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Note: This page contains sample records for the topic "thermophilic bacterium caldicellulosiruptor" from the National Library of EnergyBeta (NLEBeta).
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1

Novel monosaccharide fermentation products in Caldicellulosiruptor...  

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

Abstract: Profiles of metabolites produced by the thermophilic obligately anaerobic cellulose-degrading Gram-positive bacterium Caldicellulosiruptor saccharolyticus DSM 8903...

2

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

SciTech Connect (OSTI)

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.

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

3

Direct Conversion of Plant Biomass to Ethanol by Engineered Caldicellulosiruptor bescii  

SciTech Connect (OSTI)

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.

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

4

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

SciTech Connect (OSTI)

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.

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

5

Complete genome sequence of Thermovibrio ammonificans HB-1T, a thermophilic, chemolithoautotrophic bacterium isolated from a deep-sea hydrothermal vent  

SciTech Connect (OSTI)

Thermovibrio ammonificans type strain HB-1T is a thermophilic (Topt: 75 C), strictly anaero- bic, chemolithoautotrophic bacterium that was isolated from an active, high temperature deep-sea hydrothermal vent on the East Pacific Rise. This organism grows on mineral salts medium in the presence of CO2/H2, using NO3- or S0 as electron acceptors, which are re- duced to ammonium or hydrogen sulfide, respectively. T. ammonificans is one of only three species within the genus Thermovibrio, a member of the family Desulfurobacteriaceae, and it forms a deep branch within the phylum Aquificae. Here we report the main features of the genome of T. ammonificans strain HB-1T (DSM 15698T).

Giovannelli, Donato [Rutgers University; Ricci, Jessica [Rutgers University; Perez-Rodriguez, Ileana [Rutgers University; Hugler, Michael [Woods Hole Oceanographic Institution (WHOI), Woods Hole, MA; O'Brien, Charles [Rutgers University; Keddis, Ramaydalis [Rutgers University; Grosche, Ashley [Rutgers University; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Bruce, David [Los Alamos National Laboratory (LANL); Davenport, Karen W. [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Han, James [U.S. Department of Energy, Joint Genome Institute; Han, Cliff [Los Alamos National Laboratory (LANL); Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Vetriani, Costantino [Rutgers University

2012-01-01T23:59:59.000Z

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)

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.

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

7

Thermoflexus hugenholtzii gen. nov., sp. nov., a thermophilic, microaerophilic, filamentous bacterium representing a novel class in the Chloroflexi, Thermoflexia classis nov., and description of Thermoflexaceae fam. nov. and Thermoflexales ord. nov.  

SciTech Connect (OSTI)

A thermophilic, filamentous, heterotrophic bacterium designated strain JAD2T was isolated from sediment of Great Boiling Spring in Nevada, USA. Cells had an average diameter of 0.3 µm and length of 4.0 µm, and formed filaments typically ranging in length from 20 µm to 200 µm. Filaments were negative for the Gram stain reaction, spores were not formed, and motility was not observed. The optimum temperature for growth was 75 °C with a range from 67.5-75 °C, and the optimum pH for growth was 6.75 with a range from 6.5-7.75. Peptone, tryptone or yeast extract were able to support growth when supplemented with a vitamin solution, but no growth was observed using a variety of defined organic substrates. Strain JAD2T was a facultative microaerophile, with optimal growth at 1% v/v O2 and an upper limit of 8% O2, and anaerobic growth was stimulated by fumarate but inhibited by sulfite and elemental sulfur. The major cellular fatty acids (>5%) were C16:0, C19:0, C18:0, C20:0, and C19:1. The genomic DNA G+C content was 69.3%. Phylogenetic and phylogenomic analyses using 16S rRNA gene sequences and other conserved genes placed JAD2T and other members of the yet-uncultivated GAL35 group within the phylum Chloroflexi, but not within any existing class in this phylum. These results indicate that strain JAD2T is the first cultivated representative of a new lineage within the phylum Chloroflexi, for which we propose the name Thermoflexus hugenholtzii gen. nov., sp. nov., type strain JAD2T, within Thermoflexia classis nov., Thermoflexales ord. nov., and Thermoflexaceae fam. nov.

Dodsworth, Jeremy A.; Gevorkian, Jonathan; Despujos, Fairuz; Cole, Jesse; Murugapiran, Senthil K.; Ming, Hong; Li, Wen J.; Zhang, Gengxin; Dohnalkova, Alice; Hedlund, Brian P.

2014-06-06T23:59:59.000Z

8

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:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr May JunDatastreamsmmcrcalgovInstrumentsrucLas ConchasPassiveSubmittedStatus TomAboutManusScienceThe43068 - Energy Innovation

9

Proteogenomic Analysis of a Thermophilic Bacterial Consortium...  

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

Analysis of a Thermophilic Bacterial Consortium Adapted to Deconstruct Switchgrass. Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to Deconstruct...

10

Autoheated thermophilic aerobic digestion  

SciTech Connect (OSTI)

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.

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

11

Anaerobic thermophilic culture system  

DOE Patents [OSTI]

A mixed culture system of the newly discovered microorganism Thermoanaerobacter ethanolicus ATCC31550 and the microorganism Clostridium thermocellum ATCC31549 is described. In a mixed nutrient culture medium that contains cellulose, these microorganisms have been coupled and cultivated to efficiently ferment cellulose to produce recoverable quantities of ethanol under anaerobic, thermophilic conditions.

Ljungdahl, Lars G. (Athens, GA); Wiegel, Jurgen K. W. (Gottingen, DE)

1981-01-01T23:59:59.000Z

12

Biocorrosive Thermophilic Microbial Communities in Alaskan North Slope Oil Facilities  

E-Print Network [OSTI]

anaerobic thermophilic oil reservoir and well communities.been detected in hot oil reservoirs and production fluids (other thermophilic oil reservoirs and wells suggests that

Duncan, Kathleen E.

2010-01-01T23:59:59.000Z

13

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

SciTech Connect (OSTI)

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.

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

14

E-Print Network 3.0 - anaerobic bacterium thermoanaerobacter...  

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

.1.5 Selection of thermophilic conditions 7 1.2 Microbiology of thermophilic anaerobic methanol conversion 7 1 Source: Groningen, Rijksuniversiteit - Centre for Ecological and...

15

Thermophilic Biotrickling Filtration of Ethanol Vapors  

E-Print Network [OSTI]

Thermophilic Biotrickling Filtration of Ethanol Vapors H U U B H . J . C O X , T H O M A S S E X of ethanol vapors in biotrickling filters for air pollution control was investigated. Two reactors were adaptation phase, the removal of ethanol was similar in both reactors. At a bed contact time of 57 s

16

Biocorrosive Thermophilic Microbial Communities in Alaskan North Slope Oil Facilities  

E-Print Network [OSTI]

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

Duncan, Kathleen E.

2010-01-01T23:59:59.000Z

17

Biocorrosive Thermophilic Microbial Communities in Alaskan North Slope Oil Facilities  

E-Print Network [OSTI]

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

Duncan, Kathleen E.

2010-01-01T23:59:59.000Z

18

Caminibacter mediatlanticus sp. nov., a thermophilic, chemolithoautotrophic,  

E-Print Network [OSTI]

-ammonifying bacterium isolated from a deep-sea hydrothermal vent on the Mid-Atlantic Ridge James W. Voordeckers,1 strain TB-2T , was isolated from the walls of an active deep-sea hydrothermal vent chimney on the Mid. Growth occurred under chemolithoautotrophic conditions with H2 as the energy source and CO2 as the carbon

Vetriani, Costantino

19

Protein Dynamics in a Family of Laboratory Evolved Thermophilic Enzymes  

E-Print Network [OSTI]

, 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

Arnold, Frances H.

20

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

SciTech Connect (OSTI)

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.

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

Note: This page contains sample records for the topic "thermophilic bacterium caldicellulosiruptor" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


21

Nautilia abyssi sp. nov.,1 a novel thermophilic, chemolithoautotrophic, sulfur-reducing bacterium isolated from an East Pacific2  

E-Print Network [OSTI]

isolated from an East Pacific2 Rise hydrothermal vent3 4 Karine Alain1 , Nolwenn Callac1 , Marianne Guégan1 Rise hydrothermal vent (13°N) sample and subjected to a polyphasic27 taxonomic analysis. The cells were° as an electron acceptor and CO2 as a31 carbon source. Alternatively, strain PH1209T was able to use peptone

Boyer, Edmond

22

E-Print Network 3.0 - alkalophilic thermophilic bacillus Sample...  

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

9 Life on Earth. II The Hadean Earth Summary: ) Alkalophiles - inhabit alkaline lakes (pH10) Barophiles - high pressure Thermophiles - hot environments... of Life LUCA...

23

E-Print Network 3.0 - aerobic co-oxidizing thermophile Sample...  

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

Life LUCA may be a Thermophile Possibly more complex than some existing life 12;The Tree of Life 12... ) Alkalophiles - inhabit alkaline lakes (pH10) Barophiles -...

24

E-Print Network 3.0 - autoheated thermophilic aerobic Sample...  

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

Life LUCA may be a Thermophile Possibly more complex than some existing life 12;The Tree of Life 12... ) Alkalophiles - inhabit alkaline lakes (pH10) Barophiles -...

25

E-Print Network 3.0 - anaerobic thermophilic biogas Sample Search...  

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

biogas Search Powered by Explorit Topic List Advanced Search Sample search results for: anaerobic thermophilic biogas Page: << < 1 2 3 4 5 > >> 1 Institute for Renewable Energy Ltd...

26

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

SciTech Connect (OSTI)

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.

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

27

Pathway engineering to improve ethanol production by thermophilic bacteria  

SciTech Connect (OSTI)

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.

Lynd, L.R.

1998-12-31T23:59:59.000Z

28

Biocorrosive Thermophilic Microbial Communities in Alaskan North Slope Oil Facilities  

SciTech Connect (OSTI)

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.

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

29

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

SciTech Connect (OSTI)

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.

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

30

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

SciTech Connect (OSTI)

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.

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

31

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

SciTech Connect (OSTI)

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.

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

2010-07-20T23:59:59.000Z

32

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

E-Print Network [OSTI]

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

Gladden, J.M.

2012-01-01T23:59:59.000Z

33

Thermophilic Gram-Positive Biocatalysts for Biomass Conversion to Ethanol  

SciTech Connect (OSTI)

Production of energy from renewable sources is receiving increased attention due to the finite nature of fossil fuels and the environmental impact associated with the continued large scale use of fossil energy sources. Biomass, a CO2-neutral abundant resource, is an attractive alternate source of energy. Biomass-derived sugars, such as glucose, xylose, and other minor sugars, can be readily fermented to fuel ethanol and commodity chemicals. Extracellular cellulases produced by fungi are commercially developed for depolymerization of cellulose in biomass to glucose for fermentation by appropriate biocatalysts in a simultaneous saccharification and fermentation (SSF) process. Due to the differences in the optimum conditions for the activity of the fungal cellulases and the growth and fermentation characteristics of the current industrial biocatalysts, SSF of cellulose is envisioned at conditions that are not optimal for the fungal cellulase activity leading to higher than required cost of cellulase in SSF. We have isolated bacterial biocatalysts whose growth and fermentation requirements match the optimum conditions for commercial fungal cellulase activity (pH 5.0 and 50 deg. C). These isolates fermented both glucose and xylose, major components of cellulose and hemicellulose, respectively, to L(+)-lactic acid. Xylose was metabolized through the pentose-phosphate pathway by these organisms as evidenced by the fermentation profile and analysis of the fermentation products of 13C1-xylose by NMR. As expected for the metabolism of xylose by the pentose-phosphate pathway, 13C-lactate accounted for more than 90% of the total 13C-labeled products. All three strains fermented crystalline cellulose to lactic acid with the addition of fungal cellulase (Spezyme CE) (SSF) at an optimum of about 10 FPU/g cellulose. These isolates also fermented cellulose and sugar cane bagasse hemicellulose acid hydrolysate simultaneously. Based on fatty acid profile and 16S rRNA sequence, these isolates cluster with Bacillus coagulans although B. coagulans type strain, ATCC 7050, failed to utilize xylose as a carbon source. For successful production of ethanol from pyruvate, both pyruvate decarboxylase (PDC) and alcohol dehydrogenase (AHD) need to be produced at optimal levels in these biocatalysts. A plasmid containing the S. ventriculi pdc gene and the adh gene from geobacillus stearothermophilus was constructed using plasmid pWH1520 that was successfully used for expression of pdc in B. megaterium. The resulting portable ethanol (PET) plasmid, pJAM423, was transformed into B. megaterium. After xylose induction, a significant fraction of cell cytoplasm was composed of the S. ventriculi PDC and G. stearothermophilus ADH proteins. In preliminary experiments, the amount of ethanol produced by b. megaterium with plasmid pJAM423 was about twice (20 mM) of the bacterium without the plasmid. These results show that the PET operon is functional in B. megaterium but high level ethanol production needs further genetic and metabolic engineering. A genetic transfer system for the second generation biocatalysts needs to be developed for transferring the plasmid pJAM423 and its derivatives for engineering these organisms for ethanol production from biomass derived sugars and cellulose to ethanol. One of the new biocatalysts, strain P4-102B was found to be transformable with plasmids and the method for introducing plasmid pJAM423 into this strain and expression of the encoded DNA is being optimized. These new second generation biocatalysts have the potential to reduce the cost of SSF by minimizing the amount of fungal cellulases, a significant cost component in the use of biomass as a renewable resource for production of fuels and chemicals.

Shanmugam, K.T.; Ingram, L.O.; Maupin-Furlow, J.A.; Preston, J.F.; Aldrich, H.C.

2003-12-01T23:59:59.000Z

34

Novel monosaccharide fermentation products in Caldicellulosiruptor  

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:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmosphericNuclear Security Administration the Contributions andDataNationalNewportBig Eddyof

35

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

SciTech Connect (OSTI)

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

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

36

E-Print Network 3.0 - ammonia oxidizing bacterium Sample Search...  

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

0099-22409804.00 0 Summary: acetate oxidation with electron transfer to an anaerobic partner bacterium in the absence of ferric iron... , a syntrophic coculture of a...

37

E-Print Network 3.0 - antarctic bacterium pseudoalteromonas Sample...  

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

O-specific poly- saccharide of the marine bacterium Pseudoalteromonas tetraodonis IAM 14160(T... ., and Parrilli, M. 2005. The O-chain structure from the LPS of marine...

38

E-Print Network 3.0 - acidophilic heterotrophic bacterium Sample...  

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

acidophilic thermotolerant Archaea including Caldivirga... is the causative agent of potato late blight, cluster together without support with one cyano- bacterium... source:...

39

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

E-Print Network [OSTI]

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

Lovley, Derek

40

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

E-Print Network [OSTI]

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...

Smith, Frank Judson

1976-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "thermophilic bacterium caldicellulosiruptor" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


41

Obligate autotrophy in the ammonia oxidizing bacterium Nitrosomonas europaea.  

SciTech Connect (OSTI)

Closing report for project DOE-FG02-03ER15436. The project studied obligate autotrophy in the ammonia oxidizing bacterium Nitrosomonas europaea. Nitrosomonas europaea can obtain all of its energy and reductant for growth from the oxidation of ammonia to nitrite and is, therefore, classified as a chemolithotroph. This bacterium is also an autotroph, which can derive all cellular carbon from carbon dioxide. N. europaea seems incapable of growth with other carbon or energy sources. This restricted capability is surprising given that ammonia is a poor energy source. The main goal of the project was to examine the basis of autotrophy in N. europaea or, thought of another way, to determine the barriers to heterotrophy. The approach was enabled by the N. europaea genome sequence, stimulating new ways of thinking about this physiological paradox—an insistence on a single, albeit poor, energy source. Objective 1 was to examine the expression and regulation of the genes coding for alpha-ketoglutarate dehydrogenase, determine if the enzyme’s activity is present, and determine whether alteration of the expression levels influences autotrophic growth. Although Nitrosomonas europaea lacks measurable alpha-ketoglutarate dehydrogenase activity, the genome sequence revealed the presence of the genes encoding the enzyme. A knockout mutation was created in the sucA gene encoding the E1 subunit. Compared to wild-type cells, the mutant strain showed an accelerated loss of ammonia monooxygenase and hydroxylamine oxidoreductase activities upon entering stationary phase. In addition, unlike wild-type cells, the mutant strain showed a marked lag in the ability to resume growth in response to pH adjustments in late stationary phase. The results were published in Hommes N.G., Kurth E. G., Sayavedra-Soto L.A., and Arp D.J. (2006) Disruption of sucA, which encodes a subunit of alpha-ketoglutarate dehydrogenase, affects the survival of Nitrosomonas europaea in stationary phase. Journal of Bacteriology 188:343-347. Objective 2 was to determine the basis of fructose stimulation of growth on ammonia, examine fructose metabolism, and determine the impact of other compounds on growth on ammonia. Previous studies showed that N. europaea can utilize limited amounts of certain organic compounds, including amino acids, pyruvate, and acetate, although no organic compound has been reported to support the growth of N. europaea. The genomic sequence of N. europaea revealed a potential permease for fructose. N. europaea utilized fructose and other compounds as carbon sources to support growth. Cultures were incubated in the presence of fructose or other organic compounds in sealed bottles purged of CO(2). In these cultures, addition of either fructose or pyruvate as the sole carbon source resulted in a two- to threefold increase in optical density and protein content in 3 to 4 days. Studies with [(14)C]fructose showed that >90% of the carbon incorporated by the cells during growth was derived from fructose. Cultures containing mannose, glucose, glycerol, mannitol, citrate, or acetate showed little or no growth. N. europaea was not able to grow with fructose as an energy source, although the presence of fructose did provide an energy benefit to the cells. These results show that N. europaea can be grown in carbon dioxide free medium by using fructose and pyruvate as carbon sources and may now be considered a facultative chemolithoorganotroph. The results were published in Hommes N.G., Sayavedra-Soto L.A. and Arp. D.J. (2003). Chemolithotrophic growth of Nitrosomonas europaea on fructose. Journal of Bacteriology. 185:6809-2773. Objective 3 attempted to grow N. europaea heterotrophically through pathways predicted by the genome. Experiments with mutant strains and complementation studies were performed to test whether N. europaea can utilize other carbon sources. N. europaea was not able to grow heterotrophically in the conditions tested in this objective.

Daniel James Arp; Luis Alberto Sayavedra-Soto

2006-01-01T23:59:59.000Z

42

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

SciTech Connect (OSTI)

We present here the complete 2.4 Mb genome of the cellulolytic actinobacterial thermophile, Acidothermus cellulolyticus 11B. New secreted glycoside hydrolases and carbohydrate esterases were identified in the genome, revealing a diverse biomass-degrading enzyme repertoire far greater than previously characterized, and significantly elevating the industrial value of this organism. A sizable fraction of these hydrolytic enzymes break down plant cell walls and the remaining either degrade components in fungal cell walls or metabolize storage carbohydrates such as glycogen and trehalose, implicating the relative importance of these different carbon sources. A novel feature of the A. cellulolyticus secreted cellulolytic and xylanolytic enzymes is that they are fused to multiple tandemly arranged carbohydrate binding modules (CBM), from families 2 and 3. Interestingly, CBM3 was found to be always N-terminal to CBM2, suggesting a functional constraint driving this organization. While the catalytic domains of these modular enzymes are either diverse or unrelated, the CBMs were found to be highly conserved in sequence and may suggest selective substrate-binding interactions. For the most part, thermophilic patterns in the genome and proteome of A. cellulolyticus were weak, which may be reflective of the recent evolutionary history of A. cellulolyticus since its divergence from its closest phylogenetic neighbor Frankia, a mesophilic plant endosymbiont and soil dweller. However, ribosomal proteins and non-coding RNAs (rRNA and tRNAs) in A. cellulolyticus showed thermophilic traits suggesting the importance of adaptation of cellular translational machinery to environmental temperature. Elevated occurrence of IVYWREL amino acids in A. cellulolyticus orthologs compared to mesophiles, and inverse preferences for G and A at the first and third codon positions also point to its ongoing thermoadaptation. Additional interesting features in the genome of this cellulolytic, hot-springs dwelling prokaryote include a low occurrence of pseudogenes or mobile genetic elements, an unexpected complement of flagellar genes, and presence of three laterally-acquired genomic islands of likely ecophysiological value.

Barabote, Ravi D.; Xie, Gary; Leu, David H.; Normand, Philippe; Necsulea, Anamaria; Daubin, Vincent; Medigue, Claudine; Adney, William S.; Xu,Xin Clare; Lapidus, Alla; Detter, Chris; Pujic, Petar; Bruce, David; Lavire, Celine; Challacombe, Jean F.; Brettin, Thomas S.; Berry, Alison M.

2009-01-01T23:59:59.000Z

43

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

44

A plant growth-promoting bacterium that decreases nickel toxicity in seedlings  

SciTech Connect (OSTI)

A plant growth-promoting bacterium, Kluyvera ascorbata SUD165, that contained high levels of heavy metals was isolated from soil collected near Sudbury, Ontario, Canada. The bacterium was resistant to the toxic effects of Ni{sup 2+}, Pb{sup 2+}, Zn{sup 2+}, and CrO{sub 4}{sup {minus}}, produced a siderophore(s), and displayed 1-aminocyclopropane-1-carboxylic acid deaminase activity. Canola seeds inoculated with this bacterium and then grown under gnotobiotic conditions in the presence of high concentrations of nickel chloride were partially protected against nickel toxicity. In addition, protection by the bacterium against nickel toxicity was evident in pot experiments with canola and tomato seeds. The presence of K. ascorbata SUD165 had no measurable influence on the amount of nickel accumulated per milligram (dry weight) of either roots or shoots of canola plants. Therefore, the bacterial plant growth-promoting effect in the presence of nickel was probably not attributable to the reduction of nickel uptake by seedlings. Rather, it may reflect the ability of the bacterium to lower the level of stress ethylene induced by the nickel.

Burd, G.I.; Dixon, D.G.; Glick, B.R. [Univ. of Waterloo, Ontario (Canada). Dept. of Biology

1998-10-01T23:59:59.000Z

45

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

SciTech Connect (OSTI)

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.

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

2014-04-01T23:59:59.000Z

46

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)

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

Mosier, Annika [Stanford University] [Stanford University

2012-03-22T23:59:59.000Z

47

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)

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

Mosier, Annika [Stanford University

2013-01-22T23:59:59.000Z

48

Complete Genome Sequence of a thermotolerant sporogenic lactic acid bacterium, Bacillus coagulans strain 36D1  

SciTech Connect (OSTI)

Bacillus coagulans is a ubiquitous soil bacterium that grows at 50-55 C and pH 5.0 and fer- ments various sugars that constitute plant biomass to L (+)-lactic acid. The ability of this spo- rogenic lactic acid bacterium to grow at 50-55 C and pH 5.0 makes this organism an attrac- tive microbial biocatalyst for production of optically pure lactic acid at industrial scale not only from glucose derived from cellulose but also from xylose, a major constituent of hemi- cellulose. This bacterium is also considered as a potential probiotic. Complete genome se- quence of a representative strain, B. coagulans strain 36D1, is presented and discussed.

Rhee, Mun Su [University of Florida, Gainesville; Moritz, Brelan E. [University of Florida, Gainesville; Xie, Gary [Los Alamos National Laboratory (LANL); 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; Bruce, David [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Chertkov, Olga [Los Alamos National Laboratory (LANL); Brettin, Thomas S [ORNL; Han, Cliff [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Patel, Milind [University of Florida, Gainesville; Ou, Mark [University of Florida, Gainesville; Harbrucker, Roberta [University of Florida, Gainesville; Ingram, Lonnie O. [University of Florida; Shanmugam, Keelnathan T. [University of Florida

2011-01-01T23:59:59.000Z

49

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

SciTech Connect (OSTI)

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.

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

50

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

E-Print Network [OSTI]

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

Ismagilov, Rustem F.

51

Genome sequence of the mycorrhizal helper bacterium Pseudomonas fluorescens BBc6R8  

SciTech Connect (OSTI)

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.

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

52

A soil bacterium regulates plant acquisition of iron via deficiency-inducible mechanisms  

E-Print Network [OSTI]

A soil bacterium regulates plant acquisition of iron via deficiency-inducible mechanisms Huiming in most soils. While certain soil microbes produce chelating agents that enhance the solubility of iron understanding that select soil microbes play a signaling role in activating growth and stress responses

Paré, Paul W.

53

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

E-Print Network [OSTI]

; 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

Bae, Jin-Woo

54

The oxidation of ethylene glycol by a salt-requiring bacterium  

E-Print Network [OSTI]

by bacteria. Calcium glycolate was isolated and identified as the end-product of the growth of Bacterium aceti (Acetobacter aceti) in a medium containing CaCo with ethylene glycol as the sole source of carbon. This was sub- sequently confirmed by Seifert...

Caskey, William Horton

1975-01-01T23:59:59.000Z

55

The Sulfate-Reducing Bacterium Desulfovibrio desulfuricans ND132 as a Model for Understanding Bacterial Mercury  

E-Print Network [OSTI]

Bacterial Mercury Methylation Contact: Cynthia Gilmour (gilmourc@si.edu, 443-482-2498) DOE/Office of Science/Biological & Environmental Research ·The ORNL Mercury Science Focus Area is developing the Hg-methylating bacterium as a model for understanding bacterial mercury methylation. Appl. Environ. Microbiol. 77:3938-3951 (doi:10

56

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

SciTech Connect (OSTI)

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.

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

57

Draft Genome Sequence for Microbacterium laevaniformans Strain OR221, a Bacterium Tolerant to Metals, Nitrate, and Low pH  

SciTech Connect (OSTI)

Microbacterium laevaniformans strain OR221 was isolated from subsurface sediments obtained from the Field Research Center (FRC) in Oak Ridge, TN. It was characterized as a bacterium tolerant to heavy metals such as uranium, nickel, cobalt, cadmium, as well as nitrate and low pH. We present its draft genome sequence.

Brown, Steven D [ORNL; Palumbo, Anthony Vito [ORNL; Panikov, Nikolai [ORNL; Ariyawansa, Thilini [Northeastern University; Klingeman, Dawn Marie [ORNL; Johnson, Courtney M [ORNL; Land, Miriam L [ORNL; Utturkar, Sagar M [ORNL; Epstein, Slava [Northeastern University

2012-01-01T23:59:59.000Z

58

Effects of selected thermophilic microorganisms on crude oils at elevated temperatures and pressures; Quarterly report, January 1, 1990--March 31, 1990  

SciTech Connect (OSTI)

The objective of this program is to determine the chemical and physical effects of thermophilic organisms on crude oils and cores at elevated temperatures and pressures. Ultimately a data base will be generated which will be used in technical and economic feasibility studies leading to field application. Results of the biotreatment of the teapot Naval Petroleum Resume {number_sign}3(PR3) with BNL strain BNL-4-24 at 65{degree}C under 2000 psi of nitrogen and 80 psi of carbon dioxide are presented. Results are also briefly discussed on the biotreatment of Wilmington, CA crude with BNL-4-22 on the reduction of nickel porphyrin complex. 4 refs., 6 figs.

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

1990-03-01T23:59:59.000Z

59

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

SciTech Connect (OSTI)

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.

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

60

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

SciTech Connect (OSTI)

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.

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

Note: This page contains sample records for the topic "thermophilic bacterium caldicellulosiruptor" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


61

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)

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.

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

62

High-Quality Draft Genome Sequence of the Opitutaceae Bacterium Strain TAV1, a Symbiont of the Wood-Feeding Termite Reticulitermes flavipes  

SciTech Connect (OSTI)

Microbial communities in the termite hindgut are essential for degrading plant material. We present the high-quality draft genome sequence of the Opitutaceae bacterium strain TAV1, the first member of the phylum Verrucomicrobia to be isolated from wood-feeding termites. The genomic analysis reveals genes coding for lignocellulosic degradation and nitrogen fixation.

Isanapong, Jantiya [University of Texas, Arlington; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Bruce, David [Los Alamos National Laboratory (LANL); Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Han, James [U.S. Department of Energy, Joint Genome Institute; Han, Cliff [Los Alamos National Laboratory (LANL); Held, Brittany [Los Alamos National Laboratory (LANL); Huntemann, Marcel [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Mavromatis, K [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; Szeto, Ernest [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Rodrigues, Jorge L.M. [University of Texas, Arlington

2012-01-01T23:59:59.000Z

63

Reduction of Cr(VI) under acidic conditions by the facultative Fe(III)-reducing bacterium Acidiphilium cryptum  

SciTech Connect (OSTI)

The potential for biological reduction of Cr(VI) under acidic conditions was evaluated with the acidophilic, facultatively metal-reducing bacterium Acidiphilium cryptum strain JF-5 to explore the role of acidophilic microorganisms in the Cr cycle in low-pH environments. An anaerobic suspension of washed A. cryptum cells rapidly reduced 50 M Cr(VI) at pH 3.2; biological reduction was detected from pH 1.7-4.7. The reduction product, confirmed by XANES analysis, was entirely Cr(III) that was associated predominantly with the cell biomass (70-80%) with the residual residing in the aqueous phase. Reduction of Cr(VI) showed a pH optimum similar to that for growth and was inhibited by 5 mM HgCl2, suggesting that the reaction was enzyme-mediated. Introduction of O2 into the reaction medium slowed the reduction rate only slightly, whereas soluble Fe(III) (as ferric sulfate) increased the rate dramatically, presumably by the shuttling of electrons from bioreduced Fe(II) to Cr(VI) in a coupled biotic-abiotic cycle. Starved cells could not reduce Cr(VI) when provided as sole electron acceptor, indicating that Cr(VI) reduction is not an energy-conserving process in A. cryptum. We speculate, rather, that Cr(VI) reduction is used here as a detoxification mechanism.

David E. Cummings; Scott Fendorf; Rajesh K. Sani; Brent M. Peyton; Timothy S. Magnuson

2007-01-01T23:59:59.000Z

64

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

SciTech Connect (OSTI)

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.

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

2011-01-01T23:59:59.000Z

65

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]

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...

Gonzalez, Carlos Francisco

1972-01-01T23:59:59.000Z

66

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

SciTech Connect (OSTI)

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.

