Connection between the membrane electron transport system and Hyn hydrogenase in the purple sulfur bacterium, Thiocapsa roseopersicina BBS.

Science.gov (United States)

Tengölics, Roland; Mészáros, Lívia; Győri, E; Doffkay, Zsolt; Kovács, Kornél L; Rákhely, Gábor

2014-10-01

Thiocapsa. roseopersicina BBS has four active [NiFe] hydrogenases, providing an excellent opportunity to examine their metabolic linkages to the cellular redox processes. Hyn is a periplasmic membrane-associated hydrogenase harboring two additional electron transfer subunits: Isp1 is a transmembrane protein, while Isp2 is located on the cytoplasmic side of the membrane. In this work, the connection of HynSL to various electron transport pathways is studied. During photoautotrophic growth, electrons, generated from the oxidation of thiosulfate and sulfur, are donated to the photosynthetic electron transport chain via cytochromes. Electrons formed from thiosulfate and sulfur oxidation might also be also used for Hyn-dependent hydrogen evolution which was shown to be light and proton motive force driven. Hyn-linked hydrogen uptake can be promoted by both sulfur and nitrate. The electron flow from/to HynSL requires the presence of Isp2 in both directions. Hydrogenase-linked sulfur reduction could be inhibited by a QB site competitive inhibitor, terbutryne, suggesting a redox coupling between the Hyn hydrogenase and the photosynthetic electron transport chain. Based on these findings, redox linkages of Hyn hydrogenase are modeled. Copyright © 2014 Elsevier B.V. All rights reserved.

Disclosure of key stereoelectronic factors for efficient H2 binding and cleavage in the active site of [NiFe]-hydrogenases.

Science.gov (United States)

Bruschi, Maurizio; Tiberti, Matteo; Guerra, Alessandro; De Gioia, Luca

2014-02-05

A comparative analysis of a series of DFT models of [NiFe]-hydrogenases, ranging from minimal NiFe clusters to very large systems including both the first and second coordination sphere of the bimetallic cofactor, was carried out with the aim of unraveling which stereoelectronic properties of the active site of [NiFe]-hydrogenases are crucial for efficient H2 binding and cleavage. H2 binding to the Ni-SIa redox state is energetically favored (by 4.0 kcal mol(-1)) only when H2 binds to Ni, the NiFe metal cluster is in a low spin state, and the Ni cysteine ligands have a peculiar seesaw coordination geometry, which in the enzyme is stabilized by the protein environment. The influence of the Ni coordination geometry on the H2 binding affinity was then quantitatively evaluated and rationalized analyzing frontier molecular orbitals and populations. Several plausible reaction pathways leading to H2 cleavage were also studied. It turned out that a two-step pathway, where H2 cleavage takes place on the Ni-SIa redox state of the enzyme, is characterized by very low reaction barriers and favorable reaction energies. More importantly, the seesaw coordination geometry of Ni was found to be a key feature for facile H2 cleavage. The discovery of the crucial influence of the Ni coordination geometry on H2 binding and activation in the active site of [NiFe]-hydrogenases could be exploited in the design of novel biomimetic synthetic catalysts.

Improved growth rate in Clostridium thermocellum hydrogenase mutant via perturbed sulfur metabolism.

Science.gov (United States)

Biswas, Ranjita; Wilson, Charlotte M; Giannone, Richard J; Klingeman, Dawn M; Rydzak, Thomas; Shah, Manesh B; Hettich, Robert L; Brown, Steven D; Guss, Adam M

2017-01-01

Metabolic engineering is a commonly used approach to develop organisms for an industrial function, but engineering aimed at improving one phenotype can negatively impact other phenotypes. This lack of robustness can prove problematic. Cellulolytic bacterium Clostridium thermocellum is able to rapidly ferment cellulose to ethanol and other products. Recently, genes involved in H 2 production, including the hydrogenase maturase hydG and NiFe hydrogenase ech , were deleted from the chromosome of C. thermocellum . While ethanol yield increased, the growth rate of Δ hydG decreased substantially compared to wild type. Addition of 5 mM acetate to the growth medium improved the growth rate in C. thermocellum ∆hydG , whereas wild type remained unaffected. Transcriptomic analysis of the wild type showed essentially no response to the addition of acetate. However, in C. thermocellum ΔhydG , 204 and 56 genes were significantly differentially regulated relative to wild type in the absence and presence of acetate, respectively. Genes, Clo1313_0108-0125, which are predicted to encode a sulfate transport system and sulfate assimilatory pathway, were drastically upregulated in C. thermocellum ΔhydG in the presence of added acetate. A similar pattern was seen with proteomics. Further physiological characterization demonstrated an increase in sulfide synthesis and elimination of cysteine consumption in C. thermocellum ΔhydG . Clostridium thermocellum ΔhydGΔech had a higher growth rate than ΔhydG in the absence of added acetate, and a similar but less pronounced transcriptional and physiological effect was seen in this strain upon addition of acetate. Sulfur metabolism is perturbed in C. thermocellum ΔhydG strains, likely to increase flux through sulfate reduction to act either as an electron sink to balance redox reactions or to offset an unknown deficiency in sulfur assimilation.

Detection of the clostridial hydrogenase gene activity as a bio-index in a molasses wastewater bio-hydrogen producing system by real time PCR and FISH/ flow cytometry

International Nuclear Information System (INIS)

Jui-Jen Chang; Ping-Chi Hsu; Chi-Wa Choi; Sian-Jhong Yu; Cheng-Yu Ho; Wei-En Chen; Jiunn-Jyi Lay; Chieh-Chen Huang; Fu-Shyan Wen

2006-01-01

Hydrogenase is a key enzyme that is used by obligate, anaerobic clostridial to produce hydrogen. In this study a fermentative system with molasses wastewater as nutrient was used to produce hydrogen. For establishing the relationship between the vicissitude of clostridial hydrogenase gene activity and the hydrogen production of this system during the culturing period, total cellular RNA isolated at different growing stages were subjected to real time PCR using primer pair, which were designed according to the conserved sequence of clostridial hydrogenase genes. Cell samples at corresponding growing stages were subjected to in situ reverse transcriptase polymerase chain reaction (in situ RT-PCR) using the same primers and then to fluorescence in situ hybridization (FISH) using clostridial hydrogenase gene-specific DNA probe. Those clostridial cells expressed hydrogenase gene activity could be detected by fluorescence microscopy. This is the first time hydrogen-producing activity in a mixed culture could be successfully studied by means of FISH of hydrogenase mRNA. Besides, 16S rDNA was amplified from total cellular DNA analyzed by denaturing gradient gel electrophoresis (DGGE) to reveal the bacterial diversity in the fermentative system; FISH and flow cytometry aiming at 16S rRNA were also carried out to calculate the population of clostridia and total eubacteria in the system. (authors)

Shewanella oneidensis: a new and efficient System for Expression and Maturation of heterologous [Fe-Fe] Hydrogenase from Chlamydomonas reinhardtii

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Sybirna Kateryna

2008-09-01

Full Text Available Abstract Background The eukaryotic green alga, Chlamydomonas reinhardtii, produces H2 under anaerobic conditions, in a reaction catalysed by a [Fe-Fe] hydrogenase HydA1. For further biochemical and biophysical studies a suitable expression system of this enzyme should be found to overcome its weak expression in the host organism. Two heterologous expression systems used up to now have several advantages. However they are not free from some drawbacks. In this work we use bacterium Shewanella oneidensis as a new and efficient system for expression and maturation of HydA1 from Chlamydomonas reinhardtii. Results Based on codon usage bias and hydrogenase maturation ability, the bacterium S. oneidensis, which possesses putative [Fe-Fe] and [Ni-Fe] hydrogenase operons, was selected as the best potential host for C. reinhardtii [Fe-Fe] hydrogenase expression. Hydrogen formation by S. oneidensis strain AS52 (ΔhydAΔhyaB transformed with a plasmid bearing CrHydA1 and grown in the presence of six different substrates for anaerobic respiration was determined. A significant increase in hydrogen evolution was observed for cells grown in the presence of trimethylamine oxide, dimethylsulfoxide and disodium thiosulfate, showing that the system of S. oneidensis is efficient for heterologous expression of algal [Fe-Fe] hydrogenase. Conclusion In the present work a new efficient system for heterologous expression and maturation of C. reinhardtii hydrogenase has been developed. HydA1 of C. reinhardtii was purified and shown to contain 6 Fe atoms/molecule of protein, as expected. Using DMSO, TMAO or thiosulfate as substrates for anaerobic respiration during the cell growth, 0.4 – 0.5 mg l-1(OD600 = 1 of catalytically active HydA1 was obtained with hydrogen evolution rate of ~700 μmol H2 mg-1 min-1.

NCBI nr-aa BLAST: CBRC-DNOV-01-2127 [SEVENS

Lifescience Database Archive (English)

Full Text Available CBRC-DNOV-01-2127 ref|YP_712620.1| [NiFe] hydrogenase maturation protein HypF [Fran...kia alni ACN14a] emb|CAJ61046.1| [NiFe] hydrogenase maturation protein HypF [Frankia alni ACN14a] YP_712620.1 0.81 32% ...

Heterologous expression of an algal hydrogenase in a heterocystous cyanobacterium

Energy Technology Data Exchange (ETDEWEB)

Thorsten Heidorn; Peter Lindblad [Dept. of Physiological Botany, Uppsala University, Villavogen 6, SE-752 36 Uppsala, (Sweden)

2006-07-01

For the expression of an active algal [FeFe] hydrogenase in the heterocystous cyanobacterium Nostoc punctiforme A TCC 29133 the Chlamydomonas reinhardtii hydrogenase gene hydA1 and the accessory genes hydEF and hydG are to be introduced into the cyanobacteria cells. The genes were amplified by PCR from EST clones, cloned into the cloning vector pBluescript SK+ and sequenced. An expression vector for multi-cistronic cloning, based on pSCR202, was constructed and for a functional test GFP was inserted as a reporter gene. The GFP construct was transformed into Nostoc punctiforme A TCC 29133 by electroporation and expression of GFP was visualized by fluorescence microscopy. (authors)

Heterologous expression of an algal hydrogenase in a heterocystous cyanobacterium

International Nuclear Information System (INIS)

Thorsten Heidorn; Peter Lindblad

2006-01-01

For the expression of an active algal [FeFe] hydrogenase in the heterocystous cyanobacterium Nostoc punctiforme A TCC 29133 the Chlamydomonas reinhardtii hydrogenase gene hydA1 and the accessory genes hydEF and hydG are to be introduced into the cyanobacteria cells. The genes were amplified by PCR from EST clones, cloned into the cloning vector pBluescript SK+ and sequenced. An expression vector for multi-cistronic cloning, based on pSCR202, was constructed and for a functional test GFP was inserted as a reporter gene. The GFP construct was transformed into Nostoc punctiforme A TCC 29133 by electroporation and expression of GFP was visualized by fluorescence microscopy. (authors)

Purification and characterization of Desulfovibrio vulgaris (Hildenborough) hydrogenase expressed in Escherichia coli.

NARCIS (Netherlands)

Voordouw, G.; Hagen, W.R.; Kruse-Wolters, M.; Berkel-Arts, van A.; Veeger, C.

1987-01-01

Hydrogenase from Desulfovibrio vulgaris (Hildenborough) is a heterologous dimer of molecular mass 46 + 13.5 kDa. Its two structural genes have been cloned on a 4664-base-pair fragment of known sequence in the vector pUC9. Expression of hydrogenase polypeptides in Escherichia coli transformed with

Improving cyanobacterail O₂-tolerance using CBS hydrogenase for hydrogen production

Energy Technology Data Exchange (ETDEWEB)

Maness, Pin-Ching [National Renewable Energy Lab. (NREL), Golden, CO (United States); Eckert, Carrie [National Renewable Energy Lab. (NREL), Golden, CO (United States); Wawrousek, Karen [National Renewable Energy Lab. (NREL), Golden, CO (United States); Noble, Scott [National Renewable Energy Lab. (NREL), Golden, CO (United States); Pennington, Grant [National Renewable Energy Lab. (NREL), Golden, CO (United States); Yu, Jianping [National Renewable Energy Lab. (NREL), Golden, CO (United States)

2016-11-11

Cyanobacterial H₂ production is a viable path to renewable H₂ with water serving as the electron donor and sunlight the energy source. A grand challenge is the sensitivity of the underlying hydrogenase to O₂, the latter an inherent byproduct of oxygenic photosynthesis. This challenge has been identified as a technical barrier in the Fuel Cell Technologies Office (FCTO) Multi-year Research, Development and Deployment Plan. One solution is to express in cyanobacterium an O₂-tolerant hydrogenase to circumvent this barrier. We have uncovered an O₂-tolerant hydrogenase from a photosynthetic bacterium Rubrivivax gelatinosus CBS (Casa Bonita Strain; hereafter “CBS”) with a half-life near 21 h when exposed to ambient O₂. We sequenced the CBS genome and identified two sets of maturation machineries hyp1 and hyp2. Transcripts expression analysis and mutagenesis revealed that hyp1 is responsible for the assembly of the O₂-tolerant CO-oxidation (Coo) hydrogenase and hyp2 is involved in the maturation of a H₂-uptake hydrogenase. The structural genes encoding the O₂-tolerant hydrogenase (cooLXUH) and maturation genes hyp1FABCDE were therefore cloned and expressed in the model cyanobacterium Synechocystis sp. PCC 6803. We obtained several recombinants displaying hydrogenase activity in a Synechocystis host lacking background activity, suggesting that the CBS hydrogenase is active in Synechocystis. Yet the activity is extremely low. To ensure balanced protein expression, we systematically optimized heterologous expression of 10 CBS genes by using stronger promoters and better ribosome binding site. Moreover we attempted the expression of cooM and cooK genes, verified to be important in CBS to afford activity. CooM is a very large protein and both CooM and CooK are membrane-associated. These properties limited our success in expressing both genes in Synechocystis, although they

Minimal Influence of [NiFe] Hydrogenase on Hydrogen Isotope Fractionation in H2-Oxidizing Cupriavidus necator

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Brian J. Campbell

2017-10-01

Full Text Available Fatty acids produced by H2-metabolizing bacteria are sometimes observed to be more D-depleted than those of photoautotrophic organisms, a trait that has been suggested as diagnostic for chemoautotrophic bacteria. The biochemical reasons for such a depletion are not known, but are often assumed to involve the strong D-depletion of H2. Here, we cultivated the bacterium Cupriavidus necator H16 (formerly Ralstonia eutropha H16 under aerobic, H2-consuming, chemoautotrophic conditions and measured the isotopic compositions of its fatty acids. In parallel with the wild type, two mutants of this strain, each lacking one of two key hydrogenase enzymes, were also grown and measured. In all three strains, fractionations between fatty acids and water ranged from -173‰ to -235‰, and averaged -217‰, -196‰, and -226‰, respectively, for the wild type, SH- mutant, and MBH- mutant. There was a modest increase in δD as a result of loss of the soluble hydrogenase enzyme. Fractionation curves for all three strains were constructed by growing parallel cultures in waters with δDwater values of approximately -25‰, 520‰, and 1100‰. These curves indicate that at least 90% of the hydrogen in fatty acids is derived from water, not H2. Published details of the biochemistry of the soluble and membrane-bound hydrogenases confirm that these enzymes transfer electrons rather than intact hydride (H- ions, providing no direct mechanism to connect the isotopic composition of H2 to that of lipids. Multiple lines of evidence thus agree that in this organism, and presumably others like it, environmental H2 plays little or no direct role in controlling lipid δD values. The observed fractionations must instead result from isotope effects in the reduction of NAD(PH by reductases with flavin prosthetic groups, which transfer two electrons and acquire H+ (or D+ from solution. Parallels to NADPH reduction in photosynthesis may explain why D/H fractionations in C. necator

Heterologous expression of an algal hydrogenase in a hetero-cystous cyanobacterium

Energy Technology Data Exchange (ETDEWEB)

Thorsten Heidorn; Peter Lindblad [Dept. of Physiological Botany, Uppsala University, V illavagen 6, SE-752 36 Uppsala, (Sweden)

2006-07-01

For the expression of an active algal [FeFe] hydrogenase in the hetero-cystous cyanobacterium Nostoc punctiforme A TCC 29133 the Chlamydomonas reinhardtii hydrogenase gene hydA1 and the accessory genes hydEF and hydG are to be introduced into the cyano-bacterial cells. The genes were amplified by PCR from EST clones, cloned into the cloning vector pBluescript SK+ and sequenced. An expression vector for multi-cistronic cloning, based on pSCR202, was constructed and for a functional test GFP was inserted as a reporter gene. The GFP construct was transformed into Nostoc punctiforme A TCC 29133 by electroporation and expression of GFP was visualized by fluorescence microscopy. (authors)

Heterologous expression of an algal hydrogenase in a hetero-cystous cyanobacterium

International Nuclear Information System (INIS)

Thorsten Heidorn; Peter Lindblad

2006-01-01

For the expression of an active algal [FeFe] hydrogenase in the hetero-cystous cyanobacterium Nostoc punctiforme A TCC 29133 the Chlamydomonas reinhardtii hydrogenase gene hydA1 and the accessory genes hydEF and hydG are to be introduced into the cyano-bacterial cells. The genes were amplified by PCR from EST clones, cloned into the cloning vector pBluescript SK+ and sequenced. An expression vector for multi-cistronic cloning, based on pSCR202, was constructed and for a functional test GFP was inserted as a reporter gene. The GFP construct was transformed into Nostoc punctiforme A TCC 29133 by electroporation and expression of GFP was visualized by fluorescence microscopy. (authors)

Dissecting the hydrogenase expression and activity of transformed escherichia coli with the bidirectional NiFe-hydrogenase from synechocystis sp. PCC 6803

International Nuclear Information System (INIS)

Moon, Yu Ran; Lee, Min Hee; An, Byung Chull; Chung, Byung Yeoup; Kim, Jae Sung; Kim, Jin Hong; Park, Youn Il; Kim, Cha Soon

2009-01-01

Synechocystis bidirectional hydrogenase genes (hoxEFUYH) and their putative promoter regions and transformed into E. coli. The hox genes were transcribed in the E. coli cells carrying the vector construct of pCCIFOS::phox::hox or pCCIFOS::pT7::hox and translated into HoxEFUYH proteins, suggesting that the putative hox promoter can be constitutively activated in E. coli. Accordingly, the total hydrogenase activity was markedly increased up to 192% or 169% in the transformed cells, while the hydrogen uptake was decreased up to about 30% of the negative control. Although the gene expression of LexA, the only one transcription regulator proven for the hox genes, was substantially decreased in the pCCIFOS::phox::hox cells after γ-irradiation of 30 Gy, the expression levels of HoxEFUYH proteins were not altered significantly. Thus, it is also suggested that other transcription regulators as well as LexA might contribute to activation of the hox promoter in E. coli

A novel endo-hydrogenase activity recycles hydrogen produced by nitrogen fixation.

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Gordon Ng

Full Text Available BACKGROUND: Nitrogen (N(2 fixation also yields hydrogen (H(2 at 1:1 stoichiometric amounts. In aerobic diazotrophic (able to grow on N(2 as sole N-source bacteria, orthodox respiratory hupSL-encoded hydrogenase activity, associated with the cell membrane but facing the periplasm (exo-hydrogenase, has nevertheless been presumed responsible for recycling such endogenous hydrogen. METHODS AND FINDINGS: As shown here, for Azorhizobium caulinodans diazotrophic cultures open to the atmosphere, exo-hydrogenase activity is of no consequence to hydrogen recycling. In a bioinformatic analysis, a novel seven-gene A. caulinodans hyq cluster encoding an integral-membrane, group-4, Ni,Fe-hydrogenase with homology to respiratory complex I (NADH: quinone dehydrogenase was identified. By analogy, Hyq hydrogenase is also integral to the cell membrane, but its active site faces the cytoplasm (endo-hydrogenase. An A. caulinodans in-frame hyq operon deletion mutant, constructed by "crossover PCR", showed markedly decreased growth rates in diazotrophic cultures; normal growth was restored with added ammonium--as expected of an H(2-recycling mutant phenotype. Using A. caulinodans hyq merodiploid strains expressing beta-glucuronidase as promoter-reporter, the hyq operon proved strongly and specifically induced in diazotrophic culture; as well, hyq operon induction required the NIFA transcriptional activator. Therefore, the hyq operon is constituent of the nif regulon. CONCLUSIONS: Representative of aerobic N(2-fixing and H(2-recycling alpha-proteobacteria, A. caulinodans possesses two respiratory Ni,Fe-hydrogenases: HupSL exo-hydrogenase activity drives exogenous H(2 respiration, and Hyq endo-hydrogenase activity recycles endogenous H(2, specifically that produced by N(2 fixation. To benefit human civilization, H(2 has generated considerable interest as potential renewable energy source as its makings are ubiquitous and its combustion yields no greenhouse gases. As

A novel endo-hydrogenase activity recycles hydrogen produced by nitrogen fixation.

Science.gov (United States)

Ng, Gordon; Tom, Curtis G S; Park, Angela S; Zenad, Lounis; Ludwig, Robert A

2009-01-01

Nitrogen (N(2)) fixation also yields hydrogen (H(2)) at 1:1 stoichiometric amounts. In aerobic diazotrophic (able to grow on N(2) as sole N-source) bacteria, orthodox respiratory hupSL-encoded hydrogenase activity, associated with the cell membrane but facing the periplasm (exo-hydrogenase), has nevertheless been presumed responsible for recycling such endogenous hydrogen. As shown here, for Azorhizobium caulinodans diazotrophic cultures open to the atmosphere, exo-hydrogenase activity is of no consequence to hydrogen recycling. In a bioinformatic analysis, a novel seven-gene A. caulinodans hyq cluster encoding an integral-membrane, group-4, Ni,Fe-hydrogenase with homology to respiratory complex I (NADH: quinone dehydrogenase) was identified. By analogy, Hyq hydrogenase is also integral to the cell membrane, but its active site faces the cytoplasm (endo-hydrogenase). An A. caulinodans in-frame hyq operon deletion mutant, constructed by "crossover PCR", showed markedly decreased growth rates in diazotrophic cultures; normal growth was restored with added ammonium--as expected of an H(2)-recycling mutant phenotype. Using A. caulinodans hyq merodiploid strains expressing beta-glucuronidase as promoter-reporter, the hyq operon proved strongly and specifically induced in diazotrophic culture; as well, hyq operon induction required the NIFA transcriptional activator. Therefore, the hyq operon is constituent of the nif regulon. Representative of aerobic N(2)-fixing and H(2)-recycling alpha-proteobacteria, A. caulinodans possesses two respiratory Ni,Fe-hydrogenases: HupSL exo-hydrogenase activity drives exogenous H(2) respiration, and Hyq endo-hydrogenase activity recycles endogenous H(2), specifically that produced by N(2) fixation. To benefit human civilization, H(2) has generated considerable interest as potential renewable energy source as its makings are ubiquitous and its combustion yields no greenhouse gases. As such, the reversible, group-4 Ni,Fe-hydrogenases, such

Improved hydrogen production by uptake hydrogenase deficient mutant strain of Rhodobacter sphaeroides O.U.001

Energy Technology Data Exchange (ETDEWEB)

Kars, Goekhan; Guenduez, Ufuk; Yuecel, Meral [Department of Biological Sciences, Middle East Technical University, 06531 Ankara (Turkey); Rakhely, Gabor; Kovacs, Kornel L. [Institute of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, Szeged (Hungary); Eroglu, Inci [Department of Chemical Engineering, Middle East Technical University, 06531 Ankara (Turkey)

2008-06-15

Rhodobacter sphaeroides O.U.001 is a purple non-sulfur bacterium producing hydrogen under photoheterotrophic conditions. Hydrogen is produced by Mo-nitrogenase enzyme and substantial amount of H{sub 2} is reoxidized by a membrane-bound uptake hydrogenase in the wild type strain. To improve the hydrogen producing capacity of the cells, a suicide vector containing a gentamicin cassette in the hupSL genes was introduced into R. sphaeroiodes O.U.001 and the uptake hydrogenase genes were destroyed by site directed mutagenesis. The correct integration of the construct was confirmed by uptake hydrogenase activity measurement, PCR and subsequent sequence analysis. The wild type and the mutant cells showed similar growth patterns but the total volume of hydrogen gas evolved by the mutant was 20% higher than that of the wild type strain. This result demonstrated that the hydrogen produced by the nitrogenase was not consumed by uptake hydrogenase leading to higher hydrogen production. (author)

A hydrogen-producing, hydrogenase-free mutant strain of Nostoc punctiforme ATCC 29133

Energy Technology Data Exchange (ETDEWEB)

Lindberg, P.; Lindblad, P. [Uppsala Univ. (Sweden). Dept. of Physiological Botany; Schuetz, K.; Happe, T. [Universitaet Bonn (Germany). Botanisches Inst.

2002-12-01

The hupL gene, encoding the uptake hydrogenase large subunit, in Nostoc sp. strain ATCC 29133, a strain lacking a bidirectional hydrogenase, was inactivated by insertional mutagenesis. Recombinant strains were isolated and analysed, and one hupL{sup -} strain, NHM5, was selected for further study. Cultures of NHM5 were grown under nitrogen-fixing conditions and H{sub 2} evolution under air was observed using an H{sub 2} electrode. (Author)

Production of biohydrogen by recombinant expression of [NiFe]-hydrogenase 1 in Escherichia coli

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Kim Jaoon YH

2010-07-01

Full Text Available Abstract Background Hydrogenases catalyze reversible reaction between hydrogen (H2 and proton. Inactivation of hydrogenase by exposure to oxygen is a critical limitation in biohydrogen production since strict anaerobic conditions are required. While [FeFe]-hydrogenases are irreversibly inactivated by oxygen, it was known that [NiFe]-hydrogenases are generally more tolerant to oxygen. The physiological function of [NiFe]-hydrogenase 1 is still ambiguous. We herein investigated the H2 production potential of [NiFe]-hydrogenase 1 of Escherichia coli in vivo and in vitro. The hyaA and hyaB genes corresponding to the small and large subunits of [NiFe]-hydrogenase 1 core enzyme, respectively, were expressed in BL21, an E. coli strain without H2 producing ability. Results Recombinant BL21 expressing [NiFe]-hydrogenase 1 actively produced H2 (12.5 mL H2/(h·L in 400 mL glucose minimal medium under micro-aerobic condition, whereas the wild type BL21 did not produce H2 even when formate was added as substrate for formate hydrogenlyase (FHL pathway. The majority of recombinant protein was produced as an insoluble form, with translocation of a small fraction to the membrane. However, the membrane fraction displayed high activity (~65% of total cell fraction, based on unit protein mass. Supplement of nickel and iron to media showed these metals contribute essentially to the function of [NiFe]-hydrogenase 1 as components of catalytic site. In addition, purified E. coli [NiFe]-hydrogenase 1 using his6-tag displayed oxygen-tolerant activity of ~12 nmol H2/(min·mg protein under a normal aeration environment, compared to [FeFe]-hydrogenase, which remains inactive under this condition. Conclusions This is the first report on physiological function of E. coli [NiFe]-hydrogenase 1 for H2 production. We found that [NiFe]-hydrogenase 1 has H2 production ability even under the existence of oxygen. This oxygen-tolerant property is a significant advantage because it is

Photoinduced reduction of the medial FeS center in the hydrogenase small subunit HupS from Nostoc punctiforme.

Science.gov (United States)

Raleiras, Patrícia; Hammarström, Leif; Lindblad, Peter; Styring, Stenbjörn; Magnuson, Ann

2015-07-01

The small subunit from the NiFe uptake hydrogenase, HupSL, in the cyanobacterium Nostoc punctiforme ATCC 29133, has been isolated in the absence of the large subunit (P. Raleiras, P. Kellers, P. Lindblad, S. Styring, A. Magnuson, J. Biol. Chem. 288 (2013) 18,345-18,352). Here, we have used flash photolysis to reduce the iron-sulfur clusters in the isolated small subunit, HupS. We used ascorbate as electron donor to the photogenerated excited state of Ru(II)-trisbipyridine (Ru(bpy)3), to generate Ru(I)(bpy)3 as reducing agent. Our results show that the isolated small subunit can be reduced by the Ru(I)(bpy)3 generated through flash photolysis. Copyright © 2015 Elsevier Inc. All rights reserved.

Advances in the Function and Regulation of Hydrogenase in the Cyanobacterium Synechocystis PCC6803

Science.gov (United States)

Cassier-Chauvat, Corinne; Veaudor, Théo; Chauvat, Franck

2014-01-01

In order to use cyanobacteria for the biological production of hydrogen, it is important to thoroughly study the function and the regulation of the hydrogen-production machine in order to better understand its role in the global cell metabolism and identify bottlenecks limiting H2 production. Most of the recent advances in our understanding of the bidirectional [Ni-Fe] hydrogenase (Hox) came from investigations performed in the widely-used model cyanobacterium Synechocystis PCC6803 where Hox is the sole enzyme capable of combining electrons with protons to produce H2 under specific conditions. Recent findings suggested that the Hox enzyme can receive electrons from not only NAD(P)H as usually shown, but also, or even preferentially, from ferredoxin. Furthermore, plasmid-encoded functions and glutathionylation (the formation of a mixed-disulfide between the cysteines residues of a protein and the cysteine residue of glutathione) are proposed as possible new players in the function and regulation of hydrogen production. PMID:25365180

Diversity and transcription of proteases involved in the maturation of hydrogenases in Nostoc punctiforme ATCC 29133 and Nostoc sp. strain PCC 7120

Science.gov (United States)

2009-01-01

Background The last step in the maturation process of the large subunit of [NiFe]-hydrogenases is a proteolytic cleavage of the C-terminal by a hydrogenase specific protease. Contrary to other accessory proteins these hydrogenase proteases are believed to be specific whereby one type of hydrogenases specific protease only cleaves one type of hydrogenase. In cyanobacteria this is achieved by the gene product of either hupW or hoxW, specific for the uptake or the bidirectional hydrogenase respectively. The filamentous cyanobacteria Nostoc punctiforme ATCC 29133 and Nostoc sp strain PCC 7120 may contain a single uptake hydrogenase or both an uptake and a bidirectional hydrogenase respectively. Results In order to examine these proteases in cyanobacteria, transcriptional analyses were performed of hupW in Nostoc punctiforme ATCC 29133 and hupW and hoxW in Nostoc sp. strain PCC 7120. These studies revealed numerous transcriptional start points together with putative binding sites for NtcA (hupW) and LexA (hoxW). In order to investigate the diversity and specificity among hydrogeanse specific proteases we constructed a phylogenetic tree which revealed several subgroups that showed a striking resemblance to the subgroups previously described for [NiFe]-hydrogenases. Additionally the proteases specificity was also addressed by amino acid sequence analysis and protein-protein docking experiments with 3D-models derived from bioinformatic studies. These studies revealed a so called "HOXBOX"; an amino acid sequence specific for protease of Hox-type which might be involved in docking with the large subunit of the hydrogenase. Conclusion Our findings suggest that the hydrogenase specific proteases are under similar regulatory control as the hydrogenases they cleave. The result from the phylogenetic study also indicates that the hydrogenase and the protease have co-evolved since ancient time and suggests that at least one major horizontal gene transfer has occurred. This co

Diversity and transcription of proteases involved in the maturation of hydrogenases in Nostoc punctiforme ATCC 29133 and Nostoc sp. strain PCC 7120

Directory of Open Access Journals (Sweden)

Lindblad Peter

2009-03-01

Full Text Available Abstract Background The last step in the maturation process of the large subunit of [NiFe]-hydrogenases is a proteolytic cleavage of the C-terminal by a hydrogenase specific protease. Contrary to other accessory proteins these hydrogenase proteases are believed to be specific whereby one type of hydrogenases specific protease only cleaves one type of hydrogenase. In cyanobacteria this is achieved by the gene product of either hupW or hoxW, specific for the uptake or the bidirectional hydrogenase respectively. The filamentous cyanobacteria Nostoc punctiforme ATCC 29133 and Nostoc sp strain PCC 7120 may contain a single uptake hydrogenase or both an uptake and a bidirectional hydrogenase respectively. Results In order to examine these proteases in cyanobacteria, transcriptional analyses were performed of hupW in Nostoc punctiforme ATCC 29133 and hupW and hoxW in Nostoc sp. strain PCC 7120. These studies revealed numerous transcriptional start points together with putative binding sites for NtcA (hupW and LexA (hoxW. In order to investigate the diversity and specificity among hydrogeanse specific proteases we constructed a phylogenetic tree which revealed several subgroups that showed a striking resemblance to the subgroups previously described for [NiFe]-hydrogenases. Additionally the proteases specificity was also addressed by amino acid sequence analysis and protein-protein docking experiments with 3D-models derived from bioinformatic studies. These studies revealed a so called "HOXBOX"; an amino acid sequence specific for protease of Hox-type which might be involved in docking with the large subunit of the hydrogenase. Conclusion Our findings suggest that the hydrogenase specific proteases are under similar regulatory control as the hydrogenases they cleave. The result from the phylogenetic study also indicates that the hydrogenase and the protease have co-evolved since ancient time and suggests that at least one major horizontal gene transfer

Properties of hydrogenase from Megasphaera elsdenii

NARCIS (Netherlands)

Dijk, van C.

1980-01-01

This thesis is concerned with the purification and properties of hydrogenase from the obligate anaerobic rumen bacterium Megasphaera elsdenii. In chapter 1 the motives underlying this thesis, the physiological role of hydrogenase in some heterotrophs, including

Methanogenesis and methane genes

International Nuclear Information System (INIS)

Reeve, J.N.; Shref, B.A.

1991-01-01

An overview of the pathways leading to methane biosynthesis is presented. The steps investigated to date by gene cloning and DNA sequencing procedures are identified and discussed. The primary structures of component C of methyl coenzyme M reductase encoded by mcr operons in different methanogens are compared. Experiments to detect the primary structure of the genes encoding F420 reducing hydrogenase (frhABG) and methyl hydrogen reducing hydrogenase (mvhDGA) in methanobacterium thermoautotrophicum strain H are compared with each other and with eubacterial hydrogenase encoding genes. A biotechnological use for hydrogenases from hypermorphillic archaebacteria is suggested. (author)

Cloning, sequence determination, and expression of the genes encoding the subunits of the nickel-containing 8-hydroxy-5-deazaflavin reducing hydrogenase from Methanobacterium thermoautotrophicum ΔH

International Nuclear Information System (INIS)

Alex, L.A.; Reeve, J.N.; Orme-Johnson, W.H.; Walsh, C.T.

1990-01-01

The genes frhA (1,217 bp), frhB (845 bp), and frhG (710 bp) encoding the three known subunits, α, β, and γ, of the 8-hydroxy-5-deazaflavin (F 420 ) reducing hydrogenase (FRH) from the thermophilic methanogen Methanobacterium thermoautotrophicum ΔH have been cloned, sequenced, and shown to be tightly linked, indicative of a single transcriptional unit. The DNA sequence contains a fourth open reading frame, designated frhD (476 bp), encoding a polypeptide (δ) that does not copurify with the active enzyme. Expression of the frh gene cluster in Escherichia coli shows that four polypeptides are synthesized. When analyzed by SDS-PAGE, the proteins migrate with mobilities consistent with their calculated molecular weights. In order to understand the mechanism of H 2 oxidation by this enzyme, localization of redox cofactors (Ni, Fe/S, FAD) to specific subunits and information on their structure is needed. This has been hindered due to the refractory nature of the enzyme to denaturation methods needed in order to obtain individual subunits with cofactors intact. In this paper they discuss the possible localization of the redox cofactors as implicated from the DNA-derived protein sequences of the subunits. The amino acid sequences of the subunits of the FRH are compared with those of other Ni-containing hydrogenases, including the methyl viologen reducing hydrogenase (MVH) of M. thermoautotrophicum ΔH

[Fe]-hydrogenases in green algae: photo-fermentation and hydrogen evolution under sulfur deprivation

Energy Technology Data Exchange (ETDEWEB)

Winkler, M.; Hemschemeier, A.; Happe, T. [Botanisches Institut der Universitat Bonn (Germany); Gotor, C. [CSIC y Universidad de Sevilla (Spain). Instituto de Bioquimica Vegetal y Fotosintesis; Melis, A. [University of California, Berkeley, CA (United States). Department of Plant and Microbial Biology

2002-12-01

Recent studies indicate that [Fe]-hydrogenases and H{sub 2} metabolism are widely distributed among green algae. The enzymes are simple structured and catalyze H{sub 2} evolution with similar rates than the more complex [Fe]-hydrogenases from bacteria. Different green algal species developed diverse strategies to survive under sulfur deprivation. Chlamydomonas reinhardtii evolves large quantities of hydrogen gas in the absence of sulfur. In a sealed culture of C. reinhardtii, the photosynthetic O{sub 2} evolution rate drops below the rate of respiratory O{sub 2} consumption due to a reversible inhibition of photosystem II, thus leading to an intracellular anaerobiosis. The algal cells survive under these anaerobic conditions by switching their metabolism to a kind of photo-fermentation. Although possessing a functional [Fe]-hydrogenase gene, the cells of Scenedesmus obliquus produce no significant amounts of H{sub 2} under S-depleted conditions. Biochemical analyses indicate that S. obliquus decreases almost the complete metabolic activities while maintaining a low level of respiratory activity. (author)

Transcription and Regulation of the Bidirectional Hydrogenase in the Cyanobacterium Nostoc sp. Strain PCC 7120▿

Science.gov (United States)

Sjöholm, Johannes; Oliveira, Paulo; Lindblad, Peter

2007-01-01

The filamentous, heterocystous cyanobacterium Nostoc sp. strain PCC 7120 (Anabaena sp. strain PCC 7120) possesses an uptake hydrogenase and a bidirectional enzyme, the latter being capable of catalyzing both H2 production and evolution. The completely sequenced genome of Nostoc sp. strain PCC 7120 reveals that the five structural genes encoding the bidirectional hydrogenase (hoxEFUYH) are separated in two clusters at a distance of approximately 8.8 kb. The transcription of the hox genes was examined under nitrogen-fixing conditions, and the results demonstrate that the cluster containing hoxE and hoxF can be transcribed as one polycistronic unit together with the open reading frame alr0750. The second cluster, containing hoxU, hoxY, and hoxH, is transcribed together with alr0763 and alr0765, located between the hox genes. Moreover, alr0760 and alr0761 form an additional larger operon. Nevertheless, Northern blot hybridizations revealed a rather complex transcription pattern in which the different hox genes are expressed differently. Transcriptional start points (TSPs) were identified 66 and 57 bp upstream from the start codon of alr0750 and hoxU, respectively. The transcriptions of the two clusters containing the hox genes are both induced under anaerobic conditions concomitantly with the induction of a higher level of hydrogenase activity. An additional TSP, within the annotated alr0760, 244 bp downstream from the suggested translation start codon, was identified. Electrophoretic mobility shift assays with purified LexA from Nostoc sp. strain PCC 7120 demonstrated specific interactions between the transcriptional regulator and both hox promoter regions. However, when LexA from Synechocystis sp. strain PCC 6803 was used, the purified protein interacted only with the promoter region of the alr0750-hoxE-hoxF operon. A search of the whole Nostoc sp. strain PCC 7120 genome demonstrated the presence of 216 putative LexA binding sites in total, including recA and rec

New hypotheses for hydrogenase implication in the corrosion of mild steel

Energy Technology Data Exchange (ETDEWEB)

Mehanna, Maha; Basseguy, Regine; Delia, Marie-Line [Laboratoire de Genie Chimique (LGC) CNRS-INPT, 5 rue Paulin Talabot BP 1301, 31106 Toulouse (France); Girbal, Laurence; Demuez, Marie [Laboratoire d' Ingenierie des Systemes Biologiques et des Procedes (LISBP) CNRS-INSA, 135 Avenue de Rangueil, 31077 Toulouse (France); Bergel, Alain [Laboratoire de Genie Chimique (LGC) CNRS-INPT, 5 rue Paulin Talabot BP 1301, 31106 Toulouse (France)], E-mail: Alain.Bergel@ensiacet.fr

2008-12-01

The influence of [Fe]-hydrogenase from Clostridium acetobutylicum was studied on the anaerobic corrosion of mild steel. Two short-circuited mild steel electrodes were exposed to the same solution and hydrogenase was retained on the surface of only one electrode thanks to a dialysis membrane. The galvanic current and the electrode potential were measured as a function of time in order to monitor the difference in electrochemical behaviour induced by the presence of hydrogenase. A sharp potential decrease of around 500 mV was controlled by the deoxygenating phase. When hydrogenase was introduced after complete deoxygenation, significant heterogeneous corrosion was observed under the vivianite deposit on the electrode in contact with hydrogenase, while the other electrode only showed the vivianite deposit, which was analysed by MEB and EDX. The effect of hydrogenase was then confirmed by monitoring the free potential of single coupons exposed or not to the enzyme in a classical cell after complete deoxygenating. In both phosphate and Tris-HCl buffers, the presence of hydrogenase increased the free potential around 60 mV and induced marked general corrosion. It was concluded that [Fe]-hydrogenase acts in the absence of any final electron acceptor by catalysing direct proton reduction on the mild steel surface.

New hypotheses for hydrogenase implication in the corrosion of mild steel

International Nuclear Information System (INIS)

Mehanna, Maha; Basseguy, Regine; Delia, Marie-Line; Girbal, Laurence; Demuez, Marie; Bergel, Alain

2008-01-01

The influence of [Fe]-hydrogenase from Clostridium acetobutylicum was studied on the anaerobic corrosion of mild steel. Two short-circuited mild steel electrodes were exposed to the same solution and hydrogenase was retained on the surface of only one electrode thanks to a dialysis membrane. The galvanic current and the electrode potential were measured as a function of time in order to monitor the difference in electrochemical behaviour induced by the presence of hydrogenase. A sharp potential decrease of around 500 mV was controlled by the deoxygenating phase. When hydrogenase was introduced after complete deoxygenation, significant heterogeneous corrosion was observed under the vivianite deposit on the electrode in contact with hydrogenase, while the other electrode only showed the vivianite deposit, which was analysed by MEB and EDX. The effect of hydrogenase was then confirmed by monitoring the free potential of single coupons exposed or not to the enzyme in a classical cell after complete deoxygenating. In both phosphate and Tris-HCl buffers, the presence of hydrogenase increased the free potential around 60 mV and induced marked general corrosion. It was concluded that [Fe]-hydrogenase acts in the absence of any final electron acceptor by catalysing direct proton reduction on the mild steel surface

Inhibition of hydrogenase synthesis by DNA gyrase inhibitors in Bradyrhizobium japonicum

International Nuclear Information System (INIS)

Novak, P.D.; Maier, R.J.

1987-01-01

Derepression of an uptake hydrogenase in Bradyrhizobium japonicum is dependent on a microaerophilic environment. Addition of DNA gyrase inhibitors during derepression of hydrogenase specifically prevented expression of the hydrogenase enzyme. Antibodies to individual hydrogenase subunits failed to detect the protein after derepression in the presence of inhibitors, although there was no general inhibition of protein synthesis. The general pattern of proteins synthesized from 14 C-labeled amino acids during derepression was no significantly different whether proteins were labeled in the presence or in the absence of gyrase inhibitors. In contrast, if transcription or translation was inhibited by addition of inhibitors of those functions, virtually no proteins were labeled during derepression. This indicated that most of the 14 C-labeled proteins were synthesized de novo during derepression, synthesis of most proteins was unaffected by gyrase inhibitors, and the dependence of hydrogenase synthesis on gyrase activity was a specific one

Molecular cloning, characterization, and overexpression of a novel [Fe]-hydrogenase isolated from a high rate of hydrogen producing Enterobacter cloacae IIT-BT 08

International Nuclear Information System (INIS)

Mishra, Jayshree; Khurana, Seema; Kumar, Narendra; Ghosh, Ananta K.; Das, Debabrata

2004-01-01

Degenerate primers were designed from the conserved zone of hydA structural gene encoding for catalytic subunit of [Fe]-hydrogenase of different hydrogen producing bacteria. A 750 bp of PCR product was amplified by using the above-mentioned degenerate primers and genomic DNA of Enterobacter cloacae IIT-BT 08 as template. The amplified PCR product was cloned and sequenced. The sequence showed the presence of an ORF of 450 bp with significant similarity (40%) with C-terminal end of the conserved zone (H-cluster) of [Fe]- hydrogenase. hydA ORF was then amplified and cloned in-frame with GST in pGEX4T-1 and overexpressed in a non-hydrogen producing Escherichia coli BL-21 to produce a GST-fusion protein of a calculated molecular mass of about 42.1 kDa. Recombinant protein was purified and specifically recognized by anti-GST monoclonal antibody through Western blot. Southern hybridization confirmed the presence of this gene in E. cloacae IIT-BT 08 genome. In vitro hydrogenase assay with the overexpressed hydrogenase enzyme showed that it is catalytically active upon anaerobic adaptation. In vivo hydrogenase assay confirmed the presence of H 2 gas in the gas mixture obtained from the batch culture of recombinant E. coli BL-21. A tentative molecular mechanism has been proposed about the transfer of electron from electron donor to H-cluster without the mediation of the F-cluster

Chemistry and the iron - only hydrogenase

International Nuclear Information System (INIS)

Tard, C.; Razavet, M.; Liu, X.; Ibrahim, S.; Pickett, Ch.

2005-01-01

Complete text of publication follows: Chemistry related to the hydrogenases is developing very rapidly and providing some informative insights into how the biological systems might function. Although still very much at a blue skies stage, there is some prospect for the design of artificial assemblies, materials and devices with technological application for hydrogen production/uptake provided robust system can be designed with low over potentials for hydrogen/proton interconversion (1). The iron-only hydrogenase possesses a peculiar di-iron unit coordinated by CO and CN, ligands which are normally associated with poisoning biological function. This sub-site unit is attached to a [4Fe4S] cubane center to form the catalytic site of the hydrogenase which is known as the 'H-cluster'. The synthesis of artificial sub-sites will first be described together with how their structures, spectroscopy and reactivity provides some key insights into the natural system viz. unprecedented bridging carbonyl and Fe(I) motifs in biology (2-4). How we have approached putting together the entire iron-sulfur framework of the H-cluster will then be described together with its electron-transfer and electrocatalytic properties (4). Finally, I will describe some early work on how we are beginning to incorporate structural motifs of the active-site into conducting polymer matrices, how they function as (albeit poor) electrocatalysts for hydrogen evolution, and where we see the way ahead. (1)The Chemistry and the Hydrogenases. D.J. Evans and C.J. Pickett, Chem. Soc. Rev., 32, 268-275, 2003; (2)Electron-Transfer at a Di-thiolate-Bridged Di-Iron Assembly; Electrocatalytic Hydrogen Evolution. S.J. Borg, T. Behrsing and S.P. Best, M. Ravazet, X. Liu and C.J. Pickett, J Amer. Chem. Soc., 2004, 126, 509-533; (3) Dissecting the intimate mechanism of cyanation of [Fe2S3] complexes related to the active site of all-iron hydrogenases by DFT analysis of energetics, transition states, intermediates and

Syngas fermentation to biofuels: Effects of hydrogen partial pressure on hydrogenase efficiency

International Nuclear Information System (INIS)

Skidmore, Bradley E.; Baker, Ryan A.; Banjade, Dila R.; Bray, Jason M.; Tree, Douglas R.; Lewis, Randy S.

2013-01-01

Producing biofuels from gasified biomass (synthesis gas) via microbial fermentation is currently being pursued as one alternative in biofuels development. In synthesis gas fermentation, reducing equivalents from H 2 oxidation via hydrogenase is important towards directing more carbon towards product formation. In this work, kinetic studies of H 2 utilization via the Clostridium P11 hydrogenase enzyme were performed to determine the most appropriate model to predict hydrogenase activity as a function of H 2 partial pressure. An important aspect of this work included the proper analysis of electron acceptors used in the kinetic studies. The K H 2 model parameter governing the effect of H 2 partial pressure on activity was ∼30 kPa (absolute), independent of the type and concentration of electron acceptor. The K H 2 value indicates that H 2 partial pressures typically associated with syngas fermentation will result in compromised efficiency of the hydrogenase activity. -- Highlights: ► We model hydrogenase activity as a function of H 2 and electron acceptors. ► Model shows the H 2 kinetic parameter is independent of electron acceptor. ► Hydrogenase efficiency is compromised at H 2 levels observed in gasified biomass

The Physiological Functions and Structural Determinants of Catalytic Bias in the [FeFe]-Hydrogenases CpI and CpII of Clostridium pasteurianum Strain W5

Directory of Open Access Journals (Sweden)

Jesse B. Therien

2017-07-01

Full Text Available The first generation of biochemical studies of complex, iron-sulfur-cluster-containing [FeFe]-hydrogenases and Mo-nitrogenase were carried out on enzymes purified from Clostridium pasteurianum (strain W5. Previous studies suggested that two distinct [FeFe]-hydrogenases are expressed differentially under nitrogen-fixing and non-nitrogen-fixing conditions. As a result, the first characterized [FeFe]-hydrogenase (CpI is presumed to have a primary role in central metabolism, recycling reduced electron carriers that accumulate during fermentation via proton reduction. A role for capturing reducing equivalents released as hydrogen during nitrogen fixation has been proposed for the second hydrogenase, CpII. Biochemical characterization of CpI and CpII indicated CpI has extremely high hydrogen production activity in comparison to CpII, while CpII has elevated hydrogen oxidation activity in comparison to CpI when assayed under the same conditions. This suggests that these enzymes have evolved a catalytic bias to support their respective physiological functions. Using the published genome of C. pasteurianum (strain W5 hydrogenase sequences were identified, including the already known [NiFe]-hydrogenase, CpI, and CpII sequences, and a third hydrogenase, CpIII was identified in the genome as well. Quantitative real-time PCR experiments were performed in order to analyze transcript abundance of the hydrogenases under diazotrophic and non-diazotrophic growth conditions. There is a markedly reduced level of CpI gene expression together with concomitant increases in CpII gene expression under nitrogen-fixing conditions. Structure-based analyses of the CpI and CpII sequences reveal variations in their catalytic sites that may contribute to their alternative physiological roles. This work demonstrates that the physiological roles of CpI and CpII are to evolve and to consume hydrogen, respectively, in concurrence with their catalytic activities in vitro, with Cp

The Physiological Functions and Structural Determinants of Catalytic Bias in the [FeFe]-Hydrogenases CpI and CpII of Clostridium pasteurianum Strain W5

Science.gov (United States)

Therien, Jesse B.; Artz, Jacob H.; Poudel, Saroj; Hamilton, Trinity L.; Liu, Zhenfeng; Noone, Seth M.; Adams, Michael W. W.; King, Paul W.; Bryant, Donald A.; Boyd, Eric S.; Peters, John W.

2017-01-01

The first generation of biochemical studies of complex, iron-sulfur-cluster-containing [FeFe]-hydrogenases and Mo-nitrogenase were carried out on enzymes purified from Clostridium pasteurianum (strain W5). Previous studies suggested that two distinct [FeFe]-hydrogenases are expressed differentially under nitrogen-fixing and non-nitrogen-fixing conditions. As a result, the first characterized [FeFe]-hydrogenase (CpI) is presumed to have a primary role in central metabolism, recycling reduced electron carriers that accumulate during fermentation via proton reduction. A role for capturing reducing equivalents released as hydrogen during nitrogen fixation has been proposed for the second hydrogenase, CpII. Biochemical characterization of CpI and CpII indicated CpI has extremely high hydrogen production activity in comparison to CpII, while CpII has elevated hydrogen oxidation activity in comparison to CpI when assayed under the same conditions. This suggests that these enzymes have evolved a catalytic bias to support their respective physiological functions. Using the published genome of C. pasteurianum (strain W5) hydrogenase sequences were identified, including the already known [NiFe]-hydrogenase, CpI, and CpII sequences, and a third hydrogenase, CpIII was identified in the genome as well. Quantitative real-time PCR experiments were performed in order to analyze transcript abundance of the hydrogenases under diazotrophic and non-diazotrophic growth conditions. There is a markedly reduced level of CpI gene expression together with concomitant increases in CpII gene expression under nitrogen-fixing conditions. Structure-based analyses of the CpI and CpII sequences reveal variations in their catalytic sites that may contribute to their alternative physiological roles. This work demonstrates that the physiological roles of CpI and CpII are to evolve and to consume hydrogen, respectively, in concurrence with their catalytic activities in vitro, with CpII capturing excess

Turning cellulose waste into electricity: hydrogen conversion by a hydrogenase electrode.

Directory of Open Access Journals (Sweden)

Sergey M Abramov

Full Text Available Hydrogen-producing thermophilic cellulolytic microorganisms were isolated from cow faeces. Rates of cellulose hydrolysis and hydrogen formation were 0.2 mM L(-1 h(-1 and 1 mM L(-1 h(-1, respectively. An enzymatic fuel cell (EFC with a hydrogenase anode was used to oxidise hydrogen produced in a microbial bioreactor. The hydrogenase electrode was exposed for 38 days (912 h to a thermophilic fermentation medium. The hydrogenase activity remaining after continuous operation under load was 73% of the initial value.

Turning Cellulose Waste Into Electricity: Hydrogen Conversion by a Hydrogenase Electrode

Science.gov (United States)

Abramov, Sergey M.; Sadraddinova, Elmira R.; Shestakov, Andrey I.; Voronin, Oleg G.; Karyakin, Arkadiy A.; Zorin, Nikolay A.; Netrusov, Alexander I.

2013-01-01

Hydrogen-producing thermophilic cellulolytic microorganisms were isolated from cow faeces. Rates of cellulose hydrolysis and hydrogen formation were 0.2 mM L-1 h-1 and 1 mM L-1 h-1, respectively. An enzymatic fuel cell (EFC) with a hydrogenase anode was used to oxidise hydrogen produced in a microbial bioreactor. The hydrogenase electrode was exposed for 38 days (912 h) to a thermophilic fermentation medium. The hydrogenase activity remaining after continuous operation under load was 73% of the initial value. PMID:24312437

Oxygen limitation modulates pH regulation of catabolism and hydrogenases, multidrug transporters, and envelope composition in Escherichia coli K-12

Directory of Open Access Journals (Sweden)

Radmacher Michael D

2006-10-01

Full Text Available Abstract Background In Escherichia coli, pH regulates genes for amino-acid and sugar catabolism, electron transport, oxidative stress, periplasmic and envelope proteins. Many pH-dependent genes are co-regulated by anaerobiosis, but the overall intersection of pH stress and oxygen limitation has not been investigated. Results The pH dependence of gene expression was analyzed in oxygen-limited cultures of E. coli K-12 strain W3110. E. coli K-12 strain W3110 was cultured in closed tubes containing LBK broth buffered at pH 5.7, pH 7.0, and pH 8.5. Affymetrix array hybridization revealed pH-dependent expression of 1,384 genes and 610 intergenic regions. A core group of 251 genes showed pH responses similar to those in a previous study of cultures grown with aeration. The highly acid-induced gene yagU was shown to be required for extreme-acid resistance (survival at pH 2. Acid also up-regulated fimbriae (fimAC, periplasmic chaperones (hdeAB, cyclopropane fatty acid synthase (cfa, and the "constitutive" Na+/H+ antiporter (nhaB. Base up-regulated core genes for maltodextrin transport (lamB, mal, ATP synthase (atp, and DNA repair (recA, mutL. Other genes showed opposite pH responses with or without aeration, for example ETS components (cyo,nuo, sdh and hydrogenases (hya, hyb, hyc, hyf, hyp. A hypF strain lacking all hydrogenase activity showed loss of extreme-acid resistance. Under oxygen limitation only, acid down-regulated ribosome synthesis (rpl,rpm, rps. Acid up-regulated the catabolism of sugar derivatives whose fermentation minimized acid production (gnd, gnt, srl, and also a cluster of 13 genes in the gadA region. Acid up-regulated drug transporters (mdtEF, mdtL, but down-regulated penicillin-binding proteins (dacACD, mreBC. Intergenic regions containing regulatory sRNAs were up-regulated by acid (ryeA, csrB, gadY, rybC. Conclusion pH regulates a core set of genes independently of oxygen, including yagU, fimbriae, periplasmic chaperones, and nha

Oxidation behavior of a Ni-Fe support in SOFC anode atmosphere

DEFF Research Database (Denmark)

Xu, Na; Chen, Ming; Han, Minfang

2018-01-01

In this work, we investigated the long-term oxidation behavior of a Ni-Fe (1:1 weight ratio) support for solid oxide fuel cell (SOFC) applications. Ni-Fe supports were obtained through tape casting, high temperature sintering and pre-reducing in 97% H2/N2 (9/91)-3% H2O at 750 and 1000 °C, respect...... annealed in the two atmospheres maintained sufficiently high conductivity. The results from the current work demonstrate that the porous Ni-Fe support can be well employed in SOFCs, especially metal-supported SOFCs....

A synthetic system links FeFe-hydrogenases to essential E. coli sulfur metabolism

Directory of Open Access Journals (Sweden)

Grandl Gerald

2011-05-01

Full Text Available Abstract Background FeFe-hydrogenases are the most active class of H2-producing enzymes known in nature and may have important applications in clean H2 energy production. Many potential uses are currently complicated by a crucial weakness: the active sites of all known FeFe-hydrogenases are irreversibly inactivated by O2. Results We have developed a synthetic metabolic pathway in E. coli that links FeFe-hydrogenase activity to the production of the essential amino acid cysteine. Our design includes a complementary host strain whose endogenous redox pool is insulated from the synthetic metabolic pathway. Host viability on a selective medium requires hydrogenase expression, and moderate O2 levels eliminate growth. This pathway forms the basis for a genetic selection for O2 tolerance. Genetically selected hydrogenases did not show improved stability in O2 and in many cases had lost H2 production activity. The isolated mutations cluster significantly on charged surface residues, suggesting the evolution of binding surfaces that may accelerate hydrogenase electron transfer. Conclusions Rational design can optimize a fully heterologous three-component pathway to provide an essential metabolic flux while remaining insulated from the endogenous redox pool. We have developed a number of convenient in vivo assays to aid in the engineering of synthetic H2 metabolism. Our results also indicate a H2-independent redox activity in three different FeFe-hydrogenases, with implications for the future directed evolution of H2-activating catalysts.

Inducible hydrogenase in cyanobacteria enhances N/sub 2/ fixation. [Nostoc, anabaena

Energy Technology Data Exchange (ETDEWEB)

Tel-Or, E.; Luijk, L.W.; Packer, L.

1977-06-01

Whether hydrogenase is activated or induced, we found no evidence for activation of either consumption or production of H/sub 2/ in aerobically-grown cultures but both of these activities increased 5--20-fold when cultures are grown under H/sub 2/ gas. On the other hand, hydrogenase-catalyzed consumption of H/sub 2/ is stimulated by light and/or light plus CO/sub 2/ in hydrogenase-induced cultures. Nitrogenase activity appears to be induced in cultures grown under H/sub 2/. Studies unambiguously establish that in H/sub 2/-induced cultures hydrogenase manifests a cooperativity with nitrogenase. In the presence of H/sub 2/ the activity of nitrogenase is stimulated 3--5-fold such that rates of about 3 ..mu..mol N/sub 2/ fixed/mg chlorophyll/h are obtained if the method of Peterson and Burris is used to convert acetylene reduction data to equivalents of /sup 15/N/sub 2/ fixation to ammonia.

Studies on polyethylene glycol coating on NiFe2O4 nanoparticles for biomedical applications

International Nuclear Information System (INIS)

Phadatare, M.R.; Khot, V.M.; Salunkhe, A.B.; Thorat, N.D.; Pawar, S.H.

2012-01-01

The NiFe 2 O 4 nanoparticles were prepared by the combustion method and these nanoparticles were successfully coated with polyethylene glycol (PEG) for the possible biomedical applications such as magnetic resonance imaging, drug delivery, tissue repair, magnetic fluid hyperthermia etc. The structural and magnetic characterizations of NiFe 2 O 4 nanoparticles were carried out by x-ray diffraction and vibrating sample magnetometry techniques, respectively. The morphology of the uncoated and coated nanoparticles was studied by scanning electron microscopy. The existence of PEG layer on NiFe 2 O 4 nanoparticles was confirmed by fourier transform infrared spectroscopy technique. - Highlights: ► Synthesis of nanocrystalline NiFe 2 O 4 by the combustion method. ► Magnetic properties of the NiFe 2 O 4 nanoparticles at room temperature. ► Coating of NiFe 2 O 4 nanoparticles by Polyethylene glycol (PEG).

A hydrogenosomal [Fe]-hydrogenase from the anaerobic chytrid Neocallimastix sp L2

NARCIS (Netherlands)

Voncken, Frank G.J.; Boxma, Brigitte; Hoek, Angela H.A.M. van; Akhmanova, Anna S.; Vogels, Godfried D.; Huynen, Martijn; Veenhuis, Marten; Hackstein, Johannes H.P.

2002-01-01

The presence of a [Fe]-hydrogenase in the hydrogenosomes of the anaerobic chytridiomycete fungus Neocallimastix sp. L2 has been demonstrated by immunocytochemistry, subcellular fractionation, Western-blotting, and measurements of hydrogenase activity in the presence of various concentrations of

Novel multifunctional NiFe_2O_4/ZnO hybrids for dye removal by adsorption, photocatalysis and magnetic separation

International Nuclear Information System (INIS)

Zhu, Hua-Yue; Jiang, Ru; Fu, Yong-Qian; Li, Rong-Rong; Yao, Jun; Jiang, Sheng-Tao

2016-01-01

Graphical abstract: - Highlights: • The NiFe_2O_4 was decorated on ZnO surface by a hydrothermal method. • NiFe_2O_4/ZnO hybrids show high adsorption capacity and excellent photostability. • The main active species in dye decolorization by NiFe_2O_4/ZnO hybrids are ·OH and h"+. • NiFe_2O_4/ZnO hybrids can be easily separated by an external magnet. - Abstract: Novel multifunctional NiFe_2O_4/ZnO hybrids were prepared by a hydrothermal method and their physicochemical properties were characterized by XRD, SEM, TEM, TGA, VSM, BET and UV–vis DRS. The adsorption and photocatalytic performance of NiFe_2O_4/ZnO hybrids were systematically investigated using congo red as a model contaminant. With the introduction of NiFe_2O_4, NiFe_2O_4/ZnO hybrids can absorb the whole light from 300 nm to 700 nm. The adsorption capacity (221.73 mg g"−"1) of NiFe_2O_4/ZnO hybrids is higher than those of NiFe_2O_4, ZnO and mechanically mixed NiFe_2O_4/ZnO hybrids. The removal of congo red solution (20 mg L"−"1) by NiFe_2O_4/ZnO hybrids was about 94.55% under simulated solar light irradiation for 10 min. ·OH and h"+ play important roles in the decolorization of congo red solution by NiFe_2O_4/ZnO hybrids under simulated solar light irradiation. The decolorization efficiency of congo red solution is 97.23% for the fifth time by NiFe_2O_4/ZnO hybrids under simulate solar light irradiation, indicating the high photostability and durability. NO_3"− and Cl"− anions which are ubiquitous components in dye-containing wastewater have negligible influence on the effectiveness of NiFe_2O_4/ZnO hybrids. Moreover, the magnetic NiFe_2O_4/ZnO hybrids can be easily separated from the reacted solution by an external magnet.

Hydrogenase activity in aged, nonviable Desulfovibrio vulgaris cultures and its significance in anaerobic biocorrosion.

Science.gov (United States)

Chatelus, C; Carrier, P; Saignes, P; Libert, M F; Berlier, Y; Lespinat, P A; Fauque, G; Legall, J

1987-01-01

Batch cultures of Desulfovibrio vulgaris stored at 32 degrees C for 10 months have been found to retain 50% of the hydrogenase activity of a 1-day culture. The hydrogenase found in old cultures needs reducing conditions for its activation. Viable cell counts are negative after 6 months, showing that the hydrogenase activity does not depend on the presence of viable cells. These observations are of importance in the understanding of anaerobic biocorrosion of metals caused by depolarization phenomena. PMID:3310883

Preparation and Characterization of Lecithin-Nano Ni/Fe for Effective Removal of PCB77

OpenAIRE

Shu Ding; Lin Zhao; Yun Qi; Qian-qian Lv

2014-01-01

A kind of combined material (named lecithin-nano Ni/Fe) that is composed of lecithin and nanoscale Ni/Fe bimetal was synthesized via microemulsion method. The efficacy of such an original material was tested using 3,3′,4,4′-tetrachlorobiphenyl (PCB77) as target pollutant. A microemulsion system was optimized as template to prepare Ni/Fe nanoparticles, which was followed by an insite loading process with the deposition of lecithin carrier. It was proved by the characterization that subtle Ni/F...

Magnetic properties of electroplated nano/microgranular NiFe thin films for rf application

NARCIS (Netherlands)

Zhuang, Y.; Vroubel, M.; Rejaei, B.; Burghartz, J.N.; Attenborough, K.

2005-01-01

A granular NiFe thin film with large in-plane magnetic anisotropy and high ferromagnetic-resonance frequency developed for radio-frequency integrated circuit (IC) applications is presented. During the deposition, three-dimensional (3D) growth occurs, yielding NiFe grains (? ? 1.0??m). Nanonuclei (?

Debromination of polybrominated diphenyl ethers by Ni/Fe bimetallic nanoparticles: Influencing factors, kinetics, and mechanism

International Nuclear Information System (INIS)

Fang Zhanqiang; Qiu Xinhong; Chen Jinhong; Qiu Xiuqi

2011-01-01

Polybrominated diphenyl ethers have been identified as a new class of organic pollutants with ecological risk due to their toxicity, bioaccumulation, and global distribution. Proper remediation technologies are needed to remove them from the environment. In this paper, Ni/Fe bimetallic nanoparticles were synthesized by chemical deposition and used to degrade decabromodiphenyl ether (BDE209). The characteristics of Ni/Fe nanoparticles were analyzed by transmission electron microscopy, X-ray diffractometry, X-ray photoelectron spectroscopy, and Brunnaer-Emmett-Teller surface area analysis. Ni/Fe bimetallic nanoparticles with diameters in the order of 20-50 nm could effectively degrade BDE209 in the solvent (tetrahydrofuran/water). Influence factors, such as Ni/Fe nanoparticle dosage, initial BDE209 concentration, and Ni loading, on the removal of BDE209 were studied. The results indicated that the degradation of BDE209 followed pseudo-first-order kinetics, and the degradation rate of BDE209 increased with increasing the amount of nano Ni/Fe particles, Ni/Fe ratio, and decreasing the initial concentration of BDE209. Through analyzed the mass balance of the BDE209 removal, degradation was the main process of BDE209 removal. The mechanism of debromination was deduced by analyzing the reaction products using gas chromatography-mass spectrometry, the bromide ion in the solution and varying the solvent conditions. Stepwise hydrogen reduction is the main process of debromination, and the hydrion play an important role in the reaction. Moreover, the experiment of long term performance and leaching of Ni were also carried out to test the stability and durability of Ni/Fe nanoparticles in BDE209 degradation.

Optimization of NiFe2O4/rGO composite electrode for lithium-ion batteries

Science.gov (United States)

Li, Chen; Wang, Xia; Li, Shandong; Li, Qiang; Xu, Jie; Liu, Xiaomin; Liu, Changkun; Xu, Yuanhong; Liu, Jingquan; Li, Hongliang; Guo, Peizhi; Zhao, Xiu Song

2017-09-01

The combination of carbon compositing and the proper choice of binders in one system offer an effective strategy for improving electrode performance for lithium ion batteries (LIBs). Here, we focus on the optimization of reduced graphene oxide content in NiFe2O4/reduced graphene oxide (abbreviated to NiFe2O4/rGO) composites and the proper choice of binders to enhance the cycling stability of the NiFe2O4 electrode. The NiFe2O4/rGO composites were fabricated by a hydrothermal-annealing method, in which the mean size of spinel NiFe2O4 nanoparticles was approximately 20 nm. When tested as anode materials for LIBs, the NiFe2O4/rGO electrodes with carboxymethylcellulose (CMC) binder exhibited excellent lithium-storage performance including high reversible capacity, good cycling durability and high-rate capability. The capacity could be retained as high as 1105 mAh g-1 at a current density of 100 mA g-1 for over 50 cycles, even cycled at higher current density of 1000 mA g-1, a capacity of 800 mAh g-1can be obtained, whereas the electrode with the polyvinylidene fluoride (PVDF) binder suffered from rapid capacity decay under the same test conditions. As a result, the NiFe2O4/rGO composites with CMC binder electrode in this work are promising as anodes for high-performance LIBs, resulting from the synergistic effect of optimal graphene content and proper choice of binder.

Aquifex aeolicus membrane hydrogenase for hydrogen biooxidation: Role of lipids and physiological partners in enzyme stability and activity

Energy Technology Data Exchange (ETDEWEB)

Infossi, Pascale; Lojou, Elisabeth; Giudici-Orticoni, Marie-Therese [Unite de Bioenergetique et Ingenierie des Proteines, UPR 9036, Institut de Microbiologie de la Mediterranee - CNRS, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20 (France); Chauvin, Jean-Paul [Institut de Biologie du developpement de Marseille Luminy, UMR 6216, Parc Scientifique de Luminy, 163 Avenue de Luminy, BP 907, 13009 Marseille (France); Herbette, Gaetan [Spectropole FI 1739, Aix-Marseille Universite case 511, Faculte de St Jerome Avenue Escadrille Normandie Niemen, 13397 Marseille Cedex 20 (France); Brugna, Myriam [Unite de Bioenergetique et Ingenierie des Proteines, UPR 9036, Institut de Microbiologie de la Mediterranee - CNRS, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20 (France); Universite de Provence, 3 Place Victor Hugo, 13331 Marseille Cedex 03 (France)

2010-10-15

Hydrogenase I from the hyperthermophilic bacterium Aquifex aeolicus is a good candidate for biotechnological devices thanks to its ability to oxidize hydrogen at high temperature, even in the presence of oxygen and CO. In order to enhance the enzyme stability and the catalytic efficiency, we investigated the hydrogen oxidation process with hydrogenase I embedded in a physiological-like environment. Hydrogenase I partners in the metabolic chain, namely membrane quinone and cytochrome b, were purified and fully characterized. The complex hydrogenase I-cytochrome b was inserted into liposomes. Surface Plasmon Resonance revealed that quinone took part in the stabilization of the complex. By use of molecular modelization and electrochemistry analysis, enzyme stability has been demonstrated to be stronger and enzymatic efficiency to be five times higher when hydrogenase is embedded into the liposomes. This result raises the possibility of using hydrogenases as biocatalysts in fuel cells. (author)

Enzymatic and spectroscopic properties of a thermostable [NiFe]‑hydrogenase performing H2-driven NAD+-reduction in the presence of O2.

Science.gov (United States)

Preissler, Janina; Wahlefeld, Stefan; Lorent, Christian; Teutloff, Christian; Horch, Marius; Lauterbach, Lars; Cramer, Stephen P; Zebger, Ingo; Lenz, Oliver

2018-01-01

Biocatalysts that mediate the H 2 -dependent reduction of NAD + to NADH are attractive from both a fundamental and applied perspective. Here we present the first biochemical and spectroscopic characterization of an NAD + -reducing [NiFe]‑hydrogenase that sustains catalytic activity at high temperatures and in the presence of O 2 , which usually acts as an inhibitor. We isolated and sequenced the four structural genes, hoxFUYH, encoding the soluble NAD + -reducing [NiFe]‑hydrogenase (SH) from the thermophilic betaproteobacterium, Hydrogenophilus thermoluteolus TH-1 T (Ht). The HtSH was recombinantly overproduced in a hydrogenase-free mutant of the well-studied, H 2 -oxidizing betaproteobacterium Ralstonia eutropha H16 (Re). The enzyme was purified and characterized with various biochemical and spectroscopic techniques. Highest H 2 -mediated NAD + reduction activity was observed at 80°C and pH6.5, and catalytic activity was found to be sustained at low O 2 concentrations. Infrared spectroscopic analyses revealed a spectral pattern for as-isolated HtSH that is remarkably different from those of the closely related ReSH and other [NiFe]‑hydrogenases. This indicates an unusual configuration of the oxidized catalytic center in HtSH. Complementary electron paramagnetic resonance spectroscopic analyses revealed spectral signatures similar to related NAD + -reducing [NiFe]‑hydrogenases. This study lays the groundwork for structural and functional analyses of the HtSH as well as application of this enzyme for H 2 -driven cofactor recycling under oxic conditions at elevated temperatures. Copyright © 2017 Elsevier B.V. All rights reserved.

Novel Large Sulfur Bacteria in the Metagenomes of Groundwater-Fed Chemosynthetic Microbial Mats in the Lake Huron Basin.

Science.gov (United States)

Sharrar, Allison M; Flood, Beverly E; Bailey, Jake V; Jones, Daniel S; Biddanda, Bopaiah A; Ruberg, Steven A; Marcus, Daniel N; Dick, Gregory J

2017-01-01

Little is known about large sulfur bacteria (LSB) that inhabit sulfidic groundwater seeps in large lakes. To examine how geochemically relevant microbial metabolisms are partitioned among community members, we conducted metagenomic analysis of a chemosynthetic microbial mat in the Isolated Sinkhole, which is in a deep, aphotic environment of Lake Huron. For comparison, we also analyzed a white mat in an artesian fountain that is fed by groundwater similar to Isolated Sinkhole, but that sits in shallow water and is exposed to sunlight. De novo assembly and binning of metagenomic data from these two communities yielded near complete genomes and revealed representatives of two families of LSB. The Isolated Sinkhole community was dominated by novel members of the Beggiatoaceae that are phylogenetically intermediate between known freshwater and marine groups. Several of these Beggiatoaceae had 16S rRNA genes that contained introns previously observed only in marine taxa. The Alpena fountain was dominated by populations closely related to Thiothrix lacustris and an SM1 euryarchaeon known to live symbiotically with Thiothrix spp. The SM1 genomic bin contained evidence of H 2 -based lithoautotrophy. Genomic bins of both the Thiothrix and Beggiatoaceae contained genes for sulfur oxidation via the rDsr pathway, H 2 oxidation via Ni-Fe hydrogenases, and the use of O 2 and nitrate as electron acceptors. Mats at both sites also contained Deltaproteobacteria with genes for dissimilatory sulfate reduction ( sat, apr , and dsr ) and hydrogen oxidation (Ni-Fe hydrogenases). Overall, the microbial mats at the two sites held low-diversity microbial communities, displayed evidence of coupled sulfur cycling, and did not differ largely in their metabolic potentials, despite the environmental differences. These results show that groundwater-fed communities in an artesian fountain and in submerged sinkholes of Lake Huron are a rich source of novel LSB, associated heterotrophic and sulfate

Novel Large Sulfur Bacteria in the Metagenomes of Groundwater-Fed Chemosynthetic Microbial Mats in the Lake Huron Basin

Directory of Open Access Journals (Sweden)

Allison M. Sharrar

2017-05-01

Full Text Available Little is known about large sulfur bacteria (LSB that inhabit sulfidic groundwater seeps in large lakes. To examine how geochemically relevant microbial metabolisms are partitioned among community members, we conducted metagenomic analysis of a chemosynthetic microbial mat in the Isolated Sinkhole, which is in a deep, aphotic environment of Lake Huron. For comparison, we also analyzed a white mat in an artesian fountain that is fed by groundwater similar to Isolated Sinkhole, but that sits in shallow water and is exposed to sunlight. De novo assembly and binning of metagenomic data from these two communities yielded near complete genomes and revealed representatives of two families of LSB. The Isolated Sinkhole community was dominated by novel members of the Beggiatoaceae that are phylogenetically intermediate between known freshwater and marine groups. Several of these Beggiatoaceae had 16S rRNA genes that contained introns previously observed only in marine taxa. The Alpena fountain was dominated by populations closely related to Thiothrix lacustris and an SM1 euryarchaeon known to live symbiotically with Thiothrix spp. The SM1 genomic bin contained evidence of H2-based lithoautotrophy. Genomic bins of both the Thiothrix and Beggiatoaceae contained genes for sulfur oxidation via the rDsr pathway, H2 oxidation via Ni-Fe hydrogenases, and the use of O2 and nitrate as electron acceptors. Mats at both sites also contained Deltaproteobacteria with genes for dissimilatory sulfate reduction (sat, apr, and dsr and hydrogen oxidation (Ni-Fe hydrogenases. Overall, the microbial mats at the two sites held low-diversity microbial communities, displayed evidence of coupled sulfur cycling, and did not differ largely in their metabolic potentials, despite the environmental differences. These results show that groundwater-fed communities in an artesian fountain and in submerged sinkholes of Lake Huron are a rich source of novel LSB, associated heterotrophic

Preparation of NiFe binary alloy nanocrystals for nonvolatile memory applications

Institute of Scientific and Technical Information of China (English)

无

2010-01-01

In this work,an idea which applies binary alloy nanocrystal floating gate to nonvolatile memory application was introduced.The relationship between binary alloy’s work function and its composition was discussed theoretically.A nanocrystal floating gate structure with NiFe nanocrystals embedded in SiO2 dielectric layers was fabricated by magnetron sputtering.The micro-structure and composition deviation of the prepared NiFe nanocrystals were also investigated by TEM and EDS.

