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Description: The production of cellulases and hemicellulases was studied wi·th Trichoderrna reesei Rut-C-30. This organism produced, together with high cellulase activities, considerable amounts of xylanases and {beta}-glucosidase. Three cellulose concentrations (1, 2.5 and 5.0%) were examined to determine the maximum levels of cellulase activity obtainable in submerged culture. Temperature and pH profiling to increase viable cell mass to maximum levels and thereby enhancing fermentor productivity at the higher substrate levels is discussed. The effect of temperature, pH, Tween~80 concentration, carbon source and substrate concentration on the rates of mycelial growth and extra-cellular enzyme production are described.
Date: June 1, 1980
Creator: Tangnu, S.Kishen; Blanch, Harvey W. & Wilke, Charles R.
Partner: UNT Libraries Government Documents Department

Nanoimaging to Prevent and Treat Alzheimer’s and Parkinson’s Diseases. Scientific/Technical report

Description: This project will develop innovative approaches to characterization of the very early stages of protein aggregation that eventually can be translated to the development of early diagnostic tools and efficient treatments for Alzheimer’s, Parkinson’s and Huntington’s diseases. Funding will be used to acquire nanoimaging technology for nanoscale imaging, manipulation and analysis of biomedical materials to develop treatments that will repair disabled proteins and cure diseases that result from protein malfunction, specifically Alzheimer’s and Parkinson’s diseases. Expected outcomes include tests for early diagnosis and therapeutic treatments for these devastating neurological diseases. To elucidate the mechanisms of protein misfolding, we will establish an extensive program of experimental studies using a broad arsenal of advanced nanoscale and traditional techniques that will be integrated with molecular-scale modeling of protein misfolding and the nucleation of aggregate structures. To identify intracellular machinery or/and multicomponent complexes critically involved in protein misfolding, we will characterize interactions between targeted proteins and specific intracellular components or metabolites that impact on protein conformational pathways leading to protein misfolding accompanied by formation of toxic aggregated morphologies. To design innovative nanotechnology tools for the control of intracellular protein misfolding and aggregation processes, we will develop a predictive molecular scale model for intracellular protein misfolding and the formation of toxic aggregates. Verified through experimental studies, the objective is to establish an enabling foundation for the engineering of novel molecular diagnostics and therapeutics for various cellular pathologies.
Date: December 20, 2012
Creator: Yuri L. Lyubchenko, PhD, DSc
Partner: UNT Libraries Government Documents Department

Plasminogen activator inhibitor 1: Mechanisms of its synergistic regulation by growth factors

Description: My research is on the synergistic regulation of PAI-1 by EGF and TGF-β. The mechanism of synergistic regulation of PAI-1 by EGF and TGF-β are addressed. Methods are described for effective identification of RNA accessible sites for antisense oligodexoxynucleotides (ODNs) and siRNA. In this study effective AS-ODN sequences for both Lcn2 and Bcl2 were identified by in vitro tiled microarray studies. Our results suggest that hybridization of ODN arrays to a target mRNA under physiological conditions might be used as a rapid and reliable in vitro method to accurately identify targets on mRNA molecules for effective antisense and potential siRNA activity in vivo.
Date: December 1, 2011
Creator: Song, Xiaoling
Partner: UNT Libraries Government Documents Department

Imaging gene expression in real-time using aptamers

Description: Signal transduction pathways are usually activated by external stimuli and are transient. The downstream changes such as transcription of the activated genes are also transient. Real-time detection of promoter activity is useful for understanding changes in gene expression, especially during cell differentiation and in development. A simple and reliable method for viewing gene expression in real time is not yet available. Reporter proteins such as fluorescent proteins and luciferase allow for non-invasive detection of the products of gene expression in living cells. However, current reporter systems do not provide for real-time imaging of promoter activity in living cells. This is because of the long time period after transcription required for fluorescent protein synthesis and maturation. We have developed an RNA reporter system for imaging in real-time to detect changes in promoter activity as they occur. The RNA reporter uses strings of RNA aptamers that constitute IMAGEtags (Intracellular MultiAptamer GEnetic tags), which can be expressed from a promoter of choice. The tobramycin, neomycin and PDC RNA aptamers have been utilized for this system and expressed in yeast from the GAL1 promoter. The IMAGEtag RNA kinetics were quantified by RT-qPCR. In yeast precultured in raffinose containing media the GAL1 promoter responded faster than in yeast precultured in glucose containing media. IMAGEtag RNA has relatively short half-life (5.5 min) in yeast. For imaging, the yeast cells are incubated with their ligands that are labeled with fluorescent dyes. To increase signal to noise, ligands have been separately conjugated with the FRET (Förster resonance energy transfer) pairs, Cy3 and Cy5. With these constructs, the transcribed aptamers can be imaged after activation of the promoter by galactose. FRET was confirmed with three different approaches, which were sensitized emission, acceptor photobleaching and donor lifetime by FLIM (fluorescence lifetime imaging microscopy). Real-time transcription was measured by FLIM-FRET, which ...
Date: December 13, 2011
Creator: Shin, Il Chung
Partner: UNT Libraries Government Documents Department

