Hydrogel Tracer Beads: The Development, Modification, and Testing of an Innovative Tracer for Better Understanding LNAPL Transport in Karst Aquifers

The goal of this specific research task is to develop proxy tracers that mimic contaminant movement to better understand and predict contaminant fate and transport in karst aquifers. Hydrogel tracer beads are transported as a separate phase than water and can used as a proxy tracer to mimic the transport of non-aqueous phase liquids (NAPL). They can be constructed with different densities, sizes & chemical attributes. This poster describes the creation and optimization of the beads and the field testing of buoyant beads, including sampling, tracer analysis, and quantitative analysis. The buoyant beads are transported ahead of the dissolved solutes, suggesting that light NAPL (LNAPL) transport in karst may occur faster than predicted from traditional tracing techniques. The hydrogel beads were successful in illustrating this enhanced transport.
Date: January 1, 2012
Creator: Amanda Laskoskie, Harry M. Edenborn, and Dorothy J. Vesper
System: The UNT Digital Library

Identification of Small RNAs in Desulfovibrio vulgaris Hildenborough

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 …
Date: May 17, 2010
Creator: Burns, Andrew; Joachimiak, Marcin; Deutschbauer, Adam; Arkin, Adam & Bender, Kelly
System: The UNT Digital Library

Functional Ecological Gene Networks to Reveal the Changes Among Microbial Interactions Under Elevated Carbon Dioxide Conditions

Biodiversity and its responses to environmental changes is a central issue in ecology, and for society. Almost all microbial biodiversity researches focus on species richness and abundance but ignore the interactions among different microbial species/populations. However, determining the interactions and their relationships to environmental changes in microbial communities is a grand challenge, primarily due to the lack of information on the network structure among different microbial species/populations. Here, a novel random matrix theory (RMT)-based conceptual framework for identifying functional ecological gene networks (fEGNs) is developed with the high throughput functional gene array hybridization data from the grassland microbial communities in a long-term FACE (Free Air CO2 Enrichment) experiment. Both fEGNs under elevated CO2 (eCO2) and ambient CO2 (aCO2) possessed general characteristics of many complex systems such as scale-free, small-world, modular and hierarchical. However, the topological structure of the fEGNs is distinctly different between eCO2 and aCO2, suggesting that eCO2 dramatically altered the interactions among different microbial functional groups/populations. In addition, the changes in network structure were significantly correlated with soil carbon and nitrogen dynamics, and plant productivity, indicating the potential importance of network interactions in ecosystem functioning. Elucidating network interactions in microbial communities and their responses to environmental changes are …
Date: May 17, 2010
Creator: Deng, Ye; Zhou, Jizhong; Luo, Feng; He, Zhili; Tu, Qichao & Zhi, Xiaoyang
System: The UNT Digital Library

Regulon inference without arbitrary thresholds: three levels of sensitivity

Reconstruction of transcriptional regulatory networks is one of the major challenges facing the bioinformatics community in view of constantly growing number of complete genomes. The comparative genomics approach has been successfully used for the analysis of the transcriptional regulation of many metabolic systems in various bacteria taxa. The key step in this approach is given a position weight matrix, find an optimal threshold for the search of potential binding sites in genomes. In our previous work we proposed an approach for automatic selection of TFBS score threshold coupled with inference of regulon content. In this study we developed two modifications of this approach providing two additional levels of sensitivity.
Date: November 15, 2010
Creator: Dubchak, Pavel Novichkov, Elena Stavrovskaya, Dmitry Rodionov, Andrey Mironov, Inna; Rodionov, Dmitry; Mironov, Andrey; Dubchak, Inna & Novichkov, P.S.
System: The UNT Digital Library

In silico discovery of the dormancy regulons in a number of Actinobacteria genomes

