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End date: 2018 × Item Type: Publication × search.filters.applied.f.isOrgUnitOfPublicationTitle: College of Sciences × search.filters.applied.f.isSeriesOfPublicationTitle: Undergraduate Research Option Theses ×

Publication Search Results

Now showing 1 - 10 of 184
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Characterizing iron reducing microorganisms from anoxic ferruginous lake sediments

2018-12 , Costa, Bianca Francesca

Lake Matano, Indonesia is a well-known ancient ocean analogue as its anoxic ecosystem in the subsurface sediments allow the growth of microorganisms capable of mediating anaerobic oxidation coupled to iron reduction. An anoxic, ferric iron rich BSR was kept for 163 days to culture iron reducing bacteria in an environmental sample from Lake Matano sediment. Microscopy analysis was performed periodically to look for morphology trends using DAPI staining. Phylogenetic analysis was performed using CARD-FISH microscopy to target the Geobacter genus, known for electroactive abilities through pilA and interactions with iron particles. Cell counts correlated with iron reduction throughout the culturing period indicating iron reducing microorganisms were present in the environmental sample. Filamentous, coccus, bacillus and vibrio morphologies were observed through the culturing period with vibrio and bacillus being predominant at later stages of the culture. Particle association instances were observed at days 20, 62, 86 and 126 and DIET interactions at day 86. Characterizing these microorganisms opens a broad range of possibilities for wastewater treatment (strip mining groundwater contamination), use in bioelectrochemical systems biofilms (due to external electron transport pilA) and understanding the importance of this microorganisms in Iron cycling.

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Mitochondrial Dysfunction in Chronic Limb Ischemic Myopathy

2018-05 , Kim, Do Young Young

Critical limb ischemia (CLI), the most advanced clinical manifestation of peripheral arterial disease (PAD), is associated with cycles of ischemia and reperfusion (I/R) that are thought to compromise the bioenergetics of mitochondria. However, the specific biochemical mechanism through which the mitochondrial dysfunctions occur have not been fully characterized. In this experiment, the left femoral arteries of mice (n=3) were ligated and excised, and tibial anterior muscles were harvested on day 7 and 14. The sections were stained for hematoxylin and eosin (H&E), succinate dehydrogenase (SDH), and cytochrome C oxidase (COX). The results show significant increase in centralized nuclei in injured muscles compared to contralateral controls. SDH and COX data were inconclusive. Future studies are expected to continue identifying key mechanisms that link oxidative damage and mitochondrial dysfunction to develop targeted therapies that aim to improve the compromised bioenergetics of mitochondria, improving the prognosis of PAD and CLI patients.

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Analysis of metastatic-repressing microRNAs and determining ZEB1 as a gene candidate for siRNA knockout in mesenchymal-like ovarian and prostate cancer cell lines

2018-05 , Akbar, Amber A.

MicroRNAs (miRNAs) have been shown to play a significant role in cancer progression and metastasis through their regulation of gene expression to activate epithelial-mesenchymal transition (EMT). Understanding the genetic and molecular basis for how microRNAs induce EMT’s reciprocal mechanism, mesenchymal-epithelial transition (MET), is vital as metastatic disease is highly lethal. This study aims to identify genes involved in MET across two cancer types based on microRNA overexpressions that have previously been shown to induce MET in mesenchymal-like ovarian or prostate cancer cell lines. It also aims to understand how the same microRNAs behave in similar mesenchymal cell-lines. To elucidate the ability of different microRNAs to induce the same process of MET in two reproductive cancer cell lines, transfections to overexpress miR-429, miR-203a, and miR-205 in both ovarian cancer and prostate cancer cell lines, HEY and PC3, respectively, were performed. Using microarray analysis, differentially expressed genes were identified and comparisons of these genes to known EMT/MET genes was done to narrow down a set of genes important in both ovarian and prostate cancer MET processes. We show that miR-429 induces MET in both HEY and PC3 cells, but not through similar pathways, and that overexpression of miR-203a and miR-205 induced MET in either HEY or PC3, but not both. ZEB1 was identified as a gene candidate for siRNA knockout to recapitulate MET and further elucidate mechanisms of the three microRNAs inducing MET.

