Sample records for thermophilic cellulolytic bacterium

  1. Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations

    SciTech Connect (OSTI)

    Xie, Gary [Los Alamos National Laboratory; Detter, Chris [Los Alamos National Laboratory; Bruce, David [Los Alamos National Laboratory; Challacome, Jean F [Los Alamos National Laboratory; Brettin, Thomas S [Los Alamos National Laboratory; Barabote, Ravi D [UC DAVIS; Leu, David [UC DAVIS; Normand, Philippe [CNRS, UNIV LYON; Necsula, Anamaria [CNRS, UNIV LYON; Daubin, Vincent [CNRS, UNIV LYON; Medigue, Claudine [CNRS/GENOSCOPE; Adney, William S [NREL; Xu, Xin C [UC DAVIS; Lapidus, Alla [DOE JOINT GENOME INST.; Pujic, Pierre [CNRS, UNIV LYON; Richardson, Paul [DOE JOINT GENOME INST; Berry, Alison M [UC DAVIS

    2008-01-01T23:59:59.000Z

    We present here the complete 2.4 MB genome of the actinobacterial thermophile, Acidothermus cellulolyticus lIB, that surprisingly reveals thermophilic amino acid usage in only the cytosolic subproteome rather than its whole proteome. Thermophilic amino acid usage in the partial proteome implies a recent, ongoing evolution of the A. cellulolyticus genome since its divergence about 200-250 million years ago from its closest phylogenetic neighbor Frankia, a mesophilic plant symbiont. Differential amino acid usage in the predicted subproteomes of A. cellulolyticus likely reflects a stepwise evolutionary process of modern thermophiles in general. An unusual occurrence of higher G+C in the non-coding DNA than in the transcribed genome reinforces a late evolution from a higher G+C common ancestor. Comparative analyses of the A. cellulolyticus genome with those of Frankia and other closely-related actinobacteria revealed that A. cellulolyticus genes exhibit reciprocal purine preferences at the first and third codon positions, perhaps reflecting a subtle preference for the dinucleotide AG in its mRNAs, a possible adaptation to a thermophilic environment. Other interesting features in the genome of this cellulolytic, hot-springs dwelling prokaryote reveal streamlining for adaptation to its specialized ecological niche. These include a low occurrence of pseudogenes or mobile genetic elements, a flagellar gene complement previously unknown in this organism, and presence of laterally-acquired genomic islands of likely ecophysiological value. New glycoside hydrolases relevant for lignocellulosic biomass deconstruction were identified in the genome, indicating a diverse biomass-degrading enzyme repertoire several-fold greater than previously characterized, and significantly elevating the industrial value of this organism.

  2. Complete Genome Sequence of the Thermophilic, Piezophilic, Heterotrophic Bacterium Marinitoga piezophila KA3

    SciTech Connect (OSTI)

    Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Han, James [U.S. Department of Energy, Joint Genome Institute; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Peters, Lin [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Teshima, Hazuki [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Han, Cliff [Los Alamos National Laboratory (LANL); Tapia, Roxanne [Los Alamos National Laboratory (LANL); Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Vannier, Pauline [Ifremer, Plouzane, France; Oger, Phil [University of Lyon, France; Bartlett, Douglas [University of California, San Diego & La Jolla; Noll, Kenneth M [University of Connecticut, Storrs; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Jebbar, Mohamed [Ifremer, Plouzane, France

    2012-01-01T23:59:59.000Z

    Marinitoga piezophila KA3 is a thermophilic, anaerobic, chemoorganotrophic, sulfur-reducing bacterium isolated from the Grandbonum deep-sea hydrothermal vent site at the East Pacific Rise (13 degrees N, 2,630-m depth). The genome of M. piezophila KA3 comprises a 2,231,407-bp circular chromosome and a 13,386-bp circular plasmid. This genome was sequenced within Department of Energy Joint Genome Institute CSP 2010.

  3. Kallotenue papyrolyticum gen. nov., sp. nov., a cellulolytic and filamentous thermophile that represents a novel lineage (Kallotenuales ord. nov., Kallotenuaceae fam. nov.) within the class Chloroflexia

    SciTech Connect (OSTI)

    Cole, Jesse; Gieler, Brandon; Heisler, Devon; Palisoc, Maryknoll; Williams, Amanda; Dohnalkova, Alice; Ming, Hong; Yu, Tian T.; Dodsworth, Jeremy A.; Li, Wen J.; Hedlund, Brian P.

    2013-08-15T23:59:59.000Z

    Several closely-related, thermophilic, and cellulolytic bacterial strains, designated JKG1T, JKG2, JKG3, JKG4, and JKG5, were isolated from a cellulolytic enrichment (corn stover) incubated in the water column of Great Boiling Spring, NV. Strain JKG1T had cells of a diameter of 0.7 - 0.9 ?m and length of ~2.0 ?m that formed non-branched multicellular filaments reaching >300 ?m. Spores were not formed and dense liquid cultures were red. The temperature range for growth was 45-65 °C, with an optimum of 55 °C. The pH range for growth was 5.6-9.0, with an optimum of 7.5. JKG1T grew as an aerobic heterotroph, utilizing glucose, sucrose, xylose, arabinose, cellobiose, carboxymethylcellulose, filter paper, microcrystalline cellulose, xylan, starch, casamino acids, tryptone, peptone, yeast extract, acetate, citrate, lactate, pyruvate, and glycerol as sole carbon sources, and was not observed to photosynthesize. The cells stained Gram-negative. Phylogenetic analysis using 16S rRNA gene sequences placed the new isolates in the class Chloroflexia, but distant from other cultivated members, with the highest sequence identity of 82.5% to Roseiflexus castenholzii. The major quinone was menaquinone-9; no ubiquinones were detected. The major cellular fatty acids (>5%) were C18:0, anteiso-C17:0, iso-C18:0, and iso-C17:0. C16:0, iso-C16:0, and C17:0. The peptidoglycan amino acids were alanine, ornithine, glutamic acid, serine, and asparagine. Whole-cell sugars included mannose, rhamnose, glucose, galactose, ribose, arabinose, and xylose. Morphological, phylogenetic, and chemotaxonomic results suggest that JKG1T is representative of a new lineage within the class Chloroflexia, which we propose to designate Kallotenue papyrolyticum gen. nov., sp. nov., Kallotenuaceae fam. nov., Kallotenuales ord. nov.

  4. Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus

    SciTech Connect (OSTI)

    Saw, Jimmy H [Los Alamos National Laboratory; Mountain, Bruce W [NEW ZEALAND; Feng, Lu [NANKAI UNIV; Omelchenko, Marina V [NCBI/NLM/NIH; Hou, Shaobin [UNIV OF HAWAII; Saito, Jennifer A [UNIV OF HAWAII; Stott, Matthew B [NEW ZEALAND; Li, Dan [NANKAI UNIV; Zhao, Guang [NANKAI UNIV; Wu, Junli [NANKAI UNIV; Galperin, Michael Y [NCBI/NLM/NIH; Koonin, Eugene V [NCBI/NLM/NIH; Makarova, Kira S [NCBI/NLM/NIH; Wolf, Yuri I [NCBI/NLM/NIH; Rigden, Daniel J [UNIV OF LIVERPOOL; Dunfield, Peter F [UNIV OF CALGARY; Wang, Lei [NANKAI UNIV; Alam, Maqsudul [UNIV OF HAWAII

    2008-01-01T23:59:59.000Z

    Gram-positive bacteria of the genus Anoxybacillus have been found in diverse thermophilic habitats, such as geothermal hot springs and manure, and in processed foods such as gelatin and milk powder. Anoxybacillus flavithermus is a facultatively anaerobic bacterium found in super-saturated silica solutions and in opaline silica sinter. The ability of A. flavithermus to grow in super-saturated silica solutions makes it an ideal subject to study the processes of sinter formation, which might be similar to the biomineralization processes that occurred at the dawn of life. We report here the complete genome sequence of A. flavithermus strain WK1, isolated from the waste water drain at the Wairakei geothermal power station in New Zealand. It consists of a single chromosome of 2,846,746 base pairs and is predicted to encode 2,863 proteins. In silico genome analysis identified several enzymes that could be involved in silica adaptation and biofilm formation, and their predicted functions were experimentally validated in vitro. Proteomic analysis confirmed the regulation of biofilm-related proteins and crucial enzymes for the synthesis of long-chain polyamines as constituents of silica nanospheres. Microbial fossils preserved in silica and silica sinters are excellent objects for studying ancient life, a new paleobiological frontier. An integrated analysis of the A. flavithermus genome and proteome provides the first glimpse of metabolic adaptation during silicification and sinter formation. Comparative genome analysis suggests an extensive gene loss in the Anoxybacillus/Geobacillus branch after its divergence from other bacilli.

  5. Thermoterrabacterium ferrireducens gen. nov., sp. nov., a thermophilic anaerobic dissimilatory Fe(III)-reducing bacterium from a continental hot spring

    SciTech Connect (OSTI)

    Slobodkin, A.; Wiegel, J. [Univ. of Georgia, Athens, GA (United States); Reysenbach, A.L. [Rutgers Univ., New Brunswick, NJ (United States)] [and others

    1997-04-01T23:59:59.000Z

    A strain of a thermophilic, anaerobic, dissimilatory, Fe(III)-reducing bacterium, Thermoterrabacterium ferrireducens gen. nov., sp. nov. (type strain JW/AS-Y7{sup T}; DSM 11255), was isolated from hot springs in Yellowstone National Park and New Zealand. The gram-positive-staining cells occurred singly or in pairs as straight to slightly curved rods, 0.3 to 0.4 by 1.6 to 2.7 {mu}m, with rounded ends and exhibited a tumbling motility. Spores were not observed. The temperature range for growth was 50 to 74{degrees}C with an optimum at 65{degrees}C. The pH range for growth at 65{degrees}C was from 5.5 to 7.6, with an optimum at 6.0 to 6.2. The organism coupled the oxidation of glycerol to reduction of amorphous Fe(III) oxide or Fe(III) citrate as an electron acceptor. In the presence as well as in the absence of Fe(III) and in the presence of CO{sub 2}, glycerol was metabolized by incomplete oxidation to acetate as the only organic metabolic product; no H{sub 2} was produced during growth. The organism utilized glycerol, lactate, 1,2-propanediol, glycerate, pyruvate, glucose, fructose, mannose, and yeast extract as substrates. In the presence of Fe(III) the bacterium utilized molecular hydrogen. The organism reduced 9,10-anthraquinone-2,6-disulfonic acid, fumarate (to succinate), and thiosulfate (to elemental sulfur) but did not reduce MnO{sub 2}, nitrate, sulfate, sulfite, or elemental sulfur. The G+C content of the DNA was 41 mol% (as determined by high-performance liquid chromatography). The 16S ribosomal DNA sequence analysis placed the isolated strain as a member of a new genus within the gram-type positive Bacillus-Clostridium subphylum.

  6. Thermosyntropha lipolytica gen. nov., sp. nov., a lipolytic, anaerobic, alkalitolerant, thermophilic bacterium utilizing short- and long-chain fatty acids in syntrophic coculture with a methanogenic archaeum

    SciTech Connect (OSTI)

    Svetlitshnyi, V.; Wiegel, J. [Univ. of Georgia, Athens, GA (United States); Rainey, F. [German Collection of Microorganisms and Cell Cultures, Braunschweig (Germany)

    1996-10-01T23:59:59.000Z

    Three strains of an anaerobic thermophilic organoheterotrophic lipolytic alkalitolerant bacterium, Thermosyntropha lipolytica gen. nov., sp. nov. (type strain JW/VS-264{sup T}; DSM 11003) were isolated from alkaline hot springs of Lake Bogoria (Kenya). The cells were nonmotile, non-spore forming, straight or slightly curved rods. At 60{degrees}C, the pH range for growth determined at 25{degrees}C [pH{sup 25{degrees}C}] was 7.15 to 9.5, with an optimum between 8.1 and 8.9 (pH{sup 60{degrees}C} of 7.6 and 8.1). At a pH{sup 25{degrees}C} of 8.5 temperature range for growth was from 52 to 70{degrees}C, with an optimum between 60 and 66{degrees}C. The shortest doubling time was around 1 h. In pure culture the bacterium grew in a mineral base medium supplemented with yeast extract, tryptone, Casamino Acids, betaine, and crotonate as carbon sources, producing acetate as a major product and constitutively a lipase. During growth in the presence of olive oil, free long-chain fatty acids were accumulated in the medium but the pure culture syntrophic coculture (Methanobacterium strain JW/VS-M29) the lipolytic bacteria grew on triacylglycerols and linear saturated and unsaturated fatty acids with 4 to 18 carbon atoms, but glycerol was not utilized. Fatty acids with even numbers of carbon atoms were degraded to acetate and methane, while from odd-numbered fatty acids 1 mol of propionate per mol of fatty acid was additionally formed. 16S rDNA sequence analysis identified Syntrophospora and Syntrophomonas spp. as closest phylogenetic neighbors.

  7. Thermostable purified endoglucanase from thermophilic bacterium

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOE Office of ScienceandMesa del SolStrengthening a solidSynthesis of 2DandEnergyThermostabilized enzymeATCC

  8. acidothermus cellulolytics atcc: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    ECOLOGY Contrasts in Cellulolytic Activities of Gut Microorganisms Between the Wood-degrading microorganisms in the guts of wood-inhabiting beetles. We enriched for...

  9. Autoheated thermophilic aerobic digestion

    SciTech Connect (OSTI)

    Deeny, K. (Junkins Engineering, Morgantown, PA (United States)); Hahn, H.; Leonhard, D. (Univ. Karlsruhe (West Germany)); Heidman, J. (Environmental Protection Agency, Cincinnati, OH (United States))

    1991-10-01T23:59:59.000Z

    Autothermal thermophilic aerobic digestion (ATAD) is first and foremost a digestion process, the primary purpose of which is to decompose a portion of the waste organic solids generated from wastewater treatment. As a result of the high operating temperature, digestion is expected to occur within a short time period (6 days) and accomplish a high degree of pathogen reduction. ATAD systems are two-stage aerobic digestion processes that operate under thermophilic temperature conditions (40 to 80C) without supplemental heat. Like composting, the systems rely on the conservation of heat released during digestion itself to attain and sustain the desired operating temperature. Typical ATAD systems operate at 55C and may reach temperatures of 60 to 65C in the second-stage reactor. Perhaps because of the high operating temperature, this process has been referred to as Liquid Composting.' Major advantages associated with thermophilic operation include high biological reaction rates and a substantial degree of pathogen reduction.

  10. Characterization of cellulolytic activity from digestive fluids of Dissosteira carolina (Orthoptera: Acrididae)

    E-Print Network [OSTI]

    Jurat-Fuentes, Juan Luis

    bioethanol feedstock, characterization of insect cellulolytic systems may aid in developing applications

  11. Isolation of butyrate-utilizing bacteria from thermophilic and mesophilic methane-producing ecosystems

    SciTech Connect (OSTI)

    Henson, J.M.

    1983-01-01T23:59:59.000Z

    The ability of various ecosystems to convert butyrate to methane was studied in order to isolate the bacteria responsible for the conversion. When thermophilic digester sludge was enriched with butyrate, methane was produced without a lag period. Marine sediments enriched with butyrate required a 2-week incubation period before methanogenesis began. A thermophilic digester was studied in more detail and found by most-probable-number enumeration to have ca. 5 x 10/sup 6/ butyrate-utilizing bactera/ml of sludge. A thermophilic butyrate-utilizing bacterium was isolated in coculture with Methanobacterium thermoautotrophicum and a Methanosarcina sp. This bacterium was a gram-negative, slightly curved rod that occurred singly, was nonmotile, and did not appear to produce spores. The thermophilic digester was infused with butyrate at the rate of 10 ..mu..moles/ml of sludge per day. Biogas production increased by 150%, with the percentage of methane increasing from 58% to 68%. Acetate, propionate, and butyrate did not accumulate. Butyrate-utilizing enrichments from mesophilic ecosystems were used in obtaining cocultures of butyrate-utilizing bacteria. These cocultures served as inocula for attempts to isolate pure cultures of butyrate-utilizing bacteria by use of hydrogenase-containing membrane fragments of Escherichia coli. After a 3-week incubation period, colonies appeared only in inoculated tubes that contained membrane fragments and butyrate.

  12. Polypeptides having cellulolytic enhancing activity and polynucleotides encoding same

    SciTech Connect (OSTI)

    Maiyuran, Suchindra; Kramer, Randall; Harris, Paul

    2013-10-29T23:59:59.000Z

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  13. Polypeptides having cellulolytic enhancing activity and polynucleotides encoding the same

    SciTech Connect (OSTI)

    Tang, Lan; Liu, Ye; Duan, Junxin; Wu, Wenping; Kramer, Randall

    2013-11-19T23:59:59.000Z

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  14. Polypeptides having cellulolytic enhancing activity and polynucleotides encoding same

    DOE Patents [OSTI]

    Lopez de Leon, Alfredo (Davis, CA); Ding, Hanshu (Davis, CA); Brown, Kimberly (Elk Grove, CA)

    2011-10-25T23:59:59.000Z

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  15. Polypeptides having cellulolytic enhancing activity and polynucleotides encoding same

    SciTech Connect (OSTI)

    Lopez de Leon, Alfredo (Davis, CA); Ding, Hanshu (Davis, CA); Brown, Kimberly (Elk Grove, CA)

    2012-06-26T23:59:59.000Z

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  16. Polypeptides having cellulolytic enhancing activity and polynucleotides encoding same

    DOE Patents [OSTI]

    Tang, Lan; Liu, Ye; Duan, Junxin; Wu, Wenping; Kramer, Randall

    2014-10-21T23:59:59.000Z

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  17. Polypeptides having cellulolytic enhancing activity and polynucleotides encoding same

    SciTech Connect (OSTI)

    Tang, Lan; Liu, Ye; Duan, Junxin; Zhang, Yu; Joergensen, Christian; Kramer, Randall

    2014-09-16T23:59:59.000Z

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  18. Polypeptides having cellulolytic enhancing activity and nucleic acids encoding same

    SciTech Connect (OSTI)

    Brown, Kimberly; Harris, Paul; Zaretsky, Elizabeth; Re, Edward; Vlasenko, Elena; McFarland, Keith; Lopez de Leon, Alfredo

    2010-06-22T23:59:59.000Z

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods for producing and using the polypeptides.

  19. Polypeptides having cellulolytic enhancing activity and polynucleotides encoding same

    SciTech Connect (OSTI)

    Duan, Junxin (Beijing, CN); Liu, Ye (Beijing, CN); Tang, Lan (Beijing, CN); Wu, Wenping (Beijing, CN); Quinlan, Jason (Albany, CA); Kramer, Randall (Lincoln, CA)

    2012-03-27T23:59:59.000Z

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  20. Polypeptides having cellulolytic enhancing activity and polynucleotides encoding same

    DOE Patents [OSTI]

    Tang, Lan; Liu, Ye; Duan, Junxin; Zhang, Yu; Jorgensen, Christian Isak; Kramer, Randall

    2013-04-16T23:59:59.000Z

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  1. Polypeptides having cellulolytic enhancing activity and polynucleotides encoding the same

    DOE Patents [OSTI]

    Tang, Lan; Liu, Ye; Duan, Junxin; Zhang, Yu; Jorgensen, Christian Isak; Kramer, Randall

    2013-12-24T23:59:59.000Z

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  2. Polypeptides having cellulolytic enhancing activity and polynucleotides encoding same

    SciTech Connect (OSTI)

    Tang, Lan (Beijing, CN); Liu, Ye (Beijing, CN); Duan, Junxin (Beijing, CN); Zhang, Yu (Beijing, CN); Jorgensen, Christian Isak (Bagsvaerd, DK); Kramer, Randall (Lincoln, CA)

    2012-04-03T23:59:59.000Z

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  3. Polypeptides having cellulolytic enhancing activity and nucleic acids encoding same

    DOE Patents [OSTI]

    Brown, Kimberly; Harris, Paul; Zaretsky, Elizabeth; Re, Edward; Vlasenko, Elena; McFarland, Keith; Lopez de Leon, Alfredo

    2014-09-30T23:59:59.000Z

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods for producing and using the polypeptides.

  4. Polypeptides having cellulolytic enhancing activity and nucleic acids encoding same

    DOE Patents [OSTI]

    Brown, Kimberly; Harris, Paul; Zaretsky, Elizabeth; Re, Edward; Vlasenko, Elena; McFarland, Keith; Lopez de Leon, Alfredo

    2012-10-16T23:59:59.000Z

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods for producing and using the polypeptides.

  5. Polypeptides having cellulolytic enhancing activity and polynucleotides encoding same

    DOE Patents [OSTI]

    Duan, Junxin; Tang, Lan; Liu, Ye; Wu, Wenping; Quinlan, Jason; Kramer, Randall

    2013-06-18T23:59:59.000Z

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  6. Compositions for enhancing hydroysis of cellulosic material by cellulolytic enzyme compositions

    SciTech Connect (OSTI)

    Quinlan, Jason; Xu, Feng; Sweeney, Matthew; Johansen, Katja Salomon

    2014-09-30T23:59:59.000Z

    The present invention relates to compositions comprising a GH61 polypeptide having cellulolytic enhancing activity and an organic compound comprising a carboxylic acid moiety, a lactone moiety, a phenolic moiety, a flavonoid moiety, or a combination thereof, wherein the combination of the GH61 polypeptide having cellulolytic enhancing activity and the organic compound enhances hydrolysis of a cellulosic material by a cellulolytic enzyme compared to the GH61 polypeptide alone or the organic compound alone. The present invention also relates to methods of using the compositions.

  7. Kinetics of inactivation of indicator pathogens during thermophilic anaerobic digestion

    E-Print Network [OSTI]

    Kinetics of inactivation of indicator pathogens during thermophilic anaerobic digestion Sudeep C Thermophilic anaerobic digestion Pathogen inactivation Ascaris suum Helminth eggs Poliovirus Enteric viruses a b s t r a c t Thermophilic anaerobic sludge digestion is a promising process to divert waste

  8. Complete Genome Sequence of the Filamentous Anoxygenic Phototrophic Bacterium Chloroflexus aurantiacus

    SciTech Connect (OSTI)

    Tang, Kuo-Hsiang [Washington University, St. Louis; Barry, Kerrie [U.S. Department of Energy, Joint Genome Institute; Chertkov, Olga [Los Alamos National Laboratory (LANL); Dalin, Eileen [U.S. Department of Energy, Joint Genome Institute; Han, Cliff [Los Alamos National Laboratory (LANL); Hauser, Loren John [ORNL; Honchak, Barbara M [Washington University, St. Louis; Karbach, Lauren E [Washington University, St. Louis; Land, Miriam L [ORNL; Lapidus, Alla L. [Joint Genome Institute, Walnut Creek, California; Larimer, Frank W [ORNL; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [Joint Genome Institute, Walnut Creek, California; Pierson, Beverly K [University of Puget Sound, Tacoma, WA

    2011-01-01T23:59:59.000Z

    Chloroflexus aurantiacus is a thermophilic filamentous anoxygenic phototrophic (FAP) bacterium, and can grow phototrophically under anaerobic conditions or chemotrophically under aerobic and dark conditions. According to 16S rRNA analysis, Chloroflexi species are the earliest branching bacteria capable of photosynthesis, and Cfl. aurantiacus has been long regarded as a key organism to resolve the obscurity of the origin and early evolution of photosynthesis. Cfl. aurantiacus contains a chimeric photosystem that comprises some characters of green sulfur bacteria and purple photosynthetic bacteria, and also has some unique electron transport proteins compared to other photosynthetic bacteria.

  9. Biocorrosive Thermophilic Microbial Communities in Alaskan North Slope Oil Facilities

    E-Print Network [OSTI]

    Duncan, Kathleen E.

    2010-01-01T23:59:59.000Z

    Springs Thermophilic microbial fuel cell Horse manure "Natronoanaerobium sp. microbial fuel cell clone SHBZ503 (Clostridia" Tropical tree Microbial fuel cell Horse manure ?

  10. Biocorrosive Thermophilic Microbial Communities in Alaskan North Slope Oil Facilities

    E-Print Network [OSTI]

    Duncan, Kathleen E.

    2010-01-01T23:59:59.000Z

    due to corrosion are expensive problems in the oil industrycorrosion. The similarity of core taxa in these samples and those from other thermophilic oil

  11. acidophilic heterotrophic bacterium: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    bacterium Mannheimia succiniciproducens Biotechnology Websites Summary: production and energy generation. We have isolated a novel capnophilic bacterium, Mannheimia to...

  12. The possible symbiotic role of proteolytic and cellulolytic bacteria found in the gut of Limnoria 

    E-Print Network [OSTI]

    Traganza, Eugene Dewees

    1959-01-01T23:59:59.000Z

    THE POSSIBLE SYMBIOTIC ROLE OF PROTEOLYTIC AND CELLVLOLYTIC BACTERIA FOUND IN TBE GV1' OF LIINORIA A Thesis By Eugene Dewees Traganza ~ ~ I Submitted to the Graduate School of the Agricultural and Mechanical College of Texas in partial... fulfillment of the requirements for the degree of MASTER OF SCIENCE January 1959 Ma)or Sub5ect: Biological Oceanography THE POSSIBLE SYMBIO1'IC ROLE OF PROTEOLYTIC AND CELLULOLYTIC BACTERIA FOUND IN THE GU1' OF Like(RIA A Thesis By Eugene Dewees...

  13. The Chemical Formula of a Magnetotactic Bacterium

    E-Print Network [OSTI]

    Mittal, Aditya

    ARTICLE The Chemical Formula of a Magnetotactic Bacterium Mohit Naresh,1 Sayoni Das,1 Prashant allowed fascinating discoveries of elemental formulae of a few species that have guided the modern views in bioreactors has resulted in the discovery of the chemical formula of the magnetotactic bacterium. By devel

  14. Cellulolytic enzymes, nucleic acids encoding them and methods for making and using them

    DOE Patents [OSTI]

    Gray, Kevin A. (San Diego, CA); Zhao, Lishan (Emeryville, CA); Cayouette, Michelle H. (San Diego, CA)

    2012-01-24T23:59:59.000Z

    The invention provides polypeptides having any cellulolytic activity, e.g., a cellulase activity, a endoglucanase, a cellobiohydrolase, a beta-glucosidase, a xylanase, a mannanse, a .beta.-xylosidase, an arabinofuranosidase, and/or an oligomerase activity, polynucleotides encoding these polypeptides, and methods of making and using these polynucleotides and polypeptides. In one aspect, the invention is directed to polypeptides having any cellulolytic activity, e.g., a cellulase activity, e.g., endoglucanase, cellobiohydrolase, beta-glucosidase, xylanase, mannanse, .beta.-xylosidase, arabinofuranosidase, and/or oligomerase activity, including thermostable and thermotolerant activity, and polynucleotides encoding these enzymes, and making and using these polynucleotides and polypeptides. In one aspect, the invention provides polypeptides having an oligomerase activity, e.g., enzymes that convert recalcitrant soluble oligomers to fermentable sugars in the saccharification of biomass. The polypeptides of the invention can be used in a variety of pharmaceutical, agricultural, food and feed processing and industrial contexts. The invention also provides compositions or products of manufacture comprising mixtures of enzymes comprising at least one enzyme of this invention.

  15. Biocorrosive Thermophilic Microbial Communities in Alaskan North Slope Oil Facilities

    E-Print Network [OSTI]

    Duncan, Kathleen E.

    2010-01-01T23:59:59.000Z

    Methanogenic sludge High temperature Dagang oil field (Ekofisk oil field Mesophilic digested sludge Kamchatka hotoil field (DQ647105) FJ469331 Uncultured bacterium Bacteroidetes Anaerobic sludge

  16. Protein Dynamics in a Family of Laboratory Evolved Thermophilic Enzymes

    E-Print Network [OSTI]

    Arnold, Frances H.

    , Deqiang Zhang1,2 , Nagarajan Vaidehi1,2 Frances H. Arnold1 and William A. Goddard III1,2 * 1 DivisionProtein Dynamics in a Family of Laboratory Evolved Thermophilic Enzymes Patrick L. Wintrode1 these variants display much higher melt- ing temperatures than wild-type (up to 18 8C higher) they are both .97

  17. Complete genome sequence of the thermophilic sulfur-reducer Desulfurobacterium thermolithotrophum type strain (BSAT) from a deep-sea hydrothermal vent

    SciTech Connect (OSTI)

    Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Daligault, Hajnalka E. [Los Alamos National Laboratory (LANL); Mwirichia, Romano [Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Deshpande, Shweta [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Liolios, Konstantinos [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Palaniappan, Krishna [U.S. Department of Energy, Joint Genome Institute; Han, Cliff [Los Alamos National Laboratory (LANL); Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Pan, Chongle [ORNL; Brambilla, Evelyne-Marie [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Spring, Stefan [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Sikorski, Johannes [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Wirth, Reinhard [Universitat Regensburg, Regensburg, Germany; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Bristow, James [U.S. Department of Energy, Joint Genome Institute; Eisen, Jonathan [U.S. Department of Energy, Joint Genome Institute; Markowitz, Victor [U.S. Department of Energy, Joint Genome Institute; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany

    2011-01-01T23:59:59.000Z

    Desulfurobacterium thermolithotrophum L'Haridon et al. 1998 is the type species of the ge- nus Desulfurobacterium which belongs to the family Desulfurobacteriaceae. The species is of interest because it represents the first thermophilic bacterium that can act as a primary pro- ducer in the temperature range of 45-75 C (optimum 70 C) and is incapable of growing un- der microaerophilic conditions. Strain BSAT preferentially synthesizes high-melting-point fatty acids (C18 and C20) which is hypothesized to be a strategy to ensure the functionality of the membrane at high growth temperatures. This is the second completed genome sequence of a member of the family Desulfurobacteriaceae and the first sequence from the genus Desulfu- robacterium. The 1,541,968 bp long genome harbors 1,543 protein-coding and 51 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  18. High-solids enrichment of thermophilic microbial communities and their enzymes on bioenergy feedstocks

    E-Print Network [OSTI]

    Reddy, A. P.

    2012-01-01T23:59:59.000Z

    High-solids enrichment of thermophilic microbial communities5, upon four successive enrichments on switchgrass. Overall,the first and second enrichments increased 4-fold for

  19. Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris

    SciTech Connect (OSTI)

    Berka, Randy M.; Grigoriev, Igor V.; Otillar, Robert; Salamov, Asaf; Grimwood, Jane; Reid, Ian; Ishmael, Nadeeza; John, Tricia; Darmond, Corinne; Moisan, Marie-Claude; Henrissat, Bernard; Coutinho, Pedro M.; Lombard, Vincent; Natvig, Donald O.; Lindquist, Erika; Schmutz, Jeremy; Lucas, Susan; Harris, Paul; Powlowski, Justin; Bellemare, Annie; Taylor, David; Butler, Gregory; de Vries, Ronald P.; Allijn, Iris E.; van den Brink, Joost; Ushinsky, Sophia; Storms, Reginald; Powell, Amy J.; Paulsen, Ian T.; Elbourne, Liam D. H.; Baker, Scott. E.; Magnuson, Jon; LaBoissiere, Sylvie; Clutterbuck, A. John; Martinez, Diego; Wogulis, Mark; Lopez de Leon, Alfredo; Rey, Michael W.; Tsang, Adrian

    2011-05-16T23:59:59.000Z

    Thermostable enzymes and thermophilic cell factories may afford economic advantages in the production of many chemicals and biomass-based fuels. Here we describe and compare the genomes of two thermophilic fungi, Myceliophthora thermophila and Thielavia terrestris. To our knowledge, these genomes are the first described for thermophilic eukaryotes and the first complete telomere-to-telomere genomes for filamentous fungi. Genome analyses and experimental data suggest that both thermophiles are capable of hydrolyzing all major polysaccharides found in biomass. Examination of transcriptome data and secreted proteins suggests that the two fungi use shared approaches in the hydrolysis of cellulose and xylan but distinct mechanisms in pectin degradation. Characterization of the biomass-hydrolyzing activity of recombinant enzymes suggests that these organisms are highly efficient in biomass decomposition at both moderate and high temperatures. Furthermore, we present evidence suggesting that aside from representing a potential reservoir of thermostable enzymes, thermophilic fungi are amenable to manipulation using classical and molecular genetics.

  20. acidophilic bacterium acidithiobacillus: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    since nitrification Cohen, Michael F. 72 Pathogenesis of the carcinogenic bacterium, Helicobacter pylori MIT - DSpace Summary: Gastric cancer is the second most common...

  1. anerobic thermohalophilic bacterium: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    23 24 25 Next Page Last Page Topic Index 61 Pathogenesis of the carcinogenic bacterium, Helicobacter pylori MIT - DSpace Summary: Gastric cancer is the second most common...

  2. Pathway engineering to improve ethanol production by thermophilic bacteria

    SciTech Connect (OSTI)

    Lynd, L.R.

    1998-12-31T23:59:59.000Z

    Continuation of a research project jointly funded by the NSF and DOE is proposed. The primary project goal is to develop and characterize strains of C. thermocellum and C. thermosaccharolyticum having ethanol selectivity similar to more convenient ethanol-producing organisms. An additional goal is to document the maximum concentration of ethanol that can be produced by thermophiles. These goals build on results from the previous project, including development of most of the genetic tools required for pathway engineering in the target organisms. As well, we demonstrated that the tolerance of C. thermosaccharolyticum to added ethanol is sufficiently high to allow practical utilization should similar tolerance to produced ethanol be demonstrated, and that inhibition by neutralizing agents may explain the limited concentrations of ethanol produced in studies to date. Task 1 involves optimization of electrotransformation, using either modified conditions or alternative plasmids to improve upon the low but reproducible transformation, frequencies we have obtained thus far.

  3. Biocorrosive Thermophilic Microbial Communities in Alaskan North Slope Oil Facilities

    SciTech Connect (OSTI)

    Duncan, Kathleen E.; Gieg, Lisa M.; Parisi, Victoria A.; Tanner, Ralph S.; Green Tringe, Susannah; Bristow, Jim; Suflita, Joseph M.

    2009-09-16T23:59:59.000Z

    Corrosion of metallic oilfield pipelines by microorganisms is a costly but poorly understood phenomenon, with standard treatment methods targeting mesophilic sulfatereducing bacteria. In assessing biocorrosion potential at an Alaskan North Slope oil field, we identified thermophilic hydrogen-using methanogens, syntrophic bacteria, peptideand amino acid-fermenting bacteria, iron reducers, sulfur/thiosulfate-reducing bacteria and sulfate-reducing archaea. These microbes can stimulate metal corrosion through production of organic acids, CO2, sulfur species, and via hydrogen oxidation and iron reduction, implicating many more types of organisms than are currently targeted. Micromolar quantities of putative anaerobic metabolites of C1-C4 n-alkanes in pipeline fluids were detected, implying that these low molecular weight hydrocarbons, routinely injected into reservoirs for oil recovery purposes, are biodegraded and provide biocorrosive microbial communities with an important source of nutrients.

  4. Community dynamics and glycoside hydrolase activities of thermophilic bacterial consortia adapted to switchgrass

    SciTech Connect (OSTI)

    Gladden, J.M.; Allgaier, M.; Miller, C.S.; Hazen, T.C.; VanderGheynst, J.S.; Hugenholtz, P.; Simmons, B.A.; Singer, S.W.

    2011-05-01T23:59:59.000Z

    Industrial-scale biofuel production requires robust enzymatic cocktails to produce fermentable sugars from lignocellulosic biomass. Thermophilic bacterial consortia are a potential source of cellulases and hemicellulases adapted to harsher reaction conditions than commercial fungal enzymes. Compost-derived microbial consortia were adapted to switchgrass at 60 C to develop thermophilic biomass-degrading consortia for detailed studies. Microbial community analysis using small-subunit rRNA gene amplicon pyrosequencing and short-read metagenomic sequencing demonstrated that thermophilic adaptation to switchgrass resulted in low-diversity bacterial consortia with a high abundance of bacteria related to thermophilic paenibacilli, Rhodothermus marinus, and Thermus thermophilus. At lower abundance, thermophilic Chloroflexi and an uncultivated lineage of the Gemmatimonadetes phylum were observed. Supernatants isolated from these consortia had high levels of xylanase and endoglucanase activities. Compared to commercial enzyme preparations, the endoglucanase enzymes had a higher thermotolerance and were more stable in the presence of 1-ethyl-3-methylimidazolium acetate ([C2mim][OAc]), an ionic liquid used for biomass pretreatment. The supernatants were used to saccharify [C2mim][OAc]-pretreated switchgrass at elevated temperatures (up to 80 C), demonstrating that these consortia are an excellent source of enzymes for the development of enzymatic cocktails tailored to more extreme reaction conditions.

  5. Community dynamics and glycoside hydrolase activities of thermophilic bacterial consortia adapted to switchgrass

    E-Print Network [OSTI]

    Gladden, J.M.

    2012-01-01T23:59:59.000Z

    bacterium isolated from a  composting reactor.  Int J Syst two municipal green waste composting facilities. The firstthermophilic (30 and 60 day) composting stages. A spade was

  6. The HPr Proteins from the Thermophile Bacillus stearothermophilus Can Form Domain-swapped Dimers

    SciTech Connect (OSTI)

    Sridharan, Sudharsan; Razvi, Abbas; Scholtz, J. Martin; Sacchettini, James C. (TAM)

    2010-07-20T23:59:59.000Z

    The study of proteins from extremophilic organisms continues to generate interest in the field of protein folding because paradigms explaining the enhanced stability of these proteins still elude us and such studies have the potential to further our knowledge of the forces stabilizing proteins. We have undertaken such a study with our model protein HPr from a mesophile, Bacillus subtilis, and a thermophile, Bacillus stearothermophilus. We report here the high-resolution structures of the wild-type HPr protein from the thermophile and a variant, F29W. The variant proved to crystallize in two forms: a monomeric form with a structure very similar to the wild-type protein as well as a domain-swapped dimer. Interestingly, the structure of the domain-swapped dimer for HPr is very different from that observed for a homologous protein, Crh, from B. subtilis. The existence of a domain-swapped dimer has implications for amyloid formation and is consistent with recent results showing that the HPr proteins can form amyloid fibrils. We also characterized the conformational stability of the thermophilic HPr proteins using thermal and solvent denaturation methods and have used the high-resolution structures in an attempt to explain the differences in stability between the different HPr proteins. Finally, we present a detailed analysis of the solution properties of the HPr proteins using a variety of biochemical and biophysical methods.

  7. High-solids enrichment of thermophilic microbial communities and their enzymes on bioenergy feedstocks

    SciTech Connect (OSTI)

    Reddy, A. P.; Allgaier, M.; Singer, S.W.; Hazen, T.C.; Simmons, B.A.; Hugenholtz, P.; VanderGheynst, J.S.

    2011-04-01T23:59:59.000Z

    Thermophilic microbial communities that are active in a high-solids environment offer great potential for the discovery of industrially relevant enzymes that efficiently deconstruct bioenergy feedstocks. In this study, finished green waste compost was used as an inoculum source to enrich microbial communities and associated enzymes that hydrolyze cellulose and hemicellulose during thermophilic high-solids fermentation of the bioenergy feedstocks switchgrass and corn stover. Methods involving the disruption of enzyme and plant cell wall polysaccharide interactions were developed to recover xylanase and endoglucanase activity from deconstructed solids. Xylanase and endoglucanase activity increased by more than a factor of 5, upon four successive enrichments on switchgrass. Overall, the changes for switchgrass were more pronounced than for corn stover; solids reduction between the first and second enrichments increased by a factor of four for switchgrass while solids reduction remained relatively constant for corn stover. Amplicon pyrosequencing analysis of small-subunit ribosomal RNA genes recovered from enriched samples indicated rapid changes in the microbial communities between the first and second enrichment with the simplified communities achieved by the third enrichment. The results demonstrate a successful approach for enrichment of unique microbial communities and enzymes active in a thermophilic high-solids environment.

  8. Draft Genome Sequence of Rhizobium sp. PDO1-076, a bacterium isolated from Populus deltoides.

    SciTech Connect (OSTI)

    Brown, Steven D [ORNL; Klingeman, Dawn Marie [ORNL; Lu, Tse-Yuan [ORNL; Johnson, Courtney M [ORNL; Utturkar, Sagar M [ORNL; Land, Miriam L [ORNL; Schadt, Christopher Warren [ORNL; Doktycz, Mitchel John [ORNL; Pelletier, Dale A [ORNL

    2012-01-01T23:59:59.000Z

    Rhizobium sp. strain PDO1-076 is a plant-associated bacterium isolated from Populus deltoides, and its draft genome sequence is reported.

  9. Quantitative influences of butyrate or propionate on thermophilic production of methane from biomass

    SciTech Connect (OSTI)

    Henson, J.M.; Bordeaux, F.M.; Rivards, C.J.; Smith, P.H.

    1986-02-01T23:59:59.000Z

    Sodium butyrate and sodium propionate were continuously infused into separate 4-liter thermophilic digesters. These digesters were operated at 55/sup 0/C, had a retention time of 20 days, and had a pH of 7.8. Infusion rates were started at 10 mM day/sup -1/ and were increased incrementally when new stable external organic acid pool sizes and new stable gas production rates were observed. Stable conditions were obtained in both digesters at an infusion rate of 15 mM day/sup -1/, with methanogenesis elevated over that of control digesters. Calculations based on expected CH/sub 4/ at this infusion rate and measured CH/sub 4/ production in the treated and control digesters, however, showed an approximately 25% inhibition of methanogenesis in both digesters. A digester infused with sodium chloride showed little or no inhibition at this infusion rate, but was totally inhibited when its infusion rate was increased to 20 mM day/sup -1/, and cumulative added NaCl reached 0.38 M. The butyrate and propionate-amended digesters tolerated addition rates of 20 mM day/sup -1/, but both failed when they were increased to 25 mM day/sup -1/. These results indicate that the thermophilic digesters could function stably at higher external pool sizes of butyrate or propionate than routinely observed.

  10. Mesophilic and thermophilic anaerobic biodegradability of water hyacinth pre-treated at 80 {sup o}C

    SciTech Connect (OSTI)

    Ferrer, Ivet, E-mail: ivet.ferrer@upc.ed [Environmental Engineering Division, Department of Hydraulic, Maritime and Environmental Engineering. Technical University of Catalonia, C/ Jordi Girona 1-3, E-08034 Barcelona (Spain); Palatsi, Jordi [GIRO Technological Centre, Rambla Pompeu Fabra 1, E-08100 Mollet del Valles, Barcelona (Spain); Campos, Elena [Laboratory of Environmental Engineering, Centre UdL-IRTA, Rovira Roure 191, E-25198 Lleida (Spain); Flotats, Xavier [GIRO Technological Centre, Rambla Pompeu Fabra 1, E-08100 Mollet del Valles, Barcelona (Spain); Department of Agrifood Engineering and Biotechnology, Technical University of Catalonia, Parc Mediterrani de la Tecnologia Edifici D-4, E-08860 Castelldefels, Barcelona (Spain)

    2010-10-15T23:59:59.000Z

    Water hyacinth (Eichornia crassipes) is a fast growing aquatic plant which causes environmental problems in continental water bodies. Harvesting and handling this plant becomes an issue, and focus has been put on the research of treatment alternatives. Amongst others, energy production through biomethanation has been proposed. The aim of this study was to assess the anaerobic biodegradability of water hyacinth under mesophilic and thermophilic conditions. The effect of a thermal sludge pre-treatment at 80 {sup o}C was also evaluated. To this end, anaerobic biodegradability tests were carried out at 35 {sup o}C and 55 {sup o}C, with raw and pre-treated water hyacinth. According to the results, the thermal pre-treatment enhanced the solubilisation of water hyacinth (i.e. increase in the soluble to total chemical oxygen demand (COD)) from 4% to 12% after 30 min. However, no significant effect was observed on the methane yields (150-190 L CH{sub 4}/kg volatile solids). Initial methane production rates for thermophilic treatments were two fold those of mesophilic ones (6-6.5 L vs. 3-3.5 L CH{sub 4}/kg COD.day). Thus, higher methane production rates might be expected from thermophilic reactors working at short retention times. The study of longer low temperature pre-treatments or pre-treatments at elevated temperatures coupled to thermophilic reactors should be considered in the future.

  11. Science Blog -Bacterium cleans up uranium, generates electricity Create an account

    E-Print Network [OSTI]

    Lovley, Derek

    Science Blog - Bacterium cleans up uranium, generates electricity Create an account :: Home electricity Department of Energy-funded researchers have decoded and analyzed the genome of a bacterium with the potential to bioremediate radioactive metals and generate electricity. In an article published

  12. Effects of selected thermophilic microorganisms on crude oils at elevated temperatures and pressures. Final report

    SciTech Connect (OSTI)

    Premuzic, E.T.; Lin, M.S.

    1995-07-01T23:59:59.000Z

    During the past several years, a considerable amount of work has been carried out showing that microbially enhanced oil recovery (MEOR) is promising and the resulting biotechnology may be deliverable. At the Brookhaven National Laboratory (BNL), systematic studies have been conducted which dealt with the effects of thermophilic and thermoadapted bacteria on the chemical and physical properties of selected types of crude oils at elevated temperatures and pressures. Particular attention was paid to heavy crude oils from Venezuela, California, Alabama, Arkansas, Wyoming, Alaska, and other oil producing areas. Current studies indicate that during the biotreatment several chemical and physical properties of crude oils are affected. The oils are (1) emulsified; (2) acidified; (3) there is a qualitative and quantitative change in light and heavy fractions of the crudes; (4) there are chemical changes in fractions containing sulfur compounds; (5) there is an apparent reduction in the concentration of trace metals; (6) the qualitative and quantitative changes appear to be microbial species dependent; and (7) there is a distinction between {open_quotes}biodegraded{close_quotes} and {open_quotes}biotreated{close_quotes} oils. Preliminary results indicate the introduced microorganisms may become the dominant species in the bioconversion of oils. These studies also indicate the biochemical interactions between crude oils and microorganisms follow distinct trends, characterized by a group of chemical markers. Core-flooding experiments have shown significant additional crude oil recoveries are achievable with thermophilic microorganisms at elevated temperatures similar to those found in oil reservoirs. In addition, the biochemical treatment of crude oils has technological applications in downstream processing of crude oils such as in upgrading of low grade oils and the production of hydrocarbon based detergents.

  13. The oxidation of ethylene glycol by Bacterium T-52: mutagenesis studies

    E-Print Network [OSTI]

    Smith, Frank Judson

    1976-01-01T23:59:59.000Z

    to continue my education. TABLE OF COUTEHTS IHTRODUCTIOI'7 I'RT P IALS ARD i&THUDS Bacterial strain. Culture media, Incubationo ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ Haintenence of cultures. Growth studies' ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ !iutagenesis.... IIATEHIALS AIID IMTHODS Bacterial strain. Bacterium T-52, ATCC 270I+2, was used in all experiments. The bacterium has been previously described (12). Culture media. A mineral salts basal medium was used in all experiments. The basal medium, referred...

  14. Pathogenicity of a pseudomonad bacterium to larvae of penaeid and brine shrimp

    E-Print Network [OSTI]

    Huang, Chu-Liang

    1982-01-01T23:59:59.000Z

    OF SCIENCE August 1982 Major Subject: Veterinary Microbiology PATHOGENICITY OF A PSEUDOMONAD BACTERIUM TO LARVAE OF PENAEID AND BRINE SHRIMP A Thesis by CHU-LIANG HUANG Approved as to style and content by: (Chairman of Committee) (Member) (Member...) (Member) (Head of Department) August 1982 ABSTRACT Pathogenicity of a Pseudomonad Bacterium to Larvae of Penaeid and Brine Shrimp (August 1982) Chu-Liang Huang, B. S , National Taiwan University Chairman of Advisory Committee: Dr. Donald H. Lewis A...

  15. Effects of selected thermophilic microorganisms on crude oils at elevated temperatures and pressures. 1991 annual report

    SciTech Connect (OSTI)

    Premuzic, E.T.; Lin, M.S.

    1993-10-01T23:59:59.000Z

    During the past several years, a considerable amount of work has been carried out showing that microbially enhanced oil recovery (MEOR) is promising and the resulting biotechnology may be deliverable. In this laboratory systematic studies are being conducted which deal with the effects of thermophilic and thermoadapted bacteria on the chemical and physical properties of selected types of crude oils at elevated temperatures and pressures. Particular attention is being paid to heavy crude oils such as Boscan and Cerro Negro (Venezuela), Monterey (California) and those from Alabama and Arkansas. Current studies indicate that during the biotreatment several properties of crude oils are affected. The oils are (1) emulsified; (2) acidified; (3) there is a qualitative and quantitative change in light and heavy fractions of the crudes; (4) there are chemical changes in fractions containing sulfur compounds; (5) there is an apparent solubilization of trace metals; and (6) the qualitative and quantitative chemical and physical changes appear to be microbial species dependent. Effects on heavy crude oils are also compared to those on lighter oils such as oils from the Wyoming petroleum reserve. Microbial oil interactions are monitored routinely by a consortium of analytical techniques which are continuously upgraded and are capable of multiparameter analysis. The results generated in fiscal year 1991, describing (1) through (6), are presented and discussed in this report.

  16. Characterization of a Y-Family DNA Polymerase eta from the Eukaryotic ThermophileAlvinella pompejana

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Kashiwagi, Sayo; Kuraoka, Isao; Fujiwara, Yoshie; Hitomi, Kenichi; Cheng, Quen J.; Fuss, Jill O.; Shin, David S.; Masutani, Chikahide; Tainer, John A.; Hanaoka, Fumio; et al

    2010-01-01T23:59:59.000Z

    Human DNA polymerase?(HsPol?) plays an important role in translesion synthesis (TLS), which allows for replication past DNA damage such as UV-inducedcis-syncyclobutane pyrimidine dimers (CPDs). Here, we characterized ApPol?from the thermophilic wormAlvinella pompejana, which inhabits deep-sea hydrothermal vent chimneys. ApPol?shares sequence homology with HsPol?and contains domains for binding ubiquitin and proliferating cell nuclear antigen. Sun-induced UV does not penetrateAlvinella'senvironment; however, this novel DNA polymerase catalyzed efficient and accurate TLS past CPD, as well as 7,8-dihydro-8-oxoguanine and isomers of thymine glycol induced by reactive oxygen species. In addition, we found that ApPol?is more thermostable than HsPol?, as expected from its habitat temperature.more »Moreover, the activity of this enzyme was retained in the presence of a higher concentration of organic solvents. Therefore, ApPol?provides a robust, human-like Pol?that is more active after exposure to high temperatures and organic solvents.« less

  17. Are you protected against Pertussis? Pertussis, or whooping cough, is a highly contagious respiratory infection caused by the bacterium

    E-Print Network [OSTI]

    Are you protected against Pertussis? Pertussis, or whooping cough, is a highly contagious respiratory infection caused by the bacterium Bordetella pertussis. It causes severe coughing spells, vomiting

  18. The oxidation of ethylene glycol by a salt-requiring bacterium

    E-Print Network [OSTI]

    Caskey, William Horton

    1975-01-01T23:59:59.000Z

    THE OXIDATION OF ETHYLENE GLYCOL BY A SALT-REQUIRING BACTERIUM A Thesis by WILLIAM HORTON CASKEY Submitted to the Graduate College of Texas A&M University in partial fulfillment of the requirement for the degree of MASTER OF SCIENCE... December 1975 Major Subject: Microbiology THE OXIDATION OF ETHYLENE GLYCOL BY A SALT-REQUIRING BACTERIUM A Thesis by WILLIAM HORTON CASKEY Approved as to style and content by: '2~~m- P, &~- Chairman of Committee (Head o f D epar tment) Member...

  19. Investigations of Iron Minerals Formed by Dissimilatory Alkaliphilic Bacterium with {sup 57}Fe Moessbauer Spectroscopy

    SciTech Connect (OSTI)

    Chistyakova, N. I.; Rusakov, V. S.; Shapkin, A. A. [M.V. Lomonosov Moscow State University, Faculty of Physics, Leninskie gory, 119991 Moscow (Russian Federation); Zhilina, T. N.; Zavarzina, D. G. [Institute of Microbiology, Russian Academy of Science, 7/2, Prospekt 60-letiya Oktyabrya, 117312 Moscow (Russian Federation); Lancok, A. [Institute of Inorganic Chemistry, v.v.i., 25608 Husinec-Rez (Czech Republic); Kohout, J. [Faculty of Mathematics and Physics, Charles University, Ovocny trh 5 116 36 Praha 1 (Czech Republic)

    2010-07-13T23:59:59.000Z

    Anaerobic alkaliphilic bacterium of Geoalkalibacter ferrihydriticus type (strain Z-0531), isolated from a bottom sediment sample from the weakly mineralized soda Lake Khadyn, have been analyzed. The strain uses the amorphous Fe(III)-hydroxide (AFH) as an electron acceptor and acetate CH{sub 3}COO{sup -} as an electron donor. Moessbauer investigations of solid phase samples obtained during the process of the bacterium growth were carried out at room temperature, 77.8 K, 4.2 K without and with the presence of an external magnetic field (6 T) applied perpendicular to the {gamma}-bebam.

