteasome homolog HslV, which functions together with the AAA+ HslU; the ClpP protease with its partner AAA+ ClpX; and Anbu, a recently characterized ancestral proteasome variant. Previous bioinformatic analysis has revealed a novel bacterial member of the proteasome family Betaproteobacteria proteasome homolog (BPH). Using cluster analysis, we here affirmed that BPH evolutionarily descends from HslV. Crystal structures of the Thiobacillus denitrificans and Cupriavidus metallidurans BPHs disclosed a homo-oligomeric double-ring architecture in which the active sites face the interior of the cylinder. Using small-angle X-ray scattering (SAXS) and electron microscopy averaging, we found that BPH forms tetradecamers in solution, unlike the dodecamers seen in HslV. Although the highly acidic inner surface of BPH was in striking contrast to the cavity characteristics of the proteasome and HslV, a classical proteasomal reaction mechanism could be inferred from the covalent binding of the proteasome-specific inhibitor epoxomicin to BPH. A ligand-bound structure implied that the elongated BPH inner pore loop may be involved in substrate recognition. The apparent lack of a partner unfoldase and other unique features, such as Ser replacing Thr as the catalytic residue in certain BPH subfamilies, suggest a proteolytic function for BPH distinct from those of known bacterial self-compartmentalizing proteases. PMID:29183996

  14. Source Parameters and Rupture Directivities of Earthquakes Within the Mendocino Triple Junction

    NASA Astrophysics Data System (ADS)

    Allen, A. A.; Chen, X.

    2017-12-01

    The Mendocino Triple Junction (MTJ), a region in the Cascadia subduction zone, produces a sizable amount of earthquakes each year. Direct observations of the rupture properties are difficult to achieve due to the small magnitudes of most of these earthquakes and lack of offshore observations. The Cascadia Initiative (CI) project provides opportunities to look at the earthquakes in detail. Here we look at the transform plate boundary fault located in the MTJ, and measure source parameters of Mw≥4 earthquakes from both time-domain deconvolution and spectral analysis using empirical Green's function (EGF) method. The second-moment method is used to infer rupture length, width, and rupture velocity from apparent source duration measured at different stations. Brune's source model is used to infer corner frequency and spectral complexity for stacked spectral ratio. EGFs are selected based on their location relative to the mainshock, as well as the magnitude difference compared to the mainshock. For the transform fault, we first look at the largest earthquake recorded during the Year 4 CI array, a Mw5.72 event that occurred in January of 2015, and select two EGFs, a Mw1.75 and a Mw1.73 located within 5 km of the mainshock. This earthquake is characterized with at least two sub-events, with total duration of about 0.3 second and rupture length of about 2.78 km. The earthquake is rupturing towards west along the transform fault, and both source durations and corner frequencies show strong azimuthal variations, with anti-correlation between duration and corner frequency. The stacked spectral ratio from multiple stations with the Mw1.73 EGF event shows deviation from pure Brune's source model following the definition from Uchide and Imanishi [2016], likely due to near-field recordings with rupture complexity. We will further analyze this earthquake using more EGF events to test the reliability and stability of the results, and further analyze three other Mw≥4 earthquakes

  15. Green laser pointers for visual astronomy: how much power is enough?

    PubMed

    Bará, Salvador; Robles, Marisol; Tejelo, Isabel; Marzoa, Ramón I; González, Héctor

    2010-02-01

    Green laser pointers with output powers in the tens to hundreds of milliwatt (mW) range, clearly exceeding the limiting 5 mW of American National Standards Institute class 3a (International Electrotechnical Commission class 3R), are now easily available in the global market. They are increasingly being used in public sky observations and other nighttime outreach activities by educators and science communicators in countries where their use is not well regulated, despite the fact that such high power levels may represent a potential threat to visual health. The purpose of this study was to determine the output power reasonably required to perform satisfactorily this kind of activities. Twenty-three observers were asked to vary continuously the output power of a green laser source (wavelength 532 nm) until clearly seeing the laser beam propagating skyward through the atmosphere in a heavily light-polluted urban setting. Measurements were conducted with observers of a wide range of ages (9 to 56 years), refractions (spherical equivalents -8.50 to +1.50 diopters), and previous expertise in using lasers as pointing devices outdoors (from no experience to professional astronomers). Two measurement runs were made in different nights under different meteorological conditions. The output power chosen by observers in the first run (11 observers) averaged to 1.84 mW (+/-0.68 mW, 1 SD). The second run (17 observers) averaged to 2.91 mW (+/-1.54 mW). The global average was 2.38 mW (+/-1.30 mW). Only one observer scored 5.6 mW, just above the class 3a limit. The power chosen by the remaining 22 observers ranged from 1.37 to 3.53 mW. Green laser pointers with output powers below 5 mW (laser classes American National Standards Institute 3a or International Electrotechnical Commission 3R) appear to be sufficient for use in educational nighttime outdoors activities, providing enough bright beams at reasonable safety levels.

  16. [Recruiting and Personal Development in Surgical Departments of Large Referral Centers - Current Practice and Options for Improvement from Industry and Service Business].

    PubMed

    Homayounfar, K; König, S; Rabe, C; Beck-Broichsitter, B; Lützen, U; Ghadimi, M B; Schmidt, C

    2017-12-01

    Background Cut-throat competition, cost pressure, generation Y, shortage of qualified staff and feminisation influence human resources management in visceral surgery. The assessment of the current situation by chief surgeons (CS) as well as proof of transferability of strategies from industry and service business (ISB) have not yet been investigated. Material and Methods The CS of university hospitals and large referral centres (> 800 beds) were interviewed (n = 100) on the basis of a standardised questionnaire including 43 items. Closed questions were designed with a 5-point Likert scale and their analysis was presented as means (MW) and standard deviations (±). Ten human resources manager (HMR) of ISB were invited to participate in 45-minute telephone interviews. Results Thirty-seven CS participated in the survey, 15 of whom were full professors. Unsolicited applications (100%), job advertisements (78%) and direct approaches to final year students (78%) were the most common ways of recruitment. Only 17% of CS used a standardised form for preparation. Professional expertise (MW 2.2 ± 0.9), social skills (MW 1.9 ± 0.6) and excellent German language skills (MW 1.8 ± 0.8) were named as important qualifications for employment, while references and certificates were regarded as being less important (MW 3.2 ± 0.9). Personal development was regarded as important (MW 1.1 ± 0.2), but a defined period for residency was not guaranteed (MW 3.0 ± 1.5). Transparent selection criteria for career opportunities (MW 2.5 ± 1.1) and different career models (MW 2.7 ± 1.2) were only rarely available. Six HRM participated in the interviews. Active head-hunting (75%), Internet platforms (75%), presentations at conferences (75%), as well as hiring trainees (50%), job advertisements (50%) and social media (50%) were established options to find qualified employees. Professional and management careers were often separate career paths, while

  17. Lithology, hydraulic properties, and water quality of the Sandstone Aquifer in the northwestern part of the Bad River Indian Reservation, Wisconsin, 1998-1999

    Dunning, Charles P.

    2005-01-01

    The Precambrian sandstone aquifer in the northwestern part of the Bad River Band of Lake Superior Tribe of Chippewa Indians Reservation, Ashland County, Wisconsin, provides much of the drinking water to area residents. A study was undertaken in cooperation with the Bad River Tribe to provide specific information about the lithology, hydraulic properties, and water quality of the sandstone aquifer. During 1998 and 1999, the U.S. Geological Survey installed three monitoring wells, collected and analyzed lithologic and water samples, and conducted geophysical logging and aquifer tests to characterize the sandstone aquifer. The two monitoring wells in the southeastern part of the study area, the Diaperville Monitoring Well #1 (Diaperville MW #1) and the Tolman Monitoring Well #1 (Tolman MW #1) , are believed to have encountered older Middle Proterozoic Oronto Group sandstones. The sandstone encountered in the Ackley Monitoring Well #1 (Ackley MW #1) is believed to be Chequamegon Sandstone of the Late Proterozoic Bayfield Group. This interpretation is based on previous studies, as well as thin- section analysis of sandstone core recovered from the Ackley Monitoring Well #1. Results of aquifer tests conducted in the Diaperville Monitoring Well #1 and the Tolman Monitoring Well #1 provide ranges for hydraulic param - eter values in the sandstone aquifer: transmissivity ranges from 83 to 509 square feet per day; hydraulic conductivity ranges from 1.6 to 4.5 feet per day; storativity ranges from 0.00019 to 0.00046; and specific capacity ranges from 0.22 to 0.67 gallons per minute per foot. Though high- and low-angle fractures are present in Ackley Monitoring Well #1 core, the hydraulic properties of the bedrock appear to be due largely to the matrix porosity measured in thin section (16–21 percent) and permeability of the sandstone. The aquifer test for the Diaperville Monitoring Well #1 resulted in observed drawdown in nearby glacial wells, evidence of a hydraulic

  18. Time-resolved diode laser infrared absorption spectroscopy of the nascent HCl in the infrared laser chemistry of 1,2-dichloro-1,1-difluoroethane

    NASA Astrophysics Data System (ADS)

    Dietrich, Peter; Quack, Martin; Seyfang, George

    1990-04-01

    The IR multiphoton excitation and the frequency, fluence and intensity dependence of the IR-laser chemical yields of CF 2ClCH 2Cl have been studied in the fluence range of 1 to 10 J cm -2 yielding a steady-state constant k(st)/ I=0.74×10 6 s -1 MW -1 cm 2 which is approximately independent of intensity. Time-resolved IR absorption spectroscopy with diode laser sources has been used to observe the nascent HCl during the first few 100 ns indicating a population inversion between the levels ν=1, J=4 and ν=2, J=5. At low reactant pressures ( p⩽10 Pa) the time-resolved measurement gives a steady-state rate constant consistent with the theoretical result adjusted to the static yield measurements. The capability of state-selective and time-resolved IR spectroscopy is thus demonstrated, giving real-time determinations of rate constants.

  19. Comparative analysis of anti-polyglutamine Fab crystals grown on Earth and in microgravity.

    PubMed

    Owens, Gwen E; New, Danielle M; Olvera, Alejandra I; Manzella, Julia Ashlyn; Macon, Brittney L; Dunn, Joshua C; Cooper, David A; Rouleau, Robyn L; Connor, Daniel S; Bjorkman, Pamela J

    2016-10-01

    Huntington's disease is one of nine neurodegenerative diseases caused by a polyglutamine (polyQ)-repeat expansion. An anti-polyQ antigen-binding fragment, MW1 Fab, was crystallized both on Earth and on the International Space Station, a microgravity environment where convection is limited. Once the crystals returned to Earth, the number, size and morphology of all crystals were recorded, and X-ray data were collected from representative crystals. The results generally agreed with previous microgravity crystallization studies. On average, microgravity-grown crystals were 20% larger than control crystals grown on Earth, and microgravity-grown crystals had a slightly improved mosaicity (decreased by 0.03°) and diffraction resolution (decreased by 0.2 Å) compared with control crystals grown on Earth. However, the highest resolution and lowest mosaicity crystals were formed on Earth, and the highest-quality crystal overall was formed on Earth after return from microgravity.

  20. A linear cavity multiwavelength fiber laser with adjustable lasing line number for fixed spectral regions

    NASA Astrophysics Data System (ADS)

    Tian, J. J.; Yao, Y.

    2011-03-01

    We report an experimental demonstration of muliwavelength erbium-doped fiber laser with adjustable wavelength number based on a power-symmetric nonlinear optical loop mirror (NOLM) in a linear cavity. The intensity-dependent loss (IDL) induced by the NOLM is used to suppress the mode competition and realize the stable multiwavelength oscillation. The controlling of the wavelength number is achieved by adjusting the strength of IDL, which is dependent on the pump power. As the pump power increases from 40 to 408 mW, 1-7 lasing line(s) at fixed wavelength around 1601 nm are obtained. The output power stability is also investigated. The most power fluctuation of single wavelength is less than 0.9 dB, when the wavelength number is increased from 1-7.

  1. All Prime Contract Awards by State or Country, Place, and Contractor. Part 22 (Aua Amer-Honduras)

    DTIC Science & Technology

    1990-01-01

    5 01 񓡞i 0 La 4. U.444.4 4c 4c 41* UWl dc 4c...4C C. 0 d IL ~a.4 MW 1-1 U be 0 a 00003 0 mU 0 * a I 10.4 CD LL 00 Go G00 40 0000 1-1 qW In 0 40 t&. - 5 -4 -i..t- maoooonon 04.)m -im’ 000o >.a 0 . CV...00 t 2 Q0000000 OaN xa i004 aNO4 5 -1- J-JIJ-J 00 0 00f 0.4c 000000 0 1010CL a41 d-# 1 300000 22 1 00 wa 00000000 02 -9 a 3 4") a~ A -4-4 .4 -4-4 a 0

  2. Annual Reporting of Monitoring at Morrill, Kansas in 2015

    SciT

    LaFreniere, Lorraine M.

    In September 2005, the CCC/USDA initiated periodic sampling of groundwater, in accord with a program (Argonne 2005b) approved by the KDHE (2005), to monitor carbon tetrachloride concentrations in the groundwater. Under the KDHE-approved monitoring plan (Argonne 2005b), groundwater was sampled twice yearly for VOCs analyses through 2011. During the initial two years of monitoring, analysis for selected geochemical parameters was also conducted to aid in the evaluation of possible natural contaminant degradation (reductive dechlorination) processes in the subsurface environment. Consistently low levels of dissolved oxygen (DO) and oxidation-reduction potential (ORP) at monitoring well MW1D (in the deepest portion of themore » contaminated aquifer) and the presence of chloroform (the primary degradation product of carbon tetrachloride) suggested that some degree of reductive dechlorination was occurring.« less

  3. Three-stage linear, split-Stirling cryocooler for 1 to 2K magnetic cold stage

    NASA Technical Reports Server (NTRS)

    Longsworth, R. C.

    1993-01-01

    A long-life, linear, high efficiency 8K split Stirling cycle cryocooler was designed, built, and tested. The refrigerator is designed for cooling a 50 mW, 1.5K magnetic cold stage. Dual opposed piston compressors are driven by moving-coil linear motors. The three stage expander, although not completed, is also driven by a linear motor and is designed to produce 1 SW at 60K, 4W at 16K, and 1.2W at 8K. The cold regenerator employs a parallel gap construction for high efficiency. The key technology areas addressed include warm and cold flexible suspension bearings and a new cold regenerator geometry for high efficiency at 8K.

  4. Operation SANDSTONE. Nuclear Explosions 1948, Scientific Director’s Report of Atomic Weapon Tests. Annex 9, Parts 1, 2, 3, 4 and 5. Contamination Studies

    DTIC Science & Technology

    1949-01-01

    de - cay curves. The fit depended on the points chosen for the determination of K and L and by a suitable choice a -12- reasonably good fit could be...the previous test the crater de - cal curves indicate a mixture of Na24 and fission products. Ot)ier active materials may be present for observed...IVT N N 4-1 ui ui 0 i ’ T ; -mW 1 310 X--SH R TI ’ De A?--ŘZ (u E I EFT HAND SCA tf; t: iliT, M160 20 40 60 so 100 120 1*0 0 100 200 300 400 500 600

  5. Demonstration of a Dual-Band Mid-Wavelength HgCdTe Detector Operating at Room Temperature

    NASA Astrophysics Data System (ADS)

    Martyniuk, P.; Madejczyk, P.; Gawron, W.; Rutkowski, J.

    2018-03-01

    In this paper, the performance of sequential dual-band mid-wavelength N+-n-p-p-P+-p-p-n-n+ back-to-back HgCdTe photodiode grown by metal-organic chemical vapor deposition (MOCVD) operating at room temperature is presented. The details of the MOCVD growth procedure are given. The influence of p-type separating-barrier layer on dark current, photocurrent and response time was analyzed. Detectivity without immersion D * higher than 1 × 108 cmHz1/2/W was estimated for λ Peak = 3.2 μm and 4.2 μm, respectively. A response time of τ s ˜ 1 ns could be reached in both MW1 and MW2 ranges for the optimal P+ barrier Cd composition at the range 0.38-0.42, and extra series resistance related to the processing R Series equal to 500 Ω.

  6. Failure of Cleaning Verification in Pharmaceutical Industry Due to Uncleanliness of Stainless Steel Surface.

    PubMed

    Haidar Ahmad, Imad A; Blasko, Andrei

    2017-08-11

    The aim of this work is to identify the parameters that affect the recovery of pharmaceutical residues from the surface of stainless steel coupons. A series of factors were assessed, including drug product spike levels, spiking procedure, drug-excipient ratios, analyst-to-analyst variability, intraday variability, and cleaning procedure of the coupons. The lack of a well-defined procedure that consistently cleaned the coupon surface was identified as the major contributor to low and variable recoveries. Assessment of cleaning the surface of the coupons with clean-in-place solutions (CIP) gave high recovery (>90%) and reproducible results (Srel≤4%) regardless of the conditions that were assessed previously. The approach was successfully applied for cleaning verification of small molecules (MW <1,000 Da) as well as large biomolecules (MW up to 50,000 Da).

  7. The effect of solids retention times on the characterization of extracellular polymeric substances and soluble microbial products in a submerged membrane bioreactor.

    PubMed

    Duan, Liang; Song, Yonghui; Yu, Huibin; Xia, Siqing; Hermanowicz, Slawomir W

    2014-07-01

    In this study, the effect of solids retention times (SRTs) on extracellular polymeric substances (EPS) and soluble microbial products (SMPs) were investigated in a membrane bioreactor (MBR) at SRTs of 10, 5 and 3 days. The results showed that more carbohydrates and proteins were accumulated at short SRT, which can due to the higher biomass activity in the reactor. The molecular weight (MW) distribution analysis suggested that macromolecules (MW>30 kDa) and small molecules (MW<1 kDa) were the dominant fraction of EPS and SMP, respectively. The reactor at shorter SRT had more small molecules and less macromolecules of carbohydrates. The MW distribution of total organic carbon (TOC) suggested that other organic moieties were exuded by microbes into the solution. The shorter SRT had more undefined microbial by-product-like substances and different O − H bonds in hydroxyl functional groups. Copyright © 2014 Elsevier Ltd. All rights reserved.

  8. Gold and Iron-Gold Nanoparticles for Intracellular Tracking and in Vivo Medical Applicatons

    NASA Astrophysics Data System (ADS)

    Fu, Wei

    2005-03-01

    We have fabricated Au and Fe-Au nanoparticles for potential use in ex vivo experiments such as intracellular tracking, as well as a variety of in vivo medical applications. In order to improve their targeting potential, circulation time and flexibility, gold NPs were surface modified using a hetero-bifunctional poly(ethylene glycol) (PEG, MW 1,500) spacers. A coumarin-PEG-gold NP complex was formed and cell viability studies and optical fluorescence experiments were carried out demonstrating the use of these surface-modified gold NPs for drug delivery, gene therapy and cell trafficking experiments. Fe-Au nanoparticles were also fabricated and show significant contrast enhancement in MRI studies through a substantial reduction of the T2 relaxation time.

  9. Comparative analysis of anti-polyglutamine Fab crystals grown on Earth and in microgravity

    PubMed Central

    Owens, Gwen E.; New, Danielle M.; Olvera, Alejandra I.; Manzella, Julia Ashlyn; Macon, Brittney L.; Dunn, Joshua C.; Cooper, David A.; Rouleau, Robyn L.; Connor, Daniel S.; Bjorkman, Pamela J.

    2016-01-01

    Huntington’s disease is one of nine neurodegenerative diseases caused by a polyglutamine (polyQ)-repeat expansion. An anti-polyQ antigen-binding fragment, MW1 Fab, was crystallized both on Earth and on the International Space Station, a microgravity environment where convection is limited. Once the crystals returned to Earth, the number, size and morphology of all crystals were recorded, and X-ray data were collected from representative crystals. The results generally agreed with previous microgravity crystallization studies. On average, microgravity-grown crystals were 20% larger than control crystals grown on Earth, and microgravity-grown crystals had a slightly improved mosaicity (decreased by 0.03°) and diffraction resolution (decreased by 0.2 Å) compared with control crystals grown on Earth. However, the highest resolution and lowest mosaicity crystals were formed on Earth, and the highest-quality crystal overall was formed on Earth after return from microgravity. PMID:27710941

  10. SciT

    L. Zakharov, J. Li and Y. Wu

    The project of ASIPP (with PPPL participation), called FFRF, (R/a=4/1 m/m, Ipl=5 MA, Btor=4-6 T, PDT=50-100 MW, Pfission=80-4000 MW, 1 m thick blanket) is outlined. FFRF stands for the Fusion-Fission Research Facility with a unique fusion mission and a pioneering mission of merging fusion and fission for accumulation of design, experimental, and operational data for future hybrid applications. The design of FFRF will use as much as possible the EAST and ITER design experience. On the other hand, FFRF strongly relies on new, Lithium Wall Fusion plasma regimes, the development of which has already started in the US and China.

  11. Diversity of citrus tristeza virus isolates indicated by dsRNA analysis.

    PubMed

    Dodds, J A; Jordan, R L; Roistacher, C N; Jarupat, T

    1987-01-01

    One major dsRNA of molecular weight (MW) 13.3 X 10(6) and two others (MW 1.9 X 10(6) and 0.8 X 10(6] were routinely detected by polyacrylamide gel electrophoresis in extracts from sweet orange (Citrus sinensis) or citron (Citrus medica) infected with each of 66 isolates of citrus tristeza virus (CTV). Several additional dsRNA were also commonly detected, usually as weakly stained bands in reproducible positions in gels, but some were very prominent, e.g., a dsRNA of MW 1.7 X 10(6) associated with a seedling yellows isolate (sy-1). No dsRNA was detected in equivalent extracts from noninoculated sweet orange and citron. End-labeled [32P] probes were made from purified full-length viral RNA or polyacrylamide gel-purified full-length dsRNA of a nonseedling yellows (nsy-1) and a seedling yellows (sy-1) isolate of CTV. Each of the four probes was able to hybridize to all major and most minor dsRNAs of both isolates in composite polyacrylamide/agrarose gels, including the 1.7 X 10(6) dsRNA specific to the seedling yellows isolate, and could readily detect CTV nucleic acid sequences in extracts from bark of infected sweet orange plants spotted onto nitrocellulose membranes. One dsRNA (MW 0.5 X 10(6] was very prominent in some isolates and much less so, or undetectable, in other isolates and 66 isolates have been screened for the presence of this dsRNA. There was a strong correlation between inability to detect the 0.5 X 10(6) dsRNA and the designation of an isolate as neither a seedling yellows type nor a stem pitting isolate of grapefruit; these properties were typical for isolates of CTV from southern California.

  12. Application of a constructed wetland system for polluted stream remediation

    NASA Astrophysics Data System (ADS)

    Tu, Y. T.; Chiang, P. C.; Yang, J.; Chen, S. H.; Kao, C. M.

    2014-03-01

    ., Steroidobacter denitrificans, Hydrocarboniphaga effuse were responsible for nitrogen removal, and the dominant carbon degrading bacteria (Stenotrophomonas maltophilia, H. effuse, Alcaligenes sp., Pseudomonas sp., Fusibacter sp., Chlofoflexi, Guggenheimella bovis, Bacillus pumilus) were responsible for carbon reduction. The denaturing gradient gel electrophoresis (DGGE) and nucleotide sequence techniques provide a guide for microbial ecology evaluation, which can be used as an indication of contaminants removal. Results from this study show that constructed wetlands have the potential to be developed into an environmentally acceptable river water quality improvement and wastewater polishment alternative for practical application.

  13. Open source approaches to establishing Roseobacter clade bacteria as synthetic biology chassis for biogeoengineering.

