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Genetics in the courts

Description: Various: (1)TriState 2000 Genetics in the Courts (2) Growing impact of the new genetics on the courts (3)Human testing (4) Legal analysis - in re G.C. (5) Legal analysis - GM ''peanots'', and (6) Legal analysis for State vs Miller
Date: December 1, 2000
Creator: Coyle, Heather & Drell, Dan
Partner: UNT Libraries Government Documents Department

The Energy Budget of Steady-State Photosynthesis

Description: Our work developed a unique set of in vivo spectroscopic tools that have allowed us to probe the importance of 1) The effects of storage of proton motive force (pmf ) in the form of both electric field (Δψ) and pH difference (ΔpH); 2) alteration in the stoichiometry of proton pumping to electron transfer at key steps; 3) the influence of changes in the conductivity for proton efflux from the thylakoid of the ATP synthase; 4) the mechanisms of steps of the electron transfer process that pump protons; and 5) the mechanisms by which reactive O{sub 2} is generated as a side reaction to photosynthesis, and how these processes are minimized.
Date: June 30, 2007
Creator: Kramer, David
Partner: UNT Libraries Government Documents Department

Role of Sulfhydryl Sites on Bacterial Cell Walls in the Biosorption, Mobility and Bioavailability of Mercury and Uranium

Description: The goal of this exploratory study is to provide a quantitative and mechanistic understanding of the impact of bacterial sulfhydryl groups on the bacterial uptake, speciation, methylation and bioavailability of Hg and redox changes of uranium. The relative concentration and reactivity of different functional groups present on bacterial surfaces will be determined, enabling quantitative predictions of the role of biosorption of Hg under the physicochemical conditions found at contaminated DOE sites.The hypotheses we propose to test in this investigation are as follows- 1) Sulfhydryl groups on bacterial cell surfaces modify Hg speciation and solubility, and play an important role, specifically in the sub-micromolar concentration ranges of metals in the natural and contaminated systems. 2) Sulfhydryl binding of Hg on bacterial surfaces significantly influences Hg transport into the cell and the methylation rates by the bacteria. 3) Sulfhydryls on cell membranes can interact with hexavalent uranium and convert to insoluble tetravalent species. 4) Bacterial sulfhydryl surface groups are inducible by the presence of metals during cell growth. Our studies focused on the first hypothesis, and we examined the nature of sulfhydryl sites on three representative bacterial species: Bacillus subtilis, a common gram-positive aerobic soil species; Shewanella oneidensis, a facultative gram-negative surface water species; and Geobacter sulfurreducens, an anaerobic iron-reducing gram-negative species that is capable of Hg methylation; and at a range of Hg concentration (and Hg:bacterial concentration ratio) in which these sites become important. A summary of our findings is as follows-  Hg adsorbs more extensively to bacteria than other metals. Hg adsorption also varies strongly with pH and chloride concentration, with maximum adsorption occurring under circumneutral pH conditions for both Cl-bearing and Cl-free systems. Under these conditions, all bacterial species tested exhibit almost complete removal of Hg from the experimental solutions at relatively low bacterial concentrations.  Synchrotron based ...
Date: April 1, 2009
Creator: Myneni, Satish C.; Mishra, Bhoopesh & Fein, Jeremy
Partner: UNT Libraries Government Documents Department

Integrated Genome-Based Studies of Shewanella Ecophysiology

Description: We have constructed in-frame deletions of 7 of the 10 PAS-GGDEF-EAL proteins in Shewanella oneidensis MR-1. We are currently in the process of characterizing the deletion mutants under a wide range of growth conditions. In addition to characterizing growth, we will also examine the biofilm formation of the deletion mutants. In addition to the genetic analyses of the mutants, we are also interested in comparing the activities of the various PAS-GGDEF-EAL proteins. Proteins containing PAS, GGDEF and EAL amino acid sequence motifs may play an important role in regulating c-di-GMP signaling in response to environmental conditions. A genetic and biochemical analysis into the roles of these proteins is underway. PDE activity was observed for several PAS-GGDEF-EAL proteins. One of these proteins, SO0427, also demonstrates possible DGC activity in vitro. Currently, we are studying the growth, motility and biofilm formation characteristics of deletion mutants, as well as the activity of the purified proteins.
Date: July 12, 2011
Creator: Spormann, Alfred
Partner: UNT Libraries Government Documents Department

