Digital Commons Network^™

Predicting Rna Secondary Structures By Folding Simulation: Software And Experiments, Joel Omni Gillespie

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

We present a new method for predicting the secondary structure of RNA sequences. Using our method, each RNA nucleotide of an RNA Sequence is represented as a point on a 3D triangular lattice. Using the Simulated Annealing technique, we manipulate the location of the points on the lattice. We explore various scoring functions for judging the relative quality of the structures created by these manipulations. After near optimal configurations on the lattice have been found, we describe how the lattice locations of the nucleotides can be used to predict a secondary structure for the sequence. This prediction can be further …

Synthetic Studies Of Laulimalide Analogues, Ian Addison Mcalexander

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Chapter 1 provides some background information on the disease area of cancer and current modes of treatment. Chemotherapy treatment is discussed with a focus on the major cellular targets for these drugs: DNA and microtubules. For each target, classes of active compounds are described along with their mode of action. The microtubule stabilizing agent laulimalide is introduced and a case is made for analogue synthesis.

Chapter 2 describes our first generation efforts toward synthesis of des-methyl laulimalide. The target compound is divided into a northern and southern fragment with the synthesis of each fragment described. The preparation of landmark intermediates …

Simulation, Kriging, And Visualization Of Circular-Spatial Data, William James Morphet

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The circular dataimage is defined by displaying direction as the color at the same direction in a color wheel composed of a sequence of two-color gradients with color continuity between gradients. The resulting image of circular-spatial data is continuous with high resolution. Examples include ocean wind direction, Earth's main magnetic field, and rocket nozzle internal combustion flow. The cosineogram is defined as the mean cosine of the angle between random components of direction as a function of distance between observation locations. It expresses the spatial correlation of circular-spatial data. A circular kriging solution is developed based on a model fitted …

Naive Prey Versus Nonnative Predators: A Role For Behavior In Endangered Species Conservation, Stephanie A. Kraft

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Fish are one of the most imperiled groups of vertebrates worldwide. Threats to fish fall into one of four general categories: physical habitat loss or degradation, chemical pollution, overfishing, and nonnative species introductions. Nonnative predatory fish often have a devastating impact on native prey, especially with endemic fish, whose restricted distribution and often limited evolutionary history with predators make them particularly susceptible to nonnative predators. One reason nonnative fish are often so efficient predators is that the native fish do not recognize the predator as a threat. Although many studies have examined the role of predator odor recognition, no fish …

Prediction Of Protein Function And Functional Sites From Protein Sequences, Jing Hu

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

High-throughput genomics projects have resulted in a rapid accumulation of protein sequences. Therefore, computational methods that can predict protein functions and functional sites efficiently and accurately are in high demand. In addition, prediction methods utilizing only sequence information are of particular interest because for most proteins, 3-dimensional structures are not available. However, there are several key challenges in developing methods for predicting protein function and functional sites. These challenges include the following: the construction of representative datasets to train and evaluate the method, the collection of features related to the protein functions, the selection of the most useful features, and …

Carbohydrate Derivatives In Antibiotics Research, Yi Liang

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

In this study, we investigated the potential applications of carbohydrates in the development of new antibiotics. To tackle the problem of multidrug-resistant variants of M. tuberculosis (MDR-TB), we investigated the biosynthesis pathways of trehalose, which has contributed to significant drug resistance. Some new methods were developed for the synthesis of potential inhibitors (6-azido-trehalose and 6,6'-diazido-trehalose) that have been designed to imitate the intermediate molecule (trehalose 6-phosphate, TPP) of OtsA-OtsB pathway. At the same time, some new antibacterial agents based on trehalose have been synthesized. Members of the 1,2,3-triazole family have shown interesting biological properties. Steroid derivatives have been developed in …

Optimization Of Strongly Nonlinear Dynamical Systems Using A Modified Genetic Algorithm With Micro-Movement (Mgam), Xing Wei