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Model Selection in Gravitational Wave Astronomy

2017-12 , Napier, Katherine

The several detections of gravitational waves by the Laser Interferometer Gravitational-wave Observatory (LIGO) and the Virgo detector are providing insights about the nature of gravity in our Universe [1]. As the number of detected gravitational waves increases, it will be necessary to employ computationally inexpensive methods to extract the parameters of the gravitational wave sources. This proof of concept study utilizes principal component analysis (PCA) to try to reduce the number of vectors needed to describe binary black hole (BBH) parameter space. The results of this study suggest that performing PCA on face-on BBH systems, those at zero degrees inclination, adds an unnecessary level of complexity. However, PCA is a beneficial method to apply to waveforms that are morphologically complex such as those from edge-on BBH systems, those at 90 degrees inclination. Running PCA on a catalog of specific waveforms in one area of parameter space can inform how to construct waveforms in other regions of parameter space. If these waveforms can be constructed to a high level of accuracy using only a few principal components (PCs), it will significantly reduce the computational cost associated with generating template waveforms. Instead of creating a waveform template for every parameter combination, the PCs can be used to construct waveforms from similar areas of parameter space.

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Evolution of Cross-Feeding in a Simple Bacterial Community: Genetic Determinants

2018-05 , Alexander, Ashley Marie

Syntrophic interactions, like cross-feeding, are ubiquitous in the microbial world and occur between different species and between different ecotypes of the same species. We seek to understand the conditions that favor intraspecific syntrophy using experimental evolution. Previous experiments led us to hypothesize that a limited number of mutations, perhaps only two, favor the emergence of cross-feeding lineages from a single ancestral clone. These mutations result in the overproduction of, and restricted access to, overflow metabolites. To test this hypothesis, we used site-directed mutagenesis to introduce the two mutations into an otherwise wild-type Escherichia coli strain, K12 MG1655. This genetically engineered strain was then evolved under glucose limitation as was done in previous studies where cross-feeding was observed. The resulting experimental populations are currently being analyzed for the emergence of inter-clonal cross-feeding. The discoveries made possible by pursuing this line of inquiry promise to enhance our understanding of how metabolically complex communities emerged early on in the history of life on Earth and illuminate why certain mutational trajectories are followed in polymorphic diseases like cancer.

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In-Situ Water Quality Monitoring for Resource-Constrained Areas

2018-05 , Johnson, Ann E

Water-borne pathogens and unsafe water supplies are the cause of death for 1.7 million people every year [1]. Many of these people live in the developing world, where it can be difficult to manage water safety. The World Health Organization mandates that many countries use standardized water quality measurements, and these measurements can take up to 18 hours and require unsustainable equipment and trained operators [2]. Fluorometers provide real-time prediction of both presence and number of thermotolerant (faecal) coliforms (TTCs) in water samples. This makes a fluorimeter an ideal water quality measuring device that would reduce the large amount of time required for water testing by current WHO standards [3]. However, current fluorometers are extremely expensive and not sustainable for in-field use. We present a low-cost fluorometer that will passively and accurately collect real time water quality measurements. Our device measures a fluorescent signal called tryptophan-like fluorescence (TLF), which is produced by bacteria when exposed to light at a specific frequency. This device exploits this phenomenon to deduce the quantity of bacteria in the sample. We hypothesize that this device will have accuracy that matches the current WHO standards for water quality measurements, and will be cheaper, easier to use, and more sustainable than the current methods.

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Generation and Stability of Charged Toroidal Droplets

2018-05 , Aizenman, Aaron

In this project, we have determined the quantitative parameters governing the transition phases of charged toroidal droplets. An instability reminiscent of the Saffman-Taylor Instability (viscous fingers) has been observed when toroidal droplets are exposed to a significantly high voltage source, but this is the only recorded development of this instability in a three-dimensional situation (Alberto Fernandez-Nieves 2016). We created a silicon oil environment of extremely high viscosity with aminopropyl terminated silicon oil (ATSO) added to lower surface tension. We utilized surfactants to minimize the surface tension between the inner and outer fluids to slow down the dynamics of the system enough to give the surface a chance to reach equipotential, thus allowing us to test the theories that currently exist in the field. In an attempt to disprove the possibility that this was the Saffman-Taylor Instability, we also attempted viscosity inversion experiments. These failed, thus giving us almost conclusive proof that this was indeed the Saffman-Taylor Instability. By proving that this is indeed the Saffman-Taylor Instability, we have also proven that this three-dimensional problem can be analyzed as a series of two-dimensional problems. This approach vastly simplifies further calculations and analysis of similar systems. A secondary focus of this project was to perfect a method of automated generation of inherently unstable shapes in viscoelastic materials. By using a novel method of 3D printing, the project attempted to increase the efficiency with which we can generate samples for testing and observation while also adding uniformity and consistency to the trials and experiments.

