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Studies of the status of antioxidant enzymes and metabolites following burn injury, and the presence of antioxidant enzymes in the Aloe vera plant

Description: The effects of skin burn injury on the levels of oxidized and reduced glutthione, malondialdehyde, and on the activities of glutathione peroxidase, glutathione S-transferase, and glutathione reductase were determined in liver and lung of rabbit models, 24-h post-burn.
Date: December 1995
Creator: Sabeh, Farideh
Partner: UNT Libraries

Single cell analysis: the new frontier in 'Omics'

Description: Cellular heterogeneity arising from stochastic expression of genes, proteins, and metabolites is a fundamental principle of cell biology, but single cell analysis has been beyond the capabilities of 'Omics' technologies. This is rapidly changing with the recent examples of single cell genomics, transcriptomics, proteomics, and metabolomics. The rate of change is expected to accelerate owing to emerging technologies that range from micro/nanofluidics to microfabricated interfaces for mass spectrometry to third- and fourth-generation automated DNA sequencers. As described in this review, single cell analysis is the new frontier in Omics, and single cell Omics has the potential to transform systems biology through new discoveries derived from cellular heterogeneity.
Date: January 14, 2010
Creator: Wang, Daojing & Bodovitz, Steven
Partner: UNT Libraries Government Documents Department

Role of Glycolytic Intermediates in Global Regulation and Signal Transduction. Final Report

Description: The goal of this project is to determine the role of glycolytic intermediates in regulation of cell physiology. It is known that many glycolytic intermediates are involved in regulation of enzyme activities at the kinetic level. However, little is known regarding the role of these metabolites in global regulation and signal transduction. This project aims to investigate the role of glycolytic intermediates in the regulation of gene expression.
Date: May 8, 2000
Creator: Liao, J. C.
Partner: UNT Libraries Government Documents Department

DOE-FG02-00ER62797 Final Report

Description: Specific Aims The overall goal of this proposal has been to develop and interface a new technology, molecular gates, with microfabricated systems to add an important capability to microfabricated DNA measurement systems. This project specifically focused on demonstrating how molecular gates could be used to capture a single analyte band, among a stream of bands from a separation or a flow injection analysis experiment, and release it for later measurement, thus allowing further manipulations on the selected analyte. Since the original proposal, the molecular gate concept has been greatly expanded to allow the gates to be used as externally controllable intelligent interconnects in multilayer microfluidic networks. We have demonstrated: (1) the ability of the molecular gates to work with a much wider range of biological molecules including DNA, proteins and small metabolites; and (2) the capability of performing an electrophoretic separation and sequestering individual picoliter volume components (or even classes of components) into separate channels for further analysis. Both capabilities will enable characterization of small mass amounts of complex mixtures of DNA, proteins and even small molecules--allowing them to be further separated and chemically characterized.
Date: December 1, 2004
Creator: Sweedler, J.V.
Partner: UNT Libraries Government Documents Department

Isotopomer distributions in amino acids from a highly expressed protein as a proxy for those from total protein

Description: {sup 13}C-based metabolic flux analysis provides valuable information about bacterial physiology. Though many biological processes rely on the synergistic functions of microbial communities, study of individual organisms in a mixed culture using existing flux analysis methods is difficult. Isotopomer-based flux analysis typically relies on hydrolyzed amino acids from a homogeneous biomass. Thus metabolic flux analysis of a given organism in a mixed culture requires its separation from the mixed culture. Swift and efficient cell separation is difficult and a major hurdle for isotopomer-based flux analysis of mixed cultures. Here we demonstrate the use of a single highly-expressed protein to analyze the isotopomer distribution of amino acids from one organism. Using the model organism E. coli expressing a plasmid-borne, his-tagged Green Fluorescent Protein (GFP), we show that induction of GFP does not affect E. coli growth kinetics or the isotopomer distribution in nine key metabolites. Further, the isotopomer labeling patterns of amino acids derived from purified GFP and total cell protein are indistinguishable, indicating that amino acids from a purified protein can be used to infer metabolic fluxes of targeted organisms in a mixed culture. This study provides the foundation to extend isotopomer-based flux analysis to study metabolism of individual strains in microbial communities.
Date: June 27, 2008
Creator: Shaikh, Afshan; Shaikh, Afshan S.; Tang, Yinjie; Mukhopadhyay, Aindrila & Keasling, Jay D.
Partner: UNT Libraries Government Documents Department

