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Controlling incipient oxidation of pyrite for improved rejection. Eighth quarterly technical progress report, July 1, 1994--September 30, 1994

Description: The major objectives of this work are (1) to determine the Eh-pH conditions under which pyrite is stable, (2) to determine the mechanism of the initial stages of pyrite oxidation and (3) to determine if the semi-conducting properties of pyrite effects its oxidation behavior. It is known that moderate oxidation of pyrite produces a hydrophobic surface product. This hydrophobic product makes it extremely difficult to depress pyrite in coal flotation circuits. The eventual objective of this work is to prevent pyrite oxidation in order to better depress pyrite in coal flotation circuits. In this work clean, unoxidized pyrite surfaces are being produced by fracturing pyrite electrodes in an electrochemical cell. It has been shown that pyrite assumes a unique potential referred to as the ``stable potential`` at the instance it is fractured and that this potential is several hundred millivolts more negative than the steady state mixed potential of pyrite. It has also been shown that by holding the potential of pyrite at its stable potential during fracture, pyrite undergoes neither oxidation nor reduction. It has also been found that fresh pyrite surfaces created by fracture in an electrochemical begin to oxidize at potentials that are about 200 mV more negative than the potentials reported in the literature for pyrite oxidation. This is attributed to the fact that most work on pyrite has employed polished electrodes that have pre-existing oxidation products on the surface. The existence of a pH dependent stable potential for freshly fractured pyrite electrodes was based on studies conducted mainly on pyrite from Peru.
Date: December 31, 1994
Creator: Yoon, R.H. & Richardson, P.E.
Partner: UNT Libraries Government Documents Department

Controlling incipient oxidation of pyrite for improved rejection. Technical progress report for the ninth quarter, October 1--December 31, 1994

Description: The major objectives of this work are (1) to determine the Eh-pH conditions under which pyrite is stable, (2) to determine the mechanism of the initial stages of pyrite oxidation, and (3) to determine if the semi-conducting properties of pyrite effects its oxidation behavior. It is known that moderate oxidation of pyrite produces a hydrophobic surface product. This hydrophobic product makes it extremely difficult to depress pyrite in coal flotation circuits. The eventual objective of this work is to prevent pyrite oxidation in order to better depress pyrite in coal flotation circuits. It has been shown that by holding the potential of pyrite at its stable potential during fracture, pyrite undergoes neither oxidation nor reduction. It has also been found that fresh pyrite surfaces created by fracture in an electrochemical begin to oxidize at potentials that are about 200 mV more negative than the potentials reported in the literature for pyrite oxidation. This report period, electrochemical impedance spectroscopy (EIS) studies were continued. As discussed in the seventh quarterly progress report, the impedance of pyrite does not show the characteristics expected for either semi-conducting or metallic electrodes. Additional studies were conducted to confirm the anomalous impedance behavior. For this purpose, freshly fractured surfaces were progressively polished on 600 and 1,200 grit silicon carbide paper, and with 0.3 {micro} {alpha}-alumina and 0.05 {micro} {gamma}-alumina micropolish. Polishing is known to introduce defects in the lattice structure of semi-conducting electrodes and it was anticipated that the defects would effect the interfacial capacitance.
Date: July 1, 1995
Creator: Yoon, R.H. & Richardson, P.E.
Partner: UNT Libraries Government Documents Department

ZIRCONIUM HAZARDS RESEARCH. Summary Report No. 3655 for September 1, 1956 to August 31, 1957

