Nesting Ecology Of Bank Swallows In Interior Alaska

Thesis (M.S.) University of Alaska Fairbanks, 197

Transcriptional regulatory codes underlying Arabidopsis stress responses

Plant adaptation to stress is dependent upon the initialisation of molecular signalling networks that regulate the expression of stress-related genes. By examining high-resolution microarray datasets it has been possible to track gene expression changes over time during senescence and in response to infection by fungal pathogen Botrytis cineria in the model organism Arabidopsis thaliana. Dramatic variations in gene expression are observed at the onset of stress with different groups of genes showing different expression time-courses. This observation must, for a large part, be down to the action of different transcription factors (TFs) binding to the cis-regulatory DNA in the promoters of genes in each group and it is this regulatory code that underpins the gene regulatory networks that regulate stress responses. This thesis presents an interdisciplinary investigation of the regulatory codes that are responsible for controlling plant stress responses. Computational analysis of non-coding sequences provides a powerful approach to identify patterns within DNA that may function to regulate gene expression. This thesis covers the development of Analysis of Plant Promoter-Linked Elements (APPLES), an object-orientated software framework for the analysis of non-coding DNA. Within this environment, methods were developed to probe the regulatory codes that exist within these non-coding sequences and identify regulatory motifs that may function to regulate stress responses in Arabidopsis. APPLES methods were used to identify a novel motif that is likely to play a role in regulating drought responses in Arabidopsis, with experimental approaches providing support for this view. Using known motifs that describe previously characterised TF binding sites, it was possible to identify motifs that are associated with clusters of co-regulated genes identified from the senescence and Botrytis microarray time-course datasets. This analysis revealed cis-regulatory elements that may contribute to generating the observed expression patterns. In a contrasting approach to in silico identification of regulatory elements, the Yeast-1-Hybrid (Y1H) assay was used to experimentally identify interactions between TFs and non-coding DNA. The use of a TF library allowed the ability of approximately 1400 Arabidopsis TFs to interact with a given DNA sequence in a single assay. Using the stress-associated ANAC092 promoter as a test case, it was possible to use this highthroughput procedure to identify TFs that can bind to the promoter of this gene. This high-throughput Y1H system was then used to perform a detailed mapping of protein- DNA interactions that can occur across the core promoters of three highly related stress inducible TF-encoding genes, ANAC019, ANAC055 and ANAC072. Microarrays were used to assess the regulatory consequence of a subset of these interactions by perturbing the expression of interacting TFs and observing the effect on target gene expression during multiple stresses. This approach confirmed predicted regulatory relationships and therefore enhanced the current understanding of the transcriptional regulatory networks that operate during stress responses in Arabidopsis

Assessing Compressed Air Energy Storage (CAES) Potential in Kentucky to Augment Energy Production from Renewable Resources

Fossil fuel power plants in Kentucky have some of the highest emissions of greenhouse gasses in the United States. One potential strategy for mitigating greenhouse gasses from electric power generation is the co-installation of Compressed Air Energy Storage (CAES) and a renewable source such as photovoltaic solar electricity generation (PV solar generation). CAES with complementary co-installed PV solar generation enhances stand-alone PV solar generation because CAES power is available at night. CAES, however, requires both a site where large volumes of compressed air can be stored in the subsurface, and a heat source to prepare the stored air prior to entering the electricity-generating turbines. Co-installed PV solar electricity can provide the required thermal energy, but compressed air storage can be problematic. The two existing CAES plants, in Germany and Alabama, store compressed air in subsurface solution-mined salt caverns, however the thick salt deposits necessary to develop a compressed air storage cavern are not a part of Kentucky’s geology. Six compressed air storage models were reviewed as part of this project: acid solution-mined caverns, abandoned limestone mines, advanced energy storage in mined air storage chambers, depleted gas fields aquifer storage; and cased wellbore energy storage. Each of these models has the potential for application in Kentucky. Two issues need to be addressed in applying CAES and its variations in Kentucky: ownership of the subsurface pore space where compressed air would be stored in depleted geologic reservoirs and aquifers, and social equity of the CAES electric power generation process. Pore space ownership is addressed under both state and federal law, generally from the standpoint of natural gas storage in depleted gas fields. These storage reservoirs would require an Environmental Protection Agency (EPA) injection permit. CAES models that do not impact porosity or groundwater may require other state and federal operational permits. Because CAES is both site-flexible and easily scalable, it provides a starting point for the conversation surrounding energy equity in the U.S. CAES with co-installed PV solar electricity generation provides a path to equitable power generation for all Americans