Purification and characterization of the hydrogen uptake hydrogenase from the hyperthermpholic archaebacterium Pyrodictium brockii

International Nuclear Information System (INIS)

Pihl, T.D.; Maier, R.J.

1991-01-01

Pyrodictium brockii is a hyperthermophilic archaebacterium with an optimal growth temperature of 105C. P. brokii is also a chemolithotroph, requiring H 2 and CO 2 for growth. The authors have purified the hydrogen uptake hydrogenase from membranes of P. brockii by reactive red affinity chromatography and sucrose gradient centrifugation. Colorometric analysis of Fe and S content in reactive red-purified hydrogenase revealed 8.7 ± 0.6 mol of Fe and 6.2 ± 1.2 mol of S per mol of hydrogenase. Growth of cells in 63 NiCl 2 resulted in label incorporation into reactive red-purified hydrogenase. Temperature stability studies indicated that the membrane-bound form of the enzyme was more stable than the solubilized purified form over a period of minutes with respect to temperature. However, the membranes were not able to protect the enzyme from thermal inactivation over a period of hours. The artificial electron acceptor specificity of the pure enzyme was similar to that of the membrane-bound form, but the purified enzyme was able to evolve H 2 in the presence of reduced methyl viologen. The K m of membrane-bound hydrogenase for H 2 was approximately 19 μM with methylene blue as the electron acceptor, whereas the purified enzyme had a higher K m value

Use of molecular hydrogen as an energy substrate by human pathogenic bacteria.

Science.gov (United States)

Maier, R J

2005-02-01

Molecular hydrogen is produced as a fermentation by-product in the large intestine of animals and its production can be correlated with the digestibility of the carbohydrates consumed. Pathogenic Helicobacter species (Helicobacter pylori and H. hepaticus) have the ability to use H(2) through a respiratory hydrogenase, and it was demonstrated that the gas is present in the tissues colonized by these pathogens (the stomach and the liver respectively of live animals). Mutant strains of H. pylori unable to use H(2) are deficient in colonizing mice compared with the parent strain. On the basis of available annotated gene sequence information, the enteric pathogen Salmonella, like other enteric bacteria, contains three putative membrane-associated H(2)-using hydrogenase enzymes. From the analysis of gene-targeted mutants it is concluded that each of the three membrane-bound hydrogenases of Salmonella enterica serovar Typhimurium are coupled with an H(2)-oxidizing respiratory pathway. From microelectrode probe measurements on live mice, H(2) could be detected at approx. 50 muM levels within the tissues (liver and spleen), which are colonized by Salmonella. The half-saturation affinity of whole cells of these pathogens for H(2) is much less than this, so it is expected that the (H(2)-utilizing) hydrogenase enzymes be saturated with the reducing substrate in vivo. All three enteric NiFe hydrogenase enzymes contribute to virulence of the bacterium in a typhoid fever-mouse model, and the combined removal of all three hydrogenases resulted in a strain that is avirulent and (in contrast with the parent strain) one that is not able to pass the intestinal tract to invade liver or spleen tissue. It is proposed that H(2) utilization and specifically its oxidation, coupled with a respiratory pathway, is required for energy production to permit growth and maintain efficient virulence of a number of pathogenic bacteria during infection of animals. These would be expected to include

Replacing Electron Transport Cofactors with Hydrogenases

KAUST Repository

Laamarti, Rkia

2016-12-01

Enzymes have found applications in a broad range of industrial production processes. While high catalytic activity, selectivity and mild reaction conditions are attractive advantages of the biocatalysts, particularly costs arising from required cofactors pose a sever limitation. While cofactor-recycling systems are available, their use implies constraints for process set-up and conditions, which are a particular problem e.g. for solid-gas-phase reactions. Several oxidoreductases are able to directly exchange electrons with electrodes. Hence, the co-immobilization of both, an electron-utilizing and an electron-generating oxidoreductase on conductive nanoparticles should facilitate the direct electron flow from an enzymatic oxidation to a reduction reaction circumventing redox-cofactors requirements. In such a set-up, hydrogenases could generate and provide electrons directly form gaseous hydrogen. This thesis describes the co-immobilization of the oxygen tolerant hydrogenases from C. eutropha or C. metallidurans and cytochrome P450BM3 as test system. Conductive material in the form of carbon nanotubes (CNT) serves as a suitable support. A combination of the hydrogenase and the catalytic domain of P450BM3 immobilized on carbon nanotubes were tested for the oxidation of lauric acid in the presence of hydrogen instead of an electron-transport cofactor. The GC-MS analysis reveals the conversion of 4% of lauric acid (LA) into three products, which correspond to the hydroxylated lauric acid in three different positions with a total turnover (TON) of 34. The product distribution is similar to that obtained when using the wildtype P450BM3 with the nicotinamide adenine dinucleotide phosphate (NADPH) cofactor. Such electronic coupling couldn’t be achieved for the conversion of other substrates such as propane and cyclohexane, probably due to the high uncoupling rate within the heme-domain of cytochrome P450BM3 when unnatural substrates are introduced.

Easily Dispersible NiFe2O4/RGO Composite for Microwave Absorption Properties in the X-Band

Science.gov (United States)

Bateer, Buhe; Zhang, Jianjao; Zhang, Hongchen; Zhang, Xiaochen; Wang, Chunyan; Qi, Haiqun

2018-01-01

Composites with good dispersion and excellent microwave absorption properties have important applications. Therefore, an easily dispersible NiFe2O4/reduced graphene oxide (RGO) composite has been prepared conveniently through a simple hydrothermal method. Highly crystalline, small size (about 7 nm) monodispersed NiFe2O4 nanoparticles (NPs) are evenly distributed on the surface of RGO. The microwave absorbability revealed that the NiFe2O4/RGO composite exhibits excellent microwave absorption properties in the X-band (8-12 GHz), and the minimum reflection loss of the NiFe2O4/RGO composite is -27.7 dB at 9.2 GHz. The NiFe2O4/RGO composite has good dispersibility in nonpolar solvent, which facilitates the preparation of stable commercial microwave absorbing coatings. It can be a promising candidate for lightweight microwave absorption materials in many application fields.

Magneto-thermoelectric effects in NiFe thin films

Energy Technology Data Exchange (ETDEWEB)

Schmid, Maximilian

2015-11-01

In this thesis magneto-thermoelectric effects are investigated in a systematic way to separate the transverse spin Seebeck effect from other parasitic effects like the anomalous Nernst effect. In contrast to the first studies found in the literature, in NiFe thin films a contribution of the transverse spin Seebeck effect can be excluded. This surprising outcome was crosschecked in a variety of different sample layouts and collaborations with other universities to ensure the validity of these results. In general, this thesis solves a long time discussion about the existence of the transverse spin Seebeck effect in NiFe films and supports the importance of control measurements for the scientific community. Even if such ''negative'' results may not be the award winning ones, new discoveries should be treated with constructive criticism and be checked carefully by the scientific community.

Model synthetic complexes of the hydrogenase with different protonation sites; Complexes synthetiques modeles de l'hydrogenase avec differents sites de protonation

Energy Technology Data Exchange (ETDEWEB)

Capon, J.F.; Gloaguen, F.; Morvan, D.; Schollhammer, Ph.; Talarmin, J.; Yaouanc, J.J. [Universite de Bretagne Occidentale, UMR CNRS 6521, Chimie, Electrochimie Moleculaires et Chimie Analytique, Faculte des Sciences, 29 - Brest (France)

2005-07-01

The data obtained until now seem to indicate that the hydrogen production by hydrogenases induces a proton-hydride coupling. In taking the structures of theses enzymes active sites (determined by X-ray diffraction) as a basis, it can be thought that this proton-hydride coupling is facilitated by the juxtaposition of two protonation sites, the metallic center M and the basic group of an E ligand of the coordination sphere. Contrarily to the supposed running of the hydrogenases enzymes, the homogeneous catalysts of the protons reduction, described in the literature, present a reactivity which is either on an alone metallic site or on a metal-metal bond. This work deals then with the preparation of complexes having two juxtaposed protonation sites. Some iron dinuclear compounds have been synthesized and their properties studied. (O.M.)

Occurrence of H2-Uptake Hydrogenases in Bradyrhizobium sp. (Lupinus) and Their Expression in Nodules of Lupinus spp. and Ornithopus compressus1

Science.gov (United States)

Murillo, Jesús; Villa, Ana; Chamber, Manuel; Ruiz-Argüeso, Tomás

1989-01-01

Fifty-four strains of Bradyrhizobium sp. (Lupinus) from worldwide collections were screened by a colony hybridization method for the presence of DNA sequences homologous to the structural genes of the Bradyrhizobium japonicum hydrogenase. Twelve strains exhibited strong colony hybridization signals, and subsequent Southern blot hybridization experiments showed that they fell into two different groups on the basis of the pattern of EcoRI fragments containing the homology to the hup probe. All strains in the first group (UPM860, UPM861, and 750) expressed uptake hydrogenase activity in symbiosis with Lupinus albus, Lupinus angustifolius, Lupinus luteus, and Ornithopus compressus, but both the rate of H2 uptake by bacteroids and the relative efficiency of N2 fixation (RE = 1 - [H2 evolved in air/acetylene reduced]) by nodules were markedly affected by the legume host. L. angustifolius was the less permissive host for hydrogenase expression in symbiosis with the three strains (average RE = 0.76), and O. compressus was the more permissive (average RE = 1.0). None of the strains in the second group expressed hydrogenase activity in lupine nodules, and only one exhibited low H2-uptake activity in symbiosis with O. compressus. The inability of these putative Hup+ strains to induce hydrogenase activity in lupine nodules is discussed on the basis of the legume host effect. Among the 42 strains showing no homology to the B. japonicum hup-specific probe in the colony hybridization assay, 10 were examined in symbiosis with L. angustifolius. The average RE for these strains was 0.51. However, one strain, IM43B, exhibited high RE values (higher than 0.80) and high levels of hydrogenase activity in symbiosis with L. angustifolius, L. albus, and L. luteus. In Southern blot hybridization experiments, no homology was detected between the B. japonicum hup-specific DNA probe and total DNA from vegetative cells or bacteroids from strain IM43B even under low stringency hybridization

Synthesis and characterization of NiFe2O4–Pd magnetically recyclable catalyst for hydrogenation reaction

International Nuclear Information System (INIS)

Karaoğlu, E.; Özel, U.; Caner, C.; Baykal, A.; Summak, M.M.; Sözeri, H.

2012-01-01

Graphical abstract: Display Omitted Highlights: ► Novel superparamagnetic NiFe 2 O 4 –Pd magnetically recyclable catalyst was fabricated through co-precipitation. ► It could be reused several times without significant loss in catalytic activity for hydrogenation reaction. ► No further modification of the NiFe 2 O 4 –Pd magnetically recyclable catalyst is necessary for utilization as catalyst. -- Abstract: Herein we report the fabrication and characterization magnetically recyclable catalysts of NiFe 2 O 4 –Pd nanocomposite as highly effective catalysts for reduction reactions in liquid phase. The reduction Pd 2+ was accomplished with polyethylene glycol 400 (PEG-400) instead of sodium borohydride (NaBH 4 ) and NiFe 2 O 4 nanoparticles was prepared by sonochemically using FeCI 3 ·6H 2 O and NiCl 2 . The chemical characterization of the product was done with X-ray diffractometry, Infrared spectroscopy, transmission electron microscopy, UV–Vis spectroscopy, thermal gravimetry and inductively coupled plasma. Thus formed NiFe 2 O 4 –Pd MRCs showed a very high activity in reduction reactions of 4-nitro aniline and 1,3-dinitrobenzene in liquid phase. It was found out that the catalytic activity of NiFe 2 O 4 –Pd MRCs on the reduction of 4-nitro aniline and 1,3-dinitrobenzene in liquid phase are between 99–93% and 98–93%, respectively. Magnetic character of this system allowed recovery and multiple use without significant loss of its catalytic activity. It is found that NiFe 2 O 4 –Pd MRCs showed very efficient catalytic activity and multiple usability.

Giant magnetoimpedance effect in sputtered single layered NiFe film and meander NiFe/Cu/NiFe film

International Nuclear Information System (INIS)

Chen, L.; Zhou, Y.; Lei, C.; Zhou, Z.M.; Ding, W.

2010-01-01

Giant magnetoimpedance (GMI) effect on NiFe thin film is very promising due to its application in developing the magnetic field sensors with highly sensitivity and low cost. In this paper, the single layered NiFe thin film and NiFe/Cu/NiFe thin film with a meander structure are prepared by the MEMS technology. The influences of sputtering parameters, film structure and conductor layer width on GMI effect in NiFe single layer and meander NiFe/Cu/NiFe film are investigated. Maximum of the GMI ratio in single layer and sandwich film is 5% and 64%, respectively. The results obtained are useful for developing the high-performance magnetic sensors based on NiFe thin film.

Microstructure, AC impedance and DC electrical conductivity characteristics of NiFe2-xGdxO4 (x = 0, 0.05 and 0.075

Directory of Open Access Journals (Sweden)

K. Kamala Bharathi

2012-03-01

Full Text Available The structure and electrical characteristics of Gd doped Ni ferrite materials, namely NiFe1.95Gd0.05O4 and NiFe1.925Gd0.075O4, are reported to demonstrate their improved electrical properties compared to that of pure NiFe2O4. NiFe1.95Gd0.05O4 and NiFe1.925Gd0.075O4 compounds crystallize in the cubic inverse spinel phase with a very small amount of GdFeO3 additional phase while pure NiFe2O4 crystallize in inverse spinel phase without any impurity phase. The back scattered electron imaging analysis indicate the primary and secondary formation in NiFe1.95Gd0.05O4 and NiFe1.925Gd0.075O4 compounds. Atomic force microscopy measurements indicate that the bulk grains are ∼2-5 micron size while the grain boundaries are thin compared to bulk grains. Impedance spectroscopic analysis at different temperature indicates the different relaxation mechanisms and their variation with temperature, bulk grain and grain-boundary contributions to the electrical conductivity (Rg and capacitance (Cg of these materials. The conductivity in pure NiFeO4 is found to be predominantly due to intrinsic bulk contribution (Rg=213 kΩ and Cg=4.5 x 10-8 F. In the case of NiFe1.95Gd0.05O4 and NiFe1.925Gd0.075O4 compounds, grain and grain-boundary contributions to the conductivity are clearly observed. The DC conductivity values (at 300 K of NiFe2O4, NiFe1.95Gd0.05O4 and NiFe1.925Gd0.075O4 compounds are found to be 1.06 x 10-7 Ω-1 cm-1, 5.73 x 10-8 Ω-1 cm-1 and 1.28 x 10-8 Ω-1 cm-1 respectively.

Influence of static and dynamic dipolar fields in bulk YIG/thin film NiFe systems probed via spin rectification effect

Energy Technology Data Exchange (ETDEWEB)

Soh, Wee Tee, E-mail: a0046479@u.nus.edu [Center for Superconducting and Magnetic Materials, Department of Physics, National University of Singapore, 2 Science Drive 3, Singapore 117551 (Singapore); Tay, Z.J. [Center for Superconducting and Magnetic Materials, Department of Physics, National University of Singapore, 2 Science Drive 3, Singapore 117551 (Singapore); Yakovlev, N.L. [Institute of Materials Research and Engineering, A*STAR (Agency for Science, Technology and Research), 3 Research Link, Singapore 117602 (Singapore); Peng, Bin [State Key Laboratory of Electronic Thin Films and Integrated Devices, University of Electronic Science and Technology of China, Chengdu 610054 (China); Ong, C.K. [Center for Superconducting and Magnetic Materials, Department of Physics, National University of Singapore, 2 Science Drive 3, Singapore 117551 (Singapore); Temasek Laboratories, National University of Singapore, 5A Engineering Drive 2, Singapore 117411 (Singapore)

2017-03-15

The characteristics of the static and dynamic components of the dipolar fields originating from a bulk polycrystalline yttrium iron garnet (YIG) substrate are probed by depositing a NiFe (Permalloy) layer on it, which acts as a detector. By measuring dc voltages generated via spin rectification effect (SRE) within the NiFe layer under microwave excitation, we characterize the influence of dipolar fields from bulk YIG on the NiFe layer. It is found that the dynamic YIG dipolar fields modify the self-SRE of NiFe, driving its own rectification voltages within the NiFe layer, an effect we term as non-local SRE. This non-local SRE only occurs near the simultaneous resonance of both YIG and NiFe. On the other hand, the static dipolar field from YIG manifests itself as a negative anisotropy in the NiFe layer which shifts the latter’s ferromagnetic resonance frequency. - Highlights: • We demonstrate the quantification of both the static and dynamic components of the dipolar fields due to a YIG slab. • The detection and characterisation of such dipolar fields are important in many magnetic applications such as magnonics. • The dipolar fields can pose potential pitfalls if not properly considered in certain spin-electronics systems.

Hydrogen Activation by Biomimetic [NiFe]-Hydrogenase Model Containing Protected Cyanide Cofactors

Science.gov (United States)

Manor, Brian C.; Rauchfuss, Thomas B.

2013-01-01

Described are experiments that allow incorporation of cyanide cofactors and hydride substrate into active site models [NiFe]-hydrogenases (H2ases). Complexes of the type (CO)2(CN)2Fe(pdt)Ni(dxpe), (dxpe = dppe, 1; dxpe = dcpe, 2) bind the Lewis acid B(C6F5)3 (BArF3) to give the adducts (CO)2(CNBArF3)2Fe(pdt)Ni(dxpe), (1(BArF3)2, 2(BArF3)2). Upon decarbonylation using amine oxides, these adducts react with H2 to give hydrido derivatives Et4N[(CO)(CNBArF3)2Fe(H)(pdt)Ni(dxpe)], (dxpe = dppe, Et4N[H3(BArF3)2]; dxpe = dcpe, Et4N[H4(BArF3)2]). Crystallographic analysis shows that Et4N[H3(BArF3)2] generally resembles the active site of the enzyme in the reduced, hydride-containing states (Ni-C/R). The Fe-H…Ni center is unsymmetrical with rFe-H = 1.51(3) and rNi-H = 1.71(3) Å. Both crystallographic and 19F NMR analysis show that the CNBArF3− ligands occupy basal and apical sites. Unlike cationic Ni-Fe hydrides, [H3(BArF3)2]− and [H4(BArF3)2]− oxidize at mild potentials, near the Fc+/0 couple. Electrochemical measurements indicate that in the presence of base, [H3(BArF3)2]− catalyzes the oxidation of H2. NMR evidence indicates dihydrogen bonding between these anionic hydrides and ammonium salts, which is relevant to the mechanism of hydrogenogenesis. In the case of Et4N[H3(BArF3)2], strong acids such as HCl induce H2 release to give the chloride Et4N[(CO)(CNBArF3)2Fe(pdt)(Cl)Ni(dppe)]. PMID:23899049

CoCr double-layered media with NiFe and CoZrNb soft-magnetic layers (invited)

International Nuclear Information System (INIS)

Bernards, J.P.C.; Schrauwen, C.P.G.; Zieren, V.; Luitjens, S.B.

1988-01-01

The magnetic, structural, and recording properties of CoCr double-layered media are investigated. The underlayer materials NiFe (crystalline) and CoZrNb (amorphous) were combined with two different kinds of intermediate layers: Ti (crystalline) and Ge (amorphous). Applying a bias voltage during sputtering of NiFe results in a low coercivity of the NiFe layer and in a high coercivity of the CoCr layer. The structure of the NiFe layer influences the structure of the CoCr layer. A Ti layer between the NiFe and CoCr layers decreases the in-plane remanence of the CoCr layer. The coercivity of all CoZrNb layers is low, independent of the application of a bias voltage. The orientation and structure of CoCr on CoZrNb can be improved by using a Ge intermediate layer, which results in a low coercivity of the CoCr. A Ti intermediate layer increases the coercivity. Ring heads show a dependence of spike noise on the underlayer coercivity and on the applied normal force. A probe-type head shows a dependence of its output on the CoCr coercivity, which may be understood in terms of demagnetization and writing depth

Trichloroethene (TCE) hydrodechlorination by NiFe nanoparticles: Influence of aqueous anions on catalytic pathways.

Science.gov (United States)

Han, Yanlai; Liu, Changjie; Horita, Juske; Yan, Weile

2018-08-01

Amending bulk and nanoscale zero-valent iron (ZVI) with catalytic metals significantly accelerates hydrodechlorination of groundwater contaminants such as trichloroethene (TCE). The bimetallic design benefits from a strong synergy between Ni and Fe in facilitating the production of active hydrogen for TCE reduction, and it is of research and practical interest to understand the impacts of common groundwater solutes on catalyst and ZVI functionality. In this study, TCE hydrodechlorination reaction was conducted using fresh NiFe bimetallic nanoparticles (NiFe BNPs) and those aged in chloride, sulfate, phosphate, and humic acid solutions with concurrent analysis of carbon fractionation of TCE and its daughter products. The apparent kinetics suggest that the reactivity of NiFe BNPs is relatively stable in pure water and chloride or humic acid solutions, in contrast to significant deactivation observed of PdFe bimetallic particles in similar media. Exposure to phosphate at greater than 0.1 mM led to a severe decrease in TCE reaction rate. The change in kinetic regimes from first to zeroth order with increasing phosphate concentration is consistent with consumption of reactive sites by phosphate. Despite severe kinetic effect, there is no significant shift in TCE 13 C bulk enrichment factor between the fresh and the phosphate-aged particles. Instead, pronounced retardation of TCE reaction by NiFe BNPs in deuterated water (D 2 O) points to the importance of hydrogen spillover in controlling TCE reduction rate by NiFe BNPs, and such process can be strongly affected by groundwater chemistry. Copyright © 2018 Elsevier Ltd. All rights reserved.

Hydrogenase-3 contributes to anaerobic acid resistance of Escherichia coli.

Science.gov (United States)

Noguchi, Ken; Riggins, Daniel P; Eldahan, Khalid C; Kitko, Ryan D; Slonczewski, Joan L

2010-04-12

Hydrogen production by fermenting bacteria such as Escherichia coli offers a potential source of hydrogen biofuel. Because H(2) production involves consumption of 2H(+), hydrogenase expression is likely to involve pH response and regulation. Hydrogenase consumption of protons in E. coli has been implicated in acid resistance, the ability to survive exposure to acid levels (pH 2-2.5) that are three pH units lower than the pH limit of growth (pH 5-6). Enhanced survival in acid enables a larger infective inoculum to pass through the stomach and colonize the intestine. Most acid resistance mechanisms have been defined using aerobic cultures, but the use of anaerobic cultures will reveal novel acid resistance mechanisms. We analyzed the pH regulation of bacterial hydrogenases in live cultures of E. coli K-12 W3110. During anaerobic growth in the range of pH 5 to 6.5, E. coli expresses three hydrogenase isoenzymes that reversibly oxidize H(2) to 2H(+). Anoxic conditions were used to determine which of the hydrogenase complexes contribute to acid resistance, measured as the survival of cultures grown at pH 5.5 without aeration and exposed for 2 hours at pH 2 or at pH 2.5. Survival of all strains in extreme acid was significantly lower in low oxygen than for aerated cultures. Deletion of hyc (Hyd-3) decreased anoxic acid survival 3-fold at pH 2.5, and 20-fold at pH 2, but had no effect on acid survival with aeration. Deletion of hyb (Hyd-2) did not significantly affect acid survival. The pH-dependence of H(2) production and consumption was tested using a H(2)-specific Clark-type electrode. Hyd-3-dependent H(2) production was increased 70-fold from pH 6.5 to 5.5, whereas Hyd-2-dependent H(2) consumption was maximal at alkaline pH. H(2) production, was unaffected by a shift in external or internal pH. H(2) production was associated with hycE expression levels as a function of external pH. Anaerobic growing cultures of E. coli generate H(2) via Hyd-3 at low external pH, and

How oxygen attacks [FeFe] hydrogenases from photosynthetic organisms

Science.gov (United States)

Stripp, Sven T.; Goldet, Gabrielle; Brandmayr, Caterina; Sanganas, Oliver; Vincent, Kylie A.; Haumann, Michael; Armstrong, Fraser A.; Happe, Thomas

2009-01-01

Green algae such as Chlamydomonas reinhardtii synthesize an [FeFe] hydrogenase that is highly active in hydrogen evolution. However, the extreme sensitivity of [FeFe] hydrogenases to oxygen presents a major challenge for exploiting these organisms to achieve sustainable photosynthetic hydrogen production. In this study, the mechanism of oxygen inactivation of the [FeFe] hydrogenase CrHydA1 from C. reinhardtii has been investigated. X-ray absorption spectroscopy shows that reaction with oxygen results in destruction of the [4Fe-4S] domain of the active site H-cluster while leaving the di-iron domain (2FeH) essentially intact. By protein film electrochemistry we were able to determine the order of events leading up to this destruction. Carbon monoxide, a competitive inhibitor of CrHydA1 which binds to an Fe atom of the 2FeH domain and is otherwise not known to attack FeS clusters in proteins, reacts nearly two orders of magnitude faster than oxygen and protects the enzyme against oxygen damage. These results therefore show that destruction of the [4Fe-4S] cluster is initiated by binding and reduction of oxygen at the di-iron domain—a key step that is blocked by carbon monoxide. The relatively slow attack by oxygen compared to carbon monoxide suggests that a very high level of discrimination can be achieved by subtle factors such as electronic effects (specific orbital overlap requirements) and steric constraints at the active site. PMID:19805068

Bimetallic NiFe2O4 synthesized via confined carburization in NiFe-MOFs for efficient oxygen evolution reaction

Science.gov (United States)

Fang, Zhiqiang; Hao, Zhaomin; Dong, Qingsong; Cui, Yong

2018-04-01

Transition metal oxides that derived from metal-organic framework (MOF) precursor have intensively received attention because of their numerous electrochemical applications. Bimetallic Ni-Fe oxides have been rarely reported on the basis of MOF-related strategy. Herein, a bimetallic NiFe2O4 was successfully synthesized via confined carburization in NiFe-MOF precursors and characterized by XRD, XPS, SEM, and TEM. After conducting an investigation of oxygen evolution reaction (OER), the as-synthesized NiFe2O4 material exhibited good catalytic efficiency and high stability and durability in alkaline media. The as-synthesized NiFe2O4 material would promote the development of MOFs in non-noble-metal OER catalyst.

Accumulating the hydride state in the catalytic cycle of [FeFe]-hydrogenases

Science.gov (United States)

Winkler, Martin; Senger, Moritz; Duan, Jifu; Esselborn, Julian; Wittkamp, Florian; Hofmann, Eckhard; Apfel, Ulf-Peter; Stripp, Sven Timo; Happe, Thomas

2017-07-01

H2 turnover at the [FeFe]-hydrogenase cofactor (H-cluster) is assumed to follow a reversible heterolytic mechanism, first yielding a proton and a hydrido-species which again is double-oxidized to release another proton. Three of the four presumed catalytic intermediates (Hox, Hred/Hred and Hsred) were characterized, using various spectroscopic techniques. However, in catalytically active enzyme, the state containing the hydrido-species, which is eponymous for the proposed heterolytic mechanism, has yet only been speculated about. We use different strategies to trap and spectroscopically characterize this transient hydride state (Hhyd) for three wild-type [FeFe]-hydrogenases. Applying a novel set-up for real-time attenuated total-reflection Fourier-transform infrared spectroscopy, we monitor compositional changes in the state-specific infrared signatures of [FeFe]-hydrogenases, varying buffer pH and gas composition. We selectively enrich the equilibrium concentration of Hhyd, applying Le Chatelier's principle by simultaneously increasing substrate and product concentrations (H2/H+). Site-directed manipulation, targeting either the proton-transfer pathway or the adt ligand, significantly enhances Hhyd accumulation independent of pH.

Remediation of polybrominated diphenyl ethers in soil using Ni/Fe bimetallic nanoparticles: Influencing factors, kinetics and mechanism

International Nuclear Information System (INIS)

Xie, Yingying; Fang, Zhanqiang; Cheng, Wen; Tsang, Pokeung Eric; Zhao, Dongye

2014-01-01

Polybrominated diphenyl ethers (PBDEs) are commonly used as additive flame retardants in all kinds of electronic products. PBDEs are now ubiquitous in the environment, with soil as a major sink, especially in e-waste recycling sites. This study investigated the degradation of decabromodiphenyl ether (BDE209) in a spiked soil using Ni/Fe bimetallic nanoparticles. The results indicated that Ni/Fe bimetallic nanoparticles are able to degrade BDE209 in soil at ambient temperature and the removal efficiency can reach 72% when an initial pH of 5.6 and at a Ni/Fe dosage of 0.03 g/g. A declining trend in degradation was noticed with decreasing Ni loading and increasing of initial BDE209 concentration. The degradation products of BDE209 were analyzed by GC-MS, which showed that the degradation of BDE209 was a process of stepwise debromination from nBr to (n − 1)Br. And a possible debromination pathway was proposed. At last, the degradation process was analyzed as two-step mechanism, mass transfer and reaction. This current study shows the potential ability of Ni/Fe nanoparticles to be used for removal of PBDEs in contaminated soil. - Highlights: • Ni/Fe bimetallic nanoparticles could effectively degradate BDE209 in soil. • The effects of various factors on remediation of BDE209 in soil using Ni/Fe were considered. • The degradation of BDE209 was a process of stepwise debromination from nBr to (n − 1)Br. • A possible debromination pathway and mechanism about removal of BDE209 in soil were proposed

Second coordination sphere effects in [FeFe]-Hydrogenase mimics

NARCIS (Netherlands)

Zaffaroni, R.

2017-01-01

Iron–iron hydrogenase are fascinating metallo‐enzymes able to reversibly perform interconversion between protons and dihydrogen with high rates at low overpotentials. Nevertheless, activity and stability of synthetic analogues without the protein matrix are rarely comparable to the enzyme. This

Hydrogen Production by a Hyperthermophilic Membrane-Bound Hydrogenase in Soluble Nanolipoprotein Particles

Energy Technology Data Exchange (ETDEWEB)

Baker, S E; Hopkins, R C; Blanchette, C; Walsworth, V; Sumbad, R; Fischer, N; Kuhn, E; Coleman, M; Chromy, B; Letant, S; Hoeprich, P; Adams, M W; Henderson, P T

2008-10-22

Hydrogenases constitute a promising class of enzymes for ex vivo hydrogen production. Implementation of such applications is currently hindered by oxygen sensitivity and, in the case of membrane-bound hydrogenases (MBH), poor water solubility. Nanolipoprotein particles (NLPs), formed from apolipoproteins and phospholipids, offer a novel means to incorporate MBH into in a well-defined water-soluble matrix that maintains the enzymatic activity and is amenable to incorporation into more complex architectures. We report the synthesis, hydrogen-evolving activity and physical characterization of the first MBH-NLP assembly. This may ultimately lead to the development of biomimetic hydrogen production devices.

One-pot fabrication of NiFe2O4 nanoparticles on α-Ni(OH)2 nanosheet for enhanced water oxidation

Science.gov (United States)

Chen, Hong; Yan, Junqing; Wu, Huan; Zhang, Yunxia; Liu, Shengzhong (Frank)

2016-08-01

Water splitting has been intensively investigated as a promising solution to resolve the future environmental and energy crises. The oxygen evolution reaction (OER) of the photo- and electric field-induced water splitting limits the development of other reactions, including hydrogen evolution reaction (HER). Fe, Ni and NiFe (hydro) oxide-based catalysts are generally acknowledged among the best candidates of OER catalysts for water splitting. Herein, we developed a one-pot simple hydrothermal process to assemble NiFe2O4 nanoparticles onto the α-Ni(OH)2 nanosheets. The first formed NiFe2O4 under high temperature and pressure environment induces and assists the α-Ni(OH)2 formation without any further additives, because the distance between the neighboring Ni atoms in the cubic NiFe2O4 is similar to that in the α-Ni(OH)2 {003} facets. We have synthesized a series of NiFe2O4/α-Ni(OH)2 compounds and find that the overpotential decreases with the increase of Ni(OH)2 content while the OER kinetics stays unchanged, suggesting that Ni(OH)2 plays a major role in overpotential while NiFe2O4 mainly affects the OER kinetics. The obtained NiFe2O4/α-Ni(OH)2 compounds is also found to be a promising co-catalyst for the photocatalytic water oxidation. In fact, it is even more active than the noble PtOx with acceptable stability for the oxygen generation.

Facile synthesis of mesoporous NiFe2O4/CNTs nanocomposite cathode material for high performance asymmetric pseudocapacitors

Science.gov (United States)

Kumar, Nagesh; Kumar, Amit; Huang, Guan-Min; Wu, Wen-Wei; Tseng, Tseung Yuen

2018-03-01

Morphology and synergistic effect of constituents are the two very important factors that greatly influence the physical, chemical and electrochemical properties of a composite material. In the present work, we report the enhanced electrochemical performance of mesoporous NiFe2O4 and multiwall carbon nanotubes (MWCNTs) nanocomposites synthesized via hexamethylene tetramine (HMT) assisted one-pot hydrothermal approach. The synthesized cubic phase spinel NiFe2O4 nanomaterial possesses high specific surface area (148 m2g-1) with narrow mesopore size distribution. The effect of MWCNTs addition on the electrochemical performance of nanocomposite has been probed thoroughly in a normal three electrode configuration using 2 M KOH electrolyte at room temperature. Experimental results show that the addition of mere 5 mg MWCNTs into fixed NiFe2O4 precursors amount enhances the specific capacitance up to 1291 F g-1 at 1 A g-1, which is the highest reported value for NiFe2O4 nanocomposites so far. NiFe2O4/CNT nanocomposite exhibits small relaxation time constant (1.5 ms), good rate capability and capacitance retention of 81% over 500 charge-discharge cycles. This excellent performance can be assigned to high surface area, mesoporous structure of NiFe2O4 and conducting network formed by MWCNTs in the composite. Further, to evaluate the device performance of the composite, an asymmetric pseudocapacitor has been designed using NiFe2O4/CNT nanocomposite as a positive and N-doped graphene as a negative electrode material, respectively. Our designed asymmetric pseudocapacitor gives maximum energy density of 23 W h kg-1 at power density of 872 W kg-1. These promising results assert the potential of synthesized nanocomposite in the development of efficient practical high-capacitive energy storage devices.

Hydrogenase-3 contributes to anaerobic acid resistance of Escherichia coli.

Directory of Open Access Journals (Sweden)

Ken Noguchi

Full Text Available BACKGROUND: Hydrogen production by fermenting bacteria such as Escherichia coli offers a potential source of hydrogen biofuel. Because H(2 production involves consumption of 2H(+, hydrogenase expression is likely to involve pH response and regulation. Hydrogenase consumption of protons in E. coli has been implicated in acid resistance, the ability to survive exposure to acid levels (pH 2-2.5 that are three pH units lower than the pH limit of growth (pH 5-6. Enhanced survival in acid enables a larger infective inoculum to pass through the stomach and colonize the intestine. Most acid resistance mechanisms have been defined using aerobic cultures, but the use of anaerobic cultures will reveal novel acid resistance mechanisms. METHODS AND PRINCIPAL FINDINGS: We analyzed the pH regulation of bacterial hydrogenases in live cultures of E. coli K-12 W3110. During anaerobic growth in the range of pH 5 to 6.5, E. coli expresses three hydrogenase isoenzymes that reversibly oxidize H(2 to 2H(+. Anoxic conditions were used to determine which of the hydrogenase complexes contribute to acid resistance, measured as the survival of cultures grown at pH 5.5 without aeration and exposed for 2 hours at pH 2 or at pH 2.5. Survival of all strains in extreme acid was significantly lower in low oxygen than for aerated cultures. Deletion of hyc (Hyd-3 decreased anoxic acid survival 3-fold at pH 2.5, and 20-fold at pH 2, but had no effect on acid survival with aeration. Deletion of hyb (Hyd-2 did not significantly affect acid survival. The pH-dependence of H(2 production and consumption was tested using a H(2-specific Clark-type electrode. Hyd-3-dependent H(2 production was increased 70-fold from pH 6.5 to 5.5, whereas Hyd-2-dependent H(2 consumption was maximal at alkaline pH. H(2 production, was unaffected by a shift in external or internal pH. H(2 production was associated with hycE expression levels as a function of external pH. CONCLUSIONS: Anaerobic growing

Nanostructural and magnetic studies of virtually monodispersed NiFe2O4 nanocrystals synthesized by a liquid–solid-solution assisted hydrothermal route

International Nuclear Information System (INIS)

Li Xinghua; Tan Guoguo; Chen Wei; Zhou Baofan; Xue Desheng; Peng Yong; Li, Fashen; Mellors, Nigel J.

2012-01-01

This study presents a comprehensively and systematically structural, chemical and magnetic characterization of ∼9.5 nm virtually monodispersed nickel ferrite (NiFe 2 O 4 ) nanoparticles prepared using a modified liquid–solid-solution (LSS) assisted hydrothermal method. Lattice-resolution scanning transmission electron microscope (STEM) and converged beam electron diffraction pattern (CBED) techniques are adapted to characterize the detailed spatial morphology and crystal structure of individual NiFe 2 O 4 particles at nano scale for the first time. It is found that each NiFe 2 O 4 nanoparticle is single crystal with an fcc structure. The morphology investigation reveals that the prepared NiFe 2 O 4 nanoparticles of which the surfaces are decorated by oleic acid are dispersed individually in hexane. The chemical composition of nickel ferrite nanoparticles is measured to be 1:2 atomic ratio of Ni:Fe, indicating a pure NiFe 2 O 4 composition. Magnetic measurements reveal that the as-synthesized nanocrystals displayed superparamagnetic behavior at room temperature and were ferromagnetic at 10 K. The nanoscale characterization and magnetic investigation of monodispersed NiFe 2 O 4 nanoparticles should be significant for its potential applications in the field of biomedicine and magnetic fluid using them as magnetic materials.

Novel synthesis of Ni-ferrite (NiFe2O4) electrode material for supercapacitor applications

International Nuclear Information System (INIS)

Venkatachalam, V.; Jayavel, R.

2015-01-01

Novel nanocrystalline NiFe 2 O 4 has been synthesized through combustion route using citric acid as a fuel. Phase of the synthesized material was analyzed using powder X-ray diffraction. The XRD study revealed the formation of spinel phase cubic NiFe 2 O 4 with high crystallinity. The average crystallite size of NiFe 2 O 4 nanomaterial was calculated from scherrer equation. The electrochemical properties were realized by cyclic voltammetry, chronopotentiometry and electrochemical impedance spectroscopy. The electrode material shows a maximum specific capacitance of 454 F/g with pseudocapacitive behavior. High capacitance retention of electrode material over 1000 continuous charging-discharging cycles suggests its excellent electrochemical stability. The results revealed that the nickel ferrite electrode is a potential candidate for energy storage applications in supercapacitor

Construction and use of a Cupriavidus necator H16 soluble hydrogenase promoter (PSH fusion to gfp (green fluorescent protein

Directory of Open Access Journals (Sweden)

Bat-Erdene Jugder

2016-07-01

Full Text Available Hydrogenases are metalloenzymes that reversibly catalyse the oxidation or production of molecular hydrogen (H2. Amongst a number of promising candidates for application in the oxidation of H2 is a soluble [Ni–Fe] uptake hydrogenase (SH produced by Cupriavidus necator H16. In the present study, molecular characterisation of the SH operon, responsible for functional SH synthesis, was investigated by developing a green fluorescent protein (GFP reporter system to characterise PSH promoter activity using several gene cloning approaches. A PSH promoter-gfp fusion was successfully constructed and inducible GFP expression driven by the PSH promoter under de-repressing conditions in heterotrophic growth media was demonstrated in the recombinant C. necator H16 cells. Here we report the first successful fluorescent reporter system to study PSH promoter activity in C. necator H16. The fusion construct allowed for the design of a simple screening assay to evaluate PSH activity. Furthermore, the constructed reporter system can serve as a model to develop a rapid fluorescent based reporter for subsequent small-scale process optimisation experiments for SH expression.

Hydrogen from Water in a Novel Recombinant Cyanobacterial System

Energy Technology Data Exchange (ETDEWEB)

Weyman, Philip D [J. Craig Venter Institute; Smith, Hamillton O.

2014-12-03

Photobiological processes are attractive routes to renewable H2 production. With the input of solar energy, photosynthetic microbes such as cyanobacteria and green algae carry out oxygenic photosynthesis, using sunlight energy to extract protons and high energy electrons from water. These protons and high energy electrons can be fed to a hydrogenase system yielding H2. However, most hydrogen-evolving hydrogenases are inhibited by O2, which is an inherent byproduct of oxygenic photosynthesis. The rate of H2 production is thus limited. Certain photosynthetic bacteria are reported to have an O2-tolerant evolving hydrogenase, yet these microbes do not split water, and require other more expensive feedstocks. To overcome these difficulties, the goal of this work has been to construct novel microbial hybrids by genetically transferring O2-tolerant hydrogenases from other bacteria into a class of photosynthetic bacteria called cyanobacteria. These hybrid organisms will use the photosynthetic machinery of the cyanobacterial hosts to perform the water-oxidation reaction with the input of solar energy, and couple the resulting protons and high energy electrons to the O2-tolerant bacterial hydrogenase, all within the same microbe (Fig. 1). The ultimate goal of this work has been to overcome the sensitivity of the hydrogenase enzyme to O2 and address one of the key technological hurdles to cost-effective photobiological H2 production which currently limits the production of hydrogen in algal systems. In pursuit of this goal, work on this project has successfully completed many subtasks leading to a greatly increased understanding of the complicated [NiFe]-hydrogenase enzymes. At the beginning of this project, [NiFe] hydrogenases had never been successfully moved across wide species barriers and had never been heterologously expressed in cyanobacteria. Furthermore, the idea that whole, functional genes could be extracted from complicated, mixed-sequence meta-genomes was not

A feasibility study on SnO2/NiFe2O4 nanocomposites as anodes for Li ion batteries

International Nuclear Information System (INIS)

Balaji, S.; Vasuki, R.; Mutharasu, D.

2013-01-01

Highlights: ► The morphological analysis performed has shown the existence of nanocomposite. ► Sp. capacity after 50 cycles of pure NiFe 2 O 4 , 5 and 10 wt.% SnO 2 are 450, 750 and 780 mA h/g. ► The results are higher than the theoretical capacity of graphite (374 mA h/g). ► The capacity retention is also found to increase with SnO 2 addition in the NiFe 2 O 4 . ► Charge and discharge capacities of LiMn 2 O 4 vs. 10 wt.% SnO 2 /NiFe 2 O 4 are 232 and 138 mA h/g. -- Abstract: The SnO 2 /NiFe 2 O 4 nanocomposite samples with varying concentration of SnO 2 such as 5 wt.% and 10 wt.% were synthesized via urea assisted combustion synthesis. The kinetics of the combustion reactions were studied using thermo gravimetry analysis and from which the compound formation temperature of all the samples were observed to be below 400 °C. From the morphological analysis the grain size of NiFe 2 O 4 , 5 wt.% SnO 2 /NiFe 2 O 4 and 10 wt.% SnO 2 /NiFe 2 O 4 samples were observed to be around 1.7, 2.3 and 3.5 μm. The chrono potentiometry analyses of the samples were performed against lithium metal electrode. The capacity retention was found to be higher for composite with 10 wt.% SnO 2 . The discharge capacity of 10 wt.% SnO 2 sample with respect to Li metal and LiMn 2 O 4 electrode was observed to be around 980 mA h/g and 138 mA h/g respectively

Soft magnetic properties of hybrid ferromagnetic films with CoFe, NiFe, and NiFeCuMo layers

Energy Technology Data Exchange (ETDEWEB)

Choi, Jong-Gu [Eastern-western Biomedical Engineering, Sangji University, Wonju 220-702 (Korea, Republic of); Hwang, Do-Guwn [Dept. of Oriental Biomedical Engineering, Sangji University, Wonju 220-702 (Korea, Republic of); Rhee, Jang-Roh [Dept. of Physics, Sookmyung Women' s University, Seoul 140-742 (Korea, Republic of); Lee, Sang-Suk, E-mail: sslee@sangji.ac.kr [Dept. of Oriental Biomedical Engineering, Sangji University, Wonju 220-702 (Korea, Republic of)

2011-09-30

Two-layered ferromagnetic alloy films (NiFe and CoFe) with intermediate NiFeCuMo soft magnetic layers of different thicknesses were investigated to understand the relationship between coercivity and magnetization process by taking into account the strength of hard-axis saturation field. The thickness dependence of H{sub EC} (easy-axis coercivity), H{sub HS} (hard-axis saturation field), and {chi} (susceptibility) of the NiFeCuMo thin films in glass/Ta(5 nm)/[CoFe or NiFe(5 nm-t/2)]/NiFeCuMo(t = 0, 4, 6, 8, 10 nm)/[CoFe or NiFe(5 nm-t/2)]/Ta(5 nm) films prepared using the ion beam deposition method was determined. The magnetic properties (H{sub EC}, H{sub HS}, and {chi}) of the ferromagnetic CoFe, NiFe three-layers with an intermediate NiFeCuMo super-soft magnetic layer were strongly dependent on the thickness of the NiFeCuMo layer.

Alloyed Ni-Fe nanoparticles as catalysts for NH₃ decomposition

DEFF Research Database (Denmark)

Simonsen, Søren Bredmose; Chakraborty, Debasish; Chorkendorff, Ib

2012-01-01

A rational design approach was used to develop an alloyed Ni-Fe/Al2O3 catalyst for decomposition of ammonia. The dependence of the catalytic activity is tested as a function of the Ni-to-Fe ratio, the type of Ni-Fe alloy phase, the metal loading and the type of oxide support. In the tests with high...... temperatures and a low NH3-to-H2 ratio, the catalytic activity of the best Ni-Fe/Al2O3 catalyst was found to be comparable or even better to that of a more expensive Ru-based catalyst. Small Ni-Fe nanoparticle sizes are crucial for an optimal overall NH3 conversion because of a structural effect favoring...

Proteolytic cleavage orchestrates cofactor insertion and protein assembly in [NiFe]-hydrogenase biosynthesis.

Science.gov (United States)

Senger, Moritz; Stripp, Sven T; Soboh, Basem

2017-07-14

Metalloenzymes catalyze complex and essential processes, such as photosynthesis, respiration, and nitrogen fixation. For example, bacteria and archaea use [NiFe]-hydrogenases to catalyze the uptake and release of molecular hydrogen (H 2 ). [NiFe]-hydrogenases are redox enzymes composed of a large subunit that harbors a NiFe(CN) 2 CO metallo-center and a small subunit with three iron-sulfur clusters. The large subunit is synthesized with a C-terminal extension, cleaved off by a specific endopeptidase during maturation. The exact role of the C-terminal extension has remained elusive; however, cleavage takes place exclusively after assembly of the [NiFe]-cofactor and before large and small subunits form the catalytically active heterodimer. To unravel the functional role of the C-terminal extension, we used an enzymatic in vitro maturation assay that allows synthesizing functional [NiFe]-hydrogenase-2 of Escherichia coli from purified components. The maturation process included formation and insertion of the NiFe(CN) 2 CO cofactor into the large subunit, endoproteolytic cleavage of the C-terminal extension, and dimerization with the small subunit. Biochemical and spectroscopic analysis indicated that the C-terminal extension of the large subunit is essential for recognition by the maturation machinery. Only upon completion of cofactor insertion was removal of the C-terminal extension observed. Our results indicate that endoproteolytic cleavage is a central checkpoint in the maturation process. Here, cleavage temporally orchestrates cofactor insertion and protein assembly and ensures that only cofactor-containing protein can continue along the assembly line toward functional [NiFe]-hydrogenase. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Characterization of NiFe oxyhydroxide electrocatalysts by integrated electronic structure calculations and spectroelectrochemistry

Energy Technology Data Exchange (ETDEWEB)

Goldsmith, Zachary K.; Harshan, Aparna K.; Gerken, James B.; Vörös, Márton; Galli, Giulia; Stahl, Shannon S.; Hammes-Schiffer, Sharon

2017-03-06

NiFe oxyhydroxide materials are highly active electrocatalysts for the oxygen evolution reaction (OER), an important process for carbon-neutral energy storage. Recent spectroscopic and computational studies increasingly support iron as the site of catalytic activity but differ with respect to the relevant iron redox state. A combination of hybrid periodic density functional theory calculations and spectroelectrochemical experiments elucidate the electronic structure and redox thermodynamics of Ni-only and mixed NiFe oxyhydroxide thin-film electrocatalysts. The UV/visible light absorbance of the Ni-only catalyst depends on the applied potential as metal ions in the film are oxidized before the onset of OER activity. In contrast, absorbance changes are negligible in a 25% Fe-doped catalyst up to the onset of OER activity. First-principles calculations of proton-coupled redox potentials and magnetizations reveal that the Ni-only system features oxidation of Ni2+ to Ni3+, followed by oxidation to a mixed Ni3+/4+ state at a potential coincident with the onset of OER activity. Calculations on the 25% Fedoped system show the catalyst is redox inert before the onset of catalysis, which coincides with the formation of Fe4+ and mixed Ni oxidation states. The calculations indicate that introduction of Fe dopants changes the character of the conduction band minimum from Ni-oxide in the Ni-only to predominantly Fe-oxide in the NiFe electrocatalyst. These findings provide a unified experimental and theoretical description of the electrochemical and optical properties of Ni and NiFe oxyhydroxide electrocatalysts and serve as an important benchmark for computational characterization of mixedmetal oxidation states in heterogeneous catalysts.

Interplay between out-of-plane anisotropic L1{sub 1}-type CoPt and in-plane anisotropic NiFe layers in CoPt/NiFe exchange springs

Energy Technology Data Exchange (ETDEWEB)

Saravanan, P. [Department of Physics, National Taiwan University, Taipei 106, Taiwan (China); Defence Metallurgical Research Laboratory, Hyderabad 500058 (India); Hsu, Jen-Hwa, E-mail: jhhsu@phys.ntu.edu.tw; Tsai, C. L. [Department of Physics, National Taiwan University, Taipei 106, Taiwan (China); Tsai, C. Y.; Lin, Y. H. [Graduate Institute of Materials Science and Engineering, National Taiwan University, Taipei 106, Taiwan (China); Kuo, C. Y.; Wu, J.-C. [Department of Physics, National Chang Hua University of Education, Chang Hua 50000, Taiwan (China); Lee, C.-M. [Graduate School of Materials Science, National Yunlin University of Science and Technology, Douliou 64002, Taiwan (China)

2014-06-28

Films of L1{sub 1}-type CoPt/NiFe exchange springs were grown with different NiFe (Permalloy) layer thickness (t{sub NiFe} = 0–10 nm). X-ray diffraction analysis reveals that the characteristic peak position of NiFe(111) is not affected by the CoPt-layer—confirming the absence of any inter-diffusion between the CoPt and NiFe layers. Magnetic studies indicate that the magnetization orientation of NiFe layer can be tuned through varying t{sub NiFe} and the perpendicular magnetic anisotropy of L1{sub 1}-type CoPt/NiFe films cannot sustain for t{sub NiFe} larger than 3.0 nm due to the existence of exchange interaction at the interface of L1{sub 1}-CoPt and NiFe layers. Magnetic force microscopy analysis on the as-grown samples shows the changes in morphology from maze-like domains with good contrast to hazy domains when t{sub NiFe} ≥ 3.0 nm. The three-dimensional micro-magnetic simulation results demonstrate that the magnetization orientation in NiFe layer is not uniform, which continuously increases from the interface to the top of NiFe layer. Furthermore, the tilt angle of the topmost NiFe layers can be changed over a very wide range from a small number to about 75° by varying t{sub NiFe} from 1 to 10 nm. It is worth noting that there is an abrupt change in the magnetization direction at the interface, for all the t{sub NiFe} investigated. The results of present study demonstrate that the tunable tilted exchange springs can be realized with L1{sub 1}-type CoPt/NiFe bilayers for future applications in three-axis magnetic sensors or advanced spintronic devices demanding inclined magnetic anisotropy.

Polymer stabilized Ni-Ag and Ni-Fe alloy nanoclusters: Structural and magnetic properties

Energy Technology Data Exchange (ETDEWEB)

Kabir, L.; Mandal, A.R. [Department of Physics, Visva-Bharati, Santiniketan-731 235 (India); Mandal, S.K., E-mail: sk_mandal@hotmail.co [Department of Physics, Visva-Bharati, Santiniketan-731 235 (India)

2010-04-15

We report here the structural and magnetic behaviors of nickel-silver (Ni-Ag) and nickel-iron (Ni-Fe) nanoclusters stabilized with polymer (polypyrrole). High resolution transmission electron microscopy (HRTEM) indicates Ni-Ag nanoclusters to stabilize in core-shell configuration while that of Ni-Fe nanoclusters in a mixed type of geometry. Structural characterizations by X-ray diffraction (XRD) reveal the possibility of alloying in such bimetallic nanoclusters to some extent even at temperatures much lower than that of bulk alloying. Electron paramagnetic resonance (EPR) spectra clearly reveal two different absorption behaviors: one is ascribed to non-isolated Ni{sup 2+} clusters surrounded by either silver or iron giving rise to a broad signal, other (very narrow signal) being due to the isolated superparamagnetic Ni{sup 2+} clusters or bimetallic alloy nanoclusters. Results obtained for Ni-Ag and Ni-Fe nanoclusters have been further compared with the behavior exhibited by pure Ni nanoclusters in polypyrrole host. Temperature dependent studies (at 300 and 77 K) of EPR parameters, e.g. linewidth, g-value, line shape and signal intensity indicating the significant influence of surrounding paramagnetic silver or ferromagnetic iron within polymer host on the EPR spectra have been presented.

Polymer stabilized Ni-Ag and Ni-Fe alloy nanoclusters: Structural and magnetic properties

Science.gov (United States)

Kabir, L.; Mandal, A. R.; Mandal, S. K.

2010-04-01

We report here the structural and magnetic behaviors of nickel-silver (Ni-Ag) and nickel-iron (Ni-Fe) nanoclusters stabilized with polymer (polypyrrole). High resolution transmission electron microscopy (HRTEM) indicates Ni-Ag nanoclusters to stabilize in core-shell configuration while that of Ni-Fe nanoclusters in a mixed type of geometry. Structural characterizations by X-ray diffraction (XRD) reveal the possibility of alloying in such bimetallic nanoclusters to some extent even at temperatures much lower than that of bulk alloying. Electron paramagnetic resonance (EPR) spectra clearly reveal two different absorption behaviors: one is ascribed to non-isolated Ni 2+ clusters surrounded by either silver or iron giving rise to a broad signal, other (very narrow signal) being due to the isolated superparamagnetic Ni 2+ clusters or bimetallic alloy nanoclusters. Results obtained for Ni-Ag and Ni-Fe nanoclusters have been further compared with the behavior exhibited by pure Ni nanoclusters in polypyrrole host. Temperature dependent studies (at 300 and 77 K) of EPR parameters, e.g. linewidth, g-value, line shape and signal intensity indicating the significant influence of surrounding paramagnetic silver or ferromagnetic iron within polymer host on the EPR spectra have been presented.

Polymer stabilized Ni-Ag and Ni-Fe alloy nanoclusters: Structural and magnetic properties

International Nuclear Information System (INIS)

Kabir, L.; Mandal, A.R.; Mandal, S.K.

2010-01-01

We report here the structural and magnetic behaviors of nickel-silver (Ni-Ag) and nickel-iron (Ni-Fe) nanoclusters stabilized with polymer (polypyrrole). High resolution transmission electron microscopy (HRTEM) indicates Ni-Ag nanoclusters to stabilize in core-shell configuration while that of Ni-Fe nanoclusters in a mixed type of geometry. Structural characterizations by X-ray diffraction (XRD) reveal the possibility of alloying in such bimetallic nanoclusters to some extent even at temperatures much lower than that of bulk alloying. Electron paramagnetic resonance (EPR) spectra clearly reveal two different absorption behaviors: one is ascribed to non-isolated Ni 2+ clusters surrounded by either silver or iron giving rise to a broad signal, other (very narrow signal) being due to the isolated superparamagnetic Ni 2+ clusters or bimetallic alloy nanoclusters. Results obtained for Ni-Ag and Ni-Fe nanoclusters have been further compared with the behavior exhibited by pure Ni nanoclusters in polypyrrole host. Temperature dependent studies (at 300 and 77 K) of EPR parameters, e.g. linewidth, g-value, line shape and signal intensity indicating the significant influence of surrounding paramagnetic silver or ferromagnetic iron within polymer host on the EPR spectra have been presented.

Cyanobacterial hydrogenases and biohydrogen: present status and future potential

International Nuclear Information System (INIS)

Lindblad, P.; Tamagnini, P.

2000-01-01

Molecular hydrogen (H 2 ) is an environmentally clean energy-carrier that may be a valuable alternative to the limited fossil fuel resources of today. For photobiological H 2 production, photosynthetic cyanobacteria are among the ideal candidates since they have the simplest nutritional requirements: they can grow in air (N 2 and CO 2 ), water (electrons and reductant), and mineral salts with light (solar energy) as the only source of energy. In N 2 -fixing cyanobacteria, H 2 is mainly produced by nitrogenases, but its partial consumption is quickly catalyzed by a unidirectional uptake hydrogenase. In addition, a bidirectional (reversible) enzyme may also oxidize some of the molecular hydrogen. The same enzyme will, under certain conditions, evolve H 2 Filamentous cyanobacteria have been used in bioreactors for the photobiological conversion of water to hydrogen. However, the conversion efficiencies achieved are low because the net H 2 production is the result of H 2 evolution via a nitrogenase and H 2 consumption mainly via an uptake hydrogenase. Consequently, the improvements of the conversion efficiencies are achieved e.g. through the optimization of the conditions for H 2 evolution by nitrogenase, through the production of mutants deficient in H 2 uptake activity and by an increased H 2 -evolution by a bidirectional enzyme. Symbiotic cells are of fundamental interest since they in situ 'function as a bioreactor', High metabolism, transfer of metabolite(s) from symbiont to host but almost no growth. In the present communication we will present the general knowledge about hydrogen metabolism/hydrogenases in filamentous cyanobacteria focusing on recent advances using molecular techniques, outline strategies for improving the capacity of H 2 -production by filamentous strains, and stress the importance of international cooperations and networks. (author)

Exchange bias variations of the seed and top NiFe layers in NiFe/FeMn/NiFe trilayer as a function of seed layer thickness

International Nuclear Information System (INIS)

Sankaranarayanan, V.K.; Yoon, S.M.; Kim, C.G.; Kim, C.O.

2005-01-01

Development of exchange bias at the seed and top NiFe layers in the NiFe (t nm)/FeMn(10 nm)/NiFe(5 nm) trilayer structure is investigated as a function of seed layer thickness, in the range of 2-20 nm. The seed NiFe layer shows maximum exchange bias at 4 nm seed layer thickness. The bias shows inverse thickness dependence with increasing thickness. The top NiFe layer on the other hand shows only half the bias of the seed layer which is retained even after the sharp fall in seed layer bias. The much smaller bias for the top NiFe layer is related to the difference in crystalline texture and spin orientations at the top FeMn/NiFe interface, in comparison to the bottom NiFe/FeMn interface which grows on a saturated NiFe layer with (1 1 1) orientation

Genomic Analysis of Caldithrix abyssi, the Thermophilic Anaerobic Bacterium of the Novel Bacterial Phylum Calditrichaeota.

Science.gov (United States)

Kublanov, Ilya V; Sigalova, Olga M; Gavrilov, Sergey N; Lebedinsky, Alexander V; Rinke, Christian; Kovaleva, Olga; Chernyh, Nikolai A; Ivanova, Natalia; Daum, Chris; Reddy, T B K; Klenk, Hans-Peter; Spring, Stefan; Göker, Markus; Reva, Oleg N; Miroshnichenko, Margarita L; Kyrpides, Nikos C; Woyke, Tanja; Gelfand, Mikhail S; Bonch-Osmolovskaya, Elizaveta A

2017-01-01

The genome of Caldithrix abyssi , the first cultivated representative of a phylum-level bacterial lineage, was sequenced within the framework of Genomic Encyclopedia of Bacteria and Archaea (GEBA) project. The genomic analysis revealed mechanisms allowing this anaerobic bacterium to ferment peptides or to implement nitrate reduction with acetate or molecular hydrogen as electron donors. The genome encoded five different [NiFe]- and [FeFe]-hydrogenases, one of which, group 1 [NiFe]-hydrogenase, is presumably involved in lithoheterotrophic growth, three other produce H 2 during fermentation, and one is apparently bidirectional. The ability to reduce nitrate is determined by a nitrate reductase of the Nap family, while nitrite reduction to ammonia is presumably catalyzed by an octaheme cytochrome c nitrite reductase εHao. The genome contained genes of respiratory polysulfide/thiosulfate reductase, however, elemental sulfur and thiosulfate were not used as the electron acceptors for anaerobic respiration with acetate or H 2 , probably due to the lack of the gene of the maturation protein. Nevertheless, elemental sulfur and thiosulfate stimulated growth on fermentable substrates (peptides), being reduced to sulfide, most probably through the action of the cytoplasmic sulfide dehydrogenase and/or NAD(P)-dependent [NiFe]-hydrogenase (sulfhydrogenase) encoded by the genome. Surprisingly, the genome of this anaerobic microorganism encoded all genes for cytochrome c oxidase, however, its maturation machinery seems to be non-operational due to genomic rearrangements of supplementary genes. Despite the fact that sugars were not among the substrates reported when C. abyssi was first described, our genomic analysis revealed multiple genes of glycoside hydrolases, and some of them were predicted to be secreted. This finding aided in bringing out four carbohydrates that supported the growth of C. abyssi : starch, cellobiose, glucomannan and xyloglucan. The genomic analysis

Carbonized polydopamine coated single-crystalline NiFe2O4 nanooctahedrons with enhanced electrochemical performance as anode materials in a lithium ion battery

International Nuclear Information System (INIS)

Liu, Xinxin; Zhang, Tong; Qu, Yue; Tian, Ge; Yue, Huijuan; Zhang, Dong; Feng, Shouhua

2017-01-01

Graphical abstract: NiFe 2 O 4 @ NCweresuccessfullyfabricatedviaasubsequentcarbonizationofpolydopamine.(*) A nanocomposite containing 20% mass fraction of dopamine exhibited enhanced lithium ion battery performance with high reversible cycle capacity and good rate retention performance. - Highlights: • NiFe 2 O 4 nanooctahedrons were synthesized by a facile hydrothermal process. • A phase formation mechanism was studied by time-dependent experiments. • NiFe 2 O 4 with N-doped carbon shell was fabricated via carbonization of polydopamine. • NiFe 2 O 4 @NC 20 showed the best rate capability and cycle stability. - Abstract: Combining nanostructure engineering with conductive carbonaceous material is a promising strategy to obtain high-performance lithium ion batteries (LIBs). In this work, spinel NiFe 2 O 4 nanooctahedrons were initially synthesized at a low temperature without further annealing. We investigated the phase formation mechanism by time-dependent experiments. Next, octahedral NiFe 2 O 4 with a nitrogen-doped carbon shell (NiFe 2 O 4 @NC) were successfully fabricated via a subsequent carbonization of polydopamine (PDA). We systematically varied the dopamine content in the NiFe 2 O 4 /carbon nanocomposites and found that a nanocomposite containing 20% mass fraction of dopamine exhibited enhanced lithium ion battery performance with high reversible cycle capacity and good rate retention performance compared with the pure material. Remarkably, the hybrid nanocomposite delivered a high reversible capacity of 1297 mAh g −1 even after 50 cycles at a current density of 100 mA g −1 . Additionally, a high capacity of 1204 mAh g −1 was retained at a high current density of 500 mA g −1 after 300 cycles. This improvement in electrochemical performance is attributed to the enhanced structural stability and electrical conductivity caused by the carbon layer, and is supported by TEM and EIS measurements.

Catalytic Properties of the Isolated Diaphorase Fragment of the NAD+-Reducing [NiFe]-Hydrogenase from Ralstonia eutropha

Science.gov (United States)

Lauterbach, Lars; Idris, Zulkifli; Vincent, Kylie A.; Lenz, Oliver

2011-01-01

The NAD+-reducing soluble hydrogenase (SH) from Ralstonia eutropha H16 catalyzes the H2-driven reduction of NAD+, as well as reverse electron transfer from NADH to H+, in the presence of O2. It comprises six subunits, HoxHYFUI2, and incorporates a [NiFe] H+/H2 cycling catalytic centre, two non-covalently bound flavin mononucleotide (FMN) groups and an iron-sulfur cluster relay for electron transfer. This study provides the first characterization of the diaphorase sub-complex made up of HoxF and HoxU. Sequence comparisons with the closely related peripheral subunits of Complex I in combination with UV/Vis spectroscopy and the quantification of the metal and FMN content revealed that HoxFU accommodates a [2Fe2S] cluster, FMN and a series of [4Fe4S] clusters. Protein film electrochemistry (PFE) experiments show clear electrocatalytic activity for both NAD+ reduction and NADH oxidation with minimal overpotential relative to the potential of the NAD+/NADH couple. Michaelis-Menten constants of 56 µM and 197 µM were determined for NADH and NAD+, respectively. Catalysis in both directions is product inhibited with K I values of around 0.2 mM. In PFE experiments, the electrocatalytic current was unaffected by O2, however in aerobic solution assays, a moderate superoxide production rate of 54 nmol per mg of protein was observed, meaning that the formation of reactive oxygen species (ROS) observed for the native SH can be attributed mainly to HoxFU. The results are discussed in terms of their implications for aerobic functioning of the SH and possible control mechanism for the direction of catalysis. PMID:22016788

Optimized Expression and Purification for High-Activity Preparations of Algal [FeFe]-Hydrogenase

Energy Technology Data Exchange (ETDEWEB)

Yacoby, I.; Tegler, L. T.; Pochekailov, S.; Zhang, S.; King, P. W.

2012-04-01

Recombinant expression and purification of metallo-enzymes, including hydrogenases, at high-yields is challenging due to complex, and enzyme specific, post-translational maturation processes. Low fidelities of maturation result in preparations containing a significant fraction of inactive, apo-protein that are not suitable for biophysical or crystallographic studies. We describe the construction, overexpression and high-yield purification of a fusion protein consisting of the algal [2Fe2S]-ferredoxin PetF (Fd) and [FeFe]-hydrogenase HydA1. The maturation of Fd-HydA1 was optimized through improvements in culture conditions and media components used for expression. We also demonstrated that fusion of Fd to the N-terminus of HydA1, in comparison to the C-terminus, led to increased expression levels that were 4-fold higher. Together, these improvements led to enhanced HydA1 activity and improved yield after purification. The strong binding-affinity of Fd for DEAE allowed for two-step purification by ion exchange and StrepTactin affinity chromatography. In addition, the incorporation of a TEV protease site in the Fd-HydA1 linker allowed for the proteolytic removal of Fd after DEAE step, and purification of HydA1 alone by StrepTactin. In combination, this process resulted in HydA1 purification yields of 5 mg L{sup -1} of culture from E. coli with specific activities of 1000 U (U = 1 {micro}mol hydrogen evolved mg{sup -1} min{sup -1}). The [FeFe]-hydrogenases are highly efficient enzymes and their catalytic sites provide model structures for synthetic efforts to develop robust hydrogen activation catalysts. In order to characterize their structure-function properties in greater detail, and to use hydrogenases for biotechnological applications, reliable methods for rapid, high-yield expression and purification are required.

The key role of biochar in the rapid removal of decabromodiphenyl ether from aqueous solution by biochar-supported Ni/Fe bimetallic nanoparticles

Science.gov (United States)

Yi, Yunqiang; Wu, Juan; Wei, Yufen; Fang, Zhanqiang; Tsang, Eric Pokeung

2017-07-01

Some problems exist in the current remediation of polybrominated diphenyl ethers (PBDEs) from aqueous solution by using iron-based nanoparticles. Our efforts have contributed to the synthesis of biochar-supported Ni/Fe bimetallic nanoparticle composites (BC@Ni/Fe). Under the optimum operating parameters of BC@Ni/Fe, the morphologic analysis revealed that biochar effectively solved the agglomeration of Ni/Fe nanoparticles and the removal efficiency of BDE209 obtained by BC@Ni/Fe (91.29%) was seven times higher than the sum of biochar (2.55%) and Ni/Fe (11.22%) in 10 min. The degradation products of BDE209 in the solution and absorbed on the BC@Ni/Fe were analyzed with gas chromatography-mass spectroscopy, which indicated that the degradation of BDE209 was mainly a process of stepwise debromination. Meanwhile, compared with Ni/Fe nanoparticles, the adsorption ability of the by-products of BDE209 by BC@Ni/Fe was greater, to a certain extent, which reduced the additional environmental burden. In addition, the concentration of nickle ion leaching from the Ni/Fe nanoparticles was 3.09 mg/L; conversely, the concentration of nickle leaching from BC@Ni/Fe was not detected. This excellent performance in our study indicates a possible means to enhance the reactivity and reduce the secondary risks of Ni/Fe nanoparticles.

Hydrothermal Synthesis of NiFe2O4 nano-particles: Structural ...

Indian Academy of Sciences (India)

10

Cole plots are drawn to study electrical conduction mechanism and the kind of ... Zeiss), Transmission Electron Microscope (TEM: Model Tecnai G20, FEI, USA), JASCO ...... Z' Vs. Z" plot (Nyquist plot) of NiFe2O4 at room temperature (RT).

Biomimetic peptide-based models of [FeFe]-hydrogenases: utilization of phosphine-containing peptides

Energy Technology Data Exchange (ETDEWEB)

Roy, Souvik [Department of Chemistry and Biochemistry; Arizona State University; Tempe, USA; Nguyen, Thuy-Ai D. [Department of Chemistry and Biochemistry; Arizona State University; Tempe, USA; Gan, Lu [Department of Chemistry and Biochemistry; Arizona State University; Tempe, USA; Jones, Anne K. [Department of Chemistry and Biochemistry; Arizona State University; Tempe, USA

2015-01-01

Peptide based models for [FeFe]-hydrogenase were synthesized utilizing unnatural phosphine-amino acids and their electrocatalytic properties were investigated in mixed aqueous-organic solvents.

Cloning and knockout of formate hydrogen lyase and H{sub 2}-uptake hydrogenase genes in Enterobacter aerogenes for enhanced hydrogen production

Energy Technology Data Exchange (ETDEWEB)

Zhao, Hongxin; Ma, Kun; Lu, Yuan; Zhang, Chong; Wang, Liyan; Xing, Xin-Hui [Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Tsinghua Yuan, Beijing 100084 (China)

2009-01-15

A 5431-bp DNA fragment partially encoding the formate hydrogen lyase (FHL) gene cluster hycABCDE was isolated and identified from Enterobacter aerogenes IAM1183 chromosomal DNA. All the five putative gene products showed a high degree of homology to the reported bacterial FHL proteins. The gene hycA, encoding the FHL repressor protein, and hybO, encoding the small subunit of the uptake hydrogenase, were targeted for genetic knockout for improving the hydrogen production. The pYM-Red recombination system was adopted to form insertional mutations in the E. aerogenes genome, thereby creating mutant strains of IAM1183-A ({delta} hycA), IAM1183-O ({delta} hybO), and IAM1183-AO ({delta} hycA/ {delta} hybO double knockout). The hydrogen production experiments with these mutants showed that the maximum specific hydrogen productivities of IAM1183-A, IAM1183-O, and IAM1183-AO were 2879.466 {+-} 38.59, 2747.203 {+-} 13.25 and 3372.019 {+-} 4.39 (ml h{sup -1} g{sup -1}dry cell weight), respectively, higher than that of the wild strain (2321.861 {+-} 15.34 ml h{sup -1} g{sup -1}dry cell weight). The total H{sub 2} yields by the three mutants IAM1183-A, IAM1183-O and IAM1183-AO were 0.73, 0.78, and 0.83 mol-H{sub 2}/mol glucose, respectively, while the wild-type IAM1183 was only 0.65 mol-H{sub 2}/mol glucose. The metabolites of the mutants including acetate, ethanol, 2,3-butanediol and succinate were all increased compared with that of the wild type, implying the changed metabolic flux by the mutation. In the fermentor cultivation with IAM1183 {delta} hycA/ {delta} hybO, the total hydrogen volume after 16 h cultivation reached 4.4 L, while that for the wild type was only 2.9 L. (author)

Improved production of biohydrogen in light-powered Escherichia coli by co-expression of proteorhodopsin and heterologous hydrogenase

Directory of Open Access Journals (Sweden)

Kim Jaoon YH

2012-01-01

Full Text Available Abstract Background Solar energy is the ultimate energy source on the Earth. The conversion of solar energy into fuels and energy sources can be an ideal solution to address energy problems. The recent discovery of proteorhodopsin in uncultured marine γ-proteobacteria has made it possible to construct recombinant Escherichia coli with the function of light-driven proton pumps. Protons that translocate across membranes by proteorhodopsin generate a proton motive force for ATP synthesis by ATPase. Excess protons can also be substrates for hydrogen (H2 production by hydrogenase in the periplasmic space. In the present work, we investigated the effect of the co-expression of proteorhodopsin and hydrogenase on H2 production yield under light conditions. Results Recombinant E. coli BL21(DE3 co-expressing proteorhodopsin and [NiFe]-hydrogenase from Hydrogenovibrio marinus produced ~1.3-fold more H2 in the presence of exogenous retinal than in the absence of retinal under light conditions (70 μmole photon/(m2·s. We also observed the synergistic effect of proteorhodopsin with endogenous retinal on H2 production (~1.3-fold more with a dual plasmid system compared to the strain with a single plasmid for the sole expression of hydrogenase. The increase of light intensity from 70 to 130 μmole photon/(m2·s led to an increase (~1.8-fold in H2 production from 287.3 to 525.7 mL H2/L-culture in the culture of recombinant E. coli co-expressing hydrogenase and proteorhodopsin in conjunction with endogenous retinal. The conversion efficiency of light energy to H2 achieved in this study was ~3.4%. Conclusion Here, we report for the first time the potential application of proteorhodopsin for the production of biohydrogen, a promising alternative fuel. We showed that H2 production was enhanced by the co-expression of proteorhodopsin and [NiFe]-hydrogenase in recombinant E. coli BL21(DE3 in a light intensity-dependent manner. These results demonstrate that E. coli

Inactivation of uptake hydrogenase leads to enhanced and sustained hydrogen production with high nitrogenase activity under high light exposure in the cyanobacterium Anabaena siamensis TISTR 8012

Directory of Open Access Journals (Sweden)

Khetkorn Wanthanee

2012-10-01

Full Text Available Abstract Background Biohydrogen from cyanobacteria has attracted public interest due to its potential as a renewable energy carrier produced from solar energy and water. Anabaena siamensis TISTR 8012, a novel strain isolated from rice paddy field in Thailand, has been identified as a promising cyanobacterial strain for use as a high-yield hydrogen producer attributed to the activities of two enzymes, nitrogenase and bidirectional hydrogenase. One main obstacle for high hydrogen production by A. siamensis is a light-driven hydrogen consumption catalyzed by the uptake hydrogenase. To overcome this and in order to enhance the potential for nitrogenase based hydrogen production, we engineered a hydrogen uptake deficient strain by interrupting hupS encoding the small subunit of the uptake hydrogenase. Results An engineered strain lacking a functional uptake hydrogenase (∆hupS produced about 4-folds more hydrogen than the wild type strain. Moreover, the ∆hupS strain showed long term, sustained hydrogen production under light exposure with 2–3 folds higher nitrogenase activity compared to the wild type. In addition, HupS inactivation had no major effects on cell growth and heterocyst differentiation. Gene expression analysis using RT-PCR indicates that electrons and ATP molecules required for hydrogen production in the ∆hupS strain may be obtained from the electron transport chain associated with the photosynthetic oxidation of water in the vegetative cells. The ∆hupS strain was found to compete well with the wild type up to 50 h in a mixed culture, thereafter the wild type started to grow on the relative expense of the ∆hupS strain. Conclusions Inactivation of hupS is an effective strategy for improving biohydrogen production, in rates and specifically in total yield, in nitrogen-fixing cultures of the cyanobacterium Anabaena siamensis TISTR 8012.