Description: The sensitivity characteristics of a variety of Zr samples such as sponge, scrap, powder and process materials were studicd. Of particular interest was the determination of the relative seasitivity of these materials to such stimuli as impact, friction, electrostatic discharge, and heat. A study of the zirconium--water reaction at relatively low temperature was initiated. In general, scrap and sponge were relatively insensitive to impact. Only one proeess material, the distillation residue, exhibited any pyrophoric tendencies in this test. As anticipated, the majority of the samples tested were somewhat sensitive to friction. The dry distillation residues and Ca-reduced Zr powders, which had frequency rates of 100% in most cases, were the most sensitive of all the samples tested. Sponge was moderately sensitive, but the variation in sensitivity could not be correlated with either particle size or chemical impurities. Neither the Zr or Zircaloy scraps in the form of chips and turnings were very sensitive. The maierial which proved to be most insensitive to friction was the vapor phase residue. A frequency rate of zero was noted for all the samples tested. Using a condenser discharge to heat wire samples rapidly in aa inert atmosphere to a temperature well above the melting point, an attempt was made to determine the effect of stress on the pyrophoricity of Zr. It was found that the minimum energy requirements for fragmentation of a pure Zr wire are reduced by the application of mechanically induced stresses and bv the addition of chemical impurities such as C and/or H/sub 2/, Although the experimental phase of the study of the zirconium--water reaction has been barely- initiated, there is some evidence to indicate thai pre-treatment of a sample with N, at elevated temperatures does promote the oxidation reaction with steam. (auth)
Date: August 31, 1957
Creator: Herickes, J.A.; Richardson, P.A.; Weiss, M. & Gelernter, G.
Partner: UNT Libraries Government Documents Department

Controlling incipient oxidation of pyrite for improved rejection. Final report

Description: It is well known that superficial oxidation of pyrite produces a hydrophobic sulfur-rich surface and creates problems in separating the mineral from coal using surface-based processes such as flotation and agglomeration. Numerous studies of pyrite oxidation have been conducted but most of them were concerned with the advanced stages of oxidation, and as a result it was not possible to establish a relationship between oxidation and flotation behavior. A better understanding of the mechanisms and kinetics of the incipient oxidation reactions, which may vary with the origin, morphology, texture, and solid state properties of pyrite, can lead to the development of new processes that can improve pyrite rejection from coal. This project is aimed at better understanding of the mechanisms involved during the initial stages of pyrite oxidation to foster the development of advanced coal cleaning technologies. Studies were conducted by fracturing pyrite electrodes in-situ in an electrochemical cell to create virgin surfaces. Electrochemical and photoelectrochemical techniques were employed to characterize the incipient oxidation of pyrite in aqueous solutions. Microflotation tests were conducted to obtain information on the hydrophobicity of pyrite under controlled E{sub h} and pH conditions, and the results were correlated with electrochemical studies.
Date: April 1, 1996
Creator: Yoon, R.H.; Richardson, P.E. & Tao, D.P.
Partner: UNT Libraries Government Documents Department

Development of enhanced sulfur rejection processes

Description: Research at Virginia Tech led to the development of two complementary concepts for improving the removal of inorganic sulfur from many eastern U.S. coals. These concepts are referred to as Electrochemically Enhanced Sulfur Rejection (EESR) and Polymer Enhanced Sulfur Rejection (PESR) processes. The EESR process uses electrochemical techniques to suppress the formation of hydrophobic oxidation products believed to be responsible for the floatability of coal pyrite. The PESR process uses polymeric reagents that react with pyrite and convert floatable middlings, i.e., composite particles composed of pyrite with coal inclusions, into hydrophilic particles. These new pyritic-sulfur rejection processes do not require significant modifications to existing coal preparation facilities, thereby enhancing their adoptability by the coal industry. It is believed that these processes can be used simultaneously to maximize the rejection of both well-liberated pyrite and composite coal-pyrite particles. The project was initiated on October 1, 1992 and all technical work has been completed. This report is based on the research carried out under Tasks 2-7 described in the project proposal. These tasks include Characterization, Electrochemical Studies, In Situ Monitoring of Reagent Adsorption on Pyrite, Bench Scale Testing of the EESR Process, Bench Scale Testing of the PESR Process, and Modeling and Simulation.
Date: March 1, 1996
Creator: Yoon, R.H.; Luttrell, G.H.; Adel, G.T. & Richardson, P.E.
Partner: UNT Libraries Government Documents Department

Development of enhanced sulfur rejection processes. Final technical progress report, third quarter (8. quarterly report), July 1--September 30, 1994

