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Final technical report for DOE DE-FG02-02ER63472

Description: This document is the final report for DOE grant number DE-FG02-02ER63472: "The impact of enhanced nitrogen fixation on carbon sequestration: a reassessment of the inorganic carbon system in LNLC regions" to Patricia L. Yager at the University of Georgia School of Marine Programs. This project examined the inorganic carbon system associated with nitrogen fixation in the “low nutrient low chlorophyll” (LNLC) regions of the western tropical North Atlantic (WTNA) and subtropical Pacific Oceans. Total dissolved inorganic carbon (DIC) and alkalinity (ALK) data were measured on seven expeditions. Data have been finalized, checked for quality assurance, and uploaded to the Carbon Dioxide Information Analysis Center website (http://cdiac.ornl.gov/). Two manuscripts using this data are published or in press so far and we are current working on two others. The first (Cooley and Yager, 2006, JGR) uses a mixing model to remove the dilution effects of the Amazon River from the WTNA inorganic carbon data set. Once the physical effect is removed, the paper then estimates net community production (NCP) for each station. Enhanced rates of production (over respiration) are seen in the river plume, establishing a large biogenic atmospheric carbon sink in this region that is otherwise a source of carbon to the atmosphere. We note that this sink occurs in the absence of a measurable nitrate flux, and correlates well with the abundance of diatoms containing endosymbiotic diazotrophs, so it must be supported by nitrogen fixation. The second manuscript (Cooley et al., in press, GBC) compares our WTNA data (from Winter 2001, Spring 2001, and Summer 2003) to previously collected datasets (Ternon et al. 2000, Kortzinger et al. 2003) for the purposes of identifying seasonal and interannual variability in Amazon River-associated carbon sequestration. For the mid-salinity regions of the plume only, we estimate a carbon sink of 15±6 TgC per year. ...
Date: June 27, 2007
Creator: Yager, Patricia L.
Partner: UNT Libraries Government Documents Department

Phytoremediation of Ionic and Methylmercury Pollution

Description: Phytoremediation is defined as the use of plants to extract, resist, detoxify, and/or sequester toxic environmental pollutants. The long-term goal of the proposed research is to develop and test highly productive, field-adapted plant species that have been engineered for the phytoremediation of mercury. A variety of different genes, which should enable plants to clean mercury polluted sites are being tested as tools for mercury phytoremediation, first in model laboratory plants and then in potential field species.
Date: January 20, 2006
Creator: Meagher, Richard
Partner: UNT Libraries Government Documents Department

Identification of Novel Cell Wall Components

Description: Our DOE Biosciences-funded work focused on the fungal cell wall and morphogenesis. We are especially interested in how new cell wall material is targeted to appropriate areas for polar (asymmetric) growth. Polar growth is the only way that filamentous fungi explore the environment to find suitable substrates to degrade. Work funded by this grant has resulted in a total of twenty peer-reviewed publications. In work funded by this grant, we identified nine Aspergillus nidulans temperature-sensitive (ts) mutants that fail to send out a germ tube and show a swollen cell phenotype at restrictive temperature, the swo mutants. In other organisms, a swollen cell phenotype is often associated with misdirected growth or weakened cell walls. Our work shows that several of the A. nidulans swo mutants have defects in the establishment and maintenance of polarity. Cloning of several swo genes by complementation also showed that secondary modification of proteins seems is important in polarity. We also investigated cell wall biosynthesis and branching based on leads in literature from other organisms and found that branching and nuclear division are tied and that the cell wall reorganizes during development. In our most recent work we have focused on gene expression during the shift from isotropic to polar growth. Surprisingly we found that genes previously thought to be involved only in spore formation are important in early vegetative growth as well.
Date: October 26, 2009
Creator: Momany, Michelle
Partner: UNT Libraries Government Documents Department

