Digital Commons Network^™

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 …

The Effects Of Indoor Climbing Route Rating Manipulation On Participant Climbing Self-Efficacy, Phillip James Sandlin

Master's Theses

This quantitative study utilized a classical experiment design to explore the

effects of manipulation of indoor climbing route ratings on the climbing self-efficacy of 90 indoor rock climbers. Controversy surrounding the accuracy of the assigned ratings of indoor climbing routes is commonplace at indoor climbing facilities. For indoor rock climbers to accurately assess their abilities, set appropriate goals, and monitor their progress, they must be able to choose climbs that accurately represent their desired level of challenge. Statistical analysis of the data did not support a relationship between manipulation of climbing route ratings and any changes in participant climbing self-efficacy. …

Effect Of Nanodroplet Ink Concentration On Image Contrast For Reverse-Emulsion Electrophoretic Displays, Winston Kuantung Wang

Master's Theses

Reverse-emulsion electrophoretic display technology is based on an electro-responsive ink comprised of self-assembled nanodroplets dispersed in a non-polar liquid. The dye-containing nanodroplets are selectively driven toward or away from the viewing plane of a display by electric fields. The hypothesis of this study is that image contrast in a nanodroplet electrophoretic display is governed by concentration and steric effects that limit the intensity of the dark state. Simultaneously, steric effects as well as electrostatic screening can diminish whiteness in the light state. This hypothesis has been tested by multiphysics simulation of dilute species in electrostatic fields and experimental measurements of …

Theoretical And Experimental Exploration Of Gill Remodeling In Gambusia Affinis, Barbara Tess Douglas

Master's Theses

In this thesis, the phenomenon of gill remodeling discovered in several species of fish is explored. Gill remodeling is achieved through an increase or decrease in cells within the interlamellar space, termed the interlamellar cell mass (ILCM). The effect of the ILCM on flow is explored using a theoretical model gill section. The model gill section was compared in three states: full ILCM, half ILCM, and clear (no ILCM). Differences in surface area, total flow, flow velocities, oxygen uptake, and available oxygen were compared between the three conditions. All parameters were distinctly larger for the model without the ILCM indicating …

Western Burrowing Owl Predation In An Urban Setting In California: Do California Ground Squirrel Calls Reduce Risk?, Lisa Anne Henderson

Master's Theses

Western burrowing owls are found in ground squirrel burrows throughout the urbanized landscape of the South San Francisco bay area, where they are threatened by habitat loss and degradation, prey limitation and predation. Previous research has characterized effects of habitat loss and prey-base limitations on owls, but the interplay between ground squirrels, owls and their predators has not yet been studied. The objective of this study was to assess the rate and types of predation interactions faced by Western burrowing owls and the extent to which California ground squirrels help burrowing owls reduce risk through alarm calling at Moffett Federal …

Amphibian Mortality On Roads: A Case Study In Santa Cruz Long-Toed Salamander Habitat, Michael Thomas Hobbs

Master's Theses

Amphibian populations have been declining at higher rates than bird and mammal populations. Agriculture, urbanization, including roads, and resource extraction continue to put pressure on all species. Roads in particular, are major sources of mortality. The Santa Cruz long-toed salamander (Ambystoma macrodactylum croceum), one of the most critically endangered species in the US, is one amphibian that is declining as a result of anthropogenic impacts, especially habitat loss and fragmentation due to urban development. Migration across roads puts these salamanders at risk from road-related death. This thesis quantified the rate of road mortality to these salamanders and other common amphibians …

Benthic Invertebrate Response To Habitat Complexity In South Bay Salt Ponds, Jessica Louise Murphey