Mycobacterium tuberculosis is a dangerous Actinobacteria infecting nearly one third of the human population. It becomes dormant and phenotypically drug resistant in response to stresses. An important feature of the M. tuberculosis pathogenesis is the prevalence of latent infection without disease, making understanding of the mechanisms used by the bacteria to exist in this state and to switch to metabolically active infectious form a vital problem to consider. M. tuberculosis dormancy is regulated by the three-component regulatory system of two kinases (DosT and DevS) and transcriprional regulator (DevR). DevR activates transcription of a set of genes, which allow the bacteria to survive long periods of anaerobiosis, and may be important for long-term survival within the host during latent infection. The DevR-regulon is studied experimentally in M. tuberculosis and few other phylogenetically close Mycobacteria spp. As many other two-component systems, the devRS operon is autoregulated. However, the mechanism of the dormancy is not completely clear even for these bacteria and there is no data describing the dormancy regulons in other species.
Date: November 16, 2010
Creator: Gerasimova, Anna; Dubchak, Inna; Arkin, Adam & Gelfand, Mikhail
System: The UNT Digital Library

Alternations of Structure and Functional Activity of Below Ground Microbial Communities at Elevated Atmospheric Carbon Dioxide

The global atmospheric concentration of CO2 has increased by more than 30percent since the industrial revolution. Although the stimulating effects of elevated CO2 (eCO2) on plant growth and primary productivity have been well studied, its influences on belowground microbial communities are poorly understood and controversial. In this study, we showed a significant change in the structure and functional potential of soil microbial communities at eCO2 in a grassland ecosystem, the BioCON (Biodiversity, CO2 and Nitrogen) experimental site (http://www.biocon.umn.edu/) using a comprehensive functional gene array, GeoChip 3.0, which contains about 28,0000 probes and covers approximately 57,000 gene variants from 292 functional gene families involved in carbon, nitrogen, phosphorus and sulfur cycles as well as other functional processes. GeoChip data indicated that the functional structure of microbial communities was markedly different between ambient CO2 (aCO2) and eCO2 by detrended correspondence analysis (DCA) of all 5001 detected functional gene probes although no significant differences were detected in the overall microbial diversity. A further analysis of 1503 detected functional genes involved in C, N, P, and S cycles showed that a considerable portion (39percent) of them were only detected under either aCO2 (14percent) or eCO2 (25percent), indicating that the functional characteristics of the microbial …
Date: May 17, 2010
Creator: He, Zhili; Xu, Meiying; Deng, Ye; Kang, Sanghoon; Wu, Liyou; Van Nostrand, Joy D. et al.
System: The UNT Digital Library

Investigation of the carbon dioxide sorption capacity and structural deformation of coal

Due to increasing atmospheric CO2 concentrations causing the global energy and environmental crises, geological sequestration of carbon dioxide is now being actively considered as an attractive option to mitigate greenhouse gas emissions. One of the important strategies is to use deep unminable coal seams, for those generally contain significant quantities of coal bed methane that can be recovered by CO2 injection through enhanced coal bed natural gas production, as a method to safely store CO2. It has been well known that the adsorbing CO2 molecules introduce structural deformation, such as distortion, shrinkage, or swelling, of the adsorbent of coal organic matrix. The accurate investigations of CO2 sorption capacity as well as of adsorption behavior need to be performed under the conditions that coals deform. The U.S. Department of Energy-National Energy Technology Laboratory and Regional University Alliance are conducting carbon dioxide sorption isotherm experiments by using manometric analysis method for estimation of CO2 sorption capacity of various coal samples and are constructing a gravimetric apparatus which has a visual window cell. The gravimetric apparatus improves the accuracy of carbon dioxide sorption capacity and provides feasibility for the observation of structural deformation of coal sample while carbon dioxide molecules interact with coal …
Date: January 1, 2010
Creator: Hur, Tae-Bong; Fazio, James; Romanov, Vyacheslav & Harbert, William
System: The UNT Digital Library

Reference set of regulons in Desulfovibrionales inferred by comparative genomics approach

in this study, we carried out large-scale comparative genomics analysis of regulatory interactions in Desulfovibrio vulgaris and 12 related genomes from Desulfovibrionales order using our recently developed web server RegPredict (http://regpredict.lbl.gov). An overall reference collection of 26 Desulfovibrionales regulogs can be accessed through RegPrecise database (http://regpredict.lbl.gov).
Date: November 15, 2010
Creator: Kazakov, Alexey E.; Rodionov, Dmitry A.; Price, Morgan N.; Arkin, Adam P.; Dubchak, Inna & Novichkov, Pavel S.
System: The UNT Digital Library