Fourteenth-Sixteenth Microbial Genomics Conference-2006-2008

Description: The concept of an annual meeting on the E. coli genome was formulated at the Banbury Center Conference on the Genome of E. coli in October, 1991. The first meeting was held on September 10-14, 1992 at the University of Wisconsin, and this was followed by a yearly series of meetings, and by an expansion to include The fourteenth meeting took place September 24-28, 2006 at Lake Arrowhead, CA, the fifteenth September 16-20, 2007 at the University of Maryland, College Park, MD, and the sixteenth September 14-18, 2008 at Lake Arrowhead. The full program for the 16th meeting is attached. There have been rapid and exciting advances in microbial genomics that now make possible comparing large data sets of sequences from a wide variety of microbial genomes, and from whole microbial communities. Examining the “microbiomes”, the living microbial communities in different host organisms opens up many possibilities for understanding the landscape presented to pathogenic microorganisms. For quite some time there has been a shifting emphasis from pure sequence data to trying to understand how to use that information to solve biological problems. Towards this end new technologies are being developed and improved. Using genetics, functional genomics, and proteomics has been the recent focus of many different laboratories. A key element is the integration of different aspects of microbiology, sequencing technology, analysis techniques, and bioinformatics. The goal of these conference is to provide a regular forum for these interactions to occur. While there have been a number of genome conferences, what distinguishes the Microbial Genomics Conference is its emphasis on bringing together biology and genetics with sequencing and bioinformatics. Also, this conference is the longest continuing meeting, now established as a major regular annual meeting. In addition to its coverage of microbial genomes and biodiversity, the meetings also highlight microbial communities ...
Date: April 18, 2011
Creator: Miller, Jeffrey H
Partner: UNT Libraries Government Documents Department

Fundamental Studies of Recombinant Hydrogenases

Description: This research addressed the long term goals of understanding the assembly and organization of hydrogenase enzymes, of reducing them in size and complexity, of determining structure/function relationships, including energy conservation via charge separation across membranes, and in screening for novel H2 catalysts. A key overall goal of the proposed research was to define and characterize minimal hydrogenases that are produced in high yields and are oxygen-resistant. Remarkably, in spite of decades of research carried out on hydrogenases, it is not possible to readily manipulate or design the enzyme using molecular biology approaches since a recombinant form produced in a suitable host is not available. Such resources are essential if we are to understand what constitutes a “minimal” hydrogenase and design such catalysts with certain properties, such as resistance to oxygen, extreme stability and specificity for a given electron donor. The model system for our studies is Pyrococcus furiosus, a hyperthermophile that grows optimally at 100°C, which contains three different nickel-iron [NiFe-] containing hydrogenases. Hydrogenases I and II are cytoplasmic while the other, MBH, is an integral membrane protein that functions to both evolve H2 and pump protons. Three important breakthroughs were made during the funding period with P. furiosus soluble hydrogenase I (SHI). First, we produced an active recombinant form of SHI in E. coli by the co-expression of sixteen genes using anaerobically-induced promoters. Second, we genetically-engineered P. furiosus to overexpress SHI by an order of magnitude compared to the wild type strain. Third, we generated the first ‘minimal’ form of SHI, one that contained two rather than four subunits. This dimeric form was stable and active, and directly interacted with a pyruvate-oxidizing enzyme with any intermediate electron carrier. The research resulted in five peer-reviewed publications.
Date: January 25, 2014
Creator: Adams, Michael W
Partner: UNT Libraries Government Documents Department

