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Genomic plasticity and catabolic potential of Pseudomonas cepacia

Description: The primary goal of this project was to gain information about the size and organization of the genome of Burkholderia cepacia (formerly Pseudomonas cepacia), a microbe which continues to attract attention because of its extraordinary degradative abilities and potential as an agent of bioremediation. This bacterium is no longer considered to be a member of genus Pseudomonas nor does it belong in the gamma-subclass of the proteobacteria, in which the authentic pseudomonads are grouped. It belongs in the less well characterized beta-subclass of the proteobacteria. Technology for manipulation of large DNA fragments developed by Cantor was used to demonstrate that chromosomal multiplicity, a characteristic yet to be observed in a gamma-subclass bacterium, is common among B. cepacia strains. A derivative of Tn5 suitable for determining the chromosomal locations of various B. cepacia genes was also constructed.
Date: April 1, 1996
Creator: Lessie, T.G.
Partner: UNT Libraries Government Documents Department

SEARCH and a computational perspective of evolution

Description: This paper develops an alternate perspective of natural evolution using the SEARCH (Search Envisioned As Relation and Class Hierarchizing) framework (Kargupta, 1995). Some problems of existing views about evolutionary computation are noted. An attempt is made to fulfill these deficiencies using a new computational perspective of gene expression based on a decomposition of blackbox optimization in terms of relations, classes, samples, and partial ordering.
Date: May 1, 1996
Creator: Kargupta, H.
Partner: UNT Libraries Government Documents Department

Resolution of thylakoid polyphenol oxidase and a protein kinase

Description: The predominant protein kinase activity in octylglucoside (OG) extracts of spinach thylakoids has been attributed to a 64-kDa protein, tp64. Recent work calls into question the relation between tp64 and protein kinase activity, which were fractionated apart using fluid phase IEF and hydroxylapatite chromatography. Hind et al. sequenced tp64 from the cDNA and showed it to be a polyphenol oxidase (PPO) homolog. Its transit peptide indicates a location for the mature protein within the thylakoid lumen, where there is presumably no ATP and where it is remote from the presumed kinase substrates: the stromally exposed regions of integral PS-II membrane proteins. Here the authors suggest that the kinase is a 64-kDa protein distinct from tp64.
Date: December 31, 1995
Creator: Race, H.L.; Davenport, J.W. & Hind, G.
Partner: UNT Libraries Government Documents Department

Third International E. coli genome meeting

Description: Proceedings of the Third E. Coli Genome Meeting are provided. Presentations were divided into sessions entitled (1) Large Scale Sequencing, Sequence Analysis; (2) Databases; (3) Sequence Analysis; (4) Sequence Divergence in E. coli Strains; (5) Repeated Sequences and Regulatory Motifs; (6) Mutations, Rearrangements and Stress Responses; and (7) Origins of New Genes. The document provides a collection of abstracts of oral and poster presentations.
Date: December 31, 1994
Partner: UNT Libraries Government Documents Department

Simulation studies of vapor bubble generation by short-pulse lasers

Description: Formation of vapor bubbles is characteristic of many applications of short-pulse lasers in medicine. An understanding of the dynamics of vapor bubble generation is useful for developing and optimizing laser-based medical therapies. To this end, experiments in vapor bubble generation with laser light deposited in an aqueous dye solution near a fiber-optic tip have been performed. Numerical hydrodynamic simulations have been developed to understand and extrapolate results from these experiments. Comparison of two-dimensional simulations with the experiment shows excellent agreement in tracking the bubble evolution. Another regime of vapor bubble generation is short-pulse laser interactions with melanosomes. Strong shock generation and vapor bubble generation are common physical features of this interaction. A novel effect of discrete absorption by melanin granules within a melanosome is studied as a possible role in previously reported high Mach number shocks.
Date: October 26, 1997
Creator: Amendt, P.; London, R.A. & Strauss, M.
Partner: UNT Libraries Government Documents Department

Comparing Candidate Hospital Report Cards

Description: We present graphical and analytical methods that focus on multivariate outlier detection applied to the hospital report cards data. No two methods agree which hospitals are unusually good or bad, so we also present ways to compare the agreement between two methods. We identify factors that have a significant impact on the scoring.
Date: December 31, 1997
Creator: Burr, T.L.; Rivenburgh, R.D.; Scovel, J.C. & White, J.M.
Partner: UNT Libraries Government Documents Department