Purification and characterization of [Fe]-hydrogenase from high yielding hydrogen-producing strain, Enterobacter cloacae IIT-BT08 (MTCC 5373)

Energy Technology Data Exchange (ETDEWEB)

Dutta, Tumpa; Das, Amit Kumar; Das, Debabrata [Department of Biotechnology, Indian Institute of Technology, Kharagpur, WB 721302 (India)

2009-09-15

Fe-hydrogenase from Enterobacter cloacae IIT-BT08 was purified 1284 fold with specific activity of 335 {mu}mol H{sub 2}/min/mg protein for hydrogen evolution using reduced methyl viologen as an electron-donor at 25 C. The molecular weight of the monomeric enzyme was determined to be 51 kDa by MALDI-ToF mass spectrometry. The PI of the enzyme was {proportional_to}5.6 displaying its acidic nature. The optimal temperature and pH for hydrogen evolution was 37 C and 7-7.2 respectively. The affinity constant, K{sub m} for reduced methyl viologen was 0.57 {+-} 0.03 mM and that of reduced ferredoxin was 0.72 {+-} 0.04 {mu}M. The enzyme contained {proportional_to}11.47 gm-atom Fe/mol of Fe-hydrogenase. Electron paramagnetic resonance analysis ascertained the existence of iron molecules as [4Fe-4S] clusters. The internal amino acid sequences of trypsin digested peptides of hydrogenase as determined by ESI MS/MS Q-ToF showed 80-87% identities with the respective sequences of Clostridium sp. and Trichomonas sp. hydrogenase. (author)

Cathodic Electrodeposition of Ni-Mo on Semiconducting NiFe2 O4 for Photoelectrochemical Hydrogen Evolution in Alkaline Media.

Science.gov (United States)

Wijten, Jochem H J; Jong, Ronald P H; Mul, Guido; Weckhuysen, Bert M

2018-04-25

Photocathodes for hydrogen evolution from water were made by electrodeposition of Ni-Mo layers on NiFe 2 O 4 substrates, deposited by spin coating on F:SnO 2 -glass. Analysis confirmed the formation of two separate layers, without significant reduction of NiFe 2 O 4 . Bare NiFe 2 O 4 was found to be unstable under alkaline conditions during (photo)electrochemistry. To improve the stability significantly, the deposition of a bifunctional Ni-Mo layer through a facile electrodeposition process was performed and the composite electrodes showed stable operation for at least 1 h. Moreover, photocurrents up to -2.1 mA cm -2 at -0.3 V vs. RHE were obtained for Ni-Mo/NiFe 2 O 4 under ambient conditions, showing that the new combination functions as both a stabilizing and catalytic layer for the photoelectrochemical evolution of hydrogen. The photoelectrochemical response of these composite electrodes decreased with increasing NiFe 2 O 4 layer thickness. Transient absorption spectroscopy showed that the lifetime of excited states is short and on the ns timescale. An increase in lifetime was observed for NiFe 2 O 4 of large layer thickness, likely explained by decreasing the defect density in the primary layer(s), as a result of repetitive annealing at elevated temperature. The photoelectrochemical and transient absorption spectroscopy results indicated that a short charge carrier lifetime limits the performance of Ni-Mo/NiFe 2 O 4 photocathodes. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Ni@Fe2O3 heterodimers: controlled synthesis and magnetically recyclable catalytic application for dehalogenation reactions

Science.gov (United States)

Nakhjavan, Bahar; Tahir, Muhammad Nawaz; Natalio, Filipe; Panthöfer, Martin; Gao, Haitao; Dietzsch, Michael; Andre, Rute; Gasi, Teuta; Ksenofontov, Vadim; Branscheid, Robert; Kolb, Ute; Tremel, Wolfgang

2012-07-01

Ni@Fe2O3 heterodimer nanoparticles (NPs) were synthesized by thermal decomposition of organometallic reactants. After functionalization, these Ni@Fe2O3 heterodimers became water soluble. The pristine heterodimeric NPs were characterized by transmission electron microscopy (TEM), X-ray diffraction (XRD), Mössbauer spectroscopy and magnetic susceptibility measurements. A special advantage of the heterodimers lies in the fact that nanodomains of different composition can be used as catalysts for the removal of environmentally hazardous halogenated pollutants.Ni@Fe2O3 heterodimer nanoparticles (NPs) were synthesized by thermal decomposition of organometallic reactants. After functionalization, these Ni@Fe2O3 heterodimers became water soluble. The pristine heterodimeric NPs were characterized by transmission electron microscopy (TEM), X-ray diffraction (XRD), Mössbauer spectroscopy and magnetic susceptibility measurements. A special advantage of the heterodimers lies in the fact that nanodomains of different composition can be used as catalysts for the removal of environmentally hazardous halogenated pollutants. Electronic supplementary information (ESI) available. See DOI: 10.1039/c2nr12121b

Synthesis and characterization of nanocomposite NiFe2O4 ...

African Journals Online (AJOL)

In this work, nano ferrite spinel NiFe2O4 was synthesized by sol-gel method and characterized by SEM, XRD, FT-IR, and VSM. In second step Schiff base made from salicylaldehyde and amino propyl triethoxy silane was used for modification of the synthesized nano ferrit. In the third step removal of Ni(II) was done using ...

Reducing agent (NaBH4) dependent structure, morphology and magnetic properties of nickel ferrite (NiFe2O4) nanorods

International Nuclear Information System (INIS)

Saravanakumar, B.; Rani, B. Jansi; Ravi, G.; Thambidurai, M.; Yuvakkumar, R.

2017-01-01

Nickel ferrite (Ni-Fe 2 O 4 ) nanorods were synthesized employing a simple chemical reduction method. Reducing agent (NaBH 4 ) influence on structural, morphological and magnetic properties of NiFe 2 O 4 nanorods was investigated. XRD results clearly revealed the presence of inverse cubic spinel nickel ferrite structure characteristic peaks and confirmed the site inversion of inverse spinel structure of Fe 3+ tetrahedral A site and Ni 2+ octahedral B site. The observed Raman characteristic peak at 488 and 683 cm −1 were corresponded to E 1 g and A 1 g mode whereas A and B site respectively corresponded to tetrahedral and octahedral site of NiFe 2 O 4 inverse spinel structure. The obtained PL peaks at 530 and 542 nm were attributed to the emission spectra of Fe 3+ ions in site A of inverse spinel structure and Ni 2+ ions in site B of inverse spinel structure respectively. SEM result clearly revealed that increase in NaBH 4 concentration had remarkable impact on nanorods formation, nano-octahedron structure, homogeneity and regularity of Ni-Ferrites. VSM studies clearly revealed the soft ferromagnetic nature of NiFe 2 O 4 and increase in NaBH 4 concentration further induced raise in metal cations concentration in A- and B- site which might impact the resultant magnetization of ferrites. - Highlights: • Nano rod formation has been initiated while increase of NaBH 4 concentration. • Further increasing NaBH 4 concentration favors nano-octahedron formation. • VSM studies revealed soft ferromagnetic nature of NiFe 2 O 4 .

In-situ confined formation of NiFe layered double hydroxide quantum dots in expanded graphite for active electrocatalytic oxygen evolution

Science.gov (United States)

Guo, Jinxue; Li, Xiaoyan; Sun, Yanfang; Liu, Qingyun; Quan, Zhenlan; Zhang, Xiao

2018-06-01

Development of noble-metal-free catalysts towards highly efficient electrochemical oxygen evolution reaction (OER) is critical but challenging in the renewable energy area. Herein, we firstly embed NiFe LDHs quantum dots (QDs) into expanded graphite (NiFe LDHs/EG) via in-situ confined formation process. The interlayer spacing of EG layers acts as nanoreactors for spatially confined formation of NiFe LDHs QDs. The QDs supply huge catalytic sites for OER. The in-situ decoration endows the strong affinity between QDs with EG, thus inducing fast charge transfer. Based on the aforementioned benefits, the designed catalyst exhibits outstanding OER properties, in terms of small overpotential (220 mV required to generate 10 mA cm-2), low Tafel slope, and good durable stability, making it a promising candidate for inexpensive OER catalyst.

Hydrothermal synthesis of NiFe2O4 nano-particles: structural ...

Indian Academy of Sciences (India)

2. Experimental. In order to synthesize NiFe2O4 nano-particles, Ni(NO3)2· ... Nickel and iron nitrates are dissolved in distilled ... are in good agreement with standard JCPDS: 86-2267. The ... in order to evaluate micro-strain (ε) and crystallite size (D) using the ..... Impedance spectroscopic studies are useful for investigating.

SYNTHESIS OF MAGNETIC NANOPARTICLES OF TiO2-NiFe2O4: CHARACTERIZATION AND PHOTOCATALYTIC ACTIVITY ON DEGRADATION OF RHODAMINE B

Directory of Open Access Journals (Sweden)

Rahmayeni Rahmayeni

2012-12-01

Full Text Available Magnetic nanoparticles of TiO2-(xNiFe2O4 with x = 0.01, 0.1, and 0.3have been synthesized by mixture of titanium isopropoxide (TIP and nitric metal as precursors. The particles were characterized by XRD, SEM-EDX, and VSM. XRD pattern show the peaks at 2q = 25.3°, 38.4° and 47.9° which are referred as anatase phase of TiO2. Meanwhile NiFe2O4 phase was observed clearly for x = 0.3. The present of NiFe2O4 can prevent the transformation of TiO2 from anatase to rutile when the calcination temperature increased. Microstructure analyses by SEM show the homogeneous form and size of particles. The magnetic properties analysis by VSM indicates that TiO2-NiFe2O4 is paramagnetic behavior. TiO2 doped NiFe2O4 has higher photocatalytic activity than TiO2 synthesized for degradation of Rhodamine B in aqueous solution under solar light irradiation.

Phase and magnetic studies of the high-energy alloyed Ni-Fe

Czech Academy of Sciences Publication Activity Database

Jirásková, Yvonna; Buršík, Jiří; Turek, Ilja; Hapla, Miroslav; Titov, A.; Životský, O.

2014-01-01

Roč. 594, May (2014), s. 133-140 ISSN 0925-8388 R&D Projects: GA ČR(CZ) GAP108/11/1350 Grant - others:VŠB(CZ) CZ.1.07/2.3.00/20.0074 Institutional support: RVO:68081723 Keywords : Ni-Fe * mechanical alloying * magnetic properties * microstructure * particle interactions Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 2.999, year: 2014

Using Gas Chromatography/Isotope Ratio Mass Spectrometry to Determine the Fractionation Factor for H2 Production by Hydrogenases

International Nuclear Information System (INIS)

Yang, Hui; Ghandi, H.; Shi, Liang; Kreuzer, Helen W.; Ostrom, Nathaniel; Hegg, Eric L.

2012-01-01

Hydrogenases catalyze the reversible formation of H2, and they are key enzymes in the biological cycling of H2. H isotopes should be a very useful tool in quantifying proton trafficking in biological H2 production processes, but there are several obstacles that have thus far limited the use of this tool. In this manuscript, we describe a new method that overcomes some of these barriers and is specifically designed to measure isotopic fractionation during enzyme-catalyzed H2 evolution. A key feature of this technique is that purified hydrogenases are employed, allowing precise control over the reaction conditions and therefore a high level of precision. A custom-designed high-throughput gas chromatography-isotope ratio mass spectrometer is employed to measure the isotope ratio of the H2. Using this method, we determined that the fractionation factor of H2 production by the (NiFe)-hydrogenase from Desulfivibrio fructosovran is 0.27. This result indicates that, as expected, protons are highly favored over deuterons during H2 evolution. Potential applications of this new method are discussed.

NiFe2O4 nanoparticles decorated activated carbon nanocomposite ...

Indian Academy of Sciences (India)

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Figure S4. Standard deviation plot and DPV response of blank voltammogram on NiFe2O4-. AC/GCE……..5 ... plot (µA µM-1). m= 0.47 µA µM-1. Sm is defined as. Sm = Sbl + kσbl. (3). Where k is a number illustrating the confidence level of the detection, usually 3 and σbl is the standard deviation of the blank (0.063 µA).

Investigation of the magnetic properties of electrodeposited NiFe thin films

International Nuclear Information System (INIS)

Bakkaloglu, O. F.; Bedir, M.; Oeztas, M.; Karahan, I. H.

2002-01-01

Most magnetic devices used today are based on the magnetic thin film. Rapid and extensive developments in magnetic sensor / actuator and magnetic recording technology place a growing demand on the use of different thin film fabrication techniques for magnetic materials. The electroplating technique is especially interesting due to its low cost, high throughput and high quality of the deposits which are extensively used in the magnetic recording industry to deposit relatively thick permalloy layers. Much recent attention has focused on the electrodeposited NiFe thin films, which exhibit giant magneto resistive behaviour as well as anisotropic magnetoresistance properties. n this study, NiFe thin films were developed by using electrodeposition technique and their crystallinity structures were investigated by using x-ray diffractometer measurements. The magneto resistive properties of the samples were investigated by Wan der Pauw method with a home made electromagnet under the different magnetic fields. The magnetoresistance measurements of the samples were carried out in two configurations; current parallel ( longitudinal ) and perpendicular ( transverse ) to the magnetic field. In the longitudinal configuration giant magnetoresistance was observed while anisotropic magnetoresistance was detected in the other configuration

Evaluation of alloying effect on the formation of Ni-Fe nanosized powders by pulsed wire discharge

International Nuclear Information System (INIS)

Park, Gyu-Hyeon; Lee, Gwang-Yeob; Kim, Hyeon-Ah; Lee, A-Young; Oh, Hye-Ryeong; Kim, Song-Yi; Kim, Do-Hyang; Lee, Min-Ha

2016-01-01

Highlights: • Synthesizing Ni-Fe alloy nano-powder employing Ni-plating layer of Fe wire by PWD process. • The mean particle size is decreased with increasing the charging voltage affecting to the super heating factor (K). • The mean particle size of PWD Ni-Fe nanosized powder is accordance with applied voltage. • Uniformity of mean particel size can be controlled by adjusting charging voltage and super heating factor (K). - Abstract: This study investigates the effects of varying the explosion time and charging voltage of pulsed wire discharge (PWD) on the mean particle size, dispersibility and alloying reliability of powders produced from pure Ni and Ni-plated Fe wires. It was found that with increasing charging voltage, the mean particle size of Ni powders is reduced from 40.11 ± 0.23 to 25.63 ± 0.07 nm, which is attributed to a change in the extent of super heating with particle size. Nanosized powders of Ni-Fe alloy with a mean particle size between 25.91 ± 0.24 and 26.30 ± 0.26 nm were also successfully fabricated and found to consist of particles with a γ-(Ni/Fe) core and FeO shell. The reliability for the optimization of processing parameters to control particle sizes is also evaluated.

Evaluation of alloying effect on the formation of Ni-Fe nanosized powders by pulsed wire discharge

Energy Technology Data Exchange (ETDEWEB)

Park, Gyu-Hyeon [Advanced Functional Materials R& D Group, Korea Institute of Industrial Technology, Incheon 406-840 (Korea, Republic of); Lee, Gwang-Yeob [Advanced Analysis Center, Korea Institute of Science and Technology, Seoul 136-791 (Korea, Republic of); Deparment of Advanced Materials Engineering, Yonsei University, Seoul 120-749 (Korea, Republic of); Kim, Hyeon-Ah [Advanced Functional Materials R& D Group, Korea Institute of Industrial Technology, Incheon 406-840 (Korea, Republic of); Deparment of Advanced Materials Engineering, Yonsei University, Seoul 120-749 (Korea, Republic of); Lee, A-Young; Oh, Hye-Ryeong; Kim, Song-Yi [Advanced Functional Materials R& D Group, Korea Institute of Industrial Technology, Incheon 406-840 (Korea, Republic of); Kim, Do-Hyang [Deparment of Advanced Materials Engineering, Yonsei University, Seoul 120-749 (Korea, Republic of); Lee, Min-Ha, E-mail: mhlee1@kitech.re.kr [Advanced Functional Materials R& D Group, Korea Institute of Industrial Technology, Incheon 406-840 (Korea, Republic of)

2016-10-15

Highlights: • Synthesizing Ni-Fe alloy nano-powder employing Ni-plating layer of Fe wire by PWD process. • The mean particle size is decreased with increasing the charging voltage affecting to the super heating factor (K). • The mean particle size of PWD Ni-Fe nanosized powder is accordance with applied voltage. • Uniformity of mean particel size can be controlled by adjusting charging voltage and super heating factor (K). - Abstract: This study investigates the effects of varying the explosion time and charging voltage of pulsed wire discharge (PWD) on the mean particle size, dispersibility and alloying reliability of powders produced from pure Ni and Ni-plated Fe wires. It was found that with increasing charging voltage, the mean particle size of Ni powders is reduced from 40.11 ± 0.23 to 25.63 ± 0.07 nm, which is attributed to a change in the extent of super heating with particle size. Nanosized powders of Ni-Fe alloy with a mean particle size between 25.91 ± 0.24 and 26.30 ± 0.26 nm were also successfully fabricated and found to consist of particles with a γ-(Ni/Fe) core and FeO shell. The reliability for the optimization of processing parameters to control particle sizes is also evaluated.

An investigation of thin-film Ni-Fe oxide catalysts for the electrochemical evolution of oxygen.

Science.gov (United States)

Louie, Mary W; Bell, Alexis T

2013-08-21

A detailed investigation has been carried out of the structure and electrochemical activity of electrodeposited Ni-Fe films for the oxygen evolution reaction (OER) in alkaline electrolytes. Ni-Fe films with a bulk and surface composition of 40% Fe exhibit OER activities that are roughly 2 orders of magnitude higher than that of a freshly deposited Ni film and about 3 orders of magnitude higher than that of an Fe film. The freshly deposited Ni film increases in activity by as much as 20-fold during exposure to the electrolyte (KOH); however, all films containing Fe are stable as deposited. The oxidation of Ni(OH)2 to NiOOH in Ni films occurs at potentials below the onset of the OER. Incorporation of Fe into the film increases the potential at which Ni(OH)2/NiOOH redox occurs and decreases the average oxidation state of Ni in NiOOH. The Tafel slope (40 mV dec(-1)) and reaction order in OH(-) (1) for the mixed Ni-Fe films (containing up to 95% Fe) are the same as those for aged Ni films. In situ Raman spectra acquired in 0.1 M KOH at OER potentials show two bands characteristic of NiOOH. The relative intensities of these bands vary with Fe content, indicating a change in the local environment of Ni-O. Similar changes in the relative intensities of the bands and an increase in OER activity are observed when pure Ni films are aged. These observations suggest that the OER is catalyzed by Ni in Ni-Fe films and that the presence of Fe alters the redox properties of Ni, causing a positive shift in the potential at which Ni(OH)2/NiOOH redox occurs, a decrease in the average oxidation state of the Ni sites, and a concurrent increase in the activity of Ni cations for the OER.

In vitro hydrogen production by glucose dehydrogenase and hydrogenase

Energy Technology Data Exchange (ETDEWEB)

Woodward, J. [Oak Ridge National Lab., TN (United States)

1996-10-01

A new in vitro enzymatic pathway for the generation of molecular hydrogen from glucose has been demonstrated. The reaction is based upon the oxidation of glucose by Thermoplasma acidophilum glucose dehydrogenase with the concomitant oxidation of NADPH by Pyrococcus furiosus hydrogenase. Stoichiometric yields of hydrogen were produced from glucose with continuous cofactor recycle. This simple system may provide a method for the biological production of hydrogen from renewable sources. In addition, the other product of this reaction, gluconic acid, is a high-value commodity chemical.

Magnetic anisotropy and giant magnetoimpedance in NiFe electroplated on Cu wires

Czech Academy of Sciences Publication Activity Database

Kraus, Luděk; Butta, M.; Ripka, P.

2013-01-01

Roč. 11, č. 1 (2013), s. 53-55 ISSN 1546-198X R&D Projects: GA ČR GAP102/12/2177 Institutional research plan: CEZ:AV0Z10100520 Keywords : nife films * electrodeposition * magnetic anisotropy Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 0.558, year: 2013 http://dx.doi.org/10.1166/sl.2013.2791

Size-controlled synthesis of NiFe2O4 nanospheres via a PEG assisted hydrothermal route and their catalytic properties in oxidation of alcohols by periodic acid

International Nuclear Information System (INIS)

Paul, Bappi; Purkayastha, Debraj Dhar; Dhar, Siddhartha Sankar

2016-01-01

Graphical abstract: - Highlights: • Hydrothermal synthesis of NiFe 2 O 4 NPs with (C 4 H 9 ) 3 N as hydroxylating agent. • PEG 4000 was used as surfactant to control sizes of NPs. • The TEM images revealed the material to be spherical in shape with sizes 2–10 nm. • NiFe 2 O 4 was used as recyclable catalyst for oxidation of alcohols by periodic acid. - Abstract: A novel and facile approach for synthesis of spinel nickel ferrites (NiFe 2 O 4 ) nanoparticles (NPs) employing homogeneous chemical precipitation followed by hydrothermal heating is reported. The synthesis involves use of tributylamine (TBA) as a hydroxylating agent in synthesis of nickel ferrites. Polyethylene glycol (PEG) 4000 was used as surfactant. As-synthesized NiFe 2 O 4 NPs were characterized by powder X-ray diffraction (XRD), transmission electron microscopy (TEM), N 2 adsorption–desorption isotherm (BET) and vibrating sample magnetometry (VSM). The XRD pattern revealed formation of cubic face-centered NiFe 2 O 4 and TEM image showed spherical particles of sizes 2–10 nm. These NiFe 2 O 4 NPs were used as magnetically recoverable catalyst in oxidation of cyclic alcohols to their corresponding aldehydes by periodic acid. This eco-friendly procedure affords products in very high yield and selectivity. The reusability of the catalyst is proved to be noteworthy as the material exhibits no significant changes in its catalytic activity even after five cycles of reuse.

Cell-free H-cluster synthesis and [FeFe] hydrogenase activation: all five CO and CN⁻ ligands derive from tyrosine.

Directory of Open Access Journals (Sweden)

Jon M Kuchenreuther

Full Text Available [FeFe] hydrogenases are promising catalysts for producing hydrogen as a sustainable fuel and chemical feedstock, and they also serve as paradigms for biomimetic hydrogen-evolving compounds. Hydrogen formation is catalyzed by the H-cluster, a unique iron-based cofactor requiring three carbon monoxide (CO and two cyanide (CN⁻ ligands as well as a dithiolate bridge. Three accessory proteins (HydE, HydF, and HydG are presumably responsible for assembling and installing the H-cluster, yet their precise roles and the biosynthetic pathway have yet to be fully defined. In this report, we describe effective cell-free methods for investigating H-cluster synthesis and [FeFe] hydrogenase activation. Combining isotopic labeling with FTIR spectroscopy, we conclusively show that each of the CO and CN⁻ ligands derive respectively from the carboxylate and amino substituents of tyrosine. Such in vitro systems with reconstituted pathways comprise a versatile approach for studying biosynthetic mechanisms, and this work marks a significant step towards an understanding of both the protein-protein interactions and complex reactions required for H-cluster assembly and hydrogenase maturation.

Hydrogenase activity in Azospirillum brasilense is inhibited by nitrite, nitric oxide, carbon monoxide, and acetylene

Energy Technology Data Exchange (ETDEWEB)

Tibelius, K.H.; Knowles, R.

1984-10-01

Nitrite, NO, CO, and C/sub 2/H/sub 2/ inhibited O/sub 2/-dependent H/sub 2/ uptake (H/sup 3/H oxidation) in denitrifying Azospirillum brasilense Sp7 grown anaerobically on N/sub 2/O or NO/sub 3//sup -/. The apparent K/sub i/ values for inhibition of O/sub 2/-dependent H/sub 2/ uptake were 20 ..mu..M for NO/sub 2//sup -/, 0.4 ..mu..M for NO, 28 ..mu..M for CO, and 88 ..mu..M for C/sub 2/H/sub 2/. These inhibitors also affected methylene blue-dependent H/sub 2/ uptake, presumably by acting directly on the hydrogenase. Nitrite and NO inhibited H/sub 2/ uptake irreversibly, whereas inhibition due to CO was easily reversed by repeatedly evacuating and backfilling with N/sub 2/. The C/sub 2/H/sub 2/ inhibition was not readily reversed, partly due to difficulty in removing the last traces of this gas from solution. The NO/sub 2//sup -/ inhibition of malate-dependent respiration was readily reversed by repeatedly washing the cells, in contrast to the effect of NO/sub 2//sup -/ on H/sub 2/-dependent respiration. These results suggest that the low hydrogenase activities observed in NO/sub 3//sup -/-grown cultures of A. brasilense may be due to the irreversible inhibition of hydrogenase by NO/sub 2//sup -/ and NO produced by NO/sub 3//sup -/ reduction.

Reaction Coordinate Leading to H2 Production in [FeFe]-Hydrogenase Identified by Nuclear Resonance Vibrational Spectroscopy and Density Functional Theory.

Science.gov (United States)

Pelmenschikov, Vladimir; Birrell, James A; Pham, Cindy C; Mishra, Nakul; Wang, Hongxin; Sommer, Constanze; Reijerse, Edward; Richers, Casseday P; Tamasaku, Kenji; Yoda, Yoshitaka; Rauchfuss, Thomas B; Lubitz, Wolfgang; Cramer, Stephen P

2017-11-22

[FeFe]-hydrogenases are metalloenzymes that reversibly reduce protons to molecular hydrogen at exceptionally high rates. We have characterized the catalytically competent hydride state (H hyd ) in the [FeFe]-hydrogenases from both Chlamydomonas reinhardtii and Desulfovibrio desulfuricans using 57 Fe nuclear resonance vibrational spectroscopy (NRVS) and density functional theory (DFT). H/D exchange identified two Fe-H bending modes originating from the binuclear iron cofactor. DFT calculations show that these spectral features result from an iron-bound terminal hydride, and the Fe-H vibrational frequencies being highly dependent on interactions between the amine base of the catalytic cofactor with both hydride and the conserved cysteine terminating the proton transfer chain to the active site. The results indicate that H hyd is the catalytic state one step prior to H 2 formation. The observed vibrational spectrum, therefore, provides mechanistic insight into the reaction coordinate for H 2 bond formation by [FeFe]-hydrogenases.

Electrochemistry of Simple Organometallic Models of Iron-Iron Hydrogenases in Organic Solvent and Water.

Science.gov (United States)

Gloaguen, Frederic

2016-01-19

Synthetic models of the active site of iron-iron hydrogenases are currently the subjects of numerous studies aimed at developing H2-production catalysts based on cheap and abundant materials. In this context, the present report offers an electrochemist's view of the catalysis of proton reduction by simple binuclear iron(I) thiolate complexes. Although these complexes probably do not follow a biocatalytic pathway, we analyze and discuss the interplay between the reduction potential and basicity and how these antagonist properties impact the mechanisms of proton-coupled electron transfer to the metal centers. This question is central to any consideration of the activity at the molecular level of hydrogenases and related enzymes. In a second part, special attention is paid to iron thiolate complexes holding rigid and unsaturated bridging ligands. The complexes that enjoy mild reduction potentials and stabilized reduced forms are promising iron-based catalysts for the photodriven evolution of H2 in organic solvents and, more importantly, in water.

CO methanation over supported bimetallic Ni-Fe catalysts: From computational studies towards catalyst optimization

DEFF Research Database (Denmark)

Kustov, Arkadii; Frey, Anne Mette; Larsen, Kasper Emil

2007-01-01

with compositions 25Fe75Ni and 50Fe50Ni showed significantly better activity and in some cases also a higher selectivity to methane compared with the traditional monometallic Ni and Fe catalysts. A catalyst with composition 25Fe75Ni was found to be the most active in CO hydrogenation for the MgAl2O4 support at low...... metal loadings. At high metal concentrations, the maximum for the methanation activity was found for catalysts with composition 50Ni50Fe both on the MgAl2O4 and Al2O3 supports. This difference can be attributed to a higher reducibility of the constituting metals with increasing metal concentration......DFT calculations combined with a computational screening method have previously shown that bimetallic Ni-Fe alloys should be more active than the traditional Ni-based catalyst for CO methanation. That was confirmed experimentally for a number of bimetallic Ni-Fe catalysts supported on MgAl2O4. Here...

Effect of cathode vibration and heat treatment on electromagnetic properties of flake-shaped diatomite coated with Ni-Fe alloy by electroplating

Science.gov (United States)

Lan, Mingming; Li, Huiqin; Huang, Weihua; Xu, Guangyin; Li, Yan

2015-03-01

In this paper, flake-shaped diatomite particles were used as forming templates for the fabrication of the ferromagnetic functional fillers by way of electroplating Ni-Fe alloy method. The effects of cathode vibration frequency on the content of Ni-Fe alloy in the coating and the surface morphologies of the coatings were evaluated. The electromagnetic properties of the coated diatomite particles before and after heat treatment were also investigated in detail. The results show that the core-shell flake-shaped diatomite particles with high content of Ni-Fe alloy and good surface qualities of the coatings can be obtained by adjusting cathode vibration frequency. The coated diatomite particles with heat treatment filled paraffin wax composites exhibit a superior microwave absorbing and electromagnetic properties compared to the non-heat treated samples. Additionally, the peaks of reflection loss are found to be able to shift to lower frequency by the heat treatment process, which indicates the heat treatment can adjust microwave absorbing frequency band.

Performance of NiFe2O4-SiO2-TiO2 Magnetic Photocatalyst for the Effective Photocatalytic Reduction of Cr(VI in Aqueous Solutions

Directory of Open Access Journals (Sweden)

Mike O. Ojemaye

2017-01-01

Full Text Available Investigation into the reduction of Cr(VI in aqueous solution was carried out through some batch photocatalytic studies. The photocatalysts used were silica coated nickel ferrite nanoparticles (NiFe2O4-SiO2, nickel ferrite titanium dioxide (NiFe2O4-TiO2, nickel ferrite silica titanium dioxide (NiFe2O4-SiO2-TiO2, and titanium dioxide (TiO2. The characterization of the materials prepared via stepwise synthesis using coprecipitation and sol-gel methods were carried out with the aid of X-ray diffraction (XRD, transmission electron microscopy (TEM, scanning electron microscopy (SEM, Fourier transform infrared (FTIR spectroscopy, thermal gravimetric analysis (TGA, and vibrating sample magnetometry (VSM. The reduction efficiency was studied as a function of pH, photocatalyst dose, and contact time. The effects of silica interlayer between the magnetic photocatalyst materials reveal that reduction efficiency of NiFe2O4-SiO2-TiO2 towards Cr(VI was higher than that of NiFe2O4-TiO2. However, TiO2 was observed to have the highest reduction efficiency at all batch photocatalytic experiments. Kinetics study shows that photocatalytic reduction of Cr(VI obeyed Langmuir-Hinshelwood model and first-order rate kinetics. Regenerability study also suggested that the photocatalyst materials can be reused.

Irreversibility in room temperature current–voltage characteristics of NiFe_2O_4 nanoparticles: A signature of electrical memory effect

International Nuclear Information System (INIS)

Dey, P.; Debnath, Rajesh; Singh, Swati; Mandal, S.K.; Roy, J.N.

2017-01-01

Room temperature I–V characteristics study, both in presence and absence of magnetic field (1800 Oe), has been performed on NiFe_2O_4 nanoparticles, having different particle size (φ~14, 21 and 31 nm). Our experiments on these nanoparticles provide evidences for: (1) electrical irreversibility or hysteretic behaviour; (2) positive magnetoresistance and (3) magnetic field dependent electrical irreversibility or hysteresis in the sample. “Hysteretic” nature of I–V curve reveals the existence of electrical memory effect in the sample. Significantly, such hysteresis has been found to be tuned by magnetic field. In order to explain the observed electrical irreversibility, we have proposed a phenomenological model on the light of induced polarization in the sample. Both the positive magnetoresistance and the observed magnetic field dependence of electrical irreversibility have been explained through magnetostriction phenomenon. Interestingly, such effects are found to get reduced with increasing particle size. For NiFe_2O_4 nanoparticles having φ=31 nm, we did not observe any irreversibility effect. This feature has been attributed to the enhanced grain surface effect that in turn gives rise to the residual polarization and hence electrical memory effect in NiFe_2O_4 nanoparticles, having small nanoscopic particle size. - Highlights: • I-V characteristics study of NiFe_2O_4 nanoparticles with varying particle sizes. • Experiments evident electrical hysteretic behaviour, i.e., electrical memory effect. • Magnetic field dependent electrical irreversibility is due to magnetostriction. • A phenomenological model has been proposed on the light of induced polarization. • Such electrical irreversibility decreases with increasing particle sizes.

Effect of surface properties of NiFe2O4 nanoparticles synthesized by dc thermal plasma route on antimicrobial activity

Science.gov (United States)

Bhosale, S. V.; Ekambe, P. S.; Bhoraskar, S. V.; Mathe, V. L.

2018-05-01

The present work reports the role of surface properties of NiFe2O4 nanoparticles on the antimicrobial activity. The NiFe2O4 nanoparticles were synthesized by gas phase condensation and chemical co-precipitation route. These nanoparticles were extensively investigated using X-ray diffraction, transmission electron microscopy, Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy and electro-kinetic property measurements. The HRTEM was used to analyze surface morphology of nickel ferrite nanoparticles obtained by two different routes. Electro-kinetic properties of the nanoparticles under investigation were recorded, analyzed and correlated with the antimicrobial properties. It was observed that nickel ferrite nanoparticles synthesized by thermal plasma route (NFOTP) formed highly stable colloidal solution as compared to chemically synthesized (NFOCP), as the later tends to agglomerate due to low surface charge. The antimicrobial activity of NiFe2O4 nanoparticles were investigated on two Gram positive bacteria Staphylococcus aureus and Streptococcus pyogenes, two Gram negative bacteria Escherichia coli and Salmonella typhimurium and one fungal species Candida albicans. It was noted that the surface properties of NiFe2O4 particles have revealing effect on the antimicrobial activity. The NFOTP nanoparticles showed significant activity for gram negative E. coli bacteria however no activity was observed for other bacteria's and fungi under study. Moreover NFOCP particles did not show any significant activity for both bacteria's and fungi. Further, antimicrobial activity of nickel ferrite nanoparticles were studied even for different concentration to obtain the minimum inhibition concentration (MIC).

Mechanochemical synthesis of TiO2/NiFe2O4 magnetic catalysts for operation under RF field

International Nuclear Information System (INIS)

Houlding, Thomas K.; Gao, Pengzhao; Degirmenci, Volkan; Tchabanenko, Kirill; Rebrov, Evgeny V.

2015-01-01

Highlights: • Novel NiFe 2 O 4 –TiO 2 composite magnetic catalysts have been prepared by mechanochemical synthesis. • The synthesis time of 30 min provides the highest specific absorption rate (SAR) in RF heating. • Formation of NiTiO 3 phase during calcination decreases the SAR of the catalysts. • High stability of the NiFe 2 O 4 –TiO 2 catalyst was observed in a continuous amide bond synthesis under RF heating. - Abstract: Composite NiFe 2 O 4 –TiO 2 magnetic catalysts were prepared by mechanochemical synthesis from a mixture of titania supported nickel ferrite nanoparticles and P25 titania (Evonic). The former provides fast and efficient heating under radiofrequency field, while the latter serves as an active catalyst or catalyst support. The highest heating rate was observed over a catalyst prepared for a milling time of 30 min. The catalytic activity was measured over the sulfated composite catalysts in the condensation of aniline and 3-phenylbutyric acid in a stirred tank reactor and in a continuous RF heated flow reactor in the 140–170 °C range. The product yield of 47% was obtained over the sulfated P25 titania catalyst in the flow reactor

Microstructural changes in NiFe_2O_4 ceramics prepared with powders derived from different fuels in sol-gel auto-combustion technique

International Nuclear Information System (INIS)

Chauhan, Lalita; Sreenivas, K.; Bokolia, Renuka

2016-01-01

Structural properties of Nickel ferrite (NiFe_2O_4) ceramics prepared from powders derived from sol gel auto-combustion method using different fuels (citric acid, glycine and Dl-alanine) are compared. Changes in the structural properties at different sintering temperatures are investigated. X-ray diffraction (XRD) confirms the formation of single phase material with cubic structure. Ceramics prepared using the different powders obtained from different fuels show that that there are no significant changes in lattice parameters. However increasing sintering temperatures show significant improvement in density and grain size. The DL-alanine fuel is found to be the most effective fuel for producing NIFe_2O_4 powders by the sol-gel auto combustion method and yields highly crystalline powders in the as-burnt stage itself at a low temperature (80 °C). Subsequent use of the powders in ceramic manufacturing produces dense NiFe_2O_4 ceramics with a uniform microstructure and a large grain size.

Microstructural changes in NiFe2O4 ceramics prepared with powders derived from different fuels in sol-gel auto-combustion technique

Science.gov (United States)

Chauhan, Lalita; Bokolia, Renuka; Sreenivas, K.

2016-05-01

Structural properties of Nickel ferrite (NiFe2O4) ceramics prepared from powders derived from sol gel auto-combustion method using different fuels (citric acid, glycine and Dl-alanine) are compared. Changes in the structural properties at different sintering temperatures are investigated. X-ray diffraction (XRD) confirms the formation of single phase material with cubic structure. Ceramics prepared using the different powders obtained from different fuels show that that there are no significant changes in lattice parameters. However increasing sintering temperatures show significant improvement in density and grain size. The DL-alanine fuel is found to be the most effective fuel for producing NIFe2O4 powders by the sol-gel auto combustion method and yields highly crystalline powders in the as-burnt stage itself at a low temperature (80 °C). Subsequent use of the powders in ceramic manufacturing produces dense NiFe2O4 ceramics with a uniform microstructure and a large grain size.

Protonation/reduction dynamics at the [4Fe-4S] cluster of the hydrogen-forming cofactor in [FeFe]-hydrogenases.

Science.gov (United States)

Senger, Moritz; Mebs, Stefan; Duan, Jifu; Shulenina, Olga; Laun, Konstantin; Kertess, Leonie; Wittkamp, Florian; Apfel, Ulf-Peter; Happe, Thomas; Winkler, Martin; Haumann, Michael; Stripp, Sven T

2018-01-31

The [FeFe]-hydrogenases of bacteria and algae are the most efficient hydrogen conversion catalysts in nature. Their active-site cofactor (H-cluster) comprises a [4Fe-4S] cluster linked to a unique diiron site that binds three carbon monoxide (CO) and two cyanide (CN - ) ligands. Understanding microbial hydrogen conversion requires elucidation of the interplay of proton and electron transfer events at the H-cluster. We performed real-time spectroscopy on [FeFe]-hydrogenase protein films under controlled variation of atmospheric gas composition, sample pH, and reductant concentration. Attenuated total reflection Fourier-transform infrared spectroscopy was used to monitor shifts of the CO/CN - vibrational bands in response to redox and protonation changes. Three different [FeFe]-hydrogenases and several protein and cofactor variants were compared, including element and isotopic exchange studies. A protonated equivalent (HoxH) of the oxidized state (Hox) was found, which preferentially accumulated at acidic pH and under reducing conditions. We show that the one-electron reduced state Hred' represents an intrinsically protonated species. Interestingly, the formation of HoxH and Hred' was independent of the established proton pathway to the diiron site. Quantum chemical calculations of the respective CO/CN - infrared band patterns favored a cysteine ligand of the [4Fe-4S] cluster as the protonation site in HoxH and Hred'. We propose that proton-coupled electron transfer facilitates reduction of the [4Fe-4S] cluster and prevents premature formation of a hydride at the catalytic diiron site. Our findings imply that protonation events both at the [4Fe-4S] cluster and at the diiron site of the H-cluster are important in the hydrogen conversion reaction of [FeFe]-hydrogenases.

NiFe epitaxial films with hcp and fcc structures prepared on bcc-Cr underlayers

Energy Technology Data Exchange (ETDEWEB)

Higuchi, Jumpei, E-mail: higuchi@futamoto.elect.chuo-u.ac.jp [Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo 112-8551 (Japan); Ohtake, Mitsuru; Sato, Yoichi [Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo 112-8551 (Japan); Kirino, Fumiyoshi [Graduate School of Fine Arts, Tokyo National University of Fine Arts and Music, 12-8 Ueno-koen, Taito-ku, Tokyo 110-8714 (Japan); Futamoto, Masaaki [Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo 112-8551 (Japan)

2011-09-30

NiFe epitaxial films are prepared on Cr(211){sub bcc} and Cr(100){sub bcc} underlayers grown hetero-epitaxially on MgO single-crystal substrates by ultra-high vacuum rf magnetron sputtering. The film growth behavior and the crystallographic properties are studied by reflection high energy electron diffraction and pole figure X-ray diffraction. Metastable hcp-NiFe(11-bar 00) and hcp-NiFe(112-bar 0) crystals respectively nucleate on Cr(211){sub bcc} and Cr(100){sub bcc} underlayers, where the hcp-NiFe crystals are stabilized through hetero-epitaxial growth. The hcp-NiFe(11-bar 00) crystal is a single-crystal with the c-axis parallel to the substrate surface, whereas the hcp-NiFe(112-bar 0) crystal is a bi-crystal with the respective c-axes lying in plane and perpendicular each other. With increasing the film thickness, the hcp structure in the NiFe films starts to transform into more stable fcc structure by atomic displacement parallel to the hcp(0001) close packed plane. The resulting films consist of hcp and fcc crystals.

NiFe epitaxial films with hcp and fcc structures prepared on bcc-Cr underlayers

International Nuclear Information System (INIS)

Higuchi, Jumpei; Ohtake, Mitsuru; Sato, Yoichi; Kirino, Fumiyoshi; Futamoto, Masaaki

2011-01-01

NiFe epitaxial films are prepared on Cr(211) bcc and Cr(100) bcc underlayers grown hetero-epitaxially on MgO single-crystal substrates by ultra-high vacuum rf magnetron sputtering. The film growth behavior and the crystallographic properties are studied by reflection high energy electron diffraction and pole figure X-ray diffraction. Metastable hcp-NiFe(11-bar 00) and hcp-NiFe(112-bar 0) crystals respectively nucleate on Cr(211) bcc and Cr(100) bcc underlayers, where the hcp-NiFe crystals are stabilized through hetero-epitaxial growth. The hcp-NiFe(11-bar 00) crystal is a single-crystal with the c-axis parallel to the substrate surface, whereas the hcp-NiFe(112-bar 0) crystal is a bi-crystal with the respective c-axes lying in plane and perpendicular each other. With increasing the film thickness, the hcp structure in the NiFe films starts to transform into more stable fcc structure by atomic displacement parallel to the hcp(0001) close packed plane. The resulting films consist of hcp and fcc crystals.

Moessbauer studies of superexchange interactions in NiFe sub 2 O sub 4

CERN Document Server

Kim, S J; Kim, C S; Lee, S W

2000-01-01

NiFe sub 2 O sub 4 has been studied using Moessbauer spectroscopy and X-ray diffraction. The crystal was found to have a inverse cubic spinel structure with the lattice constant a sub 0 =8.326+-0.003 A. Moessbauer spectra of NiFe sub 2 O sub 4 was obtained at various absorber temperatures from 13 K to the Neel temperature. The Moessbauer spectra consisted of two sets of six lines corresponding to Fe sup + sup 3 at the tetrahedral (A) and the octahedral (B) sites. The temperature dependence of the magnetic hyperfine fields at sup 5 sup 7 Fe nuclei at the tetrahedral (A) and the octahedral (B) sites was analyzed by the Neel theory of ferrimagnetism. The intersublattice A-O-B and intrasublattice A-O-A superexchange interactions were found to be antiferromagnetic with strengths of J sub A sub - sub B =-25.0 k sub B and J sub A sub - sub A =-4.0 K sub B , respectively, while the intrasublattice B-O-B superexchange interaction is ferromagnetic with a strength J sub B sub - sub B =4.2 k sub B.

Effect of tungsten (W) on structural and magnetic properties of electroplated NiFe thin films for MEMS applications

Science.gov (United States)

Kannan, R.; Devaki, P.; Premkumar, P. S.; Selvambikai, M.

2018-04-01

Electrodeposition of nanocrystalline NiFe and NiFeW thin films were carried out from ammonium citrate bath at a constant current density and controlled pH of 8 by varying the bath temperature from 40 °C to 70 °C. The surface morphology and chemical composition of the electrodeposited NiFe and NiFeW soft magnetic thin films were studied by using SEM and EDAX. The SEM micrographs of the films coated at higher electrodeposited bath temperature have no micro cracks and also the films have more uniform surface morphology. The existence of crystalline nature of the coated films were analysed by XRD. The presence of predominant peaks in x-ray diffraction pattern (compared with JCPDS data) reveal that the average crystalline size was in the order of few tens of nano meters. The magnetic properties such as coercivity, saturation magnetization and magnetic flux density have been calculated from vibrating sample magnetometer analysis. The VSM result shows that the NiFeW thin film synthesised at 70 °C exhibit the lower coercivity with higher saturation magnetization. The hardness and adhesion of the electroplated films have been investigated. Reasons for variation in magnetic properties and structural characteristics are also discussed. The electroplated NiFe and NiFeW thin films can be used for Micro Electro Mechanical System (MEMS) applications due to their excellent soft magnetic behaviour.

Molecular evolution of the nif gene cluster carrying nifI1 and nifI2 genes in the Gram-positive phototrophic bacterium Heliobacterium chlorum.

Science.gov (United States)

Enkh-Amgalan, Jigjiddorj; Kawasaki, Hiroko; Seki, Tatsuji

2006-01-01

A major nif cluster was detected in the strictly anaerobic, Gram-positive phototrophic bacterium Heliobacterium chlorum. The cluster consisted of 11 genes arranged within a 10 kb region in the order nifI1, nifI2, nifH, nifD, nifK, nifE, nifN, nifX, fdx, nifB and nifV. The phylogenetic position of Hbt. chlorum was the same in the NifH, NifD, NifK, NifE and NifN trees; Hbt. chlorum formed a cluster with Desulfitobacterium hafniense, the closest neighbour of heliobacteria based on the 16S rRNA phylogeny, and two species of the genus Geobacter belonging to the Deltaproteobacteria. Two nifI genes, known to occur in the nif clusters of methanogenic archaea between nifH and nifD, were found upstream of the nifH gene of Hbt. chlorum. The organization of the nif operon and the phylogeny of individual and concatenated gene products showed that the Hbt. chlorum nif operon carrying nifI genes upstream of the nifH gene was an intermediate between the nif operon with nifI downstream of nifH (group II and III of the nitrogenase classification) and the nif operon lacking nifI (group I). Thus, the phylogenetic position of Hbt. chlorum nitrogenase may reflect an evolutionary stage of a divergence of the two nitrogenase groups, with group I consisting of the aerobic diazotrophs and group II consisting of strictly anaerobic prokaryotes.

Ir4+-Doped NiFe LDH to expedite hydrogen evolution kinetics as a Pt-like electrocatalyst for water splitting.

Science.gov (United States)

Chen, Qian-Qian; Hou, Chun-Chao; Wang, Chuan-Jun; Yang, Xiao; Shi, Rui; Chen, Yong

2018-06-06

NiFe-layered double hydroxide (NiFe LDH) is a state-of-the-art oxygen evolution reaction (OER) electrocatalyst, yet it suffers from rather poor catalytic activity for the hydrogen evolution reaction (HER) due to its extremely sluggish water dissociation kinetics, severely restricting its application in overall water splitting. Herein, we report a novel strategy to expedite the HER kinetics of NiFe LDH by an Ir4+-doping strategy to accelerate the water dissociation process (Volmer step), and thus this catalyst exhibits superior and robust catalytic activity for finally oriented overall water splitting in 1 M KOH requiring only a low initial voltage of 1.41 V delivering at 20 mA cm-2 for more than 50 h.

Requirements for construction of a functional hybrid complex of photosystem I and [NiFe]-hydrogenase.

Science.gov (United States)

Schwarze, Alexander; Kopczak, Marta J; Rögner, Matthias; Lenz, Oliver

2010-04-01

The development of cellular systems in which the enzyme hydrogenase is efficiently coupled to the oxygenic photosynthesis apparatus represents an attractive avenue to produce H(2) sustainably from light and water. Here we describe the molecular design of the individual components required for the direct coupling of the O(2)-tolerant membrane-bound hydrogenase (MBH) from Ralstonia eutropha H16 to the acceptor site of photosystem I (PS I) from Synechocystis sp. PCC 6803. By genetic engineering, the peripheral subunit PsaE of PS I was fused to the MBH, and the resulting hybrid protein was purified from R. eutropha to apparent homogeneity via two independent affinity chromatographical steps. The catalytically active MBH-PsaE (MBH(PsaE)) hybrid protein could be isolated only from the cytoplasmic fraction. This was surprising, since the MBH is a substrate of the twin-arginine translocation system and was expected to reside in the periplasm. We conclude that the attachment of the additional PsaE domain to the small, electron-transferring subunit of the MBH completely abolished the export competence of the protein. Activity measurements revealed that the H(2) production capacity of the purified MBH(PsaE) fusion protein was very similar to that of wild-type MBH. In order to analyze the specific interaction of MBH(PsaE) with PS I, His-tagged PS I lacking the PsaE subunit was purified via Ni-nitrilotriacetic acid affinity and subsequent hydrophobic interaction chromatography. Formation of PS I-hydrogenase supercomplexes was demonstrated by blue native gel electrophoresis. The results indicate a vital prerequisite for the quantitative analysis of the MBH(PsaE)-PS I complex formation and its light-driven H(2) production capacity by means of spectroelectrochemistry.

Magnetocapacidad en nanopartículas de Fe3O4 y NiFe2O4

Directory of Open Access Journals (Sweden)

Mira, J.

2010-02-01

Full Text Available We have synthesized NiFe2O4 (φ∼ 6 nm and Fe3O4 (φ∼ 30 nm magnetic nanoparticles by solvothermal synthesis; furthermore the Fe3O4 nanoparticles have been coated with a SiO2 shell of approximately 5 nm of thickness by the Stöber method. In the study of the dielectric properties as a function of the frequency, temperature and applied magnetic field, we observe a magnetocapacitive behavior (MC at room temperature and under a moderate magnetic field (H=0.5T, that is specially important in the case of the Fe3O4, nanoparticles (MC≈ 6%. On the other hand, the NiFe2O4 and Fe3O4@SiO2 samples present smaller magnetocapacitive effects: MC≈ 2% y MC≈ 1%, respectively. These MC values, that are higher than those reported in the literature for other related magnetic nanoparticles, corroborate the theoretical model proposed by Catalán in which the combination of Maxwell-Wagner effects and magnetoresistance promote the appearance of stronger magnetocapacitive effects.Hemos preparado nanopartículas magnéticas de NiFe2O4 (φ∼ 6 nm y Fe3O4 (φ∼ 30 nm mediante el método de síntesis solvotermal; además estas últimas han sido recubiertas con una capa de SiO2 de unos 5 nm de espesor mediante el método de Stöber. Al estudiar el comportamiento dieléctrico en función de la frecuencia, temperatura y campo magnético aplicado, observamos un comportamiento magnetocapacitivo (MC a temperatura ambiente y bajo un campo magnético moderado (H= 0.5 T que es especialmente importante en el caso de las nanopartículas de Fe3O4 (MC≈ 6%. Por su parte las muestras de NiFe2O4 y Fe3O4@SiO2 presentan efectos magnetocapacitivos menores: MC≈ 2% y MC≈ 1%, respectivamente. Estos valores de MC, que son considerablemente superiores a los descritos hasta el momento para otras nanopartículas magnéticas, corroboran la predicción teórica de Catalán de que la combinación de efecto Maxwell-Wagner con efectos magnetorresitivos potencian la aparición de fen

Structural Mimics of the [Fe]-Hydrogenase: A Complete Set for Group VIII Metals.

Science.gov (United States)

Barik, Chandan Kr; Ganguly, Rakesh; Li, Yongxin; Leong, Weng Kee

2018-06-18

A set of structural mimics of the [Fe]-hydrogenase active site comprising all the group VIII metals, viz., [M(2-NHC(O)C 5 H 4 N)(CO) 2 (2-S-C 5 H 4 N)], has been synthesized. They exist as a mixture of isomers in solution, and the relative stability of the isomers depends on the nature of the metal and the substituent at the 6-position of the pyridine ligand.

A study on the electrodeposition of NiFe alloy thin films using chronocoulometry and electrochemical quartz crystal microgravimetry

CERN Document Server

Myung, N S

2001-01-01

Ni, Fe and NiFe alloy thin films were electrodeposited at a polycrystalline Au surface using a range of electrolytes and potentials. Coulometry and EQCM were used for real-time monitoring of electroplating efficiency of the Ni and Fe. The plating efficiency of NiFe alloy thin films was computed with the aid of ICP spectrometry. In general, plating efficiency increased to a steady value with deposition time. Plating efficiency of Fe was lower than that of Ni at -0.85 and -1.0 V but the efficiency approached to the similar plateau value to that of Ni at more negative potentials. The films with higher content of Fe showed different stripping behavior from the ones with higher content of Ni. Finally, compositional data and real-time plating efficiency are presented for films electrodeposited using a range of electrolytes and potentials.

Using in vitro maturation and cell-free expression to explore [FeFe] hydrogenase activation and protein scaffolding requirements

Energy Technology Data Exchange (ETDEWEB)

Swartz, James [Stanford Univ., CA (United States)

2017-01-25

Final Project Report describing work to elucidate mechanisms for the activation of [FeFe]-hydrogenases and to explore the impact of the polypeptide scaffolding on the function of the Fe-S redox and catalytic centers with emphasis on improving oxygen tolerance.

Characterization of carbon nanotubes decorated with NiFe2O4 magnetic nanoparticles as a novel electrochemical sensor: Application for highly selective determination of sotalol using voltammetry

International Nuclear Information System (INIS)

Ensafi, Ali A.; Allafchian, Ali R.; Rezaei, B.; Mohammadzadeh, R.

2013-01-01

A magnetic nano‐composite of multiwall carbon nanotube, decorated with NiFe 2 O 4 nanoparticles, was synthesized with citrate sol–gel method. The multiwall carbon nanotubes decorated with NiFe 2 O 4 nanoparticles (NiFe 2 O 4 –MWCNTs) were characterized with different methods such as Fourier transform infrared spectroscopy (FT‐IR), transmission electron microscopy (TEM), atomic force microscopy (AFM), vibrating sample magnetometer (VSM), cyclic voltammetry (CV), and electrochemical impedance spectroscopy (EIS). The new nano-composite acts as a suitable electrocatalyst for the oxidation of sotalol at a potential of 500 mV at the surface of the modified electrode. Linear sweep voltammetry exhibited two wide linear dynamic ranges of 0.5–1000 μmol L −1 sotalol with a detection limit of 0.09 μmol L −1 . The modified electrode was used as a novel electrochemical sensor for the determination of sotalol in real samples such as pharmaceutical, patient and safe human urine. - Graphical abstract: Multiwall carbon nanotube, decorated with NiFe 2 O 4 nanoparticles, was prepared using citrate sol–gel method. We characterized the new nanoparticles with different spectroscopic and voltammetric methods. The nano sensor was used as a voltammetric sensor for the determination of trace amounts of sotalol at pH 7.0. Highlights: ► We synthesized and prepared new sensor, multiwall carbon nanotubes decorated with NiFe 2 O 4 . ► Several spectroscopic and voltammetric methods were used to study its characteristics. ► The nanoparticles act as suitable electrocatalyst for the oxidation of sotalol. ► Sotalol could be measured as low as 0.09 μmol L −1 using linear sweep voltammetry.

Spin-polarized scanning tunneling microscopy experiments on the rough surface of a polycrystalline NiFe film with a fine magnetic tip sensitive to a well-defined magnetization component

Directory of Open Access Journals (Sweden)

H. Matsuyama

2016-03-01

Full Text Available We developed a micrometer-sized magnetic tip integrated onto the write head of a hard disk drive for spin-polarized scanning tunneling microscopy (SP-STM in the modulated tip magnetization mode. Using SP-STM, we measured a well-defined in-plane spin-component of the tunneling current of the rough surface of a polycrystalline NiFe film. The spin asymmetry of the NiFe film was about 1.3% within the bias voltage range of -3 to 1 V. We obtained the local spin component image of the sample surface, switching the magnetic field of the sample to reverse the sample magnetization during scanning. We also obtained a spin image of the rough surface of a polycrystalline NiFe film evaporated on the recording medium of a hard disk drive.

Spin-polarized scanning tunneling microscopy experiments on the rough surface of a polycrystalline NiFe film with a fine magnetic tip sensitive to a well-defined magnetization component

Energy Technology Data Exchange (ETDEWEB)

Matsuyama, H., E-mail: matsu@phys.sci.hokudai.ac.jp [Department of Physics, Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810 (Japan); Nara, D.; Kageyama, R.; Honda, K.; Sato, T.; Kusanagi, K. [Department of Condensed Matter Physics, Graduate School of Science, Hokkaido University, Sapporo, Hokkaido 060-0810 (Japan); Srinivasan, E. [Creative Research Institution (CRIS), Hokkaido University, Sapporo, Hokkaido 001-0021 (Japan); Koike, K. [Department of Physics, Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810 (Japan); Creative Research Institution (CRIS), Hokkaido University, Sapporo, Hokkaido 001-0021 (Japan)

2016-03-15

We developed a micrometer-sized magnetic tip integrated onto the write head of a hard disk drive for spin-polarized scanning tunneling microscopy (SP-STM) in the modulated tip magnetization mode. Using SP-STM, we measured a well-defined in-plane spin-component of the tunneling current of the rough surface of a polycrystalline NiFe film. The spin asymmetry of the NiFe film was about 1.3% within the bias voltage range of -3 to 1 V. We obtained the local spin component image of the sample surface, switching the magnetic field of the sample to reverse the sample magnetization during scanning. We also obtained a spin image of the rough surface of a polycrystalline NiFe film evaporated on the recording medium of a hard disk drive.

Synthesis, characterization of spinels NiFe_2O_4 e CoFe_2O_4 and evaluation of performance in the trans esterification and esterification of cottonseed oil

International Nuclear Information System (INIS)

Dantas, J.; Silva, A.S.A.; Costa, A.C.F.M.; Freitas, N.L.

2012-01-01

The present study aimed synthesizes by combustion reaction and characterization of the spinel CoFe_2O_4 and NiFe_2O_4, and evaluation in the esterification and transesterification reaction of cottonseed oil for biodiesel. The samples were characterized by XRD, nitrogen adsorption/desorption (BET), SEM and transesterification e esterification reaction of the cottonseed oil for biodiesel. The results show that the synthesis was effective in achievement the CoFe_2O_4 and NiFe_2O_4 with surface area 23.75 and 18.18 m"2g"1. The results for esterification indicated that CoFe_2O_4 conversion 16.8 and 38.6%, however for transesterification reaction was observed that NiFe_2O_4 conversion 8.6 and 16.8% for ethanol and methanol, respectively. (author)

Transcript analysis of the extended hyp-operon in the cyanobacteria Nostoc sp. strain PCC 7120 and Nostoc punctiforme ATCC 29133

Science.gov (United States)

2011-01-01

Background Cyanobacteria harbor two [NiFe]-type hydrogenases consisting of a large and a small subunit, the Hup- and Hox-hydrogenase, respectively. Insertion of ligands and correct folding of nickel-iron hydrogenases require assistance of accessory maturation proteins (encoded by the hyp-genes). The intergenic region between the structural genes encoding the uptake hydrogenase (hupSL) and the accessory maturation proteins (hyp genes) in the cyanobacteria Nostoc PCC 7120 and N. punctiforme were analysed using molecular methods. Findings The five ORFs, located in between the uptake hydrogenase structural genes and the hyp-genes, can form a transcript with the hyp-genes. An identical genomic localization of these ORFs are found in other filamentous, N2-fixing cyanobacterial strains. In N. punctiforme and Nostoc PCC 7120 the ORFs upstream of the hyp-genes showed similar transcript level profiles as hupS (hydrogenase structural gene), nifD (nitrogenase structural gene), hypC and hypF (accessory hydrogenase maturation genes) after nitrogen depletion. In silico analyzes showed that these ORFs in N. punctiforme harbor the same conserved regions as their homologues in Nostoc PCC 7120 and that they, like their homologues in Nostoc PCC 7120, can be transcribed together with the hyp-genes forming a larger extended hyp-operon. DNA binding studies showed interactions of the transcriptional regulators CalA and CalB to the promoter regions of the extended hyp-operon in N. punctiforme and Nostoc PCC 7120. Conclusions The five ORFs upstream of the hyp-genes in several filamentous N2-fixing cyanobacteria have an identical genomic localization, in between the genes encoding the uptake hydrogenase and the maturation protein genes. In N. punctiforme and Nostoc PCC 7120 they are transcribed as one operon and may form transcripts together with the hyp-genes. The expression pattern of the five ORFs within the extended hyp-operon in both Nostoc punctiforme and Nostoc PCC 7120 is similar to

Magnetic Behavior of Ni-Fe Core-Shell and Alloy Nanowires

Science.gov (United States)

Tripathy, Jagnyaseni; Vargas, Jose; Spinu, Leonard; Wiley, John

2013-03-01

Template assisted synthesis was used to fabricate a series of Ni-Fe core-shell and alloy nanowires. By controlling reaction conditions as well as pore structure, both systems could be targeted and magnetic properties followed as a function of architectures. In the core-shell structure coercivity increases with decrease in shell thickness while for the alloys, coercivity squareness improve with increase pore diameter. Details on the systematic studies of these materials will be presented in terms of hysteretic measurements, including first order reversal curves (FORC), and FMR data. Magnetic variation as a function of structure and nanowire aspect ratios will be presented and the origins of these behaviors discussed. Advanced Material Research Institute

Radioassay for hydrogenase activity in viable cells and documentation of aerobic hydrogen-consuming bacteria living in extreme environments

International Nuclear Information System (INIS)

Schink, B.; Lupton, F.S.; Zeikus, J.G.

1983-01-01

An isotopic tracer assay based on the hydrogenase-dependent formation of tritiated water from tritium gas was developed for in life analysis of microbial hydrogen transformation. This method allowed detection of bacterial hydrogen metabolism in pure cultures or in natural samples obtained from aquatic ecosystems. A differentiation between chemical-biological and aerobic-anaerobic hydrogen metabolism was established by variation of the experimental incubation temperature or by addition of selective inhibitors. Hydrogenase activity was shown to be proportional to the consumption or production of hydrogen by cultures of Desulfovibrio vulgaris, Clostridium pasteurianum, and Methanosarcina barkeri. This method was applied, in connection with measurements of free hydrogen and most-probable-number enumerations, in aerobic natural source waters to establish the activity and document the ecology of hydrogen-consuming bacteria in extreme acid, thermal, or saline environments. The utility of the assay is based in part on the ability to quantify bacterial hydrogen transformation at natural hydrogen partial pressures, without the use of artificial electron acceptors

The genome of Paenibacillus sabinae T27 provides insight into evolution, organization and functional elucidation of nif and nif-like genes.

Science.gov (United States)

Li, Xinxin; Deng, Zhiping; Liu, Zhanzhi; Yan, Yongliang; Wang, Tianshu; Xie, Jianbo; Lin, Min; Cheng, Qi; Chen, Sanfeng

2014-08-27

Most biological nitrogen fixation is catalyzed by the molybdenum nitrogenase. This enzyme is a complex which contains the MoFe protein encoded by nifDK and the Fe protein encoded by nifH. In addition to nifHDK, nifHDK-like genes were found in some Archaea and Firmicutes, but their function is unclear. We sequenced the genome of Paenibacillus sabinae T27. A total of 4,793 open reading frames were predicted from its 5.27 Mb genome. The genome of P. sabinae T27 contains fifteen nitrogen fixation (nif) genes, including three nifH, one nifD, one nifK, four nifB, two nifE, two nifN, one nifX and one nifV. Of the 15 nif genes, eight nif genes (nifB, nifH, nifD, nifK, nifE, nifN, nifX and nifV) and two non-nif genes (orf1 and hesA) form a complete nif gene cluster. In addition to the nif genes, there are nitrogenase-like genes, including two nifH-like genes and five pairs of nifDK-like genes. IS elements on the flanking regions of nif and nif-like genes imply that these genes might have been obtained by horizontal gene transfer. Phylogenies of the concatenated 8 nif gene (nifB, nifH, nifD, nifK, nifE, nifN, nifX and nifV) products suggest that P. sabinae T27 is closely related to Frankia. RT-PCR analysis showed that the complete nif gene cluster is organized as an operon. We demonstrated that the complete nif gene cluster under the control of σ70-dependent promoter enabled Escherichia coli JM109 to fix nitrogen. Also, here for the first time we demonstrated that unlike nif genes, the transcriptions of nifHDK-like genes were not regulated by ammonium and oxygen, and nifH-like or nifD-like gene could not restore the nitrogenase activity of Klebsiella pneumonia nifH- and nifD- mutant strains, respectively, suggesting that nifHDK-like genes were not involved in nitrogen fixation. Our data and analysis reveal the contents and distribution of nif and nif-like genes and contribute to the study of evolutionary history of nitrogen fixation in Paenibacillus. For the first time we

Hierarchical 3D NiFe2O4@MnO2 core-shell nanosheet arrays on Ni foam for high-performance asymmetric supercapacitors.

Science.gov (United States)

Zhang, Xinyang; Zhang, Ziqing; Sun, Shuanggan; Sun, Qiushi; Liu, Xiaoyang

2018-02-13

Hierarchical NiFe 2 O 4 @MnO 2 core-shell nanosheet arrays (NSAs) were synthesized on Ni foam as an integrated electrode for supercapacitors, using a facile two-step hydrothermal method followed by calcination treatment. The NiFe 2 O 4 nanosheets were designed as the core and ultrathin MnO 2 nanoflakes as the shell, creating a unique three-dimensional (3D) hierarchical electrode on Ni foam. The composite electrode exhibited remarkable electrochemical performance with a high specific capacitance of 1391 F g -1 at a current density of 2 mA cm -2 and long cycling stability at a high current density of 10 mA cm -2 (only 11.4% loss after 3000 cycles). Additionally, an asymmetric supercapacitor (ASC) device was fabricated with a NiFe 2 O 4 @MnO 2 composite as the positive electrode material and activated carbon (AC) as the negative one. The ASC device exhibited a high energy density (45.2 W h kg -1 ) at a power density of 174 W kg -1 , and an excellent cycling stability over 3000 cycles with 92.5% capacitance retention. The remarkable electrochemical performance demonstrated its great potential as a promising candidate for high-performance supercapacitors.

Structural characterization of Mg substituted on A/B sites in NiFe_2O_4 nanoparticles using autocombustion method

Science.gov (United States)

De, Manojit; Tewari, H. S.

2017-07-01

In the present paper, we are reporting the synthesis of pure nickel and magnesium ferrite [NiFe_2O_4, MgFe_2O_4] and magnesium-substituted nickel ferrite (Ni_{1-x}Mg_{x/y}Fe_{2-y}O_4; x=y=0.60) on A/B sites with particles size in nanometer range using autocombustion technique. In this study, it has been observed that with increase in sintering temperature, the estimated bulk density of the materials increases. The XRD patterns of the samples show the formation of single-phase materials and the lattice parameters are estimated from XRD patterns. From Raman spectra, the Raman shift of pure NiFe_2O_4 and MgFe_2O_4 are comparable with the experimental values reported in literature. The Raman spectra give five Raman active modes (A_{{1g}} + Eg + 3F_{2g}) which are expected in the spinel structure.

Fabrication of solenoid-type inductor with electroplated NiFe magnetic core

International Nuclear Information System (INIS)

Gao Xiaoyu; Cao Ying; Zhou Yong; Ding Wen; Lei Chong; Chen Jian

2006-01-01

Solenoid-type inductor with ultra-low profile was fabricated by MEMS (Microelectromechanical systems) technique. NiFe film was electroplated as the magnetic core, and polyimide with a low relative permittivity was used as the insulation material. In the fabrication process, UV-LIGA, dry etching, fine polishing and electroplating technique have been adopted to achieve high performance of the solenoid-type inductor. The inductor was in size of 1.5 mmx0.9 mmx0.1 mm with coil width of 20 μm and aspect ratio of 5:1. The inductance and the quality factor were 0.42-0.345 μH and 1.8-5.3 in the frequency range of 1-10 MHz, respectively

Metagenomic and PCR-based diversity surveys of [FeFe]-hydrogenases combined with isolation of alkaliphilic hydrogen-producing bacteria from the serpentinite-hosted Prony hydrothermal field, New Caledonia

Directory of Open Access Journals (Sweden)

Nan Mei

2016-08-01

Full Text Available High amounts of hydrogen are emitted in the serpentinite-hosted hydrothermal field of the Prony Bay (PHF, New Caledonia, where high-pH (~11, low-temperature (<40°C and low-salinity fluids are discharged in both intertidal and shallow submarine environments. In this study, we investigated the diversity and distribution of potentially hydrogen-producing bacteria in Prony hyperalkaline springs by using metagenomic analyses and different PCR-amplified DNA sequencing methods. The retrieved sequences of hydA genes, encoding the catalytic subunit of [FeFe]-hydrogenases and, used as a molecular marker of hydrogen-producing bacteria, were mainly related to those of Firmicutes and clustered into two distinct groups depending on sampling locations. Intertidal samples were dominated by new hydA sequences related to uncultured Firmicutes retrieved from paddy soils, while submarine samples were dominated by diverse hydA sequences affiliated with anaerobic and/or thermophilic submarine Firmicutes pertaining to the orders Thermoanaerobacterales or Clostridiales. The novelty and diversity of these [FeFe]-hydrogenases may reflect the unique environmental conditions prevailing in the PHF (i.e. high-pH, low-salt, mesothermic fluids. In addition, novel alkaliphilic hydrogen-producing Firmicutes (Clostridiales and Bacillales were successfully isolated from both intertidal and submarine PHF chimney samples. Both molecular and cultivation-based data demonstrated the ability of Firmicutes originating from serpentinite-hosted environments to produce hydrogen by fermentation, potentially contributing to the molecular hydrogen balance in situ.

Metagenomic and PCR-Based Diversity Surveys of [FeFe]-Hydrogenases Combined with Isolation of Alkaliphilic Hydrogen-Producing Bacteria from the Serpentinite-Hosted Prony Hydrothermal Field, New Caledonia.

Science.gov (United States)

Mei, Nan; Postec, Anne; Monnin, Christophe; Pelletier, Bernard; Payri, Claude E; Ménez, Bénédicte; Frouin, Eléonore; Ollivier, Bernard; Erauso, Gaël; Quéméneur, Marianne

2016-01-01

High amounts of hydrogen are emitted in the serpentinite-hosted hydrothermal field of the Prony Bay (PHF, New Caledonia), where high-pH (~11), low-temperature (< 40°C), and low-salinity fluids are discharged in both intertidal and shallow submarine environments. In this study, we investigated the diversity and distribution of potentially hydrogen-producing bacteria in Prony hyperalkaline springs by using metagenomic analyses and different PCR-amplified DNA sequencing methods. The retrieved sequences of hydA genes, encoding the catalytic subunit of [FeFe]-hydrogenases and, used as a molecular marker of hydrogen-producing bacteria, were mainly related to those of Firmicutes and clustered into two distinct groups depending on sampling locations. Intertidal samples were dominated by new hydA sequences related to uncultured Firmicutes retrieved from paddy soils, while submarine samples were dominated by diverse hydA sequences affiliated with anaerobic and/or thermophilic submarine Firmicutes pertaining to the orders Thermoanaerobacterales or Clostridiales. The novelty and diversity of these [FeFe]-hydrogenases may reflect the unique environmental conditions prevailing in the PHF (i.e., high-pH, low-salt, mesothermic fluids). In addition, novel alkaliphilic hydrogen-producing Firmicutes (Clostridiales and Bacillales) were successfully isolated from both intertidal and submarine PHF chimney samples. Both molecular and cultivation-based data demonstrated the ability of Firmicutes originating from serpentinite-hosted environments to produce hydrogen by fermentation, potentially contributing to the molecular hydrogen balance in situ.

Genome-Guided Analysis and Whole Transcriptome Profiling of the Mesophilic Syntrophic Acetate Oxidising Bacterium Syntrophaceticus schinkii.

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Shahid Manzoor

Full Text Available Syntrophaceticus schinkii is a mesophilic, anaerobic bacterium capable of oxidising acetate to CO2 and H2 in intimate association with a methanogenic partner, a syntrophic relationship which operates close to the energetic limits of microbial life. Syntrophaceticus schinkii has been identified as a key organism in engineered methane-producing processes relying on syntrophic acetate oxidation as the main methane-producing pathway. However, due to strict cultivation requirements and difficulties in reconstituting the thermodynamically unfavourable acetate oxidation, the physiology of this functional group is poorly understood. Genome-guided and whole transcriptome analyses performed in the present study provide new insights into habitat adaptation, syntrophic acetate oxidation and energy conservation. The working draft genome of Syntrophaceticus schinkii indicates limited metabolic capacities, with lack of organic nutrient uptake systems, chemotactic machineries, carbon catabolite repression and incomplete biosynthesis pathways. Ech hydrogenase, [FeFe] hydrogenases, [NiFe] hydrogenases, F1F0-ATP synthase and membrane-bound and cytoplasmic formate dehydrogenases were found clearly expressed, whereas Rnf and a predicted oxidoreductase/heterodisulphide reductase complex, both found encoded in the genome, were not expressed under syntrophic growth condition. A transporter sharing similarities to the high-affinity acetate transporters of aceticlastic methanogens was also found expressed, suggesting that Syntrophaceticus schinkii can potentially compete with methanogens for acetate. Acetate oxidation seems to proceed via the Wood-Ljungdahl pathway as all genes involved in this pathway were highly expressed. This study shows that Syntrophaceticus schinkii is a highly specialised, habitat-adapted organism relying on syntrophic acetate oxidation rather than metabolic versatility. By expanding its complement of respiratory complexes, it might overcome

Preparation of NiFe2O4/graphene nanocomposite and its application as a modifier for the fabrication of an electrochemical sensor for the simultaneous determination of tramadol and acetaminophen

International Nuclear Information System (INIS)

Afkhami, Abbas; Khoshsafar, Hosein; Bagheri, Hasan; Madrakian, Tayyebeh

2014-01-01

Highlights: • A new modified electrochemical sensor was constructed and used. • NiFe 2 O 4 /graphene was used as the modifier. • The sensor was used for the determination of tramadol and acetaminophen in real samples. • Modification improved the sensitivity and detection limit of the method. • The oxidation of tramadol and acetaminophen at the surface of the electrode was studied. - Abstract: An effective electrochemical sensor for the rapid and simultaneous determination of tramadol and acetaminophen based on carbon paste electrode (CPE) modified with NiFe 2 O 4 /graphene nanoparticles was developed. The structures of the synthesized NiFe 2 O 4 /graphene nanocomposite and the electrode composition were confirmed by X-ray diffraction (XRD) spectrometry, Fourier transform infrared (FT-IR) spectrometry and scanning electron microscopy (SEM). The peak currents of square wave voltammetry of tramadol and acetaminophen increased linearly with their concentration in the range of 0.01–9 μmol L −1 . The detection limit for their determination was found to be 0.0036 and 0.0030 μmol L −1 , respectively. The results show that the combination of graphene and NiFe 2 O 4 nanoparticles causes a dramatic enhancement in the sensitivity of the sensor. The fabricated sensor exhibited high sensitivity and good stability, and would be valuable for the clinical assay of tramadol and acetaminophen

Identification of an Isothiocyanate on the HypEF Complex Suggests a Route for Efficient Cyanyl-Group Channeling during [NiFe]-Hydrogenase Cofactor Generation.

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Sven T Stripp

Full Text Available [NiFe]-hydrogenases catalyze uptake and evolution of H2 in a wide range of microorganisms. The enzyme is characterized by an inorganic nickel/ iron cofactor, the latter of which carries carbon monoxide and cyanide ligands. In vivo generation of these ligands requires a number of auxiliary proteins, the so-called Hyp family. Initially, HypF binds and activates the precursor metabolite carbamoyl phosphate. HypF catalyzes removal of phosphate and transfers the carbamate group to HypE. In an ATP-dependent condensation reaction, the C-terminal cysteinyl residue of HypE is modified to what has been interpreted as thiocyanate. This group is the direct precursor of the cyanide ligands of the [NiFe]-hydrogenase active site cofactor. We present a FT-IR analysis of HypE and HypF as isolated from E. coli. We follow the HypF-catalyzed cyanation of HypE in vitro and screen for the influence of carbamoyl phosphate and ATP. To elucidate on the differences between HypE and the HypEF complex, spectro-electrochemistry was used to map the vibrational Stark effect of naturally cyanated HypE. The IR signature of HypE could ultimately be assigned to isothiocyanate (-N=C=S rather than thiocyanate (-S-C≡N. This has important implications for cyanyl-group channeling during [NiFe]-hydrogenase cofactor generation.