Master's Theses

Wetlands are unique ecosystems that support specific flora, fauna, hydrology, and geology. These ecosystems increase groundwater availability, improve water quality, decrease flood water impacts, and help decrease shoreline erosion. In the south San Francisco Bay, the South Bay Salt Pond Restoration Project is restoring over 6,000 hectares of former salt ponds to tidal marshes and managed pond habitats. These habitats will support endangered species as well as migratory birds, diving ducks, invertebrates, and algal species. Benthic invertebrates are a vital piece of the South Bay food web as they provide the sustenance for other invertebrates, fish, shorebirds, and waterfowl. Improving …

The Effect Of Dietary Methylmercury On Na+, K+, -Atpase Activity And Growth In Fall-Run Chinook Salmon (O. Tshawytscha), John Negrey

Master's Theses

Hatchery reared Chinook salmon from California's Central Valley were fed for 67 days (Apr-Jun, 2008) on fish pellets mixed with either 0, 1, 3, or 5 µg*g-1 methylmercury hydroxide. Weight, fork length, condition factor, and Na+,K+- ATPase measurements were determined every two weeks and a 96-h seawater challenge was conducted at the conclusion of the experiment.

Results from two-way ANOVA, with treatment and date as independent variables, indicated no significant differences for weight (F3, 32 = 1.38; P = 0.280), length (F3, 32 = 0.986; P = 0.412) and condition factor (F3, 32 = 0.239; P = 0.869). Post-hoc analysis …

Metabolic Network Construction Based On The Genome Of The Marine Diatom Thalassiosira Pseudonana And The Analysis Of Genome-Wide Transcriptome Data To Investigate Triacylglyceride Accumulation, Karen Parker

Master's Theses

Algal lipids called triacylglycerols (TAGs) are essential compounds in marine ecology and are also used as the basis for commercial production of algal biofuels and omega-3 nutraceuticals. The goal of this thesis was to elucidate the biochemical processes associated with algal lipid accumulation in diatoms under different environmental conditions. The approach made use of the Mock et al. whole genome tiling microarray gene expression database for Thalassiosira pseudonana and gene annotations derived from the whole genome sequencing work of Armbrust et al. The analytical approach used bioinformatic tools, including Stanford Research Institute's (SRI) BioCyc Pathway tool and the Joint Genome …

Hydrogen/Deuterium Exchange Mass Spectrometry For The Study Of Methanol-Induced Conformational Transitions In Ubiquitin, Steven Raul Rocha

Master's Theses

In aqueous solutions with high concentrations of methanol at low pH, the global conformation of ubiquitin denatures to a structure of increased helical character at 50% methanol to a highly helical denatured structure at 90% methanol. Circular dichroism analysis and hydrogen/deuterium exchange mass spectrometry experiments have been reported for the monitoring of alcohol-induced conformational transitions of ubiquitin upon exposure to increasing concentrations of methanol. A bottom-up analysis of deuterium labeled ubiquitin was used in this study to examine the local conformational transitions of ubiquitin upon exposure to solutions of varying concentrations of methanol. Analysis of ubiquitin and nine peptide fragments, …

Spatiotemporal Variability In The Diet Of Nonbreeding Brandt's Cormorant (Phalacrocorax Penicillatus) In The Monterey Bay Region, Lisa Webb

Master's Theses

Brandt's Cormorant (Phalacrocorax penicillatus) diet composition was investigated using pellets (n = 285) collected on 19 sampling days at 3 locations during the 2006-07 and 2007-08 nonbreeding seasons in the Monterey Bay region. The conventional diet method was used, and the efficacy of the all-structure technique was evaluated. Although 29 species were consumed, Northern Anchovy (Engraulis mordax) dominated the diet and Speckled Sanddab (Citharichthys stigmaeus) also was important. Few rockfishes (Sebastes spp.) and Market Squid (Doryteuthis opalescens) were consumed compared with the number consumed in previous studies in the region during …

Behavior And Ecosystem Effects Of The Invasive Asian Clam (Corbicula Fluminea) In Urban Streams, Kayla Turek

