Digital Commons Network^™

Conformational Features Of The Human U2-U6 Snrna Complex, Ravichandra Bachu

Dissertations, Theses, and Capstone Projects

The splicing of precursor messenger (pre-m) RNA, during which noncoding intervening sequences are excised and flanking coding regions ligated, is an integral reaction of gene expression. In eukaryotes, it is carried out by a dynamic RNA-protein complex called the spliceosome, in which five small nuclear (sn) RNA components are actively involved in recognition and chemical aspects of the process. A complex formed between U2 and U6 snRNAs is implicated in the chemistry of pre-mRNA splicing. The catalytic activity of the U2-U6 snRNA complex is dependent on the presence of Mg2+ ions, and the complex has been shown to have several …

Candida Albicans Als5p Amyloid In Host-Microbe Interactions: A Ceanorhabditis Elegans Study, Michael Bois

Dissertations, Theses, and Capstone Projects

Candida albicans, a dimorphic fungus and an opportunistic pathogen, possesses a myriad of adherence factors including members of the agglutinin-like sequence (Als) family of mannoproteins. The adhesin Als5p mediates adhesion to many substrates, and is upregulated during commensal interactions, but is downregulated during active C. albicans infections[1]. An amyloid forming core sequence at residues 325-331 has been shown to be important for Als5p function, because a single amino acid substitution at position 326 (V326N) greatly reduces Als5p-mediated adherence[2]. We evaluated the role of Als5p in host-microbe interactions, using Caenorhabditis elegans as a host model and feeding them Saccharomyces cerevisiae expressing …

Transformative Science Education Through Action Research And Self-Study Practices, Olga Calderon

Dissertations, Theses, and Capstone Projects

The research studies human emotions through diverse methods and theoretical lenses. My intention in using this approach is to provide alternative ways of perceiving and interpreting emotions being experienced in the moment of arousal. Emotions are fundamental in human interactions because they are essential in the development of effective relationships of any kind and they can also mediate hostility towards others. I begin by presenting an impressionist auto-ethnography, which narrates a personal account of how science and scientific inquiry has been entrenched in me since childhood. I describe how emotions are an important part of how I perceive and respond …

Understanding Workplace Reciprocity Of Emergency Nurses: A Qualitative Study, Christine M. Corcoran

Dissertations, Theses, and Capstone Projects

Emergency nurses work with other health care providers under uncertain conditions to provide care to patients with all kinds of illnesses and afflictions from all walks of life. Despite implications that they must work together to accomplish their tasks, there are few studies that explore the relationships among emergency department personnel. Furthermore, there are even fewer that focus on the way emergency nurses work together to provide care to their patients. The purpose of the study was to understand the lived experience of workplace reciprocity of emergency nurses through the use of a qualitative phenomenological method. Nurses with three or …

Inter-Religious Relationships And Anxiety In The Regulation Of Automatic Inter-Religious Prejudice, Karla J. Felix

Dissertations, Theses, and Capstone Projects

Shared reality theory predicts and evidence suggests that inter-religious relationships are motivated to maintain or regulate interpersonal interactions with others. However, this motivation has been given little attention within the automatic attitude literature. This research is centered on the idea that automatic prejudice is moderated by two fundamental themes, shared reality and anxiety. These themes are reviewed to determine the degree to which participants socially tune to ingroup versus outgroup religious experimenters. In Experiment 1, automatic inter-religious attitudes toward Christian and Jewish experimenters were assessed via a subliminal prime procedure. Religious orientation (extrinsic, intrinsic) and regulation of inter-religious relationships were …

2d & 3d Nanomaterial Fabrication With Biological Molecular Frameworks, Kristina Ivana Fabijanic

Dissertations, Theses, and Capstone Projects

Recently, there has been a heightened amount of work done in the field of biomineralization. By taking inspiration from natures' phenomenonal individualities as a means to develop new and interesting nanostructures of varying sizes and dimensions, there is a newly developed design, namely Biomimetic Crystallization Nanolithography (BCN). With this method, the simultaneous nano-patterning and crystallization has been achieved using urease as the nucleation point and the hydrolysis of urea to obtain patterns of oxide semiconductor material, namely zinc oxide, at room temperature and aqueous solvent. The new and interesting characteristic of BCN involves the construction of amorphous inks of ZnO …