Electron transfer activation of a second water channel for proton transport in [FeFe]-hydrogenase

Energy Technology Data Exchange (ETDEWEB)

Sode, Olaseni; Voth, Gregory A., E-mail: gavoth@uchicago.edu [Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, Computation Institute, The University of Chicago, Chicago, Illinois 60637, USA and Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne, Illinois 60439 (United States)

2014-12-14

Hydrogenase enzymes are important because they can reversibly catalyze the production of molecular hydrogen. Proton transport mechanisms have been previously studied in residue pathways that lead to the active site of the enzyme via residues Cys299 and Ser319. The importance of this pathway and these residues has been previously exhibited through site-specific mutations, which were shown to interrupt the enzyme activity. It has been shown recently that a separate water channel (WC2) is coupled with electron transport to the active site of the [FeFe]-hydrogenase. The water-mediated proton transport mechanisms of the enzyme in different electronic states have been studied using the multistate empirical valence bond reactive molecular dynamics method, in order to understand any role WC2 may have in facilitating the residue pathway in bringing an additional proton to the enzyme active site. In a single electronic state A{sup 2−}, a water wire was formed through which protons can be transported with a low free energy barrier. The remaining electronic states were shown, however, to be highly unfavorable to proton transport in WC2. A double amino acid substitution is predicted to obstruct proton transport in electronic state A{sup 2-} by closing a cavity that could otherwise fill with water near the proximal Fe of the active site.

Electron transfer activation of a second water channel for proton transport in [FeFe]-hydrogenase

International Nuclear Information System (INIS)

Sode, Olaseni; Voth, Gregory A.

2014-01-01

Hydrogenase enzymes are important because they can reversibly catalyze the production of molecular hydrogen. Proton transport mechanisms have been previously studied in residue pathways that lead to the active site of the enzyme via residues Cys299 and Ser319. The importance of this pathway and these residues has been previously exhibited through site-specific mutations, which were shown to interrupt the enzyme activity. It has been shown recently that a separate water channel (WC2) is coupled with electron transport to the active site of the [FeFe]-hydrogenase. The water-mediated proton transport mechanisms of the enzyme in different electronic states have been studied using the multistate empirical valence bond reactive molecular dynamics method, in order to understand any role WC2 may have in facilitating the residue pathway in bringing an additional proton to the enzyme active site. In a single electronic state A 2− , a water wire was formed through which protons can be transported with a low free energy barrier. The remaining electronic states were shown, however, to be highly unfavorable to proton transport in WC2. A double amino acid substitution is predicted to obstruct proton transport in electronic state A 2- by closing a cavity that could otherwise fill with water near the proximal Fe of the active site

Coercivity scaling in antidot lattices in Fe, Ni, and NiFe thin films

Energy Technology Data Exchange (ETDEWEB)

Gräfe, Joachim, E-mail: graefe@is.mpg.de; Schütz, Gisela; Goering, Eberhard J., E-mail: goering@is.mpg.de

2016-12-01

Antidot lattices can be used to artificially engineer magnetic properties in thin films, however, a conclusive model that describes the coercivity enhancement in this class of magnetic nano-structures has so far not been found. We prepared Fe, Ni, and NiFe thin films and patterned each with 21 square antidot lattices with different geometric parameters and measured their hysteretic behavior. On the basis of this extensive dataset we are able to provide a model that can describe both the coercivity scaling over a wide range of geometric lattice parameters and the influence of different materials.

Structure and properties of nanosize NiFe2O4 prepared by template and precipitation methods

Czech Academy of Sciences Publication Activity Database

Ćosović, A.; Ćosović, B.; Žák, Tomáš; David, Bohumil; Talijan, N.

2013-01-01

Roč. 49, č. 3 (2013), s. 271-277 ISSN 1450-5339 R&D Projects: GA ČR(CZ) GAP108/11/1350; GA MŠk(CZ) ED1.1.00/02.0068 Institutional research plan: CEZ:AV0Z2041904 Institutional support: RVO:68081723 Keywords : nanosized NiFe2O4 * template method * precipitation route * microstructure * phase composition * magnetic properties Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.135, year: 2013

Flexible in-plane microsupercapacitors with electrospun NiFe2O4 nanofibers for portable sensing applications.

Science.gov (United States)

Li, La; Lou, Zheng; Han, Wei; Shen, Guozhen

2016-08-11

The development of wearable electronic devices in recent decades has brought new opportunities in the exploration of micro-supercapacitors as energy storage units. In this work, we report the fabrication of flexible NiFe2O4 nanofiber based in-plane micro-supercapacitors (MSCs), which can serve as energy storage receptors to drive a portable graphene pressure sensor. The obtained NiFe2O4 nanofiber electrodes exhibited a specific capacitance of 2.23 F cm(-3) at the scan rate of 100 mV s(-1), and excellent rate capability and robust cycling stability with a capacitance retention of 93.6% after 10 000 charge/discharge cycles. Moreover, the in-plane MSCs have superior flexibility and outstanding stability even after repetition of charge/discharge cycles during the convex and concave bending states. The MSCs offered a high energy density of 0.197 mWh cm(-3) and power density up to 2.07 W cm(-3). We also coupled the MSCs with a graphene pressure sensor as a micro-integrated system to implement it's pressure response function and used MATLAB to simulate this system behavior as well. The performance of the designed systems exhibited a stable pressure response, and the simulated results coincide well with the experimental data, demonstrating its feasibility in wearable electronic devices.

Synthesis and characterization of multilayered BaTiO3/NiFe2O4 thin films

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Branimir Bajac

2013-03-01

Full Text Available Presented research was focused on the fabrication of multiferroic thin film structures, composed of ferrielectric barium titanate perovskite phase and magnetostrictive nickel ferrite spinel phase. The applicability of different, solution based, deposition techniques (film growth from solution, dip coating and spin coating for thefabrication of multilayered BaTiO3 /NiFe2O4 thin films was investigated. It was shown that only spin coating produces films of desired nanostructure, thickness and smooth and crackfree surfaces.

Identification and analysis of hydrogen uptake (HUP) genes of several associative nitrogen fixing bacteria with rice plant

International Nuclear Information System (INIS)

Yuan Hongli; Wang Huixian; You Chongbiao

1990-01-01

All of the tested species (strains) in this work can reduce TTC, suggesting that they contain hydrogen uptake hydrogenase. Hybridization with Rhizobium japonicum hup gene indicated that there was homology between restricted DNA and the probe for Alcaligenes faecalis A15, Enterobacter cloacae EnSs, Klebsiella planticola DWUL2 and Pseudomonas saccharophila. Negative results were obtained for E. cloacae E26 and K. oxytoca NG13. Hup genes of A. faecalis A15 were located on chromosomal DNA, however, it was located on the larger plasmid for E. cloacae EnSs. Nif gene and hup gene are located on the same replicon. Hup gene from different hup + microorganisms was not homology inevitably

Transcription of the extended hyp-operon in Nostoc sp. strain PCC 7120

Science.gov (United States)

Agervald, Åsa; Stensjö, Karin; Holmqvist, Marie; Lindblad, Peter

2008-01-01

Background The maturation of hydrogenases into active enzymes is a complex process and e.g. a correctly assembled active site requires the involvement of at least seven proteins, encoded by hypABCDEF and a hydrogenase specific protease, encoded either by hupW or hoxW. The N2-fixing cyanobacterium Nostoc sp. strain PCC 7120 may contain both an uptake and a bidirectional hydrogenase. The present study addresses the presence and expression of hyp-genes in Nostoc sp. strain PCC 7120. Results RT-PCRs demonstrated that the six hyp-genes together with one ORF may be transcribed as a single operon. Transcriptional start points (TSPs) were identified 280 bp upstream from hypF and 445 bp upstream of hypC, respectively, demonstrating the existence of several transcripts. In addition, five upstream ORFs located in between hupSL, encoding the small and large subunits of the uptake hydrogenase, and the hyp-operon, and two downstream ORFs from the hyp-genes were shown to be part of the same transcript unit. A third TSP was identified 45 bp upstream of asr0689, the first of five ORFs in this operon. The ORFs are annotated as encoding unknown proteins, with the exception of alr0692 which is identified as a NifU-like protein. Orthologues of the four ORFs asr0689-alr0692, with a highly conserved genomic arrangement positioned between hupSL, and the hyp genes are found in several other N2-fixing cyanobacteria, but are absent in non N2-fixing cyanobacteria with only the bidirectional hydrogenase. Short conserved sequences were found in six intergenic regions of the extended hyp-operon, appearing between 11 and 79 times in the genome. Conclusion This study demonstrated that five ORFs upstream of the hyp-gene cluster are co-transcribed with the hyp-genes, and identified three TSPs in the extended hyp-gene cluster in Nostoc sp. strain PCC 7120. This may indicate a function related to the assembly of a functional uptake hydrogenase, hypothetically in the assembly of the small subunit of

Preparation of Ni-Fe bimetallic porous anode support for solid oxide fuel cells using LaGaO{sub 3} based electrolyte film with high power density

Energy Technology Data Exchange (ETDEWEB)

Ju, Young-Wan; Ida, Shintaro; Ishihara, Tatsumi [Department of Applied Chemistry, Faculty of Engineering, Kyushu University, Motooka 744, Nishi-Ku, Fukuoka 819-0395 (Japan); Eto, Hiroyuki [Mitsubishi Materials Corporation, Central Research Institute, 1002-14 Mukohyama, Naka-Shi, Ibaraki 311-0102 (Japan); Inagaki, Toru [The Kansai Electric Power Co., Inc., 11-20 Nakoji 3-Chome, Amagasaki, Hyogo 661-0974 (Japan)

2010-10-01

Optimization of sintering temperature for NiO-Fe{sub 2}O{sub 3} composite oxide substrate was studied in order to obtain a dense substrate with smooth surface. By in situ reduction, the substrate was changed to a porous Ni-Fe alloy metal. The volumetric shrinkage and porosity of the substrate were also studied systematically with the Ni-Fe substrate reduced at different temperatures. A Sr and Mg-doped LaGaO{sub 3} (LSGM) thin film was prepared on dense substrate by the pulsed laser deposition (PLD) method. The LSGM film with stoichiometric composition was successfully prepared under optimal deposition parameters and a target composition. Sm{sub 0.5}Sr{sub 0.5}CoO{sub 3} (SSC55) cathode was prepared by the slurry coating method on the deposited film. Prepared SOFC single cell shows high power density and the maximum power density (MPD) achieved was 1.79, 0.82 and 0.29 W cm{sup -2} at 973, 873 and 773 K, respectively. After thermal cycle from 973 to 298 K, the cell shows almost theoretical open circuit potential (1.1 V) and the power density of 1.62 W cm{sup -2}, which is almost the same as that at first cycles. Therefore, the Ni-Fe porous metal support made by the selective reduction is highly promising as a metal anode substrate for SOFC using LaGaO{sub 3} thin film. (author)

Structural and optical properties of NiFe2O4 synthesized via green technology

Science.gov (United States)

Patel, S.; Saleem, M.; Varshney, Dinesh

2018-05-01

The nanoparticles of NiFe2O4 were successfully synthesized via green technology using banana peel extract as the catalyst as well as the medium for reaction technique is reported. Analysis of X-ray diffraction spectrum revealed the cubic structure for the prepared spinel ferrite samples crystallized into cubic spinel structure with the space group Fd3m. The Retvield refinement was carried out which obeyed the results obtained from the XRD spectrum analysis of the sample. Raman spectrum provided confirmation for the spinel structure formation and five active Raman modes were observed. Since the optical band-gap value shows inverse response to the crystallite size, The UV-Vis spectrum study confirmed dual but reduced band-gap value.

In Situ Characterization of Ni and Ni/Fe Thin Film Electrodes for Oxygen Evolution in Alkaline Media by a Raman-Coupled Scanning Electrochemical Microscope Setup.

Science.gov (United States)

Steimecke, Matthias; Seiffarth, Gerda; Bron, Michael

2017-10-17

We present a spectroelectrochemical setup, in which Raman microscopy is combined with scanning electrochemical microscopy (SECM) in order to provide both spectroscopic and electrochemical information on the very same location of an electrode at the same time. The setup is applied to a subject of high academic and practical interest, namely, the oxygen evolution reaction at Ni and Ni/Fe electrodes. It comprises a transparent substrate electrode, onto which Ni and Ni/Fe thin films are deposited. An ultramicroelectrode (UME) is placed closely above the substrate to obtain electrochemical information, while a Raman microscope probes the same sample spot from below. To obtain information on oxygen evolution activity and structural changes, increasingly positive potentials from 0.1 up to 0.7 V vs Hg|HgO|1 M KOH were applied to the Ni/Fe-electrodes in 0.1 M KOH solution. Evolved oxygen is detected by reduction at a Pt UME, allowing for the determination of onset potentials, while the substrate current, which is recorded in parallel, is due to both overlapping oxygen evolution and the oxidation of Ni(OH) 2 to NiOOH. An optimum of 15% Fe in Ni/Fe films with respect to oxygen evolution activity was determined. At the same time, the potential-dependent formation of γ-NiOOH characterized by the Raman double band at 475 and 557 cm -1 allows for the conclusion that a certain amount of disorder introduced by Fe atoms is necessary to obtain high oxygen evolution reaction (OER) activity.

Diffusion and segregation of substrate copper in electrodeposited Ni-Fe thin films

International Nuclear Information System (INIS)

Ahadian, M.M.; Iraji zad, A.; Nouri, E.; Ranjbar, M.; Dolati, A.

2007-01-01

The Cu surface segregation is investigated in the electrodeposited Ni-Fe layers using X-ray photoelectron spectroscopy (XPS), Auger electron spectroscopy (AES), secondary ion mass spectroscopy (SIMS) and atomic force microscopy (AFM). The results indicate that Cu segregation and accumulation take place in areated and deareated baths and the amount of segregated copper increases after air exposure. This phenomenon is explained by lower interfacial tension of the Cu in comparison with Ni and Fe. Our results reveal more surface segregation in the electrodeposit than vacuum reported results. This should be due to interface charging and higher surface diffusion in applied potential. The effect of interface charging on the interfacial tension is discussed based on Lippmann equation. Increasing of the Cu accumulation after air exposure is related to selective oxidation in alloys and higher tendency of Cu to surface oxidation

Hydrogen-producing microflora and Fe-Fe hydrogenase diversities in seaweed bed associated with marine hot springs of Kalianda, Indonesia.

Science.gov (United States)

Xu, Shou-Ying; He, Pei-Qing; Dewi, Seswita-Zilda; Zhang, Xue-Lei; Ekowati, Chasanah; Liu, Tong-Jun; Huang, Xiao-Hang

2013-05-01

Microbial fermentation is a promising technology for hydrogen (H(2)) production. H(2) producers in marine geothermal environments are thermophilic and halotolerant. However, no one has surveyed an environment specifically for thermophilic bacteria that produce H(2) through Fe-Fe hydrogenases (H(2)ase). Using heterotrophic medium, several microflora from a seaweed bed associated with marine hot springs were enriched and analyzed for H(2) production. A H(2)-producing microflora was obtained from Sargassum sp., 16S rRNA genes and Fe-Fe H(2)ase diversities of this enrichment were also analyzed. Based on 16S rRNA genes analysis, 10 phylotypes were found in the H(2)-producing microflora showing 90.0-99.5 % identities to known species, and belonged to Clostridia, Gammaproteobacteria, and Bacillales. Clostridia were the most abundant group, and three Clostridia phylotypes were most related to known H(2) producers such as Anaerovorax odorimutans (94.0 % identity), Clostridium papyrosolvens (98.4 % identity), and Clostridium tepidiprofundi (93.1 % identity). For Fe-Fe H(2)ases, seven phylotypes were obtained, showing 63-97 % identities to known Fe-Fe H(2)ases, and fell into four distinct clusters. Phylotypes HW55-3 and HM55-1 belonged to thermophilic and salt-tolerant H(2)-producing Clostridia, Halothermothrix orenii-like Fe-Fe H(2)ases (80 % identity), and cellulolytic H(2)-producing Clostridia, C. papyrosolvens-like Fe-Fe H(2)ases (97 % identity), respectively. The results of both 16S rRNA genes and Fe-Fe H(2)ases surveys suggested that the thermophilic and halotolerant H(2)-producing microflora in seaweed bed of hot spring area represented previously unknown H(2) producers, and have potential application for H(2) production.

An ultra-small NiFe2O4 hollow particle/graphene hybrid: fabrication and electromagnetic wave absorption property.

Science.gov (United States)

Yan, Feng; Guo, Dong; Zhang, Shen; Li, Chunyan; Zhu, Chunling; Zhang, Xitian; Chen, Yujin

2018-02-08

Herein, ultra-small NiFe 2 O 4 hollow particles, with the diameter and wall thickness of only 6 and 1.8 nm, respectively, were anchored on a graphene surface based on the nanoscale Kirkendall effect. The hybrid exhibits an excellent electromagnetic wave absorption property, comparable or superior to that of most reported absorbers. Our strategy may open a way to grow ultra-small hollow particles on graphene for applications in many fields such as eletromagnetic wave absorption and energy storage and conversion.

Multiscale Modeling of the Active Site of [Fe] Hydrogenase: The H2 Binding Site in Open and Closed Protein Conformations

DEFF Research Database (Denmark)

Hedegård, Erik D.; Kongsted, Jacob; Ryde, Ulf

2015-01-01

A series of QM/MM optimizations of the full protein of [Fe] hydrogenase were performed. The FeGP cofactor has been optimized in the water-bound resting state (1), with a side-on bound dihydrogen (2), or as a hydride intermediate (3). For inclusion of H4MPT in the closed structure, advanced multis...... that hydride transfer from 3 has a significantly higher barrier than found in previous studies neglecting the full protein environment....

Cysteine as a ligand platform in the biosynthesis of the FeFe hydrogenase H cluster.

Science.gov (United States)

Suess, Daniel L M; Bürstel, Ingmar; De La Paz, Liliana; Kuchenreuther, Jon M; Pham, Cindy C; Cramer, Stephen P; Swartz, James R; Britt, R David

2015-09-15

Hydrogenases catalyze the redox interconversion of protons and H2, an important reaction for a number of metabolic processes and for solar fuel production. In FeFe hydrogenases, catalysis occurs at the H cluster, a metallocofactor comprising a [4Fe-4S]H subcluster coupled to a [2Fe]H subcluster bound by CO, CN(-), and azadithiolate ligands. The [2Fe]H subcluster is assembled by the maturases HydE, HydF, and HydG. HydG is a member of the radical S-adenosyl-L-methionine family of enzymes that transforms Fe and L-tyrosine into an [Fe(CO)2(CN)] synthon that is incorporated into the H cluster. Although it is thought that the site of synthon formation in HydG is the "dangler" Fe of a [5Fe] cluster, many mechanistic aspects of this chemistry remain unresolved including the full ligand set of the synthon, how the dangler Fe initially binds to HydG, and how the synthon is released at the end of the reaction. To address these questions, we herein show that L-cysteine (Cys) binds the auxiliary [4Fe-4S] cluster of HydG and further chelates the dangler Fe. We also demonstrate that a [4Fe-4S]aux[CN] species is generated during HydG catalysis, a process that entails the loss of Cys and the [Fe(CO)2(CN)] fragment; on this basis, we suggest that Cys likely completes the coordination sphere of the synthon. Thus, through spectroscopic analysis of HydG before and after the synthon is formed, we conclude that Cys serves as the ligand platform on which the synthon is built and plays a role in both Fe(2+) binding and synthon release.

Transcription of the extended hyp-operon in Nostoc sp. strain PCC 7120

Directory of Open Access Journals (Sweden)

Lindblad Peter

2008-04-01

Full Text Available Abstract Background The maturation of hydrogenases into active enzymes is a complex process and e.g. a correctly assembled active site requires the involvement of at least seven proteins, encoded by hypABCDEF and a hydrogenase specific protease, encoded either by hupW or hoxW. The N2-fixing cyanobacterium Nostoc sp. strain PCC 7120 may contain both an uptake and a bidirectional hydrogenase. The present study addresses the presence and expression of hyp-genes in Nostoc sp. strain PCC 7120. Results RT-PCRs demonstrated that the six hyp-genes together with one ORF may be transcribed as a single operon. Transcriptional start points (TSPs were identified 280 bp upstream from hypF and 445 bp upstream of hypC, respectively, demonstrating the existence of several transcripts. In addition, five upstream ORFs located in between hupSL, encoding the small and large subunits of the uptake hydrogenase, and the hyp-operon, and two downstream ORFs from the hyp-genes were shown to be part of the same transcript unit. A third TSP was identified 45 bp upstream of asr0689, the first of five ORFs in this operon. The ORFs are annotated as encoding unknown proteins, with the exception of alr0692 which is identified as a NifU-like protein. Orthologues of the four ORFs asr0689-alr0692, with a highly conserved genomic arrangement positioned between hupSL, and the hyp genes are found in several other N2-fixing cyanobacteria, but are absent in non N2-fixing cyanobacteria with only the bidirectional hydrogenase. Short conserved sequences were found in six intergenic regions of the extended hyp-operon, appearing between 11 and 79 times in the genome. Conclusion This study demonstrated that five ORFs upstream of the hyp-gene cluster are co-transcribed with the hyp-genes, and identified three TSPs in the extended hyp-gene cluster in Nostoc sp. strain PCC 7120. This may indicate a function related to the assembly of a functional uptake hydrogenase, hypothetically in the

Molecular hydrogen is involved in phytohormone signaling and stress responses in plants.

Directory of Open Access Journals (Sweden)

Jiqing Zeng

Full Text Available Molecular hydrogen (H2 metabolism in bacteria and algae has been well studied from an industrial perspective because H2 is viewed as a potential future energy source. A number of clinical trials have recently reported that H2 is a therapeutic antioxidant and signaling molecule. Although H2 metabolism in higher plants was reported in some early studies, its biological effects remain unclear. In this report, the biological effects of H2 and its involvement in plant hormone signaling pathways and stress responses were determined. Antioxidant enzyme activity was found to be increased and the transcription of corresponding genes altered when the effects of H2 on the germination of mung bean seeds treated with phytohormones was investigated. In addition, upregulation of several phytohormone receptor genes and genes that encode a few key factors involved in plant signaling pathways was detected in rice seedlings treated with HW. The transcription of putative rice hydrogenase genes, hydrogenase activity, and endogenous H2 production were also determined. H2 production was found to be induced by abscisic acid, ethylene, and jasmonate acid, salt, and drought stress and was consistent with hydrogenase activity and the expression of putative hydrogenase genes in rice seedlings. Together, these results suggest that H2 may have an effect on rice stress tolerance by modulating the output of hormone signaling pathways.

Chapter Eight - Structural Characterization of Poised States in the Oxygen Sensitive Hydrogenases and Nitrogenases

Energy Technology Data Exchange (ETDEWEB)

King, Paul W [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Mulder, David W [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Artz, Jacob H. [Washington State University; Zadvornyy, Oleg A. [Washington State University; Peters, John W. [Washington State University

2017-08-21

The crystallization of FeS cluster-containing proteins has been challenging due to their oxygen sensitivity, and yet these enzymes are involved in many critical catalytic reactions. The last few years have seen a wealth of innovative experiments designed to elucidate not just structural but mechanistic insights into FeS cluster enzymes. Here, we focus on the crystallization of hydrogenases, which catalyze the reversible reduction of protons to hydrogen, and nitrogenases, which reduce dinitrogen to ammonia. A specific focus is given to the different experimental parameters and strategies that are used to trap distinct enzyme states, specifically, oxidants, reductants, and gas-treatments. Other themes presented here include the recent use of Cryo-EM, and how coupling various spectroscopies to crystallization is opening up new approaches for structural and mechanistic analysis.

Isolation and characterization of the small subunit of the uptake hydrogenase from the cyanobacterium Nostoc punctiforme.

Science.gov (United States)

Raleiras, Patrícia; Kellers, Petra; Lindblad, Peter; Styring, Stenbjörn; Magnuson, Ann

2013-06-21

In nitrogen-fixing cyanobacteria, hydrogen evolution is associated with hydrogenases and nitrogenase, making these enzymes interesting targets for genetic engineering aimed at increased hydrogen production. Nostoc punctiforme ATCC 29133 is a filamentous cyanobacterium that expresses the uptake hydrogenase HupSL in heterocysts under nitrogen-fixing conditions. Little is known about the structural and biophysical properties of HupSL. The small subunit, HupS, has been postulated to contain three iron-sulfur clusters, but the details regarding their nature have been unclear due to unusual cluster binding motifs in the amino acid sequence. We now report the cloning and heterologous expression of Nostoc punctiforme HupS as a fusion protein, f-HupS. We have characterized the anaerobically purified protein by UV-visible and EPR spectroscopies. Our results show that f-HupS contains three iron-sulfur clusters. UV-visible absorption of f-HupS has bands ∼340 and 420 nm, typical for iron-sulfur clusters. The EPR spectrum of the oxidized f-HupS shows a narrow g = 2.023 resonance, characteristic of a low-spin (S = ½) [3Fe-4S] cluster. The reduced f-HupS presents complex EPR spectra with overlapping resonances centered on g = 1.94, g = 1.91, and g = 1.88, typical of low-spin (S = ½) [4Fe-4S] clusters. Analysis of the spectroscopic data allowed us to distinguish between two species attributable to two distinct [4Fe-4S] clusters, in addition to the [3Fe-4S] cluster. This indicates that f-HupS binds [4Fe-4S] clusters despite the presence of unusual coordinating amino acids. Furthermore, our expression and purification of what seems to be an intact HupS protein allows future studies on the significance of ligand nature on redox properties of the iron-sulfur clusters of HupS.

Enhanced photocatalytic hydrogen production from an MCM-41-immobilized photosensitizer-[Fe-Fe] hydrogenase mimic dyad.

Science.gov (United States)

Wang, Wen; Yu, Tianjun; Zeng, Yi; Chen, Jinping; Yang, Guoqiang; Li, Yi

2014-11-01

A covalently linked photosensitizer-catalytic center dyad Ps-Hy, consisting of two bis(2-phenylpyridine)(2,2'-bipyridine)iridium(iii) chromophores (Ps) and a diiron hydrogenase mimic (Hy) was constructed by using click reaction. Ps-Hy was incorporated into K(+)-exchanged molecular sieve MCM-41 to form a composite (Ps-Hy@MCM-41), which has been successfully applied to the photochemical production of hydrogen. The catalytic activity of Ps-Hy@MCM-41 is ∼3-fold higher as compared with that of Ps-Hy in the absence of MCM-41. The incorporation of Ps-Hy into MCM-41 stabilizes the catalyst, and consequently, advances the photocatalysis. The present study provides a potential strategy for improving catalytic efficiency of artificial photosynthesis systems using mesoporous molecular sieves.

Carbon monoxide and cyanide as intrinsic ligands to iron in the active site of [NiFe]-hydrogenases. NiFe(CN)2CO, biology's way to activate H2

NARCIS (Netherlands)

Pierik, A.J.; Roseboom, W.; Happe, R.P.; Bagley, K.A.; Albracht, S.P.J.

1999-01-01

Infrared-spectroscopic studies on the [NiFe]-hydrogenase of Chromatium vinosum-enriched in 15N or 13C, as well as chemical analyses, show that this enzyme contains three non-exchangeable, intrinsic, diatomic molecules as ligands to the active site, one carbon monoxide molecule and two cyanide

Synthesis of NiFe2O4 nanoparticles for energy and environment applications

Science.gov (United States)

Zhang, Ying; Rimal, Gaurab; Tang, Jinke; Dai, Qilin

2018-02-01

Magnetic nanoparticles are of great interest due to their applications in energy and environment. In this work, we developed a chemical solution based method to synthesize NiFe2O4 (NFO) nanoparticles with different sizes and structures by organic ligands and studied their applications in magnetic electrolyte concentration cells and waste water treatment. NFO nanoparticle growth is controlled by the organic passivating ligand ratios, reaction temperatures, and reaction solution concentrations to achieve the control of NFO nanoparticle size ranging from 25 nm to 160 nm. The NFO growth mechanism is controlled by aggregation related mechanism, leading to tunable magnetic properties and concentration cell device performance. Magnetic biochar consisting of biochar/NFO composite was also obtained based on the developed method. Waste water containing Rhodamine B was tested by the synthesized magnetic biochar. We believe the method developed in this work about magnetic NFO nanoparticles and magnetic biochar will shed light on the application of magnetic nanoparticles in energy and environment.

Electrochemical properties of carbon nanotubes-hydrogenase conjugates Langmuir-Blodgett films

International Nuclear Information System (INIS)

Liu, Ai-Rong; Wakayama, Tatsuki; Nakamura, Chikashi; Miyake, Jun; Zorin, Nikolay A.; Qian, Dong-Jin

2007-01-01

We report the preparation of Langmuir-Blodgett (LB) films composed of oxidized carbon nanotubes (CNTs) and hydrogenase (H 2 ase) conjugates and their electrochemical properties. Both single-walled (SWNTs) and multi-walled CNTs (MWNTs) were used to form mixed monolayers with H 2 ase on the Tris-HCl subphase surfaces. By using the LB method, the CNTs-H 2 ase monolayers were transferred onto CaF 2 and indium tin oxide (ITO) electrode surfaces. The LB film modified electrodes showed a couple of waves centered at around -500 mV (versus Ag/AgCl), which corresponding to the redox reaction of [4Fe-4S] 2+/1+ clusters in the H 2 ase. The current intensity was enhanced after co-assembly with CNTs. Because of the different diameters of CNTs, this current intensity was proportional to the scan rate (υ) for the electrodes modified with the LB films of pure H 2 ase and SWNTs-H 2 ase, but to the root of scan rate (υ 1/2 ) for those modified with the MWNTs-H 2 ase LB film. The products of diffusion coefficient and concentration (D 1/2 C) increased in the order of pure H 2 ase, SWNTs-H 2 ase, and MWNTs-H 2 ase LB films

Features of the structural and magnetic properties of Pb(TixZr1–xO3-NiFe1.98Co0.02O4 in the polarized state

Directory of Open Access Journals (Sweden)

Baev Vadim

2017-06-01

Full Text Available Composites with a 90%Pb(TixZr1-xO3-10%NiFe1.98Co0.02O4 composition have been synthesized. It has been established that the polarization of samples resulting from exposure to an electric field for 1 hour of 4 kV/mm in strength at a temperature of 400 K leads to crystal structure deformation. The compression of elementary crystal cells in some areas during polarization of the sample creates conditions suitable for the enhancement of magnetic exchange interactions. It has been found that the polarization process of such compositions leads to increases in specific magnetization and magnetic susceptibility. The analysis of Mössbauer spectra has shown that the polarization of the 90%Pb(TixZr1-xO3-10%NiFe1.98Co0.02O4 composite leads to significant changes in the effective magnetic fields of iron subspectra in various positions.

Respiratory hydrogen use by Salmonella enterica serovar Typhimurium is essential for virulence.

Science.gov (United States)

Maier, R J; Olczak, A; Maier, S; Soni, S; Gunn, J

2004-11-01

Based on available annotated gene sequence information, the enteric pathogen salmonella, like other enteric bacteria, contains three putative membrane-associated H2-using hydrogenase enzymes. These enzymes split molecular H2, releasing low-potential electrons that are used to reduce quinone or heme-containing components of the respiratory chain. Here we show that each of the three distinct membrane-associated hydrogenases of Salmonella enterica serovar Typhimurium is coupled to a respiratory pathway that uses oxygen as the terminal electron acceptor. Cells grown in a blood-based medium expressed four times the amount of hydrogenase (H2 oxidation) activity that cells grown on Luria Bertani medium did. Cells suspended in phosphate-buffered saline consumed 2 mol of H2 per mol of O2 used in the H2-O2 respiratory pathway, and the activity was inhibited by the respiration inhibitor cyanide. Molecular hydrogen levels averaging over 40 microM were measured in organs (i.e., livers and spleens) of live mice, and levels within the intestinal tract (the presumed origin of the gas) were four times greater than this. The half-saturation affinity of S. enterica serovar Typhimurium for H2 is only 2.1 microM, so it is expected that H2-utilizing hydrogenase enzymes are saturated with the reducing substrate in vivo. All three hydrogenase enzymes contribute to the virulence of the bacterium in a typhoid fever-mouse model, based on results from strains with mutations in each of the three hydrogenase genes. The introduced mutations are nonpolar, and growth of the mutant strains was like that of the parent strain. The combined removal of all three hydrogenases resulted in a strain that is avirulent and (in contrast to the parent strain) one that is unable to invade liver or spleen tissue. The introduction of one of the hydrogenase genes into the triple mutant strain on a low-copy-number plasmid resulted in a strain that was able to both oxidize H2 and cause morbidity in mice within 11

pH-Dependent isotope exchange and hydrogenation catalysed by water-soluble NiRu complexes as functional models for [NiFe]hydrogenases

OpenAIRE

Kure, Bunsho; Matsumoto, Takahiro; Ichikawa, Koji; Fukuzumi, Shunichi; Higuchi, Yoshiki; Yagi, Tatsuhiko; Ogo, Seiji

2008-01-01

The pH-dependent hydrogen isotope exchange reaction between gaseous isotopes and medium isotopes and hydrogenation of the carbonyl compounds have been investigated with water-soluble bis(mu-thiolate)(mu-hydride)NiRu complexes, Ni(II)(mu-SR)(2)(mu-H)Ru(II) {(mu-SR)(2) = N,N'-dimethyl-N,N'-bis(2-mercaptoethyl)-1,3-propanediamine}, as functional models for [NiFe]hydrogenases. In acidic media (at pH 4-6), the mu-H ligand of the Ni(II)(mu-SR)(2)(mu-H)Ru(II) complexes has H(+) properties, and the c...

Evaluation as a catalyst in ferrispinel NiFe_2O_4 esterification and transesterification

International Nuclear Information System (INIS)

Pereira, Kleberson Ricardo de Oliveira; Dantas, Joelda; Costa, Ana Cristina Figueiredo de Melo; Silva, Adriano Sant'Ana; Kiminami, Ruth Herta Goldschmidt Aliaga

2014-01-01

The advancement of nanoscience and nanotechnology, magnetic nanoparticles ferrispinels type, have found numerous applications in biochemistry, molecular biology, biomedicine, diagnosis and heterogeneous catalysis for biodiesel production. Therefore, we propose to synthesize ferrispinel NiFe_2O_4 and evaluate its performance as a catalyst for esterification and transesterification of the methyl soybean oil. The sample was obtained through combustion reaction with production of 10 g / batch and characterized by XRD, SEM and BET. The catalytic reaction was conducted in high-pressure reactor at 180 °C for 1 hour, with a molar ratio of oil:ethanol 1:12 with 2% catalyst. The results showed the formation of ferrispinel phase, morphology composed of aggregates in the form of irregular blocks formed by pre sintered particles and low interparticle porosity. As a catalyst, the conversion values presented ferrispinel 52% and 4% in the esterification and transesterification, respectively, indicating that promising material for use in biodiesel production. (author)

Engineering Synechocystis PCC6803 for hydrogen production: influence on the tolerance to oxidative and sugar stresses.

Directory of Open Access Journals (Sweden)

Marcia Ortega-Ramos

Full Text Available In the prospect of engineering cyanobacteria for the biological photoproduction of hydrogen, we have studied the hydrogen production machine in the model unicellular strain Synechocystis PCC6803 through gene deletion, and overexpression (constitutive or controlled by the growth temperature. We demonstrate that the hydrogenase-encoding hoxEFUYH operon is dispensable to standard photoautotrophic growth in absence of stress, and it operates in cell defense against oxidative (H₂O₂ and sugar (glucose and glycerol stresses. Furthermore, we showed that the simultaneous over-production of the proteins HoxEFUYH and HypABCDE (assembly of hydrogenase, combined to an increase in nickel availability, led to an approximately 20-fold increase in the level of active hydrogenase. These novel results and mutants have major implications for those interested in hydrogenase, hydrogen production and redox metabolism, and their connections with environmental conditions.

Structural features of epitaxial NiFe2O4 thin films grown on different substrates by direct liquid injection chemical vapor deposition

Science.gov (United States)

Datta, R.; Loukya, B.; Li, N.; Gupta, A.

2012-04-01

NiFe2O4 (NFO) thin films are grown on four different substrates, i.e., Lead Zinc Niobate-Lead Titanate (PZN-PT), Lead Magnesium Niobate-Lead Titanate (PMN-PT), MgAl2O4 (MAO) and SrTiO3 (STO), by a direct liquid injection chemical vapor deposition technique (DLI-CVD) under optimum growth conditions where relatively high growth rate (˜20 nm/min), smooth surface morphology and high saturation magnetization values in the range of 260-290 emu/ cm3 are obtained. The NFO films with correct stoichiometry (Ni:Fe=1:2) grow epitaxially on all four substrates, as confirmed by energy dispersive X-ray spectroscopy, transmission electron microscopy and x-ray diffraction. While the films on PMN-PT and PZN-PT substrates are partially strained, essentially complete strain relaxation occurs for films grown on MAO and STO. The formations of threading dislocations along with dark diffused contrast areas related to antiphase domains having a different cation ordering are observed on all four substrates. These crystal defects are correlated with lattice mismatch between the film and substrate and result in changes in magnetic properties of the films. Atomic resolution HAADF imaging and EDX line profiles show formation of a sharp interface between the film and the substrate with no inter-diffusion of Pb or other elements across the interface. Antiphase domains are observed to originate at the film-substrate interface.

Preparation, characterization and enhanced adsorption performance for Cr(VI) of mesoporous NiFe2O4 by twice pore-forming method

International Nuclear Information System (INIS)

Jia, Zhigang; Peng, Kuankuan; Xu, Lixin

2012-01-01

Magnetic mesoporous NiFe 2 O 4 with higher surface area has been prepared by the twice pore-forming method, including the calcination of the oxalate precursor and leaching of ZnO pore-forming agent. The X-ray diffraction (XRD), Scanning electron microscopy (SEM), Energy dispersive spectroscopy (EDS) and BET surface area measurement are used to evaluate the pore structural parameters and surface chemistry of the adsorbent respectively. The pore-forming mechanism is proposed based on the experimental results. The adsorption behavior of mesoporous NiFe 2 O 4 for Cr(VI) is investigated in detail. The results show that kinetic data follow a pseudo-second-order model and equilibrium data are well fitted by the Langmuir model. The maximum adsorption capacity is 43.68 mg g −1 at pH 2. The removal for Cr(VI) is mainly physisorption process derived from coulombic interaction. The as-prepared TPF-NiFe 2 O 4 is promising as sorbent for Cr(VI) removal because of its higher adsorption capacity, separation convenience and highly efficient reusability. -- Highlights: ► The increase of BET area was realized by leaching of ZnO from mesoporous ZnO/NiFe 2 O 4 . ► TPF-NiFe 2 O 4 demenstrates higher adsorption capacity for Cr(VI) in aqueous solution. ► TPF-NiFe 2 O 4 with magnetic sensitivity is promosing for Cr(VI) removal. ► The used TPF-NiFe 2 O 4 adsorbent can be recycled.

Electrokinetic properties of PMAA functionalized NiFe2O4 nanoparticles synthesized by thermal plasma route

Science.gov (United States)

Bhosale, Shivaji V.; Mhaske, Pravin; Kanhe, N.; Navale, A. B.; Bhoraskar, S. V.; Mathe, V. L.; Bhatt, S. K.

2014-04-01

The magnetic nickel ferrite (NiFe2O4) nanoparticles with an average size of 30nm were synthesised by Transferred arc DC Thermal Plasma route. The synthesized nickel ferrite nanoparticles were characterized by TEM and FTIR techniques. The synthesized nickel ferrite nanoparticles were further functionalized with PMAA (polymethacrylic acid) by self emulsion polymerization method and subsequently were characterized by FTIR and Zeta Analyzer. The variation of zeta potential with pH was systematically studied for both PMAA functionalized (PNFO) and uncoated nickel ferrite nanoparticles (NFO). The IEP (isoelectric points) for PNFO and NFO was determined from the graph of zeta potential vs pH. It was observed that the IEP for NFO was at 7.20 and for PNFO it was 2.52. The decrease in IEP of PNFO was attributed to the COOH functional group of PMAA.

Deformation behavior of multilayered NiFe with bimodal grain size distribution at room and elevated temperature

Energy Technology Data Exchange (ETDEWEB)

Fiebig, Jochen, E-mail: jmfiebig@ucdavis.edu [Department of Chemical Engineering and Materials Science, University of California, Davis, CA 95817 (United States); Jian, Jie [Department of Electrical and Computer Engineering, Texas A& M University, College Station, TX 77843-3128 (United States); Kurmanaeva, Lilia [Department of Chemical Engineering and Materials Science, University of California, Davis, CA 95817 (United States); McCrea, Jon [Integran Technologies Inc., Toronto (Canada); Wang, Haiyan [Department of Electrical and Computer Engineering, Texas A& M University, College Station, TX 77843-3128 (United States); Lavernia, Enrique [Department of Chemical Engineering and Materials Science, University of California, Davis, CA 95817 (United States); Department of Chemical Engineering and Materials Science, University of California, Irvine, CA 92697 (United States); Mukherjee, Amiya [Department of Chemical Engineering and Materials Science, University of California, Davis, CA 95817 (United States)

2016-02-22

We describe a study of the temperature dependent deformation behavior of a multilayered NiFe-60 wt%Fe alloy with a layer thickness of 5 μm fabricated by electrodeposition. The structure of adjacent layers alternates between a nanocrystalline and a coarse grained. Uniaxial tensile tests at temperature between 20 °C and 400 °C and strain rate of 10{sup −4}–10{sup −2} were used to determine the mechanical behavior. Microstructure observations via transmission electron microscopy and fractography were performed to provide insight into the underlying deformation mechanism. The mechanical behavior is discussed in the context of the bimodal microstructure of multilayered samples and the contribution of each sub-layer to strength and ductility. The results reveal that even at higher temperatures the nanocrystalline layer determines the mechanical performance of multilayered materials.

The characteristic of deformability and quantitative description of the microstructure of hot-deformed Ni-Fe superalloy

Directory of Open Access Journals (Sweden)

Ducki K. J.

2017-03-01

Full Text Available The paper presents the results of research concerning the influence of hot plastic working parameters on the deformability and microstructure of a Ni-Fe superalloy. The research was performed on a torsion plastometer in the range of temperatures of 900-1150°C, at a strain rates 0.1 and 1.0 s-1. Plastic properties of the alloy were characterized by the worked out flow curves and the temperature relationships of flow stress and strain limit. The structural inspections were performed on microsections taken from plastometric samples after so-called “freezing”. The stereological parameters as the recrystallized grain size, inhomogenity and grain shape have been determined. Functional relations between the Zener-Hollomon parameter and the maximum yield stress and the average grain area have been developed and the activation energy for hot working has been estimated.

Production and purification of a soluble hydrogenase from Ralstonia eutropha H16 for potential hydrogen fuel cell applications.

Science.gov (United States)

Jugder, Bat-Erdene; Lebhar, Helene; Aguey-Zinsou, Kondo-Francois; Marquis, Christopher P

2016-01-01

The soluble hydrogenase (SH) from Ralstonia eutropha H16 is a promising candidate enzyme for H2-based biofuel application as it favours H2 oxidation and is relatively oxygen-tolerant. In this report, bioprocess development studies undertaken to produce and purify an active SH are described, based on the methods previously reported [1], [2], [3], [4]. Our modifications are: •Upstream method optimizations were undertaken on heterotrophic growth media and cell lysis involving ultrasonication.•Two anion exchangers (Q Sepharose and RESOURCE Q) and size exclusion chromatographic (Superdex 200) matrices were successfully employed for purification of a hexameric SH from R. eutropha.•The H2 oxidizing activity of the SH was demonstrated spectrophotometrically in solution and also immobilized on an EPG electrode using cyclic voltammetry.

Microfabrication of magnetostrictive beams based on NiFe film doped with B and Mo for integrated sensor systems

KAUST Repository

Alfadhel, Ahmed

2012-03-09

This paper reports the development of integrated micro-sensors consisting of 1 -µm-thick magnetostrictive cantilevers or bridges with 500 µm in length and conducting interrogation elements. The thin films are fabricated by sputter deposition of NiFe doped with B and Mo, and the magnetic properties are enhanced by field annealing, resulting in a coercivity of 2.4 Oe. In operation, an alternating current applied to the interrogation elements magnetizes the magnetostrictive structures. The longitudinal resonant frequency is detected as an impedance change of the interrogation elements. The magnetostrictive micro-beams provide high resonant frequencies—2.95 MHz for the cantilever and 5.46 MHz for the bridge—which can be exploited to develop sensors of high sensitivity.

How Formaldehyde Inhibits Hydrogen Evolution by [FeFe]-Hydrogenases: Determination by ¹³C ENDOR of Direct Fe-C Coordination and Order of Electron and Proton Transfers.

Science.gov (United States)

Bachmeier, Andreas; Esselborn, Julian; Hexter, Suzannah V; Krämer, Tobias; Klein, Kathrin; Happe, Thomas; McGrady, John E; Myers, William K; Armstrong, Fraser A

2015-04-29

Formaldehyde (HCHO), a strong electrophile and a rapid and reversible inhibitor of hydrogen production by [FeFe]-hydrogenases, is used to identify the point in the catalytic cycle at which a highly reactive metal-hydrido species is formed. Investigations of the reaction of Chlamydomonas reinhardtii [FeFe]-hydrogenase with formaldehyde using pulsed-EPR techniques including electron-nuclear double resonance spectroscopy establish that formaldehyde binds close to the active site. Density functional theory calculations support an inhibited super-reduced state having a short Fe-(13)C bond in the 2Fe subsite. The adduct forms when HCHO is available to compete with H(+) transfer to a vacant, nucleophilic Fe site: had H(+) transfer already occurred, the reaction of HCHO with the Fe-hydrido species would lead to methanol, release of which is not detected. Instead, Fe-bound formaldehyde is a metal-hydrido mimic, a locked, inhibited form analogous to that in which two electrons and only one proton have transferred to the H-cluster. The results provide strong support for a mechanism in which the fastest pathway for H2 evolution involves two consecutive proton transfer steps to the H-cluster following transfer of a second electron to the active site.

Experimental Investigations on Pulsed Nd:YAG Laser Welding of C17300 Copper-Beryllium and 49Ni-Fe Soft Magnetic Alloys

International Nuclear Information System (INIS)

Mousavi, S. A. A. Akbari; Ebrahimzadeh, H.

2011-01-01

Copper-beryllium and soft magnetic alloys must be joined in electrical and electro-mechanical applications. There is a high difference in melting temperatures of these alloys which cause to make the joining process very difficult. In addition, copper-beryllium alloys are of age hardenable alloys and precipitations can brittle the weld. 49Ni-Fe alloy is very hot crack sensitive. Moreover, these alloys have different heat transfer coefficients and reflection of laser beam in laser welding process. Therefore, the control of welding parameters on the formation of adequate weld puddle composition is very difficult. Laser welding is an advanced technique for joining of dissimilar materials since it can precisely control and adjust the welding parameters. In this study, a 100W Nd:YAG pulsed laser machine was used for joining 49Ni-Fe soft magnetic to C17300 copper-beryllium alloys. Welding of samples was carried out autogenously by changing the pulse duration, diameter of beam, welding speed, voltage and frequency. The spacing between samples was set to almost zero. The ample were butt welded. It was required to apply high voltage in this study due to high reflection coefficient of copper alloys. Metallography, SEM analysis, XRD and microhardness measurement was used for survey of results. The results show that the weld strength depends upon the chemical composition of the joints. To change the wells composition and heat input of the welds, it was attempted to deviate the laser focus away from the weld centerline. The best strength was achieved by deviation of the laser beam away about 0.1mm from the weld centerline. The result shows no intermetallic compounds if the laser beam is deviated away from the joint.

Direct selenylation of mixed Ni/Fe metal-organic frameworks to NiFe-Se/C nanorods for overall water splitting

Science.gov (United States)

Xu, Bo; Yang, He; Yuan, Lincheng; Sun, Yiqiang; Chen, Zhiming; Li, Cuncheng

2017-10-01

Development of low-cost, highly active bifunctional catalyst for efficient overall water splitting based on earth-abundant metals is still a great challenging task. In this work, we report a NiFe-Se/C composite nanorod as efficient non-precious-metal electrochemical catalyst derived from direct selenylation of a mixed Ni/Fe metal-organic framework. The as-obtained catalyst requires low overpotential to drive 10 mA cm-2 for HER (160 mV) and OER (240 mV) in 1.0 M KOH, respectively, and its catalytic activity is maintained for at least 20 h. Moreover, water electrolysis using this catalyst achieves high water splitting current density of 10 mA cm-2 at cell voltage of 1.68 V.

Conduction Mechanisms in Multiferroic Multilayer BaTiO3/NiFe2O4/BaTiO3 Memristors

Science.gov (United States)

Samardzic, N.; Bajac, B.; Srdic, V. V.; Stojanovic, G. M.

2017-10-01

Memristive devices and materials are extensively studied as they offer diverse properties and applications in digital, analog and bio-inspired circuits. In this paper, we present an important class of memristors, multiferroic memristors, which are composed of multiferroic multilayer BaTiO3/NiFe2O4/BaTiO3 thin films, fabricated by a spin-coating deposition technique on platinized Si wafers. This cost-effective device shows symmetric and reproducible current-voltage characteristics for the actuating voltage amplitude of ±10 V. The origin of the conduction mechanism was investigated by measuring the electrical response in different voltage and temperature conditions. The results indicate the existence of two mechanisms: thermionic emission and Fowler-Nordheim tunnelling, which alternate with actuating voltage amplitude and operating temperature.

A Model Study on the Possible Effects of an External Electrical Field on Enzymes Having Dinuclear Iron Cluster [2Fe-2S

Directory of Open Access Journals (Sweden)

Lemi Türker

2012-01-01

Full Text Available Hydrogenases which catalyze the H2 ↔ 2H+ + 2e− reaction are metalloenzymes that can be divided into two classes, the NiFe and Fe enzymes, on the basis of their metal content. Iron-sulfur clusters [2Fe-2S] and [4Fe-4S] are common in ironhydrogenases. In the present model study, [2Fe-2S] cluster has been considered to visualize the effect of external electric field on various quantum chemical properties of it. In the model, all the cysteinyl residues are in the amide form. The PM3 type semiempirical calculations have been performed for the geometry optimization of the model structure in the absence and presence of the external field. Then, single point DFT calculations (B3LYP/6-31+G(d have been carried out. Depending on the direction of the field, the chemical reactivity of the model enzyme varies which suggests that an external electric field could, under proper conditions, improve the enzymatic hydrogen production.

Protein chaperones Q8ZP25_SALTY from Salmonella typhimurium and HYAE_ECOLI from Escherichia coli exhibit thioredoxin-like structures despite lack of canonical thioredoxin active site sequence motive

Science.gov (United States)

Parish, David; Benach, Jordi; Liu, Goahua; Singarapu, Kiran Kumar; Xiao, Rong; Acton, Thomas; Su, Min; Bansal, Sonal; Prestegard, James H.; Hunt, John; Montelione, Gaetano T.

2010-01-01

The structure of the 142-residue protein Q8ZP25_SALTY encoded in the genome of Salmonella typhimurium LT2 was determined independently by NMR and X-ray crystallography, and the structure of the 140-residue protein HYAE_ECOLI encoded in the genome of Eschericia coli was determined by NMR. The two proteins belong to Pfam [1] PF07449, which currently comprises 50 members, and belongs itself to the ‘thioredoxin-like clan’. However, protein HYAE_ECOLI and the other proteins of Pfam PF07449 do not contain the canonical Cys-X-X-Cys active site sequence motif of thioredoxin. Protein HYAE_ECOLI was previously classified as a [NiFe] hydrogenase-1 specific chaperone interacting with the twin-arginine translocation (Tat) signal peptide. The structures presented here exhibit the expected thioredoxin-like fold and support the view that members of Pfam family PF07449 specifically interact with Tat signal peptides. PMID:19039680

Protein chaperones Q8ZP25_SALTY from Salmonella typhimurium and HYAE_ECOLI from Escherichia coli exhibit thioredoxin-like structures despite lack of canonical thioredoxin active site sequence motif.

Science.gov (United States)

Parish, David; Benach, Jordi; Liu, Goahua; Singarapu, Kiran Kumar; Xiao, Rong; Acton, Thomas; Su, Min; Bansal, Sonal; Prestegard, James H; Hunt, John; Montelione, Gaetano T; Szyperski, Thomas

2008-12-01

The structure of the 142-residue protein Q8ZP25_SALTY encoded in the genome of Salmonella typhimurium LT2 was determined independently by NMR and X-ray crystallography, and the structure of the 140-residue protein HYAE_ECOLI encoded in the genome of Escherichia coli was determined by NMR. The two proteins belong to Pfam (Finn et al. 34:D247-D251, 2006) PF07449, which currently comprises 50 members, and belongs itself to the 'thioredoxin-like clan'. However, protein HYAE_ECOLI and the other proteins of Pfam PF07449 do not contain the canonical Cys-X-X-Cys active site sequence motif of thioredoxin. Protein HYAE_ECOLI was previously classified as a [NiFe] hydrogenase-1 specific chaperone interacting with the twin-arginine translocation (Tat) signal peptide. The structures presented here exhibit the expected thioredoxin-like fold and support the view that members of Pfam family PF07449 specifically interact with Tat signal peptides.

Protein Chaperones Q8ZP25_SALTY from Salmonella Typhimurium and HYAE_ECOLI from Escherichia coli Exhibit Thioredoxin-like Structures Despite Lack of Canonical Thioredoxin Active Site Sequence Motif

Energy Technology Data Exchange (ETDEWEB)

Parish, D.; Benach, J; Liu, G; Singarapu, K; Xiao, R; Acton, T; Hunt, J; Montelione, G; Szyperski, T; et. al.

2008-01-01

The structure of the 142-residue protein Q8ZP25 SALTY encoded in the genome of Salmonella typhimurium LT2 was determined independently by NMR and X-ray crystallography, and the structure of the 140-residue protein HYAE ECOLI encoded in the genome of Escherichia coli was determined by NMR. The two proteins belong to Pfam (Finn et al. 34:D247-D251, 2006) PF07449, which currently comprises 50 members, and belongs itself to the 'thioredoxin-like clan'. However, protein HYAE ECOLI and the other proteins of Pfam PF07449 do not contain the canonical Cys-X-X-Cys active site sequence motif of thioredoxin. Protein HYAE ECOLI was previously classified as a (NiFe) hydrogenase-1 specific chaperone interacting with the twin-arginine translocation (Tat) signal peptide. The structures presented here exhibit the expected thioredoxin-like fold and support the view that members of Pfam family PF07449 specifically interact with Tat signal peptides.

Nitrogen–doped graphitized carbon shell encapsulated NiFe nanoparticles: A highly durable oxygen evolution catalyst

Energy Technology Data Exchange (ETDEWEB)

Du, Lei; Luo, Langli; Feng, Zhenxing; Engelhard, Mark; Xie, Xiaohong; Han, Binghong; Sun, Junming; Zhang, Jianghao; Yin, Geping; Wang, Chongmin; Wang, Yong; Shao, Yuyan

2017-09-01

Oxygen evolution reaction (OER) plays a crucial role in various energy conversion devices such as water electrolyzers and metal–air batteries. Precious metal catalysts such as Ir, Ru and their oxides are usually used for enhancing reaction kinetics but are limited by their scarce resource. The challenges associated with alternative non–precious metal catalysts such as transition metal oxides and (oxy)hydroxides etc. are their low electronic conductivity and durability. Herein, we report a highly active (360 mV overpotential at 10 mA cm–2GEO) and durable (no degradation after 20000 cycles) OER catalyst derived from bimetallic metal–organic frameworks (MOFs) precursors. This catalyst consists of NiFe nanoparticles encapsulated by nitrogen–doped graphitized carbon shells. The electron-donation/deviation from Fe and tuned electronic structure of metal cores by Ni are revealed to be primary contributors to the enhanced OER activity, whereas N concentration contributes negligibly. We further demonstrated that the structure and morphology of encapsulating carbon shells, which are the key factors influencing the durability, are facilely controlled by the chemical state of precursors.

Cotunneling enhancement of magnetoresistance in double magnetic tunnel junctions with embedded superparamagnetic NiFe nanoparticles

International Nuclear Information System (INIS)

Dempsey, K.J.; Arena, D.; Hindmarch, A.T.; Wei, H.X.; Qin, Q.H.; Wen, Z.C.; Wang, W.X.; Vallejo-Fernandez, G.; Han, X.F.; Marrows, C.H.

2010-01-01

Temperature and bias voltage-dependent transport characteristics are presented for double magnetic tunnel junctions (DMTJs) with self-assembled NiFe nanoparticles embedded between insulating alumina barriers. The junctions with embedded nanoparticles are compared to junctions with a single barrier of comparable size and growth conditions. The embedded particles are characterized using x-ray absorption spectroscopy, transmission electron microscopy, and magnetometry techniques, showing that they are unoxidized and remain superparamagnetic to liquid helium temperatures. The tunneling magnetoresistance (TMR) for the DMTJs is lower than the control samples, however, for the DMTJs an enhancement in TMR is seen in the Coulomb blockade region. Fitting the transport data in this region supports the theory that cotunneling is the dominant electron transport process within the Coulomb blockade region, sequential tunneling being suppressed. We therefore see an enhanced TMR attributed to the change in the tunneling process due to the interplay of the Coulomb blockade and spin-dependent tunneling through superparamagnetic nanoparticles, and develop a simple model to quantify the effect, based on the fact that our nanoparticles will appear blocked when measured on femtosecond tunneling time scales.

Tuning magnetic properties of magnetoelectric BiFeO 3-NiFe 2O 4 nanostructures

Science.gov (United States)

Crane, S. P.; Bihler, C.; Brandt, M. S.; Goennenwein, S. T. B.; Gajek, M.; Ramesh, R.

2009-02-01

Multifunctional thin film nanostructures containing soft magnetic materials such as nickel ferrite are interesting for potential applications in microwave signal processing because of the possibility to shrink the size of device architecture and limit device power consumption. An essential prerequisite to future applications of such a system is a firm understanding of its magnetic properties. We show that nanostructures composed of ferrimagnetic NiFe 2O 4 pillars in a multiferroic BiFeO 3 matrix can be tuned magnetically by altering the aspect ratio of the pillars by depositing films of varying thickness. Magnetic anisotropy is studied using ferromagnetic resonance, which shows that the uniaxial magnetic anisotropy in the growth direction changes sign upon increasing the film thickness. The magnitude of this anisotropy contribution can be explained via a combination of shape and magnetostatic effects, using the object-oriented micromagnetic framework (OOMMF). The key factors determining the magnetic properties of the films are shown to be the aspect ratio of individual pillars and magnetostatic interactions between neighboring pillars.

Tuning magnetic properties of magnetoelectric BiFeO3-NiFe2O4 nanostructures

International Nuclear Information System (INIS)

Crane, S.P.; Bihler, C.; Brandt, M.S.; Goennenwein, S.T.B.; Gajek, M.; Ramesh, R.

2009-01-01

Multifunctional thin film nanostructures containing soft magnetic materials such as nickel ferrite are interesting for potential applications in microwave signal processing because of the possibility to shrink the size of device architecture and limit device power consumption. An essential prerequisite to future applications of such a system is a firm understanding of its magnetic properties. We show that nanostructures composed of ferrimagnetic NiFe 2 O 4 pillars in a multiferroic BiFeO 3 matrix can be tuned magnetically by altering the aspect ratio of the pillars by depositing films of varying thickness. Magnetic anisotropy is studied using ferromagnetic resonance, which shows that the uniaxial magnetic anisotropy in the growth direction changes sign upon increasing the film thickness. The magnitude of this anisotropy contribution can be explained via a combination of shape and magnetostatic effects, using the object-oriented micromagnetic framework (OOMMF). The key factors determining the magnetic properties of the films are shown to be the aspect ratio of individual pillars and magnetostatic interactions between neighboring pillars

Electrical transport and optical band gap of NiFe2Ox thin films

Science.gov (United States)

Bougiatioti, Panagiota; Manos, Orestis; Klewe, Christoph; Meier, Daniel; Teichert, Niclas; Schmalhorst, Jan-Michael; Kuschel, Timo; Reiss, Günter

2017-12-01

We fabricated NiFe2Ox thin films on MgAl2O4(001) by reactive dc magnetron co-sputtering varying the oxygen partial pressure. The fabrication of a material with a variable oxygen deficiency leads to controllable electrical and optical properties which are beneficial for the investigations of the transport phenomena and could, therefore, promote the use of such materials in spintronic and spin caloritronic applications. We used several characterization techniques to investigate the film properties, focusing on their structural, magnetic, electrical, and optical properties. From the electrical resistivity, we obtained the conduction mechanisms that govern the systems in the high and low temperature regimes. We further extracted low thermal activation energies which unveil extrinsic transport mechanisms. The thermal activation energy decreases in the less oxidized samples revealing the pronounced contribution of a large amount of electronic states localized in the band gap to the electrical conductivity. The Hall coefficient is negative and decreases with increasing conductivity as expected for n-type conduction, while the Hall- and the drift mobilities show a large difference. The optical band gaps were determined via ultraviolet-visible spectroscopy. They follow a similar trend as the thermal activation energies, with lower band gap values in the less oxidized samples.

Effect of 120 MeV 28Si9+ ion irradiation on structural and magnetic properties of NiFe2O4 and Ni0.5Zn0.5Fe2O4

Science.gov (United States)

Sharma, R.; Raghuvanshi, S.; Satalkar, M.; Kane, S. N.; Tatarchuk, T. R.; Mazaleyrat, F.

2018-05-01

NiFe2O4, Ni0.5Zn0.5Fe2O4 samples were synthesized using sol-gel auto combustion method, and irradiated by using 120 MeV 28Si9+ ion with ion fluence of 1×1012 ions/cm2. Characterization of pristine, irradiated samples were done using X-Ray Diffraction (XRD), Field Emission Scanning Microscopy (FE-SEM), Energy Dispersive X-ray Analysis (EDAX) and Vibrating Sample Magnetometer (VSM). XRD validates the single phase nature of pristine, irradiated Ni- Zn nano ferrite except for Ni ferrite (pristine, irradiated) where secondary phases of α-Fe2O3 and Ni is observed. FE- SEM images of pristine Ni, Ni-Zn ferrite show inhomogeneous nano-range particle size distribution. Presence of diamagnetic ion (Zn2+) in NiFe2O4 increases oxygen positional parameter (u 4¯3m ), experimental, theoretical saturation magnetization (Msexp., Msth.), while decreases the grain size (Ds) and coercivity (Hc). With irradiation Msexp., Msth. increases but not much change are observed in Hc. New antistructure modeling for the pristine, irradiated Ni and Ni-Zn ferrite samples was used for describing the surface active centers.

Genome Sequence of the Thermophilic Cyanobacterium Thermosynechococcus sp. Strain NK55a.

Energy Technology Data Exchange (ETDEWEB)

Stolyar, Sergey; Liu, Zhenfeng; Thiel, Vera; Tomsho, Lynn P.; Pinel, Nicolas; Nelson, William C.; Lindemann, Stephen R.; Romine, Margaret F.; Haruta, Shin; Schuster, Stephan C.; Bryant, Donald A.; Fredrickson, Jim K.

2014-01-02

The genome of the unicellular cyanobacterium, Thermosynechococcus sp. strain NK55a, isolated from Nakabusa hot spring, comprises a single, circular, 2.5-Mb chromosome. The genome is predicted to encode 2358 protein coding genes, including genes for all typical cyanobacterial photosynthetic and metabolic functions. No genes encoding hydrogenases or nitrogenase were identified.

The nif Gene Operon of the Methanogenic Archaeon Methanococcus maripaludis

Science.gov (United States)

Kessler, Peter S.; Blank, Carrine; Leigh, John A.

1998-01-01

Nitrogen fixation occurs in two domains, Archaea and Bacteria. We have characterized a nif (nitrogen fixation) gene cluster in the methanogenic archaeon Methanococcus maripaludis. Sequence analysis revealed eight genes, six with sequence similarity to known nif genes and two with sequence similarity to glnB. The gene order, nifH, ORF105 (similar to glnB), ORF121 (similar to glnB), nifD, nifK, nifE, nifN, and nifX, was the same as that found in part in other diazotrophic methanogens and except for the presence of the glnB-like genes, also resembled the order found in many members of the Bacteria. Using transposon insertion mutagenesis, we determined that an 8-kb region required for nitrogen fixation corresponded to the nif gene cluster. Northern analysis revealed the presence of either a single 7.6-kb nif mRNA transcript or 10 smaller mRNA species containing portions of the large transcript. Polar effects of transposon insertions demonstrated that all of these mRNAs arose from a single promoter region, where transcription initiated 80 bp 5′ to nifH. Distinctive features of the nif gene cluster include the presence of the six primary nif genes in a single operon, the placement of the two glnB-like genes within the cluster, the apparent physical separation of the cluster from any other nif genes that might be in the genome, the fragmentation pattern of the mRNA, and the regulation of expression by a repression mechanism described previously. Our study and others with methanogenic archaea reporting multiple mRNAs arising from gene clusters with only a single putative promoter sequence suggest that mRNA processing following transcription may be a common occurrence in methanogens. PMID:9515920

Metagenomic Analyses Reveal That Energy Transfer Gene Abundances Can Predict the Syntrophic Potential of Environmental Microbial Communities

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Lisa Oberding

2016-01-01

Full Text Available Hydrocarbon compounds can be biodegraded by anaerobic microorganisms to form methane through an energetically interdependent metabolic process known as syntrophy. The microorganisms that perform this process as well as the energy transfer mechanisms involved are difficult to study and thus are still poorly understood, especially on an environmental scale. Here, metagenomic data was analyzed for specific clusters of orthologous groups (COGs related to key energy transfer genes thus far identified in syntrophic bacteria, and principal component analysis was used in order to determine whether potentially syntrophic environments could be distinguished using these syntroph related COGs as opposed to universally present COGs. We found that COGs related to hydrogenase and formate dehydrogenase genes were able to distinguish known syntrophic consortia and environments with the potential for syntrophy from non-syntrophic environments, indicating that these COGs could be used as a tool to identify syntrophic hydrocarbon biodegrading environments using metagenomic data.

Insight into Energy Conservation via Alternative Carbon Monoxide Metabolism in Carboxydothermus pertinax Revealed by Comparative Genome Analysis.

Science.gov (United States)

Fukuyama, Yuto; Omae, Kimiho; Yoneda, Yasuko; Yoshida, Takashi; Sako, Yoshihiko

2018-05-04

Carboxydothermus species are some of the most studied thermophilic carboxydotrophs. Their varied carboxydotrophic growth properties suggest distinct strategies for energy conservation via CO metabolism. In this study, we used comparative genome analysis of the genus Carboxydothermus to show variations in the CO dehydrogenase/energy-converting hydrogenase gene cluster, which is responsible for CO metabolism with H 2 production (hydrogenogenic CO metabolism). Indeed, ability or inability to produce H 2 with CO oxidation is explained by the presence or absence of this gene cluster in C. hydrogenoformans , C. islandicus , and C. ferrireducens Interestingly, despite its hydrogenogenic CO metabolism, C. pertinax lacks the Ni-CO dehydrogenase catalytic subunit (CooS-I) and its transcriptional regulator encoding genes in this gene cluster probably due to inversion. Transcriptional analysis in C. pertinax showed that the Ni-CO dehydrogenase gene ( cooS-II ) and distantly encoded energy-converting hydrogenase related genes were remarkably upregulated under 100% CO. In addition, when thiosulfate was available as a terminal electron acceptor under 100% CO, C. pertinax maximum cell density and maximum specific growth rate were 3.1-fold and 1.5-fold higher, respectively, than when thiosulfate was absent. The amount of H 2 produced was only 63% of the consumed CO, less than expected according to hydrogenogenic CO oxidation: CO + H 2 O → CO 2 + H 2 Accordingly, C. pertinax would couple CO oxidation by Ni-CO dehydrogenase-II with simultaneous reduction of not only H 2 O but thiosulfate when grown under 100% CO. IMPORTANCE Anaerobic hydrogenogenic carboxydotrophs are thought to fill a vital niche with scavenging potentially toxic CO and producing H 2 as available energy source for thermophilic microbes. This hydrogenogenic carboxydotrophy relies on a Ni-CO dehydrogenase/energy-converting hydrogenase gene cluster. This feature is thought to be as common to these organisms. However

Super magnetic nanoparticles NiFe2O4, coated with aluminum-nickel oxide sol-gel lattices to safe, sensitive and selective purification of his-tagged proteins.

Science.gov (United States)

Mirahmadi-Zare, Seyede Zohreh; Allafchian, Alireza; Aboutalebi, Fatemeh; Shojaei, Pendar; Khazaie, Yahya; Dormiani, Kianoush; Lachinani, Liana; Nasr-Esfahani, Mohammad-Hossein

2016-05-01

Super magnetic nanoparticle NiFe2O4 with high magnetization, physical and chemical stability was introduced as a core particle which exhibits high thermal stability (>97%) during the harsh coating process. Instead of multi-stage process for coating, the magnetic nanoparticles was mineralized via one step coating by a cheap, safe, stable and recyclable alumina sol-gel lattice (from bohemite source) saturated by nickel ions. The TEM, SEM, VSM and XRD imaging and BET analysis confirmed the structural potential of NiFe2O4@NiAl2O4 core-shell magnetic nanoparticles for selective and sensitive purification of His-tagged protein, in one step. The functionality and validity of the nickel magnetic nanoparticles were attested by purification of three different bioactive His-tagged recombinant fusion proteins including hIGF-1, GM-CSF and bFGF. The bonding capacity of the nickel magnetics nanoparticles was studied by Bradford assay and was equal to 250 ± 84 μg Protein/mg MNP base on protein size. Since the metal ion leakage is the most toxicity source for purification by nickel magnetic nanoparticles, therefor the nickel leakage in purified final protein was determined by atomic absorption spectroscopy and biological activity of final purified protein was confirmed in comparison with reference. Also, in vitro cytotoxicity of nickel magnetic nanoparticles and trace metal ions were investigated by MTS assay analysis. The results confirmed that the synthesized nickel magnetic nanoparticles did not show metal ion toxicity and not affected on protein folding. Copyright © 2016 Elsevier Inc. All rights reserved.

Investigation of hydrogenase molecular marker to optimize hydrogen production from organic wastes and effluents of agro-food industries [abstract

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Hamilton, C.

2010-01-01

Full Text Available In recent years policy makers have started looking for alternatives to fossil fuels, not only to counter the threat of global warming, but also to reduce the risk of overdependence on imported oil and gas supplies. By contrast with hydrocarbon fuels, hydrogen (H2, whether burned directly or used in fuel cells, is intrinsically a clean energy vector with near zero emission. However the main current method of producing hydrogen, steam reforming of methane, involves the release of large quantities of greenhouse gases. So although hydrogen already accounts for around 2% of world consumption of energy, its more widespread adoption is limited by several challenges. Therefore new processes are investigated, especially those using renewable raw material, e.g. woods and organic wastes, and/or involving microorganisms. Indeed, for some algae and bacteria, the generation of molecular hydrogen is an essential part of their energy metabolism. The approach with the greatest commercial potential is fermentative hydrogen generation (dark fermentation by bacteria from the Clostridium genus. This biological process, as a part of the methane-producing anaerobic digestion process, is very promising since it allows the production of hydrogen from a wide variety of renewable resources such as carbohydrate waste from the agricultural and agro-food industries or processed urban waste and sewage. To date most publications on hydrogen production by Clostridium strains have focused on the effects of operating parameters (such as temperature, pH, dilution rate, etc.. We now need to extend this knowledge by identifying and monitoring the various different metabolic agents involved in high H2 activity. Consequently the aim of this research at the CWBI in the University of Liege is to investigate the role of [Fe] hydrogenases, the key enzymes that remove excess electrons accumulating during fermentation. Clostridium butyricum CWBI1009, the strain used for these investigations

Energy metabolism in Desulfovibrio vulgaris Hildenborough: insights from transcriptome analysis

Energy Technology Data Exchange (ETDEWEB)

Pereira, Patricia M.; He, Qiang; Valente, Filipa M.A.; Xavier, Antonio V.; Zhou, Jizhong; Pereira, Ines A.C.; Louro, Ricardo O.

2007-11-01

Sulphate-reducing bacteria are important players in the global sulphur and carbon cycles, with considerable economical and ecological impact. However, the process of sulphate respiration is still incompletely understood. Several mechanisms of energy conservation have been proposed, but it is unclear how the different strategies contribute to the overall process. In order to obtain a deeper insight into the energy metabolism of sulphate-reducers whole-genome microarrays were used to compare the transcriptional response of Desulfovibrio vulgaris Hildenborough grown with hydrogen/sulphate, pyruvate/sulphate, pyruvate with limiting sulphate, and lactate/thiosulphate, relative to growth in lactate/sulphate. Growth with hydrogen/sulphate showed the largest number of differentially expressed genes and the largest changes in transcript levels. In this condition the most up-regulated energy metabolism genes were those coding for the periplasmic [NiFeSe]hydrogenase, followed by the Ech hydrogenase. The results also provide evidence for the involvement of formate cycling and the recently proposed ethanol pathway during growth in hydrogen. The pathway involving CO cycling is relevant during growth on lactate and pyruvate, but not during growth in hydrogen as the most down-regulated genes were those coding for the CO-induced hydrogenase. Growth on lactate/thiosulphate reveals a down-regulation of several energymetabolism genes similar to what was observed in the presence of nitrite. This study identifies the role of several proteins involved in the energy metabolism of D. vulgaris and highlights several novel genes related to this process, revealing a more complex bioenergetic metabolism than previously considered.

Metagenomic analysis indicates Epsilonproteobacteria as a potential cause of microbial corrosion in pipelines injected with bisulfite

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Dongshan eAn

2016-01-01

Full Text Available Sodium bisulfite (SBS is used as an oxygen scavenger to decrease corrosion in pipelines transporting brackish subsurface water used in the production of bitumen by steam-assisted gravity drainage. Sequencing 16S rRNA gene amplicons has indicated that SBS addition increased the fraction of the sulfate-reducing bacteria (SRB Desulfomicrobium, as well as of Desulfocapsa, which can also grow by disproportionating sulfite into sulfide, sulfur and sulfate. SRB use cathodic H2, formed by reduction of aqueous protons at the iron surface, or use low potential electrons from iron and aqueous protons directly for sulfate reduction. In order to reveal the effects of SBS treatment in more detail, metagenomic analysis was performed with pipe-associated solids (PAS scraped from a pipe section upstream (PAS-616P and downstream (PAS-821TP of the SBS injection point. A major SBS-induced change in microbial community composition and in affiliated hynL genes for the large subunit of [NiFe] hydrogenase was the appearance of sulfur-metabolizing Epsilonproteobacteria of the genera Sulfuricurvum and Sulfurovum. These are chemolithotrophs, which oxidize sulfide or sulfur with O2 or reduce sulfur with H2. Because O2 was absent, this class likely catalyzed reduction of sulfur (S0 originating from the metabolism of bisulfite with cathodic H2 (or low potential electrons and aqueous protons originating from the corrosion of steel (Fe0. Overall this accelerates reaction of of S0 and Fe0 to form FeS, making this class a potentially powerful contributor to microbial corrosion. The PAS-821TP metagenome also had increased fractions of Deltaproteobacteria including the SRB Desulfomicrobium and Desulfocapsa. Altogether, SBS increased the fraction of hydrogen-utilizing Delta- and Epsilonproteobacteria in brackish-water-transporting pipelines, potentially stimulating anaerobic pipeline corrosion if dosed in excess of the intended oxygen scavenger function.