Consequences of Gut Dysbiosis on the Human Brain

The central nervous system (CNS) and the gastrointestinal (GI) tract develop in parallel and communicate with each other throughout life using neural, endocrine, and immune pathways, giving rise to the concept of a ‘gut-brain axis’ in which both organ systems intimately interact. Fundamental to the axis is the GI microbiome, which is the collective genomic aggregate of bacteria and other microorganisms that dwell within the lumen of the GI tract. Increasing evidence gathered from animal models and human studies demonstrates that perturbation of the microbiome, otherwise known as dysbiosis, can lead to specific neurological and psychiatric disorders. This chapter will provide a brief review of the literature that reveals the influence of the microbiome in CNS disease and provide perspectives in treatment through modification of the microbiome

Multi-wavelength observations of cataclysmic variable stars

Observations of the cataclysmic variable systems EX Dra, Z Cha, and OY Car using multi-wavelength data ranging from near-infrared to X-ray bands are presented and analysed. Obscuration of the white dwarf by intervening material is discussed in context of all three systems, including the confirmation of iron lines in the spectrum of OY Car and the absorbing nature of the accretion disc upon the soft X-ray band in Z Cha. Evidence for spiral shocks and slingshot prominences from the secondary star are found in EX Dra, while the extent of Z Cha's boundary layer is probed with extensive modelling of simultaneous optical and X-ray data. Combined with a spectral analysis, this leads to the conclusion of a truncated inner disc present within the system. The first radial velocity measurement of OY Car's red secondary star is presented, and used to produce a fully spectroscopic determination of the system's mass ratio which is compared to previous attempts using the photometric method. The second part of this thesis deals with the improvement of the Ultracam and Ultraspec instruments. For the former, increased colour precision is achieved by careful calibration of the instrument's filter response with respect to the SDSS system; a charge modulation problem is investigated and quantified; and the development of a software system designed to improve observation and reduction workflow is detailed. For Ultraspec, a careful analysis of the CCD parameters is performed in order to prepare the instrument for scientific quality data publication, including an analysis of spurious charge found present. It is also shown that the AC coupling of the video circuit in the CCD can cause erroneous values in the readout but can be rectified, and presence of charge trailing caused by electron traps is investigated with preliminary corrections shown

Transcriptional regulatory codes underlying Arabidopsis stress responses

Plant adaptation to stress is dependent upon the initialisation of molecular signalling networks that regulate the expression of stress-related genes. By examining high-resolution microarray datasets it has been possible to track gene expression changes over time during senescence and in response to infection by fungal pathogen Botrytis cineria in the model organism Arabidopsis thaliana. Dramatic variations in gene expression are observed at the onset of stress with different groups of genes showing different expression time-courses. This observation must, for a large part, be down to the action of different transcription factors (TFs) binding to the cis-regulatory DNA in the promoters of genes in each group and it is this regulatory code that underpins the gene regulatory networks that regulate stress responses. This thesis presents an interdisciplinary investigation of the regulatory codes that are responsible for controlling plant stress responses. Computational analysis of non-coding sequences provides a powerful approach to identify patterns within DNA that may function to regulate gene expression. This thesis covers the development of Analysis of Plant Promoter-Linked Elements (APPLES), an object-orientated software framework for the analysis of non-coding DNA. Within this environment, methods were developed to probe the regulatory codes that exist within these non-coding sequences and identify regulatory motifs that may function to regulate stress responses in Arabidopsis. APPLES methods were used to identify a novel motif that is likely to play a role in regulating drought responses in Arabidopsis, with experimental approaches providing support for this view. Using known motifs that describe previously characterised TF binding sites, it was possible to identify motifs that are associated with clusters of co-regulated genes identified from the senescence and Botrytis microarray time-course datasets. This analysis revealed cis-regulatory elements that may contribute to generating the observed expression patterns. In a contrasting approach to in silico identification of regulatory elements, the Yeast-1-Hybrid (Y1H) assay was used to experimentally identify interactions between TFs and non-coding DNA. The use of a TF library allowed the ability of approximately 1400 Arabidopsis TFs to interact with a given DNA sequence in a single assay. Using the stress-associated ANAC092 promoter as a test case, it was possible to use this highthroughput procedure to identify TFs that can bind to the promoter of this gene. This high-throughput Y1H system was then used to perform a detailed mapping of protein- DNA interactions that can occur across the core promoters of three highly related stress inducible TF-encoding genes, ANAC019, ANAC055 and ANAC072. Microarrays were used to assess the regulatory consequence of a subset of these interactions by perturbing the expression of interacting TFs and observing the effect on target gene expression during multiple stresses. This approach confirmed predicted regulatory relationships and therefore enhanced the current understanding of the transcriptional regulatory networks that operate during stress responses in Arabidopsis.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