  20. 1H, 13C, and 15N backbone and side chain resonance assignments of thermophilic Geobacillus kaustophilus cyclophilin-A

    SciTech Connect (OSTI)

    Holliday, Michael; Zhang, Fengli; Isern, Nancy G.; Armstrong, Geoffrey S.; Eisenmesser, Elan Z.

    2014-04-01T23:59:59.000Z

    Cyclophilins catalyze the reversible peptidyl-prolyl isomerization of their substrates and are present across all kingdoms of life from humans to bacteria. Although numerous biological roles have now been discovered for cyclophilins, their function was initially ascribed to their chaperone-like activity in protein folding where they catalyze the often rate-limiting step of proline isomerization. This chaperone-like activity may be especially important under extreme conditions where cyclophilins are often over expressed, such as in tumors for human cyclophilins {Lee, 2010 #1167}, but also in organisms that thrive under extreme conditions, such as theromophilic bacteria. Moreover, the reversible nature of the peptidyl-prolyl isomerization reaction catalyzed by cyclophilins has allowed these enzymes to serve as model systems for probing the role of conformational changes during catalytic turnover {Eisenmesser, 2002 #20;Eisenmesser, 2005 #203}. Thus, we present here the resonance assignments of a thermophilic cyclophilin from Geobacillus kaustophilus derived from deep-sea sediment {Takami, 2004 #1384}. This thermophilic cyclophilin may now be studied at a variety of temperatures to provide insight into the comparative structure, dynamics, and catalytic mechanism of cyclophilins.

  1. In Situ Expression of Acidic and Thermophilic Carbohydrate Active Enzymes by Filamentous Fungi (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema (OSTI)

    Mosier, Annika [Stanford University

    2013-01-22T23:59:59.000Z

    Annika Mosier, graduate student from Stanford University presents a talk titled "In Situ Expression of Acidic and Thermophilic Carbohydrate Active Enzymes by Filamentous Fungi" at the JGI User 7th Annual Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, Calif

  2. In Situ Expression of Acidic and Thermophilic Carbohydrate Active Enzymes by Filamentous Fungi (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect (OSTI)

    Mosier, Annika [Stanford University] [Stanford University

    2012-03-22T23:59:59.000Z

    Annika Mosier, graduate student from Stanford University presents a talk titled "In Situ Expression of Acidic and Thermophilic Carbohydrate Active Enzymes by Filamentous Fungi" at the JGI User 7th Annual Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, Calif

  3. Abstract The enrichment and isolation in pure culture of a bacterium, identified as a strain of Desulfovibrio, able to

    E-Print Network [OSTI]

    Leadbetter, Jared R.

    Abstract The enrichment and isolation in pure culture of a bacterium, identified as a strain of isethionate in detergents, we enriched for and isolated a bacterium able to utilize isethionate for anaerobic served as an accessory electron donor and was oxi- dized to acetate. Materials and methods Enrichment

  4. Genome sequence of the mycorrhizal helper bacterium Pseudomonas fluorescens BBc6R8

    SciTech Connect (OSTI)

    Deveau, Aurelie [French National Insitute for Agricultural Research (INRA)] [French National Insitute for Agricultural Research (INRA); Grob, Harald [University of Bonn, Germany] [University of Bonn, Germany; Morin, Emmanuelle [INRA, Nancy, France] [INRA, Nancy, France; Karpinets, Tatiana V [ORNL] [ORNL; Utturkar, Sagar M [ORNL] [ORNL; Mehnaz, Samina [University of the Punjab, Pakistan] [University of the Punjab, Pakistan; Kurz, Sven [University of Bonn, Germany] [University of Bonn, Germany; Martin, Francis [INRA, Nancy, France] [INRA, Nancy, France; Frey-Klett, Pascale [INRA, Nancy, France] [INRA, Nancy, France; Labbe, Jessy L [ORNL] [ORNL

    2014-01-01T23:59:59.000Z

    We report the draft genome sequence of the mycorrhiza helper bacterium Pseudomonas fluorescens strain BBc6R8 . Several traits which could be involved in the mycorrhiza helper ability of the bacterial strain such as multiple secretion systems, auxin metabolism and phosphate mobilization were evidenced in the genome.

  5. Abstract A two-phase partitioning bioreactor (TPPB) utilizing the bacterium Sphingomonas aromaticivorans

    E-Print Network [OSTI]

    Daugulis, Andrew J.

    Abstract A two-phase partitioning bioreactor (TPPB) utilizing the bacterium Sphingomonas of PAHs has been studied in soil slurry bioreactors (Fuchs and Braun 1995, Ober- bremer et al. 1990 extraction followed by biodegrada- tion in a two-phase partitioning bioreactor (TPPB) has been identified

  6. Salinicoccus carnicancri sp. nov., a halophilic bacterium isolated from a Korean fermented

    E-Print Network [OSTI]

    Bae, Jin-Woo

    ; BBL) supplemented with 10 % (w/v) NaCl. The following buffers were used: pH 5.0, 0.1 M acetic acid/ 0Salinicoccus carnicancri sp. nov., a halophilic bacterium isolated from a Korean fermented seafood crabs preserved in soy sauce: a traditional Korean fermented seafood. Colonies of strain CrmT were ivory

  7. Mutation of Bacterium Vibrio gazogenes for Selective Preparation of Colorants Farzaneh Alihosseini

    E-Print Network [OSTI]

    Hammock, Bruce D.

    against Escherichia coli and Staphylococcus aureus bacte- ria on the dyed products. Methyl marine bacterium strain effectively produced prodiginine type pigments. These colorants could dye wool to look for fungi and bacteria as new sources. We have previously reported that a new isolated marine

  8. Gene-targeted microfluidic cultivation validated by isolation of a gut bacterium listed in Human

    E-Print Network [OSTI]

    Ismagilov, Rustem F.

    Gene-targeted microfluidic cultivation validated by isolation of a gut bacterium listed in Human, 2014) This paper describes a microfluidics-based workflow for geneti- cally targeted isolation that enables genetically targeted cultivation of microorganisms through a combination of microfluidics and on

  9. Response to Comments on "A Bacterium That Can Grow Using Arsenic Instead of Phosphorus"

    SciTech Connect (OSTI)

    Wolfe-Simon, F; Blum, J S; Kulp, T R; Gordon, G W; Hoeft, S E; Pett-Ridge, J; Stolz, J F; Webb, S M; Weber, P K; Davies, P W; Anbar, A D; Oremland, R S

    2011-03-07T23:59:59.000Z

    Concerns have been raised about our recent study describing a bacterium that can grow using arsenic (As) instead of phosphorus (P). Our data suggested that As could act as a substitute for P in major biomolecules in this organism. Although the issues raised are of investigative interest, we contend that they do not invalidate our conclusions. We argue that while no single line of evidence we presented was sufficient to support our interpretation of the data, taken as an entire dataset we find no plausible alternative to our conclusions. Here we reply to the critiques and provide additional arguments supporting the assessment of the data we reported.

  10. Development of a gene cloning system for the hydrogen-producing marine photosynthetic bacterium Rhodopseudomonas sp

    SciTech Connect (OSTI)

    Matsunaga, T.; Matsunaga, N.; Tsubaki, K.; Tanaka, T.

    1986-10-01T23:59:59.000Z

    Seventy-six strains of marine photosynthetic bacteria were analyzed by agarose gel electrophoresis for plasmid DNA content. Among these strains, 12 carried two to four different plasmids with sizes ranging from 3.1 to 11.0 megadaltons. The marine photosynthetic bacterium Rhodopseudomonas sp. NKPB002106 had two plasmids, pRD06S and pRD06L. The smaller plasmid, pRD06S, had a molecular weight of 3.8 megadaltons and was cut at a single site by restriction endonucleases SalI, SmaI, PstI, XhoI, and BglII. Moreover, the marine photosynthetic bacterium Rhodopseudomonas sp. NKPB002106 containing plasmid pRD06 had a satisfactory growth rate (doubling time, 7.5 h), a hydrogen-producing rate of 0.96 ..mu..mol/mg (dry weight) of cells per h, and nitrogen fixation capability. Plasmid pRD06S, however, had neither drug resistance nor heavy-metal resistance, and its copy number was less than 10. Therefore, a recombinant plasmid consisting of pRD06S and Escherichia coli cloning vector pUC13 was constructed and cloned in E. coli. The recombinant plasmid was transformed into Rhodopseudomonas sp. NKPB002106. As a result, Rhodopseudomonas sp. NKPB002106 developed ampicillin resistance. Thus, a shuttle vector for gene transfer was constructed for marine photosynthetic bacteria.

  11. Abstract Carbon destined for lysine synthesis in Coryne-bacterium glutamicum ATCC 21799 can be diverted to-

    E-Print Network [OSTI]

    Sinskey, Anthony J.

    pyruvate was diverted into amino acid synthe- sis. Introduction Corynebacterium glutamicum is used in the commercial production of amino acids, primarily glutamic acid and lysine (Lessard et al. 1999). Metabolic engineering of this bacterium has sought not only to improve glutamic acid and lysine production, but also

  12. Complete genome sequence of the gliding freshwater bacterium Fluviicola taffensis type strain (RW262T)

    SciTech Connect (OSTI)

    Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Chertkov, Olga [Los Alamos National Laboratory (LANL); Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Glavina Del Rio, Tijana [U.S. Department of Energy, Joint Genome Institute; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Liolios, Konstantinos [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Huntemann, Marcel [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Palaniappan, Krishna [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Brambilla, Evelyne-Marie [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Mwirichia, Romano [Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya; Sikorski, Johannes [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Tindall, Brian [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Bristow, James [U.S. Department of Energy, Joint Genome Institute; Eisen, Jonathan [U.S. Department of Energy, Joint Genome Institute; Markowitz, Victor [U.S. Department of Energy, Joint Genome Institute; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute

    2011-01-01T23:59:59.000Z

    Fluviicola taffensis O'Sullivan et al. 2005 belongs to the monotypic genus Fluviicola within the family Cryomorphaceae. The species is of interest because of its isolated phylogenetic location in the genome-sequenced fraction of the tree of life. Strain RW262 T forms a monophyletic lineage with uncultivated bacteria represented in freshwater 16S rRNA gene libraries. A similar phylogenetic differentiation occurs between freshwater and marine bacteria in the family Flavobacteriaceae, a sister family to Cryomorphaceae. Most remarkable is the inability of this freshwater bacterium to grow in the presence of Na + ions. All other genera in the family Cryomorphaceae are from marine habitats and have an absolute requirement for Na + ions or natural sea water. F. taffensis is the first member of the family Cryomorphaceae with a completely sequenced and publicly available genome. The 4,633,577 bp long genome with its 4,082 protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  13. Thymidine uptake, thymidine incorporation, and thymidine kinase activity in marine bacterium isolates

    SciTech Connect (OSTI)

    Jeffrey, W.H.; Paul, J.H. (Univ. of South Florida, St. Petersburg (USA))

    1990-05-01T23:59:59.000Z

    One assumption made in bacterial production estimates from ({sup 3}H)thymidine incorporation is that all heterotrophic bacteria can incorporate exogenous thymidine into DNA. Heterotrophic marine bacterium isolates from Tampa Bay, Fla., Chesapeake Bay, Md., and a coral surface microlayer were examined for thymidine uptake (transport), thymidine incorporation, the presence of thymidine kinase genes, and thymidine kinase enzyme activity. Of the 41 isolates tested, 37 were capable of thymidine incorporation into DNA. The four organisms that could not incorporate thymidine also transported the thymidine poorly and lacked thymidine kinase activity. Attempts to detect thymidine kinase genes in the marine isolates by molecular probing with gene probes made from Escherichia coli and herpes simplex virus thymidine kinase genes proved unsuccessful. To determine if the inability to incorporate thymidine was due to the lack of thymidine kinase, one organism, Vibro sp. strain DI9, was transformed with a plasmid (pGQ3) that contained an E. coli thymidine kinase gene. Although enzyme assays indicated high levels of thymidine kinase activity in transformants, these cells still failed to incorporate exogenous thymidine into DNA or to transport thymidine into cells. These results indicate that the inability of certain marine bacteria to incorporate thymidine may not be solely due to the lack of thymidine kinase activity but may also be due to the absence of thymidine transport systems.

  14. Degradative capacities and bioaugmentation potential of an anaerobic benzene-degrading bacterium strain DN11

    SciTech Connect (OSTI)

    Yuki Kasai; Yumiko Kodama; Yoh Takahata; Toshihiro Hoaki; Kazuya Watanabe [Marine Biotechnology Institute, Kamaishi (Japan)

    2007-09-15T23:59:59.000Z

    Azoarcus sp. strain DN11 is a denitrifying bacterium capable of benzene degradation under anaerobic conditions. The present study evaluated strain DN11 for its application to bioaugmentation of benzene-contaminated underground aquifers. Strain DN11 could grow on benzene, toluene, m-xylene, and benzoate as the sole carbon and energy sources under nitrate-reducing conditions, although o- and p-xylenes were transformed in the presence of toluene. Phenol was not utilized under anaerobic conditions. Kinetic analysis of anaerobic benzene degradation estimated its apparent affinity and inhibition constants to be 0.82 and 11 {mu}M, respectively. Benzene-contaminated groundwater taken from a former coal-distillation plant site in Aichi, Japan was anaerobically incubated in laboratory bottles and supplemented with either inorganic nutrients (nitrogen, phosphorus, and nitrate) alone, or the nutrients plus strain DN11, showing that benzene was significantly degraded only when DN11 was introduced. Denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA gene fragments, and quantitative PCR revealed that DN11 decreased after benzene was degraded. Following the decrease in DN11 16S rRNA gene fragments corresponding to bacteria related to Owenweeksia hongkongensis and Pelotomaculum isophthalicum, appeared as strong bands, suggesting possible metabolic interactions in anaerobic benzene degradation. Results suggest that DN11 is potentially useful for degrading benzene that contaminates underground aquifers at relatively low concentrations. 50 refs., 6 figs., 1 tab.

  15. Analytical solutions to the free vibration of a double-walled carbon nanotube carrying a bacterium at its tip

    SciTech Connect (OSTI)

    Storch, Joel A. [Department of Mechanical Engineering, California State University, Northridge, CA 91330-8348 (United States); Elishakoff, Isaac [Department of Ocean and Mechanical Engineering, Florida Atlantic University, Boca Raton, FL 33431-0991 (United States)

    2013-11-07T23:59:59.000Z

    We calculate the natural frequencies and mode shapes of a cantilevered double-walled carbon nanotube carrying a rigid body—representative of a bacterium or virus—at the tip of the outer nanotube. By idealizing the nanotubes as Bernoulli-Euler beams, we are able to obtain exact expressions for both the mode shapes and characteristic frequency equation. Separate analyses are performed for the special case of a concentrated tip mass and the more complicated situation where the tip body also exhibits inertia and mass center offset from the beam tip.

  16. Direct Conversion of Plant Biomass to Ethanol by Engineered Caldicellulosiruptor bescii

    SciTech Connect (OSTI)

    Chung, Daehwan [University of Georgia, Athens, GA; Cha, Minseok [University of Georgia, Athens, GA; Guss, Adam M [ORNL; Westpheling, Janet [University of Georgia, Athens, GA

    2014-01-01T23:59:59.000Z

    Ethanol is the most widely used renewable transportation biofuel in the United States, with the production of 13.3 billion gallons in 2012 [John UM (2013) Contribution of the Ethanol Industry to the Economy of the United States]. Despite considerable effort to produce fuels from lignocellulosic biomass, chemical pretreatment and the addition of saccharolytic enzymes before microbial bioconversion remain economic barriers to industrial deployment [Lynd LR, et al. (2008) Nat Biotechnol 26(2):169-172]. We began with the thermophilic, anaerobic, cellulolytic bacterium Caldicellulosiruptor bescii, which efficiently uses unpretreated biomass, and engineered it to produce ethanol. Here we report the direct conversion of switchgrass, a nonfood, renewable feedstock, to ethanol without conventional pretreatment of the biomass. This process was accomplished by deletion of lactate dehydrogenase and heterologous expression of a Clostridium thermocellum bifunctional acetaldehyde/alcohol dehydrogenase. Whereas wild-type C. bescii lacks the ability to make ethanol, 70% of the fermentation products in the engineered strain were ethanol [12.8 mM ethanol directly from 2% (wt/vol) switchgrass, a real-world substrate] with decreased production of acetate by 38% compared with wild-type. Direct conversion of biomass to ethanol represents a new paradigm for consolidated bioprocessing, offering the potential for carbon neutral, cost-effective, sustainable fuel production.

  17. Energy transfer in an LH4-like light harvesting complex from the aerobic purple photosynthetic bacterium Roseobacter denitrificans

    SciTech Connect (OSTI)

    Niedzwiedzki, Dariusz; Fuciman, Marcel; Frank, Harry A; Blankenship, R. E.

    2011-01-01T23:59:59.000Z

    A peripheral light-harvesting complex from the aerobic purple bacterium Roseobacter (R.) denitrificans was purified and its photophysical properties characterized. The complex contains two types of pigments, bacteriochlorophyll (BChl) a and the carotenoid (Car) spheroidenone and possesses unique spectroscopic properties. It appears to lack the B850 bacteriochlorophyll a Q{sub y} band that is typical for similar light-harvesting complex 2 antennas. Circular dichroism and low temperature steady-state absorption spectroscopy revealed that the B850 band is present but is shifted significantly to shorter wavelengths and overlaps with the B800 band at room temperature. Such a spectral signature classifies this protein as a member of the light-harvesting complex 4 class of peripheral light-harvesting complexes, along with the previously known light-harvesting complex 4 from Rhodopseudomonas palustris. The influence of the spectral change on the light-harvesting ability was studied using steady-state absorption, fluorescence, circular dichroism, femtosecond and microsecond time-resolved absorption and time-resolved fluorescence spectroscopies. The results were compared to the properties of the similar (in pigment composition) light-harvesting complex 2 from aerobically grown Rhodobacter sphaeroides and are understood within the context of shared similarities and differences and the putative influence of the pigments on the protein structure and its properties.

  18. Assimilation and respiration of radioactive ethylene glycol, in the presence of high sodium chloride concentrations, by a sodium chloride requiring bacterium

    E-Print Network [OSTI]

    Gonzalez, Carlos Francisco

    1972-01-01T23:59:59.000Z

    and the contents distilled over into 5 ml of a 2X boric acid solution containing 3 ml of a O. l%%d ethanolic solution of methyl red and 5. 7 ml of a 0. 1X ethanolic 29 solution of brom cresol green. The samples were titrated, with 0. 1N HC1 using a... limits. Sodium requirement Effect of pH on growth Utilization of carbon sources. Respiration studies. Quantitation of ethylene glycol carbon Disappearance of. glucose and ammonia-nitrogen from cultures of Bacterium T-52. Possible pathways...

  19. Ruiz-Ponte, C., Cilia, V., Lambert, C., Nicolas, J.L., 1998. Roseobacter gallaeciensis sp. nov., a new marine bacterium isolated from rearings and collectors of the scallop Pecten maximus. International Journal of Systematic Bacteriology 48 Pt 2, 537-542.

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    ., a new marine bacterium isolated from rearings and collectors of the scallop Pecten maximus marine bacterium isolated from rearings and collectors of the scallop Pecten maximus. C. Ruiz-Ponte1 , V were isolated from larval cultures and collectors of the scallop Pecten maximus. They showed a high

  20. ORIGINAL ARTICLE Characterization of the cellulolytic and hydrogen-producing

    E-Print Network [OSTI]

    or acid rain (Nath and Das 2004). Moreover, H2 can be produced biologically from renew- able resources this efficiently through physicochemical techniques such as steam explo- sion and dilute-acid pretreatment, as well

  1. Activity-based protein profiling of secreted cellulolytic enzyme...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    can be applied in the short-term find great promise in the use of highly abundant and renewable lignocellulosic plant biomass.1 This material obtained from different...

  2. Kallotenue papyrolyticum gen. nov., sp. nov., a cellulolytic...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    were detected. The major cellular fatty acids (>5%) were C18:0, anteiso-C17:0, iso-C18:0, and iso-C17:0. C16:0, iso-C16:0, and C17:0. The peptidoglycan amino acids were...

  3. Targeted Mutagenesis Tool in Mesophilic Cellulolytic Clostridia Species -

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What'sis Taking Over Our InstagramStructureProposedPAGESafety Tag:8, 2013 FINALTarget Chamber TheEnergy

  4. MICROBIAL FERMENTATION OF ABUNDANT BIOPOLYMERS: CELLULOSE AND CHITIN

    SciTech Connect (OSTI)

    Leschine, Susan

    2009-10-31T23:59:59.000Z

    Our research has dealt with seven major areas of investigation: i) characterization of cellulolytic members of microbial consortia, with special attention recently given to Clostridium phytofermentans, a bacterium that decomposes cellulose and produces uncommonly large amounts of ethanol, ii) investigations of the chitinase system of Cellulomonas uda; including the purification and characterization of ChiA, the major component of this enzyme system, iii) molecular cloning, sequence and structural analysis of the gene that encodes ChiA in C. uda, iv) biofilm formation by C. uda on nutritive surfaces, v) investigations of the effects of humic substances on cellulose degradation by anaerobic cellulolytic microbes, vi) studies of nitrogen metabolism in cellulolytic anaerobes, and vii) understanding the molecular architecture of the multicomplex cellulase-xylanase system of Clostridium papyrosolvens. Also, progress toward completing the research of more recent projects is briefly summarized. Major accomplishments include: 1. Characterization of Clostridium phytofermentans, a cellulose-fermenting, ethanol-producing bacterium from forest soil. The characterization of a new cellulolytic species isolated from a cellulose-decomposing microbial consortium from forest soil was completed. This bacterium is remarkable for the high concentrations of ethanol produced during cellulose fermentation, typically more than twice the concentration produced by other species of cellulolytic clostridia. 2. Examination of the use of chitin as a source of carbon and nitrogen by cellulolytic microbes. We discovered that many cellulolytic anaerobes and facultative aerobes are able to use chitin as a source of both carbon and nitrogen. This major discovery expands our understanding of the biology of cellulose-fermenting bacteria and may lead to new applications for these microbes. 3. Comparative studies of the cellulase and chitinase systems of Cellulomonas uda. Results of these studies indicate that the chitinase and cellulase systems of this bacterium are distinct in terms of the proteins involved and the regulation of their production. 4. Characterization of the chitinase system of C. uda. A 70,000-Mr endochitinase, designated ChiA, was purified from C. uda culture supernatant fluids and characterized. 5. Analysis of chiA, which codes for the major enzymatic component of the chitinase system of C. uda. The gene encoding the endochitinase ChiA in C. uda was cloned, its complete nucleotide sequence was determined and its implications were investigated. 6. Formation of biofilms by C. uda on cellulose and chitin. Microscopic observations indicated that, under conditions of nitrogen limitation, C. uda cells grew as a biofilm attached tightly to the surface of cellulose or chitin. 7. Development of tools for a genetic approach to studies of cellulose fermentation by cellulolytic clostridia. We have explored the potential of various techniques, and obtained evidence indicating that Tn916 mutagenesis may be particularly effective in this regard. As part of this research, we identified the presence of a plasmid in one strain, which was cloned, sequenced, and analyzed for its utility in the development of vectors for genetic studies. 8. Effects of humic substances on cellulose degradation by anaerobic cellulolytic microbes. We determined that humic substances play an important role in the anaerobic cellulose decomposition and in the physiology of cellulose-fermenting soil bacteria. 9. Nitrogenases of cellulolytic clostridia. We described a nitrogenase gene from a cellulolytic clostridium and presented evidence, based on sequence analyses and conserved gene order, for lateral gene transfer between this bacterium and a methanogenic archaeon. 10. Characterization of Clostridium hungatei, a new N2-fixing cellulolytic species isolated from a methanogenic consortium from soil. 11. Understanding the molecular architecture of the multicomplex cellulase-xylanase system of Clostridium papyrosolvens. We discovered that C. papyrosolvens produces a multiprotein, multicom

  5. IMPACTS OF BIOFILM FORMATION ON CELLULOSE FERMENTATION

    SciTech Connect (OSTI)

    Leschine, Susan

    2009-10-31T23:59:59.000Z

    This project addressed four major areas of investigation: i) characterization of formation of Cellulomonas uda biofilms on cellulose; ii) characterization of Clostridium phytofermentans biofilm development; colonization of cellulose and its regulation; iii) characterization of Thermobifida fusca biofilm development; colonization of cellulose and its regulation; and iii) description of the architecture of mature C. uda, C. phytofermentans, and T. fusca biofilms. This research is aimed at advancing understanding of biofilm formation and other complex processes involved in the degradation of the abundant cellulosic biomass, and the biology of the microbes involved. Information obtained from these studies is invaluable in the development of practical applications, such as the single-step bioconversion of cellulose-containing residues to fuels and other bioproducts. Our results have clearly shown that cellulose-decomposing microbes rapidly colonize cellulose and form complex structures typical of biofilms. Furthermore, our observations suggest that, as cells multiply on nutritive surfaces during biofilms formation, dramatic cell morphological changes occur. We speculated that morphological changes, which involve a transition from rod-shaped cells to more rounded forms, might be more apparent in a filamentous microbe. In order to test this hypothesis, we included in our research a study of biofilm formation by T. fusca, a thermophilic cellulolytic actinomycete commonly found in compost. The cellulase system of T. fusca has been extensively detailed through the work of David Wilson and colleagues at Cornell, and also, genome sequence of a T. fusca strain has been determine by the DOE Joint Genome Institute. Thus, T. fusca is an excellent subject for studies of biofilm development and its potential impacts on cellulose degradation. We also completed a study of the chitinase system of C. uda. This work provided essential background information for understanding how C. uda colonizes and degrades insoluble substrates. Major accomplishments of the project include: • Development of media containing dialysis tubing (described by the manufacturer as “regenerated cellulose”) as sole carbon and energy source and a nutritive surface for the growth of cellulolytic bacteria, and development of various microscopic methods to image biofilms on dialysis tubing. • Demonstration that cultures of C. phytofermentans, an obligate anaerobe, C. uda, a facultative aerobe, and T. fusca, a filamentous aerobe, formed microbial communities on the surface of dialysis tubing, which possessed architectural features and functional characteristics typical of biofilms. • Demonstration that biofilm formation on the nutritive surface, cellulose, involves a complex developmental processes, including colonization of dialysis tubing, formation of cell clusters attached to the nutritive surface, cell morphological changes, formation of complex structures embedded in extracellular polymeric matrices, and dispersal of biofilm communities as the nutritive surface is degraded. • Determination of surface specificity and regulatory aspects of biofilm formation by C. phytofermentans, C. uda, and T. fusca. • Demonstration that biofilm formation by T. fusca forms an integral part of the life cycle of this filamentous cellulolytic bacterium, including studies on the role of mycelial pellet formation in the T. fusca life cycle and a comparison of mycelial pellets to surface-attached T. fusca biofilms. • Characterization of T. fusca biofilm EPS, including demonstration of a functional role for EPS constituents. • Correlation of T. fusca developmental life cycle and cellulase gene expression.

  6. Thermophilic Biotrickling Filtration of Ethanol Vapors

    E-Print Network [OSTI]

    .g., from the tobacco, (4) the pulp and paper, (5) and food industry (6). One option is cooling these gases containing organic packing materials: treatment of NOx at 55 °C, (7) co-treatment of methanol and R temperatures. High operating temperatures accelerate the degradation of the organic packing material, (4, 9)

  7. Proteogenomic Analysis of a Thermophilic Bacterial Consortium...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    not well-explored. Here we report on the metagenomic and proteogenomic analyses of a compost-derived bacterial consortium adapted to switchgrass at elevated temperature with high...

  8. Novel Thermophilic Cellobiohydrolase - Energy Innovation Portal

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What's Possible for Renewable Energy:Nanowire3627 Federal Register / Vol. 77,Cheaper Solar Cells; |

  9. Thermophilic Endoglucanase Enzymes Engineered for Increased Activity -

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What'sis Taking Over OurThe Iron Spin Transition in theTheoreticalEnergy Innovation Portal

  10. Thermophilic Switchgrass-Adapted Consortia Glycoside Hydrolase Activities of Thermophilic Bacterial Consortia1

    E-Print Network [OSTI]

    Hazen, Terry

    variety of potential biomass feedstocks and pretreatments5 available require tailored glycoside hydrolase

  11. The possible symbiotic role of proteolytic and cellulolytic bacteria found in the gut of Limnoria

    E-Print Network [OSTI]

    Traganza, Eugene Dewees

    1959-01-01T23:59:59.000Z

    IOGRAPHY 81 LIST OF TABLES Table No. 1 Attack of Cellulose by Limnoria Tissue Homogenates 2 Attack of Gelatin Substrate by Limnoria Tissue Homogenates; 17 Liquefaction Analysis 28 3 Attack of Gelatin Substrate by Limnoria Tissue Homogenates... of which have successfully solved the problem, while the most basic information concerning physiology and metabolism is lacking. Dr. J. R. Merkel and the author became interested in the metabolism of one type of marine borer, the small isopod crustacean...

  12. Prospecting for cellulolytic activity in insect digestive fluids Cris Oppert a

    E-Print Network [OSTI]

    Jurat-Fuentes, Juan Luis

    interest in lignocellulosic biomass as feedstock for production of ethanol biofuel (Lynd et al., 1991

  13. Pathogenesis of the carcinogenic bacterium, Helicobacter pylori

    E-Print Network [OSTI]

    Lee, Chung-Wei, Ph. D. Massachusetts Institute of Technology

    2007-01-01T23:59:59.000Z

    Gastric cancer is the second most common malignancy in the digestive system and the second leading cause of cancer-related death worldwide. Epidemiological data and experimental studies have identified several risk factors ...

  14. Laboratory Directed Research and Development Program FY 2007

    E-Print Network [OSTI]

    editor, Todd C Hansen,

    2008-01-01T23:59:59.000Z

    generating thermophilic microbial fuel cells,” submitted toof Thermophilic Microbial Fuel Cell,” American Geophysicalfrom a Thermophilic Microbial Fuel Cell,” American Society

  15. Biocorrosive Thermophilic Microbial Communities in Alaskan North Slope Oil Facilities

    E-Print Network [OSTI]

    Duncan, Kathleen E.

    2010-01-01T23:59:59.000Z

    Corrosion of metallic oilfield pipelines by microorganismsbiodegradation processes in the oilfield environment can beand is typical of ANS oilfields that collectively have

  16. anaerobic thermophiles final: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    for methane production by anaerobic digestion of animal manures. Experiences with design, construction, and operation of a two-stage heated continuous-feed digester for a herd of...

  17. anaerobic extreme thermophilic: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    for methane production by anaerobic digestion of animal manures. Experiences with design, construction, and operation of a two-stage heated continuous-feed digester for a herd of...

  18. alkalophilic thermophilic bacillus: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Huan-Xiang Zhou and Feng Dong Department of Physics caldolyticus cold shock protein (Bc-Csp) differs from the mesophilic Bacillus subtilis cold shock protein B (Bs Weston, Ken 3...

  19. anaerobic thermophiles progress: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    provides an array of positive environmental benefits such as reducing greenhouse gas emissions, replacing mineral fertilizers, producing renewable energy and treating...

  20. Biocorrosive Thermophilic Microbial Communities in Alaskan North Slope Oil Facilities

    E-Print Network [OSTI]

    Duncan, Kathleen E.

    2010-01-01T23:59:59.000Z

    in Alaskan North Slope Oil Facilities Kathleen E. Duncan,in Alaskan North Slope oil production facilities. Title:in Alaskan North Slope Oil Facilities Authors: Kathleen E.

  1. Conversion of sugarcane bagasse to carboxylic acids under thermophilic conditions 

    E-Print Network [OSTI]

    Fu, Zhihong

    2009-05-15T23:59:59.000Z

    of bio-oils: Pyrolysis and liquefaction Pyrolysis is an important thermal conversion process for biomass. Up to now, pyrolysis is less developed than gasification. Major attention was especially caused by the potential deployment of this technology... on small scale in rural areas and as feedstock for the chemical industry. Pyrolysis converts biomass at temperatures around 500?C in the absence of oxygen to liquid (bio-oil), gaseous, and solid (char) fractions (Adjaye et al. 1992; Demirbas and Balat...

  2. autoheated thermophilic aerobic: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    capacity than uninfected males, but only for small males. Discriminant function analysis suggested that aerobic capacity and display behaviour, together with male ornaments...

  3. Sulfurihydrogenibium yellowstonense sp. nov., an extremely thermophilic, facultatively heterotrophic,

    E-Print Network [OSTI]

    Reysenbach, Anna-Louise

    are proposed. The order Aquificales consists of the genera Hydrogeno- bacter, Aquifex and Hydrogenobaculum

  4. Biocorrosive Thermophilic Microbial Communities in Alaskan North Slope Oil Facilities

    E-Print Network [OSTI]

    Duncan, Kathleen E.

    2010-01-01T23:59:59.000Z

    in Alaskan North Slope oil production facilities. Title:Profiling Despite oil production from several major16) was isolated from oil-production water and has optimal

  5. Conversion of sugarcane bagasse to carboxylic acids under thermophilic conditions

    E-Print Network [OSTI]

    Fu, Zhihong

    2009-05-15T23:59:59.000Z

    ?????????????. 17 1.4 Project description????????????..?... 25 II MATERIALS AND METHODS???????????? 27 2.1 Biomass feedstock??????????????. 27 2.2 Biomass pretreatment????????????? 29 2.3 Fermentation material and methods.... This is followed by introducing promising lignocellulosic biomass feedstocks and challenges in lignocellulosic biomass conversion. Subsequently, it presents the process description and recent advances of the MixAlco process, a novel and promising biomass...

  6. anaerobic thermophilic biogas: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    for Korean food waste with high water contents (>80%). The hydrogen sulfide in the biogas was removed by a biological desulfurization equipment integrated in the horizontal...

  7. anaerobic thermophilic digestion: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    for Korean food waste with high water contents (>80%). The hydrogen sulfide in the biogas was removed by a biological desulfurization equipment integrated in the horizontal...

  8. anaerobic thermophilic bacteria: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    and tested in pilot scale for Korean food waste with high water contents (>80%). The hydrogen sulfide in the biogas was removed by a biological desulfurization equipment...

  9. Thermophilic Cellulases Compatible with Ionic Liquid Pretreatment - Energy

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What'sis Taking Over OurThe Iron Spin Transition in theTheoretical

  10. Fermentation method producing ethanol

    DOE Patents [OSTI]

    Wang, Daniel I. C. (Belmont, MA); Dalal, Rajen (Chicago, IL)

    1986-01-01T23:59:59.000Z

    Ethanol is the major end product of an anaerobic, thermophilic fermentation process using a mutant strain of bacterium Clostridium thermosaccharolyticum. This organism is capable of converting hexose and pentose carbohydrates to ethanol, acetic and lactic acids. Mutants of Clostridium thermosaccharolyticum are capable of converting these substrates to ethanol in exceptionally high yield and with increased productivity. Both the mutant organism and the technique for its isolation are provided.

  11. Closing the Carbon Balance for Fermentation by Clostridium thermocellum (ATCC 27405)

    SciTech Connect (OSTI)

    Ellis, Lucas D [Thayer School of Engineering at Dartmouth; Holwerda, Evert K [ORNL; Hogsett, David [Mascoma Corporation; Rogers, Steve [ORNL; Shao, Xiongjun [Thayer School of Engineering at Dartmouth; Tschaplinski, Timothy J [ORNL; Thorne, Phil [Mascoma Corporation; Lynd, L. [Dartmouth College

    2012-01-01T23:59:59.000Z

    Our lab and most others have not been able to close a carbon balance for fermentation by the thermophilic, cellulolytic anaerobe, Clostridium thermocellum. We undertook a detailed accounting of product formation in C. thermocellum ATCC 27405. Elemental analysis revealed that for both cellulose (Avicel) and cellobiose, {>=}92% of the substrate carbon utilized could be accounted for in the pellet, supernatant and off-gas when including sampling. However, 11.1% of the original substrate carbon was found in the liquid phase and not in the form of commonly-measured fermentation products - ethanol, acetate, lactate, and formate. Further detailed analysis revealed all the products to be <720 da and have not usually been associated with C. thermocellum fermentation, including malate, pyruvate, uracil, soluble glucans, and extracellular free amino acids. By accounting for these products, 92.9% and 93.2% of the final product carbon was identified during growth on cellobiose and Avicel, respectively.

  12. ammonia oxidizing bacterium: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Laszlo B. Kish; Maria D. King; Chiman Kwan 2009-01-20 63 Energy Savings from Floating Head Pressure in Ammonia Refrigeration Systems Texas A&M University - TxSpace Summary:...

  13. Genetic manipulation of the obligate chemolithoautotrophic bacterium Thiobacillus denitrificans

    SciTech Connect (OSTI)

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

    2011-07-15T23:59:59.000Z

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

  14. Rhodoferax ferrireducens sp. nov., a psychrotolerant, facultatively anaerobic bacterium

    E-Print Network [OSTI]

    Lovley, Derek

    included acetate, lactate, malate, propionate, pyruvate, succinate and benzoate. None of the compounds included Fe(III)­NTA (nitrilotriacetic acid), Mn(IV) oxide, nitrate, fumarate and oxygen. Phylogenetic, USA. Abbreviations: AQDS, anthraquinone-2,6-disulfonate; NTA, nitrilotri- acetic acid; PHA, poly-hydroxyalkanoate;

  15. The genome sequence of the capnophilic rumen bacterium Mannheimia succiniciproducens

    E-Print Network [OSTI]

    is further converted by microbial fermentation to volatile fatty acids (VFAs) such as acetic, propionic, an important four-carbon industrial chemical. The rumen is a fermentation vat in which the feed is collected im) are converted into succinic acid as well as acetic, formic and lactic acids by M. succiniciproducens2. Acetic

  16. antagonistic bacterium belonging: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Hugh's son. Silicon Carbide Specimen This specimen of silicon carbide, also known as carborundum or moissanite, was produced in an electric batch furnace at NC State College in the...

  17. acetic acid bacterium: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    blend. Inthe present investigation, densities and viscosities have been measured in 4 % solution of polyAcrylic Acid and Poly vinyl Acetate in DMSO using calculated and reduced...

  18. aquatic bacterium caulobacter: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    of aquatic herbicide association with herbicide appli- cations. Applications of acrolein, copper sulfate, chelated copper, diquat 29 Sustaining America's Aquatic Biodiversity...

  19. anammox bacterium kuenenia: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    a one of the essential parameter as it has significant adverse impacts on the environment. Anaerobic ammonia oxidation (ANAMMOX) is a novel process in which nitrite is used...

  20. Genetic manipulation of the obligate chemolithoautotrophic bacterium Thiobacillus denitrificans

    E-Print Network [OSTI]

    Beller, H.R.

    2012-01-01T23:59:59.000Z

    cells  into  a  centrifuge  tube,  and  spin  cells  at  resistant,  50-­?mL,  screw-­?cap   centrifuge  tube.  protocol,  use  a  centrifuge  tube  that  is  phenol-­?,  

  1. Genetic manipulation of the obligate chemolithoautotrophic bacterium Thiobacillus denitrificans

    E-Print Network [OSTI]

    Beller, H.R.

    2012-01-01T23:59:59.000Z

    hours,  may  aid   in  resuspension.   26. Add  20  µL  5  µof  70%  ethanol;  resuspension  of  the  pellet  is  not  of  70%  ethanol.    Resuspension  of  the  DNA  is  not  

  2. aerobic photosynthetic bacterium: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    capacity than uninfected males, but only for small males. Discriminant function analysis suggested that aerobic capacity and display behaviour, together with male ornaments...

  3. aerobic bacterium tetrathiobacter: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    H. Kwan; We Thank J. Decruyenaere; C. Hayes; T. Kim; T. Maclarty; S. Popma For Their 1997-01-01 10 Mate choice and aerobic capacity in red junglefowl CiteSeer Summary: In 'good...

  4. antarctica bacterium pseudoalteromonas: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    opens with a typical transmission... Tremblin, P; Schneider, N; Durand, G Al; Ashley, M C B; Lawrence, J S; Luong-Van, D M; Storey, J W V; Durand, G An; Reinert, Y; Veyssiere, C;...

  5. Spatial gradient of protein phosphorylation underlies replicative bacterium

    E-Print Network [OSTI]

    Chen, Y. Erin

    Spatial asymmetry is crucial to development. One mechanism for generating asymmetry involves the localized synthesis of a key regulatory protein that diffuses away from its source, forming a spatial gradient. Although ...

  6. anaerobic bacterium anaerocellum: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    for Korean food waste with high water contents (>80%). The hydrogen sulfide in the biogas was removed by a biological desulfurization equipment integrated in the horizontal...

  7. Abstract A novel succinic acid-producing bacterium was isolated from bovine rumen. The bacterium is a

    E-Print Network [OSTI]

    succinic acid, acetic acid and formic acid at a constant ratio of 2:1:1. When M. succiniciproducens MBEL55E of the tricarboxylic acid (TCA) cycle and also as one of the fermentation products of anaerobic metabo- lism (Gottschalk 1986; Zeikus 1980). Fermentative pro- duction of succinic acid from renewable biomass has re

  8. Process for generation of hydrogen gas from various feedstocks using thermophilic bacteria

    DOE Patents [OSTI]

    Ooteghem, Suellen Van (Morgantown, WV)

    2005-09-13T23:59:59.000Z

    A method for producing hydrogen gas is provided comprising selecting a bacteria from the Order Thermotogales, subjecting the bacteria to a feedstock and to a suitable growth environment having an oxygen concentration below the oxygen concentration of water in equilibrium with air; and maintaining the environment at a predetermined pH and at a temperature of at least approximately 45.degree. C. for a time sufficient to allow the bacteria to metabolize the feedstock.

  9. Community dynamics and glycoside hydrolase activities of thermophilic bacterial consortia adapted to switchgrass

    E-Print Network [OSTI]

    Gladden, J.M.

    2012-01-01T23:59:59.000Z

    Comparisons were made to Novozymes enzyme cocktails: NS50030pH 5.0. For comparison, a Novozymes cocktail containing bothsame pre-warmed buffer. The Novozymes enzyme preparation was

  10. Analysis of Metabolic Pathways and Fluxes in a Newly Discovered Thermophilic and

    E-Print Network [OSTI]

    Hazen, Terry

    into the physiological properties of this extremophile and explore its metabolism for bio-ethanol or other bioprocess et al., 2006), which makes it an ideal microbe for improved bio-ethanol production. Moreover

  11. A Highly Active Protein Repair Enzyme from an Extreme Thermophile: The L-Isoaspartyl Methyltransferase

    E-Print Network [OSTI]

    Clarke, Steven

    and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, California 90095 to be intermediate between those of the high-affinity human enzyme and those of the lower-affinity wheat, nematode

  12. Quantification of thermophilic archaea and bacteria in a Nevada hot spring using fluorescent in situ hybridization

    E-Print Network [OSTI]

    Walker, Lawrence R.

    in situ hybridization Abstract Previous studies of high temperature hot springs in Yellowstone National temperatures. The cells, which were concentrated from 300 liters of hot spring water through tangential flow dominate in high-temperature environments such as Yellowstone National Park. However, our study indicates

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

    SciTech Connect (OSTI)

    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.

    2014-01-02T23:59:59.000Z

    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.

  14. Thermophilic and thermoacidophilic sugar transporter genes and enzymes from Alicyclobacillus acidocaldarius and related organisms, methods

    SciTech Connect (OSTI)

    Thompson, David N; Apel, William A; Thompson, Vicki S; Reed, David W; Lacey, Jeffrey A

    2013-11-05T23:59:59.000Z

    Isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from Alicyclobacillus acidocaldarius are provided. Further provided are methods for transporting sugars across cell membranes using isolated and/or purified polypeptides and nucleic acid sequences from Alicyclobacillus acidocaldarius.

  15. Thermophilic and thermoacidophilic sugar transporter genes and enzymes from Alicyclobacillus acidocaldarius and related organisms, methods

    SciTech Connect (OSTI)

    Thompson, David N.; Apel, William A.; Thompson, Vicki S.; Reed, David W.; Lacey, Jeffrey A.

    2013-01-29T23:59:59.000Z

    Isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from Alicyclobacillus acidocaldarius are provided. Further provided are methods for transporting sugars across cell membranes using isolated and/or purified polypeptides and nucleic acid sequences from Alicyclobacillus acidocaldarius.

  16. Thermophilic and thermoacidophilic biopolymer-degrading genes and enzymes from alicyclobacillus acidocaldarius and related organisms, methods

    DOE Patents [OSTI]

    Thompson, David N; Apel, William A; Thompson, Vicki S; Reed, David W; Lacey, Jeffrey A; Henriksen, Emily D

    2013-07-30T23:59:59.000Z

    Isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from Alicyclobacillus acidocaldarius are provided. Further provided are methods of at least partially degrading, cleaving, or removing polysaccharides, lignocellulose, cellulose, hemicellulose, lignin, starch, chitin, polyhydroxybutyrate, heteroxylans, glycosides, xylan-, glucan-, galactan-, or mannan-decorating groups using isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from Alicyclobacillus acidocaldarius.

  17. Thermophilic and thermoacidophilic biopolymer-degrading genes and enzymes from Alicyclobacillus acidocaldarius and related organisms, methods

    SciTech Connect (OSTI)

    Thompson, David N; Apel, William A; Thompson, Vicki S; Reed, David W; Lacey, Jeffrey A; Henriksen, Emily D

    2013-04-23T23:59:59.000Z

    Isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from Alicyclobacillus acidocaldarius are provided. Further provided are methods of at least partially degrading, cleaving, or removing polysaccharides, lignocellulose, cellulose, hemicellulose, lignin, starch, chitin, polyhydroxybutyrate, heteroxylans, glycosides, xylan-, glucan-, galactan-, or mannan-decorating groups using isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from Alicyclobacillus acidocaldarius.

  18. Thermophilic and thermoacidophilic biopolymer-degrading genes and enzymes from alicyclobacillus acidocaldarius and related organisms, methods

    DOE Patents [OSTI]

    Thompson, David N. (Idaho Falls, ID); Apel, William A. (Jackson, WY); Thompson, Vicki S. (Idaho Falls, ID); Reed, David W. (Idaho Falls, ID); Lacey, Jeffrey A. (Idaho Falls, ID); Henriksen, Emily D. (Idaho Falls, ID)

    2010-12-28T23:59:59.000Z

    Isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from Alicyclobacillus acidocaldarius are provided. Further provided are methods of at least partially degrading, cleaving, or removing polysaccharides, lignocellulose, cellulose, hemicellulose, lignin, starch, chitin, polyhydroxybutyrate, heteroxylans, glycosides, xylan-, glucan-, galactan, or mannan-decorating groups using isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from Alicyclobacillus acidocaldarius.

  19. Thermophilic and thermoacidophilic sugar transporter genes and enzymes from alicyclobacillus acidocaldarius and related organisms, methods

    DOE Patents [OSTI]

    Thompson, David N. (Idaho Falls, ID); Apel, William A. (Jackson, WY); Thompson, Vicki S. (Idaho Falls, ID); Reed, David W. (Idaho Falls, ID); Lacey, Jeffrey A. (Idaho Falls, ID)

    2011-06-14T23:59:59.000Z

    Isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from Alicyclobacillus acidocaldarius are provided. Further provided are methods for transporting sugars across cell membranes using isolated and/or purified polypeptides and nucleic acid sequences from Alicyclobacillus acidocaldarius.

  20. Thermophilic and thermoacidophilic biopolymer-degrading genes and enzymes from Alicyclobacillus acidocaldarius and related organisms, methods

    DOE Patents [OSTI]

    Thompson, David N.; Apel, William A.; Thompson, Vicki S.; Reed, David W.; Lacey, Jeffrey A.

    2013-10-15T23:59:59.000Z

    Isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from Alicyclobacillus acidocaldarius are provided. Further provided are methods of at least partially degrading, cleaving, or removing polysaccharides, lignocellulose, cellulose, hemicellulose, lignin, starch, chitin, polyhydroxybutyrate, heteroxylans, glycosides, xylan-, glucan-, galactan-, or mannan-decorating groups using isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from Alicyclobacillus acidocaldarius.

  1. Thermophilic and thermoacidophilic sugar transporter genes and enzymes from Alicyclobacillus acidocaldarius and related organisms, methods

    SciTech Connect (OSTI)

    Thompson, David N.; Apel, William A.; Thompson, Vicki S.; Reed, David W.; Lacey, Jeffrey A.

    2013-01-15T23:59:59.000Z

    Isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from Alicyclobacillus acidocaldarius are provided. Further provided are methods for transporting sugars across cell membranes using isolated and/or purified polypeptides and nucleic acid sequences from Alicyclobacillus acidocaldarius.

  2. Thermophilic and thermoacidophilic metabolism genes and enzymes from Alicyclobacillus acidocaldarius and related organisms, methods

    DOE Patents [OSTI]

    Thompson, Vicki S; Apel, William A; Reed, David W; Lee, Brady D; Thompson, David N; Roberto, Francisco F; Lacey, Jeffrey A

    2014-05-20T23:59:59.000Z

    Isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from Alicyclobacillus acidocaldarius are provided. Further provided are methods for modulating or altering metabolism in a cell using isolated and/or purified polypeptides and nucleic acid sequences from Alicyclobacillus acidocaldarius.

  3. Thermophilic and thermoacidophilic biopolymer-degrading genes and enzymes from alicyclobacillus acidocaldarius and related organisms, methods

    DOE Patents [OSTI]

    Thompson, David N. (Idaho Falls, ID); Apel, William A. (Jackson, WY); Thompson, Vicki S. (Idaho Falls, ID); Reed, David W. (Idaho Falls, ID); Lacey, Jeffrey A. (Idaho Falls, ID); Henriksen, Emily D. (Idaho Falls, ID)

    2012-06-19T23:59:59.000Z

    Isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from Alicyclobacillus acidocaldarius are provided. Further provided are methods of at least partially degrading, cleaving, or removing polysaccharides, lignocellulose, cellulose, hemicellulose, lignin, starch, chitin, polyhydroxybutyrate, heteroxylans, glycosides, xylan-, glucan-, galactan-, or mannan-decorating groups using isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from Alicyclobacillus acidocaldarius.

  4. Thermophilic and thermoacidophilic sugar transporter genes and enzymes from Alicyclobacillus acidocaldarius and related organisms, methods

    DOE Patents [OSTI]

    Thompson, David N. (Idaho Falls, ID); Apel, William A. (Jackson, WY); Thompson, Vicki S. (Idaho Falls, ID); Reed, David W. (Idaho Falls, ID); Lacey, Jeffrey A. (Idaho Falls, ID)

    2011-12-06T23:59:59.000Z

    Isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from Alicyclobacillus acidocaldarius are provided. Further provided are methods for transporting sugars across cell membranes using isolated and/or purified polypeptides and nucleic acid sequences from Alicyclobacillus acidocaldarius.

  5. High-solids enrichment of thermophilic microbial communities and their enzymes on bioenergy feedstocks

    E-Print Network [OSTI]

    Reddy, A. P.

    2012-01-01T23:59:59.000Z

    One such community is from composting which involves theVanderGheynst et al. 1997). Composting processes typicallyaeration to simulate a composting process. Prior to

  6. Novel Thermophilic Celluloly1c Isolates Belonging to the Phylum Chloroflexi

    E-Print Network [OSTI]

    Walker, Lawrence R.

    from the food supply, the development of second-generation biofuels technology is necessary. Second-generation biofuels are produced by converting technological hurdle limiting the mass production of second-generation biofuels

  7. High-solids enrichment of thermophilic microbial communities and their enzymes on bioenergy feedstocks

    E-Print Network [OSTI]

    Reddy, A. P.

    2012-01-01T23:59:59.000Z

    strain isolated from black liquor. Bioresource Technologyhave been enriched in black liquor samples from paper

  8. 2216 Biophysical Journal Volume 84 April 2003 22162222 Electrostatic Contributions to the Stability of a Thermophilic

    E-Print Network [OSTI]

    Weston, Ken

    and Bohm, 1998; Szilagyi and Zavodszky, 2000; Petsko, 2001; Zhou, 2002d). Bacillus caldolyticus cold shock

  9. Xero-thermophilous and grassland ubiquist species dominate the weevil fauna of Swiss cities (Coleoptera, Curculionoidea)

    E-Print Network [OSTI]

    Richner, Heinz

    (Curculionoidea) was sampled in the three Swiss cities of Lucerne, Lugano and Zurich. In total, 3448 individuals from 129 species were collected (Lucerne: 64 species; Lugano: 69 species; Zurich: 83 species). The most (Soerensen index) was highest be- tween the cities of Lucerne and Zurich, which could be expected since

  10. aerobic co-oxidizing thermophile: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    capacity than uninfected males, but only for small males. Discriminant function analysis suggested that aerobic capacity and display behaviour, together with male ornaments...