Visualizing Gene Expression In Situ

Description: Visualizing bacterial cells and describing their responses to the environment are difficult tasks. Their small size is the chief reason for the difficulty, which means that we must often use many millions of cells in a sample in order to determine what the average response of the bacteria is. However, an average response can sometimes mask important events in bacterial physiology, which means that our understanding of these organisms will suffer. We have used a variety of instruments to visualize bacterial cells, all of which tell us something different about the sample. We use a fluorescence activated cell sorter to sort cells based on the fluorescence provided by bioreporter genes, and these can be used to select for particular genetic mutations. Cells can be visualized by epifluorescent microscopy, and sensitive photodetectors can be added that allow us to find a single bacterial cell that is fluorescent or bioluminescent. We have also used standard photomultipliers to examine cell aggregates as field bioreporter microorganisms. Examples of each of these instruments show how our understanding of bacterial physiology has changed with the technology.
Date: November 2, 1998
Creator: Burlage, R.S.
Partner: UNT Libraries Government Documents Department

Human genetics for non-scientists: Practical workshops for policy makers and opinion leaders

Description: These workshops form part of a series of workshops that the Banbury and the DNA Learning Centers of Cold Spring Harbor Laboratory have held for a number of years, introducing genetics, and the ways in which scientific research is done, to non-scientists. The purpose of the workshops as stated in the grant application was: {open_quotes}Our objective is to foster a better understanding of the societal impact of human genome research by providing basic information on genetics to non-scientists whose professions or special interests interface with genetic technology.... Participants will be chosen for their interest in human genetics and for their roles as opinion leaders in their own communities. Primary care physicians are of particular interest to us for this series of workshops.{close_quotes} Two workshops were held under this grant. The first was held in 21-24 April, 1994 and attended by 20 participants, and the second was held 16-19 November, 1995, and attended by 16 participants. In each case, there was a combination of concept lectures on the foundations of human molecular genetics; lectures by invited specialists; and laboratory experiments to introduce non-scientists to the techniques used in molecular genetics.
Date: December 31, 1995
Partner: UNT Libraries Government Documents Department

Allergy arising from exposure to airborne contaminants in an insect rearing facility: Health effects and exposure control

Description: In agricultural crop improvement, yield under various stress conditions and limiting factors is assessed experimentally. Of the stresses on plants which affect yield are those due to insects. Ostrinia nubilalis, the European corn borer (corn borer) is a major pest in sweet and field corn in the U.S. There are many ways to fight crop pests such as the corn borer, including (1) application of chemical insecticides, (2) application of natural predators and, (3) improving crop resistance through plant genetics programs. Randomized field trials are used to determine the effectiveness of pest management programs. These trials frequently consist of randomly selected crop plots to which well-defined input regimes are instituted. For example, corn borers might be released onto crop plots in several densities at various stages of crop development, then sprayed with different levels of pesticide. These experiments are duplicated across regions and, in some cases across the country, to determine, in this instance for example, the best pesticide application rate for a given pest density and crop development stage. In order to release these pests onto crop plots, one must have an adequate supply of the insect pest. In winter months studies are carried out in the laboratory to examine chemical and natural pesticide effectiveness, as well as such things as the role of pheromones in moth behavior. The advantage in field trials is that yield data can be garnered directly. In this country, insects are raised for crop research primarily through the US Department of Agriculture, in cooperation with public Land Grant Universities and, by the private sector agricultural concerns - seed companies and others. This study quantifies the airborne allergen exposure of persons working in a Land Grant University entomology lab were allergy to European corn borer was suspected.
Date: June 1, 1994
Creator: Wolff, D.
Partner: UNT Libraries Government Documents Department