Crystal Structure and Catalytic Mechanism of 7-Hydroxymethyl Chlorophyll a Reductase*

Science.gov (United States)

Wang, Xiao; Liu, Lin

2016-01-01

7-Hydroxymethyl chlorophyll a reductase (HCAR) catalyzes the second half-reaction in chlorophyll b to chlorophyll a conversion. HCAR is required for the degradation of light-harvesting complexes and is necessary for efficient photosynthesis by balancing the chlorophyll a/b ratio. Reduction of the hydroxymethyl group uses redox cofactors [4Fe-4S] cluster and FAD to transfer electrons and is difficult because of the strong carbon-oxygen bond. Here, we report the crystal structure of Arabidopsis HCAR at 2.7-Å resolution and reveal that two [4Fe-4S]clusters and one FAD within a very short distance form a consecutive electron pathway to the substrate pocket. In vitro kinetic analysis confirms the ferredoxin-dependent electron transport chain, thus supporting a proton-activated electron transfer mechanism. HCAR resembles a partial reconstruction of an archaeal F420-reducing [NiFe] hydrogenase, which suggests a common mode of efficient proton-coupled electron transfer through conserved cofactor arrangements. Furthermore, the trimeric form of HCAR provides a biological clue of its interaction with light-harvesting complex II. PMID:27072131

Thickness dependence of the magnetic anisotropy and dynamic magnetic response of ferromagnetic NiFe films

International Nuclear Information System (INIS)

Silva, E F; Corrêa, M A; Chesman, C; Bohn, F; Della Pace, R D; Plá Cid, C C; Kern, P R; Carara, M; Alves Santos, O; Rodríguez-Suárez, R L; Azevedo, A; Rezende, S M

2017-01-01

We investigate the thickness dependence of the magnetic anisotropy and dynamic magnetic response of ferromagnetic NiFe films. We go beyond quasi-static measurements and focus on the dynamic magnetic response by considering three complementary techniques: the ferromagnetic resonance, magnetoimpedance and magnetic permeability measurements. We verify remarkable modifications in the magnetic anisotropy, i.e. the well-known behavior of in-plane uniaxial magnetic anisotropy systems gives place to a complex magnetic behavior as the thickness increases, and splits the films in two groups according to the magnetic properties. We identify magnetoimpedance and magnetic permeability curves with multiple resonance peaks, as well as the evolution of the ferromagnetic resonance absorption spectra, as fingerprints of strong changes of the magnetic properties associated to the vanishing of the in-plane magnetic anisotropy and to the emergence of non-homogeneous magnetization configuration, local anisotropies and out-of-plane anisotropy contribution arisen as a consequence of the non-uniformities of the stress stored in the film as the thickness is increased and/or to the columnar growth of the film. We interpret the experimental results in terms of the structural and morphological properties, quasi-static magnetic behavior, magnetic domain structure and different mechanisms governing the magnetization dynamics at distinct frequency ranges. (paper)

Nitrogen–doped graphitized carbon shell encapsulated NiFe nanoparticles: A highly durable oxygen evolution catalyst

Energy Technology Data Exchange (ETDEWEB)

Du, Lei; Luo, Langli; Feng, Zhenxing; Engelhard, Mark; Xie, Xiaohong; Han, Binghong; Sun, Junming; Zhang, Jianghao; Yin, Geping; Wang, Chongmin; Wang, Yong; Shao, Yuyan

2017-09-01

Oxygen evolution reaction (OER) plays a crucial role in various energy conversion devices such as water electrolyzers and metal–air batteries. Precious metal catalysts such as Ir, Ru and their oxides are usually used for enhanced reaction kinetics but are limited by their scarce resource. The challenges associated with alternative non–precious metal catalysts such as transition metal oxides and (oxy)hydroxides etc. are their low electronic conductivity and poor durability. Here, we report OER catalysts of NiFe nanoparticles encapsulated by nitrogen–doped graphitized carbon shells derived from bimetallic metal–organic frameworks (MOFs) precursors. The optimal OER catalyst shows excellent activity (360 mV overpotential at 10 mA cm–2GEO) and durability (no obvious degradation after 20 000 cycles). The electron-donation from Fe and tuned electronic structure of metal cores by Ni are revealed to be primary contributors to the enhanced OER activity. We further demonstrated that the structure and morphology of encapsulating carbon shells, which are the key factors influencing the durability, are facilely controlled by chemical state of precursors. Severe metal particle growth probably caused by oxidation of carbon shells and encapsulated nanoparticles is believed to the main mechanism for activity degradation in these catalysts.

Lateral gene transfer and gene duplication played a key role in the evolution of Mastigamoeba balamuthi hydrogenosomes

Czech Academy of Sciences Publication Activity Database

Nývltová, E.; Stairs, C.W.; Hrdý, I.; Rídl, Jakub; Mach, J.; Pačes, Jan; Roger, A. J.; Tachezy, J.

2015-01-01

Roč. 32, č. 4 (2015), s. 1039-1055 ISSN 0737-4038 R&D Projects: GA ČR(CZ) GAP305/11/1061; GA MŠk(CZ) ED1.1.00/02.0109 Institutional support: RVO:68378050 Keywords : acetylCoA synthetase * sulfate activation pathway * PFO * glycine cleavage system * hydrogenase * succinate dehydrogenase Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 13.649, year: 2015

Characterization in Helicobacter pylori of a Nickel Transporter Essential for Colonization That Was Acquired during Evolution by Gastric Helicobacter Species

Science.gov (United States)

Turlin, Evelyne; Mancuso, Francesco; Michel, Valérie; Richaud, Pierre; Veyrier, Frédéric J.; De Reuse, Hilde; Vinella, Daniel

2016-01-01

Metal acquisition is crucial for all cells and for the virulence of many bacterial pathogens. In particular, nickel is a virulence determinant for the human gastric pathogen Helicobacter pylori as it is the cofactor of two enzymes essential for in vivo colonization, urease and a [NiFe] hydrogenase. To import nickel despite its scarcity in the human body, H. pylori requires efficient uptake mechanisms that are only partially defined. Indeed, alternative ways of nickel entry were predicted to exist in addition to the well-described NixA permease. Using a genetic screen, we identified an ABC transporter, that we designated NiuBDE, as a novel H. pylori nickel transport system. Unmarked mutants carrying deletions of nixA, niuD and/or niuB, were constructed and used to measure (i) tolerance to toxic nickel exposure, (ii) intracellular nickel content by ICP-OES, (iii) transport of radioactive nickel and (iv) expression of a reporter gene controlled by nickel concentration. We demonstrated that NiuBDE and NixA function separately and are the sole nickel transporters in H. pylori. NiuBDE, but not NixA, also transports cobalt and bismuth, a metal currently used in H. pylori eradication therapy. Both NiuBDE and NixA participate in nickel-dependent urease activation at pH 5 and survival under acidic conditions mimicking those encountered in the stomach. However, only NiuBDE is able to carry out this activity at neutral pH and is essential for colonization of the mouse stomach. Phylogenomic analyses indicated that both nixA and niuBDE genes have been acquired via horizontal gene transfer by the last common ancestor of the gastric Helicobacter species. Our work highlights the importance of this evolutionary event for the emergence of Helicobacter gastric species that are adapted to the hostile environment of the stomach where the capacity of Helicobacter to import nickel and thereby activate urease needs to be optimized. PMID:27923069

CalA, a Cyanobacterial AbrB Protein, Interacts with the Upstream Region of hypC and Acts as a Repressor of Its Transcription in the Cyanobacterium Nostoc sp. Strain PCC 7120▿ †

Science.gov (United States)

Agervald, Åsa; Zhang, Xiaohui; Stensjö, Karin; Devine, Ellenor; Lindblad, Peter

2010-01-01

The filamentous, heterocystous, nitrogen-fixing cyanobacterium Nostoc sp. strain PCC 7120 may contain, depending on growth conditions, up to two hydrogenases directly involved in hydrogen metabolism. HypC is one out of at least seven auxiliary gene products required for synthesis of a functional hydrogenase, specifically involved in the maturation of the large subunit. In this study we present a protein, CalA (Alr0946 in the genome), belonging to the transcription regulator family AbrB, which in protein-DNA assays was found to interact with the upstream region of hypC. Transcriptional investigations showed that calA is cotranscribed with the downstream gene alr0947, which encodes a putative protease from the abortive infection superfamily, Abi. CalA was shown to interact specifically not only with the upstream region of hypC but also with its own upstream region, acting as a repressor on hypC. The bidirectional hydrogenase activity was significantly downregulated when CalA was overexpressed, demonstrating a correlation with the transcription factor, either direct or indirect. In silico studies showed that homologues to both CalA and Alr0947 are highly conserved proteins within cyanobacteria with very similar physical organizations of the corresponding structural genes. Possible functions of the cotranscribed downstream protein Alr0947 are presented. In addition, we present a three-dimensional (3D) model of the DNA binding domain of CalA and putative DNA binding mechanisms are discussed. PMID:20023111

Nickel-zinc ferrite/permalloy (Ni0.5Zn0.5Fe2O4/Ni-Fe soft magnetic nanocomposites fabricated by electro-infiltration

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Xiao Wen

2016-05-01

Full Text Available Magnetically soft NiZn ferrite (Ni0.5Zn0.5Fe2O4 nanoparticles are embedded within a permalloy (Ni-Fe matrix via an electro-infiltration process as thin films intended for use as on-chip inductor cores in the MHz frequency regime. A layer of NiZn ferrite nanoparticles is first deposited, and then permalloy is electroplated through the voids to encapsulate the particles and form three-dimensional ferrite/alloy nanocomposites. The composites are estimated to contain 37% ferrite by volume and exhibit a relative permeability of ∼320, a saturation of ∼1.15 T, and an operational bandwidth of 93 MHz. Compared to a permalloy thin film of similar thickness, the nanocomposite exhibits 39% higher electrical resistivity and 50% higher bandwidth.

Effects of the shape anisotropy and biasing field on the magnetization reversal process of the diamond-shaped NiFe nano films

Science.gov (United States)

Xu, Sichen; Yin, Jianfeng; Tang, Rujun; Zhang, Wenxu; Peng, Bin; Zhang, Wanli

2017-11-01

The effects of the planar shape anisotropy and biasing field on the magnetization reversal process (MRP) of the diamond-shaped NiFe nano films have been investigated by micromagnetic simulations. Results show that when the length to width ratio (LWR) of the diamond-shaped film is small, the MRP of the diamond-shaped films are sensitive to LWR. But when LWR is larger than 2, a stable domain switching mode is observed which nucleates from the center of the diamond and then expands to the edges. At a fixed LWR, the magnitude of the switching fields decrease with the increase of the biasing field, but the domain switching mode is not affected by the biasing field. Further analysis shows that demagnetization energy dominates over the MRP of the diamond-shaped films. The above LWR dependence of MRP can be well explained by a variation of the shape anisotropic factor with LWR.

Electrochemistry of metalloproteins: protein film electrochemistry for the study of E. coli [NiFe]-hydrogenase-1.

Science.gov (United States)

Evans, Rhiannon M; Armstrong, Fraser A

2014-01-01

Protein film electrochemistry is a technique which allows the direct control of redox-active enzymes, providing particularly detailed information on their catalytic properties. The enzyme is deposited onto a working electrode tip, and through control of the applied potential the enzyme activity is monitored as electrical current, allowing for direct study of inherent activity as electrons are transferred to and from the enzyme redox center(s). No mediators are used. Because the only enzyme present in the experiment is bound at the electrode surface, gaseous and liquid phase inhibitors can be introduced and removed whilst the enzyme remains in situ. Potential control means that kinetics and thermodynamics are explored simultaneously; the kinetics of a reaction can be studied as a function of potential. Steady-state catalytic rates are observed directly as current (for a given potential) and non-steady-state rates (such as interconversions between different forms of the enzyme) are observed from the change in current with time. The more active the enzyme, the higher the current and the better the signal-to-noise. In this chapter we outline the practical aspects of PFE for studying electroactive enzymes, using the Escherichia coli [NiFe]-hydrogenase 1 (Hyd-1) as an example.

Effects of biomass-generated producer gas constituents on cell growth, product distribution and hydrogenase activity of Clostridium carboxidivorans P7T

International Nuclear Information System (INIS)

Ahmed, Asma; Cateni, Bruno G.; Huhnke, Raymond L.; Lewis, Randy S.

2006-01-01

In our previous work, we demonstrated that biomass-generated producer gas can be converted to ethanol and acetic acid using a microbial catalyst Clostridium carboxidivorans P7 T . Results showed that the producer gas (1) induced cell dormancy, (2) inhibited H 2 consumption, and (3) affected the acetic acid/ethanol product distribution. Results of this work showed that tars were the likely cause of cell dormancy and product redistribution and that the addition of a 0.025μm filter in the gas cleanup negated the effects of tars. C. carboxidivorans P7 T can adapt to the tars (i.e. grow) only after prolonged exposure. Nitric oxide, present in the producer gas at 150ppm, is an inhibitor of the hydrogenase enzyme involved in H 2 consumption. We conclude that significant conditioning of the producer gas will be required for the successful coupling of biomass-generated producer gas with fermentation to produce ethanol and acetic acid. (author)

Introduction and pinning of domain walls in 50 nm NiFe constrictions using local and external magnetic fields

International Nuclear Information System (INIS)

Zahnd, G.; Pham, V.T.; Marty, A.; Jamet, M.; Beigné, C.; Notin, L.; Vergnaud, C.; Rortais, F.; Vila, L.; Attané, J.-P.

2016-01-01

We study domain wall injection in 100 nm wide NiFe nanowires, followed by domain wall propagation and pinning on 50 nm wide constrictions. The injection is performed using local and external magnetic fields. Using several nucleation pad geometries, we show that at these small dimensions the use of an external field only does not allow obtaining a reproducible injection/pinning process. However, the use of an additional local field, created by an Oersted line, allows to nucleate a reversed domain at zero external applied field. Then, an external field of 5 mT enables the domain wall to propagate far from the Oersted line, and the pinning occurs reproducibly. We also show that notwithstanding the reproducibility of the pinning process, the depinning field is found to be stochastic, following a bimodal distribution. Using micromagnetic simulation we link two different DW configurations, vortex and transverse, to the two typical depinning fields. - Highlights: • Magnetic domain wall introduction and pinning in Permalloy nanowires with 50 nm wide constrictions. • Magnetic domain nucleation at zero external applied field. • Bimodal distribution of the domain wall configuration in the constriction.

Deletion of the hfsB gene increases ethanol production in Thermoanaerobacterium saccharolyticum and several other thermophilic anaerobic bacteria.

Science.gov (United States)

Eminoğlu, Ayşenur; Murphy, Sean Jean-Loup; Maloney, Marybeth; Lanahan, Anthony; Giannone, Richard J; Hettich, Robert L; Tripathi, Shital A; Beldüz, Ali Osman; Lynd, Lee R; Olson, Daniel G

2017-01-01

With the discovery of interspecies hydrogen transfer in the late 1960s (Bryant et al. in Arch Microbiol 59:20-31, 1967), it was shown that reducing the partial pressure of hydrogen could cause mixed acid fermenting organisms to produce acetate at the expense of ethanol. Hydrogen and ethanol are both more reduced than glucose. Thus there is a tradeoff between production of these compounds imposed by electron balancing requirements; however, the mechanism is not fully known. Deletion of the hfsA or B subunits resulted in a roughly 1.8-fold increase in ethanol yield. The increase in ethanol production appears to be associated with an increase in alcohol dehydrogenase activity, which appears to be due, at least in part, to increased expression of the adhE gene, and may suggest a regulatory linkage between hfsB and adhE . We studied this system most intensively in the organism Thermoanaerobacterium saccharolyticum ; however, deletion of hfsB also increases ethanol production in other thermophilic bacteria suggesting that this could be used as a general technique for engineering thermophilic bacteria for improved ethanol production in organisms with hfs -type hydrogenases. Since its discovery by Shaw et al. (JAMA 191:6457-64, 2009), the hfs hydrogenase has been suspected to act as a regulator due to the presence of a PAS domain. We provide additional support for the presence of a regulatory phenomenon. In addition, we find a practical application for this scientific insight, namely increasing ethanol yield in strains that are of interest for ethanol production from cellulose or hemicellulose. In two of these organisms ( T. xylanolyticum and T. thermosaccharolyticum ), the ethanol yields are the highest reported to date.

Phylogeny and phylogeography of functional genes shared among seven terrestrial subsurface metagenomes reveal N-cycling and microbial evolutionary relationships

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Maggie CY Lau

2014-10-01

Full Text Available Comparative studies on community phylogenetics and phylogeography of microorganisms living in extreme environments are rare. Terrestrial subsurface habitats are valuable for studying microbial biogeographical patterns due to their isolation and the restricted dispersal mechanisms. Since the taxonomic identity of a microorganism does not always correspond well with its functional role in a particular community, the use of taxonomic assignments or patterns may give limited inference on how microbial functions are affected by historical, geographical and environmental factors. With seven metagenomic libraries generated from fracture water samples collected from five South African mines, this study was carried out to (1 screen for ubiquitous functions or pathways of biogeochemical cycling of CH4, S and N; (2 to characterize the biodiversity represented by the common functional genes; (3 to investigate the subsurface biogeography as revealed by this subset of genes; and (4 to explore the possibility of using metagenomic data for evolutionary study. The ubiquitous functional genes are NarV, NPD, PAP reductase, NifH, NifD, NifK, NifE and NifN genes. Although these 8 common functional genes were taxonomically and phylogenetically diverse and distinct from each other, the dissimilarity between samples did not correlate strongly with either geographical, environmental or residence time of the water. Por genes homologous to those of Thermodesulfovibrio yellowstonii detected in all metagenomes were deep lineages of Nitrospirae, suggesting that subsurface habitats have preserved ancestral genetic signatures that inform the study of the origin and evolution of prokaryotes.

Production of bioplastics and hydrogen gas by photosynthetic microorganisms

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Yasuo, Asada; Masato, Miyake; Jun, Miyake

1998-03-01

Our efforts have been aimed at the technological basis of photosynthetic-microbial production of materials and an energy carrier. We report here accumulation of poly-(3-hydroxybutyrate) (PHB), a raw material of biodegradable plastics and for production of hydrogen gas, and a renewable energy carrier by photosynthetic microorganisms (tentatively defined as cyanobacteria plus photosynthetic bateria, in this report). A thermophilic cyanobacterium, Synechococcus sp. MA19 that accumulates PHB at more than 20% of cell dry wt under nitrogen-starved conditions was isolated and microbiologically identified. The mechanism of PHB accumulation was studied. A mesophilic Synechococcus PCC7942 was transformed with the genes encoding PHB-synthesizing enzymes from Alcaligenes eutrophus. The transformant accumulated PHB under nitrogen-starved conditions. The optimal conditions for PHB accumulation by a photosynthetic bacterium grown on acetate were studied. Hydrogen production by photosynthetic microorganisms was studied. Cyanobacteria can produce hydrogen gas by nitrogenase or hydrogenase. Hydrogen production mediated by native hydrogenase in cyanobacteria was revealed to be in the dark anaerobic degradation of intracellular glycogen. A new system for light-dependent hydrogen production was targeted. In vitro and in vivo coupling of cyanobacterial ferredoxin with a heterologous hydrogenase was shown to produce hydrogen under light conditions. A trial for genetic trasformation of Synechococcus PCC7942 with the hydrogenase gene from Clostridium pasteurianum is going on. The strong hydrogen producers among photosynthetic bacteria were isolated and characterized. Co-culture of Rhodobacter and Clostriumdium was applied to produce hydrogen from glucose. Conversely in the case of cyanobacteria, genetic regulation of photosynthetic proteins was intended to improve conversion efficiency in hydrogen production by the photosynthetic bacterium, Rhodobacter sphaeroides RV. A mutant acquired by

Room Temperature Gas Sensing Properties of Sn-Substituted Nickel Ferrite (NiFe2O4) Thin Film Sensors Prepared by Chemical Co-Precipitation Method

Science.gov (United States)

Manikandan, V.; Li, Xiaogan; Mane, R. S.; Chandrasekaran, J.

2018-04-01

Tin (Sn) substituted nickel ferrite (NiFe2O4) thin film sensors were prepared by a simple chemical co-precipitation method, which initially characterized their structure and surface morphology with the help of x-ray diffraction and scanning electron microscopy. Surface morphology of the sensing films reveals particles stick together with nearer particles and this formation leads to a large specific area as a large specific area is very useful for easy adsorption of gas molecules. Transmission electron microscopy and selected area electron diffraction pattern images confirm particle size and nanocrystallnity as due to formation of circular rings. Fourier transform infrared analysis has supported the presence of functional groups. The 3.69 eV optical band gap of the film was found which enabled better gas sensing. Gas sensors demonstrate better response and recovery characteristics, and the maximum response was 68.43%.

A [4Fe-4S]-Fe(CO)(CN)-l-cysteine intermediate is the first organometallic precursor in [FeFe] hydrogenase H-cluster bioassembly

Science.gov (United States)

Rao, Guodong; Tao, Lizhi; Suess, Daniel L. M.; Britt, R. David

2018-05-01

Biosynthesis of the [FeFe] hydrogenase active site (the 'H-cluster') requires the interplay of multiple proteins and small molecules. Among them, the radical S-adenosylmethionine enzyme HydG, a tyrosine lyase, has been proposed to generate a complex that contains an Fe(CO)2(CN) moiety that is eventually incorporated into the H-cluster. Here we describe the characterization of an intermediate in the HydG reaction: a [4Fe-4S][(Cys)Fe(CO)(CN)] species, 'Complex A', in which a CO, a CN- and a cysteine (Cys) molecule bind to the unique 'dangler' Fe site of the auxiliary [5Fe-4S] cluster of HydG. The identification of this intermediate—the first organometallic precursor to the H-cluster—validates the previously hypothesized HydG reaction cycle and provides a basis for elucidating the biosynthetic origin of other moieties of the H-cluster.

Effects of biomass-generated producer gas constituents on cell growth, product distribution and hydrogenase activity of Clostridium carboxidivorans P7{sup T}

Energy Technology Data Exchange (ETDEWEB)

Ahmed, Asma [Oklahoma State University, Stillwater, OK (United States). School of Chemical Engineering; Cateni, Bruno G.; Huhnke, Raymond L. [Oklahoma State University, Stillwater, OK (United States). Department of Biosystems and Agricultural Engineering; Lewis, Randy S. [Brigham Young University, Provo, UT (United States). Chemical Engineering Department

2006-07-15

In our previous work, we demonstrated that biomass-generated producer gas can be converted to ethanol and acetic acid using a microbial catalyst Clostridium carboxidivorans P7{sup T}. Results showed that the producer gas (1) induced cell dormancy, (2) inhibited H{sub 2} consumption, and (3) affected the acetic acid/ethanol product distribution. Results of this work showed that tars were the likely cause of cell dormancy and product redistribution and that the addition of a 0.025{mu}m filter in the gas cleanup negated the effects of tars. C. carboxidivorans P7{sup T} can adapt to the tars (i.e. grow) only after prolonged exposure. Nitric oxide, present in the producer gas at 150ppm, is an inhibitor of the hydrogenase enzyme involved in H{sub 2} consumption. We conclude that significant conditioning of the producer gas will be required for the successful coupling of biomass-generated producer gas with fermentation to produce ethanol and acetic acid. (author)

Escherichia coli K-12 survives anaerobic exposure at pH 2 without RpoS, Gad, or hydrogenases, but shows sensitivity to autoclaved broth products.

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Daniel P Riggins

Full Text Available Escherichia coli and other enteric bacteria survive exposure to extreme acid (pH 2 or lower in gastric fluid. Aerated cultures survive via regulons expressing glutamate decarboxylase (Gad, activated by RpoS, cyclopropane fatty acid synthase (Cfa and others. But extreme-acid survival is rarely tested under low oxygen, a condition found in the stomach and the intestinal tract. We observed survival of E. coli K-12 W3110 at pH 1.2-pH 2.0, conducting all manipulations (overnight culture at pH 5.5, extreme-acid exposure, dilution and plating in a glove box excluding oxygen (10% H2, 5% CO2, balance N2. With dissolved O2 concentrations maintained below 6 µM, survival at pH 2 required Cfa but did not require GadC, RpoS, or hydrogenases. Extreme-acid survival in broth (containing tryptone and yeast extract was diminished in media that had been autoclaved compared to media that had been filtered. The effect of autoclaved media on extreme-acid survival was most pronounced when oxygen was excluded. Exposure to H2O2 during extreme-acid treatment increased the death rate slightly for W3110 and to a greater extent for the rpoS deletion strain. Survival at pH 2 was increased in strains lacking the anaerobic regulator fnr. During anaerobic growth at pH 5.5, strains deleted for fnr showed enhanced transcription of acid-survival genes gadB, cfa, and hdeA, as well as catalase (katE. We show that E. coli cultured under oxygen exclusion (<6 µM O2 requires mechanisms different from those of aerated cultures. Extreme acid survival is more sensitive to autoclave products under oxygen exclusion.

Temperature dependence of the short-range order parameter and the concentration dependence of the order disorder temperature for Ni-Pt and Ni-Fe systems in the improved statistical pseudopotential approximation

International Nuclear Information System (INIS)

Khwaja, F.A.

1980-08-01

The calculations for the temperature dependence of the first shell short-range order (SRO) parameter for Ni 3 Fe using the cubic approximation of Tahir Kheli, and the concentration dependence of order-disorder temperature Tsub(c) for Ni-Fe and Ni-Pt systems using the linear approximation, have been carried out in the framework of pseudopotential theory. It is shown that the cubic approximation yields a good agreement between the theoretical prediction of the α 1 and the experimental data. Results for the concentration dependence of the Tsub(c) show that improvements in the statistical pseudo-potential approach are essential to achieve a good agreement with experiment. (author)

Membrane complexes of Syntrophomonas wolfei involved in syntrophic butyrate degradation and hydrogen formation

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Bryan Regis Crable

2016-11-01

Full Text Available Syntrophic butyrate metabolism involves the thermodynamically unfavorable production of hydrogen and/or formate from the high potential electron donor, butyryl-CoA. Such redox reactions can occur only with energy input by a process called reverse electron transfer. Previous studies have demonstrated that hydrogen production from butyrate requires the presence of a proton gradient, but the biochemical machinery involved has not been clearly elucidated. In this study, the gene and enzyme systems involved in reverse electron transfer by Syntrophomonas wolfei were investigated using proteomic and gene expression approaches. S. wolfei was grown in coculture with Methanospirillum hungatei or Dehalococcoides mccartyi under conditions requiring reverse electron transfer and compared to both axenic S. wolfei cultures and cocultures grown in conditions that do not require reverse electron transfer. Blue native gel analysis of membranes solubilized from syntrophically grown cells revealed the presence of a membrane-bound hydrogenase, Hyd2, which exhibited hydrogenase activity during in gel assays. Bands containing a putative iron-sulfur (FeS oxidoreductase were detected in membranes of crotonate-grown and butyrate grown S. wolfei cells. The genes for the corresponding hydrogenase subunits, hyd2ABC, were differentially expressed at higher levels during syntrophic butyrate growth when compared to growth on crotonate. The expression of the FeS oxidoreductase gene increased when S. wolfei was grown with M. hungatei. Additional membrane-associated proteins detected included FoF1 ATP synthase subunits and several membrane transporters that may aid syntrophic growth. Furthermore, syntrophic butyrate metabolism can proceed exclusively by interspecies hydrogen transfer, as demonstrated by growth with D. mccartyi, which is unable to use formate. These results argue for the importance of Hyd2 and FeS oxidoreductase in reverse electron transfer during syntrophic

Nanotextured Spikes of α-Fe2O3/NiFe2O4 Composite for Efficient Photoelectrochemical Oxidation of Water.

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Hussain, Shabeeb; Tavakoli, Mohammad Mahdi; Waleed, Aashir; Virk, Umar Siddique; Yang, Shihe; Waseem, Amir; Fan, Zhiyong; Nadeem, Muhammad Arif

2018-03-27

We demonstrate for the first time the application of p-NiFe 2 O 4 /n-Fe 2 O 3 composite thin films as anode materials for light-assisted electrolysis of water. The p-NiFe 2 O 4 /n-Fe 2 O 3 composite thin films were deposited on planar fluorinated tin oxide (FTO)-coated glass as well as on 3D array of nanospike (NSP) substrates. The effect of substrate (planar FTO and 3D-NSP) and percentage change of each component (i.e., NiFe 2 O 4 and Fe 2 O 3 ) of composite was studied on photoelectrochemical (PEC) water oxidation reaction. This work also includes the performance comparison of p-NiFe 2 O 4 /n-Fe 2 O 3 composite (planar and NSP) devices with pure hematite for PEC water oxidation. Overall, the nanostructured p-NiFe 2 O 4 /n-Fe 2 O 3 device with equal molar 1:1 ratio of NiFe 2 O 4 and Fe 2 O 3 was found to be highly efficient for PEC water oxidation as compared with pure hematite, 1:2 and 1:3 molar ratios of composite. The photocurrent density of 1:1 composite thin film on planar substrate was equal to 1.07 mA/cm 2 at 1.23 V RHE , which was 1.7 times higher current density as compared with pure hematite device (0.63 mA/cm 2 at 1.23 V RHE ). The performance of p-NiFe 2 O 4 /n-Fe 2 O 3 composites in PEC water oxidation was further enhanced by their deposition over 3D-NSP substrate. The highest photocurrent density of 2.1 mA/cm 2 at 1.23 V RHE was obtained for the 1:1 molar ratio p-NiFe 2 O 4 /n-Fe 2 O 3 composite on NSP (NF1-NSP), which was 3.3 times more photocurrent density than pure hematite. The measured applied bias photon-to-current efficiency (ABPE) value of NF1-NSP (0.206%) was found to be 1.87 times higher than that of NF1-P (0.11%) and 4.7 times higher than that of pure hematite deposited on FTO-coated glass (0.044%). The higher PEC water oxidation activity of p-NiFe 2 O 4 /n-Fe 2 O 3 composite thin film as compared with pure hematite is attributed to the Z-path scheme and better separation of electrons and holes. The increased surface area and greater light

Challenges to develop nitrogen-fixing cereals by direct nif-gene transfer.

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Curatti, Leonardo; Rubio, Luis M

2014-08-01

Some regions of the developing world suffer low cereal production yields due to low fertilizer inputs, among other factors. Biological N2 fixation, catalyzed by the prokaryotic enzyme nitrogenase, is an alternative to the use of synthetic N fertilizers. The molybdenum nitrogenase is an O2-labile metalloenzyme composed of the NifDK and NifH proteins, which biosyntheses require a number of nif gene products. A challenging strategy to increase cereal crop productivity in a scenario of low N fertilization is the direct transfer of nif genes into cereals. The sensitivity of nitrogenase to O2 and the apparent complexity of nitrogenase biosynthesis are the main barriers identified so far. Expression of active NifH requires the products of nifM, nifH, and possibly nifU and nifS, whereas active NifDK requires the products of nifH, nifD, nifK, nifB, nifE, nifN, and possibly nifU, nifS, nifQ, nifV, nafY, nifW and nifZ. Plastids and mitochondria are potential subcellular locations for nitrogenase. Both could provide the ATP and electrons required for nitrogenase to function but they differ in their internal O2 levels and their ability to incorporate ammonium into amino acids. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Fabrication and electromagnetic properties of bio-based helical soft-core particles by way of Ni-Fe alloy electroplating

Energy Technology Data Exchange (ETDEWEB)

Lan Mingming, E-mail: lan_mingming@163.com [Bionic and Micro/Nano/Bio Manufacturing Technology Research Center, School of Mechanical Engineering and Automation, Beihang University, Beijing 100191 (China); Zhang Deyuan; Cai Jun; Zhang Wenqiang; Yuan Liming [Bionic and Micro/Nano/Bio Manufacturing Technology Research Center, School of Mechanical Engineering and Automation, Beihang University, Beijing 100191 (China)

2011-12-15

Ni-Fe alloy electroplating was used as a bio-limited forming process to fabricate bio-based helical soft-core ferromagnetic particles, and a low frequency vibration device was applied to the cathode to avoid microorganism (Spirulina platens) cells adhesion to the copper net during the course of plating. The morphologies and ingredients of the coated Spirulina cells were characterized using scanning electron microscopy and energy dispersive spectrometer. The complex permittivity and permeability of the samples containing the coated Spirulina cells before and after heat treatment were measured and investigated by a vector network analyzer. The results show that the Spirulina cells after plating keep their initial helical shape, and applying low frequency vibration to the copper net cathode in the plating process can effectively prevent agglomeration and intertwinement of the Spirulina cells. The microwave absorbing and electromagnetic properties of the samples containing the coated Spirulina cells particles with heat treatment are superior to those samples containing the coated Spirulina cells particles without heat treatment. - Highlights: > We used the microorganism cells as forming template to fabricate the bio-based helical soft-core ferromagnetic particles. > Microorganism selected as forming templates was Spirulina platens, which are of natural helical shape and have high aspect ratio. > Coated Spirulina cells were a kind lightweight ferromagnetic particle.

Density functional modelling of the interaction between the uranyl ion and TiO2 and NiFe2O4 surfaces

International Nuclear Information System (INIS)

Perron, H.

2007-07-01

This study, performed within the framework of a collaboration between the IPN in Orsay and EDF, takes place within the problematic of radioactivity control in geological depository or in nuclear power plants. The interaction mechanisms of ions at solid / liquid interfaces are often very complex and thus very hard to characterize. The use of atomic modelling, and more particularly of ab initio type calculations such as the density functional theory, allow to access to surface complexes structural and energetic properties. First, this theoretical approach has been validated on the experimentally uranyl / rutile TiO 2 well-known system. The systematic comparisons between experimental data and theoretical results have allowed to demonstrate the ability of this approach to properly describe this complex system. Then, a similar study has been performed as a predictive tool on the uranyl / NiFe 2 O 4 system which is not characterized experimentally. The goal of these studies was to determine if theoretical calculations are able to bring usable and reliable data when the experimental studies are too hard to set up. (author)

pH-Dependent isotope exchange and hydrogenation catalysed by water-soluble NiRu complexes as functional models for [NiFe]hydrogenases.

Science.gov (United States)

Kure, Bunsho; Matsumoto, Takahiro; Ichikawa, Koji; Fukuzumi, Shunichi; Higuchi, Yoshiki; Yagi, Tatsuhiko; Ogo, Seiji

2008-09-21

The pH-dependent hydrogen isotope exchange reaction between gaseous isotopes and medium isotopes and hydrogenation of the carbonyl compounds have been investigated with water-soluble bis(mu-thiolate)(mu-hydride)NiRu complexes, Ni(II)(mu-SR)(2)(mu-H)Ru(II) {(mu-SR)(2) = N,N'-dimethyl-N,N'-bis(2-mercaptoethyl)-1,3-propanediamine}, as functional models for [NiFe]hydrogenases. In acidic media (at pH 4-6), the mu-H ligand of the Ni(II)(mu-SR)(2)(mu-H)Ru(II) complexes has H(+) properties, and the complexes catalyse the hydrogen isotope exchange reaction between gaseous isotopes and medium isotopes. A mechanism of the hydrogen isotope exchange reaction between gaseous isotopes and medium isotopes through a low-valent Ni(I)(mu-SR)(2)Ru(I) complex is proposed. In contrast, in neutral-basic media (at pH 7-10), the mu-H ligand of the Ni(II)(mu-SR)(2)(mu-H)Ru(II) complexes acts as H(-), and the complexes catalyse the hydrogenation of carbonyl compounds.

[Co/Pd]4–Co–Pd–NiFe spring magnets with highly tunable and uniform magnetization tilt angles

International Nuclear Information System (INIS)

Anh Nguyen, T.N.; Benatmane, N.; Fallahi, V.; Fang, Yeyu; Mohseni, S.M.; Dumas, R.K.; Åkerman, Johan

2012-01-01

By varying the Pd thickness (t Pd ) from 0 to 8 nm in [Co/Pd] 4 /Co/Pd(t Pd )/NiFe exchange springs, we demonstrate (i) continuous tailoring of the exchange coupling between a [Co/Pd] 4 /Co layer with perpendicular anisotropy, and a NiFe layer with an in-plane easy axis, (ii) tuning of the NiFe out-of-plane magnetization angle from 20 ○ to 80 ○ , and (iii) an up to two-fold increase in the NiFe damping. The partial decoupling also results in a highly uniform NiFe magnetization. These properties make [Co/Pd] 4 /Co/Pd(t Pd )/NiFe spring magnets ideal candidates for use as tilted polarizers, by combining stable and well-defined spin directions of its carriers with a high degree of angular freedom. - Highlights: ► Continuous tailoring of the exchange coupling between a [Co/Pd] 4 /Co layer and a NiFe layer. ►Tuning of the NiFe out-of-plane magnetization angle from 20° to 80°. ►A highly uniform NiFe magnetization. ►An up to two-fold increase in the NiFe damping.

Effects of particle composition and environmental parameters on catalytic hydrodechlorination of trichloroethylene by nanoscale bimetallic Ni-Fe.

Science.gov (United States)

Wei, Jianjun; Qian, Yajing; Liu, Wenjuan; Wang, Lutao; Ge, Yijie; Zhang, Jianghao; Yu, Jiang; Ma, Xingmao

2014-05-01

Catalytic nickel was successfully incorporated into nanoscale iron to enhance its dechlorination efficiency for trichloroethylene (TCE), one of the most commonly detected chlorinated organic compounds in groundwater. Ethane was the predominant product. The greatest dechlorination efficiency was achieved at 22 molar percent of nickel. This nanoscale Ni-Fe is poorly ordered and inhomogeneous; iron dissolution occurred whereas nickel was relatively stable during the 24-hr reaction. The morphological characterization provided significant new insights on the mechanism of catalytic hydrodechlorination by bimetallic nanoparticles. TCE degradation and ethane production rates were greatly affected by environmental parameters such as solution pH, temperature and common groundwater ions. Both rate constants decreased and then increased over the pH range of 6.5 to 8.0, with the minimum value occurring at pH 7.5. TCE degradation rate constant showed an increasing trend over the temperature range of 10 to 25°C. However, ethane production rate constant increased and then decreased over the range, with the maximum value occurring at 20°C. Most salts in the solution appeared to enhance the reaction in the first half hour but overall they displayed an inhibitory effect. Combined ions showed a similar effect as individual salts. Copyright © 2014 The Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences. Published by Elsevier B.V. All rights reserved.

Redox reactions of [FeFe]-hydrogenase models containing an internal amine and a pendant phosphine.

Science.gov (United States)

Zheng, Dehua; Wang, Mei; Chen, Lin; Wang, Ning; Sun, Licheng

2014-02-03

A diiron dithiolate complex with a pendant phosphine coordinated to one of the iron centers, [(μ-SCH2)2N(CH2C6H4-o-PPh2){Fe2(CO)5}] (1), was prepared and structurally characterized. The pendant phosphine is dissociated together with a CO ligand in the presence of excess PMe3, to afford [(μ-SCH2)2N(CH2C6H4-o-PPh2){Fe(CO)2(PMe3)}2] (2). Redox reactions of 2 and related complexes were studied in detail by in situ IR spectroscopy. A series of new Fe(II)Fe(I) ([3](+) and [6](+)), Fe(II)Fe(II) ([4](2+)), and Fe(I)Fe(I) (5) complexes relevant to Hox, Hox(CO), and Hred states of the [FeFe]-hydrogenase active site were detected. Among these complexes, the molecular structures of the diferrous complex [4](2+) with the internal amine and the pendant phosphine co-coordinated to the same iron center and the triphosphine diiron complex 5 were determined by X-ray crystallography. To make a comparison, the redox reactions of an analogous complex, [(μ-SCH2)2N(CH2C6H5){Fe(CO)2(PMe3)}2] (7), were also investigated by in situ IR spectroscopy in the absence or presence of extrinsic PPh3, which has no influence on the oxidation reaction of 7. The pendant phosphine in the second coordination sphere makes the redox reaction of 2 different from that of its analogue 7.

Fabrication of hydrogenase-cationic electrolyte biohybrids at interfaces and their electrochemical properties in Langmuir-Blodgett films

International Nuclear Information System (INIS)

Liu An; Zorin, Nikolay A.; Nakamura, Chikashi; Miyake, Jun; Qian Dongjin

2010-01-01

Hydrogenase (H 2 ase)-cationic electrolyte biohybrids were assembled at the air-water interface via intermolecular electrostatic interaction. The H 2 ase used was purified from the phototropic bacterium of Thiocapsa roseopersicina. Two kinds of cationic electrolyte compounds (CECs) were used, the difference of which was whether they contained viologen substituent or not. Surface pressure-area isotherms indicated that these CECs were co-existed with the H 2 ase in the monolayers, which were then transferred to substrate surfaces to form H 2 ase-CECs hybrid films by the Langmuir-Blodgett (LB) method. Uniform film was formed when polyelectrolyte was used as the subphase. Cyclic voltammograms (CVs) of the LB films showed a couple of redox waves in the potential range of -0.4 to -0.65 V vs. Ag/AgCl, which was ascribed to one electron process of either [4Fe-4S] clusters of H 2 ase or viologens of the CECs. A direct electron transfer between the H 2 ase and electrode surface was achieved in the LB films. Stronger current intensity was recorded when the CV measurements were done in H 2 saturated electrolyte solution than that in Ar. It was confirmed that the H 2 ase biocatalytic activity remained in the LB films. Thus, we suggest that the present H 2 ase-CECs biohybrids could act as potential materials for the studies of interconversion reaction of H 2 and protons.

Transcriptomic and proteomic analyses of Desulfovibrio vulgaris biofilms: carbon and energy flow contribute to the distinct biofilm growth state.

Science.gov (United States)

Clark, Melinda E; He, Zhili; Redding, Alyssa M; Joachimiak, Marcin P; Keasling, Jay D; Zhou, Jizhong Z; Arkin, Adam P; Mukhopadhyay, Aindrila; Fields, Matthew W

2012-04-16

Desulfovibrio vulgaris Hildenborough is a sulfate-reducing bacterium (SRB) that is intensively studied in the context of metal corrosion and heavy-metal bioremediation, and SRB populations are commonly observed in pipe and subsurface environments as surface-associated populations. In order to elucidate physiological changes associated with biofilm growth at both the transcript and protein level, transcriptomic and proteomic analyses were done on mature biofilm cells and compared to both batch and reactor planktonic populations. The biofilms were cultivated with lactate and sulfate in a continuously fed biofilm reactor, and compared to both batch and reactor planktonic populations. The functional genomic analysis demonstrated that biofilm cells were different compared to planktonic cells, and the majority of altered abundances for genes and proteins were annotated as hypothetical (unknown function), energy conservation, amino acid metabolism, and signal transduction. Genes and proteins that showed similar trends in detected levels were particularly involved in energy conservation such as increases in an annotated ech hydrogenase, formate dehydrogenase, pyruvate:ferredoxin oxidoreductase, and rnf oxidoreductase, and the biofilm cells had elevated formate dehydrogenase activity. Several other hydrogenases and formate dehydrogenases also showed an increased protein level, while decreased transcript and protein levels were observed for putative coo hydrogenase as well as a lactate permease and hyp hydrogenases for biofilm cells. Genes annotated for amino acid synthesis and nitrogen utilization were also predominant changers within the biofilm state. Ribosomal transcripts and proteins were notably decreased within the biofilm cells compared to exponential-phase cells but were not as low as levels observed in planktonic, stationary-phase cells. Several putative, extracellular proteins (DVU1012, 1545) were also detected in the extracellular fraction from biofilm cells

Filling Knowledge Gaps in Biological Networks: integrating global approaches to understand H2 metabolism in Chlamydomonas reinhardtii - Final Report

Energy Technology Data Exchange (ETDEWEB)

Posewitz, Matthew C

2011-06-30

The green alga Chlamydomonas reinhardtii (Chlamydomonas) has numerous genes encoding enzymes that function in fermentative pathways. Among these genes, are the [FeFe]-hydrogenases, pyruvate formate lyase, pyruvate ferredoxin oxidoreductase, acetate kinase, and phosphotransacetylase. We have systematically undertaken a series of targeted mutagenesis approaches to disrupt each of these key genes and omics techniques to characterize alterations in metabolic flux. Funds from DE-FG02-07ER64423 were specifically leveraged to generate mutants with disruptions in the genes encoding the [FeFe]-hydrogenases HYDA1 and HYDA2, pyruvate formate lyase (PFL1), and in bifunctional alcohol/aldehyde alcohol dehydrogenase (ADH1). Additionally funds were used to conduct global transcript profiling experiments of wildtype Chlamydomonas cells, as well as of the hydEF-1 mutant, which is unable to make H2 due to a lesion in the [FeFe]-hydrogenase biosynthetic pathway. In the wildtype cells, formate, acetate and ethanol are the dominant fermentation products with traces of CO2 and H2 also being produced. In the hydEF-1 mutant, succinate production is increased to offset the loss of protons as a terminal electron acceptor. In the pfl-1 mutant, lactate offsets the loss of formate production, and in the adh1-1 mutant glycerol is made instead of ethanol. To further probe the system, we generated a double mutant (pfl1-1 adh1) that is unable to synthesize both formate and ethanol. This strain, like the pfl1 mutants, secreted lactate, but also exhibited a significant increase in the levels of extracellular glycerol, acetate, and intracellular reduced sugars, and a decline in dark, fermentative H2 production. Whereas wild-type Chlamydomonas fermentation primarily produces formate and ethanol, the double mutant performs a complete rerouting of the glycolytic carbon to lactate and glycerol. Lastly, transcriptome data have been analysed for both the wildtype and hydEF-1, that correlate with our

Characterization of the hupSL promoter activity in Nostoc punctiforme ATCC 29133

Science.gov (United States)

2009-01-01

Background In cyanobacteria three enzymes are directly involved in the hydrogen metabolism; a nitrogenase that produces molecular hydrogen, H2, as a by-product of nitrogen fixation, an uptake hydrogenase that recaptures H2 and oxidize it, and a bidirectional hydrogenase that can both oxidize and produce H2.Nostoc punctiforme ATCC 29133 is a filamentous dinitrogen fixing cyanobacterium containing a nitrogenase and an uptake hydrogenase but no bidirectional hydrogenase. Generally, little is known about the transcriptional regulation of the cyanobacterial uptake hydrogenases. In this study gel shift assays showed that NtcA has a specific affinity to a region of the hupSL promoter containing a predicted NtcA binding site. The predicted NtcA binding site is centred at 258.5 bp upstream the transcription start point (tsp). To further investigate the hupSL promoter, truncated versions of the hupSL promoter were fused to either gfp or luxAB, encoding the reporter proteins Green Fluorescent Protein and Luciferase, respectively. Results Interestingly, all hupsSL promoter deletion constructs showed heterocyst specific expression. Unexpectedly the shortest promoter fragment, a fragment covering 57 bp upstream and 258 bp downstream the tsp, exhibited the highest promoter activity. Deletion of the NtcA binding site neither affected the expression to any larger extent nor the heterocyst specificity. Conclusion Obtained data suggest that the hupSL promoter in N. punctiforme is not strictly dependent on the upstream NtcA cis element and that the shortest promoter fragment (-57 to tsp) is enough for a high and heterocyst specific expression of hupSL. This is highly interesting because it indicates that the information that determines heterocyst specific gene expression might be confined to this short sequence or in the downstream untranslated leader sequence. PMID:19284581

Characterization of the hupSL promoter activity in Nostoc punctiforme ATCC 29133

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Lindberg Pia

2009-03-01

Full Text Available Abstract Background In cyanobacteria three enzymes are directly involved in the hydrogen metabolism; a nitrogenase that produces molecular hydrogen, H2, as a by-product of nitrogen fixation, an uptake hydrogenase that recaptures H2 and oxidize it, and a bidirectional hydrogenase that can both oxidize and produce H2.Nostoc punctiforme ATCC 29133 is a filamentous dinitrogen fixing cyanobacterium containing a nitrogenase and an uptake hydrogenase but no bidirectional hydrogenase. Generally, little is known about the transcriptional regulation of the cyanobacterial uptake hydrogenases. In this study gel shift assays showed that NtcA has a specific affinity to a region of the hupSL promoter containing a predicted NtcA binding site. The predicted NtcA binding site is centred at 258.5 bp upstream the transcription start point (tsp. To further investigate the hupSL promoter, truncated versions of the hupSL promoter were fused to either gfp or luxAB, encoding the reporter proteins Green Fluorescent Protein and Luciferase, respectively. Results Interestingly, all hupsSL promoter deletion constructs showed heterocyst specific expression. Unexpectedly the shortest promoter fragment, a fragment covering 57 bp upstream and 258 bp downstream the tsp, exhibited the highest promoter activity. Deletion of the NtcA binding site neither affected the expression to any larger extent nor the heterocyst specificity. Conclusion Obtained data suggest that the hupSL promoter in N. punctiforme is not strictly dependent on the upstream NtcA cis element and that the shortest promoter fragment (-57 to tsp is enough for a high and heterocyst specific expression of hupSL. This is highly interesting because it indicates that the information that determines heterocyst specific gene expression might be confined to this short sequence or in the downstream untranslated leader sequence.

Ni/Fe and Mg/Fe layered double hydroxides and their calcined derivatives: preparation, characterization and application on textile dyes removal

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Rachid Elmoubarki

2017-07-01

Full Text Available In this study, Mg/Fe and Ni/Fe layered double hydroxides (LDHs with molar ratio (M2+/Fe3+ of 3 and intercalated with carbonate ions were synthesized by co-precipitation method. The as-synthesized materials and their calcined products (CLDHs were characterized by X-ray diffraction (XRD, Fourier transform infrared spectroscopy (FT-IR, thermo-gravimetric and differential thermal analyses (TGA–DTA, transmission electron microscopy coupled with energy dispersive X-ray spectroscopy (TEM-EDX, inductively coupled plasma (ICP and elemental chemical analysis CHNSO. The materials were used as adsorbents for the removal availability of textile dyes from aqueous solution. Methylene blue (MB and malachite green (MG, representative of cationic dyes, and methyl orange (MO representative of anionic dyes were used as model molecules. Adsorption experiments were carried out under different parameters such as contact time, temperature, initial dyes concentration and solution pH. Experimental results indicate that CLDHs had much higher adsorption capacities compared to LDHs. Adsorption kinetic data fitted well the pseudo-second order kinetic model. The process was spontaneous, endothermic for cationic dyes and exothermic for the anionic dye. Equilibrium sorption data fitted the Langmuir model instead of Freundlich model.

A density functional theory study on the active center of Fe-only hydrogenase: characterization and electronic structure of the redox states.

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Liu, Zhi-Pan; Hu, P

2002-05-08

We have carried out extensive density functional theory (DFT) calculations for possible redox states of the active center in Fe-only hydrogenases. The active center is modeled by [(H(CH(3))S)(CO)(CN(-))Fe(p)(mu-DTN)(mu-CO)Fe(d)(CO)(CN(-))(L)](z)() (z is the net charge in the complex; Fe(p)= the proximal Fe, Fe(d) = the distal Fe, DTN = (-SCH(2)NHCH(2)S-), L is the ligand that bonds with the Fe(d) at the trans position to the bridging CO). Structures of possible redox states are optimized, and CO stretching frequencies are calculated. By a detailed comparison of all the calculated structures and the vibrational frequencies with the available experimental data, we find that (i) the fully oxidized, inactive state is an Fe(II)-Fe(II) state with a hydroxyl (OH(-)) group bonded at the Fe(d), (ii) the oxidized, active state is an Fe(II)-Fe(I) complex which is consistent with the assignment of Cao and Hall (J. Am. Chem. Soc. 2001, 123, 3734), and (iii) the fully reduced state is a mixture with the major component being a protonated Fe(I)-Fe(I) complex and the other component being its self-arranged form, Fe(II)-Fe(II) hydride. Our calculations also show that the exogenous CO can strongly bond with the Fe(II)-Fe(I) species, but cannot bond with the Fe(I)-Fe(I) complex. This result is consistent with experiments that CO tends to inhibit the oxidized, active state, but not the fully reduced state. The electronic structures of all the redox states have been analyzed. It is found that a frontier orbital which is a mixing state between the e(g) of Fe and the 2 pi of the bridging CO plays a key role concerning the reactivity of Fe-only hydrogenases: (i) it is unoccupied in the fully oxidized, inactive state, half-occupied in the oxidized, active state, and fully occupied in the fully reduced state; (ii) the e(g)-2 pi orbital is a bonding state, and this is the key reason for stability of the low oxidation states, such as Fe(I)-Fe(I) complexes; and (iii) in the e(g)-2 pi orbital

Sequencing and functional analysis of the nifENXorf1orf2 gene cluster of Herbaspirillum seropedicae.

Science.gov (United States)

Klassen, G; Pedrosa, F O; Souza, E M; Yates, M G; Rigo, L U

1999-12-01

A 5.1-kb DNA fragment from the nifHDK region of H. seropedicae was isolated and sequenced. Sequence analysis showed the presence of nifENXorf1orf2 but nifTY were not present. No nif or consensus promoter was identified. Furthermore, orf1 expression occurred only under nitrogen-fixing conditions and no promoter activity was detected between nifK and nifE, suggesting that these genes are expressed from the upstream nifH promoter and are parts of a unique nif operon. Mutagenesis studies indicate that nifN was essential for nitrogenase activity whereas nifXorf1orf2 were not. High homology between the C-terminal region of the NifX and NifB proteins from H. seropedicae was observed. Since the NifX and NifY proteins are important for FeMo cofactor (FeMoco) synthesis, we propose that alternative proteins with similar activities exist in H. seropedicae.

Liquid crystal based optical platform for the detection of Pb2+ ions using NiFe2O4 nanoparticles

Science.gov (United States)

Zehra, Saman; Gul, Iftikhar Hussain; Hussain, Zakir

2018-06-01

A simple, sensitive, selective and real time detection protocol was developed for Pb2+ ions in water using liquid crystals (LCs). In this method, NiFe2O4 nanoparticles were synthesized using chemical co-precipitation method. Crystallite size, morphological, functional groups and magnetization studies were confirmed using X-ray diffraction, Scanning Electron Microscopy, and Fourier transform infrared spectroscopy techniques, respectively. The nanoparticles were mono dispersed with average particle size of 20 ± 2 nm. The surfactant stabilized magnetic nanoparticles were incubated in liquid crystal based sensor system for the detection of Pb+2 ions. The bright to dark transition of LC was observed through optical microscope. When this system was further immersed with a solution containing Pb2+ ions, it caused homeotropic to planar orientation of LC. This interaction is attributed to the presence of abundant hydroxyl groups in such as M-OH, Fe-OH on the surface of spinel ferrites nanoparticles. These groups interact with metal ions at aqueous interface, causing disruption in LCs orientation giving bright texture. This sensor showed higher selectivity towards Pb2+ ions. The detection limit was estimated to be 100 ppb. The cheap and effective protocol reported here should make promising development of LC based sensor for lead ion detection.

Immobilization of hydrogenase on carbon nanotube polyelectrolytes as heterogeneous catalysts for electrocatalytic interconversion of protons and hydrogen

Energy Technology Data Exchange (ETDEWEB)

Liu, Jiang; Wu, Wen-Jie; Fang, Fang [Fudan University, Department of Chemistry (China); Zorin, Nikolay A. [Russian Academy of Sciences, Institute of Basic Biological Problems (Russian Federation); Chen, Meng; Qian, Dong-Jin, E-mail: djqian@fudan.edu.cn [Fudan University, Department of Chemistry (China)

2016-08-15

Immobilization of active enzymes on the surfaces of electrodes and nanomaterials is important in the fields of bioscience, and biotechnology. In this study, we investigated electrocatalytic properties of the interconversion of protons and hydrogen by means of hydrogenase (H{sub 2}ase)-functionalized carbon nanotube polyelectrolyte composites. Multiwalled carbon nanotube polyelectrolytes (MWNT-PEs) were synthesized through a diazonium and an addition reaction with poly(4-vinylpyridine) (P4VP), followed by another addition reaction with either methyl iodide (CH{sub 3}I) or N-methyl-N′-benzyl bromide bipyridinium (VBenBr) to produce MWNT-P4VPMe or MWNT-P4VPBenV polyelectrolytes, respectively. The MWNT-PE@H{sub 2}ase bio-nanocomposites were then prepared by means of MWNT-PEs as substrates to bind with H{sub 2}ase. The redox current density of the MWNT-PE@H{sub 2}ase-modified electrodes increased with a decrease in pH values of the Ar-saturated electrolyte solution owing to the catalytic reduction of protons (H{sub 2} production); further, it increased with the increasing pH values of the H{sub 2}-saturated solution owing to the catalytic oxidation of hydrogen. The reversible color change between blue-colored and colorless viologen (catalyzed by the MWNT-PE@H{sub 2}ase bio-nanocomposites) suggested that they may be developed as nano-biosensors for molecular H{sub 2}. The as-synthesized bio-nanocomposites showed strong long-term stability and high bioactivity.Graphical Abstract.

Liquid crystal based optical platform for the detection of Pb2+ ions using NiFe2O4 nanoparticles

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Saman Zehra

2018-06-01

Full Text Available A simple, sensitive, selective and real time detection protocol was developed for Pb2+ ions in water using liquid crystals (LCs. In this method, NiFe2O4 nanoparticles were synthesized using chemical co-precipitation method. Crystallite size, morphological, functional groups and magnetization studies were confirmed using X-ray diffraction, Scanning Electron Microscopy, and Fourier transform infrared spectroscopy techniques, respectively. The nanoparticles were mono dispersed with average particle size of 20 ± 2 nm. The surfactant stabilized magnetic nanoparticles were incubated in liquid crystal based sensor system for the detection of Pb+2 ions. The bright to dark transition of LC was observed through optical microscope. When this system was further immersed with a solution containing Pb2+ ions, it caused homeotropic to planar orientation of LC. This interaction is attributed to the presence of abundant hydroxyl groups in such as M-OH, Fe-OH on the surface of spinel ferrites nanoparticles. These groups interact with metal ions at aqueous interface, causing disruption in LCs orientation giving bright texture. This sensor showed higher selectivity towards Pb2+ ions. The detection limit was estimated to be 100 ppb. The cheap and effective protocol reported here should make promising development of LC based sensor for lead ion detection. Keywords: Chemical co-precipitation method, Fourier transform infrared spectroscopy, Liquid crystals, Nanoparticles, Sensor, X-ray diffraction

Genomes of ubiquitous marine and hypersaline Hydrogenovibrio, Thiomicrorhabdus and Thiomicrospira spp. encode a diversity of mechanisms to sustain chemolithoautotrophy in heterogeneous environments.

Science.gov (United States)

Scott, Kathleen M; Williams, John; Porter, Cody M B; Russel, Sydney; Harmer, Tara L; Paul, John H; Antonen, Kirsten M; Bridges, Megan K; Camper, Gary J; Campla, Christie K; Casella, Leila G; Chase, Eva; Conrad, James W; Cruz, Mercedez C; Dunlap, Darren S; Duran, Laura; Fahsbender, Elizabeth M; Goldsmith, Dawn B; Keeley, Ryan F; Kondoff, Matthew R; Kussy, Breanna I; Lane, Marannda K; Lawler, Stephanie; Leigh, Brittany A; Lewis, Courtney; Lostal, Lygia M; Marking, Devon; Mancera, Paola A; McClenthan, Evan C; McIntyre, Emily A; Mine, Jessica A; Modi, Swapnil; Moore, Brittney D; Morgan, William A; Nelson, Kaleigh M; Nguyen, Kimmy N; Ogburn, Nicholas; Parrino, David G; Pedapudi, Anangamanjari D; Pelham, Rebecca P; Preece, Amanda M; Rampersad, Elizabeth A; Richardson, Jason C; Rodgers, Christina M; Schaffer, Brent L; Sheridan, Nancy E; Solone, Michael R; Staley, Zachery R; Tabuchi, Maki; Waide, Ramond J; Wanjugi, Pauline W; Young, Suzanne; Clum, Alicia; Daum, Chris; Huntemann, Marcel; Ivanova, Natalia; Kyrpides, Nikos; Mikhailova, Natalia; Palaniappan, Krishnaveni; Pillay, Manoj; Reddy, T B K; Shapiro, Nicole; Stamatis, Dimitrios; Varghese, Neha; Woyke, Tanja; Boden, Rich; Freyermuth, Sharyn K; Kerfeld, Cheryl A

2018-03-09

Chemolithoautotrophic bacteria from the genera Hydrogenovibrio, Thiomicrorhabdus and Thiomicrospira are common, sometimes dominant, isolates from sulfidic habitats including hydrothermal vents, soda and salt lakes and marine sediments. Their genome sequences confirm their membership in a deeply branching clade of the Gammaproteobacteria. Several adaptations to heterogeneous habitats are apparent. Their genomes include large numbers of genes for sensing and responding to their environment (EAL- and GGDEF-domain proteins and methyl-accepting chemotaxis proteins) despite their small sizes (2.1-3.1 Mbp). An array of sulfur-oxidizing complexes are encoded, likely to facilitate these organisms' use of multiple forms of reduced sulfur as electron donors. Hydrogenase genes are present in some taxa, including group 1d and 2b hydrogenases in Hydrogenovibrio marinus and H. thermophilus MA2-6, acquired via horizontal gene transfer. In addition to high-affinity cbb 3 cytochrome c oxidase, some also encode cytochrome bd-type quinol oxidase or ba 3 -type cytochrome c oxidase, which could facilitate growth under different oxygen tensions, or maintain redox balance. Carboxysome operons are present in most, with genes downstream encoding transporters from four evolutionarily distinct families, which may act with the carboxysomes to form CO 2 concentrating mechanisms. These adaptations to habitat variability likely contribute to the cosmopolitan distribution of these organisms. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

Gene expression patterns of sulfur starvation in Synechocystis sp. PCC 6803

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Pendse Ninad D

2008-07-01

Full Text Available Abstract Background The unicellular cyanobacterium Synechocystis sp. PCC 6803 is a model microbe for studying biochemistry, genetics and molecular biology of photobiological processes. Importance of this bacterium in basic and applied research calls for a systematic, genome-wide description of its transcriptional regulatory capacity. Characteristic transcriptional responses to changes in the growth environment are expected to provide a scaffold for describing the Synechocystis transcriptional regulatory network as well as efficient means for functional annotation of genes in the genome. Results We designed, validated and used Synechocystis genome-wide oligonucleotide (70-mer microarray (representing 96.7% of all chromosomal ORFs annotated at the time of the beginning of this project to study transcriptional activity of the cyanobacterial genome in response to sulfur (S starvation. The microarray data were verified by quantitative RT-PCR. We made five main observations: 1 Transcriptional changes upon sulfate starvation were relatively moderate, but significant and consistent with growth kinetics; 2 S acquisition genes encoding for a high-affinity sulfate transporter were significantly induced, while decreased transcription of genes for phycobilisome, photosystems I and II, cytochrome b6/f, and ATP synthase indicated reduced light-harvesting and photosynthetic activity; 3 S starvation elicited transcriptional responses associated with general growth arrest and stress; 4 A large number of genes regulated by S availability encode hypothetical proteins or proteins of unknown function; 5 Hydrogenase structural and maturation accessory genes were not identified as differentially expressed, even though increased hydrogen evolution was observed. Conclusion The expression profiles recorded by using this oligonucleotide-based microarray platform revealed that during transition from the condition of plentiful S to S starvation, Synechocystis undergoes

Efficacy of resveratrol to supplement oral nifedipine treatment in pregnancy-induced preeclampsia

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Jian Ding

2017-10-01

Full Text Available Objective: Preeclampsia (PE is a complication affecting pregnant women worldwide, which usually manifests as severe maternal hypertension. Resveratrol (RESV, a naturally existing polyphenol, is known to exhibit beneficial effects in cardiovascular disease including hypertension. We evaluated the outcome of treatment combining oral nifedipine (NIFE and RESV against PE. Design and methods: Using a randomized group assignment, 400 PE patients were enrolled and received oral treatments of either NIFE + RESV or NIFE + placebo. Primary endpoints were defined as time to control blood pressure and time before a new hypertensive crisis. Secondary endpoints were defined as the number of doses needed to control blood pressure, maternal and neonatal adverse effects. Results: Compared with the NIFE + placebo group, the time needed to control blood pressure was significantly reduced in NIFE + RESV group, while time before a new hypertensive crisis was greatly delayed in NIFE + RESV group. The number of treatment doses needed to control blood pressure was also categorically lower in NIFE + RESV group. No differences in maternal or neonatal adverse effects were observed between the two treatment groups. Conclusion: Our data support the potential of RESV as a safe and effective adjuvant of oral NIFE to attenuate hypertensive symptoms among PE patients.

Resonant Ni and Fe KLL Auger spectra photoexcited from NiFe alloys

International Nuclear Information System (INIS)

Koever, L.; Cserny, I.; Berenyi, Z.; Egri, S.; Novak, M.

2005-01-01

Complete text of publication follows. KLL Auger spectra of 3d transition metal atoms in solid environment, measured using high energy resolution, give an insight into the details of the local electronic structure surrounding the particular atoms emitting the signal Auger electrons. Fine tuning the energy of the exciting monochromatic photons across the K-absorption edge, features characteristic to resonant phenomena can be identified in the spectra. The shapes of the resonantly photoexcited KLL Auger spectra induced from 3d transition metals and alloys are well interpreted by the single step model of the Auger process, based on the resonant scattering theory. The peak shapes are strongly influenced by the 4p partial density of unoccupied electronic states around the excited atom. High energy resolution studies of KLL Auger spectra of 3d transition metals using laboratory X-ray sources, however, request very demanding experiments and yield spectra of limited statistical quality making the evaluation of the fine details in the spectra difficult. The Tunable High Energy XPS (THE- XPS) instrument at BW2 offers optimum photon x and energy resolution for spectroscopy of deep core Auger transitions. For the present measurements high purity polycrystalline Ni and Fe sheets as well as NiFe alloy samples of different compositions (Ni 80 Fe 20 , Ni 50 Fe 50 , Ni 20 Fe 80 ) were used. The surfaces of the samples were cleaned by in-situ argon ion sputtering. The measurements of the Ni and Fe KL 23 L 23 Auger spectra of the metal and alloy samples were performed with the THE-XPS instrument using high electron energy resolution (0.2 eV). In Fig.1, the measured Fe KL 23 L 23 spectrum, photoexcited at the Fe K absorption edge from Fe metal, is compared with the respective spectrum excited from a Ni 50 Fe 50 alloy. A significant broadening of the 1 D 2 peak and an enhancement of the spectral intensity at the low energy loss part of this peak observed in the alloy sample, while the

A novel hydrogen oxidizer amidst the sulfur-oxidizing Thiomicrospira lineage

Science.gov (United States)

Hansen, Moritz; Perner, Mirjam

2015-01-01

Thiomicrospira species are ubiquitously found in various marine environments and appear particularly common in hydrothermal vent systems. Members of this lineage are commonly classified as sulfur-oxidizing chemolithoautotrophs. Although sequencing of Thiomicrospira crunogena's genome has revealed genes that encode enzymes for hydrogen uptake activity and for hydrogenase maturation and assembly, hydrogen uptake ability has so far not been reported for any Thiomicrospira species. We isolated a Thiomicrospira species (SP-41) from a deep sea hydrothermal vent and demonstrated that it can oxidize hydrogen. We show in vivo hydrogen consumption, hydrogen uptake activity in partially purified protein extracts and transcript abundance of hydrogenases during different growth stages. The ability of this strain to oxidize hydrogen opens up new perspectives with respect to the physiology of Thiomicrospira species that have been detected in hydrothermal vents and that have so far been exclusively associated with sulfur oxidation. PMID:25226028

CO-Bridged H-Cluster Intermediates in the Catalytic Mechanism of [FeFe]-Hydrogenase CaI.

Science.gov (United States)

Ratzloff, Michael W; Artz, Jacob H; Mulder, David W; Collins, Reuben T; Furtak, Thomas E; King, Paul W

2018-06-20

The [FeFe]-hydrogenases ([FeFe] H 2 ases) catalyze reversible H 2 activation at the H-cluster, which is composed of a [4Fe-4S] H subsite linked by a cysteine thiolate to a bridged, organometallic [2Fe-2S] ([2Fe] H ) subsite. Profoundly different geometric models of the H-cluster redox states that orchestrate the electron/proton transfer steps of H 2 bond activation have been proposed. We have examined this question in the [FeFe] H 2 ase I from Clostridium acetobutylicum (CaI) by Fourier-transform infrared (FTIR) spectroscopy with temperature annealing and H/D isotope exchange to identify the relevant redox states and define catalytic transitions. One-electron reduction of H ox led to formation of H red H + ([4Fe-4S] H 2+ -Fe I -Fe I ) and H red ' ([4Fe-4S] H 1+ -Fe II -Fe I ), with both states characterized by low frequency μ-CO IR modes consistent with a fully bridged [2Fe] H . Similar μ-CO IR modes were also identified for H red H + of the [FeFe] H 2 ase from Chlamydomonas reinhardtii (CrHydA1). The CaI proton-transfer variant C298S showed enrichment of an H/D isotope-sensitive μ-CO mode, a component of the hydride bound H-cluster IR signal, H hyd . Equilibrating CaI with increasing amounts of NaDT, and probed at cryogenic temperatures, showed H red H + was converted to H hyd . Over an increasing temperature range from 10 to 260 K catalytic turnover led to loss of H hyd and appearance of H ox , consistent with enzymatic turnover and H 2 formation. The results show for CaI that the μ-CO of [2Fe] H remains bridging for all of the "H red " states and that H red H + is on pathway to H hyd and H 2 evolution in the catalytic mechanism. These results provide a blueprint for designing small molecule catalytic analogs.

Enzymes as modular catalysts for redox half-reactions in H2-powered chemical synthesis: from biology to technology.

Science.gov (United States)

Reeve, Holly A; Ash, Philip A; Park, HyunSeo; Huang, Ailun; Posidias, Michalis; Tomlinson, Chloe; Lenz, Oliver; Vincent, Kylie A

2017-01-15

The present study considers the ways in which redox enzyme modules are coupled in living cells for linking reductive and oxidative half-reactions, and then reviews examples in which this concept can be exploited technologically in applications of coupled enzyme pairs. We discuss many examples in which enzymes are interfaced with electronically conductive particles to build up heterogeneous catalytic systems in an approach which could be termed synthetic biochemistry We focus on reactions involving the H + /H 2 redox couple catalysed by NiFe hydrogenase moieties in conjunction with other biocatalysed reactions to assemble systems directed towards synthesis of specialised chemicals, chemical building blocks or bio-derived fuel molecules. We review our work in which this approach is applied in designing enzyme-modified particles for H 2 -driven recycling of the nicotinamide cofactor NADH to provide a clean cofactor source for applications of NADH-dependent enzymes in chemical synthesis, presenting a combination of published and new work on these systems. We also consider related photobiocatalytic approaches for light-driven production of chemicals or H 2 as a fuel. We emphasise the techniques available for understanding detailed catalytic properties of the enzymes responsible for individual redox half-reactions, and the importance of a fundamental understanding of the enzyme characteristics in enabling effective applications of redox biocatalysis. © 2017 The Author(s).

Dual gas-diffusion membrane- and mediatorless dihydrogen/air-breathing biofuel cell operating at room temperature

Science.gov (United States)

Xia, Hong-qi; So, Keisei; Kitazumi, Yuki; Shirai, Osamu; Nishikawa, Koji; Higuchi, Yoshiki; Kano, Kenji

2016-12-01

A membraneless direct electron transfer (DET)-type dihydrogen (H2)/air-breathing biofuel cell without any mediator was constructed wherein bilirubin oxidase from Myrothecium verrucaria (BOD) and membrane-bound [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F (MBH) were used as biocatalysts for the cathode and the anode, respectively, and Ketjen black-modified water proof carbon paper (KB/WPCC) was used as an electrode material. The KB/WPCC surface was modified with 2-aminobenzoic acid and p-phenylenediamine, respectively, to face the positively charged electron-accepting site of BOD and the negatively charged electron-donating site of MBH to the electrode surface. A gas-diffusion system was employed for the electrodes to realize high-speed substrate supply. As result, great improvement in the current density of O2 reduction with BOD and H2 reduction with MBH were realized at negatively and postively charged surfaces, respectively. Gas diffusion system also suppressed the oxidative inactivation of MBH at high electrode potentials. Finally, based on the improved bioanode and biocathode, a dual gas-diffusion membrane- and mediatorless H2/air-breathing biofuel cell was constructed. The maximum power density reached 6.1 mW cm-2 (at 0.72 V), and the open circuit voltage was 1.12 V using 1 atm of H2 gas as a fuel at room temperature and under passive and quiescent conditions.

Mossbauer, Raman and X-ray diffraction studies of superparamagnetic NiFe2O4 nanoparticles prepared by sol-gel auto-combustion method

International Nuclear Information System (INIS)

Ahlawat, Anju; Sathe, V.G.; Reddy, V.R.; Gupta, Ajay

2011-01-01

Superparamagnetic nickel ferrite single phase nanoparticles with the average crystallite size of ∼9 nm have been synthesized at a low temperature (220 o C) by the sol-gel auto-combustion method. In the present study the as prepared powder was further calcined at different temperatures for 4 h, resulting in nanoparticles of larger size. The nanoparticles exhibited superparamagnetic behavior and changes in cation distribution as revealed by the Mossbauer, Raman and X-ray diffraction studies. The Mossbauer spectra collected at 5 K and under 5 T applied magnetic field showed mixed spinel structure and canted spin order for the nanoparticles, whereas there is collinear spin order with inverse spinel structure for larger particles. The vibrational spectra of the nanoparticles showed a redshift and broadening in the Raman line shape due to confinement effects. - Highlights: → Mossbauer spectra show a canting angle of 48 o for the nanoparticle samples measured at 5 K and 5 T applied magnetic field, the highest canting angle obtained so far in NiFe 2 O 4 nanoparticles. Site inversion in nanoparticles, thus converting it from inverse spinel to mixed spinel structure. → X-ray diffraction results showed a change in sign for the strain of the nanoparticle sample that showed mixed spinel structure. → Our Raman measurements showed a redshift and broadening for nanoparticle samples that is generally interpreted as a signature of quantum confinement.

Nickel accumulation and storage in bradyrhizobium japonicum

International Nuclear Information System (INIS)

Maier, R.J.; Pihl, T.D.; Stults, L.; Sray, W.

1990-01-01

Hydrogenase-depressed (chemolithotrophic growth conditions) and heterotrophically grown cultures of Bradyrhizobium japonicum accumulated nickel about equally over a 3-h period. Both types of cultures accumulated nickel primarily in a form that was not exchangeable with NiCl 2 , and they accumulated much more Ni than would be needed for the Ni-containing hydrogenase. The nickel accumulated by heterotrophically incubated cultures could later be mobilized to allow active hydrogenase synthesis during derepression in the absence of nickel, while cells both grown with Ni and the derepressed without nickel had low hydrogenase activities. The level of activity in cells grown with Ni and then derepressed without nickel was about the same as that in cultures derepressed in the presence of nickel. The Ni accumulated by heterotrophically grown cultures was associated principally with soluble proteins rather than particulate material, and this Ni was not lost upon dialyzing an extract containing the soluble proteins against either Ni-containing or EDTA-containing buffer. However, this Ni was lost upon pronase or low pH treatments. The soluble Ni-binding proteins were partially purified by gel filtration and DEAE chromatography. They were not antigenically related to hydrogenase peptides. Much of the 63 Ni eluted as a single peak of 48 kilodaltons. Experiments involving immunuprecipitation of 63 Ni-containing hydrogenase suggested that the stored source of Ni in heterotrophic cultures that could later be mobilized into hydrogenase resided in the nonexchangeable Ni-containing fraction rather than in loosely bound or ionic forms

Analysis of Microbial Communities in the Oil Reservoir Subjected to CO2-Flooding by Using Functional Genes as Molecular Biomarkers for Microbial CO2 Sequestration

Directory of Open Access Journals (Sweden)

Jin-Feng eLiu

2015-03-01

Full Text Available Sequestration of CO2 in oil reservoirs is considered to be one of the feasible options for mitigating atmospheric CO2 building up and also for the in situ potential bioconversion of stored CO2 to methane. However, the information on these functional microbial communities and the impact of CO2 storage on them is hardly available. In this paper a comprehensive molecular survey was performed on microbial communities in production water samples from oil reservoirs experienced CO2-flooding by analysis of functional genes involved in the process, including cbbM, cbbL, fthfs, [FeFe]-hydrogenase and mcrA. As a comparison, these functional genes in the production water samples from oil reservoir only experienced water-flooding in areas of the same oil bearing bed were also analyzed. It showed that these functional genes were all of rich diversity in these samples, and the functional microbial communities and their diversity were strongly affected by a long-term exposure to injected CO2. More interestingly, microorganisms affiliated with members of the genera Methanothemobacter, Acetobacterium and Halothiobacillus as well as hydrogen producers in CO2 injected area either increased or remained unchanged in relative abundance compared to that in water-flooded area, which implied that these microorganisms could adapt to CO2 injection and, if so, demonstrated the potential for microbial fixation and conversion of CO2 into methane in subsurface oil reservoirs.