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

67

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]

., 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

Paris-Sud XI, Université de

68

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:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmosphericNuclear Security Administration the Contributions andDataNationalNewportBig Eddyof H-2NovelSolarNovel StructuredNovel

69

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:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmosphericNuclear SecurityTensile Strain Switched Ferromagnetism in Layered NbS2 andThe1 MembersStability ofXPS.SolidInnovationEnergy

70

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

E-Print Network [OSTI]

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

Hazen, Terry

71

JOURNAL OF BACTERIOLOGY, July 2008, p. 45684575 Vol. 190, No. 13 0021-9193/08/$08.00 0 doi:10.1128/JB.00369-08  

E-Print Network [OSTI]

. The thermophilic bacterium Thermus thermophilus, with a growth temperature ranging from 45° to 85°C, belongs to one). The chromosomes are highly conserved with an identity of 94%, but variations are found, predominantly in cell), and the integral membrane components, called TpsB, of the two

Kleinschmidt, Jörg H.

72

Pathogenesis of the carcinogenic bacterium, Helicobacter pylori  

E-Print Network [OSTI]

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 ...

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

2007-01-01T23:59:59.000Z

73

Laboratory Directed Research and Development Program FY 2007  

E-Print Network [OSTI]

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

editor, Todd C Hansen,

2008-01-01T23:59:59.000Z

74

Kinetics of inactivation of indicator pathogens during thermophilic anaerobic digestion  

E-Print Network [OSTI]

relationships are necessary. ÂŞ 2010 Elsevier Ltd. All rights reserved. 1. Introduction Land application the opportunity to put sewage sludge, which otherwise needs to be disposed of, towards beneficial use such as crop, enteric viruses and Salmonella spp. Land application of Class B biosolids, which require only reduction

75

Biocorrosive Thermophilic Microbial Communities in Alaskan North Slope Oil Facilities  

E-Print Network [OSTI]

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

Duncan, Kathleen E.

2010-01-01T23:59:59.000Z

76

Conversion of sugarcane bagasse to carboxylic acids under thermophilic conditions  

E-Print Network [OSTI]

?????????????. 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...

Fu, Zhihong

2009-05-15T23:59:59.000Z

77

Biocorrosive Thermophilic Microbial Communities in Alaskan North Slope Oil Facilities  

E-Print Network [OSTI]

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

Duncan, Kathleen E.

2010-01-01T23:59:59.000Z

78

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...

79

Thermoflexus hugenholtzii gen. nov., sp. nov., a thermophilic,  

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:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmosphericNuclear SecurityTensile Strain Switched Ferromagnetism in Layered NbS2 andThe1 MembersStability ofXPS.Solid with

80

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:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmosphericNuclear SecurityTensile Strain Switched Ferromagnetism in Layered NbS2 andThe1 MembersStability ofXPS.SolidInnovation

Note: This page contains sample records for the topic "thermophilic bacterium caldicellulosiruptor" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


81

Biogenic mineral production by a novel arsenic-metabolizing thermophilic  

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:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr May JunDatastreamsmmcrcalgovInstrumentsruc DocumentationP-Series to someone6 M. Babzien, I.ProgramBig SolBiofilm assemblybacterium from the

82

Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to  

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:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmosphericNuclear Security Administration the1 - SeptemberMicroneedlesAdvanced Photon Source The

83

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...

84

Fermentation method producing ethanol  

DOE Patents [OSTI]

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.

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

1986-01-01T23:59:59.000Z

85

E-Print Network 3.0 - acidophilic bacterium acidithiobacillus...  

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

Moscow State University Collection: Biology and Medicine 52 Multiple Mechanisms of Uranium Immobilization by Cellulomonas sp. Strain ES6 Summary: released by cells. Cultures...

86

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...

87

Genetic manipulation of the obligate chemolithoautotrophic bacterium Thiobacillus denitrificans  

E-Print Network [OSTI]

water  (18-­?M?  resistance)  obtained  from  a  Milli-­?Q  Biocel  system  (Millipore,   Bedford,  MA)  or  similar  purification  system  

Beller, H.R.

2012-01-01T23:59:59.000Z

88

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;...

89

Genetic manipulation of the obligate chemolithoautotrophic bacterium Thiobacillus denitrificans  

E-Print Network [OSTI]

uranium-­?contaminated  aquifers  by   in  situ   reductive  immobilization  [i.e. ,  microbially   mediated  conversion  

Beller, H.R.

2012-01-01T23:59:59.000Z

90

Genetic manipulation of the obligate chemolithoautotrophic bacterium Thiobacillus denitrificans  

SciTech Connect (OSTI)

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.

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

2011-07-15T23:59:59.000Z

91

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

92

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...

93

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

E-Print Network [OSTI]

, USA. Abbreviations: AQDS, anthraquinone-2,6-disulfonate; NTA, nitrilotri- acetic acid; PHA, poly-hydroxyalkanoate;

Lovley, Derek

94

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

95

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

E-Print Network [OSTI]

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

Reddy, A. P.

2012-01-01T23:59:59.000Z

96

Novel Thermophilic Celluloly1c Isolates Belonging to the Phylum Chloroflexi  

E-Print Network [OSTI]

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

Walker, Lawrence R.

97

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

E-Print Network [OSTI]

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

Weston, Ken

98

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

E-Print Network [OSTI]

and their enzymes on bioenergy feedstocks Amitha P. ReddyVanderGheynst 1,2* Joint BioEnergy Institute, Emeryville, CA2009. The water footprint of bioenergy. Proceedings of the

Reddy, A. P.

2012-01-01T23:59:59.000Z

99

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

E-Print Network [OSTI]

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

Clarke, Steven

100

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

DOE Patents [OSTI]

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.

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

2013-01-15T23:59:59.000Z

Note: This page contains sample records for the topic "thermophilic bacterium caldicellulosiruptor" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


101

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

DOE Patents [OSTI]

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.

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

102

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

DOE Patents [OSTI]

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.

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

2013-11-05T23:59:59.000Z

103

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

DOE Patents [OSTI]

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.

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

2013-01-29T23:59:59.000Z

104

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

E-Print Network [OSTI]

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

Walker, Lawrence R.

105

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

SciTech Connect (OSTI)

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.

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

106

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

DOE Patents [OSTI]

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.

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

107

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

E-Print Network [OSTI]

(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

Richner, Heinz

108

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

E-Print Network [OSTI]

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

Reddy, A. P.

2012-01-01T23:59:59.000Z

109

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

E-Print Network [OSTI]

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

Gladden, J.M.

2012-01-01T23:59:59.000Z

110

E-Print Network 3.0 - acid-tolerant thermophilic bacteria Sample...  

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

Homoacetogenic bacteria - often called acetogenic' bacteria... .1.4 Selection of methanol as electron donor 6 1.1.5 Selection ... Source: Groningen, Rijksuniversiteit -...

111

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

DOE Patents [OSTI]

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.

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

112

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

DOE Patents [OSTI]

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.

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

113

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

DOE Patents [OSTI]

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.

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

2013-07-30T23:59:59.000Z

114

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

DOE Patents [OSTI]

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.

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

2013-04-23T23:59:59.000Z

115

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

DOE Patents [OSTI]

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.

Ooteghem, Suellen Van (Morgantown, WV)

2005-09-13T23:59:59.000Z

116

E-Print Network 3.0 - anaerobic thermophiles annual Sample Search...  

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

Implementation of Summary: ;12;Abstract Anaerobic digestion of dairy manure produces biogas that can be captured and used for fuel while... offering environmental benefits. Dairy...

117

E-Print Network 3.0 - anaerobic thermophiles final Sample Search...  

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

for treating this waste stream since it results in two valuable final products, biogas and ... Source: Columbia University - Waste-to-Energy Research and Technology Council...

118

E-Print Network 3.0 - anaerobic thermophilic digestion Sample...  

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

Resources which provide more detailed infor- mation on anaerobic digesters are listed. Biogas... on the source of the organic matter and the management of the anaerobic digestion...

119

E-Print Network 3.0 - anaerobic thermophiles progress Sample...  

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

due to various... returns from energy and byproduct sales. Keywords: Anaerobic digestion, biogas, cooperatives, carbon Source: Laughlin, Robert B. - Department of Physics, Stanford...

120

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 Data Center Home Page on Delicious Rank EERE:YearRound-UpHeat Pump Models |Conduct, Parent CompanyaUSAMP AMDHeavy DutyLow.4.3.100 Development of

Note: This page contains sample records for the topic "thermophilic bacterium caldicellulosiruptor" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


121

Isolation of plasmids present in thermophilic strains from hot springs in Jordan Amjad B. Khalil1,  

E-Print Network [OSTI]

in shaker and agar plate culture in Thermus medium (ATCC 697). Isolation of plasmid DNA-small scale to possess a single site for both plasmids, this enzyme is EcoRI. Introduction Plasmid purification Thermotoga strain (Akimkina et al. 1999). This report describes the development of rapid, reproducible, small

Khalil, Amjad

122

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

SciTech Connect (OSTI)

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.

Ooteghem Van, Suellen

2005-09-13T23:59:59.000Z

123

Laboratory Directed Research and Development Program FY 2006  

E-Print Network [OSTI]

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

Hansen Ed., Todd

2007-01-01T23:59:59.000Z

124

Draft genome sequence of Therminicola potens strain JR  

E-Print Network [OSTI]

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

Byrne-Bailey, K.G.

2010-01-01T23:59:59.000Z

125

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

DOE Patents [OSTI]

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.

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

2014-04-08T23:59:59.000Z

126

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

DOE Patents [OSTI]

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.

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

2013-07-23T23:59:59.000Z

127

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

E-Print Network [OSTI]

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

Weston, Ken

128

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

E-Print Network [OSTI]

and from a B. cereus food-poisoning strain. Microbiology.are known to cause food poisoning. A rare phylogeneticallyK presumably responsible for food poisoning. This pathogenic

Auger, Sandrine

2008-01-01T23:59:59.000Z

129

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

E-Print Network [OSTI]

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

Barabote, Ravi D.

2009-01-01T23:59:59.000Z

130

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

E-Print Network [OSTI]

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

Tang, Yinjie J.

2009-01-01T23:59:59.000Z

131

Thermophilic and hyperthermophilic microorganisms in 3^30C hydrothermal uids following a deep-sea volcanic eruption  

E-Print Network [OSTI]

25 (1998) 33^41 #12;ÂŁoor. Hyperthermophilic microorganisms have also recently been isolated from oil reservoirs in the North Sea, in the north slope of Alaska, and in continental reservoirs in France [5^7]. The lack of exogenous seawater in the French reservoirs, which could act as a source of hyperthermophile

Holden, James F.

132

Environmental genomics reveals a single species ecosystem deep within the Earth  

SciTech Connect (OSTI)

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.

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

133

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

E-Print Network [OSTI]

. 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...

Popova, Snezana N.

1992-01-01T23:59:59.000Z

134

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

E-Print Network [OSTI]

- degradation of naphthalene, phenanthrene, acenaphthene and anthracene at a volumetric consumption rate of 90

Daugulis, Andrew J.

135

E-Print Network 3.0 - aerobic photosynthetic bacterium Sample...  

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

& Universit Pierre-et-Marie-Curie, Paris 6 Collection: Biology and Medicine ; Renewable Energy 3 Research Focus Coloring in the tree of life Summary: -green photosynthetic...

136

E-Print Network 3.0 - anoxygenic phototrophic bacterium Sample...  

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

as filamentous anoxygenic phototrophs... as the hydrogen donor and are incapable of evolving oxy- gen. They are therefore called anoxygenic photo... in eukaryotic algae and...

137

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...

138

E-Print Network 3.0 - anammox bacterium kuenenia Sample Search...  

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

University of Florida Collection: Environmental Sciences and Ecology 74 A Calculus of Looping Sequences for Modelling Microbiological Systems Summary: and of bacteriophage...

139

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

E-Print Network [OSTI]

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

Wolf, Denise M.

2010-01-01T23:59:59.000Z

140

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

E-Print Network [OSTI]

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 –

Wolf, Denise M.

2009-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "thermophilic bacterium caldicellulosiruptor" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


141

E-Print Network 3.0 - ammonia-oxidizing bacterium nitrosomonas...  

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

Division, NASA Ames Research Center Collection: Environmental Sciences and Ecology 79 Land application of manure may contribute endocrine disrupting compounds (EDCs) such as...

142

E-Print Network 3.0 - anerobic thermohalophilic bacterium Sample...  

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

Klaus - Institut for Informatik og Matematisk Modellering, Danmarks Tekniske Universitet Collection: Computer Technologies and Information Sciences Page: << < 1 2 3 4 5 > >> Page:...

143

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

E-Print Network [OSTI]

biodegradation in activated sludge. The goal of this study is to better understand biodegradation of triclosan in activated sludge. Two specific objectives are: (i) isolating and characterizing triclosan-degrading bacteria from activated sludge, (ii...

Zhao, Fuman

2007-09-17T23:59:59.000Z

144

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

145

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

E-Print Network [OSTI]

olfe-Simon et al. (1) reported that arsenic can substitute for phosphorous in the biomolecules in the growth medium would have provided enough phosphorous (P) for all of the cell growth seen in this medium

Redfield, Rosemary J. "Rosie"

146

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

E-Print Network [OSTI]

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 ...

Bird, Lina J. (Lina Joana)

2013-01-01T23:59:59.000Z

147

E-Print Network 3.0 - anaerobic bacterium isolated Sample Search...  

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

colonies with visually distinct morphologies were restreaked several times on R2A agar... plates. Pure bacterial colonies, picked from each isolate, were boiled in 50 l...

148

E-Print Network 3.0 - anaerobic acid-resistant bacterium Sample...  

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

Quantification of Methanogenic Groups in Anaerobic... February 1994 The microbial community structure of anaerobic biological reactors was evaluated by using... ,...

149

E-Print Network 3.0 - anaerobic thermohalophilic bacterium Sample...  

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

Quantification of Methanogenic Groups in Anaerobic... February 1994 The microbial community structure of anaerobic biological reactors was evaluated by using... ,...

150

E-Print Network 3.0 - anaerobic bacterium anaerocellum Sample...  

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

Quantification of Methanogenic Groups in Anaerobic... February 1994 The microbial community structure of anaerobic biological reactors was evaluated by using... ,...

151

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

E-Print Network [OSTI]

to be related to the concentration of endotoxin (Levin and Bang, 1968). The endotosin extract of Pseudomonas (GFC- 80-9) appeared to possess potency similar to that of endotoxin of E. coli serotype 055:B5 in mediating the gelation of Limulus amebocyte lysate... of the test shrimp larvae in the present study, observations were not made to determine hemolymph gelation after exposure of the animal to live and dead Pseudomonas (GFC-80-9). 42 Levin and Bang (1968) demonstrated that 1. 62 x 10 M EDTA blocked...

Huang, Chu-Liang

1982-01-01T23:59:59.000Z

152

Complete Genome Sequence of the hyperthermophilic sulfate-reducing bacterium Thermodesulfobacterium geofontis OPF15T  

SciTech Connect (OSTI)

Thermodesulfobacterium geofontis OPF15T was isolated from Obsidian Pool, Yellowstone National Park and grows optimally at 83 oC. The OPF15T genome was finished at the Joint Genome Institute and the 1.6 Mb sequence has been annotated and deposited for future genomic studies aimed at understanding microbial processes and nutrient cycles in high-temperature environments.

Elkins, James G [ORNL; Hamilton-Brehm, Scott [ORNL; Walston Davenport, Karen [Los Alamos National Laboratory (LANL); Land, Miriam L [ORNL; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Tapia, Roxanne [Los Alamos National Laboratory (LANL); Meincke, Linda [Los Alamos National Laboratory (LANL); Detter, J C [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Cottingham, Robert W [ORNL

2013-01-01T23:59:59.000Z

153

E-Print Network 3.0 - active bacterium phylogenetically Sample...  

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

and Biological Engineering, Ohio State University Collection: Renewable Energy 14 J. theor. Biol. (1999) 196, 251261 Article No. jtbi.1998.0838, available online at...

154

E-Print Network 3.0 - aquatic bacterium caulobacter Sample Search...  

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

de Physique du Globe de Paris Collection: Geosciences 38 Diffley, J.F. (2004). Curr. Biol. 14, R778R786. Geng, Y., Yu, Q., Sicinska, E., Das, M., Schneider, J.E., Bhat-...

155

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

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

Collection: Chemistry 93 General Discussion Chapter 9: General Discussion Summary: . Soil Biol Biochem 23: 717-723. Hermansson A & Lindgren P-E (2001) Quantification of...

156

E-Print Network 3.0 - acid bacterium granulibacter Sample Search...  

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

Collection: Renewable Energy ; Energy Storage, Conversion and Utilization 87 J. theor. Biol. (1999) 196, 251261 Article No. jtbi.1998.0838, available online at http:...

157

E-Print Network 3.0 - asv-reducing bacterium implications Sample...  

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

and Information Sciences ; Biology and Medicine 3 Colicin diversity: a result of eco-evolutionary Ludo Pagie and Paulien Hogeweg Summary: of toxins makes it possible for...

158

E-Print Network 3.0 - acid bacterium isolated Sample Search Results  

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

Physics, Wageningen Universiteit Collection: Physics ; Biology and Medicine 11 J. theor. Biol. (1999) 196, 251261 Article No. jtbi.1998.0838, available online at http:...

159

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

SciTech Connect (OSTI)

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.

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

160

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

E-Print Network [OSTI]

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 ...

Frame, Caitlin H.

Note: This page contains sample records for the topic "thermophilic bacterium caldicellulosiruptor" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


161

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

E-Print Network [OSTI]

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...

Pore, Robert Scott

1962-01-01T23:59:59.000Z

162

E-Print Network 3.0 - acetic acid bacterium Sample Search Results  

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

but does not produce acid Esculin hydrolysis Acetate utilization... was isolated. The cultivation of strain FRCl in the presence of acetate ... Source: Lovley, Derek -...

163

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...

164

Proteomic Analysis of Stationary Phase in the Marine Bacterium 'Candidatus Pelagibacter ubique'  

SciTech Connect (OSTI)

Candidatus Pelagibacter ubique, an abundant marine alphaproteobacterium, subsists in nature at low ambient nutrient concentrations and may often be exposed to nutrient limitation, but its genome revealed no evidence of global regulatory adaptations to stationary phase. We used high-resolution capillary liquid chromatography (LC) coupled online to an LTQ mass spectrometer to build an Accurate Mass and Time (AMT) tag library, and employed the AMT tag approach to quantitatively examine proteome differences between exponentially growing and stationary phase Cand. P. ubique cells cultivated in a seawater medium. The AMT tag library represented 72% of the predicted protein coding genes. Stationary phase protein abundance increased for OsmC, which mitigates oxidative damage, and for molecular chaperones, enzymes involved in methionine and cysteine biosynthesis, proteins involved in rho-dependent transcription termination, and the signal transduction enzymes CheY-FisH and ChvG. Our findings indicate that Cand. P. ubique responds adaptively to stationary phase by increasing the abundance of a suite of proteins that contribute to homeostasis, but does not undergo major proteome remodeling. We speculate that this limited response may enable Cand. P. ubique to cope with ambient conditions in which nutrients are often insufficient for short periods, and the ability to resume growth overrides the capacity for long term survival afforded by more comprehensive global stationary phase responses.

Sowell, Sarah M.; Norbeck, Angela D.; Lipton, Mary S.; Nicora, Carrie D.; Callister, Stephen J.; Smith, Richard D.; Barofsky, Douglas F.; Giovannoni, Stephen J.

2008-05-01T23:59:59.000Z

165

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

E-Print Network [OSTI]

of Agriculture, Kyoto University, Kyoto, Japanm; Department of Civil & Environmental Engineering, the University and biofuels from natural gas/renewable biogas (4­6). Over the last 10 years, several novel methane

Boyer, Edmond

166

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

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:1 First Use of Energy for All Purposes (Fuel and Nonfuel),Feet) Year Jan Feb Mar Apr MayAtmospheric Optical Depth7-1D: Vegetation Proposed Newcatalyst phasesDataTranslocationDiurnalCommitteeDurable FuelNuclearFitness. |

167

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

E-Print Network [OSTI]

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

Lovley, Derek

168

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

SciTech Connect (OSTI)

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.

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

169

Evidence for Multiple Modes of Uranium Immobilization by an Anaerobic Bacterium  

SciTech Connect (OSTI)

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.

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

2011-05-15T23:59:59.000Z

170

Evidence for Multiple Modes of Uranium Immobilization by an Anaerobic Bacterium  

SciTech Connect (OSTI)

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.

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

2011-05-01T23:59:59.000Z

171

E-Print Network 3.0 - anaerobic bacterium thiobacillus Sample...  

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

14 Environmental Microbiology (2002) 4(9), 510-516 Multip,le influences of nitrate on uranium solubility Summary: of organic compounds on the growth of the chemolithotrophic...

172

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...

173

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

E-Print Network [OSTI]

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

Kersting, Roland

174

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

SciTech Connect (OSTI)

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.

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

1995-12-01T23:59:59.000Z

175

The Exiguobacterium genus: biodiversity and biogeography  

SciTech Connect (OSTI)

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.

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

2009-01-01T23:59:59.000Z

176

Subunit rotation in a single FoF1-ATP synthase in a living bacterium monitored by FRET  

E-Print Network [OSTI]

FoF1-ATP synthase is the ubiquitous membrane-bound enzyme in mitochondria, chloroplasts and bacteria which provides the 'chemical energy currency' adenosine triphosphate (ATP) for cellular processes. In Escherichia coli ATP synthesis is driven by a proton motive force (PMF) comprising a proton concentration difference {\\Delta}pH plus an electric potential {\\Delta}{\\Psi} across the lipid membrane. Single-molecule in vitro experiments have confirmed that proton-driven subunit rotation within FoF1-ATP synthase is associated with ATP synthesis. Based on intramolecular distance measurements by single-molecule fluorescence resonance energy transfer (FRET) the kinetics of subunit rotation and the step sizes of the different rotor parts have been unraveled. However, these experiments were accomplished in the presence of a PMF consisting of a maximum {\\Delta}pH ~ 4 and an unknown {\\Delta}{\\Psi}. In contrast, in living bacteria the maximum {\\Delta}pH across the plasma membrane is likely 0.75, and {\\Delta}{\\Psi} has bee...

Seyfert, Karin; Yaginuma, Hideyuki; Ernst, Stefan; Noji, Hiroyuki; Iino, Ryota; Boersch, Michael

2011-01-01T23:59:59.000Z

177

Diffusion properties of single FoF1-ATP synthases in a living bacterium unraveled by localization microscopy  

E-Print Network [OSTI]

FoF1-ATP synthases in Escherichia coli (E. coli) bacteria are membrane-bound enzymes which use an internal proton-driven rotary double motor to catalyze the synthesis of adenosine triphosphate (ATP). According to the 'chemiosmotic hypothesis', a series of proton pumps generate the necessary pH difference plus an electric potential across the bacterial plasma membrane. These proton pumps are redox-coupled membrane enzymes which are possibly organized in supercomplexes, as shown for the related enzymes in the mitochondrial inner membrane. We report diffusion measurements of single fluorescent FoF1-ATP synthases in living E. coli by localization microscopy and single enzyme tracking to distinguish a monomeric enzyme from a supercomplex-associated form in the bacterial membrane. For quantitative mean square displacement (MSD) analysis, the limited size of the observation area in the membrane with a significant membrane curvature had to be considered. The E. coli cells had a diameter of about 500 nm and a length o...

Renz, Marc; Boersch, Michael

2012-01-01T23:59:59.000Z

178

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

SciTech Connect (OSTI)

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.

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

179

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

SciTech Connect (OSTI)

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).

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

2012-02-01T23:59:59.000Z

180

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

SciTech Connect (OSTI)

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.

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

2013-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "thermophilic bacterium caldicellulosiruptor" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


181

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

E-Print Network [OSTI]

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

Lovley, Derek

182

Neptunium (V) Adsorption to a Halophilic Bacterium Under High Ionic Strength Conditions: A Surface Complexation Modeling Approach  

SciTech Connect (OSTI)

Rationale for experimental design: Np(V) -- important as analog for Pu(V) and for HLW scenarios; High ionic strength -- relevant to salt-based repositories such as the WIPP; Halophilic microorganisms -- representative of high ionic strength environments. For the first time showed: Significant adsorbant to halophilic microorganisms over entire pH range under high ionic strength conditions; Strong influence of ionic strength with increasing adsorption with increasing ionic strength (in contrast to trends of previous low ionic strength studies); Effect of aqueous Np(V) and bacterial surface site speciation on adsorption; and Developed thermodynamic models that can be incorporated into geochemical speciation models to aid in the prediction of the fate and transport of Np(V) in more complex systems.

Ams, David A [Los Alamos National Laboratory

2012-06-11T23:59:59.000Z

183

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

SciTech Connect (OSTI)

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.

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

184

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

SciTech Connect (OSTI)

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

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

185

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

SciTech Connect (OSTI)

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.

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

186

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]

(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...

Kirk, James Michael

1995-01-01T23:59:59.000Z

187

Complete Genome Sequence of the Marine Cellulose-and Xylan-Degrading Bacterium Glaciecola sp. Strain 4H-3-7+YE-5  

E-Print Network [OSTI]

of Technology, Hamburg, Germany  Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA   Los Alamos the DOE Office of Science. Oak Ridge National Laboratory is

Klippel, Barbara

2013-01-01T23:59:59.000Z

188

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

E-Print Network [OSTI]

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

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

2012-01-01T23:59:59.000Z

189

The ultimate ethanol: Technoeconomic evaluation of ethanol manufacture, comparing yeast vs Zymomonas bacterium fermentations. [Zymomonas mobilis:a5; Saccharomyces cerevisiae:a6  

SciTech Connect (OSTI)

If ethanol could be produced at a low enough price to serve as the precursor to ethylene and butadiene, it and its derivatives could account for 159 billion lb, or 50% of the US production of 316 billion lb of synthetic organic chemicals, presently valued at $113 billion. This use would consume 3.4 billion bu of corn, or {approximately}40% of the corn crop. This study evaluates advance process engineering and genetic engineering techniques that could generate savings and reduce production costs. The most rewarding development strategy appears to be to demonstrate at pilot scale the use of immobilized Zymomonas mobilis bacteria in a fluidized-bed bioreactor operating in a continuous mode over an extended period of time. Throughput should be adjusted to control product concentration at {approximately}100 g/L (i.e., as close to the threshold of inhibition as possible). There appears to be no inherent design limitation to effect the engineering improvements required in the advanced process operation. The above scenario assumes that the presently available, product-inhibited organisms would be used. In a longer-term, more difficult research effort, it might be possible to reduce or eliminate product inhibition. As a result, price would be reduced further to $1.75 for the Zymomonas system or $1.85 for the yeast fermentation. It is recommended that the engineering proveout of the advanced process be continued at a pilot scale and that a laboratory program aimed at reducing product inhibition and/or increasing specific productivity be initiated. 49 refs., 11 figs., 19 tabs.

Busche, R.M. (Bio En-Gene-Er Associates, Inc., Wilmington, DE (United States)); Scott, C.D.; Davison, B.H. (Oak Ridge National Lab., TN (United States)); Lynd, L.R. (Dartmouth Coll., Hanover, NH (United States))

1991-08-01T23:59:59.000Z

190

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

SciTech Connect (OSTI)

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.

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

191

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]

, 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

Templer, Pamela

192

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)

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.

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

193

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)

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.

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

2004-07-01T23:59:59.000Z

194

E-Print Network 3.0 - afex-treated corn stover Sample Search...  

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

Populations During High-Solids Summary: thermophilic high-solids fermentation of the bioenergy feedstocks switch- grass and corn stover. Methods... for switchgrass were more...

195

Steam-Water Relative Permeability  

Energy Savers [EERE]

Separation and Recovery of Rare Earth Elements from Low Temperature Geothermal Water 500,000 64,061 Lawrence Berkeley National Laboratory (LBNL) Engineering Thermophilic...

196

E-Print Network 3.0 - anaerobic continuously stirred Sample Search...  

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

or thermophilic... ;12;Abstract Anaerobic digestion of dairy manure produces biogas that can be captured and used for fuel while... offering environmental benefits. Dairy...

197

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...

198

A Bioreactor for Growth of Sulfate-Reducing Bacteria: Online Estimation of Specific Growth Rate and Biomass for the Deep-Sea  

E-Print Network [OSTI]

of Specific Growth Rate and Biomass for the Deep-Sea Hydrothermal Vent Thermophile Thermodesulfatator indicus, a chemolithotrophic, thermophilic, sulfate-reducing bac- terium recently isolated from a deep-sea hydrothermal vent donor and CO2 as primary carbon source. These experiments were designed to measure growth kinetics under

Reysenbach, Anna-Louise

199

Genomics of emerging infectious disease: A PLoS collection.  

E-Print Network [OSTI]

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

Eisen, Jonathan A; MacCallum, Catriona J

2009-01-01T23:59:59.000Z

200

Recoding of the stop codon UGA to glycine by a BD1-5/SN-2 bacterium and niche partitioning between Alpha- and Gammaproteobacteria in a tidal sediment microbial community naturally selected in a laboratory chemostat  

SciTech Connect (OSTI)

Sandy coastal sediments are global hot spots for microbial mineralization of organic matter and denitrification. These sediments are characterized by advective pore water flow, tidal cycling and an active and complex microbial community. Metagenomic sequencing of microbial communities sampled from such sediments showed that potential sulfuroxidizing Gammaproteobacteria and members of the enigmaticBD1-5/ SN-2 candidatephylumwereabundantinsitu (>10% and 2% respectively). By mimicking the dynamic oxic/anoxic environmental conditions of the sedimentin a laboratory chemostat, a simplified microbial community was selected from the more complex inoculum. Metagenomics, proteomics and fluorescenceinsituhybridization showed that this simplified community contained both a potential sulfuroxidizing Gamma proteobacteria (at 24 2% abundance) and a member of the BD1-5 / SN-2candidatephylum (at 7 6%abundance). Despite the abundant supply of organic substrates to the chemostat, proteomic analysis suggested that the selected gamma proteobacterium grew partially auto trophically and performed hydrogen/formate oxidation. The enrichment of a member of the BD1-5/SN-2candidatephylum enabled, for the first time, direct microscopic observation by fluorescent insitu hybridization and the experimental validation of the previously predicted translation of the stop codon UGA into glycine.