    PubMed

    Borg, Yanika; Grigonyte, Aurelija Marija; Boeing, Philipp; Wolfenden, Bethan; Smith, Patrick; Beaufoy, William; Rose, Simon; Ratisai, Tonderai; Zaikin, Alexey; Nesbeth, Darren N

    2016-01-01

    Aim. The nascent field of bio-geoengineering stands to benefit from synthetic biologists' efforts to standardise, and in so doing democratise, biomolecular research methods. Roseobacter clade bacteria comprise 15-20% of oceanic bacterio-plankton communities, making them a prime candidate for establishment of synthetic biology chassis for bio-geoengineering activities such as bioremediation of oceanic waste plastic. Developments such as the increasing affordability of DNA synthesis and laboratory automation continue to foster the establishment of a global 'do-it-yourself' research community alongside the more traditional arenas of academe and industry. As a collaborative group of citizen, student and professional scientists we sought to test the following hypotheses: (i) that an incubator capable of cultivating bacterial cells can be constructed entirely from non-laboratory items, (ii) that marine bacteria from the Roseobacter clade can be established as a genetically tractable synthetic biology chassis using plasmids conforming to the BioBrick(TM) standard and finally, (iii) that identifying and subcloning genes from a Roseobacter clade species can readily by achieved by citizen scientists using open source cloning and bioinformatic tools. Method. We cultivated three Roseobacter species, Roseobacter denitrificans, Oceanobulbus indolifexand Dinoroseobacter shibae. For each species we measured chloramphenicol sensitivity, viability over 11 weeks of glycerol-based cryopreservation and tested the effectiveness of a series of electroporation and heat shock protocols for transformation using a variety of plasmid types. We also attempted construction of an incubator-shaker device using only publicly available components. Finally, a subgroup comprising citizen scientists designed and attempted a procedure for isolating the cold resistance anf1 gene from Oceanobulbus indolifexcells and subcloning it into a BioBrick(TM) formatted plasmid. Results. All species were stable

  14. Cardiolipin deficiency causes a dissociation of the b 6 c:caa 3 megacomplex in B. subtilis membranes.

    PubMed

    García Montes de Oca, Led Yered Jafet; Cabellos Avelar, Tecilli; Picón Garrido, Gerardo Ignacio; Chagoya-López, Alicia; González de la Vara, Luis; Delgado Buenrostro, Norma Laura; Chirino-López, Yolanda Irasema; Gómez-Lojero, Carlos; Gutiérrez-Cirlos, Emma Berta

    2016-08-01

    The associations among respiratory complexes in energy-transducing membranes have been established. In fact, it is known that the Gram-negative bacteria Paracoccus denitrificans and Escherichia coli have respiratory supercomplexes in their membranes. These supercomplexes are important for channeling substrates between enzymes in a metabolic pathway, and the assembly of these supercomplexes depends on the protein subunits and membrane lipids, mainly cardiolipin, which is present in both the mitochondrial inner membrane and bacterial membranes. The Gram-positive bacterium Bacillus subtilis has a branched respiratory chain, in which some complexes generate proton motive force whereas others constitute an escape valve of excess reducing power. Some peculiarities of this respiratory chain are the following: a type II NADH dehydrogenase, a unique b 6 c complex that has a b 6 type cytochrome with a covalently bound heme, and a c-type heme attached to the third subunit, which is similar to subunit IV of the photosynthetic b 6 f complex. Cytochrome c oxygen reductase (caa 3 ) contains a c-type cytochrome on subunit I. We previously showed that the b 6 c and the caa 3 complexes form a supercomplex. Both the b 6 c and the caa 3 together with the quinol oxygen reductase aa 3 generate the proton motive force in B. subtilis. In order to seek proof that this supercomplex is important for bacterial growth in aerobic conditions we compared the b 6 c: caa 3 supercomplex from wild type membranes with membranes from two mutants lacking cardiolipin. Both mutant complexes were found to have similar activity and heme content as the wild type. Clear native electrophoresis showed that mutants lacking cardiolipin had b 6 c:caa 3 supercomplexes of lower mass or even individual complexes after membrane solubilization with digitonin. The use of dodecyl maltoside revealed a more evident difference between wild-type and mutant supercomplexes. Here we provide evidence showing that cardiolipin

  15. Far from superficial: microbial diversity associated with the skin and mucus of fish

    Cipriano, Rocco C.; Dove, Alistair; Cipriano, R.C.; Bruckner, A.W.; Shchelkunov, I.S.

    2011-01-01

    During horizontal or water-borne infection involving an obligate pathogen (e.g. – Aeromonas salmonicida, cause of furunculosis), the pathogen interacted with and influenced the microbial diversity of the dermal mucus of fish. Prior to infection, the prevalent bacterial flora cultured from juvenile Atlantic salmon (Salmo salar) included Pseudomonas fluorescens, Comomonas terrigenia, Acinetobacter sp., Moraxella sp., Pseudomonas dimunita, Alcaligenes denitrificans, Pseudomonas pseudoalcaligenes, and Pseudomonas alcaligenes, Serratia liquefaciens, Aeromonas hydrophila, other motile Aeromonas spp., and Corynebacterium aquaticum. After A. salmonicida was initially detected in this population as an external mucus infection, Acinetobacter sp., Moraxella sp., C. terrigenia, P. fluorescens, and P. dimunita, Staphylococcus sp., and A. hydrophila, were also present in appreciable numbers. Within several weeks, however, the A. salmonicida infection amplified and composed 78% of the total flora in the mucus. Only P. dimunita (4%). P. fluorescens (2%), and C. terrigenia (1%) were cultured at that time and more than a third of these fish showed evidence of a systemic A. salmonicida infection within their kidneys. Eight weeks after oral oxytetracycline treatments, A. salmonicida was no longer isolated from the mucus or kidneys of any fish and glucose inert or other oxidative microbes (e.g., P. fluorescens, C. terrigenia, Acinetobacter sp., Moraxella sp.) were beginning to repopulate the external surface of the salmon in increasing frequency. Still present and composing fairly large percentages of the total flora were A. hydrophila, as well as Enterobacter sp., and P. putrefaciens. A normal microbial diversity was re-established as the fish recovered. In another investigation, reduced biological diversity was noted in the dermal mucus among smallmouth bass that were sampled from the Jackson River (Covington, VA). In these fish, A. hydrophila and P. putrefaciens were the two

  16. Anaerobic Nitrate-Dependent Metal Bio-Oxidation

    NASA Astrophysics Data System (ADS)

    Weber, K.; Knox, T.; Achenbach, L. A.; Coates, J. D.

    2007-12-01

    TPSY, was also capable of nitrate- dependent U(IV) oxidation (8 μM over 24 hours, pseudo first order rate constant of 0.12 ± 0.02 hr-1) in washed cell suspensions. Further biochemical investigation of nitrate-dependent U(IV) oxidation in strain TPSY revealed the expression of several putative high molecular weight proteins specific to this metabolism. Together with the previously described metabolic ability of Geobacter metallireducens (Finneran et al. 2002) and Thiobacillus denitrificans (Beller 2005), these data indicate that anaerobic, metal oxidation may be a ubiquitous microbial metabolism.

  17. Nitric oxide in denitrification - an elusive signal molecule emitted from soil

    NASA Astrophysics Data System (ADS)

    Bakken, L. R.; Frostegard, A.

    2010-12-01

    Soils emit variable amounts of NO and N2O, with environmental consequences (atmosphere chemistry and global warming). Nitrification was for some time considered the main source of NO emission, but several investigations have indicated that denitrification may be a potent source as well. However, strong emission of NO from denitrifying organisms is in some conflict with common understanding of the role of NO in the regulation of denitrification, as based on paradigm model strains. NO appears to be an important signal molecule for denitrifying organisms by exerting a positive feedback on the expression of the genes coding for denitrification. On the other hand, a careful control of the NO concentrations at nanomolar concentrations has long been considered an essential fitness character for denitrifying organisms, since micromolar concentrations of NO is toxic to many organisms. For the same reason, organisms lacking genes encoding NO reductase (NOR) have been considered unfit for denitrification. This view is challenged by isolation of organisms whose primary product of denitrification is NO, either because they lack the genes for NO reductase, or because their synthesis of the denitrification proteome is extremely unbalanced, resulting in transient NO accumulation to micromolar concentrations when grown in pure culture. Such paralyzing NO concentrations are probably never reached in natural environments, however, due to diffusion and NO-absorption by adjacent organisms, be it by NOR or other NO scavenging enzymes. Hypothetically, the production of NO by denitrifying organisms may be an advantage by fending off nearby competitors. We have embarked on a comparative study of denitrification phenotypes regarding their denitrification gene expression and control of NO and N2O concentrations in response to anoxic spells. This includes model strains (Paracoccus denitrificans and Agrobacterium tumefaciens) and recently isolated strains within several genera. Some are found

  18. ANAMMOX-like performances for nitrogen removal from ammonium-sulfate-rich wastewater in an anaerobic sequencing batch reactor.

    PubMed

    Prachakittikul, Pensiri; Wantawin, Chalermraj; Noophan, Pongsak Lek; Boonapatcharoen, Nimaradee

    2016-01-01

    bacterium (Candidatus Brocadia sinica JPN1) Desulfacinum subterraneum belonging to the genus Desulfacinum and bacteria that are involved in sulfur metabolism (Pseudomonas aeruginosa strain SBTPe-001 and Paracoccus denitrificans strain IAM12479) in SRAO-AnSBR.

  19. Open source approaches to establishing Roseobacter clade bacteria as synthetic biology chassis for biogeoengineering

    PubMed Central

    Boeing, Philipp; Wolfenden, Bethan; Smith, Patrick; Beaufoy, William; Rose, Simon; Ratisai, Tonderai; Zaikin, Alexey

    2016-01-01

    Aim. The nascent field of bio-geoengineering stands to benefit from synthetic biologists’ efforts to standardise, and in so doing democratise, biomolecular research methods. Roseobacter clade bacteria comprise 15–20% of oceanic bacterio-plankton communities, making them a prime candidate for establishment of synthetic biology chassis for bio-geoengineering activities such as bioremediation of oceanic waste plastic. Developments such as the increasing affordability of DNA synthesis and laboratory automation continue to foster the establishment of a global ‘do-it-yourself’ research community alongside the more traditional arenas of academe and industry. As a collaborative group of citizen, student and professional scientists we sought to test the following hypotheses: (i) that an incubator capable of cultivating bacterial cells can be constructed entirely from non-laboratory items, (ii) that marine bacteria from the Roseobacter clade can be established as a genetically tractable synthetic biology chassis using plasmids conforming to the BioBrickTM standard and finally, (iii) that identifying and subcloning genes from a Roseobacter clade species can readily by achieved by citizen scientists using open source cloning and bioinformatic tools. Method. We cultivated three Roseobacter species, Roseobacter denitrificans, Oceanobulbus indolifexand Dinoroseobacter shibae. For each species we measured chloramphenicol sensitivity, viability over 11 weeks of glycerol-based cryopreservation and tested the effectiveness of a series of electroporation and heat shock protocols for transformation using a variety of plasmid types. We also attempted construction of an incubator-shaker device using only publicly available components. Finally, a subgroup comprising citizen scientists designed and attempted a procedure for isolating the cold resistance anf1 gene from Oceanobulbus indolifexcells and subcloning it into a BioBrickTM formatted plasmid. Results. All species were stable

  20. A Tale of Two Gases: Isotope Effects Associated with the Enzymatic Production of H2 and N2O

    NASA Astrophysics Data System (ADS)

    Yang, H.; Gandhi, H.; Kreuzer, H. W.; Moran, J.; Hill, E. A.; McQuarters, A.; Lehnert, N.; Ostrom, N. E.; Hegg, E. L.

    2014-12-01

    experiments were performed with bacterial nitric oxide reductase from Paracoccus denitrificans (cNOR). In this case both Nα and Nβ exhibited inverse isotope effects, while O had a normal isotope effect. Together, these data highlight the utility in using stable isotopes as both tracers and mechanistic probes when studying metabolic processes.

  1. Genome Analysis of the Biotechnologically Relevant Acidophilic Iron Oxidising Strain JA12 Indicates Phylogenetic and Metabolic Diversity within the Novel Genus “Ferrovum”

    PubMed Central

    Ullrich, Sophie R.; Poehlein, Anja; Tischler, Judith S.; González, Carolina; Ossandon, Francisco J.; Daniel, Rolf; Holmes, David S.; Schlömann, Michael; Mühling, Martin

    2016-01-01

    Background Members of the genus “Ferrovum” are ubiquitously distributed in acid mine drainage (AMD) waters which are characterised by their high metal and sulfate loads. So far isolation and microbiological characterisation have only been successful for the designated type strain “Ferrovum myxofaciens” P3G. Thus, knowledge about physiological characteristics and the phylogeny of the genus “Ferrovum” is extremely scarce. Objective In order to access the wider genetic pool of the genus “Ferrovum” we sequenced the genome of a “Ferrovum”-containing mixed culture and successfully assembled the almost complete genome sequence of the novel “Ferrovum” strain JA12. Phylogeny and Lifestyle The genome-based phylogenetic analysis indicates that strain JA12 and the type strain represent two distinct “Ferrovum” species. “Ferrovum” strain JA12 is characterised by an unusually small genome in comparison to the type strain and other iron oxidising bacteria. The prediction of nutrient assimilation pathways suggests that “Ferrovum” strain JA12 maintains a chemolithoautotrophic lifestyle utilising carbon dioxide and bicarbonate, ammonium and urea, sulfate, phosphate and ferrous iron as carbon, nitrogen, sulfur, phosphorous and energy sources, respectively. Unique Metabolic Features The potential utilisation of urea by “Ferrovum” strain JA12 is moreover remarkable since it may furthermore represent a strategy among extreme acidophiles to cope with the acidic environment. Unlike other acidophilic chemolithoautotrophs “Ferrovum” strain JA12 exhibits a complete tricarboxylic acid cycle, a metabolic feature shared with the closer related neutrophilic iron oxidisers among the Betaproteobacteria including Sideroxydans lithotrophicus and Thiobacillus denitrificans. Furthermore, the absence of characteristic redox proteins involved in iron oxidation in the well-studied acidophiles Acidithiobacillus ferrooxidans (rusticyanin) and Acidithiobacillus

  2. Metatranscriptomic Evidence of Chemolithoautotrophy in the Rifle (CO) Subsurface Relevant to C, S, N, and Fe Cycling

    NASA Astrophysics Data System (ADS)

    Beller, H. R.; Jewell, T. N. M.; Karaoz, U.; Thomas, B. C.; Banfield, J. F.; Brodie, E.; Williams, K. H.

    2014-12-01

    Although there is a limited understanding of the chemolithoautotrophic activity of aquifer microorganisms, such subsurface microbial activity could greatly influence the cycling of elements such as C, S, N, and Fe. Here, we present transcriptional (RNA-Seq) evidence of the emergence of such chemolithoautotrophic activities in groundwater filter samples from a 2-month experiment in which up to 1.5 mM nitrate (a native electron acceptor) was injected into a perennially suboxic/anoxic aquifer (Rifle, CO) containing a large reservoir of reduced Fe- and S-containing compounds. Illumina sequence data from rRNA-subtracted cDNA libraries was assembled and mapped to phylogenetically binned Rifle metagenome data. Indicative of the activity of Fe(II)-oxidizing bacteria, many high-abundance transcripts mapped to the Gallionellaceae family, whose known members are chemolithoautotrophic bacteria that catalyze Fe(II) oxidation. For example, included among the most abundant transcripts were a cold-shock protein and an acyl carrier protein with 96-98% protein sequence identity to Gallionella capsiferriformans and a nitrite reductase (nirS) gene likely belonging to a Sideroxydans relative. The apparent activity of Gallionellaceae members is consistent with 16S rRNA iTag analyses of these samples, which indicated that Gallionella-related taxa accounted for up to ~50% of these communities. Evidence of sulfide oxidation also was apparent in these samples. For example, highly expressed subunits of APS reductase were very similar to those of the obligately chemolithoautotrophic S- and Fe(II)-oxidizing Thiobacillus denitrificans in terms of sequence identity (98-99%) and synteny of the mapped scaffold. Also highly expressed were a ß-Proteobacterial Form II RubisCO gene and a hydrazine oxidoreductase gene (93% identity to the planctomycete KSU-1), the latter strongly indicative of anaerobic ammonia oxidation (anammox) activity, which has seldom been reported in aquifer environments. Such

  3. The Completely Sequenced Plasmid pEST4011 Contains a Novel IncP1 Backbone and a Catabolic Transposon Harboring tfd Genes for 2,4-Dichlorophenoxyacetic Acid Degradation

    PubMed Central

    Vedler, Eve; Vahter, Merle; Heinaru, Ain

    2004-01-01

    The herbicide 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading bacterium Achromobacter xylosoxidans subsp. denitrificans strain EST4002 contains plasmid pEST4011. This plasmid ensures its host a stable 2,4-D+ phenotype. We determined the complete 76,958-bp nucleotide sequence of pEST4011. This plasmid is a deletion and duplication derivative of pD2M4, the 95-kb highly unstable laboratory ancestor of pEST4011, and was self-generated during different laboratory manipulations performed to increase the stability of the 2,4-D+ phenotype of the original strain, strain D2M4(pD2M4). The 47,935-bp catabolic region of pEST4011 forms a transposon-like structure with identical copies of the hybrid insertion element IS1071::IS1471 at the two ends. The catabolic regions of pEST4011 and pJP4, the best-studied 2,4-D-degradative plasmid, both contain homologous, tfd-like genes for complete 2,4-D degradation, but they have little sequence similarity other than that. The backbone genes of pEST4011 are most similar to the corresponding genes of broad-host-range self-transmissible IncP1 plasmids. The backbones of the other three IncP1 catabolic plasmids that have been sequenced (the 2,4-D-degradative plasmid pJP4, the haloacetate-catabolic plasmid pUO1, and the atrazine-catabolic plasmid pADP-1) are nearly identical to the backbone of R751, the archetype plasmid of the IncP1 β subgroup. We show that despite the overall similarity in plasmid organization, the pEST4011 backbone is sufficiently different (51 to 86% amino acid sequence identity between individual backbone genes) from the backbones of members of the three IncP1 subgroups (the α, β, and γ subgroups) that it belongs to a new IncP1subgroup, the δ subgroup. This conclusion was also supported by a phylogenetic analysis of the trfA2, korA, and traG gene products of different IncP1 plasmids. PMID:15489427

  4. Cell biology and molecular basis of denitrification.

    PubMed Central

    Zumft, W G

    1997-01-01

    Denitrification is a distinct means of energy conservation, making use of N oxides as terminal electron acceptors for cellular bioenergetics under anaerobic, microaerophilic, and occasionally aerobic conditions. The process is an essential branch of the global N cycle, reversing dinitrogen fixation, and is associated with chemolithotrophic, phototrophic, diazotrophic, or organotrophic metabolism but generally not with obligately anaerobic life. Discovered more than a century ago and believed to be exclusively a bacterial trait, denitrification has now been found in halophilic and hyperthermophilic archaea and in the mitochondria of fungi, raising evolutionarily intriguing vistas. Important advances in the biochemical characterization of denitrification and the underlying genetics have been achieved with Pseudomonas stutzeri, Pseudomonas aeruginosa, Paracoccus denitrificans, Ralstonia eutropha, and Rhodobacter sphaeroides. Pseudomonads represent one of the largest assemblies of the denitrifying bacteria within a single genus, favoring their use as model organisms. Around 50 genes are required within a single bacterium to encode the core structures of the denitrification apparatus. Much of the denitrification process of gram-negative bacteria has been found confined to the periplasm, whereas the topology and enzymology of the gram-positive bacteria are less well established. The activation and enzymatic transformation of N oxides is based on the redox chemistry of Fe, Cu, and Mo. Biochemical breakthroughs have included the X-ray structures of the two types of respiratory nitrite reductases and the isolation of the novel enzymes nitric oxide reductase and nitrous oxide reductase, as well as their structural characterization by indirect spectroscopic means. This revealed unexpected relationships among denitrification enzymes and respiratory oxygen reductases. Denitrification is intimately related to fundamental cellular processes that include primary and secondary

  5. Phenotypic and Genetic Characterization of Carbapenemase and ESBLs Producing Gram-negative Bacteria (GNB) Isolated from Patients with Cystic Fibrosis (CF) in Tehran Hospitals

    PubMed Central

    Vali, Parisa; Shahcheraghi, Fereshteh; Seyfipour, Maryam; Zamani, Maryam Alsadat; Allahyar, Mohammad Reza; Feizabadi, Mohammad Mehdi

    2014-01-01

    Background: Cystic Fibrosis (CF) is an autosomal recessive genetic disorder in white populations caused by mutation in a gene that encodes Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) protein. Since frequent respiratory tract infections are the major problem in patients with CF, obligation to identify the causative bacteria and determining their antibiotic resistance pattern is crucial. The purpose of this project was to detect Gram-negative bacteria (GNB) isolated from sputa of CF patients and to determine their antibiotic resistance pattern. Materials and Methods: The sputum of 52 CF patients, treated as inpatients at hospitals in Tehran, was obtained between November 2011 and June 2012. Samples cultured in selective and non-selective media and GNB recognized by biochemical tests. Antimicrobial susceptibility testing to cephalosporins, aminoglycosides and carbapenems was performed by disk diffusion method and MICs of them were measured. For phenotypic detection of carbapenemase and ESBLs production, the Modified Hodge test, double disk synergy test and the combined disk methods were performed. Subsequently, the genes encoding the extended spectrum beta-lactamases (blaPER, blaCTX-M) and carbapenemases (blaIMP-1, blaGES, blaKPC, blaNDM, blaVIM-1, blaVIM-2, blaSPM, blaSIM) in Gram negative bacteria were targeted among the resistant isolates by using PCR. PFGE was used to determine any genetic relationship among the Pseudomonas aeruginosa isolated from these patients. Results: Fifty five GNB were isolated from 52 sputum samples including Pseudomonas aeruginosa, Klebsiella ozaenae, Alcaligenes xylosoxidans, Achromobacter denitrificans, Klebsiella pneumonia and Stenotrophomonas maltophilia. The rates of resistance to different antibiotic were as follows: cefixime (%80), ceftriaxone (%43), ceftazidime (%45) and meropenem (%7). The prevalence of genes encoding the ESBLs and Carbapenemases among the the phenotypically positive strains were as follows: bla

  6. Groundwater geochemical and selected volatile organic compound data, Operable Unit 1, Naval Undersea Warfare Center, Division Keyport, Washington, June 2011

    Huffman, Raegan L.; Frans, L.M.

    2012-01-01

    were similar to or slightly less than chlorinated volatile organic compound concentrations measured in previous years. For the upper aquifer beneath the southern phytoremediation plantation, chlorinated volatile organic compound concentrations in 2011 in groundwater from the piezometers were extremely high and continued to vary considerably over space and between years. At piezometer P1-9, the total chlorinated volatile organic compound concentrations increased from 9,500 micrograms per liter in 2010 to more than 44,000 micrograms per liter in 2011. Total chlorinated volatile organic compound concentrations decreased at piezometers P1-6, P1-7, and P1-10 compared to the concentrations measured in 2010. One or both of the reductive dechlorination byproducts ethane and ethene were detected at all piezometers and three of the four wells in the southern plantation. For the intermediate aquifer, concentrations of redox sensitive constituents and chlorinated volatile organic compounds in 2011 were consistent with concentrations measured in previous years, with the exception of notable decreases in sulfate and chloride concentrations at well MW1-28. Concentrations of the reductive dechlorination byproducts ethane and ethene decreased at wells MW1-25 and MW1-28 compared to previously measured concentrations.

  7. Observations of a hydrofracture induced earthquake sequence in Harrison County Ohio in 2014

    NASA Astrophysics Data System (ADS)

    Friberg, P. A.; Brudzinski, M. R.; Currie, B. S.; Skoumal, R.