  11. Process for Generation of Hydrogen Gas from Various Feedstocks Using Thermophilic Bacteria

    SciTech Connect (OSTI)

    Ooteghem Van, Suellen

    2005-09-13T23:59:59.000Z

    A method for producing hydrogen gas is provided comprising selecting a bacteria from the Order Thermotogales, subjecting the bacteria to a feedstock and to a suitable growth environment having an oxygen concentration below the oxygen concentration of water in equilibrium with air; and maintaining the environment at a predetermined pH and at a temperature of at least approximately 45 degrees C. for a time sufficient to allow the bacteria to metabolize the feedstock.

  12. Development of a thermophilic SSF system for butanol production Presentation for BETO 2015 Project Peer Review

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels DataDepartment of Energy Your Density Isn't Your Destiny:Revised Finding of No53197E T A * S HBatteries1000: Development of a Wet

  13. Insect Science (2010) 00, 115, DOI 10.1111/j.1744-7917.2010.01322.x Methods for discovery and characterization of cellulolytic

    E-Print Network [OSTI]

    Jurat-Fuentes, Juan Luis

    2010-01-01T23:59:59.000Z

    Cellulosic ethanol has been identified as a crucial biofuel resource due to its sustainability and abundance methods have been used to identify and characterize these enzymes, the advancement of genomic. This information is highly relevant to the design of improved industrial processes of biofuel production

  14. Laboratory Directed Research and Development Program FY 2006

    E-Print Network [OSTI]

    Hansen Ed., Todd

    2007-01-01T23:59:59.000Z

    a thermophilic microbial fuel cell, “in abstracts of theProject Description: In a microbial fuel cell (MFC) bacteriafrom a thermophilic microbial fuel cell and also the first

  15. Draft genome sequence of Therminicola potens strain JR

    E-Print Network [OSTI]

    Byrne-Bailey, K.G.

    2010-01-01T23:59:59.000Z

    in thermophilic microbial fuel cells. ISME J 2:1146-56. Wu,anode of a thermophilic microbial fuel cell (MFC), where it

  16. Environmental genomics reveals a single species ecosystem deep within the Earth

    SciTech Connect (OSTI)

    Chivian, Dylan; Brodie, Eoin L.; Alm, Eric J.; Culley, David E.; Dehal, Paramvir S.; DeSantis, Todd Z.; Gihring, Thomas M.; Lapidus, Alla; Lin, Li-Hung; Lowry, Stephen R.; Moser, Duane P.; Richardson, Paul; Southam, Gordon; Wanger, Greg; Pratt, Lisa M.; Andersen, Gary L.; Hazen, Terry C.; Brockman, Fred J.; Arkin, Adam P.; Onstott, Tullis C.

    2008-09-17T23:59:59.000Z

    DNA from low biodiversity fracture water collected at 2.8 km depth in a South African gold mine was sequenced and assembled into a single, complete genome. This bacterium, Candidatus Desulforudis audaxviator, comprises>99.9percent of the microorganisms inhabiting the fluid phase of this particular fracture. Its genome indicates a motile, sporulating, sulfate reducing, chemoautotrophic thermophile that can fix its own nitrogen and carbon using machinery shared with archaea. Candidatus Desulforudis audaxviator is capable of an independent lifestyle well suited to long-term isolation from the photosphere deep within Earth?s crust, and offers the first example of a natural ecosystem that appears to have its biological component entirely encoded within a single genome.

  17. Complete genome of the cellyloytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evloutionary adaptations

    E-Print Network [OSTI]

    Barabote, Ravi D.

    2009-01-01T23:59:59.000Z

    is also find in Helicobacter pylori strains annotated as:Sheeba Helicobacter hepaticus Helicobacter pylori26695 Helicobacter pylori HPAG1 Helicobacter pylori J99

  18. Analysis of Metabolic Pathways and Fluxes in a Newly Discovered Thermophilic and Ethanol-Tolerant Geobacillus Strain

    E-Print Network [OSTI]

    Tang, Yinjie J.

    2009-01-01T23:59:59.000Z

    Bacteria engineered for fuel ethanol production: currentcharacterization of two novel ethanol-tolerant facultative-Lin Y, Tanaka S. 2006. Ethanol fermentation from biomass

  19. Analysis of Metabolic Pathways and Fluxes in a Newly Discovered Thermophilic and Ethanol-Tolerant Geobacillus Strain

    E-Print Network [OSTI]

    Tang, Yinjie J.

    2009-01-01T23:59:59.000Z

    explore its metabolism for bioethanol or other bioprocessthe metabolic pathways for bioethanol production as well as

  20. Methods of combined bioprocessing and related microorganisms, thermophilic and/or acidophilic enzymes, and nucleic acids encoding said enzymes

    DOE Patents [OSTI]

    Thompson, David N; Apel, William A; Thompson, Vicki S; Ward, Thomas E

    2013-07-23T23:59:59.000Z

    A genetically modified organism comprising: at least one nucleic acid sequence and/or at least one recombinant nucleic acid isolated from Alicyclobacillus acidocaldarius and encoding a polypeptide involved in at least partially degrading, cleaving, transporting, metabolizing, or removing polysaccharides, cellulose, lignocellulose, hemicellulose, lignin, starch, sugars, sugar oligomers, carbohydrates, complex carbohydrates, chitin, heteroxylans, glycosides, xylan-, glucan-, galactan-, or mannan-decorating groups; and at least one nucleic acid sequence and/or at least one recombinant nucleic acid encoding a polypeptide involved in fermenting sugar molecules to a product. Additionally, enzymatic and/or proteinaceous extracts may be isolated from one or more genetically modified organisms. The extracts are utilized to convert biomass into a product. Further provided are methods of converting biomass into products comprising: placing the genetically modified organism and/or enzymatic extracts thereof in fluid contact with polysaccharides, cellulose, lignocellulose, hemicellulose, lignin, starch, sugars, sugar oligomers, carbohydrates, complex carbohydrates, chitin, heteroxylans, glycosides, and/or xylan-, glucan-, galactan-, or mannan-decorating groups.

  1. Methods of combined bioprocessing and related microorganisms, thermophilic and/or acidophilic enzymes, and nucleic acids encoding said enzymes

    DOE Patents [OSTI]

    Thompson, David N; Apel, William A; Thompson, Vicki S; Ward, Thomas E

    2014-04-08T23:59:59.000Z

    A genetically modified organism comprising: at least one nucleic acid sequence and/or at least one recombinant nucleic acid isolated from Alicyclobacillus acidocaldarius and encoding a polypeptide involved in at least partially degrading, cleaving, transporting, metabolizing, or removing polysaccharides, cellulose, lignocellulose, hemicellulose, lignin, starch, sugars, sugar oligomers, carbohydrates, complex carbohydrates, chitin, heteroxylans, glycosides, xylan-, glucan-, galactan-, or mannan-decorating groups; and at least one nucleic acid sequence and/or at least one recombinant nucleic acid encoding a polypeptide involved in fermenting sugar molecules to a product. Additionally, enzymatic and/or proteinaceous extracts may be isolated from one or more genetically modified organisms. The extracts are utilized to convert biomass into a product. Further provided are methods of converting biomass into products comprising: placing the genetically modified organism and/or enzymatic extracts thereof in fluid contact with polysaccharides, cellulose, lignocellulose, hemicellulose, lignin, starch, sugars, sugar oligomers, carbohydrates, complex carbohydrates, chitin, heteroxylans, glycosides, and/or xylan-, glucan-, galactan-, or mannan-decorating groups.

  2. Toward the Physical Basis of Thermophilic Proteins: Linking of Enriched Polar Interactions and Reduced Heat Capacity of Unfolding

    E-Print Network [OSTI]

    Weston, Ken

    and Bohm, 1998; Szilagyi and Zavodszky, 2000; Petsko, 2001). Whereas thermosta- bility likely results from

  3. The Genetically Remote Pathogenic Strain NVH391-98 of the Bacillus cereus Group Represents the Cluster of Thermophilic Strains

    E-Print Network [OSTI]

    Auger, Sandrine

    2008-01-01T23:59:59.000Z

    The strains Bce ATCC14579, Bwe KBAB4 and NVH391-98 are ofB. weihenstephanensis (Bwe), was proposed (14, 21). Instrains. Psychrotolerant strains Bwe KBAB4 (20, 24) and Bwe

  4. Biogeochemical controls and isotopic signatures of nitrous oxide production by a marine ammonia-oxidizing bacterium

    E-Print Network [OSTI]

    Frame, Caitlin H.

    Nitrous oxide (N2O)[N subscript 2 O] is a trace gas that contributes to the greenhouse effect and stratospheric ozone depletion. The N2O [N subscript 2 O] yield from nitrification (moles N2O-N [N subscript 2 O - N] produced ...

  5. The Pseudomonas Wilt bacterium: it's identification and role as a cotton pathogen

    E-Print Network [OSTI]

    Pore, Robert Scott

    1962-01-01T23:59:59.000Z

    inoculated after it became solid. The rela- tive amount of gelatin liquefaction was determined after 11 days (13, 15). E. Cultural characteristics. These were determined on Beef-extract broth and agar and on PDCA, Various temperatures were used, as well... cosssercial Chlorox) and cut into small sections of 1 to 2 mm in thickness. They were then dropped beck in the sodium hypochlorite for 15 to 30 seconds (the procedure varied somewhat according to the condition of the tissue and other factors) and placed...

  6. Biogenic iron mineralization accompanying the dissimilatory reduction of hydrous ferric oxide by a groundwater bacterium

    SciTech Connect (OSTI)

    Fredrickson, J.K.; Zachara, J.M.; Kennedy, D.W.; Li, S.M. [Pacific Northwest National Lab., Richland, WA (United States)] [Pacific Northwest National Lab., Richland, WA (United States); Dong, H.; Onstott, T.C. [Princeton Univ., NJ (United States). Dept. of Geosciences] [Princeton Univ., NJ (United States). Dept. of Geosciences; Hinman, N.W. [Univ. of Montana, Missoula, MT (United States). Dept. of Geology] [Univ. of Montana, Missoula, MT (United States). Dept. of Geology

    1998-10-01T23:59:59.000Z

    The purpose of this research was to investigate the bacterial reduction of hydrous ferric oxide (HFO) by Shewanella putrefaciens and the nature of biogenic secondary phase formation in the presence of different inorganic ligands (PO{sub 4} and HCO{sub 3}) under conditions that may promote or suppress the organism/oxide association (i.e., with and without an electron shuttle). The electron shuttle used, anthraquinone-2,6-disulfonate (AQDS), is both a humic acid analog and a soluble redox indicator. The goal was to provide insights on biogeochemical factors governing dissimilatory biogenic mineralization in sediment or groundwater systems. The authors have investigated the influence of AQDS on the rate and extent of HFO reduction in different buffered systems and utilized X-ray diffraction, scanning electron microscopy (SEM), and transmission electron microscopy (TEM) to evaluate the crystallographic and morphologic features of the biogenic precipitates. The biogenic phase association is interpreted in light of aqueous solution conditions, pe, solid phase thermodynamic stability, and microbiological considerations including metabolic status and growth with the intent of identifying unique microbiological contributions to secondary mineralization.

  7. Evidence for Multiple Modes of Uranium Immobilization by an Anaerobic Bacterium

    SciTech Connect (OSTI)

    Ray, Allison; Bargar, John R.; Sivaswamy, Vaideeswaran; Dohnalkova, Alice; Fujita, Yoshiko; Peyton, Brent M.; Magnuson, Timothy S.

    2011-05-15T23:59:59.000Z

    Microbial reduction of hexavalent uranium has been studied widely for its potential role in bioremediation and immobilization of soluble U(VI) in contaminated groundwater. More recently, some microorganisms have been examined for their role in immobilization of U(VI) via precipitation of uranyl phosphate minerals mediated by microbial phosphate release, alleviating the requirement for long-term redox control. Here, we investigated the mechanism of U(VI) removal mediated by an environmental isolate, strain UFO1, that is indigenous to the Field Research Center (FRC) in Oak Ridge, TN and has been detected in U(VI)-contaminated sediments. Changes in U(VI) speciation were examined in the presence and absence of the electron-shuttling moiety, anthraquinone-2,6-disulfonate (AQDS). Cell suspensions were capable of nearly complete removal of 100 ?M U(VI) from solution within 48 hours; U(VI) removal was not dependent on the presence of an exogenous electron donor or AQDS, although AQDS increased the rate of U(VI) removal. X-ray Absorption Near Edge Structure (XANES) spectroscopic measurements indicated that U(IV) was the predominant oxidation state of uranium in cell suspensions in both the absence and presence of 100 ?M AQDS. However, extended X-ray Absorption Fine Structure spectroscopy (EXAFS) measurements indicated that 17% of the cell-associated precipitates in a U(VI)-treated suspension that lacked AQDS had spectral characteristics consistent with a uranyl phosphate solid phase. The potential involvement of phosphate was consistent with observed increases in soluble phosphate concentrations over time in UFO1 cell suspensions, which suggested phosphate liberation from the cells. TEM-EDS confirmed the presence of uranyl phosphate with a U:P ratio consistent with autunite (1:1). EXAFS analyses further showed that U(IV) was present predominantly as a monomeric complex sorbed to carboxylate functional groups on biomass and also suggested that a fraction of the U(IV) was coordinated to phosphoryl ligands. These results suggest that strain UFO1 has the ability to facilitate U(VI) removal from solution via both reductive and phosphate precipitation mechanisms, and may potentially be useful for the remediation of U-contaminated sediments at the FRC or elsewhere.

  8. Evidence for Multiple Modes of Uranium Immobilization by an Anaerobic Bacterium

    SciTech Connect (OSTI)

    Allison E. Ray; John R. Bargar; Alice C. Dohnalkova; Vaidee Sivaswamy; Yoshiko Fujita; Timothy S. Magnuson

    2011-05-01T23:59:59.000Z

    ABSTRACT Microbial reduction of hexavalent uranium has been studied widely for its potential role in bioremediation and removal of soluble U(VI) from contaminated groundwater. More recently, some microorganisms have been examined for their role in immobilization of U(VI) via precipitation of uranyl phosphate minerals mediated by microbial phosphate release, alleviating the requirement for long-term redox control. Here, we investigated the mechanism of U(VI) removal mediated by an environmental isolate, strain UFO1, that is indigenous to the Field Research Center (FRC) in Oak Ridge, TN and has been detected in U(VI)-contaminated sediments. U(VI) removal was examined in the presence and absence of the electron-shuttling moiety, anthraquinone-2,6-disulfonate (AQDS). Cell suspensions were capable of the near complete removal of 100 uM U(VI) from solution within 48 hours; U(VI) removal was not dependent on the presence of an exogenous electron donor or AQDS, although AQDS increased the rate of U(VI) removal. Profiles of ortho-phosphate concentration over time suggested phosphate liberation from cells. However, X-ray Absorption Near Edge Structure (XANES) spectroscopic measurements indicated that U(IV) was the predominant oxidation state of uranium in cell suspensions in both the absence and presence of 100 uM AQDS. Extended X-ray Absorption Fine Structure spectroscopy (EXAFS) measurements indicated that 20% of the cell-associated precipitates in a U(VI)-treated suspension that lacked AQDS had spectral characteristics consistent with a uranyl phosphate solid phase. EXAFS fits further show that that U(IV) is present dominantly as a monomeric sorbed complex. TEM-EDS confirmed the presence of uranyl phosphate with a U:P ratio consistent with autunite (1:1). These results suggest that strain UFO1 has the ability to mediate U(VI) removal from solution via both reductive and phosphate precipitation mechanisms, and may potentially be useful for the remediation of U-contaminated sediments at the FRC.

  9. Comment on "A Bacterium That Can Grow by Using Arsenic Instead

    E-Print Network [OSTI]

    Redfield, Rosemary J. "Rosie"

    Wolfe-Simon et al. (Research Articles, 3 June 2011, p. 1163; published online 2 December 2010) reported of bacterial strain GFAJ-1. Although the researchers meticulously eliminated contamination of the reagents gel), and each DNA band no more than 1 mg of DNA, at least 99.9% of the carbon in these sam- ples

  10. APPLIED MICROBIAL AND CELL PHYSIOLOGY Isolation of the exoelectrogenic denitrifying bacterium

    E-Print Network [OSTI]

    September 2009 # Springer-Verlag 2009 Abstract The anode biofilm in a microbial fuel cell (MFC) is composed . Denitrifying bacteria . Microbial community. Dilution to extinction . Microbial fuel cell Introduction Microbial fuel cells (MFCs) show great promise as a method for energy production during wastewater treatment

  11. An insect symbiosis is influenced by bacterium-specific polymorphisms in

    E-Print Network [OSTI]

    Aksoy, Serap

    Center, New York, NY 10065 Edited by David L. Denlinger, Ohio State University, Columbus, OH represent beneficial and sustained ``symbiotic'' associations (1). For example, the human intestinal required to evolve (2). To date few experimental studies have been performed to deter- mine the functional

  12. Reuters AlertNet -Genome map shows how bacterium gobbles radiation Get a password

    E-Print Network [OSTI]

    Lovley, Derek

    from groundwater may also be able to generate electricity, U.S. researchers said on Thursday. Scientists who deciphered the gene map of Geobacter sulfurreducens say it has more than 100 genes that should enable it to make chemical changes in metals that would generate electricity. Writing in the journal

  13. E-Print Network 3.0 - ammonia-oxidizing bacterium nitrosococcus...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Chicago Collection: Environmental Sciences and Ecology ; Environmental Management and Restoration Technologies 48 Archaeal Communities in Surface Stream Sediments Contact: Tony...

  14. Biodegradation of triclosan by a triclosan-degrading isolate and an ammonia-oxidizing bacterium

    E-Print Network [OSTI]

    Zhao, Fuman

    2007-09-17T23:59:59.000Z

    (Glaser, 2004). Triclosan can block lipid biosynthesis by inhibiting the enzyme enoyl acyl carrier protein reductase and may induce bacterial resistance development (McMurry et al., 1998; Levy et al., 1999). Currently, Triclosan has been incorporated... and Hilton, 2004), the toxicity to ecological health (Tatarazako et al., 2004), and the formation of chlorodioxins from triclosan and its metabolites (Latch, et al., 2003). A recent study also suggested that triclosan is potentially weakly androgenic...

  15. 12 M. LAURENT. -UN PROCS les plus importantes du fromage du Limbourg: Bacterium laciis acidi

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    représente .la gente Esmeralda, la compagne du Satyre, 'la parure et la joie de la Cour des Miracles, la

  16. Effect of bacterium Oceanospirillum on the corrosion potential and oxygen reduction of AISI 4340 steel

    E-Print Network [OSTI]

    Popova, Snezana N.

    1992-01-01T23:59:59.000Z

    . In view of the electrochemical nature of metallic corrosion, it is reasonable to study MIC utilizing electrochemical techniques(1 ? 6). An excellent technical review of electrochemical techniques applied to microbiologically influenced corrosion... on a metal surface will interfere with the electrochemical reactions (hydrogen and oxygen reduction) which control the corrosion rates. Most confirmed cases of microbial corrosion are localized and include: pitting, selective leaching and stress...

  17. Draft Genome Sequence of Methylomicrobium buryatense Strain 5G, a Haloalkaline-Tolerant Methanotrophic Bacterium

    E-Print Network [OSTI]

    Boyer, Edmond

    buryatense strain 5G on methane makes it an attractive sys- tem for CH4-based biocatalysis. Here we present of the core pathways for the production of valuable chemicals from methane. Received 23 January 2013 Accepted of Sciences, Pushchino, Russiaa; Department of Chemical Engineering, University of Washington, Seattle

  18. Memory in microbes: quantifying history-Dependent behavior in a bacterium.

    E-Print Network [OSTI]

    Wolf, Denise M.

    2010-01-01T23:59:59.000Z

    The plasmid pEA18 (cmp, spc) is a vector [71] allowingP spoIIE -gfp, P aprE -dsred, cmp spc). Selection of plasmidExpress pLFKEE P spoIIG –gfp , spc P xyl -gfp , cmp spc P

  19. Memory in Microbes: Quantifying History-Dependent Behavior in a Bacterium

    E-Print Network [OSTI]

    Wolf, Denise M.

    2009-01-01T23:59:59.000Z

    The plasmid pEA18 (cmp, spc) is a vector [71] allowingP spoIIE -gfp, P aprE -dsred, cmp spc). Selection of plasmidThis study P spoIIG –gfp, spc P xyl -gfp, cmp spc P spoIIG –

  20. Effect of bacterium Oceanospirillum on the corrosion potential and oxygen reduction of AISI 4340 steel 

    E-Print Network [OSTI]

    Popova, Snezana N.

    1992-01-01T23:59:59.000Z

    methods. Agar simulates an aerobic biofilm and acts as a barrier to oxygen diffusion. The corrosion potential, E, n is always more noble when measured as a function of time in abiotic solutions ( i. e. sterilized seawa- ter) and in the presence of agar... balance equation becomes: = ? 7' N+R i)ci, b f I with the assumption of steady state &', ? 0 and R; is the homogeneous reaction which results from the presence of biofilm on the surface of the electrode. The diffusion coefficient for species i within...

  1. Interactions of Fe(II) with the iron oxidizing bacterium Rhodopseudomonas palustris TIE-1

    E-Print Network [OSTI]

    Bird, Lina J. (Lina Joana)

    2013-01-01T23:59:59.000Z

    Microbial anaerobic iron oxidation has long been of interest to biologists and geologists, both as a possible mechanism for the creation of banded iron formations before the rise of oxygen, and as a model system for organisms ...

  2. Physiological and taxonomic description of the novel autotrophic, metal oxidizing bacterium, Pseudogulbenkiania sp. strain 2002

    E-Print Network [OSTI]

    2009-01-01T23:59:59.000Z

    Anaerobic . Nitrate . Bioremediation . Uranium The GenBankhas been proposed as a bioremediation strategy (Lack et al.Natural and Accelerated Bioremediation Program, through

  3. Dying for Good: Virus-Bacterium Biofilm Co-evolution Enhances Environmental Fitness

    SciTech Connect (OSTI)

    Jin, Hongjun; Squier, Thomas C.; Long, Philip E.

    2012-07-03T23:59:59.000Z

    Commonly used in biotechnology applications, filamentous M13 phage are non-lytic viruses that infect E. coli and other bacteria, with the potential to promote horizontal gene transfer in natural populations with synthetic biology implications for engineering community systems. Using the E. coli strain TG1, we have investigated how a selective pressure involving elevated levels of toxic chromate, mimicking that found in some superfund sites, alters population dynamics following infection with either wild-type M13 phage or an M13-phage encoding a chromate reductase (Gh-ChrR) capable of the reductive immobilization of chromate (ie, M13-phageGh-ChrR). In the absence of a selective pressure, M13-phage infection results in a reduction in bacterial growth rate; in comparison, in the presence of chromate there are substantial increases in both cellular killing and biomass formation following infection of E. coli strain TG1with M13-phageGh-ChrR that is dependent on chromate-reductase activity. These results are discussed in terms of community structures that facilitate lateral gene transfer of beneficial traits that enhance phage replication, infectivity, and stability against environmental change.

  4. alkaliphilic sulfate-reducing bacterium: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Diversity and characterization of sulfate-reducing bacteria in groundwater at a uranium mill tailings site CiteSeer Summary: plays a role in both natural attenuation and...

  5. Memory in microbes: quantifying history-Dependent behavior in a bacterium.

    E-Print Network [OSTI]

    Wolf, Denise M.

    2010-01-01T23:59:59.000Z

    from T1.5 after the resuspension event. References 1.medium (SM) [58]. The resuspension time is denoted t0. Thus,grow very fast after resuspension in starvation media, and

  6. Memory in Microbes: Quantifying History-Dependent Behavior in a Bacterium

    E-Print Network [OSTI]

    Wolf, Denise M.

    2009-01-01T23:59:59.000Z

    from T1.5 after the resuspension event. References 1.medium (SM) [58]. The resuspension time is denoted t0. Thus,grow very fast after resuspension in starvation media, and

  7. Memory in Microbes: Quantifying History-Dependent Behavior in a Bacterium

    SciTech Connect (OSTI)

    Wolf, Denise M.; Fontaine-Bodin, Lisa; Bischofs, Ilka; Price, Gavin; Keasling, Jay; Arkin, Adam P.

    2007-11-15T23:59:59.000Z

    Memory is usually associated with higher organisms rather than bacteria. However, evidence is mounting that many regulatory networks within bacteria are capable of complex dynamics and multi-stable behaviors that have been linked to memory in other systems. Moreover, it is recognized that bacteria that have experienced different environmental histories may respond differently to current conditions. These"memory" effects may be more than incidental to the regulatory mechanisms controlling acclimation or to the status of the metabolic stores. Rather, they may be regulated by the cell and confer fitness to the organism in the evolutionary game it participates in. Here, we propose that history-dependent behavior is a potentially important manifestation of memory, worth classifying and quantifying. To this end, we develop an information-theory based conceptual framework for measuring both the persistence of memory in microbes and the amount of information about the past encoded in history-dependent dynamics. This method produces a phenomenologicalmeasure of cellular memory without regard to the specific cellular mechanisms encoding it. We then apply this framework to a strain of Bacillus subtilis engineered to report on commitment to sporulation and degradative enzyme (AprE) synthesisand estimate the capacity of these systems and growth dynamics to"remember" 10 distinct cell histories prior to application of a common stressor. The analysis suggests that B. subtilis remembers, both in short and long term, aspects of its cellhistory, and that this memory is distributed differently among the observables. While this study does not examine the mechanistic bases for memory, it presents a framework for quantifying memory in cellular behaviors and is thus a starting point for studying new questions about cellular regulation and evolutionary strategy.

  8. Memory in microbes: quantifying history-Dependent behavior in a bacterium.

    SciTech Connect (OSTI)

    Wolf, Denise M.; Fontaine-Bodin, Lisa; Bischofs, Ilka; Price, Gavin; Keaslin, Jay; Arkin, Adam P.

    2007-11-15T23:59:59.000Z

    Memory is usually associated with higher organisms rather than bacteria. However, evidence is mounting that many regulatory networks within bacteria are capable of complex dynamics and multi-stable behaviors that have been linked to memory in other systems. Moreover, it is recognized that bacteria that have experienced different environmental histories may respond differently to current conditions. These"memory" effects may be more than incidental to the regulatory mechanisms controlling acclimation or to the status of the metabolic stores. Rather, they may be regulated by the cell and confer fitness to the organism in the evolutionary game it participates in. Here, we propose that history-dependent behavior is a potentially important manifestation of memory, worth classifying and quantifying. To this end, we develop an information-theory based conceptual framework for measuring both the persistence of memory in microbes and the amount of information about the past encoded in history-dependent dynamics. This method produces a phenomenological measure of cellular memory without regard to the specific cellular mechanisms encoding it. We then apply this framework to a strain of Bacillus subtilis engineered to report on commitment to sporulation and degradative enzyme (AprE) synthesis and estimate the capacity of these systems and growth dynamics to 'remember' 10 distinct cell histories prior to application of a common stressor. The analysis suggests that B. subtilis remembers, both in short and long term, aspects of its cell history, and that this memory is distributed differently among the observables. While this study does not examine the mechanistic bases for memory, it presents a framework for quantifying memory in cellular behaviors and is thus a starting point for studying new questions about cellular regulation and evolutionary strategy.

  9. Complete genome sequence of the melanogenic marine bacterium Marinomonas mediterranea type strain (MMB-1T)

    SciTech Connect (OSTI)

    Lucas-Elio, Patricia [University of Murcia, Murcia, Spain; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Detter, J C [U.S. Department of Energy, Joint Genome Institute; Copeland, A [U.S. Department of Energy, Joint Genome Institute; Teshima, Hazuki [Los Alamos National Laboratory (LANL); Bruce, David [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Land, Miriam L [ORNL; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Johnston, Andrew W. B. [University of East Anglia, Norwich, United Kingdom; Sanchez-Amat, Antonio [University of Murcia, Murcia, Spain

    2012-01-01T23:59:59.000Z

    Marinomonas mediterranea MMB-1 T Solano & Sanchez-Amat 1999 belongs to the family Oceanospirillaceae within the phylum Proteobacteria. This species is of interest because it is the only species described in the genus Marinomonas to date that can synthesize melanin pigments, which is mediated by the activity of a tyrosinase. M. mediterranea expresses other oxidases of biotechnological interest, such as a multicopper oxidase with laccase activity and a novel L-lysine-epsilon-oxidase. The 4,684,316 bp long genome harbors 4,228 proteincoding genes and 98 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  10. asv-reducing bacterium implications: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    landfill waste slide, a 300,000 cubic yard landfill failure involving a geosynthetic clay liner, and a 100Landfill Instability and Its Implications for Operation, Construction,...

  11. Dying for Good: Virus-Bacterium Biofilm Co-evolution Enhances...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    in some superfund sites, alters population dynamics following infection with either wild-type M13 phage or an M13-phage encoding a chromate reductase (Gh-ChrR) capable of the...

  12. anaerobic iron-reducing bacterium: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    in oxygen deficient zones of the oceans: No evidence for the predominance of anaerobes Environmental Management and Restoration Websites Summary: is unknown. Since it is known...

  13. Why molecules move along a temperature gradient Stefan Duhr, and Dieter Braun

    E-Print Network [OSTI]

    Kersting, Roland

    and polystyrene beads, thermophoretic motion changes sign at lower temperatures. This thermophilicity toward lower

  14. Quantitative Tools for Dissection of Hydrogen-Producing Metabolic Networks-Final Report

    SciTech Connect (OSTI)

    Rabinowitz, Joshua D.; Dismukes, G.Charles.; Rabitz, Herschel A.; Amador-Noguez, Daniel

    2012-10-19T23:59:59.000Z

    During this project we have pioneered the development of integrated experimental-computational technologies for the quantitative dissection of metabolism in hydrogen and biofuel producing microorganisms (i.e. C. acetobutylicum and various cyanobacteria species). The application of these new methodologies resulted in many significant advances in the understanding of the metabolic networks and metabolism of these organisms, and has provided new strategies to enhance their hydrogen or biofuel producing capabilities. As an example, using mass spectrometry, isotope tracers, and quantitative flux-modeling we mapped the metabolic network structure in C. acetobutylicum. This resulted in a comprehensive and quantitative understanding of central carbon metabolism that could not have been obtained using genomic data alone. We discovered that biofuel production in this bacterium, which only occurs during stationary phase, requires a global remodeling of central metabolism (involving large changes in metabolite concentrations and fluxes) that has the effect of redirecting resources (carbon and reducing power) from biomass production into solvent production. This new holistic, quantitative understanding of metabolism is now being used as the basis for metabolic engineering strategies to improve solvent production in this bacterium. In another example, making use of newly developed technologies for monitoring hydrogen and NAD(P)H levels in vivo, we dissected the metabolic pathways for photobiological hydrogen production by cyanobacteria Cyanothece sp. This investigation led to the identification of multiple targets for improving hydrogen production. Importantly, the quantitative tools and approaches that we have developed are broadly applicable and we are now using them to investigate other important biofuel producers, such as cellulolytic bacteria.

  15. Laboratory Directed Research & Development program. Annual report to the Department of Energy

    SciTech Connect (OSTI)

    Ogeka, G.J.; Romano, A.J.

    1995-12-01T23:59:59.000Z

    This report briefly discusses the following projects coordinated at Brookhaven National Laboratory: investigation of the utility of max-entropy methods for the analysis of powder diffraction data; analysis of structures and interactions of nucleic acids and proteins by small angle x-ray diffraction; relaxographic MRI and functional MRI; very low temperature infra-red laser absorption as a potential analytical tool; state-resolved measurements of H{sub 2} photodesorption: development of laser probes of H{sub 2} for in-situ accelerator measurements; Siberian snake prototype development for RHIC; synthesis and characterization of novel microporous solids; ozone depletion, chemistry and physics of stratospheric aerosols; understanding the molecular basis for the synthesis of plant fatty acids possessing unusual double bond positions; structure determination of outer surface proteins of the Lyme disease spirochete; low mass, low-cost multi-wire proportional chambers for muon systems of collider experiments; theory of self-organized criticality; development of the PCR-SSCP technique for the detection, at the single cell level, of specific genetic changes; feasibility of SPECT in imaging of F-18 FDG accumulation in tumors; visible free electron laser oscillator experiment; study of possible 2 + 2 TeV muon-muon collider; ultraviolet FEL R & D; precision machining using hard x-rays; new directions in in-vivo enzyme mapping: catechol-O-methyltransferase; proposal to develop a high rate muon polarimeter; development of intense, tunable 20-femtosecond laser systems; use of extreme thermophilic bacterium thermatoga maritima as a source of ribosomal components and translation factors for structural studies; and biochemical and structural studies of Chaperon proteins from thermophilic bacteria and other experiments.

  16. The Exiguobacterium genus: biodiversity and biogeography

    SciTech Connect (OSTI)

    Vishnivetskaya, Tatiana A [ORNL; Kathariou, Sophia [North Carolina State University; Tiedje, James M. [Michigan State University, East Lansing

    2009-01-01T23:59:59.000Z

    Abstract. Bacteria of the genus Exiguobacterium are low G + C, Gram-positive facultative anaerobes that have been repeatedly isolated from ancient Siberian permafrost. In addition, Exiguobacterium spp. have been isolated from markedly diverse sources, including Greenland Glacial ice, hot springs at Yellowstone National Park, the rhizosphere of plants, and the environment of food processing plants. Strains of this hereto little known bacterium that have been retrieved from such different (and often extreme) environments are worthy of attention as they are likely to be specifically adapted to such environments and to carry variations in the genome which may correspond to psychrophilic and thermophilic adaptations. However, comparative genomic investigations of Exiguobacterium spp. from different sources have been limited. In this study, we employed different molecular approaches for the comparative analysis of 24 isolates from markedly diverse environments including ancient Siberian permafrost and hot springs at Yellowstone National Park. Pulsed-field gel electrophoresis (PFGE) with I-CeuI (an intron-encoded endonuclease), AscI and NotI were optimized for the determination of genomic fingerprints of nuclease-producing isolates. The application of a DNA macroarray for 82 putative stress-response genes yielded strain-specific hybridization profiles. Cluster analyses of 16S rRNA gene sequence data, PFGE I-CeuI restriction patterns and hybridization profiles suggested that Exiguobacterium strains formed two distinct divisions that generally agreed with temperature ranges for growth. With few exceptions (e.g., Greenland ice isolate GIC31), psychrotrophic and thermophilic isolates belonged to different divisions.

  17. System and method for introduction and stabilization of genes in Thermus sp.

    DOE Patents [OSTI]

    Kayser, Kevin J.; Park, Ho-Shin; Kilbane, II, John J.

    2005-03-01T23:59:59.000Z

    A method for introducing and stabilizing heterologous and recombinant genes in a thermophilic host in which a characteristic gene defining a detectable host characteristic is inactivated or deleted from the thermophilic host, resulting in a modified thermophilic host expressing an absence of the detectable host characteristic. A DNA fragment of interest is inserted into the modified thermophilic host together with an intact characteristic gene, whereby the detectable host characteristic is restored to the thermophilic host, thereby enabling detection and confirmation of successful transformation using plasmid vectors and integration of the DNA fragment into the chromosome of the thermophilic host.

  18. Top-Down Characterization of the Post-Translationally Modified Intact Periplasmic Proteome from the BacteriumNovosphingobium aromaticivorans

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Wu, Si; Brown, Roslyn N.; Payne, Samuel H.; Meng, Da; Zhao, Rui; Toli?, Nikola; Cao, Li; Shukla, Anil; Monroe, Matthew E.; Moore, Ronald J.; et al

    2013-01-01T23:59:59.000Z

    The periplasm of Gram-negative bacteria is a dynamic and physiologically important subcellular compartment where the constant exposure to potential environmental insults amplifies the need for proper protein folding and modifications. Top-down proteomics analysis of the periplasmic fraction at the intact protein level provides unrestricted characterization and annotation of the periplasmic proteome, including the post-translational modifications (PTMs) on these proteins. Here, we used single-dimension ultra-high pressure liquid chromatography coupled with the Fourier transform mass spectrometry (FTMS) to investigate the intact periplasmic proteome ofNovosphingobium aromaticivorans. Our top-down analysis provided the confident identification of 55 proteins in the periplasm and characterized their PTMsmore »including signal peptide removal, N-terminal methionine excision, acetylation, glutathionylation, pyroglutamate, and disulfide bond formation. This study provides the first experimental evidence for the expression and periplasmic localization of many hypothetical and uncharacterized proteins and the first unrestrictive, large-scale data on PTMs in the bacterial periplasm.« less

  19. Copyright 2003 by the Genetics Society of America A Conservative Test of Genetic Drift in the Endosymbiotic Bacterium Buchnera

    E-Print Network [OSTI]

    Herbeck, Joshua

    in recent studies of other Buchnera loci. Comparisons with Escherichia coli generally show patterns aspects of their endosymbiosis with aphidstion of genome size compared to Escherichia coli, the most for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts 02543

  20. Biological consequences of ancient gene acquisition and duplication in the large genome soil bacterium, ""solibacter usitatus"" strain Ellin6076

    SciTech Connect (OSTI)

    Challacombe, Jean F [Los Alamos National Laboratory; Eichorst, Stephanie A [Los Alamos National Laboratory; Xie, Gary [Los Alamos National Laboratory; Kuske, Cheryl R [Los Alamos National Laboratory; Hauser, Loren [ORNL; Land, Miriam [ORNL

    2009-01-01T23:59:59.000Z

    Bacterial genome sizes range from ca. 0.5 to 10Mb and are influenced by gene duplication, horizontal gene transfer, gene loss and other evolutionary processes. Sequenced genomes of strains in the phylum Acidobacteria revealed that 'Solibacter usistatus' strain Ellin6076 harbors a 9.9 Mb genome. This large genome appears to have arisen by horizontal gene transfer via ancient bacteriophage and plasmid-mediated transduction, as well as widespread small-scale gene duplications. This has resulted in an increased number of paralogs that are potentially ecologically important (ecoparalogs). Low amino acid sequence identities among functional group members and lack of conserved gene order and orientation in the regions containing similar groups of paralogs suggest that most of the paralogs were not the result of recent duplication events. The genome sizes of cultured subdivision 1 and 3 strains in the phylum Acidobacteria were estimated using pulsed-field gel electrophoresis to determine the prevalence of the large genome trait within the phylum. Members of subdivision 1 were estimated to have smaller genome sizes ranging from ca. 2.0 to 4.8 Mb, whereas members of subdivision 3 had slightly larger genomes, from ca. 5.8 to 9.9 Mb. It is hypothesized that the large genome of strain Ellin6076 encodes traits that provide a selective metabolic, defensive and regulatory advantage in the variable soil environment.

  1. Complete genome sequence of the filamentous gliding predatory bacterium Herpetosiphon aurantiacus type strain (114-95T)

    SciTech Connect (OSTI)

    Kiss, Hajnalka [Los Alamos National Laboratory (LANL); Nett, Markus [Hans Knöll Institute, Jena, Germany; Domin, Nicole [Hans Knöll Institute, Jena, Germany; Martin, Karin [Hans Knöll Institute, Jena, Germany; Maresca, Julia A. [Pennsylvania State University, University Park, PA; Copeland, A [U.S. Department of Energy, Joint Genome Institute; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Berry, Kerrie W. [United States Department of Energy Joint Genome Institute; Glavina Del Rio, Tijana [U.S. Department of Energy, Joint Genome Institute; Dalin, Eileen [U.S. Department of Energy, Joint Genome Institute; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Richardson, P M [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Schmutz, Jeremy [Stanford University; Brettin, Thomas S [ORNL; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Bryant, Donald A. [Pennsylvania State University, University Park, PA

    2011-01-01T23:59:59.000Z

    Herpetosiphon aurantiacus Holt and Lewin 1968 is the type species of the genus Herpetosiphon, which in turn is the type genus of the family Herpetosiphonaceae, type family of the order Herpe- tosiphonales in the phylum Chloroflexi. H. aurantiacus cells are organized in filaments which can rapidly glide. The species is of interest not only because of its rather isolated position in the tree of life, but also because Herpetosiphon ssp. were identified as predators capable of facultative pre- dation by a wolf pack strategy and of degrading the prey organisms by excreted hydrolytic en- zymes. The genome of H. aurantiacus strain 114-95T is the first completely sequenced genome of a member of the family Herpetosiphonaceae. The 6,346,587 bp long chromosome and the two 339,639 bp and 99,204 bp long plasmids with a total of 5,577 protein-coding and 77 RNA genes was sequenced as part of the DOE Joint Genome Institute Program DOEM 2005.

  2. Scientists decipher genome of bacterium that remediates uranium contamination, generates electricity Public release date: 11-Dec-2003

    E-Print Network [OSTI]

    Lovley, Derek

    that remediates uranium contamination, generates electricity Analysis of Geobacter sulfurreducens genes reveals easily removed. Small charges of electricity are also created through the reduction process. Geobacter electricity Public release date: 11-Dec-2003 [ Print This Article | Close This Window ] Contact: Robert Koenig

  3. Top-down characterization of the post-translationally modified intact periplasmic proteome of the bacterium Novosphingobium aromaticivorans

    SciTech Connect (OSTI)

    Wu, Si; Brown, Roslyn N.; Payne, Samuel H.; Meng, Da; Zhao, Rui; Tolic, Nikola; Cao, Li; Shukla, Anil K.; Monroe, Matthew E.; Moore, Ronald J.; Lipton, Mary S.; Pasa-Tolic, Ljiljana

    2013-03-10T23:59:59.000Z

    In this study, the intact periplasmic proteome of Novosphingobium aromaticivorans was analyzed. We identified 55 proteins in the periplasm, and characterized their post translational modifications. Proteins were first categorized based on their N-terminal processing: 17 proteins were identified with removal of signal peptides containing the canonical A-X-A motif, 8 proteins were identified with removal of signal peptides containing non A-X-A motif, 24 proteins were identified with N-terminal methione excision (NME), and 4 proteins were identified with other N-terminal processing (e.g. complex proteolysis). Only 2 proteins were identified with no N-terminal modifications. Other observed protein post-translational modifications included acetylation, glutathiolynation, pyroglutamate modification, disulfide bond formation, etc. In summary, we analyzed the intact periplasmic proteins of N. aromaticivorans in a high throughput fashion, and provided a catalogue of information on post-translational modifications observed in this dynamic subcellular fraction. This study provides the first experimental evidence for the expression and periplasmic localization of hypothetical and uncharacterized proteins, and the first unrestrictive, large-scale data on post-translational modifications in the bacterial periplasm.

  4. Differential isotopic fractionation during Cr(VI) reduction by an aquifer-derived bacterium under arobic versus denitrifying conditions

    SciTech Connect (OSTI)

    Han, R.; Qin, L.; Brown, S. T.; Christensen, J. N.; Beller, H. R.

    2012-02-01T23:59:59.000Z

    We studied Cr isotopic fractionation during Cr(VI) reduction by Pseudomonas stutzeri strain RCH2. Despite the fact that strain RCH2 reduces Cr(VI) co-metabolically under both aerobic and denitrifying conditions and at similar specific rates, fractionation was markedly different under these two conditions (ε ~2? aerobically and ~0.4? under denitrifying conditions).

  5. Targeted Enhancement of H2 and CO2 Uptake for Autotrophic Production of Biodiesel in the Lithoautotrophic Bacterium Ralsonia Eutropha

    SciTech Connect (OSTI)

    Eckert, C. A.; Sullivan, R.; Johnson, C.; Yu, J.; Maness, P. C.

    2013-01-01T23:59:59.000Z

    CO2 and H2 are promising feedstocks for production of valuable biocompounds. Ralstonia eutropha utilizes these feedstocks to generate energy (ATP) and reductant (NAD(P)H) via oxidation of H2 by a membrane-bound (MBH) and a soluble hydrogenase (SH) for CO2 fixation by the Calvin-Benson-Bassham (CBB) cycle. Increased expression of the enzyme that fixes CO2 (RubisCO) resulted in 6-fold activity improvement in vitro, while increased expression of the MBH operon or the SH operon plus MBH operon maturation factors necessary for activity resulted in a 10-fold enhancement. Current research involves genetic manipulation of two endogenous cbb operons for increased expression, analysis of expression and activity of CBB/MBH/SH, cofactor ratios, and downstream products during autotrophic growth in control versus enhanced strains, and development of strategies for long-term, optimal overexpression. These studies will improve our understanding of autotrophic metabolism and provide a chassis strain for autotrophic production of biodiesel and other valuable carbon biocompounds.

  6. Final Report on Development of Thermoanaerobacterium saccharolyticum for the conversion of lignocellulose to ethanol

    SciTech Connect (OSTI)

    Herring, Christopher D.; Kenealy, William R.; Shaw, A. Joe; Raman, Babu; Tschaplinski, Timothy J.; Brown, Steven D.; Davison, Brian H.; Covalla, Sean F.; Sillers, W. Ryan; Xu, Haowen; Tsakraklides, Vasiliki; Hogsett, David A.

    2012-01-24T23:59:59.000Z

    This project addressed the need for economical technology for the conversion of lignocellulosic biomass to fuels, specifically the conversion of pretreated hardwood to ethanol. The technology developed is a set of strains of the bacterium Thermoanaerobacterium saccharolyticum and an associated fermentation process for pretreated hardwood. Tools for genetic engineering and analysis of the organism were developed, including a markerless mutation method, a complete genome sequence and a set of gene expression profiles that show the activity of its genes under a variety of conditions relevant to lignocellulose conversion. Improved strains were generated by selection and genetic engineering to be able to produce higher amounts of ethanol (up to 70 g/L) and to be able to better tolerate inhibitory compounds from pretreated hardwood. Analysis of these strains has generated useful insight into the genetic basis for desired properties of biofuel producing organisms. Fermentation conditions were tested and optimized to achieve ethanol production targets established in the original project proposal. The approach proposed was to add cellulase enzymes to the fermentation, a method called Simultaneous Saccharification and Fermentation (SSF). We had reason to think SSF would be an efficient approach because the optimal temperature and pH for the enzymes and bacterium are very close. Unfortunately, we discovered that commercially available cellulases are inactivated in thermophilic SSF by a combination of low redox potential and ethanol. Despite this, progress was made against the fermentation targets using bacterial cellulases. Thermoanaerobacterium saccharolyticum may still prove to be a commercially viable technology should cellulase enzyme issues be addressed. Moreover, the organism was demonstrated to produce ethanol at approximately theoretical yield from oligomeric hemicellulose extracts, an ability that may prove to be uniquely valuable in pretreatment configurations in which cellulose and hemicellulose are separated.

  7. evaluation of the bioconversion of genetically modified switchgrass using simultaneous saccharification and fermentation ans a consolidated bioprocessing approach

    SciTech Connect (OSTI)

    Yee, Kelsey L [ORNL; Rodriguez, Jr., Miguel [ORNL; Tschaplinski, Timothy J [ORNL; Engle, Nancy L [ORNL; Martin, Madhavi Z [ORNL; Fu, Chunxiang [Noble Foundation; Wang, Zeng-Yu [Noble Foundation; Hamilton-Brehm, Scott [ORNL; Mielenz, Jonathan R [ORNL

    2012-01-01T23:59:59.000Z

    Abstract Background: The inherent recalcitrance of lignocellulosic biomass is one of the major economic hurdles for the production of fuels and chemicals from biomass. Additionally, lignin is recognized as having a negative impact on enzymatic hydrolysis of biomass, and as a result much interest has been placed on modifying the lignin pathway to improve bioconversion of lignocellulosic feedstocks. Results: Previous results showed down-regulation of the caffeic acid 3-O-methyl transferase (COMT) gene in the lignin pathway yielded switchgrass (Panicum virgatum) that was more susceptible to bioconversion after dilute acid pretreatment. Here we examined the response of these plant lines to milder pretreatment conditions with yeast-based SSF, CBP with Clostridium thermocellum, and fermentations with the cellulolytic extreme thermophiles, Caldicellulosiruptor bescii and Caldicellulosiruptor obsidiansis. Unlike the S. cerevisiae SSF conversions, fermentations of pretreated down-regulated COMT transgenic switchgrass with C. thermocellum showed an apparent inhibition of fermentation not observed in the wild-type switchgrass. This inhibition can be eliminated by hot water extraction of the pretreated biomass which resulted in superior conversion yield with transgenic versus wild-type switchgrass for C. thermocellum, also exceeding the yeast-based SSF yield. Further fermentation evaluation of the transgenic switchgrass indicated differential inhibition for the Caldicellulosiruptor strains, which could not be rectified by additional processing conditions. Gas chromatography-mass spectrometry metabolite profiling was used to examine the fermentation broth to elucidate the relative abundance of lignin derived aromatic compounds. The types and abundance of fermentation-derived lignin constituents varied between C. thermocellum and each of the Caldicellulosiruptor strains. Conclusions: The down-regulation of the COMT gene improves the bioconversion of switchgrass relative to the wild-type regardless of the pretreatment condition or fermentation microorganism. However, bacterial fermentations demonstrated strain-dependent sensitivity to the COMT transgenic biomass, likely due to additional soluble lignin pathway-derived constituents resulting from the COMT gene disruption. Removal of these inhibitory constituents permitted completion of fermentation by C. thermocellum, but not by the Caldicellulosiruptor strains. The reason for this difference needs to be explored further.

  8. Profile of Secreted Hydrolases, Associated Proteins, and SlpA in Thermoanaerobacterium saccharolyticum during the Degradation of Hemicellulose

    SciTech Connect (OSTI)

    Currie, Devin [Dartmouth College; Guss, Adam M [ORNL; Herring, Christopher [Mascoma Corporation; Giannone, Richard J [ORNL; Johnson, Courtney M [ORNL; Lankford, Patricia K [ORNL; Brown, Steven D [ORNL; Hettich, Robert {Bob} L [ORNL; Lynd, Lee R [Thayer School of Engineering at Dartmouth

    2014-01-01T23:59:59.000Z

    Thermoanaerobacterium saccharolyticum, a Gram-positive thermophilic anaerobic bacterium, grows robustly on insoluble hemicellulose, which requires a specialized suite of secreted and transmembrane proteins. We report here the characterization of proteins secreted by this organism. Cultures were grown on hemicellulose, glucose, xylose, starch, and xylan in pH-controlled bioreactors, and samples were analyzed via spotted microarrays and liquid chromatography-mass spectrometry. Key hydrolases and transporters employed by T. saccharolyticum for growth on hemicellulose were, for the most part, hitherto uncharacterized and existed in two clusters (Tsac_1445 through Tsac_1464 for xylan/xylose and Tsac_1344 through Tsac_1349 for starch). A phosphotransferase system subunit, Tsac_0032, also appeared to be exclusive to growth on glucose. Previously identified hydrolases that showed strong conditional expression changes included XynA (Tsac_1459), XynC (Tsac_0897), and a pullulanase, Apu (Tsac_1342). An omnipresent transcript and protein making up a large percentage of the overall secretome, Tsac_0361, was tentatively identified as the primary S-layer component in T. saccharolyticum, and deletion of the Tsac_0361 gene resulted in gross morphological changes to the cells. The view of hemicellulose degradation revealed here will be enabling for metabolic engineering efforts in biofuel-producing organisms that degrade cellulose well but lack the ability to catabolize C5 sugars

  9. Comparison of Chloroflexus aurantiacus strain J-10-fl proteomes of cells grown chemoheterotrophically and photoheterotrophically

    SciTech Connect (OSTI)

    Cao, Li; Bryant, Donald A.; Schepmoes, Athena A.; Vogl, Kajetan; Smith, Richard D.; Lipton, Mary S.; Callister, Stephen J.

    2012-01-17T23:59:59.000Z

    Chloroflexus aurantiacus J-10-fl is a thermophilic green bacterium, a filamentous anoxygenic phototroph, and the model organism of the phylum Chloroflexi. We applied high-throughput, liquid chromatography-mass spectrometry in a global quantitative proteomics investigation of C. aurantiacus cells grown under oxic (chemoorganoheterotrophically) and anoxic (photoorganoheterotrophically) redox states. Our global analysis identified 13,524 high-confidence peptides that matched to 1,286 annotated proteins, 242 of which were either uniquely identified or significantly increased in abundance under anoxic culture conditions. Fifty-three of the 242 proteins are previously characterized photosynthesis-related proteins, including chlorosome proteins, proteins involved in the bacteriochlorophyll biosynthesis, 3-hydroxypropionate (3-OHP) CO2 fixation pathway, and components of electron transport chains. The remaining 190 proteins have not previously been reported. Of these, five proteins were found to be encoded by genes from a novel operon and observed only in photoheterotrophically grown cells. These proteins candidates may prove useful in further deciphering the phototrophic physiology of C. aurantiacus and other filamentous anoxygenic phototrophs.