Hanke, Anna [Max Planck Institute for Marine Microbiology; Hamann, Emmo [Max Planck Institute for Marine Microbiology; Sharma, Ritin [ORNL; Geelhoed, Jeanine [Max Planck Institute for Marine Microbiology; Hargesheimer, Theresa [Max Planck Institute for Marine Microbiology; Kraft, Beate [Max Planck Institute for Marine Microbiology; Meyer, Volker [Max Planck Institute for Marine Microbiology; Lenk, Sabine [Max Planck Institute for Marine Microbiology; Osmers, Harald [Max Planck Institute for Marine Microbiology; Wu, Rong [Delft University of Technology, Delft, Netherlands; Makinwa, Kofi [Delft University of Technology, Delft, Netherlands; Hettich, Robert {Bob} L [ORNL; Banfield, Jillian F. [University of California, Berkeley; Tegetmeyer, Halina [Max Planck Institute for Marine Microbiology; Strouss, Marc [University of Calgary, ALberta, Canada

2014-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "thermophilic bacterium caldicellulosiruptor" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


201

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

SciTech Connect (OSTI)

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.

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

202

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

SciTech Connect (OSTI)

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)

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

1980-01-01T23:59:59.000Z

203

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

E-Print Network [OSTI]

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...

Dulin, Jennifer Natalie

2013-02-22T23:59:59.000Z

204

E-Print Network 3.0 - anaerobic xylose fermentation Sample Search...  

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

(Glucose... ) Thermophilic Fermentation (Xylose) Wet oxidation 196C, 12 Bar O2 NaCO2 Biogas Ethanol 55C 32C 70C 12... or transport 6.4 Ris Energy Report 2 Introduction...

205

E-Print Network 3.0 - anaerobic ethanol oxidation Sample Search...  

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

) Thermophilic Fermentation (Xylose) Wet oxidation 196C, 12 Bar O2 NaCO2 Biogas Ethanol 55C 32C 70C 12... 90% of new cars have engines specially designed to...

206

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]

Characterization of allosteric properties of phosphofructokinase from the extreme thermophile Thermus thermophilus (TtPFK) using thermodynamic linkage analysis revealed several peculiarities. Inhibition and activation of Fru-6-P binding...

Shubina-McGresham, Maria

2012-10-19T23:59:59.000Z

207

A comparative study of HPr proteins from extremophilic organisms  

E-Print Network [OSTI]

of the proteins were derived from moderate thermophiles (Streptococcus thermophilus and Bacillus staerothermophilus) and two from haloalkaliphilic organisms (Bacillus halodurans and Oceanobacillus iheyensis); these proteins were compared with HPr from...

Syed Ali, Abbas Razvi

2006-04-12T23:59:59.000Z

208

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

SciTech Connect (OSTI)

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.

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

209

Optimized procedures for extractioin, purification and characterization of exopolymeric substances (eps) from two bacteria (sagittula stellata and pseudomonas fluorescens biovar ii) with relevance to the study of actinide binding in aquatic environments  

E-Print Network [OSTI]

The extracellular polymeric substances (EPS) of marine bacterium Sagittula stellata and soil bacterium Pseudomonas fluorescens Biovar II, were extracted by six methods referred to the bibliography, efficacies of which were compared based on the EPS...

Xu, Chen

2009-05-15T23:59:59.000Z

210

Dispersant solutions for dispersing hydrocarbons  

DOE Patents [OSTI]

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

Tyndall, Richard L. (Clinton, TN)

1997-01-01T23:59:59.000Z

211

Dispersant solutions for dispersing hydrocarbons  

DOE Patents [OSTI]

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

Tyndall, R.L.

1997-03-11T23:59:59.000Z

212

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

E-Print Network [OSTI]

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

Reysenbach, Anna-Louise

213

Sustainable syntrophic growth of Dehalococcoides ethenogenes strain 195 with Desulfovibrio vulgaris Hildenborough and Methanobacterium congolense: Global transcriptomic and proteomic analyses  

E-Print Network [OSTI]

2005). Genome sequence of the PCE-dechlorinating bacteriumHong Kong. chloroethene (PCE) and trichloroethene (TCE) toexperimental co-culture, PCE was dechlorinated to vinyl

Men, Y.

2012-01-01T23:59:59.000Z

214

Harnessing the Bacterial Power of Nanomagnets  

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

a method for producing large quantities of highly crystalline magnetite and cobalt ferrite (CoFe2O4) nanoparticles using the Fe(III)-reducing bacterium, Geobacter...

215

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

E-Print Network [OSTI]

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

2012-01-01T23:59:59.000Z

216

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

E-Print Network [OSTI]

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

Malmirchegini, Ghulam Reza Khan

2013-01-01T23:59:59.000Z

217

Comparative genomics reveals mechanism for short-term and long-term clonal transitions in pandemic Vibrio cholerae  

SciTech Connect (OSTI)

Vibrio cholerae, the causative agent of cholera, is a bacterium autochthonous to the aquatic environment, and a serious public health threat.

Chun, Jongsik; Grim, Christopher J.; Hasan, Nur A.; Lee, Je H.; Choi, Seon Y.; Haley, Bradd J.; Taviani, Elisa; Jeon, Yoon-Seong; Kim, Dong W.; Lee, Jae-Hak; Brettin, T.; Bruce, David; Challacombe, Jean; Detter, J. C.; Han, Cliff F.; Munk, A. C.; Chertkov, Olga; Meincke, Linda; Saunders, Elizabeth; Walters, Ronald A.; Huq, Anwar; Nair, G. B.; Colwell, Rita R.

2009-09-08T23:59:59.000Z

218

E-Print Network 3.0 - antimicrobial susceptibilities phage Sample...  

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

of infection), by increasing exposure to susceptible hosts (Rhodes & Anderson 1996; Boots & Sasaki 1999... plant bacterium Pseudomonas fluorescens strain SBW25 (Rainey & Bailey...

219

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...

220

E-Print Network 3.0 - active marine methylotrophs Sample Search...  

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

TM-1 are active during acetate metabolism to methane. In nongastrointestinal... methane-producing bacterium isolated from marine sediments. Appl. Environ. Microbiol. 47:971-978....

Note: This page contains sample records for the topic "thermophilic bacterium caldicellulosiruptor" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


221

E-Print Network 3.0 - alkaliphilic anaerobe isolated Sample Search...  

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

campinasensis sp. nov., a Summary: Paenibacillus campinasensis sp. nov., a cyclodextrin-producing bacterium isolated in Brazil Jung-Hoon Yoon,1... , College of Food Engineering...

222

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...

223

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...

224

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...

225

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...

226

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...

227

Purification of soluble and active RaxH, a transmembrane histidine protein kinase from Xanthomonas oryzae pv. oryzae required for AvrXa21 activity.  

E-Print Network [OSTI]

of the plant pathogenic bacterium Xanthomonas campestris pv.oryzae pv. oryzae isolates in transgenic plants. Mol. Plant–Xanthomonas oryzae pv. oryzae. Mol. Plant–Microbe Interact.

Stolov, Avital; Valverde, Angel; Ronald, Pamela; Burdman, Saul

2007-01-01T23:59:59.000Z

228

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...

229

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

E-Print Network [OSTI]

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

Hazen, Terry

230

Geobiology (2008), 6, 481502 DOI: 10.1111/j.1472-4669.2008.00179.x 2008 The Authors  

E-Print Network [OSTI]

by diverse mesophilic and thermophilic microbial life. In addition, outflow waters and condensed steam from formation was restricted to the vicinity of the air­water interface (AWI) where evaporation and condensation and this indicated that silica precipitation, i.e. sinter growth, was aided by the surfaces provided by the thick

Benning, Liane G.

231

A Novel Kingdom of Parasitic Archaea Karl O. Stetter1,2* | Michael J. Hohn1 | Harald Huber1  

E-Print Network [OSTI]

discovered in terrestrial high temperature environments like solfataras, hot springs, smoldering coal refuse piles, and deep, geothermally- heated rocks. In addition, submarine high temperature environments like- thermophiles which are adapted to the high salinity of sea water (Stetter 1999). Hyperthermophiles occur within

Ahmad, Sajjad

232

Eos, Vol. 87, No. 4, 24 January 2006 Geophysics program and the NOAA Ocean Ex-  

E-Print Network [OSTI]

: Relationships between hydrothermal and volcanic processes,Geophys.Res.Lett.,22(2),143­146. Holden.A.Feely (1987), Cataclysmic hydrothermal venting on the Juan de Fuca Ridge,Nature,329, 149­151. Bohnenstiehl,D,J.F.,M.Summit,and J.A.Baross (1998), Thermophilic and hyperthermophilic microorgan- isms in 3­30°C hydrothermal fluids

233

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

E-Print Network [OSTI]

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

Stoltz, Brian M.

234

References 170 RREEFFEERREENNCCEESS  

E-Print Network [OSTI]

, Comparison Between Dynamics and Control Performance of Mesophilic and Thermophilic Anaerobic Sludge Digesters Controller for Distillation Columns in the Presence of Strong Directionality and Model Errors, Industrial Reactor Case Study, Industrial and Engineering Chemistry Research, 29: 1218-1226 Coughauowr, D.R., 1991

Skogestad, Sigurd

235

proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS PROTS: A fragment based protein  

E-Print Network [OSTI]

which live at elevated temperatures as high as 1138C.5 Thus, the proteins produced by thermophiles and practically.1­8 Protein-based drugs have become increasingly attractive because of their high efficiency at higher temperature, which can lead to more efficient industrial processes because chemical reactions

Zhang, Yang

236

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

E-Print Network [OSTI]

) 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

Paris-Sud XI, Université de

1990-01-01T23:59:59.000Z

237

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

E-Print Network [OSTI]

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

Paris-Sud XI, Université de

2007-01-01T23:59:59.000Z

238

RESEARCH PAPER A review of the microbiology of the Rehai geothermal  

E-Print Network [OSTI]

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

Ahmad, Sajjad

239

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

DOE Patents [OSTI]

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.

Dees, H. Craig (Lenoir City, TN)

1998-01-01T23:59:59.000Z

240

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

E-Print Network [OSTI]

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

Tessmer, Stuart

Note: This page contains sample records for the topic "thermophilic bacterium caldicellulosiruptor" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


241

Biochemistry and physiology of anaerobic bacteria  

SciTech Connect (OSTI)

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.

NONE

2000-05-18T23:59:59.000Z

242

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)

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.

Laurinavichius, K.S.

1998-09-30T23:59:59.000Z

243

Mixed oxide nanoparticles and method of making  

DOE Patents [OSTI]

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.

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

244

Nucleotide sequences encoding a thermostable alkaline protease  

DOE Patents [OSTI]

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.

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

1998-01-01T23:59:59.000Z

245

PETROLEUM BIOREFINING FOR POLLUTION PREVENTION  

SciTech Connect (OSTI)

The objective of this project was to isolate and characterize thermophilic bacterial cultures that can be used for the selective removal of nitrogen, sulfur, and/or metals in the biorefining of petroleum. The project was completed on schedule and no major difficulties were encountered. Significant progress was made on multiple topics relevant to the development of a petroleum biorefining process capable of operating at thermophilic temperatures. New cultures capable of selectively cleaving C-N or C-S bonds in molecules relevant to petroleum were obtained, and the genes encoding the enzymes for these unique biochemical reactions were cloned and sequenced. Genetic tools were developed that enable the use of Thermus thermophilus as a host to express any gene of interest, and information was obtained regarding the optimum conditions for the growth of T. thermophilus. The development of a practical biorefining process still requires further research and the future research needs identified in this project include the development of new enzymes and pathways for the selective cleavage of C-N or C-S bonds that have higher specific activities, increased substrate range, and are capable of functioning at thermophilic temperatures. Additionally, there is a need for process engineering research to determine the maximum yield of biomass and cloned gene products that can be obtained in fed-batch cultures using T. thermophilus, and to determine the best configuration for a process employing biocatalysts to treat petroleum.

John J. Kilbane II

2002-03-01T23:59:59.000Z

246

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

SciTech Connect (OSTI)

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.

John J. Kilbane II

2000-12-15T23:59:59.000Z

247

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

E-Print Network [OSTI]

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 ...

Grote, Jana

2011-01-01T23:59:59.000Z

248

Review of the Impacts of Crumb Rubber in Artificial Turf Applications  

E-Print Network [OSTI]

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

Simon, Rachel

2010-01-01T23:59:59.000Z

249

Sensing Applications of Fluctuations and Noise  

E-Print Network [OSTI]

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...

Chang, Hung-Chih

2011-02-22T23:59:59.000Z

250

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

E-Print Network [OSTI]

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 ...

Bell, John Alexander

2014-06-28T23:59:59.000Z

251

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

E-Print Network [OSTI]

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 ...

Demain, Arnold L.

252

Interactions of microbes in aquatic systems Uncultured populations of bacteria were analyzed in aquatic systems and populations related  

E-Print Network [OSTI]

Rotsee (Lucerne, Switzerland), and were subsequently expanded to studies on the interaction of aggregate-actions that presumably resemble a source-sink rela-tionship for sulfide between the sulfate-reducing bacterium growing

Aspbury, Andrea S. - Department of Biology, Texas State University

253

Helicobacter pylori moves through mucus by reducing mucin viscoelasticity  

E-Print Network [OSTI]

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 ...

So, Peter T. C.

254

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]

(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

van den Brink, Jeroen

255

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

E-Print Network [OSTI]

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

Paris-Sud XI, Université de

256

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

E-Print Network [OSTI]

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

Wirth, Thierry

257

TRENDS in Genetics Vol.18 No.12 December 2002 http://tig.trends.com 0168-9525/02/$ see front matter 2002 Elsevier Science Ltd. All rights reserved. PII: S0168-9525(02)02793-2  

E-Print Network [OSTI]

repeats and conversion events are the main mechanism of divergence between closely related primate genomes on the biochemical pathways by which the bacterium `reduces' and precipitates chromium, uranium and other toxic

Utrecht, Universiteit

258

The effect of gender on Helicobacter pylori and gastric cancer  

E-Print Network [OSTI]

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 ...

Sheh, Alexander

2011-01-01T23:59:59.000Z

259

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

E-Print Network [OSTI]

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

Lovley, Derek

260

Radial and Spiral Stream Formation in Proteus mirabilis Colonies  

E-Print Network [OSTI]

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: ...

Xue, Chuan

Note: This page contains sample records for the topic "thermophilic bacterium caldicellulosiruptor" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


261

Xanthomonas oryzae pathovars: model pathogens of a model crop.  

E-Print Network [OSTI]

the plant pathogen Xanthomonas campestris pv. vesicatoria.of the plant pathogenic bacterium Xanthomonas campestris pv.pv. oryzae in artificially inoculated and naturally infected rice seeds and plants

Nińo-Liu, David O; Ronald, Pamela C; Bogdanove, Adam J

2006-01-01T23:59:59.000Z

262

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

E-Print Network [OSTI]

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 ...

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

2009-01-01T23:59:59.000Z

263

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

264

Complete Genome Sequences of Bacillus subtilis subsp. subtilis Laboratory Strains JH642 (AG174) and AG1839  

E-Print Network [OSTI]

The Gram-positive bacterium Bacillus subtilis is widely used for studies of cellular and molecular processes. We announce the complete genomic sequences of strain AG174, our stock of the commonly used strain JH642, and ...

Smith, Janet L.

265

Structural Basis for Activation of Cholera Toxin  

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

2005 00:00 Cholera is a serious disease that claims thousands of victims each year in third-world, war-torn, and disaster-stricken nations. The culprit is the bacterium Vibrio...

266

Structural Basis for Activation of Cholera Toxin  

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

Toxin Print Cholera is a serious disease that claims thousands of victims each year in third-world, war-torn, and disaster-stricken nations. The culprit is the bacterium Vibrio...

267

Comparative Analysis of Microbial Community Composition Throughout Three Perennially Ice-Covered Lake Systems in the McMurdo Dry Valleys, Antarctica and its Relationship With Lake Geochemistry  

E-Print Network [OSTI]

Delta Proteobacteria F12, F18 Uncultured eubacterium AB16 (Delta Proteobacteria F12, F18 Rhodoferax antarcticus strainDelta Proteobacteria F12, F18 Uncultured bacterium clone

Foo, Wilson

2009-01-01T23:59:59.000Z

268

Antimicrobial product and process  

DOE Patents [OSTI]

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.

Barrett, K.B.

1997-12-16T23:59:59.000Z

269

Antimicrobial product and process  

DOE Patents [OSTI]

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.

Barrett, Karen B. (Idaho Falls, ID)

1997-01-01T23:59:59.000Z

270

Combination biological and microwave treatments of used rubber products  

DOE Patents [OSTI]

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.

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

2002-01-01T23:59:59.000Z

271

High ethanol producing derivatives of Thermoanaerobacter ethanolicus  

DOE Patents [OSTI]

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).

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

1983-05-24T23:59:59.000Z

272

High ethanol producing derivatives of Thermoanaerobacter ethanolicus  

DOE Patents [OSTI]

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).

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

1983-01-01T23:59:59.000Z

273

Results an data on the growth of the microorganisms  

SciTech Connect (OSTI)

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.

Laurinavichius, K.S.

1995-10-09T23:59:59.000Z

274

Production of extremophilic bacterial cellulase enzymes in aspergillus niger.  

SciTech Connect (OSTI)

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.

Gladden, John Michael

2013-09-01T23:59:59.000Z

275

Cellulase producing microorganism ATCC 55702  

DOE Patents [OSTI]

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.

Dees, H.C.

1997-12-30T23:59:59.000Z

276

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

DOE Patents [OSTI]

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.

Dees, H.C.

1998-05-26T23:59:59.000Z

277

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

DOE Patents [OSTI]

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.

Dees, H.C.

1997-12-16T23:59:59.000Z

278

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

DOE Patents [OSTI]

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.

Dees, H.C.

1998-07-14T23:59:59.000Z

279

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

DOE Patents [OSTI]

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.

Dees, H. Craig (Lenoir City, TN)

1998-01-01T23:59:59.000Z

280

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

DOE Patents [OSTI]

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.

Dees, H. Craig (Lenoir City, TN)

1997-12-16T23:59:59.000Z

Note: This page contains sample records for the topic "thermophilic bacterium caldicellulosiruptor" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


281

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

DOE Patents [OSTI]

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.

Dees, H. Craig (Lenoir City, TN)

1998-01-01T23:59:59.000Z

282

Cellulase producing microorganism ATCC 55702  

DOE Patents [OSTI]

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.

Dees, H. Craig (Lenoir City, TN)

1997-01-01T23:59:59.000Z

283

Thermal ecology of Naegleria fowleri from a power plant cooling reservoir  

SciTech Connect (OSTI)

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.

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

1990-07-01T23:59:59.000Z

284

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

SciTech Connect (OSTI)

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.

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

285

Hydrogen, Fuel Cells, and Infrastructure Technologies FY 2002 Progress Report Section II. Hydrogen Production and Delivery  

E-Print Network [OSTI]

.A Biological Processes II.A.1 Biological Water Gas Shift Development Gary R. Vanzin, Sharon Smolinski, Karen the overall water-gas shift (WGS) pathway by serving as an inducer, a substrate, and an inhibitor. · Elucidate the specific CO shift kinetics of the photosynthetic bacterium Rubrivivax (Rx.) gelatinosus CBS. Approach

286

Aromatic hydrocarbon metabolism by Rhodococcus sp. I24 : computational, biochemical and transcriptional analysis  

E-Print Network [OSTI]

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 ...

Parker, Jefferson A. (Jefferson Alexander), 1974-

2004-01-01T23:59:59.000Z

287

1 | P a g e Chem 124H Organic Chemistry Case Study #2: "Overcoming Bacterial  

E-Print Network [OSTI]

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

Reed, Christopher A.

288

The prevalence of multidrug-resistant bacterial strains has substantially  

E-Print Network [OSTI]

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

Nizet, Victor

289

Antimicrobial protein protects grapevines from pathogen  

E-Print Network [OSTI]

to block infection Your evening glass of wine will still be available--despite the potential attack of a bacterium that causes Pierce's Disease and poses a significant threat to the California wine industry chlorosis disease in Brazil Operated by Los Alamos National Security, LLC for the Department of Energy

290

Bioremediation of nanomaterials  

DOE Patents [OSTI]

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.

Chen, Frank Fanqing; Keasling, Jay D; Tang, Yinjie J

2013-05-14T23:59:59.000Z

291

Guardian Unlimited | The Guardian | Scientists see big role for uranium clean-up bug Sign in Register  

E-Print Network [OSTI]

Guardian 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 The Guardian Scientists have sequenced the DNA of a bacterium which can help to remove uranium from

Lovley, Derek

292

Spatially-Correlated Mass Spectrometric Analysis of Microbe-Mineral Interactions  

SciTech Connect (OSTI)

A new methodology for examining the interactions of microbes with heterogeneous minerals is presented. Imaging laser-desorption Fourier transform mass spectrometry was used to examine the colonization patterns of Burkholderia vietnamiensis (Burkholderia cepacia) G4 on a heterogeneous basalt sample. Depth-profile imaging found that the bacterium preferentially colonized the plagioclase mineral phases within the basalt.

Jill R. Scott; Beizhan Yan; Daphne L. Stoner

2006-11-01T23:59:59.000Z

293

EHS 7-7 August 2007 DEPARTMENT OF ENVIRONMENTAL HEALTH & SAFETY  

E-Print Network [OSTI]

EHS 7-7 August 2007 DEPARTMENT OF ENVIRONMENTAL HEALTH & SAFETY Biological Safety Office 1200 subjects? Yes No Recombinant DNA molecules host cells Check one: Plant* Animal* Bacterium Fungus Animal or animal pathogens. Vector to be used: Describe the inserted recombinant DNA materials: (if applicable

Sura, Philip

294

Methods for targetted mutagenesis in gram-positive bacteria  

SciTech Connect (OSTI)

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.

Yang, Yunfeng

2014-05-27T23:59:59.000Z

295

Copyright 2011, The Ohio State University Family and Consumer Sciences  

E-Print Network [OSTI]

Staphylococcusaureusisacommoncauseoffoodborne illness. Commonly called "Staph aureus," this bacterium produces a poison/toxin that cause are employedinhospitals.Althoughfoodhandlersareusually the main source of food contamination in food poison- ing outbreaks. Symptoms of illness Symptoms of staphylococcal food poisoning usually occur within a few hours of eating

296

Composite Surface for Blocking Bacterial Adsorption on Protein Biochips  

E-Print Network [OSTI]

in the present study. This bacterium causes serious food poisoning (Farber and Peterkin, 1991) and has been of Electrical and Computer Engineering, 4 Molecular Food Microbiology Laboratory, Department of Food Science, 5 of the Association of Official Analytical Chemists (AOAC) for detecting bacteria in clinical, food, and industrial

Bashir, Rashid

297

Biophysical Journal Volume 73 August 1997 703-721 703 Protein Turbines 1: The Bacterial Flagellar Motor  

E-Print Network [OSTI]

flagellar motor (BFM) is a rotary engine that derives its energy from the electrochemical gradient estab to their swimming mode, the bacterium's direction has been randomly reoriented. Normally, reversals occur components and their relative sizes (Francis et al., 1994; Schuster and Khan, 1994). The energy

Oster, George

298

Production of amino acids using auxotrophic mutants of methylotrophic bacillus  

SciTech Connect (OSTI)

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.

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

299

Adsorption of rare earth elements onto bacterial cell walls and its implication for REE sorption onto natural microbial mats  

E-Print Network [OSTI]

Adsorption of rare earth elements onto bacterial cell walls and its implication for REE sorption of rare earth elements (REE) onto the cell walls of Bacillus subtilis (a gram-positive bacterium of the rocks in the geological record. D 2005 Elsevier B.V. All rights reserved. Keywords: Rare earth elements

300

normally occur in the environment. How it recognizes this compound was the subject  

E-Print Network [OSTI]

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

Sakaluk, Scott

Note: This page contains sample records for the topic "thermophilic bacterium caldicellulosiruptor" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


301

Molecular Biology of the Cell Vol. 16, 48524866, October 2005  

E-Print Network [OSTI]

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

Paris-Sud XI, Université de

302

RESEARCH Open Access Helicobacter pylori interferes with an embryonic  

E-Print Network [OSTI]

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

Paris-Sud XI, Université de

303

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]

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

Bordenstein, Seth

304

Expression of the Helicobacter pylori adhesin SabA is controlled via phase variation and the ArsRS  

E-Print Network [OSTI]

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

Forsyth, Mark

305

NOTTINGHAM TRENT UNIVERSITY -INVESTING IN EXCELLENCE VICE-CHANCELLOR'S PHD SCHOLARSHIP SCHEME 2014 & SCHOOL PHD SCHOLARSHIPS  

E-Print Network [OSTI]

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

Evans, Paul

306

Distinguishing human ethnic groups by means of sequences from Helicobacter pylori  

E-Print Network [OSTI]

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

Wirth, Thierry

307

Lovley lands $8.9m grant for microbial studies Page 1 Vol. XVII, Issue 39 for the Amherst campus of the University of Massachusetts July 26, 2002  

E-Print Network [OSTI]

as the production of electricity. The grant, from the U.S. Department of Energy, is part of a larger $103 million effort involving six national laboratories, 16 universities and research hospitals, and four private; another looked at the same bacterium's ability to produce electricity from mud and other organic waste

Lovley, Derek

308

Microfluidic capture and release of bacteria in a conical nanopore array Peng Guo,ab  

E-Print Network [OSTI]

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

Zare, Richard N.

309

Fire blight of apple blossoms Fireblight of apples and pears, caused by the  

E-Print Network [OSTI]

Fire blight of apple blossoms Fireblight of apples and pears, caused by the bacterium Erwinia. W. Lightner. 1990. Predicting apple blossom infections by Erwinia amylovora using the Maryblyt model for forecasting fire blight disease in apples and pears. University of Maryland, College Park, MD. #12;

310

Radiation-resistant microorganism  

DOE Patents [OSTI]

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.

Fliermans, Carl B.

2010-06-15T23:59:59.000Z

311

Marine Fisheries Review Vol. 40, No, 10  

E-Print Network [OSTI]

., Seattle, WA 98105. Publication of material from sources outside the Service is not an en- dorsement of the Lobster, Homarl/S americanus James E. S,ewart 5 A New Bacterium (Presumptive Vibrio Species) Causing: An Abstract Louis LeibovilZ 9 Vibriosis in Maine and ~ew Hampshire Salmonids Evelyn S. Sawyer 10 Anaerobic

312

Heavy Metal Tolerance in Stenotrophomonas maltophilia Delphine Pages1,2,3  

E-Print Network [OSTI]

Heavy Metal Tolerance in Stenotrophomonas maltophilia Delphine Pages1,2,3 , Jerome Rose4 , Sandrine, this bacterium tolerates high levels (0.1 to 50 mM) of various toxic metals, such as Cd, Pb, Co, Zn, Hg, Ag mechanisms to overcome metal toxicity, reduction of oxyanions to non-toxic elemental ions and detoxification

Paris-Sud XI, Université de

313

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]

-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

Nori, Franco

2011-01-01T23:59:59.000Z

314

Redfield (PIN 28084) Regulation of CRP-S promoters in H. influenzae and E. coli $169,310 Introduction  

E-Print Network [OSTI]

. 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

Redfield, Rosemary J. "Rosie"

315

Lactobacillus kimchiensis sp. nov., isolated from a fermented food  

E-Print Network [OSTI]

& 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

Bae, Jin-Woo

316

Alien invasion Getting to the root of radiation  

E-Print Network [OSTI]

'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

Dawson, Jeff W.

317

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

318

THE GREENTECH MEDIA WEEKLY NEWSLETTER  

E-Print Network [OSTI]

: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

Lovley, Derek

319

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

320

Fuel-producing Geobacter receives support from new research May 3rd, 2010 in Technology / Energy  

E-Print Network [OSTI]

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

Lovley, Derek

Note: This page contains sample records for the topic "thermophilic bacterium caldicellulosiruptor" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


321

April 30, 2010 Getting the Bugs Out, a New Approach to Renewable  

E-Print Network [OSTI]

. 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

Lovley, Derek

322

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

323

Republican photo: David Molnar University of Massachusetts graduate  

E-Print Network [OSTI]

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

Lovley, Derek

324

Electric germs Source: scenta Rate this item  

E-Print Network [OSTI]

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

Lovley, Derek

325

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

326

2,4-Dichlorophenol Degradation Using Streptomyces viridosporus T7A Lignin Peroxidase  

E-Print Network [OSTI]

2,4-Dichlorophenol Degradation Using Streptomyces viridosporus T7A Lignin Peroxidase Dennis C. Yee, California 92697-2575 The Streptomyces viridosporus T7A bacterium produces the extracellular lignin from the ping- pong bireactant system that is typically used for horseradish peroxidase and lignin

Wood, Thomas K.

327

Proc. Natl. Acad. Sci. USA Vol. 74, No. 7, pp. 2963-2967, July 1977  

E-Print Network [OSTI]

for experiments that require the large-scale purification of nif DNA. MATERIALS AND METHODS Bacterial Strains) genes of the enteric bacterium Klebsiella pneumoniae on the small amplifiable bacterial plasmid pMB9.2. Nitrogen-free medium (NFDM) for nitrogenase assays has been described previously (9). Purification of DNA

Ausubel, Frederick M.

328

Comparison of the Prevalence and Genotypic Characteristics of Clostridium difficile in a Closed and Integrated Human and Swine Population in Texas  

E-Print Network [OSTI]

difficile moxalactam norfloxacin agar MIC Minimum inhibitory concentration MLVA Multilocus variable-number tandem-repeat analysis NAP North American pulsed-field type PCR Polymerase chain reaction PFGE Pulsed-field gel electrophoresis PYG Peptone... ............................................................................................... 69 3.3 Isolation of bacterium ........................................................................... 70 3.4 Molecular analysis ................................................................................ 73 3.5 Antibiotic...

Norman, Keri Noelle

2011-10-21T23:59:59.000Z

329

Solvent Immersion Imprint Lithography  

SciTech Connect (OSTI)

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.

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

330

Complete genome sequence of Anabaena variabilis ATCC 29413  

SciTech Connect (OSTI)

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.

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

331

Presence of pathogenic amoebae in power plant cooling waters. Final report, October 15, 1977-September 30, 1979. [Naegleria fowleri  

SciTech Connect (OSTI)

Cooling-water-associated algae and sediments from five northern and five southern or western electric power plants were tested for the presence of pathogenic amoebae. In addition, water algae and sediments from five northern and five southern/western sites not associated with power plants were tested. There was a significant correlation at northern power plants between the presence of thermophilic, pathogenic amoebae in cooling waters and thermal additions. Presence of the pathogenic did not correlate with salinity, pH, conductivity, or a variety of various chemical components of the cooling waters. Selected pathogenic isolates were tested serologically and were classified as Naegleria fowleri. Although thermal additions were shown to be contributing factor in predisposing cooling waters to the growth of pathogenic amoebae, the data suggest the involvement of other currently undefined parameters associated with the presence of the pathogenic amoebae. 35 refs., 21 tabs.

