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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, …

Determining The Intracellular Concentrations Of Flavonoids In Mda-Mb-231 Cells Using Hplc-Coupled Mass Spectrometry, Anh Dang Pham

Master's Theses

Flavonoids are polyphenolic compounds found in a wide variety of plants. In recent years, flavonoids have been found to be beneficial to human health. Our lab has investigated the ability of flavonoids to induce cytotoxicity in human breast cancer cell lines. We have discovered that some compounds can induce cytotoxicity very readily, whereas others cannot. We hypothesized that this difference is attributable to a compound's ability to transverse the cell membrane. Therefore, we used LC-MS to measure the amount of each flavonoid that is able to enter into MDA-MB-231 cells, human breast cancer cells. We tested 14 flavonoids. MDA-MB-231 cells …

Design Of A 4-Seat, General Aviation, Electric Aircraft, Arvindhakshan Rajagopalan Srilatha

Master's Theses

Range and payload of current electric aircraft is limited primarily due to low energy density of batteries. However, recent advances in battery technology promise storage of more than 1 kWh of energy per kilogram of weight in the near future. This kind of energy storage makes possible the design of an electric aircraft comparable to, if not better than existing state-of-the art general aviation aircraft powered by internal combustion engines. This thesis explores through parametric studies the effect of lift-to-drag ratio, flight speed, and cruise altitude on required thrust power and battery energy and presents the conceptual and preliminary design …

Classical Models Of The Spin 1/2 System, Carlos Harold Salazar-Lazaro

Master's Theses

We proposed a Quaternionic mechanical system motivated by the Foucault

pendulum as a classical model for the dynamics of the spin 1/2 system. We showed

that this mechanical system contains the dynamics of the spin state of the electron

under a uniform magnetic field as it is given by the Schrodinger-Pauli-Equation

(SPE). We closed with a characterization of the dynamics of this generalized

classical system by showing that it is equivalent with the dynamics of the

Schrodinger Pauli Equation as long as the solutions to the generalized classical

system are roots of the Lagrangian, that is the condition L = …

Profiling Flavonoid Cytotoxicity In Human Breast Cancer Cell Lines, Sina Yadegarynia

Master's Theses

Flavonoids are part of a large family of polyphenols that are found extensively in fruits and vegetables. This class of compounds has been of considerable medical interest due to their anti-inflammatory and anti-cancer activities. Although extensive effort has been made to identify the biological effects responsible for the chemopreventive activity of these compounds, the exact molecular mechanisms involved are not fully understood. In this study, we focused on the cytotoxic effects of fourteen different flavonoids against a series of breast cancer cell lines and evaluated the induction of cell cycle arrest at G1 or G2/M phase as result of such …

Eye-Tracking Analysis Of Next Generation Air Transportation (Nextgen) Taxiing And Departure Concepts, Christina Kunkle

Master's Theses

The Next Generation Air Transportation System (NextGen) is comprised of concepts and technology that will help change the national airspace system. In the current experiment, we analyzed eye-tracking in a NextGen experiment that examined a concept of taxi-out operations that are commonly referred to as surface trajectory-based operation (STBO). This study was built on previous research investigating taxiing from the gate to the runway based on speed and time commands to include speed-based taxiing with bounds. Commercial airline pilots, both current and recently retired, participated in this study at the Human-Centered Systems Lab at NASA Ames Research Center. This study …

A Descriptive Study Of Old-Growth Sequoia Sempervirens Growth Form And Canopy Structure On A Pygmy Forest Ecotone In Mendocino County, Zuhayl Rochin Lambert

Master's Theses

The tallest tree in the world is the coast redwood, Sequoia sempervirens, a species endemic to a 16-km-wide coastal belt extending from Big Sur, California, to southern Oregon. Old-growth redwood forests are home to other plant and animal species that depend on structural characteristics that have formed over hundreds of years. While a great deal of research regarding growth form and structure has taken place on highly productive stands, little work has been done on marginal sites, where redwoods are on the edge of their ecological tolerance. In the Northern California County of Mendocino, hydrophobic spodosol are host to …