Frequency doubling and tripling of ultrashort laser pulses in biological tissues

Description: Structural proteins such as collagen and elastin are known to generate second harmonic at high laser intensities. Second and third harmonic generations (SHG, THG) of 0.4 ps Ti-Sapphire laser radiation at 800 nm were observed in various biological tissues. Dependence of SHG on laser pulse energy and pulse width was investigated. Reflected second harmonic yield was measured for animal tissue <i>in vitro</i> and human skin <i>in vivo</i>. The yield varies about a factor of 20 for various areas of the skin while the scattered laser radiation (diffuse reflectance) varies only by a factor of 2. In some cases the THG efficiency was comparable to the SHG. Possible applications of higher harmonic radiation for diagnostics and microscopy are discussed.
Date: July 24, 1998
Creator: Da Silva, L. B.; Eichler, J.; Joslin, E. J. & Kim, B.-M.
Partner: UNT Libraries Government Documents Department

Porphyrin Interactions with Wild Type and Mutant Mouse Ferrochelatase

Description: Ferrochelatase (EC, the terminal enzyme of the heme biosynthetic pathway, catalyzes Fe<sup>2+</sup> chelation into protoporphyrin IX. Resonance Raman and W-visible absorbance spectroscopes of wild type and engineered variants of murine ferrochelatase were used to examine the proposed structural mechanism for iron insertion into protoporphyrin by ferrochelatase. The recombinant variants (i.e., H207N and E287Q) are enzymes in which the conserved amino acids histidine-207 and glutamate-287 of murine ferrochelatase were substituted with asparagine and glutamine, respectively. Both of these residues are at the active site of the enzyme as deduced from the Bacillus subtilis ferrochelatase three-dimensional structure. Addition of free base or metalated porphyrins to wild type ferrochelatase and H207N variant yields a quasi 1:1 complex, possibly a monomeric protein-bound species. In contrast, the addition of porphyrin (either free base or metalated) to E287Q is sub-stoichiometric, as this variant retains bound porphyrin in the active site during isolation and purification. The specificity of porphyrin binding is confirmed by the narrowing of the structure-sensitive resonance Raman lines and the vinyl vibrational mode. Resonance Raman spectra of free base and metalated porphyrins bound to the wild type ferrochelatase indicate a nonplanar distortion of the porphyrin macrocycle, although the magnitude of the distortion cannot be determined without first defining the specific type of deformation. Significantly, the extent of the nonplanar distortion varies in the case of H207N- and E287Q-bound porphyrins. In fact, resonance Raman spectral decomposition indicates a homogeneous ruffled distortion for the nickel protoporphyrin bound to the wild type ferrochelatase, whereas both a planar and ruffled conformations are present for the H207N-bound porphyrin. Perhaps more revealing is the unusual resonance , 3 Raman spectrum of the endogenous E287Q-bound porphyrin, which has the structure-sensitive lines greatly upshifted relative to those of the free base protoporphyrin in solution. This could be interpreted as an equilibrium ...
Date: May 19, 1999
Creator: Ferreira, Gloria C.; Franco, Ricardo; Lu, Yi; Ma, Jian-Guo & Shelnutt, John A.
Partner: UNT Libraries Government Documents Department

Identifying Calcium Channels and Porters in Plant Membranes

Description: The overall objectives of the proposal submitted in 6/90 was to understand how Ca was transported across plant membranes, and how these transport pathways were regulated. Ca participates in many cellular processes, including the transduction of hormonal and environmental signals, secretion, and protein folding. These processes depend on the coordination of passive Ca fluxes via channels and active Ca pumps; however these transport pathways are poorly understood in plants. We had, therefore, proposed to identify and characterize Ca transport proteins, such as the inositol-1 ,4,5-trisphosphate (IP3)-sensitive Ca channels and Ca pumps. We have had difficulties characterizing and cloning the IP3-sensitive Ca channel, but have made considerable progress on the biochemical characterization, and partial purification of a 120 kD Ca-pumping ATPase. We have begun to determine the structure of Ca pumps by molecular cloning and have already obtained a partial cDNA with features characteristic of Ca pumps.
Date: April 1, 1998
Creator: Sze, Heven
Partner: UNT Libraries Government Documents Department