Master's Theses

Invasive species can be detrimental to freshwater ecosystems. By completing laboratory and field studies to observe processes and behaviors of the invasive Asian Clam (Corbicula fluminea), I documented pathways whereby this invasive species impacts aquatic ecosystems under conditions typical of urbanized streams I found. The predominant pathways by which clams impacted nitrogen (N) cycling was through excretion thus increasing ammonium (NH4+) flux out of sediment and through bioturbation, which increased nitrate (NO3-) diffusion to the sediment and dinitrogen gas (N2) production (i.e., denitrification). The effect was greater under urban conditions, where C. fluminea population density and water column NO3- were …

Alpha-Synuclein Aggregates Activate The Nlrp3 Inflammasome Following Vesicle Rupture, Rudy Orlando Cedillos

Master's Theses

Parkinson's disease (PD) and related synucleinopathies are progressive neurodegenerative disorders that feature the accumulation of intracellular inclusions known as Lewy bodies (LBs) in the brain. The presynaptic protein α-synuclein is the primary constituent of LBs and has been documented to play a major role in the pathogenesis of synucleinopathies. Recently, aggregated α-synuclein has been implicated in prompting microglia-mediated inflammation, a process associated with the progression of neuronal death in neurodegenerative disorders. Although the mechanisms surrounding the induction of neuroinflammation are not well understood, the recently discovered inflammasome-forming NLR proteins have emerged as regulators of inflammation. In this study, we sought …

Snail Induces Mesenchymal Transition And Promotes Egfr Tki Resistance In Nsclc Cells Harboring Efgr Kinase Domain Mutations, Rutu Gandhi

Master's Theses

Lung cancer is the leading cause of cancer related death, accounting for one third of all deaths from cancer worldwide. About 85-90% of lung cancers are non-small cell lung cancers (NSCLCs). Molecular targeted therapies such as epidermal growth factor receptor tyrosine kinase inhibitors (EGFR TKIs) provide an effective treatment option for oncogene addicted NSCLC. However, the development of resistance to EGFR TKIs continues to be the major limitation in the treatment of NSCLC. Resistance to EGFR TKIs has been associated with the loss of canonical epithelial protein E-cadherin, suggesting involvement of epithelial to mesenchymal transition (EMT) in conferring EGFR TKI …

Development Of Cell Based Reporter Assay To Measure Pkc-Delta Promoter Activity, Kushal Prajapati

Master's Theses

Protein kinase C- δ (PKC-δ) acts as a tumor suppressor in skin cancer and is lost in 30% of human Squamous Cell Carcinoma (SCC). This loss is at the transcriptional level and involves the pathway leading to PKC-δ promoter repression after activation of Ras,PI3K,Fyn, and NF-κB. We proposed development of a high throughput, cell-based luciferase reporter assay on Ras transformed keratinocyte cell line, HaCaT-Ras to screen compounds having potential to inhibit this pathway and re-induce PKC-δ expression. First we developed a stable, PKC-δ promoter-reporter transfected HaCaT-Ras cell line. Next, we tested 13 compounds for their abilities to induce PKC-δ …

Social-Environmental Predictors Of Health-Related Quality Of Life In Youth With Spina Bifida, Caitlin Beth Murray

Master's Theses

Health-related quality of life (HRQOL) is a multidimensional construct including an individual's physical and mental health and psychosocial well-being (De Civita et al., 2005), and the measurement of HRQOL has been recognized as a key marker of health outcomes in pediatric populations (Eiser & Jenney, 2007). Due to medical and technological advances, an increasing number of individuals with chronic illnesses are living longer. As such, research that investigates improvements in HRQOL in youth with chronic illnesses has become essential. Indeed, the number of studies examining HRQOL in pediatric populations has increased markedly; spina bifida (SB) is one among several chronic …

Evidence For Renewal And Reconstitution Of Marginal Zone Macrophages In Young And Aged Mice, Erika Bahamon