Tyndall, R.L.; Willaert, E.; Stevens, A.R.

1981-03-01T23:59:59.000Z

332

In situ thermally enhanced biodegradation of petroleum fuel hydrocarbons and halogenated organic solvents  

DOE Patents [OSTI]

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.

Taylor, R.T.; Jackson, K.J.; Duba, A.G.; Chen, C.I.

1998-05-19T23:59:59.000Z

333

In situ thermally enhanced biodegradation of petroleum fuel hydrocarbons and halogenated organic solvents  

DOE Patents [OSTI]

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.

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

334

Survival of Salmonella typhimurium in soil  

E-Print Network [OSTI]

~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...

Zibilske, Larry Marvin

1975-01-01T23:59:59.000Z

335

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

E-Print Network [OSTI]

named Bacterium monocytogenes because of the large mononuclear leucocytosis that developed due to its presence (Murray and others 1926), but its genus was renamed Listeria by J. H. Harvey Pirie (1940) in 1940. Thereafter, many reports... truncated inlA and inlB with no activity (Nightingale and others 2005; Nightingale and others 2007; Van Stelten and Nightingale 2008). This sort of observation is of particular interest to the food industry as some isolates from foods have been shown...

Brandt, Alex Lamar

2011-02-22T23:59:59.000Z

336

Regulation of the genes involved in nitrification.  

SciTech Connect (OSTI)

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.

Arp, D.J.; Sayavedra-Soto, L.A.

2003-08-14T23:59:59.000Z

337

Development of a Proteoliposome Model to Probe Transmembrane Electron-Transfer Reactions  

SciTech Connect (OSTI)

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.

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

338

Microbially-Promoted Solubilization of Steel Corrosion Products and Fate of Associated Actinides  

SciTech Connect (OSTI)

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

Gill Geesey; Timothy Magnuson; Andrew Neal

2002-06-15T23:59:59.000Z

339

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 Data Center Home Page on Delicious RankCombustion | Department of Energy Low-Temperature CombustionGlassMackle Company: ProposedBacterium

340

Investigations on the diagnosis, colonization, and epidemiology of grapevines with Pierce's disease  

E-Print Network [OSTI]

, or susceptible to PD (23,24). Fry et 6 al. (23) showed that ?French Colombard?, a susceptible Vitis vinifera cultivar, appeared to be a more conducive habitat for the bacterium than ?Carlos? and ?Noble?, both V. rotundifolia cultivars native... multiply and colonize at different rates in grapevines that vary in susceptibility (40). ?Cynthiana? (Norton), Vitis aestivalis, appears to have tolerance to PD (46). ?Cabernet Sauvignon?, V. vinifera, is considered moderately susceptible...

Vest, Mandi Ann

2005-02-17T23:59:59.000Z

Note: This page contains sample records for the topic "thermophilic bacterium caldicellulosiruptor" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


341

Efficient breakdown of lignocellulose using mixed-microbe populations for bioethanol production.  

SciTech Connect (OSTI)

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.

Murton, Jaclyn K.; Ricken, James Bryce; Powell, Amy Jo

2009-11-01T23:59:59.000Z

342

Final report for DOE grant FG02-06ER15805  

SciTech Connect (OSTI)

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.

Daniel Gage

2012-05-31T23:59:59.000Z

343

IMPACT OF WATER TEMPERATURE ON ZEBRA MUSSEL MORTALITY  

SciTech Connect (OSTI)

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.

Daniel P. Molloy

2002-08-07T23:59:59.000Z

344

Determination of the occurrence of Arcobacter butzleri in beef and dairy cattle from Texas using two isolation methods  

E-Print Network [OSTI]

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...

Golla, Steven Craig

2000-01-01T23:59:59.000Z

345

Development of More Effective Biosurfactants for Enhanced Oil Recovery  

SciTech Connect (OSTI)

The objectives of this were two fold. First, core displacement studies were done to determine whether microbial processes could recover residual oil at elevated pressures. Second, the importance of biosurfactant production for the recovery of residual oil was studies. In these studies, a biosurfactant-producing, microorganisms called Bacillus licheniformis strain JF-2 was used. This bacterium produces a cyclic peptide biosurfactant that significantly reduces the interfacial tension between oil and brine (7). The use of a mutant deficient in surfactant production and a mathematical MEOR simulator were used to determine the major mechanisms of oil recovery by these two strains.

McInerney, J.J.; Han, S.O.; Maudgalya, S.; Mouttaki, H.; Folmsbee, M.; Knapp, R.; Nagle, D.; Jackson, B.E.; Stuadt, M.; Frey, W.

2003-01-16T23:59:59.000Z

346

The Case for a Hot Archean Climate and its Implications to the History of the Biosphere  

E-Print Network [OSTI]

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...

Schwartzman, David W

2015-01-01T23:59:59.000Z

347

Increase in ethanol yield via elimination of lactate production in an ethanol-tolerant mutant of Clostridium thermocellum  

SciTech Connect (OSTI)

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.

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

348

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)

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.

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

349

Entropic stabilization of proteins and its proteomic consequences  

E-Print Network [OSTI]

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

Igor N. Berezovsky; William W. Chen; Paul J. Choi; Eugene I. Shakhnovich

2005-06-22T23:59:59.000Z

350

Computational design of an endo-1,4-[beta]-xylanase ligand binding site  

SciTech Connect (OSTI)

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.

Morin, Andrew; Kaufmann, Kristian W.; Fortenberry, Carie; Harp, Joel M.; Mizoue, Laura S.; Meiler, Jens (Vanderbilt)

2012-09-05T23:59:59.000Z

351

Oxidation and methylation of dissolved elemental mercury by anaerobic bacteria  

SciTech Connect (OSTI)

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.

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

352

Isolation and characterization of a fluoranthene-utilizing strain of pseudomonas paucimobilis  

SciTech Connect (OSTI)

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.

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

353

MICROBIAL FERMENTATION OF ABUNDANT BIOPOLYMERS: CELLULOSE AND CHITIN  

SciTech Connect (OSTI)

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

Leschine, Susan

2009-10-31T23:59:59.000Z

354

Final Report - "CO2 Sequestration in Cell Biomass of Chlorobium Thiosulfatophilum"  

SciTech Connect (OSTI)

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.

James L. Gaddy, PhD; Ching-Whan Ko, PhD

2009-05-04T23:59:59.000Z

355

The Genome Sequence of the psychrophilic archaeon, Methanococcoides burtonii: the Role of Genome Evolution in Cold-adaptation  

SciTech Connect (OSTI)

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.

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

356

Structure-Function, Stability, and Chemical Modification of the Cyanobacterial Cytochrome b[subscript 6]f Complex from Nostoc sp. PCC 7120  

SciTech Connect (OSTI)

The crystal structure of the cyanobacterial cytochrome b{sub 6}f complex has previously been solved to 3.0-{angstrom} resolution using the thermophilic Mastigocladus laminosus whose genome has not been sequenced. Several unicellular cyanobacteria, whose genomes have been sequenced and are tractable for mutagenesis, do not yield b{sub 6}f complex in an intact dimeric state with significant electron transport activity. The genome of Nostoc sp. PCC 7120 has been sequenced and is closer phylogenetically to M. laminosus than are unicellular cyanobacteria. The amino acid sequences of the large core subunits and four small peripheral subunits of Nostoc are 88 and 80% identical to those in the M. laminosus b{sub 6}f complex. Purified b{sub 6}f complex from Nostoc has a stable dimeric structure, eight subunits with masses similar to those of M. laminosus, and comparable electron transport activity. The crystal structure of the native b{sub 6}f complex, determined to a resolution of 3.0{angstrom} (PDB id: 2ZT9), is almost identical to that of M. laminosus. Two unique aspects of the Nostoc complex are: (i) a dominant conformation of heme b{sub p} that is rotated 180 deg. about the {alpha}- and {gamma}-meso carbon axis relative to the orientation in the M. laminosus complex and (ii) acetylation of the Rieske iron-sulfur protein (PetC) at the N terminus, a post-translational modification unprecedented in cyanobacterial membrane and electron transport proteins, and in polypeptides of cytochrome bc complexes from any source. The high spin electronic character of the unique heme cn is similar to that previously found in the b{sub 6}f complex from other sources.

Baniulis, Danas; Yamashita, Eiki; Whitelegge, Julian P.; Zatsman, Anna I.; Hendrich, Michael P.; Hasan, S. Saif; Ryan, Christopher M.; Cramer, William A.; (Semel); (Purdue); (Osaka)

2009-06-08T23:59:59.000Z

357

Fair Oaks Dairy Farms Cellulosic Ethanol Technology Review Summary  

SciTech Connect (OSTI)

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.

Andrew Wold; Robert Divers

2011-06-23T23:59:59.000Z

358

Crystal structure of a thermostable Old Yellow Enzyme from Thermus scotoductus SA-01  

SciTech Connect (OSTI)

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.

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

359

Does aspartic acid racemization constrain the depth limit of the subsurface biosphere?  

SciTech Connect (OSTI)

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.

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

360

Mechanism of N[superscript 10]-formyltetrahydrofolate synthetase derived from complexes with intermediates and inhibitors  

SciTech Connect (OSTI)

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.

Celeste, Lesa R.; Chai, Geqing; Bielak, Magdalena; Minor, Wladek; Lovelace, Leslie L.; Lebioda, Lukasz (SC); (UV)

2012-09-05T23:59:59.000Z

Note: This page contains sample records for the topic "thermophilic bacterium caldicellulosiruptor" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


361

Life Redefined: Microbes Built with Arsenic  

SciTech Connect (OSTI)

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.

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

362

Nucleic acids, compositions and uses thereof  

DOE Patents [OSTI]

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.

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

363

Nucleic acid compositions and the encoding proteins  

SciTech Connect (OSTI)

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.

Preston, III, James F.; Chow, Virginia; Nong, Guang; Rice, John D.; St. John, Franz J.

2014-09-02T23:59:59.000Z

364

Engineered plant biomass particles coated with biological agents  

DOE Patents [OSTI]

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.

Dooley, James H.; Lanning, David N.

2014-06-24T23:59:59.000Z

365

Recombinant glucose uptake system  

DOE Patents [OSTI]

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.

Ingrahm, Lonnie O. (Gainesville, FL); Snoep, Jacob L. (Groede, NL); Arfman, Nico (Delft, NL)

1997-01-01T23:59:59.000Z

366

Complete genome sequence of Halorhodospira halophila SL1  

SciTech Connect (OSTI)

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.

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

367

Complete genome sequence of Paenibacillus sp. strain JDR-2  

SciTech Connect (OSTI)

Paenibacillus sp. strain JDR-2, an aggressively xylanolytic bacterium isolated from sweetgum (Liquidambar styraciflua) wood, is able to efficiently depolymerize, assimilate and metabolize 4-O-methylglucuronoxylan, the predominant structural component of hardwood hemicelluloses. A basis for this capability was first supported by the identification of genes and characterization of encoded enzymes and has been further defined by the sequencing and annotation of the complete genome, which we describe. In addition to genes implicated in the utilization of -1,4-xylan, genes have also been identified for the utilization of other hemicellulosic polysaccharides. The genome of Paenibacillus sp. JDR-2 contains 7,184,930 bp in a single replicon with 6,288 protein-coding and 122 RNA genes. Uniquely prominent are 874 genes encoding proteins involved in carbohydrate transport and metabolism. The prevalence and organization of these genes support a metabolic potential for bioprocessing of hemicellulose fractions derived from lignocellulosic resources.

Chow, Virginia [University of Florida; Nong, Guang [University of Florida; St. John, Franz J. [US Forest Service, Forest Products Laboratory, Madison, Wisconsin, USA; Dickstein, Ellen [University of Florida; Chertkov, Olga [Los Alamos National Laboratory (LANL); Bruce, David [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Brettin, Thomas S [ORNL; Han, James [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; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Martin, Joel [U.S. Department of Energy, Joint Genome Institute; Copeland, A [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Jones, Jeffrey B. [University of Florida; Ingram, Lonnie O. [University of Florida; Shanmugam, Keelnathan T. [University of Florida; Preston, James F. [University of Florida

2012-01-01T23:59:59.000Z

368

Strength and stability of microbial plugs in porous media  

SciTech Connect (OSTI)

Mobility reduction induced by the growth and metabolism of bacteria in high-permeability layers of heterogeneous reservoirs is an economically attractive technique to improve sweep efficiency. This paper describes an experimental study conducted in sandpacks using an injected bacterium to investigate the strength and stability of microbial plugs in porous media. Successful convective transport of bacteria is important for achieving sufficient initial bacteria distribution. The chemotactic and diffusive fluxes are probably not significant even under static conditions. Mobility reduction depends upon the initial cell concentrations and increase in cell mass. For single or multiple static or dynamic growth techniques, permeability reduction was approximately 70% of the original permeability. The stability of these microbial plugs to increases in pressure gradient and changes in cell physiology in a nutrient-depleted environment needs to be improved.

Sarkar, A.K. [NIPER/BDM-Oklahoma, Inc., Bartlesville, OK (United States); Sharma, M.M.; Georgiou, G. [Univ. of Texas, Austin, TX (United States)

1995-12-31T23:59:59.000Z

369

Biological production of ethanol from coal. Task 4 report, Continuous reactor studies  

SciTech Connect (OSTI)

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.

Not Available

1992-10-01T23:59:59.000Z

370

Sugar Transport and Metabolism in Thermotoga  

SciTech Connect (OSTI)

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.

Noll, Kenneth M.; Romano, Antonio H.

2003-02-11T23:59:59.000Z

371

R/BHC: fast Bayesian hierarchical clustering for microarray data  

E-Print Network [OSTI]

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...

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

372

Complete Genome sequence of Burkholderia phymatum STM815, a broad host range and efficient nitrogen-fixing symbiont of Mimosa species  

SciTech Connect (OSTI)

Burkholderia phymatum is a soil bacterium able to develop a nitrogen-fixing symbiosis with species of the legume genus Mimosa, and is frequently found associated specifically with Mimosa pudica. The type strain of the species, STM 815T, was isolated from a root nodule in French Guiana in 2000. The strain is an aerobic, motile, non-spore forming, Gram-negative rod, and is a highly competitive strain for nodulation compared to other Mimosa symbionts, as it also nodulates a broad range of other legume genera and species. The 8,676,562 bp genome is composed of two chromosomes (3,479,187 and 2,697,374 bp), a megaplasmid (1,904,893 bp) and a plasmid hosting the symbiotic functions (595,108 bp).

Moulin, Lionel [UMR, France] [UMR, France; Klonowska, Agnieszka [UMR, France] [UMR, France; Caroline, Bournaud [UMR, France] [UMR, France; Booth, Kristina [University of Massachusetts] [University of Massachusetts; Vriezen, Jan A.C. [University of Massachusetts] [University of Massachusetts; Melkonian, Remy [UMR, France] [UMR, France; James, Euan [James Hutton Institute, Dundee, United Kingdom] [James Hutton Institute, Dundee, United Kingdom; Young, Peter W. [University of York, United Kingdom] [University of York, United Kingdom; Bena, Gilles [UMR, France] [UMR, France; Hauser, Loren John [ORNL] [ORNL; Land, Miriam L [ORNL] [ORNL; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute] [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Los Alamos National Laboratory (LANL)] [Los Alamos National Laboratory (LANL); Chain, Patrick S. G. [Lawrence Livermore National Laboratory (LLNL)] [Lawrence Livermore National Laboratory (LLNL); Copeland, A [U.S. Department of Energy, Joint Genome Institute] [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [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; Lizotte-Waniewski, Michelle [University of Massachusetts] [University of Massachusetts; Bristow, James [U.S. Department of Energy, Joint Genome Institute] [U.S. Department of Energy, Joint Genome Institute; Riley, Monica [Woods Hole Oceanographic Institution (WHOI), Woods Hole] [Woods Hole Oceanographic Institution (WHOI), Woods Hole

2014-01-01T23:59:59.000Z

373

High resolution structure of the large ribosomal subunit from a Mesophilic Eubacterium  

SciTech Connect (OSTI)

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.

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

374

Anaerobic microbial dissolution of lead and production of organic acids  

DOE Patents [OSTI]

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.

Francis, A.J.; Dodge, C.; Chendrayan, K.

1986-02-28T23:59:59.000Z

375

Respiratory arsenate reductase as a bidirectional enzyme  

SciTech Connect (OSTI)

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.

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

376

Crystallization and preliminary X-ray crystallographic studies of the outer membrane cytochrome OmcA from Shewanella oneidensis MR-1  

SciTech Connect (OSTI)

The outer membrane cytochrome OmcA functions as a terminal metal reductase in the dissimilatory metal-reducing bacterium Shewanella oneidensis MR-1. The ten-heme centers shuttle electrons from the transmembrane donor complex to extracellular electron acceptors. Here, the crystallization and preliminary crystallographic analysis of OmcA are reported. Crystals of OmcA were grown by the sitting-drop vapor-diffusion method using PEG 20 000 as a precipitant. The OmcA crystals belonged to space group P21, with unit-cell parameters a = 93.0, b = 246.0, c = 136.6 A ° , * = 90, * = 97.8, * = 90*. X-ray diffraction data were collected to a maximum resolution of 3.25 A ° .

Tomanicek, S. J.; Johs, Alexander; Sawhney, M. S.; Shi, Liang; Liang, L.

2012-01-01T23:59:59.000Z

377

Discrimination of Bacillus anthracis from closely related microorganisms by analysis of 16S and 23S rRNA with oligonucleotide microchips  

DOE Patents [OSTI]

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.

Bavykin, Sergei G. (Darien, IL); Mirzabekova, legal representative, Natalia V. (Westmont, IL); Mirzabekov, deceased, Andrei D. (Westmont, IL)

2007-12-04T23:59:59.000Z

378

Discrimination of Bacillus anthracis from closely related microorganisms by analysis of 16S and 23S rRNA with oligonucleotide microchips  

DOE Patents [OSTI]

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.

Bavykin, Sergei G. (Darien, IL); Mirzabekov, Andrei D. (Moscow, RU)

2007-10-30T23:59:59.000Z

379

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)

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.

Maness, P. C.

2014-06-01T23:59:59.000Z

380

Data Gathering in Networks of Bacteria Colonies: Collective Sensing and Relaying Using Molecular Communication  

E-Print Network [OSTI]

The prospect of new biological and industrial applications that require communication in micro-scale, encourages research on the design of bio-compatible communication networks using networking primitives already available in nature. One of the most promising candidates for constructing such networks is to adapt and engineer specific types of bacteria that are capable of sensing, actuation, and above all, communication with each other. In this paper, we describe a new architecture for networks of bacteria to form a data collecting network, as in traditional sensor networks. The key to this architecture is the fact that the node in the network itself is a bacterial colony; as an individual bacterium (biological agent) is a tiny unreliable element with limited capabilities. We describe such a network under two different scenarios. We study the data gathering (sensing and multihop communication) scenario as in sensor networks followed by the consensus problem in a multi-node network. We will explain as to how th...

Einolghozati, Arash; Beirami, Ahmad; Fekri, Faramarz

2012-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "thermophilic bacterium caldicellulosiruptor" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


381

Microbial engineering of nano-heterostructures; biological synthesis of a magnetically-recoverable palladium nanocatalyst  

SciTech Connect (OSTI)

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.

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

382

Sorption of cadmium to bacterial extracellular polymeric sediment coatings under estuarine conditions  

SciTech Connect (OSTI)

Microbial extracellular polymeric substances (EPS) are ubiquitous features in aquatic environments. Produced by surface-adherent bacteria and microalgae, EPS are often present as coatings on surfaces of sediment particles and exhibit high affinities for divalent cationic metals. Thus, EPS sediment coatings may participate in the fate of potentially toxic metals. The authors coated particulate silica with EPS produced by NISC1, a bacterium isolated from estuarine sediments, in order to measure the metal binding characteristics of these coatings. They used the radioisotope {sup 109}Cd to measure effects of salinity, Cd concentration, and pH on Cd sorption to EPS-coated (EPS-silica) silica and to noncoated silica (NC-silica). Also, Cd sorption by NISC1 EPS coatings was compared to coatings of polymers formed by the bacterium, Alteromonas atlantica and the alga, Macrocystis porifera. Under all circumstances, EPS coatings increased the affinity of silica for Cd. Extracellular polymeric substance-particulate aggregates rapidly sorbed up to 90% of Cd from aqueous solution. Extracellular polymeric substance sediment coatings exhibited a maximum log distribution coefficient (K{sub d}) of 6.5 at 2.5%. Sorption of Cd to NC-silica was affected by salinity and metal concentration, whereas sorption of Cd to EPS-silica was only affected by salinity under high metal concentrations. Changes in pH had a dramatic effect on Cd sorption, with the proportion of free Cd to sorbed Cd changing from approximately 90% at pH 5 to 5% at pH 9. Desorption of Cd from EPS-silica was enhanced with increasing salinity. These experiments suggest that EPS coatings actively participate in binding dissolved overlying and pore-water metals in estuarine sediments.

Schlekat, C.E.; Decho, A.W.; Chandler, G.T. [Univ. of South Carolina, Columbia, SC (United States). Dept. of Environmental Health Sciences

1998-09-01T23:59:59.000Z

383

Post-Translational Modifications of Desulfovibrio vulgaris Hildenborough Sulfate Reduction Pathway Proteins  

SciTech Connect (OSTI)

Recent developments in shotgun proteomics have enabled high-throughput studies of a variety of microorganisms at a proteome level and provide experimental validation for predicted open reading frames in the corresponding genome. More importantly, advances in mass spectrometric data analysis now allow mining of large proteomics data sets for the presence of post-translational modifications(PTMs). Although PTMs are a critical aspectof cellular activity, such information eludes cell-wide studies conducted at the transcript level. Here, we analyze several mass spectrometric data sets acquired using two-dimensional liquid chromatography tandem mass spectrometry, 2D-LC/MS/MS, for the sulfate reducing bacterium, Desulfovibrio vulgaris Hildenborough. Our searches of the raw spectra led us to discover several post-translationally modified peptides in D. vulgaris. Of these, several peptides containing a lysine with a +42 Da modification were found reproducibly across all data sets. Both acetylation and trimethylation have the same nominal +42 Da mass, and are therefore candidates for this modification. Several spectra were identified having markers for trimethylation, while one is consistent with an acetylation. Surprisingly, these modified peptides predominantly mapped to proteins involved in sulfate respiration. Other highly expressed proteins in D. vulgaris, such as enzymes involved in electron transport and other central metabolic processes, did not contain this modification. Decoy database searches were used to control for random spectrum/sequence matches. Additional validation for these modifications was provided by alternate workflows, for example, two-dimensional gel electrophoresis followed by mass spectrometry analysis of the dissimilatory sulfite reductase gamma-subunit(DsrC) protein. MS data for DsrC in this alternate workflow also contained the +42 Da modification at the same loci. Furthermore, the DsrC homologue in another sulfate reducing bacterium, Desulfovibrio desulfuricans G20, also showed similar +42 Da modifications in the same pathway. Here, we discuss our methods and implications of potential trimethylation in the D. vulgaris sulfate reduction pathway.

Gaucher, S.P.; Redding, A.M.; Mukhopadhyay, A.; Keasling, J.D.; Singh, A.K.

2008-03-01T23:59:59.000Z

384

Combined inactivation of the Clostridium cellulolyticum lactate and malate dehydrogenase genes substantially increases ethanol yield from cellulose and switchgrass fermentations  

SciTech Connect (OSTI)

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.

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

385

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

SciTech Connect (OSTI)

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.

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

2012-10-19T23:59:59.000Z

386

Identification of Small RNAs in Desulfovibrio vulgaris Hildenborough  

SciTech Connect (OSTI)

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.

Burns, Andrew; Joachimiak, Marcin; Deutschbauer, Adam; Arkin, Adam; Bender, Kelly

2010-05-17T23:59:59.000Z

387

Microbial enhanced oil recovery research. Final report, Annex 5  

SciTech Connect (OSTI)

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.

Sharma, M.M.; Gerogiou, G.

1993-07-01T23:59:59.000Z

388

Clostridium thermocellum Transcriptomic Profiles after Exposure to Furfural or Heat Stress  

SciTech Connect (OSTI)

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.

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

389

Final Report: Structural studies of archatelthermophilic adenylate kinase, September 15, 1996 - September 14, 1998  

SciTech Connect (OSTI)

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.

Konisky, Jordan

1998-09-14T23:59:59.000Z

390

Final technical report for award NO. DE-FG02-95ER20206  

SciTech Connect (OSTI)

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.

James P. Shapleigh

2010-02-23T23:59:59.000Z

391

A STUDY ON LEGIONELLA PNEUMOPHILA, WATER CHEMISTRY, AND ATMOSPHERIC CONDITIONS IN COOLING TOWERS AT THE SAVANNAH RIVER SITE  

SciTech Connect (OSTI)

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.

Smith, C.; Brigmon, R.

2009-10-20T23:59:59.000Z

392

Linear and Nonlinear Spectroscopic Probing of Solute Interactions with Chemically Modified Silica Surfaces  

SciTech Connect (OSTI)

Solar energy conversion through biology would provide a renewable and nonpolluting abundance of energy. The bacterium Halobacterium salinarum converts solar to electrical energy by virtue of a transmembrane protein, bacteriorhodopsin. This transmembrane protein pumps protons across a nonconducting bilayer upon irradiation with green light. The bacterium evolved to perform this function inefficiently. If we were able to understand this process to engineer this protein for efficiency, then inexpensive energy production could be achieved. There are tens of thousands of different types of halobacteria, giving the opportunity to study different efficiencies and relating these to the protein structures. Technology does not yet exist to perform such screening. The goal of this research is to generate new separation technology that can ultimately enable such screening. This involves creating a method for separating oriented and functional transmembrane proteins that remain in an electrically insulating lipid bilayer, with aqueous solutions on either side of the bilayer. A pH change across the lipid bilayer upon irradiation of a known concentration of proteins would probe function. Differences in proton pumping efficiency for different proteins variants would provide structure-function information for engineering the proteins. A schematic diagram from the original proposal is shown here. The idea is that (a) a lipid bilayer supported on a hydrophilic polymer film will make the bilayer fluid, and (b) applying an electric field will cause electrophoretic migration of the transmembrane proteins. We demonstrated this concept experimentally in a paper that was published just after this new grant period started (Lipid Bilayers on Polyacrylamide Brushes for Inclusion of Membrane Proteins, Emily A. Smith, Jason W. Coym, Scott M. Cowell, Victor J. Hruby, Henry I. Yamamura, Mary J. Wirth, Langmuir, 21, 9644-9650, 2005). The electrophoretic mobility was slow (10{sup -8} cm{sup 2}/Vs), and we project that a two order of magnitude increase would make this a practical tool. We are investigating two ways of improving electrophoretic mobility: better polymer supports, and a novel nanoporous medium that suspends the bilayer over free solution.

Wirth, Mary J

2011-02-09T23:59:59.000Z

393

Syntrophic Effects in a Subsurface Clostridial Consortium on Fe(III)-(Oxyhydr)oxide Reduction and Secondary Mineralization  

SciTech Connect (OSTI)

In this study, we cultivated from subsurface sediments an anaerobic Clostridia 25 consortium that was composed of a fermentative Fe-reducer Clostridium species (designated as 26 strain FGH) and a novel sulfate-reducing bacterium belonging to the Clostridia family 27 Vellionellaceae (designated as strain RU4). In pure culture, Clostridium sp. strain FGH mediated 28 the reductive dissolution/transformation of iron oxides during growth on peptone. When 29 Clostridium sp. FGH was grown with strain RU4 on peptone, the rates of iron oxide reduction 30 were significantly higher. Iron reduction by the consortium was mediated by multiple 31 mechanisms, including biotic reduction by Clostridium sp. FGH and biotic/abiotic reactions 32 involving biogenic sulfide by strain RU4. The Clostridium sp. FGH produced hydrogen during 33 fermentation, and the presence of hydrogen inhibited growth and iron reduction activity. The 34 sulfate-reducing partner strain RU4 was stimulated by the presence of H2 gas and generated 35 reactive sulfide which promoted the chemical reduction of the iron oxides. Characterization of 36 Fe(II) mineral products showed the formation of magnetite during ferrihydrite reduction, and 37 the precipitation of iron sulfides during goethite and hematite reduction. The results suggest an 38 important pathway for iron reduction and secondary mineralization by fermentative sulfate-39 reducing microbial consortia is through syntrophy-driven biotic/abiotic reactions with biogenic 40 sulfide.

Shah, Madhavi; Lin, Chu-Ching; Kukkadapu, Ravi K.; Engelhard, Mark H.; Zhao, Xiuhong; Wang, Yangping; Barkay, Tamar; Yee, Nathan

2013-12-02T23:59:59.000Z

394

Electrocatalytic reduction of S-nitrosoglutathione at electrodes modified with an electropolymerized film of a pyrrole-derived viologen system and their application to cellular S-nitrosoglutathione determinations  

SciTech Connect (OSTI)

The preparation, electrochemical characterization, and analytical applications of glassy carbon (GC) electrodes modified with electropolymerized films of the cation N,N{prime}-di(3-pyrrol-1-yl-propyl)-4,4{prime}-bipyridine (DPPB) are described. Electropolymerized films of DPPB on GC electrodes exhibit two one-electron redox processes centered at {minus}0.45 and {minus}0.85 V, respectively. S-Nitrosoglutathione (GSNO) can be electrocatalytically reduced at electrodes modified with electropolymerized films of DPPB at approximately {minus}0.4 V vs sodium-saturated calomel electrode, which represents a dramatic diminution of about 600 mV in the overpotential in comparison with the reaction carried out at a bare GC electrode. The kinetics of the catalytic reaction have been characterized using cyclic voltammetry and rotated disk electrode techniques from which a value of (1.3 {+-} 0.2) {times} 10{sup 3} M{sup {minus}1} s{sup {minus}1} was obtained. Using electrodes modified with an electropolymerized film of DPPB the authors have carried out preliminary studies of the determination of intracellular GSNO concentrations in two strains of the bacterium Rhodobacter sphaeroides.