Taxa-area Relationship (TAR) of Microbial Functional Genes with Long-TGerm Fertilization

Diversity and spatial patterns in plant and animal communities are well documented as a positive-power law of a taxa-area relationship (TAR). At present little is known whether this also applies to soil microbial communities and whether long-term fertilization has an influence on the underlying microbial diversity. To test the effects of long-term fertilization on above-ground botanical diversity and below-ground microbial diversity, a nested sampling approach on Park Grass plots (12d& 11/2c) of Rothamsted Reseach in United Kingdom, both at ~;; pH 5 but with plant diversities of between 42 and 13 respectively were used. GeoChip 3.0, covering approximately 57, 000 gene sequences of 292 gene families involved in nitrogen, carbon, sulfur and phosphorus cycling, metal reduction and resistance, and organic contaminant degradation, was used to determine the gene area relationships for both functional and phylogenetic groups and the relationship to plant diversity. Our analysis indicated that the microbial communities were separated by different plant diversity based on DCA. The soil microbial diversity was in accord with plant diversity. Soil microbial community exhibited different z value with different plant diversity, z = 0.0449 with higher plant diversity and z = 0.0583 with lower plant diversity (P< 0.0001). These results suggest that …
Date: May 17, 2010
Creator: Liang, Yuting; Wu, Liyou; Clark, Ian; Xue, Kai; Van Nostrand, Joy D.; Deng, Ye et al.
System: The UNT Digital Library

Two Component Signal Transduction in Desulfovibrio Species

The environmentally relevant Desulfovibrio species are sulfate-reducing bacteria that are of interest in the bioremediation of heavy metal contaminated water. Among these, the genome of D. vulgaris Hildenborough encodes a large number of two component systems consisting of 72 putative response regulators (RR) and 64 putative histidinekinases (HK), the majority of which are uncharacterized. We classified the D. vulgaris Hildenborough RRs based on their output domains and compared the distribution of RRs in other sequenced Desulfovibrio species. We have successfully purified most RRs and several HKs as His-tagged proteins. We performed phospho-transfer experiments to verify relationships between cognate pairs of HK and RR, and we have also mapped a few non-cognate HK-RR pairs. Presented here are our discoveries from the Desulfovibrio RR categorization and results from the in vitro studies using purified His tagged D. vulgaris HKs and RRs.
Date: May 17, 2010
Creator: Luning, Eric; Rajeev, Lara; Ray, Jayashree & Mukhopadhyay, Aindrila
System: The UNT Digital Library

Syntrophic Degradation of Lactate in Methanogenic Co-cultures

In environments where the amount of the inorganic electron acceptors (oxygen, nitrate, sulfate, sulfur oroxidized metal ions (Fe3+;Mn4+) is insufficient for complete breakdown of organic matter, methane is formed as the major reduced end product. In such methanogenic environments organic acids are degraded by syntrophic associations of fermenting, acetogenic bacteria (e.g., sulfate-reducing bacteria (SRB) as"secondary fermenters") and methanogenic archaea. In these consortia, the conversion of lactate to acetate, CO2 and methane depends on the cooperating activities of both metabolically distinct microbial groups that are tightly linked by the need to maintain the exchanged metabolites (hydrogenandformate) at very low concentrations.
Date: May 17, 2010
Creator: Meyer, Birte & Stahl, David
System: The UNT Digital Library

Durability of Polymeric Encapsulation Materials for Concentrating Photovoltaic Systems [Poster]

