Digital Commons Network^™

Computational Study On Protein Docking With Vascular Disease Application, Lohitha Reddy Shanigaram

Master's Theses

This thesis investigates how computational methods can help us understand protein docking and vascular diseases by integrating machine learning. The main goal of this research is to develop a system that can predict whether variants in the SOX17 gene are associated to Pulmonary Arterial Hypertension (PAH), a significant vascular condition. To do this, a dataset of 1,063 SOX17 variants was created using publicly available sources such as ClinVar, gnomAD, LOVD, and Ensembl. The study included cleaning and structuring the dataset, encoding genomic data and training a Random Forest classifier to classify variants as positive, negative, or unknown for disease association. …

Data Driven Analysis Of Samara Seed Kinematics And Dynamics, Shashwat Sparsh

Master's Theses

Samara Seeds are a class of fruit most famously belonging to the Acer species and are characterized by their single-bladed geometry and their auto-rotation response during descent. This steady-state auto-rotation response is the subject of aerodynamic analysis which aim to quantify the performance. The period prior to the beginning of steady-state auto-rotation is classified as the transition regime and has not been the subject of intense scrutiny.

This thesis employs a data-driven approach to analyzing the kinematic and dynamic response of these seeds during both the transition and auto-rotation stages of flight to quantify the performance with respect to the …

Influence Of Prescribed Burning On Coast Redwood (Sequoia Sempervirens) Forest Wildfire Resistance, Resilience, And Risk Of Repeated Fire, Sky B. Biblin

Master's Theses

Land managers need tools to mitigate wildfire proliferation in the western United States. Prescribed burning may be an effective tool to reduce wildfire severity and promote healthy landscapes. In 2020, a large-scale wildfire provided a rare opportunity to compare early postfire data between areas with and without a history of prescribed burning. Field data were collected approximately one year after a wildfire in fifty 20-meter plots from sites treated with prescribed fire in either 1999, 2007, or 2011 and fifty from sites without a history of prescribed fire. The influence of prescribed burning on forest resistance, resilience, and risk of …

Exosense: A Novel Technology For Selective Purification Of Cd63+ Exosomes From Neural Cells, Kristen Hope Hutson Truelove

Master's Theses

Exosomes are extracellular, cell signaling microvesicles that contain unique genomic and proteomic signatures reflective of the host cell’s pathophysiological conditions. In recent years, the study of exosomes has increased tremendously because many have been recognized as molecular biomarkers with the potential to advance methods of disease diagnostics and therapeutics as well as contribute to physiological analyses of multiple organism types. With the promising potential that exosomes offer to the field of molecular biology, it is vital to establish an efficient and consistently reliable mechanism of exosome isolation from biological samples. Many isolation techniques currently available typically yield exosome samples with …

Play Behavior And The Development Of Boldness And Caution In Juvenile Belding’S Ground Squirrels (Urocitellus Beldingi), Madelene Shehan

Master's Theses

The ubiquity of play among juvenile mammals suggests it provides adaptive benefits, potentially through influences on the development of temperament in young animals. Juvenile Belding’s ground squirrels (Urocitellus beldingi) must balance competing demands for boldness and caution imposed by the fundamental trade-off between their short active season and their vulnerability to predation. In this study, I evaluated whether play helps to facilitate the development of an appropriate balance between boldness and caution in juvenile U. beldingi.I observed the play behavior of juvenile U. beldingiand conducted flight-initiation distance tests to measure boldness-caution at the beginning and toward …

Investigations And Analysis Of Dynamical And Steady State Properties Of Chemical Reaction Systems, Diego Ortega Hernandez

Master's Theses

In this paper, we investigate results from chemical reaction network theory and a list of techniques to test for the reaction-coordinates dynamical system to have a partial order induced by a positive orthant cone. A successful result from one of these tests guarantees mono-stationarity (and indeed convergence). We also investigate a recently published algorithmic and computational approach to determine whether a reaction network establishes mono- or multi-stationarity. We test new reactions that have not been previously introduced in the literature for mono- or multi-stationarity using this approach. This includes the two-site phosphorylation reaction network and a modified double phosphorylation reaction …

Role Of Daxx As A Predictive Biomarker In Breast Cancer, Michelle Lucia Fernandez

