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Purification and characterization of glycogen synthase from Ascaris suum

Description: Glycogen synthase, the enzyme that catalyzes the rate-limiting reaction of glycogen syntheses has been purified and characterized from Ascaris suum muscle. Glycogen in the crude extract was digested to release the enzyme, eluted from a DE52 cellulose column and then applied to a Sepharose affinity column. The purified Ascaris enzyme was found to be homologous to the mammalian enzyme with regard to subunit and holoenzyme Mr^3 allosteric activation, substrate affinity and covalent modification. However, the association between Ascaris glycogen synthase and endogenous glycogen differed from that in mammalian systems.
Date: August 1985
Creator: Hannigan, Linda L. (Linda Lucile)
Partner: UNT Libraries

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

Whole-genome analyses of the speciation events in the pathogenic Brucellae

Description: Despite their high DNA identity and a proposal to group classical Brucella species as biovars of B. melitensis, the commonly recognized Brucella species can be distinguished by distinct biochemical and fatty acid characters as well as by a marked host range (e.g. B. suis for swine, B. melitensis for sheep and goats, B. abortus for cattle). Here we present the genome of B. abortus 2308, the virulent prototype biovar 1 strain, and its comparison to the two other human pathogenic Brucellae species and to the B. abortus field isolate 9-941. The global distribution of pseudogenes, deletions and insertions support previous indications that B. abortus and B. melitensis share a common ancestor that diverged from B. suis. With the exception of a dozen genes, the genetic complement of both B. abortus strains is identical, whereas the three species differ in gene content and pseudogenes. The pattern of species-specific gene inactivations affecting transcriptional regulators and outer membrane proteins suggest that these inactivations may play an important role in the establishment of host-specificity and may have been a primary driver of speciation in the Brucellae. Despite being non-motile, the Brucellae contain flagellum gene clusters and display species-specific flagellar gene inactivations, which lead to the putative generation of different versions of flagellum-derived structures, and may contribute to differences in host-specificity and virulence. Metabolic changes such as the lack of complete metabolic pathways for the synthesis of numerous compounds (e.g. glycogen, biotin, NAD, and choline) are consistent with adaptation of Brucellae to an intracellular lifestyle.
Date: July 14, 2005
Creator: Chain, P; Comerci, D; Tolmasky, M; Larimer, F; Malfatti, S; Vergez, L et al.
Partner: UNT Libraries Government Documents Department

The Complete Genome Sequence of the Marine, Chemolithoautotrophic, Ammonia-Oxidizing Bacterium Nitrosococcus oceani ATCC19707

Description: The Gammaproteobacterium, Nitrosococcus oceani (ATCC 19707), is a Gram-negative obligate chemolithoautotroph capable of extracting energy and reducing power from the oxidation of ammonia to nitrite. Sequencing and annotation of the genome revealed a single circular chromosome (3,481,691 bp; 50.4% G+C) and a plasmid (40,420 bp) that contain 3052 and 41 candidate protein-encoding genes, respectively. The genes encoding proteins necessary for the function of known modes of lithotrophy and autotrophy were identified. In contrast to betaproteobacterial nitrifier genomes, the N. oceani genome contained two complete rrn operons. In contrast, only one copy of the genes needed to synthesize functional ammonia monooxygenase and hydroxylamine oxidoreductase, as well as the proteins that relay the extracted electrons to a terminal electron acceptor were identified. The N. oceani genome contained genes for 13 complete two-component systems. The genome also contained all the genes needed to reconstruct complete central pathways, the tricarboxylic acid cycle and the Embden-Meyerhof-Parnass and pentose phosphate pathways. The N. oceani genome contains the genes required to store and utilize energy from glycogen inclusion bodies and sucrose. Polyphosphate and pyrophosphate appear to be integrated in this bacterium's energy metabolism, stress tolerance and the ability to assimilate carbon via gluconeogenesis. One set of genes for type I RuBisCO was identified, while genes necessary for methanotrophy and for carboxysome formation were not identified. The N. oceani genome contains two copies each of the genes or operons necessary to assemble functional complexes I and IV as well as ATP synthase (one H{sup +}-dependent F{sub 0}F{sub 1}-type, one Na{sup +}-dependent V-type).
Date: August 3, 2006
Creator: Klotz, M G; Arp, D J; Chain, P S; El-Sheikh, A F; Hauser, L J; Hommes, N G et al.
Partner: UNT Libraries Government Documents Department