  10. Novel monosaccharide fermentation products in Caldicellulosiruptor saccharolyticus identified using NMR spectroscopy

    SciTech Connect (OSTI)

    Isern, Nancy G.; Xue, Junfeng; Rao, Jaya V.; Cort, John R.; Ahring, Birgitte K.

    2013-04-03T23:59:59.000Z

    Profiles of metabolites produced by the thermophilic obligately anaerobic cellulose-degrading Gram-positive bacterium Caldicellulosiruptor saccharolyticus DSM 8903 strain following growth on different monosaccharides (D-glucose, D-mannose, L-arabinose, D-arabinose, D-xylose, L-fucose, and D-fucose) as carbon sources revealed several unexpected fermentation products, suggesting novel metabolic capacities and unexplored metabolic pathways in this organism. Both 1H and 13C nuclear magnetic resonance (NMR) spectroscopy were used to determine intracellular and extracellular metabolite profiles. Metabolite profiles were determined from 1-D 1H NMR spectra by curve fitting against spectral libraries provided in Chenomx software. To reduce uncertainties due to unassigned, overlapping, or poorly-resolved peaks, metabolite identifications were confirmed with 2-D homonuclear and heteronuclear NMR experiments. In addition to expected metabolites such as acetate, lactate, glycerol, and ethanol, several novel fermentation products were identified: ethylene glycol (from growth on D-arabinose, though not L-arabinose), acetoin and 2,3-butanediol (from D-glucose and L-arabinose), and hydroxyacetone (from D-mannose and L-arabinose). Production of ethylene glycol from D-arabinose was particularly notable, with around 10% of the substrate carbon converted into this uncommon fermentation product. The novel products have not previously been reported to be produced by C. saccharolyticus, nor would they be easily predicted from the current genome annotation, and show new potentials for using this strain for production of bioproducts.

  11. Syntrophic exchange in synthetic microbial communities Michael T. Meea,b

    E-Print Network [OSTI]

    Collins, James J.

    recently described including the bioconversion of unprocessed cellulolytic feedstocks into biofuel isobutanol using fungal­bacterial communities (4) and biofuel precursor methyl halides using yeast using engineered quorum-sensing Escherichia coli (7, 8). These advances paint an exciting future

  12. The transcriptional landscape of the deep-sea bacterium Photobacterium profundum in both a toxR mutant and its parental strain

    E-Print Network [OSTI]

    Campanaro, Stefano; Pascale, Fabio; Telatin, Andrea; Schiavon, Riccardo; Bartlett, Douglas H; Valle, Giorgio

    2012-01-01T23:59:59.000Z

    involved in the biosynthesis of riboflavin. The biologicallythiamin (vitamin B1) and riboflavin (vitamin B2) are TPP anda possible role of riboflavin in deep-sea adaptation. P.

  13. Biotransformation of Two-Line Silica-Ferrihydrite by a Dissimilatory Fe(III)-Reducing Bacterium: Formation of Carbonate Green Rust in the Presence of Phosphate

    SciTech Connect (OSTI)

    Kukkadapu, Ravi K.; Zachara, John M.; Fredrickson, Jim K.; Kennedy, David W.

    2004-07-01T23:59:59.000Z

    The reductive biotransformation of two Si-ferrihydrite (0.01 and 0.05 mole% Si) coprecipiates by Shewanella putrefaciens, strain CN32, was investigated in 1,4-piperazinediethanesulfonic acid-buffered media (pH ~7) with lactate as the electron donor. Anthraquinone-2,6-disulfonate (electron shuttle) that stimulates respiration was present in the media. Experiments were performed without and with PO43- (ranging from 1 to 20 mmol/L in media containing 50 mmol/L Fe). Our objectives were to define the combined effects of SiO44- and PO43- on the bioreducibility and biomineralization of ferrihydrites under anoxic conditions. Iron reduction was measured as a function of time, solids were characterized by powder X-ray diffraction (XRD) and Mossbauer spectroscopy, and aqueous solutions were analyzed for Si, P, Cl- and inorganic carbon. Both of the ferrihydrites were rapidly reduced regardless of the Si content. Si concentration had no effect on the reduction rate or mineralization products. Magnetite was formed in the absence of PO43- whereas carbonate green rust GR(CO32-) ([FeII(6-x)FeIIIx(OH)12]x+(CO32-)0.5x.yH2O) and vivianite [Fe3(PO4)2.8H2O], were formed when PO43- was present. GR(CO32-) dominated as a mineral product in samples with < 4 mmol/L PO43-. The Fe(II)/Fe(III) ratio of GR(CO32-) varied with PO43- concentration; it was 2 in the 1 mmol/L PO43- and approached 1 in the 4- and 10-mmol/L PO43- samples. GR appeared to form by solid-state transformation of ferrihydrite. Medium PO43- concentration dictated the mechanism of transformation. In 1 mmol/L PO43- media, an intermediate Fe(II)/Fe(III) phase with structural Fe(II), which we tentatively assigned to a protomagnetite phase, slowly transformed to GR with time. In contrast, in medium with >4 mmol/L PO43-, a residual ferrihydrite with sorbed Fe2+ phase transformed to GR. Despite similar chemistries, PO43- was shown to have a profound effect on ferrihydrite biotransformations while that of SiO44- was minimal.

  14. The transcriptional landscape of the deep-sea bacterium Photobacterium profundum in both a toxR mutant and its parental strain

    E-Print Network [OSTI]

    Campanaro, Stefano; Pascale, Fabio; Telatin, Andrea; Schiavon, Riccardo; Bartlett, Douglas H; Valle, Giorgio

    2012-01-01T23:59:59.000Z

    major human pathogen Helicobacter pylori. Nature 15. Toledo-like that of Helicobacter pylori revealed an unexpectedlyusing RNA-seq in Helicobacter pylori where 87.5% of the

  15. Complete genome sequence of the halophilic bacterium Spirochaeta africana type strain (Z-7692T) from the alkaline Lake Magadi in the East African Rift

    SciTech Connect (OSTI)

    Liolios, Konstantinos [U.S. Department of Energy, Joint Genome Institute; Abt, Birte [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Scheuner, Carmen [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Teshima, Hazuki [Los Alamos National Laboratory (LANL); Held, Brittany [Los Alamos National Laboratory (LANL); Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Deshpande, Shweta [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Huntemann, Marcel [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Palaniappan, Krishna [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Tindall, Brian [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Bristow, James [U.S. Department of Energy, Joint Genome Institute; Eisen, Jonathan [U.S. Department of Energy, Joint Genome Institute; Markowitz, Victor [U.S. Department of Energy, Joint Genome Institute; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute

    2013-01-01T23:59:59.000Z

    Spirochaeta africana Zhilina et al. 1996 is an anaerobic, aerotolerant, spiral-shaped bacte- rium that is motile via periplasmic flagella. The type strain of the species, Z-7692T, was iso- lated in 1993 or earlier from a bacterial bloom in the brine under the trona layer in a shallow lagoon of the alkaline equatorial Lake Magadi in Kenya. Here we describe the features of this organism, together with the complete genome sequence, and annotation. Considering the pending reclassification of S. caldaria to the genus Treponema, S. africana is only the second 'true' member of the genus Spirochaeta with a genome-sequenced type strain to be pub- lished. The 3,285,855 bp long genome of strain Z-7692T with its 2,817 protein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  16. Subcellular localization of the magnetosome protein MamC in the marine magnetotactic bacterium Magnetococcus marinus strain MC-1 using immunoelectron microscopy

    SciTech Connect (OSTI)

    Valverde-Tercedor, C [Universidad de Granada; Abada-Molina, F [Universidad de Granada; Martinez-Bueno, M [Universidad de Granada; Pineda-Molina, Estela [Laboratorio de Estudios Cristalograficos; Chen, Lijun [Ohio State University; Oestreicher, Zachery [Ohio State University; Lower, Brian H [Ohio State University; Lower, Steven K [Ohio State University; Bazylinski, Dennis A [Ames Laboratory; Jimenez-Lopez, C [Universidad de Granada

    2014-04-24T23:59:59.000Z

    Magnetotactic bacteria are a diverse group of prokaryotes that biomineralize intracellular magnetosomes, composed of magnetic (Fe3O4) crystals each enveloped by a lipid bilayer membrane that contains proteins not found in other parts of the cell. Although partial roles of some of these magnetosome proteins have been determined, the roles of most have not been completely elucidated, particularly in how they regulate the biomineralization process. While studies on the localization of these proteins have been focused solely on Magnetospirillum species, the goal of the present study was to determine, for the first time, the localization of the most abundant putative magnetosome membrane protein, MamC, in Magnetococcus marinus strain MC-1. MamC was expressed in Escherichia coli and purified. Monoclonal antibodies were produced against MamC and immunogold labeling TEM was used to localize MamC in thin sections of cells of M. marinus. Results show that MamC is located only in the magnetosome membrane of Mc. marinus. Based on our findings and the abundance of this protein, it seems likely that it is important in magnetosome biomineralization and might be used in controlling the characteristics of synthetic nanomagnetite.

  17. Marulanda A, Barea JM, Azcon R. 2006. An indigenous drought-tolerant strain of Glomus intraradices associated with a native bacterium improves

    E-Print Network [OSTI]

    Templer, Pamela

    , Glomus intraradices, nuclear DNA content. Meetings Multi-factor global change experiments: what have we dynamics (Lin et al., 2010). However, it is not always possible to predict the impacts of environmental should consider not only the complexity of changes in the environment, but also the underlying structure

  18. CO2 exposure at pressure impacts metabolism and stress responses in the model sulfate-reducing bacterium Desulfovibrio vulgaris strain Hildenborough

    SciTech Connect (OSTI)

    Wilkins, Michael J.; Hoyt, David W.; Marshall, Matthew J.; Alderson, Paul A.; Plymale, Andrew E.; Markillie, Lye Meng; Tucker, Abigail E.; Walter, Eric D.; Linggi, Bryan E.; Dohnalkova, Alice; Taylor, Ronald C.

    2014-09-01T23:59:59.000Z

    Geologic carbon dioxide (CO2) sequestration drives physical and geochemical changes in deep subsurface environments that impact indigenous microbial activities. The combined effects of pressurized CO2 on a model sulfate-reducing microorganism, Desulfovibrio vulgaris, have been assessed using a suite of genomic and kinetic measurements. Novel high-pressure NMR time-series measurements using 13C-lactate were used to track D. vulgaris metabolism. We identified cessation of respiration at CO2 pressures of 10 bar, 25 bar, 50 bar, and 80 bar. Concurrent experiments using N2 as the pressurizing phase had no negative effect on microbial respiration, as inferred from reduction of sulfate to sulfide. Complementary pressurized batch incubations and fluorescence microscopy measurements supported NMR observations, and indicated that non-respiring cells were mostly viable at 50 bar CO2 for at least four hours, and at 80 bar CO2 for two hours. The fraction of dead cells increased rapidly after four hours at 80 bar CO2. Transcriptomic (RNA-Seq) measurements on mRNA transcripts from CO2-incubated biomass indicated that cells up-regulated the production of certain amino acids (leucine, isoleucine) following CO2 exposure at elevated pressures, likely as part of a general stress response. Evidence for other poorly understood stress responses were also identified within RNA-Seq data, suggesting that while pressurized CO2 severely limits the growth and respiration of D. vulgaris cells, biomass retains intact cell membranes at pressures up to 80 bar CO2. Together, these data show that geologic sequestration of CO2 may have significant impacts on rates of sulfate reduction in many deep subsurface environments where this metabolism is a key respiratory process.

  19. Effects of nitrogen source and concentration upon glutamine synthetase and protease activity in the rumen bacterium Prevotella ruminicola strain B1 4

    E-Print Network [OSTI]

    Kirk, James Michael

    1995-01-01T23:59:59.000Z

    (mineral salts, essential volatile fatty acids, vitamin cofactors, 12 mM glucose, cysteine-HCL as a reductant and sodium carbonate) with variable amounts of ammonium chloride, pepticase or casein as the nitrogen source. The results indicated that when...

  20. Targeted Discovery of Glycoside Hydrolases from a Switchgrass-Adapted Compost Community

    E-Print Network [OSTI]

    Reddy, Amitha

    2012-01-01T23:59:59.000Z

    thermophilic composting in a bioreactor to select for aday 0) and final (day 31) bioreactor sample and for a samplesamples of the compost bioreactor. Overlapping bars indicate

  1. Characterization of the Allosteric Properties of Thermus thermophilus Phosphofructokinase and the Sources of Strong Inhibitor Binding Affinity and Weak Inhibitory Response 

    E-Print Network [OSTI]

    Shubina-McGresham, Maria

    2012-10-19T23:59:59.000Z

    Characterization of allosteric properties of phosphofructokinase from the extreme thermophile Thermus thermophilus (TtPFK) using thermodynamic linkage analysis revealed several peculiarities. Inhibition and activation of ...

  2. High level expression of Acidothermus cellulolyticus ?-1, 4-endoglucanase in transgenic rice enhances the hydrolysis of its straw by cultured cow gastric fluid

    SciTech Connect (OSTI)

    Chou, Hong L.; Dai, Ziyu; Hsieh, Chia W.; Ku, Maurice S.

    2011-12-10T23:59:59.000Z

    Large-scale production of effective cellulose hydrolytic enzymes is the key to the bioconversion of agricultural residues to ethanol. The goal of this study was to develop a rice plant as a bioreactor for the large-scale production of cellulose hydrolytic enzymes via genetic transformation, and to simultaneously improve rice straw as an efficient biomass feedstock for conversion of cellulose to glucose. In this study, the cellulose hydrolytic enzyme {beta}-1, 4-endoglucanase (E1) from the thermophilic bacterium Acidothermus cellulolyticus was overexpressed in rice through Agrobacterium-mediated transformation. The expression of the bacterial gene in rice was driven by the constitutive Mac promoter, a hybrid promoter of Ti plasmid mannopine synthetase promoter and cauliflower mosaic virus 35S promoter enhancer with the signal peptide of tobacco pathogenesis-related protein for targeting the protein to the apoplastic compartment for storage. A total of 52 transgenic rice plants from six independent lines expressing the bacterial enzyme were obtained, which expressed the gene at high levels with a normal phenotype. The specific activities of E1 in the leaves of the highest expressing transgenic rice lines were about 20 fold higher than those of various transgenic plants obtained in previous studies and the protein amounts accounted for up to 6.1% of the total leaf soluble protein. Zymogram and temperature-dependent activity analyses demonstrated the thermostability of the enzyme and its substrate specificity against cellulose, and a simple heat treatment can be used to purify the protein. In addition, hydrolysis of transgenic rice straw with cultured cow gastric fluid yielded almost twice more reducing sugars than wild type straw. Taken together, these data suggest that transgenic rice can effectively serve as a bioreactor for large-scale production of active, thermostable cellulose hydrolytic enzymes. As a feedstock, direct expression of large amount of cellulases in transgenic rice may also facilitate saccharification of cellulose in rice straw and significantly reduce the costs for hydrolytic enzymes.

  3. New generation NMR bioreactor coupled with high-resolution NMR spectroscopy leads to novel discoveries in Moorella thermoaceticum metabolic profiles

    SciTech Connect (OSTI)

    Xue, Junfeng; Isern, Nancy G.; Ewing, R James; Liyu, Andrey V.; Sears, Jesse A.; Knapp, Harlan; Iversen, Jens; Sisk, Daniel R.; Ahring, Birgitte K.; Majors, Paul D.

    2014-06-20T23:59:59.000Z

    An in-situ nuclear magnetic resonance (NMR) bioreactor was developed and employed to monitor microbial metabolism under batch-growth conditions in real time. We selected Moorella thermoacetica ATCC 49707 as a test case. M. thermoacetica (formerly Clostridium thermoaceticum) is a strictly anaerobic, thermophilic, acetogenic, gram-positive bacterium with potential for industrial production of chemicals. The metabolic profiles of M. thermoacetica were characterized during growth in batch mode on xylose (a component of lignocellulosic biomass) using the new generation NMR bioreactor in combination with high-resolution, high sensitivity NMR (HR-NMR) spectroscopy. In-situ NMR measurements were performed using water-suppressed H-1 NMR spectroscopy at an NMR frequency of 500 MHz, and aliquots of the bioreactor contents were taken for 600 MHz HR-NMR spectroscopy at specific intervals to confirm metabolite identifications and expand metabolite coverage. M. thermoacetica demonstrated the metabolic potential to produce formate, ethanol and methanol from xylose, in addition to its known capability of producing acetic acid. Real-time monitoring of bioreactor conditions showed a temporary pH decrease, with a concomitant increase in formic acid during exponential growth. Fermentation experiments performed outside of the magnet showed that the strong magnetic field employed for NMR detection did not significantly affect cell metabolism. Use of the in-situ NMR bioreactor facilitated monitoring of the fermentation process in real time, enabling identification of intermediate and end-point metabolites and their correlation with pH and biomass produced during culture growth. Real-time monitoring of culture metabolism using the NMR bioreactor in combination with the HR-NMR spectroscopy will allow optimization of the metabolism of microorganisms producing valuable bioproducts.

  4. Bioreduction of hematite nanoparticles by the dissimilatory iron...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    nanoparticles by the dissimilatory iron reducing bacterium Shewanella oneidensis MR-1. Bioreduction of hematite nanoparticles by the dissimilatory iron reducing bacterium...

  5. Genomics of emerging infectious disease: A PLoS collection.

    E-Print Network [OSTI]

    Eisen, Jonathan A; MacCallum, Catriona J

    2009-01-01T23:59:59.000Z

    Salama NR (2009) Helicobacter pylori’s unconventional rolewith the bacterium Helicobacter pylori (which causes peptic

  6. Effect of a probiotic on caecal microbial digestion in the pony A de Vaux, V Julliand

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    ponies caecally fistulated were fed a maintenance ration of a complete meal (89% dry matter, 16 adapted from those of Leedle and Hespell (1981). The number of cellulolytic bacteria was deter- mined nitrogenous nutrient availability. Halliwell G, Bryant MP (1953) J Gen Microbiol 32, 441-448 Leedle JAZ

  7. Dissimilatory reduction of Fe(III) and other electron acceptors by a Thermus isolate

    SciTech Connect (OSTI)

    Kieft, T.L. [New Mexico Inst. of Mining and Technology, Socorro, NM (United States). Dept. of Biology; Fredrickson, J.K. [Pacific Northwest National Lab., Richland, WA (United States); Onstott, T.C. [Princeton Univ., NJ (United States). Dept. of Geosciences] [and others

    1999-03-01T23:59:59.000Z

    A thermophilic bacterium that can use O{sub 2}, NO{sub 3}{sup {minus}}, Fe(III), and S{sup 0} as terminal electron acceptors for growth was isolated from groundwater sampled at a 3.2-km depth in a South African gold mine. This organism, designated SA-01, clustered most closely with members of the genus Thermus, as determined by 16S rRNA gene (rDNA) sequence analysis. The 16S rDNA sequence of SA-01 was >98% similar to that of Thermus strain NMX2 A.1, which was previously isolated by other investigators from a thermal spring in New Mexico. Strain NMX2 A.1 was also able to reduce Fe(III) and other electron acceptors. Neither SA-01 nor NMX2 A.1 grew fermentatively, i.e., addition of an external electron acceptor was required for anaerobic growth. Thermus strain SA-01 reduced soluble Fe(III) complexed with citrate or nitrilotriacetic acid (NTA); however, it could reduce only relatively small quantities of hydrous ferric oxide except when the humic acid analog 2,6-anthraquinone disulfonate was added as an electron shuttle, in which case 10 mM Fe(III) was reduced. Fe(III)-NTA was reduced quantitatively to Fe(II); reduction of Fe(III)-NTA was coupled to the oxidation of lactate and supported growth through three consecutive transfers. Suspensions of Thermus strain SA-01 cells also reduced Mn(IV), Co(III)-EDTA, Cr(VI), and U(VI). Mn(IV)-oxide was reduce in the presence of either lactate or H{sub 2}. Both strains were also able to mineralize NTA to CO{sub 2} and to couple its oxidation to Fe(III) reduction and growth. The optimum temperature for growth and Fe(III) reduction by Thermus strains SA-01 and NMX2 A.1 is approximately 65 C; their optimum pH is 6.5 to 7.0. This is the first report of a Thermus sp. being able to couple the oxidation of organic compounds to the reduction of Fe, Mn, or S.

  8. The use of single tryptophan variants to study protein folding and stability 

    E-Print Network [OSTI]

    Dulin, Jennifer Natalie

    2013-02-22T23:59:59.000Z

    Studies on the kinetics of protein folding of the histidine-containing phosphocarrier protein (HPr) from the thermophile Bacillus stearothermophilus (Bst) will contribute much to the understanding of the origins of its enhanced thermal stability...

  9. Ecological Monographs, 83(4), 2013, pp. 419439 2013 by the Ecological Society of America

    E-Print Network [OSTI]

    Fortunat, Joos

    to global warming WILLY TINNER,1,2,3,11 DANIELE COLOMBAROLI,1,2 OLIVER HEIRI,1,2 PAUL D. HENNE,1,2,3 MARCO human impact was negligible, corroborate the Holocene evidence. Thermophilous Mediterranean A. alba

  10. Microbiology and physiology of anaerobic fermentations of cellulose. Progress report, September 1, 1979-May 15, 1980

    SciTech Connect (OSTI)

    Peck, H.D. Jr.; Ljungdahl, L.G.

    1980-01-01T23:59:59.000Z

    Reseach progress is reported for the period September, 1979 to May, 1980. Studies on the mesophilic and thermophilic microorganisms fermenting cellulose to various products (ethanol, acetate, CO/sub 2/, H/sub 2/, and methane) are summarized. (ACR)

  11. Reduction of Antibiotic-Resistant Bacteria Present in Food Animal Manures by Composting and Anaerobic Digestion

    E-Print Network [OSTI]

    Jones, Michelle

    Reduction of Antibiotic-Resistant Bacteria Present in Food Animal Manures by Composting digestion and composting at mesophilic or moderate temperature significantly reduced the antimicrobial resistance in animal manure. The most effective treatment was composting at thermophilic or high temperature

  12. The use of single tryptophan variants to study protein folding and stability

    E-Print Network [OSTI]

    Dulin, Jennifer Natalie

    2013-02-22T23:59:59.000Z

    Studies on the kinetics of protein folding of the histidine-containing phosphocarrier protein (HPr) from the thermophile Bacillus stearothermophilus (Bst) will contribute much to the understanding of the origins of its enhanced thermal stability...

  13. The winds of (evolutionary) change: Breathing new life into microbiology

    SciTech Connect (OSTI)

    Olsen, G.J.; Woese, C.R. [Univ. of Illinois, Urbana, IL (United States). Dept. of Microbiology; Overbeek, R.A. [Argonne National Lab., IL (United States)

    1996-03-01T23:59:59.000Z

    To date, over 1500 prokaryotes have been characterized by small subunit rRNA sequencing and molecular phylogeny has had an equally profound effect on our understanding of relationship among eukaryotic microorganisms. The universal phylogenetic tree readily shows however how artificial the strong distinction between the eukaryote and prokaryotes has become. The split between the Archaea and the Bacteria is now recognized as the primary phylogenetic division and that the Eucarya have branched from the same side of the tree as the Archaea. Both prokaryotic domains would seem to be of thermophilic origin suggesting that life arose in a very warm environment. Among the Archaea, all of the Crenarchaeota cultured to date are thermophiles, and the deepest euryarchaeal branchings are represented exclusively by thermophiles. Among the Bacteria, the deepest known branchings are again represented exclusively by thermophiles, and thermophilia is widely scattered throughout the domain. The Archaea comprise a small number of quite disparate phenotypes that grow in unusual niches. All are obligate or facultative anaerobes. All cultured crenarchaeotes are thermophilic, some even growing optimally above the normal boiling temperature of water. The Archaeoglobales are sulfate reducers growing at high temperatures. The extreme halophiles grow only in highly saline environments. The methanogens are confined to a variety of anaerobic niches, often thermophilic. The Bacteria, on the other hand, are notable as being the source of life`s photosynthetic capacity. Five kingdoms of bacteria contain photosynthetic species; and each of the five manifests a distinct type of (chlorophyll-based) photosynthesis.

  14. INTERNATIONAL JOURNAL OF SYSTEMATIC BACTERIOLOGY, 0020-7713/97/$04.00 0

    E-Print Network [OSTI]

    Reysenbach, Anna-Louise

    (III) the bacterium utilized molecular hydrogen. The organism reduced 9,10-anthraquinone-2,6-disulfonic acid, fumarate

  15. Dispersant solutions for dispersing hydrocarbons

    DOE Patents [OSTI]

    Tyndall, Richard L. (Clinton, TN)

    1997-01-01T23:59:59.000Z

    A dispersant solution includes a hydrocarbon dispersing solution derived from a bacterium from ATCC 75527, ATCC 75529, or ATCC 55638.

  16. Dispersant solutions for dispersing hydrocarbons

    DOE Patents [OSTI]

    Tyndall, R.L.

    1997-03-11T23:59:59.000Z

    A dispersant solution includes a hydrocarbon dispersing solution derived from a bacterium from ATCC 75527, ATCC 75529, or ATCC 55638.

  17. Mobility of Source Zone Heavy Metals and Radionuclides: The Mixed Roles of Fermentative Activity on Fate and Transport of U and Cr

    SciTech Connect (OSTI)

    Apel, William; Peyton, Brent; Gerlach, Robin; Lee, Brady

    2006-06-01T23:59:59.000Z

    Predicting the potential migration of metals and radionuclides from waste pits and trenches will require understanding the effects of carbon and electron flow through these environments. Important aspects of this flow include the physiological activity of cellulolytic and non-cellulolytic fermentative microbial populations, as well as the subsequent activity of metal and radionuclide reducing bacteria. The activity of subsurface fermentative microbial populations is significantly understudied even though these organisms can affect contaminant migration by at least two mechanisms. In the first mechanism, products of the fermentation process can act as chelators for metals and radionuclides increasing their transport through underlying geological media. The second mechanism is the reduction and immobilization of metals and radionuclides since some fermentative bacteria have been shown to directly reduce metals and radionuclides, while their fermentation products can provide carbon and energy for respiratory metal reducing bacteria that can also reduce oxidized metals and radionuclides.

  18. Exo-endo cellulase fusion protein

    DOE Patents [OSTI]

    Bower, Benjamin S. (Palo Alto, CA); Larenas, Edmund A. (Palo Alto, CA); Mitchinson, Colin (Palo Alto, CA)

    2012-01-17T23:59:59.000Z

    The present invention relates to a heterologous exo-endo cellulase fusion construct, which encodes a fusion protein having cellulolytic activity comprising a catalytic domain derived from a fungal exo-cellobiohydrolase and a catalytic domain derived from an endoglucanase. The invention also relates to vectors and fungal host cells comprising the heterologous exo-endo cellulase fusion construct as well as methods for producing a cellulase fusion protein and enzymatic cellulase compositions.

  19. Degradation of cellulosic biomass and its subsequent utilization for the production of chemical feedstocks. Progress report, March 1-August 31, 1980

    SciTech Connect (OSTI)

    Wang, D. I.C.

    1980-09-01T23:59:59.000Z

    Progress is reported in this coordinated research program to effect the microbiological degradation of cellulosic biomass by anaerobic microorganisms possessing cellulolytic enzymes. Three main areas of research are discussed: increasing enzyme levels through genetics, mutations, and genetic manipulation; the direct conversion of cellulosic biomass to liquid fuel (ethanol); and the production of chemical feedstocks from biomass (acrylic acid, acetone/butanol, and acetic acid). (DMC)

  20. A study of over-production and enhanced secretion of enzymes. Quarterly report 2

    SciTech Connect (OSTI)

    Dashek, W.V.

    1993-04-08T23:59:59.000Z

    This project is concerned with the over-production of ligno-cellulolytic enzymes which are relevant to the paper-pulp industry and agricultural community. Since ligno-cellulosics are components of wood, the project involves the forest, a renewable energy resource. Attention is focused on the following: over-production of polyphenol oxidase; establishment of the route of polyphenol oxidase secretion; regulation of polyphenol oxidase secretion; purification of extracellular oxidase.

  1. Global transcriptomic analysis of Cyanothece 51142 reveals robust...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    photosynthetic bacterium Citation: Stockel J, EA Welsh, ML Liberton, RV Kunnavakkam, R Aurora, and HB Pakrasi.2008."Global transcriptomic analysis of Cyanothece 51142 reveals...

  2. Reduction And Immobilization Of Hexavalent Chromium By Microbially...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    bacterium Geobacter sulfurreducens with acetate as the sole electron donor and anthraquinone-2,6-disulfate (AQDS) as electron shuttle in synthetic groundwater (pH 7). Biogenic...

  3. asbestos-related pleuropulmonary diseases: Topics by E-print...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    diseases Ulcer treatment has been revolutionized by recently discovered knowledge about Helicobacter pylori, a bacterium commonly found in the human gastrointestinal tract. These...

  4. anthropometry gastrointestinal dysfunction: Topics by E-print...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    diseases Ulcer treatment has been revolutionized by recently discovered knowledge about Helicobacter pylori, a bacterium commonly found in the human gastrointestinal tract. These...

  5. advanced gastrointestinal stromal: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    diseases Ulcer treatment has been revolutionized by recently discovered knowledge about Helicobacter pylori, a bacterium commonly found in the human gastrointestinal tract. These...

  6. acute gastrointestinal hemorrhage: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    diseases Ulcer treatment has been revolutionized by recently discovered knowledge about Helicobacter pylori, a bacterium commonly found in the human gastrointestinal tract. These...

  7. adnexal diseases: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    diseases Ulcer treatment has been revolutionized by recently discovered knowledge about Helicobacter pylori, a bacterium commonly found in the human gastrointestinal tract. These...

  8. acrylonitrile-induced gastrointestinal bleeding: Topics by E...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    diseases Ulcer treatment has been revolutionized by recently discovered knowledge about Helicobacter pylori, a bacterium commonly found in the human gastrointestinal tract. These...

  9. anus diseases: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    diseases Ulcer treatment has been revolutionized by recently discovered knowledge about Helicobacter pylori, a bacterium commonly found in the human gastrointestinal tract. These...

  10. attenuates postprandial gastrointestinal: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    diseases Ulcer treatment has been revolutionized by recently discovered knowledge about Helicobacter pylori, a bacterium commonly found in the human gastrointestinal tract. These...

  11. activities gastrointestinal fermentation: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    diseases Ulcer treatment has been revolutionized by recently discovered knowledge about Helicobacter pylori, a bacterium commonly found in the human gastrointestinal tract. These...

  12. acute upper gastrointestinal: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    diseases Ulcer treatment has been revolutionized by recently discovered knowledge about Helicobacter pylori, a bacterium commonly found in the human gastrointestinal tract. These...

  13. acute gastrointestinal bleeding: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    diseases Ulcer treatment has been revolutionized by recently discovered knowledge about Helicobacter pylori, a bacterium commonly found in the human gastrointestinal tract. These...

  14. acid peptic disease: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    is an imbalance between offensive and defensive gastric factors. A bacterium called Helicobacter pylori has been considered a major causative agent for gastric and duodenal...

  15. attenuate gastrointestinal motility: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    diseases Ulcer treatment has been revolutionized by recently discovered knowledge about Helicobacter pylori, a bacterium commonly found in the human gastrointestinal tract. These...

  16. autoimmune gastrointestinal dysmotility: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    diseases Ulcer treatment has been revolutionized by recently discovered knowledge about Helicobacter pylori, a bacterium commonly found in the human gastrointestinal tract. These...

  17. active gastrointestinal bleeding: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    diseases Ulcer treatment has been revolutionized by recently discovered knowledge about Helicobacter pylori, a bacterium commonly found in the human gastrointestinal tract. These...

  18. 800 MHz NMR Denali (Liquids) | EMSL

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Publications Dying for Good: Virus-Bacterium Biofilm Co-evolution Enhances Environmental Fitness. Commonly used in biotechnology applications, filamentous M13 phage...

  19. Biotransformation of Two-Line Silica-Ferrihydrite by a Dissimilatory...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    by a Dissimilatory Fe(III)-Reducing Bacterium: Formation of Carbonate Green Biotransformation of Two-Line Silica-Ferrihydrite by a Dissimilatory Fe(III)-Reducing...

  20. High content live cell imaging for the discovery of new antimalarial marine natural products

    E-Print Network [OSTI]

    2012-01-01T23:59:59.000Z

    Staphylococcus aureus (MRSA) and vancomycin-resistantresistant Staphylococcus aureus (MRSA); vancomycin-resistantand ARCA, respectively). MRSA is a patho- genic bacterium

  1. Structural and Molecular Basis of Heme Acquisition by the Gram-positive Pathogens Staphylococcus aureus and Listeria monocytogenes

    E-Print Network [OSTI]

    Malmirchegini, Ghulam Reza Khan

    2013-01-01T23:59:59.000Z

    Staphylococcus aureus (MRSA) is a growing problem, worldwideand Prevention (CDC) estimated that MRSA was responsible forresistant S. aureus (MRSA) carriers (20). The bacterium

  2. RNA Type III Secretion Signals that require Hfq. | EMSL

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    that require Hfq. RNA Type III Secretion Signals that require Hfq. Abstract: effector proteins from the bacterium to a host cell; however, the secretion signal is poorly...

  3. Alice Dohnalkova | EMSL

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Alice Dohnalkova Recent Highlights Lipid Biofuels By revealing a novel molecular pathway involved in microbial lipid accumulation in the bacterium Rhodobacter sphaeroides, this...

  4. CO2 exposure at pressure impacts metabolism and stress responses...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    in the model sulfate-reducing bacterium Desulfovibrio vulgaris Abstract: Geologic carbon dioxide (CO2) sequestration drives physical and geochemical changes in deep...

  5. Lait (1990) 70,411-423 Elsevier/INRA

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    1990-01-01T23:59:59.000Z

    ) and artificial acidification (addition of citric acid) were used for the manufacture of water-buffalo Mozzarella cheese. Whey acidity, fermentation end-products and microbial populations were monitored during cheese. Cheeses produced with the thermophilic multiple strain starter and citric acid addition obtained

  6. Lait 87 (2007) 7177 INRA, EDP Sciences, 2007

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    2007-01-01T23:59:59.000Z

    was found for acetic acid level. In the beverages produced using mesophilic cultures the amount of this compound was higher than in beverages containing thermophilic bacte- ria. Due to the fact that acetic acid of analysis. free fatty acid profile / fermented beverage / ewe's milk ­ / / Résumé ­ Profils des

  7. HYDROTHERMAL TREATMENT OF WHEAT STRAW ON PILOT PLANT SCALE Anders Thygesena

    E-Print Network [OSTI]

    with lignin (15-20% w/w). The polysaccharides in lignocellulosic materials can be used for bioethanol bioethanol production. The cellulose cannot be enzymatically hydrolyzed to glucose without a physical be converted to bioethanol by thermophilic microorganisms. One of the objectives of the EU

  8. Extremophilic iron-reducing bacteria: Their implications for possible life in extraterrestrial environments

    SciTech Connect (OSTI)

    Zhou, J.; Liu, S.V.; Zhang, C.; Palumbo, A.V.; Phelps, T.J.

    1998-06-01T23:59:59.000Z

    Iron reduction is believed to be an early form of respiration and iron-reducing bacteria might have evolved very early on Earth. To support this hypothesis, the authors began to search for both thermophilic and psychrophilic iron-reducing bacteria because iron-reducing capacity may be a widely distributed trait if ancestral microorganisms include extremophilic iron-reducing bacteria. To date, they have obtained thermophilic Fe(III)-reducing and magnetite-forming enrichment cultures from geologically and hydrologically isolated, millions of years-old deep terrestrial subsurface samples. Three dominant bacteria were identified based on 16S ribosomal RNA gene sequences. Phylogenetical analysis indicated that these bacteria were closely related to Thermoanaerobacter ethanoliticus. Two pure thermophilic iron-reducing bacteria have been isolated and characterized from these enrichments, they also are able to degrade cellulose and xylan. Geological evidence indicated that these bacteria were separated from modern organisms for about 200 million years, and they are the oldest isolated bacteria available now. Evolutionary sequence analysis showed that the 16S rRNA genes evolved extremely slowly in these bacteria. In addition, the authors have obtained about 30 psychrophilic iron-reducing bacteria in samples from Siberia and Alaska permafrost soils, Pacific marine sediments and Hawaii deep sea water. These bacteria were also able to reduce other heavy metals. The isolation of both thermophilic and psychrophilic iron-reducing bacteria from surface and subsurface environments has significant implications for microbial evolution and for studying the origin of life in extraterrestrial environments.

  9. RESEARCH PAPER A review of the microbiology of the Rehai geothermal

    E-Print Network [OSTI]

    Ahmad, Sajjad

    RESEARCH PAPER A review of the microbiology of the Rehai geothermal field in Tengchong, Yunnan Geomicrobiology; Thermophile; Yunnan; Rehai; Tengchong; PIRE Abstract The Rehai Geothermal Field, located geothermal field in China. A wide physicochemical diver- sity of springs (ambient to w97 C; pH from 1

  10. Targeted Discovery of Glycoside Hydrolases from a Switchgrass-Adapted Compost Community

    E-Print Network [OSTI]

    Hazen, Terry

    Targeted Discovery of Glycoside Hydrolases from a Switchgrass-Adapted Compost Community Martin avenue of research in this area. Here we added a green-waste compost inoculum to switchgrass (Panicum virgatum) and simulated thermophilic composting in a bioreactor to select for a switchgrass

  11. Geothermics, Vol. 15, No. 3, pp. 347-358, 1986. Printed inGreatBritain.

    E-Print Network [OSTI]

    Ahmad, Sajjad

    Geothermics, Vol. 15, No. 3, pp. 347-358, 1986. Printed inGreatBritain. 0375 - 6505/86 $3.130 + 0.00 Pergamon Journals Ltd. © 1986 CNR. THERMOPHILIC MICROORGANISMS IN THE HOT SPRINGS OF TENGCHONG GEOTHERMAL volcanicgeothermalenvironmentsis discussed. INTRODUCTION In recent years biologists have been attaching great importance to thermal

  12. Nucleosides, Nucleotides, and Nucleic Acids, 25:915, 2006 Copyright C Taylor & Francis Group, LLC

    E-Print Network [OSTI]

    Stoltz, Brian M.

    Nucleosides, Nucleotides, and Nucleic Acids, 25:9­15, 2006 Copyright C Taylor & Francis Group, LLC-LABELED NUCLEOTIDE SPACER ARM ON INCORPORATION BY THERMOPHILIC DNA POLYMERASES Christopher J. Lacenere 2 Division incor- porate fluorescently labeled nucleotides sequentially was analyzed by a gel based primer

  13. Bioelectrical SPMs (G. Gomila, UB-IBEC) Bioelectric Scanning Probe Microscopies

    E-Print Network [OSTI]

    Ritort, Felix

    -Surface Topography 900nm E.Coli Bacterium E.Coli Bacterium AFM Topography (2D colour image) 3D image measure with an SPM? 2-In addition to topography some other physical property depending on the type of SPM are softer. Topography Bioelectrical SPMs (G. Gomila, UB-IBEC) 1. Introduction Bioelectric scanning probe

  14. Method for the detection of Salmonella enterica serovar Enteritidis

    DOE Patents [OSTI]

    Agron, Peter G. (Castro Valley, CA); Andersen, Gary L. (Berkeley, CA); Walker, Richard L. (Davis, CA)

    2008-10-28T23:59:59.000Z

    Described herein is the identification of a novel Salmonella enterica serovar Enteritidis locus that serves as a marker for DNA-based identification of this bacterium. In addition, three primer pairs derived from this locus that may be used in a nucleotide detection method to detect the presence of the bacterium are also disclosed herein.

  15. 460 NATURE PHYSICS | VOL 9 | AUGUST 2013 | www.nature.com/naturephysics news & views

    E-Print Network [OSTI]

    Loss, Daniel

    is to continue along that course. In Escherichia coli, a well-studied bacterium, cells `run' along a smooth a cell is swimming up the gradient than when it is swimming down2 . E. coli manages this because it has, it was found in a study4 of a polarly flagellated marine bacterium, Vibrio alginolyticus, that a cell swims

  16. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Dec. 2003, p. 75277530 Vol. 69, No. 12 0099-2240/03/$08.00 0 DOI: 10.1128/AEM.69.12.75277530.2003

    E-Print Network [OSTI]

    Ruby, Edward G.

    (Fig. 1A). Cells of Escherichia coli also form two rings on tryptone-based soft agar, with the outer colonized by the biolu- minescent marine bacterium Vibrio fischeri. Motility is required to establish Hawaiian squid, Euprymna scolopes, is specifically colonized by the lumi- nous marine bacterium Vibrio

  17. RAPID COMMUNICATIONS PHYSICAL REVIEW E 84, 060901(R) (2011)

    E-Print Network [OSTI]

    Tessmer, Stuart

    pili of the metal-reducing bacterium Geobacter sulfurreducens probed by scanning tunneling microscopy; published 6 December 2011) The metal-reducing bacterium Geobacter sulfurreducens produces conductive protein. These processes can be harnessed for the bioremediation of toxic metals and the generation of electricity

  18. Processing of cellulosic material by a cellulase-containing cell-free fermentate produced from cellulase-producing bacteria, ATCC 55702

    DOE Patents [OSTI]

    Dees, H. Craig (Lenoir City, TN)

    1998-01-01T23:59:59.000Z

    Bacteria which produce large amounts of a cellulase-containing cell-free fermentate, have been identified. The original bacterium (ATCC 55703) was genetically altered using nitrosoguanidine (MNNG) treatment to produce the enhanced cellulase degrading bacterium ATCC 55702, which was identified through replicate plating. ATCC 55702 has improved characteristics and qualities for the degradation of cellulosic materials.

  19. Nitrogen Metabolism in Bos indicus and Bos taurus Cattle Consuming Low-quality Forages

    E-Print Network [OSTI]

    Weldon, Kyle

    2013-05-22T23:59:59.000Z

    regions. Subspecies differences: Digestion The reticulo-rumen is the primary site of fermentation in the ruminant animal, with a diverse microbial population degrading cellulolytic material to produce microbial crude protein and volatile fatty acids... numerically more OM in the reticulo-rumen than Bt (90 versus 83%). They did conclude that the greater apparent ruminal OM digestion for Bi ? Bt compared to Bt (1.68 versus 1.53 kg/d), was balanced by less OM digestion post ruminally in Bi ? Bt versus Bt (0...

  20. Methods for degrading lignocellulosic materials

    SciTech Connect (OSTI)

    Vlasenko, Elena (Davis, CA); Cherry, Joel (Davis, CA); Xu, Feng (Davis, CA)

    2011-05-17T23:59:59.000Z

    The present invention relates to methods for degrading a lignocellulosic material, comprising: treating the lignocellulosic material with an effective amount of one or more cellulolytic enzymes in the presence of at least one surfactant selected from the group consisting of a secondary alcohol ethoxylate, fatty alcohol ethoxylate, nonylphenol ethoxylate, tridecyl ethoxylate, and polyoxyethylene ether, wherein the presence of the surfactant increases the degradation of lignocellulosic material compared to the absence of the surfactant. The present invention also relates to methods for producing an organic substance, comprising: (a) saccharifying a lignocellulosic material with an effective amount of one or more cellulolytic enzymes in the presence of at least one surfactant selected from the group consisting of a secondary alcohol ethoxylate, fatty alcohol ethoxylate, nonylphenol ethoxylate, tridecyl ethoxylate, and polyoxyethylene ether, wherein the presence of the surfactant increases the degradation of lignocellulosic material compared to the absence of the surfactant; (b) fermenting the saccharified lignocellulosic material of step (a) with one or more fermenting microorganisms; and (c) recovering the organic substance from the fermentation.

  1. Effects of oil spill dispersants and drilling fluids on substrate specificity of marine bacteria

    SciTech Connect (OSTI)

    Okpokwasili, G.C.; Nnubia, C. [Univ. of Port Harcourt (Nigeria). Dept. of Microbiology] [Univ. of Port Harcourt (Nigeria). Dept. of Microbiology

    1995-12-31T23:59:59.000Z

    The effects of oil spill dispersants and drilling fluids on the sizes of populations of specific heterotroph subgroups of marine bacteria were monitored in this study. The bacteria were isolated from drill cuttings recovered from Agbara--an offshore oilfield located some 100 nautical miles off the Atlantic coast of Nigeria. Numbers of cellulolytic, proteolytic, starch-hydrolyzing and lipolytic bacteria in the drill cuttings were monitored for 28 days in the presence of oil spill dispersants and drilling fluids. The percentages of these bacterial subgroups within the total heterotrophic population enumerated on tryptic soy agar (10% with 3% NaCl) fluctuated between 3.0 and 17.0%, 0.0 and 27.0%, 4.0 and 25.0% and 3.0 and 18.0% for cellulolytic, proteolytic, starch-hydrolyzing and lipolytic bacteria respectively. These results indicate that oil spill dispersants and drilling fluids affect the ability of marine bacteria to metabolize these substrates in the environment.

  2. Methods for degrading lignocellulosic materials

    DOE Patents [OSTI]

    Vlasenko, Elena (Davis, CA); Cherry, Joel (Davis, CA); Xu, Feng (Davis, CA)

    2008-04-08T23:59:59.000Z

    The present invention relates to methods for degrading a lignocellulosic material, comprising: treating the lignocellulosic material with an effective amount of one or more cellulolytic enzymes in the presence of at least one surfactant selected from the group consisting of a secondary alcohol ethoxylate, fatty alcohol ethoxylate, nonylphenol ethoxylate, tridecyl ethoxylate, and polyoxyethylene ether, wherein the presence of the surfactant increases the degradation of lignocellulosic material compared to the absence of the surfactant. The present invention also relates to methods for producing an organic substance, comprising: (a) saccharifying a lignocellulosic material with an effective amount of one or more cellulolytic enzymes in the presence of at least one surfactant selected from the group consisting of a secondary alcohol ethoxylate, fatty alcohol ethoxylate, nonylphenol ethoxylate, tridecyl ethoxylate, and polyoxyethylene ether, wherein the presence of the surfactant increases the degradation of lignocellulosic material compared to the absence of the surfactant; (b) fermenting the saccharified lignocellulosic material of step (a) with one or more fermentating microoganisms; and (c) recovering the organic substance from the fermentation.

  3. Integrated ‘omics analysis for studying the microbial community response to a pH perturbation of a cellulose-degrading bioreactor culture

    SciTech Connect (OSTI)

    Boaro, Amy A.; Kim, Young-Mo; Konopka, Allan; Callister, Stephen J.; Ahring, Birgitte K.

    2014-12-01T23:59:59.000Z

    Integrated ‘omics have been used on pure cultures and co-cultures, yet they have not been applied to complex microbial communities to examine questions of perturbation response. In this study, we used integrated ‘omics to measure the perturbation response of a cellulose-degrading bioreactor community fed with microcrystalline cellulose (Avicel). We predicted that a pH decrease by addition of a pulse of acid would reduce microbial community diversity and temporarily reduce reactor function such as cellulose degradation. However, 16S rDNA pyrosequencing results revealed increased alpha diversity in the microbial community after the perturbation, and a persistence of the dominant community members over the duration of the experiment. Proteomics results showed a decrease in activity of proteins associated with Fibrobacter succinogenes two days after the perturbation followed by increased protein abundances six days after the perturbation. The decrease in cellulolytic activity suggested by the proteomics was confirmed by the accumulation of Avicel in the reactor. Metabolomics showed a pattern similar to that of the proteome, with amino acid production decreasing two days after the perturbation and increasing after six days. This study demonstrated that community ‘omics data provides valuable information about the interactions and function of anaerobic cellulolytic community members after a perturbation.

  4. Dynamic compartmentalization of bacteria: accurate division in E. coli

    E-Print Network [OSTI]

    Martin Howard; Andrew D. Rutenberg; Simon de Vet

    2001-12-07T23:59:59.000Z

    Positioning of the midcell division plane within the bacterium E. coli is controlled by the min system of proteins: MinC, MinD and MinE. These proteins coherently oscillate from end to end of the bacterium. We present a reaction--diffusion model describing the diffusion of min proteins along the bacterium and their transfer between the cytoplasmic membrane and cytoplasm. Our model spontaneously generates protein oscillations in good agreement with experiments. We explore the oscillation stability, frequency and wavelength as a function of protein concentration and bacterial length.

  5. Biochemistry and physiology of anaerobic bacteria

    SciTech Connect (OSTI)

    NONE

    2000-05-18T23:59:59.000Z

    We welcome you to The Power of Anaerobes. This conference serves two purposes. One is to celebrate the life of Harry D. Peck, Jr.,who was born May 18, 1927 and would have celebrated his 73rd birthday at this conference. He died November 20, 1998. The second is to gather investigators to exchange views within the realm of anaerobic microbiology, an area in which tremendous progress has been seen during recent years. It is sufficient to mention discoveries of a new form of life (the archaea), hyper or extreme thermophiles, thermophilic alkaliphiles and anaerobic fungi. With these discoveries has come a new realization about physiological and metabolic properties of microorganisms, and this in turn has demonstrated their importance for the development, maintenance and sustenance of life on Earth.

  6. Improvements of biomass deconstruction enzymes

    SciTech Connect (OSTI)

    Sale, K. L.

    2012-03-01T23:59:59.000Z

    Sandia National Laboratories and DSM Innovation, Inc. collaborated on the investigation of the structure and function of cellulases from thermophilic fungi. Sandia's role was to use its expertise in protein structure determination and X-ray crystallography to solve the structure of these enzymes in their native state and in their substrate and product bound states. Sandia was also tasked to work with DSM to use the newly solved structure to, using computational approaches, analyze enzyme interactions with both bound substrate and bound product; the goal being to develop approaches for rationally designing improved cellulases for biomass deconstruction. We solved the structures of five cellulases from thermophilic fungi. Several of these were also solved with bound substrate/product, which allowed us to predict mutations that might enhance activity and stability.

  7. Experimental Investigation of Microbially Induced Corrosion of Test Samples and Effect of Self-Assembled Hydrophobic Monolayers. Exposure of Test Samples to Continuous Microbial Cultures, Chemical Analysis, and Biochemical Studies

    SciTech Connect (OSTI)

    Laurinavichius, K.S.

    1998-09-30T23:59:59.000Z

    The study of biocorrosion of aluminum and beryllium samples were performed under conditions of continuous fermentation of thermophilic anaerobic microorganisms of different groups. This allowed us to examine the effect of various types of metabolic reactions of reduction-oxidation proceeding at different pH and temperatures under highly reduced conditions on aluminum and beryllium corrosion and effect of self-assembled hydrophobic monolayers.

  8. Mixed oxide nanoparticles and method of making

    DOE Patents [OSTI]

    Lauf, Robert J. (Oak Ridge, TN); Phelps, Tommy J. (Knoxville, TN); Zhang, Chuanlun (Columbia, MO); Roh, Yul (Oak Ridge, TN)

    2002-09-03T23:59:59.000Z

    Methods and apparatus for producing mixed oxide nanoparticulates are disclosed. Selected thermophilic bacteria cultured with suitable reducible metals in the presence of an electron donor may be cultured under conditions that reduce at least one metal to form a doped crystal or mixed oxide composition. The bacteria will form nanoparticles outside the cell, allowing easy recovery. Selection of metals depends on the redox potentials of the reducing agents added to the culture. Typically hydrogen or glucose are used as electron donors.

  9. Nucleotide sequences encoding a thermostable alkaline protease

    DOE Patents [OSTI]

    Wilson, David B. (Ithaca, NY); Lao, Guifang (Bethesda, MD)

    1998-01-01T23:59:59.000Z

    Nucleotide sequences, derived from a thermophilic actinomycete microorganism, which encode a thermostable alkaline protease are disclosed. Also disclosed are variants of the nucleotide sequences which encode a polypeptide having thermostable alkaline proteolytic activity. Recombinant thermostable alkaline protease or recombinant polypeptide may be obtained by culturing in a medium a host cell genetically engineered to contain and express a nucleotide sequence according to the present invention, and recovering the recombinant thermostable alkaline protease or recombinant polypeptide from the culture medium.

  10. A comparative study of HPr proteins from extremophilic organisms

    E-Print Network [OSTI]

    Syed Ali, Abbas Razvi

    2006-04-12T23:59:59.000Z

    . Sequence, in turn, defines structure as studied in the field of protein folding. Sequence is also the variable which organisms change as they evolve to adapt their proteins to the environments they inhabit. The sequence... associated with protein folding and ?G, the free energy of protein stabilization. Proteins from thermophiles alter their sequence in a way such that it optimizes the interactions holding their conformations together; these optimizations...