Wu, Q.; Storrier, G.D.; Wu, K.R.; Shapleigh, J.P.; Abruna, H.D. [Cornell Univ., Ithaca, NY (United States)] [Cornell Univ., Ithaca, NY (United States)

1998-10-01T23:59:59.000Z

395

Complete genome sequence of Desulfomicrobium baculatum type strain (XT)  

SciTech Connect (OSTI)

Desulfomicrobium baculatum is the type species of the genus Desulfomicrobium, which is the type genus of the family Desulfomicrobiaceae. It is of phylogenetic interest because of the isolated location of the family Desulfomicrobiaceae within the order Desulfovibrionales. D. baculatum strain XT is a Gram-negative, motile, sulfate-reducing bacterium isolated from water-saturated manganese carbonate ore. It is strictly anaerobic and does not require NaCl for growth, although NaCl concentrations up to 6percent (w/v) are tolerated. The metabolism is respiratory or fermentative. In the presence of sulfate, pyruvate and lactate are incompletely oxidized to acetate and CO2. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the deltaproteobacterial family Desulfomicrobiaceae, and this 3,942,657 bp long single replicon genome with its 3494 protein-coding and 72 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

Copeland, Alex; Spring, Stefan; Goker, Markus; Schneider, Susanne; Lapidus, Alla; Glavina Del Rio, Tijana; Tice, Hope; Cheng, Jan-Fang; Lucas, Susan; Chen, Feng; Nolan, Matt; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Ivanova, Natalia; Mavrommatis, Konstantinos; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jefferies, Cynthia C; Meincke, Linda; Sims, David; Brettin, Thomas; Detter, John C; Han, Cliff; Chain, Patrick; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Klenk, Hans-Peter; Kyrpides, Nikos C; Lucas, Susan

2009-05-20T23:59:59.000Z

396

Bioremediation of uranium contaminated soils and wastes  

SciTech Connect (OSTI)

Contamination of soils, water, and sediments by radionuclides and toxic metals from uranium mill tailings, nuclear fuel manufacturing and nuclear weapons production is a major concern. Studies of the mechanisms of biotransformation of uranium and toxic metals under various microbial process conditions has resulted in the development of two treatment processes: (1) stabilization of uranium and toxic metals with reduction in waste volume and (2) removal and recovery of uranium and toxic metals from wastes and contaminated soils. Stabilization of uranium and toxic metals in wastes is accomplished by exploiting the unique metabolic capabilities of the anaerobic bacterium, Clostridium sp. The radionuclides and toxic metals are solubilized by the bacteria directly by enzymatic reductive dissolution, or indirectly due to the production of organic acid metabolites. The radionuclides and toxic metals released into solution are immobilized by enzymatic reductive precipitation, biosorption and redistribution with stable mineral phases in the waste. Non-hazardous bulk components of the waste volume. In the second process uranium and toxic metals are removed from wastes or contaminated soils by extracting with the complexing agent citric acid. The citric-acid extract is subjected to biodegradation to recover the toxic metals, followed by photochemical degradation of the uranium citrate complex which is recalcitrant to biodegradation. The toxic metals and uranium are recovered in separate fractions for recycling or for disposal. The use of combined chemical and microbiological treatment process is more efficient than present methods and should result in considerable savings in clean-up and disposal costs.

Francis, A.J.

1998-12-31T23:59:59.000Z

397

Zn Sorption Mechanisms onto Sheathed Leptothrix Discophora and the Impact of the Nanoparticulate Biogenic Mn Oxide Coating  

SciTech Connect (OSTI)

Zinc sorption on sheathed Leptothrix discophora bacterium, the isolated extracellular polymeric substances (EPS) sheath, and Mn oxide-coated bacteria was investigated with macroscopic and spectroscopic techniques. Complexation with L. discophora was dominated by the outer membrane phosphoryl groups of the phospholipid bilayer while sorption to isolated EPS was dominated by carboxyl groups. Precipitation of nanoparticulate Mn oxide coatings on the cell surface increased site capacity by over twenty times with significant increase in metal sorption. XAS analysis of Zn sorption in the coated system showed Mn oxide phase contributions of 18 to 43% through mononuclear inner-sphere complexes. The coordination environments in coprecipitation samples were identical to those of sorption samples, indicating that, even in coprecipitation, Zn is not incorporated into the Mn oxide structure. Rather, through enzymatic oxidation by L. discophora, Mn(II) is oxidized and precipitated onto the biofilm providing a large surface for metal sequestration. The nanoparticulate Mn oxide coating exhibited significant microporosity (75%) suggesting contributions from intraparticle diffusion. Transient studies conducted over 7 months revealed a 170% increase in Zn loading. However, the intraparticle diffusivity of 10{sup -19} cm{sup 2} s{sup -1} is two orders of magnitude smaller than that for abiotic Mn oxide which we attribute to morphological changes such as reduced pore sizes in the nanoparticulate oxide. Our results demonstrate that the cell-bound Mn oxide particles can sorb significant amounts of Zn over long periods of time representing an important surface for sequestration of metal contaminants.

Boonfueng, T.; Axe, L; Yee, N; Hahn, D; Ndiba, P

2009-01-01T23:59:59.000Z

398

Whole-genome shotgun optical mapping of rhodospirillumrubrum  

SciTech Connect (OSTI)

Rhodospirillum rubrum is a phototrophic purple non-sulfur bacterium known for its unique and well-studied nitrogen fixation and carbon monoxide oxidation systems, and as a source of hydrogen and biodegradable plastics production. To better understand this organism and to facilitate assembly of its sequence, three whole-genome restriction maps (Xba I, Nhe I, and Hind III) of R. rubrum strain ATCC 11170 were created by optical mapping. Optical mapping is a system for creating whole-genome ordered restriction maps from randomly sheared genomic DNA molecules extracted directly from cells. During the sequence finishing process, all three optical maps confirmed a putative error in sequence assembly, while the Hind III map acted as a scaffold for high resolution alignment with sequence contigs spanning the whole genome. In addition to highlighting optical mapping's role in the assembly and validation of genome sequence, our work underscores the unique niche in resolution occupied by the optical mapping system. With a resolution ranging from 6.5 kb (previously published) to 45 kb (reported here), optical mapping advances a ''molecular cytogenetics'' approach to solving problems in genomic analysis.

Reslewic, Susan; Zhou, Shiguo; Place, Mike; Zhang, Yaoping; Briska, Adam; Goldstein, Steve; Churas, Chris; Runnheim, Rod; Forrest,Dan; Lim, Alex; Lapidus, Alla; Han, Cliff S.; Roberts, Gary P.; Schwartz,David C.

2004-07-01T23:59:59.000Z

399

Single-cell analysis of growth in budding yeast and bacteria reveals a common size regulation strategy  

E-Print Network [OSTI]

Unicellular organism from various kingdoms of life face the challenge of regulating their size. Despite decades of research, we still do not have a good understanding of the molecular mechanisms involved in this regulation, and how cells coordinate the different events of the cell cycle, such as growth, division and DNA replication is still unclear. Here, we report on experimental results for the budding yeast Saccharomyces cerevisiae and the bacterium Escherichia coli, showing that, remarkably, they share a common strategy for cell size control. We collected data on single-cell growth and cell cycle progression in S. cerevisiae in several growth media and estimated the distributions of size at birth and interdivision time as well as their correlations throughout cell lineages. We also performed the same analysis on previously collected data on single-cell growth and division in E. coli. The results are in quantitative agreement with the predictions of the incremental model, which leads to the addition of a constant volume (up to fluctuations), independent of size at birth, between birth and division; we show that in both organisms size at birth and size at division exhibit a linear relationship with slope one. This result, together with extended additional analysis supporting the incremental model, argues against the existing "critical size" paradigm for cell size control in bacteria and yeast.

Ilya Soifer; Lydia Robert; Naama Barkai; Ariel Amir

2014-10-23T23:59:59.000Z

400

Permanent draft genome sequence of Dethiosulfovibrio peptidovorans type strain (SEBR 4207T)  

SciTech Connect (OSTI)

Dethiosulfovibrio peptidovorans Magot et al. 1997 is the type species of the genus Dethiosulfovibrio of the family Synergistaceae in the recently created phylum Sysnergistetes. The strictly anaerobic, vibrio-shaped, thiosulfate-reducing bacterium utilizes only peptides and amino acids, but no sugars or fatty acids. It was isolated from an offshore oil well where it is supposed to be involved in pitting corrosion of mild steel. While initially (1997) described as a distantly related to the genus Thermoanaerobacter, but not assigned to any specific genus, it is meanwhile taxonomically established within the novel phylum Synergistetes. A large number of repeats on the distal portions of the main contig prevented an economically justifiable closure of the last gaps. This is already the third published genome from a member of the phylum Synergistetes. The 2,576,359 bp long genome consists of three contigs with 2,458 protein-coding and 59 RNA genes and is part of the Genomic Encyclopedia of Bacteria and Archaea project.

LaButti, Kurt [U.S. Department of Energy, Joint Genome Institute; Mayilraj, Shanmugam [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Clum, Alicia [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; Nolan, Matt [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; 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; Ovchinnikova, Galina [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); 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; Chang, Yun-Juan [ORNL; Jeffries, Cynthia [Oak Ridge National Laboratory (ORNL); Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Spring, Stefan [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 [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; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute

2010-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "thermophilic bacterium caldicellulosiruptor" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


401

Complete genome sequence of Actinosynnema mirum type strain (101T)  

SciTech Connect (OSTI)

Actinosynnema mirum Hasegawa et al. 1978 is the type species of the genus, and is of phylogenetic interest because of its central phylogenetic location in the Actino-synnemataceae, a rapidly growing family within the actinobacterial suborder Pseudo-nocardineae. A. mirum is characterized by its motile spores borne on synnemata and as a producer of nocardicin antibiotics. It is capable of growing aerobically and under a moderate CO2 atmosphere. The strain is a Gram-positive, aerial and substrate mycelium producing bacterium, originally isolated from a grass blade collected from the Raritan River, New Jersey. 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 family Actinosynnemataceae, and only the second sequence from the actinobacterial suborder Pseudonocardineae. The 8,248,144 bp long single replicon genome with its 7100 protein-coding and 77 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

Land, Miriam L [ORNL; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Mayilraj, Shanmugam [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Chen, Feng [U.S. Department of Energy, Joint Genome Institute; Copeland, A [U.S. Department of Energy, Joint Genome Institute; Glavina Del Rio, Tijana [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; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Chertkov, Olga [Los Alamos National Laboratory (LANL); Bruce, David [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; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Pati, Amrita [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; Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Palaniappan, Krishna [U.S. Department of Energy, Joint Genome Institute; Hauser, Loren John [ORNL; Chang, Yun-Juan [ORNL; Jeffries, Cynthia [Oak Ridge National Laboratory (ORNL); Brettin, Thomas S [ORNL; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Han, Cliff [Los Alamos National Laboratory (LANL); Chain, Patrick S. G. [Lawrence Livermore National Laboratory (LLNL); Tindall, Brian [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; 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

2009-01-01T23:59:59.000Z

402

Complete genome sequence of Actinosynnema mirum type strain (101T)  

SciTech Connect (OSTI)

Actinosynnema mirum Hasegawa et al. 1978 is the type species of the genus, and is of phylogenetic interest because of its central phylogenetic location in the Actino-synnemataceae, a rapidly growing family within the actinobacterial suborder Pseudo-nocardineae. A. mirum is characterized by its motile spores borne on synnemata and as a producer of nocardicin antibiotics. It is capable of growing aerobically and under a moderate CO2 atmosphere. The strain is a Gram-positive, aerial and substrate mycelium producing bacterium, originally isolated from a grass blade collected from the Raritan River, New Jersey. 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 family Actinosynnemataceae, and only the second sequence from the actinobacterial suborder Pseudonocardineae. The 8,248,144 bp long single replicon genome with its 7100 protein-coding and 77 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

Land, Miriam; Lapidus, Alla; Mayilraj, Shanmugam; Chen, Feng; Copeland, Alex; Glavina Del Rio, Tijana; Nolan, Matt; Lucas, Susan; Tice, Hope; Cheng, Jan-Fang; Chertkov, Olga; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Rohde, Manfred; Goker, Markus; Pati, Amrita; Ivanova, Natalia; Mavrommatis, Konstantinos; Chen, Amy; Palaniappan, Krishna; Hauser, Loren; Chang, Yun-Juan; Jefferies, Cynthia; Brettin, Thomas; Detter, John C.; Han, Cliff; Chain, Patrick; Tindall, Brian; Bristow, James; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans-Peter

2009-05-20T23:59:59.000Z

403

Complete genome sequence of Kytococcus sedentarius type strain (strain 541T)  

SciTech Connect (OSTI)

Kytococcus sedentarius (ZoBell and Upham 1944) Stackebrandt et al. 1995 is the type strain of the species, and is of phylogenetic interest because of its location in the Dermacoccaceae, a poorly studied family within the actinobacterial suborder Micrococcineae. K. sedentarius is known for the production of oligoketide antibiotics as well as for its role as an opportunistic pathogen causing valve endocarditis, hemorrhagic pneumonia, and pitted keratolysis. It is strictly aerobic and can only grow when several amino acids are provided in the medium. The strain described in this report is a free-living, nonmotile, Gram-positive bacterium, originally isolated from a marine environment. 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 family Dermacoccaceae and the 2,785,024 bp long single replicon genome with its 2639 protein-coding and 64 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

Sims, David; Brettin, Thomas; Detter, John C.; Han, Cliff; Lapidus, Alla; Copeland, Alex; Glavina Del Rio, Tijana; Nolan, Matt; Chen, Feng; Lucas, Susan; Tice, Hope; Cheng, Jan-Fang; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Ovchinnikova, Galina; Pati, Amrita; Ivanova, Natalia; Mavrommatis, Konstantinos; Chen, Amy; Palaniappan, Krishna; D'haeseleer, Patrick; Chain, Patrick; Bristow, James; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Schneider, Susanne; Goker, Markus; Pukall, Rudiger; Kyrpides, Nikos C.; Klenk, Hans-Peter

2009-05-20T23:59:59.000Z

404

Generalized schemes for high throughput manipulation of the Desulfovibrio vulgaris Hildenborough genome  

SciTech Connect (OSTI)

The ability to conduct advanced functional genomic studies of the thousands of sequenced bacteria has been hampered by the lack of available tools for making high- throughput chromosomal manipulations in a systematic manner that can be applied across diverse species. In this work, we highlight the use of synthetic biological tools to assemble custom suicide vectors with reusable and interchangeable DNA “parts” to facilitate chromosomal modification at designated loci. These constructs enable an array of downstream applications including gene replacement and creation of gene fusions with affinity purification or localization tags. We employed this approach to engineer chromosomal modifications in a bacterium that has previously proven difficult to manipulate genetically, Desulfovibrio vulgaris Hildenborough, to generate a library of over 700 strains. Furthermore, we demonstrate how these modifications can be used for examining metabolic pathways, protein-protein interactions, and protein localization. The ubiquity of suicide constructs in gene replacement throughout biology suggests that this approach can be applied to engineer a broad range of species for a diverse array of systems biological applications and is amenable to high-throughput implementation.

Chhabra, S.R.; Butland, G.; Elias, D.; Chandonia, J.-M.; Fok, V.; Juba, T.; Gorur, A.; Allen, S.; Leung, C.-M.; Keller, K.; Reveco, S.; Zane, G.; Semkiw, E.; Prathapam, R.; Gold, B.; Singer, M.; Ouellet, M.; Sazakal, E.; Jorgens, D.; Price, M.; Witkowska, E.; Beller, H.; Hazen, T.C.; Biggin, M.; Auer, M.; Wall, J.; Keasling, J.

2011-07-15T23:59:59.000Z

405

Effect of Growth Temperature and Culture Medium on the Cryotolerance of Permafrost Exiguobacterium Sibiricum 255-15 by Proteome-Wide Mass Mapping  

SciTech Connect (OSTI)

Exiguobacterium sibiricum 255-15 has shown significantly improved cryotolerance after liquid broth growth at 4oC and agar surface growth at both 4oC and 25oC compared with liquid broth growth at 25oC. The ability to survive freeze-thaw stress is expected to depend on the physiological state and protein composition of cells prior to freezing. Using 2-D liquid separation and an ESI-TOF MS-based mass mapping technique, we examined the differences in the proteomic profiles of the permafrost bacterium E. sibiricum 255-15 grown at two temperatures (4oC and 25oC) and two media (liquid broth and agar surface) before freeze-thawing treatments. In this study, a total of 330 proteins were identified. The cells cultured under the growth conditions associated with the improved cryotolerance have revealed a general downregulation of enzymes involved in major metabolic processes (glycolysis, anaerobic respiration, ATP synthesis, fermentation, electron transport, and sugar metabolism) as well as in the metabolism of lipids, amino acids, nucleotides and nucleic acids. In addition, eight proteins (2 -5 RNA ligase, hypoxanthine phosphoribosyl transferase, FeS assembly ATPase SufC, thioredoxin reductase and four hypothetical proteins) were observed to be up-regulated. This suggests these eight proteins might have a potential role to induce the improved cryotolerance.

Qiu, Yinghua [University of Michigan; Vishnivetskaya, Tatiana A [ORNL; Qiu, Weilian [University of Michigan; Lubman, David M [University of Michigan

2009-01-01T23:59:59.000Z

406

Characterization of the Cobalamin and Fep Operons in Methylobium petrolphilum PM1  

SciTech Connect (OSTI)

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.

Ewing, J

2005-09-06T23:59:59.000Z

407

Field application of a genetically engineered microorganism for polycyclic aromatic hydrocarbon bioremediation process monitoring and control  

SciTech Connect (OSTI)

On October 30, 1996, the US Environmental Protection Agency (EPA) commenced the first test release of genetically engineered microorganisms (GEMs) for use in bioremediation. The specific objectives of the investigation were multifaceted and include (1) testing the hypothesis that a GEM can be successfully introduced and maintained in a bioremediation process, (2) testing the concept of using, at the field scale, reporter organisms for direct bioremediation process monitoring and control, and (3) acquiring data that can be used in risk assessment decision making and protocol development for future field release applications of GEMs. The genetically engineered strain under investigation is Pseudomonas fluorescens strain HK44 (King et al., 1990). The original P. fluorescens parent strain was isolated from polycyclic aromatic hydrocarbon (PAH) contaminated manufactured gas plant soil. Thus, this bacterium is able to biodegrade naphthalene (as well as other substituted naphthalenes and other PAHs) and is able to function as a living bioluminescent reporter for the presence of naphthalene contamination, its bioavailability, and the functional process of biodegradation. A unique component of this field investigation was the availability of an array of large subsurface soil lysimeters. This article describes the experience associated with the release of a genetically modified microorganism, the lysimeter facility and its associated instrumentation, as well as representative data collected during the first eighteen months of operation.

Sayler, G.S.; Cox, C.D.; Ripp, S.; Nivens, D.E.; Werner, C.; Ahn, Y.; Matrubutham, U. [Univ. of Tennessee, Knoxville, TN (United States); Burlage, R. [Oak Ridge National Lab., TN (United States). Environmental Sciences Div.

1998-11-01T23:59:59.000Z

408

Rapid electron exchange between surface-exposed bacterial cytochromes and Fe(III) minerals  

SciTech Connect (OSTI)

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.

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

409

One simple step in the identification of the cofactors signals, one giant leap for the solution structure determination of multiheme proteins  

SciTech Connect (OSTI)

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.

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

410

Role of microbial iron reduction in the dissolution of iron hydroxysulfate minerals - article no. G01012  

SciTech Connect (OSTI)

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.

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

411

How the xap Locus Put Electrical “Zap” in Geobacter sulfurreducens Biofilms  

SciTech Connect (OSTI)

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

Magnuson, Timothy S.

2011-03-01T23:59:59.000Z

412

Outer-membrane cytochrome-c, OmcF, from Geobacter sulfurreducens : high structural similarity to an algal cytochrone c{sub 6}.  

SciTech Connect (OSTI)

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.

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

413

Research and engineering assessment of biological solubilization of phosphate  

SciTech Connect (OSTI)

This research and engineering assessment examined a microbial phosphate solubilization process as a method of recovering phosphate from phosphorus containing ore compared to the existing wet acid and electric arc methods. A total of 860 microbial isolates, collected from a range of natural environments were tested for their ability to solubilize phosphate from rock phosphate. A bacterium (Pseudomonas cepacia) was selected for extensive characterization and evaluation of the mechanism of phosphate solubilization and of process engineering parameters necessary to recover phosphate from rock phosphate. These studies found that concentration of hydrogen ion and production of organic acids arising from oxidation of the carbon source facilitated microbial solubilization of both pure chemical insoluble phosphate compounds and phosphate rock. Genetic studies found that phosphate solubilization was linked to an enzyme system (glucose dehydrogenase). Process-related studies found that a critical solids density of 1% by weight (ore to liquid) was necessary for optimal solubilization. An engineering analysis evaluated the cost and energy requirements for a 2 million ton per year sized plant, whose size was selected to be comparable to existing wet acid plants.

Rogers, R.D.; McIlwain, M.E.; Losinski, S.J.; Taylor, D.D.

1993-03-01T23:59:59.000Z

414

Adhesion and formation of microbial biofilms in complex microfluidic devices  

SciTech Connect (OSTI)

Shewanella oneidensis is a metal reducing bacterium, which is of interest for bioremediation and clean energy applications. S. oneidensis biofilms play a critical role in several situations such as in microbial energy harvesting devices. Here, we use a microfluidic device to quantify the effects of hydrodynamics on the biofilm morphology of S. oneidensis. For different rates of fluid flow through a complex microfluidic device, we studied the spatiotemporal dynamics of biofilms, and we quantified several morphological features such as spatial distribution, cluster formation and surface coverage. We found that hydrodynamics resulted in significant differences in biofilm dynamics. The baffles in the device created regions of low and high flow in the same device. At higher flow rates, a nonuniform biofilm develops, due to unequal advection in different regions of the microchannel. However, at lower flow rates, a more uniform biofilm evolved. This depicts competition between adhesion events, growth and fluid advection. Atomic force microscopy (AFM) revealed that higher production of extra-cellular polymeric substances (EPS) occurred at higher flow velocities.

Kumar, Aloke [ORNL; Karig, David K [ORNL; Neethirajan, Suresh [University of Guelph; Suresh, Anil K [ORNL; Srijanto, Bernadeta R [ORNL; Mukherjee, Partha P [ORNL; Retterer, Scott T [ORNL; Doktycz, Mitchel John [ORNL

2012-01-01T23:59:59.000Z

415

Metabolic Profiling Directly from the Petri Dish Using Nanospray Desorption Electrospray Ionization Imaging Mass Spectrometry  

SciTech Connect (OSTI)

Understanding molecular interaction pathways in complex biological systems constitutes a treasure trove of knowledge that might facilitate the specific, chemical manipulation of the countless microbiological systems that occur throughout our world. However, there is a lack of methodologies that allow the direct investigation of chemical gradients and interactions in living biological systems, in real time. Here, we report the use of nanospray desorption electrospray ionization (nanoDESI) imaging mass spectrometry for in vivo metabolic profiling of living bacterial colonies directly from the Petri dish with absolutely no sample preparation needed. Using this technique, we investigated single colonies of Shewanella oneidensis MR-1, Bacillus subtilis 3610, and Streptomyces coelicolor A3(2) as well as a mixed biofilm of S. oneidensis MR-1 and B. subtilis 3610. Data from B. subtilis 3610 and S. coelicolor A3(2) provided a means of validation for the method while data from S. oneidensis MR-1 and the mixed biofilm showed a wide range of compounds that this bacterium uses for the dissimilatory reduction of extracellular metal oxides, including riboflavin, iron-bound heme and heme biosynthetic intermediates, and the siderophore putrebactin.

Watrous, Jeramie D.; Roach, Patrick J.; Heath, Brandi S.; Alexandrov, Theodore; Laskin, Julia; Dorrestein, Pieter C.

2013-11-05T23:59:59.000Z

416

Dissimilatory Bacterial Reduction of Al-Substituted Goethite in Subsurface Sediments  

SciTech Connect (OSTI)

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.

Kukkadapu, Ravi K.; Zachara, John M.; Smith, Steven C.; Fredrickson, Jim K.; Liu, Chongxuan

2001-09-13T23:59:59.000Z

417

Redox reactions of reduced flavin mononucleotide (FMN), riboflavin (RBF), and anthraquinone-2,6-disulfonate (AQDS) with ferrihydrite and lepidocrocite  

SciTech Connect (OSTI)

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.

Shi, Zhi; Zachara, John M.; Shi, Liang; Wang, Zheming; Moore, Dean A.; Kennedy, David W.; Fredrickson, Jim K.

2012-11-01T23:59:59.000Z

418

Metagenomic analysis of phosphorus removing sludgecommunities  

SciTech Connect (OSTI)

Enhanced Biological Phosphorus Removal (EBPR) is not wellunderstood at the metabolic level despite being one of the best-studiedmicrobially-mediated industrial processes due to its ecological andeconomic relevance. Here we present a metagenomic analysis of twolab-scale EBPR sludges dominated by the uncultured bacterium, "CandidatusAccumulibacter phosphatis." This analysis resolves several controversiesin EBPR metabolic models and provides hypotheses explaining the dominanceof A. phosphatis in this habitat, its lifestyle outside EBPR and probablecultivation requirements. Comparison of the same species from differentEBPR sludges highlights recent evolutionary dynamics in the A. phosphatisgenome that could be linked to mechanisms for environmental adaptation.In spite of an apparent lack of phylogenetic overlap in the flankingcommunities of the two sludges studied, common functional themes werefound, at least one of them complementary to the inferred metabolism ofthe dominant organism. The present study provides a much-needed blueprintfor a systems-level understanding of EBPR and illustrates thatmetagenomics enables detailed, often novel, insights into evenwell-studied biological systems.

Garcia Martin, Hector; Ivanova, Natalia; Kunin, Victor; Warnecke,Falk; Barry, Kerrie; McHardy, Alice C.; Yeates, Christine; He, Shaomei; Salamov, Asaf; Szeto, Ernest; Dalin, Eileen; Putnam, Nik; Shapiro, HarrisJ.; Pangilinan, Jasmyn L.; Rigoutsos, Isidore; Kyrpides, Nikos C.; Blackall, Linda Louise; McMahon, Katherine D.; Hugenholtz, Philip

2006-02-01T23:59:59.000Z

419

Genetics and Molecular Biology of Hydrogen Metabolism in Sulfate-Reducing Bacteria  

SciTech Connect (OSTI)

The degradation of our environment and the depletion of fossil fuels make the exploration of alternative fuels evermore imperative. Among the alternatives is biohydrogen which has high energy content by weight and produces only water when combusted. Considerable effort is being expended to develop photosynthetic systems -- algae, cyanobacteria, and anaerobic phototrophs -- for sustainable H2 production. While promising, this approach also has hurdles such as the harvesting of light in densely pigmented cultures that requires costly constant mixing and large areas for exposure to sunlight. Little attention is given to fermentative H2 generation. Thus understanding the microbial pathways to H2 evolution and metabolic processes competing for electrons is an essential foundation that may expand the variety of fuels that can be generated or provide alternative substrates for fine chemical production. We studied a widely found soil anaerobe of the class Deltaproteobacteria, a sulfate-reducing bacterium to determine the electron pathways used during the oxidation of substrates and the potential for hydrogen production.

Wall, Judy D. [University of Missouri-Columbia

2014-12-23T23:59:59.000Z

420

Biohydrogenesis in the Thermotogales  

SciTech Connect (OSTI)

The production and consumption of molecular hydrogen drives the physiology and bioenergetics of many microorganisms in hydrothermal environments. As such, the potential of these microorganisms as model systems to probe fundamental issues related to biohydrogen production merits consideration. It is important to understand how carbon/energy sources relate to the disposition of reducing power and, ultimately, the formation of molecular hydrogen by high temperature microorganisms. This project focused on bacteria in the thermophilic order Thermotogales, fermentative anaerobes that produce H2 from simple and complex carbohydrates. The major thrusts of the project are summarized in the Objectives listed below: OBJECTIVE 1: Examine the regulation of substrate catabolic proteins and pathways as this relates to carbon partitioning, disposition of reducing power, and H2 generation in Thermotoga maritima. OBJECTIVE 2: Apply classical genetics and develop molecular genetic tools for Thermotoga species to dissect catabolic and regulatory pathways related to sugar metabolism and H2 evolution. OBJECTIVE 3: Thermotogales biodiversity arises from adaptive specialization that expands on a conserved minimal genome; physiological characterization of selected novel traits will be done to expand understanding of biohydrogenesis. Four species within the genus Thermotoga were examined to understand similarities and differences in the mechanisms by which simple and complex carbohydrates were utilized and converted to molecular hydrogen. Although the core genome of these four species represented 75% of open reading frames (ORFs), there were significant differences in carbohydrate utilization patterns. New ABC transporters were identified within the Thermotogales through genomic and biochemical analysis. Molecular genetics tools were developed to examine Thermotoga maritima physiology. Cell lines were created in which both H2 and acetate levels were elevated on a per cell basis relative to the wild type, while lactate remained undetectable. Genome resequencing indicated that the primary genetic target for these phenotypic changes was the ATP binding component of a maltose ABC transporter. High temperature anaerobic [14C]-maltose transport assays demonstrated maltose uptake was reduced in the H2 overproducing cell lines. This suggested normal rates of maltose transport in the wild type organism lead to a metabolic imbalance that limited H2 synthesis. The microbial ecology of T. maritima was examined through functional genomics experiments. Under low nutrient conditions, T. maritima was observed to produce a range of putative peptides, some of which were related to ?-carbon cyclic peptides produced by Bacillus subtilus. Finally, the role of ‘toga’ in these novel microorganisms was shown to involve association with insoluble growth substrates. The ‘toga’ distends from the cytoplasmic membrane-enclosed portion of the cells as they enter the late exponential/stationary phase of growth. Some of the genes encoding toga-associated proteins were up-regulated during this phase of growth and the distension is caused by continued growth of the toga, and not shrinkage of the cytoplasmic aspect of the cells. This increase in cell surface area may have selective value to provide a larger anchor for polysaccharide hydrolytic enzymes during a time of nutritional stress. This project led to many interesting insights about the Thermotogales that have both scientific and technological implications. Ongoing work will leverage these developments to further elucidate many interesting features of these novel microorganisms.