    2015-12-01

    On October 7, 2014, a Mw 1.9 earthquake was detected and located using the IRIS Earthscope Transportable Array stations in Ohio. The earthquake was located at a depth of ~3 km near the interface of the Paleozoic sedimentary rocks with the crystalline Precambrian basement. The location is within a few kilometers laterally of a 2013 earthquake sequence that was linked to hydraulic fracturing (HF) operations on three wells in Harrison county (Friberg et al, 2014). Using the Mw 1.9 event as a template in a multi-component cross correlation detector on station O53A, over 1000 matching detections were revealed between September 26 - October 17, 2014. These detections were all coincident in time with HF operations on 3 nearby (< 1km away) horizontally drilled wells (Tarbert 1H, 3H, and 5H) in the Utica formation (~2.4 km depth). The HF operations at two of the wells (1H and 5H) were coincident with the majority of the detected events. The final well (3H) stimulated in the series, produced only about 20 identified events. In addition to the coincident timing with nearby HF operations, the time clustered nature of the detections were similar to the 2013 sequence and two other Ohio HF induced sequences in 2014 (Skoumal et al, 2015). All of the other HF induced earthquake sequences in Ohio were related to operations in the Utica formation. Interestingly, this sequence of earthquakes did not follow a simple Gutenberg-Richter magnitude frequency relationship and was deficient in positive magnitude events; the magnitude 1.9 was preceded by a magnitude 1.7, and only a ½ dozen events slightly above magnitude 0.0. The majority of the events detected were below magnitude 0.0, with some as low as magnitude -2.0. While the majority of detections are too small to locate, high similarity in waveform character indicate they are spatially near to the magnitude 1.9 event. Furthermore, gradual shifts in P phase arrival relative to S phases indicate events are moving away from the station

  8. Surface modification of esophageal stent materials by a polyethylenimine layer aiming at anti-cancer function.

    PubMed

    Zhang, Kun; Bai, Yuxin; Wang, Xiaofeng; Li, Qian; Guan, Fangxia; Li, Jingan

    2017-08-01

    Esophageal cancer is difficult to cure globally and possesses high mortality rate, and it is generally accepted that palliative care such as stent implantation is the main therapy method for esophageal cancer in later period. However, the restenosis caused by tumor cells and inflammatory cells seriously interferes the stent clinical application and limits its long-term services. To solve this problem, series of drug delivery stents were developed and proven rather effective in the early stage of implantation, but more serious restenosis occurred after the drug delivery was over, which endangered the patients' life. Therefore, endowing the esophageal stent continuous anti-cancer function become an ideal strategy for inhibiting the restenosis. In this contribution, the functional layer composed of polydopamine (PDA) and Poly-ethylenimine (PEI) with series of molecular weights (MW, 1.8 × 10 3 , 1 × 10 4 , 2.5 × 10 4 and 7 × 10 4  Da) were fabricated onto the esophageal stent material 317L stainless steel (317L SS) surface. The surface characterization including amine quantitative, atomic force microscopy (AFM) and water contact angle measurement indicated successful preparation of the PDA/PEI layer. The Eca109 cells culture results proved that the PDA/PEI layers significantly improve Eca109 cells apoptosis and necrosis, suggesting excellent anti-cancer function. In addition, we also found that the anti-cancer function of the PDA/PEI layers was positively correlated to the immobilized PEIs' MW. All the results demonstrated the potential application of the PDA/PEI layers on the surface modification of esophageal stent for continuous anti-cancer function. It is generally accepted that the restenosis caused by tumor cells seriously interferes the esophageal stent clinical application. Thus, endowing the esophageal stent continuous anti-cancer function is the ideal strategy for inhibiting the restenosis. In this work, we fabricated functional layers

  9. Non-thermal Plasma Exposure Rapidly Attenuates Bacterial AHL-Dependent Quorum Sensing and Virulence.

    PubMed

    Flynn, Padrig B; Busetti, Alessandro; Wielogorska, Ewa; Chevallier, Olivier P; Elliott, Christopher T; Laverty, Garry; Gorman, Sean P; Graham, William G; Gilmore, Brendan F

    2016-05-31

    The antimicrobial activity of atmospheric pressure non-thermal plasma has been exhaustively characterised, however elucidation of the interactions between biomolecules produced and utilised by bacteria and short plasma exposures are required for optimisation and clinical translation of cold plasma technology. This study characterizes the effects of non-thermal plasma exposure on acyl homoserine lactone (AHL)-dependent quorum sensing (QS). Plasma exposure of AHLs reduced the ability of such molecules to elicit a QS response in bacterial reporter strains in a dose-dependent manner. Short exposures (30-60 s) produce of a series of secondary compounds capable of eliciting a QS response, followed by the complete loss of AHL-dependent signalling following longer exposures. UPLC-MS analysis confirmed the time-dependent degradation of AHL molecules and their conversion into a series of by-products. FT-IR analysis of plasma-exposed AHLs highlighted the appearance of an OH group. In vivo assessment of the exposure of AHLs to plasma was examined using a standard in vivo model. Lettuce leaves injected with the rhlI/lasI mutant PAO-MW1 alongside plasma treated N-butyryl-homoserine lactone and n-(3-oxo-dodecanoyl)-homoserine lactone, exhibited marked attenuation of virulence. This study highlights the capacity of atmospheric pressure non-thermal plasma to modify and degrade AHL autoinducers thereby attenuating QS-dependent virulence in P. aeruginosa.

  10. VHH antibodies: Emerging reagents for the analysis of environmental chemicals

    PubMed Central

    Bever, Candace S.; Dong, Jie-Xian; Vasylieva, Natalia; Barnych, Bogdan; Cui, Yongliang; Xu, Zhen-Lin; Hammock, Bruce D.; Gee, Shirley J.

    2016-01-01

    A VHH antibody (or nanobody) is the antigen binding fragment of heavy chain only antibodies. Discovered nearly 25 years ago, they have been investigated for their use in clinical therapeutics and immunodiagnostics, and more recently for environmental monitoring applications. A new and valuable immunoreagent for the analysis of small molecular weight environmental chemicals, VHH will overcome many pitfalls encountered with conventional reagents. In the work so far, VHH antibodies often perform comparably to conventional antibodies for small molecule analysis, are amenable to numerous genetic engineering techniques, and show ease of adaption to other immunodiagnostic platforms for use in environmental monitoring. Recent reviews cover the structure and production of VHH antibodies as well as their use in clinical settings. However, no report focuses on the use of these VHH antibodies to small environmental chemicals (MW <1,500 Da). This review article summarizes the efforts made to produce VHHs to various environmental targets, compares the VHH-based assays with conventional antibody assays, and discusses the advantages and limitations in developing these new antibody reagents particularly to small molecule targets. PMID:27209591

  11. A Proton Flare Triggered the Mw 8.1 Chiapos Mexican Earthquake

    NASA Astrophysics Data System (ADS)

    Elfaki, H.; Yousef, S.

    2017-12-01

    In a 2015 Cairo University M.Sc. thesis by Sarah Khodairy, very strong earthquakes were found to be highly correlated with proton flares. Strange blue and green bright flashes of light across Mexico accompanied the 8th of September 2017 Mw 1.8 Chiapas earthquake. Those lights were contemporary with a solar proton flare. Those green and blue lights are indicative of the arrival of proton streams over Mexico and their interaction with atmospheric Oxygen and Nitrogen atoms respectively in analogy with aurora lights. The proton streams attacked the weak spots of tectonic plates where the Coscos plate is being subducted below the North American plate. It is suggested that they induced telluric electric currents in the ground and in the magma thus caused motion and more subduction in the tectonic plates. Such motion immediately trigged the Chiapas earthquake in the near vicinity. The Bz component of the interplanetary magnetic field was highly negative, a door was opened in the magnetosphere and the proton stream easily leaked inside and targeted Mexico. This proton flare was accompanied by coronal mass ejection and extremely strong X.9.3- class X-ray flare as well as magnetic storms. On the other hand, the 19th of September Mw 7.1 Puebla central Mexico earthquake was initiated by fast solar wind coronal hole stream. Such stream if they hit ground they cause earthquakes, if they hit narrow seas like the Red Sea they cause flash floods. However if they target Oceans they initiate hurricanes.

  12. Surface segregation and surface tension of polydisperse polymer melts.

    PubMed

    Minnikanti, Venkatachala S; Qian, Zhenyu; Archer, Lynden A

    2007-04-14

    The effect of polydispersity on surface segregation of a lower molecular weight polymer component in a higher molecular weight linear polymer melt host is investigated theoretically. We show that the integrated surface excess zM of a polymer component of molecular weight M satisfies a simple relation zM=2Ue(M/Mw-1)phiM, where Mw is the weight averaged molecular weight, phiM is the polymer volume fraction, and Ue is the attraction of polymer chain ends to the surface. Ue is principally of entropic origin, but also reflects any energetic preference of chain ends to the surface. We further show that the surface tension gammaM of a polydisperse melt of high molar mass components depends on the number average degree of polymerization Mn as, gammaM=gammainfinity+2UerhobRT/Mn. The parameter gammainfinity is the asymptotic surface tension of an infinitely long polymer of the same chemistry, rhob is the bulk density of the polymer, R is the universal gas constant, and T is the temperature. The predicted gammaM compare favorably with surface tension values obtained from self-consistent field theory simulations that include equation of state effects, which account for changes in polymer density with molecular weight. We also compare the predicted surface tension with available experimental data.

  13. Design and performance of a 4He-evaporator at <1.0 K

    NASA Astrophysics Data System (ADS)

    Das, N. K.; Pradhan, J.; Naser, Md. Z. A.; Roy, A.; Mandal, B. Ch.; Mallik, C.; Bhandari, R. K.

    2012-12-01

    A helium evaporator for obtaining 1 K temperature has been built and tested in laboratory. This will function primarily as the precooling stage for the circulating helium isotopic gas mixture. This works on evaporative cooling by way of pumping out the vapour from the top of the pot. A precision needle valve is used initially to fill up the pot and subsequently a permanent flow impedance maintains the helium flow from the bath into the pot to replenish the evaporative loss of helium. Considering the cooling power of 10 mW @1.0 K, a 99.0 cm3 helium evaporator was designed, fabricated from OFE copper and tested in the laboratory. A pumping station comprising of a roots pump backed by a dry pump was used for evacuation. The calibrated RuO thermometer and kapton film heater were used for measuring the temperature and cooling power of the system respectively. The continuously filled 1 K bath is tested in the laboratory and found to offer a temperature less than 1.0 K by withdrawing vapour from the evaporator. In order to minimize the heat load and to prevent film creep across the pumping tube, size optimization of the pumping line and pump-out port has been performed. The results of test run along with relevant analysis, mechanical fabrication of flow impedance are presented here.

  14. Transformation of Sordaria macrospora to hygromycin B resistance: characterization of transformants by electrophoretic karyotyping and tetrad analysis.

    PubMed

    Walz, M; Kück, U

    1995-12-01

    The ascomycete Sordaria macrospora was transformed using different plasmid molecules containing the bacterial hygromycin B resistance gene (hph) under the control of different expression signals. The highest transformation frequency was obtained with vector pMW1. On this plasmid molecule, expression of the hph gene is directed by the upstream region of the isopenicillin N synthetase gene (pcbC) from the deuteromycete Acremonium chrysogenum. Southern analysis suggests that the vector copies are integrated as tandem repeats into the S. macrospora chromosomes and that duplicated sequences are most probably not inactivated by methylation during meiosis. Furthermore, the hygromycin B resistance (hygR) is not correlated with the number of integrated vector molecules. Electrophoretic karyotyping was used to further characterize S. macrospora transformants. Five chromosomal bands were separated by pulsed-field gel electrophoresis (PFGE) representing seven chromosomes with a total genome size of 39.5Mb. Hybridization analysis revealed ectopic integration of vector DNA into different chromosomes. In a few transformants, major rearrangements were detected. Transformants were sexually propagated to analyze the fate of the heterologous vector DNA. Although the hygR phenotype is stably maintained during mitosis, about a third of all lines tested showed loss of the resistance marker gene after meiosis. However, as was concluded from electrophoretic karyotyping, the resistant spores showed a Mendelian segregation of the integrated vector molecules in at least three consecutive generations. Our data indicate that heterologous marker genes can be used for transformation tagging, or the molecular mapping of chromosomal loci in S. macrospora.

  15. A glycoconjugate of Haemophilus influenzae Type b capsular polysaccharide with tetanus toxoid protein: hydrodynamic properties mainly influenced by the carbohydrate.

    PubMed

    Abdelhameed, Ali Saber; Adams, Gary G; Morris, Gordon A; Almutairi, Fahad M; Duvivier, Pierre; Conrath, Karel; Harding, Stephen E

    2016-02-26

    Three important physical properties which may affect the performance of glycoconjugate vaccines against serious disease are molar mass (molecular weight), heterogeneity (polydispersity), and conformational flexibility in solution. The dilute solution behaviour of native and activated capsular polyribosylribitol (PRP) polysaccharides extracted from Haemophilus influenzae type b (Hib), and the corresponding glycoconjugate made by conjugating this with the tetanus toxoid (TT) protein have been characterized and compared using a combination of sedimentation equilibrium and sedimentation velocity in the analytical ultracentrifuge with viscometry. The weight average molar mass of the activated material was considerably reduced (Mw ~ 0.24 × 10(6) g.mol(-1)) compared to the native (Mw ~ 1.2 × 10(6) g.mol(-1)). Conjugation with the TT protein yielded large polydisperse structures (of Mw ~ 7.4 × 10(6) g.mol(-1)), but which retained the high degree of flexibility of the native and activated polysaccharide, with frictional ratio, intrinsic viscosity, sedimentation conformation zoning behaviour and persistence length all commensurate with highly flexible coil behaviour and unlike the previously characterised tetanus toxoid protein (slightly extended and hydrodynamically compact structure with an aspect ratio of ~3). This non-protein like behaviour clearly indicates that it is the carbohydrate component which mainly influences the physical behaviour of the glycoconjugate in solution.

  16. Size and resin fractionations of dissolved organic matter and trihalomethane precursors from four typical source waters in China.

    PubMed

    Wei, Qunshan; Wang, Dongsheng; Wei, Qia; Qiao, Chunguang; Shi, Baoyou; Tang, Hongxiao

    2008-06-01

    Dissolved organic matter (DOM) and its potential to form disinfection by-products (DBPs) during drinking water treatment raise challenges to water quality control. Understanding both chemical and physical characteristics of DOM in source waters is key to better water treatment. In this study, the DOM from four typical source waters in China was fractionated by XAD resin adsorption (RA) and ultrafiltration (UF) techniques. The trihalomethane formation potential (THMFP) of all fractions in the DOM were investigated to reveal the major THM precursors. The fraction distributions of DOM could be related to their geographical origins in a certain extent. The dominant chemical fraction as THM precursors in the DOM from south waters (East-Lake reservoir in Shenzhen and Peal rivers in Guangzhou) was hydrophobic acid (HoA). The size fraction with molecular weight (MW) <1 kDa in both south waters had the highest THMFP. The results of cluster analysis showed that the parameters of fractions including DOC percentage (DOC%), UV254%, SUVA254 (specific UV254 absorbance) and THMFP were better for representing the differences of DOM from the studied waters than specific THMFP (STHMFP). The weak correlation between SUVA254 and STHMFP for either size or XAD fractions suggests that whether SUVA254 can be used as an indicator for the reactivity of THM formation is highly dependent on the nature of organic matter.

  17. Effect of different molecular weight organic components on the increase of microbial growth potential of secondary effluent by ozonation.

    PubMed

    Zhao, Xin; Hu, Hong-Ying; Yu, Tong; Su, Chang; Jiang, Haochi; Liu, Shuming

    2014-11-01

    Ozonation has been widely applied in advanced wastewater treatment. In this study, the effect of ozonation on assimilable organic carbon (AOC) levels in secondary effluents was investigated, and AOC variation of different molecular weight (MW) organic components was analyzed. Although the removal efficiencies were 47%-76% and 94%-100% for UV254 and color at ozone dosage of 10mg/L, dissolved organic carbon (DOC) in secondary effluents was hardly removed by ozonation. The AOC levels increased by 70%-780% at an ozone dosage range of 1-10mg/L. AOC increased significantly in the instantaneous ozone demand phase, and the increase in AOC was correlated to the decrease in UV254 during ozonation. The results of MW distribution showed that, ozonation led to the transformation of larger molecules into smaller ones, but the increase in low MW (<1kDa) fraction did not contribute much to AOC production. The change of high MW (>100kDa and 10-100kDa) fractions itself during ozonation was the main reason for the increase of AOC levels. Furthermore, the oxidation of organic matters with high MWs (>100kDa and 10-100kDa) resulted in more AOC production than those with low MWs (1-10kDa and <1kDa). The results indicated that removing large molecules in secondary effluents could limit the increase of AOC during ozonation. Copyright © 2014. Published by Elsevier B.V.

  18. The application of liquid air energy storage for large scale long duration solutions to grid balancing

    NASA Astrophysics Data System (ADS)

    Brett, Gareth; Barnett, Matthew

    2014-12-01

    Liquid Air Energy Storage (LAES) provides large scale, long duration energy storage at the point of demand in the 5 MW/20 MWh to 100 MW/1,000 MWh range. LAES combines mature components from the industrial gas and electricity industries assembled in a novel process and is one of the few storage technologies that can be delivered at large scale, with no geographical constraints. The system uses no exotic materials or scarce resources and all major components have a proven lifetime of 25+ years. The system can also integrate low grade waste heat to increase power output. Founded in 2005, Highview Power Storage, is a UK based developer of LAES. The company has taken the concept from academic analysis, through laboratory testing, and in 2011 commissioned the world's first fully integrated system at pilot plant scale (300 kW/2.5 MWh) hosted at SSE's (Scottish & Southern Energy) 80 MW Biomass Plant in Greater London which was partly funded by a Department of Energy and Climate Change (DECC) grant. Highview is now working with commercial customers to deploy multi MW commercial reference plants in the UK and abroad.

  19. The effect of adding selective mixed culture of alternative electricity production based on tempe wastewater on tubular microbial fuel cell

    NASA Astrophysics Data System (ADS)

    Mariana, Elisabeth, Utami, Tania Surya; Arbianti, Rita; Hermansyah, Heri

    2017-05-01

    Bacteria has long been known could produce electricity. MFC (Microbial Fuel Cell) is a technology that uses bacteria. MFC is potential as producer of alternative renewable energy through the conversion of waste by bacteria into electrical energy. However, this technology cannot reach the target value of the minimum voltage. This research is focused on reviewing the effect of the addition of gram positive and negative bacteria (selective mixed culture) contained in tempe wastewater as well as the optimal volume additions gram using a tubular single chamber membranless reactor. The result shows that the addition of selective mixed culture can increase voltage of MFC. Gram negative bacteria dominate tempe wastewater and has better ability to transfer electrons than gram-positive. The voltage increases with increasing amount of bacteria up to a certain maximum point. Addition of 1 mL gram-negative bacteria improve electrical output and provide the most optimal results of 0.0697 mW/m2 mV or 92.14% excalation against the initial control experiment with the average power density of 0.0702 mW1m2. Additions of most optimum variation also give good results on the use of industrial waste, with electrical voltage and power density high of 8.90 mV and 0.02 mW/m2.

  20. The effects of ILLLI on peripheral blood T lymphocytes subpopulation & NK cells in psoriasis treatment

    NASA Astrophysics Data System (ADS)

    Zhu, Jing; Nie, Fan

    2005-07-01

    Objective: To research the effects of Intravascular low level laser irradiation (ILLLI) on the immulogic function of cells in treatment of psoriasis. Method: 49 patients suffered from psoriasis were treated by Intravascular low level laser irradiation (laser output power: 4-5mw, 1 hour per day, a course of treatment is 10 days). We checked the function of T lymphocyte subgroup and NK cell in peripheral blood between pre and post treatment. Results: 1.The mean value of CD3+ in post treatment is higher. P<0.05. Significant difference is showed between pre and post treatment 2. The mean value of CD4+ in post treatment dropped slightly while the mean value of CD4/CD8, NK cell in post treatment increased little, nearly approach the mean value of natural person. 3.The mean value of CD4+,CD8+,NK cell which is under 30% increased the percent obviously after the treatment; The mean value of CD4+,CD8+ u higher than 30% obviously drop the percent, P#0.05 and <0.01. Related statistical analysis showed significant and much significant difference between pre and post treatment. Conclusions: The low level laser irradiation (ILLLI) in treatment of psoriasis has bidirectional ajustive effect which can balance the immulogic function of cell.

  1. A Self-Powered and Flexible Organometallic Halide Perovskite Photodetector with Very High Detectivity.

    PubMed

    Leung, Siu-Fung; Ho, Kang-Ting; Kung, Po-Kai; Hsiao, Vincent K S; Alshareef, Husam N; Wang, Zhong Lin; He, Jr-Hau

    2018-02-01

    Flexible and self-powered photodetectors (PDs) are highly desirable for applications in image sensing, smart building, and optical communications. In this paper, a self-powered and flexible PD based on the methylammonium lead iodide (CH 3 NH 3 PBI 3 ) perovskite is demonstrated. Such a self-powered PD can operate even with irregular motion such as human finger tapping, which enables it to work without a bulky external power source. In addition, with high-quality CH 3 NH 3 PBI 3 perovskite thin film fabricated with solvent engineering, the PD exhibits an impressive detectivity of 1.22 × 10 13 Jones. In the self-powered voltage detection mode, it achieves a large responsivity of up to 79.4 V mW -1 cm -2 and a voltage response of up to ≈90%. Moreover, as the PD is made of flexible and transparent polymer films, it can operate under bending and functions at 360 ° of illumination. As a result, the self-powered, flexible, 360 ° omnidirectional perovskite PD, featuring high detectivity and responsivity along with real-world sensing capability, suggests a new direction for next-generation optical communications, sensing, and imaging applications. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Power measurement system of ECRH on HL-2A

    NASA Astrophysics Data System (ADS)

    Wang, He; Lu, Zhihong; Kubo, Shin; Chen, Gangyu; Wang, Chao; Zhou, Jun; Huang, Mei; Rao, Jun

    2015-03-01

    Electron Cyclotron Resonance Heating (ECRH) is one of the main auxiliary heating systems for HL-2A tokamak. The ECRH system with total output power 5MW has been equipped on HL-2A which include 6 sets of 0.5MW/1.0s at a frequency of 68GHz and 2 sets of 1MW/3s at a frequency of 140GHz. The power is one of important parameters in ECRH system. In this paper, the method for measuring the power of ECRH system on HL-2A is introduced which include calorimetric techniques and directional coupler. Calorimetric techniques is an existing method, which is used successfully in ECRH commissioning and experiment, and the transmission efficiency of ECRH system is achieved by measuring the absorbed microwave power in the Match Optical Unit (MOU), gyrotron output window and tours window of the EC system use this method. Now base on the theory of electromagnetic coupling through apertures, directional couplers are being designed, which is a new way for us.

  3. Burning plasma regime for Fussion-Fission Research Facility

    NASA Astrophysics Data System (ADS)

    Zakharov, Leonid E.

    2010-11-01

    The basic aspects of burning plasma regimes of Fusion-Fission Research Facility (FFRF, R/a=4/1 m/m, Ipl=5 MA, Btor=4-6 T, P^DT=50-100 MW, P^fission=80-4000 MW, 1 m thick blanket), which is suggested as the next step device for Chinese fusion program, are presented. The mission of FFRF is to advance magnetic fusion to the level of a stationary neutron source and to create a technical, scientific, and technology basis for the utilization of high-energy fusion neutrons for the needs of nuclear energy and technology. FFRF will rely as much as possible on ITER design. Thus, the magnetic system, especially TFC, will take advantage of ITER experience. TFC will use the same superconductor as ITER. The plasma regimes will represent an extension of the stationary plasma regimes on HT-7 and EAST tokamaks at ASIPP. Both inductive discharges and stationary non-inductive Lower Hybrid Current Drive (LHCD) will be possible. FFRF strongly relies on new, Lithium Wall Fusion (LiWF) plasma regimes, the development of which will be done on NSTX, HT-7, EAST in parallel with the design work. This regime will eliminate a number of uncertainties, still remaining unresolved in the ITER project. Well controlled, hours long inductive current drive operation at P^DT=50-100 MW is predicted.

  4. Structural characterization of a glucuronoarabinoxylan from pineapple (Ananas comosus (L.) Merrill) gum exudate.

    PubMed

    Simas-Tosin, Fernanda F; de Souza, Lauro M; Wagner, Ricardo; Pereira, Graciele C Z; Barraza, Ruth R; Wendel, Cinthia F; Sassaki, Guilherme L; Iacomini, Marcello; Gorin, Philip A J

    2013-04-15

    Native polysaccharide from pineapple gum (PANP) was obtained following alkaline extraction of gum and fractionation with cetylpyridinium chloride. It was characterized as a glucuronoarabinoxylan using NMR, methylation data, controlled Smith degradation, carboxy-reduction, and ESI-MS of oligosaccharides produced on mild acid hydrolysis of PANP. HSPEC-MALLS-RI of carboxy-reduced fraction showed homogeneous profile (Mw 1.943×10(5) g/mol). PANP was composed of Ara, Xyl, Gal, and GlcpA (40:23:7:30 molar ratio). Its main chain presented (1→4)-linked β-xylan, highly substituted at O-2 and O-3 by side chains of 3-O- and 3,5-di-O-linked α-Araf, 2-O- and 4-O-linked α-GlcpA, and nonreducing end-units of α-Araf, β-Arap, β-Galp, and α-GlcpA. ESI-MS of a mixture of oligosaccharides formed on the mild acid hydrolysis of PANP was consistent with repetitive structures of α-GlcpA O-3 linked at β-Xylp units, whereas in others glucuronoarabinoxylan-type gum exudates, α-GlcpA units had been previously found to be linked at O-2. Copyright © 2013 Elsevier Ltd. All rights reserved.