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The genetic algorithm (GA) is a popular random search and optimization method inspired by the concepts of crossover, random mutation, and natural selection from evolutionary biology. The real-valued genetic algorithm (RGA) is an improved version of the genetic algorithm designed for direct operation on real-valued variables. In this work, a modified version of a genetic algorithm is introduced, which is called a modified genetic algorithm with micro-movement (MGAM). It implements a particle swarm optimization (PSO)-inspired micro-movement phase that helps to improve the convergence rate, while employing the efficient GA mechanism for maintaining population diversity. In order to test the capability …

Sustaining The Allideghi Grassland Of Ethiopia: Influences Of Pastoralism And Vegetation Change, Almaz Tadesse Kebede

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The Allideghi Wildlife Reserve in the Amibara District of Afar Regional State, Ethiopia, has international significance for harboring endangered Grevy's Zebra and other wildlife dependent on grasslands. The reserve is increasingly used by pastoral people and their herds. Impacts of livestock on native vegetation include direct effects of grazing and indirect effects from livestock-facilitated dispersal of an invasive plant, Prosopis juliflora. The main research objective was to determine effects of pastoralism and vegetation change on prospects for sustaining the Allideghi Wildlife Reserve as grassland habitat for Grevy's Zebra. Methods included use of driving surveys to quantify resource use by …

Reinterpreting The Comedy Of Errors: Exploring "Madness" And The Need To Belong, William K. Smith

Undergraduate Honors Capstone Projects

Since The Comedy of Errors' rescue from the literary bargain bin where it was tossed by nineteenth and early twentieth-century critics, many modern scholars have provided insightful cultural, linguistic, and theatrical commentaries on a play that is clearly more complex than it first seems. One area these recent discussions frequently address is the play's portrayal of madness in early modern society. However, what many of these discussions fail to remember is that ultimately Errors is a comedy "performed for the Delight of the Beholders" and that no one in the play is actually mad. Therefore, this essay argues that The …

Grounding To Place And Past: Motherhood In The Novels Of Native American Writers Louise Erdrich And Linda Hogan, Elise Doney

Undergraduate Honors Capstone Projects

The interconnectedness in both form and content ofNative American literature originates from the complex relationship between cultural and personal identity as inextricably intertwined with spiritual and natural realms. In Louise Erdrich's Tracks and Linda Hogan's Solar Storms and Power motherhoodliesatthecenter ofthisinterconnectedweb ofrelationships among identity, community, tradition, and landscape. Each novel centers on a protagonist who is, in some form, distanced from her primary mother/daughter relationship, consequently literally and figuratively displaced. The disrupted maternal relationship results in the child's displacement, functioning as a metaphor for the community's severance from tradition and the land. However, surrogate mother/daughter relationships develop in each novel …

Loss Translated: Saudade In The Poetry Of Elizabeth Bishop, Corey D. Clawson

Undergraduate Honors Capstone Projects

In 1954, former U.S. poet laureate Elizabeth Bishop wrote in a letter from Brazil to Robert Lowell, a dear friend and fellow poet: "With much love and saudades as they say here, a very nice word that seems to include all the sentiments of missing friends in one.” This insightful observation illuminates a concept central to Brazilian culture which has been designated one of the most difficult words to translate. Later, Bishop defined the idea as “the characteristic Brazilian longing or nostalgia,” which she “strongly associates with homesickness.” Bishop’s fascination with the concept, I argue, is more than that of …

Convergence And Divergence In Attachment Style Across Male And Female College Students' Friendships And Romantic Relationships, Victoria Jean Van Uitert

Undergraduate Honors Capstone Projects

Attachment representations in friendship and romantic relationship contexts were examined in a sample of 398 college students. Analyses examined patterns of attachment style in both relationship contexts, divergence and convergence in attachment style, and links between attachment representations and negative peer and romantic relationship experiences (i.e., relational and physical victimization and betrayal). The majority of participants reported more secure attachment representations, relative to preoccupied or dismissing attachment. However, analysis of biological sex indicated that males reported more dismissing attachment styles with both friends and romantic partners, relative to females. Additionally, significant links were observed between negative peer and romantic relationship …

A Comparison Of Ffr Measures Of Young Adults With Biomark Normative Values, Kathryn Eileen Pitts