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Frustrated Magnetism and Searching For Quantum Spin Liquid Phases in Novel Materials

2018-05 , Bender, Darian Marie

In my research, I wish to classify and identify a possible Quantum Spin-Liquid (QSL) phase on novel quantum materials. Materials of interest include the two triangular lattice materials, Li4CoTeO6 and Li4NiTeO6, in which Ni and Co ions with effective spin-1 and spin-1/2 each occupy a triangular lattice. We performed thermodynamic and magnetization measurements which indicate a possible exotic magnetic ground-state in both materials. We then performed elastic neutron scattering, providing additional evidence for exotic magnetism in these materials. Inelastic neutron scattering measurements are still necessary to probe the nature of the magnetic correlations and to confirm a QSL phase. Another material of interest is the kagomé lattice material, KFe3(OH)6(SO4)2 (known as Fe-Jarosite). This material is a popular QSL.1, 2 Small crystals of Fe-Jarosite have been created by hydrothermal synthesis in Mourigal Lab, and preliminary measurements of magnetization are in good agreement with known values.1, 3 Neutron scattering is required to study this material’s spin-dynamics, however, scattering is weak. Therefore, further synthesis attempts must be performed in order to increase the size of single-crystals of Fe-Jarosite from 2.6 mm to 1.0 cm.

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Towards More Efficient ab initio Computation of Physical Properties

2018-05 , Zott, Michael D.

The introduction of the modern computer has been a boon to myriad scientific communities. Scientific experiment can be categorized into the categories of physical experiment and thought experiment. In the chemical arena, these thought experiments are now able to be tested for validity through advanced semi-empirical and ab initio computational methods. Theoretical chemistry continues to increase in efficacy, and the spread of classical, wavefunction, and density functional methods into experimental communities is now undeniable. An aspiration of computational chemistry is to provide predictive power to lower the number of physical experiments that need to be performed. This is especially important when systems arise that are difficult to study experimentally. This has the possibility to lower financial and environmental costs, in addition to reducing the time needed to perform physical experiments. Here, methods to computationally study solvent effects and crystal lattice energies are reported on. Both of these physical properties have substantial relevance to human-focused enterprises such as targeted drug design. For example, drugs are often delivered in solid, crystalline form and must dissolve into molecular form prior to being pharmaceutically active. Although the specific research reported on here does not use systems directly related to such applications, it is posited that fundamental advances in computational methods for computing physical properties for arbitrary systems will contribute to solving problems in drug design, material development, and biomolecule recognition.

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Rotifer Growth Under Astaxanthin Enrichment

2017-12 , Siegfried, Emma

Rotifers and astaxanthin both play an important part in the aquaculture industry. Rotifers are used as a substitute for copepods, the main source of food for larval fish in natural systems, due to the ease with which they can be cultured. Astaxanthin is a carotenoid and antioxidant which brightens the coloring of fish and improves fish health. Rotifers are believed to be a method through which astaxanthin can be bioencapsulated and vectored to larval fish. As a result, it is important to understand the effect of astaxanthin on rotifers themselves. This experiment uses a multitude of different protocols to determine how different astaxanthin compounds effects rotifers on both the individual and population levels. Reproductive tables and fluorescent imaging were used to assess the health of individual rotifers; population density measurements in mass cultures were used to assess rotifer population health. The reproductive ability of rotifers was significantly different from control under multiple astaxanthin treatments. Astaxanthin enrichment also created a higher stable population density in the mass cultures. The fluorescent imaging showed that the rotifers reached peak astaxanthin concentration within the rotifer gut after 3 hours, and but concentration returned to control levels within 24 hours of removal from astaxanthin. These results all point to the fact that astaxanthin helps to increase rotifer health and fitness, and that these rotifers could be used as a vector for astaxanthin to larval fish.

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