  5. Production of copolymer, poly (hydroxybutyrate-co-hydroxyvalerate) by Halomonas campisalis MCM B-1027 using agro-wastes.

    PubMed

    Kulkarni, S O; Kanekar, P P; Jog, J P; Sarnaik, S S; Nilegaonkar, S S

    2015-01-01

    For cost effective production of PHA, agro-wastes like fruit peels, bagasse and deoiled cakes were screened as a sole source of carbon. Halomonas campisalis MCM B-1027, which was isolated from one of the extreme environment, i.e. Lonar Lake, India, was explored for the production of PHA using fruit peels and bagasse having fermentable sugars. Among the agro-wastes tested, 1% (v/v) aqueous extract of bagasse was found to be the optimum carbon source with 47% PHA production on dry cell weight basis. Significant amount of total sugars are utilized and converted into cell mass and PHA, e.g. 62% sugar utilized from bagasse extract, 84% from orange peel extract and 71% from banana peel extract as compared to 51% in case of maltose. Hence the cost of production would be positively reduced. The detailed characterization of PHA formed by H. campisalis using bagasse extract as sole carbon source revealed that the organism produces a copolymer of PHB-co-PHV (94.4:5.6) having molecular weight M(w) 1.394 × 10(6) and melting temperature 168.9 °C. Production of PHA by H. campisalis using aqueous extract of fruit peels and a copolymer PHB-co-PHV using aqueous extract of bagasse is presumably the first report. Copyright © 2014 Elsevier B.V. All rights reserved.

  6. The physicochemical properties of a new class of anticancer fungal polysaccharides: a comparative study.

    PubMed

    Ren, Lu; Reynisson, Jóhannes; Perera, Conrad; Hemar, Yacine

    2013-08-14

    The structural and physicochemical properties of polysaccharides isolated from fungi with anticancer properties were investigated. The majority of the polysaccharides considered, have the β-d-Glcp component mostly connected by 1→3 and 1→6 linkages in the backbones and the short branches, respectively. The established parameters of lead-like, drug-like and of known dug space (KDS) were used and the repeating units of the polysaccharides exhibit some overlap with these. It was found that a unique region of chemical space is occupied by the polysaccharides, with MW: 1.0 x 10(5) to 2.5 x 10(5) g mol(-1); LogP: -3.0 x 10(3) to -1.0 x 10(3); HD: 1.0 x 10(3) to 5.0 x 10(3); HA: 5.0 x 10(3) to 1.0 x 10(4); PSA: 5.0 x 10(4) to 1.0 x 10(5) and RB: 5.0 x 10(3) to 1.0 x 10(4). These findings can be exploited in antitumor drug discovery projects. Copyright © 2013 Elsevier Ltd. All rights reserved.

  7. N-acetylcysteine and acute retinal laser lesions in the colubrid snake eye

    NASA Astrophysics Data System (ADS)

    Elliott, William R., III; Rentmeister-Bryant, Heike K.; Barsalou, Norman; Beer, Jeremy; Zwick, Harry

    2004-07-01

    This study examined the role of oxidative stress and the effect of a single dose treatment with N-Acetylcysteine (NAC) on the temporal development of acute laser-induced retinal injury. We used the snake eye/Scanning Laser Ophthalmoscope (SLO) model, an in vivo, non-invasive ocular imaging technique, which has the ability to image cellular retinal detail and allows for studying morphological changes of retinal injury over time. For this study 12 corn-snakes (Elaphe g. guttata) received 5 laser exposures per eye, followed by either a single dose of the antioxidant NAC (150mg/kg, IP in sterile saline) or placebo. Laser exposures were made with a Nd: VO4 DPSS, 532nm laser, coaxially aligned to the SLO. Shuttered pulses were 20msec x 50 mW; 1mJ each. Retinal images were taken using a Rodenstock cSLO and were digitally recorded at 1, 6, 24-hrs, and at 3-wks post-exposure. Lesions were assessed by two raters blind to the conditions of the study yielding measures of damaged area and counts of missing or damaged photoreceptors. Treated eyes showed a significant beneficial effect overall, and these results suggest that oxidative stress plays a role in laser-induced retinal injury. The use of NAC or a similar antioxidant shows promise as a therapeutic tool.

  8. Search for W' $$\\to $$ tb decays in the lepton + jets final state in pp collisions at $$\\sqrt{s}$$ = 8 TeV

    DOE PAGES

    Chatrchyan, Serguei

    2014-05-23

    Results are presented from a search for the production of a heavy gauge boson W' decaying into a top and a bottom quark, using a data set collected by the CMS experiment at sqrt(s) = 8 TeV and corresponding to an integrated luminosity of 19.5 inverse femtobarns. Various models of W'-boson production are studied by allowing for an arbitrary combination of left- and right-handed couplings. The analysis is based on the detection of events with a lepton (e, mu), jets, and missing transverse energy in the final state. No evidence for W'-boson production is found and 95% confidence level uppermore » limits on the production cross section times branching fraction are obtained. For W' bosons with purely right-handed couplings, and for those with left-handed couplings assuming no interference effects, the observed 95% confidence level limit is M(W') > 2.05 TeV. For W' bosons with purely left-handed couplings, including interference effects, the observed 95% confidence level limit is M(W') > 1.84 TeV. The results presented in this paper are the most stringent limits published to date.« less

  9. One Minute, Sub-One-Watt Photothermal Tumor Ablation Using Porphysomes, Intrinsic Multifunctional Nanovesicles

    PubMed Central

    Jin, Cheng S.; Lovell, Jonathan F.; Zheng, Gang

    2013-01-01

    We recently developed porphysomes as intrinsically multifunctional nanovesicles. A photosensitizer, pyropheophorbide α, was conjugated to a phospholipid and then self-assembled to liposome-like spherical vesicles. Due to the extremely high density of porphyrin in the porphyrin-lipid bilayer, porphysomes generated large extinction coefficients, structure-dependent fluorescence self-quenching, and excellent photothermal efficacy. In our formulation, porphysomes were synthesized using high pressure extrusion, and displayed a mean particle size around 120 nm. Twenty-four hr post-intravenous injection of porphysomes, the local temperature of the tumor increased from 30 °C to 62 °C rapidly upon one minute exposure of 750 mW (1.18 W/cm2), 671 nm laser irradiation. Following the complete thermal ablation of the tumor, eschars formed and healed within 2 weeks, while in the control groups the tumors continued to grow and all reached the defined end point within 3 weeks. These data show how porphysomes can be used as potent photothermal therapy (PTT) agents. PMID:24084712

  10. Research of epidermal cellular vegetal cycle of intravascular low level laser irradiation in treatment of psoriasis

    NASA Astrophysics Data System (ADS)

    Zhu, Jing; Bao, Xiaoqing; Zhang, Mei-Jue

    2005-07-01

    Objective: To research epidermal cellular vegetal cycle and the difference of DNA content between pre and post Intravascular Low Level Laser Irradiation treatment of psoriasis. Method: 15 patients suffered from psoriasis were treated by intravascular low level laser irradiation (output power: 4-5mw, 1 hour per day, a course of treatment is 10 days). We checked the different DNA content of epidermal cell between pre and post treatment of psoriasis and 8 natural human. Then the percentage of each phase among the whole cellular cycle was calculated and the statistical analysis was made. Results: The mean value of G1/S phase is obviously down while G2+M phase increased obviously. T test P<0.05.The related statistical analysis showed significant difference between pre and post treatments. Conclusions: The Intravascular Low Level Laser Irradiation (ILLLI) in treatment of psoriasis is effective according to the research of epidermal cellular vegetal cycle and the difference DNA content of Intravascular Low Level Laser Irradiation between pre and post treatment of psoriasis

  11. The effect of ILLLI on peripheral blood SOD, MDA in psoriasis treatment

    NASA Astrophysics Data System (ADS)

    Zhu, Jing; Nie, Fan

    2005-07-01

    Objective: To research the effect of Intravascular low level laser irradiation (ILLLI) on the SOD,MDA in the treatment of psoriasis. Method :47 patients suffering from psoriasis from five groups were treated by Intravascular low level laser irradiation (power:4-5mw,1h per day, period of treatment: 10 days) .We checked the change of SOD,MDA peripheral blood in 10 normal people between pre and post treatment. Group A were treated by He-Ne laser combined with drug, group B were treated by semi-conductor laser combined with drug, group C were treated only by He-Ne laser, group D were treated only by semiconductor laser, group E were treated only by drug . Results: The levels of SOD in red cell of psoriatic patients from five groups after treatment were significantly lower than that of controlled group. The levels of SOD of them were significantly increased and nearly closed to that of controlled group; the levels of MDA in red cell of psoriatic patients from five groups after treatment were significantly higher than that of controlled group; the levels of MDA of them are decreased ,however, they were still not recovered to normal levels. Conclusions: ILLLI, both He-Ne laser and semiconductor laser, can activate SOD in psoriasis patients and enhance their ability of anti-oxidation.

  12. Is skin penetration a determining factor in skin sensitization ...

    EPA Pesticide Factsheets

    Summary:Background. It is widely accepted that substances that cannot penetrate through the skin will not be sensitisers. Thresholds based on relevant physicochemical parameters such as a LogKow > 1 and a MW 1 is a true requirement for sensitisation.Methods. A large dataset of substances that had been evaluated for their skin sensitisation potential, together with measured LogKow values was compiled from the REACH database. The incidence of skin sensitisers relative to non-skin sensitisers below and above the LogKow = 1 threshold was evaluated. Results. 1482 substances with associated skin sensitisation outcomes and measured LogKow values were identified. 305 substances had a measured LogKow < 0 and of those, 38 were sensitisers.Conclusions. There was no significant difference in the incidence of skin sensitisation above and below the LogKow = 1 threshold. Reaction chemistry considerations could explain the skin sensitisation observed for the 38 sensitisers with a LogKow < 0. The LogKow threshold is a self-evident truth borne out from the widespread misconception that the ability to efficiently penetrate the stratum corneum is a key determinant of skin sensitisation potential and potency. Using the REACH data extracted to test out the validity of common assumptions in the skin sensitization AOP. Builds on trying to develop a proof of concept IATA

  13. Molecular weight distribution of organic matter by ozonation and biofiltration.

    PubMed

    Lin, Yen-Hui

    2012-01-01

    Molecular weight (MW) distribution of organic matter by ozonation and biofiltration was evaluated using gel chromatography. The MW distribution of organic matter by Sephadex G-25 was observed from groups 2 (MW = 1,029-7,031 g/mol) and 3 (MW = 303-1,029 g/mol) shifted to groups 2, 3 and 4 (MW < 303 g/mol) under ozone doses of 0.1 and 0.4 mg O₃/mg total organic carbon (TOC). The shift in MW increases as ozone dosage increases. Biofiltration effectively degraded the organic molecule of group 2; however, the biofiltration only slightly degraded the organic molecule of group 4. Increased ozone dose destroyed functional groups C═C in phenolic and C-O in alcoholic compounds and increased UV-insensitive biodegradable organic carbon for subsequent biofiltration. Biofiltration effectively degraded organic compounds of alcohols and alkenes at an ozone dose of 0.1 mg O₃/mg TOC. Experimental approaches in this study can be applied to evaluate and diagnose the function of a full-scale process combining ozonation and biofiltration in drinking water treatment plants.

  14. Nutritional stress enhances cell viability of odontoblast-like cells subjected to low level laser irradiation

    NASA Astrophysics Data System (ADS)

    Tagliani, M. M.; Oliveira, C. F.; Lins, E. M. M.; Kurachi, C.; Hebling, J.; Bagnato, V. S.; de Souza Costa, C. A.

    2010-03-01

    In spite of knowing that cells under stress are biostimulated by low level laser (LLL) irradiation, the ideal condition of stress to different cell lines has not yet been established. Consequently, the aim of the present in vitro study was to evaluate the effects of a defined parameter of LLL irradiation applied on stressed odontoblast-like pulp cells (MDPC-23). The cells were seeded (12500 cells/cm2) in wells of 24-well plates using complete culture medium (DMEM) and incubated for 24 hours. Then, the DMEM was replaced by a new medium with low concentrations (nutritional stress condition) of fetal bovine serum (FBS) giving rise to the following experimental groups: G1: 2% FBS; G2: 5% FBS; and G3: 10% FBS. The cells were irradiated three times with LLL in specific parameters (808±3 nm, 100 mW, 1.5 J/cm2) every 24 hours. No irradiation was carried out in groups G4 (2% FBS-Control), G5 (5% FBS-Control), and G6 (10% FBS-Control). For all groups, the cell metabolism (MTT assay) and morphology (SEM) was evaluated. The experimental groups showed enhanced cell metabolism and normal cell morphology regardless of FBS concentration. A slight increase in the cell metabolism was observed only in group G2. It was concluded that cell nutritional stress caused by reducing the concentration of FBS to 5% is the most suitable method to assess the biostimulation of LLL irradiated MDPC-23 cells.

  15. 100 GeV SLAC Linac

    NASA Astrophysics Data System (ADS)

    Farkas, Z. D.

    2002-03-01

    The SLAC beam energy can be increased from the current 50 GeV to 100 GeV, if we change the operating frequency from the present 2856 MHz to 11424 MHz, using technology developed for the NLC. We replace the power distribution system with a proposed NLC distribution system as shown in Fig. 1. The four 3 meter s-band 820 nS .ll time accelerator sections are replaced by six 2 meter x-band 120 nS .ll time sections. Thus the accelerator length per klystron retains the same length, 12 meters. The 4050 65MW- 3.5microS klystrons are replaced by 75MW-1.5microS permanent magnet klystrons developed here and in Japan. The present input to the klystrons would be multiplied by a factor of 4 and possibly ampli.ed. The SLED cavities have to be replaced. The increase in beam voltage is due to the higher elastance to group velocity ratio, higher compression ratio and higher unloaded to external Q ratio of the new SLED cavities. The average power input is reduced because of the narrower klystron pulse width and because the klystron electro-magnets are replaced by permanent magnets.

  16. The effects of a low-intensity red laser on bacterial growth, filamentation and plasmid DNA

    NASA Astrophysics Data System (ADS)

    Roos, C.; Santos, J. N.; Guimarães, O. R.; Geller, M.; Paoli, F.; Fonseca, A. S.

    2013-07-01

    Exposure of nonphotosynthesizing microorganisms to light could increase cell division in cultures, a phenomenon denominated as biostimulation. However, data concerning the importance of the genetic characteristics of cells on this effect are as yet scarce. The aim of this work was to evaluate the effects of a low-intensity red laser on the growth, filamentation and plasmids in Escherichia coli cells proficient and deficient in DNA repair. E. coli cultures were exposed to a laser (658 nm, 10 mW, 1 and 8 J cm-2) to study bacterial growth and filamentation. Also, bacterial cultures hosting pBSK plasmids were exposed to the laser to study DNA topological forms from the electrophoretic profile in agarose gels. Data indicate the low-intensity red laser: (i) had no effect on the growth of E. coli wild type and exonuclease III deficient cells; (ii) induced bacterial filamentation, (iii) led to no alteration in the electrophoretic profile of plasmids from exonuclease III deficient cells, but plasmids from wild type cells were altered. A low-intensity red laser at the low fluences used in phototherapy has no effect on growth, but induces filamentation and alters the topological forms of plasmid DNA in E. coli cultures depending on the DNA repair mechanisms.

  17. Antioxidant Extracts from Acorns (Quercus ilex L.) Effectively Protect Ready-to-Eat (RTE) Chicken Patties Irrespective of Packaging Atmosphere.

    PubMed

    Ferreira, Valquíria C S; Morcuende, David; Hérnandez-López, Silvia H; Madruga, Marta S; Silva, Fábio A P; Estévez, Mario

    2017-03-01

    This study evaluated the impact of a phenolic-rich acorn extract (200 ppm gallic acid equivalents) and the concentration of oxygen in the packaging system (low-oxygen modified atmosphere; 5% vs. normal-oxygen; 21%) on lipid and protein oxidation and consumers acceptance of the ready-to-eat chicken patties. Samples were subjected to cooking (electric oven, 170 °C/16 min), cold storage (14 d at 4 °C), and reheating (microwave, 600 mW/1 min). Samples treated with acorn extract kept thiobarbituric acid-reactive substances numbers and lipid-derived volatiles at basal levels throughout the whole processing irrespective of the oxygen concentration in the packaging atmosphere. Consistently, treated patties had lower protein carbonyls than control ones. The acorn extract also controlled color and texture deterioration during chilled storage and reheating and improved the color and odor acceptance of the products. Formulating with acorn extract is a feasible strategy to inhibit the oxidation-driven changes and preserve the quality of reheated samples as if there were freshly cooked. Compared to the effect of the antioxidant extract, the concentration of oxygen in the packaging system was negligible in terms of quality preservation. © 2017 Institute of Food Technologists®.

  18. Fractionation and identification of novel antioxidant peptides from buffalo and bovine casein hydrolysates.

    PubMed

    Shazly, Ahmed Behdal; He, Zhiyong; El-Aziz, Mahmoud Abd; Zeng, Maomao; Zhang, Shuang; Qin, Fang; Chen, Jie

    2017-10-01

    Buffalo and bovine caseins were hydrolysed by alcalase and trypsin to produce novel antioxidant peptides. The casein hydrolysates were purified using ultrafiltration (UF) and further characterized by RP-HPLC. The fractions produced higher antioxidant activities were identified for their peptides using LC MS/MS. All UF-VI (MW<1kDa) fractions showed higher antioxidant activity. Hydrolysate produced by alcalase for buffalo casein (UF-VI with 54.84-fold purification) showed higher antioxidant activity than that obtained by trypsin. Trypsin hydrolysate contained high amount of hydrophobic amino acids while alcalase hydrolysate consisted mainly of Ser, Arg, Ala and Leu. The antioxidant peptides identified by LC MS/MS were RELEE, MEDNKQ and TVA, EQL in buffalo casein hydrolysates produced by trypsin and alcalase, respectively. Mechanism and reaction pathways of selected antioxidant peptides with ABTS were proposed. Conclusively, buffalo casein provided antioxidant peptides similar to bovine, suggesting that buffalo casein is a novel source of antioxidant. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. Earthquake source properties of a shallow induced seismic sequence in SE Brazil

    NASA Astrophysics Data System (ADS)

    Agurto-Detzel, Hans; Bianchi, Marcelo; Prieto, Germán. A.; Assumpção, Marcelo

    2017-04-01

    We study source parameters of a cluster of 21 very shallow (<1 km depth) small-magnitude (Mw < 2) earthquakes induced by percolation of water by gravity in SE Brazil. Using a multiple empirical Green's functions (meGf) approach, we estimate seismic moments, corner frequencies, and static stress drops of these events by inversion of their spectral ratios. For the studied magnitude range (-0.3 < Mw < 1.9), we found an increase of stress drop with seismic moment. We assess associated uncertainties by considering different signal time windows and by performing a jackknife resampling of the spectral ratios. We also calculate seismic moments by full waveform inversion to independently validate our moments from spectral analysis. We propose repeated rupture on a fault patch at shallow depth, following continuous inflow of water, as the cause for the observed low absolute stress drop values (<1 MPa) and earthquake size dependency. To our knowledge, no other study on earthquake source properties of shallow events induced by water injection with no added pressure is available in the literature. Our study suggests that source parameter characterization may provide additional information of induced seismicity by hydraulic stimulation.

  20. Evaluating the biosafety of conventional and O3-BAC process and its relationship with NOM characteristics.

    PubMed

    Liao, Xiaobin; Zou, Rusen; Chen, Chao; Yuan, Baoling; Zhou, Zhenming; Zhang, Xiaojian

    2018-01-01

    It is the priority to guarantee biosafety for drinking water treatment. The objective of this study was to evaluate the impact of widely applied conventional and ozone-biological activated carbon (O 3 -BAC) advanced treatment technology on biosafety of drinking water. The items, including assimilable organic carbon (AOC), biodegradable dissolved organic carbon (BDOC), heterotrophic plate counts (HPCs) and the microorganism community structures, were used to evaluate the biosafety. Moreover, their relationships with molecular weights (MWs) and fluorescence intensity of dissolved organic matter were investigated. The results indicated that the technology provided a considerable gain in potable water quality by decreasing dissolved organic carbon (DOC, from 5.05 to 1.71 mg/L), AOC (from 298 to 131 μg/L), BDOC (from 1.39 to 0.24 mg/L) and HPCs (from 275 to 10 CFU/mL). Ozone brought an increase in DOC with low MW <1 kDa, which accompanies with an increase in AOC/BDOC concentration, which could be reduced effectively by subsequent BAC process. The formation of AOC/BDOC was closely related to DOC with low MWs and aromatic protein. Bacteria could be released from BAC filter, resulting in an increase in HPC and the presence of pathogenic bacteria in effluent, while the post sand filter could further guarantee the biosafety of finished water.

  1. Characterization of gold kiwifruit pectin from fruit of different maturities and extraction methods.

    PubMed

    Yuliarti, Oni; Matia-Merino, Lara; Goh, Kelvin K T; Mawson, John; Williams, Martin A K; Brennan, Charles

    2015-01-01

    Studies on gold kiwifruit pectins are limited. In this work, the characterization of pectin isolated from two different stages of maturity of gold kiwifruit, namely early harvested fruit (EHF) and main harvested fruit (MHF) isolated by three methods (acid, water, enzymatic) was carried out. Pectins isolated from MHF were higher in galacturonic acid content (52-59% w/w) and weight-average molecular weights (Mw, 1.7-3.8 × 10(6)g/mol) compared with EHF pectins (29-49% w/w and 0.2-1.7 × 10(6)g/mol respectively). Enzymatic treatment gave the highest yield but lowest in Mw, viscosity and mechanical spectra for both maturities. The pectin of both maturities was classified as high-methoxyl pectin with the degree of esterification ranged from 82% to 90%. Water-extracted MHF pectin molecules had the highest RMS radius (182.7 nm) and Mw (3.75 × 10(6)g/mol). The water extraction method appeared to retain the native state of pectin molecules compared with acid and enzymatic extraction methods based on the Mw and viscosity data. Copyright © 2014 Elsevier Ltd. All rights reserved.

  2. Environmental impacts of large-scale CSP plants in northwestern China.

    PubMed

    Wu, Zhiyong; Hou, Anping; Chang, Chun; Huang, Xiang; Shi, Duoqi; Wang, Zhifeng

    2014-01-01

    Several concentrated solar power demonstration plants are being constructed, and a few commercial plants have been announced in northwestern China. However, the mutual impacts between the concentrated solar power plants and their surrounding environments have not yet been addressed comprehensively in literature by the parties involved in these projects. In China, these projects are especially important as an increasing amount of low carbon electricity needs to be generated in order to maintain the current economic growth while simultaneously lessening pollution. In this study, the authors assess the potential environmental impacts of large-scale concentrated solar power plants. Specifically, the water use intensity, soil erosion and soil temperature are quantitatively examined. It was found that some of the impacts are favorable, while some impacts are negative in relation to traditional power generation techniques and some need further research before they can be reasonably appraised. In quantitative terms, concentrated solar power plants consume about 4000 L MW(-1) h(-1) of water if wet cooling technology is used, and the collectors lead to the soil temperature changes of between 0.5 and 4 °C; however, it was found that the soil erosion is dramatically alleviated. The results of this study are helpful to decision-makers in concentrated solar power site selection and regional planning. Some conclusions of this study are also valid for large-scale photovoltaic plants.

  3. Tissue response to peritoneal implants

    NASA Technical Reports Server (NTRS)

    Picha, G. J.

    1980-01-01

    Peritoneal implants were fabricated from poly 2-OH, ethyl methacrylate (HEMA), polyetherurethane (polytetramethylene glycol 1000 MW, 1,4 methylene disocynate, and ethyl diamine), and untreated and sputter treated polytetrafluoroethylene (PTFE). The sputter treated PTFE implants were produced by an 8 cm diameter argon ion source. The treated samples consisted of ion beam sputter polished samples, sputter etched samples (to produce a microscopic surface cone texture) and surface pitted samples (produced by ion beam sputtering to result in 50 microns wide by 100 microns deep square pits). These materials were implanted in rats for periods ranging from 30 minutes to 14 days. The results were evaluated with regard to cell type and attachment kinetics onto the different materials. Scanning electron microscopy and histological sections were also evaluated. In general the smooth hydrophobic surfaces attracted less cells than the ion etched PTFE or the HEMA samples. The ion etching was observed to enhance cell attachment, multinucleated giant cell (MNGC) formation, cell to cell contact, and fibrous capsule formation. The cell responsed in the case of ion etched PTFE to an altered surface morphology. However, equally interesting was the similar attachment kinetics of HEMA verses the ion etched PTFE. However, HEMA resulted in a markedly different response with no MNGC's formation, minimal to no capsule formation, and sample coverage by a uniform cell layer.