Coexistence of unipolar and bipolar resistive switching behaviors in NiFe2O4 thin film devices by doping Ag nanoparticles

Science.gov (United States)

Hao, Aize; Ismail, Muhammad; He, Shuai; Huang, Wenhua; Qin, Ni; Bao, Dinghua

2018-02-01

The coexistence of unipolar and bipolar resistive switching (RS) behaviors of Ag-nanoparticles (Ag-NPs) doped NiFe2O4 (NFO) based memory devices was investigated. The switching voltages of required operations in the unipolar mode were smaller than those in the bipolar mode, while ON/OFF resistance levels of both modes were identical. Ag-NPs doped NFO based devices could switch between the unipolar and bipolar modes just by preferring the polarity of RESET voltage. Besides, the necessity of identical compliance current during the SET process of unipolar and bipolar modes provided an additional advantage of simplicity in device operation. Performance characteristics and cycle-to-cycle uniformity (>103 cycles) in unipolar operation were considerably better than those in bipolar mode (>102 cycles) at 25 °C. Moreover, good endurance (>600 cycles) at 200 °C was observed in unipolar mode and excellent nondestructive retention characteristics were obtained on memory cells at 125 °C and 200 °C. On the basis of temperature dependence of resistance at low resistance state, it was believed that physical origin of the RS mechanism involved the formation/rupture of the conducting paths consisting of oxygen vacancies and Ag atoms, considering Joule heating and electrochemical redox reaction effects for the unipolar and bipolar resistive switching behaviors. Our results demonstrate that 0.5% Ag-NPs doped nickel ferrites are promising resistive switching materials for resistive access memory applications.

The study of structural properties of carbon nanotubes decorated with NiFe₂O₄ nanoparticles and application of nano-composite thin film as H₂S gas sensor.

Science.gov (United States)

Hajihashemi, R; Rashidi, Ali M; Alaie, M; Mohammadzadeh, R; Izadi, N

2014-11-01

Nano-composite of multiwall carbon nanotube, decorated with NiFe2O4 nanoparticles (NiFe2O4-MWCNT), was synthesized using the sol-gel method. NiFe2O4-MWCNTs were characterized using different methods such as X-ray diffraction (XRD), field emission scanning electron microscopy (FESEM), high resolution transmission electron microscopy (HRTEM), atomic force microscopy (AFM) and vibrating sample magnetometer (VSM). The average size of the crystallites is 23.93 nm. The values of the saturation magnetization (MS), coercivity (HC) and retentivity (MR) of NiFe2O4-MWCNTs are obtained as 15 emu g(-1), 21Oe and 5 emu g(-1), respectively. In this research, NiFe2O4-MWCNT thin films were prepared with the spin-coating method. These thin films were used as the H2S gas sensor. The results suggest the possibility of the utilization of NiFe2O4-MWCNT nano-composite, as the H2S detector. The sensor shows appropriate response towards 100 ppm of H2S at 300°C. Copyright © 2014 Elsevier B.V. All rights reserved.

Determination of intrinsic spin Hall angle in Pt

Energy Technology Data Exchange (ETDEWEB)

Wang, Yi; Deorani, Praveen; Qiu, Xuepeng; Kwon, Jae Hyun; Yang, Hyunsoo, E-mail: eleyang@nus.edu.sg [Department of Electrical and Computer Engineering, National University of Singapore, 117576 (Singapore)

2014-10-13

The spin Hall angle in Pt is evaluated in Pt/NiFe bilayers by spin torque ferromagnetic resonance measurements and is found to increase with increasing the NiFe thickness. To extract the intrinsic spin Hall angle in Pt by estimating the total spin current injected into NiFe from Pt, the NiFe thickness dependent measurements are performed and the spin diffusion in the NiFe layer is taken into account. The intrinsic spin Hall angle of Pt is determined to be 0.068 at room temperature and is found to be almost constant in the temperature range of 13–300 K.

Determination of intrinsic spin Hall angle in Pt

International Nuclear Information System (INIS)

Wang, Yi; Deorani, Praveen; Qiu, Xuepeng; Kwon, Jae Hyun; Yang, Hyunsoo

2014-01-01

The spin Hall angle in Pt is evaluated in Pt/NiFe bilayers by spin torque ferromagnetic resonance measurements and is found to increase with increasing the NiFe thickness. To extract the intrinsic spin Hall angle in Pt by estimating the total spin current injected into NiFe from Pt, the NiFe thickness dependent measurements are performed and the spin diffusion in the NiFe layer is taken into account. The intrinsic spin Hall angle of Pt is determined to be 0.068 at room temperature and is found to be almost constant in the temperature range of 13–300 K.

Single-Amino Acid Modifications Reveal Additional Controls on the Proton Pathway of [FeFe]-Hydrogenase

Energy Technology Data Exchange (ETDEWEB)

Cornish, Adam J.; Ginovska, Bojana; Thelen, Adam; da Silva, Julio C. S.; Soares, Thereza A.; Raugei, Simone; Dupuis, Michel; Shaw, Wendy J.; Hegg, Eric L.

2016-06-07

The proton pathway of [FeFe]-hydrogenase is essential for enzymatic H2 production and oxidation and is composed of four residues and a modeled water molecule. Recently, a computational analysis of this pathway revealed that the solvent-exposed residue of the pathway (Glu282) could form hydrogen bonds to two residues outside of the pathway (Arg286 and Ser320), implicating that these residues could function in regulating proton transfer. Substituting Arg286 with leucine eliminates hydrogen bonding with Glu282 and results in a 2.5-fold enhancement in H2 production activity, suggesting that Arg286 serves an important role in controlling the rate of proton delivery. In contrast, substitution of Ser320 with alanine reduces the rate approximately 5-fold, implying that it either acts as a member of the pathway or influences Glu282 to enable proton transfer. Interestingly, QM/MM and molecular dynamics calculations indicate that Ser320 does not play an electronic or structural role. QM calculations also estimate that including Ser320 in the pathway does not significantly change the barrier to proton movement, providing further support for its role as a member of the proton pathway. While further studies are needed to quantify the role of Ser320, collectively, these data provide evidence that the enzyme scaffold plays a significant role in modulating the activity of the enzyme, demonstrating that the rate of intraprotein proton transfer can be accelerated, particularly in a non-biological context. This work was supported by the DOE Great Lakes Bioenergy Research Center (DOE BER Office of Science, DE-FC02-07ER64494). In addition, support from the DOE Office of Science Early Career Research Program through the Office of Basic Energy Sciences (WJS, BGP, SR) is gratefully acknowledged. Computational resources were provided at W. R. Wiley Environmental Molecular Science Laboratory (EMSL), a national scientific user facility sponsored by the Department of Energy’s Office of

Investigation on nickel ferrite nanowire device exhibiting negative differential resistance — a first-principles investigation

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V. Nagarajan

2017-06-01

Full Text Available The electronic property of NiFe_2O_4 nanowire device is investigated through nonequilibrium Green’s functions (NEGF in combination with density functional theory (DFT. The electronic transport properties of NiFe_2O_4 nanowire are studied in terms of density of states, transmission spectrum and I–V characteristics. The density of states gets modified with the applied bias voltage across NiFe_2O_4 nanowire device, the density of charge is observed both in the valence band and in the conduction band on increasing the bias voltage. The transmission spectrum of NiFe_2O_4 nanowire device gives the insights on the transition of electrons at different energy intervals. The findings of the present work suggest that NiFe_2O_4 nanowire device can be used as negative differential resistance (NDR device and its NDR property can be tuned with the bias voltage, which may be used in microwave device, memory devices and in fast switching devices.

Role of the antiferromagnetic pinning layer on spin wave properties in IrMn/NiFe based spin-valves

Energy Technology Data Exchange (ETDEWEB)

Gubbiotti, G., E-mail: gubbiotti@fisica.unipg.it; Tacchi, S. [Istituto Officina dei Materiali del CNR (IOM-CNR), Unità di Perugia, I-06123 Perugia (Italy); Del Bianco, L. [Department of Physics and Astronomy, University of Bologna, I-40127 Bologna (Italy); Department of Physics and Earth Sciences and CNISM, University of Ferrara, I-44122 Ferrara (Italy); Bonfiglioli, E.; Giovannini, L.; Spizzo, F.; Zivieri, R. [Department of Physics and Earth Sciences and CNISM, University of Ferrara, I-44122 Ferrara (Italy); Tamisari, M. [Department of Physics and Earth Sciences and CNISM, University of Ferrara, I-44122 Ferrara (Italy); Dipartimento di Fisica e Geologia, Università di Perugia, I-06123 Perugia (Italy)

2015-05-07

Brillouin light scattering (BLS) was exploited to study the spin wave properties of spin-valve (SV) type samples basically consisting of two 5 nm-thick NiFe layers (separated by a Cu spacer of 5 nm), differently biased through the interface exchange coupling with an antiferromagnetic IrMn layer. Three samples were investigated: a reference SV sample, without IrMn (reference); one sample with an IrMn underlayer (10 nm thick) coupled to the bottom NiFe film; one sample with IrMn underlayer and overlayer of different thickness (10 nm and 6 nm), coupled to the bottom and top NiFe film, respectively. The exchange coupling with the IrMn, causing the insurgence of the exchange bias effect, allowed the relative orientation of the NiFe magnetization vectors to be controlled by an external magnetic field, as assessed through hysteresis loop measurements by magneto-optic magnetometry. Thus, BLS spectra were acquired by sweeping the magnetic field so as to encompass both the parallel and antiparallel alignment of the NiFe layers. The BLS results, well reproduced by the presented theoretical model, clearly revealed the combined effects on the spin dynamic properties of the dipolar interaction between the two NiFe films and of the interface IrMn/NiFe exchange coupling.

Passivation of bimetallic catalysts used in water treatment: prevention and reactivation.

Science.gov (United States)

Chen, Jianming; Gillham, Robert W; Gui, Lai

2013-01-01

With respect to degradation rates and the range in contaminants treated, bimetals such as Ni-Fe or Pd-Fe generally outperform unamended granular iron. However, the catalytic enhancement is generally short-lived, lasting from a few days to months. To take advantage of the significant benefits of bimetals, this study aims at developing an effective method for the rejuvenation of passivated bimetals and alternatively, the prevention of rapid reactivity loss of bimetals. Because the most likely cause of Ni-Fe and Pd-Fe passivation is the deposition of iron oxide films over the catalyst sites, it is hypothesized that removal of the iron oxide films will restore the lost reactivity or avoiding the deposition of iron oxide films will prevent passivation. Two organic ligands (ethylenediaminetetraacetic acid (EDTA), and [s,s]-ethylenediaminedisuccinate acid ([s,s]-EDDS)) and two acids (citric acid and sulphuric acid) were tested as possible chemical reagents for both passivation rejuvenation and prevention. Trichloroethene (TCE) and Ni-Fe were chosen as probes for chlorinated solvents and bimetals respectively. The test was carried out using small glass columns packed with Ni-Fe. TCE solution containing a single reagent at various concentrations was pumped through the Ni-Fe columns with a residence time in the Ni-Fe of about 6.6 min. TCE concentrations in the influent and effluent were measured to evaluate the performance of each chemical reagent. The results show that (i) for passivated Ni-Fe, flushing with a low concentration of acid or ligand solution without mechanical mixing can fully restore the lost reactivity; and (ii) for passivation prevention, adding a small amount of a ligand or an acid to the feed solution can successfully prevent or at least substantially reduce Ni-Fe passivation. All four chemicals tested are effective in both rejuvenation and prevention, but sulphuric acid and citric acid are considered to be the most practical reagents due to their

NCBI nr-aa BLAST: CBRC-AGAM-02-0168 [SEVENS

Lifescience Database Archive (English)

Full Text Available CBRC-AGAM-02-0168 ref|YP_001226076.1| Hydrogenase/urease accessory protein [Synecho...coccus sp. WH 7803] emb|CAK24779.1| Hydrogenase/urease accessory protein [Synechococcus sp. WH 7803] YP_001226076.1 1.0 28% ...

Isolation and characterization of mutant strains of Escherichia coli altered in H2 metabolism

International Nuclear Information System (INIS)

Lee, J.H.; Patel, P.; Sankar, P.; Shanmugam, K.T.

1985-01-01

A positive selection procedure is described for the isolation of hydrogenase-defective mutant strains of Escherichia coli. Mutant strains isolated by this procedure can be divided into two major classes. Class II mutants produced hydrogenase activity (determined by using a tritium-exchange assay) and formate hydrogenlyase activity but lacked the ability to reduce benzyl viologen or fumarate with H 2 as the electron donor. Class I mutants failed to produce active hydrogenase and hydrogenase-dependent activities. All the mutant strains produced detectable levels of formate dehydrogenase-1 and -2 and fumarate reductase. The mutation in class I mutants mapped near 65 min of the E. coli chromosome, whereas the mutation in class II mutants mapped between srl and cys operons (58 and 59 min, respectively) in the genome. The class II Hyd mutants can be further subdivided into two groups (hydA and hydB) based on the cotransduction characteristics with cys and srl. These results indicate that there are two hyd operons and one hup operon in the E. coli chromosome. The two hyd operons are needed for the production of active hydrogenase, and all three are essential for hydrogen-dependent growth of the cell

Photosynthetic Versatility in the Genome of Geitlerinema sp. PCC 9228 (Formerly Oscillatoria limnetica 'Solar Lake'), a Model Anoxygenic Photosynthetic Cyanobacterium.

Science.gov (United States)

Grim, Sharon L; Dick, Gregory J

2016-01-01

Anoxygenic cyanobacteria that use sulfide as the electron donor for photosynthesis are a potentially influential but poorly constrained force on Earth's biogeochemistry. Their versatile metabolism may have boosted primary production and nitrogen cycling in euxinic coastal margins in the Proterozoic. In addition, they represent a biological mechanism for limiting the accumulation of atmospheric oxygen, especially before the Great Oxidation Event and in the low-oxygen conditions of the Proterozoic. In this study, we describe the draft genome sequence of Geitlerinema sp. PCC 9228, formerly Oscillatoria limnetica 'Solar Lake', a mat-forming diazotrophic cyanobacterium that can switch between oxygenic photosynthesis and sulfide-based anoxygenic photosynthesis (AP). Geitlerinema possesses three variants of psbA , which encodes protein D1, a core component of the photosystem II reaction center. Phylogenetic analyses indicate that one variant is closely affiliated with cyanobacterial psbA genes that code for a D1 protein used for oxygen-sensitive processes. Another version is phylogenetically similar to cyanobacterial psbA genes that encode D1 proteins used under microaerobic conditions, and the third variant may be cued to high light and/or elevated oxygen concentrations. Geitlerinema has the canonical gene for sulfide quinone reductase (SQR) used in cyanobacterial AP and a putative transcriptional regulatory gene in the same operon. Another operon with a second, distinct sqr and regulatory gene is present, and is phylogenetically related to sqr genes used for high sulfide concentrations. The genome has a comprehensive nif gene suite for nitrogen fixation, supporting previous observations of nitrogenase activity. Geitlerinema possesses a bidirectional hydrogenase rather than the uptake hydrogenase typically used by cyanobacteria in diazotrophy. Overall, the genome sequence of Geitlerinema sp. PCC 9228 highlights potential cyanobacterial strategies to cope with fluctuating

NCBI nr-aa BLAST: CBRC-XTRO-01-2348 [SEVENS

Lifescience Database Archive (English)

Full Text Available CBRC-XTRO-01-2348 ref|YP_594815.1| hydrogenase-1 small subunit [Lawsonia intracellu...laris PHE/MN1-00] emb|CAJ54493.1| hydrogenase-1 small subunit [Lawsonia intracellularis PHE/MN1-00] YP_594815.1 6.0 27% ...

Electrical and optical properties of nickel ferrite/polyaniline nanocomposite

Directory of Open Access Journals (Sweden)

M. Khairy

2015-07-01

Full Text Available Polyaniline–NiFe2O4 nanocomposites (PANI–NiFe2O4 with different contents of NiFe2O4 (2.5, 5 and 50 wt% were prepared via in situ chemical oxidation polymerization, while the nanoparticles nickel ferrite were synthesized by sol–gel method. The prepared samples were characterized using some techniques such as Fourier transforms infrared (FTIR, X-ray diffraction (XRD, scanning electron microscopy (SEM and thermogravimetric analysis (TGA. Moreover, the electrical conductivity and optical properties of the nanocomposites were investigated. Pure (PANI and the composites containing 2.5 and 5 wt% NiFe2O4 showed amorphous structures, while the one with 50 wt% NiFe2O4 showed a spinel crystalline structure. The SEM images of the composites showed different aggregations for the different nickel ferrite contents. FTIR spectra revealed to the formation of some interactions between the PANI macromolecule and the NiFe2O4 nanoparticles, while the thermal analyses indicated an increase in the composites stability for samples with higher NiFe2O4 nanoparticles contents. The electrical conductivity of PANI–NiFe2O4 nanocomposite was found to increase with the rise in NiFe2O4 nanoparticle content, probably due to the polaron/bipolaron formation. The optical absorption experiments illustrate direct transition with an energy band gap of Eg = 1.0 for PANI–NiFe2O4 nanocomposite.

The Role of Hydrogen for Sulfurimonas denitrificans’ Metabolism

Science.gov (United States)

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

Influence of Ni-dopant on the properties of synthetic goethite

International Nuclear Information System (INIS)

Krehula, Stjepko; Music, Svetozar; Popovic, Stanko

2005-01-01

The influence of Ni-dopant on the properties of α-FeOOH was investigated by XRD, FT-IR, 57 Fe Moessbauer spectroscopy and transmission electron microscopy. α-FeOOH was synthesized at a highly alkaline pH by precipitation from the FeCl 3 solution with the addition of tetramethylammonium hydroxide and autoclaving at 160 o C. The samples doped with Ni 2+ ions were precipitated in the same way, but in the presence of varying concentrations of NiCl 2 . Solid solutions, having the structure of α-FeOOH, were observed in samples with the Ni/Fe ratio up to 0.05. Upon increasing the amount of Ni-dopant the XRD lines were gradually broadened. The sample with the ratio Ni/Fe=0.10 showed NiFe 2 O 4 , besides the dominant phase having the structure type of α-FeOOH. Shifts of IR bands at 892 and 796cm -1 were not observed in all samples doped with Ni. For the ratio Ni/Fe=0.10, the IR bands centered at 631 and 404cm -1 were significantly broadened. RT Moessbauer spectrum of undoped α-FeOOH and Ni-doped α-FeOOH showed distributions of hyperfine magnetic fields. B hf decreased from 35.1T for an undoped α-FeOOH to 32.1T for α-FeOOH containing Ni 2+ ions (Ni/Fe=0.05). The saturation of the α-FeOOH structure with Ni 2+ ions in amounts higher than ∼5mol% was also observed by Moessbauer spectroscopy. The particle size (length) of acicular α-FeOOH particles with a maximum in the interval 180-220nm was slightly decreased with Ni-doping, but the distribution of the length/width ratio showed no change, having a maximum at 4-5. TEM photographs additionally showed small populations of cubic-shaped or pseudocubic particles of ∼10nm in size for the ratio Ni/Fe=0.05 and about 10-20nm in size for the ratio Ni/Fe=0.10. These particles were assigned to NiFe 2 O 4

Hydrogen production by recombinant Escherichia coli strains

Science.gov (United States)

Maeda, Toshinari; Sanchez‐Torres, Viviana; Wood, Thomas K.

2012-01-01

Summary The production of hydrogen via microbial biotechnology is an active field of research. Given its ease of manipulation, the best‐studied bacterium Escherichia coli has become a workhorse for enhanced hydrogen production through metabolic engineering, heterologous gene expression, adaptive evolution, and protein engineering. Herein, the utility of E. coli strains to produce hydrogen, via native hydrogenases or heterologous ones, is reviewed. In addition, potential strategies for increasing hydrogen production are outlined and whole‐cell systems and cell‐free systems are compared. PMID:21895995

Preparation of nickel ferrite/carbon nanotubes composite by microwave irradiation technique for use as catalyst in photo-fenton reaction

Energy Technology Data Exchange (ETDEWEB)

Foletto, E.L.; Rigo, C.; Severo, E.C.; Mazutti, M.A.; Dotto, G.L.; Jahn, S.L.; Sales, J.C. [Universidade Federal de Santa Maria (UFSM), RS (Brazil); Chiavone-Filho, O. [Universidade Federal do Rio Grande do Sul (UFRGS), RS (Brazil); Gundel, A.; Lucchese, M. [Universidade Federal do Pampa (UNIPAMPA), Bage, RS (Brazil)

2016-07-01

Full text: Nickel ferrite/multi-walled carbon nanotubes (NiFe2O4/MWCNTs) composite has been rapidly synthesized via microwave irradiation technique. The structural properties of the formed product was investigated by X-ray diffraction (XRD), N2 adsorption/desorption isotherms, thermogravimetric analysis (TGA), Raman spectroscopy and, scanning electron microscopy (SEM). The catalytic behavior of composite material was evaluated by the degradation of Amaranth dye in the photo-Fenton reaction under visible light irradiation. The overall results showed that the prepared composite was successfully synthesized, demonstrating good performance in the dye degradation, with higher degradation rate compared to the NiFe2O4. The high efficiency in dye degradation can be attributed to synergism between NiFe2O4 and MWCNTs. Therefore, NiFe2O4/MWCNTs composite can be used as promising photo-Fenton catalyst to degrade Amaranth dye from aqueous solutions. (author)

Effect of interface intermixing on giant magnetoresistance in NiFe/Cu and Co/NiFe/Co/Cu multilayers

International Nuclear Information System (INIS)

Nagamine, L.C.C.M.; Biondo, A.; Pereira, L.G.; Mello, A.; Schmidt, J.E.; Chimendes, T.W.; Cunha, J.B.M.; Saitovitch, E.B.

2003-01-01

This article reports on the important influence of the spontaneously built-in paramagnetic interfacial layers on the magnetic and magnetoresistive properties of NiFe/Cu and Co/NiFe/Co/Cu multilayers grown by magnetron sputtering. A computational simulation, based on a semiclassical model, has been used to reproduce the variations of the resistivity and of the magnetoresistance (MR) amplitude with the thickness of the NiFe, Cu, and Co layers. We showed that the compositionally intermixed layers at NiFe/Cu interfaces, which are paramagnetic, reduce the flow of polarized electrons and produce a masking on the estimated mean-free path of both types of electrons due to the reduction of their effective values, mainly for small NiFe thickness. Moreover, the transmission coefficients for the electrons decrease when Fe buffer layers are replaced by NiFe ones. This result is interpreted in terms of the variations of the interfacial intermixing and roughness at the interfaces, leading to an increase of the paramagnetic interfacial layer thickness. The effect provoked by Co deposition at the NiFe 16 A/Cu interfaces has also been investigated. The maximum of the MR amplitudes was found at 5 A of Co, resulting in the quadruplication of the MR amplitude. This result is partially attributed to the interfacial spin-dependent scattering due to the increase of the magnetic order at interfaces. Another effect observed here was the increase of the spin-dependent scattering events in the bulk NiFe due to a larger effective NiFe thickness, since the paramagnetic interfacial layer thickness is decreased

Addressing the challenges of using ferromagnetic electrodes in the magnetic tunnel junction-based molecular spintronics devices

International Nuclear Information System (INIS)

Tyagi, Pawan; Friebe, Edward; Baker, Collin

2015-01-01

Addressing the challenges of using high-Curie temperature ferromagnetic (FM) electrodes is critical for molecular spintronics devices (MSDs) research. Two FM electrodes simultaneously chemically bonded with a thiol-functionalized molecule can produce novel MSDs to exploring new quantum mechanical phenomenon and computer technologies. For developing a commercially viable MSD, it is crucial to developing a device fabrication scheme that carefully considers FM electrodes’ susceptibility to oxidation, chemical etching, and stress-induced deformations during fabrication and usage. This paper studies NiFe, an alloy extensively used in present-day memory devices and high-temperature engineering applications, as a candidate FM electrode for the fabrication of MSDs. Our spectroscopic reflectance studies show that NiFe oxidized aggressively after heating beyond ∼90 °C. The NiFe surfaces, aged for several months or heated for several minutes below ∼90 °C, exhibited remarkable electrochemical activity and were found suitable for chemical bonding with the thiol-functionalized molecular device elements. NiFe also demonstrated excellent etching resistance against commonly used solvents and lithography related chemicals. Additionally, NiFe mitigated the adverse effects of mechanical stress by subsiding the stress-induced deformities. A magnetic tunnel junction-based MSD approach was designed by carefully considering the merits and limitations of NiFe. The device fabrication protocol considers the safe temperature limit to avoiding irreversible surface oxidation, the effect of mechanical stresses, surface roughness, and chemical etching. This paper provides foundational experimental insights in realizing a versatile MSD allowing a wide range of transport and magnetic studies

SPINE: SParse eIgengene NEtwork linking gene expression clusters in Dehalococcoides mccartyi to perturbations in experimental conditions.

Directory of Open Access Journals (Sweden)

Cresten B Mansfeldt

Full Text Available We present a statistical model designed to identify the effect of experimental perturbations on the aggregate behavior of the transcriptome expressed by the bacterium Dehalococcoides mccartyi strain 195. Strains of Dehalococcoides are used in sub-surface bioremediation applications because they organohalorespire tetrachloroethene and trichloroethene (common chlorinated solvents that contaminate the environment to non-toxic ethene. However, the biochemical mechanism of this process remains incompletely described. Additionally, the response of Dehalococcoides to stress-inducing conditions that may be encountered at field-sites is not well understood. The constructed statistical model captured the aggregate behavior of gene expression phenotypes by modeling the distinct eigengenes of 100 transcript clusters, determining stable relationships among these clusters of gene transcripts with a sparse network-inference algorithm, and directly modeling the effect of changes in experimental conditions by constructing networks conditioned on the experimental state. Based on the model predictions, we discovered new response mechanisms for DMC, notably when the bacterium is exposed to solvent toxicity. The network identified a cluster containing thirteen gene transcripts directly connected to the solvent toxicity condition. Transcripts in this cluster include an iron-dependent regulator (DET0096-97 and a methylglyoxal synthase (DET0137. To validate these predictions, additional experiments were performed. Continuously fed cultures were exposed to saturating levels of tetrachloethene, thereby causing solvent toxicity, and transcripts that were predicted to be linked to solvent toxicity were monitored by quantitative reverse-transcription polymerase chain reaction. Twelve hours after being shocked with saturating levels of tetrachloroethene, the control transcripts (encoding for a key hydrogenase and the 16S rRNA did not significantly change. By contrast

Synthesize and characterization of a novel anticorrosive cobalt ferrite nanoparticles dispersed in silica matrix (CoFe2O4-SiO2) to improve the corrosion protection performance of epoxy coating

International Nuclear Information System (INIS)

Gharagozlou, M.; Ramezanzadeh, B.; Baradaran, Z.

2016-01-01

Highlights: • An anticorrosive cobalt ferrite nanopigment dispersed in silica matrix was synthesized. • The nanopigment showed proper inhibition performance in solution study. • The nanopigment significantly improved the corrosion resistance of the epoxy coating. - Abstract: This study aimed at studying the effect of an anticorrosive nickel ferrite nanoparticle dispersed in silica matrix (NiFe 2 O 4 -SiO 2 ) on the corrosion protection properties of steel substrate. NiFe 2 O 4 and NiFe 2 O 4 -SiO 2 nanopigments were synthesized and then characterized by X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FT-IR) and transmission electron microscope (TEM). Then, 1 wt.% of nanopigments was dispersed in an epoxy coating and the resultant nanocomposites were applied on the steel substrates. The corrosion inhibition effects of nanopigments were tested by an electrochemical impedance spectroscopy (EIS) and salt spray test. Results revealed that dispersing nickel ferrite nanoparticles in a silica matrix (NiFe 2 O 4 -SiO 2 ) resulted in the enhancement of the nanopigment dispersion in the epoxy coating matrix. Inclusion of 1 wt.% of NiFe 2 O 4 -SiO 2 nanopigment into the epoxy coating enhanced its corrosion protection properties before and after scratching.

Biomarkers’ Responses to Reductive Dechlorination Rates and Oxygen Stress in Bioaugmentation Culture KB-1TM

Directory of Open Access Journals (Sweden)

Gretchen L. W. Heavner

2018-02-01

Full Text Available Using mRNA transcript levels for key functional enzymes as proxies for the organohalide respiration (OHR rate, is a promising approach for monitoring bioremediation populations in situ at chlorinated solvent-contaminated field sites. However, to date, no correlations have been empirically derived for chlorinated solvent respiring, Dehalococcoides mccartyi (DMC containing, bioaugmentation cultures. In the current study, genome-wide transcriptome and proteome data were first used to confirm the most highly expressed OHR-related enzymes in the bioaugmentation culture, KB-1TM, including several reductive dehalogenases (RDases and a Ni-Fe hydrogenase, Hup. Different KB-1™ DMC strains could be resolved at the RNA and protein level through differences in the sequence of a common RDase (DET1545-like homologs and differences in expression of their vinyl chloride-respiring RDases. The dominant strain expresses VcrA, whereas the minor strain utilizes BvcA. We then used quantitative reverse-transcriptase PCR (qRT-PCR as a targeted approach for quantifying transcript copies in the KB-1TM consortium operated under a range of TCE respiration rates in continuously-fed, pseudo-steady-state reactors. These candidate biomarkers from KB-1TM demonstrated a variety of trends in terms of transcript abundance as a function of respiration rate over the range: 7.7 × 10−12 to 5.9 × 10−10 microelectron equivalents per cell per hour (μeeq/cell∙h. Power law trends were observed between the respiration rate and transcript abundance for the main DMC RDase (VcrA and the hydrogenase HupL (R2 = 0.83 and 0.88, respectively, but not transcripts for 16S rRNA or three other RDases examined: TceA, BvcA or the RDase DET1545 homologs in KB1TM. Overall, HupL transcripts appear to be the most robust activity biomarker across multiple DMC strains and in mixed communities including DMC co-cultures such as KB1TM. The addition of oxygen induced cell stress that caused respiration

Biomarkers' Responses to Reductive Dechlorination Rates and Oxygen Stress in Bioaugmentation Culture KB-1TM.

Science.gov (United States)

Heavner, Gretchen L W; Mansfeldt, Cresten B; Debs, Garrett E; Hellerstedt, Sage T; Rowe, Annette R; Richardson, Ruth E

2018-02-08

Using mRNA transcript levels for key functional enzymes as proxies for the organohalide respiration (OHR) rate, is a promising approach for monitoring bioremediation populations in situ at chlorinated solvent-contaminated field sites. However, to date, no correlations have been empirically derived for chlorinated solvent respiring, Dehalococcoides mccartyi (DMC) containing, bioaugmentation cultures. In the current study, genome-wide transcriptome and proteome data were first used to confirm the most highly expressed OHR-related enzymes in the bioaugmentation culture, KB-1 TM , including several reductive dehalogenases (RDases) and a Ni-Fe hydrogenase, Hup. Different KB-1™ DMC strains could be resolved at the RNA and protein level through differences in the sequence of a common RDase (DET1545-like homologs) and differences in expression of their vinyl chloride-respiring RDases. The dominant strain expresses VcrA, whereas the minor strain utilizes BvcA. We then used quantitative reverse-transcriptase PCR (qRT-PCR) as a targeted approach for quantifying transcript copies in the KB-1 TM consortium operated under a range of TCE respiration rates in continuously-fed, pseudo-steady-state reactors. These candidate biomarkers from KB-1 TM demonstrated a variety of trends in terms of transcript abundance as a function of respiration rate over the range: 7.7 × 10 -12 to 5.9 × 10 -10 microelectron equivalents per cell per hour (μeeq/cell∙h). Power law trends were observed between the respiration rate and transcript abundance for the main DMC RDase (VcrA) and the hydrogenase HupL (R² = 0.83 and 0.88, respectively), but not transcripts for 16S rRNA or three other RDases examined: TceA, BvcA or the RDase DET1545 homologs in KB1 TM . Overall, HupL transcripts appear to be the most robust activity biomarker across multiple DMC strains and in mixed communities including DMC co-cultures such as KB1 TM . The addition of oxygen induced cell stress that caused respiration rates

Perturbation of formate pathway for hydrogen production by expressions of formate hydrogen lyase and its transcriptional activator in wild Enterobacter aerogenes and its mutants

Energy Technology Data Exchange (ETDEWEB)

Lu, Yuan; Zhao, Hongxin; Zhang, Chong; Lai, Qiheng; Xing, Xin-Hui [Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084 (China)

2009-06-15

To examine perturbation effects of formate pathway on hydrogen productivity in Enterobacter aerogenes (Ea), formate dehydrogenase FDH-H gene (fdhF) and formate hydrogen lyase activator protein FHLA gene (fhlA) originated from Escherichia coli, were overexpressed in the wild strain Ea, its hycA-deleted mutant (A) by knockout the formate hydrogen lyase repressor and hybO-deleted mutant (O) by knockout of the uptake hydrogenase, respectively. Overexpression of fdhF and fhlA promoted cell growth and volumetric hydrogen production rates of all the strains, and the hydrogen production per gram cell dry weight (CDW) for Ea, A and O was increased by 38.5%, 21.8% and 5.25%, respectively. The fdhF and fhlA overexpression improved the hydrogen yield per mol glucose of strains Ea and A, but declined that of strain O. The increase of hydrogen yield of the strain Ea with fdhF and fhlA expression was mainly attributed to the increase of formate pathway, while for the mutant A, the improved hydrogen yield with fdhF and fhlA expression was mainly due to the increase of NADH pathway. Analysis of the metabolites and ratio of ethanol-to-acetate showed that the cellular redox state balance and energy level were also changed for these strains by fdhF and fhlA expression. These findings demonstrated that the hydrogen production was not only dependent on the hydrogenase genes, but was also affected by the regulation of the whole metabolism. Therefore, fdhF and fhlA expression in different strains of E. aerogenes could exhibit different perturbation effects on the metabolism and the hydrogen productivity. (author)

Dark hydrogen production in nitrogen atmosphere - An approach for sustainability by marine cyanobacterium Leptolyngbya valderiana BDU 20041

Energy Technology Data Exchange (ETDEWEB)

Prabaharan, D.; Arun Kumar, D.; Uma, L.; Subramanian, G. [National Facility for Marine Cyanobacteria (Sponsored by DBT, Govt. of India), Department of Marine Biotechnology, Bharathidasan University, Tiruchirapalli 620 024 (India)

2010-10-15

Biological hydrogen production is an ideal system for three main reasons i) forms a renewable energy source, ii) gives clean fuel and iii) serves as a good supplement to oil reserves. The major challenges faced in biological hydrogen production are the presence of uptake hydrogenase and lack of sustainability in the cyanobacterial hydrogen production system. Three different marine cyanobacterial species viz. Leptolyngbya valderiana BDU 20041, Dichothrix baueriana BDU 40481 and Nostoc calcicola BDU 40302 were studied for their potential use in hydrogen production. Among these, L. valderiana BDU 20041, was found to produce hydrogen even in 100% nitrogen atmosphere which was 85% of the hydrogen produced in argon atmosphere. This is the first report of such a high rate of production of hydrogen in a nitrogen atmosphere by a cyanobacterium, which makes it possible to develop sustained hydrogen production systems. L. valderiana BDU 20041, a dark hydrogen producer uses the reductant essentially supplied by the respiratory pathway for hydrogen production. Using inhibitors, this organism was found to produce hydrogen due to the activities of both nitrogenase and bidirectional hydrogenase, while it had no 'uptake' hydrogenase activity. The other two organisms though had low levels of bidirectional hydrogenase, possessed considerable 'uptake' hydrogenase activity and hence could not release much hydrogen either in argon or nitrogen atmosphere. (author)

Permanent Draft Genome of Strain ESFC-1: Ecological Genomics of a Newly Discovered Lineage of Filamentous Diazotrophic Cyanobacteria

Science.gov (United States)

Everroad, R. Craig; Stuart, Rhona K.; Bebout, Brad M.; Detweiler, Angela M.; Lee, Jackson Zan; Woebken, Dagmar; Bebout, Leslie E.; Pett-Ridge, Jennifer

2016-01-01

The nonheterocystous filamentous cyanobacterium, strain ESFC-1, is a recently described member of the order Oscillatoriales within the Cyanobacteria. ESFC-1 has been shown to be a major diazotroph in the intertidal microbial mat system at Elkhorn Slough, CA, USA. Based on phylogenetic analyses of the 16S RNA gene, ESFC-1 appears to belong to a unique, genus-level divergence; the draft genome sequence of this strain has now been determined. Here we report features of this genome as they relate to the ecological functions and capabilities of strain ESFC-1. The 5,632,035 bp genome sequence encodes 4914 protein-coding genes and 92 RNA genes. One striking feature of this cyanobacterium is the apparent lack of either uptake or bi-directional hydrogenases typically expected within a diazotroph. Additionally, a large genomic island is found that contains numerous low GC-content genes and genes related to extracellular polysaccharide production and cell wall synthesis and maintenance.

Enzymatic recovery of platinum (IV) from industrial wastewater using ...

African Journals Online (AJOL)

highest hydrogen-dependent platinum (IV) reducing activity in the presence of hydrogenase and its physiological electron carrier, cytochrome c3. When the purified hydrogenase enzyme (with and without cytochrome c3) was used with the industrial effluent, containing 7.9 mg.l-1 platinum, only 10 – 15% recovery was noted ...

Fiscal 1998 R and D project on global environmental industrial technology. R and D result report on environment- friendly production technology (advanced chemical synthesis reactor); 1998 nendo chikyu kankyo sangyo gijutsu kenkyu kaihatsu jigyo. Kankyo chowagata seisan gijutsu (kokino kagaku gosei bio reactor) kenkyu kaihatsu seika hokokusho

Energy Technology Data Exchange (ETDEWEB)

NONE

1999-03-01

For high-efficiency production of substances by bioreactor, study was made on a bio-control mechanism as its elementary technology. On the study of breeding technology by expression control, the structure design of a control region and development of new expression vectors had been finished, and study was made on breeding of high-efficiency recombinant production cells by using candidate expression vectors. On the study of breeding technology by multi-stage enzyme reaction control, the enzyme gene of a system synthesizing cysteine from glycerol was searched, and hydroxypyruvaldehyde hydrogenase gene was isolated as substance production model. Cysteine production Escherichia coli combined with serineacetyl transferase gene was also prepared. In addition, study started on cloning of hydroxyacetone oxidase gene. On development of reactor system technology, for conversion of serine to cysteine, study was made on optimization of a reaction condition by theory of enzyme reaction rate. (NEDO)

Laboratoire de Chimie Bactérienne C.N.R.S., Marsielle, France.

Science.gov (United States)

Chippaux, M; Giudici, D; Abou-Jaoudé, A; Casse, F; Pascal, M C

1978-04-06

Mutants of E. coli, completely devoid of nitrite reductase activity with glucose or formate as donor were studied. Biochemical analysis indicates that they are simultaneously affected in nitrate reductase, nitrite reductase, fumarate reductase and hydrogenase activities as well as in cytochrome C552 biosynthesis. The use of an antiserum specific for nitrate reductase shows that the nitrate reductase protein is probably missing. A single mutation is responsible for this phenotype: the gene affected, nir R, is located close to tyr R i.e. at 29 min on the chromosomal map.

Investigation on reactivity of iron nickel oxides in chemical looping dry reforming

International Nuclear Information System (INIS)

Huang, Zhen; He, Fang; Chen, Dezhen; Zhao, Kun; Wei, Guoqiang; Zheng, Anqing; Zhao, Zengli; Li, Haibin

2016-01-01

Iron nickel oxides as oxygen carriers were investigated to clarify the reaction mechanism of NiFe_2O_4 material during the chemical looping dry reforming (CLDR) process. The thermodynamic analysis showed that metallic Fe can be oxidized into Fe_3O_4 by CO_2, but metallic Ni cannot. The oxidizability of the four oxygen carriers was in the order of NiO > synthetic NiFe_2O_4 spinel > NiO-Fe_2O_3 mixed oxides > Fe_2O_3, and the reducibility sequence of their reduced products was synthetic NiFe_2O_4 spinel > NiO-Fe_2O_3 mixed oxides > Fe_2O_3 > NiO. The NiO showed the best oxidizability but it was easy to cause CH_4 cracking and its reduced product (Ni) did not recover lattice oxygen under CO_2 atmosphere. It only produced 74 mL CO for 1 g Fe_2O_3 during the CO_2 reforming because of its weak oxidizability. The Redox ability of synthetic NiFe_2O_4 was obvious higher than that of NiO-Fe_2O_3 mixed oxides due to the synergistic effect of metallic Fe-Ni in the spinel structure. 1 g synthetic NiFe_2O_4 can produce 238 mL CO, which was twice higher than that of 1 g NiO-Fe_2O_3 mixed oxides (111 mL). A part of Fe element was divorced from the NiFe_2O_4 spinel structure after one cycle, which was the major reason for degradation of reactivity of NiFe_2O_4 oxygen carrier. - Highlights: • A synergistic effect of Fe/Ni can improve the reactivity of oxygen carrier (OC). • The oxidizability sequence of four OCs is NiO > NiFe_2O_4 > mixed NiO + Fe_2O_3 > Fe_2O_3. • The reducibility sequence of four OCs is NiFe_2O_4 > mixed NiO + Fe_2O_3 > Fe_2O_3 > NiO. • The formation of Fe (Ni) alloy phase facilitates more CO_2 reduced into CO. • Part of Fe is divorced from the spinel structure, leading to the degeneration of OC reactivity.

Photosynthetic versatility in the genome of Geitlerinema sp. PCC 9228 (formerly Oscillatoria limnetica ‘Solar Lake’, a model anoxygenic photosynthetic cyanobacterium

Directory of Open Access Journals (Sweden)

Sharon L Grim

2016-10-01

Full Text Available Anoxygenic cyanobacteria that use sulfide as the electron donor for photosynthesis are a potentially influential but poorly constrained force on Earth’s biogeochemistry. Their versatile metabolism may have boosted primary production and nitrogen cycling in euxinic coastal margins in the Proterozoic. In addition, they represent a biological mechanism for limiting the accumulation of atmospheric oxygen, especially before the Great Oxidation Event and in the low-oxygen conditions of the Proterozoic. In this study, we describe the draft genome sequence of Geitlerinema sp. PCC 9228, formerly Oscillatoria limnetica ‘Solar Lake’, a mat-forming diazotrophic cyanobacterium that can switch between oxygenic photosynthesis and sulfide-based anoxygenic photosynthesis. Geitlerinema possesses three variants of psbA, which encodes protein D1, a core component of the photosystem II reaction center. Phylogenetic analyses indicate that one variant is closely affiliated with cyanobacterial psbA genes that code for a D1 protein used for oxygen-sensitive processes. Another version is phylogenetically similar to cyanobacterial psbA genes that encode D1 proteins used under microaerobic conditions, and the third variant may be cued to high light and/or elevated oxygen concentrations. Geitlerinema has the canonical gene for sulfide quinone reductase (SQR used in cyanobacterial anoxygenic photosynthesis and a putative transcriptional regulatory gene in the same operon. Another operon with a second, distinct sqr and regulatory gene is present, and is phylogenetically related to sqr genes used for high sulfide concentrations. The genome has a comprehensive nif gene suite for nitrogen fixation, supporting previous observations of nitrogenase activity. Geitlerinema possesses a bidirectional hydrogenase rather than the uptake hydrogenase typically used by cyanobacteria in diazotrophy. Overall, the genome sequence of Geitlerinema sp. PCC 9228 highlights potential

Photosynthetic Versatility in the Genome of Geitlerinema sp. PCC 9228 (Formerly Oscillatoria limnetica ‘Solar Lake’), a Model Anoxygenic Photosynthetic Cyanobacterium

Science.gov (United States)

Grim, Sharon L.; Dick, Gregory J.

2016-01-01

Anoxygenic cyanobacteria that use sulfide as the electron donor for photosynthesis are a potentially influential but poorly constrained force on Earth’s biogeochemistry. Their versatile metabolism may have boosted primary production and nitrogen cycling in euxinic coastal margins in the Proterozoic. In addition, they represent a biological mechanism for limiting the accumulation of atmospheric oxygen, especially before the Great Oxidation Event and in the low-oxygen conditions of the Proterozoic. In this study, we describe the draft genome sequence of Geitlerinema sp. PCC 9228, formerly Oscillatoria limnetica ‘Solar Lake’, a mat-forming diazotrophic cyanobacterium that can switch between oxygenic photosynthesis and sulfide-based anoxygenic photosynthesis (AP). Geitlerinema possesses three variants of psbA, which encodes protein D1, a core component of the photosystem II reaction center. Phylogenetic analyses indicate that one variant is closely affiliated with cyanobacterial psbA genes that code for a D1 protein used for oxygen-sensitive processes. Another version is phylogenetically similar to cyanobacterial psbA genes that encode D1 proteins used under microaerobic conditions, and the third variant may be cued to high light and/or elevated oxygen concentrations. Geitlerinema has the canonical gene for sulfide quinone reductase (SQR) used in cyanobacterial AP and a putative transcriptional regulatory gene in the same operon. Another operon with a second, distinct sqr and regulatory gene is present, and is phylogenetically related to sqr genes used for high sulfide concentrations. The genome has a comprehensive nif gene suite for nitrogen fixation, supporting previous observations of nitrogenase activity. Geitlerinema possesses a bidirectional hydrogenase rather than the uptake hydrogenase typically used by cyanobacteria in diazotrophy. Overall, the genome sequence of Geitlerinema sp. PCC 9228 highlights potential cyanobacterial strategies to cope with

Enzymatic recovery of platinum (IV) from industrial wastewater using ...

African Journals Online (AJOL)

SERVER

2008-04-17

Apr 17, 2008 ... A hydrogenase from sulphate reducing consortium was purified by a ... diation. The present work reports on the use of SRB cells from the resting .... hydrogenase fraction had a half life of 35 minutes (t1/2 = 35). ... balance (Hughes and Poole, 1997). ... an enzyme efficiency (Kcat) (turnover number) of 3.6 s-1.

Model and Subcomponent Development for a Pulse-Combustor-Driven Microgenerator

Science.gov (United States)

2004-08-31

sputtering of thin magnetic and dielectric layers [4]; and mechanical lamination of polymer -coated NiFe foils [5]. Although these approaches have...photomicrograph of the fabricated device is given in Figure 4.2-6. 3d solenoid- like Cu coil EPOXY SU8 NIFE LAMINATE D CORE Figure 4.2-6 Photomicrograph

Sol-gel synthesis and characterization of single-phase Ni ferrite nanoparticles dispersed in SiO2 matrix

International Nuclear Information System (INIS)

Nadeem, K.; Traussnig, T.; Letofsky-Papst, I.; Krenn, H.; Brossmann, U.; Wuerschum, R.

2010-01-01

Nanoparticles of NiFe 2 O 4 dispersed in SiO 2 (25 wt%) matrix were synthesized by sol-gel method using tetraethyl orthosilicate (TEOS), as a precursor for SiO 2 . The sol-gel method for nanocomposites normally provides multi-phase nanoparticles. We investigated by a synopsis of different analysis methods, X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR) and SQUID-magnetometry, how the various chemical phases are transformed to a single-phase spinel structure during the various stages of annealing from 300 to 900 o C. We have developed a full phase diagram of chemical phases as a function of annealing temperature. The average particle size lies in the range 16-27 nm. The chemical phases formed below 900 o C are NiFe, NiO, γ-Fe 2 O 3 , α-Fe 2 O 3 , and NiFe 2 O 4 , respectively. The role of the TEOS prepared SiO 2 matrix is to restrict the particle size in a small range in order to rule out particle size effects. In the mid-infrared, a shift of the vibrational Fe-O bond is observed from 568 to 586 cm -1 for annealing between 500 and 700 o C which indicates an increasing NiFe 2 O 4 phase formation. A systematic study of coercivity field (ranging from 32 to 200 Oe) and saturation magnetic moment (ranging from 12.2 to 32.1 emu/g) for differently annealed samples supports our findings about the evolution of single-phase NiFe 2 O 4 at 900 o C. The opposite trend of saturation magnetic moment and coercivity with respect to annealing temperature clearly separates the different phases of metallic, antiferromagnetic, and finally single-phase spinel NiFe 2 O 4 .

Journal of Chemical Sciences | Indian Academy of Sciences

Indian Academy of Sciences (India)

The NiFe2O4-AC-modified glassy carbon electrode (GCE) showed excellent electrocatalytic activity towards DA compared to NiFe2O4/GCE and AC/GCE. This is attributed to the synergistic action and the large surface area of the nanocomposite.Differential pulse voltammetry (DPV) was employed for the detection of DA ...

A study on electrodeposited NixFe1−x alloy films

Indian Academy of Sciences (India)

Several techniques such as X-ray diffraction [9], VSM. [10], Mössbauer spectroscopy [11], four-point probe [12] etc. are used to investigate the crystallographic, magnetic and magnetotransport properties of NiFe systems. In this study our aim is to prepare NiFe alloy films relatively thicker (in µm scale) than those reported in ...

Bio-Prospecting for Improved Hydrogen-Producing Organisms

Science.gov (United States)

2011-06-01

including soil, sediment, seawater, thermophilic compost, and geothermal sites. Cyanobacterial production of hydrogen and oxygen in natural habitats...Berelson and Corsetti at USC-, experiments were conducted to analyze the hydrogenase enzymes and microbial community of a novel cyanobacterially...another. Future work should involve rate and flux experiments, further investigation of the hydrogenase enzymes involved and follow up work with D:H ratio

Pulsed laser deposition of epitaxial YBa{sub 2}Cu{sub 3}O{sub 7-y}/oxide multilayers onto textured NiFe substrates for coated conductor applications

Energy Technology Data Exchange (ETDEWEB)

Tomov, R I [Department of Materials Science and IRC in Superconductivity, University of Cambridge, Cambridge (United Kingdom); Kursumovic, A; Kang, D -J; Glowacki, B A; Evetts, J E [Department of Materials Science and IRC in Superconductivity, University of Cambridge, Cambridge (United Kingdom); Majoros, M [IRC in Superconductivity, University of Cambridge, Cambridge (United Kingdom)

2002-04-01

Pulsed laser depositions of double-buffer and triple-buffer YBa{sub 2}Cu{sub 3}O{sub 7-y} (YBCO)/Y{sub 2}O{sub 3}(YSZ)/CeO{sub 2} heterostructures have been performed in situ onto commercially available biaxially textured NiFe 50%/50% tape. The deposition in the forming gas (4% H{sub 2}/Ar) from a CeO{sub 2} target and the deposition in vacuum from a CeO{sub 2}:Pd composite target have been explored as two possible routes for cube-on-cube growth of the first buffer layer. The influence of the critical processing parameters on the texture is investigated and some of the issues involved in the reduction of NiO (111) and the formation of cube-on-cube NiO (200) growth are discussed. X-ray diffraction has been used for texture evaluation of the substrate and subsequent deposited layers. The substrate-buffer interface region has been studied by focused ion beam cross section electron microscopy. Both the buffers and YBCO layers show biaxial alignment with {omega} and {phi} scans having optimum YBCO full width at half maximum (FWHM) values of 4.3 deg. and 8.8 deg., respectively. The morphology has been characterized using atomic force microscopy and scanning electron microscopy. The value of T{sub c} (onset) has been measured at 90 K ({delta}T{sub c}=10 K). The critical current density, J{sub c}, has been measured by transport measurements and magnetic measurements performed in a dc SQUID magnetometer. (author)

CoCr/NiFe double layers studied by FMR and VSM

NARCIS (Netherlands)

Stam, M.T.H.C.W.; Gerritsma, G.J.; Lodder, J.C.; Popma, T.J.A.

1987-01-01

CoCr/NiFe double layers were investigated by FMR and VSM. The FMR linewidth of NiFe of the double layer is about twice that of a single NiFe layer. The resonance field is the same in both cases. Using the VSM the coercive field of the CoCr layer of the double layer was obtained. It is approximately

Biomimetic hydrogen production

Energy Technology Data Exchange (ETDEWEB)

Krassen, Henning

2009-05-15

Hydrogenases catalyze the reduction of protons to molecular hydrogen with outstanding efficiency. An electrode surface which is covered with active hydrogenase molecules becomes a promising alternative to platinum for electrochemical hydrogen production. To immobilize the hydrogenase on the electrode, the gold surface was modified by heterobifunctional molecules. A thiol headgroup on one side allowed the binding to the gold surface and the formation of a self-assembled monolayer. The other side of the molecules provided a surface with a high affinity for the hydrogenase CrHydA1 from Chlamydomonas reinhardtii. With methylviologen as a soluble energy carrier, electrons were transferred from carboxy-terminated electrodes to CrHydA1 and conducted to the active site (H-cluster), where they reduce protons to molecular hydrogen. A combined approach of surface-enhanced infrared absorption spectroscopy, gas chromatography, and surface plasmon resonance allowed quantifying the hydrogen production on a molecular level. Hydrogen was produced with a rate of 85 mol H{sub 2} min{sup -1} mol{sup -1}. On a 1'- benzyl-4,4'-bipyridinum (BBP)-terminated surface, the electrons were mediated by the monolayer and no soluble electron carrier was necessary to achieve a comparable hydrogen production rate (approximately 50% of the former system). The hydrogen evolution potential was determined to be -335 mV for the BBP-bound hydrogenase and -290 mV for the hydrogenase which was immobilized on a carboxy-terminated mercaptopropionic acid SAM. Therefore, both systems significantly reduce the hydrogen production overpotential and allow electrochemical hydrogen production at an energy level which is close to the commercially applied platinum electrodes (hydrogen evolution potential of -270 mV). In order to couple hydrogen production and photosynthesis, photosystem I (PS1) from Synechocystis PCC 6803 and membrane-bound hydrogenase (MBH) from Ralstonia eutropha were bound to each other

Renewable Bio-Solar Hydrogen Production From Robust Oxygenic Phototrophs: The Second Generation

Science.gov (United States)

2014-07-14

adds a layer of complexity due to oxygen’s natural prevalence in air. Furthermore, oxygenic photosynthesis, the most effective photosynthesis, is...between the oxic and anoxic layers as well as the anaerobic water and benthic layers . (c) We have tested the hypothesis that sequence variations...both hydrogenase and urease in Helicobacter pylori, Mol Microbiol, 39 (2001) 176-182. [199] L. Forzi, R.G. Sawers, Maturation of [NiFe]-hydrogenases

Damage buildup and edge dislocation mobility in equiatomic multicomponent alloys

Science.gov (United States)

Granberg, F.; Djurabekova, F.; Levo, E.; Nordlund, K.

2017-02-01

A new class of single phase metal alloys of equal atomic concentrations has shown very promising mechanical properties and good corrosion resistance. Moreover, a significant reduction in damage accumulation during prolonged irradiation has also been observed in these equiatomic multicomponent alloys. A comparison of elemental Ni with the two component NiFe- and the three component NiCoCr-alloy showed a substantial reduction in damage in both alloys, and an even larger difference was seen if only larger clusters were considered. One of the factors limiting the damage build-up in the alloys compared to the elemental material was seen to be dislocation mobility (Granberg et al., 2016). In this Article, we focus on a more thorough investigation of the mobility of edge dislocations in different cases of the Ni-, NiFe- and NiCoCr-samples. We find that even though the saturated amount of defects in the alloys is lower than in elemental Ni, the defect buildup in the early stages is faster in the alloys. We also find that the dislocation mobility in NiFe is lower than in Ni, at low stresses, and that the onset stress in NiFe is higher than in Ni. The same phenomenon was seen in comparison between NiFe and NiCoCr, since the three component alloy had lower dislocation mobility and higher onset stress. The dislocation velocity in elemental Ni plateaued out just under the forbidden velocity, whereas the alloys showed a more complex behaviour.

Biological H{sub 2} from syngas and from H{sub 2}O

Energy Technology Data Exchange (ETDEWEB)

Weaver, P.; Maness, P.C.; Markov, S.; Martin, S. [National Renewable Energy Lab., Golden, CO (United States)

1996-10-01

The two stand-alone objectives of the research are to economically produce neat H{sub 2} in the near term from biomass (thermally gasified to syngas) and in the mid term from H{sub 2}O using cyanobacteria or algae with an oxygen-tolerant bacterial hydrogenase. Photosynthetic bacteria have four different terminal enzymes that mediate their H{sub 2} metabolisms-nitrogenase, uptake hydrogenase, fermentative hydrogenase, and carbon monoxide-linked hydrogenase. Each has been microbiologically and biochemically examined for their potential to specifically generate H{sub 2} in large-scale processes. Based on measurements of maximal activities, stabilities, energy requirements, equilibria, and partial pressures of the H{sub 2} producing reactions, the CO-linked hydrogenase is easily the most suited for practical applications. The enzyme mediates H{sub 2} production from CO at rates up to 1.5 mmol/min/g cell dry weight at near ambient temperature and pressure. Hydrogen can be produced and evolved at linear rates up to at least 2 atmospheres of partial pressure (100% CO). The rate-limiting step with high cell density suspensions is the mass transfer of CO into the aqueous phase. Bioreactor designs have been examined which enhance the mass transfer. Hollow-fiber bioreactors with bacterial cells immobilized on the fiber surfaces evolve H{sub 2} at ambient pressure at rates of about 0.3-0.7 mmol/min/g cdw. One such reactor has been producing H{sub 2} from CO continuously for 9 months with only occasional changes of liquid medium. A trickle-filter reactor with bacteria immobilized on beads removed from a bulk water phase and a pumped-bubble coil reactor with bacteria in suspension are also being examined.

Ferrites nanoparticles MFe2O4 (M = Ni and Zn: hydrothermal synthesis and magnetic properties

Directory of Open Access Journals (Sweden)

Pérez Mazariego, J. L.

2008-06-01

Full Text Available MFe2O4 (M = Ni and Zn nanoparticles were prepared by the hydrothermal method. The obtained samples were characterized by X-ray and electron diffraction, Scanning and Transmission Electron Microscopy and Mössbauer spectroscopy. The transmission images show homogeneous shape and particle size ranging from 10 to 40 nm, depending on the nature of the M cation. Mössbauer spectroscopy yields to a ratio of occupancy between the A and B sites of 0.7 in the case of NiFe2O4 oxide. DC magnetization (2-300 K measurements reveal a superparamagnetic behaviour for the ZnFe2O4 sample with a blocking temperature of 20 K. By contrast, in the case of the NiFe2O4 ferrite the blocking temperature appears to be above 300 K and at lower temperature, it shows a ferrimagnetic behaviour arising from the superexchange interactions that take place in this inverse spinel. Mössbauer spectroscopy results confirm the bulk magnetic measurements.Se han preparado mediante el método hidrotermal nanopartículas de ferritas MFe2O4 (M = Ni, Zn. Las muestras obtenidas fueron caracterizadas mediante difracción de rayos X y electrones, microscopía electrónica de transmisión y barrido y espectroscopia Mössbauer. Las imágenes de transmisión muestran partículas de forma y tamaño homogéneo de 10 a 40 nm según la naturaleza del catión M. La espectroscopia Mössbauer revela una relación de ocupación entre los sitios A y B por los átomos de hierro de 0.7 en el caso del óxido NiFe2O4. Las medidas de magnetización DC (2 – 300 K muestran un comportamiento superparamagnético para la muestra ZnFe2O4 con una temperatura de bloqueo de 20 K. En el caso de las nanopartículas de NiFe2O4 la temperatura de bloqueo parece estar por encima de los 300 K mostrando por debajo de la misma, comportamiento ferrimagnético provocado por las interacciones de superintercambio que tienen lugar en esta espinela inversa. Los resultados de espectroscopia Mössbauer confirman los datos de las

Synthesis of NiFe2O4 with PEG as Template Via Hydrothermal Method%PEG为软模板水热法合成NiFe2O4

Institute of Scientific and Technical Information of China (English)

张俊玲; 杨巧珍; 王晶; 滕红霞

2012-01-01

以聚乙二醇(PEG)为软模板,采用水热法合成了尖晶石型NiFe2O4纳米晶,考察了PEG分子量对样品的影响,并对样品进行了X射线衍射,振动样品磁强计,扫描电镜,低温氮吸脱附和原子发射光谱表征.结果表明合成的NiFe2O4纳米晶具有尖晶石结构且粒度分布较为均匀.以PEG-400为软模板水热合成的样品粒度小、比表面积较大、饱和磁化强度较高；PEG-1500合成的样品粒度稍大、饱和磁化强度较高.%NiFe2O4 nanocrystals were synthesized by hydrothermal method with polyethylene glycol (PEG) as a soft template. The effect of PEG molecular weight on properties of the sample was investigated. The samples were characterized by XRD, VSM.SEM.BET and ICP. The results show that as-synthesized NiFe2O4 nanocrystals with spinel cyrstal structure and unifor-mer particle distribution. The sample synthesized with PEG-400 as soft template has small particle size , higher specific surface and saturation magnetization ; as-synthesized sample with PEG-1500 has larger particle size and higher saturation magnetization.

Flexibility of syntrophic enzyme systems in Desulfovibrio species ensures their adaptation capability to environmental changes.

Science.gov (United States)

Meyer, Birte; Kuehl, Jennifer V; Deutschbauer, Adam M; Arkin, Adam P; Stahl, David A

2013-11-01

The mineralization of organic matter in anoxic environments relies on the cooperative activities of hydrogen producers and consumers obligately linked by interspecies metabolite exchange in syntrophic consortia that may include sulfate reducing species such as Desulfovibrio. To evaluate the metabolic flexibility of syntrophic Desulfovibrio to adapt to naturally fluctuating methanogenic environments, we studied Desulfovibrio alaskensis strain G20 grown in chemostats under respiratory and syntrophic conditions with alternative methanogenic partners, Methanococcus maripaludis and Methanospirillum hungatei, at different growth rates. Comparative whole-genome transcriptional analyses, complemented by G20 mutant strain growth experiments and physiological data, revealed a significant influence of both energy source availability (as controlled by dilution rate) and methanogen on the electron transfer systems, ratios of interspecies electron carriers, energy generating systems, and interspecies physical associations. A total of 68 genes were commonly differentially expressed under syntrophic versus respiratory lifestyle. Under low-energy (low-growth-rate) conditions, strain G20 further had the capacity to adapt to the metabolism of its methanogenic partners, as shown by its differing gene expression of enzymes involved in the direct metabolic interactions (e.g., periplasmic hydrogenases) and the ratio shift in electron carriers used for interspecies metabolite exchange (hydrogen/formate). A putative monomeric [Fe-Fe] hydrogenase and Hmc (high-molecular-weight-cytochrome c3) complex-linked reverse menaquinone (MQ) redox loop become increasingly important for the reoxidation of the lactate-/pyruvate oxidation-derived redox pair, DsrC(red) and Fd(red), relative to the Qmo-MQ-Qrc (quinone-interacting membrane-bound oxidoreductase; quinone-reducing complex) loop. Together, these data underscore the high enzymatic and metabolic adaptive flexibility that likely sustains

Formate dehydrogenases and hydrogenases in syntrophic propionate-oxidizing communities : gene analysis and transcritional profiling

NARCIS (Netherlands)

Worm, P.

2010-01-01

Many places on earth are without oxygen (anaerobic) such as rice paddy fields, swamps
and sediments of freshwater lakes and oceans. When oxygen, nitrate or other electron
acceptors are not present, organic material is degraded to carbon dioxide and methane
by mixed microbial

Screening of NiFe₂O₄ Nanoparticles as Oxygen Carrier in Chemical Looping Hydrogen Production

DEFF Research Database (Denmark)

Liu, Shuai; He, Fang; Huang, Zhen

2016-01-01

) methods were used to prepare NiFe2O4 oxygen carriers. Samples were characterized by X-ray diffraction (XRD), Raman spectroscopy, scanning electron microscopy (SEM), X-ray photoelectron spectroscopy (XPS), Brunauer-Emmett-Teller (BET) surface area measurement, as well as Barrett-Joyner-Halenda (BJH......The objective of this paper is to systematically investigate the influences of different preparation methods on the properties of NiFe2O4 nanoparticles as oxygen carrier in chemical looping hydrogen production (CLH). The solid state (SS), coprecipitation (CP), hydrothermal (HT), and sol-gel (SG...... gas (24% H2 + 24% CO + 12% CO2 + N2 balance), then reacted with steam to produce H2, and finally fully oxidized by air. The NiFe2O4 oxygen carrier prepared by the sol gel method showed the best capacity for hydrogen production and the highest recovery degree of lattice oxygen, in agreement...

Selected Test Results from the Encell Technology Nickel Iron Battery

Energy Technology Data Exchange (ETDEWEB)

Ferreira, Summer Kamal Rhodes [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Advanced Power Sources R& D; Baca, Wes Edmund [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Advanced Power Sources R& D; Avedikian, Kristan [Encell Technology, Alachua, FL (United States)

2014-09-01

The performance of the Encell Nickel Iron (NiFe) battery was measured. Tests included capacity, capacity as a function of rate, capacity as a function of temperature, charge retention (28-day), efficiency, accelerated life projection, and water refill evaluation. The goal of this work was to evaluate the general performance of the Encell NiFe battery technology for stationary applications and demonstrate the chemistry's capabilities in extreme conditions. Test results have indicated that the Encell NiFe battery technology can provide power levels up to the 6C discharge rate, ampere-hour efficiency above 70%. In summary, the Encell batteries have met performance metrics established by the manufacturer. Long-term cycle tests are not included in this report. A cycle test at elevated temperature was run, funded by the manufacturer, which Encell uses to predict long-term cycling performance, and which passed their prescribed metrics.

Damage buildup and edge dislocation mobility in equiatomic multicomponent alloys

Energy Technology Data Exchange (ETDEWEB)

Granberg, F., E-mail: fredric.granberg@helsinki.fi [Department of Physics, P.O. Box 43, FIN-00014 University of Helsinki (Finland); Djurabekova, F. [Department of Physics, P.O. Box 43, FIN-00014 University of Helsinki (Finland); Helsinki Institute of Physics, P.O. Box 43, FIN-00014 University of Helsinki (Finland); Levo, E.; Nordlund, K. [Department of Physics, P.O. Box 43, FIN-00014 University of Helsinki (Finland)

2017-02-15

Highlights: • We studied the damage buildup in equiatomic multicomponent alloys by MD simulations. • Edge dislocation mobility was lower in the studied alloys compared to elemental Ni. • Damage buildup in alloys saturated at lower levels than in elemental Ni. • Initial damage buildup is faster in alloys compared to elemental Ni. - Abstract: A new class of single phase metal alloys of equal atomic concentrations has shown very promising mechanical properties and good corrosion resistance. Moreover, a significant reduction in damage accumulation during prolonged irradiation has also been observed in these equiatomic multicomponent alloys. A comparison of elemental Ni with the two component NiFe- and the three component NiCoCr-alloy showed a substantial reduction in damage in both alloys, and an even larger difference was seen if only larger clusters were considered. One of the factors limiting the damage build-up in the alloys compared to the elemental material was seen to be dislocation mobility (Granberg et al., 2016). In this Article, we focus on a more thorough investigation of the mobility of edge dislocations in different cases of the Ni-, NiFe- and NiCoCr-samples. We find that even though the saturated amount of defects in the alloys is lower than in elemental Ni, the defect buildup in the early stages is faster in the alloys. We also find that the dislocation mobility in NiFe is lower than in Ni, at low stresses, and that the onset stress in NiFe is higher than in Ni. The same phenomenon was seen in comparison between NiFe and NiCoCr, since the three component alloy had lower dislocation mobility and higher onset stress. The dislocation velocity in elemental Ni plateaued out just under the forbidden velocity, whereas the alloys showed a more complex behaviour.

Photoproduction of hydrogen - A potential system of solar energy bioconversion

Energy Technology Data Exchange (ETDEWEB)

Das, V S.R.

1979-10-01

The photoproduction of hydrogen from water utilizing the photosynthetic capacity of green plants is discussed as a possible means of solar energy conversion. Advantages of the biological production of H/sub 2/ over various physical and chemical processes are pointed out, and the system used for the production of hydrogen by biological agents, which comprises the photosynthetic electron transport chain, ferredoxin and hydrogenase, is examined in detail. The various types of biological hydrogen production systems in bacteria, algae, symbiotic systems and isolated chloroplast-ferredoxin-hydrogenase systems are reviewed. The limitations and the scope for further improvement of the promising symbiotic Azolli-Anabena azollae and chloroplast-ferredoxin-hydrogenase are discussed, and it is concluded that future research should concern itself with the identification of the environmental conditions that would maximize solar energy conversion efficiency, the elimination of the oxygen inhibition of biological hydrogen production, and the definition of the metabolic state for the maximal production of hydrogen.

A novel synthesis of magnetic and photoluminescent graphene quantum dots/MFe2O4 (M = Ni, Co) nanocomposites for catalytic application

Science.gov (United States)

Naghshbandi, Zhwan; Arsalani, Nasser; Zakerhamidi, Mohammad Sadegh; Geckeler, Kurt E.

2018-06-01

In recent year, the research is focused on the nanostructured catalyst with increase physiochemical properties. Herein, Different magnetic nanocomposites of graphene quantum dots (GQD) and MFe2O4 (M = Ni, Co) with intrinsic photoluminescent and ferromagnetic properties were synthesized by a convenient co-precipitation method. The structure, morphology, and properties of these nanocomposites as well as the catalytic activity of the nanocomposites for the reduction of p-nitrophenol were investigated. The catalytic activity was found to be in the order of NiFe2O4/GQD > CoFe2O4/GQD > NiFe2O4 > CoFe2O4. The sample NiFe2O4/GQD exhibited the best catalytic activity with an apparent rate constant of 3.56 min-1 and a reduction completion time to p-aminophenol of 60 s. The catalysts can be reused by a magnetic field and display good stability, which can be recycled for six successive experiment with a conversion percentage of more than 95%. These results demonstrate that the nanocomposite NiFe2O4/GQD is an efficient catalyst for the reduction of p-nitrophenol compound. Also, the new nanocomposites have shown a significant reduction in the direct and indirect energy bandgaps when compared to pure GQD and the corresponding magnetic metal oxides.

Density functional theory study on the structures, electronic and magnetic properties of the MFe3n‑1O4n (n = 1–3) (M=Mn, Co and Ni) clusters

Science.gov (United States)

Li, Zhi; Zhao, Zhen; Wang, Qi; Yin, Xi-tao

2018-04-01

The structures, electronic and magnetic properties of the MFe3n‑1O4n (n = 1–3) (M=Mn, Co and Ni) clusters are obtained by using the GGA-PBE functional. The results found that the CoFe3n‑1O4n (n = 1–3) clusters are more stable than the corresponding NiFe3n‑1O4n and MnFe3n‑1O4n clusters. The NiFe2O4, MnFe5O8 and CoFe5O8 clusters have higher kinetic stability than their neighbors. The average magnetic moments of MFe3n‑1O4n (n = 1–3) (M=Mn, Co and Ni) clusters are successively: NiFe3n‑1O4n > CoFe3n‑1O4n > MnFe3n‑1O4n. For NiFe3n‑1O4n and CoFe3n‑1O4n clusters, the average magnetic moments are decreased with the cluster size increasing while for MnFe3n‑1O4n, the opposite situation is occur. The difference of 3d orbital electrons of M (M=Mn, Co and Ni) atoms influence the magnetic properties of MFe3n‑1O4n clusters.

Occurrence and characterisation of the hydrogen-evolving enzyme in Frankia sp.

Energy Technology Data Exchange (ETDEWEB)

Mohapatra, A.; Leul, M.; Sellstedt, A. [Umeaa Plant Science Centre, Department of Plant Physiology, Umeaa University, S-901 87 Umeaa (Sweden); Sandstroem, G. [Karolinska Institutet, Department of Laboratory Medicine, Division of Clinical Bacteriology, Karelinska University Hospital, Huddinge, S-141 86 Stockholm (Sweden)

2006-09-15

An increase in hydrogen evolution from the hydrogen-evolving enzyme in the actinomycete Frankia was recorded in the presence of nickel. Immunogold localisation analysis of the intracellular distribution of hydrogenase proteins indicated that they were evenly distributed in the membranes and cytosol of both hyphae and vesicles. In addition, molecular characterisation of the hydrogen-evolving enzyme at the proteomic level, using two-dimensional gel electrophoresis combined with mass spectrometry, confirmed that the Frankia hydrogen-evolving enzyme is similar to the cyanobacterial bidirectional hydrogenase of Anabena siamensis. (author)

Systems Level Approaches to Understanding and Manipulating Heterocyst Differentiation in Nostoc Punctiforme: Sites of Hydrogenase and Nitrogenase Synthesis and Activity

Energy Technology Data Exchange (ETDEWEB)

Meeks, John C. [University of California, Davis, CA (United States)

2015-04-02

Heterocysts are specialized cells that establish a physiologically low oxygen concentration; they function as the sites of oxygen-sensitive nitrogen fixation and hydrogen metabolism in certain filamentous cyanobacteria. They are present at a frequency of less than 10% of the cells and singly in a nonrandom spacing pattern in the filaments. The extent of differential gene expression during heterocyst differentiation was defined by DNA microarray analysis in wild type and mutant cultures of Nostoc punctiforme. The results in wild-type cultures identified two groups of genes; approximately 440 that are unique to heterocyst formation and function, and 500 that respond positively and negatively to the transient stress of nitrogen starvation. Nitrogen fixation is initiated within 24 h after induction, but the cultures require another 24 h before growth is reinitiated. Microarray analyses were conducted on strains with altered expression of three genes that regulate the presence and spacing of heterocysts in the filaments; loss of function or over expression of these genes increases the heterocyst frequency 2 to 3 fold compared to the wild-type. Mutations in the genes hetR and hetF result in the inability to differentiate heterocysts, whereas over expression of each gene individually yields multiple contiguous heterocysts at sites in the filaments; they are positive regulatory elements. Mutation of the gene patN results in an increase in heterocysts frequency, but, in this case, the heterocysts are singly spaced in the filaments with a decrease in the number of vegetative cells in the interval between heterocysts; this is a negative regulatory element. However, over expression of patN resulted in the wild-type heterocyst frequency and spacing pattern. Microarray results indicated HetR and HetF influence the transcription of a common set of about 395 genes, as well as about 350 genes unique to each protein. HetR is known to be a transcriptional regulator and HetF is

Biohydrogen production from soluble condensed molasses fermentation using anaerobic fermentation

Energy Technology Data Exchange (ETDEWEB)

Lay, Chyi-How; Lin, Chiu-Yue [Department of Environmental Engineering and Science, Feng Chia University, Taichung 40724 (China); Wu, Jou-Hsien; Hsiao, Chin-Lang [Department of Water Resource Engineering, Feng Chia University (China); Chang, Jui-Jen [Department of Life Sciences, National Chung Hsing University (China); Chen, Chin-Chao [Environmental Resources Laboratory, Department of Landscape Architecture, Chungchou Institute of Technology (China)

2010-12-15

Using anaerobic micro-organisms to convert organic waste to produce hydrogen gas gives the benefits of energy recovery and environmental protection. The objective of this study was to develop a biohydrogen production technology from food wastewater focusing on hydrogen production efficiency and micro-flora community at different hydraulic retention times. Soluble condensed molasses fermentation (CMS) was used as the substrate because it is sacchariferous and ideal for hydrogen production. CMS contains nutrient components that are necessary for bacterial growth: microbial protein, amino acids, organic acids, vitamins and coenzymes. The seed sludge was obtained from the waste activated sludge from a municipal sewage treatment plant in Central Taiwan. This seed sludge was rich in Clostridium sp. A CSTR (continuously stirred tank reactor) lab-scale hydrogen fermentor (working volume, 4.0 L) was operated at a hydraulic retention time (HRT) of 3-24 h with an influent CMS concentration of 40 g COD/L. The results showed that the peak hydrogen production rate of 390 mmol H{sub 2}/L-d occurred at an organic loading rate (OLR) of 320 g COD/L-d at a HRT of 3 h. The peak hydrogen yield was obtained at an OLR of 80 g COD/L-d at a HRT of 12 h. At HRT 8 h, all hydrogenase mRNA detected were from Clostridium acetobutylicum-like and Clostridium pasteurianum-like hydrogen-producing bacteria by RT-PCR analysis. RNA based hydrogenase gene and 16S rRNA gene analysis suggests that Clostridium exists in the fermentative hydrogen-producing system and might be the dominant hydrogen-producing bacteria at tested HRTs (except 3 h). The hydrogen production feedstock from CMS is lower than that of sucrose and starch because CMS is a waste and has zero cost, requiring no added nutrients. Therefore, producing hydrogen from food wastewater is a more commercially feasible bioprocess. (author)

Design of heterogeneous catalysts

DEFF Research Database (Denmark)

Frey, Anne Mette

was inspired by a computational screening, suggesting that alloys such as Ni-Fe, Co-Ni, and Co-Fe should show superior activity to the industrially used nickel catalyst. Especially the Ni-Fe system was considered to be interesting, since such alloy catalysts should be both more active and cheaper than the Ni...... catalyst. The results from the screening were experimentally verified for CO hydrogenation, CO2 hydrogenation, and simultaneous CO and CO2 hydrogenation by bimetallic Ni-Fe catalysts. These catalysts were found to be highly active and selective. The Co-Ni and Co-Fe systems were investigated for CO...... well, and the best catalyst prepared had a C5+ yield almost a factor of two higher than a standard air calcined Co catalyst. In the NH3-SCR reaction it is desirable to develop an active and stable catalyst for NOx removal in automotive applications, since the traditionally used vanadium-based catalyst...