The genome of black cottonwood, Populus trichocarpa (Torr.&Gray)

Description: We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. Over 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event, with approximately 8,000 pairs of duplicated genes from that event surviving in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication and gross chromosomal rearrangement appear to proceed substantially slower in Populus relative to Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average between 1.4-1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with disease resistance, meristem development, metabolite transport and lignocellulosic wall biosynthesis.
Date: September 1, 2006
Creator: Tuskan, G. A.; DiFazio, S.; Jansson, S.; Bohlmann, J.; Grigoriev,I.; Hellsten, U. et al.
Partner: UNT Libraries Government Documents Department

Genomic islands predict functional adaptation in marine actinobacteria

Description: Linking functional traits to bacterial phylogeny remains a fundamental but elusive goal of microbial ecology 1. Without this information, it becomes impossible to resolve meaningful units of diversity and the mechanisms by which bacteria interact with each other and adapt to environmental change. Ecological adaptations among bacterial populations have been linked to genomic islands, strain-specific regions of DNA that house functionally adaptive traits 2. In the case of environmental bacteria, these traits are largely inferred from bioinformatic or gene expression analyses 2, thus leaving few examples in which the functions of island genes have been experimentally characterized. Here we report the complete genome sequences of Salinispora tropica and S. arenicola, the first cultured, obligate marine Actinobacteria 3. These two species inhabit benthic marine environments and dedicate 8-10percent of their genomes to the biosynthesis of secondary metabolites. Despite a close phylogenetic relationship, 25 of 37 secondary metabolic pathways are species-specific and located within 21 genomic islands, thus providing new evidence linking secondary metabolism to ecological adaptation. Species-specific differences are also observed in CRISPR sequences, suggesting that variations in phage immunity provide fitness advantages that contribute to the cosmopolitan distribution of S. arenicola 4. The two Salinispora genomes have evolved by complex processes that include the duplication and acquisition of secondary metabolite genes, the products of which provide immediate opportunities for molecular diversification and ecological adaptation. Evidence that secondary metabolic pathways are exchanged by Horizontal Gene Transfer (HGT) yet are fixed among globally distributed populations 5 supports a functional role for their products and suggests that pathway acquisition represents a previously unrecognized force driving bacterial diversification
Date: April 1, 2009
Creator: Penn, Kevin; Jenkins, Caroline; Nett, Markus; Udwary, Daniel; Gontang, Erin; McGlinchey, Ryan et al.
Partner: UNT Libraries Government Documents Department

Invariability of Central Metabolic Flux Distribution in Shewanella oneidensis MR-1 Under Environmental or Genetic Perturbations

Description: An environmentally important bacterium with versatile respiration, Shewanella oneidensis MR-1, displayed significantly different growth rates under three culture conditions: minimal medium (doubling time {approx} 3 hrs), salt stressed minimal medium (doubling time {approx} 6 hrs), and minimal medium with amino acid supplementation (doubling time {approx}1.5 hrs). {sup 13}C-based metabolic flux analysis indicated that fluxes of central metabolic reactions remained relatively constant under the three growth conditions, which is in stark contrast to the reported significant changes in the transcript and metabolite profiles under various growth conditions. Furthermore, ten transposon mutants of S. oneidensis MR-1 were randomly chosen from a transposon library and their flux distributions through central metabolic pathways were revealed to be identical, even though such mutational processes altered the secondary metabolism, for example, glycine and C1 (5,10-Me-THF) metabolism.
Date: April 21, 2009
Creator: Tang, Yinjie; Martin, Hector Garcia; Deutschbauer, Adam; Feng, Xueyang; Huang, Rick; Llora, Xavier et al.
Partner: UNT Libraries Government Documents Department

Merging Models and Biomonitoring Data to Characterize Sources andPathways of Human Exposure to Organophosphorous Pesticides in the SalinasValley of California