  4. The intravascular low level laser irradiation (ILLLI) in treatment of psoriasis clinically

    NASA Astrophysics Data System (ADS)

    Zhu, Jing; Nie, Fan; Shi, Hong-Min

    2005-07-01

    Objective: The title is research curative effect of intravascular low level laser irradiation (ILLLI) in treatment of psoriasis. Method: 478 patients with psoriasis from five groups to observe their efficacy. Group1 were treated by He-Ne laser combined with drug. Group 2 were treated by semi-conductor laser combined with drug. Group 3 were treated only by He-He laser. Group 4 were treated by semi-conductor laser. Group 5 were treated only by drug. The Ridit statistical analysis was applied to all of these data. The treatment of intravascular low level laser irradiation is as follow: laser power:4-5mw, 1 hour per day and 10 days as a period combined with vit C 2.0 g iv and inhalation of O2. Results: The clinical results: the near efficient rate was 100%, in group1-4, if combined with drugs it would be better. Ridit statistical analysis showed no significant difference between group1-4, p>0.05. The efficient rate 72.97% in group5.There were showed very significant difference with group1-4, p<0.01. 2.There were no significant differences between He-Ne laser (632.8nm) and semiconductor laser(650nm); 3.The efficacy of ILLLI in psoriasis was positive correlation to the ILLLI times. Conclusions: It can improve curative effect of intravascular low levellaser irradiation (ILLLI) in treatment of psoriasis.

  5. Non-thermal Plasma Exposure Rapidly Attenuates Bacterial AHL-Dependent Quorum Sensing and Virulence

    PubMed Central

    Flynn, Padrig B.; Busetti, Alessandro; Wielogorska, Ewa; Chevallier, Olivier P.; Elliott, Christopher T.; Laverty, Garry; Gorman, Sean P.; Graham, William G.; Gilmore, Brendan F.

    2016-01-01

    The antimicrobial activity of atmospheric pressure non-thermal plasma has been exhaustively characterised, however elucidation of the interactions between biomolecules produced and utilised by bacteria and short plasma exposures are required for optimisation and clinical translation of cold plasma technology. This study characterizes the effects of non-thermal plasma exposure on acyl homoserine lactone (AHL)-dependent quorum sensing (QS). Plasma exposure of AHLs reduced the ability of such molecules to elicit a QS response in bacterial reporter strains in a dose-dependent manner. Short exposures (30–60 s) produce of a series of secondary compounds capable of eliciting a QS response, followed by the complete loss of AHL-dependent signalling following longer exposures. UPLC-MS analysis confirmed the time-dependent degradation of AHL molecules and their conversion into a series of by-products. FT-IR analysis of plasma-exposed AHLs highlighted the appearance of an OH group. In vivo assessment of the exposure of AHLs to plasma was examined using a standard in vivo model. Lettuce leaves injected with the rhlI/lasI mutant PAO-MW1 alongside plasma treated N-butyryl-homoserine lactone and n-(3-oxo-dodecanoyl)-homoserine lactone, exhibited marked attenuation of virulence. This study highlights the capacity of atmospheric pressure non-thermal plasma to modify and degrade AHL autoinducers thereby attenuating QS-dependent virulence in P. aeruginosa. PMID:27242335

  6. Chandra Low Energy Transmission Grating Spectrum of SS Cygni in Outburst

    NASA Astrophysics Data System (ADS)

    Mauche, Christopher W.

    2004-07-01

    We have fitted the Chandra Low Energy Transmission Grating (LETG) spectrum of SS Cygni in outburst with a single-temperature blackbody suffering the photoelectric opacity of a neutral column density and the scattering opacity of an outflowing wind. We find that this simple model is capable of reproducing the essential features of the observed spectrum with the blackbody temperature Tbl~250+/-50 kK, hydrogen column density NH~5.0+2.9-1.5×1019cm-2, fractional emitting area f~5.6+60-4.5×10-3, boundary layer luminosity Lbl~5+18-3×1033ergss-1, wind velocity v~2500kms-1, wind mass-loss rate Mw~1.1×1016gs-1, and arbitrary values of the wind ionization fractions of 20 ions of O, Ne, Mg, Si, S, and Fe. Given that in outburst the accretion disk luminosity Ldisk~1×1035ergss-1, Lbl/Ldisk~0.05+0.18-0.03, which can be explained if the white dwarf (or an equatorial belt thereon) is rotating with an angular velocity Ωwd~0.7+0.1-0.2 Hz, hence Vrotsini~2300kms-1. This paper is dedicated to the memory and accomplishments of my colleague and friend Janet Akyüz Mattei, who died on 2004 March 22 after a long battle with acute myelogenous leukemia. Her passing is a great loss to the astronomical community, both amateur and professional.

  7. Scalable Method to Produce Biodegradable Nanoparticles that Rapidly Penetrate Human Mucus

    PubMed Central

    Xu, Qingguo; Boylan, Nicholas J.; Cai, Shutian; Miao, Bolong; Patel, Himatkumar; Hanes, Justin

    2013-01-01

    Mucus typically traps and rapidly removes foreign particles from the airways, gastrointestinal tract, nasopharynx, female reproductive tract and the surface of the eye. Nanoparticles capable of rapid penetration through mucus can potentially avoid rapid clearance, and open significant opportunities for controlled drug delivery at mucosal surfaces. Here, we report an industrially scalable emulsification method to produce biodegradable mucus-penetrating particles (MPP). The emulsification of diblock copolymers of poly(lactic-co-glycolic acid) and polyethylene glycol (PLGA-PEG) using low molecular weight (MW) emulsifiers forms dense brush PEG coatings on nanoparticles that allow rapid nanoparticle penetration through fresh undiluted human mucus. In comparison, conventional high MW emulsifiers, such as polyvinyl alcohol (PVA), interrupts the PEG coating on nanoparticles, resulting in their immobilization in mucus owing to adhesive interactions with mucus mesh elements. PLGA-PEG nanoparticles with a wide range of PEG MW (1, 2, 5, and 10 kDa), prepared by the emulsification method using low MW emulsifiers, all rapidly penetrated mucus. A range of drugs, from hydrophobic small molecules to hydrohilic large biologics, can be efficiently loaded into biodegradable MPP using the method described. This readily scalable method should facilitate the production of MPP products for mucosal drug delivery, as well as potentially longer-circulating particles following intravenous administration. PMID:23751567

  8. DDE remediation and degradation.

    PubMed

    Thomas, John E; Ou, Li-Tse; All-Agely, Abid

    2008-01-01

    breakdown of DDE by the extracellular lignolytic enzymes produced by white rot fungi. The addition of adjutants such as sodium ion, surfactants, and cellulose increased the rate of DDT aerobic or anaerobic degradation but did little to enhance the rate of DDE disappearance under anaerobic conditions. Only in the past decade has it been demonstrated that DDE can undergo reductive dechlorination under methanogenic and sulfidogenic conditions to form the degradation product DDMU, 1-chloro-2,2'-bis-(4'-chlorophenyl)ethane. The only pure culture reported to degrade DDE under anaerobic conditions was the denitrifier Alcaligens denitrificans. The degradation of DDE by this bacterium was enhanced by glucose, whereas biphenyl fumes had no effect. Abiotic remediation by DDE volatilization was enhanced by flooding and irrigation and deepplowing inhibited the volatilization. The use of zero-valent iron and surfactants in flooded soils enhanced DDT degradation but did not significantly alter the rate of DDE removal. Other catalysts (palladized magnesium, palladium on carbon, and nickel/aluminum alloys) degraded DDT and its metabolites, including DDE. However, these systems are often biphasic or involve explosive gases or both. Safer abiotic alternatives use UV light with titanium oxide or visible light with methylene green to degrade DDT, DDD, and DDE in aqueous or mixed solvent systems. Remediation and degradation of DDE in soil and water by phytoextraction, aerobic and anaerobic microorganisms, or abiotic methods can be accomplished. However, success has been limited, and great care must be taken that the method does not transfer the contaminants to another locale (by volatilization, deep plowing, erosion, or runoff) or to another species (by ingestion of accumulating plants or contaminated water). Although the remediation of DDT-, DDD-, and DDE-contaminated soil and water is beset with myriad problems, there remain many open avenues of research.

  9. Molecular approaches to understand the regulation of N2O emission from denitrifying bacteria - model strains and soil communities (Invited)

    NASA Astrophysics Data System (ADS)

    Frostegard, A.; Bakken, L. R.

    2010-12-01

    in intact soil samples from long-term liming experiments. Expression of nirS (encoding nitrite reductase) and nosZ (encoding N2OR) was generally lower at pH6 compared to pH8, but the nosZ/nirS transcript ratios were similar or even higher at pH6. These results were largely corroborated in refined experiments using extracted bacterial communities from the same soils, which allowed us to better control the pH levels experienced by the cells. The findings indicated that the higher N2O/N2 product ratios at pH6 were due to a post-transcriptional effect. Pure culture experiments using Paracoccus denitrificans demonstrated very low N2O/N2 ratios at pH7 while N2O reduction was severely inhibited by suboptimal pH, and that this inhibition occurred during protein synthesis/assembly rather than at the transcription level. The results are important for the understanding of main factors affecting N2O emissions from terrestrial ecosystems.

  10. The Salem Smart Power Center: An Assessment of Battery Performance and Economic Potential

    SciT

    Balducci, Patrick J.; Alam, M. J.E.; Viswanathan, Vilayanur

    This paper presents an assessment of the economic potential of a 5 MW/1.25 MWh Energy Storage System (ESS) installed at the Salem Smart Power Center (SSPC), a smart grid technology demonstration facility owned and operated by Portland General Electric (PGE) in Salem, Oregon. The ESS and the grid conditions in which it operates were modeled using Pacific Northwest National Laboratory’s Battery Storage Evaluation Tool (BSET) to explore tradeoffs between services, and to develop optimal control strategies. This assessment monetized the value derived from nine services the SSPC could provide to PGE and the customers it serves. The ESS and themore » grid conditions in which it operates were modeled using PNNL’s in-house optimization tool BSET to explore tradeoffs between services, and to develop optimal control strategies. The analysis resulted in a number of lessons that provide crucial insights into the practical application of ESS, including; The SSPC, which was originally conceived as a research and test facility and built with the prevailing maturity technology level, was built at a cost ($20.4 million) that exceeds current day prices ($5.4 million) for a similarly designed and built 5 MW/1.25 MWh system; In terms of economic operation, the SSPC is currently underutilized, deployed only for primary frequency response. PNNL modeling indicates that optimal operation of the ESS could generate an additional value of $2.3 million over 20 years. It should also be noted that primary frequency response is the highest benefit application but requires a response from the SSPC only 17 hours each year. While optimally engaged, the ESS would provide arbitrage and ancillary services 78 percent of the time, but those services generate only 27 percent of the total value; Participation in Western EIM represents an interesting opportunity for PGE with a potential to generate $2.1 million value in PV terms over 20 years in the 5-min real-time market; With an energy to power

  11. Microstructural studies of wear mechanisms in cast aluminum alloys

    NASA Astrophysics Data System (ADS)

    Elmadagli, Mustafa

    2005-07-01

    The microstructural basis of wear and surface degradation mechanisms in Al-Si alloys has been investigated in order to improve the current understanding of the requirements for wear resistant aluminum alloy design. The wear behaviour of three commercial alloys namely: a sand cast A390 (Al-18.4%Si), a spray formed Al-25%Si, and a die cast 383 (Al-9.5%Si) have been investigated. Dry sliding wear tests were performed using a block on ring type tribometer under controlled environments. The experiments were performed in a load range between 0.2 N and 300 N at a constant speed of 1 m/s. The testing environments were a dry air (5% RH), a humid air (95% RH), and an argon atmosphere. In dry air (5% RH), two main wear regimes namely, mild wear (MW), and severe wear (SW) were identified. The (MW) regime consisted of two sub-regimes: first and second regimes of mild wear, (MW-1) and (MW-2). The mild wear was controlled by the formation and destruction (spallation) of hardened tribolayers composed of Fe, Al, Si, and O which gave rise to steady state wear rates in both sub-regimes. The transition to second sub-regime was attributed to the destabilization and partial removal of the tribolayers on the contact surfaces. Severe wear occurred at loads exceeding 150 N irrespective of the alloy when the contact surface temperature reached a critical value (210-240°C). The wear rates (W) in each sub-regime of the MW obeyed the relation, W=CLn, where C and n were the wear coefficient and the wear exponent, respectively. The wear exponents, n, were similar in each of the sub-regimes for all three alloys, indicating that the same mechanisms controlled the wear rates. However, the wear coefficients, C, and the transition loads to the second sub-regime were considerably different for each alloy. A method of analyzing the wear coefficients and the transition loads of the alloys, based on pair-wise comparison between them, was developed. This method demonstrated that small equiaxed silicon

  12. Ground-water quality, water year 1995, and statistical analysis of ground-water-quality data, water years 1994-95, at the Chromic Acid Pit site, US Army Air Defense Artillery Center and Fort Bliss, El Paso, Texas

    Abeyta, Cynthia G.; Roybal, R.G.

    1996-01-01

    The Chromic Acid Pit site is an inactive waste disposal site that is regulated by the Resource Conservation and Recovery Act of 1976. The 2.2-cubic-yard cement-lined pit was operated from 1980 to 1983 by a contractor to the U.S. Army Air Defense Artillery Center and Fort Bliss. The pit, located on the Fort Bliss military reservation in El Paso, Texas, was used for disposal and evaporation of chromic acid waste generated from chrome plating operations. The site was closed in 1989, and the Texas Natural Resources Conservation Commission issued permit number HW-50296 (U.S. Environmental Protection Agency number TX4213720101), which approved and implemented post-closure care for the Chromic Acid Pit site. In accordance with an approved post-closure plan, the U.S. Geological Survey is cooperating with the U.S. Army in monitoring and evaluating ground-water quality at the site. One upgradient ground-water monitoring well (MW1) and two downgradient ground-water monitoring wells (MW2 and MW3), installed adjacent to the chromic acid pit, are monitored on a quarterly basis. Ground-water sampling of these wells by the U.S. Geological Survey began in December 1993. The ground-water level, measured in a production well located approximately 1,700 feet southeast of the Chromic Acid Pit site, has declined about 29.43 feet from 1982 to 1995. Depth to water at the Chromic Acid Pit site in September 1995 was 284.2 to 286.5 feet below land surface; ground-water flow at the water table is assumed to be toward the southeast. Ground-water samples collected from monitoring wells at the Chromic Acid Pit site during water year 1995 contained dissolved- solids concentrations of 481 to 516 milligrams per liter. Total chromium concentrations detected above the laboratory reporting limit ranged from 0.0061 to 0.030 milligram per liter; dissolved chromium concentrations ranged from 0.0040 to 0.010 milligram per liter. Nitrate as nitrogen concentrations ranged from 2.1 to 2.8 milligrams per

  13. Hydrophobic matrix-free graphene-oxide composites with isotropic and nematic states

    NASA Astrophysics Data System (ADS)

    Wåhlander, Martin; Nilsson, Fritjof; Carlmark, Anna; Gedde, Ulf W.; Edmondson, Steve; Malmström, Eva

    2016-08-01

    We demonstrate a novel route to synthesise hydrophobic matrix-free composites of polymer-grafted graphene oxide (GO) showing isotropic or nematic alignment and shape-memory effects. For the first time, a cationic macroinitiator (MI) has been immobilised on anionic GO and subsequently grafted with hydrophobic polymer grafts. Dense grafts of PBA, PBMA and PMMA with a wide range of average graft lengths (MW: 1-440 kDa) were polymerised by surface-initiated controlled radical precipitation polymerisation from the statistical MI. The surface modification is designed similarly to bimodal graft systems, where the cationic MI generates nanoparticle repulsion, similar to dense short grafts, while the long grafts offer miscibility in non-polar environments and cohesion. The state-of-the-art dispersions of grafted GO were in the isotropic state. Transparent and translucent matrix-free GO-composites could be melt-processed directly using only grafted GO. After processing, birefringence due to nematic alignment of grafted GO was observed as a single giant Maltese cross, 3.4 cm across. Permeability models for composites containing aligned 2D-fillers were developed, which were compared with the experimental oxygen permeability data and found to be consistent with isotropic or nematic states. The storage modulus of the matrix-free GO-composites increased with GO content (50% increase at 0.67 wt%), while the significant increases in the thermal stability (up to 130 °C) and the glass transition temperature (up to 17 °C) were dependent on graft length. The tuneable matrix-free GO-composites with rapid thermo-responsive shape-memory effects are promising candidates for a vast range of applications, especially selective membranes and sensors.We demonstrate a novel route to synthesise hydrophobic matrix-free composites of polymer-grafted graphene oxide (GO) showing isotropic or nematic alignment and shape-memory effects. For the first time, a cationic macroinitiator (MI) has been

  14. Eagleworks Laboratories: Advanced Propulsion Physics Research

    NASA Technical Reports Server (NTRS)

    White, Harold; March, Paul; Williams, Nehemiah; ONeill, William

    2011-01-01

    NASA/JSC is implementing an advanced propulsion physics laboratory, informally known as "Eagleworks", to pursue propulsion technologies necessary to enable human exploration of the solar system over the next 50 years, and enabling interstellar spaceflight by the end of the century. This work directly supports the "Breakthrough Propulsion" objectives detailed in the NASA OCT TA02 In-space Propulsion Roadmap, and aligns with the #10 Top Technical Challenge identified in the report. Since the work being pursued by this laboratory is applied scientific research in the areas of the quantum vacuum, gravitation, nature of space-time, and other fundamental physical phenomenon, high fidelity testing facilities are needed. The lab will first implement a low-thrust torsion pendulum (<1 uN), and commission the facility with an existing Quantum Vacuum Plasma Thruster. To date, the QVPT line of research has produced data suggesting very high specific impulse coupled with high specific force. If the physics and engineering models can be explored and understood in the lab to allow scaling to power levels pertinent for human spaceflight, 400kW SEP human missions to Mars may become a possibility, and at power levels of 2MW, 1-year transit to Neptune may also be possible. Additionally, the lab is implementing a warp field interferometer that will be able to measure spacetime disturbances down to 150nm. Recent work published by White [1] [2] [3] suggests that it may be possible to engineer spacetime creating conditions similar to what drives the expansion of the cosmos. Although the expected magnitude of the effect would be tiny, it may be a "Chicago pile" moment for this area of physics.

  15. Stress drop estimates and hypocenter relocations of induced earthquakes near Fox Creek, Alberta

    NASA Astrophysics Data System (ADS)

    Clerc, F.; Harrington, R. M.; Liu, Y.; Gu, Y. J.

    2016-12-01

    This study investigates the physical differences between induced and naturally occurring earthquakes using a sequence of events potentially induced by hydraulic fracturing near Fox Creek, Alberta. We perform precise estimations of static stress drop to determine if the range of values is low compared to values estimated for naturally occurring events, as has been suggested by previous studies. Starting with the Natural Resources Canada earthquake catalog and using waveform data from regional networks, we use a spectral ratio method to calculate the static stress drop values of a group of relocated earthquakes occurring in close proximity to hydraulic fracturing wells from December 2013 to June 2015. The spectral ratio method allows us to precisely constrain the corner frequencies of the amplitude spectra by eliminating the path and site effects of co-located event pairs. Our estimated stress drop values range from 0.1 - 149 MPa over the full range of observed magnitudes, Mw 1.5-4, which are on the high side of the typical reported range of tectonic events, but consistent with other regional studies [Zhang et al., 2016; Wang et al., 2016]. , Stress drops values range from 11 to 93 MPa and appear to be scale invariant over the magnitude range Mw 3 - 4, and are less well constrained at lower magnitudes due to noise and bandwidth limitations. We observe no correlation between event stress drop and hypocenter depth or distance from the wells. Relocated hypocenters cluster around corresponding injection wells and form fine-scale lineations, suggesting the presence and orientation of fault planes. We conclude that neither the range of stress drops nor their scaling with respect to magnitude can be used to conclusively discriminate induced and tectonic earthquakes, as stress drop values may be greatly affected by the regional setting. Instead, the double-difference relocations may be a more reliable indicator of induced seismicity.

  16. Boronization in textor

    NASA Astrophysics Data System (ADS)

    Winter, J.; Esser, H. G.; Könen, L.; Philipps, V.; Reimer, H.; Seggern, J. v.; Schlüter, J.; Vietzke, E.; Waelbroeck, F.; Wienhold, P.; Banno, T.; Ringer, D.; Vepřek, S.

    1989-04-01

    The liner and limiters of TEXTOR have been coated in situ with a boron containing carbon film using a RG discharge in a throughflow of 0.8 He + 0.1 B 2H 6 +0.1 CH 4. The average film thickness was 30-50 nm, the ratio of boron and carbon in the layer was about 1:1 according to Auger Electron Spectroscopy. Subsequent tokamak discharges are characterized by a small fraction of radiated power (< 0.3) even during high power ICRF heating (2.6 MW, 1.6 s). A concomitant strong increase of the convective power loading of the limiters is observed. Values of Z eff lower than 1.2 are derived from conductivity measurements. The most prominent change in the impurity concentration compared to good conditions in a carbonized surrounding is measured for oxygen. The value OVI/ n¯e of the OVI intensity normalized to the averaged plasma density overlinene decreases by more than a factor of four. The decrease in the oxygen content manifests itself also as a reduction of the CO and CO 2 partial pressures measured during and after the discharge with a sniffer probe. The carbon levels are reduced by a factor of about two as measured by the normalized intensity CII/ overlinene of the CII line and via the ratio of the C fluxes and deuterium fluxes measured at the limiter (CI/D α). The wall shows a pronounced sorption of hydrogen from the plasma, easing the density control and the establishment of low recycling conditions. The beneficial conditions did not show a significant deterioration during more than 200 discharges, including numerous shots at ICRH power levels > 2 MW.

  17. Long-term survival of a randomized phase III trial of head and neck cancer patients receiving concurrent chemoradiation therapy with or without low-level laser therapy (LLLT) to prevent oral mucositis.

    PubMed

    Antunes, Héliton S; Herchenhorn, Daniel; Small, Isabele A; Araújo, Carlos M M; Viégas, Celia Maria Pais; de Assis Ramos, Gabriela; Dias, Fernando L; Ferreira, Carlos G

    2017-08-01

    The impact of low-level laser therapy (LLLT) to prevent oral mucositis in patients treated with exclusive chemoradiation therapy remains unknown. This study evaluated the overall, disease-free and progression-free survival of these patients. Overall, disease-free and progression-free survival of 94 patients diagnosed with oropharynx, nasopharynx, and hypopharynx cancer, who participated on a phase III study, was evaluated from 2007 to 2015. The patients were subjected to conventional radiotherapy plus cisplatin every 3weeks. LLLT was applied with an InGaAlP diode (660nm-100mW-1J-4J/cm 2 ). With a median follow-up of 41.3months (range 0.7-101.9), patients receiving LLLT had a statistically significant better complete response to treatment than those in the placebo group (LG=89.1%; PG=67.4%; p=0.013). Patients subjected to LLLT also displayed increase in progression-free survival than those in the placebo group (61.7% vs. 40.4%; p=0.030; HR:1:93; CI 95%: 1.07-3.5) and had a tendency for better overall survival (57.4% vs. 40.4%; p=0.90; HR:1.64; CI 95%: 0.92-2.91). This is the first study to suggest that LLLT may improve survival of head and neck cancer patients treated with chemoradiotherapy. Further studies, with a larger sample, are necessary to confirm our findings. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Applying polarity rapid assessment method and ultrafiltration to characterize NDMA precursors in wastewater effluents.

