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Widefield laser doppler velocimeter: development and theory.

Description: The widefield laser Doppler velocimeter is a new measurement technique that significantly expands the functionality of a traditional scanning system. This new technique allows full-field velocity measurements without scanning, a drawback of traditional measurement techniques. This is particularly important for tests in which the sample is destroyed or the motion of the sample is non-repetitive. The goal of creating ''velocity movies'' was accomplished during the research, and this report describes the current functionality and operation of the system. The mathematical underpinnings and system setup are thoroughly described. Two prototype experiments are then presented to show the practical use of the current system. Details of the corresponding hardware used to collect the data and the associated software to analyze the data are presented.
Date: March 1, 2007
Creator: Hansche, Bruce David; Reu, Phillip L. & Massad, Jordan Elias
Partner: UNT Libraries Government Documents Department

Fracture Dissolution of Carbonate Rock: An Innovative Process for Gas Storage

Description: The goal of the project is to develop and assess the feasibility and economic viability of an innovative concept that may lead to commercialization of new gas-storage capacity near major markets. The investigation involves a new approach to developing underground gas storage in carbonate rock, which is present near major markets in many areas of the United States. Because of the lack of conventional gas storage and the projected growth in demand for storage capacity, many of these areas are likely to experience shortfalls in gas deliverability. Since depleted gas reservoirs and salt formations are nearly non-existent in many areas, alternatives to conventional methods of gas storage are required. The need for improved methods of gas storage, particularly for ways to meet peak demand, is increasing. Gas-market conditions are driving the need for higher deliverability and more flexibility in injection/withdrawal cycling. In order to meet these needs, the project involves an innovative approach to developing underground storage capacity by creating caverns in carbonate rock formations by acid dissolution. The basic concept of the acid-dissolution method is to drill to depth, fracture the carbonate rock layer as needed, and then create a cavern using an aqueous acid to dissolve the carbonate rock. Assessing feasibility of the acid-dissolution method included a regional geologic investigation. Data were compiled and analyzed from carbonate formations in six states: Indiana, Ohio, Kentucky, West Virginia, Pennsylvania, and New York. To analyze the requirements for creating storage volume, the following aspects of the dissolution process were examined: weight and volume of rock to be dissolved; gas storage pressure, temperature, and volume at depth; rock solubility; and acid costs. Hydrochloric acid was determined to be the best acid to use because of low cost, high acid solubility, fast reaction rates with carbonate rock, and highly soluble products (calcium chloride) ...
Date: October 31, 2006
Creator: Castle, James W.; Falta, Ronald W.; Bruce, David; Murdoch, Larry; Brame, Scott E. & Brooks, Donald
Partner: UNT Libraries Government Documents Department

Pregnancy-Resolution Correlates: An Exploratory Study into Demographic and Personality Variables

Description: This study was designed to explore possible demographic and personality correlates of pregnancy-resolution alternatives. A total of 146 female college students were given the Marlowe-Crowne Social Desirability Scale, the Intrinsic Extrinsic Religious Orientation Scale, a demographic questionnaire, and a Pregnancy-Resolution Questionnaire. The data were analyzed by means of the chi-square statistic and discriminant analysis.
Date: December 1983
Creator: Nystrom, Bruce D. (Bruce David)
Partner: UNT Libraries