Consortium to develop the medical uses of NMR imaging, NMR spectroscopy, and positron emission tomography. Final technical report

Description: The goal of this work is to, perform clinically relevant studies using a new whole-body 4.1 T NMR imaging spectrometer. Initially we will develop and approach for the assessment of the severity of skeletal muscle involvement in ischemic peripheral vascular disease.
Date: June 1, 1998
Creator: Pohost, G.M.
Partner: UNT Libraries Government Documents Department

NREL Creates New Pathways for Producing Biofuels and Acids from Cyanobacteria (Fact Sheet)

Description: Cyanobacteria use photosynthesis to convert carbon dioxide into glycogen, a carbohydrate that is stored in the cells as an energy source. However, researchers at the National Renewable Energy Laboratory (NREL) have discovered that this photosynthesis can be redirected to produce lipids and valuable organic acids. The research could yield a new source of biofuels, because the lipids can potentially be extracted from the bacteria and converted into biodiesel.
Date: October 1, 2012
Partner: UNT Libraries Government Documents Department

Metabolomic Functional Analysis of Bacterial Genomes: Final Report

Description: The availability of the complete DNA sequence of the bacterial genome of Nitrosomonas europaea offered the opportunity for unprecedented and detailed investigations of function. We studied the function of genes involved in carbohydrate and Fe metabolism. N. europaea has genes for the synthesis and degradation of glycogen and sucrose but cannot grow on substrates other than ammonia and CO2. Granules of glycogen were detected in whole cells by electron microscopy and quantified in cell-free extracts by enzymatic methods. The cellular glycogen and sucrose content varied depending on the composition of the growth medium and cellular growth stage. N. europaea also depends heavily on iron for metabolism of ammonia, is particularly interesting since it lacks genes for siderophore production, and has genes with only low similarity to known iron reductases, yet grows relatively well in medium containing low Fe. By comparing the transcriptomes of cells grown in iron-replete medium versus iron-limited medium, 247 genes were identified as differentially expressed. Mutant strains deficient in genes for sucrose, glycogen and iron metabolism were created and are being used to further our understanding of ammonia oxidizing bacteria.
Date: January 1, 2008
Creator: Sayavedra-Soto, Daniel J. Arp Luis A.
Partner: UNT Libraries Government Documents Department

Integrated genome-based studies of Shewanella ecophysiology

Description: This project was a component of the Shewanella Federation and, as such, contributed to the overall goal of applying the genomic tools to better understand eco-physiology and speciation of respiratory-versatile members of Shewanella genus. Our role at Boston University was to perform bioreactor and high throughput gene expression microarrays, and combine dynamic flux balance modeling with experimentally obtained transcriptional and gene expression datasets from different growth conditions. In the first part of project, we designed the S. oneidensis microarray probes for Affymetrix Inc. (based in California), then we identified the pathways of carbon utilization in the metal-reducing marine bacterium Shewanella oneidensis MR-1, using our newly designed high-density oligonucleotide Affymetrix microarray on Shewanella cells grown with various carbon sources. Next, using a combination of experimental and computational approaches, we built algorithm and methods to integrate the transcriptional and metabolic regulatory networks of S. oneidensis. Specifically, we combined mRNA microarray and metabolite measurements with statistical inference and dynamic flux balance analysis (dFBA) to study the transcriptional response of S. oneidensis MR-1 as it passes through exponential, stationary, and transition phases. By measuring time-dependent mRNA expression levels during batch growth of S. oneidensis MR-1 under two radically different nutrient compositions (minimal lactate and nutritionally rich LB medium), we obtain detailed snapshots of the regulatory strategies used by this bacterium to cope with gradually changing nutrient availability. In addition to traditional clustering, which provides a first indication of major regulatory trends and transcription factors activities, we developed and implemented a new computational approach for Dynamic Detection of Transcriptional Triggers (D2T2). This new method allows us to infer a putative topology of transcriptional dependencies, with special emphasis on the nodes at which external stimuli are expected to affect the internal dynamics. In parallel, we addressed the question of how to compare transcriptional profiles across different ...
Date: February 14, 2012
Creator: Daniel, Segre & Qasim, Beg
Partner: UNT Libraries Government Documents Department