Polymeric encapsulation materials are typically used in concentrating photovoltaic (CPV) modules to protect the cell from the field environment. Because it is physically located adjacent to the cell, the encapsulation is exposed to a high optical flux, often including light in the ultraviolet (UV) and infrared (IR) wavelengths. The durability of encapsulants used in CPV modules is critical to the technology, but is presently not well understood. This work seeks to identify the appropriate material types, field-induced failure mechanisms, and factors of influence (if possible) of polymeric encapsulation. These results will ultimately be weighed against those of future qualification and accelerated life test procedures.
Date: February 1, 2011
Creator: Miller, D. C.; Kempe, M. D.; Araki, K.; Kennedy, C. E. & Kurtz, S. R.
System: The UNT Digital Library

2011 DOE Occupational Radiation Exposure Summary poster

This poster graphically presents data pertaining to occupational radiation exposure in terms of total effective dose (TED), primarily, but also collective dose and average measureable dose.
Date: December 12, 2012
Creator: Oak Ridge Associated Universities
System: The UNT Digital Library

Mapping the Two-component Regulatory Networks in Desulfovibrio vulgaris

D. vulgaris Hildenborough has 72 response regulators. The Desulfovibrio are sulfate reducing bacteria that are important in the sulfur and carbon cycles in anoxic habitats. Its large number of two componenent systems are probably critical to its ability to sense and respond to its environment. Our goal is to map these RRs to the genes they regulate using a DNA-affinity-purification-chip (DAP-chip) protocol. First target determined usuing EMSA. A positive target was determined for as many RRs as possible using EMSA. Targets were selected based on gene proximity, regulon predictions and/or predicted sigma54 dependent promoters. qPCR was used to ensure that the target was enriched from sheared genomic DNA before proceeding to the DAP-chip.
Date: May 17, 2010
Creator: Rajeev, Lara; Luning, Eric; Dehal, Paramvir; Joachimiak, Marcin & Mukhopadhyay, Aindrila
System: The UNT Digital Library

Investigating the role of CheA-3 in Dusulfovibrio Vulgaris Hildenborough

Multiple sets of chemotaxis genes including three cheA homologs were identified in the genome sequence of the anaerobic bacterium Desulfovibrio vulgaris Hildenborough. Each CheA is a histidine kinase (HK) and part of a two component signal transduction system. Knock out mutants in the three cheA genes were created using single cross-over homologous recombination insertion. We studied the phenotypes of the cheA mutants in detail and discovered that ?cheA-3 has a non swarming/swimming phenotype both in the soft agar plates and Palleroni chamber assays. CheA-3 shows similarity to the Shewanella oneidensis CheA-3 and the Vibrio cholerae CheA-2 that are responsible for chemotaxis in the respective organisms. We did not find any morphological or structural differences between the three Delta cheA mutants and the wild type cells in electron microscopy. Our results from these studies are presented.
Date: May 22, 2010
Creator: Ray, Jayashee; Keller, Kimberley; Krierim, Bernhard; Auer, Manfred; Keasling, Jay; Wall, Judy et al.
System: The UNT Digital Library

New National Wind Potential Estimates for Modern and Near-Future Turbine Technologies

Recent advancements in utility-scale wind turbine technology and pricing have vastly increased the potential land area where turbines can be deployed in the United States. This presentation quantifies the new developable land potential (e.g., capacity curves), visually identifies new areas for possible development (e.g., new wind resource maps), and begins to address deployment barriers to wind in new areas for modern and future turbine technology.
Date: January 1, 2014
Creator: Roberts, J. O.
System: The UNT Digital Library

The Role of the Tetraheme Cytochrome c3 in Desulfovibrio vulgaris Hildenborough Metabolism