Roles of Calcium Ions and Cyclic AMP in Olfactory Transduction

Description: The roles of Ca2 + and cAMP in olfactory transduction were explored using agents which affect calcium channels and second messenger systems. These agents were applied at certain calculated final concentrations onto olfactory epithelia of urethane-anesthetized frogs (Sana PiPlens) by two-sec aerosol spray. During extracellular recording, saturated vapors of isoamyl acetate were delivered every 100 sec in 0.3 sec pulses to produce an electroolfactogram (EOG). Inorganic cations that block inward calcium currents inhibit EOG responses with the following rank order: (La3+) > (Zn2+, Cd2+) > (Al3+, Ca2+, Sr2+) > (Co2+). Application of 7.5 mM La3+ eradicates £0G's, while Ba2+ (which can carry more current that Ca2+) initially produces significant enhancement (F=43.04, p<0.001, df=19). Magnesium ion has no effect on EOG's at 7.5 mM, while 1.5 X 10"4M Ca2+ is significantly inhibitory (F=5.74; p=0.0355; df=12). Control aerosol sprays of distilled water depress EOG's by an average of 5%. The organic calcium channel antagonists diltiazem and verapamil inhibit EOG's by 17% and 36X, respectively, at a concentration of 1.5 X 10~*M. Verapamil produces significant inhibition (F=17.17; p=0.002; df=ll) at 1.5 X 10" 5 M, while the 1,4-dihydropyridine calcium channel antagonists, nicardipine and nifedipine, do not inhibit beyond 1% DMSO controls. Several calmodulin antagonists decrease EOG's, but without correlation to their anti-calmodulin potency. Application of 1.5 X 10"*M chlorpromazine and N-(6-aminohexyl)-5-chloro-l-naphthalenesulfonamide inhibit EOG's by 31% and 27%, respectively, while trifluoperazine inhibits by 23%. Dibutyryl cAMP, a lipophilic mimic of cAMP, produces 54% inhibition at 1.5 X 10" *M. Dibutyryl cGMP, cGMP, cAMP, and adenosine all decrease EOG's by less than 15% compared to distilled water controls. Forskolin, a reversible activator of adenylate cyclase, inhibits EOG's by 57% at 1.5 X 10"5M, which is significant beyond the 1% DMSO controls (F=17.17; p=0.002; df=ll). These data support the hypothesis that Ca2+ participates in olfactory transduction. ...
Date: December 1986
Creator: Winegar, Bruce D. (Bruce David)
Partner: UNT Libraries

BASIC ENGINEERING RESEARCH FOR D&amp;D OF R REACTOR STORAGE POND SLUDGE: ELECTROKINETICS, CARBON DIOXIDE EXTRACTION, AND SUPERCRITICAL WATER OXIDATION

Description: Large quantities of mixed low level waste (MLLW) that fall under the Toxic Substances Control Act (TSCA) exist and will continue to be generated during D&amp;D operations at DOE sites across the country. Currently, the volume of these wastes is approximately 23,500 m3, and the majority of these wastes (i.e., almost 19,000 m3) consist of PCBs and PCB-contaminated materials. Further, additional PCB-contaminated waste will be generated during D&amp;D operations in the future. The standard process for destruction of this waste is incineration, which generates secondary waste that must be disposed, and the TSCA incinerator at Oak Ridge has an uncertain future. Beyond incineration, no proposed process for the recovery and/or destruction of these persistent pollutants has emerged as the preferred choice for DOE cleanup. The main objective of the project was to investigate and develop a deeper understanding of the thermodynamic and kinetic reactions involved in the extraction and destruction of polychlorinated biphenyls (PCBs) from low-level mixed waste solid matrices in order to provide data that would permit the design of a combined-cycle extraction/destruction process. The specific research objectives were to investigate benign dense-fluid extraction with either carbon dioxide (USC) or hot water (CU), followed by destruction of the extracted PCBs via either electrochemical (USC) or hydrothermal (CU) oxidation. Two key advantages of the process are that it isolates and concentrates the PCBs from the solid matrices (thereby reducing waste volume greatly and removing the remaining low-level mixed waste from TSCA control), and little, if any, secondary solvent or solid wastes are generated. This project was a collaborative effort involving the University of South Carolina (USC), Clemson University (CU), and Westinghouse Savannah River Company (WSRC) (including the Savannah River Technology Center, Facilities Decommissioning Division and Regulatory Compliance). T he project was directed and coordinated by the South Carolina Universities Research ...
Date: December 31, 2001
Creator: Matthews, Michael A.; Bruce,David; Davis,Thomas; Thies, Mark; Weidner, John & White, Ralph
Partner: UNT Libraries Government Documents Department