The Effects Of Restored Aquatic Large Woody Debris Structures On Invertebrate Populations In The Napa River, Clayton Christopher Leal

Master's Theses

Agricultural encroachment and habitat destruction within the riparian zone of many California ecosystems have created a need for restoration of stream hydrology in order to enhance and support native flora and fauna. On the Napa River, adjacent vineyards have caused the channel to become deeply incised, so that the stream now lacks geomorphic variability and biodiversity. In order to restore channel complexity, large woody debris (LWD) structures were installed in the river in the summer of 2010. In this study I evaluated the effects of installing LWD structures within the Napa River on benthic invertebrates in the first year after …

Investigation Of The Role Of Dietary Flavonoids On Cell Death: Evidence To Support A Non-Classical Apoptotic Mechanism, Tetiana Lialiutska

Master's Theses

Flavonoids are polyphenolic compounds widely distributed in plants and have been shown to be cytotoxic to cancer cells. Our lab has previously shown that some flavonoids are able to induce cytotoxicity and inhibit caspase activity in human breast cancer cell lines. The goal of our study was to identify the specific molecular pathways required for flavonoid-induced cytotoxicity. MDA-MB-231 cells, mouse embryonic fibroblasts (MEFs) lacking caspase 3 and 7, and primary baby mouse kidney epithelial cells lacking Bax and Bak were cultured. Flavonoid-treated MDA-MB-231 cells showed cytochrome c release. We detected caspase 3 activation and PARP cleavage in MDA-MB-231 cells after …

Ethics And Wolf Management: Attitudes Toward And Tolerance Of Wolves In Washington State, Julie Callahan

Master's Theses

Approximately seventy-five years after extirpation from Washington State, gray wolves (Canis lupus) returned. As of December 2012, eight packs had arrived from adjacent states and provinces. Delisted from the Federal Endangered Species List in the eastern one-third of Washington, state wildlife managers now have the authority to manage wolves without federal supervision. As a result, one seven-wolf pack has been destroyed. The current study was developed to provide information for managers and policymakers to modify wolf management policies to fit the new regulatory context. Effects of a range of cultural and demographic factors on attitudes toward wolves and tolerance of …

A Study On Taiwanese International Students And Taiwanese American Students: The Interface Between Naming And Identity, Yi-An Chen

Master's Theses

In this study, I analyze how Chinese and English naming practices influence name adoption and explicate how the use and choice of names by Taiwanese international students and Taiwanese American students at San José State University, California, are structured through social interaction and cultural context. The data were collected from in-depth interviews with 10 Taiwanese international students and 10 Taiwanese American students. The interviews focused on how they construct their identities and produce social relations with others through their choice and use of ethnic and/or English names.

The study findings help to illuminate areas that until now have not received …

Measurement Of Laser-Induced Thermo-Elastic Deformation In An Optic Using Polarization-Based Lateral Shearing Interferometry, Mark A. Cordier

Master's Theses

polarization-based shearing interferometer is presented that is capable of measuring the thermal deformation of a mirror subject to heating from absorption of a Gaussian laser beam. The shear is generated by spatial walk-off in a birefringent crystal. By adjusting the orientation of the crystal, the components of the wavefront gradient can be independently measured to allow determination of the full wavefront vector gradate as well as reconstruction of the wavefront. Furthermore, the monolithic nature of the birefringent crystal allows non-critical alignment of the interferometer's components. The interferogram is modulated, and a homodyne detection algorithm analyzes the modulated interferograms to extract …

Rural Water Development In Sub-Saharan Africa: A Comparative Study Between Uganda And Tanzania, Paola De Cecco