The role of tetraheme cytochrome c3 (CycA) in the metabolism of the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough (DvH) was investigated by deletion of the cycA gene using a marker-exchange deletion strategy. A highly abundant periplasmic cytochrome, CycA has the important function of transferring electrons from periplasmic hydrogenases (Hyd, Hyn, Hys) to transmembrane complexes which transport the electrons to the cytoplasm where sulfate is reduced. Previous studies have indicated that during its interaction with periplasmic hydrogenases, CycA is also involved in the reduction of toxic metals. Growth of the cycA mutant strain on lactate as the electron donor and sulfate as the terminal electron acceptor showed that, despite its abundance, CycA is not essential for DvH growth. However, the rate of growth of the mutant strain was significantly lower, and the extent of growth less, than rates and extents of growth of the wild type and complement strains on lactate/sulfate medium. This indicates that a portion of the electrons generated from cytoplasmic lactate oxidation are transported by CycA for energy production, possibly in a hydrogen cycling mechanism employed to generate ATP. Failure of the mutant strain to grow on either formate or H2, with sulfate or sulfite as electron acceptors, further …
Date: May 17, 2010
Creator: Semkiw, Elizabeth; Zane, Grant & Wall, Judy
System: The UNT Digital Library

Analysis of a US Department of Energy Emergent Technologies Cohort

As a major user of engineered nanoparticles, the U.S. Department of Energy (DOE) uses various methods to monitor the health of emergent technologies workers (ETW) who handle or could potentially be exposed to unbound engineered nanoparticles (UNP). Using data from DOE’s Illness and Injury Surveillance Program (IISP), Oak Ridge Associated Universities (ORAU) created a registry of ETWs. IISP currently tracks 125,000 workers at 14 DOE facilities. Workers in IISP, who were classified as ETWs, were placed in a separate database using Microsoft Access. Using SAS (Version 9.2; Cary, NC), the health status of this cohort was analyzed by a variety of different variables such as age, gender, occupation, years of employment, number of years classified as an ETW, and site.
Date: December 12, 2012
Creator: Strader, Cliff; Ellis, Elizabeth; Barrie, Martin D; Tankersley, William & Wallace, Phil
System: The UNT Digital Library

HuMiChip: Development of a Functional Gene Array for the Study of Human Microbiomes

Microbiomes play very important roles in terms of nutrition, health and disease by interacting with their hosts. Based on sequence data currently available in public domains, we have developed a functional gene array to monitor both organismal and functional gene profiles of normal microbiota in human and mouse hosts, and such an array is called human and mouse microbiota array, HMM-Chip. First, seed sequences were identified from KEGG databases, and used to construct a seed database (seedDB) containing 136 gene families in 19 metabolic pathways closely related to human and mouse microbiomes. Second, a mother database (motherDB) was constructed with 81 genomes of bacterial strains with 54 from gut and 27 from oral environments, and 16 metagenomes, and used for selection of genes and probe design. Gene prediction was performed by Glimmer3 for bacterial genomes, and by the Metagene program for metagenomes. In total, 228,240 and 801,599 genes were identified for bacterial genomes and metagenomes, respectively. Then the motherDB was searched against the seedDB using the HMMer program, and gene sequences in the motherDB that were highly homologous with seed sequences in the seedDB were used for probe design by the CommOligo software. Different degrees of specific probes, including gene-specific, …
Date: May 17, 2010
Creator: Tu, Q.; Deng, Ye; Lin, Lu; Hemme, Chris L.; He, Zhili & Zhou, Jizhong
System: The UNT Digital Library

Rapid Field Measurement of Dissolved Inorganic Carbon Based on CO{sub 2} Analysis

Dissolved inorganic carbon (DIC) is commonly measured in water and is an important parameter for understanding carbonate equilibrium, carbon cycling, and water-rock interaction. While accurate measurements can be made in the analytical laboratory, we have developed a rapid, portable technique that can be used to obtain accurate and precise data in the field as well.
Date: January 1, 2012
Creator: VESPER, DJ, Edenborn, Harry
System: The UNT Digital Library

Microarray-based analysis of survival of soil microbial community during ozonation