Catalytic Process for the Conversion of Coal-derived Syngas to Ethanol

Description: The catalytic conversion of coal-derived syngas to C{sub 2+} alcohols and oxygenates has attracted great attention due to their potential as chemical intermediates and fuel components. This is particularly true of ethanol, which can serve as a transportation fuel blending agent, as well as a hydrogen carrier. A thermodynamic analysis of CO hydrogenation to ethanol that does not allow for byproducts such as methane or methanol shows that the reaction: 2 CO + 4 H{sub 2} {yields} C{sub 2}H{sub 5}OH + H{sub 2}O is thermodynamically favorable at conditions of practical interest (e.g,30 bar, {approx}&lt; 250 C). However, when methane is included in the equilibrium analysis, no ethanol is formed at any conditions even approximating those that would be industrially practical. This means that undesired products (primarily methane and/or CO{sub 2}) must be kinetically limited. This is the job of a catalyst. The mechanism of CO hydrogenation leading to ethanol is complex. The key step is the formation of the initial C-C bond. Catalysts that are selective for EtOH can be divided into four classes: (a) Rh-based catalysts, (b) promoted Cu catalysts, (c) modified Fischer-Tropsch catalysts, or (d) Mo-sulfides and phosphides. This project focuses on Rh- and Cu-based catalysts. The logic was that (a) Rh-based catalysts are clearly the most selective for EtOH (but these catalysts can be costly), and (b) Cu-based catalysts appear to be the most selective of the non-Rh catalysts (and are less costly). In addition, Pd-based catalysts were studied since Pd is known for catalyzing CO hydrogenation to produce methanol, similar to copper. Approach. The overall approach of this project was based on (a) computational catalysis to identify optimum surfaces for the selective conversion of syngas to ethanol; (b) synthesis of surfaces approaching these ideal atomic structures, (c) specialized characterization to determine the extent to which the ...
Date: July 29, 2011
Creator: Spivery, James; Harrison, Doug; Earle, John; Goodwin, James; Bruce, David; Mo, Xunhau et al.
Partner: UNT Libraries Government Documents Department

Basic Engineering Research for D&amp;D of R. Reactor Storage Pond Sludge: Electrokinetics, Carbon Dioxide Extraction, and Supercritical Water Oxidation

Description: Collaborating researchers at the University of South Carolina (USC), Clemson University (CU), and the Savannah River Site (SRS) are investigating the fundamentals of a combined extraction and destruction process for the decontamination and decommissioning (D&amp;D) of PCB-contaminated materials as found at DOE sites. Currently, the volume of PCBs and PCB contaminated wastes at DOE sites nationwide is approximately 19,000 m3. While there are a number of existing and proposed processes for the recovery and/or destruction of these persistent 4 pollutants, none has emerged as the preferred choice. Therefore, this research focuses on combining novel processes to solve the problem. The research objectives are to investigate benign dense-fluid extraction with either carbon dioxide (USC) or hot water (CU), followed by destruction of the extracted PCBs via either electrochemical (USC) or hydrothermal (CU) oxidation. Based on the results of these investigations, a combined extraction and destruction process that incorporates the most successful elements of the various processes will be recommended for application to contaminated DOE sites.
Date: June 1, 1999
Creator: Hamilton, Edward A.; Bruce, David A.; Oji, Lawrence; White, Ralph E.; Matthews, Michael A. & Thies, Mark C.
Partner: UNT Libraries Government Documents Department

The Methanosarcina barkeri genome: comparative analysis withMethanosarcina acetivorans and Methanosarcina mazei reveals extensiverearrangement within methanosarcinal genomes

