Matching Items (123)
Description
Ponderosa pine forests are a dominant land cover type in semiarid montane areas. Water supplies in major rivers of the southwestern United States depend on ponderosa pine forests since these ecosystems: (1) receive a significant amount of rainfall and snowfall, (2) intercept precipitation and transpire water, and (3) indirectly influence runoff by impacting the infiltration rate. However, the hydrologic patterns in these ecosystems with strong seasonality are poorly understood. In this study, we used a distributed hydrologic model evaluated against field observations to improve our understandings on spatial controls of hydrologic patterns, appropriate model resolution to simulate ponderosa pine ecosystems and hydrologic responses in the context of contrasting winter to summer transitions. Our modeling effort is focused on the hydrologic responses during the North American Monsoon (NAM), winter and spring periods. In Chapter 2, we utilized a distributed model explore the spatial controls on simulated soil moisture and temporal evolution of these spatial controls as a function of seasonal wetness. Our findings indicate that vegetation and topographic curvature are spatial controls. Vegetation controlled patterns during dry summer period switch to fine-scale terrain curvature controlled patterns during persistently wet NAM period. Thus, a climatic threshold involving rainfall and weather conditions during the NAM is identified when high rainfall amount (such as 146 mm rain in August, 1997) activates lateral flux of soil moisture and frequent cloudy cover (such as 42% cloud cover during daytime of August, 1997) lowers evapotranspiration. In Chapter 3, we investigate the impacts of model coarsening on simulated soil moisture patterns during the NAM. Results indicate that model aggregation quickly eradicates curvature features and its spatial control on hydrologic patterns. A threshold resolution of ~10% of the original terrain is identified through analyses of homogeneity indices, correlation coefficients and spatial errors beyond which the fidelity of simulated soil moisture is no longer reliable. Based on spatial error analyses, we detected that the concave areas (~28% of hillslope) are very sensitive to model coarsening and root mean square error (RMSE) is higher than residual soil moisture content (~0.07 m3/m3 soil moisture) for concave areas. Thus, concave areas need to be sampled for capturing appropriate hillslope response for this hillslope. In Chapter 4, we investigate the impacts of contrasting winter to summer transitions on hillslope hydrologic responses. We use a distributed hydrologic model to generate a consistent set of high-resolution hydrologic estimates. Our model is evaluated against the snow depth, soil moisture and runoff observations over two water years yielding reliable spatial distributions during the winter to summer transitions. We find that a wet winter followed by a dry summer promotes evapotranspiration losses (spatial averaged ~193 mm spring ET and ~ 600 mm summer ET) that dry the soil and disconnect lateral fluxes in the forested hillslope, leading to soil moisture patterns resembling vegetation patches. Conversely, a dry winter prior to a wet summer results in soil moisture increases due to high rainfall and low ET during the spring (spatially averaged 78 mm ET and 232 mm rainfall) and summer period (spatially averaged 147 mm ET and 247 mm rainfall) which promote lateral connectivity and soil moisture patterns with the signature of terrain curvature. An opposing temporal switch between infiltration and saturation excess runoff is also identified. These contrasting responses indicate that the inverse relation has significant consequences on hillslope water availability and its spatial distribution with implications on other ecohydrological processes including vegetation phenology, groundwater recharge and geomorphic development. Results from this work have implications on the design of hillslope experiments, the resolution of hillslope scale models, and the prediction of hydrologic conditions in ponderosa pine ecosystems. In addition, our findings can be used to select future hillslope sites for detailed ecohydrological investigations. Further, the proposed methodology can be useful for predicting responses to climate and land cover changes that are anticipated for the southwestern United States.