Information on a Major New Initiative: Mapping and Sequencing the Human Genome (1986 DOE Memorandum)

Description: In the history of the Human Genome Program, Dr. Charles DeLisi and Dr. Alvin Trivelpiece of the Department of Energy (DOE) were instrumental in moving the seeds of the program forward. This May 1986 memo from DeLisi to Trivelpiece, director of DOE's Office of Energy Research, documents this fact. Following the March 1986 Santa Fe workshop on the subject of mapping and sequencing the human genome, Delisi's memo outlines workshop conclusions, explains the relevance of this project to DOE and the importance of the Department's laboratories and capabilities, notes the critical experience of DOE in managing projects of this scale and potential magnitude, and recognizes the fact that the project will impact biomedical science in ways which could not be fully anticipated at the time. Subsequently, program guidance was further sought from the DOE Health Effects Research Advisory Committee (HERAC) and the April 1987 HERAC report recommmended that DOE and the nation commit to a large, multidisciplinary, scientific and technological undertaking to map and sequence the human genome.
Date: May 6, 1986
Creator: DeLisi, Charles (Associate Director, Heath and Environmental Research, DOE Office of Energy Research)
Partner: UNT Libraries Government Documents Department


Description: SV40 minichromosomes were reacted with (+)7{beta},8{alpha}-dihydroxy-9{alpha},10{alpha}-epoxy- 7,8,9,10-tetrahydrobenzo[a]pyrene (BaP diol epoxide). Low levels of modification (< 5 DNA adducts/minichromosome) did not detectably alter the structure of the minichromosomes but high levels (> 200 DNA adducts/minichromosome) led to extensive fragmentation. Relative to naked SV40 DNA BaP diol epoxide induced alkylation and strand scission of minichromosomal DNA was reduced or enhanced by factors of 1.5 and 2.0, respectively. The reduction in covalent binding was attributed to the presence of histones, which competed with DNA for the hydrocarbon and reduced the probability of BaP diol epoxide intercalation by tightening the helix. The enhancement of strand scission was probably due to the catalytic effect of histones on the rate of S-elimination at apurinic sites, although an altered adduct profile or the presence of a repair endonuclease were not excluded. Staphylococcal nuclease digestion indicated that BaP dial epoxide randomly alkylated the minichromosomal DNA. This is in contrast to studies with cellular chromatin where internucleosomal DNA was preferentially modified. Differences in the minichromosomal protein complement were responsible for this altered susceptibility.
Date: March 1, 1980
Creator: Gamper, Howard B.; Yokota, Hisao A. & Bartholomew, James C.
Partner: UNT Libraries Government Documents Department


Description: Isolated cells from leaves of Spinacea oleracea have been maintained in a state capable of high rates of photosynthetic CO{sub 2} fixation for more than 60 h. The incorporation of {sup 14}CO{sub 2} under saturating CO{sub 2} conditions into carbohydrates, carboxylic acids, and amino acids, and the effect of ammonia on this incorporation have been studied. Total incorporation, specific radioactivity and pool size have been determined as a function of time for most of the protein amino acids and for {gamma}-aminobutyric acid. the measurements of specific activities and of the approaches to {sup 14}C "saturation" of some amino acids indicate the presence and relative sizes of metabolically active and passive pools of these amino acids. Added ammonia decreased carbon fixation into carbohydrates and increased fixation into carboxylic acids and amino acids. Different amino acids were, however, affected in different and highly specific ways. Ammonia caused large stimulatory effects in incorporation of {sup 14}C into glutamine (a factor of 16), No effect or slight decreases were seen in glycine, serine, phenylalanine, and tyrosine labeling, In.the case of glutamate, {sup 14}C-labeling decreased, but specific activity increased. The production of labeled {gamma}-aminobutyric acid was virtually stopped by ammonia. The results indicate that added ammonia stimulates the reactions mediated by pyruvate kinase and phosphoenolpyruvate carboxylase, as seen with other plant systems. The data on the effects of added ammonia on total labeling, pool sizes, and specific activities of several amino acids provides a number of indications about the intracellular sites of principal synthesis from carbon skeletons of these amino acids and the selective nature of effects of increased intracellular ammonia concentration on such synthesis.
Date: October 1, 1980
Creator: Larsen, Peder Olesen; Cornwell, Karen L.; Gee, Sherry L. & Bassham, James A.
Partner: UNT Libraries Government Documents Department