Kelly, Robert M [North Carolina State University

2014-12-13T23:59:59.000Z

Note: This page contains sample records for the topic "thermophilic bacterium caldicellulosiruptor" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


421

Nitrogen availability and indirect measurements of greenhouse gas emissions from aerobic and anaerobic biowaste digestates applied to agricultural soils  

SciTech Connect (OSTI)

Highlights: • Nitrogen release in digestate-amended soil depends on the digestate type. • Overall N release is modulated by digestate mineral and mineralisable N contents. • Microbial immobilisation does not influence overall release of digestate N in soil. • Digestate physical properties and soil type interact to affect overall N recovery. • High labile C inputs in digestate may promote denitrification in fine-textured soil. - Abstract: Recycling biowaste digestates on agricultural land diverts biodegradable waste from landfill disposal and represents a sustainable source of nutrients and organic matter (OM) to improve soil for crop production. However, the dynamics of nitrogen (N) release from these organic N sources must be determined to optimise their fertiliser value and management. This laboratory incubation experiment examined the effects of digestate type (aerobic and anaerobic), waste type (industrial, agricultural and municipal solid waste or sewage sludge) and soil type (sandy loam, sandy silt loam and silty clay) on N availability in digestate-amended soils and also quantified the extent and significance of the immobilisation of N within the soil microbial biomass, as a possible regulatory mechanism of N release. The digestate types examined included: dewatered, anaerobically digested biosolids (DMAD); dewatered, anaerobic mesophilic digestate from the organic fraction of municipal solid waste (DMADMSW); liquid, anaerobic co-digestate of food and animal slurry (LcoMAD) and liquid, thermophilic aerobic digestate of food waste (LTAD). Ammonium chloride (NH{sub 4}Cl) was included as a reference treatment for mineral N. After 48 days, the final, maximum net recoveries of mineral N relative to the total N (TN) addition in the different digestates and unamended control treatments were in the decreasing order: LcoMAD, 68%; LTAD, 37%, DMAD, 20%; and DMADMSW, 11%. A transient increase in microbial biomass N (MBN) was observed with LTAD application, indicating greater microbial activity in amended soil and reflecting the lower stability of this OM source, compared to the other, anaerobic digestate types, which showed no consistent effects on MBN compared to the control. Thus, the overall net release of digestate N in different soil types was not regulated by N transfer into the soil microbial biomass, but was determined primarily by digestate properties and the capacity of the soil type to process and turnover digestate N. In contrast to the sandy soil types, where nitrate (NO{sub 3}{sup -}) concentrations increased during incubation, there was an absence of NO{sub 3}{sup -} accumulation in the silty clay soil amended with LTAD and DMADMSW. This provided indirect evidence for denitrification activity and the gaseous loss of N, and the associated increased risk of greenhouse gas emissions under certain conditions of labile C supply and/or digestate physical structure in fine-textured soil types. The significance and influence of the interaction between soil type and digestate stability and physical properties on denitrification processes in digestate-amended soils require urgent investigation to ensure management practices are appropriate to minimise greenhouse gas emissions from land applied biowastes.

Rigby, H.; Smith, S.R., E-mail: s.r.smith@imperial.ac.uk

2013-12-15T23:59:59.000Z

422

Integrated genome-based studies of Shewanella ecophysiology  

SciTech Connect (OSTI)

This project was a component of the Shewanella Federation and, as such, contributed to the overall goal of applying the genomic tools to better understand eco-physiology and speciation of respiratory-versatile members of Shewanella genus. Our role at Boston University was to perform bioreactor and high throughput gene expression microarrays, and combine dynamic flux balance modeling with experimentally obtained transcriptional and gene expression datasets from different growth conditions. In the first part of project, we designed the S. oneidensis microarray probes for Affymetrix Inc. (based in California), then we identified the pathways of carbon utilization in the metal-reducing marine bacterium Shewanella oneidensis MR-1, using our newly designed high-density oligonucleotide Affymetrix microarray on Shewanella cells grown with various carbon sources. Next, using a combination of experimental and computational approaches, we built algorithm and methods to integrate the transcriptional and metabolic regulatory networks of S. oneidensis. Specifically, we combined mRNA microarray and metabolite measurements with statistical inference and dynamic flux balance analysis (dFBA) to study the transcriptional response of S. oneidensis MR-1 as it passes through exponential, stationary, and transition phases. By measuring time-dependent mRNA expression levels during batch growth of S. oneidensis MR-1 under two radically different nutrient compositions (minimal lactate and nutritionally rich LB medium), we obtain detailed snapshots of the regulatory strategies used by this bacterium to cope with gradually changing nutrient availability. In addition to traditional clustering, which provides a first indication of major regulatory trends and transcription factors activities, we developed and implemented a new computational approach for Dynamic Detection of Transcriptional Triggers (D2T2). This new method allows us to infer a putative topology of transcriptional dependencies, with special emphasis on the nodes at which external stimuli are expected to affect the internal dynamics. In parallel, we addressed the question of how to compare transcriptional profiles across different time-course experiments. Our growth derivative mapping (GDM) method makes it possible to relate with each other points that correspond to the same relative growth rate in different media sets. This mapping allowed us to discriminate between genes that display an environment-independent behavior, and genes whose transcription seems to be tuned by specific environmental factors. Our analysis highlighted the importance of some specific pathways, whose metabolic relevance was confirmed by dynamic flux balance analysis (dFBA) calculations. In particular, we found that oxygen limitation potentially triggers the activation of genes previously shown to be relevant for anaerobic respiration, and that nitrogen limitation is coupled to storage of glycogen. Both observations have been corroborated by measurement of relevant intracellular and extracellular metabolites, as well as by complementary analyses of literature information and competitive fitness assay data. The pipeline of experimental and computational approaches applied and developed for this work could be extended to other microbes and additional conditions.

Segre Daniel; Beg Qasim

2012-02-14T23:59:59.000Z

423

BNL Citric Acid Technology: Pilot Scale Demonstration  

SciTech Connect (OSTI)

The objective of this project is to remove toxic metals such as lead and cadmium from incinerator ash using the Citric Acid Process developed at Brookhaven National Laboratory. In this process toxic metals in bottom ash from the incineration of municipal solid waste were first extracted with citric acid followed by biodegradation of the citric acid-metal extract by the bacterium Pseudomonas fluorescens for metals recovery. The ash contained the following metals: Al, As, Ba, Ca, Cd, Cr, Cu, Fe, Mg, Mn, Ni, Pb, Se, Sr, Ti, and Zn. Optimization of the Citric Acid Process parameters which included citric acid molarity, contact time, the impact of mixing aggressiveness during extraction and pretreatment showed lead and cadmium removal from incinerator ash of >90%. Seeding the treated ash with P. fluorescens resulted in the removal of residual citric acid and biostabilization of any leachable lead, thus allowing it to pass EPA?s Toxicity Characteristic Leaching Procedure. Biodegradation of the citric acid extract removed >99% of the lead from the extract as well as other metals such as Al, Ca, Cu, Fe, Mg, Mn, Ti, and Zn. Speciation of the bioprecipitated lead by Extended X-ray Absorption Fine Structure at the National Synchrotron Light Source showed that the lead is predominantly associated with the phosphate and carboxyl functional groups in a stable form. Citric acid was completely recovered (>99%) from the extract by sulfide precipitation technique and the extraction efficiency of recovered citric acid is similar to that of the fresh citric acid. Recycling of the citric acid should result in considerable savings in the overall treatment cost. We have shown the potential application of this technology to remove and recover the metal contaminants from incinerator ash as well as from other heavy metal bearing wastes (i.e., electric arc furnace dust from steel industry) or soils. Information developed from this project is being applied to demonstrate the remediation of lead paint contaminated soils on Long Island.

FRANCIS, A J; DODGE,; J, C; GILLOW, J B; FORRESTER, K E

1999-09-24T23:59:59.000Z

424

Bacterial reduction of selenium in coal mine tailings pond sediment  

SciTech Connect (OSTI)

Sediment from a storage facility for coal tailings solids was assessed for its capacity to reduce selenium (Se) by native bacterial community. One Se{sup 6+}-reducing bacterium Enterobacter hormaechei (Tar11) and four Se{sup 4+}-reducing bacteria, Klebsiella pneumoniae (Tar1), Pseudomonasfluorescens (Tar3), Stenotrophomonas maltophilia (Tar6), and Enterobacter amnigenus (Tar8) were isolated from the sediment. Enterobacter horinaechei removed 96% of the added Se{sup 6+} (0.92 mg L{sup -1} from the effluents when Se6+ was determined after 5 d of incubation. Analysis of the red precipitates showed that Se{sup 6+} reduction resulted in the formation of spherical particles ({lt}1.0 {mu} m) of Se 0 as observed under scanning electron microscope (SEM) and confirmed by EDAX. Selenium speciation was performed to examine the fate of the added Se{sup 6+} in the sediment with or without addition of Enterobacter hormaechei cells. More than 99% of the added Se{sup 6+} (about 2.5 mg L{sup -1}) was transformed in the nonsterilized sediment (without Enterobacter hormaechei cells) as well as in the sterilized (heat-killed) sediment (with Enterobacter hormaechei cells). The results of this study suggest that the lagoon sediments at the mine site harbor Se{sup 6+}- and Se{sup 4+} -reducing bacteria and may be important sinks for soluble Se (Se{sup 6+} and Se{sup 4+}). Enterobacter hormaechei isolated from metal-contaminated sediment may have potential application in removing Se from industrial effluents.

Siddique, T.; Arocena, J.M.; Thring, R.W.; Zhang, Y.Q. [University of North British Columbia, Prince George, BC (Canada)

2007-05-15T23:59:59.000Z

425

Rapid imaging of mycoplasma in solution using Atmospheric Scanning Electron Microscopy (ASEM)  

SciTech Connect (OSTI)

Highlights: Black-Right-Pointing-Pointer Mycoplasma mobile was observed in buffer with the Atmospheric Scanning Electron Microscope. Black-Right-Pointing-Pointer Characteristic protein localizations were visualized using immuno-labeling. Black-Right-Pointing-Pointer M. mobile attached to sialic acid on the SiN film surface within minutes. Black-Right-Pointing-Pointer Cells were observed at low concentrations. Black-Right-Pointing-Pointer ASEM should promote study and early-stage diagnosis of mycoplasma. -- Abstract: Mycoplasma is a genus of bacterial pathogen that causes disease in vertebrates. In humans, the species Mycoplasma pneumoniae causes 15% or more of community-acquired pneumonia. Because this bacterium is tiny, corresponding in size to a large virus, diagnosis using optical microscopy is not easy. In current methods, chest X-rays are usually the first action, followed by serology, PCR amplification, and/or culture, but all of these are particularly difficult at an early stage of the disease. Using Mycoplasma mobile as a model species, we directly observed mycoplasma in buffer with the newly developed Atmospheric Scanning Electron Microscope (ASEM). This microscope features an open sample dish with a pressure-resistant thin film window in its base, through which the SEM beam scans samples in solution, from below. Because of its 2-3 {mu}m-deep scanning capability, it can observe the whole internal structure of mycoplasma cells stained with metal solutions. Characteristic protein localizations were visualized using immuno-labeling. Cells were observed at low concentrations, because suspended cells concentrate in the observable zone by attaching to sialic acid on the silicon nitride (SiN) film surface within minutes. These results suggest the applicability of the ASEM for the study of mycoplasmas as well as for early-stage mycoplasma infection diagnosis.

Sato, Chikara, E-mail: ti-sato@aist.go.jp [Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566 (Japan)] [Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566 (Japan); Manaka, Sachie [Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566 (Japan)] [Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566 (Japan); Nakane, Daisuke [Department of Biology, Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585 (Japan)] [Department of Biology, Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585 (Japan); Nishiyama, Hidetoshi; Suga, Mitsuo [Advanced Technology Division, JEOL Ltd., Akishima, Tokyo 196-8558 (Japan)] [Advanced Technology Division, JEOL Ltd., Akishima, Tokyo 196-8558 (Japan); Nishizaka, Takayuki [Department of Physics, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588 (Japan)] [Department of Physics, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588 (Japan); Miyata, Makoto [Department of Biology, Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585 (Japan)] [Department of Biology, Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585 (Japan); Maruyama, Yuusuke [Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566 (Japan)] [Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566 (Japan)

2012-01-27T23:59:59.000Z

426

Redirection of metabolism for hydrogen production  

SciTech Connect (OSTI)

This project is to develop and apply techniques in metabolic engineering to improve the biocatalytic potential of the bacterium Rhodopseudomonas palustris for nitrogenase-catalyzed hydrogen gas production. R. palustris, is an ideal platform to develop as a biocatalyst for hydrogen gas production because it is an extremely versatile microbe that produces copious amounts of hydrogen by drawing on abundant natural resources of sunlight and biomass. Anoxygenic photosynthetic bacteria, such as R. palustris, generate hydrogen and ammonia during a process known as biological nitrogen fixation. This reaction is catalyzed by the enzyme nitrogenase and normally consumes nitrogen gas, ATP and electrons. The applied use of nitrogenase for hydrogen production is attractive because hydrogen is an obligatory product of this enzyme and is formed as the only product when nitrogen gas is not supplied. Our challenge is to understand the systems biology of R. palustris sufficiently well to be able to engineer cells to produce hydrogen continuously, as fast as possible and with as high a conversion efficiency as possible of light and electron donating substrates. For many experiments we started with a strain of R. palustris that produces hydrogen constitutively under all growth conditions. We then identified metabolic pathways and enzymes important for removal of electrons from electron-donating organic compounds and for their delivery to nitrogenase in whole R. palustris cells. For this we developed and applied improved techniques in 13C metabolic flux analysis. We identified reactions that are important for generating electrons for nitrogenase and that are yield-limiting for hydrogen production. We then increased hydrogen production by blocking alternative electron-utilizing metabolic pathways by mutagenesis. In addition we found that use of non-growing cells as biocatalysts for hydrogen gas production is an attractive option, because cells divert all resources away from growth and to hydrogen. Also R. palustris cells remain viable in a non-growing state for long periods of time.

Harwood, Caroline S.

2011-11-28T23:59:59.000Z

427

Study of red-sore disease in alligators. Final report, September 1, 1976-September 3, 1980. [Predisposing factors  

SciTech Connect (OSTI)

Necropsies of eight alligators which died following capture within a thermally-altered reservoir demonstrated the presence of the gram negative, pathogenic bacterium Aeromonas hydrophila, in internal tissues. A study designed to demonstrate whether A. hydrophila were capable of causing infection and death of the ecologically threatened alligator and, if so, the mechanism of exposure and infection in natural habitats was undertaken. The pathology and response to infection were also studied. When juvenile alligators were exposed under experimental conditions to increasing concentrations of A. hydrophila in water, by oral inoculation, or by intramuscular injections at 20/sup 0/, 25/sup 0/, 30/sup 0/, and 35/sup 0/C, they developed external lesions. These lesions were likely to become severe and lead to death of the animal at 30 and 35/sup 0/C. Infected animals produced: (a) increased numbers of white blood cells; (b) increased specific antibody titer; and (c) alpha 2 peaks higher than albumen peaks (except at 35/sup 0/C). Biweekly intraperitoneal injections of live, washed A. hydrophila were apparently more effective in the prevention of infection and of external lesions than were the antibiotics Kanamycin and OTH-Puramycin. Topical applications of Neosporin ointment resulted in the healing of severe lesions on confined animals. Alligators which were shown to be exposed to A. hydrophila in their natural habitats showed no external evidence of infection by the bacteria. It is recommended that exposure to conditions of stress, including water temperatures greater than 30/sup 0/C, be kept to a minimum during the capture, transport, and captivity of alligators. (ERB)

Gorden, R.E.; Esch, G.W.

1980-01-01T23:59:59.000Z

428

BIOREMEDIATION OF URANIUM CONTAMINATED SOILS AND WASTES.  

SciTech Connect (OSTI)

Contamination of soils, water, and sediments by radionuclides and toxic metals from uranium mill tailings, nuclear fuel manufacturing and nuclear weapons production is a major concern. Studies of the mechanisms of biotransformation of uranium and toxic metals under various microbial process conditions has resulted in the development of two treatment processes: (i) stabilization of uranium and toxic metals with reduction in waste volume and (ii) removal and recovery of uranium and toxic metals from wastes and contaminated soils. Stabilization of uranium and toxic metals in wastes is accomplished by exploiting the unique metabolic capabilities of the anaerobic bacterium, Clostridium sp. The radionuclides and toxic metals are solubilized by the bacteria directly by enzymatic reductive dissolution, or indirectly due to the production of organic acid metabolites. The radionuclides and toxic metals released into solution are immobilized by enzymatic reductive precipitation, biosorption and redistribution with stable mineral phases in the waste. Non-hazardous bulk components of the waste such as Ca, Fe, K, Mg and Na released into solution are removed, thus reducing the waste volume. In the second process uranium and toxic metals are removed from wastes or contaminated soils by extracting with the complexing agent citric acid. The citric-acid extract is subjected to biodegradation to recover the toxic metals, followed by photochemical degradation of the uranium citrate complex which is recalcitrant to biodegradation. The toxic metals and uranium are recovered in separate fractions for recycling or for disposal. The use of combined chemical and microbiological treatment process is more efficient than present methods and should result in considerable savings in clean-up and disposal costs.

FRANCIS,A.J.

1998-09-17T23:59:59.000Z

429

c-Type Cytochrome-Dependent Formation of U(IV) Nanoparticles by Shewanella oneidensis  

SciTech Connect (OSTI)

Modern approaches for bioremediation of radionuclide contaminated environments are based on the ability of microorganisms to effectively catalyze changes in the oxidation states of metals that in turn influence their solubility. Although microbial metal reduction has been identified as an effective means for immobilizing highly-soluble uranium(VI) complexes in situ, the biomolecular mechanisms of U(VI) reduction are not well understood. Here, we show that c-type cytochromes of a dissimilatory metal reducing bacterium, Shewanella oneidensis MR-1 are essential for the reduction of U(VI) and formation of extracelluar UO2 nanoparticles. In particular, the outer membrane (OM) decaheme cytochrome MtrC, previously implicated in Mn(IV) and Fe(III) reduction, directly transferred electrons to U(VI). Additionally, deletions of mtrC and/or omcA significantly affected the in vivo U(VI) reduction rate relative to wild type MR-1. Similar to the wild type, the mutants accumulated UO2 nanoparticles extracellularly to high densities in association with an exopolymeric substance (EPS). In wild type cells, this UO2-EPS matrix exhibited glycocalyx-like properties, contained multiple elements of the OM, polysaccharide, and heme containing proteins. Using a novel combination of methods including synchrotron-based X-ray fluorescence microscopy and high resolution immune-electron microscopy, we demonstrate a close association of the extracellular UO2 nanoparticles with MtrC and OmcA. This is the first study to directly localize the OM-associated cytochromes with EPS, which contains biogenic UO2 nanoparticles. In the environment, such association of UO2 nanoparticles with biopolymers may exert a strong influence on subsequent behavior including susceptibility to oxidation by O2 or transport in soils and sediments.

Marshall, Matthew J.; Beliaev, Alex S.; Dohnalkova, Alice; Kennedy, David W.; Shi, Liang; Wang, Zheming; Boyanov, Maxim I.; Lai, Barry; Kemner, Kenneth M.; Mclean, Jeffrey S.; Reed, Samantha B.; Culley, David E.; Bailey, Vanessa L.; Simonson, Cody J.; Saffarini, Daad; Romine, Margaret F.; Zachara, John M.; Fredrickson, Jim K.

2006-08-08T23:59:59.000Z

430

Systems biology analysis of Zymomonas mobilis ZM4 ethanol stress responses  

SciTech Connect (OSTI)

Zymomonas mobilis ZM4 is a capable ethanogenic bacterium with high ethanol productivity and high level of ethanol tolerance. Previous studies indicated that several stress-related proteins and changes in the ZM4 membrane lipid composition may contribute to ethanol tolerance. However, the molecular mechanisms of ethanol stress response have not been elucidated fully. In this study, ethanol stress responses were investigated using systems biology tools. Medium supplementation with an initial 47.3 g/L (6% v/v) ethanol reduced Z. mobilis ZM4 glucose consumption, growth rate and ethanol productivity compared to that of untreated controls. Metabolomic profiling showed that ethanol-treated ZM4 cells accumulated greater amounts of glycerol during the entire fermentation process, which may indicate an important role for this metabolite. A proteomic analysis of early exponential growth identified about one thousand proteins, or approximately 56% of the predicted ZM4 proteome. Proteins related to metabolism and stress response such as chaperones and key regulators were more abundant in the early ethanol stress condition. Transcriptomic studies indicated the response of ZM4 to ethanol is dynamic, complex and involves many genes from all the different functional categories. There were fewer genes significantly differentially expressed in the exponential phase compared to that of stationary phase and early stationary phase. Most down-regulated genes were related to translation and ribosome biogenesis, while the ethanol-upregulated genes were mostly related to cellular processes and metabolism. Correlations among the transcriptomics, proteomics and metabolism were examined and among significantly expressed genes or proteins, we observe higher correlation coefficients when fold-change values are higher. This systems biology study elucidates key Z. mobilis ZM4 metabolites, genes and proteins that form the foundation of its distinctive physiology and its multifaceted response to ethanol stress.

Yang, Shihui [ORNL; Pan, Chongle [ORNL; Tschaplinski, Timothy J [ORNL; Hurst, Gregory {Greg} B [ORNL; Engle, Nancy L [ORNL; Zhou, Wen [University of Georgia, Athens, GA; Dam, Phuongan [ORNL; Xu, Ying [University of Georgia, Athens, GA; Dice, Lezlee T [ORNL; Davison, Brian H [ORNL; Brown, Steven D [ORNL

2013-01-01T23:59:59.000Z

431

Thermal-induced conformational changes in the product release area drive the enzymatic activity of xylanases 10B: Crystal structure, conformational stability and functional characterization of the xylanase 10B from Thermotoga petrophila RKU-1  

SciTech Connect (OSTI)

Research highlights: {yields} The hyperthermostable xylanase 10B from Thermotoga petrophila RKU-1 produces exclusively xylobiose at the optimum temperature. {yields} Circular dichroism spectroscopy suggests a coupling effect of temperature-induced structural changes with its enzymatic behavior. {yields} Crystallographic and molecular dynamics studies indicate that conformational changes in the product release area modulate the enzyme action mode. -- Abstract: Endo-xylanases play a key role in the depolymerization of xylan and recently, they have attracted much attention owing to their potential applications on biofuels and paper industries. In this work, we have investigated the molecular basis for the action mode of xylanases 10B at high temperatures using biochemical, biophysical and crystallographic methods. The crystal structure of xylanase 10B from hyperthermophilic bacterium Thermotoga petrophila RKU-1 (TpXyl10B) has been solved in the native state and in complex with xylobiose. The complex crystal structure showed a classical binding mode shared among other xylanases, which encompasses the -1 and -2 subsites. Interestingly, TpXyl10B displayed a temperature-dependent action mode producing xylobiose and xylotriose at 20 {sup o}C, and exclusively xylobiose at 90 {sup o}C as assessed by capillary zone electrophoresis. Moreover, circular dichroism spectroscopy suggested a coupling effect of temperature-induced structural changes with this particular enzymatic behavior. Molecular dynamics simulations supported the CD analysis suggesting that an open conformational state adopted by the catalytic loop (Trp297-Lys326) provokes significant modifications in the product release area (+1,+2 and +3 subsites), which drives the enzymatic activity to the specific release of xylobiose at high temperatures.

Santos, Camila Ramos; Meza, Andreia Navarro [Laboratorio Nacional de Biociencias (LNBio), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP (Brazil)] [Laboratorio Nacional de Biociencias (LNBio), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP (Brazil); Hoffmam, Zaira Bruna; Silva, Junio Cota; Alvarez, Thabata Maria; Ruller, Roberto [Laboratorio Nacional de Ciencia e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP (Brazil)] [Laboratorio Nacional de Ciencia e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP (Brazil); Giesel, Guilherme Menegon; Verli, Hugo [Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS (Brazil)] [Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS (Brazil); Squina, Fabio Marcio [Laboratorio Nacional de Ciencia e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP (Brazil)] [Laboratorio Nacional de Ciencia e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP (Brazil); Prade, Rolf Alexander [Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK (United States)] [Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK (United States); Murakami, Mario Tyago, E-mail: mario.murakami@lnbio.org.br [Laboratorio Nacional de Biociencias (LNBio), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP (Brazil)

2010-12-10T23:59:59.000Z

432

Anti-bacterial immunity to Listeria monocytogenes in allogeneic bone marrow chimera in mice  

SciTech Connect (OSTI)

Protection and delayed-type hypersensitivity (DTH) to the facultative intracellular bacterium Listeria monocytogenes (L.m.) were studied in allogeneic and syngeneic bone marrow chimeras. Lethally irradiated AKR (H-2k) mice were successfully reconstituted with marrow cells from C57BL/10 (B10) (H-2b), B10 H-2-recombinant strains or syngeneic mice. Irradiated AKR mice reconstituted with marrow cells from H-2-compatible B10.BR mice, (BR----AKR), as well as syngeneic marrow cells, (AKR----AKR), showed a normal level of responsiveness to the challenge stimulation with the listeria antigens when DTH was evaluated by footpad reactions. These mice also showed vigorous activities in acquired resistance to the L.m. By contrast, chimeric mice that had total or partial histoincompatibility at the H-2 determinants between donor and recipient, (B10----AKR), (B10.AQR----AKR), (B10.A(4R)----AKR), or (B10.A(5R)----AKR), were almost completely unresponsive in DTH and antibacterial immunity. However, when (B10----AKR) H-2-incompatible chimeras had been immunized with killed L.m. before challenge with live L.m., these mice manifested considerable DTH and resistance to L.m. These observations suggest that compatibility at the entire MHC between donor and recipient is required for bone marrow chimeras to be able to manifest DTH and protection against L.m. after a short-term immunization schedule. However, this requirement is overcome by a preceding or more prolonged period of immunization with L.m. antigens. These antigens, together with marrow-derived antigen-presenting cells, can then stimulate and expand cell populations that are restricted to the MHC (H-2) products of the donor type.

Onoe, K.; Good, R.A.; Yamamoto, K.

1986-06-01T23:59:59.000Z

433

Microbial reduction of SO{sub 2} and NO{sub x} as a means of by-product recovery/disposal from regenerable processes for the desulfurization of flue gas. Technical progress report, September 11, 1992--December 11, 1992  

SciTech Connect (OSTI)

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

Sublette, K.L.

1992-12-31T23:59:59.000Z

434

The Genome Organization of Thermotoga maritima Reflects Its Lifestyle  

SciTech Connect (OSTI)

Recent studies have revealed that microbial genomes have many more organizational features than previously thought. Here, an integrated approach utilizing multiple ‘omics’ datasets and bioinformatics tools is established that elucidates genomic features spanning various levels of cellular organization. This methodology produces gene annotation improvements and includes the definition of transcription units. These enhancements to the annotation enable identification of a set of genetic elements instrumental to gene expression and regulation including promoters, ribosome binding sites (RBSs) and untranslated regions (UTRs). This was applied to characterize the genome organization of Thermotoga maritima—a phylogenetically deep-branching, hyperthermophilic bacterium with a small 1.86 Mb genome. Analysis derived from this multiomics approach in combination with bioinformatics tools demonstrate that the genome organization of T. maritima reflects its lifestyle, both with respect to its extreme growth temperature and compact genome. Comparative analysis of genome features suggests that thermodynamic limitations on binding kinetics for RNA polymerase and the ribosome necessitate increased sequence conservation of promoters and RBSs. Thus, restricting the sequences capable of initiating transcription and translation. Furthermore, this organism has uncharacteristically short 5’UTRs (11-17 nucleotides), which reduce the potential for 5’UTR regulatory interactions. The short intergenic distances in the T. maritima genome (5 bp on average) leave little space for regulation through transcription factor binding. The net effect of these constraints, temperature and genomic space, is a reduced ability to tune gene expression. This effect is readily apparent in global gene expression patterns, which show a high fraction of genes expressed independent of growth state with a tight, linear mRNA/protein correlation (Pearson r = 0.62, p < 2.2 x 10-16 t-test). This methodology for characterizing the genome organization is applicable to any culturable bacteria, and as similar studies are completed in diverse taxa, comparative analysis of genome features may provide insights into microbial evolution.

Latif, Haythem; Lerman, Joshua A.; Portnoy, Vasiliy A.; Tarasova, Yekaterina; Nagarajan, Harish; Rutledge, Alexandra C.; Smith, Richard D.; Adkins, Joshua N.; Lee, Dae-Hee; Qiu, Yu; Zengler, Karsten

2013-04-25T23:59:59.000Z

435

Solid State Electron Transfer via Bacterial Nanowires: Contributions Toward a Mechanistic Understanding of Geophysical Response of Biostimulated Subsurface  

SciTech Connect (OSTI)

The degradation of organic matter by microorganisms provides a source of electrical potential or so-called 'self potential' (SP) that can be measured by using a voltmeter. During this process electrons are being produced as a waste-product and bacterial cells have to dispose of these to allow for the complete biodegradation of organic matter. Especially in anaerobic microbial communities, exo-cellular electron transfer is the most important driving force behind this process and organisms have developed different, but also similar, ways to transfer electrons to other microorganisms. Recently, it has been postulated that direct electron transfer from cell-to-cell is actually done by 'hard-wired' microorganisms. This shuttling of electrons is most likely done by certain c-type cytochromes that form the functional part of electrically conductive nanowires. In this study we investigated if nanowires can explain the geoelectrical (self potential and spectral induced polarization) signals observed at some biostimulated environments such as DOE sites. The objectives of our project are to: (1) investigate any temporal changes in the geophysical signatures (Self Potential (SP) and Induced Polarization (IP)) associated with nanowires of the bacterium Shewanella oneidensis MR-1, wild type and mtrc/omcA deletion mutant, (2) demonstrate that mutant strains of bacteria that produce nonconductive nanowires do not contribute to geoelectrical responses. We accomplished the following: (1) Provided training to students and a postdoctoral fellow that worked on the project, (2) Conducted several SP & IP measurements correlating the distribution of nanowires and SIP/SP signals in partial fulfillment of object No. 1 and 2. On the following we will report and discuss the results of our last experiment with some emphasis on the source mechanisms of both SP and IP associated with Shewanella oneidensis MR-1, wild type in sand columns.