Master's Theses

Global transnational efforts to achieve the Millennium Development Goal of halving the world population lacking access to improved water supplies are failing to address sustainable development in sub-Saharan rural communities. These efforts have been driven largely by water governance strategies centered on the controversial principle that water is an economic good, and as such, the development of water services shall be left to the supply-demand mechanisms regulating commodities' markets. Uganda and Tanzania have embraced these strategies to varying degrees and have made strikingly different progress in developing their rural water sector. Uganda has maintained a steady rate of improvement in …

Mexican Photography Collected: Graciela Iturbide And Tina Modotti, Camille F. Porter

Master's Theses

The act of collecting has increasingly become a focus of art historians in the last

thirty years. Susan Pearce, Mieke Bal, Bruce Althuser and other scholars have written

theoretical perspectives illuminating the ways in which the collecting of art influences the identity of a particular collector and in turn the ways in which the process of collecting art itself attaches meanings to objects.

In the last twenty years, there has been a surge in the collecting of Mexican

photography dating from the 1920s to the contemporary period. Mexican photography

has a long history of being at once an art form …

Reproductive Success Of Gulls In The Larus Glaucescens-Occidentalis Complex On Protection Island, Washington, Libby C. Megna

Master's Theses

Glaucous-winged Gulls (Larus glaucescens) and Western Gulls (Larus occidentalis) hybridize extensively where their ranges meet along the coasts of Washington and Oregon, producing a continuum of phenotypic intergrades between the two parental species. Previous work has shown that hybrids can experience greater reproductive success than parental types by combining adaptive behaviors, such as nest site selection, of both parental species, although success of hybrids may be affected by shifts in the ecotone between marine upwelling and non-upwelling environments. I investigated whether there is a correlation between phenotype, reproductive success, and nest site choice for gulls in Protection Island National Wildlife …

Temporal Dynamics Of Galapagos Marine Iguna (Amblyhynchus Cristatus) Haulout, Brianna Gale Payne

Master's Theses

Galápagos marine iguanas (Amblyrhynchus cristatus) briefly forage in marine habitats but spend their remaining time hauled out on land. A wide range of diurnal activities, from social and thermoregulatory behaviors to sleep and food processing, occurs during haulout. To understand the dynamics of haulout and foraging in relation to environmental factors, I fit compartmental models derived from ordinary differential equations to field data collected daily from 30 April to 16 May 2011 at two sites—one Sandy and one Rocky—at Cabo Douglas, Isla Fernandina. The best model for haulout at the Sandy site accounts for 77–80% of observed variability and includes …

Protology And Eschatology In The Writings Of John C. Polkinghorne: A Study Of Contrastive Roles Of Scripture, H. Nicholas De Lima

Master's Theses

Problem The focus of this thesis is to address the problem of the contrastive roles of Scripture in protology and eschatology in the writings of John C. Polkinghorne. On the one hand, Polkinghorne rejects a univocal understanding of Gen 1-2, by invoking symbolic/analogical language for Gen 1-2, so that he can accept scientific protology. On the other hand, Polkinghorne introduces an apparent, relative univocity of biblical language in order to obtain his eschatology, contrary to the claims of pure scientific eschatology. This seems to suggest a dimension of internal methodological and theological incoherence in his system. Methodology This thesis provides …

Anthropomorphic And Zoomorphic Figurines Of Tall Jalul From 1992 To 2007, Sean Patrick Porras

Master's Theses

Problem. The seasons at Tall Jalul conducted between 1992-2007 yielded 77 terracotta fragments of objects commonly called figurines. These figurine fragments are styled after humans and animals. This present study has two major objectives: (1) to catalog the 77 exemplars of various types found at Tall Jalul and (2) to analyze that catalog with respect to factors such as figurine type, date, geographical locus, and archaeological context. -- Method. Forty-two fragments out of the total 77 were examined in the Horn Archaeological Museum at Andrews University. Those that have been allocated to the Department of Antiquities of Jordan were examined …