Genomic Characterization of Methanomicrobiales Reveals Three Classes of Methanogens

Energy Technology Data Exchange (ETDEWEB)

Anderson, Iain; Ulrich, Luke E.; Lupa, Boguslaw; Susanti, Dwi; Porat, Iris; Hooper, Sean D.; Lykidis, Athanasios; Sieprawska-Lupa, Magdalena; Dharmarajan, Lakshmi; Goltsman, Eugene; Lapidus, Alla; Saunders, Elizabeth; Han, Cliff; Land, Miriam; Lucas, Susan; Mukhopadhyay, Biswarup; Whitman, William B.; Woese, Carl; Bristow, James; Kyrpides, Nikos

2009-05-01

Methanomicrobiales is the least studied order of methanogens. While these organisms appear to be more closely related to the Methanosarcinales in ribosomal-based phylogenetic analyses, they are metabolically more similar to Class I methanogens. In order to improve our understanding of this lineage, we have completely sequenced the genomes of two members of this order, Methanocorpusculum labreanum Z and Methanoculleus marisnigri JR1, and compared them with the genome of a third, Methanospirillum hungatei JF-1. Similar to Class I methanogens, Methanomicrobiales use a partial reductive citric acid cycle for 2-oxoglutarate biosynthesis, and they have the Eha energy-converting hydrogenase. In common with Methanosarcinales, Methanomicrobiales possess the Ech hydrogenase and at least some of them may couple formylmethanofuran formation and heterodisulfide reduction to transmembrane ion gradients. Uniquely, M. labreanum and M. hungatei contain hydrogenases similar to the Pyrococcus furiosus Mbh hydrogenase, and all three Methanomicrobiales have anti-sigma factor and anti-anti-sigma factor regulatory proteins not found in other methanogens. Phylogenetic analysis based on seven core proteins of methanogenesis and cofactor biosynthesis places the Methanomicrobiales equidistant from Class I methanogens and Methanosarcinales. Our results indicate that Methanomicrobiales, rather than being similar to Class I methanogens or Methanomicrobiales, share some features of both and have some unique properties. We find that there are three distinct classes of methanogens: the Class I methanogens, the Methanomicrobiales (Class II), and the Methanosarcinales (Class III).

Magnetization switching of NiFeSiB free layers for magnetic tunnel junctions

International Nuclear Information System (INIS)

Chun, B.S.; Ko, S.P.; Oh, B.S.; Hwang, J.Y.; Rhee, J.R.; Kim, T.W.; Saito, S.; Yoshimura, S.; Tsunoda, M.; Takahashi, M.; Kim, Y.K.

2006-01-01

Ferromagnetic amorphous Ni 16 Fe 62 Si 8 B 14 layer have been studied as free layers for magnetic tunnel junctions (MTJs) to enhance cell switching performance. Traditional MTJ free layer materials such as NiFe and CoFe were also prepared for switching comparison purposes. Both NiFeSiB and NiFe resulted in an order of magnitude smaller switching fields compared to the CoFe. The switching field was further reduced for the synthetic antiferromagnetic NiFeSiB free layered structure

Effect of Ta buffer and NiFe seed layers on pulsed-DC magnetron sputtered Ir{sub 20}Mn{sub 80}/Co{sub 90}Fe{sub 10} exchange bias

Energy Technology Data Exchange (ETDEWEB)

Oksuezoglu, Ramis Mustafa, E-mail: rmoksuzoglu@anadolu.edu.t [University of Anadolu, Faculty of Engineering and Architecture, Department of Materials Sciences and Engineering, Iki Eyluel Campus, 26555 Eskisehir (Turkey); Yildirim, Mustafa; Cinar, Hakan [University of Anadolu, Faculty of Engineering and Architecture, Department of Materials Sciences and Engineering, Iki Eyluel Campus, 26555 Eskisehir (Turkey); Hildebrandt, Erwin; Alff, Lambert [Department of Materials Sciences, Darmstadt University of Technology, Petersenstrasse 23, D-64287 Darmstadt (Germany)

2011-07-15

A systematic investigation has been done on the correlation between texture, grain size evolution and magnetic properties in Ta/Ni{sub 81}Fe{sub 19}/Ir{sub 20}Mn{sub 80}/Co{sub 90}Fe{sub 10}/Ta exchange bias in dependence of Ta buffer and NiFe seed layer thickness in the range of 2-10 nm, deposited by pulsed DC magnetron sputtering technique. A strong dependence of <1 1 1> texture on the Ta/NiFe thicknesses was found, where the reducing and increasing texture was correlated with exchange bias field and unidirectional anisotropy energy constant at both NiFe/IrMn and IrMn/CoFe interfaces. However, a direct correlation between average grain size in IrMn and H{sub ex} and H{sub c} was not observed. L1{sub 2} phase IrMn{sub 3} could be formed by thickness optimization of Ta/NiFe layers by deposition at room temperature, for which the maximum exchange coupling parameters were achieved. We conclude finally that the coercivity is mainly influenced by texture induced interfacial effects at NiFe/IrMn/CoFe interfaces developing with Ta/NiFe thicknesses. - Research highlights: We discussed the influence of Ta/NiFe thicknesses on structure and grain size in AF layer and texture. A direct correlation between the <1 1 1> texture and exchange coupling was found. A direct relation between average grain size and H{sub ex} and H{sub c} was not observed. L1{sub 2} phase IrMn{sub 3} was formed by deposition at room temperature for Ta (5-6 nm)/NiFe (6-8 nm). We conclude that the coercivity is influenced by order/disorder at NiFe/IrMn/CoFe interfaces.

Genes and Gene Therapy

Science.gov (United States)

... correctly, a child can have a genetic disorder. Gene therapy is an experimental technique that uses genes to ... or prevent disease. The most common form of gene therapy involves inserting a normal gene to replace an ...

Sequencing and promoter analysis of the nifENXorf3orf5fdxAnifQ operon from Azospirillum brasilense Sp7

Directory of Open Access Journals (Sweden)

Potrich D.P.

2001-01-01

Full Text Available A 40-kb DNA region containing the major cluster of nif genes has been isolated from the Azospirillum brasilense Sp7 genome. In this region three nif operons have been identified: nifHDKorf1Y, nifENXorf3orf5fdxAnifQ and orf2nifUSVorf4. The operons containing nifENX and nifUSV genes are separated from the structural nifHDKorf1Y operon by about 5 kb and 10 kb, respectively. The present study shows the sequence analysis of the 6045-bp DNA region containing the nifENX genes. The deduced amino acid sequences from the open reading frames were compared to the nif gene products of other diazotrophic bacteria and indicate the presence of seven ORFs, all reading in the same direction as that of the nifHDKorf1Y operon. Consensus sigma54 and NifA-binding sites are present only in the promoter region upstream of the nifE gene. This promoter is activated by NifA protein and is approximately two-times less active than the nifH promoter, as indicated by the ß-galactosidase assays. This result suggests the differential expression of the nif genes and their respective products in Azospirillum.

A new group in the Leptospirillum clade: cultivation-independent community genomics, proteomics and transcriptomics of the new species Leptospirillum group IV UBA BS.

Energy Technology Data Exchange (ETDEWEB)

Goltsman, Daniela [University of California, Berkeley; Dasari, Mauna [University of California, Berkeley; Thomas, BC [University of California, Berkeley; Shah, Manesh B [ORNL; Verberkmoes, Nathan C [ORNL; Hettich, Robert {Bob} L [ORNL; Banfield, Jillian F. [University of California, Berkeley

2013-01-01

Leptospirillum spp. are widespread members of acidophilic microbial communities that catalyze ferrous iron oxidation, thereby increasing sulfide mineral dissolution rates. These bacteria play important roles in environmental acidification and are harnessed for bioleaching-based metal recovery. Known members of the Leptospirillum clade of the Nitrospira phylum are Leptospirillum ferrooxidans (group I), Leptospirillum ferriphilum and Leptospirillum rubarum (group II), and Leptospirillum ferrodiazotrophum (group III). In the Richmond Mine acid mine drainage (AMD) system, biofilm formation is initiated by L. rubarum; L. ferrodiazotrophum appears in later developmental stages. Here we used community metagenomic data from unusual, thick floating biofilms to identify distinguishing metabolic traits in a rare and uncultivated community member, the new species Leptospirillum group IV UBA BS. These biofilms typically also contain a variety of Archaea, Actinobacteria, and a few other Leptospirillum spp. The Leptospirillum group IV UBA BS species shares 98% 16S rRNA sequence identity and 70% average amino acid identity between orthologs with its closest relative, L. ferrodiazotrophum. The presence of nitrogen fixation and reverse tricarboxylic acid (TCA) cycle proteins suggest an autotrophic metabolism similar to that of L. ferrodiazotrophum, while hydrogenase proteins suggest anaerobic metabolism. Community transcriptomic and proteomic analyses demonstrate expression of a multicopper oxidase unique to this species, as well as hydrogenases and core metabolic genes. Results suggest that the Leptospirillum group IV UBA BS species might play important roles in carbon fixation, nitrogen fixation, hydrogen metabolism, and iron oxidation in some acidic environments.

Lichen symbiosis: nature's high yielding machines for induced hydrogen production.

Directory of Open Access Journals (Sweden)

Aikaterini Papazi

Full Text Available Hydrogen is a promising future energy source. Although the ability of green algae to produce hydrogen has long been recognized (since 1939 and several biotechnological applications have been attempted, the greatest obstacle, being the O2-sensitivity of the hydrogenase enzyme, has not yet been overcome. In the present contribution, 75 years after the first report on algal hydrogen production, taking advantage of a natural mechanism of oxygen balance, we demonstrate high hydrogen yields by lichens. Lichens have been selected as the ideal organisms in nature for hydrogen production, since they consist of a mycobiont and a photobiont in symbiosis. It has been hypothesized that the mycobiont's and photobiont's consumption of oxygen (increase of COX and AOX proteins of mitochondrial respiratory pathways and PTOX protein of chrolorespiration establishes the required anoxic conditions for the activation of the phycobiont's hydrogenase in a closed system. Our results clearly supported the above hypothesis, showing that lichens have the ability to activate appropriate bioenergetic pathways depending on the specific incubation conditions. Under light conditions, they successfully use the PSII-dependent and the PSII-independent pathways (decrease of D1 protein and parallel increase of PSaA protein to transfer electrons to hydrogenase, while under dark conditions, lichens use the PFOR enzyme and the dark fermentative pathway to supply electrons to hydrogenase. These advantages of lichen symbiosis in combination with their ability to survive in extreme environments (while in a dry state constitute them as unique and valuable hydrogen producing natural factories and pave the way for future biotechnological applications.

Lichen Symbiosis: Nature's High Yielding Machines for Induced Hydrogen Production

Science.gov (United States)

Papazi, Aikaterini; Kastanaki, Elizabeth; Pirintsos, Stergios; Kotzabasis, Kiriakos

2015-01-01

Hydrogen is a promising future energy source. Although the ability of green algae to produce hydrogen has long been recognized (since 1939) and several biotechnological applications have been attempted, the greatest obstacle, being the O2-sensitivity of the hydrogenase enzyme, has not yet been overcome. In the present contribution, 75 years after the first report on algal hydrogen production, taking advantage of a natural mechanism of oxygen balance, we demonstrate high hydrogen yields by lichens. Lichens have been selected as the ideal organisms in nature for hydrogen production, since they consist of a mycobiont and a photobiont in symbiosis. It has been hypothesized that the mycobiont’s and photobiont’s consumption of oxygen (increase of COX and AOX proteins of mitochondrial respiratory pathways and PTOX protein of chrolorespiration) establishes the required anoxic conditions for the activation of the phycobiont’s hydrogenase in a closed system. Our results clearly supported the above hypothesis, showing that lichens have the ability to activate appropriate bioenergetic pathways depending on the specific incubation conditions. Under light conditions, they successfully use the PSII-dependent and the PSII-independent pathways (decrease of D1 protein and parallel increase of PSaA protein) to transfer electrons to hydrogenase, while under dark conditions, lichens use the PFOR enzyme and the dark fermentative pathway to supply electrons to hydrogenase. These advantages of lichen symbiosis in combination with their ability to survive in extreme environments (while in a dry state) constitute them as unique and valuable hydrogen producing natural factories and pave the way for future biotechnological applications. PMID:25826211

The Evolution of Dinitrogen Fixation

International Nuclear Information System (INIS)

Broda, E.

1984-01-01

It is argued that nitrogenase originated monophyletically in obligate anaerobes similar to Clostridia. The enzyme system was later inherited, without much change, by photosynthetic bacteria, by prokaryotic plants (blue-greens) and by aerobic bacteria. The hydrogenase function of the enzyme complex preceded the nitrogenase function, and was useful in hydrogen fermentations. The consumption of ATP served to assure disposal of electrons in the form of hydrogen gas. The present need of the enzyme system, whether acting as hydrogenase or as nitrogenase, for ATP may be a relic from the period when the biosphere was still reducing. (author)

Gene expression and gene therapy imaging

International Nuclear Information System (INIS)

Rome, Claire; Couillaud, Franck; Moonen, Chrit T.W.

2007-01-01

The fast growing field of molecular imaging has achieved major advances in imaging gene expression, an important element of gene therapy. Gene expression imaging is based on specific probes or contrast agents that allow either direct or indirect spatio-temporal evaluation of gene expression. Direct evaluation is possible with, for example, contrast agents that bind directly to a specific target (e.g., receptor). Indirect evaluation may be achieved by using specific substrate probes for a target enzyme. The use of marker genes, also called reporter genes, is an essential element of MI approaches for gene expression in gene therapy. The marker gene may not have a therapeutic role itself, but by coupling the marker gene to a therapeutic gene, expression of the marker gene reports on the expression of the therapeutic gene. Nuclear medicine and optical approaches are highly sensitive (detection of probes in the picomolar range), whereas MRI and ultrasound imaging are less sensitive and require amplification techniques and/or accumulation of contrast agents in enlarged contrast particles. Recently developed MI techniques are particularly relevant for gene therapy. Amongst these are the possibility to track gene therapy vectors such as stem cells, and the techniques that allow spatiotemporal control of gene expression by non-invasive heating (with MRI guided focused ultrasound) and the use of temperature sensitive promoters. (orig.)

Functional organization of a single nif cluster in the mesophilic archaeon Methanosarcina mazei strain Gö1

Directory of Open Access Journals (Sweden)

Claudia Ehlers

2002-01-01

Full Text Available The mesophilic methanogenic archaeon Methanosarcina mazei strain Gö1 is able to utilize molecular nitrogen (N2 as its sole nitrogen source. We have identified and characterized a single nitrogen fixation (nif gene cluster in M. mazei Gö1 with an approximate length of 9 kbp. Sequence analysis revealed seven genes with sequence similarities to nifH, nifI1, nifI2, nifD, nifK, nifE and nifN, similar to other diazotrophic methanogens and certain bacteria such as Clostridium acetobutylicum, with the two glnB-like genes (nifI1 and nifI2 located between nifH and nifD. Phylogenetic analysis of deduced amino acid sequences for the nitrogenase structural genes of M. mazei Gö1 showed that they are most closely related to Methanosarcina barkeri nif2 genes, and also closely resemble those for the corresponding nif products of the gram-positive bacterium C. acetobutylicum. Northern blot analysis and reverse transcription PCR analysis demonstrated that the M. mazei nif genes constitute an operon transcribed only under nitrogen starvation as a single 8 kb transcript. Sequence analysis revealed a palindromic sequence at the transcriptional start site in front of the M. mazei nifH gene, which may have a function in transcriptional regulation of the nif operon.

Ferromagnetic resonance study of sputtered NiFe/V/NiFe heterostructures

Energy Technology Data Exchange (ETDEWEB)

Alayo, W., E-mail: willian.rodriguez@ufpel.edu.br [Departamento de Física – IFM, Universidade Federal de Pelotas, 96010-900 Rio Grande do Sul (Brazil); Pelegrini, F. [Instituto de Física, Universidade Federal de Goiás, Goiânia, 74001-970 (Brazil); Baggio-Saitovitch, E. [Centro Brasileiro de Pesquisas Físicas, Rio de Janeiro, RJ, 22290-180 (Brazil)

2015-03-01

The Ni{sub 81}Fe{sub 19}/V/Ni{sub 81}Fe{sub 19} heterostructures has been produced by magnetron sputtering and analyzed by ferromagnetic resonance. Two systems were investigated: the non symmetrical NiFe(50 Å)/V(t)/NiFe(30 Å) trilayers and the symmetrical NiFe(80 Å)/V(t)/NiFe(80 Å) trilayers, with variable ultrathin V thickness t. Ferromagnetic exchange coupling was evidenced for t below 10 Å by the excitation of the optic mode, in the case of the non symmetrical samples, and by the observation of a single resonance mode for the symmetrical trilayers. For larger V thickness, all samples exhibited two modes, which were attributed to the resonance of the individual NiFe layers with different effective magnetizations. The analysis with the equilibrium and resonance conditions provided the exchange coupling constants and effective magnetizations. - Highlights: • We present a study of symmetrical and non symmetrical NiFe/V/NiFe trilayers deposited on Si single crystals by ferromagnetic resonance (FMR) at room temperature. • For the non symmetrical trilayers, the FMR spectra show the optic and acoustic modes for samples with very thin V layer thicknesses, evidencing ferromagnetic exchange coupling, whereas, for larger V thickness, the spectra exhibited two well resolved modes associated to each independent NiFe layer. For the symmetrical trilayers, strong ferromagnetic exchange coupling is evidenced by the observation of a single resonance mode. • The analysis with the equilibrium condition and dispersion relation provides the exchange coupling constants and effective magnetizations.

Ferromagnetic resonance study of structure and relaxation of magnetization in NiFe/Ru superlattices

Energy Technology Data Exchange (ETDEWEB)

Alayo, W., E-mail: willian.rodriguez@ufpel.edu.br [Depto. de Física, Univ. Federal de Pelotas, Campus Universitário, 96010-900, Pelotas, RS (Brazil); Landi Jr, S. [Instituto Federal Goiano, Rio Verde 75901-970 (Brazil); Pelegrini, F. [Instituto de Física, Universidade Federal de Goiás, Goiânia 74001-970 (Brazil); Baggio-Saitovitch, E. [Centro Brasileiro de Pesquisas Físicas, Rio de Janeiro 22290-180 (Brazil)

2014-01-15

The structural properties and relaxation processes of magnetization in [Ni{sub 81}Fe{sub 19}(t{sub 1})/Ru(t{sub 2})]{sub N} superlattices (N=number of bilayers) were analyzed by ferromagnetic resonance (FMR) with a fixed microwave frequency. One series of samples was deposited with constant NiFe layer thickness (t{sub 1}) and variable Ru layer thickness (t{sub 2}); the other series, with constant t{sub 2} and variable t{sub 1}. A single FMR mode was observed for t{sub 2}<15 Å and t{sub 1}>75 Å and it has been attributed to the resonance of the exchange-coupled NiFe layers across the Ru interlayers. For the other values of t{sub 1} and t{sub 2}, several FMR modes appeared and they were associated to non-coupled magnetic phases with different effective magnetization formed during the multilayer growth. The FMR linewidths were analyzed as a function of the magnetic layer thickness and a strong dependence on t{sub 1}{sup −2} was observed. It was attributed to the contribution of the two-magnon scattering mechanism for the linewidth. - Highlights: • We present a study of magnetic properties of NiFe/Ru superlattices by ferromagnetic resonance (FMR). • The FMR spectra show several modes for large Ru thicknesses and for low NiFe thicknesses. • The above behavior is correlated with the interlayer exchange coupling. • The two-magnon scattering mechanism is revealed by the dependence of the FMR linewidth on the NiFe thickness.

Alloys of nickel-iron and nickel-silicon do not swell under fast neutron irradiation

International Nuclear Information System (INIS)

Silvestre, G.; Silvent, A.; Regnard, C.; Sainfort, G.

1975-01-01

This research is concerned with the effect of fast-neutron irradiation on the swelling of nickel and nickel alloys. Ni-Fe (0-60at%Fe) and Ni-Si (0-8at%Si) were studied, and the fluences were in the range 10 20 -4.3x10 22 n/cm 2 . In dilute alloys, the added elements are dissolved and reduce swelling, silicon being particularly effective. In more concentrated alloys, irradiation of Ni-Fe and Ni-Si alloys brings about the formation of plate-shaped precipitates of Ni 3 X and these alloys do not swell. (Auth.)

Imaging gene expression in gene therapy

International Nuclear Information System (INIS)

Wiebe, Leonard I.

1997-01-01

Full text. Gene therapy can be used to introduce new genes, or to supplement the function of indigenous genes. At the present time, however, there is non-invasive test to demonstrate efficacy of the gene transfer and expression processes. It has been postulated that scintigraphic imaging can offer unique information on both the site at which the transferred gene is expressed, and the degree of expression, both of which are critical issue for safety and clinical efficacy. Many current studies are based on 'suicide gene therapy' of cancer. Cells modified to express these genes commit metabolic suicide in the presence of an enzyme encoded by the transferred gene and a specifically-convertible pro drug. Pro drug metabolism can lead to selective metabolic trapping, required for scintigraphy. Herpes simplex virus type-1 thymidine kinase (H S V-1 t k + ) has been use for 'suicide' in vivo tumor gene therapy. It has been proposed that radiolabelled nucleosides can be used as radiopharmaceuticals to detect H S V-1 t k + gene expression where the H S V-1 t k + gene serves a reporter or therapeutic function. Animal gene therapy models have been studied using purine-([ 18 F]F H P G; [ 18 F]-A C V), and pyrimidine- ([ 123 / 131 I]I V R F U; [ 124 / 131I ]) antiviral nucleosides. Principles of gene therapy and gene therapy imaging will be reviewed and experimental data for [ 123 / 131I ]I V R F U imaging with the H S V-1 t k + reporter gene will be presented

Imaging gene expression in gene therapy

Energy Technology Data Exchange (ETDEWEB)

Wiebe, Leonard I. [Alberta Univ., Edmonton (Canada). Noujaim Institute for Pharmaceutical Oncology Research

1997-12-31

Full text. Gene therapy can be used to introduce new genes, or to supplement the function of indigenous genes. At the present time, however, there is non-invasive test to demonstrate efficacy of the gene transfer and expression processes. It has been postulated that scintigraphic imaging can offer unique information on both the site at which the transferred gene is expressed, and the degree of expression, both of which are critical issue for safety and clinical efficacy. Many current studies are based on `suicide gene therapy` of cancer. Cells modified to express these genes commit metabolic suicide in the presence of an enzyme encoded by the transferred gene and a specifically-convertible pro drug. Pro drug metabolism can lead to selective metabolic trapping, required for scintigraphy. Herpes simplex virus type-1 thymidine kinase (H S V-1 t k{sup +}) has been use for `suicide` in vivo tumor gene therapy. It has been proposed that radiolabelled nucleosides can be used as radiopharmaceuticals to detect H S V-1 t k{sup +} gene expression where the H S V-1 t k{sup +} gene serves a reporter or therapeutic function. Animal gene therapy models have been studied using purine-([{sup 18} F]F H P G; [{sup 18} F]-A C V), and pyrimidine- ([{sup 123}/{sup 131} I]I V R F U; [{sup 124}/{sup 131I}]) antiviral nucleosides. Principles of gene therapy and gene therapy imaging will be reviewed and experimental data for [{sup 123}/{sup 131I}]I V R F U imaging with the H S V-1 t k{sup +} reporter gene will be presented

Water-splitting-based, sustainable and efficient H2 production in green algae as achieved by substrate limitation of the Calvin-Benson-Bassham cycle.

Science.gov (United States)

Nagy, Valéria; Podmaniczki, Anna; Vidal-Meireles, André; Tengölics, Roland; Kovács, László; Rákhely, Gábor; Scoma, Alberto; Tóth, Szilvia Z

2018-01-01

Photobiological H 2 production has the potential of becoming a carbon-free renewable energy source, because upon the combustion of H 2 , only water is produced. The [Fe-Fe]-type hydrogenases of green algae are highly active, although extremely O 2 -sensitive. Sulphur deprivation is a common way to induce H 2 production, which, however, relies substantially on organic substrates and imposes a severe stress effect resulting in the degradation of the photosynthetic apparatus. We report on the establishment of an alternative H 2 production method by green algae that is based on a short anaerobic induction, keeping the Calvin-Benson-Bassham cycle inactive by substrate limitation and preserving hydrogenase activity by applying a simple catalyst to remove the evolved O 2 . Cultures remain photosynthetically active for several days, with the electrons feeding the hydrogenases mostly derived from water. The amount of H 2 produced is higher as compared to the sulphur-deprivation procedure and the process is photoautotrophic. Our protocol demonstrates that it is possible to sustainably use algal cells as whole-cell catalysts for H 2 production, which enables industrial application of algal biohydrogen production.

Hydrogen production of Enterobacter aerogenes altered by extracellular and intracellular redox states

Energy Technology Data Exchange (ETDEWEB)

Nakashimada, Y.; Rachman, M.A.; Kakizono, T.; Nishio, N. [Hiroshima University, Higashi-Hiroshima (Japan). Graduate School of Advanced Sciences of Matter, Department of Molecular Biotechnology

2002-12-01

Enterobacter aerogenes HU-101, tested for its hydrogen production in batch cultures on various substrates, produced the highest amount of hydrogen when the substrate was glycerol. The yield of hydrogen is a function of the degree to which the substrates are reduced. To examine the effect of intracellular redox state on hydrogen yield, glucose-limiting chemostat cultures were carried out at various pH using strain HU-101 and its mutant AY-2. For both strains, the molar yield and the production rate of hydrogen and the hydrogenase activity in the cell-free extract were optimal at the culture pH of 6.3. The highest NADH/NAD ratio in both strains was also observed at pH 6.3, at which the ratio in AY-2 was more than two-fold that of HU-101. Furthermore, NAD(P)H-dependent hydrogen formation was observed in the cell-free extract of AY-2, and hydrogenase activity was found not in the cytoplasmic but in the cell membrane fraction, suggesting that a high intracellular redox state, that is a high NADH/NAD ratio, would accelerate hydrogen production by driving membrane-bound NAD(P)H-dependent hydrogenase. (author)

The generation of molecular hydrogen by cyanobacteria. Die Gewinnung von molekularem Wasserstoff durch Cyanobakterien

Energy Technology Data Exchange (ETDEWEB)

Kentemich, T.; Haverkamp, G.; Bothe, H. (Koeln Univ. (Germany, F.R.). Botanisches Inst.)

1990-01-01

Currently there is renewed interest in projects on solar-energy conversion by microorganisms. Among all organisms, cyanobacteria are first choice for such projects. Hydrogen production by cyanobacteria is light-dependent and catalyzed by the enzyme complex nitrogenase which concomitantly catalyzes the reduction of N{sub 2} to ammonia. The cyanobacterium Anabaena variabilis can express an alternative, vanadium-containing nitrogenase which produces more hydrogen than the conventional, molybdenum-containing enzyme. In intact cells, most of the H{sub 2} produced by nitrogenase is immediatley reutilized by the hydrogenase enzymes. Maximal hydrogen production requires the genetic blockage of H{sub 2} utilization by the hydrogenases. (orig.).

Preparation and magnetic properties of nano size nickel ferrite particles using hydrothermal method

Directory of Open Access Journals (Sweden)

Nejati Kamellia

2012-03-01

Full Text Available Abstract Background Nickel ferrite, a kind of soft magnetic materials is one of the most attracting class of materials due to its interesting and important properties and has many technical applications, such as in catalysis, sensors and so on. In this paper the synthesis of NiFe2O4 nanoparticles by the hydrothermal method is reported and the inhibition of surfactant (Glycerol or Sodium dodecyl sulfate on the particles growth is investigated. Methods For investigation of the inhibition effect of surfactant on NiFe2O4 particles growth, the samples were prepared in presence of Glycerol and Sodium dodecyl sulfate. The X-ray powder diffraction (XRD, transmission electron microscopy (TEM, Fourier transform infrared spectroscopy (FT-IR, vibrating sample magnetometer (VSM and inductively coupled plasma atomic emission spectrometer (ICP-AES techniques were used to characterize the samples. Results The results of XRD and ICP-AES show that the products were pure NiFe2O4 and also nanoparticles grow with increasing the temperature, while surfactant prevents the particle growth under the same condition. The average particle size was determined from the Scherrer's equation and TEM micrographs and found to be in the range of 50-60 nm that decreased up to 10-15 nm in presence of surfactant. The FT-IR results show two absorption bands near to 603 and 490 cm-1 for the tetrahedral and octahedral sites respectively. Furthermore, the saturated magnetization and coercivity of NiFe2O4 nanoparticles were in the range of 39.60 emu/g and 15.67 Qe that decreased for samples prepared in presence of surfactant. As well as, the nanoparticles exhibited a superparamagnetic behavior at room temperature. Conclusions Nanosized nickel ferrite particles were synthesized with and without surfactant assisted hydrothermal methods. The results show that with increasing of temperature, the crystallinity of nanoparticles is increased. In the presence of surfactants, the crystallinity of

High-frequency electromagnetic properties of soft magnetic metal-polyimide hybrid thin films

Energy Technology Data Exchange (ETDEWEB)

Kim, Sang Woo [Nano-Materials Research Center, Korea Institute of Science and Technology, 39-1 Haweoulgog-dong, Sungbuk-gu, Seoul 136-791 (Korea, Republic of)]. E-mail: swkim@kist.re.kr; Yoon, Chong S. [Division of Advanced Materials Science, Hanyang University, Seoul 133-791 (Korea, Republic of)

2007-09-15

Although there are a lot of demands for suppression of unwanted high-frequency electromagnetic noise in highly integrated electronic devices such as mobile phones and notebook computers, electromagnetic thin films that effectively work in the high-frequency range have still been underdeveloped. Soft magnetic metal-polyimide (PI) hybrid films with high electrical resistivity were prepared by thermal imidization and selective oxidation between the metal alloy layer and polyamic acid (PAA) layer. Electromagnetic properties of the hybrid thin films in the radio-frequency range were characterized by using the microstrip line method and were correlated with their material parameters. Although anisotropy field of the CoFe/NiFe hybrid film was two times lower than that of the NiFe hybrid film, the saturation magnetization of the CoFe/NiFe hybrid film was three times higher than that of the NiFe hybrid film. The CoFe/NiFe hybrid film showed higher power loss in the frequency range of 3-6 GHz compared to the NiFe hybrid film. The high power loss of the CoFe/NiFe hybrid film was caused by high relative permeability and high ferromagnetic resonance (FMR) frequency due to high saturation magnetization.

High-frequency electromagnetic properties of soft magnetic metal-polyimide hybrid thin films

International Nuclear Information System (INIS)

Kim, Sang Woo; Yoon, Chong S.

2007-01-01

Although there are a lot of demands for suppression of unwanted high-frequency electromagnetic noise in highly integrated electronic devices such as mobile phones and notebook computers, electromagnetic thin films that effectively work in the high-frequency range have still been underdeveloped. Soft magnetic metal-polyimide (PI) hybrid films with high electrical resistivity were prepared by thermal imidization and selective oxidation between the metal alloy layer and polyamic acid (PAA) layer. Electromagnetic properties of the hybrid thin films in the radio-frequency range were characterized by using the microstrip line method and were correlated with their material parameters. Although anisotropy field of the CoFe/NiFe hybrid film was two times lower than that of the NiFe hybrid film, the saturation magnetization of the CoFe/NiFe hybrid film was three times higher than that of the NiFe hybrid film. The CoFe/NiFe hybrid film showed higher power loss in the frequency range of 3-6 GHz compared to the NiFe hybrid film. The high power loss of the CoFe/NiFe hybrid film was caused by high relative permeability and high ferromagnetic resonance (FMR) frequency due to high saturation magnetization

Localized excitation of magnetostatic surface spin waves in yttrium iron garnet by shorted coaxial probe detected via spin pumping and rectification effect

International Nuclear Information System (INIS)

Soh, Wee Tee; Ong, C. K.; Peng, Bin

2015-01-01

We demonstrate the localized excitation and dc electrical detection of magnetostatic surface spin waves (MSSWs) in yttrium iron garnet (YIG) by a shorted coaxial probe. Thin films of NiFe and Pt are patterned at different regions onto a common bulk YIG substrate. A shorted coaxial probe is used to excite spin precession locally near various patterned regions. The dc voltages across the corresponding regions are recorded. For excitation of the Pt regions, the dc voltage spectra are dominated by the spin pumping of MSSWs from YIG, where various modes can be clearly distinguished. For the NiFe region, it is also found that spin pumping from MSSWs generated in YIG dominated the spectra, indicating that the spin pumped currents are dissipated into charge currents via the inverse Spin Hall effect (ISHE) in NiFe. For all regions, dc signals from YIG MSSWs are observed to be much stronger than the ferromagnetic resonance (FMR) uniform mode, likely due to the nature of the microwave excitation. The results indicate the potential of this probe for microwave imaging via dc detection of spin dynamics in continuous and patterned films

Moessbauer and XRD study of pulse plated Fe-P and Fe-Ni thin layers

International Nuclear Information System (INIS)

Miko, Annamaria; Kuzmann, Erno; Lakatos-Varsanyi, Magda; Kakay, Attila; Nagy, Ferenc; Varga, Lajos Karoly

2005-01-01

57 Fe conversion electron Moessbauer spectroscopy, X-ray diffraction, electrochemical and magnetic measurements were used to study pulse electroplated Fe-P and Ni-Fe coatings. XRD and 57 Fe CEMS measurements revealed the amorphous character of the novel pulse plated Fe-P alloys. CEM spectra indicated significant differences in the short range order and in the magnetic anisotropy between the Fe-P deposits pulse plated at medium long deposition time (t on = 2 ms), with short relaxation time (t off = 9 ms) and low current density (I p = 0.05 Acm -2 ) or at short deposition time (t on = 1 ms) with long relaxation time (t off = 250 ms) and high current density (I p = 1.0 Acm -2 ). The broad peaks centred around the fcc reflections in XRD of the pulse plated Ni-22 wt.% Fe deposit reflected a microcrystalline Ni-Fe alloy with a very fine, 5-8 nm, grain size. The CEM spectrum of the pulse plated Ni-22 wt.% Fe coating corresponded to a highly disordered solid solution alloy containing a minute amount of ferrihydrite. Extreme favourable soft magnetic properties were observed with these Ni-Fe and Fe-P pulse plated thin layers.

GoGene: gene annotation in the fast lane.

Science.gov (United States)

Plake, Conrad; Royer, Loic; Winnenburg, Rainer; Hakenberg, Jörg; Schroeder, Michael

2009-07-01

High-throughput screens such as microarrays and RNAi screens produce huge amounts of data. They typically result in hundreds of genes, which are often further explored and clustered via enriched GeneOntology terms. The strength of such analyses is that they build on high-quality manual annotations provided with the GeneOntology. However, the weakness is that annotations are restricted to process, function and location and that they do not cover all known genes in model organisms. GoGene addresses this weakness by complementing high-quality manual annotation with high-throughput text mining extracting co-occurrences of genes and ontology terms from literature. GoGene contains over 4,000,000 associations between genes and gene-related terms for 10 model organisms extracted from more than 18,000,000 PubMed entries. It does not cover only process, function and location of genes, but also biomedical categories such as diseases, compounds, techniques and mutations. By bringing it all together, GoGene provides the most recent and most complete facts about genes and can rank them according to novelty and importance. GoGene accepts keywords, gene lists, gene sequences and protein sequences as input and supports search for genes in PubMed, EntrezGene and via BLAST. Since all associations of genes to terms are supported by evidence in the literature, the results are transparent and can be verified by the user. GoGene is available at http://gopubmed.org/gogene.

Magnetoresistance Effect in NiFe/BP/NiFe Vertical Spin Valve Devices

Directory of Open Access Journals (Sweden)

Leilei Xu

2017-01-01

Full Text Available Two-dimensional (2D layered materials such as graphene and transition metal dichalcogenides are emerging candidates for spintronic applications. Here, we report magnetoresistance (MR properties of a black phosphorus (BP spin valve devices consisting of thin BP flakes contacted by NiFe ferromagnetic (FM electrodes. The spin valve effect has been observed from room temperature to 4 K, with MR magnitudes of 0.57% at 4 K and 0.23% at 300 K. In addition, the spin valve resistance is found to decrease monotonically as temperature is decreased, indicating that the BP thin film works as a conductive interlayer between the NiFe electrodes.

Protein (Cyanobacteria): 515868638 [PGDBj - Ortholog DB

Lifescience Database Archive (English)

Full Text Available ... hydrogenase nickel incorporation protein HypA Nodosilinea nodulosa MHETDMTKALILTVRDWWEAQPGQPAIEKVHLTVGKFTC... WP_017299262.1 ... 1117:21745 ... 1150:31644 1301283:50549 ... 1120752:1645 416001:1645 ...

Radionuclide reporter gene imaging for cardiac gene therapy

International Nuclear Information System (INIS)

Inubushi, Masayuki; Tamaki, Nagara

2007-01-01

In the field of cardiac gene therapy, angiogenic gene therapy has been most extensively investigated. The first clinical trial of cardiac angiogenic gene therapy was reported in 1998, and at the peak, more than 20 clinical trial protocols were under evaluation. However, most trials have ceased owing to the lack of decisive proof of therapeutic effects and the potential risks of viral vectors. In order to further advance cardiac angiogenic gene therapy, remaining open issues need to be resolved: there needs to be improvement of gene transfer methods, regulation of gene expression, development of much safer vectors and optimisation of therapeutic genes. For these purposes, imaging of gene expression in living organisms is of great importance. In radionuclide reporter gene imaging, ''reporter genes'' transferred into cell nuclei encode for a protein that retains a complementary ''reporter probe'' of a positron or single-photon emitter; thus expression of the reporter genes can be imaged with positron emission tomography or single-photon emission computed tomography. Accordingly, in the setting of gene therapy, the location, magnitude and duration of the therapeutic gene co-expression with the reporter genes can be monitored non-invasively. In the near future, gene therapy may evolve into combination therapy with stem/progenitor cell transplantation, so-called cell-based gene therapy or gene-modified cell therapy. Radionuclide reporter gene imaging is now expected to contribute in providing evidence on the usefulness of this novel therapeutic approach, as well as in investigating the molecular mechanisms underlying neovascularisation and safety issues relevant to further progress in conventional gene therapy. (orig.)

Gene cluster statistics with gene families.

Science.gov (United States)

Raghupathy, Narayanan; Durand, Dannie

2009-05-01

Identifying genomic regions that descended from a common ancestor is important for understanding the function and evolution of genomes. In distantly related genomes, clusters of homologous gene pairs are evidence of candidate homologous regions. Demonstrating the statistical significance of such "gene clusters" is an essential component of comparative genomic analyses. However, currently there are no practical statistical tests for gene clusters that model the influence of the number of homologs in each gene family on cluster significance. In this work, we demonstrate empirically that failure to incorporate gene family size in gene cluster statistics results in overestimation of significance, leading to incorrect conclusions. We further present novel analytical methods for estimating gene cluster significance that take gene family size into account. Our methods do not require complete genome data and are suitable for testing individual clusters found in local regions, such as contigs in an unfinished assembly. We consider pairs of regions drawn from the same genome (paralogous clusters), as well as regions drawn from two different genomes (orthologous clusters). Determining cluster significance under general models of gene family size is computationally intractable. By assuming that all gene families are of equal size, we obtain analytical expressions that allow fast approximation of cluster probabilities. We evaluate the accuracy of this approximation by comparing the resulting gene cluster probabilities with cluster probabilities obtained by simulating a realistic, power-law distributed model of gene family size, with parameters inferred from genomic data. Surprisingly, despite the simplicity of the underlying assumption, our method accurately approximates the true cluster probabilities. It slightly overestimates these probabilities, yielding a conservative test. We present additional simulation results indicating the best choice of parameter values for data

Gene therapy prospects--intranasal delivery of therapeutic genes.

Science.gov (United States)

Podolska, Karolina; Stachurska, Anna; Hajdukiewicz, Karolina; Małecki, Maciej

2012-01-01

Gene therapy is recognized to be a novel method for the treatment of various disorders. Gene therapy strategies involve gene manipulation on broad biological processes responsible for the spreading of diseases. Cancer, monogenic diseases, vascular and infectious diseases are the main targets of gene therapy. In order to obtain valuable experimental and clinical results, sufficient gene transfer methods are required. Therapeutic genes can be administered into target tissues via gene carriers commonly defined as vectors. The retroviral, adenoviral and adeno-associated virus based vectors are most frequently used in the clinic. So far, gene preparations may be administered directly into target organs or by intravenous, intramuscular, intratumor or intranasal injections. It is common knowledge that the number of gene therapy clinical trials has rapidly increased. However, some limitations such as transfection efficiency and stable and long-term gene expression are still not resolved. Consequently, great effort is focused on the evaluation of new strategies of gene delivery. There are many expectations associated with intranasal delivery of gene preparations for the treatment of diseases. Intranasal delivery of therapeutic genes is regarded as one of the most promising forms of pulmonary gene therapy research. Gene therapy based on inhalation of gene preparations offers an alternative way for the treatment of patients suffering from such lung diseases as cystic fibrosis, alpha-1-antitrypsin defect, or cancer. Experimental and first clinical trials based on plasmid vectors or recombinant viruses have revealed that gene preparations can effectively deliver therapeutic or marker genes to the cells of the respiratory tract. The noninvasive intranasal delivery of gene preparations or conventional drugs seems to be very encouraging, although basic scientific research still has to continue.

Gene-gene interactions and gene polymorphisms of VEGFA and EG-VEGF gene systems in recurrent pregnancy loss.

Science.gov (United States)

Su, Mei-Tsz; Lin, Sheng-Hsiang; Chen, Yi-Chi; Kuo, Pao-Lin

2014-06-01

Both vascular endothelial growth factor A (VEGFA) and endocrine gland-derived vascular endothelial growth factor (EG-VEGF) systems play major roles in angiogenesis. A body of evidence suggests VEGFs regulate critical processes during pregnancy and have been associated with recurrent pregnancy loss (RPL). However, little information is available regarding the interaction of these two major major angiogenesis-related systems in early human pregnancy. This study was conducted to investigate the association of gene polymorphisms and gene-gene interaction among genes in VEGFA and EG-VEGF systems and idiopathic RPL. A total of 98 women with history of idiopathic RPL and 142 controls were included, and 5 functional SNPs selected from VEGFA, KDR, EG-VEGF (PROK1), PROKR1 and PROKR2 were genotyped. We used multifactor dimensionality reduction (MDR) analysis to choose a best model and evaluate gene-gene interactions. Ingenuity pathways analysis (IPA) was introduced to explore possible complex interactions. Two receptor gene polymorphisms [KDR (Q472H) and PROKR2 (V331M)] were significantly associated with idiopathic RPL (P<0.01). The MDR test revealed that the KDR (Q472H) polymorphism was the best loci to be associated with RPL (P=0.02). IPA revealed EG-VEGF and VEGFA systems shared several canonical signaling pathways that may contribute to gene-gene interactions, including the Akt, IL-8, EGFR, MAPK, SRC, VHL, HIF-1A and STAT3 signaling pathways. Two receptor gene polymorphisms [KDR (Q472H) and PROKR2 (V331M)] were significantly associated with idiopathic RPL. EG-VEGF and VEGFA systems shared several canonical signaling pathways that may contribute to gene-gene interactions, including the Akt, IL-8, EGFR, MAPK, SRC, VHL, HIF-1A and STAT3.

Protein (Cyanobacteria): 493036452 [PGDBj - Ortholog DB

Lifescience Database Archive (English)

Full Text Available oration protein HypA Coleofasciculus chthonoplastes MHETDMTKALILTVRQWWEEQPSRPQIDTIH... WP_006104069.1 ... 1117:21745 ... 1150:63074 1301283:85471 ... 669368:4227 64178:4227 ... hydrogenase nickel incorp

Gene doping: gene delivery for olympic victory

OpenAIRE

Gould, David

2012-01-01

With one recently recommended gene therapy in Europe and a number of other gene therapy treatments now proving effective in clinical trials it is feasible that the same technologies will soon be adopted in the world of sport by unscrupulous athletes and their trainers in so called ‘gene doping’. In this article an overview of the successful gene therapy clinical trials is provided and the potential targets for gene doping are highlighted. Depending on whether a doping gene product is secreted...

FunGene: the functional gene pipeline and repository.

Science.gov (United States)

Fish, Jordan A; Chai, Benli; Wang, Qiong; Sun, Yanni; Brown, C Titus; Tiedje, James M; Cole, James R

2013-01-01

Ribosomal RNA genes have become the standard molecular markers for microbial community analysis for good reasons, including universal occurrence in cellular organisms, availability of large databases, and ease of rRNA gene region amplification and analysis. As markers, however, rRNA genes have some significant limitations. The rRNA genes are often present in multiple copies, unlike most protein-coding genes. The slow rate of change in rRNA genes means that multiple species sometimes share identical 16S rRNA gene sequences, while many more species share identical sequences in the short 16S rRNA regions commonly analyzed. In addition, the genes involved in many important processes are not distributed in a phylogenetically coherent manner, potentially due to gene loss or horizontal gene transfer. While rRNA genes remain the most commonly used markers, key genes in ecologically important pathways, e.g., those involved in carbon and nitrogen cycling, can provide important insights into community composition and function not obtainable through rRNA analysis. However, working with ecofunctional gene data requires some tools beyond those required for rRNA analysis. To address this, our Functional Gene Pipeline and Repository (FunGene; http://fungene.cme.msu.edu/) offers databases of many common ecofunctional genes and proteins, as well as integrated tools that allow researchers to browse these collections and choose subsets for further analysis, build phylogenetic trees, test primers and probes for coverage, and download aligned sequences. Additional FunGene tools are specialized to process coding gene amplicon data. For example, FrameBot produces frameshift-corrected protein and DNA sequences from raw reads while finding the most closely related protein reference sequence. These tools can help provide better insight into microbial communities by directly studying key genes involved in important ecological processes.

FunGene: the Functional Gene Pipeline and Repository

Directory of Open Access Journals (Sweden)

Jordan A. Fish

2013-10-01

Full Text Available Ribosomal RNA genes have become the standard molecular markers for microbial community analysis for good reasons, including universal occurrence in cellular organisms, availability of large databases, and ease of rRNA gene region amplification and analysis. As markers, however, rRNA genes have some significant limitations. The rRNA genes are often present in multiple copies, unlike most protein-coding genes. The slow rate of change in rRNA genes means that multiple species sometimes share identical 16S rRNA gene sequences, while many more species share identical sequences in the short 16S rRNA regions commonly analyzed. In addition, the genes involved in many important processes are not distributed in a phylogenetically coherent manner, potentially due to gene loss or horizontal gene transfer.While rRNA genes remain the most commonly used markers, key genes in ecologically important pathways, e.g., those involved in carbon and nitrogen cycling, can provide important insights into community composition and function not obtainable through rRNA analysis. However, working with ecofunctional gene data requires some tools beyond those required for rRNA analysis. To address this, our Functional Gene Pipeline and Repository (FunGene; http://fungene.cme.msu.edu/ offers databases of many common ecofunctional genes and proteins, as well as integrated tools that allow researchers to browse these collections and choose subsets for further analysis, build phylogenetic trees, test primers and probes for coverage, and download aligned sequences. Additional FunGene tools are specialized to process coding gene amplicon data. For example, FrameBot produces frameshift-corrected protein and DNA sequences from raw reads while finding the most closely related protein reference sequence. These tools can help provide better insight into microbial communities by directly studying key genes involved in important ecological processes.

Mining disease genes using integrated protein-protein interaction and gene-gene co-regulation information.

Science.gov (United States)

Li, Jin; Wang, Limei; Guo, Maozu; Zhang, Ruijie; Dai, Qiguo; Liu, Xiaoyan; Wang, Chunyu; Teng, Zhixia; Xuan, Ping; Zhang, Mingming

2015-01-01

In humans, despite the rapid increase in disease-associated gene discovery, a large proportion of disease-associated genes are still unknown. Many network-based approaches have been used to prioritize disease genes. Many networks, such as the protein-protein interaction (PPI), KEGG, and gene co-expression networks, have been used. Expression quantitative trait loci (eQTLs) have been successfully applied for the determination of genes associated with several diseases. In this study, we constructed an eQTL-based gene-gene co-regulation network (GGCRN) and used it to mine for disease genes. We adopted the random walk with restart (RWR) algorithm to mine for genes associated with Alzheimer disease. Compared to the Human Protein Reference Database (HPRD) PPI network alone, the integrated HPRD PPI and GGCRN networks provided faster convergence and revealed new disease-related genes. Therefore, using the RWR algorithm for integrated PPI and GGCRN is an effective method for disease-associated gene mining.

Silicification-induced cell aggregation for the sustainable production of H2 under aerobic conditions.

Science.gov (United States)

Xiong, Wei; Zhao, Xiaohong; Zhu, Genxing; Shao, Changyu; Li, Yaling; Ma, Weimin; Xu, Xurong; Tang, Ruikang

2015-10-05

Photobiological hydrogen production is of great importance because of its promise for generating clean renewable energy. In nature, green algae cannot produce hydrogen as a result of the extreme sensitivity of hydrogenase to oxygen. However, we find that silicification-induced green algae aggregates can achieve sustainable photobiological hydrogen production even under natural aerobic conditions. The core-shell structure of the green algae aggregates creates a balance between photosynthetic electron generation and hydrogenase activity, thus allowing the production of hydrogen. This finding provides a viable pathway for the solar-driven splitting of water into hydrogen and oxygen to develop green energy alternatives by using rationally designed cell-material complexes. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Gene-gene, gene-environment, gene-nutrient interactions and single nucleotide polymorphisms of inflammatory cytokines.

Science.gov (United States)

Nadeem, Amina; Mumtaz, Sadaf; Naveed, Abdul Khaliq; Aslam, Muhammad; Siddiqui, Arif; Lodhi, Ghulam Mustafa; Ahmad, Tausif

2015-05-15

Inflammation plays a significant role in the etiology of type 2 diabetes mellitus (T2DM). The rise in the pro-inflammatory cytokines is the essential step in glucotoxicity and lipotoxicity induced mitochondrial injury, oxidative stress and beta cell apoptosis in T2DM. Among the recognized markers are interleukin (IL)-6, IL-1, IL-10, IL-18, tissue necrosis factor-alpha (TNF-α), C-reactive protein, resistin, adiponectin, tissue plasminogen activator, fibrinogen and heptoglobins. Diabetes mellitus has firm genetic and very strong environmental influence; exhibiting a polygenic mode of inheritance. Many single nucleotide polymorphisms (SNPs) in various genes including those of pro and anti-inflammatory cytokines have been reported as a risk for T2DM. Not all the SNPs have been confirmed by unifying results in different studies and wide variations have been reported in various ethnic groups. The inter-ethnic variations can be explained by the fact that gene expression may be regulated by gene-gene, gene-environment and gene-nutrient interactions. This review highlights the impact of these interactions on determining the role of single nucleotide polymorphism of IL-6, TNF-α, resistin and adiponectin in pathogenesis of T2DM.

Biochemical factors affecting the quantum efficiency of hydrogen production by membranes of green photosynthetic bacteria

Energy Technology Data Exchange (ETDEWEB)

Bernstein, J.D.; Olson, J.M.

1981-01-01

Photohydrogen production, 200-700 ..mu..mol H/sub 2/ h/sup -1/ (mg bacteriochlorophyll a)/sup -1/ has been obtained in a system containing unit membrane vesicles (Complex I) from the green photosynthetic bacterium Chlorobium limicola f. thiosulfatophilum, ascorbate, N,N,N',N'-tetramethyl-p-phenylenediamine, dithioerythritol, an oxygen scavenging mixture, either methyl viologen (MV) or clostridial ferredoxin (CPS Fd) as electron carrier, and either CPS hydrogenase or platinum asbestos as catalyst. All components are necessary for maximum activity, and spinach Fd cannot be substituted for CPS Fd. Higher rates of photohydrogen production are obtained using MV or CPS Fd with hydrogenase than with MV and Pt asbestos. The highest quantum efficiencies (7-10% at 0.2-0.9 mW absorbed light and over 20% at lower light) were obtained with CPS Fd, hydrogenase and non-saturating 812 nm light. With saturating white light, however, rates of photohydrogen production varied relatively little among the various combinations of electron carrier and catalyst tested. The reaction rate is unaffected by 0.03% Triton X-100, and is insensitive to treatment with antimycin a or m-chloro-carbonyl cyanide phenylhydrazone.This indicates that neither electron flow through an endogenous cyclic chain, nor maintenance of a proton gradient are involved in this process.

Effect of light on respiration and development of photosynthetic cells. Progress report, September 1, 1975--June 1, 1976

Energy Technology Data Exchange (ETDEWEB)

Gibbs, M

1976-06-01

Adaptation and deadaptation of unicellular algal cells to a hydrogen metabolism may involve not only hydrogenase but also the site of entry of electrons from NADH. NADPH can also serve as an electron donor in a chloroplast preparation fortified with hydrogenase but the rate of photoevolution falls off rapidly perhaps due to competition with NADP for electrons. The evolution of H/sub 2/ with reduced pyridine nucleotide as electron donor is coupled to ATP formation. Evidence is presented that soluble ferredoxin may not be the immediate donor of H/sub 2/. Hydrogenases from Chlamydomonas and Scenedesmus have been highly purified and will be used to test the stoichiometry of NADH disappearance, ATP and H/sub 2/ formation and also whether H/sub 2/-photoevolution in contrast to dark evolution is ferredoxin dependent. Studies with intact Chlamydomonas provide evidence that a reduced carbon compound and not water is the source of H/sub 2/. The presence of acetate eliminates the CO/sub 2/ production. The ratio of CO/sub 2/:H/sub 2/ is 1:2 and evolution is blocked by inhibitors of glycolysis. Acetate has a strong effect on H/sub 2/O. Cells starved over a long period still retain photoreduction but will not evolve H/sub 2/ until glucose is added.

Suicide genes or p53 gene and p53 target genes as targets for cancer gene therapy by ionizing radiation

International Nuclear Information System (INIS)

Liu Bing; Chinese Academy of Sciences, Beijing; Zhang Hong

2005-01-01

Radiotherapy has some disadvantages due to the severe side-effect on the normal tissues at a curative dose of ionizing radiation (IR). Similarly, as a new developing approach, gene therapy also has some disadvantages, such as lack of specificity for tumors, limited expression of therapeutic gene, potential biological risk. To certain extent, above problems would be solved by the suicide genes or p53 gene and its target genes therapies targeted by ionizing radiation. This strategy not only makes up the disadvantage from radiotherapy or gene therapy alone, but also promotes success rate on the base of lower dose. By present, there have been several vectors measuring up to be reaching clinical trials. This review focused on the development of the cancer gene therapy through suicide genes or p53 and its target genes mediated by IR. (authors)

Neighboring Genes Show Correlated Evolution in Gene Expression

Science.gov (United States)

Ghanbarian, Avazeh T.; Hurst, Laurence D.

2015-01-01

When considering the evolution of a gene’s expression profile, we commonly assume that this is unaffected by its genomic neighborhood. This is, however, in contrast to what we know about the lack of autonomy between neighboring genes in gene expression profiles in extant taxa. Indeed, in all eukaryotic genomes genes of similar expression-profile tend to cluster, reflecting chromatin level dynamics. Does it follow that if a gene increases expression in a particular lineage then the genomic neighbors will also increase in their expression or is gene expression evolution autonomous? To address this here we consider evolution of human gene expression since the human-chimp common ancestor, allowing for both variation in estimation of current expression level and error in Bayesian estimation of the ancestral state. We find that in all tissues and both sexes, the change in gene expression of a focal gene on average predicts the change in gene expression of neighbors. The effect is highly pronounced in the immediate vicinity (genes increasing their expression in humans tend to avoid nuclear lamina domains and be enriched for the gene activator 5-hydroxymethylcytosine, we conclude that, most probably owing to chromatin level control of gene expression, a change in gene expression of one gene likely affects the expression evolution of neighbors, what we term expression piggybacking, an analog of hitchhiking. PMID:25743543

Genome analysis of Elusimicrobium minutum, the first cultivated representative of the Elusimicrobia phylum (formerly Termite Group 1)

Energy Technology Data Exchange (ETDEWEB)

Herlemann, D. P. R.; Geissinger, O.; Ikeda-Ohtsubo, W.; Kunin, V.; Sun, H.; Lapidus, A.; Hugenholtz, P.; Brune, A.

2009-02-01

The candidate phylum Termite group 1 (TG1), is regularly 1 encountered in termite hindguts but is present also in many other habitats. Here we report the complete genome sequence (1.64 Mbp) of Elusimicrobium minutum strain Pei191{sup T}, the first cultured representative of the TG1 phylum. We reconstructed the metabolism of this strictly anaerobic bacterium isolated from a beetle larva gut and discuss the findings in light of physiological data. E. minutum has all genes required for uptake and fermentation of sugars via the Embden-Meyerhof pathway, including several hydrogenases, and an unusual peptide degradation pathway comprising transamination reactions and leading to the formation of alanine, which is excreted in substantial amounts. The presence of genes encoding lipopolysaccharide biosynthesis and the presence of a pathway for peptidoglycan formation are consistent with ultrastructural evidence of a Gram-negative cell envelope. Even though electron micrographs showed no cell appendages, the genome encodes many genes putatively involved in pilus assembly. We assigned some to a type II secretion system, but the function of 60 pilE-like genes remains unknown. Numerous genes with hypothetical functions, e.g., polyketide synthesis, non-ribosomal peptide synthesis, antibiotic transport, and oxygen stress protection, indicate the presence of hitherto undiscovered physiological traits. Comparative analysis of 22 concatenated single-copy marker genes corroborated the status of Elusimicrobia (formerly TG1) as a separate phylum in the bacterial domain, which was so far based only on 16S rRNA sequence analysis.

Protein (Cyanobacteria): 504995873 [PGDBj - Ortholog DB

Lifescience Database Archive (English)

Full Text Available Hydrogenase-3 nickel incorporation protein HypA Microcoleus sp. PCC 7113 MHEVGIMQNTLDIALEYANRQGAAQIHRMTLRIGQ... WP_015182975.1 ... 1117:21745 ... 1150:36937 1301283:56429 ... 44471:3321 1173027:436 ...

Protein (Cyanobacteria): 504985265 [PGDBj - Ortholog DB

Lifescience Database Archive (English)

Full Text Available poration protein HypA Geitlerinema sp. PCC 7407 MTKALLMTLHDWWESQPDRPKIDKVHLVVGQFTCV... WP_015172367.1 ... 1117:21745 ... 1150:57512 1301283:79291 ... 63132:2365 1173025:1620 ... hydrogenase nickel incor

Protein (Cyanobacteria): 504993053 [PGDBj - Ortholog DB

Lifescience Database Archive (English)

Full Text Available Hydrogenase-3 nickel incorporation protein HypA Microcoleus sp. PCC 7113 MHETDMTKALIVTVRDWWEAQPEHPKISHIYLTVG... WP_015180155.1 ... 1117:21745 ... 1150:36937 1301283:56429 ... 44471:3321 1173027:436 ...

Gene Therapy

Science.gov (United States)

Gene therapy Overview Gene therapy involves altering the genes inside your body's cells in an effort to treat or stop disease. Genes contain your ... that don't work properly can cause disease. Gene therapy replaces a faulty gene or adds a new ...

Imaging reporter gene for monitoring gene therapy

International Nuclear Information System (INIS)

Beco, V. de; Baillet, G.; Tamgac, F.; Tofighi, M.; Weinmann, P.; Vergote, J.; Moretti, J.L.; Tamgac, G.

2002-01-01

Scintigraphic images can be obtained to document gene function at cellular level. This approach is presented here and the use of a reporter gene to monitor gene therapy is described. Two main ways are presented: either the use of a reporter gene coding for an enzyme the action of which will be monitored by radiolabeled pro-drug, or a cellular receptor gene, the action of which is documented by a radio labeled cognate receptor ligand. (author)

Gene-Gene and Gene-Environment Interactions in the Etiology of Breast Cancer

National Research Council Canada - National Science Library

Adegoke, Olufemi

2003-01-01

The objective of this CDA is to evaluate the gene-gene and gene-environment interactions in the etiology of breast cancer in two ongoing case-control studies, the Shanghai Breast Cancer Study (SBCS...

Gene doping: gene delivery for olympic victory.

Science.gov (United States)

Gould, David

2013-08-01

With one recently recommended gene therapy in Europe and a number of other gene therapy treatments now proving effective in clinical trials it is feasible that the same technologies will soon be adopted in the world of sport by unscrupulous athletes and their trainers in so called 'gene doping'. In this article an overview of the successful gene therapy clinical trials is provided and the potential targets for gene doping are highlighted. Depending on whether a doping gene product is secreted from the engineered cells or is retained locally to, or inside engineered cells will, to some extent, determine the likelihood of detection. It is clear that effective gene delivery technologies now exist and it is important that detection and prevention plans are in place. © 2012 The Author. British Journal of Clinical Pharmacology © 2012 The British Pharmacological Society.

Electrolytic materials for hydrogen production by water electrolysis; Materiais eletroliticos para a producao de hidrogenio por eletrolise da agua

Energy Technology Data Exchange (ETDEWEB)

Gonzalez, E R; Avaca, L A; Motheo, A J [Sao Paulo Univ., Sao Carlos, SP (Brazil). Inst. de Fisica e Quimica; Carvalho, J de [Alagoas Univ., Maceio, AL (Brazil)

1985-12-31

The hydrogen and oxygen evolution reactions in the electrolysis of water were studied on Ni-Fe and Ni-Co co deposits, respectively, in 28% KOH solution at 60 deg C. The studies were carried out on micro and macro electrodes and the results compared to those obtained with conventional materials. In the HER is observed a significant improvement in the electrocatalytic activity which points out the Ni-Fe co deposits as good substitutes for the conventional mild steel electrodes. In contrast, the Ni-Co co deposits don`t present enhanced activity when compared to Ni electro deposits. However the higher mechanic resistance observed make its utilization attractive. (author). 3 tabs., 2 figs., 11 refs

Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization

Directory of Open Access Journals (Sweden)

Gelfand Mikhail S

2009-02-01

Full Text Available Abstract Background Nickel (Ni and cobalt (Co are trace elements required for a variety of biological processes. Ni is directly coordinated by proteins, whereas Co is mainly used as a component of vitamin B12. Although a number of Ni and Co-dependent enzymes have been characterized, systematic evolutionary analyses of utilization of these metals are limited. Results We carried out comparative genomic analyses to examine occurrence and evolutionary dynamics of the use of Ni and Co at the level of (i transport systems, and (ii metalloproteomes. Our data show that both metals are widely used in bacteria and archaea. Cbi/NikMNQO is the most common prokaryotic Ni/Co transporter, while Ni-dependent urease and Ni-Fe hydrogenase, and B12-dependent methionine synthase (MetH, ribonucleotide reductase and methylmalonyl-CoA mutase are the most widespread metalloproteins for Ni and Co, respectively. Occurrence of other metalloenzymes showed a mosaic distribution and a new B12-dependent protein family was predicted. Deltaproteobacteria and Methanosarcina generally have larger Ni- and Co-dependent proteomes. On the other hand, utilization of these two metals is limited in eukaryotes, and very few of these organisms utilize both of them. The Ni-utilizing eukaryotes are mostly fungi (except saccharomycotina and plants, whereas most B12-utilizing organisms are animals. The NiCoT transporter family is the most widespread eukaryotic Ni transporter, and eukaryotic urease and MetH are the most common Ni- and B12-dependent enzymes, respectively. Finally, investigation of environmental and other conditions and identity of organisms that show dependence on Ni or Co revealed that host-associated organisms (particularly obligate intracellular parasites and endosymbionts have a tendency for loss of Ni/Co utilization. Conclusion Our data provide information on the evolutionary dynamics of Ni and Co utilization and highlight widespread use of these metals in the three

Moving protons with pendant amines: proton mobility in a nickel catalyst for oxidation of hydrogen.

Science.gov (United States)

O'Hagan, Molly; Shaw, Wendy J; Raugei, Simone; Chen, Shentan; Yang, Jenny Y; Kilgore, Uriah J; DuBois, Daniel L; Bullock, R Morris

2011-09-14

homogeneous catalysts and enzymes in general, with specific implications for the proton channel in the Ni-Fe hydrogenase enzyme.

Protein (Cyanobacteria): 648410610 [PGDBj - Ortholog DB

Lifescience Database Archive (English)

Full Text Available WP_026102361.1 NZ_KB235920 1117:21745 ... 52604:1915 ... 44474:816 118161:1544 ... hydrogenase nickel incorpora...tion protein HypA Pleurocapsa sp. PCC 7319 MHETDMTKALILTMKDWYVSQPEQRKIEKVHLIVGQFTCV

Genes2FANs: connecting genes through functional association networks

Science.gov (United States)

2012-01-01

Background Protein-protein, cell signaling, metabolic, and transcriptional interaction networks are useful for identifying connections between lists of experimentally identified genes/proteins. However, besides physical or co-expression interactions there are many ways in which pairs of genes, or their protein products, can be associated. By systematically incorporating knowledge on shared properties of genes from diverse sources to build functional association networks (FANs), researchers may be able to identify additional functional interactions between groups of genes that are not readily apparent. Results Genes2FANs is a web based tool and a database that utilizes 14 carefully constructed FANs and a large-scale protein-protein interaction (PPI) network to build subnetworks that connect lists of human and mouse genes. The FANs are created from mammalian gene set libraries where mouse genes are converted to their human orthologs. The tool takes as input a list of human or mouse Entrez gene symbols to produce a subnetwork and a ranked list of intermediate genes that are used to connect the query input list. In addition, users can enter any PubMed search term and then the system automatically converts the returned results to gene lists using GeneRIF. This gene list is then used as input to generate a subnetwork from the user’s PubMed query. As a case study, we applied Genes2FANs to connect disease genes from 90 well-studied disorders. We find an inverse correlation between the counts of links connecting disease genes through PPI and links connecting diseases genes through FANs, separating diseases into two categories. Conclusions Genes2FANs is a useful tool for interpreting the relationships between gene/protein lists in the context of their various functions and networks. Combining functional association interactions with physical PPIs can be useful for revealing new biology and help form hypotheses for further experimentation. Our finding that disease genes in

2D NiFe/CeO2 Basic-Site-Enhanced Catalyst via in-Situ Topotactic Reduction for Selectively Catalyzing the H2 Generation from N2H4·H2O.

Science.gov (United States)

Wu, Dandan; Wen, Ming; Gu, Chen; Wu, Qingsheng

2017-05-17

An economical catalyst with excellent selectivity and high activity is eagerly desirable for H 2 generation from the decomposition of N 2 H 4 ·H 2 O. Here, a bifunctional two-dimensional NiFe/CeO 2 nanocatalyst with NiFe nanoparticles (∼5 nm) uniformly anchored on CeO 2 nanosheets supports has been successfully synthesized through a dynamic controlling coprecipitation process followed by in-situ topotactic reduction. Even without NaOH as catalyst promoter, as-designed Ni 0.6 Fe 0.4 /CeO 2 nanocatalyst can show high activity for selectively catalyzing H 2 generation (reaction rate (mol N2H4 mol -1 NiFe h -1 ): 5.73 h -1 ). As ceria is easily reducible from CeO 2 to CeO 2-x , the surface of CeO 2 could supply an extremely large amount of Ce 3+ , and the high-density electrons of Ce 3+ can work as Lewis base to facilitate the absorption of N 2 H 4 , which can weaken the N-H bond and promote NiFe active centers to break the N-H bond preferentially, resulting in the high catalytic selectivity (over 99%) and activity for the H 2 generation from N 2 H 4 ·H 2 O.

Amorphous NiFe-OH/NiFeP Electrocatalyst Fabricated at Low Temperature for Water Oxidation Applications

KAUST Repository

Liang, Hanfeng

2017-04-11

Water splitting driven by electricity or sunlight is one of the most promising ways to address the global terawatt energy needs of future societies; however, its large-scale application is limited by the sluggish kinetics of the oxygen evolution reaction (OER). NiFe-based compounds, mainly oxides and hydroxides, are well-known OER catalysts and have been intensively studied; however, the utilization of the synergistic effect between two different NiFe-based materials to further boost the OER performance has not been achieved to date. Here, we report the rapid conversion of NiFe double hydroxide into metallic NiFeP using PH3 plasma treatment and further construction of amorphous NiFe hydroxide/NiFeP/Ni foam as efficient and stable oxygen-evolving anodes. The strong electronic interactions between NiFe hydroxide and NiFeP significantly lower the adsorption energy of H2O on the hybrid and thus lead to enhanced OER performance. As a result, the hybrid catalyst can deliver a geometrical current density of 300 mA cm–2 at an extremely low overpotential (258 mV, after ohmic-drop correction), along with a small Tafel slope of 39 mV decade–1 and outstanding long-term durability in alkaline media.

Moessbauer and XRD study of pulse plated Fe-P and Fe-Ni thin layers

Energy Technology Data Exchange (ETDEWEB)

Miko, Annamaria [Bay Zoltan Institute for Material Science (Hungary); Kuzmann, Erno, E-mail: kuzmann@para.chem.elte.hu [Eoetvoes Lorand University, Research Group for Nuclear Methods in Structural Chemistry, Hungarian Academy of Sciences, Department of Nuclear Chemistry (Hungary); Lakatos-Varsanyi, Magda [Bay Zoltan Institute for Material Science (Hungary); Kakay, Attila [Research Institute for Solid State Physics and Optics (Hungary); Nagy, Ferenc [Eoetvoes Lorand University, Research Group for Nuclear Methods in Structural Chemistry, Hungarian Academy of Sciences, Department of Nuclear Chemistry (Hungary); Varga, Lajos Karoly [Research Institute for Solid State Physics and Optics (Hungary)

2005-09-15

{sup 57}Fe conversion electron Moessbauer spectroscopy, X-ray diffraction, electrochemical and magnetic measurements were used to study pulse electroplated Fe-P and Ni-Fe coatings. XRD and {sup 57}Fe CEMS measurements revealed the amorphous character of the novel pulse plated Fe-P alloys. CEM spectra indicated significant differences in the short range order and in the magnetic anisotropy between the Fe-P deposits pulse plated at medium long deposition time (t{sub on} = 2 ms), with short relaxation time (t{sub off} = 9 ms) and low current density (I{sub p} = 0.05 Acm{sup -2}) or at short deposition time (t{sub on} = 1 ms) with long relaxation time (t{sub off} = 250 ms) and high current density (I{sub p} = 1.0 Acm{sup -2}). The broad peaks centred around the fcc reflections in XRD of the pulse plated Ni-22 wt.% Fe deposit reflected a microcrystalline Ni-Fe alloy with a very fine, 5-8 nm, grain size. The CEM spectrum of the pulse plated Ni-22 wt.% Fe coating corresponded to a highly disordered solid solution alloy containing a minute amount of ferrihydrite. Extreme favourable soft magnetic properties were observed with these Ni-Fe and Fe-P pulse plated thin layers.

Classifying genes to the correct Gene Ontology Slim term in Saccharomyces cerevisiae using neighbouring genes with classification learning

Directory of Open Access Journals (Sweden)

Tsatsoulis Costas

2010-05-01

Full Text Available Abstract Background There is increasing evidence that gene location and surrounding genes influence the functionality of genes in the eukaryotic genome. Knowing the Gene Ontology Slim terms associated with a gene gives us insight into a gene's functionality by informing us how its gene product behaves in a cellular context using three different ontologies: molecular function, biological process, and cellular component. In this study, we analyzed if we could classify a gene in Saccharomyces cerevisiae to its correct Gene Ontology Slim term using information about its location in the genome and information from its nearest-neighbouring genes using classification learning. Results We performed experiments to establish that the MultiBoostAB algorithm using the J48 classifier could correctly classify Gene Ontology Slim terms of a gene given information regarding the gene's location and information from its nearest-neighbouring genes for training. Different neighbourhood sizes were examined to determine how many nearest neighbours should be included around each gene to provide better classification rules. Our results show that by just incorporating neighbour information from each gene's two-nearest neighbours, the percentage of correctly classified genes to their correct Gene Ontology Slim term for each ontology reaches over 80% with high accuracy (reflected in F-measures over 0.80 of the classification rules produced. Conclusions We confirmed that in classifying genes to their correct Gene Ontology Slim term, the inclusion of neighbour information from those genes is beneficial. Knowing the location of a gene and the Gene Ontology Slim information from neighbouring genes gives us insight into that gene's functionality. This benefit is seen by just including information from a gene's two-nearest neighbouring genes.

Protein Scaffolding for Small Molecule Catalysts

Energy Technology Data Exchange (ETDEWEB)

Baker, David [Univ. of Washington, Seattle, WA (United States)

2014-09-14

We aim to design hybrid catalysts for energy production and storage that combine the high specificity, affinity, and tunability of proteins with the potent chemical reactivities of small organometallic molecules. The widely used Rosetta and RosettaDesign methodologies will be extended to model novel protein / small molecule catalysts in which one or many small molecule active centers are supported and coordinated by protein scaffolding. The promise of such hybrid molecular systems will be demonstrated with the nickel-phosphine hydrogenase of DuBois et. al.We will enhance the hydrogenase activity of the catalyst by designing protein scaffolds that incorporate proton relays and systematically modulate the local environment of the catalyticcenter. In collaboration with DuBois and Shaw, the designs will be experimentally synthesized and characterized.

Evolution from a respiratory ancestor to fill syntrophic and fermentative niches: comparative fenomics of six Geobacteraceae species

Directory of Open Access Journals (Sweden)

Lovley Derek R

2009-03-01

Full Text Available Abstract Background The anaerobic degradation of organic matter in natural environments, and the biotechnical use of anaerobes in energy production and remediation of subsurface environments, both require the cooperative activity of a diversity of microorganisms in different metabolic niches. The Geobacteraceae family contains members with three important anaerobic metabolisms: fermentation, syntrophic degradation of fermentation intermediates, and anaerobic respiration. Results In order to learn more about the evolution of anaerobic microbial communities, the genome sequences of six Geobacteraceae species were analyzed. The results indicate that the last common Geobacteraceae ancestor contained sufficient genes for anaerobic respiration, completely oxidizing organic compounds with the reduction of external electron acceptors, features that are still retained in modern Geobacter and Desulfuromonas species. Evolution of specialization for fermentative growth arose twice, via distinct lateral gene transfer events, in Pelobacter carbinolicus and Pelobacter propionicus. Furthermore, P. carbinolicus gained hydrogenase genes and genes for ferredoxin reduction that appear to permit syntrophic growth via hydrogen production. The gain of new physiological capabilities in the Pelobacter species were accompanied by the loss of several key genes necessary for the complete oxidation of organic compounds and the genes for the c-type cytochromes required for extracellular electron transfer. Conclusion The results suggest that Pelobacter species evolved parallel strategies to enhance their ability to compete in environments in which electron acceptors for anaerobic respiration were limiting. More generally, these results demonstrate how relatively few gene changes can dramatically transform metabolic capabilities and expand the range of environments in which microorganisms can compete.

High hydrostatic pressure adaptive strategies in an obligate piezophile Pyrococcus yayanosii

KAUST Repository

Michoud, Gregoire; Jebbar, Mohamed

2016-01-01

Pyrococcus yayanosii CH1, as the first and only obligate piezophilic hyperthermophilic microorganism discovered to date, extends the physical and chemical limits of life on Earth. It was isolated from the Ashadze hydrothermal vent at 4,100 m depth. Multi-omics analyses were performed to study the mechanisms used by the cell to cope with high hydrostatic pressure variations. In silico analyses showed that the P. yayanosii genome is highly adapted to its harsh environment, with a loss of aromatic amino acid biosynthesis pathways and the high constitutive expression of the energy metabolism compared with other non-obligate piezophilic Pyrococcus species. Differential proteomics and transcriptomics analyses identified key hydrostatic pressure-responsive genes involved in translation, chemotaxis, energy metabolism (hydrogenases and formate metabolism) and Clustered Regularly Interspaced Short Palindromic Repeats sequences associated with Cellular apoptosis susceptibility proteins.