    PubMed

    Chen, Chao; Leavey, Shannon; Krasner, Stuart W; Mel Suffet, I H

    2014-06-15

    Certain nitrosamines in water are disinfection byproducts that are probable human carcinogens. Nitrosamines have diverse and complex precursors that include effluent organic matter, some anthropogenic chemicals, and natural (likely non-humic) substances. An easy and selective tool was first developed to characterize nitrosamine precursors in treated wastewaters, including different process effluents. This tool takes advantages of the polarity rapid assessment method (PRAM) and ultrafiltration (UF) (molecular weight distribution) to locate the fractions with the strongest contributions to the nitrosamine precursor pool in the effluent organic matter. Strong cation exchange (SCX) and C18 solid-phase extraction cartridges were used for their high selectivity for nitrosamine precursors. The details of PRAM operation, such as cartridge clean-up, capacity, pH influence, and quality control were included in this paper, as well as the main parameters of UF operation. Preliminary testing of the PRAM/UF method with effluents from one wastewater treatment plant gave very informative results. SCX retained 45-90% of the N-nitrosodimethylamine (NDMA) formation potential (FP)-a measure of the precursors-in secondary and tertiary wastewater effluents. These results are consistent with NDMA precursors likely having a positively charged amine group. C18 adsorbed 30-45% of the NDMAFP, which indicates that a substantial portion of these precursors were non-polar. The small molecular weight (MW) (<1 kDa) and large MW (>10 kDa) fractions obtained from UF were the primary contributors to NDMAFP. The combination of PRAM and UF brings important information on the characteristics of nitrosamine precursors in water with easy operation. Copyright © 2014 Elsevier Ltd. All rights reserved.

  19. A linear lattice model for polyglutamine in CAG-expansion diseases.

    PubMed

    Bennett, Melanie J; Huey-Tubman, Kathryn E; Herr, Andrew B; West, Anthony P; Ross, Scott A; Bjorkman, Pamela J

    2002-09-03

    Huntington's disease and several other neurological diseases are caused by expanded polyglutamine [poly(Gln)] tracts in different proteins. Mechanisms for expanded (>36 Gln residues) poly(Gln) toxicity include the formation of aggregates that recruit and sequester essential cellular proteins [Preisinger, E., Jordan, B. M., Kazantsev, A. & Housman, D. (1999) Phil. Trans. R. Soc. London B 354, 1029-1034; Chen, S., Berthelier, V., Yang, W. & Wetzel, R. (2001) J. Mol. Biol. 311, 173-182] and functional alterations, such as improper interactions with other proteins [Cummings, C. J. & Zoghbi, H. Y. (2000) Hum. Mol. Genet. 9, 909-916]. Expansion above the "pathologic threshold" ( approximately 36 Gln) has been proposed to induce a conformational transition in poly(Gln) tracts, which has been suggested as a target for therapeutic intervention. Here we show that structural analyses of soluble huntingtin exon 1 fusion proteins with 16 to 46 glutamine residues reveal extended structures with random coil characteristics and no evidence for a global conformational change above 36 glutamines. An antibody (MW1) Fab fragment, which recognizes full-length huntingtin in mouse brain sections, binds specifically to exon 1 constructs containing normal and expanded poly(Gln) tracts, with affinity and stoichiometry that increase with poly(Gln) length. These data support a "linear lattice" model for poly(Gln), in which expanded poly(Gln) tracts have an increased number of ligand-binding sites as compared with normal poly(Gln). The linear lattice model provides a rationale for pathogenicity of expanded poly(Gln) tracts and a structural framework for drug design.

  20. Surface modification of biomaterials based on high-molecular polylactic acid and their effect on inflammatory reactions of primary human monocyte-derived macrophages: perspective for personalized therapy.

    PubMed

    Stankevich, Ksenia S; Gudima, Alexandru; Filimonov, Victor D; Klüter, Harald; Mamontova, Evgeniya M; Tverdokhlebov, Sergei I; Kzhyshkowska, Julia

    2015-06-01

    Polylactic acid (PLA) based implants can cause inflammatory complications. Macrophages are key innate immune cells that control inflammation. To provide higher biocompatibility of PLA-based implants with local innate immune cells their surface properties have to be improved. In our study surface modification technique for high-molecular PLA (MW=1,646,600g/mol) based biomaterials was originally developed and successfully applied. Optimal modification conditions were determined. Treatment of PLA films with toluene/ethanol=3/7 mixture for 10min with subsequent exposure in 0.001M brilliant green dye (BGD) solution allows to entrap approximately 10(-9)mol/cm(2) model biomolecules. The modified PLA film surface was characterized by optical microscopy, SERS, FT-IR, UV and TG/DTA/DSC analysis. Tensile strain of modified films was determined as well. The effect of PLA films modified with BGD on the inflammatory reactions of primary human monocyte-derived macrophages was investigated. We developed in vitro test-system by differentiating primary monocyte-derived macrophages on a coating material. Type 1 and type 2 inflammatory cytokines (TNFα, CCL18) secretion and histological biomarkers (CD206, stabilin-1) expression were analyzed by ELISA and confocal microscopy respectively. BGD-modified materials have improved thermal stability and good mechanical properties. However, BGD modifications induced additional donor-specific inflammatory reactions and suppressed tolerogenic phenotype of macrophages. Therefore, our test-system successfully demonstrated specific immunomodulatory effects of original and modified PLA-based biomaterials, and can be further applied for the examination of improved coatings for implants and identification of patient-specific reactions to implants. Copyright © 2015. Published by Elsevier B.V.

  1. 808-nm laser therapy with a flat-top handpiece photobiomodulates mitochondria activities of Paramecium primaurelia (Protozoa).

    PubMed

    Amaroli, Andrea; Ravera, Silvia; Parker, Steven; Panfoli, Isabella; Benedicenti, Alberico; Benedicenti, Stefano

    2016-05-01

    Photobiomodulation is proposed as a non-linear process, and only low-level laser therapy (LLLT) is assumed to stimulate exposed cells, whereas high powered laser and fluences can cause negative effects, exhausting the cell's energy reserve as a consequence of excessive photon-based stimulation. In our work, we investigated and compared the effects of 808-nm diode laser (CW) with a new flat-top handpiece. To this purpose, we tested the photobiomodulation effects of 1 and 3 J/cm(2) fluence, both generated by 100 mW or 1 W of laser power and of 64 J/cm(2) of fluence generated by 100 mW, 1 W, 1.5 W or 2 W, as expressed through oxygen consumption and ATP synthesis of Paramecium. Data collected indicates the incremental consumption of oxygen through irradiation with 3 J/cm(2)-100 mW or 64 J/cm(2)-1 W correlates with an increase in Paramecium ATP synthesis. The Paramecium respiration was inhibited by fluences 64 J/cm(2)-100 mW or 64 J/cm(2)-2 W and was followed by a decrease in the endogenous ATP concentration. The 1 J/cm(2)-100 mW or 1 W and 3 J/cm(2)-1 W did not affect mitochondrial activity. The results show that the fluence of 64 J/cm(2)-1 W more than the 3 J/cm(2)-100 mW causes greater efficiency in Paramecium mitochondria respiratory chain activity. Our results suggest that thanks to flat-top handpiece we used, high fluences by high-powered laser have to be reconsidered as an effective and non-invasive therapy. Possible associated benefits of deeper tissue penetration would increase treatment effectiveness and reduced irradiation time.

  2. Polyanion-Induced Self Association of Complement Factor H1

    PubMed Central

    Pangburn, Michael K.; Rawal, Nenoo; Cortes, Claudio; Alam, M. Nurul; Ferreira, Viviana P.; Atkinson, Mark A. L.

    2008-01-01

    Factor H is the primary soluble regulator of activation of the alternative pathway of complement. It prevents activation of complement on host cells and tissues upon association with C3b and surface polyanions such as sialic acids, heparin and other glycosaminoglycans. Here we show that interaction with polyanions causes self-association forming tetramers of the 155,000 Da glycosylated protein. Monomeric human factor H is an extended flexible protein that exhibits an apparent size of 330,000 Da, relative to globular standards, during gel filtration chromatography in the absence of polyanions. In the presence of dextran sulfate (5,000 Da) or heparin an intermediate species of apparent m.w. 700,000 and a limit species of m.w. 1,400,000 were observed by gel filtration. Sedimentation equilibrium analysis by analytical ultracentrifugation indicated a monomer Mr of 163,000 in the absence of polyanions and a Mr of 607,000, corresponding to a tetramer, in the presence of less than a 2-fold molar excess of dextran sulfate. Increasing concentrations of dextran sulfate increased binding of factor H to zymosan-C3b 4.5-fold. This was accompanied by an increase in both the decay accelerating and cofactor activity of factor H on these cells. An expressed fragment encompassing the C-terminal polyanion binding site (complement control protein domains 18–20) also exhibited polyanion-induced self association, suggesting that the C-terminal ends of factor H mediate self-association. The results suggest that recognition of polyanionic markers on host cells and tissues by factor H, and the resulting regulation of complement activation, may involve formation of dimers and tetramers of factor H. PMID:19124749

  3. A capacitive power sensor based on the MEMS cantilever beam fabricated by GaAs MMIC technology

    NASA Astrophysics Data System (ADS)

    Yi, Zhenxiang; Liao, Xiaoping

    2013-03-01

    In this paper, a novel capacitive power sensor based on the microelectromechanical systems (MEMS) cantilever beam at 8-12 GHz is proposed, fabricated and tested. The presented design can not only realize a cantilever beam instead of the conventional fixed-fixed beam, but also provide fine compatibility with the GaAs monolithic microwave integrated circuit (MMIC) process. When the displacement of the cantilever beam is very small compared with the initial height of the air gap, the capacitance change between the measuring electrode and the cantilever beam has an approximately linear dependence on the incident radio frequency (RF) power. Impedance compensating technology, by modifying the slot width of the coplanar waveguide transmission line, is adopted to minimize the effect of the cantilever beam on the power sensor; its validity is verified by the simulation of high frequency structure simulator software. The power sensor has been fabricated successfully by Au surface micromachining using polyimide as the sacrificial layer on the GaAs substrate. Optimization of the design with impedance compensating technology has resulted in a measured return loss of less than -25 dB and an insertion loss of around 0.1 dB at 8-12 GHz, which shows the slight effect of the cantilever beam on the microwave performance of this power sensor. The measured capacitance change starts from 0.7 fF to 1.3 fF when the incident RF power increases from 100 to 200 mW and an approximate linear dependence has been obtained. The measured sensitivities of the sensor are about 6.16, 6.27 and 6.03 aF mW-1 at 8, 10 and 12 GHz, respectively.

  4. Characteristics of molecular weight distribution of dissolved organic matter in bromide-containing water and disinfection by-product formation properties during treatment processes.

    PubMed

    Zhang, Ying; Zhang, Ning; Zhao, Peng; Niu, Zhiguang

    2018-03-01

    The characteristics of dissolved organic matter (DOM) and bromide ion concentration have a significant influence on the formation of disinfection by-products (DBPs). In order to identify the main DBP precursors, DOM was divided into five fractions based on molecular weight (MW), trihalomethane formation potential and haloacetic acid formation potential were determined for fractions, and the change in contents of different fractions and total DBPs during treatment processes (pre-chlorination, coagulation, sand filtration, disinfection) were studied. Moreover, the relationship between bromide concentration and DBP generation characteristics in processes was also analyzed. The results showed that the main DBP precursors were the fraction with MW <1kDa and fraction with MW 3-10kDa, and the DBP's generation ability of lower molecular weight DOM (<10kDa) was higher than that of higher molecular weight DOM. During different processes, pre-chlorination and disinfection had limited effect on removing organics but could alter the MW distribution, and coagulation and filtration could effectively remove organics with higher MW. For DBPs, trihalomethanes (THMs) were mainly generated in pre-chlorination and disinfection, while haloacetic acids (HAAs) were mostly generated during pre-chlorination; coagulation and sand filtration had little effect on THMs but resulted in a slight removal of HAAs. In addition, the results of ANOVA tests suggested that molecular sizes and treatment processes have significant influence on DBP formation. With increasing bromide concentration, the brominated DBPs significantly increased, but the bromine incorporation factor in the processes was basically consistent at each concentration. Copyright © 2017. Published by Elsevier B.V.

  5. Size-fractionation and characterization of landfill leachate and the improvement of Cu{sup 2+} adsorption capacity in soil and aged refuse

    SciT

    Lou Ziyang; State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, Shanghai 200092; Chai Xiaoli

    2009-01-15

    Leachate was collected from an anaerobic lagoon at Shanghai Laogang refuse landfill, the largest landfill in China, and the sample was separated into six fractions using micro-filtration membranes, followed by ultra-filtration membranes. Several parameters of the samples were measured, including chemical oxygen demand (COD), total organic carbon (TOC), total solids (TS), pH, total phosphate (TP), total nitrogen (TN), fixed solids (FS), NH{sub 4}{sup +}, orthophosphate, color, turbidity, and conductivity. These parameters were then quantitatively correlated with the molecular weight cutoff of the membrane used. Organic matter in the dissolved fraction (MW < 1 kDa) predominated in the leachate, accounting formore » 65% of TOC. Thermal infrared spectroscopy was used to characterize the filter residues. Asymmetric and symmetric stretching of methyl and methylene groups, and of functional groups containing nitrogen and oxygen atoms, were observed. In addition, the ability of two different samples to adsorb heavy metals was tested. Cu{sup 2+} was chosen as the representative heavy metal in this study, and the samples were soil; aged refuse, which had spent 8 years in a conventional sanitary landfill; and samples of soil and aged refuse treated for 48 h with leachate in the ratio of 5 g of sample per 50 ml of leachate. Cu{sup 2+} uptake by the raw soil was {approx}4.60 {mu}g/g, while uptake by the leachate-contacted soil and leachate-contacted aged refuse were 5.66 and 5.11 {mu}g/g, respectively. These results show that the organic matter in the leachate enhanced the capacity of aqueous solutions to adsorb Cu{sup 2+}.« less

  6. Hydraulic Fracture Induced Seismicity During A Multi-Stage Pad Completion in Western Canada: Evidence of Activation of Multiple, Parallel Faults

    NASA Astrophysics Data System (ADS)

    Maxwell, S.; Garrett, D.; Huang, J.; Usher, P.; Mamer, P.

    2017-12-01

    Following reports of injection induced seismicity in the Western Canadian Sedimentary Basin, regulators have imposed seismic monitoring and traffic light protocols for fracturing operations in specific areas. Here we describe a case study in one of these reservoirs, the Montney Shale in NE British Columbia, where induced seismicity was monitored with a local array during multi-stage hydraulic fracture stimulations on several wells from a single drilling pad. Seismicity primarily occurred during the injection time periods, and correlated with periods of high injection rates and wellhead pressures above fracturing pressures. Sequential hydraulic fracture stages were found to progressively activate several parallel, critically-stressed faults, as illuminated by multiple linear hypocenter patterns in the range between Mw 1 and 3. Moment tensor inversion of larger events indicated a double-couple mechanism consistent with the regional strike-slip stress state and the hypocenter lineations. The critically-stressed faults obliquely cross the well paths which were purposely drilled parallel to the minimum principal stress direction. Seismicity on specific faults started and stopped when fracture initiation points of individual injection stages were proximal to the intersection of the fault and well. The distance ranges when the seismicity occurs is consistent with expected hydraulic fracture dimensions, suggesting that the induced fault slip only occurs when a hydraulic fracture grows directly into the fault and the faults are temporarily exposed to significantly elevated fracture pressures during the injection. Some faults crossed multiple wells and the seismicity was found to restart during injection of proximal stages on adjacent wells, progressively expanding the seismogenic zone of the fault. Progressive fault slip is therefore inferred from the seismicity migrating further along the faults during successive injection stages. An accelerometer was also deployed close

  7. The Space Motion of Leo I: The Mass of the Milky Way's Dark Matter Halo

    NASA Astrophysics Data System (ADS)

    Boylan-Kolchin, Michael; Bullock, James S.; Sohn, Sangmo Tony; Besla, Gurtina; van der Marel, Roeland P.

    2013-05-01

    We combine our Hubble Space Telescope measurement of the proper motion of the Leo I dwarf spheroidal galaxy (presented in a companion paper) with the highest resolution numerical simulations of Galaxy-size dark matter halos in existence to constrain the mass of the Milky Way's dark matter halo (M vir, MW). Despite Leo I's large Galactocentric space velocity (200 km s-1) and distance (261 kpc), we show that it is extremely unlikely to be unbound if Galactic satellites are associated with dark matter substructure, as 99.9% of subhalos in the simulations are bound to their host. The observed position and velocity of Leo I strongly disfavor a low-mass Milky Way: if we assume that Leo I is the least bound of the Milky Way's classical satellites, then we find that M vir, MW > 1012 M ⊙ at 95% confidence for a variety of Bayesian priors on M vir, MW. In lower mass halos, it is vanishingly rare to find subhalos at 261 kpc moving as fast as Leo I. Should an additional classical satellite be found to be less bound than Leo I, this lower limit on M vir, MW would increase by 30%. Imposing a mass-weighted ΛCDM prior, we find a median Milky Way virial mass of M vir, MW = 1.6 × 1012 M ⊙, with a 90% confidence interval of [1.0-2.4] × 1012 M ⊙. We also confirm a strong correlation between subhalo infall time and orbital energy in the simulations and show that proper motions can aid significantly in interpreting the infall times and orbital histories of satellites.

  8. Laser-based satellite communication systems stabilized by non-mechanical electro-optic scanners

    NASA Astrophysics Data System (ADS)

    Ziemkiewicz, Michael; Davis, Scott R.; Rommel, Scott D.; Gann, Derek; Luey, Benjamin; Gamble, Joseph D.; Anderson, Mike

    2016-05-01

    Laser communications systems provide numerous advantages for establishing satellite-to-ground data links. As a carrier for information, lasers are characterized by high bandwidth and directionality, allowing for fast and secure transfer of data. These systems are also highly resistant to RF influences since they operate in the infrared portion of the electromagnetic spectrum, far from radio bands. In this paper we will discuss an entirely non-mechanical electro-optic (EO) laser beam steering technology, with no moving parts, which we have used to form robust 400 Mbps optical data connections through air. This technology will enable low cost, compact, and rugged free space optical (FSO) communication modules for small satellite applications. The EO beam-steerer at the heart of this system is used to maintain beam pointing as the satellite orbits. It is characterized by extremely low values for size, weight and power consumption (SWaP) - approximately 300 cm3, 300 g, and 5 W respectively, which represents a marked improvement compared to heavy, and power-consuming gimbal mechanisms. It is capable of steering a 500 mW, 1 mm short wave infrared (SWIR) beam over a field of view (FOV) of up to 50° x 15°, a range which can be increased by adding polarization gratings, which provide a coarse adjust stage at the EO beam scanner output. We have integrated this device into a communication system and demonstrated the capability to lock on and transmit a high quality data stream by modulation of SWIR power.

  9. Application of M-type cathodes to high-power cw klystrons

    NASA Astrophysics Data System (ADS)

    Isagawa, S.; Higuchi, T.; Kobayashi, K.; Miyake, S.; Ohya, K.; Yoshida, M.

    1999-05-01

    Two types of high-power cw klystrons have been widely used at KEK in both TRISTAN and KEKB e +e - collider projects: one is a 0.8 MW/1.0 MW tube, called YK1302/YK1303 (Philips); the other is a 1.2 MW tube, called E3786/E3732 (Toshiba). Normally, the dispenser cathodes of the `B-type' and the `S-type' have been used, respectively, but for improved versions they have been replaced by low-temperature cathodes, called the `M-type'. An Os/Ru coating was applied to the former, whereas an Ir one was applied to the latter. Until now, all upgraded tubes installing M-type cathodes, 9 and 8 in number, respectively, have worked successfully without any dropout. A positive experience concerning the lifetime under real operation conditions has been obtained. M-type cathodes are, however, more easily poisoned. One tube installing an Os/Ru-coated cathode showed a gradual, and then sudden decrease in emission during an underheating test, although the emission could fortunately be recovered by aging at the KEK test field. Once sufficiently aged, the emission of an Ir-coated cathode proved to be very high and stable, and its lifetime is expected to be very long. One disadvantage of this cathode is, however, susceptibility to gas poisoning and the necessity of long-term initial aging. New techniques, like ion milling and fine-grained tungsten top layers, were not as successful as expected from their smaller scale applications to shorten the initial aging period. A burn-in process at higher cathode loading was efficient to make the poisoned cathode active and to decrease unwanted Wehnelt emission. On top of that, the emission cooling, and thus thermal conductivity near the emitting layer could play an important role in such large-current cathodes as ours.

  10. Low stress drops observed for aftershocks of the 2011 Mw 5.7 Prague, Oklahoma, earthquake

    NASA Astrophysics Data System (ADS)

    Sumy, Danielle F.; Neighbors, Corrie J.; Cochran, Elizabeth S.; Keranen, Katie M.

    2017-05-01

    In November 2011, three Mw ≥ 4.8 earthquakes and thousands of aftershocks occurred along the structurally complex Wilzetta fault system near Prague, Oklahoma. Previous studies suggest that wastewater injection induced a Mw 4.8 foreshock, which subsequently triggered a Mw 5.7 mainshock. We examine source properties of aftershocks with a standard Brune-type spectral model and jointly solve for seismic moment (M0), corner frequency (f0), and kappa (κ) with an iterative Gauss-Newton global downhill optimization method. We examine 934 earthquakes with initial moment magnitudes (Mw) between 0.33 and 4.99 based on the pseudospectral acceleration and recover reasonable M0, f0, and κ for 87 earthquakes with Mw 1.83-3.51 determined by spectral fit. We use M0 and f0 to estimate the Brune-type stress drop, assuming a circular fault and shear-wave velocity at the hypocentral depth of the event. Our observations suggest that stress drops range between 0.005 and 4.8 MPa with a median of 0.2 MPa (0.03-26.4 MPa with a median of 1.1 MPa for Madariaga-type), which is significantly lower than typical eastern United States intraplate events (>10 MPa). We find that stress drops correlate weakly with hypocentral depth and magnitude. Additionally, we find the stress drops increase with time after the mainshock, although temporal variation in stress drop is difficult to separate from spatial heterogeneity and changing event locations. The overall low median stress drop suggests that the fault segments may have been primed to fail as a result of high pore fluid pressures, likely related to nearby wastewater injection.

  11. Extraction of the same novel homoglycan mixture from two different strains of Bifidobacterium animalis and three strains of Bifidobacterium breve.

    PubMed

    Alhudhud, M; Sadiq, S; Ngo, H N; Hidalgo-Cantabrana, C; Ruas-Madiedo, P; van Sinderen, D; Humphreys, P N; Laws, A P

    2018-06-15

    Three strains of Bifidobacterium breve (JCM 7017, JCM 7019 and JCM 2258) and two strains of Bifidobacterium animalis subsp. lactis (AD011 and A1dOxR) were grown in broth cultures or on plates, and a standard exopolysaccharide extraction method was used in an attempt to recover exocellular polysaccharides. When the extracted materials were analysed by NMR it was clear that mixtures of polysaccharides were being isolated including exopolysaccharides (EPS) cell wall polysaccharides and intracellular polysaccharides. Treatment of the cell biomass from the B. breve strains, or the B. animalis subsp. lactis AD011 strain, with aqueous sodium hydroxide provided a very similar mixture of polysaccharides but without the EPS. The different polysaccharides were partially fractionated by selective precipitation from an aqueous solution upon the addition of increasing percentages of ethanol. The polysaccharides extracted from B. breve JCM 7017 grown in HBM media supplemented with glucose (or isotopically labelled D-glucose-1- 13 C) were characterised using 1D and 2D-NMR spectroscopy. Addition of one volume of ethanol generated a medium molecular weight glycogen (Mw=1×10 5 Da, yield 200 mg/l). The addition of two volumes of ethanol precipitated an intimate mixture of a low molecular weight β-(1→6)-glucan and a low molecular weight β-(1→6)-galactofuranan which could not be separated (combined yield 46 mg/l). When labelled D-glucose-1- 13 C was used as a carbon supplement, the label was incorporated into >95% of the anomeric carbons of each polysaccharide confirming they were being synthesised in situ. Similar 1 H NMR profiles were obtained for polysaccharides recovered from the cells of B. animalis subsp. lactis AD011and A1dOxR (in combination with an EPS), B. breve JCM 7017, B. breve JCM 7019, B. breve JCM 2258 and from an EPS (-ve) mutant of B. breve 7017 (a non-EPS producer).