Description: We report here a comparative analysis of the genome sequence of Methanosarcina barkeri with those of Methanosarcina acetivorans and Methanosarcina mazei. All three genomes share a conserved double origin of replication and many gene clusters. M. barkeri is distinguished by having an organization that is well conserved with respect to the other Methanosarcinae in the region proximal to the origin of replication with interspecies gene similarities as high as 95%. However it is disordered and marked by increased transposase frequency and decreased gene synteny and gene density in the proximal semi-genome. Of the 3680 open reading frames in M. barkeri, 678 had paralogs with better than 80% similarity to both M. acetivorans and M. mazei while 128 nonhypothetical orfs were unique (non-paralogous) amongst these species including a complete formate dehydrogenase operon, two genes required for N-acetylmuramic acid synthesis, a 14 gene gas vesicle cluster and a bacterial P450-specific ferredoxin reductase cluster not previously observed or characterized in this genus. A cryptic 36 kbp plasmid sequence was detected in M. barkeri that contains an orc1 gene flanked by a presumptive origin of replication consisting of 38 tandem repeats of a 143 nt motif. Three-way comparison of these genomes reveals differing mechanisms for the accrual of changes. Elongation of the large M. acetivorans is the result of multiple gene-scale insertions and duplications uniformly distributed in that genome, while M. barkeri is characterized by localized inversions associated with the loss of gene content. In contrast, the relatively short M. mazei most closely approximates the ancestral organizational state.
Date: May 19, 2006
Creator: Maeder, Dennis L.; Anderson, Iain; Brettin, Thomas S.; Bruce,David C.; Gilna, Paul; Han, Cliff S. et al.
Partner: UNT Libraries Government Documents Department

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

Description: 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 ...
Date: January 1, 2009
Creator: Barabote, Ravi D.; Xie, Gary; Leu, David H.; Normand, Philippe; Necsulea, Anamaria; Daubin, Vincent et al.
Partner: UNT Libraries Government Documents Department

High-resolution metagenomics targets major functional types in complex microbial communities

Description: Most microbes in the biosphere remain uncultured and unknown. Whole genome shotgun (WGS) sequencing of environmental DNA (metagenomics) allows glimpses into genetic and metabolic potentials of natural microbial communities. However, in communities of high complexity metagenomics fail to link specific microbes to specific ecological functions. To overcome this limitation, we selectively targeted populations involved in oxidizing single-carbon (C{sub 1}) compounds in Lake Washington (Seattle, USA) by labeling their DNA via stable isotope probing (SIP), followed by WGS sequencing. Metagenome analysis demonstrated specific sequence enrichments in response to different C{sub 1} substrates, highlighting ecological roles of individual phylotypes. We further demonstrated the utility of our approach by extracting a nearly complete genome of a novel methylotroph Methylotenera mobilis, reconstructing its metabolism and conducting genome-wide analyses. This approach allowing high-resolution genomic analysis of ecologically relevant species has the potential to be applied to a wide variety of ecosystems.
Date: August 1, 2009
Creator: Kalyuzhnaya, Marina G.; Lapidus, Alla; Ivanova, Natalia; Copeland, Alex C.; McHardy, Alice C.; Szeto, Ernest et al.
Partner: UNT Libraries Government Documents Department

Complete genome sequence of Tolumonas auensis type strain (TA 4T)

Description: Tolumonas auensis (Fischer-Romero et al. 1996) is currently the only validly named species of the genus Tolumonas in the family Aeromonadaceae. The strain is of interest because of its ability to produce toluene from phenylalanine and other phenyl precursors, as well as phenol from tyrosine. This is of interest because toluene is normally considered to be a tracer of anthropogenic pollution in lakes, but T. auensis represents a biogenic source of toluene. Other than Aeromonas hydrophila subsp. hydrophila, T. auensis strain TA 4T is the only other member in the family Aeromonadaceae with a completely sequenced type-strain genome. The 3,471,292-bp chromosome with a total of 3,288 protein-coding and 116 RNA genes was sequenced as part of the DOE Joint Genome Institute Program JBEI 2008.
Date: October 4, 2011
Creator: Chertkov, Olga; Copeland, Alex; Lucas1, Susa; Lapidus, Alla; Berry, KerrieW.; Detter, JohnC. et al.
Partner: UNT Libraries Government Documents Department

Complete genome sequence of Acidimicrobium ferrooxidans type strain (ICPT)

Description: Acidimicrobium ferrooxidans (Clark and Norris 1996) is the sole and type species of the genus, which until recently was the only genus within the actinobacterial family Acidimicrobiaceae and in the order Acidomicrobiales. Rapid oxidation of iron pyrite during autotrophic growth in the absence of an enhanced CO2 concentration is characteristic for A. ferrooxidans. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the order Acidomicrobiales, and the 2,158,157 bp long single replicon genome with its 2038 protein coding and 54 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
Date: May 20, 2009
Creator: Clum, Alicia; Nolan, Matt; Lang, Elke; Glavina Del Rio, Tijana; Tice, Hope; Copeland, Alex et al.
Partner: UNT Libraries Government Documents Department