  11. Elucidation of Beta-Oxidation Pathways in Ralstonia Eutropha H16 by Examination of Global Gene Expression

    E-Print Network [OSTI]

    Zeng, Qiandong

    Ralstonia eutropha H16 is capable of growth and polyhydroxyalkanoate production on plant oils and fatty acids. However, little is known about the triacylglycerol and fatty acid degradation pathways of this bacterium. We ...

  12. Helicobacter pylori moves through mucus by reducing mucin viscoelasticity

    E-Print Network [OSTI]

    So, Peter T. C.

    The ulcer-causing gastric pathogen Helicobacter pylori is the only bacterium known to colonize the harsh acidic environment of the human stomach. H. pylori survives in acidic conditions by producing urease, which catalyzes ...

  13. Evolutionary History of Helicobacter pylori Sequences Reflect Past Human Migrations in Southeast Asia

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    Evolutionary History of Helicobacter pylori Sequences Reflect Past Human Migrations in Southeast analyse housekeeping gene sequences of the human stomach bacterium Helicobacter pylori from various, Dieye FB, et al. (2011) Evolutionary History of Helicobacter pylori Sequences Reflect Past Human

  14. Molecular Ecology (2005) 14, 32893306 doi: 10.1111/j.1365-294X.2005.02687.x 2005 Blackwell Publishing Ltd

    E-Print Network [OSTI]

    Wirth, Thierry

    of viruses, and the bacterium Helicobacter pylori, can be used as genetic tracers for one of the most sampling and analysis. Keywords: co-evolution, evolution, Helicobacter pylori, human migrations, microbes

  15. In Vitro Inhibition of Listeria Monocytogenes by Novel Combinations of Food Antimicrobials 

    E-Print Network [OSTI]

    Brandt, Alex Lamar

    2011-02-22T23:59:59.000Z

    Listeria monocytogenes is a foodborne pathogenic bacterium responsible for ~500 deaths and a financial burden of ~$2.3 billion each year in the United States. Though a zero tolerance policy is enforced with regard to its ...

  16. The effect of gender on Helicobacter pylori and gastric cancer

    E-Print Network [OSTI]

    Sheh, Alexander

    2011-01-01T23:59:59.000Z

    Gastric cancer is the 2nd leading cause of cancer death worldwide and the 4th most commonly diagnosed cancer worldwide. Helicobacter pylori infection is the major risk factor of gastric cancer, and as such, this bacterium ...

  17. Radial and Spiral Stream Formation in Proteus mirabilis Colonies

    E-Print Network [OSTI]

    Xue, Chuan

    The enteric bacterium Proteus mirabilis, which is a pathogen that forms biofilms in vivo, can swarm over hard surfaces and form a variety of spatial patterns in colonies. Colony formation involves two distinct cell types: ...

  18. Production of Clostridium difficile toxin in a medium totally free of both animal and dairy proteins or digests

    E-Print Network [OSTI]

    Demain, Arnold L.

    In the hope of developing a vaccine against Clostridium difficile based on its toxin(s), we have developed a fermentation medium for the bacterium that results in the formation of Toxin A and contains no meat or dairy ...

  19. Selection and optimization of gene targets for the metabolic engineering of E. coli

    E-Print Network [OSTI]

    Fischer, Curt R., Ph. D. Massachusetts Institute of Technology

    2009-01-01T23:59:59.000Z

    This thesis is about identifying genetic interventions that improve the performance of targeted pathways in the metabolism of the bacterium Escherichia coli. Three case studies illustrate three disparate approaches to ...

  20. NATURE|Vol 437|29 September 2005 NEWS & VIEWS (as occurred in the 1960s compared with the

    E-Print Network [OSTI]

    Elowitz, Michael

    -levelcircuitry.Similarassays,applied in yeast and the bacterium Escherichia coli, have detected both sources of noise and shown how: achieving a better understanding of that variability is one of the next challenges in marine biogeochemistry

  1. Programmed population control by cellcell communication

    E-Print Network [OSTI]

    You, Lingchong

    that autonomously regulates the density of an Escherichia coli population. The cell density is broadcasted from the marine bacterium Vibrio fischeri13,14 synthesizes a small, diffusible acyl-homoserine lactone

  2. JOURNAL OF BACTERIOLOGY, Mar. 2005, p. 20582065 Vol. 187, No. 6 0021-9193/05/$08.00 0 doi:10.1128/JB.187.6.20582065.2005

    E-Print Network [OSTI]

    McFall-Ngai, Margaret

    of the enteric bac- teria Escherichia coli and Salmonella enterica serovar Typhi- murium have been well. The symbiosis between the marine bacterium Vibrio fischeri and the Hawaiian squid Euprymna scolopes provides

  3. Cloning and nucleotide sequence of the Bartonella bacilliformis gene: alaS and leuS, which encode aminoacyl tRNA synthetases; pyrF, which encodes orotidine 5' monophosphate decarboxylase; and txpA, an ABC transporter-like protein similar to the Agrobacterium tumefaciens chvA gene 

    E-Print Network [OSTI]

    Upeslacis, Erik

    1996-01-01T23:59:59.000Z

    Biosynthetic genes, putatively identified as pyrf, alas and leus and the putative transport gene txpa, have been cloned and sequenced from the gram negative, hemotrophic, flagellated bacterium Barionella bacilliformis. The ...

  4. High quality genome-scale metabolic network reconstruction of mycobacterium tuberculosis and comparison with human metabolic network: application for drug targets identification 

    E-Print Network [OSTI]

    Kalapanulak, Saowalak

    2009-01-01T23:59:59.000Z

    Mycobacterium tuberculosis (Mtb), a pathogenic bacterium, is the causative agent in the vast majority of human tuberculosis (TB) cases. Nearly one-third of the world’s population has been affected by TB and annually two ...

  5. Interference with histidyl-tRNA synthetase by a CRISPR spacer sequence as a factor in the evolution of Pelobacter carbinolicus

    E-Print Network [OSTI]

    Lovley, Derek

    carbinolicus, a bacterium of the family Geobacteraceae, cannot reduce Fe(III) directly or produce electricity for interference with hisS. Spacer #1 inhibited growth of a transgenic strain of Geobacter sulfurreducens in which

  6. Cellulose degradation system of Cytophaga hutchinsonii 

    E-Print Network [OSTI]

    Liu, Chao-Kuo

    2012-11-30T23:59:59.000Z

    In this project, Cytophaga hutchinsonii, an aerobic gliding bacterium with cellulose-degrading ability, was studied, since its cellulase system was unknown and might be very different from those of other cellulose-degrading ...

  7. Draft genome sequence of strain HIMB100, a cultured representative of the SAR116 clade of marine Alphaproteobacteria

    E-Print Network [OSTI]

    Grote, Jana

    2011-01-01T23:59:59.000Z

    Strain HIMB100 is a planktonic marine bacterium in the class Alphaproteobacteria. This strain is of interest because it is one of the first known isolates from a globally ubiquitous clade of marine bacteria known as SAR116 ...

  8. Methods for dispersing hydrocarbons using autoclaved bacteria

    DOE Patents [OSTI]

    Tyndall, R.L.

    1996-11-26T23:59:59.000Z

    A method of dispersing a hydrocarbon includes the following steps: providing a bacterium selected from the following group: ATCC 85527, ATCC 75529, and ATCC 55638, a mutant of any one of these bacteria possessing all the identifying characteristics of any one of these bacteria, and mixtures; autoclaving the bacterium to derive a dispersant solution; and contacting the dispersant solution with a hydrocarbon to disperse the hydrocarbon. Moreover, a method for preparing a dispersant solution includes the following steps: providing a bacterium selected from the following group: ATCC 75527, ATCC 75529, and ATCC 55638, a mutant of any one of these bacteria possessing all the identifying characteristics of any one of these bacteria, and mixtures; and autoclaving the bacterium to derive a dispersant solution.

  9. Review of the Impacts of Crumb Rubber in Artificial Turf Applications

    E-Print Network [OSTI]

    Simon, Rachel

    2010-01-01T23:59:59.000Z

    Staphylococcus aureus (CA-MRSA): the latest sports epidemic.Taussig, M.E. Lane (2003). MRSA outbreak in a state prison:Staphylococcus aureus (MRSA) is a drug-resistant bacterium

  10. Sensing Applications of Fluctuations and Noise

    E-Print Network [OSTI]

    Chang, Hung-Chih

    2011-02-22T23:59:59.000Z

    Noise and time-dependent fluctuations are usually undesirable signals. However, they have many applications. This dissertation deals with two kinds of sensing applications of fluctuation and noise: soil bulk density assessment and bacterium sensing...

  11. The Temperature Dependent Development of Bactericera cockerelli (Sulc) from south Texas (Hemiptera: Triozidae)

    E-Print Network [OSTI]

    Lewis, Olin M

    2014-11-06T23:59:59.000Z

    Bactericera cockerelli (Sulc) (Hemiptera: Triozidae) is a pest of potato (Solanum tuberosum L.) that vectors the bacterium that putatively causes zebra chip disease in potatoes, ‘Candidatus Liberibacter solanacearum.’ The economic risk of zebra chip...

  12. RESEARCH ARTICLE Open Access Survival of taylorellae in the environmental

    E-Print Network [OSTI]

    Boyer, Edmond

    Hébert6 Abstract Background: Taylorella equigenitalis is the causative agent of contagious equine natural ecological niche. Keywords: Taylorella equigenitalis, Taylorella asinigenitalis, Contagious equine-negative betaproteo- bacterium of the Alcaligenaceae family. It is the causative agent of Contagious Equine Metritis

  13. Carbon based nutrition of Staphylococcus aureus and the role of sugar phosphate transporters in intracellular bacterial replication 

    E-Print Network [OSTI]

    Bell, John Alexander

    2014-06-28T23:59:59.000Z

    The Gram positive bacterium Staphylococcus aureus is a major cause of human disease in industrialized countries. This multifaceted pathogen is adapted to thrive in a variety of host niches, including the intracellular ...

  14. A cell needs all the players within its cell envelope in order to fullfill its tasks efficiently. Proteins have an essential role in this picture; they are required for many biological functions and their

    E-Print Network [OSTI]

    van den Brink, Jeroen

    (such as tyrosinase and hemocyanin), which are capable of transporting oxygen in their active site. The protein, which was mainly tyrosinase from the soil bacterium Streptomyces antibioticus, has been

  15. Large scale total synthesis of apoptolidinone and progress towards the total synthesis of ammocidin 

    E-Print Network [OSTI]

    Liu, Qingsong

    2009-05-15T23:59:59.000Z

    Apoptolidin 1.1 was isolated in 1997 by Hayakawa and co-workers from a soil bacterium Nocardiopsis sp. during screening for specific apoptosis inducers. The primary biological test revealed that this polyketide macrolide ...

  16. National Aeronautics and Space Administration thVIIaeMpacS

    E-Print Network [OSTI]

    581g Artwork (Lynette Cook/NASA); 38) Dreath Star (NASA/G. Bacon); 43) Transiting planets (NASA/Tim Pyle); 45) Habitable Zones (NASA/Kepler); 61) Solar Probe (JHU/APL); 73) Bacterium (NASA/Jodi Blum); 81

  17. Thermostabilization of desulfurization enzymes from Rhodococcos sp. IGTS8. Final technical report

    SciTech Connect (OSTI)

    John J. Kilbane II

    2000-12-15T23:59:59.000Z

    The objective of this project was to develop thermophilic cultures capable of expressing the desulfurization (dsz) operon of Rhodococcus sp. IGTS8. The approaches taken in this project included the development of plasmid and integrative expression vectors that function well in Thermus thermophilus, the cloning of Rhodococcus dsz genes in Thermus expression vectors, and the isolation of bacterial cultures that express the dsz operon at thermophilic temperatures. This project has resulted in the development of plasmid and integrative expression vectors for use in T. thermophilus. The dsz genes have been expressed at moderately thermophilic temperatures (52 C) in Mycobacterium phlei and at temperatures as high as 72 C in T. thermophilus. The tools and methods developed in this project will be generally useful for the expression of heterologous genes in Thermus. Key developments in the project have been the isolation of a Mycobacterium phlei culture capable of expressing the desulfurization operon at 52 C, development of plasmid and integrative expression vectors for Thermus thermophilus, and the development of a host-vector system based on the malate dehydrogenase gene that allows plasmids to be stably maintained in T. thermophilus and provides a convenient reporter gene for the accurate quantification of gene expression. Publications have been prepared regarding each of these topics; these preprints are included.

  18. Antimicrobial product and process

    DOE Patents [OSTI]

    Barrett, Karen B. (Idaho Falls, ID)

    1997-01-01T23:59:59.000Z

    A composition for controlling a plant disease caused by a plant pathogenic bacterium is disclosed. The composition comprises an activity for inhibiting the growth of the plant pathogenic bacterium and is extracted in an aqueous solvent from particles of malted cereal grain. The composition is used either in dry or wet form by application to plant parts, such as potato seed pieces, that are to be protected from the pathogenic bacteria.

  19. Antimicrobial product and process

    DOE Patents [OSTI]

    Barrett, K.B.

    1997-12-16T23:59:59.000Z

    A composition for controlling a plant disease caused by a plant pathogenic bacterium is disclosed. The composition comprises an activity for inhibiting the growth of the plant pathogenic bacterium and is extracted in an aqueous solvent from particles of malted cereal grain. The composition is used either in dry or wet form by application to plant parts, such as potato seed pieces, that are to be protected from the pathogenic bacteria. 6 figs.

  20. Nitrogen and Sulfur Requirements for Clostridium thermocellum and Caldicellulosiruptor bescii on Cellulosic Substrates in Minimal Nutrient Media

    SciTech Connect (OSTI)

    Kridelbaugh, Donna M [ORNL; Nelson, Josh C [ORNL; Engle, Nancy L [ORNL; Tschaplinski, Timothy J [ORNL; Graham, David E [ORNL

    2013-01-01T23:59:59.000Z

    Growth media for cellulolytic Clostridium thermocellum and Caldicellulosiruptor bescii bacteria usually contain excess nutrients that would increase costs for consolidated bioprocessing for biofuel production and create a waste stream with nitrogen, sulfur and phosphate. C. thermocellum was grown on crystalline cellulose with varying concentrations of nitrogen and sulfur compounds, and growth rate and alcohol production response curves were determined. Both bacteria assimilated sulfate in the presence of ascorbate reductant, increasing the ratio of oxidized to reduced fermentation products. From these results, a low ionic strength, defined minimal nutrient medium with decreased nitrogen, sulfur, phosphate and vitamin supplements was developed for the fermentation of cellobiose, cellulose and acid-pretreated Populus. Carbon and electron balance calculations indicate the unidentified residual fermentation products must include highly reduced molecules. Both bacterial populations were maintained in co-cultures with substrates containing xylan or hemicellulose in defined medium with sulfate and basal vitamin supplements.

  1. Development of a commercial enzymes system for lignocellulosic biomass saccharification

    SciTech Connect (OSTI)

    Kumar, Manoj

    2012-12-20T23:59:59.000Z

    DSM Innovation Inc., in its four year effort was able to evaluate and develop its in-house DSM fungal cellulolytic enzymes system to reach enzyme efficiency mandates set by DoE Biomass program MYPP goals. DSM enzyme cocktail is uniquely active at high temperature and acidic pH, offering many benefits and product differentiation in 2G bioethanol production. Under this project, strain and process development, ratio optimization of enzymes, protein and genetic engineering has led to multitudes of improvement in productivity and efficiency making development of a commercial enzyme system for lignocellulosic biomass saccharification viable. DSM is continuing further improvement by additional biodiversity screening, protein engineering and overexpression of enzymes to continue to further lower the cost of enzymes for saccharification of biomass.

  2. A study of overproduction and enhanced secretion of enzymes. Quarterly report

    SciTech Connect (OSTI)

    Dashek, W.V.

    1993-09-01T23:59:59.000Z

    Wood decay within forests, a significant renewable photosynthetic energy resource, is caused primarily by Basidiomycetous fungi, e.g., white rot fungi. These organisms possess the ability to degrade lignin, cellulose and hemicellulose, the main organic polymers of wood. In the case of the white rot fungi, e.g., Coriolus versicolor, the capacity results from the fungus` ability to elaborate extracellular cellulolytic and ligninolytic enzymes. With regard to the latter, at least one of the enzymes, polyphenol oxidase (PPO) appears within a defined growth medium. This proposal focuses on the over-production and enhanced secretion of PPO, cellulase and lignin peroxidase. There are two major sections to the proposal: (1) overproduction of lignocellulolytic enzymes by genetic engineering methodologies and hyper-production and enhanced secretion of these enzymes by biochemical/electro microscopical techniques and (2) the biochemical/electron microscopical method involves substrate induction and the time-dependent addition of respiration and PPO enzymes.

  3. Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis

    SciTech Connect (OSTI)

    Fernandez-Fueyo, Elena; Ruiz-Duenas, Francisco J.; Ferreira, Patrica; Floudas, Dimitrios; HIbbett, David S.; Canessa, Paulo; Larrondo, Luis F.; James, Tim Y.; Seelenfreund, Daniela; Lobos, Sergio; Polanco, Ruben; Tello, Mario; Honda, Yoichi; Watanabe, Takahito; Watanabe, Takashi; Ryu, Jae San; Kubicek, Christian P.; Schmoll, Monika; Gaskell, Jill; Hammel, Kenneth E.; St. John, Franz J.; Vanden Wymelenberg, Amber; Sabat, Grzegorz; Splinter BonDurant, Sandra; Syed, Khajamohiddin; Yadav, Jagjit S.; Doddapaneni, Harshavardhan; Subramanian, Venkataramanan; Lavin, Jose L.; Oguiza, Jose A.; Perez, Gumer; Pisabarro, Antonio G.; Ramirez, Lucia; Santoyo, Francisco; Master, Emma; Coutinho, Pedro M.; Henrissat, Bernard; Lombard, Vincent; Magnuson, Jon Karl; Kues, Ursula; Hori, Chiaki; Igarashi, Kiyohiko; Samejima, Masahiro; Held, Benjamin W.; Barry, Kerrie W.; LaButti, Kurt M.; Lapidus, Alla; Lindquist, Erika A.; Lucas, Susan M.; Riley, Robert; Salamov, Asaf A.; Hoffmeister, Dirk; Schwenk, Daniel; Hadar, Yitzhak; Yarden, Oded; de Vries, Ronald P.; Wiebenga, Ad; Stenlid, Jan; Eastwood, Daniel; Grigoriev, Igor V.; Berka, Randy M.; Blanchette, Robert A.; Kersten, Phil; Martinez, Angel T.; Vicuna, Rafael; Cullen, Dan

    2011-12-06T23:59:59.000Z

    Efficient lignin depolymerization is unique to the wood decay basidiomycetes, collectively referred to as white rot fungi. Phanerochaete chrysosporium simultaneously degrades lignin and cellulose, whereas the closely related species, Ceriporiopsis subvermispora, also depolymerizes lignin but may do so with relatively little cellulose degradation. To investigate the basis for selective ligninolysis, we conducted comparative genome analysis of C. subvermispora and P. chrysosporium. Genes encoding manganese peroxidase numbered 13 and five in C. subvermispora and P. chrysosporium, respectively. In addition, the C. subvermispora genome contains at least seven genes predicted to encode laccases, whereas the P. chrysosporium genome contains none. We also observed expansion of the number of C. subvermispora desaturase-encoding genes putatively involved in lipid metabolism. Microarray-based transcriptome analysis showed substantial up-regulation of several desaturase and MnP genes in wood-containing medium. MS identified MnP proteins in C. subvermispora culture filtrates, but none in P. chrysosporium cultures. These results support the importance of MnP and a lignin degradation mechanism whereby cleavage of the dominant nonphenolic structures is mediated by lipid peroxidation products. Two C. subvermispora genes were predicted to encode peroxidases structurally similar to P. chrysosporium lignin peroxidase and, following heterologous expression in Escherichia coli, the enzymes were shown to oxidize high redox potential substrates, but not Mn2. Apart from oxidative lignin degradation, we also examined cellulolytic and hemicellulolytic systems in both fungi. In summary, the C. subvermispora genetic inventory and expression patterns exhibit increased oxidoreductase potential and diminished cellulolytic capability relative to P. chrysosporium.

  4. Identification of a haloalkaliphilic and thermostable cellulase with improved ionic liquid tolerance

    SciTech Connect (OSTI)

    Zhang, Tao; Datta, Supratim; Eichler, Jerry; Ivanova, Natalia; Axen, Seth D.; Kerfeld, Cheryl A.; Chen, Feng; Kyrpides, Nikos; Hugenholtz, Philip; Cheng, Jan-Fang; Sale, Kenneth L.; Simmons, Blake; Rubin, Eddy

    2011-02-17T23:59:59.000Z

    Some ionic liquids (ILs) have been shown to be very effective solvents for biomass pretreatment. It is known that some ILs can have a strong inhibitory effect on fungal cellulases, making the digestion of cellulose inefficient in the presence of ILs. The identification of IL-tolerant enzymes that could be produced as a cellulase cocktail would reduce the costs and water use requirements of the IL pretreatment process. Due to their adaptation to high salinity environments, halophilic enzymes are hypothesized to be good candidates for screening and identifying IL-resistant cellulases. Using a genome-based approach, we have identified and characterized a halophilic cellulase (Hu-CBH1) from the halophilic archaeon, Halorhabdus utahensis. Hu-CBH1 is present in a gene cluster containing multiple putative cellulolytic enzymes. Sequence and theoretical structure analysis indicate that Hu-CBH1 is highly enriched with negatively charged acidic amino acids on the surface, which may form a solvation shell that may stabilize the enzyme, through interaction with salt ions and/or water molecules. Hu-CBH1 is a heat tolerant haloalkaliphilic cellulase and is active in salt concentrations up to 5 M NaCl. In high salt buffer, Hu-CBH1 can tolerate alkali (pH 11.5) conditions and, more importantly, is tolerant to high levels (20percent w/w) of ILs, including 1-allyl-3-methylimidazolium chloride ([Amim]Cl). Interestingly, the tolerances to heat, alkali and ILs are found to be salt-dependent, suggesting that the enzyme is stabilized by the presence of salt. Our results indicate that halophilic enzymes are good candidates for the screening of IL-tolerant cellulolytic enzymes.

  5. Comparison of different liquid anaerobic digestion effluents as inocula and nitrogen sources for solid-state batch anaerobic digestion of corn stover

    SciTech Connect (OSTI)

    Xu Fuqing; Shi Jian [Department of Food, Agricultural and Biological Engineering, Ohio State University, Ohio Agricultural Research and Development Center, 1680 Madison Ave., Wooster, OH 44691 (United States); Lv Wen; Yu Zhongtang [Department of Animal Sciences, Ohio State University, Columbus, OH 43210 (United States); Li Yebo, E-mail: li.851@osu.edu [Department of Food, Agricultural and Biological Engineering, Ohio State University, Ohio Agricultural Research and Development Center, 1680 Madison Ave., Wooster, OH 44691 (United States)

    2013-01-15T23:59:59.000Z

    Highlights: Black-Right-Pointing-Pointer Compared methane production of solid AD inoculated with different effluents. Black-Right-Pointing-Pointer Food waste effluent (FWE) had the largest population of acetoclastic methanogens. Black-Right-Pointing-Pointer Solid AD inoculated with FWE produced the highest methane yield at F/E ratio of 4. Black-Right-Pointing-Pointer Dairy waste effluent (DWE) was rich of cellulolytic and xylanolytic bacteria. Black-Right-Pointing-Pointer Solid AD inoculated with DWE produced the highest methane yield at F/E ratio of 2. - Abstract: Effluents from three liquid anaerobic digesters, fed with municipal sewage sludge, food waste, or dairy waste, were evaluated as inocula and nitrogen sources for solid-state batch anaerobic digestion of corn stover in mesophilic reactors. Three feedstock-to-effluent (F/E) ratios (i.e., 2, 4, and 6) were tested for each effluent. At an F/E ratio of 2, the reactor inoculated by dairy waste effluent achieved the highest methane yield of 238.5 L/kgVS{sub feed}, while at an F/E ratio of 4, the reactor inoculated by food waste effluent achieved the highest methane yield of 199.6 L/kgVS{sub feed}. The microbial population and chemical composition of the three effluents were substantially different. Food waste effluent had the largest population of acetoclastic methanogens, while dairy waste effluent had the largest populations of cellulolytic and xylanolytic bacteria. Dairy waste also had the highest C/N ratio of 8.5 and the highest alkalinity of 19.3 g CaCO{sub 3}/kg. The performance of solid-state batch anaerobic digestion reactors was closely related to the microbial status in the liquid anaerobic digestion effluents.

  6. High ethanol producing derivatives of Thermoanaerobacter ethanolicus

    DOE Patents [OSTI]

    Ljungdahl, Lars G. (Athens, GA); Carriera, Laura H. (Athens, GA)

    1983-01-01T23:59:59.000Z

    Derivatives of the newly discovered microorganism Thermoanaerobacter ethanolicus which under anaerobic and thermophilic conditions continuously ferment substrates such as starch, cellobiose, glucose, xylose and other sugars to produce recoverable amounts of ethanol solving the problem of fermentations yielding low concentrations of ethanol using the parent strain of the microorganism Thermoanaerobacter ethanolicus are disclosed. These new derivatives are ethanol tolerant up to 10% (v/v) ethanol during fermentation. The process includes the use of an aqueous fermentation medium, containing the substrate at a substrate concentration greater than 1% (w/v).

  7. Results an data on the growth of the microorganisms

    SciTech Connect (OSTI)

    Laurinavichius, K.S.

    1995-10-09T23:59:59.000Z

    The study of biocorrosion of aluminum and its alloy was performed under conditions of continuous fermentation of thermophilic anaerobic microorganisms of different groups. This allowed us to examine the effect of various types of metabolic reactions of reduction-oxidation proceeding at different pH and temperatures under highly reduced conditions on aluminum corrosion. Besides, the experiments were performed where the part of the standard sample was exposed under strictly anaerobic conditions with an active microbiological process, and the second half was exposed under aerobic conditions. Thus the sample was exposed in gradient of oxidized-reduced conditions.

  8. Combination biological and microwave treatments of used rubber products

    DOE Patents [OSTI]

    Fliermans, Carl B. (Augusta, GA); Wicks, George G. (Aiken, SC)

    2002-01-01T23:59:59.000Z

    A process and resulting product is provided in which a vulcanized solid particulate, such as vulcanized crumb rubber, has select chemical bonds altered by biotreatment with thermophillic microorganisms selected from natural isolates from hot sulfur springs. Following the biotreatment, microwave radiation is used to further treat the surface and to treat the bulk interior of the crumb rubber. The resulting combined treatments render the treated crumb rubber more suitable for use in new rubber formulations. As a result, larger loading levels and sizes of the treated crumb rubber can be used in new rubber mixtures and good properties obtained from the new recycled products.

  9. Production of extremophilic bacterial cellulase enzymes in aspergillus niger.

    SciTech Connect (OSTI)

    Gladden, John Michael

    2013-09-01T23:59:59.000Z

    Enzymes can be used to catalyze a myriad of chemical reactions and are a cornerstone in the biotechnology industry. Enzymes have a wide range of uses, ranging from medicine with the production of pharmaceuticals to energy were they are applied to biofuel production. However, it is difficult to produce large quantities of enzymes, especially if they are non-native to the production host. Fortunately, filamentous fungi, such as Aspergillus niger, are broadly used in industry and show great potential for use a heterologous enzyme production hosts. Here, we present work outlining an effort to engineer A. niger to produce thermophilic bacterial cellulases relevant to lignocellulosic biofuel production.

  10. High ethanol producing derivatives of Thermoanaerobacter ethanolicus

    DOE Patents [OSTI]

    Ljungdahl, L.G.; Carriera, L.H.

    1983-05-24T23:59:59.000Z

    Derivatives of the newly discovered microorganism Thermoanaerobacter ethanolicus which under anaerobic and thermophilic conditions continuously ferment substrates such as starch, cellobiose, glucose, xylose and other sugars to produce recoverable amounts of ethanol solving the problem of fermentations yielding low concentrations of ethanol using the parent strain of the microorganism Thermoanaerobacter ethanolicus are disclosed. These new derivatives are ethanol tolerant up to 10% (v/v) ethanol during fermentation. The process includes the use of an aqueous fermentation medium, containing the substrate at a substrate concentration greater than 1% (w/v).

  11. Cellulase producing microorganism ATCC 55702

    DOE Patents [OSTI]

    Dees, H. Craig (Lenoir City, TN)

    1997-01-01T23:59:59.000Z

    Bacteria which produce large amounts of cellulase--containing cell-free fermentate have been identified. The original bacterium (ATCC 55703) was genetically altered using nitrosoguanidine (MNNG) treatment to produce the enhanced cellulase producing bacterium (ATCC 55702), which was identified through replicate plating. ATCC 55702 has improved characteristics and qualifies for the degradation of cellulosic waste materials for fuel production, food processing, textile processing, and other industrial applications. ATCC 55702 is an improved bacterial host for genetic manipulations using recombinant DNA techniques, and is less likely to destroy genetic manipulations using standard mutagenesis techniques.

  12. Cellulase producing microorganism ATCC 55702

    DOE Patents [OSTI]

    Dees, H.C.

    1997-12-30T23:59:59.000Z

    Bacteria which produce large amounts of cellulase--containing cell-free fermentate have been identified. The original bacterium (ATCC 55703) was genetically altered using nitrosoguanidine (MNNG) treatment to produce the enhanced cellulase producing bacterium (ATCC 55702), which was identified through replicate plating. ATCC 55702 has improved characteristics and qualifies for the degradation of cellulosic waste materials for fuel production, food processing, textile processing, and other industrial applications. ATCC 55702 is an improved bacterial host for genetic manipulations using recombinant DNA techniques, and is less likely to destroy genetic manipulations using standard mutagenesis techniques. 5 figs.

  13. Detergent composition comprising a cellulase containing cell-free fermentate produced from microorganism ATCC 55702 or mutant thereof

    DOE Patents [OSTI]

    Dees, H.C.

    1998-07-14T23:59:59.000Z

    Bacteria which produce large amounts of a cellulase-containing cell-free fermentate have been identified. The original bacterium (ATCC 55703) was genetically altered using nitrosoguanidine (MNNG) treatment to produce the enhanced cellulase producing bacterium (ATCC 55702), which was identified through replicate plating. ATCC 55702 has improved characteristics and qualities for the degradation of cellulosic waste materials for fuel production, food processing, textile processing, and other industrial applications. ATCC 55702 is an improved bacterial host for genetic manipulations using recombinant DNA techniques, and is less likely to destroy genetic manipulations using standard mutagenesis techniques. 5 figs.

  14. Method of producing a cellulase-containing cell-free fermentate produced from microorganism ATCC 55702

    DOE Patents [OSTI]

    Dees, H.C.

    1998-05-26T23:59:59.000Z

    Bacteria which produce large amounts of cellulose-containing cell-free fermentate have been identified. The original bacterium (ATCC 55703) was genetically altered using nitrosoguanidine (MNNG) treatment to produce the enhanced cellulase producing bacterium (ATCC 55702), which was identified through replicate plating. ATCC 55702 has improved characteristics and qualities for the degradation of cellulosic waste materials for fuel production, food processing, textile processing, and other industrial applications. ATCC 55702 is an improved bacterial host for genetic manipulations using recombinant DNA techniques, and is less likely to destroy genetic manipulations using standard mutagenesis techniques. 5 figs.

  15. Cellulase-containing cell-free fermentate produced from microorganism ATCC 55702

    DOE Patents [OSTI]

    Dees, H.C.

    1997-12-16T23:59:59.000Z

    Bacteria which produce large amounts of cellulase-containing cell-free fermentate have been identified. The original bacterium (ATCC 55703) was genetically altered using nitrosoguanidine (MNNG) treatment to produce the enhanced cellulase producing bacterium (ATCC 55702), which was identified through replicate plating. ATCC 55702 has improved characteristics and qualities for the degradation of cellulosic waste materials for fuel production, food processing, textile processing, and other industrial applications. ATCC 55702 is an improved bacterial host for genetic manipulations using recombinant DNA techniques, and is less likely to destroy genetic manipulations using standard mutagenesis techniques. 5 figs.

  16. Cellulase-containing cell-free fermentate produced from microorganism ATCC 55702

    DOE Patents [OSTI]

    Dees, H. Craig (Lenoir City, TN)

    1997-12-16T23:59:59.000Z

    Bacteria which produce large amounts of cellulase-containing cell-free fermentate have been identified. The original bacterium (ATCC 55703) was genetically altered using nitrosoguanidine (MNNG) treatment to produce the enhanced cellulase producing bacterium (ATCC 55702), which was identified through replicate plating. ATCC 55702 has improved characteristics and qualities for the degradation of cellulosic waste materials for fuel production, food processing, textile processing, and other industrial applications. ATCC 55702 is an improved bacterial host for genetic manipulations using recombinant DNA techniques, and is less likely to destroy genetic manipulations using standard mutagenesis techniques.

  17. Detergent composition comprising a cellulase containing cell-free fermentate produced from microorganism ATCC 55702 or mutant thereof

    DOE Patents [OSTI]

    Dees, H. Craig (Lenoir City, TN)

    1998-01-01T23:59:59.000Z

    Bacteria which produce large amounts of a cellulase-containing cell-free fermentate have been identified. The original bacterium (ATCC 55703) was genetically altered using nitrosoguanidine (MNNG) treatment to produce the enhanced cellulase producing bacterium (ATCC 55702), which was identified through replicate plating. ATCC 55702 has improved characteristics and qualities for the degradation of cellulosic waste materials for fuel production, food processing, textile processing, and other industrial applications. ATCC 55702 is an improved bacterial host for genetic manipulations using recombinant DNA techniques, and is less likely to destroy genetic manipulations using standard mutagenesis techniques.

  18. Method of producing a cellulase-containing cell-free fermentate produced from microorganism ATCC 55702

    DOE Patents [OSTI]

    Dees, H. Craig (Lenoir City, TN)

    1998-01-01T23:59:59.000Z

    Bacteria which produce large amounts of cellulose-containing cell-free fermentate have been identified. The original bacterium (ATCC 55703) was genetically altered using nitrosoguanidine (MNNG) treatment to produce the enhanced cellulase producing bacterium (ATCC 55702), which was identified through replicate plating. ATCC 55702 has improved characteristics and qualities for the degradation of cellulosic waste materials for fuel production, food processing, textile processing, and other industrial applications. ATCC 55702 is an improved bacterial host for genetic manipulations using recombinant DNA techniques, and is less likely to destroy genetic manipulations using standard mutagenesis techniques.

  19. Thermal ecology of Naegleria fowleri from a power plant cooling reservoir

    SciTech Connect (OSTI)

    Huizinga, H.W. (Illinois State Univ., Normal (USA)); McLaughlin, G.L. (Univ. of Illinois, Urbana (USA))

    1990-07-01T23:59:59.000Z

    The pathogenic, free-living amoeba Naegleria fowleri is the causative agent of human primary amebic meningoencephalitis. N. fowleri has been isolated from thermally elevated aquatic environments worldwide, but temperature factors associated with occurrence of the amoeba remain undefined. In this study, a newly created cooling reservoir (Clinton Lake, Illinois) was surveyed for Naegleria spp. before and after thermal additions from a nuclear power plant. Water and sediment samples were collected from heated and unheated arms of the reservoir and analyzed for the presence of thermophilic Naegleria spp. and pathogenic N. fowleri. Amoebae were identified by morphology, in vitro cultivation, temperature tolerance, mouse pathogenicity assay, and DNA restriction fragment length analysis. N. fowleri was isolated from the thermally elevated arm but not from the ambient-temperature arm of the reservoir. The probability of isolating thermophilic Naegleria and pathogenic N. fowleri increased significantly with temperature. Repetitive DNA restriction fragment profiles of the N. fowleri Clinton Lake isolates and a known N. fowleri strain of human origin were homogeneous.

  20. Probing the mechanism of rubredoxin thermal unfolding in the absence of salt bridges by temperature jump experiments

    SciTech Connect (OSTI)

    Henriques, Barbara J. [Instituto Tecnologia Quimica e Biologica, Universidade Nova de Lisboa, Oeiras (Portugal); Saraiva, Ligia M. [Instituto Tecnologia Quimica e Biologica, Universidade Nova de Lisboa, Oeiras (Portugal); Gomes, Claudio M. [Instituto Tecnologia Quimica e Biologica, Universidade Nova de Lisboa, Oeiras (Portugal)]. E-mail: gomes@itqb.unl.pt

    2005-08-05T23:59:59.000Z

    Rubredoxins are the simplest type of iron-sulphur proteins and in recent years they have been used as model systems in protein folding and stability studies, especially the proteins from thermophilic sources. Here, we report our studies on the rubredoxin from the hyperthermophile Methanococcus jannaschii (T {sub opt} = 85 deg C), which was investigated in respect to its thermal unfolding kinetics by temperature jump experiments. Different spectroscopic probes were used to monitor distinct structural protein features during the thermal transition: the integrity of the iron-sulphur centre was monitored by visible absorption spectroscopy, whereas tertiary structure was followed by intrinsic tryptophan fluorescence and exposure of protein hydrophobic patches was sensed by 1-anilinonaphthalene-8-sulphonate fluorescence. The studies were performed at acidic pH conditions in which any stabilising contributions from salt bridges are annulled due to protonation of protein side chain groups. In these conditions, M. jannaschii rubredoxin assumes a native-like, albeit more flexible and open conformation, as indicated by a red shift in the tryptophan emission maximum and 1-anilinonaphthalene-8-sulphonate binding. Temperature jumps were monitored by the three distinct techniques and showed that the protein undergoes thermal denaturation via a simple two step mechanism, as loss of tertiary structure, hydrophobic collapse, and disintegration of the iron-sulphur centre are concomitant processes. The proposed mechanism is framed with the multiphasic one proposed for Pyrococcus furiosus rubredoxin, showing that a common thermal unfolding mechanism is not observed between these two closely related thermophilic rubredoxins.

  1. Determining the crystal structure of SseB, a product of the Salmonella Pathogenicity Island II Type III Secretion System of Salmonella typhimurium

    E-Print Network [OSTI]

    Patel, Bhavini Narendrakumar

    2008-03-20T23:59:59.000Z

    Salmonella typhimurium is a bacterium that causes many food-borne illnesses such as gastrointestinal infections, diarrhea, and abdominal cramps. It affects 700,000 to 3.8 million people each year. The SseB protein, a part of the Salmonella...

  2. Penn State University Pilot-scale Tests of Fixed Bed

    E-Print Network [OSTI]

    Penn State University Pilot-scale Tests of Fixed Bed Reactors for Perchlorate Degradation: Plastic for inoculation #12;Penn State University PSU-O4 Process Patent: Perchlorate degradation in a fixed bed bioreactor in a packed bed reactor · Reactor performance compared with other studies · Stability of the bacterium used

  3. normally occur in the environment. How it recognizes this compound was the subject

    E-Print Network [OSTI]

    Sakaluk, Scott

    and sodium, then broke down a solid intermediate of the reaction by heating. This generated a fused pack bacterium, Synechococcus elongatus. This shuttles bicarbonate through its cell membrane by means.365 (2008) Sodium; ethanol; heat; sound waves: those easy-to-come-by, cheap ingredients are all that John

  4. Molecular Biology of the Cell Vol. 16, 48524866, October 2005

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    Molecular Biology of the Cell Vol. 16, 4852­4866, October 2005 Helicobacter pylori VacA Cytotoxin cytotoxin VacA is a major virulence factor of Helicobacter pylori, a bacterium responsible for gastrodu-independent mechanism, and routed to the degradative compartment. INTRODUCTION Gastric infection by Helicobacter pylori

  5. APMIS 114: 12730, 2006 C 2006 The Authors Printed in Denmark . All rights reserved

    E-Print Network [OSTI]

    Gelb, Michael

    A2 against Helicobacter pylori in vitro HEIKKI T. HUHTINEN,1 JUHA O. GRO¨ NROOS,2 JUHA M. GRO¨ NROOS Helicobacter pylori in vitro. APMIS 2006;114:127­30. Group IIA phospholipase A2 (PLA2-IIA) is an enzyme which properties of recombinant human PLA2-IIA and PLA2-XIIA against Helicobacter pylori, a Gram-negative bacterium

  6. RESEARCH Open Access Helicobacter pylori interferes with an embryonic

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    RESEARCH Open Access Helicobacter pylori interferes with an embryonic stem cell micro RNA cluster. In this work we report that Helicobacter pylori, a human stomach-colonizing bacterium responsible for severe defense mechanism against bacterial infections. Keywords: microRNAs, cell cycle, Helicobacter pylori

  7. JOURNAL OF BACTERIOLOGY, Dec. 2010, p. 61266135 Vol. 192, No. 23 0021-9193/10/$12.00 doi:10.1128/JB.01081-10

    E-Print Network [OSTI]

    Bordenstein, Seth

    Evolution of the Helicobacter pylori Vacuolating Toxin Gene vacA Kelly A. Gangwer,1,2 Carrie L. Shaffer,1, Nashville, Tennessee7 Received 10 September 2010/Accepted 15 September 2010 Helicobacter pylori separately from the core genome. Helicobacter pylori is a Gram-negative bacterium that persis- tently

  8. Expression of the Helicobacter pylori adhesin SabA is controlled via phase variation and the ArsRS

    E-Print Network [OSTI]

    Forsyth, Mark

    Expression of the Helicobacter pylori adhesin SabA is controlled via phase variation and the Ars epithelium, are essential for persistent colonization of the human stomach by Helicobacter pylori. INTRODUCTION Helicobacter pylori is a Gram-negative bacterium that infects more than half the world

  9. NOTTINGHAM TRENT UNIVERSITY -INVESTING IN EXCELLENCE VICE-CHANCELLOR'S PHD SCHOLARSHIP SCHEME 2014 & SCHOOL PHD SCHOLARSHIPS

    E-Print Network [OSTI]

    Evans, Paul

    genomic analysis of Helicobacter pylori within-host microevolution. PROJECT LEAD: Dr Jody Winter Helicobacter pylori is a bacterium that infects the stomachs of around 50% of the world's population. Infection of Helicobacter pylori in the diseased stomach. Candidates should have a UK 2:1/1st class Batchelor's degree (or

  10. Distinguishing human ethnic groups by means of sequences from Helicobacter pylori

    E-Print Network [OSTI]

    Wirth, Thierry

    Distinguishing human ethnic groups by means of sequences from Helicobacter pylori: Lessons from from Helicobacter pylori, a bacterium that colonizes the stomachs of most humans and is usually in this respect to classical human genetic markers. H. pylori from Buddhists and Muslims, the two major ethnic

  11. "Red Sore Disease"in Game Fish1 Peggy Reed and Ruth Francis-Floyd2

    E-Print Network [OSTI]

    Watson, Craig A.

    VM85 "Red Sore Disease"in Game Fish1 Peggy Reed and Ruth Francis-Floyd2 1. This document is VM85 fish is generically referred to as "red sore disease." This problem usually occurs in the spring on their fish. Typically, "red sore disease" is caused by two organisms, Aeromonas hydrophila , a bacterium

  12. Like that circuit maze, Newman's career path--set in motion by her

    E-Print Network [OSTI]

    fruitful." One particular environment that currently holds Newman's attention is the human lung. She fibrosis (CF), a chronic lung disease. It also is an im- portant hospital-acquired bacterium for people who are explor- ing how these bacteria manage to thrive in the lungs of CF patients. "So far, it seems that one

  13. Radiation-resistant microorganism

    DOE Patents [OSTI]

    Fliermans, Carl B.

    2010-06-15T23:59:59.000Z

    An isolated and purified bacterium is provided which was isolated from a high-level radioactive waste site of mixed waste. The isolate has the ability to degrade a wide variety of organic contaminants while demonstrating high tolerance to ionizing radiation. The organism is uniquely suited to bioremediation of a variety or organic contaminants while in the presence of ionizing radiation.

  14. IOP PUBLISHING JOURNAL OF PHYSICS: CONDENSED MATTER J. Phys.: Condens. Matter 23 (2011) 234101 (11pp) doi:10.1088/0953-8984/23/23/234101

    E-Print Network [OSTI]

    Nori, Franco

    2011-01-01T23:59:59.000Z

    -loop mechanism of PMF generation, taking place in the nitrate respiratory chain of the E. coli bacterium that both models can be described by the same approach, which can be significantly simplified if the system, temperature, and other system parameters. We show that the quantum yield in our models can be up to 100

  15. Redfield (PIN 28084) Regulation of CRP-S promoters in H. influenzae and E. coli $169,310 Introduction

    E-Print Network [OSTI]

    Redfield, Rosemary J. "Rosie"

    . Background The following sections first introduce H. influenzae and its natural competence system. I understanding of both this novel regulatory mechanism and the signals that induce DNA uptake in both organisms gram-negative bacterium is usually commensal in the human upper respiratory tract but is also a common

  16. Lactobacillus kimchiensis sp. nov., isolated from a fermented food

    E-Print Network [OSTI]

    Bae, Jin-Woo

    & Kim, 2010) and organic acids (e.g., lactic, acetic, succinic and propionic acids) duringLactobacillus kimchiensis sp. nov., isolated from a fermented food Jandi Kim,3 Joon Yong Kim,3 Min bacterium was isolated from a traditional fermented food, kimchi. The morphology, physiology, biochemical

  17. Alien invasion Getting to the root of radiation

    E-Print Network [OSTI]

    Dawson, Jeff W.

    's tsunami, as well as ongoing threats to global energy supplies and national security, has been felt around with a bacterium they hope will produce enough electrical current to power city generators. If their research troublesome alien plants in North America, among other faculty research stories. As usual, you will also hear

  18. SGM Special Moving folded proteins across the bacterial cell

    E-Print Network [OSTI]

    Palmer, Tracy

    -containing proteins are essential for most types of bacterial respiratory and photo- synthetic energy metabolism by the transmembrane proton electrochemical gradient. The TatA protein probably forms the transport channel while metabolism in most environments depends upon the bacterium being able to produce cofactor-containing pro

  19. Microfluidic capture and release of bacteria in a conical nanopore array Peng Guo,ab

    E-Print Network [OSTI]

    Zare, Richard N.

    Microfluidic capture and release of bacteria in a conical nanopore array Peng Guo,ab Eric W. Hall a microfluidic device. As an example, we demonstrate that cyanobacteria can be captured, one bacterium per pore, in a conical nanoporous membrane (CNM) integrated into a microfluidic chip. This study, to our knowledge

  20. Antimicrobial protein protects grapevines from pathogen

    E-Print Network [OSTI]

    it and transmits widely to the grapevines. The key to the project's success is the fact that early in an X it is infected, much as the body's immune system naturally recognizes a pathogen and takes action to defeat it of the Gram- negative bacterium, Xf," said Gupta, thus allowing the plant to fight back the infection. Sap

  1. Methods for targetted mutagenesis in gram-positive bacteria

    DOE Patents [OSTI]

    Yang, Yunfeng

    2014-05-27T23:59:59.000Z

    The present invention provides a method of targeted mutagenesis in Gram-positive bacteria. In particular, the present invention provides a method that effectively integrates a suicide integrative vector into a target gene in the chromosome of a Gram-positive bacterium, resulting in inactivation of the target gene.

  2. PUBLISHED ONLINE: 7 JULY 2013 | DOI: 10.1038/NPHYS2676 Bacteria can exploit a flagellar buckling instability

    E-Print Network [OSTI]

    Loss, Daniel

    in the locomotion of bacteria with multiple flagella (peritrichous), such as Escherichia coli, which bundles its a single flagellum (monotrichous), including 90% of motile marine bacteria3 , and how they reorient has long remained unclear. Only recently has the monotrichous marine bacterium Vibrio alginolyticus been

  3. Rapid chemotactic response enables marine bacteria to exploit ephemeral microscale nutrient patches

    E-Print Network [OSTI]

    Entekhabi, Dara

    chemotaxis model Escherichia coli, leading to twice the nutrient exposure. We demonstrate that such rapidRapid chemotactic response enables marine bacteria to exploit ephemeral microscale nutrient patches mechanisms dissipate them. Here we show that the rapid chemo- tactic response of the marine bacterium

  4. JOURNAL OF BACTERIOLOGY, Mar. 2007, p. 25712574 Vol. 189, No. 6 0021-9193/07/$08.00 0 doi:10.1128/JB.01761-06

    E-Print Network [OSTI]

    McFall-Ngai, Margaret

    of the family Enterobac- teriaceae (e.g., Escherichia coli), the activity of AC becomes enhanced by its assembly in E. coli (25). Insights into the control of c-di-GMP production and its targets have come from our investigations of motility in the marine bac- terium Vibrio fischeri. This bacterium, found

  5. JOURNAL OF BACTERIOLOGY, 0021-9193/98/$04.00 0

    E-Print Network [OSTI]

    Ruby, Edward G.

    in Escherichia coli by the alternative sigma factor encoded by rpoS. Further, the level of expression of the cloned katA gene in an E. coli rpoS mutant is much lower than in wild-type E. coli. Catalase activity. fischeri and its squid host. The luminous marine bacterium Vibrio fischeri occupies a unique niche

  6. JOURNAL OF BACTERIOLOGY, Jan. 1996, p. 209215 Vol. 178, No. 1 0021-9193/96/$04.00 0

    E-Print Network [OSTI]

    McFall-Ngai, Margaret

    but not secreted in E. coli; however, it is secreted from a heterologous marine Vibrio species. We have named amino acid sequence of an ADP-ribosyltransferase secreted from the marine bacterium Vibrio fischeri (V that was used to clone a cross-hybridizing DNA fragment from V. fischeri genomic DNA. Recombinant Escherichia

  7. Proc. Natl. Acad. Sci. USA Vol. 94, pp. 1443314437, December 1997

    E-Print Network [OSTI]

    Croquette, Vincent

    (protons) or, in alkalophilic or marine bacteria, Na . In Escherichia coli, the motor can rotate in either ABSTRACT A cell of the bacterium Escherichia coli was tethered covalently to a glass coverslip by a single. coli rotate at over 100 Hz and are difficult to observe directly, tethered cells rotate at 10 Hz

  8. Cryobiology 52 (2006) 417429 www.elsevier.com/locate/ycryo

    E-Print Network [OSTI]

    Swanson, Brian D.

    2006-01-01T23:59:59.000Z

    was detected in the killed controls for strain 34H (or in Escherichia coli controls), which included TCA to increasingly lower temperatures, so far to ¡20 °C. To date, the metabolic activities of marine psychrophilic fractionated biochemically) by the marine psychrophilic bacterium Colwellia psychrerythraea strain 34H over

  9. JOURNAL OF BACTERIOLOGY, 0021-9193/00/$04.00 0

    E-Print Network [OSTI]

    Ruby, Edward G.

    of the Escherichia coli gene for 3,4-dihydroxy-2- butanone 4-phosphate synthase, a key enzyme for riboflavin* Center of Marine Biotechnology, University of Maryland Biotechnology Institute, Baltimore, Maryland 21202R genes were first identified in the marine bioluminescent bacterium Vibrio fischeri (20, 23). At present

  10. Production of amino acids using auxotrophic mutants of methylotrophic bacillus

    DOE Patents [OSTI]

    Hanson, Richard S. (Wayzata, MN); Flickinger, Michael C. (St. Paul, MN); Schendel, Frederick J. (Falcon Heights, MN); Guettler, Michael V. (Waconia, MN)

    2001-07-17T23:59:59.000Z

    A method of producing amino acids by culturing an amino acid auxotroph of a biologically pure strain of a type I methylotrophic bacterium of the genus Bacillus which exhibits sustained growth at 50.degree. C. using methanol as a carbon and energy source and requiring vitamin B.sub.12 and biotin is provided.