Socially Constructing God: Gender, Culture, And A Stratified Trinity, Landon P. Schnabel

Master's Theses

The Problem. Both hierarchicalist and equivalentist evangelicals use Trinitarian relations to argue for their opposing views on gender roles. How can this stalemate be broken if the Bible, the typical evangelical foundation for resolving doctrinal disputes, is used by both sides to argue their contrasting positions? -- Methods and Procedures. I explored the cultural determination of worldview, bringing the fields of sociology, psychology, history, and philosophy to bear on this theological debate and considered whether it may be differing presuppositions and subsequent opposing interpretations that cause the conflicting positions, rather than what the biblical text means. By looking through the …

God's Mission To The "Nations" And Hindus: Three Old Testament Narrative Models, Andrew J. Tompkins

Master's Theses

Background to the Problem. The world’s religions outside of Christianity have still hardly been touched by the gospel. This is especially true of Hindus, which make up the third largest religious group in the world. The time for new understandings and approaches is long overdue. -- Problem. The challenge of understanding how to present the God of the Bible to Hindus in a meaningful and lasting way continues to perplex the mission-minded person. For centuries this challenge has been present, and yet the gap between Christians and Hindus in many ways appears to be increasing. This study looks at God’s …

Automatic Document Classification In Small Environments, Jonathan David Mcelroy

Master's Theses

Document classification is used to sort and label documents. This gives users quicker access to relevant data. Users that work with large inflow of documents spend time filing and categorizing them to allow for easier procurement. The Automatic Classification and Document Filing (ACDF) system proposed here is designed to allow users working with files or documents to rely on the system to classify and store them with little manual attention. By using a system built on Hidden Markov Models, the documents in a smaller desktop environment are categorized with better results than the traditional Naive Bayes implementation of classification.

Beating The Odds? An Analysis Of Dialectical Tensions Experienced By First Generation College Students, Laurina Jane Lanham

Master's Theses

Current scholarly research on first generation college (FGC) students is concerned with attrition rates of these students and other ways institutions of higher education count FGC students. However, much of this research focuses on negative characteristics (e.g., "at-risk," low income) often associated with the FGC student community. Not only do these reports exclude the success rates of FGC students, but they also overlook the other identities that these students experience, such as working class identity. We know little of how these students negotiate this identity in their communication with others and how this process affects their communication in college classrooms. …

Exposure To Community Violence And Social Maladjustment Among Urban African American Youth: The Role Of Emotion Dysregulation, Devin Colleen Carey

Master's Theses

The goal of the present study was to further previous research that has focused on the detrimental outcomes of violence exposure by identifying the mechanisms that influence children's psychosocial vulnerabilities. Specifically, it examined emotion regulation as a possible mediator of community violence exposure to social adjustment. Moreover, because of the evidence that children living in inner city communities are chronically exposed to violence, this study longitudinally explored the reciprocal and perpetuating relationship between exposure to violence and child social maladjustment. Participants were 268 African American students (M age = 11.65 years, 40% males and 60% females) from six inner city …

The Effect Of Glucose On Transcription At Cpxr- And Ompr-Regulated Promoters, Andrew Charles Cosgrove

Master's Theses

While reversible acetylation of proteins has been well studied in eukaryotes and is now recognized in bacteria, global protein acetylation in bacteria is a recently appreciated phenomenon. Protein acetylation is known to affect almost every aspect of cellular physiology in eukaryotes and there is proteomic evidence that this may also hold true in bacteria. In eukaryotes, lysines are acetylated by acetyltransferases that use acetyl-CoA as the acetyl group source, and de-acetylated by deacetylases. In bacteria, this reversible process uses enzymes homologous to those used by eukaryotes.