Physiological, Molecular and Genetic Mechanisms of Long-Term Habituation

Description: Work funded on this grant has explored the mechanisms of long-term habituation, a ubiquitous form of learning that plays a key role in basic cognitive functioning. Specifically, behavioral, physiological, and molecular mechanisms of habituation have been explored using a simple model system, the tail-elicited siphon-withdrawal reflex (T-SWR) in the marine mollusk Aplysia californica. Substantial progress has been made on the first and third aims, providing some fundamental insights into the mechanisms by which memories are stored. We have characterized the physiological correlates of short- and long-term habituation. We found that short-term habituation is accompanied by a robust sensory adaptation, whereas long-term habituation is accompanied by alterations in sensory and interneuron synaptic efficacy. Thus, our data indicates memories can be shifted between different sites in a neural network as they are consolidated from short to long term. At the molecular level, we have accomplished microarray analysis comparing gene expression in both habituated and control ganglia. We have identified a network of putatively regulated transcripts that seems particularly targeted towards synaptic changes (e.g. SNAP25, calmodulin) . We are now beginning additional work to confirm regulation of these transcripts and build a more detailed understanding of the cascade of molecular events leading to the permanent storage of long-term memories. On the third aim, we have fostered a nascent neuroscience program via a variety of successful initiatives. We have funded over 11 undergraduate neuroscience scholars, several of whom have been recognized at national and regional levels for their research. We have also conducted a pioneering summer research program for community college students which is helping enhance access of underrepresented groups to life science careers. Despite minimal progress on the second aim, this project has provided a) novel insight into the network mechanisms by which short-term memories are permanently stored, and b) a strong foundation ...
Date: September 12, 2009
Creator: Calin-Jageman, Robert J
Partner: UNT Libraries Government Documents Department

Ferric Ion-Specific Sequestering Agents. 7. Synthesis, Iron Exchange Kinetics, and Stability Constants of N-Substituted, Sulfonated Catechoylamide Analogues of Enterobactin.

Description: For treatment of chronic iron overload (as occurs in Cooley's anemia), ferric ion sequestering agents with specific properties are necessary. Two analogues of enterobactin [a microbial chelating agent with the greatest stability constant known for an Fe(III) complex] are reported which exhibit: i) hydrolytic stability; ii) water solubility; iii) N-substitution to block peptidase hydrolysis. The first compound, N,N',N"- trimethyl-N,N',N"-tris(2,3-dihydroxysulfobenzoyl)1,3,5-triaminomethyl- benzene, [Me{sub 3}MECAMS, 6] was prepared from the amide of trimesloyl chloride (1) and MeNH{sub 2}. The resulting amide was reduced to the triamine (3) and converted in three steps to the final product 6 in 6% overall yield. The proton-dependent formation constant (log K*) for the reaction: Fe{sup 3+} + H{sub 3}L{sup 6-} = FeL{sup 6-} + 3H{sup +} is 4.87, which gives an equilibrium concentration of [Fe{sup 3+}] at pH 7.4 of 2 x 10{sup -27} M for 10{sup -5} M L (6) and 10{sup -6} M total Fe{sup 3+}. The estimated formation constant (log {beta}{sub 110}) is 40. At low pH the FeL{sup 6-} complex undergoes a series of three, one-proton reactions which probably gives a tris-salicylate complex formed by the carbonyl and ortho-catechol oxygen of the 2,3~dihydroxybenzoyl units (the same reaction that occurs with ferric enterobactin). After six hours in the presence of 6 mM ascorbate, Me{sub 3}MECAMS (6.0 mM) removed 3.7% of the ferric ion initially sequestered by the iron storage protein, ferritin. The human iron transport protein transferrin goves up iron to Me{sub 3}MECAMS with a pseudo first-order rate constant of 1.9 x 10{sup -3}min{sup -1} (ligand concentration 2 X 10{sup -4} M). This rate is comparable to that of enterobactin and other catechoyl amide sequestering agents. and greatly exceeds that of desferrioxamine B (Desferal{reg-sign}). the current drug of choice in treating iron overload. Two related compounds have been prepared in which the catechol ring ...
Date: October 1, 1980
Creator: Pecoraro, Vincent L.; Weitl, Frederick L. & Raymond, Kenneth N.
Partner: UNT Libraries Government Documents Department

On the multiscale origins of fracture resistance in human bone and its biological degradation

Description: Akin to other mineralized tissues, human cortical bone can resist deformation and fracture due to the nature of its hierarchical structure, which spans the molecular to macroscopic length-scales. Deformation at the smallest scales, mainly through the composite action of the mineral and collagen, contributes to bone?s strength or intrinsic fracture resistance, while crack-tip shielding mechanisms active on the microstructural scale contribute to the extrinsic fracture resistance once cracking begins. The efficiency with which these structural features can resist fracture at both small and large length-scales becomes severely degraded with such factors as aging, irradiation and disease. Indeed aging and irradiation can cause changes to the cross-link profile at fibrillar length-scales as well as changes at the three orders of magnitude larger scale of the osteonal structures, both of which combine to inhibit the bone's overall resistance to the initiation and growth of cracks.
Date: March 9, 2012
Creator: Zimmermann, Elizabeth A.; Barth, Holly D. & Ritchie, Robert O.
Partner: UNT Libraries Government Documents Department

Evolutionary and Geologic Consequences of Organic Carbon Fixing in the Primitive Anoxic Ocean