Biochemistry and genetics of autotrophy in Methanococcus

Description: The project investigated fundamental aspects of carbon metabolism and genetics in the methane-producing archaeon Methanococcus maripaludis. The project yielded 23 peer-reviewed publications and five reviews from 1997-2007. PDFs of the peer-reviewed publications are included in the next section. Some papers of special interest are listed below. The pathway of pyruvate biosynthesis was elucidated by a combination of biochemical and physiological studies. This work characterized the very oxygen sensitive pyruvate oxidoreductase and showed that the enzyme was irreversible under physiological conditions. Evidence for the flow of electrons from the energy coupling hydrogenase b (Ehb) was presented. These results were published in the following papers. Yang, Y.L., J.N. Gluska, and W.B. Whitman (2002) Intracellular pyruvate flux in the methane-producing archaeon Methanococcus maripaludis. Arch. Microbiol. 178: 493-498. Lin, W.C., Y.L. Yang, and W.B. Whitman (2003) The anabolic pyruvate oxidoreductase from Methanococcus maripaludis. Arch. Microbiol. 179: 444-456. Lin, W., and W.B. Whitman (2004) The importance of porE and porF in the anabolic pyruvate oxidoreductase of Methanococcus maripaludis. Arch. Microbiol. 181: 68-73. Porat, I., W. Kim, E.L. Hendrickson, Q. Xia, Y. Zhang, T. Wang, F. Taub, B.C. Moore, I.J. Anderson, M. Hackett, J.A. Leigh, and W.B. Whitman (2006) Disruption of the Ehb hydrogenase operon limits anabolic CO2 assimilation in the archaeon Methanococcus maripaludis. J. Bacteriol. 188: 1373-1380. The presence of a novel pathway of aromatic amino acid biosynthesis was discovered and elucidated as part of these studies. These results were published in the following papers. Tumbula, D. L., Q. Teng, M. G. Bartlett, and W. B. Whitman (1997) Ribose biosynthesis and evidence for an alternative first step in the common aromatic amino acid pathway in Methanococcus maripaludis. J. Bacteriol. 179:6010-6013. Porat, I., B.W. Waters, Q. Teng, and W.B. Whitman (2004) Two biosynthetic pathways for the aromatic amino acids in the archaeon Methanococcus maripaludis. J. Bacteriol. ...
Date: March 31, 2009
Creator: Whitman, William B.
Partner: UNT Libraries Government Documents Department

Structures and Functions of Oligosaccharins: The Role of Endoglycanases

Description: The research proposed will investigate two projects that involve studies of the chemistry and biology of protein/protein and protein/carbohydrate interactions involved in host/pathogen interactions. Specifically, the projects involve (i) the interactions between fungal endopolygalacturonases and plant polygalacturonase-inhibiting proteins and (ii) the interactions between fungal endoxylanases and plant arabinoxylans. During pathogenesis fungi secrete families of endoglycanases that fragment the cell wall polysaccharides of the plant host. The result of endoglycanase action on cell wall polysaccharides can include weakening of the wall, penetration of host cells by the pathogen, solubilization of carbohydrate nutrients, and formation of oligosaccharins (oligosaccharides with regulatory function) that can stimulate plant defenses. We have made significant advances during the last funding period to support the hypothesis that the outcome of attempted pathogenesis can be influenced by protein/protein and protein/carbohydrate interactions in the extracellular matrices of the host and pathogen. We plan to expand on those successes by further exploring the mechanism of action of the endoglycanases and their plant-derived inhibitors, the expression of the various members of the endoglycanase families at various stages of infection and their role in the release of oligosaccharins and in pathogenicity, as well as the role played by the polysaccharide substrates in both pathogenicity and endoglycanase-inhibitor interactions.
Date: December 5, 2008
Creator: Bergmann, Carl W.
Partner: UNT Libraries Government Documents Department

Biorefinery and Carbon Cycling Research Project

Description: In this project we focused on several aspects of technology development that advances the formation of an integrated biorefinery. These focus areas include: [ 1] pretreatment of biomass to enhance quality of products from thermochemical conversion; [2] characterization of and development of coproduct uses; [3] advancement in fermentation of lignocellulosics and particularly C5 and C6 sugars simultaneously, and [ 4] development of algal biomass as a potential substrate for the biorefinery. These advancements are intended to provide a diverse set of product choices within the biorefinery, thus improving the cost effectiveness of the system. Technical effectiveness was demonstrated in the thermochemical product quality in the form of lower tar production, simultaneous of use of multiple sugars in fermentation, use ofbiochar in environmental (ammonia adsorption) and agricultural applications, and production of algal biomass in wastewaters. Economic feasibility of algal biomass production systems seems attractive, relative to the other options. However, further optimization in all paths, and testing/demonstration at larger scales are required to fully understand the economic viabilities. The coproducts provide a clear picture that multiple streams of value can be generated within an integrated biorefinery, and these include fuels and products.
Date: June 8, 2012
Creator: Das, K. C., Adams; Thomas, T; Eiteman, Mark A; Kastner, James R; Mani, Sudhagar & Adolphson, Ryan
Partner: UNT Libraries Government Documents Department