Our lab has recently found that acetylation of RNA polymerase (RNAP) can activate transcription …

Family In Context: (Re)Entry Narratives Of Formerly Incarcerated Individuals, Jennifer Elena Cossyleon

Master's Theses

The current study is informed by narrative accounts of 39 released prisoners, who provide day-to-day understandings of how they have experienced and continue to experience community reintegration. This study digs deeper into the intricacies of returning to free society, one that often disenfranchises and labels ex-offenders, and attempts to reveal how released prisoners themselves see family as pertinent in their reentry experiences. Respondents' stories are telling of the resources they draw upon, and in particular how their families are involved in that process. Findings suggest that families at times provide material and emotional support, but may also facilitate drug use …

Evaluation Of The Performance Of Non-Covalent Molecular Mechanical Models For Zn2+ And Mg2+ Metal Ions, Maria Magdalena Kamm

Master's Theses

Computer simulations using molecular dynamics (MD) on classical molecular mechanical

(MM) interatomic potentials can provide valuable information and quantitative

predictions about these systems. In MD calculations binding free energies of ions to

host molecules can be studied if correct ion solvation free energies in aqueous solution

are obtained. However, no MM models exist that parametrize various Zn2+ and

transition metals consistently and consider both structural and thermodynamic data

simultaneously.

The first part of our work focused on MD free energy perturbation (FEP) simulations

to derive MM interaction parameters for Zn2+ and Mg2+ ions in aqueous

solution. To obtain these parameters …

Justice Efficacy And Argument Strength In Mock Juror Decision-Making In A Civil Trial, Katharina Kluwe

Master's Theses

In 2005, 48,300 state and federal civil jury trials occurred in the United States (National Center for State Courts, 2009). Approximately 15% of the verdicts juries render are inaccurate (Spencer, 2007). Therefore, it is of utmost important to increase juror accuracy. The current thesis investigated jurors' justice efficacy as it relates to persuasion. Mock jurors' levels of justice efficacy were manipulated by giving them false feedback on a moral reasoning task. Participants read a civil trial summary, and received weak or strong statements by potential other jurors. The relation between argument strength and verdict did not depend on the feedback …

Characterization Of The Clostridium Difficile Biofilm, Michelle Laning

Master's Theses

Clostridium difficile is a Gram-positive, spore forming bacterium and an opportunistic gastrointestinal pathogen. Clostridium difficile infection (CDI) is a common nosocomial infection. Upon antibiotic treatment, patients can be colonized with C. difficile from ingestion of spores. After colonization, cells produce toxins creating symptoms from diarrhea to pseudomembranous colitis, and many patients develop recurrent infections. Interactions between host epithelium and the bacteria is a critical step in infection, yet the interaction is not well understood. It is not known how C. difficile evades host immune responses. These are important mechanisms to answer in advancing CDI treatment. A biofilm could contribute to …

Deconstructing Demand For Women And Girls' Education, Linda Lu

Master's Theses

There is an increasing focus on the recognition of women and girls' education as a universal right. Many feminist scholars have questioned this rights-based approach to gender education and evaluated the challenges and solutions based on the international policy discourse. What is notably absent from this scholarship is a comprehensive look at how women and girls' demand for education is constructed though such universal declarations.

This thesis uses a postcolonial feminist framework to analyze how women and girls' demand for education is constructed through international gender education policy. Ultimately, through an analysis of policy and an assessment of the feminist …

(Women's) Archival Spaces And Trans Voices? A (Re)Search And Proposal, Jeremy Curtis Main

Master's Theses

Transgender has been silenced, exiled, forgotten, erased, ignored, maltreated, killed, and ultimately, in a major theme of this research project, excluded from histories. Yet, like women, African-Americans, and gay men and lesbians before them, transgender and their allies are working toward inclusion and independence. History, it seems, can no longer ignore them. One of the surest ways to "prove" a history is to have the original items of that history in an archives. So, what representation do we find among various United States' archives concerning transgender people? Unfortunately, like with many other marginalized groups, much work has to be investigated …