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Undergraduate Honors Theses

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Analysis of carbohydrates in dissolved organic matter in peat porewaters by electrospray ionization mass spectrometry
Analysis of carbohydrates in dissolved organic matter in peat porewaters by electrospray ionization mass spectrometry
Summary: Vast amounts of carbon are stored in peatlands worldwide. As these reserves of organic matter slowly decompose, they release methane, carbon dioxide and other greenhouse gases to the atmosphere. The effects of global warming on the rate of organic matter decomposition in peats have come into question. To understand these effects, the behavior of organic matter, both solid and dissolved, must be understood in the context of changing thermal and hydrological conditions. This project focused on carbohydrates in the dissolved organic matter (DOM) phase of peatland porewaters. Carbohydrates are an important component of DOM because they act as indicators of organic matter reactivity. This project attempted to develop a method to analyze for both free and total hydrolysable carbohydrates in porewaters from the Lake Agassiz Peatland in Northern Minnesota. Analyses were performed using a JEOL AccuTOF mass spectrometer equipped with a nano-electrospray ionization source. Because mass alone cannot distinguish isomers, this study focused on identification of carbohydrates based on class. In addition, the fragmentation patterns of each class were studied in an attempt to find a common fragment that could be used for selective ion monitoring in conjunction with liquid chromatography. While analysis of hydrolysable carbohydrates was unsuccessful, both qualitative and quantitative analysis of free carbohydrates was achieved. The results show that the concentrations of free carbohydrates increased with depth in both fen and bog systems. This may reflect the turnover of older DOM; however, future studies are necessary to confirm this hypothesis., Advisor: Dr. William Cooper, Florida State University, College of Arts and Sciences, Dept. of Chemistry., Thesis (Honors paper)--Florida State University, 2009., Includes bibliographical references.
Analysis of rheological response of high molecular weight cyclic polymer melts to percolation caused by trace contamination from linear chains
Analysis of rheological response of high molecular weight cyclic polymer melts to percolation caused by trace contamination from linear chains
Melts of cyclic polymers intentionally contaminated with linear polymer fractions were studied using the bond-fluctuation model and sol-gel transition theory analysis to determine the threshold concentration at which percolation spans these melts. These results were then compared to recent experimental results that reported the threshold concentration of a sample of cyclic polystyrenes to be approximately 50 times below the overlap concentration of the chains. The experimental study mentioned also attempted to explain why the threshold concentration found experimentally was that low, by suggesting that the end-to-end distance of the linear chains was a relevant factor in the capture of the surrounding cyclic chains. Our results showed some agreement with the percolation threshold values found experimentally; however, our theoretical estimations on the enhanced entrapment volume with which linear chains capture cyclic chains resulted in a concentration approximately 20 times smaller than the overlap concentration of linear chains. Our study was then expanded to look for an improved estimate of the distance required for entanglement in linear chains, this time omitting the presence of rings. Our results provide two important conclusions; first, the existence of a bridging mechanism that allows distant linear chains to interconnect by means of a common cyclic chain seems to be evident, in agreement with previous studies; second, the use of the end-to-end distance as an indicator of linear chain entanglement results in an underestimation of this condition. It is proposed that a more appropriate parameter would be the critical distance, which was found in this study to be approximately 1.09 times greater than the end-to-end distance for each chain. We also suggest that this parameter be treated as a radius rather than an end-to-end vector, in the same way as the radius of gyration is employed to calculate the overlapping concentration., Advisor: Dr. Sachin Shanbhag, Florida State University, College of Engineering, Dept. of Chemical & Biomedical Engineering., Thesis (Honors paper)--Florida State University, 2010., Includes bibliographical references.