ContributorsMahmood, Taufique Hasan (Author) / Vivoni, Enrique R. (Thesis advisor) / Whipple, Kelin X. (Committee member) / Shock, Everett (Committee member) / Heimsath, Arjun M. (Committee member) / Ruddell, Benjamin (Committee member) / Arizona State University (Publisher)
Created2012
Description
Early spacecraft missions to Mars, including the Marnier and Viking orbiters and landers revealed a morphologically and compositionally diverse landscape that reshaped widely held views of Mars. More recent spacecraft including Mars Global Surveyor, Mars Odyssey, Mars Express, Mars Reconnaissance Orbiter, and the Mars Exploration Rovers have further refined, enhanced, and diversified our understanding of Mars. In this dissertation, I take a multiple-path approach to planetary and Mars science including data analysis and instrument development. First, I present several tools necessary to effectively use new, complex datasets by highlighting unique and innovative data processing techniques that allow for the regional to global scale comparison of multiple datasets. Second, I present three studies that characterize several processes on early Mars, where I identify a regional, compositionally distinct, in situ, stratigraphically significant layer in Ganges and Eos Chasmata that formed early in martian history. This layer represents a unique period in martian history where primitive mantle materials were emplaced over large sections of the martian surface. While I originally characterized this layer as an effusive lava flow, based on the newly identified regional or global extent of this layer, I find the only likely scenario for its emplacement is the ejecta deposit of the Borealis Basin forming impact event. I also re-examine high thermal inertia, flat-floored craters identified in Viking data and conclude they are typically more mafic than the surrounding plains and were likely infilled by primitive volcanic materials during, or shortly after the Late Heavy Bombardment. Furthermore, the only plausible source for these magmas is directly related to the impact process, where mantle decompression melting occurs as result of the removal of overlying material by the impactor. Finally, I developed a new laboratory microscopic emission and reflectance spectrometer designed to help improve the interpretation of current remote sensing or in situ data from planetary bodies. I present the design, implementation, calibration, system performance, and preliminary results of this instrument. This instrument is a strong candidate for the next generation in situ rover instruments designed to definitively assess sample mineralogy and petrology while preserving geologic context.
ContributorsEdwards, Christopher (Author) / Christensen, Philip R. (Thesis advisor) / Bell, James (Committee member) / Sharp, Thomas (Committee member) / Clarke, Amanda B (Committee member) / Shock, Everett (Committee member) / Arizona State University (Publisher)
Created2012
Description
Single cell analysis has become increasingly important in understanding disease onset, progression, treatment and prognosis, especially when applied to cancer where cellular responses are highly heterogeneous. Through the advent of single cell computerized tomography (Cell-CT), researchers and clinicians now have the ability to obtain high resolution three-dimensional (3D) reconstructions of single cells. Yet to date, no live-cell compatible version of the technology exists. In this thesis, a microfluidic chip with the ability to rotate live single cells in hydrodynamic microvortices about an axis parallel to the optical focal plane has been demonstrated. The chip utilizes a novel 3D microchamber design arranged beneath a main channel creating flow detachment into the chamber, producing recirculating flow conditions. Single cells are flowed through the main channel, held in the center of the microvortex by an optical trap, and rotated by the forces induced by the recirculating fluid flow. Computational fluid dynamics (CFD) was employed to optimize the geometry of the microchamber. Two methods for the fabrication of the 3D microchamber were devised: anisotropic etching of silicon and backside diffuser photolithography (BDPL). First, the optimization of the silicon etching conditions was demonstrated through design of experiment (DOE). In addition, a non-conventional method of soft-lithography was demonstrated which incorporates the use of two positive molds, one of the main channel and the other of the microchambers, compressed together during replication to produce a single ultra-thin (<200 µm) negative used for device assembly. Second, methods for using thick negative photoresists such as SU-8 with BDPL have been developed which include a new simple and effective method for promoting the adhesion of SU-8 to glass. An assembly method that bonds two individual ultra-thin (<100 µm) replications of the channel and the microfeatures has also been demonstrated. Finally, a pressure driven pumping system with nanoliter per minute flow rate regulation, sub-second response times, and < 3% flow variability has been designed and characterized. The fabrication and assembly of this device is inexpensive and utilizes simple variants of conventional microfluidic fabrication techniques, making it easily accessible to the single cell analysis community.
ContributorsMyers, Jakrey R (Author) / Meldrum, Deirdre (Thesis advisor) / Johnson, Roger (Committee member) / Frakes, David (Committee member) / Arizona State University (Publisher)
Created2012
Description
Molybdenum and uranium isotope variations are potentially powerful tools for reconstructing the paleoredox history of seawater. Reliable application and interpretation of these proxies requires not only detailed knowledge about the fractionation factors that control the distribution of molybdenum and uranium isotopes in the marine system, but also a thorough understanding of the diagenetic processes that may affect molybdenum and uranium isotopes entering the rock record. Using samples from the Black Sea water column, the first water column profile of 238U/235U variations from a modern euxinic basin has been measured. This profile allows the direct determination of the 238U/235U fractionation factor in a euxinic marine setting. More importantly however, these data demonstrate the extent of Rayleigh fractionation of U isotopes that can occur in euxinic restricted basins. Because of this effect, the offset of 238U/235U between global average seawater and coeval black shales deposited in restricted basins is expected to depend on the degree of local uranium drawdown from the water column, potentially complicating the interpretation 238U/235U paleorecords. As an alternative to the black shales typically used for paleoredox reconstructions, molybdenum and uranium isotope variations in bulk carbonate sediments from the Bahamas are examined. The focus of this work was to determine what processes, if any, fractionate molybdenum and uranium isotopes during incorporation into bulk carbonate sediments and their subsequent diagenesis. The results demonstrate that authigenic accumulation of molybdenum and uranium from anoxic and sulfidic pore waters is a dominant process controlling the concentration and isotopic composition of these sediments during early diagenesis. Examination of ODP drill core samples from the Bahamas reveals similar behavior for sediments during the first ~780ka of burial, but provides important examples where isolated cores and samples occasionally demonstrate additional fractionation, the cause of which remains poorly understood.