Ethanologenic Enzymes of Zymomonas mobilis

Description: Zymomonas mobilis is a unique microorganism in being both obligately fermentative and utilizing a Entner-Doudoroff pathway for glycolysis. Glycolytic flux in this organism is readily measured as evolved carbon dioxide, ethanol, or glucose consumed and exceeds 1 {micro}mole glucose/min per mg cell protein. To support this rapid glycolysis, approximately 50% of cytoplasmic protein is devoted to the 13 glycolytic and fermentative enzymes which constitute this central catabolic pathway. Only 1 ATP (net) is produced from each glucose metabolized. During the past grant period, we have completed the characterization of 11 of the 13 glycolytic genes from Z. mobilis together with complementary but separate DOE-fimded research by a former post-dot and collaborator, Dr. Tyrrell Conway. Research funded in my lab by DOE, Division of Energy Biosciences can be divided into three sections: A. Fundamental studies; B. Applied studies and utility; and C. Miscellaneous investigations.
Date: March 1, 1999
Creator: Ingram, Lonnie O'Neal
Partner: UNT Libraries Government Documents Department

Manpower Assessment Brief {number_sign}43: Health Physics Enrollments and Degrees Decreased at all Levels in 1997

Description: Undergraduate degrees decreased from 84 to 62 students in 1997. As with enrollments, most of the The Health Physics Enrollments and Degrees, degrees were awarded within the health physics/ 1997 survey consisted of 51 institutions offering a radiation protection or radiation health major (79 major in health physics/radiation protection or radiation percent), while health physics/radiation protection health, or an option program equivalent to a major (for engineering programs accounted for 15 percent of the example, in radiobiology or biophysics) that prepare the undergraduates. graduates to perform as health physicists. Of the 51 programs, 1 was reported as inactive, and 5 programs MASTER`S ENROLLMENTS AND DEGREES have been suspended; 1 reported last degrees in 1996, 2 reported last degrees in 1997, and 2 programs were In 1997, the number of master`s enrollments allowing students to complete their degrees. The data decreased from 460 students to 413, or by 10 percent, for 5 programs were estimated. continuing the downward trend since 1993.
Date: June 1, 1998
Partner: UNT Libraries Government Documents Department

[Hydrodyne quarterly report]

Description: In order that this report might stand by itself, a brief description of its goals is as follows. The equipment to tenderize meat by immersing the meat in water in which a small amount of high explosive is detonated was to be designed, fabricated and tested. The equipment was then to be shipped and installed near the ARS Meat Science Laboratory in Beltsville, MD. There further testing was to be done to establish performance characteristics. It was to be shown as an operating plant to meat producers who were potential customers. This document is in letter format; main headings include design of the equipment; new patent; fabrication; testing of unit; prototype plant in Virginia; new developments; tests and potential users; basic investigation.
Date: March 1, 1996
Partner: UNT Libraries Government Documents Department

Comparison of soft and hard tissue ablation with sub-ps and ns pulse lasers

Description: Tissue ablation with ultrashort laser pulses offers several unique advantages. The nonlinear energy deposition is insensitive to tissue type, allowing this tool to be used for soft and hard tissue ablation. The localized energy deposition lead to precise ablation depth and minimal collateral damage. This paper reports on efforts to study and demonstrate tissue ablation using an ultrashort pulse laser. Ablation efficiency and extent of collateral damage for 0.3 ps and 1000 ps duration laser pulses are compared. Temperature measurements of the rear surface of a tooth section is also presented.
Date: May 1, 1996
Creator: Da Silva, L.B.; Stuart, B.C.; Celliers, P.M.; Feit, M.D.; Glinsky, M.E.; Heredia, N.J. et al.
Partner: UNT Libraries Government Documents Department

Algorithms for biomagnetic source imaging with prior anatomical and physiological information

Description: This dissertation derives a new method for estimating current source amplitudes in the brain and heart from external magnetic field measurements and prior knowledge about the probable source positions and amplitudes. The minimum mean square error estimator for the linear inverse problem with statistical prior information was derived and is called the optimal constrained linear inverse method (OCLIM). OCLIM includes as special cases the Shim-Cho weighted pseudoinverse and Wiener estimators but allows more general priors and thus reduces the reconstruction error. Efficient algorithms were developed to compute the OCLIM estimate for instantaneous or time series data. The method was tested in a simulated neuromagnetic imaging problem with five simultaneously active sources on a grid of 387 possible source locations; all five sources were resolved, even though the true sources were not exactly at the modeled source positions and the true source statistics differed from the assumed statistics.
Date: December 1995
Creator: Hughett, P. W.
Partner: UNT Libraries Government Documents Department