Master's Theses

Breast cancer is the most commonly diagnosed form of cancer in women, besides skin cancer, and second only to lung cancer for cause of mortality. It is divided into three subtypes, depending on different molecular or pathologic characteristics, including estrogen or progesterone receptor-positive (ER/PR+), human epidermal growth factor receptor-2-positive (HER2+) and triple negative breast cancer (TNBC). There are several therapies used to target these subtypes, but there is still a chance that the cancer will recur into a more aggressive, resistant form even if the therapies were successful before. This recurrence is believed to be due to the Cancer Stem …

The Effects Of Spinal Cord Injury On Expression Of Pain-Relevant Genes In The Colon, Noelle Mckearney

Master's Theses

Spinal cord injury (SCI) results in varying degrees of paralysis, loss of normal sensory function and, oftentimes, chronic pain originating below the level of injury. Post-SCI pain tends to be resistant to traditional analgesic therapies and has been shown to impair recovery of function, making it a significant healthcare concern. Approximately one third of SCI patients report abdominal pain as a primary and severe symptom with marked similarity to other functional gastrointestinal pain disorders (e.g. irritable bowel). The etiology of this intense pain phenotype is unclear given that visceral organs are left uninjured in SCI. Here we examine changes in …

Bird Abundance At Bird Feeders In Response To Temperature, Wind Speed And Precipitation During The Winter Season, Siddhant Kahal

Master's Theses

The goal of this project is to explore how 23 different bird species respond to 3 climatic attributes. These attributes are lower than average temperatures, wind speed and precipitation level. Information about the bird species and all of the data associated with them is provided by Project FeederWatch (PFW). This is a citizen based survey study that provides key information about bird species abundance through the use of backyard and community feeders. The study volunteers from across the United States and Canada monitor these bird feeders and note important information about the species such as the number of individuals seen. …

Preparation And Characterization Of A (Viologen) Containing Main Chain Peg-Carbon Nanotubes Phase For Hybrid Supercapacitor Application, Kanishka Rana

Master's Theses

Supercapacitors (SCs) and batteries are recognized as the two most important electrical energy storage devices. SCs have some distinct advantages such as high-power density and long cycle life when compared to batteries. However, they have yet to match the energy densities of batteries. In an effort to improve the energy density of SCs, a hybrid supercapacitor was developed using a pair of single-walled carbon nanotube electrodes and two polyethylene glycol (PEG-400) gel-polymer electrolytes (GPEs) containing redox additives of viologen (V) and ferrocene dicarboxylic acid (Fc), respectively. The introduction of V and Fc, was expected to improve the energy performance of …

Cux2-Positive Radial Glial Cells Generate Diverse Subtypes Of Neocortical Projection Neurons And Macroglia, Ton Dan Nguyen

Master's Theses

The mammalian neocortex is 6-layered structure that develops in an “inside-out” manner, with cells of the deep layers (Layers 5-6) born first. Cells of the superficial outer layers (Layers 2-4) are generated subsequently and must migrate past older born cells to their final laminar position. Pioneering transplant studies suggested a progressive lineage restriction model, which posits that early neural stem cells (or radial glial cells, RGCs) are multipotent and sequentially generate different types of cortical neurons based on birthdate. Recently published work from Franco et al. (2012) argues against this paradigm, and proposes the existence of a subclass of neural …

Early Round Goby (Neogobius Melanostomus) Invasion Into Lake Michigan Tributaries And Competitive Interactions With Two Native Benthic Fishes., Margaret Ann Malone

Master's Theses

The round goby is a prolific invasive species and is currently spreading into Great Lake tributary streams. There is a high potential for negative impacts on native benthic fishes in these stream habitats and the aim of this study is to assess the impacts of the round goby on two native darter species in particular (johnny darter and blackside darter). I review the history of round goby invasion in the Great Lakes and summarize hypotheses of the invasive characters of the round goby. Using game theory, I provide a G-function approach to understanding the outcomes of the round goby invasion …

Characterization Of Gut Associated Circulating Invariant Natural Killer T Cells (Inkt) In Chronic Inflammation Of The Intestine, Venus Allahyarzadeh

Master's Theses

The incidence of chronic intestinal diseases such as Crohn’s disease (CD), ulcerative colitis (UC), and celiac disease is steadily rising in pediatric patients in the United States. Although there is an influx of helper T cells to the gastrointestinal (GI) tract in these diseases, the immunopathologic mechanisms of specific T cell subsets are not clearly understood and diagnosis between these diseases is difficult. We hypothesized that the frequency of specific subsets of circulating invariant natural killer T (iNKT) cells and their surface trafficking receptor (TR) phenotype indicate location and degree of inflammation in patients and further help to distinguish between …