Description: Pyrite becomes hydrophobic upon superficial oxidation and floats without a collector. The flotation begins to occur at potentials above the stable potentials identified by the chronoamperometry experiments conducted with freshly fractured pyrite. This finding suggests that iron polysulfide, formed during the initial stages of oxidation, is responsible for the flotation. The collectorless flotation is suppressed above the potential where the mineral is aggressively oxidized, forming iron hydroxide and soluble sulfoxy species. The collectorless flotation is less significant at pH 9.2 than at pH 4.6, possibly due to the formation of iron hydroxide. At pH 9.2, the collectorless flotation increases in the presence of EDTA and hydrocarbon oil. The collectorless flotation of pyrite can be suppressed by galvanically coupling the mineral with reactive metals such as aluminum, manganese, and zinc. This effectively prevents the mineral from oxidation. The microflotation tests conducted with mono-sized pyrite samples show that the collectorless flotation can be suppressed effectively in the presence of metal powders. Bench-scale flotation experiments conducted using Denver laboratory flotation cell and a 2-inch diameter Microcel flotation column, also demonstrates that the collectorless flotation can be suppressed in the presence of the reactive metals. It has been established that the most important parameters determining the effectiveness of suppressing pyrite flotation by the galvanic coupling technique are the surface area of the galvanic contractors and the solids concentration of the slurry during conditioning.
Date: March 20, 1996
Creator: Yoon, R.H.; Luttrell, G.H.; Tao, D.P.; Lu, M.X. & Richardson, P.E.
Partner: UNT Libraries Government Documents Department

Genome of Methylobacillus flagellatus, Molecular Basis for Obligate Methylotrophy, and Polyphyletic Origin of Methylotrophy

Description: Along with methane, methanol and methylated amines represent important biogenic atmospheric constituents; thus, not only methanotrophs but also nonmethanotrophic methylotrophs play a significant role in global carbon cycling. The complete genome of a model obligate methanol and methylamine utilizer, Methylobacillus flagellatus (strain KT) was sequenced. The genome is represented by a single circular chromosome of approximately 3 Mbp, potentially encoding a total of 2,766 proteins. Based on genome analysis as well as the results from previous genetic and mutational analyses, methylotrophy is enabled by methanol and methylamine dehydrogenases and their specific electron transport chain components, the tetrahydromethanopterin-linked formaldehyde oxidation pathway and the assimilatory and dissimilatory ribulose monophosphate cycles, and by a formate dehydrogenase. Some of the methylotrophy genes are present in more than one (identical or nonidentical) copy. The obligate dependence on single-carbon compounds appears to be due to the incomplete tricarboxylic acid cycle, as no genes potentially encoding alpha-ketoglutarate, malate, or succinate dehydrogenases are identifiable. The genome of M. flagellatus was compared in terms of methylotrophy functions to the previously sequenced genomes of three methylotrophs, Methylobacterium extorquens (an alphaproteobacterium, 7 Mbp), Methylibium petroleiphilum (a betaproteobacterium, 4 Mbp), and Methylococcus capsulatus (a gammaproteobacterium, 3.3 Mbp). Strikingly, metabolically and/or phylogenetically, the methylotrophy functions in M. flagellatus were more similar to those in M. capsulatus and M. extorquens than to the ones in the more closely related M. petroleiphilum species, providing the first genomic evidence for the polyphyletic origin of methylotrophy in Betaproteobacteria.
Date: July 24, 2007
Creator: Chistoserdova, L; Lapidus, A; Han, C; Godwin, L; Saunders, L; Brettin, T et al.
Partner: UNT Libraries Government Documents Department

A Les Houches Interface for BSM Generators

Description: We propose to combine and slightly extend two existing 'Les Houches Accords' to provide a simple generic interface between beyond-the-standard-model parton-level and event-level generators. All relevant information--particle content, quantum numbers of new states, masses, cross sections, parton-level events, etc.--is collected in one single file, which adheres to the Les Houches Event File (LHEF) standard.
Date: December 1, 2007
Creator: Alwall, J.; Boos, E.; Dudko, L.; Gigg, M.; Herquet, M.; Pukhov, A. et al.
Partner: UNT Libraries Government Documents Department

A Les Houches Interface for BSM Generators

Description: We propose to combine and slightly extend two existing 'Les Houches Accords' to provide a simple generic interface between beyond-the-standard-model parton-level and event-level generators. All relevant information--particle content, quantum numbers of new states, masses, cross sections, parton-level events, etc.--is collected in one single file, which adheres to the Les Houches Event File (LHEF) standard.
Date: January 23, 2008
Creator: Alwall, J.; Boos, E.; Dudko, L.; Gigg, M.; Herquet, M.; Pukhov, A. et al.
Partner: UNT Libraries Government Documents Department