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

Description: We present here the complete 2.4 Mb genome of the cellulolytic actinobacterial thermophile, Acidothermus cellulolyticus 11B. New secreted glycoside hydrolases and carbohydrate esterases were identified in the genome, revealing a diverse biomass-degrading enzyme repertoire far greater than previously characterized, and significantly elevating the industrial value of this organism. A sizable fraction of these hydrolytic enzymes break down plant cell walls and the remaining either degrade components in fungal cell walls or metabolize storage carbohydrates such as glycogen and trehalose, implicating the relative importance of these different carbon sources. A novel feature of the A. cellulolyticus secreted cellulolytic and xylanolytic enzymes is that they are fused to multiple tandemly arranged carbohydrate binding modules (CBM), from families 2 and 3. Interestingly, CBM3 was found to be always N-terminal to CBM2, suggesting a functional constraint driving this organization. While the catalytic domains of these modular enzymes are either diverse or unrelated, the CBMs were found to be highly conserved in sequence and may suggest selective substrate-binding interactions. For the most part, thermophilic patterns in the genome and proteome of A. cellulolyticus were weak, which may be reflective of the recent evolutionary history of A. cellulolyticus since its divergence from its closest phylogenetic neighbor Frankia, a mesophilic plant endosymbiont and soil dweller. However, ribosomal proteins and non-coding RNAs (rRNA and tRNAs) in A. cellulolyticus showed thermophilic traits suggesting the importance of adaptation of cellular translational machinery to environmental temperature. Elevated occurrence of IVYWREL amino acids in A. cellulolyticus orthologs compared to mesophiles, and inverse preferences for G and A at the first and third codon positions also point to its ongoing thermoadaptation. Additional interesting features in the genome of this cellulolytic, hot-springs dwelling prokaryote include a low occurrence of pseudogenes or mobile genetic elements, an unexpected complement of flagellar genes, and presence of three ...
Date: January 1, 2009
Creator: Barabote, Ravi D.; Xie, Gary; Leu, David H.; Normand, Philippe; Necsulea, Anamaria; Daubin, Vincent et al.
Partner: UNT Libraries Government Documents Department

Effects of Mine Waste Contamination on Fish and Wildlife Habitat at Multiple Levels of Biological Organization in the Methow River, 2001-2002 Annual Report.

Description: A three-year multidisciplinary study was conducted on the relationship between mine waste contamination and the effects on aquatic and terrestrial habitats in the Methow River below abandoned mines near Twisp in Okanogan County, Washington (U.S.A.). Ore deposits in the area were mined for gold, silver, copper and zinc until the early 1950's. An above-and-below-mine approach was used to study potentially impacted sites. Although the dissolved metal content of water in the Methow River was below the limits of detection, eleven chemicals of potential environmental concern were identified in the tailings, mine effluents, groundwater, streamwater and sediments (Al, As, B, Ba, Cd, Cr, Cu, Mn, Pb, Se and Zn). The potential for ecosystem level impacts was reflected in the risk of contamination in the mine waste to communities and populations that are valued for their functional properties related to energy storage and nutrient cycling. Dissolved and sediment metal contamination changed the benthic insect community structure in a tributary of the Methow River below Alder Mine, and at the population level, caddisfly larval development in the Methow River was delayed. Arsenic accumulation in bear hair and Cd in fish liver suggest top predators are effected. In situ exposure of juvenile triploid trout (Oncorhynchus mykiss) to conditions at the downstream site resulted in reduced growth and increased mortality among exposed individuals. Histopathological studies of their tissues revealed extensive glycogen inclusions suggesting food is being converted into glycogen and stored in the liver but the glycogen is not being converted back normally into glucose for distribution to other tissues in the body. Subcellular observations revealed mitochondrial changes including a decrease in the number and increase in the size of electron-dense metrical granules, the presence of glycogen bodies in the cytoplasm, and glycogen nuclei in exposed trout hepatocytes, which are signs that Type IV Glycogen ...
Date: June 1, 2002
Creator: Peplow, Dan & Edmonds, Robert.
Partner: UNT Libraries Government Documents Department