Undergraduate Honors Capstone Projects

The BioMARK (Biological Marker of Auditory Processing) test, formerly known as BioMAP, is a measure of the frequency following response (FFR) in children to a speech stimulus. The test was designed for 8 to 12 year old children. Other tests of the auditory brainstem such as auditory brainstem responses, have normative values that are valid for listeners from age 2 to adulthood. The goal of the present study was to evaluate the speech-evoked FFR of young adult listeners to determine if a separate set of normative values is needed for this age group. FFR tests using the BioMARK with thirteen …

Effects Of Direct And Indirect Predator Cues On Heteromyid Seed Selection And Seed Fate, Kelly J. Sivy

Undergraduate Honors Capstone Projects

Many factors affect foraging behavior of rodents, including predation risk, which is thought to influence seed selection and seed handling by desert rodents in patchy environments. Understanding forces that drive seed selection and seed fate can aid understanding of rodents' impacts on vegetation structure and dynamics. In a feeding arena study, we tested how indirect and direct predation cues influence seed selection and handling behaviors (e.g., scatterhoarding and larderhoarding) of two heteromyid rodents, Dipodomys ordii (Ord's kangaroo rat) and Perognathus parvus (Great Basin pocket mouse), foraging on three seed species. The indirect cue was shrub cover: one half of the …

Hydrologic Information Systems: Advancing Cyberinfrastructure For Environmental Observatories, Jeffery S. Horsburgh

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Recently, community initiatives have emerged for the establishment of large-scale environmental observatories. Cyberinfrastructure is the backbone upon which these observatories will be built, and scientists' ability to access and use the data collected within observatories to address research questions will depend on the successful implementation of cyberinfrastructure. The research described in this dissertation advances the cyberinfrastructure available for supporting environmental observatories. This has been accomplished through both development of new cyberinfrastructure components as well as through the demonstration and application of existing tools, with a specific focus on point observations data. The cyberinfrastructure that was developed and deployed to support …

On The Applicability Of Genetic Algorithms To Fast Solar Spectropolarimetric Inversions For Vector Magnetography, Brian J. Harker

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The measurement of vector magnetic fields on the sun is one of the most important diagnostic tools for characterizing solar activity. The ubiquitous solar wind is guided into interplanetary space by open magnetic field lines in the upper solar atmosphere. Highly-energetic solar flares and Coronal Mass Ejections (CMEs) are triggered in lower layers of the solar atmosphere by the driving forces at the visible ``surface'' of the sun, the photosphere. The driving forces there tangle and interweave the vector magnetic fields, ultimately leading to an unstable field topology with large excess magnetic energy, and this excess energy is suddenly and …

An Empirical Investigation Of The Adaptive Nature Of Shame, Elizabeth Jacqueline Dansie

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Throughout the empirical psychological literature on emotion, the general consensus is that shame is maladaptive, while guilt is the adaptive moral emotion. Conversely, evolutionary psychology concludes that all emotions serve adaptive functions. Specifically, shame serves an appeasement function in social relationships. In order to investigate the true nature of shame, the current study used an experimental design. Specifically, a 2 (high shame, no shame) X 2 (high guilt, no guilt) design with a no-mistakes control group was implemented, and shame and guilt were operationalized through an evolutionary lens (i.e., shame as a nonverbal display, guilt as verbalizations of apology). Participants …

A Comparative Study Of The Structural Features And Kinetic Properties Of The Mofe And Vfe Proteins From Azotobacter Vinelandii, Miguel Alejandro Pabon Sanclemente

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Biological nitrogen fixation is accomplished in the bacterium Azotobacter vinelandii by means of three metalloenzymes: The molybdenum, vanadium, and iron-only nitrogenase. The knowledge regarding biological nitrogen fixation has come from studies on the Mo-dependent reaction. However, the V- and Fe-only-dependent reduction of nitrogen remains largely unknown.