Estella Atekwana

2012-05-08T23:59:59.000Z

436

Your World Magazine - Microbes: Parts and Potential  

SciTech Connect (OSTI)

Microorganisms are tiny, but together, they make up more than 60 percent of the earth's living matter. Often people think only of bacteria when they talk about microbes, but viruses, fungi, protozoa, and microalgae are also microbes. Scientists estimate that there are 2 to 3 billion species of microorganisms. By learning what genes microbes contain and how they are arranged, what they do, and how they are expressed, researchers get a better grasp on how microbes have evolved, new possibilities for diagnosing and treating diseases, and ideas for ways to clean up the environment and produce energy. You can be a part of this exciting work in many ways. Figuring out the genes in microbes, or microbial genomics, is a field that gets a lot of help from computer science and mathematics. You could go into bioinformatics, which uses computers to collect and sort information about living matter. Or you could try computational modeling and help develop simple models of what an organism would look like and how it would function. Researchers want to understand microbes genetics well enough to build useful ones. As we move toward that possibility, we need to think about how that ability can be used wisely or poorly. Enjoy learning about microbial genomics in this issue of Your World, and think about what part you'd like to take in exploring this vital field. Some current uses of microbes are: (1) Saccharomyces cerevisiae (baker's yeast) - produces the CO{sub 2} that makes bread rise and is also used to make beer; (2) Streptomyces - soil bacteria that make streptomycin, an antibiotic, used to treat infections; (3) Pseudomonas putida - one of many microbes used to clean wastes from sewage at water treatment plants; (4) Escherichia coli - one of many kinds of microbes that live in your gut and help digest your food; and (5) Bacillus thuringiensis - a common soil bacterium that acts as a natural pest-killer in gardens and on crops.

Biotechnology Institute

2005-04-01T23:59:59.000Z

437

Evaluation of terrestrial microcosms for assessing the fate and effects of genetically engineered microorganisms on ecological processes  

SciTech Connect (OSTI)

This project evaluates and modifies the existing US Environmental Protection Agency's Office of Pesticides and Toxic Substances (EPA/OPTS) terrestrial microcosm test system and test protocols such that they can be used to determine the environmental fate and ecological hazards of genetically engineered microorganisms (GEMs). The intact soil-core microcosm represents terrestrial ecosystems, and when coupled with appropriate test protocols, such microcosms may be appropriate to define and limit risks associated with the intentional release of GEMs. The terrestrial microcosm test system was used to investigate the survival and transport of two model GEMs (Azospirillum lipoferum and Pseudomonas sp. Tn5 mutants) to various trophic levels and niches and through intact soil cores. Subsequent effects on nutrient cycling and displacement of indigenous microorganisms were evaluated. The model organisms were a diazotrophic root-colonizing bacterium (A. lipoferum) and a wheat root growth-inhibiting rhizobacterium (Pseudomonas sp.). The transposable element Tn5 was used as a genetic marker for both microorganisms in two separate experiments. The organisms were subjected to transposon mutagenesis using a broad host-range-mobilizable suicide plasmid. The transposon Tn5 conferred levels of kanamycin resistance up to 500 ..mu..g/ml (Pseudomonas sp.), which allowed for selection of the bacteria from environmental samples. The presence of Tn5 DNA in the genome of the model GEMs also allowed the use of Tn5 gene probes to confirm and enumerate the microorganisms in different samples from the microcosms. Two types of root growth-inhibiting Pseudomonas sp. Tn5 mutants were obtained and used in microcosm studies: those that lacked the ability to inhibit either wheat root growth or the growth of other microorganisms in vitro (tox/sup /minus//) and those which retained these properties (tox/sup +/). 53 refs., 7 figs., 6 tabs.

Fredrickson, J.K.; Bentjen, S.A.; Bolton, H. Jr.; Li, S.W.; Ligotke, M.W.; McFadden, K.M.; Van Voris, P.

1989-04-01T23:59:59.000Z

438

The Structure and Function of an Arabinan-specific [alpha]-1,2-Arabinofuranosidase Identified from Screening the Activities of Bacterial GH43 Glycoside Hydrolases  

SciTech Connect (OSTI)

Reflecting the diverse chemistry of plant cell walls, microorganisms that degrade these composite structures synthesize an array of glycoside hydrolases. These enzymes are organized into sequence-, mechanism-, and structure-based families. Genomic data have shown that several organisms that degrade the plant cell wall contain a large number of genes encoding family 43 (GH43) glycoside hydrolases. Here we report the biochemical properties of the GH43 enzymes of a saprophytic soil bacterium, Cellvibrio japonicus, and a human colonic symbiont, Bacteroides thetaiotaomicron. The data show that C. japonicus uses predominantly exo-acting enzymes to degrade arabinan into arabinose, whereas B. thetaiotaomicron deploys a combination of endo- and side chain-cleaving glycoside hydrolases. Both organisms, however, utilize an arabinan-specific {alpha}-1,2-arabinofuranosidase in the degradative process, an activity that has not previously been reported. The enzyme can cleave {alpha}-1,2-arabinofuranose decorations in single or double substitutions, the latter being recalcitrant to the action of other arabinofuranosidases. The crystal structure of the C. japonicus arabinan-specific {alpha}-1,2-arabinofuranosidase, CjAbf43A, displays a five-bladed {beta}-propeller fold. The specificity of the enzyme for arabinan is conferred by a surface cleft that is complementary to the helical backbone of the polysaccharide. The specificity of CjAbf43A for {alpha}-1,2-L-arabinofuranose side chains is conferred by a polar residue that orientates the arabinan backbone such that O2 arabinose decorations are directed into the active site pocket. A shelflike structure adjacent to the active site pocket accommodates O3 arabinose side chains, explaining how the enzyme can target O2 linkages that are components of single or double substitutions.

Cartmell, Alan; McKee, Lauren S.; Pena, Maria J.; Larsbrink, Johan; Brumer, Harry; Kaneko, Satoshi; Ichinose, Hitomi; Lewis, Richard J.; Vikso-Nielsen, Anders; Gilbert, Harry; Marles-Wright, Jon (Newcastle); (National Food Research Institute); (Novozymes A/S); (RITS); (Georgia)

2012-03-26T23:59:59.000Z

439

Determination of thiol functional groups on bacteria and natural organic matter in environmental systems  

SciTech Connect (OSTI)

Organic thiols (R-SH) are known to react and form complexes with some toxic soft metals such as mercury (Hg) in both biotic and abiotic systems. However, a clear understanding of these interactions is currently limited because quantifying thiols in environmental matrices is difficult due to their low abundance, susceptibility to oxidation, and measurement interference by non-thiol compounds in samples. Here, we report a fluorescence-labeling method using a maleimide containing probe, ThioGlo-1 (TG-1), to determine total thiols directly on bacterial cells and natural organic matter (NOM). We systematically evaluated the optimal thiol labeling conditions and interference from organic compounds such as disulfide, methionine, thiourea, and amine, and inorganic ions such as Na+, K+, Ca2+, Fe2+, Cl-, SO42-, HCO3-, and SCN-, and found that the method is highly sensitive and selective. Only relatively high levels of sulfide (S2-) and sulfite (SO32-) significantly interfere with the thiol analysis. The method was successful in determining thiols in a bacterium Geobacter sulfurreducens PCA and its mutants in a phosphate buffered saline solution. The measured value of ~2.1 104 thiols cell-1 (or ~0.07 mol g-1 wet cells) is in good agreement with that observed during reactions between Hg and PCA cells. Using the standard addition, we determined the total thiols of two reference NOM samples, the reduced Elliot soil humic acid and Suwanee River NOM, to be 3.6 and 0.7 mol g-1, respectively, consistent with those obtained based on their reactions with Hg.

Anandha Rao, Balaji [ORNL] [ORNL; Lin, Hui [ORNL] [ORNL; Liang, Liyuan [ORNL] [ORNL; Gu, Baohua [ORNL] [ORNL

2014-01-01T23:59:59.000Z

440

The genome of Pelobacter carbinolicus reveals surprising metabolic capabilities and physiological features  

SciTech Connect (OSTI)

Background: The bacterium Pelobacter carbinolicus is able to grow by fermentation, syntrophic hydrogen/formate transfer, or electron transfer to sulfur from short-chain alcohols, hydrogen or formate; it does not oxidize acetate and is not known to ferment any sugars or grow autotrophically. The genome of P. carbinolicus was sequenced in order to understand its metabolic capabilities and physiological features in comparison with its relatives, acetate-oxidizing Geobacter species. Results: Pathways were predicted for catabolism of known substrates: 2,3-butanediol, acetoin, glycerol, 1,2-ethanediol, ethanolamine, choline and ethanol. Multiple isozymes of 2,3-butanediol dehydrogenase, ATP synthase and [FeFe]-hydrogenase were differentiated and assigned roles according to their structural properties and genomic contexts. The absence of asparagine synthetase and the presence of a mutant tRNA for asparagine encoded among RNA-active enzymes suggest that P. carbinolicus may make asparaginyl-tRNA in a novel way. Catabolic glutamate dehydrogenases were discovered, implying that the tricarboxylic acid (TCA) cycle can function catabolically. A phosphotransferase system for uptake of sugars was discovered, along with enzymes that function in 2,3-butanediol production. Pyruvate: ferredoxin/flavodoxin oxidoreductase was identified as a potential bottleneck in both the supply of oxaloacetate for oxidation of acetate by the TCA cycle and the connection of glycolysis to production of ethanol. The P. carbinolicus genome was found to encode autotransporters and various appendages, including three proteins with similarity to the geopilin of electroconductive nanowires. Conclusions: Several surprising metabolic capabilities and physiological features were predicted from the genome of P. carbinolicus, suggesting that it is more versatile than anticipated.

Aklujkar, Muktak [University of Massachusetts, Amherst; Haveman, Shelley [University of Massachusetts, Amherst; DiDonatoJr., Raymond [University of Massachusetts, Amherst; Chertkov, Olga [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Land, Miriam L [ORNL; Brown, Peter [University of Massachusetts, Amherst; Lovley, Derek [University of Massachusetts, Amherst

2012-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "thermophilic bacterium caldicellulosiruptor" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


441

Genomic Analyses of Bacterial Porin-Cytochrome Gene Clusters  

SciTech Connect (OSTI)

The porin-cytochrome (Pcc) protein complex is responsible for trans-outer membrane electron transfer during extracellular reduction of Fe(III) by the dissimilatory metal-reducing bacterium Geobacter sulfurreducens PCA. The identified and characterized Pcc complex of G. sulfurreducens PCA consists of a porin-like outer-membrane protein, a periplasmic 8-heme c type cytochrome (c-Cyt) and an outer-membrane 12-heme c-Cyt, and the genes encoding the Pcc proteins are clustered in the same regions of genome (i.e., the pcc gene clusters) of G. sulfurreducens PCA. A survey of additionally microbial genomes has identified the pcc gene clusters in all sequenced Geobacter spp. and other bacteria from six different phyla, including Anaeromyxobacter dehalogenans 2CP-1, A. dehalogenans 2CP-C, Anaeromyxobacter sp. K, Candidatus Kuenenia stuttgartiensis, Denitrovibrio acetiphilus DSM 12809, Desulfurispirillum indicum S5, Desulfurivibrio alkaliphilus AHT2, Desulfurobacterium thermolithotrophum DSM 11699, Desulfuromonas acetoxidans DSM 684, Ignavibacterium album JCM 16511, and Thermovibrio ammonificans HB-1. The numbers of genes in the pcc gene clusters vary, ranging from two to nine. Similar to the metal-reducing (Mtr) gene clusters of other Fe(III)-reducing bacteria, such as Shewanella spp., additional genes that encode putative c-Cyts with predicted cellular localizations at the cytoplasmic membrane, periplasm and outer membrane often associate with the pcc gene clusters. This suggests that the Pcc-associated c-Cyts may be part of the pathways for extracellular electron transfer reactions. The presence of pcc gene clusters in the microorganisms that do not reduce solid-phase Fe(III) and Mn(IV) oxides, such as D. alkaliphilus AHT2 and I. album JCM 16511, also suggests that some of the pcc gene clusters may be involved in extracellular electron transfer reactions with the substrates other than Fe(III) and Mn(IV) oxides.

Shi, Liang; Fredrickson, Jim K.; Zachara, John M.

2014-11-26T23:59:59.000Z

442

Detecting bacteria and Determining Their Susceptibility to Antibiotics by Stochastic Confinement in Nanoliter Droplets using Plug-Based Microfluidics  

SciTech Connect (OSTI)

This article describes plug-based microfluidic technology that enables rapid detection and drug susceptibility screening of bacteria in samples, including complex biological matrices, without pre-incubation. Unlike conventional bacterial culture and detection methods, which rely on incubation of a sample to increase the concentration of bacteria to detectable levels, this method confines individual bacteria into droplets nanoliters in volume. When single cells are confined into plugs of small volume such that the loading is less than one bacterium per plug, the detection time is proportional to plug volume. Confinement increases cell density and allows released molecules to accumulate around the cell, eliminating the pre-incubation step and reducing the time required to detect the bacteria. We refer to this approach as stochastic confinement. Using the microfluidic hybrid method, this technology was used to determine the antibiogram - or chart of antibiotic sensitivity - of methicillin-resistant Staphylococcus aureus (MRSA) to many antibiotics in a single experiment and to measure the minimal inhibitory concentration (MIC) of the drug cefoxitin (CFX) against this strain. In addition, this technology was used to distinguish between sensitive and resistant strains of S. aureus in samples of human blood plasma. High-throughput microfluidic techniques combined with single-cell measurements also enable multiple tests to be performed simultaneously on a single sample containing bacteria. This technology may provide a method of rapid and effective patient-specific treatment of bacterial infections and could be extended to a variety of applications that require multiple functional tests of bacterial samples on reduced timescales.

Boedicker, J.; Li, L; Kline, T; Ismagilov, R

2008-01-01T23:59:59.000Z

443

Short-term antibiotic treatment has differing long-term impacts on the human throat and gut microbiome  

SciTech Connect (OSTI)

Antibiotic administration is the standard treatment for the bacterium Helicobacter pylori, the main causative agent of peptic ulcer disease and gastric cancer. However, the long-term consequences of this treatment on the human indigenous microbiota are relatively unexplored. Here we studied short- and long-term effects of clarithromycin and metronidazole treatment, a commonly used therapy regimen against H. pylori, on the indigenous microbiota in the throat and in the lower intestine. The bacterial compositions in samples collected over a four year period were monitored by analyzing the 16S rRNA gene using 454-based pyrosequencing and terminal-restriction fragment length polymorphism (T-RFLP). While the microbial communities of untreated control subjects were relatively stable over time, dramatic shifts were observed one week after antibiotic treatment with reduced bacterial diversity in all treated subjects in both locations. While the microbiota of the different subjects responded uniquely to the antibiotic treatment some general trends could be observed; such as a dramatic decline in Actinobacteria in both throat and feces immediately after treatment. Although the diversity of the microbiota subsequently recovered to resemble the pre treatment states, the microbiota remained perturbed in some cases for up to four years post treatment. In addition, four years after treatment high levels of the macrolide resistance gene erm(B) were found, indicating that antibiotic resistance, once selected for, can persist for longer periods of time than previously recognized. This highlights the importance of a restrictive antibiotic usage in order to prevent subsequent treatment failure and potential spread of antibiotic resistance.

Jakobsson, H.; Jernberg, C.; Andersson, A.F.; Sjolund-Karlsson, M.; Jansson, J.K.; Engstrand, L.

2010-01-15T23:59:59.000Z

444

The metagenome of an anaerobic microbial community decomposing poplar wood chips  

SciTech Connect (OSTI)

This study describes the composition and metabolic potential of a lignocellulosic biomass degrading community that decays poplar wood chips under anaerobic conditions. We examined the community that developed on poplar biomass in a non-aerated bioreactor over the course of a year, with no microbial inoculation other than the naturally occurring organisms on the woody material. The composition of this community contrasts in important ways with biomass-degrading communities associated with higher organisms, which have evolved over millions of years into a symbiotic relationship. Both mammalian and insect hosts provide partial size reduction, chemical treatments (low or high pH environments), and complex enzymatic 'secretomes' that improve microbial access to cell wall polymers. We hypothesized that in order to efficiently degrade coarse untreated biomass, a spontaneously assembled free-living community must both employ alternative strategies, such as enzymatic lignin depolymerization, for accessing hemicellulose and cellulose and have a much broader metabolic potential than host-associated communities. This would suggest that such a community would make a valuable resource for finding new catalytic functions involved in biomass decomposition and gaining new insight into the poorly understood process of anaerobic lignin depolymerization. Therefore, in addition to determining the major players in this community, our work specifically aimed at identifying functions potentially involved in the depolymerization of cellulose, hemicelluloses, and lignin, and to assign specific roles to the prevalent community members in the collaborative process of biomass decomposition. A bacterium similar to Magnetospirillum was identified among the dominant community members, which could play a key role in the anaerobic breakdown of aromatic compounds. We suggest that these compounds are released from the lignin fraction in poplar hardwood during the decay process, which would point to lignin-modification or depolymerization under anaerobic conditions.

van der Lelie D.; Taghavi, S.; McCorkle, S. M.; Li, L.-L.; Malfatti, S. A.; Monteleone, D.; Donohoe, B. S.; Ding, S.-Y.; Adney, W. S.; Himmel, M. E.; Tringe, S. G.

2012-05-01T23:59:59.000Z

445

Metagenome of an Anaerobic Microbial Community Decomposing Poplar Wood Chips  

SciTech Connect (OSTI)

This study describes the composition and metabolic potential of a lignocellulosic biomass degrading community that decays poplar wood chips under anaerobic conditions. We examined the community that developed on poplar biomass in a non-aerated bioreactor over the course of a year, with no microbial inoculation other than the naturally occurring organisms on the woody material. The composition of this community contrasts in important ways with biomass-degrading communities associated with higher organisms, which have evolved over millions of years into a symbiotic relationship. Both mammalian and insect hosts provide partial size reduction, chemical treatments (low or high pH environments), and complex enzymatic 'secretomes' that improve microbial access to cell wall polymers. We hypothesized that in order to efficiently degrade coarse untreated biomass, a spontaneously assembled free-living community must both employ alternative strategies, such as enzymatic lignin depolymerization, for accessing hemicellulose and cellulose and have a much broader metabolic potential than host-associated communities. This would suggest that such a community would make a valuable resource for finding new catalytic functions involved in biomass decomposition and gaining new insight into the poorly understood process of anaerobic lignin depolymerization. Therefore, in addition to determining the major players in this community, our work specifically aimed at identifying functions potentially involved in the depolymerization of cellulose, hemicelluloses, and lignin, and to assign specific roles to the prevalent community members in the collaborative process of biomass decomposition. A bacterium similar to Magnetospirillum was identified among the dominant community members, which could play a key role in the anaerobic breakdown of aromatic compounds. We suggest that these compounds are released from the lignin fraction in poplar hardwood during the decay process, which would point to lignin-modification or depolymerization under anaerobic conditions.

van der Lelie, D.; Taghavi, S.; McCorkle, S. M.; Li, L. L.; Malfatti, S. A.; Monteleone, D.; Donohoe, B. S.; Ding, S. Y.; Adney, W. S.; Himmel, M. E.; Tringe, S. G.

2012-05-01T23:59:59.000Z

446

Manganese sulfide formation via concomitant microbial manganese oxide and thiosulfate reduction  

SciTech Connect (OSTI)

The dissimilatory metal-reducing bacterium, Shewanella oneidensis MR-1 produced {gamma}-MnS (rambergite) nanoparticles during the concurrent reduction of MnO{sub 2} and thiosulfate coupled to H{sub 2} oxidation. To investigate effect of direct microbial reduction of MnO{sub 2} on MnS formation, two MR-1 mutants defective in outer membrane c-type cytochromes ({Delta}mtrC/{Delta}omcA and {Delta}mtrC/{Delta}omcA/{Delta}mtrF) were also used and it was determined that direct reduction of MnO{sub 2} was dominant relative to chemical reduction by biogenic sulfide generated from thiosulfate reduction. Although bicarbonate was excluded from the medium, incubations of strain MR-1 with lactate as the electron donor produced MnCO{sub 3} (rhodochrosite) as well as MnS in nearly equivalent amounts as estimated by micro X-ray diffraction (micro-XRD) analysis. It was concluded that carbonate released from lactate metabolism promoted MnCO{sub 3} formation and that Mn(II) mineralogy was strongly affected by carbonate ions even in the presence of abundant sulfide and weakly alkaline conditions expected to favor the precipitation of MnS. Formation of MnS, as determined by a combination of micro-XRD, transmission electron microscopy, energy dispersive X-ray spectroscopy, and selected area electron diffraction analyses was consistent with equilibrium speciation modeling predictions. Biogenic manganese sulfide may be a manganese sink in the Mn biogeochemical cycle in select environments such as deep anoxic marine basins within the Baltic Sea.

Lee, Ji-Hoon; Kennedy, David W.; Dohnalkova, Alice; Moore, Dean A.; Nachimuthu, Ponnusamy; Reed, Samantha B.; Fredrickson, Jim K.

2011-12-13T23:59:59.000Z

447

Manganese sulfide formation via concomitant microbial manganese oxide and thiosulfate reduction.  

SciTech Connect (OSTI)

The dissimilatory metal-reducing bacterium, Shewanella oneidensis MR-1 produced ?-MnS (rambergite) nanoparticles under the concurrent reduction of synthetic MnO2 and thiosulfate coupled to H2 oxidation. Using two MR-1 mutants defective in outer membrane c-type cytochromes (?mtrC/?omcA and ?mtrC/?omcA/?mtrF) to eliminate the direct reduction pathway for solid electron acceptors, it was determined that respiratory reduction of MnO2 was dominant relative to chemical reduction by biogenic sulfide generated from bacterial thiosulfate reduction. Although bicarbonate was excluded from the medium, incubations of MR-1 using lactate as the sole electron donor produced MnCO3 (rhodochrosite) as well as MnS in nearly equivalent amounts as estimated by micro X-ray diffraction (micro-XRD) analysis. It was concluded that carbonate released from lactate metabolism promoted MnCO3 formation and that Mn(II) mineralogy was strongly affected by carbonate ions even in the presence of abundant sulfide and weakly alkaline conditions that favor the precipitation of MnS. Formation of the biogenic MnS, as determined by a combination of micro-XRD, transmission electron microscopy, energy dispersive X-ray spectroscopy, and selected area electron diffraction analyses was consistent with equilibrium speciation modeling predictions. Although biogenic MnS likely only forms and is stable over a relatively narrow range of conditions, it may be a significant sink for Mn in anoxic marine basins and terrestrial subsurface sediments where Mn and sulfur compounds are undergoing concurrent reduction.

Lee, Ji-Hoon; Kennedy, David W.; Dohnalkova, Alice; Moore, Dean A.; Nachimuthu, Ponnusamy; Reed, Samantha B.; Fredrickson, Jim K.

2011-12-27T23:59:59.000Z

448

Reductive Dissolution of Goethite and Hematite by Reduced Flavins  

SciTech Connect (OSTI)

The abiotic reductive dissolution of goethite and hematite by the reduced forms of flavin mononucleotide (FMNH2) and riboflavin (RBFH2), electron transfer mediators (ETM) secreted by the dissimilatory iron-reducing bacterium Shewanella, was investigated under stringent anaerobic conditions. In contrast to the rapid redox reaction rate observed for ferrihydrite and lepidocrocite (Shi et al., 2012), the reductive dissolution of crystalline goethite and hematite was slower, with the extent of reaction limited by the thermodynamic driving force at circumneutral pH. Both the initial reaction rate and reaction extent increased with decreasing pH. On a unit surface area basis, goethite was less reactive than hematite between pH 4.0 and 7.0. AH2DS, the reduced form of the well-studied synthetic ETM anthraquinone-2,6-disulfonate (AQDS), yielded higher rates than FMNH2 under most reaction conditions, despite the fact that FMNH2 was a more effective reductant than AH2DS for ferryhydrite and lepidocrocite. Two additional model compounds, methyl viologen and benzyl viologen, were investigated under similar reaction conditions to explore the relationship between reaction rate and thermodynamic properties. Relevant kinetic data from the literature were also included in the analysis to span a broad range of half-cell potentials. Other conditions being equal, the surface area normalized initial reaction rate (ra) increased as the redox potential of the reductant became more negative. A non-linear, parabolic relationship was observed between log ra and the redox potential for eight reducants at pH 7.0, as predicted by Marcus theory for electron transfer. When pH and reductant concentration were fixed, log ra was positively correlated to the redox potential of four Fe(III) oxides over a wide pH range, following a non-linear parabolic relationship as well.

Shi, Zhi; Zachara, John M.; Wang, Zheming; Shi, Liang; Fredrickson, Jim K.

2013-10-02T23:59:59.000Z

449

Gene expression profiles of Nitrosomonas europaea, an obligate chemolitotroph  

SciTech Connect (OSTI)

Nitrosomonas europaea is an aerobic lithoautotrophic bacterium that uses ammonia (NH3) as its energy source. As a nitrifier, it is an important participant in the nitrogen cycle, which can also influence the carbon cycle. The focus of this work was to explore the genetic structure and mechanisms underlying the lithoautotrophic growth style of N. europaea. Whole genome gene expression. The gene expression profile of cells in exponential growth and during starvation was analyzed using microarrays. During growth, 98% of the genes increased in expression at least two fold compared to starvation conditions. In growing cells, approximately 30% of the genes were expressed eight fold higher, Approximately 10% were expressed more than 15 fold higher. Approximately 3% (91 genes) were expressed to more than 20 fold of their levels in starved cells. Carbon fixation gene expression. N. europaea fixes carbon via the Calvin-Benson-Bassham (CBB) cycle via a type I ribulose bisphosphate carboxylase/oxygenase (RubisCO). This study showed that transcription of cbb genes was up-regulated when the carbon source was limited, while amo, hao and other energy harvesting related genes were down-regulated. Iron related gene expression. Because N. europaea has a relatively high content of hemes, sufficient Fe must be available in the medium for it to grow. The genome revealed that approximately 5% of the coding genes in N. europaea are dedicated to Fe transport and assimilation. Nonetheless, with the exception of citrate biosynthesis genes, N. europaea lacks genes for siderophore production. The Fe requirements for growth and the expression of the putative membrane siderophore receptors were determined. The N. europaea genome has over 100 putative genes ({approx}5% of the coding genes) related to Fe uptake and its siderophore receptors could be grouped phylogenetically in four clusters. Fe related genes, such as a number of TonB-dependent Fe-siderophore receptors for ferrichrome and enterobactin, and diffusion protein OmpC were expressed to higher levels under Fe limitation. N. europaea has a high Fe requirement and under Fe limiting conditions (0.2 ?M), is capable to assimilate up to 70% of the available Fe without the ability to produce siderophores.

Daniel J Arp

2005-06-15T23:59:59.000Z

450

Gene expression profiles of Nitrosomonas europaea, an obligate chemolitotroph  

SciTech Connect (OSTI)

Nitrosomonas europaea is an aerobic lithoautotrophic bacterium that uses ammonia (NH3) as its energy source. As a nitrifier, it is an important participant in the nitrogen cycle, which can also influence the carbon cycle. The focus of this work was to explore the genetic structure and mechanisms underlying the lithoautotrophic growth style of N. europaea. Whole genome gene expression: The gene expression profile of cells in exponential growth and during starvation was analyzed using microarrays. During growth, 98% of the genes increased in expression at least two fold compared to starvation conditions. In growing cells, approximately 30% of the genes were expressed eight fold higher, Approximately 10% were expressed more than 15 fold higher. Approximately 3% (91 genes) were expressed to more than 20 fold of their levels in starved cells. Carbon fixation gene expression: N. europaea fixes carbon via the Calvin-Benson-Bassham (CBB) cycle via a type I ribulose bisphosphate carboxylase/oxygenase (RubisCO). This study showed that transcription of cbb genes was up-regulated when the carbon source was limited, while amo, hao and other energy harvesting related genes were down-regulated. Iron related gene expression: Because N. europaea has a relatively high content of hemes, sufficient Fe must be available in the medium for it to grow. The genome revealed that approximately 5% of the coding genes in N. europaea are dedicated to Fe transport and assimilation. Nonetheless, with the exception of citrate biosynthesis genes, N. europaea lacks genes for siderophore production. The Fe requirements for growth and the expression of the putative membrane siderophore receptors were determined. The N. europaea genome has over 100 putative genes ({approx}5% of the coding genes) related to Fe uptake and its siderophore receptors could be grouped phylogenetically in four clusters. Fe related genes, such as a number of TonB-dependent Fe-siderophore receptors for ferrichrome and enterobactin, and diffusion protein OmpC were expressed to higher levels under Fe limitation. N. europaea has a high Fe requirement and under Fe limiting conditions (0.2 {micro}M), is capable to assimilate up to 70% of the available Fe without the ability to produce siderophores.

Daniel J. Arp

2005-05-25T23:59:59.000Z

451

Crystal structures of MW1337R and lin2004: Representatives of a novel protein family that adopt a four-helical bundle fold  

SciTech Connect (OSTI)

To extend the structural coverage of proteins with unknown functions, we targeted a novel protein family (Pfam accession number PF08807, DUF1798) for which we proposed and determined the structures of two representative members. The MW1337R gene of Staphylococcus aureus subsp. aureus Rosenbach (Wood 46) encodes a protein with a molecular weight of 13.8 kDa (residues 1-116) and a calculated isoelectric point of 5.15. The lin2004 gene of the nonspore-forming bacterium Listeria innocua Clip11262 encodes a protein with a molecular weight of 14.6 kDa (residues 1-121) and a calculated isoelectric point of 5.45. MW1337R and lin2004, as well as their homologs, which, so far, have been found only in Bacillus, Staphylococcus, Listeria, and related genera (Geobacillus, Exiguobacterium, and Oceanobacillus), have unknown functions and are annotated as hypothetical proteins. The genomic contexts of MW1337R and lin2004 are similar and conserved in related species. In prokaryotic genomes, most often, functionally interacting proteins are coded by genes, which are colocated in conserved operons. Proteins from the same operon as MW1337R and lin2004 either have unknown functions (i.e., belong to DUF1273, Pfam accession number PF06908) or are similar to ypsB from Bacillus subtilis. The function of ypsB is unclear, although it has a strong similarity to the N-terminal region of DivIVA, which was characterized as a bifunctional protein with distinct roles during vegetative growth and sporulation. In addition, members of the DUF1273 family display distant sequence similarity with the DprA/Smf protein, which acts downstream of the DNA uptake machinery, possibly in conjunction with RecA. The RecA activities in Bacillus subtilis are modulated by RecU Holliday-junction resolvase. In all analyzed cases, the gene coding for RecU is in the vicinity of MW1337R, lin2004, or their orthologs, but on a different operon located in the complementary DNA strand. Here, we report the crystal structures of MW1337R and lin2004, which were determined using the semiautomated, high-throughput pipeline of the Joint Center for Structural Genomics (JCSG), part of the National Institute of General Medical Sciences Protein Structure Initiative.