Description: Detailed methods are described for the sorting and cell cycle synchronization by means of centrifugal elutriation of an established mouse liver epithelial cell line(NMuLi). In a comparison between three different elutriation media and between two different temperatures(4° and 20° C), the NMuLi cells were found to be most reproducibly sorted in the cell cycle when run in growth medium in the absence of serum and at the lower temperature. Under these conditions. and using decrements of rotor speed calculated from an empirically derived algorithm as described in the text an initially asynchronous population (38% G{sub 1}, 36% S, and 28% G{sub 2}M) was sorted into fractions enriched to 60% G{sub 1}, 75% S, and 50% G{sub 2}M. Of the cells loaded into the rotor, 30% were lost in the elutriation process, and about 20% recovered as aggregates. The remainder appeared in the various synchronized fractions. Epithelial cells sorted in this manner demonstrated no loss of viability, and upon replating showed significant movement in the cell cycle by 6 hrs post elutriation. The degree of synchronous movement through the cell cycle achieved by elutriation depended on the part of the cell cycle from which the original elutriated fraction came. Cells collected as late S and G{sub 2}M moved through the cell cycle with the tightest sychrony.
Date: June 1, 1980
Creator: Pearlman, Andrew L. & Bartholomew, James C.
Partner: UNT Libraries Government Documents Department


Description: The isolation and chromatographic purification of chromophore-containing peptides from the P{sub R} form of phytochrome treated with pepsin and thermolysin are described. From the amino acid sequence and {sup 1}H NMR spectral analysis of phytochromobiliundeca peptide (2) , the structure of the P{sub R) phytochrome chromophore and the nature of the thioether linkage joining pigment to peptide have been established. Confirmatory evidence was obtained from similar analysis of phytochromobilioctapeptide (3) . The implications of this structural assignment with respect to the mechanism of the P{sub R} to P{sub FR} phototransformation is considered.
Date: December 1, 1979
Creator: Lagarias, J.C. & Rapoport, H.
Partner: UNT Libraries Government Documents Department


Description: We have examined the photoadducts of 4'-hydroxymethyl- 4,5',8-trirnethylpsoralen (HMT) and native DNA. Five DNA-HMT monoaddition products have been isolated and characterized, corresponding to three deoxythymidine-HMT and two deoxyuridine (derived from deoxycytidine) -HMT adducts. Structural assignments are based on high resolution mass spectrometry and {sup 1}H NMR studies, including homonuclear spin decoupling and nuclear Overhauser effect (NOE) experiments. The results of this study indicate that (1) a limited number of nucleoside-psoralen adducts are formed with native, double-stranded DNA, and (2) the stereochemistry of the adducts is apparently determined by the geomertry of the non-covalent intercalative complex formed by HMT and DNA prior to irradiation.
Date: September 1, 1980
Creator: Straub, Kenneth; Kanne, David; Hearst, John E. & Rapoport, Henry
Partner: UNT Libraries Government Documents Department


Description: Male Swiss albino CD-1 mice given a single injection of a cerebral protein synthesis inhibitor, anisomycin (ANI) (1 mg/animal), 20 min prior to single trial passive avoidance training demonstrated impaired retention at tests given 3 hr, 6 hr, 1 day, and 7 days after training. Retention was not significantly different from saline controls when tests were given 0.5 or 1.5 hr after training. Prolonging inhibition of brain protein synthesis by giving either 1 or 2 additional injections of ANI 2 or 2 and 4 hr after training did not prolong short-term retention performance. The temporal development of impaired retention in ANI treated mice could not be accounted for by drug dosage, duration of protein synthesis inhibition, or nonspecific sickness at test. In contrast to the suggestion that protein synthesis inhibition prolongs short-term memory (Quinton, 1978), the results of this experiment indicate that short-term memory is not prolonged by antibiotic drugs that inhibit cerebral protein synthesis. All evidence seems consistent with the hypothesis that short-term memory is protein synthesis independent and that the establishment of long-term memory depends upon protein synthesis during or shortly after training. Evidence for a role of protein synthesis in memory maintenance is discussed.
Date: September 1, 1980
Creator: Davis, Hasker P.; Rosenzweig, Mark R. & Jones, Oliver W.
Partner: UNT Libraries Government Documents Department