Phytoremediation of ionic and methylmercury pollution

Description: Our long-term goal is to enable highly productive plant species to extract, resist, detoxify, and sequester the toxic elemental pollutants, like the heavy metal mercury. Our current working hypothesis is that transgenic plants controlling the transport, chemical speciation, electrochemical state. volatilization, and aboveground binding of mercury will: a) tolerate mercury and grow rapidly in mercury contaminated environments; b) prevent methylmercury from entering the food chain; c) remove mercury from polluted soil and . water; and d) hyperaccumulate mercury in aboveground tissues for later harvest. Progress toward these specific aims is reported: to increase the transport of mercury into roots and to aboveground vegetative organs; to increase biochemical sinks and storage for mercury in leaves; to increase leaf cell vacuolar storage of mercury; and to demonstrate that several stacked transgenes, when functioning in concert, enhance mercury resistance and hyperaccumulation to high levels.
Date: April 28, 2010
Creator: Meagher, Richard B
Partner: UNT Libraries Government Documents Department

Characterization of Laccase-like Multicopper Oxidases (LMCOs) in Arabidopsis thaliana

Description: Laccase-like multicopper oxidases (LMCOs) have repeatedly been associated with the process of lignification in plants, and previous work suggested that these enzymes might be acting as specific marker for highly localized, small-scale lignification events in tissues not typically thought of as lignified. However, plant LMCOs typically occur as members of gene families and different family members can display disparate enzyme activities and overlapping patterns of expression in bulk tissues. This study used reporter genes and knockout mutants to document the involvement of a specific Arabidopsis thaliana LMCO family member (At2g30210 ) in early root development, specifically with development of endodermal tissues. Expression of the gene product was found to be under the control of sucrose levels, but the gene also responded to fluctuations in salt concentrations. The expression patterns of this gene were consistent with its involvement in the formation of suberin in the Casparian strip of root endodermis. An additional LMCO (At5g58910) displayed a more generalized expression in the radicles emergent seedlings. Additional members of the Arabidopsis LMCO family (At2g29130, At5g01190, and At5g05390) were also investigated with reporter gene constructs and knockout mutants. Expression of these LMCOs was associated with lignifying xylem, and the genes had over-lapping expression. Single knockout mutants did not display obvious phenotypes, suggesting that the gene products might have degenerate functionality that could compensate for loss of a single LMCO function.
Date: June 9, 2008
Creator: Dean, Jeffrey F.D.
Partner: UNT Libraries Government Documents Department

Process Design for the Biocatalysis of Value-Added Chemicals from Carbon Dioxide

Description: This report describes results toward developing a process to sequester CO{sub 2} centered on the enzyme pyruvate carboxylase. The process involves the use of bacteria to convert CO{sub 2} and glucose as a co-substrate and generates succinic acid as a commodity chemical product. The phases of research have included strain development and process development. Though we continue to work on one important component of strain development, the research has principally focused on process development. In the previous year we constructed several strains which would serve as templates for the CO{sub 2} sequestration, including the knock-out of genes involved in the formation of undesirable byproducts. This project period the focus has been on the integration of the pyruvate carboxylase gene (pyc) onto the E. coli chromosome. This has proven to be a difficult task because of relatively low expression of the gene and resulting low enzyme activity when only one copy of the gene is present on the chromosome. Several molecular biology techniques have been applied, with some success, to improve the level of protein activity as described herein. Progress in process development has come as a result of conducting numerous fermentation experiments to select optimal conditions for CO{sub 2} sequestration. This process-related research has progressed in four areas. First, we have clarified the range of pH which results in the optimal rate of sequestration. Second, we have determined how the counterion used to control the pH affects the sequestration rate. Third, we have determined how CO{sub 2} gas phase composition impacts sequestration rate. Finally, we have made progress in determining the affect of several potential gaseous impurities on CO{sub 2} sequestration; in particular we have completed a study using NO{sub 2}. Although the results provide significant guidance as to process conditions for CO{sub 2} sequestration and succinate production, in some ...
Date: July 31, 2006
Creator: Eiteman, Mark A.
Partner: UNT Libraries Government Documents Department