Synthesis And Characterization Of C8 And N2 2'-Deoxyguanosine Adducts Of 6-Nitrochrysene, A Cancer-Causing Agent, Kimberly R. Rebello

Master's Theses

Nitropolycyclic aromatic hydrocarbons are ubiquitous in the environment, and many compounds of this family are carcinogenic. 6-Nitrochrysene, a representative member of this group, is a suspected human carcinogen that has been shown to cause lung, breast, and other forms of cancer in rodents. It is believed that this derivative of chrysene causes cancer by forming DNA adducts, which, in turn, induce mutations in critical gene sequences. The goal of my research is to synthesize one or more of the major DNA adducts formed by 6-nitrochrysene, which will be introduced in DNA in order to study their biological effects.

The initiation …

Exploring The Physiological Role Of Vibrio Fischeri Pepn, Sally L. Cello

Master's Theses

The primary contributor to Vibrio fischeri aminopeptidase activity is aminopeptidase N, PepN. Colonization assays revealed the pepN mutant strain to be deficient at forming dense aggregates and populating the host’s light organ compared to wildtype within the first 12 hours of colonization; however the mutant competed normally at 24 hours. To address the role of PepN in colonization initiation and establish additional phenotypes for the pepN mutant strain, stress response and other physiological assays were employed. Marked differences were found between pepN mutant and wildtype strain in response to salinity, acidity, and antibiotic tolerance. This study has provided a foundation …

Conservation Of Bridle Shiner (Notropis Bifrenatus) In Connecticut: Issues In Detecting An Elusive Species, Kasey C. Pregler

Master's Theses

Bridle Shiner (Notropis bifrenatus) is apparently declining over most of its range and is currently listed as a species of concern in Connecticut. Using an occupancy modeling framework in program PRESENCE, my study compared seining and electrofishing backpack unit detection probabilities of Bridle Shiner. This research indicated the apparent decline of Bridle Shiner in the state was in part due to changes in sampling gear used for statewide surveys. Seining used 50 years ago was demonstrably more effective at capturing Bridle Shiner than the currently favored and more frequently used electrofishing gear. In light of this recent finding, …

Synthesis Of Hybrid Inositol Glycan Analogues, Sudi Sabet

Master's Theses

A 2010 study by Centers for Disease Control and Prevention has projected that one of three US adults could have diabetes by the year 2050. More than 90% of the diagnosed cases are Type II diabetes, a condition characterized by insulin resistance. In search of new antidiabetic drugs, a class of natural, phosphorylated, inositol-containing pseudosaccharides called inositol glycans (IGs) has been studied for years. These compounds have insulin-mimetic activity in insulin-sensitive cells and can stimulate processes such as lipogenesis and glucose transport. Due to the heterogeneity of IGs, it is very difficult to isolate them from their natural sources, and …

Comparative Gene Analysis And Prediction Of Innate Immunity And Apoptosis Machinery In Hydrothermal Vent Tubeworms, Corey M. Bunce

Master's Theses

Siboglinid tubeworms are an emerging model system for symbiosis in extreme conditions. At deep-sea hydrothermal vents in the Pacific Ocean, they harbor a chemoautotrophic symbiont in a specialized organ, the trophosome, where the bacteria carry out primary production via oxidation of reduced sulfur compounds. The trophosome of siboglinid worms is suggested to be tightly regulated, symbiont-responsive, and developmentally homeostatic. The purported mechanism involves a cellular proliferative or apoptotic response to bacterial signals, environmental cues, or nutrition. Though these processes are well understood in more amenable model systems, there has been little work uncovering the tubeworm’s genetic potential for sensing and …

Analysis Of Post-Cranial Traits For The Assessment Of Biological Distance Among Temporally Distinct New World Populations Of African Descent, Claire Marie Dansereau