Description: The nonexchangeable base protons and the hydrogen- bonding NH-N imino protons were used to study the conformations and the helix-coil transitions in the following oligonucleotides: (I) dCT{sub 5}G + dCA{sub 5}G, (II) rCU{sub 5}G + rCA{sub 5}G, (III) dCT{sub 5}G + rCA{sub 5}G, (IV) rCU{sub 5}G + dCA{sub 5}G. The first three mixtures all form stable double-helical structures at 5{degrees}C, whereas IV forms a triple strand with a ratio of 2:1 rCU{sub 5}G:dCA{sub 5}G. The chemical shifts of the imino protons in the double strands indicate that I, II, and III have different conformations in solution. For example, the hydrogen-bonded proton of one of the C-G base pairs is more shielded (a 0.4-ppm upfield shift) in helix I than in helix II or III. This implies a significant change in helical parameters, such as the winding angle, the distance between base pairs, or overlap of the bases. The coupling constants of the H1’ sugar protons show that helix I has 90% 2’-endo sugar conformation, whereas helix III has greater than 85% 3’-endo conformation for the observed sugar rings. The sugar pucker data are consistent with helix I having B-family geometry; III has A-family geometry. The chemical shifts of the nonexchangeable base protons in system I were followed with increasing temperature. The midpoints for the transitions, T{sub m}’s, for all the base protons were 28-30 {degrees}C; this indicates an all-or-none transition.
Date: November 1, 1980
Creator: Pardi, Arthur; Martin, Francis H. & Tinoco, Jr., Ignacio
Partner: UNT Libraries Government Documents Department


Description: Extended X-ray Absorption Fine Structure (EXAFS) studies on the manganese contained in spinach chloroplasts and on certain di-u-oxo bridged manganese dimers of the form (X{sub 2}Mn)O{sub 2}(MnX{sub 2} (X=2,2'-bypyridine and 1,10-phenanthroline) are reported. From these studies, the manganese associated with photosynthetic oxygen evolution is suggested to occur as a bridged transition metal dimer with most likely another manganese. Extensive details on the analysis are included.
Date: November 1, 1980
Creator: Kirby, J.A.; Robertson, A.S.; Smith, J.P.; Thompson, A.C.; Thompson, A.C. & Klein, M.P.
Partner: UNT Libraries Government Documents Department


Description: X-ray absorption spectra at the Manganese K-edge are presented for spinach chloroplasts, and chloroplasts which have been Tris-treated and hence unable to evolve oxygen. A significant change in the electronic environment of manganese is observed and is attributed to the release of manganese from the thylakoid membranes with a concomitant change in oxidation state. A correlation of the K-edge energy, defined as the energy at the first inflection point, with coordination charge has been established for a number of manganese compounds of known structure and oxidation state. Comparison of the manganese K-edge energies of the chloroplast samples with the reference compounds places the average oxidation state of the chloroplasts between +2 and +3. Using the edge spectra for Tris-treated membranes which were osmotically shocked to remove the released manganese, difference edge spectra were synthesized to approximate the active pool of manganese. Coordination charge predictions for this fraction are consistent with an average resting oxidation state higher than +2. The shape at the edge is also indicative of heterogeneity of the manganese site, of low symmetry, or both.
Date: November 1, 1980
Creator: Kirby, J.A.; Goodin, D.B.; Wydrzynski, T.; Robertson, A.S. & Klein, M.P.
Partner: UNT Libraries Government Documents Department