  12. On current drive by Ohkawa mechanism of electron cyclotron wave in large inverse aspect ratio tokamaks

    NASA Astrophysics Data System (ADS)

    Zheng, Pingwei; Gong, Xueyu; Lu, Xingqiang; He, Lihua; Cao, Jingjia; Huang, Qianhong; Deng, Sheng

    2018-03-01

    A localized and efficient current drive method in the outer-half region of the tokamak with a large inverse aspect ratio is proposed via the Ohkawa mechanism of electron cyclotron (EC) waves. Further off-axis Ohkawa current drive (OKCD) via EC waves was investigated in high electron beta β e HL-2M-like tokamaks with a large inverse aspect ratio, and in EAST-like tokamaks with a low inverse aspect ratio. OKCD can be driven efficiently, and the driven current profile is spatially localized in the radial region, ranging from 0.62 to 0.85, where the large fraction of trapped electrons provides an excellent advantage for OKCD. Furthermore, the current drive efficiency increases with an increase in minor radius, and then drops when the minor radius beyond a certain value. The effect of trapped electrons greatly enhances the current driving capability of the OKCD mechanism. The highest current drive efficiency can reach 0.183 by adjusting the steering mirror to change the toroidal and poloidal incident angle, and the total driven current by OKCD can reach 20-32 kA MW-1 in HL-2M-like tokamaks. The current drive is less efficient for the EAST-like scenario due to the lower inverse aspect ratio. The results show that OKCD may be a valuable alternative current drive method in large inverse aspect ratio tokamaks, and the potential capabilities of OKCD can be used to suppress some important magnetohydrodynamics instabilities in the far off-axis region.

  13. Variable-period surface-wave magnitudes: A rapid and robust estimator of seismic moments

    Bonner, J.; Herrmann, R.; Benz, H.

    2010-01-01

    We demonstrate that surface-wave magnitudes (Ms), measured at local, regional, and teleseismic distances, can be used as a rapid and robust estimator of seismic moment magnitude (Mw). We used the Russell (2006) variable-period surface-wave magnitude formula, henceforth called Ms(VMAX), to estimate the Ms for 165 North American events with 3.2 Mw = 1.91 + 0.66Msx (VMAX) for 2

  14. Hydrophobic matrix-free graphene-oxide composites with isotropic and nematic states.

    PubMed

    Wåhlander, Martin; Nilsson, Fritjof; Carlmark, Anna; Gedde, Ulf W; Edmondson, Steve; Malmström, Eva

    2016-08-21

    We demonstrate a novel route to synthesise hydrophobic matrix-free composites of polymer-grafted graphene oxide (GO) showing isotropic or nematic alignment and shape-memory effects. For the first time, a cationic macroinitiator (MI) has been immobilised on anionic GO and subsequently grafted with hydrophobic polymer grafts. Dense grafts of PBA, PBMA and PMMA with a wide range of average graft lengths (MW: 1-440 kDa) were polymerised by surface-initiated controlled radical precipitation polymerisation from the statistical MI. The surface modification is designed similarly to bimodal graft systems, where the cationic MI generates nanoparticle repulsion, similar to dense short grafts, while the long grafts offer miscibility in non-polar environments and cohesion. The state-of-the-art dispersions of grafted GO were in the isotropic state. Transparent and translucent matrix-free GO-composites could be melt-processed directly using only grafted GO. After processing, birefringence due to nematic alignment of grafted GO was observed as a single giant Maltese cross, 3.4 cm across. Permeability models for composites containing aligned 2D-fillers were developed, which were compared with the experimental oxygen permeability data and found to be consistent with isotropic or nematic states. The storage modulus of the matrix-free GO-composites increased with GO content (50% increase at 0.67 wt%), while the significant increases in the thermal stability (up to 130 °C) and the glass transition temperature (up to 17 °C) were dependent on graft length. The tuneable matrix-free GO-composites with rapid thermo-responsive shape-memory effects are promising candidates for a vast range of applications, especially selective membranes and sensors.

  15. Characterization and biotoxicity assessment of dissolved organic matter in RO concentrate from a municipal wastewater reclamation reverse osmosis system.

    PubMed

    Sun, Ying-Xue; Gao, Yue; Hu, Hong-Ying; Tang, Fang; Yang, Zhe

    2014-12-01

    Reverse osmosis (RO) concentrate from municipal wastewater reclamation reverse osmosis (mWRRO) system containing organic compounds may associate with toxic risk, and its discharge might pose an environmental risk. To identify a basis for the selection of feasible technology in treating RO concentrates, the characteristics and biotoxicity of different fractions of dissolved organic matter (DOM) in RO concentrates from an mWRRO system were investigated. The results indicated that the hydrophilic neutrals (HIN), hydrophobic acids (HOA) and hydrophobic bases (HOB) accounted for 96% of the dissolved organic carbon (DOC) of the total DOM in the RO concentrate. According to the SEC chromatograph detected at 254 nm wavelength of UV, the DOM with molecular weight (MW) 1-3 kDa accounted for the majority of the basic and neutral fractions. The fluorescence spectra of the excitation emission matrix (EEM) indicated that most aromatic proteins, humic/fulvic acid-like and soluble microbial by-product-like substances existed in the fractions HOA and hydrophobic neutrals (HON). The genotoxicity and anti-estrogenic activity of the RO concentrate were 1795.6 ± 57.2 μg 4-NQOL(-1) and 2.19 ± 0.05 mg TAM L(-1), respectively. The HIN, HOA, and HOB contributed to the genotoxicity of the RO concentrate, and the HIN was with the highest genotoxic level of 1007.9 ± 94.8 μg 4-NQOL(-1). The HOA, HON, and HIN lead to the total anti-estrogenic activity of the RO concentrate, and HOA occupied approximately 60% of the total, which was 1.3 ± 0.17 mg TAM L(-1). Copyright © 2014 Elsevier Ltd. All rights reserved.

  16. AGN Luminosity and Stellar Age: Two Missing Ingredients for AGN Unification as Seen with iPTF Supernovae

    NASA Astrophysics Data System (ADS)

    Villarroel, Beatriz; Nyholm, Anders; Karlsson, Torgny; Comerón, Sébastien; Korn, Andreas J.; Sollerman, Jesper; Zackrisson, Erik

    2017-03-01

    Active galactic nuclei (AGNs) are extremely powerful cosmic objects, driven by accretion of hot gas upon super-massive black holes. The zoo of AGN classes is divided into two major groups, with Type-1 AGNs displaying broad Balmer emission lines and Type-2 narrow ones. For a long time it was believed that a Type-2 AGN is a Type-1 AGN viewed through a dusty kiloparsec-sized torus, but an emerging body of observations suggests more than just the viewing angle matters. Here we report significant differences in supernova (SN) counts and classes in the first study to date of SNe near Type-1 and Type-2 AGN host galaxies, using data from the intermediate Palomar Transient Factory, the Sloan Digital Sky Survey Data Release 7, and Galaxy Zoo. We detect many more SNe in Type-2 AGN hosts (size of effect ˜5.1σ) compared to Type-1 hosts, which shows that the two classes of AGN are located inside host galaxies with different properties. In addition, Type-1 and Type-2 AGNs that are dominated by star formation according to Wide-field Infrared Survey Explorer colors {m}W1-{m}W2< 0.5 and are matched in 22 μm absolute magnitude differ by a factor of ten in L[O III] λ5007 luminosity, suggesting that when residing in similar types of host galaxies Type-1 AGNs are much more luminous. Our results demonstrate two more factors that play an important role in completing the current picture: the age of stellar populations and the AGN luminosity. This has immediate consequences for understanding the many AGN classes and galaxy evolution.

  17. The roles of carbohydrates, proteins and lipids in the process of aggregation of natural marine organic matter investigated by means of 2D correlation spectroscopy applied to infrared spectra.

    PubMed

    Mecozzi, Mauro; Pietrantonio, Eva; Pietroletti, Marco

    2009-01-01

    In this paper the marine organic matter soluble in an alkaline medium called extractable humic substance (EHS), was extracted from three sediment samples of Tyrrhenian Sea and separated by precipitation at pH 2 in the two fractions of fulvic acids (FAs) and humic acids (HAs). FAs were further fractionated in seven sub-samples of different molecular weight (mw) by means of seven different ultrafiltration membranes operating in the range between mw<1 kDa and mw>100 kDa. Then the qualitative composition of each sample of fractionated FAs and HAs was studied by means of one-dimensional Fourier transform infrared spectroscopy in reflectance mode (FTIR-DRIFT) and by two-dimensional (2D) correlation spectroscopy both in wavelength-wavelength (WW) and in sample-sample (SS) mode. The application of 2D correlation WW spectroscopy allows to elucidate the different roles played by carbohydrates and proteins with respect to some lipid compounds such as fatty acids and ester fatty acids during the process of aggregate formations from mw approximately 1 kDa to higher size aggregates. In addition, 2D correlation WW spectroscopy allows to observe some peculiar interactions between carbohydrates and proteins in the formation of EHS aggregates, interactions which vary from a sample to another sample. The results of 2D correlation SS spectroscopy confirm the general evidences obtained by 2D WW spectroscopy and moreover, they also describe the formation of EHS aggregates as a complex process where evolutionary links and connectivity between aggregates of neighbour molecular size ranges are not evident. Two-dimensional correlation spectroscopy applied to FTIR spectroscopy shows to be a powerful tool for the investigation of the mechanisms involved in EHS aggregation because it supports the acquisition of structural information which sometimes can be hardly obtained by one-dimensional FTIR spectroscopy.

  18. The effect of oxidation on the enzyme-catalyzed hydrolytic biodegradation of poly(urethane)s.

    PubMed

    Labow, Rosalind S; Tang, Yiwen; McCloskey, Christopher B; Santerre, J Paul

    2002-01-01

    Although the biodegradation of polyurethanes (PU) by oxidative and hydrolytic agents has been studied extensively, few investigations have reported on the combination of their effects. Since neutrophils (PMN) arrive at an implanted device first and release HOCl, followed by monocyte-derived macrophages (MDM) which have potent esterase activities and oxidants of their own, the combined effect of oxidative and hydrolytic degradation on radiolabeled polycarbonate-polyurethanes (PCNU)s was investigated and compared to that of a polyester-PU (PESU) and a polyether-PU (PEU). The PCNUs were synthesized with PCN (MW = 1,000), and butanediol (14C-BD) and one of two diisocyanates, hexane-1,6-diisocyanate (14C-HDI) or methylene bis-p-phenyl diisocyanate (MDI). The PESU and PEU were synthesized using toluene-diisocyanate (14C-TDI), with polycaprolactone and polytetramethylene oxide as soft segments respectively, and ethylene diamine as the chain extender. The effect of pre-treatment with 0.1 mM HOC1 for 1 week on the HDI-based PCNUs and both TDI-based PUs resulted in a significant inhibition of radiolabel release (RR) elicited by cholesterol esterase (CE), when compared to buffer alone, whereas the MDI-based PCNU showed a small but significant increase. When PMN were activated on the HDI-based PCNU surface with phorbol myristate acetate (PMA), HOCl was released for 3 h, and was almost completely abolished by sodium azide (AZ). Simultaneously, the PMN-elicited RR, shown previously to be due to the esterolytic cleavage by serine proteases, was inhibited approximately 75% by PMA-activation of the cells, but significantly increased relative to the latter when AZ was added. Both in vitro oxidation by HOCl and the release of HOCI by PMN were associated with the inhibition of RR and suggest perturbations between oxidative and hydrolytic mechanisms of biodegradation.

  19. Synthetic polymeric substrates as potent pro-oxidant versus anti-oxidant regulators of cytoskeletal remodeling and cell apoptosis.

    PubMed

    Sung, Hak-Joon; Chandra, Prafulla; Treiser, Matthew D; Liu, Er; Iovine, Carmine P; Moghe, Prabhas V; Kohn, Joachim

    2009-03-01

    The role of reactive oxygen species (ROS)-mediated cell signal transduction pathways emanating from engineered cell substrates remains unclear. To elucidate the role, polymers derived from the amino acid L-tyrosine were used as synthetic matrix substrates. Variations in their chemical properties were created by co-polymerizing hydrophobic L-tyrosine derivatives with uncharged hydrophilic poly(ethylene glycol) (PEG, Mw = 1,000 Da), and negatively charged desaminotyrosyl-tyrosine (DT). These substrates were characterized for their intrinsic ability to generate ROS, as well as their ability to elicit Saos-2 cell responses in terms of intracellular ROS production, actin remodeling, and apoptosis. PEG-containing substrates induced both exogenous and intracellular ROS production, whereas the charged substrates reduced production of both types, indicating a coupling of exogenous ROS generation and intracellular ROS production. Furthermore, PEG-mediated ROS induction caused nuclear translocation of glyceraldehyde-3-phosphate dehydrogenase and an increase in caspase-3 activity, confirming a link with apoptosis. PEG-rich pro-oxidant substrates caused cytoskeletal actin remodeling through beta-actin cleavage by caspase-3 into fractins. The fractins co-localized to the mitochondria and reduced the mitochondrial membrane potential. The remnant cytosolic beta-actin was polymerized and condensed, events consistent with apoptotic cell shrinkage. The cytoskeletal remodeling was integral to the further augmentation of intracellular ROS production. Conversely, the anti-oxidant DT-containing charged substrates suppressed the entire cascade of apoptotic progression. We demonstrate that ROS activity serves an important role in "outside-in" signaling for cells grown on substrates: the ROS activity couples exogenous stress, driven by substrate composition, to changes in intracellular signaling. This signaling causes cell apoptosis, which is mediated by actin remodeling.

  20. Diagnosis at a glance of biological non-Newtonian fluids with Film Interference Flow Imaging (FIFI)

    NASA Astrophysics Data System (ADS)

    Hidema, R.; Yamada, N.; Furukawa, H.

    2012-04-01

    In the human body, full of biological non-Newtonian fluids exist. For example, synovial fluids exist in our joints, which contain full of biopolymers, such as hyaluronan and mucin. It is thought that these polymers play critical roles on the smooth motion of the joint. Indeed, luck of biopolymers in synovial fluid cause joint pain. Here we study the effects of polymer in thin liquid layer by using an original experimental method called Film Interference Flow Imaging (FIFI). A vertically flowing soap film containing polymers is made as two-dimensional flow to observe turbulence. The thickness of water layer is about 4 μm sandwiched between surfactant mono-layers. The interference pattern of the soap film is linearly related to the flow velocity in the water layer through the change in the thickness of the film. Thus the flow velocity is possibly analyzed by the single image analysis of the interference pattern, that is, FIFI. The grid turbulence was made in the flowing soap films containing the long flexible polymer polyethyleneoxide (PEO, Mw=3.5x106), and rigid polymer hydroxypropyl cellulose (HPC, Mw > 1.0 x106). The decaying process of the turbulence is affected by PEO and HPC at several concentrations. The effects of PEO are sharply seen even at low concentrations, while the effects of HPC are gradually occurred at much higher concentration compared to the PEO. It is assumed that such a difference between PEO and HPC is due to the polymer stretching or polymer orientation under turbulence, which is observed and analyzed by FIFI. We believe the FIFI will be applied in the future to examine biological fluids such as synovial fluids quickly and quantitatively.

  1. Lipids characterization of ultrasound and microwave processed germinated sorghum.

    PubMed

    Hassan, Sadia; Imran, Muhammad; Ahmad, Nazir; Khan, Muhammad Kamran

    2017-06-27

    Cereal crops and oilseeds provide diverse pool of fatty acids with characteristic properties. Sorghum (Sorghum bicolor (L.) Moench) provides the staple food with serving as main source of energy and protein. Germination of sorghum generally increases the nutritive value of seeds and the effects of germination on lipids composition of seeds vary greatly with processing conditions. Therefore, the current study was conducted to compare the effect of emerging processing techniques such as ultrasound (US) and microwave (MW) on fatty acids composition and oil yield of sorghum seeds before and after germination. Initially sorghum grains were soaked with 5% NaOCl (sodium hypochlorite) for surface sterilization. Afterwards, grains were soaked in excess water for 22 h at room temperature and were divided into four portions. The first portion (100 g grains) was subjected to germination without applying any microwave and ultrasonic treatment (T 0 ). Second portion was further divided into four groups (T 1 , T 2 , T 3 , T 4 ) (100 g of each group) and grains were subjected to ultrasonic treatments using two different ultrasonic intensities (US 1 : 40%; US 2 : 60%) within range of 0-100% and with two different time durations (t US1 : 5 min; t US2 : 10 min) at constant temperature. Third portion was also divided into four groups (T 1 , T 2 , T 3 , T 4 ) (100 g of each group) and exposed to microwave treatments at two different power levels (MW 1 : 450 watt; MW 2 : 700 watt) within the range of 100-900 W for two different time durations (t MW1 : 15 s; t MW2 : 30s). Similarly, fourth portion was divided into four groups (T 1 , T 2 , T 3 , T 4 ) (100 g of each group). Each group was exposed to both MW (MW 1 , MW 2 ) (100-900 watt power) & US (US 1 , US 2 ) (0-100% intensity) treatments at two different time levels (t US , t MW ). Then, germination was carried out and pre-treated raw and pre-treated germinated sorghum grains were analyzed for total oil yield, fatty acid

  2. Explicit macroscopic singlet oxygen modeling for benzoporphyrin derivative monoacid ring A (BPD)-mediated photodynamic therapy.

    PubMed

    Kim, Michele M; Penjweini, Rozhin; Liang, Xing; Zhu, Timothy C

    2016-11-01

    Photodynamic therapy (PDT) is an effective non-ionizing treatment modality that is currently being used for various malignant and non-malignant diseases. In type II PDT with photosensitizers such as benzoporphyrin monoacid ring A (BPD), cell death is based on the creation of singlet oxygen ( 1 O 2 ). With a previously proposed empirical five-parameter macroscopic model, the threshold dose of singlet oxygen ([ 1 O 2 ] rx,sh ]) to cause tissue necrosis in tumors treated with PDT was determined along with a range of the magnitude of the relevant photochemical parameters: the photochemical oxygen consumption rate per light fluence rate and photosensitizer concentration (ξ), the probability ratio of 1 O 2 to react with ground state photosensitizer compared to a cellular target (σ), the ratio of the monomolecular decay rate of the triplet state photosensitizer (β), the low photosensitizer concentration correction factor (δ), and the macroscopic maximum oxygen supply rate (g). Mice bearing radiation-induced fibrosarcoma (RIF) tumors were treated interstitially with a linear light source at 690nm with total energy released per unit length of 22.5-135J/cm and source power per unit length of 12-150mW/cm to induce different radii of necrosis. A fitting algorithm was developed to determine the photochemical parameters by minimizing the error function involving the range between the calculated reacted singlet oxygen ([ 1 O 2 ] rx ) at necrosis radius and the [ 1 O 2 ] rx,sh . [ 1 O 2 ] rx was calculated based on explicit dosimetry of the light fluence distribution, the tissue optical properties, and the BPD concentration. The initial ground state oxygen concentration ([ 3 O 2 ] 0 ) was set to be 40μM in this study. The photochemical parameters were found to be ξ=(55±40)×10 -3 cm 2 mW -1 s -1 , σ=(1.8±3)×10 -5 μM -1 , and g=1.7±0.7μMs -1 . We have taken the literature values for δ=33μM, and β=11.9μM. [ 1 O 2 ] rx has shown promise to be a more effective dosimetry quantity for predicting necrosis than either light dose or PDT dose, where the latter is simplistically a temporal integral of the products of the photosensitizer concentration and light fluence rate. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. Orbits of massive satellite galaxies - II. Bayesian estimates of the Milky Way and Andromeda masses using high-precision astrometry and cosmological simulations

    NASA Astrophysics Data System (ADS)

    Patel, Ekta; Besla, Gurtina; Mandel, Kaisey

    2017-07-01

    In the era of high-precision astrometry, space observatories like the Hubble Space Telescope (HST) and Gaia are providing unprecedented 6D phase-space information of satellite galaxies. Such measurements can shed light on the structure and assembly history of the Local Group, but improved statistical methods are needed to use them efficiently. Here we illustrate such a method using analogues of the Local Group's two most massive satellite galaxies, the Large Magellanic Cloud (LMC) and Triangulum (M33), from the Illustris dark-matter-only cosmological simulation. We use a Bayesian inference scheme combining measurements of positions, velocities and specific orbital angular momenta (j) of the LMC/M33 with importance sampling of their simulated analogues to compute posterior estimates of the Milky Way (MW) and Andromeda's (M31) halo masses. We conclude that the resulting host halo mass is more susceptible to bias when using measurements of the current position and velocity of satellites, especially when satellites are at short-lived phases of their orbits (I.e. at pericentre). Instead, the j value of a satellite is well conserved over time and provides a more reliable constraint on host mass. The inferred virial mass of the MW (M31) using j of the LMC (M33) is {{M}}_{vir, MW} = 1.02^{+0.77}_{-0.55} × 10^{12} M⊙ ({{M}}_{vir, M31} = 1.37^{+1.39}_{-0.75} × 10^{12} M⊙). Choosing simulated analogues whose j values are consistent with the conventional picture of a previous (<3 Gyr ago), close encounter (<100 kpc) of M33 about M31 results in a very low virial mass for M31 (˜1012 M⊙). This supports the new scenario put forth in Patel, Besla & Sohn, wherein M33 is on its first passage about M31 or on a long-period orbit. We conclude that this Bayesian inference scheme, utilizing satellite j, is a promising method to reduce the current factor of 2 spread in the mass range of the MW and M31. This method is easily adaptable to include additional satellites as new 6D

  4. Earthquake Complex Network Analysis Before and After the Mw 8.2 Earthquake in Iquique, Chile

    NASA Astrophysics Data System (ADS)

    Pasten, D.

    2017-12-01

    The earthquake complex networks have shown that they are abble to find specific features in seismic data set. In space, this networkshave shown a scale-free behavior for the probability distribution of connectivity, in directed networks and theyhave shown a small-world behavior, for the undirected networks.In this work, we present an earthquake complex network analysis for the large earthquake Mw 8.2 in the north ofChile (near to Iquique) in April, 2014. An earthquake complex network is made dividing the three dimensional space intocubic cells, if one of this cells contain an hypocenter, we name this cell like a node. The connections between nodes aregenerated in time. We follow the time sequence of seismic events and we are making the connections betweennodes. Now, we have two different networks: a directed and an undirected network. Thedirected network takes in consideration the time-direction of the connections, that is very important for the connectivityof the network: we are considering the connectivity, ki of the i-th node, like the number of connections going out ofthe node i plus the self-connections (if two seismic events occurred successive in time in the same cubic cell, we havea self-connection). The undirected network is made removing the direction of the connections and the self-connectionsfrom the directed network. For undirected networks, we are considering only if two nodes are or not connected.We have built a directed complex network and an undirected complex network, before and after the large earthquake in Iquique. We have used magnitudes greater than Mw = 1.0 and Mw = 3.0. We found that this method can recognize the influence of thissmall seismic events in the behavior of the network and we found that the size of the cell used to build the network isanother important factor to recognize the influence of the large earthquake in this complex system. This method alsoshows a difference in the values of the critical exponent γ (for the probability

  5. Conversion of Local and Surface-Wave Magnitudes to Moment Magnitude for Earthquakes in the Chinese Mainland

    NASA Astrophysics Data System (ADS)

    Li, X.; Gao, M.

    2017-12-01

    The magnitude of an earthquake is one of its basic parameters and is a measure of its scale. It plays a significant role in seismology and earthquake engineering research, particularly in the calculations of the seismic rate and b value in earthquake prediction and seismic hazard analysis. However, several current types of magnitudes used in seismology research, such as local magnitude (ML), surface wave magnitude (MS), and body-wave magnitude (MB), have a common limitation, which is the magnitude saturation phenomenon. Fortunately, the problem of magnitude saturation was solved by a formula for calculating the seismic moment magnitude (MW) based on the seismic moment, which describes the seismic source strength. Now the moment magnitude is very commonly used in seismology research. However, in China, the earthquake scale is primarily based on local and surface-wave magnitudes. In the present work, we studied the empirical relationships between moment magnitude (MW) and local magnitude (ML) as well as surface wave magnitude (MS) in the Chinese Mainland. The China Earthquake Networks Center (CENC) ML catalog, China Seismograph Network (CSN) MS catalog, ANSS Comprehensive Earthquake Catalog (ComCat), and Global Centroid Moment Tensor (GCMT) are adopted to regress the relationships using the orthogonal regression method. The obtained relationships are as follows: MW=0.64+0.87MS; MW=1.16+0.75ML. Therefore, in China, if the moment magnitude of an earthquake is not reported by any agency in the world, we can use the equations mentioned above for converting ML to MW and MS to MW. These relationships are very important, because they will allow the China earthquake catalogs to be used more effectively for seismic hazard analysis, earthquake prediction, and other seismology research. We also computed the relationships of and (where Mo is the seismic moment) by linear regression using the Global Centroid Moment Tensor. The obtained relationships are as follows: logMo=18

  6. Coseismic and aseismic deformations of the rock mass around deep level mining in South Africa - Joint South African and Japanese study

    NASA Astrophysics Data System (ADS)

    Milev, A. M.; Yabe, Y.; Naoi, M. M.; Nakatani, M.; Durrheim, R. J.; Ogasawara, H.; Scholz, C. H.