ContributorsRomaniello, Stephen J. (Author) / Anbar, Ariel (Thesis advisor) / Hartnett, Hilairy (Committee member) / Herrmann, Achim (Committee member) / Shock, Everett (Committee member) / Wadhwa, Meenakshi (Committee member) / Arizona State University (Publisher)
Created2012
Description
Background: Human papillomavirus (HPV) is the cause of 99.7% of cervical cancers. Research of cervical cancer has made this disease mostly curable in the developing world. Head and neck cancer, which is increasingly caused by HPV, still is associated with a mortality rate of 50,000 in the US annually. This study proposed to evaluate the biology of HPV-16 in head and neck tumors by using RT-qPCR to measure the RNA expression and its relation to physical status of the virus. Methods: This study was to develop an assay that uses RT-qPCR to determine the quantitative expression of HPV-16 RNA coding for proteins E1, E2, E4, E5, E6, and E7 in tumor samples. The assay development started with creation of primers. It went on to test the primers on template DNA through traditional PCR and then on DNA from HPV-16 positive cell lines, SiHa and CaSki, using RT-qPCR. This paper also describes the troubleshooting methods taken for the PCR reaction. Once the primers are verified, the RT-qPCR process can be carried out on RNA purified from tumor samples. Results: No primer sets have been confirmed to produce a product through PCR or RT-qPCR. The primer sequences match up correctly with known sequences for HPV-16 E1, E2, E4, E5, E6, and E7. RT-qPCR showed results consistent with the hypothesis. Conclusion: The RT-qPCR protocol must be optimized to confirm the primer sequences work as desired. Then primers will be used to study physical status and RNA expression in HPV-positive and HPV-negative head and neck tumor samples. This assay can help shed light on which proteins are expressed most in tumors of the head and neck and will aid in the development of future screening and treatment options.
ContributorsKhazanovich, Jakob (Author) / Anderson, Karen (Thesis director) / Mangone, Marco (Committee member) / Sundaresan, Sri Krishna (Committee member) / Barrett, The Honors College (Contributor)
Created2015-05
Description
Duchenne Muscular Dystrophy (DMD) is an X-linked recessive disease characterized by progressive muscle loss and weakness. This disease arises from a mutation that occurs on a gene that encodes for dystrophin, which results in observable muscle death and inflammation; however, the genetic changes that result from dystrophin's dysfunctionality remain unknown. Current DMD research uses mdx mice as a model, and while very useful, does not allow the study of cell-autonomous transcriptome changes during the progression of DMD due to the strong inflammatory response, perhaps hiding important therapeutic targets. C. elegans, which has a very weak inflammatory response compared to mdx mice and humans, has been used in the past to study DMD with some success. The worm ortholog of the dystrophin gene has been identified as dys-1 since its mutation phenocopies the progression of the disease and a portion of the human dystrophin gene alleviates symptoms. Importantly, the extracted RNA transcriptome from dys-1 worms showed significant change in gene expression, which needs to be further investigated with the development of a more robust model. Our lab previously published a method to isolate high-quality muscle-specific RNA from worms, which could be used to study such changes at higher resolution. We crossed the dys-1 worms with our muscle-specific strain and demonstrated that the chimeric strain exhibits similar behavioral symptoms as DMD patients as characterized by a shortened lifespan, difficulty in movement, and a decrease in speed. The presence of dys-1 and other members of the dystrophin complex in the body muscle were supported by the development of a resulting phenotype due to RNAi knockdown of each component in the body muscle; however, further experimentation is needed to reinforce this conclusion. Thus, the constructed chimeric C. elegans strain possesses unique characteristics that will allow the study of genetic changes, such as transcriptome rearrangements and dysregulation of miRNA, and how they affect the progression of DMD.