Description: TA3 ascites tumor cells maintained in vitro as a dilute suspension in 0.9% NaCl solution (physiological saline) were found to undergo time-dependent degenerative processes leading to alterations in both membrane characteristics and tumor transplantation properties. A 30% decrease in the negative cellular surface charge density occurred within 2 hr. when TA3 cells were incubated in a 0.9% NaCl solution at 23 °C. A similar reduction in negative surface charge density occurred within 0.5 hr. when the medium was maintained at 37 °C. This time-dependent reduction in surface charge was prevented when cellular metabolism was blocked either by maintaining the medium at 4 °C. or by adding 1 mM cyanide ion to a 23 °C medium. TA3 cells incubated as a dilute suspension in 0.9% NaCl solution at 23 °C also exhibited a large 9 time-dependent reduction in proliferative capacity in isogeneic LAF1/J hosts, as indicated by an increase in the tumor dose for 50% mortality (TD50). Lowering the temperature of the medium to 4 °C was observed to slow the onset of the degenerative processes that lead to a decreased transplantability of TA3 cells. The modification in growth properties of TA3 cells maintained in vitro was found to be attributable in part to an alteration in tumor histocompatibility. This effect was demonstrated by comparing the tumor growth kinetics and TD50 values in normal hosts versus hosts that had been immunosuppressed by whole-body irradiation. Following the in vitro maintenance of TA3 cells, nigrosin dye exclusion tests were performed as a means of assessing cell viability. Evidence obtained in this series of experiments indicated that vital staining is an inadequate criterion for judging either the extent of cell membrane damage or the loss of cellular proliferative capacity.
Date: December 1, 1980
Creator: Tenforde, T.S.; Richards, W.R. & Kelly, L.S.
Partner: UNT Libraries Government Documents Department

Workshop on ENU Mutagenesis: Planning for Saturation, July 25-28, 2002

Description: The goal of the conference is to enhance the development of improved technologies and new approaches to the identification of genes underlying chemically-induced mutant phenotypes. The conference brings together ENU mutagenesis experts from the United States and aborad for a small, intensive workshop to consider these issues.
Date: July 25, 2002
Creator: Nadeau, Joseph H
Partner: UNT Libraries Government Documents Department


Description: The Gordon Research Conference on MICROBIAL STRESS RESPONSE was held at Mount Holyoke College, South Hadley, Massachusetts, July 15-20, 2012. The Conference was well-attended with 180 participants. The 2012 Microbial Stress Responses Gordon Research Conference will provide a forum for the open reporting of recent discoveries on the diverse mechanisms employed by microbes to respond to stress. Approaches range from analysis at the molecular level (how are signals perceived and transmitted to change gene expression or function) to cellular and microbial community responses. Gordon Research Conferences does not permit publication of meeting proceedings.
Date: July 25, 2012
Creator: Donohue, Timothy
Partner: UNT Libraries Government Documents Department


Description: The delicate balance among cellular pathways that control mutagenic changes in DNA will be the focus of the 2012 Mutagenesis Gordon Research Conference. Mutagenesis is essential for evolution, while genetic stability maintains cellular functions in all organisms from microbes to metazoans. Different systems handle DNA lesions at various times of the cell cycle and in different places within the nucleus, and inappropriate actions can lead to mutations. While mutation in humans is closely linked to disease, notably cancers, mutational systems can also be beneficial. The conference will highlight topics of beneficial mutagenesis, including full establishment of the immune system, cell survival mechanisms, and evolution and adaptation in microbial systems. Equal prominence will be given to detrimental mutation processes, especially those involved in driving cancer, neurological diseases, premature aging, and other threats to human health. Provisional session titles include Branching Pathways in Mutagenesis; Oxidative Stress and Endogenous DNA Damage; DNA Maintenance Pathways; Recombination, Good and Bad; Problematic DNA Structures; Localized Mutagenesis; Hypermutation in the Microbial World; and Mutation and Disease.
Date: August 23, 2012
Creator: Demple, Bruce
Partner: UNT Libraries Government Documents Department


Description: The Gordon Research Conference on CELLULAR & MOLECULAR FUNGAL BIOLOGY was held at Holderness School, Holderness New Hampshire, June 17 - 22, 2012. The 2012 Gordon Conference on Cellular and Molecular Fungal Biology (CMFB) will present the latest, cutting-edge research on the exciting and growing field of molecular and cellular aspects of fungal biology. Topics will range from yeast to filamentous fungi, from model systems to economically important organisms, and from saprophytes and commensals to pathogens of plants and animals. The CMFB conference will feature a wide range of topics including systems biology, cell biology and morphogenesis, organismal interactions, genome organisation and regulation, pathogenesis, energy metabolism, biomass production and population genomics. The Conference was well-attended with 136 participants. Gordon Research Conferences does not permit publication of meeting proceedings.
Date: June 22, 2012
Creator: Berman, Judith
Partner: UNT Libraries Government Documents Department