  11. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Dec. 2008, p. 73487355 Vol. 74, No. 23 0099-2240/08/$08.00 0 doi:10.1128/AEM.01639-08

    E-Print Network [OSTI]

    . Comparison of Electrode Reduction Activities of Geobacter sulfurreducens and an Enriched Consortium in an Air, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan5 Received 16 July 2008/Accepted 29 September 2008 An electricity-generating bacterium, Geobacter sulfurreducens PCA, was inoculated into a single-chamber, air-cathode microbial fuel

  12. THE GREENTECH MEDIA WEEKLY NEWSLETTER

    E-Print Network [OSTI]

    Lovley, Derek

    :56 PM Electricity-Generating Geobacter Bacteria Made Stronger Geobacter. It's a bacterium that turns waste into electricity in its naturally oxygen-free environment ­ and if you stress it out, it adapts of Massachusetts at Amherst into Geobacter's potential to make microbial fuel cells ­ fuel cells made from living

  13. APPLIED MICROBIAL AND CELL PHYSIOLOGY Enhanced electrode-reducing rate during the enrichment

    E-Print Network [OSTI]

    # Springer-Verlag 2012 Abstract The improvement in electricity generation during the enrichment process related to the known exoelec- trogenic bacterium, Geobacter sulfurreducens, showed an increase showed the increase of Geobacter-like phylotypes from 53% to 72%. These results suggest

  14. Fuel-producing Geobacter receives support from new research May 3rd, 2010 in Technology / Energy

    E-Print Network [OSTI]

    Lovley, Derek

    genetically modified the Geobacter bacterium so that it acts like a reverse fuel cell, using electricity electricity, Geobacter could be used as a microbial fuel cell, converting organic waste matter - includingFuel-producing Geobacter receives support from new research grant May 3rd, 2010 in Technology

  15. April 30, 2010 Getting the Bugs Out, a New Approach to Renewable

    E-Print Network [OSTI]

    Lovley, Derek

    . Geobacter and Shewanella are uniquely constructed, in that they generate electricity. The bacteria make long of ClimateWire The Geobacter bacterium could be the biofuel-generating machine of the future, producing of funding. The Geobacter project is part of a new wave of biofuel generation experiments that feed

  16. Received 10 May 2013 | Accepted 10 Oct 2013 | Published 8 Nov 2013 Probing single-to multi-cell level charge transport

    E-Print Network [OSTI]

    -cell level charge transport in Geobacter sulfurreducens DL-1 Xiaocheng Jiang1,*, Jinsong Hu2,*, Emily R energy into electricity, represent a potentially sustainable energy technology for the future. Here we report the single-bacterium level current measurements of Geobacter sulfurreducens DL-1 to elucidate

  17. Republican photo: David Molnar University of Massachusetts graduate

    E-Print Network [OSTI]

    Lovley, Derek

    of University of Massachusetts graduate and undergraduate students is hoping a hungry, electricity the physics and microbiology departments have been looking at the electrical properties of the power-producing bacterium genus Geobacter for the last few years. While physics is often theoretical, Malvankar, a recipient

  18. Electric germs Source: scenta Rate this item

    E-Print Network [OSTI]

    Lovley, Derek

    Electric germs Source: scenta Rate this item People in remote areas could benefit from fuel cells that contain bacteria that grows prolifically on the graphite anodes of fuel cells and can conduct electricity that isolating a bacterium generated pow er in fuel cells efficiently. Geobacter sulfurreducens is bacteria

  19. Biosensors and Bioelectronics 25 (2009) 105111 Contents lists available at ScienceDirect

    E-Print Network [OSTI]

    June 2009 Available online 10 June 2009 Keywords: Electricity generation Photosynthetic bacteria, and a dissimilatory iron-reducing bacterium, Geobacter sulfurreducens. Pure culture tests confirmed that PNS to light (Cao et al., 2008; He et al., 2009; Malik et al., 2009; Xing et al., 2008b). Direct electricity

  20. Guardian Unlimited | The Guardian | Scientists see big role for uranium clean-up bug Sign in Register

    E-Print Network [OSTI]

    Lovley, Derek

    The Guardian Scientists have sequenced the DNA of a bacterium which can help to remove uranium fromGuardian Unlimited | The Guardian | Scientists see big role for uranium clean-up bug Sign big role for uranium clean-up bug Alok Jha, science correspondent Friday December 12, 2003

  1. AQUACULTURE EXTENSION Illinois -Indiana Sea Grant Program

    E-Print Network [OSTI]

    by this bacterium primarily affects freshwater fish such as cattfish, several species of bass, and many species and Treatment of "Aeromonas hydrophila" Infection of Fish LaDon Swann Illinois-Indiana Sea Grant Program Purdue University Introduction Aeromonas hydrophila causes disease in fish known as "Motile Aeromonas Septicemia

  2. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 0099-2240/98/$04.00 0

    E-Print Network [OSTI]

    Tebo, Brad

    but kinet- ically slow process under most natural conditions. In the envi- ronment, however, Mn(II). In this bacterium, it is the spores that catalyze Mn(II) and Co(II) oxidation (19, 29) under environmentallyAPPLIED AND ENVIRONMENTAL MICROBIOLOGY, 0099-2240/98/$04.00 0 Mar. 1998, p. 1123­1129 Vol. 64, No

  3. ORIGINAL RESEARCH ARTICLE published: 08 October 2014

    E-Print Network [OSTI]

    Paré, Paul W.

    Arabidopsis thaliana. Here we examined the effect of this beneficial soil bacterium on salt tolerance supplemented with 0, 50, 100, or 150 mM NaCl water into soil. Growth parameters, chlorophyll content+ contents were determined at the time of harvest. White clover plants grown in GB03-inoculated soil were

  4. Effects of Bt-corn decomposition on the composition of the soil meso-and macrofauna

    E-Print Network [OSTI]

    Richner, Heinz

    to the environment. At this point genetically modified corn, expressing Cry proteins of the soil bacterium Bacillus bags Soil invertebrates a b s t r a c t Genetically modified Bt-corn is able to fight main insect pests than 4%. All corn varieties were likewise used as food resource by decomposers, thus the Bt

  5. ENGI 4421 Probability and Statistics Faculty of Engineering and Applied Science

    E-Print Network [OSTI]

    George, Glyn

    L in this waste water and find the uncertainty in this estimate. 5. The lifetime in months X of an electronic the arrival of telephone calls, electronic messages, accidents in industry, customers in queuing models of a certain type of bacterium in a waste water sample. She puts a 0.5 mL sample of the waste water

  6. 1 | P a g e Chem 124H Organic Chemistry Case Study #2: "Overcoming Bacterial

    E-Print Network [OSTI]

    Reed, Christopher A.

    resistance worldwide: causes, challenges and responses" Nat. Med. 2004, 10, pS122. c) "MRSA" (wikipedia, http://en.wikipedia.org/wiki/Mrsa. The most notable resistant bacterium is Methicillin Resistant Staphylococcus Aureus (MRSA, "Superbug and sterilization are essential in hospitals to prevent the spread of MRSA and other resistant bacterial infections

  7. The prevalence of multidrug-resistant bacterial strains has substantially

    E-Print Network [OSTI]

    Nizet, Victor

    against methicillin-resistant Staphylococcus aureus (MRSA). S. aureus is the leading cause of many human infections, particularly those of the skin and soft tissues. Moreover, MRSA -- a variation of this bacterium MRSA. Such virulence-factor-based approaches offer a new direction for therapies targeting multidrug

  8. Radiation-resistant microorganism

    DOE Patents [OSTI]

    Fliermans, Carl B.

    2007-01-09T23:59:59.000Z

    An isolated and purified bacterium is provided which was isolated from a high-level radioactive waste site of mixed waste. The isolate has the ability to degrade a wide variety of organic contaminants while demonstrating high tolerance to ionizing radiation. The organism is uniquely suited to bioremediation of a variety or organic contaminants while in the presence of ionizing radiation.

  9. Aromatic hydrocarbon metabolism by Rhodococcus sp. I24 : computational, biochemical and transcriptional analysis

    E-Print Network [OSTI]

    Parker, Jefferson A. (Jefferson Alexander), 1974-

    2004-01-01T23:59:59.000Z

    Rhodococcus sp. 124 is a Gram-positive soil bacterium being developed for the manufacture of (-)cis-(1S,2R)-1-aminoindan-2-ol, a key precursor in the production of the HIV-1 protease inhibitor CrixivanTM, from the aromatic ...

  10. Bioremediation of nanomaterials

    DOE Patents [OSTI]

    Chen, Frank Fanqing; Keasling, Jay D; Tang, Yinjie J

    2013-05-14T23:59:59.000Z

    The present invention provides a method comprising the use of microorganisms for nanotoxicity study and bioremediation. In some embodiment, the microorganisms are bacterial organisms such as Gram negative bacteria, which are used as model organisms to study the nanotoxicity of the fullerene compounds: E. coli W3110, a human related enterobacterium and Shewanella oneidensis MR-1, an environmentally important bacterium with versatile metabolism.

  11. Characterization and Control of Biological Microrobots

    E-Print Network [OSTI]

    magnetic system is five orders-of-magnitude less than the propulsion force gener- ated by the flagellum proposed for propulsion: extracting energy from an ex- ternal magnetic field [4], or extracting energy from of Magnetotactic Bacterium (MTB) which can be considered as a biological microrobot. Magnetic dipole moment

  12. MasterProof The Proton-Driven Rotor of ATP Synthase: Ohmic Conductance (10 fS),

    E-Print Network [OSTI]

    Steinhoff, Heinz-Jürgen

    MasterProof The Proton-Driven Rotor of ATP Synthase: Ohmic Conductance (10 fS), and Absence ABSTRACT The membrane portion of F0F1-ATP synthase, F0, translocates protons by a rotary mechanism. Proton conduction by F0 was studied in chromatophores of the photosynthetic bacterium Rhodobacter capsulatus

  13. Man vs. Microbe After the Centers for Disease Control and Prevention (CDC) published a paper about a

    E-Print Network [OSTI]

    Chen, Keh-Hsun

    predispose them to infection. Vibrio on the Rise In the United States, raw oysters are the primary vehicle a mysterious bacterium that appeared to be the cause of several human deaths, graduate student Michael Poole occur at far higher rates than those caused by Vibrio, the fatality rates for Vibrio give one pause

  14. A long-term toxicology study on pigs fed a combined genetically modified (GM) soy and

    E-Print Network [OSTI]

    Porter, Warren P.

    of genetically modified (GM) crops have been approved to enter human food and animal feed since 1996, including released into fields in the USA in 1996 (USDA, 2011). The main traits in GM crops to date have been bacterium, Bacillus thuringiensis (ANZFA, NDb). Hence these crops are also called Bt crops. Of the GM crops

  15. Characterization and analysis of the molecular weight of lignin for biorefining studies

    SciTech Connect (OSTI)

    Tolbert, Allison [Georgia Institute of Technology, Atlanta] [Georgia Institute of Technology, Atlanta; Akinosho, Hannah [Georgia Institute of Technology, Atlanta] [Georgia Institute of Technology, Atlanta; Khunsupat, Taya Ratayakorn [ORNL] [ORNL; Naskar, Amit K [ORNL] [ORNL; Ragauskas, Arthur [Georgia Institute of Technology, Atlanta] [Georgia Institute of Technology, Atlanta

    2014-01-01T23:59:59.000Z

    The molecular weight of lignin is a fundamental property that infl uences the recalcitrance of biomass and the valorization of lignin. The determination of the molecular weight of lignin in native biomass is dependent on the bioresources used and the isolation and purifi cation procedures employed. The three most commonly employed isolation methods are milled wood lignin (MWL), cellulolytic enzyme lignin (CEL), and enzymatic mild acidolysis lignin (EMAL). Common characterization techniques for determining the molecular weight of lignin will be addressed, with an emphasis on gel permeation chromatography (GPC). This review also examines the mechanisms behind several biological, physical, and chemical pre-treatments and their impact on the molecular weight of lignin. The number average molecular weight (Mn), weight average molecular weight (Mw) and polydispersity index (D) all vary in magnitude depending on the biomass source, pre-treatment conditions, and isolation method. Additionally, there is a growing body of literature that supports changes in the molecular weight of lignin in response to genetic modifi cations in the lignin biosynthetic pathways. This review summarizes different procedures for obtaining the molecular weight of lignin that have been used in recent years and highlight future opportunities for applications of lignin.

  16. Complete genome sequence of Anabaena variabilis ATCC 29413

    SciTech Connect (OSTI)

    Thiel, Teresa [University of Missouri, St. Louis] [University of Missouri, St. Louis; Pratte, Brenda S. [University of Missouri, St. Louis] [University of Missouri, St. Louis; Zhong, Jinshun [University of Missouri, St. Louis] [University of Missouri, St. Louis; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL)] [Los Alamos National Laboratory (LANL); Copeland, A [U.S. Department of Energy, Joint Genome Institute] [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute] [U.S. Department of Energy, Joint Genome Institute; Han, Cliff [Los Alamos National Laboratory (LANL)] [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute] [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL] [ORNL; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute] [U.S. Department of Energy, Joint Genome Institute; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute] [U.S. Department of Energy, Joint Genome Institute

    2013-01-01T23:59:59.000Z

    Anabaena variabilis ATCC 29413 is a filamentous, heterocyst-forming cyanobacterium that has served as a model organism, with an extensive literature extending over 40 years. The strain has three distinct nitrogenases that function under different environmental conditions and is capable of photoautotrophic growth in the light and true heterotrophic growth in the dark using fructose as both carbon and energy source. While this strain was first isolated in 1964 in Mississippi and named Ana-baena flos-aquae MSU A-37, it clusters phylogenetically with cyanobacteria of the genus Nostoc. The strain is a moderate thermophile, growing well at approximately 40 C. Here we provide some additional characteristics of the strain, and an analysis of the complete genome sequence.

  17. Solvent Immersion Imprint Lithography

    SciTech Connect (OSTI)

    Vasdekis, Andreas E.; Wilkins, Michael J.; Grate, Jay W.; Kelly, Ryan T.; Konopka, Allan; Xantheas, Sotiris S.; Chang, M. T.

    2014-06-21T23:59:59.000Z

    The mechanism of polymer disolution was explored for polymer microsystem prototyping, including microfluidics and optofluidics. Polymer films are immersed in a solvent, imprinted and finally brought into contact with a non-modified surface to permanently bond. The underlying polymer-solvent interactions were experimentally and theoretically investigated, and enabled rapid polymer microsystem prototyping. During imprinting, small molecule integration in the molded surfaces was feasible, a principle applied to oxygen sensing. Polystyrene (PS) was employed for microbiological studies at extreme environmental conditions. The thermophile anaerobe Clostridium Thermocellum was grown in PS pore-scale micromodels, revealing a double mean generation lifetime than under ideal culture conditions. Microsystem prototyping through directed polymer dissolution is simple and accessible, while simultaneous patterning, bonding, and surface/volume functionalization are possible in less than one minute.

  18. In situ thermally enhanced biodegradation of petroleum fuel hydrocarbons and halogenated organic solvents

    DOE Patents [OSTI]

    Taylor, Robert T. (Livermore, CA); Jackson, Kenneth J. (San Leandro, CA); Duba, Alfred G. (Livermore, CA); Chen, Ching-I (Danville, CA)

    1998-01-01T23:59:59.000Z

    An in situ thermally enhanced microbial remediation strategy and a method for the biodegradation of toxic petroleum fuel hydrocarbon and halogenated organic solvent contaminants. The method utilizes nonpathogenic, thermophilic bacteria for the thermal biodegradation of toxic and carcinogenic contaminants, such as benzene, toluene, ethylbenzene and xylenes, from fuel leaks and the chlorinated ethenes, such as trichloroethylene, chlorinated ethanes, such as 1,1,1-trichloroethane, and chlorinated methanes, such as chloroform, from past solvent cleaning practices. The method relies on and takes advantage of the pre-existing heated conditions and the array of delivery/recovery wells that are created and in place following primary subsurface contaminant volatilization efforts via thermal approaches, such as dynamic underground steam-electrical heating.

  19. In situ thermally enhanced biodegradation of petroleum fuel hydrocarbons and halogenated organic solvents

    DOE Patents [OSTI]

    Taylor, R.T.; Jackson, K.J.; Duba, A.G.; Chen, C.I.

    1998-05-19T23:59:59.000Z

    An in situ thermally enhanced microbial remediation strategy and a method for the biodegradation of toxic petroleum fuel hydrocarbon and halogenated organic solvent contaminants are described. The method utilizes nonpathogenic, thermophilic bacteria for the thermal biodegradation of toxic and carcinogenic contaminants, such as benzene, toluene, ethylbenzene and xylenes, from fuel leaks and the chlorinated ethenes, such as trichloroethylene, chlorinated ethanes, such as 1,1,1-trichloroethane, and chlorinated methanes, such as chloroform, from past solvent cleaning practices. The method relies on and takes advantage of the pre-existing heated conditions and the array of delivery/recovery wells that are created and in place following primary subsurface contaminant volatilization efforts via thermal approaches, such as dynamic underground steam-electrical heating. 21 figs.

  20. Crystallization and preliminary X-ray diffraction studies of tetrameric malate dehydrogenase from the novel Antarctic psychrophile Flavobacterium frigidimaris KUC-1

    SciTech Connect (OSTI)

    Fujii, Tomomi [Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011 (Japan); Oikawa, Tadao; Muraoka, Ikuo [Department of Life Science and Biotechnology, Faculty of Chemistry, Materials and Bioengineering, Kansai University, Suita, Osaka 564-8680 (Japan); Soda, Kenji [Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011 (Japan); Department of Life Science and Biotechnology, Faculty of Chemistry, Materials and Bioengineering, Kansai University, Suita, Osaka 564-8680 (Japan); Hata, Yasuo, E-mail: hata@scl.kyoto-u.ac.jp [Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011 (Japan)

    2007-11-01T23:59:59.000Z

    A psychrophilic malate dehydrogenase from the novel Antarctic bacterium F. frigidimaris KUC-1 was crystallized using the hanging-drop vapour-diffusion method. The crystals contained one tetrameric molecule per asymmetric unit. The best crystal diffracted to 1.8 Å resolution. Flavobacterium frigidimaris KUC-1 is a novel psychrotolerant bacterium isolated from Antarctic seawater. Malate dehydrogenase (MDH) is an essential metabolic enzyme in the citric acid cycle and has been cloned, overexpressed and purified from F. frigidimaris KUC-1. In contrast to the already known dimeric form of MDH from the psychrophile Aquaspirillium arcticum, F. frigidimaris MDH exists as a tetramer. It was crystallized at 288 K by the hanging-drop vapour-diffusion method using ammonium sulfate as the precipitating agent. The crystal diffracted to a maximum resolution of 1.80 Å. It contains one tetrameric molecule in the asymmetric unit.

  1. Development of a Proteoliposome Model to Probe Transmembrane Electron-Transfer Reactions

    SciTech Connect (OSTI)

    White, Gaye F.; Shi, Zhi; Shi, Liang; Dohnalkova, Alice; Fredrickson, Jim K.; Zachara, John M.; Butt, Julea N.; Richardson, David J.; Clarke, Thomas

    2012-12-01T23:59:59.000Z

    The mineral respiring bacterium Shewanella oneidensis uses a protein complex, MtrCAB, composed of two decaheme cytochromes brought together inside a transmembrane porin to transport electrons across the outer membrane to a variety of mineral-based electron acceptors. A proteoliposome system has been developed that contains methyl viologen (MV) as an internalised electron acceptor and valinomycin (V) as a membrane associated cation exchanger. These proteoliposomes can be used as a model system to investigate MtrCAB function.

  2. Microbially-Promoted Solubilization of Steel Corrosion Products and Fate of Associated Actinides

    SciTech Connect (OSTI)

    Gill Geesey; Timothy Magnuson; Andrew Neal

    2002-06-15T23:59:59.000Z

    Microorganisms have the capacity to modify iron oxides during anaerobic respiration. When the dissimilatory sulfate-reducing bacterium Desulfovibrio desulfuricans G20 respires soluble sulfate during colonization of the solid-phase iron oxide hematite, the sulfide product reacts with the iron to produce the insoluble iron sulfide, pyrrhotite. When soluble uranium is present as uranyl ion, these microorganisms reduce the U(VI) to U(IV) as insoluble uraninite on the hematite surface. There is also evidence that a stable form of U is produced under these conditions that displays an oxidation state between U(VI) and U(iv). The dissimilatory iron reducing bacterium, Shewanella oneidensis MR1 can utilize insoluble hematite as the sole electron acceptor for anaerobic respiration during growth and biofilm development on the mineral. The growth rate, maximum cell density and detachment rate for this bacterium are significantly greater on hematite than on magnetite (111) and (100). The difference could not be attributed to iron site density in the iron oxide. A gene (ferA) encoding a c-tyoe cytochrome involved in dissimulatory iron reduction in the bacterium Geobacter sulfurreducens was completed sequenced and characterized. The sequence information was used to develop an in-situ reverse transcriptase polymerase chain reaction assay that could detect expression of the gene during growth and biofilm development on ferrihydrite at the single cell and microcolony level. X-ray photoelectron spectroscopic analysis revealed that the ferrihydrite was reduced during expression of this gene. The assay was extended to detect expression of genes involved in sulfate reduction and hydrogen reduction in sulfate-reducing bacteria. This assay will be useful to assess mechanisms of biotransformation of minerals including corrosion products on buried metal containers containing radionuclide waste. In summary, the research has shown that dissimilatory sulfate and iron reducing bacteria can modify the iron oxide surfaces that they colonize and promote the reduction and precipitation of actinides such as uranium at these sites

  3. Regulation of the genes involved in nitrification.

    SciTech Connect (OSTI)

    Arp, D.J.; Sayavedra-Soto, L.A.

    2003-08-14T23:59:59.000Z

    OAK-B135 This project focuses on the characterization of the regulation of the genes involved in nitrification in the bacterium Nitrosomonas europaea. The key genes in the nitrification pathway, amo and hao, are present in multiple copies in the genome. The promoters for these genes were identified and characterized. It was shown that there were some differences in the transcriptional regulation of the copies of these genes.

  4. Understanding the lytic domain of A2: the maturation protein of ssRNA bacteriophage QBeta

    E-Print Network [OSTI]

    Langlais, Carrie-Lynn

    2009-05-15T23:59:59.000Z

    of ssRNA Bacteriophage Q?. (May 2007) Carrie-Lynn Langlais, B.S., University of Great Falls Chair of Advisory Committee: Dr. Ryland F. Young, III Most bacteriophage escape the confines of the host bacterium by compromising the integrity of its... to thank Superman, the invisible jet, red rocket and the leaning blue house for adding plenty of color and strength to this journey. vi TABLE OF CONTENTS Page ABSTRACT????????????????????????????. iii ACKNOWLEDGMENTS...

  5. Atrophic Rhinitis

    E-Print Network [OSTI]

    Lawhorn, D. Bruce

    2002-01-31T23:59:59.000Z

    and rate of gain. Atrophic rhinitis (AR) is the term com- monly used to refer to the condition of a sneezing pig with a crooked, bleeding snout and tear-stained face. The term ?atrophic? means that the turbinate bones inside the snout are shrunken... a crooked nose, is called ?turbinate atrophy.? Producers and veterinarians often refer to any or all of these conditions as atrophic rhinitis. Bacterial Causes Bordetella bronchioseptica was the first bacterium discovered to cause AR. More recently...

  6. Studies of the C-terminal Region of the Gamma Subunit of the Chloroplast ATP Synthase

    E-Print Network [OSTI]

    He, Feng

    2008-06-18T23:59:59.000Z

    and Girvin 1999). 4. The Binding Change Mechanism and Rotational Catalysis of the ATP Synthase Isotopic exchange studies of 18 O and 32 P revealed that the ? phosphate bond of the nucleotide is broken and reformed with oxygen from water during... et al. 2003). The ? rotation has also been observed in EcF 1 (Omote, Sambonmatsu et al. 1999) and hybrid F 1 that contained ? and ? subunits from the bacterium Rhodospirillum rubrum and ? subunit from spinach chloroplast F 1 (Tucker, Schwarz et...

  7. Survival of Salmonella typhimurium in soil

    E-Print Network [OSTI]

    Zibilske, Larry Marvin

    1975-01-01T23:59:59.000Z

    ~th' in Soil. (August 1975) Larry Marvin Zibilskes B. S. , Texas AAM University Chairman of Advisory Committee: Dr. Richard Lleaver Land application is a desirable alternative for the disposal and utilization of cattle manure because nutri- ents... in the manure may be used by plants for growth. This practice may constitute a health hazard to animals coming into contact with manured soil. Salmonella ~t h- imurium is a commonly encountered intestinal bacterium which is pathogenic for warm...

  8. Characterization of trapped lignin-degrading microbes in tropical forest soil

    SciTech Connect (OSTI)

    DeAngelis, K.M.; Allgaier, M.; Chavarria, Y.; Fortney, J.L.; Hugenholz, P.; Simmons, B.; Sublette, K.; Silver, W.L.; Hazen, T.C.

    2011-03-01T23:59:59.000Z

    Lignin is often the most difficult portion of plant biomass to degrade, with fungi generally thought to dominate during late stage decomposition. Lignin in feedstock plant material represents a barrier to more efficient plant biomass conversion and can also hinder enzymatic access to cellulose, which is critical for biofuels production. Tropical rain forest soils in Puerto Rico are characterized by frequent anoxic conditions and fluctuating redox, suggesting the presence of lignin-degrading organisms and mechanisms that are different from known fungal decomposers and oxygen-dependent enzyme activities. We explored microbial lignin-degraders by burying bio-traps containing lignin-amended and unamended biosep beads in the soil for 1, 4, 13 and 30 weeks. At each time point, phenol oxidase and peroxidase enzyme activity was found to be elevated in the lignin-amended versus the unamended beads, while cellulolytic enzyme activities were significantly depressed in lignin-amended beads. Quantitative PCR of bacterial communities showed more bacterial colonization in the lignin-amended compared to the unamended beads after one and four weeks, suggesting that the lignin supported increased bacterial abundance. The microbial community was analyzed by small subunit 16S ribosomal RNA genes using microarray (PhyloChip) and by high-throughput amplicon pyrosequencing based on universal primers targeting bacterial, archaeal, and eukaryotic communities. Community trends were significantly affected by time and the presence of lignin on the beads. Lignin-amended beads have higher relative abundances of representatives from the phyla Actinobacteria, Firmicutes, Acidobacteria and Proteobacteria compared to unamended beads. This study suggests that in low and fluctuating redox soils, bacteria could play a role in anaerobic lignin decomposition.

  9. Characterization of Trapped Lignin-Degrading Microbes in Tropical Forest Soil

    SciTech Connect (OSTI)

    DeAngelis, Kristen M.; Allgaier, Martin; Chavarria, Yaucin; Fortney, Julian L.; Hugenholtz, Philip; Simmons, Blake A.; Sublette, Kerry; Silver, Whendee; Hazen, Terry C.

    2011-04-29T23:59:59.000Z

    Lignin is often the most difficult portion of plant biomass to degrade, with fungi generally thought to dominate during late stage decomposition. Lignin in feedstock plant material represents a barrier to more efficient plant biomass conversion and can also hinder enzymatic access to cellulose, which is critical for biofuels production. Tropical rain forest soils in Puerto Rico are characterized by frequent anoxic conditions and fluctuating redox, suggesting the presence of lignin-degrading organisms and mechanisms that are different from known fungal decomposers and oxygen-dependent enzyme activities. We explored microbial lignin-degraders by burying bio-traps containing lignin-amended and unamended biosep beads in the soil for 1, 4, 13 and 30 weeks. At each time point, phenol oxidase and peroxidase enzyme activity was found to be elevated in the lignin-amended versus the unamended beads, while cellulolytic enzyme activities were significantly depressed in lignin-amended beads. Quantitative PCR of bacterial communities showed more bacterial colonization in the lignin-amended compared to the unamended beads after one and four weeks, suggesting that the lignin supported increased bacterial abundance. The microbial community was analyzed by small subunit 16S ribosomal RNA genes using microarray (PhyloChip) and by high-throughput amplicon pyrosequencing based on universal primers targeting bacterial, archaeal, and eukaryotic communities. Community trends were significantly affected by time and the presence of lignin on the beads. Lignin-amended beads have higher relative abundances of representatives from the phyla Actinobacteria, Firmicutes, Acidobacteria and Proteobacteria compared to unamended beads. This study suggests that in low and fluctuating redox soils, bacteria could play a role in anaerobic lignin decomposition.

  10. Characterization of Trapped Lignin-Degrading Microbes in Tropical Forest Soil

    SciTech Connect (OSTI)

    DeAngelis, Kristen; Allgaier, Martin; Chavarria, Yaucin; Fortney, Julian; Hugenholtz, Phillip; Simmons, Blake; Sublette, Kerry; Silver, Whendee; Hazen, Terry

    2011-07-14T23:59:59.000Z

    Lignin is often the most difficult portion of plant biomass to degrade, with fungi generally thought to dominate during late stage decomposition. Lignin in feedstock plant material represents a barrier to more efficient plant biomass conversion and can also hinder enzymatic access to cellulose, which is critical for biofuels production. Tropical rain forest soils in Puerto Rico are characterized by frequent anoxic conditions and fluctuating redox, suggesting the presence of lignin-degrading organisms and mechanisms that are different from known fungal decomposers and oxygen-dependent enzyme activities. We explored microbial lignin-degraders by burying bio-traps containing lignin-amended and unamended biosep beads in the soil for 1, 4, 13 and 30 weeks. At each time point, phenol oxidase and peroxidase enzyme activity was found to be elevated in the lignin-amended versus the unamended beads, while cellulolytic enzyme activities were significantly depressed in lignin-amended beads. Quantitative PCR of bacterial communities showed more bacterial colonization in the lignin-amended compared to the unamended beads after one and four weeks, suggesting that the lignin supported increased bacterial abundance. The microbial community was analyzed by small subunit 16S ribosomal RNA genes using microarray (PhyloChip) and by high-throughput amplicon pyrosequencing based on universal primers targeting bacterial, archaeal, and eukaryotic communities. Community trends were significantly affected by time and the presence of lignin on the beads. Lignin-amended beads have higher relative abundances of representatives from the phyla Actinobacteria, Firmicutes, Acidobacteria and Proteobacteria compared to unamended beads. This study suggests that in low and fluctuating redox soils, bacteria could play a role in anaerobic lignin decomposition.

  11. Genome, transcriptome, and secretome analysis of wood decay fungus postia placenta supports unique mechanisms of lignocellulose conversion

    SciTech Connect (OSTI)

    Martinez, Diego [Los Alamos National Laboratory; Challacombe, Jean F [Los Alamos National Laboratory; Misra, Monica [Los Alamos National Laboratory; Xie, Gary [Los Alamos National Laboratory; Brettin, Thomas [Los Alamos National Laboratory; Morgenstern, Ingo [CLARK UNIV; Hibbett, David [CLARK UNIV.; Schmoll, Monika [UNIV WIEN; Kubicek, Christian P [UNIV WIEN; Ferreira, Patricia [CIB, CSIC, MADRID; Ruiz - Duenase, Francisco J [CIB, CSIC, MADRID; Martinez, Angel T [CIB, CSIC, MADRID; Kersten, Phil [FOREST PRODUCTS LAB; Hammel, Kenneth E [FOREST PRODUCTS LAB; Vanden Wymelenberg, Amber [U. WISCONSIN; Gaskell, Jill [FOREST PRODUCTS LAB; Lindquist, Erika [DOE JGI; Sabati, Grzegorz [U. WISCONSIN; Bondurant, Sandra S [U. WISCONSIN; Larrondo, Luis F [U. CATHOLICA DE CHILE; Canessa, Paulo [U. CATHOLICA DE CHILE; Vicunna, Rafael [U. CATHOLICA DE CHILE; Yadavk, Jagiit [U. CINCINATTI; Doddapaneni, Harshavardhan [U. CINCINATTI; Subramaniank, Venkataramanan [U. CINCINATTI; Pisabarro, Antonio G [PUBLIC U. NAVARRE; Lavin, Jose L [PUBLIC U. NAVARRE; Oguiza, Jose A [PUBLIC U. NAVARRE; Master, Emma [U. TORONTO; Henrissat, Bernard [CNRS, MARSEILLE; Coutinho, Pedro M [CNRS, MARSEILLE; Harris, Paul [NOVOZYMES, INC.; Magnuson, Jon K [PNNL; Baker, Scott [PNNL; Bruno, Kenneth [PNNL; Kenealy, William [MASCOMA, INC.; Hoegger, Patrik J [GEORG-AUGUST-U.; Kues, Ursula [GEORG-AUGUST-U; Ramaiva, Preethi [NOVOZYMES, INC.; Lucas, Susan [DOE JGI; Salamov, Asaf [DOE JGI; Shapiro, Harris [DOE JGI; Tuh, Hank [DOE JGI; Chee, Christine L [UNM; Teter, Sarah [NOVOZYMES, INC.; Yaver, Debbie [NOVOZYMES, INC.; James, Tim [MCMASTER U.; Mokrejs, Martin [CHARLES U.; Pospisek, Martin [CHARLES U.; Grigoriev, Igor [DOE JGI; Rokhsar, Dan [DOE JGI; Berka, Randy [NOVOZYMES; Cullen, Dan [FOREST PRODUCTS LAB

    2008-01-01T23:59:59.000Z

    Brown-rot fungi such as Postia placenta are common inhabitants of forest ecosystems and are also largely responsible for the destructive decay of wooden structures. Rapid depolymerization of cellulose is a distinguishing feature of brown-rot, but the biochemical mechanisms and underlying genetics are poorly understood. Systematic examination of the P. placenta genome, transcriptome and secretome revealed unique extracellular enzyme systems, including an unusual repertoire of extracellular glycoside hydrolases. Genes encoding exocellobiohydrolases and cellulose-binding domains, typical of cellulolytic microbes, are absent in this efficient cellulose-degrading fungus. When P. placenta was grown in medium containing cellulose as sole carbon source, transcripts corresponding to many hemicellulases and to a single putative {beta}-1-4 endoglucanase were expressed at high levels relative to glucose grown cultures. These transcript profiles were confirmed by direct identification of peptides by liquid chromatography-tandem mass spectrometry (LC{center_dot}MSIMS). Also upregulated during growth on cellulose medium were putative iron reductases, quinone reductase, and structurally divergent oxidases potentially involved in extracellular generation of Fe(II) and H202. These observations are consistent with a biodegradative role for Fenton chemistry in which Fe(II) and H202 react to form hydroxyl radicals, highly reactive oxidants capable of depolymerizing cellulose. The P. placenta genome resources provide unparalleled opportunities for investigating such unusual mechanisms of cellulose conversion. More broadly, the genome offers insight into the diversification of lignocellulose degrading mechanisms in fungi. Comparisons to the closely related white-rot fungus Phanerochaete chrysosporium support an evolutionary shift from white-rot to brown-rot during which the capacity for efficient depolymerization of lignin was lost.

  12. Efficient breakdown of lignocellulose using mixed-microbe populations for bioethanol production.

    SciTech Connect (OSTI)

    Murton, Jaclyn K.; Ricken, James Bryce; Powell, Amy Jo

    2009-11-01T23:59:59.000Z

    This report documents progress in discovering new catalytic technologies that will support the development of advanced biofuels. The global shift from petroleum-based fuels to advanced biofuels will require transformational breakthroughs in biomass deconstruction technologies, because current methods are neither cost effective nor sufficiently efficient or robust for scaleable production. Discovery and characterization of lignocellulolytic enzyme systems adapted to extreme environments will accelerate progress. Obvious extreme environments to mine for novel lignocellulolytic deconstruction technologies include aridland ecosystems (ALEs), such as those of the Sevilleta Long Term Ecological Research (LTER) site in central New Mexico (NM). ALEs represent at least 40% of the terrestrial biosphere and are classic extreme environments, with low nutrient availability, high ultraviolet radiation flux, limited and erratic precipitation, and extreme variation in temperatures. ALEs are functionally distinct from temperate environments in many respects; one salient distinction is that ALEs do not accumulate soil organic carbon (SOC), in marked contrast to temperate settings, which typically have large pools of SOC. Low productivity ALEs do not accumulate carbon (C) primarily because of extraordinarily efficient extracellular enzyme activities (EEAs) that are derived from underlying communities of diverse, largely uncharacterized microbes. Such efficient enzyme activities presumably reflect adaptation to this low productivity ecosystem, with the result that all available organic nutrients are assimilated rapidly. These communities are dominated by ascomycetous fungi, both in terms of abundance and contribution to ecosystem-scale metabolic processes, such as nitrogen and C cycling. To deliver novel, robust, efficient lignocellulolytic enzyme systems that will drive transformational advances in biomass deconstruction, we have: (1) secured an award through the Department of Energy (DoE) Joint Genome Institute (JGI) to perform metatranscriptomic functional profiling of eukaryotic microbial communities of blue grama grass (Bouteloua gracilis) rhizosphere (RHZ) soils and (2) isolated and provided initial genotypic and phenotypic characterization data for thermophilic fungi. Our preliminary results show that many strains in our collection of thermophilic fungi frequently outperform industry standards in key assays; we also demonstrated that this collection is taxonomically diverse and phenotypically compelling. The studies summarized here are being performed in collaboration with University of New Mexico and are based at the Sevilleta LTER research site.

  13. Investigating the ?Trojan Horse? Mechanism of Yersinia pestis Virulence

    SciTech Connect (OSTI)

    McCutchen-Maloney, S L; Fitch, J P

    2005-02-08T23:59:59.000Z

    Yersinia pestis, the etiological agent of plague, is a Gram-negative, highly communicable, enteric bacterium that has been responsible for three historic plague pandemics. Currently, several thousand cases of plague are reported worldwide annually, and Y. pestis remains a considerable threat from a biodefense perspective. Y. pestis infection can manifest in three forms: bubonic, septicemic, and pneumonic plague. Of these three forms, pneumonic plague has the highest fatality rate ({approx}100% if left untreated), the shortest intervention time ({approx}24 hours), and is highly contagious. Currently, there are no rapid, widely available vaccines for plague and though plague may be treated with antibiotics, the emergence of both naturally occurring and potentially engineered antibiotic resistant strains makes the search for more effective therapies and vaccines for plague of pressing concern. The virulence mechanism of this deadly bacterium involves induction of a Type III secretion system, a syringe-like apparatus that facilitates the injection of virulence factors, termed Yersinia outer membrane proteins (Yops), into the host cell. These virulence factors inhibit phagocytosis and cytokine secretion, and trigger apoptosis of the host cell. Y. pestis virulence factors and the Type III secretion system are induced thermally, when the bacterium enters the mammalian host from the flea vector, and through host cell contact (or conditions of low Ca{sup 2+} in vitro). Apart from the temperature increase from 26 C to 37 C and host cell contact (or low Ca{sup 2+} conditions), other molecular mechanisms that influence virulence induction in Y. pestis are largely uncharacterized. This project focused on characterizing two novel mechanisms that regulate virulence factor induction in Y. pestis, immunoglobulin G (IgG) binding and quorum sensing, using a real-time reporter system to monitor induction of virulence. Incorporating a better understanding of the mechanisms of virulence and pathogenicity into detection systems, may allow us to anticipate both natural and engineered evolution of infectious diseases while laying the foundation for next-generation detection of biothreat agents.

  14. Determination of the occurrence of Arcobacter butzleri in beef and dairy cattle from Texas using two isolation methods

    E-Print Network [OSTI]

    Golla, Steven Craig

    2000-01-01T23:59:59.000Z

    Arcobactt r brit, leri is a pathogenic bacterium tha& has been found in d ury cattle, pigs, poultry and humans. As of this v riling, there arc, no data to report the prevalcncc of occurrence of A. bn(zleri in beef' cattle. Also, there arc numerous culture... CHAPTF'R I Ii&& TRODUCTIO'&i Many consuincrs perceive that the food supply is no&. sal'e (5). Biolog&cal harards arc the most leared by tod;&y's consumers because they can cause serious illness and even death. Over 90%& of toodb&irne illnesses...

  15. IMPACT OF WATER TEMPERATURE ON ZEBRA MUSSEL MORTALITY

    SciTech Connect (OSTI)

    Daniel P. Molloy

    2002-08-07T23:59:59.000Z

    These tests conducted this past quarter have indicated that the bacterium Pseudomonas fluorescens strain CL0145A is effective at killing zebra mussels at water temperatures ranging from 7 to 23 C. Percent kill will likely be somewhat lower at very low temperatures, e.g., 7 C, but even at such low temperatures high mussel kill can still be achieved (>70% kill). This is significant because the development of a zebra mussel control method that is efficacious in such a wide range of temperatures broadens its usefulness as a potential commercial product.

  16. Non-contiguous finished genome sequence of Aminomonas paucivorans type strain (GLU-3T)

    SciTech Connect (OSTI)

    Pitluck, Sam [Joint Genome Institute, Walnut Creek, California; Yasawong, Montri [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Held, Brittany [Los Alamos National Laboratory (LANL); Lapidus, Alla L. [Joint Genome Institute, Walnut Creek, California; Nolan, Matt [Joint Genome Institute, Walnut Creek, California; Copeland, A [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [Joint Genome Institute, Walnut Creek, California; Glavina Del Rio, Tijana [Joint Genome Institute, Walnut Creek, California; Tice, Hope [Joint Genome Institute, Walnut Creek, California; Cheng, Jan-Fang [Joint Genome Institute, Walnut Creek, California; Chertkov, Olga [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Tapia, Roxanne [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Liolios, Konstantinos [Joint Genome Institute, Walnut Creek, California; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Ovchinnikova, Galina [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [Joint Genome Institute, Walnut Creek, California; Palaniappan, Krishna [Joint Genome Institute, Walnut Creek, California; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Chang, Yun-Juan [ORNL; Jeffries, Cynthia [Oak Ridge National Laboratory (ORNL); Pukall, Rudiger [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Spring, Stefan [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Sikorski, Johannes [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Woyke, Tanja [Joint Genome Institute, Walnut Creek, California; Bristow, James [Joint Genome Institute, Walnut Creek, California; Eisen, Jonathan [Joint Genome Institute, Walnut Creek, California; Markowitz, Victor [Joint Genome Institute, Walnut Creek, California; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [Joint Genome Institute, Walnut Creek, California; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany

    2010-01-01T23:59:59.000Z

    Aminomonas paucivorans Baena et al. 1999 is the type species of the genus Aminomonas, which belongs to the family Synergistaceae. The species is of interest because it is an asaccharolytic chemoorganotrophic bacterium which ferments quite a number of amino acids. This is the first completed genome sequence (with one gap in a rDNA region) of a member of the genus Aminomonas and the third sequence from the family Synergistaceae. The 2,630,120 bp long genome with its 2,433 protein-coding and 61 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  17. Klebsiella pneumoniae inoculants for enhancing plant growth

    DOE Patents [OSTI]

    Triplett, Eric W. (Middleton, WI); Kaeppler, Shawn M. (Oregon, WI); Chelius, Marisa K. (Greeley, CO)

    2008-07-01T23:59:59.000Z

    A biological inoculant for enhancing the growth of plants is disclosed. The inoculant includes the bacterial strains Herbaspirillum seropedicae 2A, Pantoea agglomerans P101, Pantoea agglomerans P102, Klebsiella pneumoniae 342, Klebsiella pneumoniae zmvsy, Herbaspirillum seropedicae Z152, Gluconacetobacter diazotrophicus PA15, with or without a carrier. The inoculant also includes strains of the bacterium Pantoea agglomerans and K. pneumoniae which are able to enhance the growth of cereal grasses. Also disclosed are the novel bacterial strains Herbaspirillum seropedicae 2A, Pantoea agglomerans P101 and P102, and Klebsiella pneumoniae 342 and zmvsy.

  18. Final report for DOE grant FG02-06ER15805

    SciTech Connect (OSTI)

    Daniel Gage

    2012-05-31T23:59:59.000Z

    DOE funding was used to investigate the role of the phosphotransferase system (PTS) in the symbiotic, nodulating bacterium Sinorhizobium meliloti. This system is well studied in several bacterial species. However, itâ??s organization and function in S. meliloti is substantially different than in the those other, well-studied bacteria. The S. meliloti PTS, through our DOE-funded work, has become a model for how this important signal transduction system works in the a-proteobacteria. We have found that the PTS is relatively simple, used for only signal transduction and not transport, and is involved in regulation of carbon metabolism in response to carbon availability and nitrogen availability.

  19. Genome Sequence of the Ethene- and Vinyl Chloride-Oxidizing Actinomycete Nocardioides sp Strain JS614

    SciTech Connect (OSTI)

    Coleman, Nicholas V [University of Sydney, Australia; Wilson, Neil L [University of Sydney, Australia; Barry, Kerrie [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Los Alamos National Laboratory (LANL); Copeland, A [U.S. Department of Energy, Joint Genome Institute; Dalin, Eileen [U.S. Department of Energy, Joint Genome Institute; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Glavina Del Rio, Tijana [U.S. Department of Energy, Joint Genome Institute; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Hammon, Nancy [U.S. Department of Energy, Joint Genome Institute; Han, Shunsheng [Los Alamos National Laboratory (LANL); Hauser, Loren John [ORNL; Israni, Sanjay [U.S. Department of Energy, Joint Genome Institute; Kim, Edwin [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Larimer, Frank W [ORNL; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Richardson, Paul [U.S. Department of Energy, Joint Genome Institute; Schmutz, Jeremy [Stanford University; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Thompson, Sue [Los Alamos National Laboratory (LANL); Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Spain, Jim C [Georgia Institute of Technology; Gossett, James G [Cornell University; Mattes, Timothy E [University of Iowa

    2011-01-01T23:59:59.000Z

    Nocardioides sp. strain JS614 grows on ethene and vinyl chloride (VC) as sole carbon and energy sources and is of interest for bioremediation and biocatalysis. Sequencing of the complete genome of JS614 provides insight into the genetic basis of alkene oxidation, supports ongoing research into the physiology and biochemistry of growth on ethene and VC, and provides biomarkers to facilitate detection of VC/ethene oxidizers in the environment. This is the first genome sequence from the genus Nocardioides and the first genome of a VC/ethene-oxidizing bacterium.

  20. The Vroman effect: a molecular level description of fibrinogen displacement

    E-Print Network [OSTI]

    Jung, Seung-Yong

    2005-02-17T23:59:59.000Z

    is free to rearrange its position on the surface to maximize its interactions with an incoming multivalent protein, virus, bacterium, or toxin.2,66,67 For example, in the case of anti-2,4 dinitrophenyl IgG antibodies interacting with a supported... the effect of ligand density and cholesterol content on the binding of anti-2,4 dinitrophenyl IgG antibodies with DNP-Cap PE lipids in phosphatidylcholine membranes. The antibodies were labeled with Texas Red dye so that they could be visualized...

  1. Bacteriophage ?MAM1, a Viunalikevirus, Is a Broad-Host-Range, High-Efficiency Generalized Transducer That Infects Environmental and Clinical Isolates of the Enterobacterial Genera Serratia and Kluyvera

    E-Print Network [OSTI]

    Matilda, Miguel A.; Salmond, George P. C.

    2014-01-01T23:59:59.000Z

      The generated transducing particles adsorb normally and inject DNA into a recipient 63  bacterium. The injected bacterial DNA may integrate by homologous recombination into 64  the genome of the recipient host, resulting in a stable bacterial transductant (14... .o.i. The mixture was incubated at 30 169  ºC for 30 minutes (1 h for Sma 12), pelleted by centrifugation (4.000 g for 10 min at 4 ºC) 170  8    and washed twice with 10 ml of LB to remove any remaining lysate. The cells were 171  resuspended in 5 ml of LB and 100...

  2. Made Famous By Erin Brockovich: A Potent Pollutant and its Nemesis

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels DataDepartment of Energy Your Density Isn't YourTransport(FactDepartment ofLetterEconomyDr. ErnestMID-CAREERofBacterium | Department of

  3. Madelyn Creedon Confirmed as Principal Deputy Administrator for the

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels DataDepartment of Energy Your Density Isn't YourTransport(FactDepartment ofLetterEconomyDr. ErnestMID-CAREERofBacterium | Department

  4. Madhav Manjrekar and Elena Arvanitis, Siemens Corporate Research, Research

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels DataDepartment of Energy Your Density Isn't YourTransport(FactDepartment ofLetterEconomyDr. ErnestMID-CAREERofBacterium |

  5. Magnesium Front End Design And Development (AMD603) | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels DataDepartment of Energy Your Density Isn't YourTransport(FactDepartment ofLetterEconomyDr. ErnestMID-CAREERofBacterium |Magna E-Car

  6. Magnesium Front End Design and Development | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels DataDepartment of Energy Your Density Isn't YourTransport(FactDepartment ofLetterEconomyDr. ErnestMID-CAREERofBacterium |Magna E-Carand

  7. Magnesium Front End Development (AMD 603/604/904) | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels DataDepartment of Energy Your Density Isn't YourTransport(FactDepartment ofLetterEconomyDr. ErnestMID-CAREERofBacterium |Magna E-Carand2 DOE

  8. Magnesium Front End Development (AMD 603/604/904) | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels DataDepartment of Energy Your Density Isn't YourTransport(FactDepartment ofLetterEconomyDr. ErnestMID-CAREERofBacterium |Magna E-Carand2

  9. Magnesium Front End Research And Development (AMD604) | Department of

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels DataDepartment of Energy Your Density Isn't YourTransport(FactDepartment ofLetterEconomyDr. ErnestMID-CAREERofBacterium |Magna

  10. Magnesium Front End Research and Development AMD 604 | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels DataDepartment of Energy Your Density Isn't YourTransport(FactDepartment ofLetterEconomyDr. ErnestMID-CAREERofBacterium |Magna10 DOE Vehicle

  11. Magnesium Front End Research and Development AMD 604 | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels DataDepartment of Energy Your Density Isn't YourTransport(FactDepartment ofLetterEconomyDr. ErnestMID-CAREERofBacterium |Magna10 DOE

  12. Magnesium Powertrain Cast Components Project (AMD 304) | Department of

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels DataDepartment of Energy Your Density Isn't YourTransport(FactDepartment ofLetterEconomyDr. ErnestMID-CAREERofBacterium |Magna10

  13. Magnesium Powertrain Cast Components | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels DataDepartment of Energy Your Density Isn't YourTransport(FactDepartment ofLetterEconomyDr. ErnestMID-CAREERofBacterium |Magna10Components

  14. Magnesium Projects | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels DataDepartment of Energy Your Density Isn't YourTransport(FactDepartment ofLetterEconomyDr. ErnestMID-CAREERofBacterium

  15. Nutrient requirements and growth physiology of the photoheterotrophic Acidobacterium, Chloracidobacterium thermophilum

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Tank, Marcus; Bryant, Donald A.

    2015-03-27T23:59:59.000Z

    A novel thermophilic, microaerophilic, anoxygenic, and chlorophototrophic member of the phylum Acidobacteria, Chloracidobacterium thermophilum strain BT, was isolated from a cyanobacterial enrichment culture derived from microbial mats associated with Octopus Spring, Yellowstone National Park, Wyoming. C. thermophilum is strictly dependent on light and oxygen and grows optimally as a photoheterotroph at irradiance values between 20 and 50 µmol photons m?² s?¹. C. thermophilum is unable to synthesize branched-chain amino acids (AAs), L-lysine, and vitamin B??, which are required for growth. Although the organism lacks genes for autotrophic carbon fixation, bicarbonate is also required. Mixtures of other AAs and 2-oxoglutarate stimulatemore »growth. As suggested from genomic sequence data, C. thermophilum requires a reduced sulfur source such as thioglycolate, cysteine, methionine, or thiosulfate. The organism can be grown in a defined medium at 51° (Topt; range 44–58°C) in the pH range 5.5–9.5 (pHopt = ~7.0). Using the defined growth medium and optimal conditions, it was possible to isolate new C. thermophilum strains directly from samples of hot springs mats in Yellowstone National Park, Wyoming. The new isolates differ from the type strain with respect to pigment composition, morphology in liquid culture, and temperature adaptation.« less

  16. Computational design of an endo-1,4-[beta]-xylanase ligand binding site

    SciTech Connect (OSTI)

    Morin, Andrew; Kaufmann, Kristian W.; Fortenberry, Carie; Harp, Joel M.; Mizoue, Laura S.; Meiler, Jens (Vanderbilt)

    2012-09-05T23:59:59.000Z

    The field of computational protein design has experienced important recent success. However, the de novo computational design of high-affinity protein-ligand interfaces is still largely an open challenge. Using the Rosetta program, we attempted the in silico design of a high-affinity protein interface to a small peptide ligand. We chose the thermophilic endo-1,4-{beta}-xylanase from Nonomuraea flexuosa as the protein scaffold on which to perform our designs. Over the course of the study, 12 proteins derived from this scaffold were produced and assayed for binding to the target ligand. Unfortunately, none of the designed proteins displayed evidence of high-affinity binding. Structural characterization of four designed proteins revealed that although the predicted structure of the protein model was highly accurate, this structural accuracy did not translate into accurate prediction of binding affinity. Crystallographic analyses indicate that the lack of binding affinity is possibly due to unaccounted for protein dynamics in the 'thumb' region of our design scaffold intrinsic to the family 11 {beta}-xylanase fold. Further computational analysis revealed two specific, single amino acid substitutions responsible for an observed change in backbone conformation, and decreased dynamic stability of the catalytic cleft. These findings offer new insight into the dynamic and structural determinants of the {beta}-xylanase proteins.