By using homology modeling techniques, the protein folds that contain the metal cluster active sites for the V- and Fe-only nitrogenases were constructed. The models uncovered similarities and differences existing among the nitrogenases regarding the identity of the amino acid residues lining pivotal structural features for the correct functioning of the proteins. These differences, …

Vegetation Characteristics Of Wyoming Big Sagebrush Communities Historically Seeded With Crested Wheatgrass In Northeastern Great Basin, Usa, Justin Rodney Williams

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Crested wheatgrass (Agropyron cristatum [L.] Gaertn.) is one of the most commonly seeded grass species in the western United States and dominates thousands of hectares in the Great Basin. Although many degraded Wyoming big sagebrush (Artemisia tridentata ssp. wyomingensis) plant communities have been seeded with crested wheatgrass, successional pathways, influence of soil attributes, and cultivation history on the vegetation of these communities have not been fully characterized. I sought to identify community phases, vegetative differences, and soil attributes that explain variation among 35 Wyoming big sagebrush communities historically seeded with crested wheatgrass. All communities were more than …

Goatsrue (Galega Officinalis) Seed Biology, Control, And Toxicity, Michelle Oldham

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Goatsrue is an introduced perennial plant that has proven to have great invasive potential, leading to its classification as a noxious weed in many states and at the federal level. This research focused on seed biology, herbicide control, and toxic dynamics of goatsrue. Physical dormancy of mature goatsrue seed was tested through scarification using sulfuric acid with exposures of up to 60 minutes resulting in 100% germination. Comparison of dormancy for 26-year-old and 6-month-old goatsrue seed indicated aged seeds had reduced dormancy levels compared to newly harvested seeds, but had similar viability. Goatsrue seedling emergence was inversely related to burial …

The Effect Of An Ambient Olfactory Intervention On Time-On-Task And Performance During Participant Interaction With An Electronic Flashcard System, Aaron J. Loewer

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The purpose of this study was to measure the influence of an ambient peppermint aroma on participants' time-on-task and performance while using FACTOR, an open-source e-Learning application. I proposed time-on-task was moderating between olfactory stimulation and performance.

A 2x2 research design measured interaction of group (nonscented, scented) and gender of participants (N = 65). The learning content consisted of 28 African countries. Two methods for measuring time-on-task were employed: participant self-report at six learning intervals, and second, video recordings captured by, and stored on each participant's computer.

Independent samples t tests were used to measure group and gender differences …

An Investigation Of Postzygotic Reproductive Isolation And Phenotypic Divergence In The Bark Beetle Dendroctonus Ponderosae, Ryan R. Bracewell

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Understanding reproductive isolation and divergence is the focus of speciation research. Recent evidence suggested that some Dendroctonus ponderosae populations produced hybrids with reproductive incompatibilities, a reproductive boundary undetected by phylogeographic analyses using molecular markers. Additionally, the unique bifurcated distribution of D. ponderosae and the proposed isolation-by-distance gene flow pattern around the Great Basin Desert provided a unique opportunity to investigate the evolution of postmating (postyzygotic) isolation while also understanding phenotypic divergence along latitudinal (climatic) gradients. First, I characterized the strength, biological pattern, and geographic pattern of postzygotic isolation in D. ponderosae by crossing increasingly divergent populations in a common garden …

Optimal Fractional Order Proportional And Integral Controller For Processes With Random Time Delays, Varsha Bhambhani

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

This thesis developed a new practical tuning method for fractional order proportional and integral controllers (FO-PI / PI^α) for varying time-delay systems like networked control systems (NCS), sensor networks, etc. Based on previously proposed FO-PI controller tuning rules using fractional Ms constrained integral gain optimization (F-MIGO), simultaneous maximization of the jitter margin and integrated time weighted absolute error (ITAE) performance for a set of hundred gain delay time-constant (KLT) systems having different time-constants and time-delay values are achieved. A multi-objective optimization algorithm is used to simultaneously maximize the ITAE factor and jitter margin of the plants at initial …

The Bioactive Properties Of Syringomycin E-Rhamnolipid Mixtures And Syringopeptins, Mekki F. Bensaci

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The need for new antimicrobial agents has become important in the last decade due to emerging resistance to a number of conventional antimicrobial agents. New approaches and sources are needed to generate novel and effective antimicrobials. For example, synergistic combinations between two or more agents may lead to new antimicrobial therapies. Furthermore, the increase in health problems caused by the exposure to agricultural crop pesticides and synthetic fungicides and the emerging development of organic farming has increased the necessity to develop natural products than can be used safely in controlling crop diseases.