Phylogenetic Trees And Their Analysis, Eric Ford

Dissertations, Theses, and Capstone Projects

Determining the best possible evolutionary history, the lowest-cost phylogenetic tree, to fit a given set of taxa and character sequences using maximum parsimony is an active area of research due to its underlying importance in understanding biological processes. As several steps in this process are NP-Hard when using popular, biologically-motivated optimality criteria, significant amounts of resources are dedicated to both both heuristics and to making exact methods more computationally tractable. We examine both phylogenetic data and the structure of the search space in order to suggest methods to reduce the number of possible trees that must be examined to find …

Mechanism Of Phospho-Alpha-Tubulin-Driven Motility In Human Breast Epithelial Cells, Shatarupa De

Dissertations, Theses, and Capstone Projects

Protein kinase C (PKC), an enzyme important in signaling pathways that give rise to various cell phenotypes, has been closely associated with metastatic phenotypes of breast cancer. Tissues from patients of varying degrees of tumorgenicity have shown an elevated expression of the PKCα isoform as well as other diacylglycerol (DAG)-sensitive isoforms. Moreover, independent studies with highly invasive breast cell lines, such as MDA-MB-231 cells, have also shown an elevated level of PKCα. Therefore, PKCα has long been a therapeutic target for breast cancer. Among its known substrates (recently identified by our laboratory), α6-tubulin will, upon phosphorylation by PKC, enhance migration …

Migration Plasticity As An Adaptation To Climate Change: The Spatial Distribution And Abundance Of A Subset Of Neotropical Migrant Landbirds Wintering In The Northeastern United States, Juliette Goulet

Dissertations, Theses, and Capstone Projects

There is a need for accurate predictions of the effects of climate change on wildlife populations. Bioclimatic relationships however are potentially complicated by various environmental factors operating at multiple spatial and temporal scales. Therefore, in order to test the hypothesis that climate constraints of winter bird distributions are modified by species-specific responses to weather and climate, I relied on Christmas Bird Count data (CBC). With nearly 100 years of data, the CBC is a valuable source of information on historic and recent changes in the status and distribution of birds during the early winter period in the United States and …

How Important Is Land-Based Foraging To Polar Bears (Ursus Maritimus) During The Ice-Free Season In Western Hudson Bay? An Examination Of Dietary Shifts, Compositional Patterns, Behavioral Observations And Energetic Contributions, Linda J. Gormezano

Dissertations, Theses, and Capstone Projects

Trophic mismatches between predators and their prey are increasing as climate change causes decoupling of phenological relationships. Predators linked to the life histories of a particular prey will have a more difficult time persisting through environmental change unless they can alter their behavior to maintain the historical match or possess the ability to pursue alternate prey. Arctic predators typically possess flexible foraging strategies to survive in the labile environment, however, quantifying the limits of those strategies can be difficult when life history information is incomplete. In such cases, piecing together different aspects of a predator's foraging behavior, particularly when environmental …

Using Otoacoustic Emissions To Evaluate Efferent Auditory Function In Humans, Simon Henin

Dissertations, Theses, and Capstone Projects

The auditory system continually adapts to changes in the acoustic environment over short periods of time. This fine-tuning of its dynamics is mediated in part by the medial olivocochlear (MOC) bundle, a neural feedback loop which aids in the regulation of cochlear micro-mechanics. The ability to measure the response of the MOC system in humans may provide significant insight into unique cochlear functions, such as its sharp frequency selectivity and wide dynamic range. In humans the efferent system can be investigated non-invasively using otoacoustic emissions (OAEs). However, how OAEs can best be used to evaluate efferent function, the pitfalls associated …

An Ethnobotanical, Ecological And Lc-Ms-Based Chemometric Investigation Of Phaleria Nisidai, A Traditional Adaptogen Containing Diterpene Esters From Palau, Micronesia, Daniel Kulakowski

Dissertations, Theses, and Capstone Projects

An ethnobotanical, ecological and LC-MS-based chemometric investigation of Phaleria nisidai, a traditional adaptogen containing diterpene esters from Palau, Micronesia

Palau is a country with a rich heritage of traditional medicine still being practiced. One of the most popular and respected remedies in Palau is a tea made from fresh leaves of Phaleria nisidai Kaneh. (Thymelaeaceae). Interviews conducted to determine the use of this plant revealed that it is employed non-specifically to treat a variety of general health concerns. Its use as a prophylactic to keep away sickness, as a 'system cleaner', as well as for strength and energy indicate …