Unusual Gene Order and Organization of the Sea Urchin Hox Cluster

Description: The highly consistent gene order and axial colinear expression patterns found in vertebrate hox gene clusters are less well conserved across the rest of bilaterians. We report the first deuterostome instance of an intact hox cluster with a unique gene order where the paralog groups are not expressed in a sequential manner. The finished sequence from BAC clones from the genome of the sea urchin, Strongylocentrotus purpuratus, reveals a gene order wherein the anterior genes (Hox1, Hox2 and Hox3) lie nearest the posterior genes in the cluster such that the most 3 gene is Hox5. (The gene order is : 5-Hox1, 2, 3, 11/13c, 11/13b, 11/13a, 9/10, 8, 7, 6, 5 - 3). The finished sequence result is corroborated by restriction mapping evidence and BAC-end scaffold analyses. Comparisons with a putative ancestral deuterostome Hox gene cluster suggest that the rearrangements leading to the sea urchin gene order were many and complex.
Date: October 11, 2005
Creator: Cameron, R A; Rowen, L; Nesbitt, R; Bloom, S; Rast, J P; Berney, K et al.
Partner: UNT Libraries Government Documents Department

Large microchannel array fabrication and results for DNA sequencing

Description: We have developed a process for the production of microchannel arrays on bonded glass substrates up to I4 x 58 cm, for DNA sequencing. Arrays of 96 and 384 microchannels, each 46 cm long have been built. This technology offers significant advantages over discrete capillaries or conventional slab-gel approaches. High throughput DNA sequencing with over 550 base pairs resolution has been achieved. With custom fabrication apparatus, microchannels are etched in a borosilicate substrate, and then fusion bonded to a top substrate 1.1 mm thick that has access holes formed in it. SEM examination shows a typical microchannel to be 40 x 180 micrometers by 46 cm Iong; the etch is approximately isotropic, leaving a key undercut, for forming a rounded channel. The surface roughness at the bottom of the 40 micrometer deep channel has been profilometer measured to be as low as 20 nm; the roughness at the top surface was 2 nm. Etch uniformity of about 5% has been obtained using a 22% vol. HF / 78% Acetic acid solution. The simple lithography, etching, and bonding of these substrates enables efficient production of these arrays and extremely precise replication From master masks and precision machining with a mandrel. Keywords: microchannels, microchannel plates, DNA sequencing, electrophoresis, borosilicate glass
Date: January 7, 1999
Creator: Pastrone, R L; Balch, J W; Brewer, L R; Copeland, A C; Davidson , J C; Fitch, J P et al.
Partner: UNT Libraries Government Documents Department

The Calyptogena magnifica chemoautotrophic symbiont genome

Description: Chemoautotrophic endosymbionts are the metabolic cornerstone of hydrothermal vent communities, providing invertebrate hosts with nearly all of their nutrition. The Calyptogena magnifica (Bivalvia: Vesicomyidae) symbiont, Candidatus Ruthia magnifica, is the first intracellular sulfur-oxidizing endosymbiont to have its genome sequenced, revealing a suite of metabolic capabilities. The genome encodes major chemoautotrophic pathways as well as pathways for biosynthesis of vitamins, cofactors, and all 20 amino acids required by the clam.
Date: March 1, 2007
Creator: Newton, I.L.; Woyke, T.; Auchtung, T.A.; Dilly, G.F.; Dutton,R.J.; Fisher, M.C. et al.
Partner: UNT Libraries Government Documents Department

A microchannel electrophoresis DNA sequencing system

Description: Last year, the Joint Genome Institute was the third leading sequencing group in the world with over 20 million bases of human DNA finished. The goal of the human genome project is to sequence the 3 billion bases of human DNA sequence by 2003. In order to increase the DNA sequencing throughput of the Joint Genome Institute, we have developed a microchannel electrophoresis system. One critical new and unique element of this system is a process for production of 96 and 384 microchannels on bonded glass substrates up to 14 x 58 cm. In order to utilize these instruments for DNA production sequencing, we have been evaluating and implementing software to convert raw electropherograms into called DNA bases with an associated probability of error. Our original intent was to utilize the DNA base calling software known as Plan and Phred developed by the University of Washington. In our tests and evaluations of this software applied to microchannel data, we observed that the electropherograms are of a different statistical and underlying signal structure compared to slab gels. We have modified Plan and Phred to improve base calling performance for the microchannel data. In this paper, we will present 1) the microchannel DNA sequencing system and show the advantages compared to current slab gel and capillary systems. 2) The signal processing modules needed for DNA base calling including correction of multiple wavelength channels, signal averaging, non-uniform sampling, variable DNA mobility, and peak shape and spreading effects. 3) A comparison of the DNA base signatures in the raw data of microchannels vs. slab gels including some simple modeling results. This will be propagated through the base calling software to show the impact on DNA sequencing.
Date: February 1, 1999
Creator: Balch, J W; Bass, M S; Brewer, L R; Copeland, A C; Davidson, J C; Fitch, J P et al.
Partner: UNT Libraries Government Documents Department