MEME-LaB : motif analysis in clusters

Genome-wide expression analysis can result in large numbers of clusters of co-expressed genes. While there are tools for ab initio discovery of transcription factor binding sites, most do not provide a quick and easy way to study large numbers of clusters. To address this, we introduce a web-tool called MEME-LaB. The tool wraps MEME (an ab initio motif finder), providing an interface for users to input multiple gene clusters, retrieve promoter sequences, run motif finding, and then easily browse and condense the results, facilitating better interpretation of the results from large-scale datasets

Paper Session I-A - Robust Low Cost Liquid Rocket Combustion Chamber By Advanced Vacuum Plasma Process

Next-generation, regeneratively cooled rocket engines require materials that can meet high temperatures while resisting the corrosive oxidation-reduction reaction of combustion known as blanching, the main cause of engine failure. A project was initiated at NASA-Marshall Space Flight Center (MSFC) to combine three existing technologies to build and demonstrate an advanced liquid rocket engine combustion chamber that would provide a 100-mission life. Technology developed in microgravity research to build cartridges for space furnaces was utilized to vacuum plasma spray (VPS) a functional gradient coating on the hot wall of the combustion liner as one continuous operation, eliminating any bondline between the coating and the liner. (See Figure 1) The coating was NiCrAlY, developed previously as durable protective coatings on space shuttle high-pressure fuel turbopump (HPFTP) turbine blades. A thermal model showed that 0.035” NiCrAlY applied to the hot wall of the combustion liner would reduce the hot wall temperature 200°F, a 20% reduction, for longer life. Cu-8Cr-4Nb alloy, which was developed by NASA-Glenn Research Center (GRC), and which possesses excellent high-temperature strength, creep resistance, and low cycle fatigue behavior combined with exceptional thermal stability, was utilized as the liner material in place of NARloy-Z. The Cu-8Cr-4Nb material exhibits better mechanical properties at 650°C (1200°F) than NARloy-Z does at 538°C (1000°F). VPS formed Cu-8Cr-4Nb combustion chamber liners with a protective NiCrAlY functional gradient coating have been hot fire tested, successfully demonstrating a durable coating for the first time. Hot fire tests along with tensile and low cycle fatigue properties of the VPS formed combustion chamber liners and witness panel specimens are discussed

Zircon U-Pb Geochronology of Two Basement Cores (Kentucky, USA): Implications for Late Mesoproterozoic Sedimentation and Tectonics in the Eastern Midcontinent

Basement cores from two wells drilled west and east of the Grenville front consist of feldspathic litharenite and granitic orthogneiss, respectively. Detrital zircon U-Pb ages for the litharenite define a broad dominant U-Pb age mode at ca. 1115 Ma. The dominant mode matches that for the type locality of the Middle Run Formation in the Ohio subsurface and is interpreted to consist of detrital zircons sourced from East Continent Rift volcanic sources (ca. 1100 Ma) and Grenville Shawinigan granites/gneisses (1120–1180 Ma). The youngest detrital zircon ages (ca. 1020 Ma) require a maximum depositional age that is at least 70 My younger than the time of Midcontinent and East Continent rifting and magmatism. We propose that the litharenite is correlative with the Middle Run Formation in Ohio and was deposited in an evolving late Grenville rift/foreland basin adjacent to the exhuming Grenville orogen. Zircon U-Pb secondary-ion mass spectrometry ages from orthogneiss define a discordant array with intercepts of ca. 1500 and 1000 Ma. The oldest concordant dates (ca. 1450 Ma, from oscillatory-zoned cores) are interpreted as the crystallization age of the igneous protolith of the orthogneiss. Metamorphic zircon rims define a weighted mean U-Pb age of 1018 ± 19 Ma (2σ) Ma, interpreted to represent the time of high-grade metamorphism during the late Ottawan phase of the Grenville orogeny. This age pattern matches that of exposed basement in the Central Gneiss Belt of the Grenville Province (Ontario) and similar basement orthogneisses in Ohio and Kentucky that are interpreted to be of Eastern Granite-Rhyolite Province affinity. All age data are consistent with a provenance model of an actively exhuming Grenville orogen at ca. 1000 Ma producing sediment that is mixing with recycled East Continent Rift sediments