    2010-12-01

    Two underground sites in a deep level gold mine in South Africa were instrumented by the Council for Scientific and Industrial Research (CSIR) with tilt meters and seismic monitors. One of the sites was also instrumented by JApanese-German Underground Acoustic emission Research in South Africa (JAGUARS) with a small network, approx. 40 m span, of eight Acoustic Emission (AE) sensors. The rate of tilt, defined as quasi-static deformations, and the seismic ground motion, defined as dynamic deformations, were analysed in order to understand the rock mass behavior around deep level mining. In addition the high frequency AE events recorded at hypocentral distances of about 50m were analysed. This was the first implementation of high frequency AE events at such a great depth (3300m below the surface). A good correspondence between the dynamic and quasi-static deformations was found. The rate of coseismic and aseismic tilt, as well as seismicity recorded by the mine seismic network, are approximately constant until the daily blasting time, which takes place from about 19:30 until shortly before 21:00. During the blasting time and the subsequent seismic events the coseismic and aseismic tilt shows a rapid increase indicated by a rapid change of the tilt during the seismic event. Much of the quasi-static deformation, however, occurs independently of the seismic events and was described as ‘slow’ or aseismic events. During the monitoring period a seismic event with MW 1.9 (2.1) occurred in the vicinity of the instrumented site. This event was recorded by both the CSIR integrated monitoring system and JAGUARS acoustic emotion network. The tilt changes associated with this event showed a well pronounced after-tilt. More than 21,000 AE aftershocks were located in the first 150 hours after the main event. Using the distribution of the AE events the position of the fault in the source area was successfully delineated. The distribution of the AE events following the main shock

  7. Construction, Geologic, and Hydrologic Data from Five Exploratory Wells on Rota, Commonwealth of the Northern Mariana Islands, 1999

    Carruth, Rob

    2005-01-01

    Rota is the southernmost of the 14 small islands that make up the Commonwealth of the Northern Mariana Islands. Reduced springflow at Matan Hanom and As Onan springs occurred during a drought associated with the 1997-98 El Nino. Water from the two developed springs constituted the only municipal water source for the island at that time. In April 1998, reduced water supplies forced the Commonwealth Utilities Corporation to restrict water service in the principal villages of Songsong and Sinapalu for the duration of the dry season. In 1999, Five exploratory wells, EX-1 through EX-5 (CUC wells SP-MW1, SP-1, -2, -3, and SP-MW2), were drilled in the Sinapalu region of Rota to (1) assess the availability of fresh ground-water resources in an area where no other well information were available, and (2) to provide a new water source to help mitigate the impacts of drought associated with recurring El Nino weather events. The wells penetrated mainly light colored (dirty white to brownish), fragmental limestones containing abundant coral remains. Sustained-rate, recovery, and step-drawdown aquifer tests were attempted at each of the five exploratory wells to estimate aquifer properties in the vicinity of the wells and to assess the potential for new water sources. At wells EX-1 (CUC well SPMW1) and EX-5 (CUC well SP-MW2), attempts to conduct sustained-rate aquifer tests resulted in excessive drawdown to the pump intakes in the vicinity of the wells. At well EX-2 (CUC well SP-1), the maximum drawdown measured in the pumped well was 3.93 ft during 8 days of sustained pumping at an average rate of 187 gal/min. At well EX-3 (CUC well SP-2), the maximum drawdown measured in the pumped well was 2.31 ft during 8 days of sustained pumping at an average rate of 108 gal/min, and at well EX-4 (CUC well SP-3), the maximum drawdown measured in the pumped well was 3.27 ft during 8 days of sustained pumping at an average rate of 139 gal/min. Specific conductance at the end of 8 days of

  8. Recovery of nitrogen and phosphorus from alkaline fermentation liquid of waste activated sludge and application of the fermentation liquid to promote biological municipal wastewater treatment.

    PubMed

    Tong, Juan; Chen, Yinguang

    2009-07-01

    In previous publications we reported that by controlling the pH at 10.0 the accumulation of short-chain fatty acids (SCFA) during waste activated sludge (WAS) fermentation was remarkably improved [Yuan, H., Chen, Y., Zhang, H., Jiang, S., Zhou, Q., Gu, G., 2006. Improved bioproduction of short-chain fatty acids (SCFAs) from excess sludge under alkaline conditions. Environ. Sci. Technol. 40, 2025-2029], but significant ammonium nitrogen (NH(4)-N) and soluble ortho-phosphorus (SOP) were released [Chen, Y., Jiang, S., Yuan, H., Zhou, Q., Gu, G., 2007. Hydrolysis and acidification of waste activated sludge at different pHs. Water Res. 41, 683-689]. This paper investigated the simultaneous recovery of NH(4)-N and SOP from WAS alkaline fermentation liquid and the application of the fermentation liquid as an additional carbon source for municipal wastewater biological nitrogen and phosphorus removal. The central composite design (CCD) of the response surface methodology (RSM) was employed to optimize and model the simultaneous NH(4)-N and SOP recovery from WAS alkaline fermentation liquid. Under the optimum conditions, the predicted and experimental recovery efficiency was respectively 73.4 and 75.7% with NH(4)-N, and 82.0 and 83.2% with SOP, which suggested that the developed models described the experiments well. After NH(4)-N and SOP recovery, the alkaline fermentation liquid was added to municipal wastewater, and the influence of volume ratio of fermentation liquid to municipal wastewater (FL/MW) on biological nitrogen and phosphorus removal was investigated. The addition of fermentation liquid didn't significantly affect nitrification. Both SOP and total nitrogen (TN) removal were increased with fermentation liquid, but there was no significant increase at FL/MW greater than 1/35. Compared to the blank test, the removal efficiency of SOP and TN at FL/MW=1/35 was improved from 44.0 to 92.9%, and 63.3 to 83.2%, respectively. The enhancement of phosphorus and nitrogen

  9. Selected natural attenuation monitoring data, Operable Unit 1, Naval Undersea Warfare Center, Division Keyport, Washington, June 2002

    Dinicola, Richard S.

    2004-01-01

    Previous investigations indicated that natural attenuation and biodegradation of chlorinated volatile organic compounds (CVOCs) are substantial in shallow ground water beneath the 9-acre former landfill at Operable Unit 1 (OU 1), Naval Undersea Warfare Center (NUWC), Division Keyport, Washington. The U.S. Geological Survey (USGS) has continued to monitor ground-water geochemistry to assure that conditions remain favorable for contaminant biodegradation. This report presents the geochemical and selected CVOC data for ground water at OU 1, collected by the USGS during June 10-14, 2002, in support of long-term monitoring for natural attenuation. Overall, the geochemical data for June 2002 indicate that redox conditions in the upper-aquifer water remain favorable for reductive dechlorination of chlorinated VOCs because strongly reducing conditions persisted beneath much of the former landfill. Redox conditions in the intermediate aquifer downgradient of the landfill also remained favorable for reductive dechlorination, although the 2002 dissolved hydrogen (H2) concentration from well MW1-28 is questionable. Changes in redox conditions were observed at certain wells during 2002, but a longer monitoring period and more thorough interpretation are needed to ascertain if phytoremediation activities are affecting redox conditions and if biodegradation processes are changing over time. The Navy intends to complete a more thorough interpretation in preparation for the 5-year review of OU 1 scheduled for 2004. There were a few substantial differences between the 2002 concentrations and previously observed concentrations of volatile organic compounds. Total CVOC concentrations in 2002 samples decreased substantially in all piezometers sampled in the northern plantation, and the largest percentages of decrease were for the compounds trichloroethene (TCE) and cis-1,2-dichloroethene (cis-DCE). Changes in total CVOC concentrations in the southern plantation were less consistent

  10. Dual-responsive polyplexes with enhanced disassembly and endosomal escape for efficient delivery of siRNA.

    PubMed

    Zhu, Jia; Qiao, Mingxi; Wang, Qi; Ye, Yuqing; Ba, Shuang; Ma, Jingjing; Hu, Haiyang; Zhao, Xiuli; Chen, Dawei

    2018-04-01

    Despite the extracellular barriers for siRNA delivery have been overcome by utilizing advanced nanoparticle delivery systems, the key intracellular barriers after internalization including efficient disassembly of siRNA and endosomal escape still remains challenging. To address the issues, we developed a unique pH- and redox potential-responsive polyplex delivery system based on the copolymer of mPEG-b-PLA-PHis-ssPEI1.8 k, which is composed of a pH-responsive copolymer of PEG-b-PLA-PHis (Mw 5 k) and a branched PEI (Mw1.8 k) linked with redox cleavable disulfide bond. The copolymer showed excellent siRNA complexation and protection abilities against endogenous substances at the relatively low N/P ratio of 6. The siRNA release from the polyplexes (N/P 6) was markedly increased from 13.62% to 58.67% under conditions simulating the endosomal microenvironment. Fluorescence resonance energy transfer (FRET) test also indicated a higher disassembly extent of siRNA from the copolymer. The accelerated siRNA release from the polyplexes was markedly restrained when the N/P ratio was raised above 10 due to the increasing of electrostatic interactions. The efficient endosomal escape of siRNA after internalization was confirmed by confocal microscopy, which was attributed to the cleavaged PEI chains inducing membrane destabilization, the "proton sponge effect" of PHis and PEI as well as the relative small size of after disassembly. The enhanced disassembly and endosomal escape were elucidated as the leading cause for polyplexes (N/P 6) showed more efficient Bcl-2 silencing (85.45%) than those polyplexes with higher N/P ratios (N/P 10 and 15). In vivo results further demonstrated that polyplexes (N/P 6) delivery of siBcl-2 significantly inhibited the MCF-7 breast tumor growth as compared to its counterparts. The incorporation of convertible non-electrical interactions at a balance with electrostatic interactions in complexation siRNA has been demonstrated as an effective

  11. Seismic monitoring at the Decatur, Ill., CO2 sequestration demonstration site

    Kaven, Joern; Hickman, Stephen H.; McGarr, Arthur F.; Walter, Steve R.; Ellsworth, William L.

    2014-01-01

    The viability of carbon capture and storage (CCS) to reduce emissions of greenhouse gases depends on the ability to safely sequester large quantities of CO2 over geologic time scales. One concern with CCS is the potential of induced seismicity. We report on ongoing seismic monitoring by the U.S. Geological Survey (USGS) at a CCS demonstration site in Decatur, IL, in an effort to understand the potential hazards posed by injection-induced seismicity associated with geologic CO2 sequestration. At Decatur, super-critical CO2 is injected at 2.1 km depth into the 550-m-thick Mt. Simon Sandstone, which directly overlies granitic basement. The primary sealing cap rock is the Eau Claire Shale, a 100- to 150-m-thick unit at a depth of roughly 1.5 km. The USGS seismic network consists of 12 stations, three of which have surface accelerometers and three-component borehole geophones. We derived a one-dimensional velocity models from a vertical seismic profile acquired by Archer-Daniels-Midland (ADM) and the Illinois State Geological Survey (ISGS) to a depth of 2.2 km, tied into shallow acoustic logs from our borehole stations and assuming a 6 km/sec P-wave velocity for granite below 2.2 km. We further assume a constant ratio of P- to S-wave velocities of 1.83, as derived from velocity model inversions. We use this velocity model to locate seismic events, all of which are within the footprint of our network. So far magnitudes of locatable events range from Mw = -1.52 to 1.07. We further improved the hypocentral precision of microseismic events when travel times and waveforms are sufficiently similar by employing double-difference relocation techniques, with relative location errors less than 80 m horizontally and 100 m vertically. We observe tend to group in three distinct clusters: ∼0.4 to 1.0 km NE, 1.6 to 2.4 km N, and ∼1.8 to 2.6 km WNW from the injection well. The first cluster of microseismicity forms a roughly linear trend, which may represent a pre-existing geologic

  12. Halo Substructure and the Power Spectrum

    NASA Astrophysics Data System (ADS)

    Zentner, Andrew R.; Bullock, James S.

    2003-11-01

    We present a semianalytic model to investigate the merger history, destruction rate, and survival probability of substructure in hierarchically formed dark matter halos and use it to study the substructure content of halos as a function of input primordial power spectrum. For a standard cold dark matter ``concordance'' cosmology (ΛCDM n=1, σ8=0.95) we successfully reproduce the subhalo velocity function and radial distribution profile seen in N-body simulations and determine that the rate of merging and disruption peaks ~10-12 Gyr in the past for Milky Way-like halos, while surviving substructures are typically accreted within the last ~0-8 Gyr. We explore power spectra with normalizations and spectral ``tilts'' spanning the ranges σ8~=1-0.65 and n~=1-0.8, and include a ``running-index'' model with dn/dlnk=-0.03 similar to the best-fit model discussed in the first-year Wilkinson Microwave Anisotropy Probe (WMAP) report. We investigate spectra with truncated small-scale power, including a broken-scale inflation model and three warm dark matter cases with mW=0.75-3.0 keV. We find that the mass fraction in substructure is relatively insensitive to the tilt and overall normalization of the primordial power spectrum. All of the CDM-type models yield projected substructure mass fractions that are consistent with, but on the low side, of published estimates from strong lens systems: f9=0.4%-1.5% (64th percentile) for subhalos smaller than 109 Msolar within projected cylinders of radius r<10 kpc. Truncated models produce significantly smaller fractions, f9=0.02%-0.2% for mW~=1 keV, and are disfavored by lensing estimates. This suggests that lensing and similar probes can provide a robust test of the CDM paradigm and a powerful constraint on broken-scale inflation/warm particle masses, including masses larger than the ~1 keV upper limits of previous studies. We compare our predicted subhalo velocity functions with the dwarf satellite population of the Milky Way. Assuming that dwarfs have isotropic velocity dispersions, we find that the standard n=1 model overpredicts the number of Milky Way satellites at Vmax<~35 km s-1, as expected. Models with less small-scale power do better because subhalos are less concentrated and the mapping between observed velocity dispersion and halo Vmax is significantly altered. The running-index model, or a fixed tilt with σ8~0.75, can account for the local dwarfs without the need for differential feedback (for Vmax>~20 km s-1) however, these comparisons depend sensitively on the assumption of isotropic velocities in satellite galaxies.

  13. Solving the Meteorological Challenges of Creating a Sustainable Energy System (Invited)

    NASA Astrophysics Data System (ADS)

    Marquis, M.

    2010-12-01

    Global energy demand is projected to double from 13 TW at the start of this century to 28 TW by the middle of the century. This translates into obtaining 1000 MW (1 GW, the amount produced by an average nuclear or coal power plant) of new energy every single day for the next 40 years. The U.S. Department of Energy has conducted three feasibility studies in the last two years identifying the costs, challenges, impacts, and benefits of generating large portions of the nation’s electricity from wind and solar energy, in the new two decades. The 20% Wind by 2030 report found that the nation could meet one-fifth of its electricity demand from wind energy by 2030. The second report, the Eastern Wind Integration and Transmission Study, considered similar costs, challenges, and benefits, but considered 20% wind energy in the Eastern Interconnect only, with a target date of 2024. The third report, the Western Wind and Solar Integration Study, considered the operational impact of up to 35% penetration of wind, photovoltaics (PVs) and, concentrating solar power (CSP) on the power system operated by the WestConnect group, with a target date of 2017. All three studies concluded that it is technically feasible to obtain these high penetration levels of renewable energy, but that increases in the balancing area cooperation or coordination, increased utilization of transmission and building of transmission in some cases, and improved weather forecasts are needed. Current energy systems were designed for dispatchable fuels, such as coal, natural gas and nuclear energy. Fitting weather-driven renewable energy into today's energy system is like fitting a square peg into a round hole. If society chooses to meet a significant portion of new energy demand from weather-driven renewable energy, such as wind and solar energy, a number of obstacles must be overcome. Some of these obstacles are meteorological and climatological issues that are amenable to scientific research. For variable

  14. An Interactive Computer Session to Initiate Physical Activity in Sedentary Cardiac Patients: Randomized Controlled Trial.

    PubMed

    Almeida, Fabio A; Smith-Ray, Renae L; Dzewaltowski, David A; Glasgow, Russell E; Lee, Rebecca E; Thomas, Deborah S K; Xu, Stanley; Estabrooks, Paul A

    2015-08-24

    ; 59% female, 78% white, 12% black, 11% Hispanic) completed a baseline assessment and an interactive computer session. PA increased across the study sample (F1,441=30.03, P<.001). However, a time by condition interaction (F3,441=8.33, P<.001) followed by post hoc analyses indicated that SC participants exhibited a significant increase in weekly PA participation (mean 45.1, SD 10.2) compared to CON (mean -2.5, SD 10.8, P=.004) and ENV (mean 8.3, SD 8.1, P<.05). Additionally, COMBO participants exhibited a significant increase in weekly PA participation (mean 53.4, SD 8.9) compared to CON (P<.001) and ENV (P=.003) participants. There were no significant differences between ENV and CON or between SC and COMBO. A brief, computer-based, interactive personal action planning session may be an effective tool to initiate PA within a health care setting, in particular as part of the ETT system. Clinicaltrials.gov NCT00432133, http://clinicaltrials.gov/ct2/show/NCT00432133 (Archived by WebCite at http://www.webcitation.org/6aa8X3mw1).

  15. Pathology in patients with ventricular assist devices: a study of 21 autopsies, 24 ventricular apical core biopsies and 24 explanted hearts.

    PubMed

    Rose, Alan G; Park, Soon J

    2005-01-01

    .35)/1.75 (S.D.=1.26; NS); and MW: 1.50 (S.D.=1.22)/0.59 (S.D.=0.73; P<.01). Acquired aortic stenosis developed in six hearts, and one heart showed thrombotic occlusion of the left ventricular outflow tract below an aortic bioprosthesis. VAD significantly reduced the amount of CN, MC and MW in the left ventricle but may lead to acquired aortic stenosis of native aortic valves or total occlusive thrombosis of aortic prosthetic valves. Proximate cause of death was, most often, VAD related.

  16. Final report : groundwater monitoring at Centralia, Kansas, inSeptember-October 2005 and March 2006, with expansion of the monitoringnetwork in January 2006.

    SciT

    LaFreniere, L. M.

    2006-12-07

    This document reports the results of groundwater sampling in September-October 2005 and March 2006 at the grain storage facility formerly operated at Centralia, Kansas, by the Commodity Credit Corporation of the U.S. Department of Agriculture (CCC/USDA). These activities were the first and second twice yearly sampling events of the two-year monitoring program approved by the CCC/USDA and Kansas Department of Health and Environment (KDHE) project managers. The initial monitoring network sampled in September and October 2005 consisted of six monitoring wells (MW1-MW6) installed in 2004, plus five groundwater piezometers (SB01, SB04, SB05, SB08, SB09) installed in 2002. The combined September-Octobermore » 2005 sampling was the first monitoring event in the planned two-year program for Centralia. The groundwater samples collected in both September and October were analyzed for volatile organic compounds (VOCs), and samples collected in September were analyzed for dissolved hydrogen and additional groundwater parameters to aid in evaluating the potential for reductive dechlorination processes. After the monitoring in September-October 2005, Argonne recommended expansion of the initial monitoring network. Previous sampling (August 2004) had already suggested that this network of six monitoring wells and five piezometers was inadequate to delineate the extent of the carbon tetrachloride plume. With the approval of the CCC/USDA and KDHE project managers, the monitoring network was expanded in January 2006 through the installation of four additional monitoring wells (MW7-MW10) and one new piezometer (SB07R) to replace a damaged piezometer (the former SB07). Details of the monitoring well and piezometer installations are reported in this document. The expanded monitoring network of ten monitoring wells (MW01-MW10) and six piezometers (SB01, SB04, SB05, SB07R, SB08, and SB09) was sampled in March 2006. This March 2006 sampling was the second monitoring event in the planned

  17. SciT

    LaFreniere, L. M.

    program approved by the state (KDHE 2005), to monitor carbon tetrachloride concentrations in the groundwater. Under the KDHE-approved monitoring plan (Argonne 2005b), groundwater was initially sampled twice yearly for a period of two years. The samples were analyzed for VOCs, as well as for selected geochemical parameters to aid in the evaluation of possible natural contaminant degradation (reductive dechlorination) processes in the subsurface environment. The data have been inconclusive overall, possibly because of the relatively low contaminant concentrations in the plume. Nevertheless, consistently low levels of dissolved oxygen (DO) and oxidation-reduction potential (ORP) at monitoring well MW1D (in the deepest portion of the contaminated aquifer) and the presence of chloroform (the primary degradation product of carbon tetrachloride) suggest that some degree of reductive dechlorination is occurring.« less

  18. Producing Martian Lithologies with Geophysically-Constrained Martian Mantle Compositions

    NASA Astrophysics Data System (ADS)

    Minitti, M. E.; Fei, Y.; Bertka, C. M.

    2008-12-01

    The Martian meteorites, rocks measured by the Mars Exploration Rovers (MER) and lithologies detected by orbital assets represent a diversity of igneous rocks that collectively provide insight into the formation and evolution of Mars. Experimental studies aimed at reproducing the observed igneous lithologies have met with varying degrees of success [e.g., 1,2,3], No study has yet been able to reproduce both Martian meteorite parent magmas and the basalts measured by MER at Gusev Crater [e.g., 1,3]. We attempted a different approach to successfully reproducing Martian igneous lithologies by using geophysical constraints on Martian bulk Fe (wt.%), Fe/Si and mantle Mg# [4,5] to identify mixtures of chondrite compositions that formed plausible Martian mantle compositions. We identified two candidate chondrite mixtures for Mars, CM+L and H+L. We synthesized the CM+L and H+L compositions from oxide, carbonate and phosphate powders and fixed them at an oxygen fugacity below the magnetite-wüstite buffer (MW-1). We conducted experiments at 2 GPa (corresponding to ~150 km in the Martian mantle) between 1300-1600 °C for 4-48 hours in the end-loaded piston cylinder apparatus at the Geophysical Laboratory. Thusfar, we have also conducted experiments at 4 GPa (corresponding to ~320 km in the Martian mantle) between 1425-1475 °C for 210-240 minutes in a Walker-type multi-anvil apparatus at the Geophysical Laboratory. We utilized an 18/11 (octahedron edge length/truncated edge length, in mm) assembly. In both assembly types, the sample was contained within a graphite capsule welded into a Pt tube. We analyzed the experiment products in electron probes at either the Geophysical Laboratory or Arizona State University. Fe and Mg contents of olivine, orthopyroxene and melt were used to assess the attainment of equilibrium for each run product. No significant difference exists between the CM+L and H+L experiment products. The near-solidus phase assemblage of the 2-GPa experiments is

  19. Rivers of Carbon: Carbon Fluxes in a Watershed Context

    NASA Astrophysics Data System (ADS)

    Wohl, E.; Tom, B.; Hovius, N.

    2017-12-01

    Research within the past decade has identified the roles of diverse terrestrial processes in mobilizing terrestrial carbon from bedrock, soil, and vegetation and in redistributing this carbon among the atmosphere, biota, geosphere, and oceans. Rivers are central to carbon redistribution, serving as the primary initial receptor of mobilized terrestrial carbon, as well as governing the proportions of carbon sequestered within sediment, transported to oceans, or released to the atmosphere. We use a riverine carbon budget to examine how key questions regarding carbon dynamics can be addressed across diverse spatial and temporal scales from sub-meter areas over a few hours on a single gravel bar to thousands of square kilometers over millions of years across an entire large river network. The portion of the budget applying to the active channel(s) takes the form of ,in which Cs is organic carbon storage over time t. Inputs are surface and subsurface fluxes from uplands (CIupl) and the floodplain (CIfp), including fossil, soil, and biospheric organic carbon; surface and subsurface fluxes of carbon dioxide to the channel (CICO2); and net primary productivity in the channel (CINPP). Outputs occur via respiration within the channel and carbon dioxide emissions (COgas) and fluxes of dissolved and particulate organic carbon to the floodplain and downstream portions of the river network (COriver). The analogous budget for the floodplain portion of a river corridor is .