A microchannel electrophoresis DNA sequencing system

Description: In order to increase the DNA sequencing throughput of the Joint Genome Institute, we have developed a microchannel electrophoresis system. The critical new and unique elements of this system include 1) a process for the production of arrays of 96 and 384 microchannels on bonded glass substrates up to 14 x 58 cm and 2) new sieving media for high resolution and high speed separations. With custom fabrication apparatus, microchannels are etched in a borosilicate substrate, and then fusion bonded to a top substrate 1.1 mm thick that has access holes formed in it. SEM examination shows a typical microchannel to be 40 micrometers deep x 180 micrometers wide by 46 cm long. This technology offers significant advantages over discrete capillaries or conventional slab-gel approaches. High throughput DNA sequencing with over 550 base pairs resolution has been achieved in roughly half the time of conventional sequencers. In February 1999, we begin a pre-production evaluation protocol for the microchannel and for three glass capillary electrophoresis systems (two from industry and one developed by Lawrence Berkeley National Laboratory for the Joint Genome Institute). In order to utilize these instruments for DNA production sequencing, we have been evaluating and implementing software to convert raw electropherograms into called DNA bases with an associated probability of error. Our original intent was to utilize the DNA base calling software known as Plan and Phred developed by the University of Washington. This software has been outstanding for our slab gel electrophoresis systems currently in the production facility. In our tests and evaluations of this software applied to microchannel data, we observed that the electropherograms are of a different statistical and underlying signal structure compared to slab gels. Even with substantial modifications to the software, base calling performance was not satisfactory for the microchannel data. In this paper, ...
Date: January 1, 1999
Creator: Madabhushi, R S; Warth, T; Balch, J W; Bass, M; Brewer, L R; Copeland, A C et al.
Partner: UNT Libraries Government Documents Department

Searching for R-parity violation at run-II of the tevatron.

Description: The authors present an outlook for possible discovery of supersymmetry with broken R-parity at Run II of the Tevatron. They first present a review of the literature and an update of the experimental bounds. In turn they then discuss the following processes: (1) resonant slepton production followed by R{sub P} decay, (a) via LQD{sup c} and (b) via LLE{sup c}; (2) how to distinguish resonant slepton production from Z{prime} or W{prime} production; (3) resonant slepton production followed by the decay to neutralino LSP, which decays via LQD{sup c}; (4) resonant stop production followed by the decay to a chargino, which cascades to the neutralino LSP; (5) gluino pair production followed by the cascade decay to charm squarks which decay directly via L{sub 1}Q{sub 2}D{sub 1}{sup c}; (6) squark pair production followed by the cascade decay to the neutralino LSP which decays via L{sub 1}Q{sub 2}D{sub 1}{sup c}; (7) MSSM pair production followed by the cascade decay to the LSP which decays (a) via LLE{sup c}, (b) via LQD{sup c}, and (c) via U{sup c}D{sup c}D{sup c}, respectively; and (8) top quark and top squark decays in spontaneous R{sub P}.
Date: June 22, 1999
Creator: Allanach, B.; Banerjee, S.; Berger, E. L.; Chertok, M.; Diaz, M. A.; Dreiner, H. et al.
Partner: UNT Libraries Government Documents Department

A Repository for Beyond-the-Standard-Model Tools

Description: To aid phenomenological studies of Beyond-the-Standard-Model (BSM) physics scenarios, a web repository for BSM calculational tools has been created. We here present brief overviews of the relevant codes, ordered by topic as well as by alphabet.
Date: May 1, 2005
Creator: Skands, P.; /Fermilab; Richardson, P.; Allanach, B.C.; Baer, H.; Belanger, G. et al.
Partner: UNT Libraries Government Documents Department

Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000

Description: The complete genomic sequence of Pseudomonas syringae pathovar syringae B728a (Pss B728a), has been determined and is compared with that of Pseudomonas syringae pv. tomato DC3000 (Pst DC3000). The two pathovars of this economically important species of plant pathogenic bacteria differ in host range and other interactions with plants, with Pss having a more pronounced epiphytic stage of growth and higher abiotic stress tolerance and Pst DC3000 having a more pronounced apoplastic growth habitat. The Pss B728a genome (6.1 megabases) contains a circular chromosome and no plasmid, whereas the Pst DC3000 genome is 6.5 mbp in size, composed of a circular chromosome and two plasmids. While a high degree of similarity exists between the two sequenced Pseudomonads, 976 protein-encoding genes are unique to Pss B728a when compared to Pst DC3000, including large genomic islands likely to contribute to virulence and host specificity. Over 375 repetitive extragenic palindromic sequences (REPs) unique to Pss B728a when compared to Pst DC3000 are widely distributed throughout the chromosome except in 14 genomic islands, which generally had lower GC content than the genome as a whole. Content of the genomic islands vary, with one containing a prophage and another the plasmid pKLC102 of P. aeruginosa PAO1. Among the 976 genes of Pss B728a with no counterpart in Pst DC3000 are those encoding for syringopeptin (SP), syringomycin (SR), indole acetic acid biosynthesis, arginine degradation, and production of ice nuclei. The genomic comparison suggests that several unique genes for Pss B728a such as ectoine synthase, DNA repair, and antibiotic production may contribute to epiphytic fitness and stress tolerance of this organism.
Date: July 14, 2005
Creator: Feil, H; Feil, W S; Chain, P; Larimer, F; DiBartolo, G; Copeland, A et al.
Partner: UNT Libraries Government Documents Department

Comparison of multiple ecogenomics methods for determining ecosystem function in uranium-contaminated environments

Description: Background: Bioremediation may offer the only feasiblestrategy for the nearly intractable problem of metal and radionuclidecontamination of soil and groundwater. To understand bioremediation incontaminated environments, it is critical to determine the organismspresent in these environments, analyze their responses to stressconditions, and elucidate functional position in the environment.Methods: We used multiple molecular techniques on both sediment andgroundwater to develop a better understanding of the functionalcapability and stress level within the microbial community inrelationship to over one hundred geochemical parameters. Due to the lowpH (3.5-4.5) and high contaminant levels (e.g., uranium) microbialdensities and activities were low. We used a phage polymeraseamplification system to construct large and small insert DNA libraries,performed metagenome sequencing, constructed clonal libraries of selectfunctional genes (SSU rRNA gene, nirK, nirS, amoA, pmoA, and dsrAB), useda SSU rDNA Phylochip microarray (9,000 taxa), and a functional gene array(23K genes). A complete comparison for community differences andsimilarities between the different techniques was assessed using severalbioinformatics techniques. Results: SSU rDNA analysis revealed thepresence of distinct bacterial phyla, including proteobacteria,acidobacteria, and planctomycetes along the contaminant gradient.Metagenome analysis identified many of the same organisms, and diversitywas lower in water than sediment. Analysis with functional gene arrays,phylochip, and specific probes for genes and organisms involved inbiogeochemical cycling of C, N, and S, metal resistance, stress response,and contaminant degradation suggested that the dominant species could bebiostimulated during in situ uranium reduction. Several other findings ofdifference and similarities between methods are presented. Conclusion:These systems biology field studies could be enabling for strategies toattenuate nletal and radionuclide contamination.
Date: January 10, 2007
Creator: Hazen, T.C.; Dehal, P.; Arkin, A.P.; Fields, M.W.; Keller, M.; Zhou, J. et al.
Partner: UNT Libraries Government Documents Department

The genome of obligately intracellular Ehrlichia canis revealsthemes of complex membrane structure and immune evasion strategies