Description: By drawing on human biomonitoring data and limited environmental samples together with outputs from the CalTOX multimedia, multipathway source-to-dose model, we characterize cumulative intake of organophosphorous (OP) pesticides in an agricultural region of California. We assemble regional OP pesticide use, environmental sampling, and biological tissue monitoring data for a large and geographically dispersed population cohort of 592 pregnant Latina women in California (the CHAMACOS cohort). We then use CalTOX with regional pesticide usage data to estimate the magnitude and uncertainty of exposure and intake from local sources. We combine model estimates of intake from local sources with food intake based on national residue data to estimate for the CHAMACOS cohort cumulative median OP intake, which corresponds to expected levels of urinary dialkylphosphate (DAP) metabolite excretion for this cohort. From these results we develop premises about relative contributions from different sources and pathways of exposure. We evaluate these premises by comparing the magnitude and variation of DAPs in the CHAMACOS cohort with the whole U.S. population using data from the National Health and Nutrition Evaluation Survey (NHANES). This comparison supports the premise that in both populations diet is the common and dominant exposure pathway. Both the model results and biomarker comparison supports the observation that the CHAMACOS population has a statistically significant higher intake of OP pesticides that appears as an almost constant additional dose among all participants. We attribute the magnitude and small variance of this intake to non-dietary exposure in residences from local sources.
Date: June 1, 2006
Creator: McKone, Thomas E.; Castorina, Rosemary; Kuwabara, Yu; Harnly,Martha E.; Eskenazi, Brenda & Bradman, Asa
Partner: UNT Libraries Government Documents Department

STRATEGIES FOR QUANTIFYING PET IMAGING DATA FROM TRACER STUDIES OF BRAIN RECEPTORS AND ENZYMES.

Description: A description of some of the methods used in neuroreceptor imaging to distinguish changes in receptor availability has been presented in this chapter. It is necessary to look beyond regional uptake of the tracer since uptake generally is affected by factors other than the number of receptors for which the tracer has affinity. An exception is the infusion method producing an equilibrium state. The techniques vary in complexity some requiring arterial blood measurements of unmetabolized tracer and multiple time uptake data. Others require only a few plasma and uptake measurements and those based on a reference region require no plasma measurements. We have outlined some of the limitations of the different methods. Laruelle (1999) has pointed out that test/retest studies to which various methods can be applied are crucial in determining the optimal method for a particular study. The choice of method will also depend upon the application. In a clinical setting, methods not involving arterial blood sampling are generally preferred. In the future techniques for externally measuring arterial plasma radioactivity with only a few blood samples for metabolite correction will extend the modeling options of clinical PET. Also since parametric images can provide information beyond that of ROI analysis, improved techniques for generating such images will be important, particularly for ligands requiring more than a one-compartment model. Techniques such as the wavelet transform proposed by Turkheimer et al. (2000) may prove to be important in reducing noise and improving quantitation.
Date: April 2, 2001
Creator: Logan, J.
Partner: UNT Libraries Government Documents Department

Metabolic engineering of Saccharomyces cerevisiae for the production of n-butanol

Description: BackgroundIncreasing energy costs and environmental concerns have motivated engineering microbes for the production of ?second generation? biofuels that have better properties than ethanol.Results& ConclusionsSaccharomyces cerevisiae was engineered with an n-butanol biosynthetic pathway, in which isozymes from a number of different organisms (S. cerevisiae, Escherichia coli, Clostridium beijerinckii, and Ralstonia eutropha) were substituted for the Clostridial enzymes and their effect on n-butanol production was compared. By choosing the appropriate isozymes, we were able to improve production of n-butanol ten-fold to 2.5 mg/L. The most productive strains harbored the C. beijerinckii 3-hydroxybutyryl-CoA dehydrogenase, which uses NADH as a co-factor, rather than the R. eutropha isozyme, which uses NADPH, and the acetoacetyl-CoA transferase from S. cerevisiae or E. coli rather than that from R. eutropha. Surprisingly, expression of the genes encoding the butyryl-CoA dehydrogenase from C. beijerinckii (bcd and etfAB) did not improve butanol production significantly as previously reported in E. coli. Using metabolite analysis, we were able to determine which steps in the n-butanol biosynthetic pathway were the most problematic and ripe for future improvement.
Date: November 25, 2008
Creator: Steen, EricJ.; Chan, Rossana; Prasad, Nilu; Myers, Samuel; Petzold, Christopher; Redding, Alyssa et al.
Partner: UNT Libraries Government Documents Department