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

Description: 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.
Date: May 20, 2009
Creator: Land, Miriam; Lapidus, Alla; Mayilraj, Shanmugam; Chen, Feng; Copeland, Alex; Glavina Del Rio, Tijana et al.
Partner: UNT Libraries Government Documents Department

Complete genome sequence of Capnocytophaga ochracea type strain (VPI 2845T)

Description: Capnocytophaga ochracea (Prevot et al. 1956) Leadbetter et al. 1982 is the type species of the genus Capnocytophaga. It is of interest because of its location in the Flavobacteriaceae, a genomically yet uncharted family within the order Flavobacteriales. The species grows as fusiform to rod shaped cells which tend to form clumps and are able to move by gliding. C. ochracea is known as a capnophilic organism with the ability to grow under anaerobic as well as under aerobic conditions (oxygen concentration larger than 15percent), here only in the presence of 5percent CO2. Strain VPI 2845T, the type strain of the species, is portrayed in this report as a gliding, Gram-negative bacterium, originally isolated from a human oral cavity. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first completed genome sequence from the flavobacterial genus Capnocytophaga, and the 2,612,925 bp long single replicon genome with its 2193 protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
Date: May 20, 2009
Creator: Mavromatis, Konstantinos; Gronow, Sabine; Saunders, Elizabeth; Land, Miriam; Lapidus, Alla; Copeland, Alex et al.
Partner: UNT Libraries Government Documents Department

Complete genome sequence of Catenulispora acidiphila type strain (ID 139908T)

Description: Catenulispora acidiphila Busti et al. 2006 is the type species of the genus Catenulispora, and is of interest because of the rather isolated phylogenetic location of the genomically little studied suborder Catenulisporineae within the order Actinomycetales. C. acidiphilia is known for its acidophilic, aerobic lifestyle, but can also grow scantly under anaerobic conditions. Under regular conditions C. acidiphilia grows in long filaments of relatively short aerial hyphae with marked septation. It is a free living, non motile, Gram-positive bacterium isolated from a forest soil sample taken from a wooded area in Gerenzano, Italy. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first complete genome sequence of the actinobacterial family Catenulisporaceae, and the 10,467,782 bp long single replicon genome with its 9056 protein-coding and 69 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
Date: May 20, 2009
Creator: Copeland, Alex; Lapidus, Alla; Rio, Tijana GlavinaDel; Nolan, Matt; Lucas, Susan; Chen, Feng et al.
Partner: UNT Libraries Government Documents Department

Complete genome sequence of Cryptobacterium curtum type strain (12-3T)

Description: Cryptobacterium curtum Nakazawa et al. 1999 is the type species of the genus, and is of phylogenetic interest because of its very distant and isolated position within the family Coriobacteriaceae. C. curtum is an asaccharolytic, opportunistic pathogen with a typical occurrence in the oral cavity, involved in dental and oral infections like periodontitis, inflammations and abscesses. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the actinobacterial family Coriobacteriaceae, and this 1,617,804 bp long single replicon genome with its 1364 protein-coding and 58 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
Date: May 20, 2009
Creator: Mavromatis, Konstantinos; Pukall, Rudiger; Rohde, Christine; Sims, David; Brettin, Thomas; Kuske, Cheryl et al.
Partner: UNT Libraries Government Documents Department

Complete genome sequence of Dyadobacter fermentans type strain (NS114T)

Description: Dyadobacter fermentans (Chelius MK and Triplett EW, 2000) is the type species of the genus Dyadobacter. It is of phylogenetic interest because of its location in the Cytophagaceae, a very diverse family within the order 'Sphingobacteriales'. D. fermentans has a mainly respiratory metabolism, stains Gram-negative, is non-motile and oxidase and catalase positive. It is characterized by the production of cell filaments in ageing cultures, a flexirubin-like pigment and its ability to ferment glucose, which is almost unique in the aerobically living members of this taxonomically difficult family. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the 'sphingobacterial' genus Dyadobacter, and this 6,967,790 bp long single replicon genome with its 5804 protein-coding and 50 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
Date: May 20, 2009
Creator: Lang, Elke; Lapidus, Alla; Chertkov, Olga; Brettin, Thomas; Detter, John C.; Han, Cliff et al.
Partner: UNT Libraries Government Documents Department