Hydrodynamic And Mass Transport Properties Of Microfluidic Geometries, Thomas F. Leary

Dissertations, Theses, and Capstone Projects

Microfluidic geometries allow direct observation of microscale phenomena while conserving liquid volumes. They also enable modeling of experimental data using simplified transport equations and static force balances. This is possible because the length scales of these geometries ensure low Re conditions approaching the Stokesian limit, where the flow profile is laminar, viscous forces are dominant and inertial forces are negligible. This work presents results on two transport problems in microfluidic geometries. The first examines the heterogeneous binding kinetics in a microbead array, where beads with different chemical functionalities are sequentially captured in a well geometry over which analyte solution is …

Vegf Treatment During Status Epilepticus Alters Long-Term Hippocampal Astrocyte Morphology: A Detailed Description Of Astrocyte Morphology And Glutamate Transporter Patterns With And Without Administration Of Vegf And Seizure Induction, Janice Rene Lenzer

Dissertations, Theses, and Capstone Projects

VEGF treatment during pilocarpine-induced status epilepticus (SE) causes enduring preservation of behavioral function in rats in the absence of enduring neuroprotection (Nicoletti et al., 2010). In addition, VEGF treatment reduces hyperexcitability in hippocampal slices without altering neuronal membrane properties (McCloskey et al, 2005). Combined, these data suggest the possibility that other cells or mechanisms could be involved in the beneficial effects of VEGF during SE. Our laboratory is interested in the potential contribution of astrocytes to these effects. Astrocytes are not only reported to contribute to epileptiform discharges in the hippocampus (Tian et al., 2005; Kang et al., 2005) but …

Analysis Of Dna Motifs In The Human Genome, Yupu Liang

Dissertations, Theses, and Capstone Projects

DNA motifs include repeat elements, promoter elements and gene regulator elements, and play a critical role in the human genome. This thesis describes a genome-wide computational study on two groups of motifs: tandem repeats and core promoter elements.

Tandem repeats in DNA sequences are extremely relevant in biological phenomena and diagnostic tools. Computational programs that discover tandem repeats generate a huge volume of data, which can be difficult to decipher without further organization. A new method is presented here to organize and rank detected tandem repeats through clustering and classification. Our work presents multiple ways of expressing tandem repeats using …

The Privileged "In-Between" Status Of Latino Jews In The Northeastern United States, Laura Limonic

Dissertations, Theses, and Capstone Projects

This study is an in-depth look at how religion, class, and ethno-racial status interact and intersect to affect assimilation and integration prospects for new immigrants. The research focuses on Latin American Jewish immigrants in the Northeastern United States, a particularly interesting group to study because they are not easily classified within the American racial and ethnic system and existing ethno-racial categories. As a result, they are presented with a number of ethnic options that they can call upon. The choices they make as well as the constraints they face in making these choices, can broaden our understanding of contemporary immigrant …

Why Should One Reproduce? The Rationality And Morality Of Human Reproduction, Lantz Fleming Miller

Dissertations, Theses, and Capstone Projects

Human reproduction has long been assumed to be an act of the blind force of nature, to which humans were subject, like the weather. However, with recent concerns about the environmental impact of human population, particularly resource depletion, human reproduction has come to be seen as a moral issue. That is, in general, it may be moral or immoral for people to continue propagating their species. The past decade's philosophical discussions of the question have yielded varying results. This dissertation takes on the issue in a broader moral perspective and asks not only whether it is moral to reproduce but …

The Characterization Of Pb2+ Toxicity In Rat Neural Development: An Assessment Of Pb2+ Effects On The Gaba Shift In Neural Networks And Implications For Learning And Memory Disruption, Lorenz Simon Neuwirth

Dissertations, Theses, and Capstone Projects

The toxic effects of Pb2+ on the developing rat nervous system has been investigated to assess early developmental GABAergic disruption and its implications with altering inhibitory learning and memory. This goal was achieved using a multi-systems approach: blood lead levels (clinical physiology), qRT-PCR (molecular genetics), brain and primary neuronal culture immunology (immunohistochemical and cellular approaches), physiological cellular components (synaptosomes and protein expression) and finally through learning and memory assessment with GABA mimetic drug manipulations in the intact animal (behavioral pharmacology). The influence of a 956ppm Pb2+ gestational diet (i.e. from birth to sacrifice) resulted in pup mean blood lead levels …