ELECTRON PARAMAGNETIC RESONANCE IN BIOLOGY

Description: A review of the theories of electron paramagnetic resonance in biology is presented, including a discussion of the nature of the physical observation, followed by examples of materials of biological interest. Iq discussing these examples, information is presented in terms of the nature of the starting material under observation rather than the nature of the magnetic entities observed. The examples proceed from the simpler molecules of biological interest (metabolites, vitamins, cofactors) into the more complex materials (polymers, proteins, nucleic acids) toward cellular organelles (mitochondria, chloroplasts) and, finally, to whole cells, organisms and organs. The observation of photoinduced unpaired electrons in photosynthetic material is described and the various parameters controlling it are discussed. The basic observation is interpreted in terms of a primary photophysical act of quantum conversion.
Date: August 15, 1961
Creator: Androes, G.M. & Calvin, Melvin.
Partner: UNT Libraries Government Documents Department

IN SITU URANIUM STABILIZATION BY MICROBIAL METABOLITES

Description: Soil contaminated with U was the focus of this study in order to develop in-situ, U bio-immobilization technology. We have demonstrated microbial production of a metal chelating biopolymer, pyomelanin, in U contaminated soil from the Tims Branch area of the Department of Energy (DOE) Savannah River Site (SRS) as a result of tyrosine amendments. Bacterial densities of pyomelanin producers were >106 cells/g wet soil. Pyomelanin demonstrated U chelating and mineral binding capacities at pH 4 and 7. In laboratory studies, in the presence of goethite or illite, pyomelanin enhanced U sequestration by these minerals. Tyrosine amended soils in field tests demonstrated increased U sequestration capacity following pyomelanin production up to 13 months after tyrosine treatments.
Date: November 29, 2006
Creator: Turick, C; Anna Knox, A; Chad L Leverette,C & Yianne Kritzas, Y
Partner: UNT Libraries Government Documents Department

Field Deployment for In-situ Metal and Radionuclide Stabilization by Microbial Metabolites

Description: A novel biotechnology is reported here that was demonstrated at SRS that facilitates metal and actinide immobilization by incorporating the physiology and ecology of indigenous bacteria. This technology is based on our previous work with pyomelanin-producing bacteria isolated from SRS soils. Through tyrosine supplementation, overproduction of pyomelanin was achieved, which lead ultimately to metal and actinide immobilization, both in-vitro and in-situ. Pyomelanin is a recalcitrant microbial pigment and a humic type compound in the class of melanin pigments. Pyomelanin has electron shuttling and metal chelation capabilities and thus accelerates the bacterial reduction and/or immobilization of metals. Pyomelanin is produced outside the cell and either diffuses away or attaches to the cell surface. In either case, the reduced pyomelanin is capable of transferring electrons to metals as well as chelating metals. Because of its recalcitrance and redox cycling properties, pyomelanin molecules can be used over and over again for metal transformation. When produced in excess, pyomelanin produced by one bacterial species can be used by other species for metal reduction, thereby extending the utility of pyomelanin and further accelerating metal immobilization rates. Soils contaminated with Ni and U were the focus of this study in order to develop in-situ, metal bioimmobilization technologies. We have demonstrated pyomelanin production in soil from the Tims Branch area of SRS as a result of tyrosine amendments. These results were documented in laboratory soil column studies and field deployment studies. The amended soils demonstrated increased redox behavior and sequestration capacity of U and transition metals following pyomelanin production. Treatments incorporating tyrosine and lactate demonstrated the highest levels of pyomelanin production. In order to determine the potential use of this technology at other areas of SRS, pyomelanin producing bacteria were also quantified from metal contaminated soils at TNX and D areas of SRS. A bacterial culture collection ...
Date: September 26, 2005
Creator: Turick, C. E.; Knox, A. S.; Dixon, K. L.; Roseberry, R. J. & Kritzas, Y. G
Partner: UNT Libraries Government Documents Department

GLUCOSE METABOLITE PATTERNS AS MARKERS OF FUNCTIONAL DIFFERENTIATION IN FRESHLY ISOLATED AND CULTURED MOUSE MAMMARY EPITHELIAL CELLS