Master's Theses

This investigation examines change in post-cranial osteometric markers in temporally distinct New World populations of African ancestry: Newton Plantation series (17th-19th century Barbados; N = 16); two subsamples from the Hamann-Todd (HT) series (U.S.) based on birth year, 1865-1900 (N = 66) and 1901-1915 (N = 62); and the Forensic Databank Collection (FDB) (20th century U.S.; N = 137). It was anticipated that individuals from Newton would exhibit less admixture than those from H-T or FDB. They were also predicted to demonstrate greater skeletal robusticity due to mechanical loading. Additionally, it was expected that stature would increase over time due …

Effect Of Positional Dependence In Recognizing Transcription Factor Binding Sites, Saad A. Quader

Master's Theses

Background: Many consensus-based and Position Weight Matrix-based methods for recognizing transcription factor binding sites are not well suited to the variability in the lengths of binding sites. Besides, many methods discard known binding sites while building the model. Moreover, the impact of Information Content (IC) and the positional dependence of nucleotides within an aligned set of TFBSs has not been well researched for modeling variable-length binding sites. In this paper, we propose ML-Consensus, a consensus model for variable-length binding sites which does not exclude any input binding sites. We consider Pairwise Score (PS) as a measure of positional dependence of …

Perceptions Of Psychology Among Seminary And Biology Students At Andrews University, Sandro Moraes

Master's Theses

Problem. Both pastors and biologists frequently interact with individuals. These contacts often involve conversations that deal with an individual’s feelings, behaviors, and the relationship between mind and body. Thus, how seminarians and biologists perceive psychology will greatly affect such interactions. Therefore it is important to know how both professionals perceive psychology. This is not all that different from the research biologists perform as they learn about the brain. Because of the interrelatedness between these two professions, what are the perceptions of psychology among seminary and biology students at Andrews University? -- Method. The data gathered from the responses of biology …

Local Adaptation Of Two Cryptic Species, Lasthenia Californica And Lasthenia Gracilis, To Distinct Regions Within A Serpentine Outcrop, Teri Barry

Master's Theses

Intraspecific variation providing tolerance to specific edaphic conditions may contribute to population differentiation, speciation, and species coexistence. This process is often examined using reciprocal transplant experiments of closely related species in contrasting edaphic conditions. The two cryptic species Lasthenia californica and L. gracilis occur on a serpentine outcrop in parapatry at Jasper Ridge Biological Preserve. I hypothesized that each species would demonstrate greater fitness in its home range. A reciprocal transplant experiment was conducted in the field to determine home site advantage. Seedlings from each species were planted in both home ranges and in the transition zone where both species …

Mastermind-Like 1-Dependent Notch Target Gene Activation Requires A Sequence-Paired Site And A Tata Box, Cassandra Agbayani Ramos

Master's Theses

Notch signaling plays an important role in mammalian cellular proliferation, apoptosis, and differentiation. To activate target genes, the Notch intracellular domain (NICD) forms a complex with CBF1 and Mastermind-like protein (MAM). The Notch activation complex binds to a response element containing the consensus sequence RTGRGAR (R= purine) on target gene promoters. The promoter of one well characterized target gene, Hes1, contains four Notch response elements (NREs). Site-directed mutagenesis and reporter gene assays were used to examine the activation of Hes1 by mutating individual and combinations of NREs. Results indicated that NREs 2 and 4 are important for Hes1 activity, confirming …

Hydrodynamic Focused Passive Separation Under Continuous Flow In A Microfluidic Chip, Jad Kanbar

Master's Theses

A continuous flow, passive separation device was designed using an equivalent circuit to create variable flow rates for hydrodynamic focusing to drain channels and collection outlets. By varying the diameter of the sample inlet connection into the reservoir, the particle position was influenced significantly, which enabled desired separations. Additionally it was noted that the relative, horizontal position of the inlet also had a significant influence on particle position within the device. A dimensionless number, the Characteristic Sample Inlet, was developed to relate geometric properties of the inlet reservoir to downstream particle distribution. It was found that a 2:1 ratio between …

Synthesis Of Half-Loaded Nitroimidazole Indocyanine Green Dyes Attached To Carbon Nanotubes, Courtney L. Stanford

Master's Theses

Indocyanine green dye is the only FDA approved NIR fluorescent dye that can be used in humans. 2-Nitroimidazoles are very effective radiosensitizers, have low cytotoxicity, and target hypoxic tissue. By coupling the two together, hypoxic tumors can be targeted and imaged. Previous work has been done to couple 2-nitroimidazole to both sides of the indocyanine green dye. This work focuses on expanding that concept to couple 2-nitroimidazole to only one side of the dye, thus allowing for the other end to be available to couple to another compound, generating a half loaded 2-nitroimidazole indocyanine green dye. In theory, this half-loaded …