Dispersion of Metals from Abandoned Mines and their Effect on Biota in the Methow River, Okanogan County, Washington: Final Report 2002-2003.

Description: A study of mine-waste contamination effects on Methow River habitat on the eastern slopes of the north Cascade Mountains in Washington state, U.S.A., revealed impacts at ecosystem, community, population, individual, tissue, and cellular levels. Ore deposits in the area were mined for gold, silver, copper and zinc until the early 1950's, but the mines are now inactive. An above-and-below-mine approach was used to compare potentially impacted to control sites. The concentrations of eleven trace elements (i.e., Al, As, B, Ba, Cd, Cr, Cu, Mn, Pb, Se, and Zn) in Methow River sediments downstream from the abandoned mine sites were higher than background levels. Exposed trout and caddisfly larvae in the Methow River showed reduced growth compared to controls. Samples of liver from juvenile trout and small intestine from exposed caddisfly larvae were examined for evidence of metal accumulation, cytopathological change, and chemical toxicity. Morphological changes that are characteristic of nuclear apoptosis were observed in caddisfly small intestine columnar epithelial and trout liver nuclei where extensive chromatin condensation and margination was observed. Histopathological studies revealed glycogen bodies were present in the cytosol and nuclei, which are indicators of Type IV Glycogen Storage Disease (GSD IV). This suggests food is being converted into glycogen and stored in the liver but the glycogen is not being converted back normally into glucose for distribution to other tissues in the body resulting in poor growth. Examination of trout hepatocytes by transmission electron microscopy revealed the accumulation of electron dense granules in the mitochondrial matrix. Matrix granules contain mixtures of Cd, Cu, Au, Pb, Ni, and Ti. Contaminated sediments caused adverse biological effects at different levels of biological organization, from the cellular to ecosystem-level responses, even where dissolved metal concentrations in the corresponding surface water met water-quality criteria.
Date: May 15, 2003
Creator: Peplow, Dan & Edmonds, Robert
Partner: UNT Libraries Government Documents Department

The bioenergetics of salt tolerance

Description: The aim of this project was to try to understand the adaptive mechanisms that organisms develop in order to respond to a sudden transformation in their environment to a salt shock.'' To study this problem we used a fresh water oxygenic photosynthetic cyanobacterium known as Synecoccus 6311. This organism suffers injury after this sudden exposure to high concentrations of sodium chloride equivalent to or even higher than that in sea water. Yet they are able to re-establish their photosynthetic activity which is partially injured and return to virtually normal growth rates. Identification of the temporal sequence of changes involved in adaptation to this stress was the rationale. Indeed this project employed a wide variety of biochemical and biophysical methods, including electron spin resonance techniques and nuclear magnetic resonance to study the bioenergetics and transport mechanisms, growth and energy changes in these organisms and how the structural components of the cells changed in response to adaptation to growth at high salinity. The problem has relevance for higher plants because most of the arable farmland in the work is already under use and that which is not used is usually in salite environments. Hence, understanding basic mechanisms of salt tolerance is a fundamental biological problem with great applications for bioproductivity and agriculture. 18 refs.
Date: January 1, 1991
Creator: Packer, L.
Partner: UNT Libraries Government Documents Department