Description: In the mammary gland of nonruminant animals, glucose is utilized in a characteristic and unique way during lactation. We have measured the incorporation of glucose carbon from [U-{sup 14}C] glucose into intermediary metabolites and metabolic products in mammary epithelial cells from virgin, pregnant, and lactating mice and demonstrate that glucose metabolite patterns can be used to recognize stages of differentiated function. For these cells, the rates of synthesis of glycogen and lactose, the ratio of lactate to alanine, and the ratio of citrate to malate were important parameters in identifying the degree of expression of differentiation. We further show that these patterns can be used as markers to determine the differentiated state of cultured mammary epithelial cells. Cells maintained on plastic substrates lose their distinctive glucose metabolite patterns while those on floating collagen gels do not. Cells from pregnant mice have a pattern similar to freshly isolated cells from pregnant mice. The pattern of cells from lactating mice is different from that of the cells of origin, and resembles that of the cells from pregnant mice. Our findings suggest that the floating collagen gels under the culture conditions used in these experiments provide an environment for the functional expression of the pregnant state, while additional factors are needed for the expression of the lactating state.
Date: June 1, 1980
Creator: Emerman, J.T.; Bartley, J.C. & Bissell, M.J.
Partner: UNT Libraries Government Documents Department

Effects of Cigarette Smoke Condensates on Cultured Human Lymphocytes and Separation of Benzo-α-Pyrene Metabolites by High Pressure Liquid Chromatography

Description: Cigarette smoke condensates from all cigarettes tested were found to be potent inducers of AHH enzyme in cultured human lymphocytes and, with the exception of Kent Lights and Carlton CSC's, all were found to be toxic under the experiment conditions. Most of the AHH inducing activity was found in basic and neutral fractions of the lAl standard cigarettes. A radiometric assay of BP metabolites in cultured human lymphocytes was developed in which we were able to separate the primary metabolites and the secondary metabolites from the parent compound (BP) by neutral alumnia HPLC. The primary metabolites were further separated by a selective enzyme hydrolysis and/or reverse phase HPLC.
Date: August 1979
Creator: Ghanayem, Burhan I.
Partner: UNT Libraries

Methods and applications of HPLC-AMS (WBio 5)

Description: Pharmacokinetics of physiologic doses of nutrients, pesticides, and herbicides can easily be traced in humans using a {sup 14}C-labelled compound. Basic kinetics can be monitored in blood or urine by measuring the elevation in the {sup 14}C content above the control predose tissue and converting to equivalents of the parent compound. High Performance Liquid Chromatography (HPLC) is an excellent method for the chemical separation of complex mixtures whose profiles afford estimation of biochemical pathways of metabolism. Compounds elute from the HPLC systems with characteristic retention times and can be collected in fractions that can then be graphitized for AMS measurement. Unknowns are identified by coelution with known standards and chemical tests that reveal functional groupings. Metabolites are quantified with the {sup 14}C signal. Thoroughly accounting for the carbon inventory in the LC solvents, ion-pairing agents, samples, and carriers adds some complexity to the analysis. In most cases the total carbon inventory is dominated by carrier. Baseline background and stability need to be carefully monitored. Limits of quantitation near 10 amol of {sup 14}C per HPLC fraction are typically achieved. Baselines are maintained by limiting injected {sup 14}C activity <0.17 Bq (4.5 pCi) on the HPLC column.
Date: September 29, 1999
Creator: Bucholz, B A; Clifford, A J; Duecker, S R; Lin, Y & Vogel, J S
Partner: UNT Libraries Government Documents Department

N-Acylethanolamine (NAE) Profiles Change During Arabidopsis Thaliana Seed Germination and Seedling Growth

Description: An understanding of the potential roles as lipid mediators of a family of bioactive metabolites called N-acylethanolamines (NAEs) depends on their accurate identification and quantification. The levels of 18C unsaturated NAEs (e.g. NAE18:2, NAE 18:3, etc.) in wild-type seeds (about 2000 ng/g fw) generally decreased by about 80% during germination and post-germinative growth. In addition, results suggest NAE-degradative fatty acid amide hydrolase (FAAH) expression does not play a major role in normal NAE metabolism as previously thought. Seedlings germinated and grown in the presence of abscisic acid (ABA), an endogenous plant hormone, exhibited growth arrest and secondary dormancy, similar to the treatment of seedlings with exogenous N­lauroylethanolamine (NAE12:0). ABA-mediated growth arrest was associated with higher levels of unsaturated NAEs. Overall, these results are consistent with the concept that NAE metabolism is activated during seed germination and suggest that the reduction in unsaturated NAE levels is under strict temporal control and may be a requirement for normal seed germination and post-germinative growth.
Date: August 2006
Creator: Wiant, William C.
Partner: UNT Libraries