  17. Increase in ethanol yield via elimination of lactate production in an ethanol-tolerant mutant of Clostridium thermocellum

    SciTech Connect (OSTI)

    Biswas, Ranjita [ORNL] [ORNL; Prabhu, Sandeep [ORNL] [ORNL; Lynd, Lee R [Thayer School of Engineering at Dartmouth] [Thayer School of Engineering at Dartmouth; Guss, Adam M [ORNL] [ORNL

    2014-01-01T23:59:59.000Z

    Large-scale production of lignocellulosic biofuel is a potential solution to sustainably meet global energy needs. One-step consolidated bioprocessing (CBP) is a potentially advantageous approach for the production of biofuels, but requires an organism capable of hydrolyzing biomass to sugars and fermenting the sugars to ethanol at commercially viable titers and yields. Clostridium thermocellum, a thermophilic anaerobe, can ferment cellulosic biomass to ethanol and organic acids, but low yield, low titer, and ethanol sensitivity remain barriers to industrial production. Here, we deleted the hypoxanthine phosphoribosyltransferase gene in ethanol tolerant strain of C. thermocellum adhE*(EA) in order to allow use of previously developed gene deletion tools, then deleted lactate dehydrogenase (ldh) to redirect carbon flux towards ethanol. Upon deletion of ldh, the adhE*(EA) ldh strain produced 30% more ethanol than wild type on minimal medium. The adhE*(EA) ldh strain retained tolerance to 5% v/v ethanol, resulting in an ethanol tolerant platform strain of C. thermocellum for future metabolic engineering efforts.

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

    SciTech Connect (OSTI)

    Alex, L.A. (Harvard Medical School, Boston, MA (USA) Massachusetts Institute of Technology, Cambridge (USA)); Reeve, J.N. (Ohio State Univ., Columbus (USA)); Orme-Johnson, W.H. (Massachusetts Institute of Technology, Cambridge (USA)); Walsh, C.T. (Harvard Medical School, Cambridge, MA (USA))

    1990-08-07T23:59:59.000Z

    The genes frhA (1,217 bp), frhB (845 bp), and frhG (710 bp) encoding the three known subunits, {alpha}, {beta}, and {gamma}, of the 8-hydroxy-5-deazaflavin (F{sub 420}) reducing hydrogenase (FRH) from the thermophilic methanogen Methanobacterium thermoautotrophicum {Delta}H 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 ({delta}) 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{sub 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 {Delta}H.

  19. ENHANCED PRACTICAL PHOTOSYNTHETIC CO2 MITIGATION

    SciTech Connect (OSTI)

    Dr. David J. Bayless; Dr. Morgan Vis; Dr. Gregory Kremer; Dr. Michael Prudich; Dr. Keith Cooksey; Dr. Jeff Muhs

    2001-01-16T23:59:59.000Z

    This is the first quarterly report of the project Enhanced Practical Photosynthetic CO{sub 2} Mitigation. The official project start date, 10/02/2000, was delayed until 10/31/2000 due to an intellectual property dispute that was resolved. However, the delay forced a subsequent delay in subcontracting with Montana State University, which then delayed obtaining a sampling permit from Yellowstone National Park. However, even with these delays, the project moved forward with some success. Accomplishments for this quarter include: Culturing of thermophilic organisms from Yellowstone; Testing of mesophilic organisms in extreme CO{sub 2} conditions; Construction of a second test bed for additional testing; Purchase of a total carbon analyzer dedicated to the project; Construction of a lighting container for Oak Ridge National Laboratory optical fiber testing; Modified lighting of existing test box to provide more uniform distribution; Testing of growth surface adhesion and properties; Experimentation on water-jet harvesting techniques; and Literature review underway regarding uses of biomass after harvesting. Plans for next quarter's work and an update on the project's web page are included in the conclusions.

  20. Distinct symmetry and limited peptide refolding activity of the thermosomes from the acidothermophilic archaea Acidianus tengchongensis S5{sup T}

    SciTech Connect (OSTI)

    Wang, Li [The State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101 (China)] [The State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101 (China); Hu, Zhong-jun [National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China)] [National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China); Luo, Yuan-ming [The State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101 (China)] [The State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101 (China); Huo, Yan-wu [National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China)] [National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China); Ma, Qing [The State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101 (China) [The State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101 (China); The College of Life Sciences, Beijing Normal University, Beijing 100875 (China); He, Yong-zhi; Zhang, Yu-ying [The State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101 (China)] [The State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101 (China); Sun, Fei, E-mail: feisun@ibp.ac.cn [National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China)] [National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China); Dong, Zhi-yang, E-mail: dongzy@sun.im.ac.cn [The State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101 (China)] [The State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101 (China)

    2010-03-05T23:59:59.000Z

    Recombinant thermosomes from the Acidianus tengchongensis strain S5{sup T} were purified to homogeneity and assembled in vitro into homo-oligomers (rATcpn{alpha} or rATcpn{beta}) and hetero-oligomers (rATcpn{alpha}{beta}). The symmetries of these complexes were determined by electron microscopy and image analysis. The rATcpn{alpha} homo-oligomer was shown to possess 8-fold symmetry while both rATcpn{beta} and rATcpn{alpha}{beta} oligomers adopted 9-fold symmetry. rATcpn{alpha}{beta} oligomers were shown to contain the {alpha} and {beta} subunits in a 1:2 ratio. All of the complexes prevented the irreversible inactivation of yeast alcohol dehydrogenase at 55 {sup o}C and completely prevented the formation of aggregates during thermal inactivation of citrate synthase at 45 {sup o}C. All rATcpn complexes showed trace ATP hydrolysis activity. Furthermore, rATcpn{beta} sequestered fully chemically denatured substrates (GFP and thermophilic malic dehydrogenase) in vitro without refolding them in an ATP-dependent manner. This property is similar to previously reported properties of chaperonins from Sulfolobus tokodaii and Sulfolobus acidocaldarius. These features are consistent with the slow growth rates of these species of archaea in their native environment.

  1. The Case for a Hot Archean Climate and its Implications to the History of the Biosphere

    E-Print Network [OSTI]

    Schwartzman, David W

    2015-01-01T23:59:59.000Z

    The case for a much warmer climate on the early Earth than now is presented. The oxygen isotope record in sedimentary chert and the compelling case for a near constant isotopic oxygen composition of seawater over geologic time support thermophilic surface temperatures prevailing in the Archean, with some support for hot conditions lasting until about 1.5 billion years ago, aside from lower temperatures including glacial episodes at 2.1-2.4 Ga and possibly an earlier one at 2.9 Ga. Other evidence includes the following: 1) Melting temperatures of proteins resurrected from sequences inferred from robust molecular phylogenies give paleotemperatures at emergence consistent with a very warm early climate. 2) High atmospheric pCO2 levels in the Archean are consistent with high climatic temperatures near the triple point of primary iron minerals in banded iron formations, the formation of Mn-bicarbonate clusters leading to oxygenic photosynthesis and generally higher weathering intensities on land. These higher weat...

  2. Structural and Functional Features of a nNDP Kinase from the Hyperthermophile Crenarchaeon Pyrobaculum Aerophilum

    SciTech Connect (OSTI)

    Pedelacq,J.; Waldo, G.; Cabantous, S.; Liong, E.; Terwilliger, T.

    2005-01-01T23:59:59.000Z

    Nucleoside diphosphate (NDP) kinases are ubiquitous enzymes that transfer {gamma}-phosphates from nucleoside triphosphates to nucleoside diphosphates via a ping-pong mechanism. The important role of this large family of enzymes in controlling cellular functions and developmental processes along with their crystallizability has made them good candidates for structural studies. We recently determined the structure of an evolved version of an NDP kinase from Pyrobaculum aerophilum, an extreme thermophile. This NDP kinase has similarity to the 42 other NDP kinases deposited in the Protein Data Bank (PDB) but differs significantly in sequence, structure, and biophysical properties. The P. aerophilum NDP kinase sequence contains two unique segments not present in other NDP kinases, comprising residues 66-100 and 156-165. We show that deletion mutants of the P. aerophilum NDP kinase lacking either or both of these inserts have an altered substrate specificity, allowing dGTP as the phosphate donor. A structural analysis of the evolved NDP kinase in conjunction with mutagenesis experiments suggests that the substrate specificity of the P. aerophilum NDP kinase is related to the presence of these two inserts.

  3. Entropic stabilization of proteins and its proteomic consequences

    E-Print Network [OSTI]

    Igor N. Berezovsky; William W. Chen; Paul J. Choi; Eugene I. Shakhnovich

    2005-06-22T23:59:59.000Z

    We report here a new entropic mechanism of protein thermostability due to residual dynamics of rotamer isomerization in native state. All-atom simulations show that Lysines have much greater number of accessible rotamers than Arginines in folded states of proteins. This finding suggests that Lysines would preferentially entropically stabilize the native state. Indeed we show in computational experiments that Arginine-to-Lysine amino acid substitutions result in noticeable stabilization of proteins. We then hypothesize that if evolution uses this physical mechanisms in its strategies of thermophilic adaptation then hyperthermostable organisms would have much greater content of Lysines in their proteomes than of comparable in size and similarly charged Arginines.. Consistent with that, high-throughput comparative analysis of complete proteomes shows extremely strong bias towards Arginine-to-Lysine replacement in hyperthermophilic organisms and overall much greater content of Lysines than Arginines in hyperthermophiles. This finding cannot be explained by GC compositional biases. Our study provides an example of how analysis of a delicate physical mechanism of thermostability helps to resolve a puzzle in comparative genomics as to why aminoacid compositions of hyperthermophilic proteomes are significantly biased towards Lysines but not Arginines

  4. High-solids anaerobic digestion of mixed municipal and industrial waste

    SciTech Connect (OSTI)

    Oleszkiewicz, J.A.; Poggi-Varaldo, H.M. [Univ. of Manitoba, Winnipeg, Manitoba (Canada). Dept. of Civil Engineering

    1997-11-01T23:59:59.000Z

    Laboratory studies on dry anaerobic digestion of mixture of paper, kitchen food waste, and sewage sludge have demonstrated the optimum performance at total solids (TS) at the range of 30--35% TS. The thermophilic process (at 55 C) was found to be superior to a mesophilic (35 C) one, both in terms of volatile solid (VS) reduction and specific gas production, but was somewhat less stable at short mass retention times (MRT). The efficiency of total volatile solids destruction and the decrease in the oxygen demand were found to be proportional to the product of the mass retention time and temperature (d {center_dot} C). Pilot studies, conducted on a mixture of sewage sludge, mixed paper, food waste, and solids from a potato processing conducted on site in Portage la Prairie, Manitoba, Canada, have demonstrated the feasibility of running the process at loads exceeding 9 kg TS/m{sup 3} {center_dot} d and producing biogas at 140 m{sup 3} of wet solids fed to the composter. The residual oxygen demand per unit mass of the dry compost was 20 mg O{sub 2}/g {center_dot} h, which indicated a need for aerobic postcuring of the anaerobically produced compost.

  5. Oxidation and methylation of dissolved elemental mercury by anaerobic bacteria

    SciTech Connect (OSTI)

    Hu, Haiyan [ORNL] [ORNL; Lin, Hui [ORNL] [ORNL; Zheng, Wang [ORNL] [ORNL; Tomanicek, Stephen J [ORNL] [ORNL; Johs, Alexander [ORNL] [ORNL; Feng, Xinbin [ORNL] [ORNL; Elias, Dwayne A [ORNL] [ORNL; Liang, Liyuan [ORNL] [ORNL; Liang, Liyuan [ORNL] [ORNL; Gu, Baohua [ORNL] [ORNL

    2013-01-01T23:59:59.000Z

    Methylmercury is a neurotoxin that poses significant health risks to humans. Some anaerobic sulphate- and iron-reducing bacteria can methylate oxidized forms of mercury, generating methylmercury1-4. One strain of sulphate-reducing bacteria (Desulfovibrio desulfuricans ND132) can also methylate elemental mercury5. The prevalence of this trait among different bacterial strains and species remains unclear, however. Here, we compare the ability of two strains of the sulphate-reducing bacterium Desulfovibrio and one strain of the iron-reducing bacterium Geobacter to oxidise and methylate elemental mercury in a series of laboratory incubations. Experiments were carried out under dark, anaerobic conditions, in the presence of environmentally-relevant concentrations of elemental mercury. We report differences in the ability of these organisms to oxidise and methylate elemental mercury. In line with recent findings5, we show that Desulfovibrio desulfuricans ND132 can both oxidise and methylate elemental mercury. However, the rate of methylation of elemental mercury is only about one third the rate of methylation of oxidized mercury. We also show that Desulfovibrio alaskensis G20 can oxidise, but not methylate, elemental mercury. Geobacter sulfurreducens PCA is able to oxidise and methylate elemental mercury in the presence of cysteine. We suggest that the activity of methylating and non-methylating bacteria may together enhance the formation of methylmercury in anaerobic environments.

  6. Isolation and characterization of a fluoranthene-utilizing strain of pseudomonas paucimobilis

    SciTech Connect (OSTI)

    Mueller, J.G.; Chapman, P.J.; Pritchard, P.H.; Blattmann, B.O. (Environmental Protection Agency Environmental Research Laboratory, Gulf Breeze, FL (USA))

    1990-04-01T23:59:59.000Z

    A soil bacterium capable of utilizing fluoranthene as the sole source of carbon and energy for growth was purified from a seven-member bacterial community previously isolated from a creosote waste site for its ability to degrade polycyclic aromatic hydrocarbons. By standard bacteriological methods, this bacterium was characterized taxonomically as a strain of Pseudomonas paucimobilis and was designated strain EPA505. Utilization of fluoranthene by strain EPA505 was demonstrated by increase in bacterial biomass, decrease in aqueous fluoranthene concentration, and transient formation of transformation products in liquid cultures where fluoranthene was supplied as the sole carbon source. Resting cells grown in complex medium showed activity toward anthraquinone, benzo(b)fluorene, biphenyl, chrysene, and pyrene as demonstrated by the disappearance of parent compounds or changes in their UV absorption spectra. Fluoranthene-grown resting cells were active against these compounds as well as 2,3-dimethylnaphthalene, anthracene, fluoranthene, fluorene, naphthalene, and phenanthrene. These studies demonstrate that organic compounds not previously reported to serve as growth substrates can be utilized by axenic cultures of microorganisms. Such organisms may possess novel degradative systems that are active toward other compounds whose biological degradation has been limited because inherent structural considerations or because of low aqueous solubility.

  7. Stable zymomonas mobilis xylose and arabinose fermenting strains

    SciTech Connect (OSTI)

    Zhang, Min (Lakewood, CO); Chou, Yat-Chen (Taipei, TW)

    2008-04-08T23:59:59.000Z

    The present invention briefly includes a transposon for stable insertion of foreign genes into a bacterial genome, comprising at least one operon having structural genes encoding enzymes selected from the group consisting of xylAxylB, araBAD and tal/tkt, and at least one promoter for expression of the structural genes in the bacterium, a pair of inverted insertion sequences, the operons contained inside the insertion sequences, and a transposase gene located outside of the insertion sequences. A plasmid shuttle vector for transformation of foreign genes into a bacterial genome, comprising at least one operon having structural genes encoding enzymes selected from the group consisting of xylAxylB, araBAD and tal/tkt, at least one promoter for expression of the structural genes in the bacterium, and at least two DNA fragments having homology with a gene in the bacterial genome to be transformed, is also provided.The transposon and shuttle vectors are useful in constructing significantly different Zymomonas mobilis strains, according to the present invention, which are useful in the conversion of the cellulose derived pentose sugars into fuels and chemicals, using traditional fermentation technology, because they are stable for expression in a non-selection medium.

  8. Engineering yeast consortia for surface-display of complex cellulosome structures

    SciTech Connect (OSTI)

    Chen, Wilfred [University of Delaware

    2014-03-31T23:59:59.000Z

    As our society marches toward a more technologically advanced future, energy and environmental sustainability are some of the most challenging problems we face today. Biomass is one of the most abundant renewable-feedstock for sustainable production of biofuels. However, the main technological obstacle to more widespread uses of this resource is the lack of low-cost technologies to overcome the recalcitrant nature of the cellulosic structure, especially the hydrolysis step on highly ordered celluloses. In this proposal, we successfully engineered several efficient and inexpensive whole-cell biocatalysts in an effort to produce economically compatible and sustainable biofuels, namely cellulosic ethanol. Our approach was to display of a highly efficient cellulolytic enzyme complex, named cellulosome, on the surface of a historical ethanol producer Saccharomyces cerevisiae for the simultaneous and synergistic saccharification and fermentation of cellulose to ethanol. We first demonstrated the feasibility of assembling a mini-cellulosome by incubating E. coli lysates expressing three different cellulases. Resting cells displaying mini-cellulosomes produced 4-fold more ethanol from phosphoric acid-swollen cellulose (PASC) than cultures with only added enzymes. The flexibility to assemble the mini-cellulosome structure was further demonstrated using a synthetic yeast consortium through intracellular complementation. Direct ethanol production from PASC was demonstrated with resting cell cultures. To create a microorganism suitable for a more cost-effective process, called consolidated bioprocessing (CBP), a synthetic consortium capable of displaying mini-cellulosomes on the cell surface via intercellular complementation was created. To further improve the efficiency, a new adaptive strategy of employing anchoring and adaptor scaffoldins to amplify the number of enzymatic subunits was developed, resulting in the creation of an artificial tetravalent cellulosome on the yeast surface and a significant improvement in cellulosic ethanol production. Although this adaptive strategy is ideal for assembling more complex cellulosome for large-scale production of cellulosic ethanol, a substantially larger number of enzymes (up to 10 to 12) is needed to better mimic the natural cellulosome structures for practical usage of the technology.

  9. Improvement of cellulose catabolism in Clostridium cellulolyticum by sporulation abolishment and carbon alleviation

    SciTech Connect (OSTI)

    Li, Yongchao [ORNL] [ORNL; Xu, Tao [University of Oklahoma, Norman] [University of Oklahoma, Norman; Tschaplinski, Timothy J [ORNL] [ORNL; Engle, Nancy L [ORNL] [ORNL; Graham, David E [ORNL] [ORNL; He, Zhili [University of Oklahoma, Norman] [University of Oklahoma, Norman; Zhou, Jizhong [University of Oklahoma, Norman] [University of Oklahoma, Norman

    2014-01-01T23:59:59.000Z

    Background Clostridium cellulolyticum can degrade lignocellulosic biomass, and ferment the soluble sugars to produce valuable chemicals such as lactate, acetate, ethanol and hydrogen. However, the cellulose utilization efficiency of C. cellulolyticum still remains very low, impeding its application in consolidated bioprocessing for biofuels production. In this study, two metabolic engineering strategies were exploited to improve cellulose utilization efficiency, including sporulation abolishment and carbon overload alleviation. Results The spo0A gene at locus Ccel_1894, which encodes a master sporulation regulator was inactivated. The spo0A mutant abolished the sporulation ability. In a high concentration of cellulose (50 g/l), the performance of the spo0A mutant increased dramatically in terms of maximum growth, final concentrations of three major metabolic products, and cellulose catabolism. The microarray and gas chromatography mass spectrometry (GC-MS) analyses showed that the valine, leucine and isoleucine biosynthesis pathways were up-regulated in the spo0A mutant. Based on this information, a partial isobutanol producing pathway modified from valine biosynthesis was introduced into C. cellulolyticum strains to further increase cellulose consumption by alleviating excessive carbon load. The introduction of this synthetic pathway to the wild-type strain improved cellulose consumption from 17.6 g/l to 28.7 g/l with a production of 0.42 g/l isobutanol in the 50 g/l cellulose medium. However, the spo0A mutant strain did not appreciably benefit from introduction of this synthetic pathway and the cellulose utilization efficiency did not further increase. A technical highlight in this study was that an in vivo promoter strength evaluation protocol was developed using anaerobic fluorescent protein and flow cytometry for C. cellulolyticum. Conclusions In this study, we inactivated the spo0A gene and introduced a heterologous synthetic pathway to manipulate the stress response to heavy carbon load and accumulation of metabolic products. These findings provide new perspectives to enhance the ability of cellulolytic bacteria to produce biofuels and biocommodities with high efficiency and at low cost directly from lignocellulosic biomass.

  10. Final Report - "CO2 Sequestration in Cell Biomass of Chlorobium Thiosulfatophilum"

    SciTech Connect (OSTI)

    James L. Gaddy, PhD; Ching-Whan Ko, PhD

    2009-05-04T23:59:59.000Z

    World carbon dioxide emissions from the combustion of fossil fuels have increased at a rate of about 3 percent per year during the last 40 years to over 24 billion tons today. While a number of methods have been proposed and are under study for dealing with the carbon dioxide problem, all have advantages as well as disadvantages which limit their application. The anaerobic bacterium Chlorobium thiosulfatophilum uses hydrogen sulfide and carbon dioxide to produce elemental sulfur and cell biomass. The overall objective of this project is to develop a commercial process for the biological sequestration of carbon dioxide and simultaneous conversion of hydrogen sulfide to elemental sulfur. The Phase I study successfully demonstrated the technical feasibility of utilizing this bacterium for carbon dioxide sequestration and hydrogen sulfide conversion to elemental sulfur by utilizing the bacterium in continuous reactor studies. Phase II studies involved an advanced research and development to develop the engineering and scale-up parameters for commercialization of the technology. Tasks include culture isolation and optimization studies, further continuous reactor studies, light delivery systems, high pressure studies, process scale-up, a market analysis and economic projections. A number of anaerobic and aerobic microorgansims, both non-photosynthetic and photosynthetic, were examined to find those with the fastest rates for detailed study to continuous culture experiments. C. thiosulfatophilum was selected for study to anaerobically produce sulfur and Thiomicrospira crunogena waws selected for study to produce sulfate non-photosynthetically. Optimal conditions for growth, H2S and CO2 comparison, supplying light and separating sulfur were defined. The design and economic projections show that light supply for photosynthetic reactions is far too expensive, even when solar systems are considered. However, the aerobic non-photosynthetic reaction to produce sulfate with T. crunogena produces a reasonable return when treating a sour gas stream of 120 million SCFD containing 2.5 percent H2S. In this case, the primary source of revenue is from desulfurization of the gas stream. While the technology has significant application in sequestering carbon dioxide in cell biomass or single cell proten (SCP), perhaps the most immediate application is in desulfurizing LGNG or other gas streams. This biological approach is a viable economical alternative to existing hydrogen sulfide removal technology, and is not sensitive to the presence of hydrocarbons which act as catalyst poisons.

  11. End-to-end gene fusions and their impact on the production of multifunctional biomass degrading enzymes

    SciTech Connect (OSTI)

    Rizk, Mazen, E-mail: mazen.rizk@tuhh.de [Institute of Technical Microbiology, Hamburg University of Technology (TUHH), Kasernenstr. 12, D-21073 Hamburg (Germany)] [Institute of Technical Microbiology, Hamburg University of Technology (TUHH), Kasernenstr. 12, D-21073 Hamburg (Germany); Antranikian, Garabed, E-mail: antranikian@tuhh.de [Institute of Technical Microbiology, Hamburg University of Technology (TUHH), Kasernenstr. 12, D-21073 Hamburg (Germany)] [Institute of Technical Microbiology, Hamburg University of Technology (TUHH), Kasernenstr. 12, D-21073 Hamburg (Germany); Elleuche, Skander, E-mail: skander.elleuche@tuhh.de [Institute of Technical Microbiology, Hamburg University of Technology (TUHH), Kasernenstr. 12, D-21073 Hamburg (Germany)] [Institute of Technical Microbiology, Hamburg University of Technology (TUHH), Kasernenstr. 12, D-21073 Hamburg (Germany)

    2012-11-09T23:59:59.000Z

    Highlights: Black-Right-Pointing-Pointer Multifunctional enzymes offer an interesting approach for biomass degradation. Black-Right-Pointing-Pointer Size and conformation of separate constructs play a role in the effectiveness of chimeras. Black-Right-Pointing-Pointer A connecting linker allows for maximal flexibility and increased thermostability. Black-Right-Pointing-Pointer Genes with functional similarities are the best choice for fusion candidates. -- Abstract: The reduction of fossil fuels, coupled with its increase in price, has made the search for alternative energy resources more plausible. One of the topics gaining fast interest is the utilization of lignocellulose, the main component of plants. Its primary constituents, cellulose and hemicellulose, can be degraded by a series of enzymes present in microorganisms, into simple sugars, later used for bioethanol production. Thermophilic bacteria have proven to be an interesting source of enzymes required for hydrolysis since they can withstand high and denaturing temperatures, which are usually required for processes involving biomass degradation. However, the cost associated with the whole enzymatic process is staggering. A solution for cost effective and highly active production is through the construction of multifunctional enzyme complexes harboring the function of more than one enzyme needed for the hydrolysis process. There are various strategies for the degradation of complex biomass ranging from the regulation of the enzymes involved, to cellulosomes, and proteins harboring more than one enzymatic activity. In this review, the construction of multifunctional biomass degrading enzymes through end-to-end gene fusions, and its impact on production and activity by choosing the enzymes and linkers is assessed.

  12. The Genome Sequence of the psychrophilic archaeon, Methanococcoides burtonii: the Role of Genome Evolution in Cold-adaptation

    SciTech Connect (OSTI)

    Allen, Michelle A.; Lauro, Federico M.; Williams, Timothy J.; Burg, Dominic; Siddiqui, Khawar S.; De Francisci, David; Chong, Kevin W.Y.; Pilak, Oliver; Chew, Hwee H.; De Maere, Matthew Z.; Ting, Lily; Katrib, Marilyn; Ng, Charmaine; Sowers, Kevin R.; Galperin, Michael Y.; Anderson, Iain J.; Ivanova, Natalia; Dalin, Eileen; Martinez, Michelle; Lapidus, Alla; Hauser, Loren; Land, Miriam; Thomas, Torsten; Cavicchioli, Ricardo

    2009-04-01T23:59:59.000Z

    Psychrophilic archaea are abundant and perform critical roles throughout the Earth's expansive cold biosphere. Here we report the first complete genome sequence for a psychrophilic methanogenic archaeon, Methanococcoides burtonii. The genome sequence was manually annotated including the use of a five tiered Evidence Rating system that ranked annotations from Evidence Rating (ER) 1 (gene product experimentally characterized from the parent organism) to ER5 (hypothetical gene product) to provide a rapid means of assessing the certainty of gene function predictions. The genome is characterized by a higher level of aberrant sequence composition (51%) than any other archaeon. In comparison to hyper/thermophilic archaea which are subject to selection of synonymous codon usage, M. burtonii has evolved cold adaptation through a genomic capacity to accommodate highly skewed amino acid content, while retaining codon usage in common with its mesophilic Methanosarcina cousins. Polysaccharide biosynthesis genes comprise at least 3.3% of protein coding genes in the genome, and Cell wall/membrane/envelope biogenesis COG genes are over-represented. Likewise, signal transduction (COG category T) genes are over-represented and M. burtonii has a high 'IQ' (a measure of adaptive potential) compared to many methanogens. Numerous genes in these two over-represented COG categories appear to have been acquired from {var_epsilon}- and {delta}-proteobacteria, as do specific genes involved in central metabolism such as a novel B form of aconitase. Transposases also distinguish M. burtonii from other archaea, and their genomic characteristics indicate they play an important role in evolving the M. burtonii genome. Our study reveals a capacity for this model psychrophile to evolve through genome plasticity (including nucleotide skew, horizontal gene transfer and transposase activity) that enables adaptation to the cold, and to the biological and physical changes that have occurred over the last several thousand years as it adapted from a marine, to an Antarctic lake environment.

  13. Mechanisms of thermal adaptation revealed from the genomes of the Antarctic

    SciTech Connect (OSTI)

    Saunders, Neil F.W.; Thomas, Torsten; Curmi, Paul M.G.; Mattick, John S.; Kuczek, Elizabeth; Slade, Rob; Davis, John; Franzmann, Peter; Boone, David; Rusterholtz, Karl; Feldman, Robert; Gates, Chris; Bench, Shellie; Sowers, Kevin; Kadner, Kristen; Aerts, Andrea; Dehal, Paramvir; Detter, Chris; Glavina, Tijana; Lucas, Susan; Richardson, Paul; Larimer, Frank; Hauser , Frank; Hauser, Loren; Land, Miriam; Cavicchioli, Richard

    2003-03-01T23:59:59.000Z

    We generated draft genome sequences for two cold-adapted Archaea, Methanogenium frigidum and Methanococcoides burtonii, to identify genotypic characteristics that distinguish them from Archaea with a higher optimal growth temperature (OGT). Comparative genomics revealed trends in amino acid and tRNA composition, and structural features of proteins. Proteins from the cold-adapted Archaea are characterized by a higher content of non-charged polar amino acids, particularly Gln and Thr and a lower content of hydrophobic amino acids, particularly Leu. Sequence data from nine methanogen genomes (OGT 15-98 C) was used to generate 1 111 modeled protein structures. Analysis of the models from the cold-adapted Archaea showed a strong tendency in the solvent accessible area for more Gln, Thr an hydrophobic residues and fewer charged residues. A cold shock domain (CSD) protein (CspA homolog) was identified in M. frigidum, two hypothetical proteins with CSD-folds in M. burtonii, and a unique winged helix DNA-binding domain protein in M. burtonii. This suggests that these types of nucleic acid binding proteins have a critical role in cold-adapted Archaea. Structural analysis of tRNA sequences from the Archaea indicated that GC content is the major factor influencing tRNA stability in hyperthermophiles, but not in the psychrophiles, mesophiles or moderate thermophiles. Below an OGT of 60 C, the GC content in tRNA was largely unchanged, indicating that any requirement for flexibility of tRNA in psychrophiles is mediated by other means. This is the first time that comparisons have been performed with genome data from Archaea spanning the growth temperature extremes from psychrophiles to hyperthermophiles.

  14. Crystal structure of a thermostable Old Yellow Enzyme from Thermus scotoductus SA-01

    SciTech Connect (OSTI)

    Opperman, Diederik J. [Department of Microbial, Biochemical and Food Biotechnology, BioPAD Metagenomics Platform, University of the Free State, Bloemfontein 9300 (South Africa)] [Department of Microbial, Biochemical and Food Biotechnology, BioPAD Metagenomics Platform, University of the Free State, Bloemfontein 9300 (South Africa); Sewell, Bryan T. [Electron Microscope Unit, University of Cape Town, Rondebosch 7701 (South Africa)] [Electron Microscope Unit, University of Cape Town, Rondebosch 7701 (South Africa); Litthauer, Derek [Department of Microbial, Biochemical and Food Biotechnology, BioPAD Metagenomics Platform, University of the Free State, Bloemfontein 9300 (South Africa)] [Department of Microbial, Biochemical and Food Biotechnology, BioPAD Metagenomics Platform, University of the Free State, Bloemfontein 9300 (South Africa); Isupov, Mikhail N.; Littlechild, Jennifer A. [School of Biosciences, Henry Wellcome Building for Biocatalysis, University of Exeter, Stocker Road, Exeter EX4 4QD (United Kingdom)] [School of Biosciences, Henry Wellcome Building for Biocatalysis, University of Exeter, Stocker Road, Exeter EX4 4QD (United Kingdom); Heerden, Esta van, E-mail: vheerde.sci@ufs.ac.za [Department of Microbial, Biochemical and Food Biotechnology, BioPAD Metagenomics Platform, University of the Free State, Bloemfontein 9300 (South Africa)

    2010-03-12T23:59:59.000Z

    Recent characterization of the chromate reductase (CrS) from the thermophile Thermus scotoductus SA-01 revealed this enzyme to be related to the Old Yellow Enzyme (OYE) family. Here, we report the structure of a thermostable OYE homolog in its holoform at 2.2 A as well as its complex with p-hydroxybenzaldehyde (pHBA). The enzyme crystallized as octamers with the monomers showing a classical TIM barrel fold which upon dimerization yields the biologically active form of the protein. A sulfate ion is bound above the si-side of the non-covalently bound FMN cofactor in the oxidized solved structure but is displaced upon pHBA binding. The active-site architecture is highly conserved as with other members of this enzyme family. The pHBA in the CrS complex is positioned by hydrogen bonding to the two conserved catalytic-site histidines. The most prominent structural difference between CrS and other OYE homologs is the size of the 'capping domain'. Thermostabilization of the enzyme is achieved in part through increased proline content within loops and turns as well as increased intersubunit interactions through hydrogen bonding and complex salt bridge networks. CrS is able to reduce the C=C bonds of {alpha},{beta}-unsaturated carbonyl compounds with a preference towards cyclic substrates however no activity was observed towards {beta}-substituted substrates. Mutational studies have confirmed the role of Tyr177 as the proposed proton donor although reduction could still occur at a reduced rate when this residue was mutated to phenylalanine.

  15. Does aspartic acid racemization constrain the depth limit of the subsurface biosphere?

    SciTech Connect (OSTI)

    Onstott, T. C. [Princeton University] [Princeton University; Aubrey, A.D. [Jet Propulsion Laboratory, Pasadena, CA] [Jet Propulsion Laboratory, Pasadena, CA; Kieft, T L [New Mexico Institute of Mining and Technology] [New Mexico Institute of Mining and Technology; Silver, B J [Jet Propulsion Laboratory, Pasadena, CA] [Jet Propulsion Laboratory, Pasadena, CA; Phelps, Tommy Joe [ORNL] [ORNL; Van Heerden, E. [University of the Free State] [University of the Free State; Opperman, D. J. [University of the Free State] [University of the Free State; Bada, J L. [Geosciences Research Division, Scripps Instition of Oceanography, Univesity of California San Diego,] [Geosciences Research Division, Scripps Instition of Oceanography, Univesity of California San Diego,

    2014-01-01T23:59:59.000Z

    Previous studies of the subsurface biosphere have deduced average cellular doubling times of hundreds to thousands of years based upon geochemical models. We have directly constrained the in situ average cellular protein turnover or doubling times for metabolically active micro-organisms based on cellular amino acid abundances, D/L values of cellular aspartic acid, and the in vivo aspartic acid racemization rate. Application of this method to planktonic microbial communities collected from deep fractures in South Africa yielded maximum cellular amino acid turnover times of ~89 years for 1 km depth and 27 C and 1 2 years for 3 km depth and 54 C. The latter turnover times are much shorter than previously estimated cellular turnover times based upon geochemical arguments. The aspartic acid racemization rate at higher temperatures yields cellular protein doubling times that are consistent with the survival times of hyperthermophilic strains and predicts that at temperatures of 85 C, cells must replace proteins every couple of days to maintain enzymatic activity. Such a high maintenance requirement may be the principal limit on the abundance of living micro-organisms in the deep, hot subsurface biosphere, as well as a potential limit on their activity. The measurement of the D/L of aspartic acid in biological samples is a potentially powerful tool for deep, fractured continental and oceanic crustal settings where geochemical models of carbon turnover times are poorly constrained. Experimental observations on the racemization rates of aspartic acid in living thermophiles and hyperthermophiles could test this hypothesis. The development of corrections for cell wall peptides and spores will be required, however, to improve the accuracy of these estimates for environmental samples.

  16. Mechanism of N[superscript 10]-formyltetrahydrofolate synthetase derived from complexes with intermediates and inhibitors

    SciTech Connect (OSTI)

    Celeste, Lesa R.; Chai, Geqing; Bielak, Magdalena; Minor, Wladek; Lovelace, Leslie L.; Lebioda, Lukasz (SC); (UV)

    2012-09-05T23:59:59.000Z

    N{sup 10}-formyltetrahydrofolate synthetase (FTHFS) is a folate enzyme that catalyzes the formylation of tetrahydrofolate (THF) in an ATP dependent manner. Structures of FTHFS from the thermophilic homoacetogen, Moorella thermoacetica, complexed with (1) a catalytic intermediate-formylphosphate (XPO) and product-ADP; (2) with an inhibitory substrate analog-folate; (3) with XPO and an inhibitory THF analog, ZD9331, were used to analyze the enzyme mechanism. Nucleophilic attack of the formate ion on the gamma phosphate of ATP leads to the formation of XPO and the first product ADP. A channel that leads to the putative formate binding pocket allows for the binding of ATP and formate in random order. Formate binding is due to interactions with the gamma-phosphate moiety of ATP and additionally to two hydrogen bonds from the backbone nitrogen of Ala276 and the side chain of Arg97. Upon ADP dissociation, XPO reorients and moves to the position previously occupied by the beta-phosphate of ATP. Conformational changes that occur due to the XPO presence apparently allow for the recruitment of the third substrate, THF, with its pterin moiety positioned between Phe384 and Trp412. This position overlaps with that of the bound nucleoside, which is consistent with a catalytic mechanism hypothesis that FTHFS works via a sequential ping-pong mechanism. More specifically, a random bi uni uni bi ping-pong ter ter mechanism is proposed. Additionally, the native structure originally reported at a 2.5 {angstrom} resolution was redetermined at a 2.2 {angstrom} resolution.

  17. Fair Oaks Dairy Farms Cellulosic Ethanol Technology Review Summary

    SciTech Connect (OSTI)

    Andrew Wold; Robert Divers

    2011-06-23T23:59:59.000Z

    At Fair Oaks Dairy, dried manure solids (''DMS'') are currently used as a low value compost. United Power was engaged to evaluate the feasibility of processing these DMS into ethanol utilizing commercially available cellulosic biofuels conversion platforms. The Fair Oaks Dairy group is transitioning their traditional ''manure to methane'' mesophilic anaerobic digester platform to an integrated bio-refinery centered upon thermophilic digestion. Presently, the Digested Manure Solids (DMS) are used as a low value soil amendment (compost). United Power evaluated the feasibility of processing DMS into higher value ethanol utilizing commercially available cellulosic biofuels conversion platforms. DMS was analyzed and over 100 potential technology providers were reviewed and evaluated. DMS contains enough carbon to be suitable as a biomass feedstock for conversion into ethanol by gasification technology, or as part of a conversion process that would include combined heat and power. In the first process, 100% of the feedstock is converted into ethanol. In the second process, the feedstock is combusted to provide heat to generate electrical power supporting other processes. Of the 100 technology vendors evaluated, a short list of nine technology providers was developed. From this, two vendors were selected as finalists (one was an enzymatic platform and one was a gasification platform). Their selection was based upon the technical feasibility of their systems, engineering expertise, experience in commercial or pilot scale operations, the ability or willingness to integrate the system into the Fair Oaks Biorefinery, the know-how or experience in producing bio-ethanol, and a clear path to commercial development.

  18. On the possibility of cosmic ray-induced ionizing radiation-powered life in subsurface environments in the Universe

    E-Print Network [OSTI]

    Atri, Dimitra

    2015-01-01T23:59:59.000Z

    Photosynthesis is a highly efficient mechanism developed by terrestrial life to utilize the energy from photons of solar origin for biological use. Subsurface regions are isolated from the photosphere, and consequently are incapable of utilizing this energy. This opens up the opportunity for life to cultivate alternative mechanisms in order to take advantage of other available energy sources. Studies have shown that in subsurface environments, life can use energy generated from geochemical and geothermal processes to sustain a minimal metabolism. Another mechanism is radiolysis, in which particles emitted by radioactive substances are indirectly utilized for metabolism. One such example is the bacterium fueled by radiation, found 2 miles deep in a South African mine, which consumes hydrogen formed from particles emitted by radioactive U, Th and K present in rock. An additional source of radiation in the subsurface environments is secondary particles, such as muons generated by Galactic Cosmic Rays (GCRs). It ...

  19. Microbial engineering of nano-heterostructures; biological synthesis of a magnetically-recoverable palladium nanocatalyst

    SciTech Connect (OSTI)

    Coker, V. S.; Bennett, J. A.; Telling, N.; Charnock, J. M.; van der Laan, G.; Pattrick, R. A. D.; Pearce, C. I; Cutting, R. S.; Shannon, I. J.; Wood, J.; Arenholz, E.; Vaughan, D. J.; Lloyd, J. R.

    2009-12-01T23:59:59.000Z

    Precious metals supported on ferrimagnetic particles form a diverse range of catalysts. Here we show a novel biotechnological route for the synthesis of a heterogeneous catalyst consisting of reactive palladium nanoparticles arrayed on a biomagnetite support. The magnetic support was synthesized at ambient temperature by the Fe(III)-reducing bacterium, Geobacter sulfurreducens, and facilitated ease of recovery of the catalyst with superior performance due to reduced agglomeration. Arrays of palladium nanoparticles were deposited on the nanomagnetite using a simple one-step method without the need to modify the biomineral surface most likely due to an organic coating priming the surface for Pd adsorption. A combination of EXAFS and XPS showed the particles to be predominantly metallic in nature. The Pd{sup 0}-biomagnetite was tested for catalytic activity in the Heck Reaction coupling iodobenzene to ethyl acrylate or styrene and near complete conversion to ethyl cinnamate or stilbene was achieved within 90 and 180 min, respectively.

  20. Respiratory arsenate reductase as a bidirectional enzyme

    SciTech Connect (OSTI)

    Richey, Christine [Department of Biological Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, PA 15282 (United States)] [Department of Biological Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, PA 15282 (United States); Chovanec, Peter [Department of Biological Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, PA 15282 (United States) [Department of Biological Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, PA 15282 (United States); Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, PA 15282 (United States); Hoeft, Shelley E.; Oremland, Ronald S. [U.S. Geological Survey, 345 Middlefield Rd., MS 480, Menlo Park, CA 94025 (United States)] [U.S. Geological Survey, 345 Middlefield Rd., MS 480, Menlo Park, CA 94025 (United States); Basu, Partha [Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, PA 15282 (United States)] [Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, PA 15282 (United States); Stolz, John F., E-mail: stolz@duq.edu [Department of Biological Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, PA 15282 (United States)

    2009-05-01T23:59:59.000Z

    The haloalkaliphilic bacterium Alkalilimnicola ehrlichii is capable of anaerobic chemolithoautotrophic growth by coupling the oxidation of arsenite (As(III)) to the reduction of nitrate and carbon dioxide. Analysis of its complete genome indicates that it lacks a conventional arsenite oxidase (Aox), but instead possesses two operons that each encode a putative respiratory arsenate reductase (Arr). Here we show that one homolog is expressed under chemolithoautotrophic conditions and exhibits both arsenite oxidase and arsenate reductase activity. We also demonstrate that Arr from two arsenate respiring bacteria, Alkaliphilus oremlandii and Shewanella sp. strain ANA-3, is also biochemically reversible. Thus Arr can function as a reductase or oxidase. Its physiological role in a specific organism, however, may depend on the electron potentials of the molybdenum center and [Fe-S] clusters, additional subunits, or constitution of the electron transfer chain. This versatility further underscores the ubiquity and antiquity of microbial arsenic metabolism.

  1. Anaerobic microbial dissolution of lead and production of organic acids

    DOE Patents [OSTI]

    Francis, A.J.; Dodge, C.; Chendrayan, K.

    1986-02-28T23:59:59.000Z

    The present invention relates to a method of solubilizing lead, in the form of lead oxide, found in industrial wastes, before these wastes are dumped into the environment. The lead is solubilized by dissolving the lead oxide in the wastes through contact with an anaerobic bacterial culture containing the bacterium ATCC No. 53464. The solubilized lead can then be removed from the wastes by chemical separation. It could also be removed by extending the contact period with the bacterial culture. As the culture grows, the solubilized lead is removed from the wastes by bioaccumulation by the microorganism or by immobilization by a polymer-like material produced by the microorganism. At this point, the lead is then removed from the wastes when the waste material is separated from the bacterial culture. If desired, the bacterial culture could be digested at this point to yield relatively pure lead for further industrial use.

  2. Nucleic acids, compositions and uses thereof

    DOE Patents [OSTI]

    Preston, III, James F. (Micanopy, FL); Chow, Virginia (Gainesville, FL); Nong, Guang (Gainesville, FL); Rice, John D. (Gainesville, FL); St. John, Franz J. (Baltimore, MD)

    2012-02-21T23:59:59.000Z

    The subject invention provides at least one nucleic acid sequence encoding an aldouronate-utilization regulon isolated from Paenibacillus sp. strain JDR-2, a bacterium which efficiently utilizes xylan and metabolizes aldouronates (methylglucuronoxylosaccharides). The subject invention also provides a means for providing a coordinately regulated process in which xylan depolymerization and product assimilation are coupled in Paenibacillus sp. strain JDR-2 to provide a favorable system for the conversion of lignocellulosic biomass to biobased products. Additionally, the nucleic acid sequences encoding the aldouronate-utilization regulon can be used to transform other bacteria to form organisms capable of producing a desired product (e.g., ethanol, 1-butanol, acetoin, 2,3-butanediol, 1,3-propanediol, succinate, lactate, acetate, malate or alanine) from lignocellulosic biomass.

  3. Nucleic acid compositions and the encoding proteins

    DOE Patents [OSTI]

    Preston, III, James F.; Chow, Virginia; Nong, Guang; Rice, John D.; St. John, Franz J.

    2014-09-02T23:59:59.000Z

    The subject invention provides at least one nucleic acid sequence encoding an aldouronate-utilization regulon isolated from Paenibacillus sp. strain JDR-2, a bacterium which efficiently utilizes xylan and metabolizes aldouronates (methylglucuronoxylosaccharides). The subject invention also provides a means for providing a coordinately regulated process in which xylan depolymerization and product assimilation are coupled in Paenibacillus sp. strain JDR-2 to provide a favorable system for the conversion of lignocellulosic biomass to biobased products. Additionally, the nucleic acid sequences encoding the aldouronate-utilization regulon can be used to transform other bacteria to form organisms capable of producing a desired product (e.g., ethanol, 1-butanol, acetoin, 2,3-butanediol, 1,3-propanediol, succinate, lactate, acetate, malate or alanine) from lignocellulosic biomass.

  4. Engineered plant biomass particles coated with biological agents

    DOE Patents [OSTI]

    Dooley, James H.; Lanning, David N.

    2014-06-24T23:59:59.000Z

    Plant biomass particles coated with a biological agent such as a bacterium or seed, characterized by a length dimension (L) aligned substantially parallel to a grain direction and defining a substantially uniform distance along the grain, a width dimension (W) normal to L and aligned cross grain, and a height dimension (H) normal to W and L. In particular, the L.times.H dimensions define a pair of substantially parallel side surfaces characterized by substantially intact longitudinally arrayed fibers, the W.times.H dimensions define a pair of substantially parallel end surfaces characterized by crosscut fibers and end checking between fibers, and the L.times.W dimensions define a pair of substantially parallel top and bottom surfaces.

  5. Complete genome sequence of Intrasporangium calvumtype strain (7 KIPT)

    SciTech Connect (OSTI)

    Glavina Del Rio, Tijana [Joint Genome Institute, Walnut Creek, California; Chertkov, Olga [Los Alamos National Laboratory (LANL); Yasawong, Montri [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Lucas, Susan [Joint Genome Institute, Walnut Creek, California; Deshpande, Shweta [Joint Genome Institute, Walnut Creek, California; Cheng, Jan-Fang [Joint Genome Institute, Walnut Creek, California; Detter, J. Chris [Joint Genome Institute, Walnut Creek, California; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [Joint Genome Institute, Walnut Creek, California; Liolios, Konstantinos [Joint Genome Institute, Walnut Creek, California; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [Joint Genome Institute, Walnut Creek, California; Palaniappan, Krishna [Joint Genome Institute, Walnut Creek, California; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Chang, Yun-Juan [ORNL; Jeffries, Cynthia [Oak Ridge National Laboratory (ORNL); Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Pukall, Rudiger [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Sikorski, Johannes [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Woyke, Tanja [Joint Genome Institute, Walnut Creek, California; Bristow, James [Joint Genome Institute, Walnut Creek, California; Eisen, Jonathan [Joint Genome Institute, Walnut Creek, California; Markowitz, Victor [Joint Genome Institute, Walnut Creek, California; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [Joint Genome Institute, Walnut Creek, California; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Lapidus, Alla L. [Joint Genome Institute, Walnut Creek, California

    2010-01-01T23:59:59.000Z

    Intrasporangium calvum Kalakoutskii et al. 1967 is the type species of the genus Intrasporangium, which belongs to the actinobacterial family Intrasporangiaceae. The species is a Gram-positive bacterium that forms a branching mycelium, which tends to break into irregular fragments. The mycelium of this strain may bear intercalary vesicles but does not contain spores. The strain described in this study is an airborne organism that was isolated from a school dining room in 1967. One particularly interesting feature of I. calvum is that the type of its menaquinone is different from all other representatives of the family Intrasporangiaceae. This is the first completed genome sequence from a member of the genus Intrasporangium and also the first sequence from the family Intrasporangiaceae. The 4,024,382 bp long genome with its 3,653 protein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  6. Complete genome sequence of Kangiella koreensis type strain (SW-125T)

    SciTech Connect (OSTI)

    Han, Cliff [Los Alamos National Laboratory (LANL); Sikorski, Johannes [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Lapidus, Alla L. [Joint Genome Institute, Walnut Creek, California; Nolan, Matt [Joint Genome Institute, Walnut Creek, California; Glavina Del Rio, Tijana [Joint Genome Institute, Walnut Creek, California; Tice, Hope [Joint Genome Institute, Walnut Creek, California; Cheng, Jan-Fang [Joint Genome Institute, Walnut Creek, California; Lucas, Susan [Joint Genome Institute, Walnut Creek, California; Chen, Feng [Joint Genome Institute, Walnut Creek, California; Copeland, A [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Ovchinnikova, Galina [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Joint Genome Institute, Walnut Creek, California; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [Joint Genome Institute, Walnut Creek, California; Chen, Amy [Joint Genome Institute, Walnut Creek, California; Palaniappan, Krishna [Joint Genome Institute, Walnut Creek, California; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Chang, Yun-Juan [ORNL; Jeffries, Cynthia [Oak Ridge National Laboratory (ORNL); Chain, Patrick S. G. [Lawrence Livermore National Laboratory (LLNL); Saunders, Elizabeth H [Los Alamos National Laboratory (LANL); Brettin, Thomas S [ORNL; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Tindall, Brian [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Bristow, James [Joint Genome Institute, Walnut Creek, California; Eisen, Jonathan [Joint Genome Institute, Walnut Creek, California; Markowitz, Victor [Joint Genome Institute, Walnut Creek, California; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [Joint Genome Institute, Walnut Creek, California; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Detter, J. Chris [Joint Genome Institute, Walnut Creek, California

    2009-11-01T23:59:59.000Z

    Kangiella koreensis (Yoon et al. 2004) is the type species of the genus and is of phylogenetic interest because of the very isolated location of the genus Kangiella in the gammaproteobac-terial order Oceanospirillales. K. koreensis SW-125T is a Gram-negative, non-motile, non-spore-forming bacterium isolated from tidal flat sediments at Daepo Beach, Yellow Sea, Ko-rea. Here we describe the features of this organism, together with the complete genome se-quence, and annotation. This is the first completed genome sequence from the genus Kangiel-la and only the fourth genome from the order Oceanospirillales. This 2,852,073 bp long sin-gle replicon genome with its 2647 protein-coding and 48 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  7. Complete genome sequence of Isosphaera pallida type strain (IS1BT)

    SciTech Connect (OSTI)

    Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Cleland, David M [ORNL; Saunders, Elizabeth H [Los Alamos National Laboratory (LANL); Lapidus, Alla L. [Joint Genome Institute, Walnut Creek, California; Nolan, Matt [Joint Genome Institute, Walnut Creek, California; Lucas, Susan [Joint Genome Institute, Walnut Creek, California; Hammon, Nancy [Joint Genome Institute, Walnut Creek, California; Deshpande, Shweta [Joint Genome Institute, Walnut Creek, California; Cheng, Jan-Fang [Joint Genome Institute, Walnut Creek, California; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [Joint Genome Institute, Walnut Creek, California; Liolios, Konstantinos [Joint Genome Institute, Walnut Creek, California; Pagani, Ioanna [Joint Genome Institute, Walnut Creek, California; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [Joint Genome Institute, Walnut Creek, California; Palaniappan, Krishna [Joint Genome Institute, Walnut Creek, California; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Chang, Yun-Juan [ORNL; Jeffries, Cynthia [Oak Ridge National Laboratory (ORNL); Detter, J. Chris [Joint Genome Institute, Walnut Creek, California; Beck, Brian [ATCC - American Type Culture Collection; Woyke, Tanja [Joint Genome Institute, Walnut Creek, California; Bristow, James [Joint Genome Institute, Walnut Creek, California; Eisen, Jonathan [Joint Genome Institute, Walnut Creek, California; Markowitz, Victor [Joint Genome Institute, Walnut Creek, California; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [Joint Genome Institute, Walnut Creek, California; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany

    2011-01-01T23:59:59.000Z

    Isosphaera pallida (ex Woronichin 1927) Giovannoni et al. 1995 is the type species of the genus Isosphaera. The species is of interest because it was the first heterotrophic bacterium known to be phototactic, and it occupies an isolated phylogenetic position within the Planctomycetaceae. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first complete genome sequence of a member of the genus Isosphaera and the third of a member of the family Planctomycetaceae. The 5,472,964 bp long chromosome and the 56,340 bp long plasmid with a total of 3,763 protein-coding and 60 RNA genes are part of the Genomic Encyclopedia of Bacteria and Archaea project.