In this work, I present the first studies …

Cognitive Inference And Resulting Behaviors In Response To Ambiguous Threat In The Coyote, Canis Latrans, Sarah Shawnee Dawson

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

While antipredator strategies have been a focus of behavioral research for decades, scientists generally study the responses of prey toward overt, explicit threat. However, risk can also be significant when a threat is covert, such as when an ambush predator may be nearby or a secondary threat remains after a predator's departure. Little is known about the mechanism that prey use to assess risk in a predator's absence. Tests were conducted to determine the manner in which coyotes respond to these ambiguous threats. Specifically, I tested whether coyotes respond to prior anthropogenic activity that has occurred near their only food …

Seed Banks Of Sagebrush Communities Seeded With Crested Wheatgrass, Kevin L. Gunnell

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Crested wheatgrass (Agropyron cristatum [L.] Gaertn.) is one of the most commonly seeded exotic species in the western United States. Although many degraded Wyoming big sagebrush (Artemisia tridentata ssp. wyomingensis) plant communities have been seeded with crested wheatgrass during rehabilitation efforts, seed banks of these communities have not been characterized. I sought to characterize and explain the variation among 33 seeded communities in the northeastern Great Basin. Hierarchical clustering and principal components analysis identified four possible seed bank categories in these communities. Seed bank categories varied from high to low crested wheatgrass dominance. The crested wheatgrass-dominated category …

Mechanisms Of Induced Cell Death In Bluetongue Virus Challenged Human Cell Lines, Justin Darrel Hoopes

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Bluetongue virus (BTV) is a pathogenic member of the Reoviridae family. BTV does not cause disease in humans, but is capable of selectively infecting and killing certain transformed human cell lines. Understanding BTV's oncotrophism may lead to new therapeutics for treating cancer. This study focused on the underlying mechanisms of BTV-induced cell death in carcinoma cell lines. It was our hypothesis that BTV infects human carcinoma transformed cells, produces mRNA and protein, induces a strong inflammatory response, induces mitogen activated protein kinase (MAPK)-based pro-apoptotic signaling, inhibits PKB-based signaling, and eventually kills the cell by inducing apoptosis.

Three carcinoma cell lines …

The Correlation Between A Pre-Engineering Student's Spatial Ability And Achievement In An Electronics Fundamentals Course, Mark E. Smith

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Though there is ample evidence showing a positive relationship between a student's spatial ability and achievement in many fields of science, technology, and engineering, this study was seeking evidence that a relationship exists between a pre-engineering student's spatial ability and achievement in an electronics fundamentals course.

The importance of spatial ability to mentally design, develop, and manipulate images has been linked to measures of practical and mechanical abilities that are quite useful in technical occupations. Spatial abilities are frequently attributed to creative and higher order thinking skills in science and mathematics. Spatial imagery is tremendously important in art and creative …

Effects Of Targeted Grazing And Prescribed Burning On Fire Behavior And Community Dynamics Of A Cheatgrass (Bromus Tectorum)-Dominated Landscape, Joel M. Diamond

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Studies were conducted to determine the effectiveness of using targeted grazing and prescribed burning as tools to reduce fire hazards and cheatgrass (Bromus tectorum) dominance on rangelands in the northern Great Basin. A field study, with four grazing-burning treatments (graze and no-burn, graze and burn, no-graze and burn, and no-graze and no-burn), was conducted on a B. tectorum-dominated site near McDermitt, Nevada from 2005-2007. Cattle removed 80-90% of standing biomass in grazed plots in May 2005 and 2006 when B. tectorum was in the boot (phenological) stage. Grazed and ungrazed plots were burned in October 2005 and …

Sonication Assisted Synthesis Of Oligomannosides, Christabel Tomla Tanifum

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Oligomannosides prevalently exist as cell surface antigens. They play important roles in diseases such as viral infection and cancer, and they have been shown to be useful as candidates for vaccines. HIV, one of the most devastating modern diseases, has a high content of mannose sugars on its envelope glycoprotein gp120. Oligomannosides of the HIV virus, also called Man9, which are found on the glycoprotein gp120, have been shown to play a protective role for the HIV virus, shielding highly conserved protein domains of gp120 from proteolytic attacks. Thus gp120 plays an important role in HIV infection of cells, being …