Description: A model is proposed for a group of Archean pre-prokaryotes primary producers (termed Anoxium), that derived their energy from geothermal hydrogen sulfide discharged at oceanic vents. With time, competition developed for available S{sup =} due to organic oxidation and loss of sulfur to sediments. As a consequence, evolutionary advantage shifted to Anoxium isolates that could use alternative energy sources such as light to supplement diminished supplies of S{sup =}. Subsequent carbon fixing and deposition of organic carbon improved both the quality and quantity of light reaching the ocean surface so that eventually photosynthesis replaced sulfur chemosynthesis as the primary carbon dioxide-fixing mechanism. Organisms occupying niches similar to those of modern purple and green sulfur bacteria, thiobacilli and cyanobacteria could have evolved from the Anoxium complex as the environment was organically modified by the consequences of carbon fixing.
Date: September 1, 1980
Creator: Berry, W. B.N. & Wilde, P.
Partner: UNT Libraries Government Documents Department

In Silico Biology, Biological Networks: From Genomics to Epidemiology

Description: Grant was issued to Georgia Tech Research Corporation (Georgia Tech} in 2003 to provide some travel funds for 20 grad students/post docs to attend the In Silico Biology International Conference. Conference name "Biological Networks: From Genomics to Epidemiology." Dates Nov 13- 16, 2003 Web site of the conference is as follows (DOE is shown as the Gold level sponsor) http://opal.biology.gatech.edu/GeneMark/conference03/
Date: December 1, 2003
Creator: Borodovsky, Mark
Partner: UNT Libraries Government Documents Department

RTE1, A Novel Regulator of Ethylene Receptor Function

Description: RTE1 is a novel conserved gene found in both plants and animals. The main aims of this project were to: 1) examine Arabidopsis RTE1 function using genetic and cell biological analyses, and 2) determine whether the Arabidopsis RTH gene plays a role similar to that of RTE1 in ethylene signaling.
Date: February 5, 2013
Creator: Chang, Caren
Partner: UNT Libraries Government Documents Department

2013 Plant Lipids Gordon Research Conference and Gordon Research Seminar (January 27-February 1, 2013 - Hotel Galvez, Galveston TX)

Description: Presenters will discuss the latest advances in plant and algal lipid metabolism, oil synthesis, lipid signaling, lipid visualization, lipid biotechnology and its applications, the physiological and developmental roles of lipids, and plant lipids in health. Sessions include: Producing Nutritional Lipids; Metabolic biochemistry in the next decade; Triacylglycerols: Metabolism, function, and as a target for engineering; Lipids in Protection, Reproduction, and Development; Genetic and Lipidomic Approaches to Understanding Lipid Metabolism and Signaling; Lipid Signaling in Stress Responses; New Insights on the Path to Triacylglycerols; Membrane Lipid Signaling; Lipid Visualization; Development of Biofuels and Industrial Lipids.
Date: November 1, 2012
Creator: Welti, Ruth
Partner: UNT Libraries Government Documents Department

Research Frontiers in Bioinspired Energy: Molecular-Level Learning from Natural Systems: A Workshop

Description: An interactive, multidisciplinary, public workshop, organized by a group of experts in biochemistry, biophysics, chemical and biomolecular engineering, chemistry, microbial metabolism, and protein structure and function, was held on January 6-7, 2011 in Washington, DC. Fundamental insights into the biological energy capture, storage, and transformation processes provided by speakers was featured in this workshop�which included topics such as microbes living in extreme environments such as hydrothermal vents or caustic soda lakes (extremophiles)� provided a fascinating basis for discussing the exploration and development of new energy systems. Breakout sessions and extended discussions among the multidisciplinary groups of participants in the workshop fostered information sharing and possible collaborations on future bioinspired research. Printed and web-based materials that summarize the committee�s assessment of what transpired at the workshop were prepared to advance further understanding of fundamental chemical properties of biological systems within and between the disciplines. In addition, webbased materials (including two animated videos) were developed to make the workshop content more accessible to a broad audience of students and researchers working across disciplinary boundaries. Key workshop discussion topics included: Exploring and identifying novel organisms; Identifying patterns and conserved biological structures in nature; Exploring and identifying fundamental properties and mechanisms of known biological systems; Supporting current, and creating new, opportunities for interdisciplinary education, training, and outreach; and Applying knowledge from biology to create new devices and sustainable technology.
Date: March 28, 2012
Creator: Zolandz, Dorothy
Partner: UNT Libraries Government Documents Department

Integrated Genome-Based Studies of Shewanella Ecophysiology

Description: The aim of the work reported is to study Shewanella population genomics, and to understand the evolution, ecophysiology, and speciation of Shewanella. The tasks supporting this aim are: to study genetic and ecophysiological bases defining the core and diversification of Shewanella species; to determine gene content patterns along redox gradients; and to Investigate the evolutionary processes, patterns and mechanisms of Shewanella.
Date: January 8, 2014
Creator: Tiedje, James M.; Konstantinidis, Kostas & Worden, Mark
Partner: UNT Libraries Government Documents Department


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