Complete genome sequence of Leptotrichia buccalis type strain (C-1013-bT)

Description: Leptotrichia buccalis (Robin 1853) Trevisan 1879 is the type species of the genus, and is of phylogenetic interest because of its isolated location in the sparsely populated and neither taxonomically nor genomically adequately accessed family 'Leptotrichiaceae' within the phylum 'Fusobacteria'. Species of Leptotrichia are large fusiform non-motile, non-sporulating rods, which often populate the human oral flora. L. buccalis is anaerobic to aerotolerant, and saccharolytic. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first complete genome sequence of the order 'Fusobacteriales' and no more than the second sequence from the phylum 'Fusobacteria'. The 2,465,610 bp long single replicon genome with its 2306 protein-coding and 61 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
Date: May 20, 2009
Creator: Ivanova, Natalia; Gronow, Sabine; Lapidus, Alla; Copeland, Alex; Glavina Del Rio, Tijana; Nolan, Matt et al.
Partner: UNT Libraries Government Documents Department

Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3T)

Description: Pedobacter heparinus (Payza and Korn 1956) Steyn et al. 1998 comb. nov. is the type species of the rapidly growing genus Pedobacter within the family Sphingobacteriaceae of the phylum 'Bacteroidetes'. P. heparinus is of interest, because it was the first isolated strain shown to grow with heparin as sole carbon and nitrogen source and because it produces several enzymes involved in the degradation of mucopolysaccharides. All available data about this species are based on a sole strain that was isolated from dry soil. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first report on a complete genome sequence of a member of the genus Pedobacter, and the 5,167,383 bp long single replicon genome with its 4287 protein-coding and 54 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
Date: May 20, 2009
Creator: Han, Cliff; Spring, Stefan; Lapidus, Alla; Glavina Del Rio, Tijana; Tice, Hope; Copeland, Alex et al.
Partner: UNT Libraries Government Documents Department

Complete genome sequence of Saccharomonospora viridis type strain (P101T)

Description: Saccharomonospora viridis (Schuurmans et al. 1956) Nonomurea and Ohara 1971 is the type species of the genus Saccharomonospora which belongs to the family Pseudonocardiaceae. S. viridis is of interest because it is a Gram-negative organism classified amongst the usually Gram-positive actinomycetes. Members of the species are frequently found in hot compost and hay, and its spores can cause farmer?s lung disease, bagassosis, and humidifier fever. Strains of the species S. viridis have been found to metabolize the xenobiotic pentachlorophenol (PCP). The strain described in this study has been isolated from peat-bog in Ireland. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the family Pseudonocardiaceae, and the 4,308,349 bp long single replicon genome with its 3906 protein-coding and 64 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
Date: May 20, 2009
Creator: Pati, Amrita; Sikorski, Johannes; Nolan, Matt; Lapidus, Alla; Copeland, Alex; Glavina Del Rio, Tijana et al.
Partner: UNT Libraries Government Documents Department

Complete genome sequence of Desulfomicrobium baculatum type strain (XT)

Description: 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.
Date: May 20, 2009
Creator: Copeland, Alex; Spring, Stefan; Goker, Markus; Schneider, Susanne; Lapidus, Alla; Glavina Del Rio, Tijana et al.
Partner: UNT Libraries Government Documents Department

The Complete Genome Sequence of Bacillus thuringiensis AlHakam

Description: Bacillus thuringiensis is an insect pathogen that is widelyused as a biopesticide (3). Here we report the finished, annotated genomesequence of B. thuringiensis Al Hakam, which was collected in Iraq by theUnited Nations Special Commission (2).
Date: April 1, 2007
Creator: Challacombe, Jean F.; Altherr, Michael R.; Xie, Gary; Bhotika,Smriti S.; Brown, Nancy; Bruce, David et al.
Partner: UNT Libraries Government Documents Department