ContributorsNguyen, Thuy-Duyen Cao (Author) / Mangone, Marco (Thesis director) / Newbern, Jason (Committee member) / Duchaine, Thomas (Committee member) / School of Social Transformation (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
microRNAs (miRNAs) are short ~22nt non-coding RNAs that regulate gene output at the post-transcriptional level. Via targeting of degenerate elements primarily in 3'untranslated regions (3'UTR) of mRNAs, miRNAs can target thousands of varying genes and suppress their protein translation. The precise mechanistic function and bio- logical role of miRNAs is not fully understood and yet it is a major contributor to a pleth- ora of diseases, including neurological disorders, muscular disorders, and cancer. Cer- tain model organisms are valuable in understanding the function of miRNA and there- fore fully understanding the biological significance of miRNA targeting. Here I report a mechanistic analysis of miRNA targeting in C. elegans, and a bioinformatic approach to aid in further investigation of miRNA targeted sequences. A few of the biologically significant mechanisms discussed in this thesis include alternative polyadenylation, RNA binding proteins, components of the miRNA recognition machinery, miRNA secondary structures, and their polymorphisms. This thesis also discusses a novel bioinformatic approach to studying miRNA biology, including computational miRNA target prediction software, and sequence complementarity. This thesis allows a better understanding of miRNA biology and presents an ideal strategy for approaching future research in miRNA targeting.
ContributorsWeigele, Dustin Keith (Author) / Mangone, Marco (Thesis director) / Katchman, Benjamin (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor) / School of Life Sciences (Contributor)
Created2014-12
Description
The Cannabis plant has historical roots with human beings. The plant produces compounds called cannabinoids, which are responsible for the physiological affects of Cannabis and make it a research candidate for medicinal use. Analysis of the plant and its components will help build a better database that could be used to develop a complete roster of medicinal benefits. Research regarding the cellular protein receptors that bind the cannabinoids may not only help provide reasons explaining why the Cannabis plant could be medicinally relevant, but will also help explain how the receptors originated. The receptors may have been present in organisms before the present day Cannabis plant. So why would there be receptors that bind to cannabinoids? Searching for an endocannabinoid system could help explain the purpose of the cannabinoid receptors and their current structures in humans. Using genetic technologies we are able to take a closer look into the evolutionary history of cannabinoids and the receptors that bind them.
ContributorsSalasnek, Reed Samuel (Author) / Capco, David (Thesis director) / Mangone, Marco (Committee member) / Stump, Edmund (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2014-05
Description
A coincidence reporter construct, consisting of the p21-promoter and two luciferase genes (Firefly and Renilla), was constructed for the screening of drugs that might inhibit Olig2's tumorigenic role in glioblastoma. The reporter construct was tested using an Olig2 inhibitor, HSP990, as well as short hairpin RNA targeting Olig2. Further confirmatory analysis is needed before the reporter cell line is ready for high-throughput screening at the NIH and lead compound selection.
ContributorsCusimano, Joseph Michael (Author) / LaBaer, Joshua (Thesis director) / Mangone, Marco (Committee member) / Mehta, Shwetal (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor)
Created2014-05
Description
Background: Breast cancer is the most frequently diagnosed cancer and the leading cause of cancer deaths in females worldwide, accounting for 23% of all new cancer cases and 14% of all total cancer deaths in 2008. Five tumor-normal pairs of primary breast epithelial cells were treated for infinite proliferation by using a ROCK inhibitor and mouse feeder cells. Methods: Raw paired-end, 100x coverage RNA-Seq data was aligned to the Human Reference Genome Version 19 using BWA and Tophat. Gene differential expression analysis was completed using Cufflinks and Cuffdiff. Interactive Genome Viewer was used for data visualization. Results: 15 genes were found to be down-regulated by at least one log-fold change in 4/5 of tumor samples. 75 genes were found to be down-regulated in 3/5 of our tumor samples by at least one log-fold change. 11 genes were found to be up-regulated in 4/5 of our tumor samples, and 68 genes were identified to be up-regulated in 3/5 of the tumor samples by at least one-fold change. Conclusion: Expression changes in genes such as AZGP1, AGER, ALG11, and S1007 suggest a disruption in the glycosylation pathway. No correlation was found between Cufflink's Her2 gene-expression and DAKO score classification.
ContributorsHernandez, Fernando (Author) / Anderson, Karen (Thesis director) / Mangone, Marco (Committee member) / Park, Jin (Committee member) / Barrett, The Honors College (Contributor) / Department of Information Systems (Contributor)
Created2013-05