  8. Complete genome sequence of Desulfarculus baarsii type strain (2st14T)

    SciTech Connect (OSTI)

    Sun, Christine [University of California, Berkeley; Spring, Stefan [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Lapidus, Alla L. [Joint Genome Institute, Walnut Creek, California; Davenport, Karen W. [Los Alamos National Laboratory (LANL); Glavina Del Rio, Tijana [Joint Genome Institute, Walnut Creek, California; Tice, Hope [Joint Genome Institute, Walnut Creek, California; Nolan, Matt [Joint Genome Institute, Walnut Creek, California; Copeland, A [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [Joint Genome Institute, Walnut Creek, California; Lucas, Susan [Joint Genome Institute, Walnut Creek, California; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [Joint Genome Institute, Walnut Creek, California; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [Joint Genome Institute, Walnut Creek, California; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Ovchinnikova, Galina [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [Joint Genome Institute, Walnut Creek, California; Palaniappan, Krishna [Joint Genome Institute, Walnut Creek, California; Hauser, Loren John [ORNL; Chang, Yun-Juan [ORNL; Jeffries, Cynthia [Oak Ridge National Laboratory (ORNL); Detter, J. Chris [Joint Genome Institute, Walnut Creek, California; Han, Cliff [Los Alamos National Laboratory (LANL); Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Brambilla, Evelyne-Marie [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Woyke, Tanja [Joint Genome Institute, Walnut Creek, California; Bristow, James [Joint Genome Institute, Walnut Creek, California; Eisen, Jonathan [Joint Genome Institute, Walnut Creek, California; Markowitz, Victor [Joint Genome Institute, Walnut Creek, California; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [Joint Genome Institute, Walnut Creek, California; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Land, Miriam L [ORNL

    2010-01-01T23:59:59.000Z

    Desulfarculus baarsii (Widdel 1981) Kuever et al. 2006 is the type and only species of the genus Desulfarculus, which represents the family Desulfarculaceae and the order Desulfarculales. This species is a mesophilic sulfate-reducing bacterium with the capability to oxidize acetate and fatty acids of up to 18 carbon atoms completely to CO2. The acetyl-CoA/CODH (Wood-Ljungdahl) pathway is used by this species for the complete oxidation of carbon sources and autotrophic growth on formate. The type strain 2st14T was isolated from a ditch sediment collected near the University of Konstanz, Germany. This is the first completed genome sequence of a member of the order Desulfarculales. The 3,655,731 bp long single replicon genome with its 3,303 protein-coding and 52 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  9. Complete genome sequence of Bacteroides helcogenes type strain (P 36-108T)

    SciTech Connect (OSTI)

    Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Gronow, Sabine [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Zeytun, Ahmet [Los Alamos National Laboratory (LANL); Lapidus, Alla L. [Joint Genome Institute, Walnut Creek, California; Nolan, Matt [Joint Genome Institute, Walnut Creek, California; Hammon, Nancy [Joint Genome Institute, Walnut Creek, California; Deshpande, Shweta [Joint Genome Institute, Walnut Creek, California; Cheng, Jan-Fang [Joint Genome Institute, Walnut Creek, California; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [Joint Genome Institute, Walnut Creek, California; Liolios, Konstantinos [Joint Genome Institute, Walnut Creek, California; Pagani, Ioanna [Joint Genome Institute, Walnut Creek, California; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [Joint Genome Institute, Walnut Creek, California; Palaniappan, Krishna [Joint Genome Institute, Walnut Creek, California; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Chang, Yun-Juan [ORNL; Jeffries, Cynthia [Oak Ridge National Laboratory (ORNL); Detter, J. Chris [Joint Genome Institute, Walnut Creek, California; Brambilla, Evelyne-Marie [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Woyke, Tanja [Joint Genome Institute, Walnut Creek, California; Bristow, James [Joint Genome Institute, Walnut Creek, California; Eisen, Jonathan [Joint Genome Institute, Walnut Creek, California; Markowitz, Victor [Joint Genome Institute, Walnut Creek, California; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [Joint Genome Institute, Walnut Creek, California; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Lucas, Susan [Joint Genome Institute, Walnut Creek, California

    2011-01-01T23:59:59.000Z

    Bacteroides helcogenes Benno et al. 1983 is of interest because of its isolated phylogenetic location and, although it has been found in pig feces and is known to be pathogenic for pigs, occurrence of this bacterium is rare and it does not cause significant damage in intensive animal husbandry. The genome of B. helcogenes P 36-108T is already the fifth completed and published type strain genome from the genus Bacteroides in the family Bacteroidaceae. The 3,998,906 bp long genome with its 3,353 protein-coding and 83 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  10. ANAEROBIC RESISTANCE TO HIGH LEVELS OF CADMIUM AND OTHER TOXIC METALS IN A FACULTATIVE ANAEROBE ISOLATED FROM PRISTINE SALT MARSH SEDIMENTS

    SciTech Connect (OSTI)

    SHARMA,P.K.; VAIRAVAMURTHY,A.; KIELECZAWA,J.

    1999-06-20T23:59:59.000Z

    The authors have isolated many Cd (II) resistant bacterial strains from relatively pristine sediments collected from salt marshes in Shelter Island, New York. Detailed studies are being performed on one isolate, strain Cd-1. Strain Cd-1 is metabolically diverse, halotolerant, Gram-negative, facultative anaerobe. It can resist high amounts of Cd (II), Cr (VI), As (V), Se (IV), Co (II), Pb (II), or Zn (II) under defined anaerobic conditions. With pyruvate as the energy source, Cd-1 can grow well at examined Cd (II) concentrations ranging up to 15 mM. It can resist Cd (II) with or without marine level NaCl concentration, under acidic or neutral conditions. It can resist Cd (II) under aerobic conditions as well. These features are novel for a heavy metal resistant bacterium.

  11. Biological production of ethanol from coal. Task 4 report, Continuous reactor studies

    SciTech Connect (OSTI)

    Not Available

    1992-10-01T23:59:59.000Z

    The production of ethanol from synthesis gas by the anaerobic bacterium C. ljungdahlii has been demonstrated in continuous stirred tank reactors (CSTRs), CSTRs with cell recycle and trickle bed reactors. Various liquid media were utilized in these studies including basal medium, basal media with 1/2 B-vitamins and no yeast extract and a medium specifically designed for the growth of C. ljungdahlii in the CSTR. Ethanol production was successful in each of the three reactor types, although trickle bed operation with C. ljungdahlii was not as good as with the stirred tank reactors. Operation in the CSTR with cell recycle was particularly promising, producing 47 g/L ethanol with only minor concentrations of the by-product acetate.

  12. Sugar Transport and Metabolism in Thermotoga

    SciTech Connect (OSTI)

    Noll, Kenneth M.; Romano, Antonio H.

    2003-02-11T23:59:59.000Z

    The work conducted under this grant demonstrated that the hyperthermophilic bacterium Thermotoga neapolitana carries out glucose and lactose transport in a sodium-dependent manner and that energization of anaerobic cells is required to observe transport. We also demonstrated that Thermotoga maritima carries out maltose and glucose transport using periplasmic sugar binding proteins. We began defining patterns of expression of genes encoding sugar transport and catabolic functions in both T. maritima and T. neapolitana. We began a collaborative effort to identify all the genes regulated at the transcriptional level in response to sugars substrates. These funds also allowed us to begin an examination of the functions of several periplasmic substrate binding proteins encoded in the genome of T. maritima.

  13. Complete genome sequence of Desulfurispirillum indicum strain S5T

    SciTech Connect (OSTI)

    Bini, Elisabetta [Rutgers University; Rauschenbach, Ines [Rutgers University; Narasingarao, Priya [Rutgers University; Starovoytov, Valentin [Rutgers University; Hauser, Loren John [ORNL; Jeffries, Cynthia [Oak Ridge National Laboratory (ORNL); Land, Miriam L [ORNL; Bruce, David [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Held, Brittany [Los Alamos National Laboratory (LANL); Tapia, Roxanne [Los Alamos National Laboratory (LANL); Copeland, A [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Pennacchio, Len [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Haggblom, Max [Rutgers University

    2011-01-01T23:59:59.000Z

    Desulfurispirillum indicum strain S5T is a strictly anaerobic bacterium isolated from river se- diment in Chennai, India. D. indicum belongs to the deep branching phylum of Chrysioge- netes, which currently only includes three other cultured species. Strain S5T is the type strain of the species and it is capable of growth using selenate, selenite, arsenate, nitrate or nitrite as terminal electron acceptors. The 2,928,377 bp genome encodes 2,619 proteins and 49 RNA genes, and the information gained from its sequence will be relevant to the elucidation of mi- crobially-mediated transformations of arsenic and selenium, in addition to deepening our knowledge of the underrepresented phylum of Chrysiogenetes.

  14. Life Redefined: Microbes Built with Arsenic

    SciTech Connect (OSTI)

    Webb, Sam (SLAC and Felisa Wolfe-Simon, NASA and U.S. Geological Survey) [SLAC and Felisa Wolfe-Simon, NASA and U.S. Geological Survey

    2011-03-22T23:59:59.000Z

    Life can survive in many harsh environments, from extreme heat to the presence of deadly chemicals. However, life as we know it has always been based on the same six elements -- carbon, oxygen, nitrogen, hydrogen, sulfur and phosphorus. Now it appears that even this rule has an exception. In the saline and poisonous environment of Mono Lake, researchers have found a bacterium that can grow by incorporating arsenic into its structure in place of phosphorus. X-ray images taken at SLAC's synchrotron light source reveal that this microbe may even use arsenic as a building block for DNA. Please join us as we describe this discovery, which rewrites the textbook description of how living cells work.

  15. Recombinant glucose uptake system

    DOE Patents [OSTI]

    Ingrahm, Lonnie O. (Gainesville, FL); Snoep, Jacob L. (Groede, NL); Arfman, Nico (Delft, NL)

    1997-01-01T23:59:59.000Z

    Recombinant organisms are disclosed that contain a pathway for glucose uptake other than the pathway normally utilized by the host cell. In particular, the host cell is one in which glucose transport into the cell normally is coupled to PEP production. This host cell is transformed so that it uses an alternative pathway for glucose transport that is not coupled to PEP production. In a preferred embodiment, the host cell is a bacterium other than Z. mobilis that has been transformed to contain the glf and glk genes of Z. mobilis. By uncoupling glucose transport into the cell from PEP utilization, more PEP is produced for synthesis of products of commercial importance from a given quantity of biomass supplied to the host cells.

  16. Complete genome sequence of Halorhodospira halophila SL1

    SciTech Connect (OSTI)

    Challacombe, Jean F [ORNL; Majid, Sophia [University of Chicago; Deole, Ratnakar [Oklahoma State University; Brettin, Thomas S. [Argonne National Laboratory (ANL); Bruce, David [Los Alamos National Laboratory (LANL); Delano, Susana [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Gleasner, Cheryl D. [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Misra, Monica [Los Alamos National Laboratory (LANL); Reitenga, Krista K. [Los Alamos National Laboratory (LANL); Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Copeland, A [U.S. Department of Energy, Joint Genome Institute; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Saunders, Elizabeth H [Los Alamos National Laboratory (LANL); Tapia, Roxanne [Los Alamos National Laboratory (LANL); Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Hoff, Wouter D. [Oklahoma State University

    2013-01-01T23:59:59.000Z

    Halorhodospira halophila is among the most halophilic organisms known. It is an obligately photosynthetic and anaerobic purple sulfur bacterium that exhibits autotrophic growth up to saturated NaCl concentrations. The type strain H. halophila SL1 was isolated from a hypersaline lake in Oregon. Here we report the determination of its entire genome in a single contig. This is the first genome of a phototrophic extreme halophile. The genome consists of 2,678,452 bp, encoding 2493 predicted genes as determined by automated genome annotation. Of the 2407 predicted proteins, 1905 were assigned to a putative function. Future detailed analysis of this genome promises to yield insights into the halophilic adaptations of this organism, its ability for photoautotrophic growth under extreme conditions, and its characteristic sulfur metabolism.

  17. R/BHC: fast Bayesian hierarchical clustering for microarray data

    E-Print Network [OSTI]

    Savage, Richard S; Heller, Katherine; Xu, Yang; Ghahramani, Zoubin; Truman, William M; Grant, Murray; Denby, Katherine J; Wild, David L

    2009-08-06T23:59:59.000Z

    activity (3.99× 10?4) chitinase activity (6.02× 10?3) intracellular ligand-gated ion channel activity (1.51× 10?2) multi-organism process (2.21× 10?2) apoplast (2.60× 10?2) response to bacterium (2.76× 10?2) ligand-gated channel activity (3.22× 10... transporter activity (6.64× 10?3) asparagine synthase (glutamine-hydrolyzing) activity (9.96× 10?3) sinapate 1-glucosyltransferase activity (1.33× 10?2) NAD+ ADP-ribosyltransferase activity (1.99× 10?2) fatty acid (omega-1)-hydroxylase activity (2.32× 10...

  18. High resolution structure of the large ribosomal subunit from a Mesophilic Eubacterium

    SciTech Connect (OSTI)

    Harms, Joerg; Schluenzen, Frank; Zarivach, Raz; Bashan, Anat; Gat, Sharon; Agmon, Ilana; Bartels, Heike; Franceschi, Francois; Yonath, Ada (Weizmann Inst Israel); (Mac Planck Germany); (Max Planck Germany)

    2009-10-07T23:59:59.000Z

    We describe the high resolution structure of the large ribosomal subunit from Deinococcus radiodurans (D50S), a gram-positive mesophile suitable for binding of antibiotics and functionally relevant ligands. The over-all structure of D50S is similar to that from the archae bacterium Haloarcula marismortui (H50S); however, a detailed comparison revealed significant differences, for example, in the orientation of nucleotides in peptidyl transferase center and in the structures of many ribosomal proteins. Analysis of ribosomal features involved in dynamic aspects of protein biosynthesis that are partially or fully disordered in H50S revealed the conformations of intersubunit bridges in unbound subunits, suggesting how they may change upon subunit association and how movements of the L1-stalk may facilitate the exit of tRNA.

  19. Discrimination of Bacillus anthracis from closely related microorganisms by analysis of 16S and 23S rRNA with oligonucleotide microchips

    DOE Patents [OSTI]

    Bavykin, Sergei G. (Darien, IL); Mirzabekova, legal representative, Natalia V. (Westmont, IL); Mirzabekov, deceased, Andrei D. (Westmont, IL)

    2007-12-04T23:59:59.000Z

    The present invention relates to methods and compositions for using nucleotide sequence variations of 16S and 23S rRNA within the B. cereus group to discriminate a highly infectious bacterium B. anthracis from closely related microorganisms. Sequence variations in the 16S and 23S rRNA of the B. cereus subgroup including B. anthracis are utilized to construct an array that can detect these sequence variations through selective hybridizations and discriminate B. cereus group that includes B. anthracis. Discrimination of single base differences in rRNA was achieved with a microchip during analysis of B. cereus group isolates from both single and in mixed samples, as well as identification of polymorphic sites. Successful use of a microchip to determine the appropriate subgroup classification using eight reference microorganisms from the B. cereus group as a study set, was demonstrated.

  20. Discrimination of Bacillus anthracis from closely related microorganisms by analysis of 16S and 23S rRNA with oligonucleotide microchips

    DOE Patents [OSTI]

    Bavykin, Sergei G. (Darien, IL); Mirzabekov, Andrei D. (Moscow, RU)

    2007-10-30T23:59:59.000Z

    The present invention is directed to a novel method of discriminating a highly infectious bacterium Bacillus anthracis from a group of closely related microorganisms. Sequence variations in the 16S and 23S rRNA of the B. cereus subgroup including B. anthracis are utilized to construct an array that can detect these sequence variations through selective hybridizations. The identification and analysis of these sequence variations enables positive discrimination of isolates of the B. cereus group that includes B. anthracis. Discrimination of single base differences in rRNA was achieved with a microchip during analysis of B. cereus group isolates from both single and in mixed probes, as well as identification of polymorphic sites. Successful use of a microchip to determine the appropriate subgroup classification using eight reference microorganisms from the B. cereus group as a study set, was demonstrated.

  1. Novel Biological Conversion of Hydrogen and Carbon Dioxide Directly into Biodiesel: Cooperative Research and Development Final Report, CRADA Number: CRD-10-408

    SciTech Connect (OSTI)

    Maness, P. C.

    2014-06-01T23:59:59.000Z

    OPX Biotechnologies, Inc. (OPX), the National Renewable Energy Laboratory (NREL), and Johnson Matthey will develop and optimize a novel, engineered microorganism that directly produces biodiesel from renewable hydrogen (H2) and carbon dioxide (CO2). The proposed process will fix CO2 utilizing H2 to generate an infrastructure-compatible, energy-dense fuel at costs of less than $2.50 per gallon, with water being produced as the primary byproduct. NREL will perform metabolic engineering on the bacterium Cupriavidus necator (formerly Ralstonia eutropha) and a techno-economic analysis to guide future scale-up work. H2 and CO2 uptakes rates will be genetically increased, production of free fatty acids will be enhanced and their degradation pathway blocked in order to meet the ultimate program goals.

  2. Combined inactivation of the Clostridium cellulolyticum lactate and malate dehydrogenase genes substantially increases ethanol yield from cellulose and switchgrass fermentations

    SciTech Connect (OSTI)

    Li, Yongchao [ORNL; Tschaplinski, Timothy J [ORNL; Engle, Nancy L [ORNL; Hamilton, Choo Yieng [ORNL; Rodriguez, Jr., Miguel [ORNL; Liao, James C [ORNL; Schadt, Christopher Warren [ORNL; Guss, Adam M [ORNL; Yang, Yunfeng [ORNL; Graham, David E [ORNL

    2012-01-01T23:59:59.000Z

    Background: The model bacterium Clostridium cellulolyticum efficiently hydrolyzes crystalline cellulose and hemicellulose, using cellulosomes to degrade lignocellulosic biomass. Although it imports and ferments both pentose and hexose sugars to produce a mixture of ethanol, acetate, lactate, H2 and CO2, the proportion of ethanol is low, which impedes its use in consolidated bioprocessing for biofuels. Therefore genetic engineering will likely be required to improve the ethanol yield. Random mutagenesis, plasmid transformation, and heterologous expression systems have previously been developed for C. cellulolyticum, but targeted mutagenesis has not been reported for this organism. Results: The first targeted gene inactivation system was developed for C. cellulolyticum, based on a mobile group II intron originating from the Lactococcus lactis L1.LtrB intron. This markerless mutagenesis system was used to disrupt both the paralogous L-lactate dehydrogenase (Ccel_2485; ldh) and L-malate dehydrogenase (Ccel_0137; mdh) genes, distinguishing the overlapping substrate specificities of these enzymes. Both mutations were then combined in a single strain. This double mutant produced 8.5-times more ethanol than wild-type cells growing on crystalline cellulose. Ethanol constituted 93% of the major fermentation products (by molarity), corresponding to a molar ratio of ethanol to organic acids of 15, versus 0.18 in wild-type cells. During growth on acid-pretreated switchgrass, the double mutant also produced four-times as much ethanol as wild-type cells. Detailed metabolomic analyses identified increased flux through the oxidative branch of the mutant s TCA pathway. Conclusions: The efficient intron-based gene inactivation system produced the first gene-targeted mutations in C. cellulolyticum. As a key component of the genetic toolbox for this bacterium, markerless targeted mutagenesis enables functional genomic research in C. cellulolyticum and rapid genetic engineering to significantly alter the mixture of fermentation products. The initial application of this system successfully engineered a strain with high ethanol productivity from complex biomass substrates.

  3. Microbial enhanced oil recovery research. Final report, Annex 5

    SciTech Connect (OSTI)

    Sharma, M.M.; Gerogiou, G.

    1993-07-01T23:59:59.000Z

    The objective of this project was to develop an engineering framework for the exploitation of microorganisms to enhance oil recovery. An order of magnitude analysis indicated that selective plugging and the production of biosurfactants are the two most likely mechanisms for the mobilization of oil in microbial enhanced oil recovery (MEOR). The latter, biosurfactant production, is easier to control within a reservoir environment and was investigated in some detail. An extensive literature survey indicated that the bacterium Bacillus licheniformis JF-2 produces a very effective surface active agent capable of increasing the capillary number to values sufficiently low for oil mobilization. In addition, earlier studies had shown that growth of this bacterium and biosurfactant production occur under conditions that are typically encountered in MEOR, namely temperatures up to 55{degrees}C, lack of oxygen and salinities of up to 10% w/v. The chemical structure of the surfactant, its interfacial properties and its production by fermentation were characterized in some detail. In parallel, a set of experiments as conducted to measure the transport of Bacillus licheniformis JF-2 in sandpacks. It was shown that the determining parameters for cell transport in porous media are: cell size and degree of coagulation, presence of dispersants, injection velocity and cell concentration. The mechanisms of bacteria retention within the pores of the reservoir were analyzed based on heuristic arguments. A mathematical simulator of MEOR was developed using conservation equations in which the mechanisms of bacteria retention and the growth kinetics of the cells were incorporated. The predictions of the model agreed reasonably well with experimental results.

  4. Identification of Small RNAs in Desulfovibrio vulgaris Hildenborough

    SciTech Connect (OSTI)

    Burns, Andrew; Joachimiak, Marcin; Deutschbauer, Adam; Arkin, Adam; Bender, Kelly

    2010-05-17T23:59:59.000Z

    Desulfovibrio vulgaris is an anaerobic sulfate-reducing bacterium capable of facilitating the removal of toxic metals such as uranium from contaminated sites via reduction. As such, it is essential to understand the intricate regulatory cascades involved in how D. vulgaris and its relatives respond to stressors in such sites. One approach is the identification and analysis of small non-coding RNAs (sRNAs); molecules ranging in size from 20-200 nucleotides that predominantly affect gene regulation by binding to complementary mRNA in an anti-sense fashion and therefore provide an immediate regulatory response. To identify sRNAs in D. vulgaris, a bacterium that does not possess an annotated hfq gene, RNA was pooled from stationary and exponential phases, nitrate exposure, and biofilm conditions. The subsequent RNA was size fractionated, modified, and converted to cDNA for high throughput transcriptomic deep sequencing. A computational approach to identify sRNAs via the alignment of seven separate Desulfovibrio genomes was also performed. From the deep sequencing analysis, 2,296 reads between 20 and 250 nt were identified with expression above genome background. Analysis of those reads limited the number of candidates to ~;;87 intergenic, while ~;;140 appeared to be antisense to annotated open reading frames (ORFs). Further BLAST analysis of the intergenic candidates and other Desulfovibrio genomes indicated that eight candidates were likely portions of ORFs not previously annotated in the D. vulgaris genome. Comparison of the intergenic and antisense data sets to the bioinformatical predicted candidates, resulted in ~;;54 common candidates. Current approaches using Northern analysis and qRT-PCR are being used toverify expression of the candidates and to further develop the role these sRNAs play in D. vulgaris regulation.

  5. Final technical report for award NO. DE-FG02-95ER20206

    SciTech Connect (OSTI)

    James P. Shapleigh

    2010-02-23T23:59:59.000Z

    ABSTRACT Initial work focused on the regulation of nitrite reductase, the defining reaction of denitrification as well as nitric oxide (NO) reductase. Expression of the genes encoding both proteins was controlled by NnrR. This regulator was shown to be responsive to NO. More recent work has shown NnrR function is also likely inhibited by oxygen. Therefore, it is this protein that sets the oxygen level at which nitrate respiration takes over from aerobic respiration. The gene encoding NO reductase appears to only require NnrR for expression. Expression of the gene encoding nitrite reductase is more complex. In addition to NnrR, a two component sensor regulator complex termed PrrA and PrrB is also required for expression. These proteins are global regulators and serve to link denitrification with other bioenergetic processes in the cell. They also provide an additional layer of oxygen dependent regulation. The sequencing of the R. sphaeroides 2.4.3 genome allowed us to identify several other genes regulated by NnrR. Surprisingly, most of the genes were not essential for denitrification. Their high level of conservation in related denitrifiers suggests they do provide a selectable benefit to the bacterium, however. We also examined the role of nitrate reductase in contributing to denitrification in R. sphaeroides. Strain 2.4.3 is unusual in having two distinct, but related clusters of genes encoding nitrate reductase. One of these genes clusters is expressed under high oxygen conditions but is repressed, likely by PrrB-PrrA, under low oxygen conditions. The other cluster is expressed only under low oxygen conditions. This cluster expresses the nitrate reductase used during denitrification. The high oxygen expressed cluster encodes a protein used for redox homeostasis. Surprisingly, both clusters are fully expressed even in the absence of nitrate. During the course of this work we found that the type strain of R. sphaeroides, 2.4.1, is a partial denitrifier because it has the nitrate and NO reductases but lacks nitrite reductase. Like 2.4.3 it uses NnrR to regulate NO reductase. This unexpected arrangement suggested that it may use NO reductase to detoxify NO produced in its environment. Using a green fluorescent protein based reporter system we were able to demonstrate that NO produced by a denitrifier such as 2.4.3 can induce expression of NO reductase in 2.4.1. We then went on to show that the NO produced by denitrifiers can induce a stress response in other non-denitrifying bacteria. This suggests that the NO produced during denitrification will have a significant impact on the non-denitrifiers present in the surrounding environment. We also expanded our studies to include the denitrifier Agrobacterium tumefaciens. We demonstrated that the expression of the nitrite and NO reductase genes in this bacterium follows the same general scheme as in R. sphaeroides. We also were able to show that this bacterium would induce NO reductase in response to the NO produced by plants. Importantly, we were able to demonstrate that A. tumefaciens had difficulty transitioning from aerobic respiration to denitrification if the transition was sudden. This difficulty manifested as an accumulation of NO. In some conditions cells were slowly able to switch modes of respiration but in other cases NO accumulations seemed to kill the cells. The difficulty in transition appears to be due to an inability to produce enough energy once the oxygen has been completely consumed.

  6. Clostridium thermocellum Transcriptomic Profiles after Exposure to Furfural or Heat Stress

    SciTech Connect (OSTI)

    Wilson, Charlotte M [ORNL; Yang, Shihui [ORNL; Rodriguez, Jr., Miguel [ORNL; Ma, Qin [University of Georgia, Athens, GA; Johnson, Courtney M [ORNL; Dice, Lezlee T [ORNL; Xu, Ying [University of Georgia, Athens, GA; Brown, Steven D [ORNL

    2013-01-01T23:59:59.000Z

    Background The thermophilic anaerobe Clostridium thermocellum is a candidate consolidated bioprocessing (CBP)biocatalyst for cellulosic ethanol production. It is capable of both cellulose solubilization and its fermentation to produce lignocellulosic ethanol. Intolerance to stresses routinely encountered during industrial fermentations may hinder the commercial development of this organism. A previous C. thermocellum ethanol stress study showed that largest transcriptomic response was in genes and proteins related to nitrogen uptake and metabolism. Results In this study, C. thermocellum was grown to mid-exponential phase and treated with furfural or heat to a final concentration of 3 g.L-1 or 68 C respectively to investigate general and specific physiological and regulatory stress responses. Samples were taken at 10, 30, 60 and 120 min post-shock, and from untreated control fermentations, for transcriptomic analyses and fermentation product determinations and compared to a published dataset from an ethanol stress study. Urea uptake genes were induced following furfural stress, but not to the same extent as ethanol stress and transcription from these genes was largely unaffected by heat stress. The largest transcriptomic response to furfural stress was genes for sulfate transporter subunits and enzymes in the sulfate assimilatory pathway, although these genes were also affected late in the heat and ethanol stress responses. Lactate production was higher in furfural treated culture, although the lactate dehydrogenase gene was not differentially expressed under this condition. Other redox related genes such as a copy of the rex gene, a bifunctional acetaldehyde-CoA/alcohol dehydrogenase and adjacent genes did show lower expression after furfural stress compared to the control, heat and ethanol fermentation profiles. Heat stress induced expression from chaperone related genes and overlap was observed with the responses to the other stresses. This study suggests the involvement of C. thermocellum genes with functions in oxidative stress protection, electron transfer, detoxification, sulfur and nitrogen acquisition, and DNA repair mechanisms in its stress responses and the use of different regulatory networks to coordinate and control adaptation. Conclusions This study has identified C. thermocellum gene regulatory motifs and aspects of physiology and gene regulation for further study. The nexus between future systems biology studies and recently developed genetic tools for C. thermocellum offers the potential for more rapid strain development and for broader insights into this organism s physiology and regulation.

  7. Final Report: Structural studies of archatelthermophilic adenylate kinase, September 15, 1996 - September 14, 1998

    SciTech Connect (OSTI)

    Konisky, Jordan

    1998-09-14T23:59:59.000Z

    Through this DOE sponsored program Konisky has studied the evolution and molecular biology of microbes that live in extreme environments. The emphasis of this work has been the determination of the structural features of thermophilic enzymes that allow them to function optimally at near 100%. The laboratory has focused on a comparative study of adenylate kinase (ADK), an enzyme that functions to interconvert adenine nucleotides. Because of the close phylogenetic relatedness of members of the methanococci, differences in the structure of their ADKs will be dominated by structural features that reflect contributions to their optimal temperature for activity, rather than differences due to phylogenetic divergence. The authors have cloned, sequenced and modeled the secondary structure for several methanococcal ADKs. using molecular modeling threading approaches that are based on the solved structure for the porcine ADK, they have also proposed a general low resolution three dimensional structure for each of the methanococcal enzymes. These analyzes have allowed them to propose structural features that confer hyperthermoactivity to those enzymes functioning in the hyperthermophilic members of the Methanococci. Using protein engineering methodologies, they have tested their hypotheses by examining the effects of selective structural changes on thermoactivity. Despite possessing between 68--83% sequence identity, the methanococcal AKs had significantly different stability against thermal denaturation, with melting points ranging from 69--103 C. The construction of several chimerical AKs by linking regions of the MVO and MJA AKs demonstrated the importance of cooperative interactions between amino- and carboxyl-terminal regions in influencing thermostability. Addition of MJA terminal fragments to the MVO AK increased thermal stability approximately 20 C while maintaining 88% of the mesophilic sequence. Further analysis using structural models suggested that hydrophobic interactions are largely responsible for determining the thermostability of the methanococcal AKs. Construction of chimerical enzyme also demonstrated a distinct separation between thermostability and enzymatic temperature optima, suggesting that overall protein flexibility and stability are not dependently linked. Sequence comparisons and model buildings of highly related archaeal adenylate kinases has allowed the prediction of interactions responsible for the large temperature variation in temperatures for of optimal catalytic activity and temperature stability. The tertiary structure for these ADK have been predicted by using homology modeling to further investigate the potential of specific interactions on thermal stability and activity.

  8. SPINE: SParse eIgengene NEtwork Linking Gene Expression Clusters in Dehalococcoides mccartyi to Perturbations in Experimental Conditions

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Mansfeldt, Cresten B.; Logsdon, Benjamin A.; Debs, Garrett E.; Richardson, Ruth E.; Mande, Shekhar C.

    2015-02-25T23:59:59.000Z

    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 100more »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, transcripts for DET0137 and DET0097 displayed a 46.8±11.5 and 14.6±9.3 fold up-regulation, respectively, supporting the model. This is the first study to identify transcripts in Dehalococcoides that potentially respond to tetrachloroethene solvent-toxicity conditions that may be encountered near contamination source zones in sub-surface environments.« less

  9. A STUDY ON LEGIONELLA PNEUMOPHILA, WATER CHEMISTRY, AND ATMOSPHERIC CONDITIONS IN COOLING TOWERS AT THE SAVANNAH RIVER SITE

    SciTech Connect (OSTI)

    Smith, C.; Brigmon, R.

    2009-10-20T23:59:59.000Z

    Legionnaires disease is a pneumonia caused by the inhalation of the bacterium Legionella pneumophila. The majority of illnesses have been associated with cooling towers since these devices can harbor and disseminate the bacterium in the aerosolized mist generated by these systems. Historically, Savannah River Site (SRS) cooling towers have had occurrences of elevated levels of Legionella in all seasons of the year and in patterns that are difficult to predict. Since elevated Legionella in cooling tower water are a potential health concern a question has been raised as to the best control methodology. In this work we analyze available chemical, biological, and atmospheric data to determine the best method or key parameter for control. The SRS 4Q Industrial Hygiene Manual, 4Q-1203, 1 - G Cooling Tower Operation and the SRNL Legionella Sampling Program, states that 'Participation in the SRNL Legionella Sampling Program is MANDATORY for all operating cooling towers'. The resulting reports include L. pneumophila concentration information in cells/L. L. pneumophila concentrations >10{sup 7} cells/L are considered elevated and unsafe so action must be taken to reduce these densities. These remedial actions typically include increase biocide addition or 'shocking'. Sometimes additional actions are required if the problem persists including increase tower maintenance (e.g. cleaning). Evaluation of 14 SRS cooling towers, seven water quality parameters, and five Legionella serogroups over a three-plus year time frame demonstrated that cooling tower water Legionella densities varied widely though out this time period. In fact there was no one common consistent significant variable across all towers. The significant factors that did show up most frequently were related to suspended particulates, conductivity, pH, and dissolved oxygen, not chlorine or bromine as might be expected. Analyses of atmospheric data showed that there were more frequent significant elevated Legionella concentrations when the dew point temperature was high--a summertime occurrence. However, analysis of the three years of Legionella monitoring data of the 14 different SRS Cooling Towers demonstrated that elevated concentrations are observed at all temperatures and seasons. The objective of this study is to evaluate the ecology of L. pneumophila including serogroups and population densities, chemical, and atmospheric data, on cooling towers at SRS to determine whether relationships exist among water chemistry, and atmospheric conditions. The goal is to more fully understand the conditions which inhibit or encourage L. pneumophila growth and supply this data and associated recommendations to SRS Cooling Tower personnel for improved management of operation. Hopefully this information could then be used to help control L. pneumophila growth more effectively in SRS cooling tower water.

  10. Enhanced Practical Photosynthetic CO2 Mitigation

    SciTech Connect (OSTI)

    Gregory Kremer; David J. Bayless; Morgan Vis; Michael Prudich; Keith Cooksey; Jeff Muhs

    2006-01-15T23:59:59.000Z

    This final report highlights significant achievements in the Enhanced Practical Photosynthetic CO{sub 2} Mitigation Project during the period from 10/1/2001 through 01/02/2006. As indicated in the list of accomplishments below, our efforts during this project were focused on the selection of candidate organisms and growth surfaces and initiating long-term tests in the bench-scale and pilot-scale bioreactor test systems. Specific results and accomplishments for the program include: (1) CRF-2 test system: (a) Sampling test results have shown that the initial mass of algae loaded into the Carbon Recycling Facility Version 2 (CRF-2) system can be estimated with about 3% uncertainty using a statistical sampling procedure. (b) The pressure shim header pipe insert design was shown to have better flow for harvesting than the drilled-hole design. (c) The CRF-2 test system has undergone major improvements to produce the high flow rates needed for harvesting (as determined by previous experiments). The main changes to the system are new stainless steel header/frame units, with increased flow capacity and a modified pipe-end-sealing method to improve flow uniformity, and installation and plumbing for a new high flow harvesting pump. Qualitative system tests showed that the harvesting system performed wonderfully, cleaning the growth surfaces within a matter of seconds. (d) Qualitative tests have shown that organisms can be repopulated on a harvested section of a bioreactor screen, demonstrating that continuous bioreactor operation is feasible, with continuous cycles of harvesting and repopulating screens. (e) Final preparations are underway for quantitative, long-term tests in the CRF-2 with weekly harvesting. (2) Pilot-scale test system: (a) The construction of the pilot-scale bioreactor was completed, including the solar collector and light distribution system. Over the course of the project, the solar collector used in the light delivery system showed some degradation, but performed well overall. (b) Testing confirmed that algae can be grown in a sustainable fashion in the pilot bioreactor, even with intermittent availability of sunlight. (c) The pilot-scale tests indicated that algal growth rate followed photon delivery during productivity testing. (3) Organisms and Growth Surfaces: (a) The aeration of growth media with 5% CO{sub 2} in air stimulates cyanobacterial growth 10-20 times over that with air alone. It is possible that the rate of the stimulation of cyanobacterial growth in the CRF will be higher because cyanobacteria will be grown as a biofilm. We plan to increase the concentration to 15% CO{sub 2} in air. (b) Tests have shown a doubling time of the cyanobacterial culture of about 7.5 hours with illumination of about 170 {micro}mol m{sup -2} sec{sup -1}. All lower levels of illumination led to a decrease in the cyanobacterial growth rate. (c) Macroscopical and microscopical observations suggest that the culture of this isolate undergoes significant morphological changes after 60-70 hours of incubation in the batch culture mode. First of all, the culture begins to clump. This clumping could lead to the decrease of effective illumination of culture and may reflect a medium alkalinization. (d) Organization of our collection of the thermophilic cyanobacteria isolated from Yellowstone National Park has resulted in 13 unialgal cultures of thermophilic cyanobacteria. (e) A new species (even probably a new genus) of cyanobacteria, 5.2 s. c. 1, isolated from LaDuke Spring in Great Yellowstone Basin, demonstrates an elevated resistance to some compounds of iron. This might be very important for our project, because plant gases may have elevated amount of iron. Our study of the effect of different concentration of FeCl{sub 3}* 6H{sub 2}O on the growth of the 5.2 s.c.1 isolate showed that iron additions stimulated rather then inhibited the growth of the isolate. Because of this we would recommend this isolate for further experiments. (f) The shape of the Chlorogloeopsis siderophila cells (cyanobacteria) was found to be affected b

  11. Rapid electron exchange between surface-exposed bacterial cytochromes and Fe(III) minerals

    SciTech Connect (OSTI)

    White, Gaye F.; Shi, Zhi; Shi, Liang; Wang, Zheming; Dohnalkova, Alice; Marshall, Matthew J.; Fredrickson, Jim K.; Zachara, John M.; Butt, Julea N.; Richardson, David; Clarke, Thomas A.

    2013-04-16T23:59:59.000Z

    The mineral respiring bacterium Shewanella oneidensis uses a protein complex, MtrCAB, composed of two decaheme cytochromes brought together inside a transmembrane porin to transport electrons across the outer membrane to a variety of mineral-based electron acceptors. A proteoliposome system that contains methyl viologen as an internalised electron carrier has been used to investigate how the topology of the MtrCAB complex relates to its ability to transport electrons across a lipid bilayer to externally-located Fe(III) oxides. With MtrA facing the interior and MtrC exposed on the outer surface of the phospholipid bilayer, direct electron transfer from the interior through MtrCAB to solid-phase Fe(III) oxides was demonstrated. The observed rates of conduction through the protein complex were 2 to 3 orders of magnitude higher than that observed in whole cells, demonstrating that direct electron exchange between MtrCAB and Fe(III) oxides is efficient enough to support in-vivo, anaerobic, solid phase iron respiration.

  12. One simple step in the identification of the cofactors signals, one giant leap for the solution structure determination of multiheme proteins

    SciTech Connect (OSTI)

    Morgado, Leonor; Fernandes, Ana P. [Requimte-CQFB, Departamento de Quimica, Faculdade de Ciencias e Tecnologia, Universidade Nova de Lisboa, Campus Caparica, 2829-516 Caparica (Portugal)] [Requimte-CQFB, Departamento de Quimica, Faculdade de Ciencias e Tecnologia, Universidade Nova de Lisboa, Campus Caparica, 2829-516 Caparica (Portugal); Londer, Yuri Y. [Biosciences Division, Argonne National Laboratory, Argonne, IL 60439 (United States)] [Biosciences Division, Argonne National Laboratory, Argonne, IL 60439 (United States); Bruix, Marta [Departamento de Espectroscopia y Estructura Molecular, Instituto de Quimica-Fisica 'Rocasolano', CSIC, Serrano 119, 28006 Madrid (Spain)] [Departamento de Espectroscopia y Estructura Molecular, Instituto de Quimica-Fisica 'Rocasolano', CSIC, Serrano 119, 28006 Madrid (Spain); Salgueiro, Carlos A., E-mail: csalgueiro@dq.fct.unl.pt [Requimte-CQFB, Departamento de Quimica, Faculdade de Ciencias e Tecnologia, Universidade Nova de Lisboa, Campus Caparica, 2829-516 Caparica (Portugal)

    2010-03-12T23:59:59.000Z

    Multiheme proteins play major roles in various biological systems. Structural information on these systems in solution is crucial to understand their functional mechanisms. However, the presence of numerous proton-containing groups in the heme cofactors and the magnetic properties of the heme iron, in particular in the oxidised state, complicates significantly the assignment of the NMR signals. Consequently, the multiheme proteins superfamily is extremely under-represented in structural databases, which constitutes a severe bottleneck in the elucidation of their structural-functional relationships. In this work, we present a strategy that simplifies the assignment of the NMR signals in multiheme proteins and, concomitantly, their solution structure determination, using the triheme cytochrome PpcA from the bacterium Geobacter sulfurreducens as a model. Cost-effective isotopic labeling was used to double label ({sup 13}C/{sup 15}N) the protein in its polypeptide chain, with the correct folding and heme post-translational modifications. The combined analysis of {sup 1}H-{sup 13}C HSQC NMR spectra obtained for labeled and unlabeled samples of PpcA allowed a straight discrimination between the heme cofactors and the polypeptide chain signals and their confident assignment. The results presented here will be the foundations to assist solution structure determination of multiheme proteins, which are still very scarce in the literature.

  13. Role of microbial iron reduction in the dissolution of iron hydroxysulfate minerals - article no. G01012

    SciTech Connect (OSTI)

    Jones, E.J.P.; Nadeau, T.L.; Voytek, M.A.; Landa, E.R. [US Geological Survey, Reston, VA (United States)

    2006-03-28T23:59:59.000Z

    Reduction of structural sulfate in the iron-hydroxysulfate mineral jarosite by sulfate-reducing bacteria has previously been demonstrated. The primary objective of this work was to evaluate the potential for anaerobic dissolution of the iron-hydroxysulfate minerals jarosite and schwertmannite at neutral pH by iron-reducing bacteria. Mineral dissolution was tested using a long-term cultivar, Geobacter metallireducens strain GS-15, and a fresh isolate Geobacter sp. strain ENN1, previously undescribed. ENN1 was isolated from the discharge site of Shadle Mine, in the southern anthracite coalfield of Pennsylvania, where schwertmannite was the predominant iron-hydroxysulfate mineral. When jarosite from Elizabeth Mine (Vermont) was provided as the sole terminal electron acceptor, resting cells of both G. metallireducens and ENN1 were able to reduce structural Fe(III), releasing Fe{sup +2}, SO{sub 4}{sup -2}, and K{sup +} ions. A lithified jarosite sample from Utah was more resistant to microbial attack, but slow release of Fe{sup +2} was observed. Neither bacterium released Fe{sup +2} from poorly crystalline synthetic schwertmannite. Our results indicate that exposure of jarosite to iron-reducing conditions at neutral pH is likely to promote the mobility of hazardous constituents and should therefore be considered in evaluating waste disposal and/or reclamation options involving jarosite-bearing materials.

  14. How the xap Locus Put Electrical “Zap” in Geobacter sulfurreducens Biofilms

    SciTech Connect (OSTI)

    Magnuson, Timothy S.

    2011-03-01T23:59:59.000Z

    Investigation of microbial mineral respiration remains an experimental challenge. In this issue of Journal of Bacteriology, Rollefson et al. (11) present a foundational study on the functionality of the biofilm matrix in Geobacter sulfurreducens, a model dissimilatory metal respiring bacterium (DMRB). In this study, the investigators identify an extracellular polysaccharide scaffold or network that entraps redox-active proteins, thus positioning these proteins for optimal electron transfer from the membrane-bound respiratory supercomplexes to a mineral phase electron acceptor. The distinguishing feature of this study is the perspective, in that the team examined specifically exopolysaccharide formation and how it enables entrapment and tethering of redox proteins in the vicinity of the cell. Previous studies on Geobacter (10) and Shewanella (4) have focused primarily on the presence and functionality of conductive pili and nanowires, proteinaceous structures that also enable and enhance extracellular electron transfer. Rollefson et al. remind investigators in this field that many microbial systems have redundancy in essential functions, and in the case of DMRB, it is clearly critical that more than one mechanism exists to ensure

  15. Outer-membrane cytochrome-c, OmcF, from Geobacter sulfurreducens : high structural similarity to an algal cytochrone c{sub 6}.

    SciTech Connect (OSTI)

    Pokkuluri, P. R.; Londer, Y. Y.; Wood, S. J.; Duke, N. E. C.; Morgado, L.; Salgueiro, C. A.; Schiffer, M.; Biosciences Division; Univ. Nova de Lisboa, Campus Caparica

    2009-01-01T23:59:59.000Z

    Putative outer membrane c-type cytochromes have been implicated in metal ion reducing properties of Geobacter sulfurreducens. OmcF (GSU2432), OmcB (GSU2731), and OmcC are three such proteins that have predicted lipid anchors. MmcF is a monoheme cytochrome, whereas OmcB and OmcC are multiheme cytochromes. Deletion of OmcF was reported to affect the expression of OmcB and OmcC in G. sulfurreducens. The OmcF deficient strain was impaired in its ability to both reduce and grow on Fe(III) citrate probably because the expression fo OmcB, which is crucial for iron reduction, is low in this strain. U(VI) reduction activity of this bacterium is also lower on deletion of OmcB or OmcF. The U(VI) reduction activity is affected more by the deletion of OmcF than by the deletion of OmcB.

  16. Dissimilatory Bacterial Reduction of Al-Substituted Goethite in Subsurface Sediments

    SciTech Connect (OSTI)

    Kukkadapu, Ravi K.; Zachara, John M.; Smith, Steven C.; Fredrickson, Jim K.; Liu, Chongxuan

    2001-09-13T23:59:59.000Z

    Microbiologic reduction of the 0.2-2.0 mm size fraction of an Atlantic coastal plain sediment (Eatontown) was investigated using a dissimilatory Fe(III)-reducing bacterium (Shewanella putrefaciens, strain CN32) to evaluate mineralogic controls on the rate and extent of Fe(III) reduction and resulting distribution of biogenic Fe(II). Mössbauer spectroscopy, X-ray diffraction (XRD), and scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM/EDX) was used to show that the sedimentary Fe(III) oxide was Al-substituted goethite (11-17% Al) that existed as 1-5 mm aggregates of indistinct morphology. Bioreduction experiments were performed in two buffers [HCO3-, 1,4-piperazinediethansulfonic acid (PIPES)] both without and with 2,6-anthraquinone disulfonate (AQDS), an electron shuttle. The production of biogenic Fe(II) and the distribution of Al (aqueous and sorbed) were followed over time, as was formation of Fe(II) biominerals and physical/chemical changes to the goethite.

  17. Redox reactions of reduced flavin mononucleotide (FMN), riboflavin (RBF), and anthraquinone-2,6-disulfonate (AQDS) with ferrihydrite and lepidocrocite

    SciTech Connect (OSTI)

    Shi, Zhi; Zachara, John M.; Shi, Liang; Wang, Zheming; Moore, Dean A.; Kennedy, David W.; Fredrickson, Jim K.

    2012-11-01T23:59:59.000Z

    Flavins are secreted by the dissimilatory iron-reducing bacterium Shewanella and can function as endogenous electron transfer mediators (ETM). In order to assess the potential importance of flavins in Fe(III) bioreduction, we investigated the redox reaction kinetics of reduced flavins (FMNH2 and RBFH2) with ferrihydrite and lepidocrocite. The organic reductants rapidly reduced and dissolved ferrihydrite and lepidocrocite in the pH range 4-8. The rate constant k for 2-line ferrihydrite reductive dissolution by FMNH2 was 87.5 ? 3.5 M-1?s-1 at pH 7.0 in batch reactors, and the k was similar for RBFH2. For lepidocrocite, the k was 500 ? 61 M-1?s-1 for FMNH2, and 236 ? 22 M-1?s-1 for RBFH2. The surface area normalized initial reaction rates (ra) were between 0.08 and 77 ?moles?m-2?s-1 for various conditions in stopped-flow experiments. Initial rates (ro) were first-order with respect to Fe(III) oxide concentration, and ra increased with decreasing pH. Poorly crystalline 2-line ferrihydrite yielded the highest ra, followed by more crystalline 6-line ferrihydrite, and crystalline lepidocrocite. Compared to a previous whole-cell study with Shewanella oneidensis strain MR-1, our findings suggest that ETM reduction by the Mtr pathway coupled to lactate oxidation are rate limiting, rather than heterogeneous electron transfer to the Fe(III) oxide.

  18. Characterization of the Cobalamin and Fep Operons in Methylobium petrolphilum PM1

    SciTech Connect (OSTI)

    Ewing, J

    2005-09-06T23:59:59.000Z

    The bacterium Methylobium petroleophilum PM1 is economically important due to its ability to degrade methyl tert-butyl ether (MTBE), a fuel additive. Because PM1 is a representative of all MTBE degraders, it is important to understand the transport pathways critical for the organism to survive in its particular environment. In this study, the cobalamin pathway and select iron transport genes will be characterized to help further understand all metabolic pathways in PM1. PM1 contains a total of four cobalamin operons. A single operon is located on the chromosome. Located on the megaplasmid are two tandem repeats of cob operons and a very close representative of the cob operon located on the chromosome. The fep operon, an iron transport mechanism, lies within the multiple copies of the cob operon. The cob operon and the fep operon appear to be unrelated except for a shared need for the T-on-B-dependent energy transduction complex to assist the operons in moving large molecules across the outer membrane of the cell. A genomic study of the cob and the fep operons with that of phylogenetically related organisms helped to confirm the identity of the cob and fep operons and to represent the pathways. More study of the pathways should be done to find the relationship that positions the two seemingly unrelated cob and fep genes together in what appears to be one operon.

  19. Carotenoid biosynthesis in bacteria: In vitro studies of a crt/bch transcription factor from Rhodobacter capsulatus and carotenoid enzymes from Erwinia herbicola

    SciTech Connect (OSTI)

    O'Brien, D.A.

    1992-11-01T23:59:59.000Z

    A putative transcription factor in Rhodobactor capsulatus which binds upstream of the crt and bch pigment biosynthesis operons and appears to play a role in the adaptation of the organism from the aerobic to the anaerobic-photosynthetic growth mode was characterized. Chapter 2 describes the identification of this factor through an in vitro mobility shift assay, as well as the determination of its binding properties and sequence specificity. Chapter 3 focuses on the isolation of this factor. Biochemistry of later carotenoid biosynthesis enzymes derived from the non-photosynthetic bacterium, Erwinia herbicola. Chapter 4 describes the separate overexpression and in vitro analysis of two enzymes involved in the main sequence of the carotenoid biosynthesis pathway, lycopene cyclase and 5-carotene hydroxylase. Chapter 5 examines the overexpression and enzymology of functionally active zeaxanthin glucosyltransferase, an enzyme which carries out a more unusual transformation, converting a carotenoid into its more hydrophilic mono- and diglucoside derivatives. In addition, amino acid homology with other glucosyltransferases suggests a putative binding site for the UDP-activated glucose substrate.

  20. Spatial distribution of an uranium-respiring betaproteobacterium at the rifle, CO field research site

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Koribanics, Nicole M.; Tuorto, Steven J.; Lopez-Chiaffarelli, Nora; McGuinness, Lora R.; Häggblom, Max M.; Williams, Kenneth H.; Long, Philip E.; Kerkhof, Lee J.; Morais, Paula V

    2015-04-13T23:59:59.000Z

    The Department of Energy’s Integrated Field-Scale Subsurface Research Challenge Site (IFRC) at Rifle, Colorado was created to address the gaps in knowledge on the mechanisms and rates of U(VI) bioreduction in alluvial sediments. Previous studies at the Rifle IFRC have linked microbial processes to uranium immobilization during acetate amendment. Several key bacteria believed to be involved in radionuclide containment have been described; however, most of the evidence implicating uranium reduction with specific microbiota has been indirect. Here, we report on the cultivation of a microorganism from the Rifle IFRC that reduces uranium and appears to utilize it as a terminalmore »electron acceptor for respiration with acetate as electron donor. Furthermore, this bacterium constitutes a significant proportion of the subsurface sediment community prior to biostimulation based on TRFLP profiling of 16S rRNA genes. 16S rRNA gene sequence analysis indicates that the microorganism is a betaproteobacterium with a high similarity to Burkholderia fungorum. This is, to our knowledge, the first report of a betaproteobacterium capable of uranium respiration. Our results indicate that this microorganism occurs commonly in alluvial sediments located between 3-6 m below ground surface at Rifle and may play a role in the initial reduction of uranium at the site.« less