Description: Ehrlichia canis, a small obligately intracellular, tick-transmitted, gram-negative, a-proteobacterium is the primary etiologic agent of globally distributed canine monocytic ehrlichiosis. Complete genome sequencing revealed that the E. canis genome consists of a single circular chromosome of 1,315,030 bp predicted to encode 925 proteins, 40 stable RNA species, and 17 putative pseudogenes, and a substantial proportion of non-coding sequence (27 percent). Interesting genome features include a large set of proteins with transmembrane helices and/or signal sequences, and a unique serine-threonine bias associated with the potential for O-glycosylation that was prominent in proteins associated with pathogen-host interactions. Furthermore, two paralogous protein families associated with immune evasion were identified, one of which contains poly G:C tracts, suggesting that they may play a role in phase variation and facilitation of persistent infections. Proteins associated with pathogen-host interactions were identified including a small group of proteins (12) with tandem repeats and another with eukaryotic-like ankyrin domains (7).
Date: September 1, 2005
Creator: Mavromatis, K.; Kuyler Doyle, C.; Lykidis, A.; Ivanova, N.; Francino, P.; Chain, P. et al.
Partner: UNT Libraries Government Documents Department

The Pathogenomic Sequence Analysis of B. cereus and B. Thuringiensis isolates closely related to Bacillus anthracis

Description: The sequencing and analysis of two close relatives of Bacillus anthracis are reported. AFLP analysis of over 300 isolates of B. cereus, B. thuringiensis and B. anthracis identified two isolates as being very closely related to B. anthracis. One, a B. cereus, BcE33L, was isolated from a zebra carcass in Nambia; the second, a B. thuringiensis, 97-27, was isolated from a necrotic human wound. The B. cereus appears to be the closest anthracis relative sequenced to date. A core genome of over 3,900 genes was compiled for the Bacillus cereus group, including B anthracis. Comparative analysis of these two genomes with other members of the B. cereus group provides insight into the evolutionary relationships among these organisms. Evidence is presented that differential regulation modulates virulence, rather than simple acquisition of virulence factors. These genome sequences provide insight into the molecular mechanisms contributing to the host range and virulence of this group of organisms.
Date: October 12, 2005
Creator: Han, C S; Xie, G; Challacombe, J F; Altherr, M R; Bhotika, S S; Bruce, D et al.
Partner: UNT Libraries Government Documents Department

The genome of the diatom Thalassiosira pseudonana: Ecology, evolution, and metabolism

Description: Diatoms are unicellular algae with plastids acquired by secondary endosymbiosis. They are responsible for {approx}20% of global carbon fixation. We report the 34 Mbp draft nuclear genome of the marine diatom, Thalassiosira pseudonana and its 129 Kbp plastid and 44 Kbp mitochondrial genomes. Sequence and optical restriction mapping revealed 24 diploid nuclear chromosomes. We identified novel genes for silicic acid transport and formation of silica-based cell walls, high-affinity iron uptake, biosynthetic enzymes for several types of polyunsaturated fatty acids, utilization of a range of nitrogenous compounds and a complete urea cycle, all attributes that allow diatoms to prosper in the marine environment. Diatoms are unicellular, photosynthetic, eukaryotic algae found throughout the world's oceans and freshwater systems. They form the base of short, energetically-efficient food webs that support large-scale coastal fisheries. Photosynthesis by marine diatoms generates as much as 40% of the 45-50 billion tonnes of organic carbon produced each year in the sea (1), and their role in global carbon cycling is predicted to be comparable to that of all terrestrial rainforests combined (2, 3). Over geological time, diatoms may have influenced global climate by changing the flux of atmospheric carbon dioxide into the oceans (4). A defining feature of diatoms is their ornately patterned silicified cell wall or frustule, which displays species-specific nano-structures of such fine detail that diatoms have long been used to test the resolution of optical microscopes. Recent attention has focused on biosynthesis of these nano-structures as a paradigm for future silica nanotechnology (5). The long history (over 180 million years) and dominance of diatoms in the oceans is reflected by their contributions to vast deposits of diatomite, most cherts and a significant fraction of current petroleum reserves (6). As photosynthetic heterokonts, diatoms reflect a fundamentally different evolutionary history from the higher plants that dominate photosynthesis ...
Date: September 1, 2004
Creator: Ambrust, E.V.; Berges, J.; Bowler, C.; Green, B.; Martinez, D.; Putnam, N. et al.
Partner: UNT Libraries Government Documents Department