A Conservation Plan For Reservoir Canyon Natural Reserve, San Luis Obispo, Ca, Brian M. Provenzale

Master's Theses

My thesis project is to create a conservation plan for the Reservoir Canyon Natural Reserve (RCNR) in San Luis Obispo, California. It is a professional project for the City of San Luis Obispo with the goal of eventual adoption by the City Council. The plan was motivated by City policy, which advises creating conservation plans for open spaces, and by a particular need to address management issues in RCNR that include plant and wildlife conservation, trail access, erosion, electrical utility easements, and other legal matters. The project consists of two main components: the conservation plan and a companion paper. The …

Utilization Of Protein Tertiary Contacts To Improve Protein Structure Prediction Using Sequence Homology, Trung Thanh Nguyen

Master's Theses

The structure of a protein ultimately determines its function; therefore, knowledge of three-dimensional structure is essential for understanding its function and mechanism of action. The two most common methods for determining protein structure are x-ray crystallography and Nuclear Magnetic Resonance (NMR) spectroscopy. These methods are quite successful but can be very time-intensive and costly. An alternative method is protein structure prediction, where structure is computationally predicted from amino acid sequence. As opposed to x-ray crystallography and NMR spectroscopy, protein structure prediction is not encumbered by potential experimental problems. In this research, we attempted to determine if certain protein structure features, …

Chemical, Biological, And Preliminary In Vitro Studies Of Novel Vanadium(Iv) Complexes With Schiff Bases And Thiosemicarbazone Ligands, Nerissa Abigail Lewis

Master's Theses

9-Anthraldehyde-N(4)-methylthiosemicarbazone (MeATSC), potassium (E)-2-(2-hydroxybenzylideneamino)-3-(1H-indol-3-yl)propanoate (K[(Sal-L-tryp)] and 2-(2-hydroxybenzylamino)-3-(1H-indol-3-yl)propanoic acid (the reduced Schiff base) were prepared using known synthetic procedures. Two novel thiosemicarbazone ligands, (E)-N-ethyl-2-(4-hydroxy-3-methoxybenzylidene)hydrazinecarbothioamide (N-Ethhymethohcarbthio) and (E)-N-ethyl-2-(1-(thiazol-2-yl)ethylidene)hydrazinecarbothioamide (acetylethTSC), were also prepared. All ligands were characterized by FT IR and electrochemistry. N-Ethhymethohcarbthio were characterized by elemental analysis whereas the reduced Schiff base and K[(Sal-L-tryp)] were characterized by ESI MS. X-ray crystallography was also used to characterize acetylethTSC. The ligands were then reacted with [VO(Sal-L-tryp)(H2O)] (1) (Sal-L-tryp = N-salicylidene-L-tryptophanate) to produce the …

Accurate Estimation Of Isoform And Gene Expression Levels From Next Generation Sequencing Data, Marius Nicolae

Master's Theses

Massively parallel transcriptome sequencing is quickly replacing microarrays as the technology of choice for performing gene expression profiling due to its wider dynamic range and digital quantitation capabilities. However, accurate estimation of expression levels from sequencing data remains challenging due to the short read length delivered by current sequencing technologies and still poorly understood protocol- and technology-specific biases.

To date, two main transcriptome sequencing protocols have been proposed in the literature. The most commonly used one, referred to as RNA-Seq, generates short (single or paired) sequencing tags from the ends of randomly generated cDNA fragments. An alternative protocol, referred to …

Surface Nitriding And Oxidation Of Nitinol, Edin Bazochaharbakhsh

Master's Theses

Nitinol has been widely employed in biomedical devices due to its unique mechanical properties such as superelasticity, shape memory, and good biocompatibility. However, nickel ion release from the surface of the Nitinol is an issue. Surface nitriding and oxidation was performed on the Nitinol specimens to develop a nickel-free oxide layer on the surface. Nitinol specimens were nitrided in nitrogen + 4% hydrogen at 800 - 1000oC for 10 - 30 min and further nitrided in nitrogen + 5% ammonia at 500 - 675oC for 0 - 30 min. The thickness and chemical composition, specifically the nickel content of the …