A 15 h ozonation was performed on bioremediated soil to remove recalcitrant residual oil. To monitor the survival of indigenous microorganisms in the soil during in-situ chemical oxidation(ISCO) culturing and a functional genearray, GeoChip, was used to examine the functional genes and structure of the microbial community during ozonation (0h, 2h, 4h, 6h, 10hand15h). Breakthrough ozonation decreased the population of cultivable heterotrophic bacteria by about 3 orders of magnitude. The total functional gene abundance and diversity decreased during ozonation, as the number of functional genes was reduced by 48percent after 15 h. However, functional genes were evenly distributed during ozonation as judged by the Shannon-Weaver Evenness index. A sharp decrease in gene number was observed in the first 6 h of ozonation followed by a slower decrease in the next 9 h, which was consistent with microbial populations measured by a culture based method. Functional genes involved in carbon, nitrogen, phosphors and sulfur cycling, metal resistance and organic remediation were detected in all samples. Though the pattern of gene categories detected was similar for all time points, hierarchica lcluster of all functional genes and major functional categories all showed a time-serial pattern. Bacteria, archaea and fungi decreased by 96.1percent, 95.1percent …
Date: May 17, 2010
Creator: Wang, Jian; Van Nostrand, Joy D.; He, Zhili; Wu, Liyou; Deng, Ye; Zhang, Xu et al.
System: The UNT Digital Library

Phylogenetic Analysis of Shewanella Strains by DNA Relatedness Derived from Whole Genome Microarray DNA-DNA Hybridization and Comparison with Other Methods

Phylogenetic analyses were done for the Shewanella strains isolated from Baltic Sea (38 strains), US DOE Hanford Uranium bioremediation site [Hanford Reach of the Columbia River (HRCR), 11 strains], Pacific Ocean and Hawaiian sediments (8 strains), and strains from other resources (16 strains) with three out group strains, Rhodopseudomonas palustris, Clostridium cellulolyticum, and Thermoanaerobacter ethanolicus X514, using DNA relatedness derived from WCGA-based DNA-DNA hybridizations, sequence similarities of 16S rRNA gene and gyrB gene, and sequence similarities of 6 loci of Shewanella genome selected from a shared gene list of the Shewanella strains with whole genome sequenced based on the average nucleotide identity of them (ANI). The phylogenetic trees based on 16S rRNA and gyrB gene sequences, and DNA relatedness derived from WCGA hybridizations of the tested Shewanella strains share exactly the same sub-clusters with very few exceptions, in which the strains were basically grouped by species. However, the phylogenetic analysis based on DNA relatedness derived from WCGA hybridizations dramatically increased the differentiation resolution at species and strains level within Shewanella genus. When the tree based on DNA relatedness derived from WCGA hybridizations was compared to the tree based on the combined sequences of the selected functional genes (6 loci), we …
Date: May 17, 2010
Creator: Wu, Liyou; Yi, T. Y.; Van Nostrand, Joy & Zhou, Jizhong
System: The UNT Digital Library

Effect of Increasing Nitrogen Deposition on Soil Microbial Communities

Increasing nitrogen deposition, increasing atmospheric CO2, and decreasing biodiversity are three main environmental changes occurring on a global scale. The BioCON (Biodiversity, CO2, and Nitrogen) ecological experiment site at the University of Minnesota's Cedar Creek Ecosystem Science Reserve started in 1997, to better understand how these changes would affect soil systems. To understand how increasing nitrogen deposition affects the microbial community diversity, heterogeneity, and functional structure impact soil microbial communities, 12 samples were collected from the BioCON plots in which nitrogenous fertilizer was added to simulate the effect of increasing nitrogen deposition and 12 samples from without added fertilizer. DNA from the 24 samples was extracted using a freeze-grind protocol, amplified, labeled with a fluorescent dye, and then hybridized to GeoChip, a functional gene array containing probes for genes involved in N, S and C cycling, metal resistance and organic contaminant degradation. Detrended correspondence analysis (DCA) of all genes detected was performed to analyze microbial community patterns. The first two axes accounted for 23.5percent of the total variation. The samples fell into two major groups: fertilized and non-fertilized, suggesting that nitrogenous fertilizer had a significant impact on soil microbial community structure and diversity. The functional gene numbers detected in fertilized …
Date: May 17, 2010
Creator: Xiao, Shengmu; Xue, Kai; He, Zhili; VanNostrand, Joy D.; Liu, Jianshe; Hobbie, Sarah E. et al.
System: The UNT Digital Library