Development Of A Model Of Participation Of Community-Based, Discretionary Activities By People Who Use Wheelchairs, Anita Perr

Dissertations, Theses, and Capstone Projects

This cross-sectional research analyzed an existing data set of 302 wheelchair users to identify the psychosocial predictors of participation in community-based, discretionary activities. Two defining elements of participation were studied: the extent of participation and satisfaction with participation. Descriptive analyses of the participants' demographic information and portions of four assessments were completed first. Regression analyses were then used to systematically eliminate potential covariates until the significant psychosocial covariates of the extent of and satisfaction with participation were identified. Perceived control over one's life and perceived reintegration to social function were found to predict the extent of participation. Perceived control also …

Comparative Modeling And Functional Characterization Of Two Enzymes Of The Cyclooxygenase Pathway In Drosophila Melanogaster, Yan Qi

Dissertations, Theses, and Capstone Projects

Eicosanoids are biologically active molecules oxygenated from twenty carbon polyunsaturated fatty acids. Natural eicosanoids exert potent biological effects in humans, and a great deal of pharmaceutical research has led to the discovery of compounds for selective inhibition of specific enzymes in eicosanoid biosynthesis. Coupled with different receptors, eicosanoids mediate various physiological and pathophysiological processes, including fever generation, pain response, vasoconstriction, vasodilation, platelet aggregation, platelet declumping, body temperature maintenance and sleep-wake cycle regulation. In mammals, the eicosanoid biosynthesis has three pathways: the cyclooxygenase (COX) pathway, the lipoxygenase (LOX) pathway and the epoxygenase pathway. The COX pathway synthesizes prostanoids, which are important …

Metabolic Checkpoints In Cancer Cell Cycle, Mahesh Saqcena

Dissertations, Theses, and Capstone Projects

Growth factors (GFs) as well as nutrient sufficiency regulate cell division in metazoans. The vast majority of mutations that contribute to cancer are in genes that regulate progression through the G1 phase of the cell cycle. A key regulatory site in G1 is the growth factor-dependent Restriction Point (R), where cells get permissive signals to divide. In the absence of GF instructions, cells enter the quiescent G0 state. Despite fundamental differences between GF signaling and nutrient sensing, they both have been confusingly referred to as R and therefore by definition considered to be a singular event in G1. Autonomy from …

Quantitative Evaluation Of Microglial Activation And Vascularization In Suicide, Tatiana Pavlovna Schnieder

Dissertations, Theses, and Capstone Projects

Accumulated evidence points to immunological factors in psychiatric disorders. In a variety of chronic neurological disorders, exacerbation is associated with inflammation and a loss of integrity of the blood-brain barrier. Microglia, the principal brain immunological cells in the healthy state, respond to changes in the internal environment of the brain through a sequence of activated states. This study compared microglial phenotypes in the white matter of autopsy brains from 11 suicide victims and 25 subjects who died involuntarily. Both groups included cases with and without major psychiatric disorders, which were determined by PA interviews. Cases were matched for sex, age, …

Xenakis In America, Charles Wolcott Turner

Dissertations, Theses, and Capstone Projects

Iannis Xenakis had a long-standing interest in the U.S., but given the five years he spent here, little has been written about his experiences. This study attempts, through archival research and interviews, to document Xenakis’ time in the United States. Its subject is his relationship to American cultural institutions, and in what lured Xenakis here for musical composition and research.

The narrative treats the period from Copland’s invitation to Tanglewood in 1963, through Xenakis’ 1972 investment by France as a state-supported artist. While he visited the U.S. many times thereafter, he no longer sought long-term engagement with U.S. institutions, but …

Phylogeny And Population Genetics Of The Endangered Dwarf Bear-Poppy, Arctomecon Humilis Coville (Papaveraceae) Using Microsatellite Markers, Joshua Simpson

Dissertations, Theses, and Capstone Projects

The genus Arctomecon (Papaveraceae) is comprised of three narrowly endemic rare species that are largely restricted to gypsum soils of the eastern Mojave Desert. The small, remaining populations of these species have become increasingly isolated by urban development and habitat fragmentation. Arctomecon humilis is federally listed as endangered due to its limited distribution within a ~15 km radius of an actively expanding city. Organizations involved with land management and conservation have called for greater insight into the genetic variation and population structure of the remaining subpopulations as they make important decisions regarding where to focus their efforts and resources.