Development of UV-LED Phosphor Coatings for High Efficiency Solid State Lighting

Description: The University of Georgia, in collaboration with GE Global Research, is investigating the relevant quenching mechanism of phosphor coatings used in white light devices based on UV LEDs in a focused eighteen month program. The final goal is the design of high-efficacy white UV-LEDs through improved and optimized phosphor coatings. At the end of the first year, we have reached a fundamental understanding of quenching processes in UV-LED phosphors and have observed severe quenching in standard devices under extreme operating conditions. Relationships are being established that describe the performance of the phosphor as a function of photon flux, temperature, and phosphor composition. These relationships will provide a road map for the design of efficient white light LEDs during the final six months of the project.
Date: January 1, 2005
Creator: Happek, U.
Partner: UNT Libraries Government Documents Department

Development of Efficient UV-LED Phosphor Coatings for Energy Saving Solid State Lighting

Description: The University of Georgia, in collaboration with GE Global Research, has investigated the relevant quenching mechanism of phosphor coatings used in white light devices based on UV LEDs. The final goal of the project was the design and fabrication of a high-efficacy white light UV-LED device through improved geometry and optimized phosphor coatings. At the end of the research period, which was extended to seamlessly carry over the research to a follow-up program, we have demonstrated a two-fold improvement in the conversion efficiency of a white light LED device, where the increase efficacy is due to both improved phosphor quantum efficiency and lamp geometry. Working prototypes have been displayed at DOE sponsored meetings and during the final presentation at the DOE Headquarters in Washington, DC. During the first phase of the project, a fundamental understanding of quenching processes in UV-LEDs was obtained, and the relationships that describe the performance of the phosphor as a function of photon flux, temperature, and phosphor composition were established. In the second phase of the project, these findings were then implemented to design the improved UV-LED lamp. In addition, our research provides a road map for the design of efficient white light LEDs, which will be an important asset during a follow-up project led by GE.
Date: May 15, 2006
Creator: Happek, Uwe
Partner: UNT Libraries Government Documents Department

Mechanisms and Determinants of RNA Turnover: Plant IRESs and Polycistrons for Metabolic Engineering

Description: There is a strong need for tools that allow multiple transgenes to be expressed in genetically engineered plants. For the last 30 years it has been believed that nearly all eukaryotic mRNAs were monocistronic, with ribosomes entering at the 5' end and scanning through the 5'UTR to the first AUG codon. It is now clear that perhaps 3% of vertebrate and yeast mRNAs utilize IRESs (Internal Ribosome Entry Sites) within their 5'UTRs to promote the internal entry of ribosomes to mRNAs and subsequent translation of protein without scanning. The working hypothesis behind this proposal is that IRES sequences function in plants and can be used to engineer the efficient co-expression of multiple proteins from polycistronic transcripts. Our goal was to translate multiple proteins from single polycistroic mRNAs. We cloned four IRESs from the following sources: CrTMV (plant virus), EMCV (human encephalomyocarditis virus), eIF4G (human), and c-myc (human). All four IRES were cloned into a specially designed test vector with the strong constitutive ACT2 actin regulatory sequences and flanked by multicloning sites for two reporter genes. These four IRESs were tested in three different test systems with strong paired reporter activities: two fluorescent proteins, two mercury resistance enzymes, and two biosynthetic enzymes making thiolpeptides. All of the four IRES constructs with the fluorescent protein reporter genes were tested for transient expression after particle gun bombardment of tobacco BY2 cells. Three of the IRESs gave reasonable activity (10%-40%) for the second cistron fluorescent reporter (DsRFP) relative to the first cistron reporter (GFP). As a control, translational blocking sequence placed at the 5' end of duplicate constructs had little effect on activity from the second cistron, but blocked the first cistron. These initial positive data lead us to examine the four IRES constructs with three pairs of reporters in hundreds of transgenic Arabidopsis ...
Date: August 1, 2002
Creator: Meagher, Richard B.
Partner: UNT Libraries Government Documents Department