Analysis of somatic driver genes in pediatric medulloblastoma
Analysis of somatic driver genes in pediatric medulloblastoma
Medulloblastoma is the most common malignant pediatric brain tumor. The early incidence of medulloblastoma and low prevalence of germline mutations suggest that somatic mutations have a significant effect on medulloblastoma development. This thesis focuses on the analysis of somatic driver genes to identify aberrant pathways contributing to the genetic architecture of medulloblastoma incidence. These signaling pathways were determined through gene set enrichment analysis on the medulloblastoma driver genes. Additionally, single nucleotide variant data was utilized to generate medulloblastoma’s mutational profile to understand the mutational processes that contribute to its development. In SHH-activated medulloblastoma, the contribution of somatic driver genes to the activation of the SHH pathway was inconclusive. In contrast, the Wnt signaling pathway in Wnt-activated medulloblastoma was significantly upregulated by somatic driver gene mutations. In Group 3 medulloblastoma, gain-of-function mutations in an inhibitor of pro-inflammatory cytokines, HIVEP3, could aid in explaining the poor prognosis of this subgroup. Group 4 medulloblastoma samples had driver gene mutations in molecules that may activate the Wnt pathway but inhibit the SHH pathway. Analysis of medulloblastoma’s mutational profile demonstrated an abundance of cytosine to thymine transitions. Decomposition of this profile into known mutational signatures revealed two significant mutational processes: spontaneous deamination of 5-methylcytosine and defective DNA mismatch repair. Understanding the genetic architecture of medulloblastoma through the analysis of somatic driver gene mutations and aberrant signaling pathways may help in revealing the molecular mechanisms of these tumors that ultimately assist in the development of drugs for targeted therapy., Keywords: Medulloblastoma, Cancer, Biochemistry, Wnt, SHH, Mutational signatures, Gene set enrichment analysis
Analysis of the 1st–3rd December 2018 South Georgia and North Florida Flooding Event
Analysis of the 1st–3rd December 2018 South Georgia and North Florida Flooding Event
The purpose of this project is to determine what caused the 3-day heavy rainfall event in the North Florida and South Georgia region from December 1st through December 3rd, 2018 as well as why it was climatologically abnormal for the month of December. This will be done by 1. Determining the surface features and fronts responsible for providing the lift and moisture to help produce the heavy rainfall, 2. Analyzing upper-air data as a second way to identify the systems and to see what the atmospheric column was like in terms of moisture content and instability to produce the heavy rainfall in the region, and 3. Examining in-depth the radar loops from the four radar sites in the area to show how the event unfolded. This will also serve as a visual explanation for why certain areas received significantly more rainfall than others.In the end, by showing the overall synoptic setup and radar imagery that caused the heavy rainfall event over our region, the results will serve as an example for future winter flash flood events if they were to occur again.
Analysis of the Extratropical Flow Response to Recurving Atlantic Tropical Cyclones
Analysis of the Extratropical Flow Response to Recurving Atlantic Tropical Cyclones
There is a significant frequency of Atlantic tropical cyclones that complete extratropical transition and recurve in the mid-latitudes. Using a climatological approach, this study will analyze the extratropical flow response to recurving Atlantic tropical cyclones and compare the results to those from the Western North Pacific, as examined by Archambault et al. (2013). This investigation includes 54 recurving Atlantic tropical cyclones occurring between 2007 and 2013. The extratropical flow response will be quantified using potential vorticity. Characteristics of tropical cyclones, the extratropical jet stream, and the dynamical "phasing" of their interaction will be examined to determine the features that lead to significantly amplified extratropical flow. Results show the extratropical flow to be insensitive to the wind speed, latitude, and month of recurvature. However, there is an association between low mean sea level pressure and a larger amplification of flow. Finally, tropical cyclones recurving on the east side of the nearest trough are shown to have "favorable phasing," which yields amplification of the extratropical flow., Keywords: Extratropical Flow Response, Extratropical Transition, Recurving Atlantic Tropical Cyclones, Submitted Note: A Thesis submitted to the Department of Earth, Ocean, and Atmospheric Science in partial fulfillment of the requirements for graduation with Honors in the Major., Degree Awarded: Spring Semester, 2015., Date of Defense: April 10, 2015.
Analyzing Gaps and Hurricane Rain Coverage to Inform NASA Satellite Proposal
Analyzing Gaps and Hurricane Rain Coverage to Inform NASA Satellite Proposal
Remote sensing has become an increasingly popular way to use the absorptivity, emissivity, and scattering of several key atmospheric constituents to estimate relevant properties of various meteorological and oceanographic phenomena, such as precipitation, sea surface temperature (SST), surface vector winds, and ocean surface currents. However, because many of the techniques are sensitive to rain, surface observations suffer from considerable ‘rain contamination’ during heavy rain events that make it difficult to view the surface. In these conditions, high resolution surface observations typically come from operational aircraft that are used to observe and study tropical cyclones (TCs) and other weather systems. Furthermore, most current satellites either measure with long wavelengths over an area much larger than desired hurricane features, or with too short a wavelength and can’t see the surface through the clouds or rain. Other techniques that provide high resolution surface observations through rain also suffer somewhat from rain contamination and are very sparse in space and time. One characteristic that has not been studied is the distribution of gap sizes in moderate to heavy rainbands that circulate around the main low pressure center of a TC. Aircraft data from the National Oceanic and Atmospheric Administration’s (NOAA’s) WP-3D turboprop aircraft will be used to create Lower Fuselage (LF) radar snapshots in plane-relative coordinates to determine the spatial distribution and size estimation of moderate to heavy rainband gaps, or near-zero reflectivity regions, near and around the core of hurricanes. The distribution of these gap sizes will provide very useful information on the satellite instrument characteristics needed to see the surface through these gaps. This information is expected to aid in hurricane-related applications of a new higher-resolution satellite.

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