DNA sequence pattern recognition methods in GRAIL

Description: The goal of the GRAIL project has been to create a comprehensive analysis environment where a host of questions about genes and genome structure can be answered as quickly and accurately as possible. Constructing this system has entailed solving a number of significant technical challenges including: (a) making coding recognition in sequence more sensitive and accurate, (b) compensating for isochore base compositional effects in coding prediction, (c) developing methods to determine which parts of each strand of a long genomic DNA are the coding strand, (d) improving the accuracy of splice site prediction and recognizing non-consensus sites, and (e) recognizing variable regulatory structures such as polymerase II promoters. An additional challenge has been to construct algorithms which compensate for the deleterious effects of insertion or deletion (indel) errors in the coding region recognition process. This paper addresses progress on these technical issues and the current state of sequence feature recognition methods.
Date: December 31, 1995
Creator: Uberbacher, E.C.; Xu, Ying; Shah, M.; Matis, S.; Guan, X. & Mural, R.J.
Partner: UNT Libraries Government Documents Department

Vertical cavity surface-emitting laser scanning cytometer for high speed analysis of cells

Description: We have constructed a new semiconductor laser device that may be useful in high speed characterization of cell morphology for diagnosis of disease. This laser device has critical advantages over conventional cell fluorescence detection methods since it provides intense, monochromatic, low-divergence fight signals that are emitted from lasing modes confined by a cell. Further, the device integrates biological structures with semiconductor materials at the wafer level to reduce device size and simplify cell preparation. In this paper we discuss operational characteristics of the prototype cytometer and present preliminary data for blood cells and dielectric spheres.
Date: December 31, 1995
Creator: Gourley, P.L.; McDonald, A.E. & Gourley, M.F.
Partner: UNT Libraries Government Documents Department

DNA sequencing technology, walking with modular primers. Final report

Description: The success of the Human Genome Project depends on the development of adequate technology for rapid and inexpensive DNA sequencing, which will also benefit biomedical research in general. The authors are working on DNA technologies that eliminate primer synthesis, the main bottleneck in sequencing by primer walking. They have developed modular primers that are assembled from three 5-mer, 6-mer or 7-mer modules selected from a presynthesized library of as few as 1,000 oligonucleotides ({double_bond}4, {double_bond}5, {double_bond}7). The three modules anneal contiguously at the selected template site and prime there uniquely, even though each is not unique for the most part when used alone. This technique is expected to speed up primer walking 30 to 50 fold, and reduce the sequencing cost by a factor of 5 to 15. Time and expensive will be saved on primer synthesis itself and even more so due to closed-loop automation of primer walking, made possible by the instant availability of primers. Apart from saving time and cost, closed-loop automation would also minimize the errors and complications associated with human intervention between the walks. The author has also developed two additional approaches to primer-library based sequencing. One involves a branched structure of modular primers which has a distinctly different mechanism of achieving priming specificity. The other introduces the concept of ``Differential Extension with Nucleotide Subsets`` as an approach increasing priming specificity, priming strength and allowing cycle sequencing. These approaches are expected to be more robust than the original version of the modular primer technique.
Date: December 31, 1996
Creator: Ulanovsky, L.
Partner: UNT Libraries Government Documents Department

From photons to protons in the photocycle of bacterial reaction center

Description: The detailed knowledge of the atomic coordinates of the bacterial reaction center (RC) has permitted a close scrutiny of structure/function relationships not only of the quinones but of the protein itself with its internal water structure. Protonatable groups were identified as intrinsic part of the redox reactions, providing charge compensation and forming channels for the movement of hydrogen ions to QB2-. The nature and position of these groups give rise to electrostatic profiles that determine the kinetics and energetics of proton transport. Fine tuning or dramatic variations of protein delivery pathways can adapt the photocycle to changes in bulk phase pH value, buffering capacities and primary structure of the RC.
Date: December 31, 1995
Creator: Maroti, P., Osvath, S., Tapai, C., Hanson, D.K.
Partner: UNT Libraries Government Documents Department