Kozbial, Piotr; Xu, Qingping; Chiu, Hsiu-Ju; McMullan, Daniel; Krishna, S. Sri; Miller, Mitchell D.; Abdubek, Polat; Acosta, Claire; Astakhova, Tamara; Axelrod, Herbert L.; Carlton, Dennis; Clayton, Thomas; Deller, Marc; Duan, Lian; Elias, Ylva; Elsliger, Marc-André; Feuerhelm, Julie; Grzechnik, Slawomir K.; Hale, Joanna; Han, Gye Won; Jaroszewski, Lukasz; Jin, Kevin K.; Klock, Heath E.; Knuth, Mark W.; Koesema, Eric; Kumar, Abhinav; Marciano, David; Morse, Andrew T.; Murphy, Kevin D.; Nigoghossian, Edward; Okach, Linda; Oommachen, Silvya; Reyes, Ron; Rife, Christopher L.; Spraggon, Glen; Trout, Christina V.; ban den Bedem, Henry; Weekes, Dana; White, Aprilfawn; Wolf, Guenter; Zubieta, Chloe; Hodgson, Keith O.; Wooley, John; Deacon, Ashley M.; Godzik, Adam; Lesley, Scott A.; Wilson, Ian A. (Scripps); (SSRL); (JCSG); (UCSD); (Burnham)

2009-08-28T23:59:59.000Z

452

Adaptation of the Biolog Phenotype MicroArrayTM Technology to Profile the Obligate Anaerobe Geobacter metallireducens  

SciTech Connect (OSTI)

The Biolog OmniLog? Phenotype MicroArray (PM) plate technology was successfully adapted to generate a select phenotypic profile of the strict anaerobe Geobacter metallireducens (G.m.). The profile generated for G.m. provides insight into the chemical sensitivity of the organism as well as some of its metabolic capabilities when grown with a basal medium containing acetate and Fe(III). The PM technology was developed for aerobic organisms. The reduction of a tetrazolium dye by the test organism represents metabolic activity on the array which is detected and measured by the OmniLog(R) system. We have previously adapted the technology for the anaerobic sulfate reducing bacterium Desulfovibrio vulgaris. In this work, we have taken the technology a step further by adapting it for the iron reducing obligate anaerobe Geobacter metallireducens. In an osmotic stress microarray it was determined that the organism has higher sensitivity to impermeable solutes 3-6percent KCl and 2-5percent NaNO3 that result in osmotic stress by osmosis to the cell than to permeable non-ionic solutes represented by 5-20percent ethylene glycol and 2-3percent urea. The osmotic stress microarray also includes an array of osmoprotectants and precursor molecules that were screened to identify substrates that would provide osmotic protection to NaCl stress. None of the substrates tested conferred resistance to elevated concentrations of salt. Verification studies in which G.m. was grown in defined medium amended with 100mM NaCl (MIC) and the common osmoprotectants betaine, glycine and proline supported the PM findings. Further verification was done by analysis of transcriptomic profiles of G.m. grown under 100mM NaCl stress that revealed up-regulation of genes related to degradation rather than accumulation of the above-mentioned osmoprotectants. The phenotypic profile, supported by additional analysis indicates that the accumulation of these osmoprotectants as a response to salt stress does not occur in G.m. and response to stress must occur by other mechanisms. The Phenotype MicroArray technology can be reliably used as a rapid screening tool for characterization in anaerobic microbial ecology.

Joyner, Dominique; Fortney, Julian; Chakraborty, Romy; Hazen, Terry

2010-05-17T23:59:59.000Z

453

Intercellular Genomics of Subsurface Microbial Colonies  

SciTech Connect (OSTI)

This report summarizes progress in the second year of this project. The objective is to develop methods and software to predict the spatial configuration, properties and temporal evolution of microbial colonies in the subsurface. To accomplish this, we integrate models of intracellular processes, cell-host medium exchange and reaction-transport dynamics on the colony scale. At the conclusion of the project, we aim to have the foundations of a predictive mathematical model and software that captures the three scales of these systems – the intracellular, pore, and colony wide spatial scales. In the second year of the project, we refined our transcriptional regulatory network discovery (TRND) approach that utilizes gene expression data along with phylogenic similarity and gene ontology analyses and applied it successfully to E.coli, human B cells, and Geobacter sulfurreducens. We have developed a new Web interface, GeoGen, which is tailored to the reconstruction of microbial TRNs and solely focuses on Geobacter as one of DOE’s high priority microbes. Our developments are designed such that the frameworks for the TRND and GeoGen can readily be used for other microbes of interest to the DOE. In the context of modeling a single bacterium, we are actively pursuing both steady-state and kinetic approaches. The steady-state approach is based on a flux balance that uses maximizing biomass growth rate as its objective, subjected to various biochemical constraints, for the optimal values of reaction rates and uptake/release of metabolites. For the kinetic approach, we use Karyote, a rigorous cell model developed by us for an earlier DOE grant and the DARPA BioSPICE Project. We are also investigating the interplay between bacterial colonies and environment at both pore and macroscopic scales. The pore scale models use detailed representations for realistic porous media accounting for the distribution of grain size whereas the macroscopic models employ the Darcy-type flow equations and up-scaled advective-diffusive transport equations for chemical species. We are rigorously testing the relationship between these two scales by evaluating macroscopic parameters using the volume averaging methodology applied to pore scale model results.

Ortoleva, Peter; Tuncay, Kagan; Gannon, Dennis; Meile, Christof

2007-02-14T23:59:59.000Z

454

Bioavailability of Fe(III) in Loess Sediments: An Important Source of Electron Acceptors  

SciTech Connect (OSTI)

A quantitative study was conducted to understand if Fe (III) in loess sediments is available for microbial respiration by using a common metal reducing bacterium, Shewanella putrefaciens, CN32. The loess samples were collected from three different sites: St. Louis (Peoria), Missouri, USA; Huanxia (HX) and Yanchang (YCH), Shanxi Province of China. Wet chemical analyses indicated that the total Fe concentration for the three samples was 1.69%, 2.76%, and 3.29%, respectively, of which 0.48%, 0.67%, and 1.27% was Fe(III). All unreduced loess sediments contained iron oxides and phyllosilicates (smectite, illite, chlorite, vermiculite), in addition to common minerals such as quartz, feldspar, plagioclase, calcite, and dolomite. Bioreduction experiments were performed at a loess concentration of 20 mg/mL using lactate as the sole electron donor, Fe(III) in loess as the sole electron acceptor in the presence and absence of anthraquinone-2, 6-disulfonate (AQDS) as an electron shuttle. Experiments were performed in non-growth (bicarbonate buffer) and growth (M1) media with a cell concentration of ~2.8 x 107 and 2.1 x 107 cells/mL, respectively. The unreduced and bioreduced solids were analyzed by X-ray diffraction (XRD), Mössbauer spectroscopy, diffuse reflection spectroscopy (DRS), and scanning electron microscopy/energy dispersive spectroscopy (SEM/EDS) methods. Despite many similarities among the three loess samples, the extent and rate of Fe (III) reduction varied significantly. For example, in presence of AQDS the extent of reduction in the non-growth experiment was 25% in HX, 34% in Peoria, and 38% in YCH. The extent of reduction in the growth experiment was 72% in HX, 94% in Peoria, and 56% in YCH. The extent of bioreduction was lower in absence of AQDS. Overall, AQDS and the M1 growth medium significantly enhanced the rate and extent of bioreduction. Fe(III) in iron oxides and Fe(III)-containing phyllosilicates was bioreduced. Biogenic illite, siderite, and vivianite formed. The results of this study suggest that Fe (III) in loess sediments represents a potentially important source of electron acceptors to support microbial activity in dry environments.

Bishop, Michael E.; Jaisi, Deb P.; Dong, Hailiang; Kukkadapu, Ravi K.; Ji, Junfeng

2010-08-01T23:59:59.000Z

455

Bacterial reduction of crystalline Fe{sup 3+} oxides in single phase suspensions and subsurface materials  

SciTech Connect (OSTI)

Microbiologic reduction of synthetic and geologic Fe{sup 3+} oxides associated with four Pleistocene-age, Atlantic coastal plain sediments was investigated using a dissimilatory Fe reducing bacterium (Shewanella putrefaciens, strain CN32) in bicarbonate buffer. Experiments investigated whether phosphate and anthraquinone-2,6-disulfonate, (AQDS, a humic acid analogue) influenced the extent of crystalline Fe{sup 3+} oxide bioreduction and whether crystalline Fe{sup 3+} oxides in geologic materials are more or less reducible than comparable synthetic phases. Anaerobic incubations (10{sup 8} organisms/mL) were performed both with and without PO{sub 4} and AQDS that functions as an electron repository and shuttle. The production of Fe{sup 2+} (solid and aqueous) was followed with time, as was mineralogy by X-ray diffraction. The synthetic oxides were reduced in a qualitative trend consistent with their surface area and free energy: hydrous ferric oxide (HFO) > goethite > hematite. Bacterial reduction of the crystalline oxides was incomplete in spite of excess electron donor. Biogenic formation of vivianite [Fe{sub 3}(PO{sub 4}){sub 2}{center_dot}8H{sub 2}O] and siderite (FeCO{sub 3}) was observed; the conditions of their formation was consistent with their solubility. The geologic Fe{sup 3+} oxides showed a large range in reducibility, approaching 100% in some materials. The natural oxides were equally or more reducible than their synthetic counterparts, in spite of association with non-reducible mineral phases (e.g., kaolinite). The reducibility of the synthetic and geologic oxides was weakly effected by PO{sub 4}, but was accelerated by AQDS. CN32 produced the hydroquinone form of AQDS (AHDS), that, in turn, had thermodynamic power to reduce the Fe{sup 3+} oxides. As a chemical reductant, it could reach physical regions of the oxide not accessible by the organism. Electron microscopy showed that crystallite size was not the primary factor that caused differences in reducibility between natural and synthetic crystalline Fe{sup 3+} oxide phases. Crystalline disorder and microheterogeneities may be more important.

Zachara, J.M.; Fredrickson, J.K.; Li, S.M.; Kennedy, D.W.; Smith, S.C.; Gassman, P.L. [Pacific Northwest National Lab., Richland, WA (United States)

1998-11-01T23:59:59.000Z

456

Reduction And Immobilization Of Hexavalent Chromium By Microbially Reduced Fe-bearing Clay Minerals  

SciTech Connect (OSTI)

Hexavalent chromium (Cr6+) is a major contaminant in the environment. As a redox-sensitive element, the fate and toxicity of chromium is controlled by reduction-oxidation (redox) reactions. Previous research has shown the ability of structural Fe(II) in naturally present and chemically reduced clay minerals to reduce Cr6+ to Cr(III) as a way of immobilization and detoxification. However, it is still poorly known whether or not structural Fe(II) in biologically reduced clay minerals exhibits a similar reactivity and if so, what the kinetics and mechanisms of Cr6+ reduction are. The objective of this study was to determine the kinetics and possible mechanisms of Cr6+ reduction by structural Fe(II) in microbially reduced clay minerals and the nature of reduced Cr(III). Structural Fe(III) in nontronite (NAu-2), montmorillonite (SWy-2), chlorite (CCa-2), and clay-rich sediments from the Ringold Formation of the Hanford site of Washington State, USA was first bioreduced to Fe(II) by an iron-reducing 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 Fe(II) was then used to reduce aqueous Cr6+ at three different temperatures, 10°, 20°, and 30°C, in order to determine the temperature dependence of the redox reaction between Cr6+ and clay-Fe(II). The results showed that nontronite and montmorillonite were most effective in reducing aqueous Cr6+ at all three temperatures. In contrast, most Fe(II) in chlorite was not reactive towards Cr6+ reduction at 10°C, though at 30°C there was some reduction. For all the clay minerals, the ratio of total Fe(II) oxidized to Cr6+ reduced was close to the expected stoichiometric value of 3. Characterization of the Cr-clay reaction product with scanning electron microscopy with focused ion beam and transmission electron microscopy with electron energy loss spectroscopy revealed that reduced chromium was possibly in the form of sub-nanometer Cr2O3 in association with residual clay minerals as micro-aggregates. This textural association was expected to minimize the chance of Cr(III) reoxidation upon exposure to oxidants. These results are important for our understanding of how various clay minerals may be used to reductively immobilize the heavy metal contaminant Cr in the environment.

Bishop, Michael E.; Glasser, Paul; Dong, Hailiang; Arey, Bruce W.; Kovarik, Libor

2014-05-15T23:59:59.000Z

457

Engineering and Coordination of Regulatory Networks and Intracellular Complexes to Maximize Hydrogen Production by Phototrophic Microorganisms  

SciTech Connect (OSTI)

This project is a collaboration with F. R. Tabita of Ohio State. Our major goal is to understand the factors and regulatory mechanisms that influence hydrogen production. The organisms to be utilized in this study, phototrophic microorganisms, in particular nonsulfur purple (NSP) bacteria, catalyze many significant processes including the assimilation of carbon dioxide into organic carbon, nitrogen fixation, sulfur oxidation, aromatic acid degradation, and hydrogen oxidation/evolution. Our part of the project was to develop a modeling technique to investigate the metabolic network in connection to hydrogen production and regulation. Organisms must balance the pathways that generate and consume reducing power in order to maintain redox homeostasis to achieve growth. Maintaining this homeostasis in the nonsulfur purple photosynthetic bacteria is a complex feat with many avenues that can lead to balance, as these organisms possess versatile metabolic capabilities including anoxygenic photosynthesis, aerobic or anaerobic respiration, and fermentation. Growth is achieved by using H{sub 2} as an electron donor and CO{sub 2} as a carbon source during photoautotrophic and chemoautotrophic growth, where CO{sub 2} is fixed via the Calvin-Benson-Bassham (CBB) cycle. Photoheterotrophic growth can also occur when alternative organic carbon compounds are utilized as both the carbon source and electron donor. Regardless of the growth mode, excess reducing equivalents generated as a result of oxidative processes, must be transferred to terminal electron acceptors, thus insuring that redox homeostasis is maintained in the cell. Possible terminal acceptors include O{sub 2}, CO{sub 2}, organic carbon, or various oxyanions. Cells possess regulatory mechanisms to balance the activity of the pathways which supply energy, such as photosynthesis, and those that consume energy, such as CO{sub 2} assimilation or N{sub 2} fixation. The major route for CO{sub 2} assimilation is the CBB reductive pentose phosphate pathway, whose key enzyme is ribulose 1,5-biphosphate carboxylase/oxygenase (RubisCO). In addition to providing virtually all cellular carbon during autotrophic metabolism, RubisCO-mediated CO{sub 2} assimilation is also very important for nonsulfur purple photosynthetic bacteria under photoheterotrophic growth conditions since CO{sub 2} becomes the major electron sink under these conditions. In this work, Ensemble Modeling (EM) was developed to examine the behavior of CBB-compromised RubisCO knockout mutant strains of the nonsulfur purple photosynthetic bacterium Rhodobacter sphaeroides. Mathematical models of metabolism can be a great aid in studying the effects of large perturbations to the system, such as the inactivation of RubisCO. Due to the complex and highly-interconnected nature of these networks, it is not a trivial process to understand what the effect of perturbations to the metabolic network will be, or vice versa, what enzymatic perturbations are necessary to yield a desired effect. Flux distribution is controlled by multiple enzymes in the network, often indirectly linked to the pathways of interest. Further, depending on the state of the cell and the environmental conditions, the effect of a perturbation may center around how it effects the carbon flow in the network, the balancing of cofactors, or both. Thus, it is desirable to develop mathematical models to describe, understand, and predict network behavior. Through the development of such models, one may gain the ability to generate a set of testable hypotheses for system behavior.

James C. Liao

2012-05-22T23:59:59.000Z

458

Molecular Characterization of Bacterial Respiration on Minerals  

SciTech Connect (OSTI)

The overall aim of this project was to contribute to our fundamental understanding of proteins and biological processes under extreme environmental conditions. We sought to define the biochemical and physiological mechanisms that underlie biodegradative and other cellular processes in normal, extreme, and engineered environments. Toward that end, we sought to understand the substrate oxidation pathways, the electron transport mechanisms, and the modes of energy conservation employed during respiration by bacteria on soluble iron and insoluble sulfide minerals. In accordance with these general aims, the specific aims were two-fold: To identify, separate, and characterize the extracellular biomolecules necessary for aerobic respiration on iron under strongly acidic conditions; and to elucidate the molecular principles whereby these bacteria recognize and adhere to their insoluble mineral substrates under harsh environmental conditions. The results of these studies were described in a total of nineteen manuscripts. Highlights include the following: 1. The complete genome of Acidithiobacillus ferrooxidans ATCC 23270 (type strain) was sequenced in collaboration with the DOE Joint Genome Institute; 2. Genomic and mass spectrometry-based proteomic methods were used to evaluate gene expression and in situ microbial activity in a low-complexity natural acid mine drainage microbial biofilm community. This was the first effort to successfully analyze a natural community using these techniques; 3. Detailed functional and structural studies were conducted on rusticyanin, an acid-stable electron transfer protein purified from cell-free extracts of At. ferrooxidans. The three-dimensional structure of reduced rusticyanin was determined from a combination of homonuclear proton and heteronuclear 15N- and 13C-edited NMR spectra. Concomitantly, the three-dimensional structure of oxidized rusticyanin was determined by X-ray crystallography to a resolution of 1.9 A by multiwavelength anomalous dispersion (MAD) phasing; 4. An acid-stable red cytochrome with a novel absorbance peak at 579 nm was purified from cell-free extracts of L. ferriphilum. Functional studies demonstrated that this cytochrome was an important component of the aerobic iron respiratory chain in this organism; 5. The specific adhesion of At. ferrooxidans to pyrite is mediated by an extracellular protein that was identified as aporusticyanin. The adhesion of At. ferrooxidans to minerals was characterized by high affinity binding that exhibited a high specificity for pyrite over other sulfide minerals. The principal biopolymer involved in this high-affinity adhesion to pyrite was isolated by mineral affinity chromatography and identified as aporusticyanin. The adhesion of purified aporusticyanin to minerals was observed to adhere to different mineral with a pattern of reactivity identical to that observed with the intact bacterium. Further, preincubation of pyrite with excess exogenous aporusticyanin served to inhibit the adherence of intact cells to the surface of the mineral, indicating that the protein and the cells adhered to the pyrite in a mutually exclusive manner. Taken together, these observations support a model where aporusticyanin located on the surface of the bacterial cell acts as a mineral-specific receptor for the initial adherence of At. ferrooxidans to solid pyrite; 6. The specific adhesion of L. ferriphilum to pyrite was mediated by a different acid-stable extracellular protein than aporusticyanin; and 7. A prototype integrating cavity absorption meter (ICAM) was assembled to determine whether this novel spectrophotometer could be used to study cellular respiration in situ.

Blake, Robert C.

2013-04-26T23:59:59.000Z

459

Structural and Functional Proteomic Analysis of a Developing Energy Transducing Membrane  

SciTech Connect (OSTI)

While much is known about the light reactions of photosynthesis in purple bacteria, comparatively little information is available on how the requisite integral membrane proteins are assembled, their patterns of cellular localization are established or their apoproteins cooperate with numerous assembly factors in their insertion into the growing intracytoplasmic membrane (ICM). This problem was approached through a detailed structural and functional proteomic analysis of ICM assembly process in the well-characterized purple bacterium Rhodobacter sphaeroides. Proteomic approaches have focused upon identification of membrane proteins temporally expressed during ICM development and spatially localized in both membrane growth initiation sites and in mature ICM vesicles. Protocols were established for ICM induction under reduced aeration and ICM remodeling in cells adapting to low intensity illumination, which permitted isolation, in sucrose density gradients, of ICM growth initiation sites as an upper pigmented band (UPB) and mature ICM vesicles as the main (chromatophore) band. Non-denaturing clear native gel electrophoresis (CNE) of these isolated membrane fractions gave rise to pigmented bands containing the peripheral light-harvesting 2 (LH2) antenna and the reaction center-light-harvesting 1 (RC-LH1) core complex, together with a full array of other ICM proteins, which were subjected to proteomic analysis. Proteomic analysis of the gel bands from chromatophores revealed developmental changes including increasing levels of the LH2 complex as ICM development proceeded, as well as a large array of other associated proteins including high spectral counts for the F1FO� ATP synthase subunits, given the inability to detect this coupling factor, as well as the more abundant cytochrome bc1 complex by atomic force microscopy (AFM). Significant levels of general membrane assembly factors were encountered, as well as high counts for RSP6124, a protein of unknown function, correlated with increasing LH2 levels. RC-LH1-containing CNE gel bands from the UPB were enriched in cytoplasmic membrane (CM) markers, including electron transfer and transport proteins, as well as general membrane assembly factors relative to chromatophore bands. This confirms the origin of the UPB from both peripheral respiratory membrane and sites of CM invagination. Significant levels of preprotein translocases YidC, YajC and SecY, bacterial type 1 signal peptidase and twin arg translocation subunit TatA were found. Such general membrane assembly factors were significantly enriched in the UPB RC-LH1 gel bands, confirming the active role of membrane invagination sites in pigment-protein complex assembly. Functional correlates of proteomics approaches were provided by near-IR fluorescence induction/relaxation transients arising from LH-BChl components. A linear relation was found between increasing functional absorption cross-section and slowing of RC electron transfer turnover rate, thought to arise from the imposition of constraints upon free UQ diffusion between the RC and cytochrome bc1 complex as the membrane became saturated with new LH2 rings. In cells undergoing ICM induction in which generation of the electrochemical proton gradient was uncoupled with CCCP, blockage in membrane insertion of the LH and RC polypetides was demonstrated. This was reflected in a diminution of quantum yield of the primary charge separation, a cessation in expansion of functional absorption cross-section and a >4-fold slowing in RC electron transfer turnover. The ICM insertion of ATP synthase and transhydrogenase was also significantly diminished. Importantly, for the UPB fraction, CCCP treatment resulted in accumulation of ~2-fold greater levels of the preprotein translocase SecY, the SecA translocation ATPase, Sec D and SecF insertion components, and chaperonins DnaJ and DnaK, suggesting that these general membrane assembly factors had accumulated in association with nascent LH and RC assembly intermediates. In addition to spectrally homogeneous bands c

Niederman, Robert A

2012-06-04T23:59:59.000Z

460

Harnessing microbial subsurface metal reduction activities to synthesise nanoscale cobalt ferrite with enhanced magnetic properties  

SciTech Connect (OSTI)

Nanoscale ferrimagnetic particles have a diverse range of uses from directed cancer therapy and drug delivery systems to magnetic recording media and transducers. Such applications require the production of monodisperse nanoparticles with well-controlled size, composition, and magnetic properties. To fabricate these materials purely using synthetic methods is costly in both environmental and economical terms. However, metal-reducing microorganisms offer an untapped resource to produce these materials. Here, the Fe(III)-reducing bacterium Geobacter sulfurreducens is used to synthesize magnetic iron oxide nanoparticles. A combination of electron microscopy, soft X-ray spectroscopy, and magnetometry techniques was employed to show that this method of biosynthesis results in high yields of crystalline nanoparticles with a narrow size distribution and magnetic properties equal to the best chemically synthesized materials. In particular, it is demonstrated here that cobalt ferrite (CoFe{sub 2}O{sub 4}) nanoparticles with low temperature coercivity approaching 8 kOe and an effective anisotropy constant of {approx} 10{sup 6} erg cm{sup -3} can be manufactured through this biotechnological route. The dramatic enhancement in the magnetic properties of the nanoparticles by the introduction of high quantities of Co into the spinel structure represents a significant advance over previous biomineralization studies in this area using magnetotactic bacteria. The successful production of nanoparticulate ferrites achieved in this study at high yields could open up the way for the scaled-up industrial manufacture of nanoparticles using environmentally benign methodologies. Production of ferromagnetic nanoparticles for pioneering cancer therapy, drug delivery, chemical sensors, catalytic activity, photoconductive materials, as well as more traditional uses in data storage embodies a large area of inorganic synthesis research. In particular, the addition of transition metals other than Fe into the structure of magnetite (Fe{sub 3}O{sub 4}) has been shown to greatly enhance the magnetic properties of the particles, tailoring them to different commercial uses. However, synthesis of magnetic nanoparticles is often carried out at high temperatures with toxic solvents resulting in high environmental and energy costs. Additionally, these ferrite nanoparticles are not intrinsically biocompatible, and to make them suitable for insertion into the human body is a rather intricate task. A relatively unexplored resource for magnetic nanomaterial production is subsurface Fe(III)-reducing bacteria, as these microorganisms are capable of producing large quantities of nanoscale magnetite (Fe{sub 3}O{sub 4}) at ambient temperatures. Metal-reducing bacteria live in environments deficient in oxygen and conserve energy for growth through the oxidation of hydrogen or organic electron donors, coupled to the reduction of oxidized metals such as Fe(III)-bearing minerals. This can result in the formation of magnetite via the extracellular reduction of amorphous Fe(III)-oxyhydroxides causing the release of soluble Fe(II) and resulting in complete recrystallization of the amorphous mineral into a new phase. Some previous studies have reported altering the composition of biogenic magnetite produced by Fe(III)-reducing bacteria for industrial and environmental applications. However, research into the commercial exploitation of bacteria to form magnetic minerals has focused primarily on magnetotactic bacteria which form magnetosomal magnetite internally using very different pathways to those bacteria forming magnetite outside the cell. Magnetotactic bacteria live at the sediment-water interface and use internal nanomagnets to guide them to their preferred environmental niche using the Earth's magnetic field. Since magnetotactic bacteria generally grow optimally under carefully controlled microaerobic conditions, the culturing processes for these organisms are challenging and result in low yields of nanomagnetite. Despite these limitations, magnetotactic bacteria have bee

Coker, Victoria S.; Telling, Neil D.; van der Laan, Gerrit; Pattrick, Richard A.D.; Pearce, Carolyn I.; Arenholz, Elke; Tuna, Floriana; Winpenny, Richard E.P.; Lloyd, Jonathan R.

2009-03-24T23:59:59.000Z

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461

Assessing the Role of Iron Sulfides in the Long Term Sequestration of Uranium by Sulfate-Reducing Bacteria  

SciTech Connect (OSTI)

This overarching aim of this project was to identify the role of biogenic and synthetic iron-sulfide minerals in the long-term sequestration of reduced U(IV) formed under sulfate-reducing conditions when subjected to re-oxidizing conditions. The work reported herein was achieved through the collaborative research effort conducted at Arizona State University (ASU) and the University of Michigan (UM). Research at ASU, focused on the biogenesis aspects, examined the biogeochemical bases for iron-sulfide production by Desulfovibrio vulgaris, a Gram-negative bacterium that is one of the most-studied strains of sulfate-reducing bacteria. A series of experimental studies were performed to investigate comprehensively important metabolic and environmental factors that affect the rates of sulfate reduction and iron-sulfide precipitation, the mineralogical characteristics of the iron sulfides, and how uranium is reduced or co-reduced by D. vulagaris. FeS production studies revealed that controlling the pH affected the growth of D. vulgaris and strongly influenced the formation and growth of FeS solids. In particular, lower pH produced larger-sized mackinawite (Fe1+xS). Greater accumulation of free sulfide, from more sulfate reduction by D. vulgaris, also led to larger-sized mackinawite and stimulated mackinawite transformation to greigite (Fe3S4) when the free sulfide concentration was 29.3 mM. On the other hand, using solid Fe(III) (hydr)oxides as the iron source led to less productivity of FeS due to their slow and incomplete dissolution and scavenging of sulfide. Furthermore, sufficient free Fe2+, particularly during Fe(III) (hydr)oxide reductions, led to the additional formation of vivianite [Fe3(PO4)2•8(H2O)]. The U(VI) reduction studies revealed that D. vulgaris reduced U(VI) fastest when accumulating sulfide from concomitant sulfate reduction, since direct enzymatic and sulfide-based reductions of U(VI) occurred in parallel. The UO2 produced in presence of ferrous iron was poorly crystalline. At UM, laboratory-scale reactor studies were performed to assess the potential for the predominant abiotic reductants formed under sulfate reducing conditions (SRCs) to: (1) reduce U(VI) in contaminated groundwater sediments), and (2) inhibit the re-oxidation of U(IV) species, and in particular, uraninite (UO2(s)). Under SRCs, mackinawite and aqueous sulfide are the key reductants expected to form. To assess their potential for abiotic reduction of U(VI) species, a series of experiments were performed in which either FeS or S(-II) was added to solutions of U(VI), with the rates of conversion to U(IV) solids monitored as a function of pH, and carbonate and calcium concentration. In the presence of FeS and absence of oxygen or carbonate, U(IV) was completely reduced uraninite. S(-II) was also found to be an effective reductant of aqueous phase U(VI) species and produced uraninite, with the kinetics and extent of reduction depending on geochemical conditions. U(VI) reduction to uraninite was faster under higher S(-II) concentrations but was slowed by an increase in the dissolved Ca or carbonate concentration. Rapid reduction of U(VI) occurred at circumneutral pH but virtually no reduction occurred at pH 10.7. In general, dissolved Ca and carbonate slowed abiotic U(VI) reduction by forming stable Ca-U(VI)-carbonate soluble complexes that are resistant to reaction with aqueous sulfide. To investigate the stability of U(IV) against re-oxidation in the presence of iron sulfides by oxidants in simulated groundwater environments, and to develop a mechanistic understanding the controlling redox processes, continuously-mixed batch reactor (CMBR) and flow-through reactor (CMFR) studies were performed at UM. In these studies a series of experiments were conducted under various oxic groundwater conditions to examine the effectiveness of FeS as an oxygen scavenger to retard UO2 dissolution. The results indicate that FeS is an effective oxygen scavenger, and can lower the rate of oxidative dissolution of UO2 by over an order of magnitude compared to

Hayes, Kim F.; Bi, Yuqiang; Carpenter, Julian; Hyng, Sung Pil; Rittmann, Bruce E.; Zhou, Chen; Vannela, Raveender; Davis, James A.

2014-01-01T23:59:59.000Z