High hydrostatic pressure adaptive strategies in an obligate piezophile Pyrococcus yayanosii

KAUST Repository

Michoud, Gregoire

2016-06-02

Pyrococcus yayanosii CH1, as the first and only obligate piezophilic hyperthermophilic microorganism discovered to date, extends the physical and chemical limits of life on Earth. It was isolated from the Ashadze hydrothermal vent at 4,100 m depth. Multi-omics analyses were performed to study the mechanisms used by the cell to cope with high hydrostatic pressure variations. In silico analyses showed that the P. yayanosii genome is highly adapted to its harsh environment, with a loss of aromatic amino acid biosynthesis pathways and the high constitutive expression of the energy metabolism compared with other non-obligate piezophilic Pyrococcus species. Differential proteomics and transcriptomics analyses identified key hydrostatic pressure-responsive genes involved in translation, chemotaxis, energy metabolism (hydrogenases and formate metabolism) and Clustered Regularly Interspaced Short Palindromic Repeats sequences associated with Cellular apoptosis susceptibility proteins.

High hydrostatic pressure adaptive strategies in an obligate piezophile Pyrococcus yayanosii

Science.gov (United States)

Michoud, Grégoire; Jebbar, Mohamed

2016-01-01

Pyrococcus yayanosii CH1, as the first and only obligate piezophilic hyperthermophilic microorganism discovered to date, extends the physical and chemical limits of life on Earth. It was isolated from the Ashadze hydrothermal vent at 4,100 m depth. Multi-omics analyses were performed to study the mechanisms used by the cell to cope with high hydrostatic pressure variations. In silico analyses showed that the P. yayanosii genome is highly adapted to its harsh environment, with a loss of aromatic amino acid biosynthesis pathways and the high constitutive expression of the energy metabolism compared with other non-obligate piezophilic Pyrococcus species. Differential proteomics and transcriptomics analyses identified key hydrostatic pressure-responsive genes involved in translation, chemotaxis, energy metabolism (hydrogenases and formate metabolism) and Clustered Regularly Interspaced Short Palindromic Repeats sequences associated with Cellular apoptosis susceptibility proteins. PMID:27250364

Method for the enzymatic production of hydrogen

Science.gov (United States)

Woodward, J.; Mattingly, S.M.

1999-08-24

The present invention is an enzymatic method for producing hydrogen comprising the steps of: (a) forming a reaction mixture within a reaction vessel comprising a substrate capable of undergoing oxidation within a catabolic reaction, such as glucose, galactose, xylose, mannose, sucrose, lactose, cellulose, xylan and starch; the reaction mixture also comprising an amount of glucose dehydrogenase in an amount sufficient to catalyze the oxidation of the substrate, an amount of hydrogenase sufficient to catalyze an electron-requiring reaction wherein a stoichiometric yield of hydrogen is produced, an amount of pH buffer in an amount sufficient to provide an environment that allows the hydrogenase and the glucose dehydrogenase to retain sufficient activity for the production of hydrogen to occur and also comprising an amount of nicotinamide adenine dinucleotide phosphate sufficient to transfer electrons from the catabolic reaction to the electron-requiring reaction; (b) heating the reaction mixture at a temperature sufficient for glucose dehydrogenase and the hydrogenase to retain sufficient activity and sufficient for the production of hydrogen to occur, and heating for a period of time that continues until the hydrogen is no longer produced by the reaction mixture, wherein the catabolic reaction and the electron-requiring reactions have rates of reaction dependent upon the temperature; and (c) detecting the hydrogen produced from the reaction mixture. 8 figs.

Parallel ferromagnetic resonance and spin-wave excitation in exchange-biased NiFe/IrMn bilayers

Energy Technology Data Exchange (ETDEWEB)

Sousa, Marcos Antonio de, E-mail: marcossharp@gmail.com [Instituto de Física, Universidade Federal de Goiás, Goiânia, 74001-970 (Brazil); Pelegrini, Fernando [Instituto de Física, Universidade Federal de Goiás, Goiânia, 74001-970 (Brazil); Alayo, Willian [Departamento de Física, Universidade Federal de Pelotas, Pelotas, 96010-900 (Brazil); Quispe-Marcatoma, Justiniano; Baggio-Saitovitch, Elisa [Centro Brasileiro de Pesquisas Físicas, Rio de Janeiro, 22290-180 (Brazil)

2014-10-01

Ferromagnetic Resonance study of sputtered Ru(7 nm)/NiFe(t{sub FM})/IrMn(6 nm)/Ru(5 nm) exchange-biased bilayers at X and Q-band microwave frequencies reveals the excitation of spin-wave and NiFe resonance modes. Angular variations of the in-plane resonance fields of spin-wave and NiFe resonance modes show the effect of the unidirectional anisotropy, which is about twice larger for the spin-wave mode due to spin pinning at the NiFe/IrMn interface. At Q-band frequency the angular variations of in-plane resonance fields also reveal the symmetry of a uniaxial anisotropy. A modified theoretical model which also includes the contribution of a rotatable anisotropy provides a good description of the experimental results.

Electric-field tunable spin diode FMR in patterned PMN-PT/NiFe structures

Energy Technology Data Exchange (ETDEWEB)

Ziętek, Slawomir, E-mail: zietek@agh.edu.pl; Skowroński, Witold; Stobiecki, Tomasz [AGH University of Science and Technology, Department of Electronics, Al. Mickiewicza 30, 30-059 Kraków (Poland); Ogrodnik, Piotr, E-mail: piotrogr@if.pw.edu.pl [AGH University of Science and Technology, Department of Electronics, Al. Mickiewicza 30, 30-059 Kraków (Poland); Faculty of Physics, Warsaw University of Technology, ul. Koszykowa 75, 00-662 Warszawa (Poland); Stobiecki, Feliks [Institute of Molecular Physics, Polish Academy of Sciences, ul. Smoluchowskiego 17, 60-179 Poznań (Poland); Dijken, Sebastiaan van [NanoSpin, Department of Applied Physics, Aalto University School of Science, P.O. Box 15100, FI-00076 Aalto (Finland); Barnaś, Józef [Faculty of Physics, Adam Mickiewicz University, ul. Umultowska 85, 61-614 Poznań (Poland); Institute of Molecular Physics, Polish Academy of Sciences, ul. Smoluchowskiego 17, 60-179 Poznań (Poland)

2016-08-15

Dynamic properties of NiFe thin films on PMN-PT piezoelectric substrate are investigated using the spin-diode method. Ferromagnetic resonance (FMR) spectra of microstrips with varying width are measured as a function of magnetic field and frequency. The FMR frequency is shown to depend on the electric field applied across the substrate, which induces strain in the NiFe layer. Electric field tunability of up to 100 MHz per 1 kV/cm is achieved. An analytical model based on total energy minimization and the Landau-Lifshitz-Gilbert equation, taking into account the magnetostriction effect, is used to explain the measured dynamics. Based on this model, conditions for optimal electric-field tunable spin diode FMR in patterned NiFe/PMN-PT structures are derived.

Sexy gene conversions: locating gene conversions on the X-chromosome.

Science.gov (United States)

Lawson, Mark J; Zhang, Liqing

2009-08-01

Gene conversion can have a profound impact on both the short- and long-term evolution of genes and genomes. Here, we examined the gene families that are located on the X-chromosomes of human (Homo sapiens), chimpanzee (Pan troglodytes), mouse (Mus musculus) and rat (Rattus norvegicus) for evidence of gene conversion. We identified seven gene families (WD repeat protein family, Ferritin Heavy Chain family, RAS-related Protein RAB-40 family, Diphosphoinositol polyphosphate phosphohydrolase family, Transcription Elongation Factor A family, LDOC1-related family, Zinc Finger Protein ZIC, and GLI family) that show evidence of gene conversion. Through phylogenetic analyses and synteny evidence, we show that gene conversion has played an important role in the evolution of these gene families and that gene conversion has occurred independently in both primates and rodents. Comparing the results with those of two gene conversion prediction programs (GENECONV and Partimatrix), we found that both GENECONV and Partimatrix have very high false negative rates (i.e. failed to predict gene conversions), which leads to many undetected gene conversions. The combination of phylogenetic analyses with physical synteny evidence exhibits high resolution in the detection of gene conversions.

Unique flexibility in energy metabolism allows mycobacteria to combat starvation and hypoxia.

Directory of Open Access Journals (Sweden)

Michael Berney

Full Text Available Mycobacteria are a group of obligate aerobes that require oxygen for growth, but paradoxically have the ability to survive and metabolize under hypoxia. The mechanisms responsible for this metabolic plasticity are unknown. Here, we report on the adaptation of Mycobacterium smegmatis to slow growth rate and hypoxia using carbon-limited continuous culture. When M. smegmatis is switched from a 4.6 h to a 69 h doubling time at a constant oxygen saturation of 50%, the cells respond through the down regulation of respiratory chain components and the F1Fo-ATP synthase, consistent with the cells lower demand for energy at a reduced growth rate. This was paralleled by an up regulation of molecular machinery that allowed more efficient energy generation (i.e. Complex I and the use of alternative electron donors (e.g. hydrogenases and primary dehydrogenases to maintain the flow of reducing equivalents to the electron transport chain during conditions of severe energy limitation. A hydrogenase mutant showed a 40% reduction in growth yield highlighting the importance of this enzyme in adaptation to low energy supply. Slow growing cells at 50% oxygen saturation subjected to hypoxia (0.6% oxygen saturation responded by switching on oxygen scavenging cytochrome bd, proton-translocating cytochrome bc1-aa3 supercomplex, another putative hydrogenase, and by substituting NAD+-dependent enzymes with ferredoxin-dependent enzymes thus highlighting a new pattern of mycobacterial adaptation to hypoxia. The expression of ferredoxins and a hydrogenase provides a potential conduit for disposing of and transferring electrons in the absence of exogenous electron acceptors. The use of ferredoxin-dependent enzymes would allow the cell to maintain a high carbon flux through its central carbon metabolism independent of the NAD+/NADH ratio. These data demonstrate the remarkable metabolic plasticity of the mycobacterial cell and provide a new framework for understanding their

Optimal Reference Genes for Gene Expression Normalization in Trichomonas vaginalis

Science.gov (United States)

dos Santos, Odelta; de Vargas Rigo, Graziela; Frasson, Amanda Piccoli; Macedo, Alexandre José; Tasca, Tiana

2015-01-01

Trichomonas vaginalis is the etiologic agent of trichomonosis, the most common non-viral sexually transmitted disease worldwide. This infection is associated with several health consequences, including cervical and prostate cancers and HIV acquisition. Gene expression analysis has been facilitated because of available genome sequences and large-scale transcriptomes in T. vaginalis, particularly using quantitative real-time polymerase chain reaction (qRT-PCR), one of the most used methods for molecular studies. Reference genes for normalization are crucial to ensure the accuracy of this method. However, to the best of our knowledge, a systematic validation of reference genes has not been performed for T. vaginalis. In this study, the transcripts of nine candidate reference genes were quantified using qRT-PCR under different cultivation conditions, and the stability of these genes was compared using the geNorm and NormFinder algorithms. The most stable reference genes were α-tubulin, actin and DNATopII, and, conversely, the widely used T. vaginalis reference genes GAPDH and β-tubulin were less stable. The PFOR gene was used to validate the reliability of the use of these candidate reference genes. As expected, the PFOR gene was upregulated when the trophozoites were cultivated with ferrous ammonium sulfate when the DNATopII, α-tubulin and actin genes were used as normalizing gene. By contrast, the PFOR gene was downregulated when the GAPDH gene was used as an internal control, leading to misinterpretation of the data. These results provide an important starting point for reference gene selection and gene expression analysis with qRT-PCR studies of T. vaginalis. PMID:26393928

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

Science.gov (United States)

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

Stable isotopes can provide considerable insight into enzymatic mechanisms and fluxes in various biological processes. In our studies, we used stable isotopes to characterize both enzyme-catalyzed H2 and N2O production. H2 is a potential alternative clean energy source and also a key metabolite in many microbial communities. Biological H2 production is generally catalyzed by hydrogenases, enzymes that combine protons and electrons to produce H2 under anaerobic conditions. In our study, H isotopes and fractionation factors (α) were used to characterize two types of hydrogenases: [FeFe]- and [NiFe]-hydrogenases. Due to differences in the active site, the α associated with H2 production for [FeFe]- and [NiFe]-hydrogenases separated into two distinct clusters (αFeFe > αNiFe). The calculated kinetic isotope effects indicate that hydrogenase-catalyzed H2 production has a preference for light isotopes, consistent with the relative bond strengths of O-H and H-H bonds. Interestingly, the isotope effects associated with H2 consumption and H2-H2O exchange reactions were also characterized, but in this case no specific difference was observed between the different enzymes. N2O is a potent greenhouse gas with a global warming potential 300 times that of CO2, and the concentration of N2O is currently increasing at a rate of ~0.25% per year. Thus far, bacterial and fungal denitrification processes have been identified as two of the major sources of biologically generated N2O. In this study, we measured the δ15N, δ18O, δ15Nα (central N atom in N2O), and δ15Nβ (terminal N atom in N2O) of N2O generated by purified fungal P450 nitric oxide reductase (P450nor) from Histoplasma capsulatum. We observed normal isotope effects for δ18O and δ15Nα, and inverse isotope effects for bulk δ15N (the average of Nα and Nβ) and δ15Nβ. The observed isotope effects have been used in conjunction with DFT calculations to provide important insight into the mechanism of P450nor. Similar

Patenting human genes: Chinese academic articles' portrayal of gene patents.

Science.gov (United States)

Du, Li

2018-04-24

The patenting of human genes has been the subject of debate for decades. While China has gradually come to play an important role in the global genomics-based testing and treatment market, little is known about Chinese scholars' perspectives on patent protection for human genes. A content analysis of academic literature was conducted to identify Chinese scholars' concerns regarding gene patents, including benefits and risks of patenting human genes, attitudes that researchers hold towards gene patenting, and any legal and policy recommendations offered for the gene patent regime in China. 57.2% of articles were written by law professors, but scholars from health sciences, liberal arts, and ethics also participated in discussions on gene patent issues. While discussions of benefits and risks were relatively balanced in the articles, 63.5% of the articles favored gene patenting in general and, of the articles (n = 41) that explored gene patents in the Chinese context, 90.2% supported patent protections for human genes in China. The patentability of human genes was discussed in 33 articles, and 75.8% of these articles reached the conclusion that human genes are patentable. Chinese scholars view the patent regime as an important legal tool to protect the interests of inventors and inventions as well as the genetic resources of China. As such, many scholars support a gene patent system in China. These attitudes towards gene patents remain unchanged following the court ruling in the Myriad case in 2013, but arguments have been raised about the scope of gene patents, in particular that the increasing numbers of gene patents may negatively impact public health in China.

Research progress in machine learning methods for gene-gene interaction detection.

Science.gov (United States)

Peng, Zhe-Ye; Tang, Zi-Jun; Xie, Min-Zhu

2018-03-20

Complex diseases are results of gene-gene and gene-environment interactions. However, the detection of high-dimensional gene-gene interactions is computationally challenging. In the last two decades, machine-learning approaches have been developed to detect gene-gene interactions with some successes. In this review, we summarize the progress in research on machine learning methods, as applied to gene-gene interaction detection. It systematically examines the principles and limitations of the current machine learning methods used in genome wide association studies (GWAS) to detect gene-gene interactions, such as neural networks (NN), random forest (RF), support vector machines (SVM) and multifactor dimensionality reduction (MDR), and provides some insights on the future research directions in the field.

Gene Circuit Analysis of the Terminal Gap Gene huckebein

Science.gov (United States)

Ashyraliyev, Maksat; Siggens, Ken; Janssens, Hilde; Blom, Joke; Akam, Michael; Jaeger, Johannes

2009-01-01

The early embryo of Drosophila melanogaster provides a powerful model system to study the role of genes in pattern formation. The gap gene network constitutes the first zygotic regulatory tier in the hierarchy of the segmentation genes involved in specifying the position of body segments. Here, we use an integrative, systems-level approach to investigate the regulatory effect of the terminal gap gene huckebein (hkb) on gap gene expression. We present quantitative expression data for the Hkb protein, which enable us to include hkb in gap gene circuit models. Gap gene circuits are mathematical models of gene networks used as computational tools to extract regulatory information from spatial expression data. This is achieved by fitting the model to gap gene expression patterns, in order to obtain estimates for regulatory parameters which predict a specific network topology. We show how considering variability in the data combined with analysis of parameter determinability significantly improves the biological relevance and consistency of the approach. Our models are in agreement with earlier results, which they extend in two important respects: First, we show that Hkb is involved in the regulation of the posterior hunchback (hb) domain, but does not have any other essential function. Specifically, Hkb is required for the anterior shift in the posterior border of this domain, which is now reproduced correctly in our models. Second, gap gene circuits presented here are able to reproduce mutants of terminal gap genes, while previously published models were unable to reproduce any null mutants correctly. As a consequence, our models now capture the expression dynamics of all posterior gap genes and some variational properties of the system correctly. This is an important step towards a better, quantitative understanding of the developmental and evolutionary dynamics of the gap gene network. PMID:19876378

Gene expression

International Nuclear Information System (INIS)

Hildebrand, C.E.; Crawford, B.D.; Walters, R.A.; Enger, M.D.

1983-01-01

We prepared probes for isolating functional pieces of the metallothionein locus. The probes enabled a variety of experiments, eventually revealing two mechanisms for metallothionein gene expression, the order of the DNA coding units at the locus, and the location of the gene site in its chromosome. Once the switch regulating metallothionein synthesis was located, it could be joined by recombinant DNA methods to other, unrelated genes, then reintroduced into cells by gene-transfer techniques. The expression of these recombinant genes could then be induced by exposing the cells to Zn 2+ or Cd 2+ . We would thus take advantage of the clearly defined switching properties of the metallothionein gene to manipulate the expression of other, perhaps normally constitutive, genes. Already, despite an incomplete understanding of how the regulatory switch of the metallothionein locus operates, such experiments have been performed successfully

Genes from scratch--the evolutionary fate of de novo genes.

Science.gov (United States)

Schlötterer, Christian

2015-04-01

Although considered an extremely unlikely event, many genes emerge from previously noncoding genomic regions. This review covers the entire life cycle of such de novo genes. Two competing hypotheses about the process of de novo gene birth are discussed as well as the high death rate of de novo genes. Despite the high death rate, some de novo genes are retained and remain functional, even in distantly related species, through their integration into gene networks. Further studies combining gene expression with ribosome profiling in multiple populations across different species will be instrumental for an improved understanding of the evolutionary processes operating on de novo genes. Copyright © 2015 The Author. Published by Elsevier Ltd.. All rights reserved.

Matrix composition effects on the tensile properties of tungsten-molybdenum heavy alloys

International Nuclear Information System (INIS)

Bose, A.; German, R.N.

1990-01-01

Tungsten-base heavy alloys are liquid-phase sintered from mixed tungsten, nickel, and iron powders. The sintered product is a composite consisting of interlaced tungsten and solidified matrix (W-Ni-Fe) phases. These alloys are most useful in applications requiring high density, strength, and toughness. The design of improved tungsten heavy alloys has been the subject of several research investigations. Much success has taken place through improved processing, but parallel compositional studies have resulted in new microstructure-property combinations. As part of these investigations, the Ni/Fe ratio has been varied, with the general conclusion that optimal strength and ductility occur with a ratio between 2 and 4. Brittle intermetallic phases can form outside of this composition range. Historically, a 7/3 Ni/Fe ratio has been selected for processing studies. Recently, others reported higher ductilities and impact energies for 90 and 93 pct W heavy alloys with the 8/2 Ni/Fe ratio. Alternatively, these alloys can be strengthened by both solid solution and grain size refinement through incorporation of molybdenum, tantalum, or rhenium. These additions are soluble in both the tungsten and matrix phases and retard solution-reprecipitation during liquid phase sintering. In this study, the alloy composition was varied in the nickel/iron ratio and molybdenum was partially substituted for tungsten. The sintered tensile properties are assessed vs these compositional variations

Ordered mesoporous MFe(2)O(4) (M = Co, Cu, Mg, Ni, Zn) thin films with nanocrystalline walls, uniform 16 nm diameter pores and high thermal stability: template-directed synthesis and characterization of redox active trevorite.

Science.gov (United States)

Haetge, Jan; Suchomski, Christian; Brezesinski, Torsten

2010-12-20

In this paper, we report on ordered mesoporous NiFe(2)O(4) thin films synthesized via co-assembly of hydrated ferric nitrate and nickel chloride with an amphiphilic diblock copolymer, referred to as KLE. We establish that the NiFe(2)O(4) samples are highly crystalline after calcination at 600 °C, and that the conversion of the amorphous inorganic framework comes at little cost to the ordering of the high quality cubic network of pores averaging 16 nm in diameter. We further show that the synthesis method employed in this work can be readily extended to other ferrites, such as CoFe(2)O(4), CuFe(2)O(4), MgFe(2)O(4), and ZnFe(2)O(4), which could pave the way for innovative device design. While this article focuses on the self-assembly and characterization of these materials using various state-of-the-art techniques, including electron microscopy, grazing incidence small-angle X-ray scattering (GISAXS), time-of-flight secondary ion mass spectrometry (TOF-SIMS), X-ray photoelectron spectroscopy (XPS), as well as UV-vis and Raman spectroscopy, we also examine the electrochemical properties and show the benefits of combining a continuous mesoporosity with nanocrystalline films. KLE-templated NiFe(2)O(4) electrodes exhibit reasonable levels of lithium ion storage at short charging times which stem from facile pseudocapacitance.

Gene Duplicability of Core Genes Is Highly Consistent across All Angiosperms.

Science.gov (United States)

Li, Zhen; Defoort, Jonas; Tasdighian, Setareh; Maere, Steven; Van de Peer, Yves; De Smet, Riet

2016-02-01

Gene duplication is an important mechanism for adding to genomic novelty. Hence, which genes undergo duplication and are preserved following duplication is an important question. It has been observed that gene duplicability, or the ability of genes to be retained following duplication, is a nonrandom process, with certain genes being more amenable to survive duplication events than others. Primarily, gene essentiality and the type of duplication (small-scale versus large-scale) have been shown in different species to influence the (long-term) survival of novel genes. However, an overarching view of "gene duplicability" is lacking, mainly due to the fact that previous studies usually focused on individual species and did not account for the influence of genomic context and the time of duplication. Here, we present a large-scale study in which we investigated duplicate retention for 9178 gene families shared between 37 flowering plant species, referred to as angiosperm core gene families. For most gene families, we observe a strikingly consistent pattern of gene duplicability across species, with gene families being either primarily single-copy or multicopy in all species. An intermediate class contains gene families that are often retained in duplicate for periods extending to tens of millions of years after whole-genome duplication, but ultimately appear to be largely restored to singleton status, suggesting that these genes may be dosage balance sensitive. The distinction between single-copy and multicopy gene families is reflected in their functional annotation, with single-copy genes being mainly involved in the maintenance of genome stability and organelle function and multicopy genes in signaling, transport, and metabolism. The intermediate class was overrepresented in regulatory genes, further suggesting that these represent putative dosage-balance-sensitive genes. © 2016 American Society of Plant Biologists. All rights reserved.

Advances in study of reporter gene imaging for monitoring gene therapy

International Nuclear Information System (INIS)

Mu Chuanjie; Zhou Jiwen

2003-01-01

To evaluate the efficiency of gene therapy, it is requisite to monitor localization and expression of the therapeutic gene in vivo. Monitoring expression of reporter gene using radionuclide reporter gene technique is the best method. Adenoviral vectors expressing reporter gene are constructed using gene fusion, bicistronic, double promoter or bidirectional transcriptional recombination techniques, and transferred into target cells and tissues, then injected radiolabeled reporter probes which couple to the reporter genes. The reporter genes can be imaged invasively, repeatedly, quantitatively with γ-camera, PET and SPECT. Recently, several reporter gene and reporter probe systems have been used in studies of gene therapy. The part of them has been used for clinic trials

Global transcriptome analysis of the heat shock response ofshewanella oneidensis

Energy Technology Data Exchange (ETDEWEB)

Gao, Haichun; Wang, Sarah; Liu, Xueduan; Yan, Tinfeng; Wu, Liyou; Alm, Eric; Arkin, Adam P.; Thompson, Dorothea K.; Zhou, Jizhong

2004-04-30

Shewanella oneidensis is an important model organism for bioremediation studies because of its diverse respiratory capabilities. However, the genetic basis and regulatory mechanisms underlying the ability of S. oneidensis to survive and adapt to various environmentally relevant stresses is poorly understood. To define this organism's molecular response to elevated growth temperatures, temporal gene expression profiles were examined in cells subjected to heat stress using whole-genome DNA microarrays for S. oneidensis MR-1. Approximately 15 percent (711) of the predicted S. oneidensis genes represented on the microarray were significantly up- or down-regulated (P < 0.05) over a 25-min period following shift to the heat shock temperature (42 C). As expected, the majority of S. oneidensis genes exhibiting homology to known chaperones and heat shock proteins (Hsps) were highly and transiently induced. In addition, a number of predicted genes encoding enzymes in glycolys is and the pentose cycle, [NiFe] dehydrogenase, serine proteases, transcriptional regulators (MerR, LysR, and TetR families), histidine kinases, and hypothetical proteins were induced in response to heat stress. Genes encoding membrane proteins were differentially expressed, suggesting that cells possibly alter their membrane composition or structure in response to variations in growth temperature. A substantial number of the genes encoding ribosomal proteins displayed down-regulated co-expression patterns in response to heat stress, as did genes encoding prophage and flagellar proteins. Finally, based on computational comparative analysis of the upstream promoter regions of S.oneidensis heat-inducible genes, a putative regulatory motif, showing high conservation to the Escherichia coli sigma 32-binding consensus sequence, was identified.

Down-Regulation of Gene Expression by RNA-Induced Gene Silencing

Science.gov (United States)

Travella, Silvia; Keller, Beat

Down-regulation of endogenous genes via post-transcriptional gene silencing (PTGS) is a key to the characterization of gene function in plants. Many RNA-based silencing mechanisms such as post-transcriptional gene silencing, co-suppression, quelling, and RNA interference (RNAi) have been discovered among species of different kingdoms (plants, fungi, and animals). One of the most interesting discoveries was RNAi, a sequence-specific gene-silencing mechanism initiated by the introduction of double-stranded RNA (dsRNA), homologous in sequence to the silenced gene, which triggers degradation of mRNA. Infection of plants with modified viruses can also induce RNA silencing and is referred to as virus-induced gene silencing (VIGS). In contrast to insertional mutagenesis, these emerging new reverse genetic approaches represent a powerful tool for exploring gene function and for manipulating gene expression experimentally in cereal species such as barley and wheat. We examined how RNAi and VIGS have been used to assess gene function in barley and wheat, including molecular mechanisms involved in the process and available methodological elements, such as vectors, inoculation procedures, and analysis of silenced phenotypes.

Therapeutic genes for anti-HIV/AIDS gene therapy.

Science.gov (United States)

Bovolenta, Chiara; Porcellini, Simona; Alberici, Luca

2013-01-01

The multiple therapeutic approaches developed so far to cope HIV-1 infection, such as anti-retroviral drugs, germicides and several attempts of therapeutic vaccination have provided significant amelioration in terms of life-quality and survival rate of AIDS patients. Nevertheless, no approach has demonstrated efficacy in eradicating this lethal, if untreated, infection. The curative power of gene therapy has been proven for the treatment of monogenic immunodeficiensies, where permanent gene modification of host cells is sufficient to correct the defect for life-time. No doubt, a similar concept is not applicable for gene therapy of infectious immunodeficiensies as AIDS, where there is not a single gene to be corrected; rather engineered cells must gain immunotherapeutic or antiviral features to grant either short- or long-term efficacy mostly by acquisition of antiviral genes or payloads. Anti-HIV/AIDS gene therapy is one of the most promising strategy, although challenging, to eradicate HIV-1 infection. In fact, genetic modification of hematopoietic stem cells with one or multiple therapeutic genes is expected to originate blood cell progenies resistant to viral infection and thereby able to prevail on infected unprotected cells. Ultimately, protected cells will re-establish a functional immune system able to control HIV-1 replication. More than hundred gene therapy clinical trials against AIDS employing different viral vectors and transgenes have been approved or are currently ongoing worldwide. This review will overview anti-HIV-1 infection gene therapy field evaluating strength and weakness of the transgenes and payloads used in the past and of those potentially exploitable in the future.

the tnfluence of breed, castration and age on muscle fibre type and ...

African Journals Online (AJOL)

For histochemical demonstration of succinic de- hydrogenase situated in the ..... centage coefficient of variation elucidates the matter. At. 34/' in the case of the .... metabolic and functional properties of skeletal muscle in relation to meat quality,.

Discovering implicit entity relation with the gene-citation-gene network.

Directory of Open Access Journals (Sweden)

Min Song

Full Text Available In this paper, we apply the entitymetrics model to our constructed Gene-Citation-Gene (GCG network. Based on the premise there is a hidden, but plausible, relationship between an entity in one article and an entity in its citing article, we constructed a GCG network of gene pairs implicitly connected through citation. We compare the performance of this GCG network to a gene-gene (GG network constructed over the same corpus but which uses gene pairs explicitly connected through traditional co-occurrence. Using 331,411 MEDLINE abstracts collected from 18,323 seed articles and their references, we identify 25 gene pairs. A comparison of these pairs with interactions found in BioGRID reveal that 96% of the gene pairs in the GCG network have known interactions. We measure network performance using degree, weighted degree, closeness, betweenness centrality and PageRank. Combining all measures, we find the GCG network has more gene pairs, but a lower matching rate than the GG network. However, combining top ranked genes in both networks produces a matching rate of 35.53%. By visualizing both the GG and GCG networks, we find that cancer is the most dominant disease associated with the genes in both networks. Overall, the study indicates that the GCG network can be useful for detecting gene interaction in an implicit manner.

Reduced rates of gene loss, gene silencing, and gene mutation in Dnmt1-deficient embryonic stem cells

NARCIS (Netherlands)

Chan, M.F.; van Amerongen, R.; Nijjar, T.; Cuppen, E.; Jones, P.A.; Laird, P.W.

2001-01-01

Tumor suppressor gene inactivation is a crucial event in oncogenesis. Gene inactivation mechanisms include events resulting in loss of heterozygosity (LOH), gene mutation, and transcriptional silencing. The contribution of each of these different pathways varies among tumor suppressor genes and by

A hybrid approach of gene sets and single genes for the prediction of survival risks with gene expression data.

Science.gov (United States)

Seok, Junhee; Davis, Ronald W; Xiao, Wenzhong

2015-01-01

Accumulated biological knowledge is often encoded as gene sets, collections of genes associated with similar biological functions or pathways. The use of gene sets in the analyses of high-throughput gene expression data has been intensively studied and applied in clinical research. However, the main interest remains in finding modules of biological knowledge, or corresponding gene sets, significantly associated with disease conditions. Risk prediction from censored survival times using gene sets hasn't been well studied. In this work, we propose a hybrid method that uses both single gene and gene set information together to predict patient survival risks from gene expression profiles. In the proposed method, gene sets provide context-level information that is poorly reflected by single genes. Complementarily, single genes help to supplement incomplete information of gene sets due to our imperfect biomedical knowledge. Through the tests over multiple data sets of cancer and trauma injury, the proposed method showed robust and improved performance compared with the conventional approaches with only single genes or gene sets solely. Additionally, we examined the prediction result in the trauma injury data, and showed that the modules of biological knowledge used in the prediction by the proposed method were highly interpretable in biology. A wide range of survival prediction problems in clinical genomics is expected to benefit from the use of biological knowledge.

Probing the oxidation kinetics of small permalloy particles

International Nuclear Information System (INIS)

Dong, Xiaolei; Song, Xiao; Yin, Shiliu; Shirolkar, Mandar M.; Li, Ming; Wang, Haiqian

2017-01-01

The oxidation of permalloys is important to apply in a wide range. The oxidation and diffusion mechanisms of small permalloy particles with different Fe content are studied by using thermal gravimetric analysis (TGA) and microstructure characterizations. Fe 2 O 3 /(Ni, Fe) 3 O 4 plays a key role in the morphology evolution and diffusion mechanisms of small NiFe particles upon oxidation. The activation energies of grain boundary diffusion for the NiFe alloys increase from 141 kJ/mol to 208 kJ/mol as the Fe content increases from 0 to ~50 wt%. We have developed a diffusion process resolved temperature programed oxidation (PR-TPO) analysis method. Three diffusion mechanisms have been recognized by using this method: In addition to the grain boundary diffusion and lattice diffusion, our TGA analysis suggests that the phase conversion from Fe 2 O 3 to (Ni, Fe) 3 O 4 induces diffusion change and affects the diffusion process at the intermediate temperature. Relevant oxidation kinetics and diffusion mechanisms are discussed. - Graphical abstract: The oxidation mechanisms of small Permalloy particles with different Fe content is studied by using thermal gravimetric analysis (TGA) and microstructure characterizations. The activation energies of grain boundary diffusion for the NiFe alloys increases from 140 kJ/mol to 208 kJ/mol as the Fe content increases from 0 to 50 wt% as determined by TGA. We have developed a diffusion process resolved temperature programed oxidation (DPR-TPO) analysis method, and three diffusion mechanisms have been recognized by using this method: In addition to the well-known grain boundary diffusion and lattice diffusion, we found that the phase conversion from Fe 2 O 3 to (Ni, Fe) 3 O 4 will induce diffusion changes and affect the diffusion process at the intermediate temperature. The diffusion processes can be characterized by the corresponding characteristic peak temperatures in temperature programmed oxidation (TPO) analysis. This work not only

Moessbauer spectroscopic characterization of ferrite ceramics

International Nuclear Information System (INIS)

Music, S.; Ristic, M.

1999-01-01

The principle of Moessbauer effect and the nature of hyperfine interactions were presented. The discovery of the Moessbauer effect was the basis of a new spectroscopic technique, called Moessbauer spectroscopy, which has already made important contribution to research in physics, chemistry, metallurgy, mineralogy and biochemistry. In the present work the selected ferrites such as spinel ferrite, NiFe 2 O 4 , and some rare earth orthoferrites and garnets were investigated using Moessbauer spectroscopy. X-ray powder diffraction and Fourier transform infrared spectroscopy were used as complementary techniques. The formation of NiFe 2 O 4 was monitored during the thermal decomposition of mixed salt (Ni(NO 3 ) 2 +2Fe(NO 3 ) 3 )nH 2 O. The ferritization of Ni 2+ ions was observed at 500 deg. C and after heating at 1300 deg. C the stoichiometric NiFe 2 O 4 was produced. The Moessbauer parameters obtained for NiFe 2 O 4 , d Fe = 0.36 mm s -1 and HMF = 528 kOe, can be ascribed to Fe 3+ ions in the octahedral sublattice, while parameters d Fe = 0.28 mm s -1 and HMF = 494 kOe can be ascribed to Fe 3+ ions in the tetrahedral lattice. The effect of ball-milling of NiFe 2 O 4 was monitored. The formation of oxide phases and their properties in the systems Nd 2 O 3 -Fe 2 O 3 , Sm 2 O 3 -Fe 2 O 3 , Gd 2 O 3 -Fe 2 O 3 , Eu 2 O 3 -Fe 2 O 3 and Er 2 O 3 -Fe 2 O 3 were also investigated. Quantitative distributions of oxide phases, a-Fe 2 O 3 , R 2 O 3 , R 3 Fe 5 O 12 and RFeO 3 , R = Gd or Eu, were determined for the systems xGd 2 O 3 +(1-x)Fe 2 O 3 and xEu 2 O 3 +(1-x)Fe 2 O 3 . The samples, prepared by chemical coprecipitation in the system xEu 2 O 3 +(1-x)Fe 2 O 3 , 0≤x≤1, were completely amorphous as observed by XRD, even at the relatively high temperature of the sample preparation (600 deg. C). Similar behavior was observed during the formation of Er 3 Fe 5 O 12 . Moessbauer spectroscopy indicated that this 'amorphous' phase is actually composed of very small and/or poor

Time-Course Gene Set Analysis for Longitudinal Gene Expression Data.

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Boris P Hejblum

2015-06-01

Full Text Available Gene set analysis methods, which consider predefined groups of genes in the analysis of genomic data, have been successfully applied for analyzing gene expression data in cross-sectional studies. The time-course gene set analysis (TcGSA introduced here is an extension of gene set analysis to longitudinal data. The proposed method relies on random effects modeling with maximum likelihood estimates. It allows to use all available repeated measurements while dealing with unbalanced data due to missing at random (MAR measurements. TcGSA is a hypothesis driven method that identifies a priori defined gene sets with significant expression variations over time, taking into account the potential heterogeneity of expression within gene sets. When biological conditions are compared, the method indicates if the time patterns of gene sets significantly differ according to these conditions. The interest of the method is illustrated by its application to two real life datasets: an HIV therapeutic vaccine trial (DALIA-1 trial, and data from a recent study on influenza and pneumococcal vaccines. In the DALIA-1 trial TcGSA revealed a significant change in gene expression over time within 69 gene sets during vaccination, while a standard univariate individual gene analysis corrected for multiple testing as well as a standard a Gene Set Enrichment Analysis (GSEA for time series both failed to detect any significant pattern change over time. When applied to the second illustrative data set, TcGSA allowed the identification of 4 gene sets finally found to be linked with the influenza vaccine too although they were found to be associated to the pneumococcal vaccine only in previous analyses. In our simulation study TcGSA exhibits good statistical properties, and an increased power compared to other approaches for analyzing time-course expression patterns of gene sets. The method is made available for the community through an R package.

Study of dipole interaction in micron-width NiFe/Cu/NiFe/NiO wire using exchange anisotropy

International Nuclear Information System (INIS)

Kimura, Takashi; Itagaki, Yoshio; Wakaya, Fujio; Gamo, Kenji

2001-01-01

The dipole interaction between a NiFe layer pinned by a NiO and a free NiFe layer in a micron-wide NiFe/Cu/NiFe/NiO wire was studied by changing the direction of the exchange bias from the NiO layer. The effect of the dipole interaction when the exchange bias was perpendicular to the wire axis was larger than that when the exchange bias was parallel to the wire axis, and was consistently explained by the stray field caused by the magnetic charges of the pinned layer. It was demonstrated that this method, using exchange anisotropy, is useful for investigating the dipole interaction between ferromagnetic materials separated by a nonmagnetic material in small-scale magnetic multilayers. [copyright] 2001 American Institute of Physics

Room-temperature ferromagnetism in Dy films doped with Ni

International Nuclear Information System (INIS)

Edelman, I.; Ovchinnikov, S.; Markov, V.; Kosyrev, N.; Seredkin, V.; Khudjakov, A.; Bondarenko, G.; Kesler, V.

2008-01-01

Temperature, magnetic field and spectral dependences of magneto-optical effects (MOEs) in bi-layer films Dy (1-x) Ni x -Ni and Dy (1-x) (NiFe) x -NiFe were investigated, x changes from 0 to 0.06. Peculiar behavior of the MOEs was revealed at temperatures essentially exceeding the Curie temperature of bulk Dy which is explained by the magnetic ordering of the Dy layer containing Ni under the action of two factors: Ni impurities distributed homogeneously over the whole Dy layer and atomic contact of this layer with continues Ni layer. The mechanism of the magnetic ordering is suggested to be associated with the change of the density of states of the alloy Dy (1-x) Ni x owing to hybridization with narrow peaks near the Fermi level character for Ni

Norrie disease gene is distinct from the monoamine oxidase genes

OpenAIRE

Sims, Katherine B.; Ozelius, Laurie; Corey, Timothy; Rinehart, William B.; Liberfarb, Ruth; Haines, Jonathan; Chen, Wei Jane; Norio, Reijo; Sankila, Eeva; de la Chapelle, Albert; Murphy, Dennis L.; Gusella, James; Breakefield, Xandra O.

1989-01-01

The genes for MAO-A and MAO-B appear to be very close to the Norrie disease gene, on the basis of loss and /or disruption of the MAO genes and activities in atypical Norrie disease patients deleted for the DXS7 locus; linkage among the MAO genes, the Norrie disease gene, and the DXS7 locus; and mapping of all these loci to the chromosomal region Xp11. The present study provides evidence that the MAO genes are not disrupted in “classic” Norrie disease patients. Genomic DNA from these “nondelet...

A genetic ensemble approach for gene-gene interaction identification

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Ho Joshua WK

2010-10-01

Full Text Available Abstract Background It has now become clear that gene-gene interactions and gene-environment interactions are ubiquitous and fundamental mechanisms for the development of complex diseases. Though a considerable effort has been put into developing statistical models and algorithmic strategies for identifying such interactions, the accurate identification of those genetic interactions has been proven to be very challenging. Methods In this paper, we propose a new approach for identifying such gene-gene and gene-environment interactions underlying complex diseases. This is a hybrid algorithm and it combines genetic algorithm (GA and an ensemble of classifiers (called genetic ensemble. Using this approach, the original problem of SNP interaction identification is converted into a data mining problem of combinatorial feature selection. By collecting various single nucleotide polymorphisms (SNP subsets as well as environmental factors generated in multiple GA runs, patterns of gene-gene and gene-environment interactions can be extracted using a simple combinatorial ranking method. Also considered in this study is the idea of combining identification results obtained from multiple algorithms. A novel formula based on pairwise double fault is designed to quantify the degree of complementarity. Conclusions Our simulation study demonstrates that the proposed genetic ensemble algorithm has comparable identification power to Multifactor Dimensionality Reduction (MDR and is slightly better than Polymorphism Interaction Analysis (PIA, which are the two most popular methods for gene-gene interaction identification. More importantly, the identification results generated by using our genetic ensemble algorithm are highly complementary to those obtained by PIA and MDR. Experimental results from our simulation studies and real world data application also confirm the effectiveness of the proposed genetic ensemble algorithm, as well as the potential benefits of

The Mycoplasma hominis vaa gene displays a mosaic gene structure

DEFF Research Database (Denmark)

Boesen, Thomas; Emmersen, Jeppe M. G.; Jensen, Lise T.

1998-01-01

Mycoplasma hominis contains a variable adherence-associated (vaa) gene. To classify variants of the vaa genes, we examined 42 M. hominis isolated by PCR, DNA sequencing and immunoblotting. This uncovered the existence of five gene categories. Comparison of the gene types revealed a modular...

Identification of Hematopoietic Stem Cell Engraftment Genes in Gene Therapy Studies.

Science.gov (United States)

Powers, John M; Trobridge, Grant D

2013-09-01

Hematopoietic stem cell (HSC) therapy using replication-incompetent retroviral vectors is a promising approach to provide life-long correction for genetic defects. HSC gene therapy clinical studies have resulted in functional cures for several diseases, but in some studies clonal expansion or leukemia has occurred. This is due to the dyregulation of endogenous host gene expression from vector provirus insertional mutagenesis. Insertional mutagenesis screens using replicating retroviruses have been used extensively to identify genes that influence oncogenesis. However, retroviral mutagenesis screens can also be used to determine the role of genes in biological processes such as stem cell engraftment. The aim of this review is to describe the potential for vector insertion site data from gene therapy studies to provide novel insights into mechanisms of HSC engraftment. In HSC gene therapy studies dysregulation of host genes by replication-incompetent vector proviruses may lead to enrichment of repopulating clones with vector integrants near genes that influence engraftment. Thus, data from HSC gene therapy studies can be used to identify novel candidate engraftment genes. As HSC gene therapy use continues to expand, the vector insertion site data collected will be of great interest to help identify novel engraftment genes and may ultimately lead to new therapies to improve engraftment.

Gene Duplicability of Core Genes Is Highly Consistent across All Angiosperms[OPEN

Science.gov (United States)

Li, Zhen; Van de Peer, Yves; De Smet, Riet

2016-01-01

Gene duplication is an important mechanism for adding to genomic novelty. Hence, which genes undergo duplication and are preserved following duplication is an important question. It has been observed that gene duplicability, or the ability of genes to be retained following duplication, is a nonrandom process, with certain genes being more amenable to survive duplication events than others. Primarily, gene essentiality and the type of duplication (small-scale versus large-scale) have been shown in different species to influence the (long-term) survival of novel genes. However, an overarching view of “gene duplicability” is lacking, mainly due to the fact that previous studies usually focused on individual species and did not account for the influence of genomic context and the time of duplication. Here, we present a large-scale study in which we investigated duplicate retention for 9178 gene families shared between 37 flowering plant species, referred to as angiosperm core gene families. For most gene families, we observe a strikingly consistent pattern of gene duplicability across species, with gene families being either primarily single-copy or multicopy in all species. An intermediate class contains gene families that are often retained in duplicate for periods extending to tens of millions of years after whole-genome duplication, but ultimately appear to be largely restored to singleton status, suggesting that these genes may be dosage balance sensitive. The distinction between single-copy and multicopy gene families is reflected in their functional annotation, with single-copy genes being mainly involved in the maintenance of genome stability and organelle function and multicopy genes in signaling, transport, and metabolism. The intermediate class was overrepresented in regulatory genes, further suggesting that these represent putative dosage-balance-sensitive genes. PMID:26744215

Effect of the absolute statistic on gene-sampling gene-set analysis methods.

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Nam, Dougu

2017-06-01

Gene-set enrichment analysis and its modified versions have commonly been used for identifying altered functions or pathways in disease from microarray data. In particular, the simple gene-sampling gene-set analysis methods have been heavily used for datasets with only a few sample replicates. The biggest problem with this approach is the highly inflated false-positive rate. In this paper, the effect of absolute gene statistic on gene-sampling gene-set analysis methods is systematically investigated. Thus far, the absolute gene statistic has merely been regarded as a supplementary method for capturing the bidirectional changes in each gene set. Here, it is shown that incorporating the absolute gene statistic in gene-sampling gene-set analysis substantially reduces the false-positive rate and improves the overall discriminatory ability. Its effect was investigated by power, false-positive rate, and receiver operating curve for a number of simulated and real datasets. The performances of gene-set analysis methods in one-tailed (genome-wide association study) and two-tailed (gene expression data) tests were also compared and discussed.

Human Gene Therapy: Genes without Frontiers?

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Simon, Eric J.

2002-01-01

Describes the latest advancements and setbacks in human gene therapy to provide reference material for biology teachers to use in their science classes. Focuses on basic concepts such as recombinant DNA technology, and provides examples of human gene therapy such as severe combined immunodeficiency syndrome, familial hypercholesterolemia, and…

Sequence Classification: 258180 [

Lifescience Database Archive (English)

Full Text Available Non-TMB Non-TMH Non-TMB Non-TMB Non-TMB Non-TMB >gi|71909593|ref|YP_287180.1| HupH hydrogenase express...ion protein, C-terminal conserved region || http://www.ncbi.nlm.nih.gov/protein/71909593 ...

Gene function prediction based on Gene Ontology Hierarchy Preserving Hashing.

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Zhao, Yingwen; Fu, Guangyuan; Wang, Jun; Guo, Maozu; Yu, Guoxian

2018-02-23

Gene Ontology (GO) uses structured vocabularies (or terms) to describe the molecular functions, biological roles, and cellular locations of gene products in a hierarchical ontology. GO annotations associate genes with GO terms and indicate the given gene products carrying out the biological functions described by the relevant terms. However, predicting correct GO annotations for genes from a massive set of GO terms as defined by GO is a difficult challenge. To combat with this challenge, we introduce a Gene Ontology Hierarchy Preserving Hashing (HPHash) based semantic method for gene function prediction. HPHash firstly measures the taxonomic similarity between GO terms. It then uses a hierarchy preserving hashing technique to keep the hierarchical order between GO terms, and to optimize a series of hashing functions to encode massive GO terms via compact binary codes. After that, HPHash utilizes these hashing functions to project the gene-term association matrix into a low-dimensional one and performs semantic similarity based gene function prediction in the low-dimensional space. Experimental results on three model species (Homo sapiens, Mus musculus and Rattus norvegicus) for interspecies gene function prediction show that HPHash performs better than other related approaches and it is robust to the number of hash functions. In addition, we also take HPHash as a plugin for BLAST based gene function prediction. From the experimental results, HPHash again significantly improves the prediction performance. The codes of HPHash are available at: http://mlda.swu.edu.cn/codes.php?name=HPHash. Copyright © 2018 Elsevier Inc. All rights reserved.

A Nonlinear Model for Gene-Based Gene-Environment Interaction

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Jian Sa

2016-06-01

Full Text Available A vast amount of literature has confirmed the role of gene-environment (G×E interaction in the etiology of complex human diseases. Traditional methods are predominantly focused on the analysis of interaction between a single nucleotide polymorphism (SNP and an environmental variable. Given that genes are the functional units, it is crucial to understand how gene effects (rather than single SNP effects are influenced by an environmental variable to affect disease risk. Motivated by the increasing awareness of the power of gene-based association analysis over single variant based approach, in this work, we proposed a sparse principle component regression (sPCR model to understand the gene-based G×E interaction effect on complex disease. We first extracted the sparse principal components for SNPs in a gene, then the effect of each principal component was modeled by a varying-coefficient (VC model. The model can jointly model variants in a gene in which their effects are nonlinearly influenced by an environmental variable. In addition, the varying-coefficient sPCR (VC-sPCR model has nice interpretation property since the sparsity on the principal component loadings can tell the relative importance of the corresponding SNPs in each component. We applied our method to a human birth weight dataset in Thai population. We analyzed 12,005 genes across 22 chromosomes and found one significant interaction effect using the Bonferroni correction method and one suggestive interaction. The model performance was further evaluated through simulation studies. Our model provides a system approach to evaluate gene-based G×E interaction.

Vertebrate gene predictions and the problem of large genes

DEFF Research Database (Denmark)

Wang, Jun; Li, ShengTing; Zhang, Yong

2003-01-01

To find unknown protein-coding genes, annotation pipelines use a combination of ab initio gene prediction and similarity to experimentally confirmed genes or proteins. Here, we show that although the ab initio predictions have an intrinsically high false-positive rate, they also have a consistent...

Reranking candidate gene models with cross-species comparison for improved gene prediction

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Pereira Fernando CN

2008-10-01

Full Text Available Abstract Background Most gene finders score candidate gene models with state-based methods, typically HMMs, by combining local properties (coding potential, splice donor and acceptor patterns, etc. Competing models with similar state-based scores may be distinguishable with additional information. In particular, functional and comparative genomics datasets may help to select among competing models of comparable probability by exploiting features likely to be associated with the correct gene models, such as conserved exon/intron structure or protein sequence features. Results We have investigated the utility of a simple post-processing step for selecting among a set of alternative gene models, using global scoring rules to rerank competing models for more accurate prediction. For each gene locus, we first generate the K best candidate gene models using the gene finder Evigan, and then rerank these models using comparisons with putative orthologous genes from closely-related species. Candidate gene models with lower scores in the original gene finder may be selected if they exhibit strong similarity to probable orthologs in coding sequence, splice site location, or signal peptide occurrence. Experiments on Drosophila melanogaster demonstrate that reranking based on cross-species comparison outperforms the best gene models identified by Evigan alone, and also outperforms the comparative gene finders GeneWise and Augustus+. Conclusion Reranking gene models with cross-species comparison improves gene prediction accuracy. This straightforward method can be readily adapted to incorporate additional lines of evidence, as it requires only a ranked source of candidate gene models.

Hydrogen utilization potential in subsurface sediments

DEFF Research Database (Denmark)

Adhikari, Rishi Ram; Glombitza, Clemens; Nickel, Julia

2016-01-01

Pacific, and Gulf of Mexico) with different predominant electron-acceptors. Hydrogenases constitute a diverse family of enzymes expressed by microorganisms that utilize molecular hydrogen as a metabolic substrate, product, or intermediate. The assay reveals the potential for utilizing molecular hydrogen...

Evolution of homeobox genes.

Science.gov (United States)

Holland, Peter W H

2013-01-01

Many homeobox genes encode transcription factors with regulatory roles in animal and plant development. Homeobox genes are found in almost all eukaryotes, and have diversified into 11 gene classes and over 100 gene families in animal evolution, and 10 to 14 gene classes in plants. The largest group in animals is the ANTP class which includes the well-known Hox genes, plus other genes implicated in development including ParaHox (Cdx, Xlox, Gsx), Evx, Dlx, En, NK4, NK3, Msx, and Nanog. Genomic data suggest that the ANTP class diversified by extensive tandem duplication to generate a large array of genes, including an NK gene cluster and a hypothetical ProtoHox gene cluster that duplicated to generate Hox and ParaHox genes. Expression and functional data suggest that NK, Hox, and ParaHox gene clusters acquired distinct roles in patterning the mesoderm, nervous system, and gut. The PRD class is also diverse and includes Pax2/5/8, Pax3/7, Pax4/6, Gsc, Hesx, Otx, Otp, and Pitx genes. PRD genes are not generally arranged in ancient genomic clusters, although the Dux, Obox, and Rhox gene clusters arose in mammalian evolution as did several non-clustered PRD genes. Tandem duplication and genome duplication expanded the number of homeobox genes, possibly contributing to the evolution of developmental complexity, but homeobox gene loss must not be ignored. Evolutionary changes to homeobox gene expression have also been documented, including Hox gene expression patterns shifting in concert with segmental diversification in vertebrates and crustaceans, and deletion of a Pitx1 gene enhancer in pelvic-reduced sticklebacks. WIREs Dev Biol 2013, 2:31-45. doi: 10.1002/wdev.78 For further resources related to this article, please visit the WIREs website. The author declares that he has no conflicts of interest. Copyright © 2012 Wiley Periodicals, Inc.

Horizontal acquisition of multiple mitochondrial genes from a parasitic plant followed by gene conversion with host mitochondrial genes

Science.gov (United States)

2010-01-01

Background Horizontal gene transfer (HGT) is relatively common in plant mitochondrial genomes but the mechanisms, extent and consequences of transfer remain largely unknown. Previous results indicate that parasitic plants are often involved as either transfer donors or recipients, suggesting that direct contact between parasite and host facilitates genetic transfer among plants. Results In order to uncover the mechanistic details of plant-to-plant HGT, the extent and evolutionary fate of transfer was investigated between two groups: the parasitic genus Cuscuta and a small clade of Plantago species. A broad polymerase chain reaction (PCR) survey of mitochondrial genes revealed that at least three genes (atp1, atp6 and matR) were recently transferred from Cuscuta to Plantago. Quantitative PCR assays show that these three genes have a mitochondrial location in the one species line of Plantago examined. Patterns of sequence evolution suggest that these foreign genes degraded into pseudogenes shortly after transfer and reverse transcription (RT)-PCR analyses demonstrate that none are detectably transcribed. Three cases of gene conversion were detected between native and foreign copies of the atp1 gene. The identical phylogenetic distribution of the three foreign genes within Plantago and the retention of cytidines at ancestral positions of RNA editing indicate that these genes were probably acquired via a single, DNA-mediated transfer event. However, samplings of multiple individuals from two of the three species in the recipient Plantago clade revealed complex and perplexing phylogenetic discrepancies and patterns of sequence divergence for all three of the foreign genes. Conclusions This study reports the best evidence to date that multiple mitochondrial genes can be transferred via a single HGT event and that transfer occurred via a strictly DNA-level intermediate. The discovery of gene conversion between co-resident foreign and native mitochondrial copies suggests

Horizontal acquisition of multiple mitochondrial genes from a parasitic plant followed by gene conversion with host mitochondrial genes

Directory of Open Access Journals (Sweden)

Hao Weilong

2010-12-01

Full Text Available Abstract Background Horizontal gene transfer (HGT is relatively common in plant mitochondrial genomes but the mechanisms, extent and consequences of transfer remain largely unknown. Previous results indicate that parasitic plants are often involved as either transfer donors or recipients, suggesting that direct contact between parasite and host facilitates genetic transfer among plants. Results In order to uncover the mechanistic details of plant-to-plant HGT, the extent and evolutionary fate of transfer was investigated between two groups: the parasitic genus Cuscuta and a small clade of Plantago species. A broad polymerase chain reaction (PCR survey of mitochondrial genes revealed that at least three genes (atp1, atp6 and matR were recently transferred from Cuscuta to Plantago. Quantitative PCR assays show that these three genes have a mitochondrial location in the one species line of Plantago examined. Patterns of sequence evolution suggest that these foreign genes degraded into pseudogenes shortly after transfer and reverse transcription (RT-PCR analyses demonstrate that none are detectably transcribed. Three cases of gene conversion were detected between native and foreign copies of the atp1 gene. The identical phylogenetic distribution of the three foreign genes within Plantago and the retention of cytidines at ancestral positions of RNA editing indicate that these genes were probably acquired via a single, DNA-mediated transfer event. However, samplings of multiple individuals from two of the three species in the recipient Plantago clade revealed complex and perplexing phylogenetic discrepancies and patterns of sequence divergence for all three of the foreign genes. Conclusions This study reports the best evidence to date that multiple mitochondrial genes can be transferred via a single HGT event and that transfer occurred via a strictly DNA-level intermediate. The discovery of gene conversion between co-resident foreign and native

Gene coexpression network analysis as a source of functional annotation for rice genes.

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Kevin L Childs

Full Text Available With the existence of large publicly available plant gene expression data sets, many groups have undertaken data analyses to construct gene coexpression networks and functionally annotate genes. Often, a large compendium of unrelated or condition-independent expression data is used to construct gene networks. Condition-dependent expression experiments consisting of well-defined conditions/treatments have also been used to create coexpression networks to help examine particular biological processes. Gene networks derived from either condition-dependent or condition-independent data can be difficult to interpret if a large number of genes and connections are present. However, algorithms exist to identify modules of highly connected and biologically relevant genes within coexpression networks. In this study, we have used publicly available rice (Oryza sativa gene expression data to create gene coexpression networks using both condition-dependent and condition-independent data and have identified gene modules within these networks using the Weighted Gene Coexpression Network Analysis method. We compared the number of genes assigned to modules and the biological interpretability of gene coexpression modules to assess the utility of condition-dependent and condition-independent gene coexpression networks. For the purpose of providing functional annotation to rice genes, we found that gene modules identified by coexpression analysis of condition-dependent gene expression experiments to be more useful than gene modules identified by analysis of a condition-independent data set. We have incorporated our results into the MSU Rice Genome Annotation Project database as additional expression-based annotation for 13,537 genes, 2,980 of which lack a functional annotation description. These results provide two new types of functional annotation for our database. Genes in modules are now associated with groups of genes that constitute a collective functional

The drug target genes show higher evolutionary conservation than non-target genes.

Science.gov (United States)

Lv, Wenhua; Xu, Yongdeng; Guo, Yiying; Yu, Ziqi; Feng, Guanglong; Liu, Panpan; Luan, Meiwei; Zhu, Hongjie; Liu, Guiyou; Zhang, Mingming; Lv, Hongchao; Duan, Lian; Shang, Zhenwei; Li, Jin; Jiang, Yongshuai; Zhang, Ruijie

2016-01-26

Although evidence indicates that drug target genes share some common evolutionary features, there have been few studies analyzing evolutionary features of drug targets from an overall level. Therefore, we conducted an analysis which aimed to investigate the evolutionary characteristics of drug target genes. We compared the evolutionary conservation between human drug target genes and non-target genes by combining both the evolutionary features and network topological properties in human protein-protein interaction network. The evolution rate, conservation score and the percentage of orthologous genes of 21 species were included in our study. Meanwhile, four topological features including the average shortest path length, betweenness centrality, clustering coefficient and degree were considered for comparison analysis. Then we got four results as following: compared with non-drug target genes, 1) drug target genes had lower evolutionary rates; 2) drug target genes had higher conservation scores; 3) drug target genes had higher percentages of orthologous genes and 4) drug target genes had a tighter network structure including higher degrees, betweenness centrality, clustering coefficients and lower average shortest path lengths. These results demonstrate that drug target genes are more evolutionarily conserved than non-drug target genes. We hope that our study will provide valuable information for other researchers who are interested in evolutionary conservation of drug targets.

Identifying potential maternal genes of Bombyx mori using digital gene expression profiling

Science.gov (United States)

Xu, Pingzhen

2018-01-01

Maternal genes present in mature oocytes play a crucial role in the early development of silkworm. Although maternal genes have been widely studied in many other species, there has been limited research in Bombyx mori. High-throughput next generation sequencing provides a practical method for gene discovery on a genome-wide level. Herein, a transcriptome study was used to identify maternal-related genes from silkworm eggs. Unfertilized eggs from five different stages of early development were used to detect the changing situation of gene expression. The expressed genes showed different patterns over time. Seventy-six maternal genes were annotated according to homology analysis with Drosophila melanogaster. More than half of the differentially expressed maternal genes fell into four expression patterns, while the expression patterns showed a downward trend over time. The functional annotation of these material genes was mainly related to transcription factor activity, growth factor activity, nucleic acid binding, RNA binding, ATP binding, and ion binding. Additionally, twenty-two gene clusters including maternal genes were identified from 18 scaffolds. Altogether, we plotted a profile for the maternal genes of Bombyx mori using a digital gene expression profiling method. This will provide the basis for maternal-specific signature research and improve the understanding of the early development of silkworm. PMID:29462160

Novel gene sets improve set-level classification of prokaryotic gene expression data.

Science.gov (United States)

Holec, Matěj; Kuželka, Ondřej; Železný, Filip

2015-10-28

Set-level classification of gene expression data has received significant attention recently. In this setting, high-dimensional vectors of features corresponding to genes are converted into lower-dimensional vectors of features corresponding to biologically interpretable gene sets. The dimensionality reduction brings the promise of a decreased risk of overfitting, potentially resulting in improved accuracy of the learned classifiers. However, recent empirical research has not confirmed this expectation. Here we hypothesize that the reported unfavorable classification results in the set-level framework were due to the adoption of unsuitable gene sets defined typically on the basis of the Gene ontology and the KEGG database of metabolic networks. We explore an alternative approach to defining gene sets, based on regulatory interactions, which we expect to collect genes with more correlated expression. We hypothesize that such more correlated gene sets will enable to learn more accurate classifiers. We define two families of gene sets using information on regulatory interactions, and evaluate them on phenotype-classification tasks using public prokaryotic gene expression data sets. From each of the two gene-set families, we first select the best-performing subtype. The two selected subtypes are then evaluated on independent (testing) data sets against state-of-the-art gene sets and against the conventional gene-level approach. The novel gene sets are indeed more correlated than the conventional ones, and lead to significantly more accurate classifiers. The novel gene sets are indeed more correlated than the conventional ones, and lead to significantly more accurate classifiers. Novel gene sets defined on the basis of regulatory interactions improve set-level classification of gene expression data. The experimental scripts and other material needed to reproduce the experiments are available at http://ida.felk.cvut.cz/novelgenesets.tar.gz.

Facile synthesis, dielectric properties and electrocatalytic activities of PMMA-NiFe2O4 nanocomposite

International Nuclear Information System (INIS)

Maji, Pranabi; Choudhary, Ram Bilash

2017-01-01

The paper deals with the dielectric and catalytic properties of poly (methyl methacrylate)-nikel ferrite (PMMA-NiFe 2 O 4 ) nanocomposite. The nanocomposite was prepared by using a general and facile synthesis strategy. Fourier transform infrared (FTIR) and X-ray diffraction (XRD) spectra confirmed the formation of PMMA-NiFe 2 O 4 nanocomposite. Field effect scanning electron microscopic (FESEM) and transmission electron microscopic (TEM) images revealed that NiFe 2 O 4 nanoparticles were uniformly distributed and were tightly adhered with PMMA matrix owing to surface modification with 3-methacryloyloxy propyl trimethoxy silane (KH-570). Thermal stability was enhanced by incorporation of NiFe 2 O 4 nanofillers. The nanocomposite showed high dielectric constant and low dielectric loss. The achieved dielectric and thermal property inferred the potential application of this material in energy storage and embedded electronics devices. Further, the as prepared nanocomposite also offered a remarkable electrochemical performance towards hydrogen peroxide (H 2 O 2 ) sensing. - Highlights: • PMMA-NiFe 2 O 4 nanocomposite was synthesized via free radical polymerization. • The nanocomposite exhibited high value of dielectric constant (51) and tanδ (0.3). • Thermal stability of the PMMA matrix was improved by the incorporation of NiFe 2 O 4. • The H 2 O 2 detection limit was estimated 44 μM when signal to noise (S/N) ration was 3. • The electrochemical sensitivity of H 2 O 2 was calculated 0.6727 μA mM -1 .

Removal of Cr(VI Ions from Aqueous Solutions Using Nickel Ferrite Nanoparticles: Kinetic and Equilibrium Study

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Raziyeh Zandi Pak

2017-01-01

Full Text Available Background & Aims of the Study: Heavy metals are the most important and main pollutants because of their accumulation and high toxicity even at very low dose and cause serious hazards to ecological system as well as human health. Thus, their removal has been challenged from drinking water and industrial waters with different technologies. The purpose of this work is to investigate the removal of Cr(VI from aqueous solutions. Materials & Methods: NiFe2O4 nanoparticles was prepared by the co-precipitation method and then applied for adsorption of Cr(VI ions from water. Characterization of nanoparticles was carried out via TEM, EDX, XRD and BET analysis. Various physico-chemical parameters like the effect of contact time, pH and adsorbent dose were studied, using batch process to optimize conditions for maximum adsorption. Results: The results demonstrated that the size of the NiFe2O4 nanoparticles was about 12 nm and had selectivity for Cr(VI adsorption. Also, adsorption process was found to be fast with equilibrium time of 55 min. Optimum pH was found to be 3. Maximum adsorption capacity (qm as calculated from Langmuir isotherm was found to be 294.1 mg g-1. Analysis of adsorption kinetics indicated better applicability of pseudo-second-order kinetic model. Conclusions: The results of this study represented that the synthesized NiFe2O4 nanoparticles could be useful for the simultaneous removal of anionic ions from wastewaters.

[Gene doping: gene transfer and possible molecular detection].

Science.gov (United States)

Argüelles, Carlos Francisco; Hernández-Zamora, Edgar

2007-01-01

The use of illegal substances in sports to enhance athletic performance during competition has caused international sports organizations such as the COI and WADA to take anti doping measures. A new doping method know as gene doping is defined as "the non-therapeutic use of genes, genetic elements and/or cells that have the capacity to enhance athletic performance". However, gene doping in sports is not easily identified and can cause serious consequences. Molecular biology techniques are needed in order to distinguish the difference between a "normal" and an "altered" genome. Further, we need to develop new analytic methods and biological molecular techniques in anti-doping laboratories, and design programs that avoid the non therapeutic use of genes.

Delimiting Coalescence Genes (C-Genes) in Phylogenomic Data Sets.

Science.gov (United States)

Springer, Mark S; Gatesy, John

2018-02-26

coalescence methods have emerged as a popular alternative for inferring species trees with large genomic datasets, because these methods explicitly account for incomplete lineage sorting. However, statistical consistency of summary coalescence methods is not guaranteed unless several model assumptions are true, including the critical assumption that recombination occurs freely among but not within coalescence genes (c-genes), which are the fundamental units of analysis for these methods. Each c-gene has a single branching history, and large sets of these independent gene histories should be the input for genome-scale coalescence estimates of phylogeny. By contrast, numerous studies have reported the results of coalescence analyses in which complete protein-coding sequences are treated as c-genes even though exons for these loci can span more than a megabase of DNA. Empirical estimates of recombination breakpoints suggest that c-genes may be much shorter, especially when large clades with many species are the focus of analysis. Although this idea has been challenged recently in the literature, the inverse relationship between c-gene size and increased taxon sampling in a dataset-the 'recombination ratchet'-is a fundamental property of c-genes. For taxonomic groups characterized by genes with long intron sequences, complete protein-coding sequences are likely not valid c-genes and are inappropriate units of analysis for summary coalescence methods unless they occur in recombination deserts that are devoid of incomplete lineage sorting (ILS). Finally, it has been argued that coalescence methods are robust when the no-recombination within loci assumption is violated, but recombination must matter at some scale because ILS, a by-product of recombination, is the raison d'etre for coalescence methods. That is, extensive recombination is required to yield the large number of independently segregating c-genes used to infer a species tree. If coalescent methods are powerful

Influence of Reduced Graphene Oxide on Effective Absorption Bandwidth Shift of Hybrid Absorbers.

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Shahid Ameer

Full Text Available The magnetic nanoparticle composite NiFe2O4 has traditionally been studied for high-frequency microwave absorption with marginal performance towards low-frequency radar bands (particularly L and S bands. Here, NiFe2O4 nanoparticles and nanohybrids using large-diameter graphene oxide (GO sheets are prepared via solvothermal synthesis for low-frequency wide bandwidth shielding (L and S radar bands. The synthesized materials were characterized using XRD, SEM, FTIR and microwave magneto dielectric spectroscopy. The dimension of these solvothermally synthesized pristine particles and hybrids lies within 30-58 nm. Microwave magneto-dielectric spectroscopy was performed in the low-frequency region in the 1 MHz-3 GHz spectrum. The as-synthesized pristine nanoparticles and hybrids were found to be highly absorbing for microwaves throughout the L and S radar bands ( 4 GHz with limited selective bandwidth.

The fabrication and the coercivity mechanism of segmented (Ni/Fe)m composite nanowire arrays

International Nuclear Information System (INIS)

Xue, D S; Shi, H G; Si, M S

2004-01-01

Arrays of segmented (Ni/Fe) m (m = 1,2,3,4,5) composite nanowires about 3 μm in length and with aspect ratios of about 60 were electrodeposited on anodic porous alumina templates using a dual bath. The structure, morphology and magnetic properties of the samples were characterized by means of x-ray diffraction, transmission electron microscopy and vibrating sample magnetometry, respectively. It is found that Fe(110) and Ni(111) orientations along nanowire axis are preferred. The large aspect ratio of the composite nanowires reveals a strong shape magnetic anisotropy. As the number of the Ni/Fe composite segments m increases, the coercivity of the nanowire arrays, with the magnetic field applied parallel to the wire, gradually increases. The coercivity variation of the segmented composite nanowires is closely related to the effective exchange coupling between the Ni and Fe segments

Gene therapy of cancer and development of therapeutic target gene

Energy Technology Data Exchange (ETDEWEB)

Kim, Chang Min; Kwon, Hee Chung

1998-04-01

We applied HSV-tk/GCV strategy to orthotopic rat hepatoma model and showed anticancer effects of hepatoma. The increased expression of Lac Z gene after adenovirus-mediated gene delivery throughout hepatic artery was thought that is increased the possibility of gene therapy for curing hepatoma. With the construction of kGLP-laboratory, it is possible to produce a good quantity and quality of adenovirus in lage-scale production and purification of adenovirus vector. Also, the analysis of hepatoma related genes by PCR-LOH could be used for the diagnosis of patients and the development of therapeutic gene.

Gene therapy of cancer and development of therapeutic target gene

International Nuclear Information System (INIS)

Kim, Chang Min; Kwon, Hee Chung

1998-04-01

We applied HSV-tk/GCV strategy to orthotopic rat hepatoma model and showed anticancer effects of hepatoma. The increased expression of Lac Z gene after adenovirus-mediated gene delivery throughout hepatic artery was thought that is increased the possibility of gene therapy for curing hepatoma. With the construction of kGLP-laboratory, it is possible to produce a good quantity and quality of adenovirus in lage-scale production and purification of adenovirus vector. Also, the analysis of hepatoma related genes by PCR-LOH could be used for the diagnosis of patients and the development of therapeutic gene

DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis

Directory of Open Access Journals (Sweden)

Baseler Michael W

2007-11-01

Full Text Available Abstract Background Due to the complex and distributed nature of biological research, our current biological knowledge is spread over many redundant annotation databases maintained by many independent groups. Analysts usually need to visit many of these bioinformatics databases in order to integrate comprehensive annotation information for their genes, which becomes one of the bottlenecks, particularly for the analytic task associated with a large gene list. Thus, a highly centralized and ready-to-use gene-annotation knowledgebase is in demand for high throughput gene functional analysis. Description The DAVID Knowledgebase is built around the DAVID Gene Concept, a single-linkage method to agglomerate tens of millions of gene/protein identifiers from a variety of public genomic resources into DAVID gene clusters. The grouping of such identifiers improves the cross-reference capability, particularly across NCBI and UniProt systems, enabling more than 40 publicly available functional annotation sources to be comprehensively integrated and centralized by the DAVID gene clusters. The simple, pair-wise, text format files which make up the DAVID Knowledgebase are freely downloadable for various data analysis uses. In addition, a well organized web interface allows users to query different types of heterogeneous annotations in a high-throughput manner. Conclusion The DAVID Knowledgebase is designed to facilitate high throughput gene functional analysis. For a given gene list, it not only provides the quick accessibility to a wide range of heterogeneous annotation data in a centralized location, but also enriches the level of biological information for an individual gene. Moreover, the entire DAVID Knowledgebase is freely downloadable or searchable at http://david.abcc.ncifcrf.gov/knowledgebase/.

Evolutionary dynamics of human autoimmune disease genes and malfunctioned immunological genes

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Podder Soumita

2012-01-01

Full Text Available Abstract Background One of the main issues of molecular evolution is to divulge the principles in dictating the evolutionary rate differences among various gene classes. Immunological genes have received considerable attention in evolutionary biology as candidates for local adaptation and for studying functionally important polymorphisms. The normal structure and function of immunological genes will be distorted when they experience mutations leading to immunological dysfunctions. Results Here, we examined the fundamental differences between the genes which on mutation give rise to autoimmune or other immune system related diseases and the immunological genes that do not cause any disease phenotypes. Although the disease genes examined are analogous to non-disease genes in product, expression, function, and pathway affiliation, a statistically significant decrease in evolutionary rate has been found in autoimmune disease genes relative to all other immune related diseases and non-disease genes. Possible ways of accumulation of mutation in the three steps of the central dogma (DNA-mRNA-Protein have been studied to trace the mutational effects predisposed to disease consequence and acquiring higher selection pressure. Principal Component Analysis and Multivariate Regression Analysis have established the predominant role of single nucleotide polymorphisms in guiding the evolutionary rate of immunological disease and non-disease genes followed by m-RNA abundance, paralogs number, fraction of phosphorylation residue, alternatively spliced exon, protein residue burial and protein disorder. Conclusions Our study provides an empirical insight into the etiology of autoimmune disease genes and other immunological diseases. The immediate utility of our study is to help in disease gene identification and may also help in medicinal improvement of immune related disease.

Carboxylesterase 1 genes

DEFF Research Database (Denmark)

Rasmussen, Henrik Berg; Madsen, Majbritt Busk

2018-01-01

The carboxylesterase 1 gene (CES1) encodes a hydrolase that metabolizes commonly used drugs. The CES1-related pseudogene, carboxylesterase 1 pseudogene 1 (CES1P1), has been implicated in gene exchange with CES1 and in the formation of hybrid genes including the carboxylesterase 1A2 gene (CES1A2...

Bayesian assignment of gene ontology terms to gene expression experiments

Science.gov (United States)

Sykacek, P.

2012-01-01

Motivation: Gene expression assays allow for genome scale analyses of molecular biological mechanisms. State-of-the-art data analysis provides lists of involved genes, either by calculating significance levels of mRNA abundance or by Bayesian assessments of gene activity. A common problem of such approaches is the difficulty of interpreting the biological implication of the resulting gene lists. This lead to an increased interest in methods for inferring high-level biological information. A common approach for representing high level information is by inferring gene ontology (GO) terms which may be attributed to the expression data experiment. Results: This article proposes a probabilistic model for GO term inference. Modelling assumes that gene annotations to GO terms are available and gene involvement in an experiment is represented by a posterior probabilities over gene-specific indicator variables. Such probability measures result from many Bayesian approaches for expression data analysis. The proposed model combines these indicator probabilities in a probabilistic fashion and provides a probabilistic GO term assignment as a result. Experiments on synthetic and microarray data suggest that advantages of the proposed probabilistic GO term inference over statistical test-based approaches are in particular evident for sparsely annotated GO terms and in situations of large uncertainty about gene activity. Provided that appropriate annotations exist, the proposed approach is easily applied to inferring other high level assignments like pathways. Availability: Source code under GPL license is available from the author. Contact: peter.sykacek@boku.ac.at PMID:22962488

Bayesian assignment of gene ontology terms to gene expression experiments.

Science.gov (United States)

Sykacek, P