The …

The Effect Of Malintent On Visual Attention, David Brian Wallace

Dissertations, Theses, and Capstone Projects

Malintent is a relatively unexplored phenomenon, despite the practical and theoretical interest in its detection. The four studies presented here, informed by the Guilty Knowledge Test and Guided Search model of visual attention, illustrate how eye tracking can (and cannot) be utilized to detect malicious intent. Malintent, induced in two different mock crime paradigms (murder; theft), boosted the frequency and duration of fixations that fell upon objects relevant to their task. The size of the malintent effect ranged from moderate (fixation duration) to large (fixation frequency). The increased visual attention given to task-relevant objects was not unique to malintent; benign …

An Experimental Investigation Into The Mechanisms Of Bacterial Evolution, Zhenmao Wan

Dissertations, Theses, and Capstone Projects

This thesis studies the two fundamental mechanisms of bacterial evolution — horizontal gene transfer and spontaneous mutation, in the bacterium Escherichia coli through novel experimental assays and mathematical simulations. First, I will develop a growth assay utilizing the quantitative polymerase chain reaction (qPCR) to provide real-time enumeration of genetic marker abundance within bacterial populations. Second, I will focus on horizontal gene transfer in E. coli occurring through a process called conjugation. By fitting the qPCR data to a resource limited, logistic growth model, I will obtain estimated values of several key parameters governing the dynamics of DNA transfer through conjugation …

Numerical Study Of Canopy Flows In Complex Terrain, Xiyan Xu

Dissertations, Theses, and Capstone Projects

Canopy flow plays a substantial role in regulating atmosphere-biosphere exchanges of mass and energy. The worldwide FLUXNET has been developed to quantify the net ecosystem exchange of mass and energy through fluid dynamics in and above vegetation canopy using tower-based eddy covariance (EC) technique. However, EC measurements are subject to advection errors in complex terrain, particularly during nights when atmospheric stability is strong. Because EC measurements are one-dimensional (1D), three-dimensional (3D) air movement, CO2 transport, and temperature variation around the instrumented tower are unknown. We employ a Computational Fluid Dynamics (CFD) model to investigate the impact on CO2 transport of …

Acts Of Belonging: Perceptions Of Citizenship Among Queer Turkish Women In Germany, Ilgin Yorukoglu

Dissertations, Theses, and Capstone Projects

This thesis examines how people who have multiple identifications develop a sense of belonging. It focuses on those with politicized, romanticized, and stigmatized identifications which are assumed to be in conflict with one another. My particular case is that of "queer" women of Turkish descent in Germany with Berlin as my main study site.

These people embody what is considered to be an oxymoron: being queer yet also Turkish, being a lesbian yet having a Muslim background, being of immigrant origin yet also German. In short, they are between all worlds and thus, seemingly, do not belong anywhere. Their ambiguous …

Mechanisms Of Deadenylation Regulation Under Different Cellular Conditions, Xiaokan Zhang

Dissertations, Theses, and Capstone Projects

Control of gene expression by regulating mRNA stability after DNA damage has the potential to contribute to the cells rapid response to stress. The main focus of this dissertation is to elucidate the role(s) of nuclear PARN deadenylase in controlling mRNA stability, hence gene expression, of factors in the p53 signaling pathway during the DNA damage response (DDR). Understanding the mechanisms of these regulatory pathways will provide new insights on how the control of gene expression upon DNA damage decides cellular fate, offering new opportunities for therapeutics. In Chapter II, I presented evidence that PARN along with the cleavage factor …

The Inner Workings Of Text Summarization Systems, Hope Cotton

Dissertations, Theses, and Capstone Projects

This paper investigates automatic text summarization systems (ATS). To begin, a general description of how some ATS systems operate is provided. Following is a report on the testing of two summarization systems, Mead and SweSum. News articles from online sources were used for testing. Analyzing each system's output under different parameter settings helped to uncover (to some extent) the architecture of these summarizers. Both systems were compared as to how user-focused they are, how informative the summaries are in relation to the source document, and how punctuation and format are reconstructed in a summary.