Master's Theses

Aging in humans and mice correlates with decline in immune health, affecting both innate and adaptive immunity. Response against blood-borne bacterial pathogens is compromised because of the deterioration of the marginal zones of the spleen and decrease in frequency of marginal zone macrophages (MZM). This thesis asked if low cell turnover is the cause for the decrease of MZM, using cell proliferation to indicate cell turnover in spleens of mice. First, evidence showed MZM proliferation occurred in spleens of young mice and was decreased in the MZM from aged mice. Second, transfer of young bone marrow into old mice replenished …

Aquatic Macroinvertebrate Response To Invasion And Subsequent Removal Of Typha × Glauca From Great Lakes Coastal Marshes, Kimberly Anne Greene

Master's Theses

Aquatic macroinvertebrates are important in wetland ecosystems; many fish and wildlife species depend upon them for food resources and they aid in nutrient cycling. Wetland macroinvertebrate communities are influenced by plant community composition; as such, this study examined two implications of invasive hybrid cattail, Typha × glauca (Typha), on aquatic macroinvertebrate communities in northern Great Lakes coastal wetlands: 1) how the presence of nearly monotypic stands of Typha alters wetland aquatic macroinvertebrate communities and 2) how manual removal of Typha, via mowing and manual tilling, impacts these invertebrate communities along with wetland plant communities. I found that …

Legislating The Risk Of Light Teachers In 1950s And 1970s America, Kevin Vincent Heffernan

Master's Theses

The existence of gay and lesbian teachers remains for many a dangerous notion. Indeed, education and schooling are terrains in which homosexuality has historically been highly charged. Underlying this are problematic assumptions about the suitability of gays and lesbians as school workers, assumptions that feed into larger questions about gays and lesbians in general. This thesis will explore these assumptions - and their consequences for gay and lesbian teachers - against the backdrop of both the 1950s, when the burgeoning Cold War created an "age of anxiety," and the 1970s, when the rise of the religious right began to transform …

I Am Relieved To Discover My Symptoms Are Normal For My Condition: An Analysis Of Two Irritable Bowel Syndrome Support Communities, Erin Hvizdak

Master's Theses

Symptoms of Irritable Bowel Syndrome (IBS), a "medically unexplained illness," are present in up to 20% of the United States population. Individuals experiencing symptoms of IBS often report that physicians dismiss their experiential and embodied knowledge, leading to a sense of isolation and frustration. Many of these individuals attempt to diminish isolation and also exchange their knowledge in a community setting. In order to enable a more complete understanding of IBS, a survey about community participation was sent to members of a large online support group for IBS located on Facebook, with 81 completed surveys received. Further, an open-ended questionnaire …

Characterization Of Inducible Regulatory T Cells: An Umbilical Cord Blood Model, Rebecca Anne Krier

Master's Theses

The immune system is a group of structures and processes that protect us from disease. To function properly it must recognize a wide variety of pathogens such as viruses and bacteria. T cells play a crucial role in an immune response; however, an overactive immune response can lead to autoimmune diseases, therefore it is important that the immune system has the ability to negatively regulate an immune response. In the periphery, regulatory T cells (CD4⁺CD25⁺Foxp3⁺) are involved in the maintenance of self-tolerance and immune homeostasis. Mechanisms involved in the induction of iTregs from naïve …

Activity Patterns And Spatial Resource Selection Of The Eastern Garter Snake (Thamnophis Sirtalis Sirtalis), Matthew Gregory Most

Master's Theses

Snake species usually exhibit seasonal variations in activity patterns, home-range size and the use of respective habitat. Using mark-recapture protocols I marked 96 individual Thamnophis sirtalis sirtalis specimens in Lake Forest, IL to determine the independent variables that best explained habitat selection in a population of Eastern Garter Snakes (T. s. sirtalis). Specifically, I focused on the relationship between seasonal movement and home range size of male and female garter snakes. I analyzed the habitat preferences and spatial ecology of Eastern Garter Snakes during the 2011 sampling season and modeled the relationship between preferred or avoided habitat, in conjunction with …

Exosomes: Antiviral Agents In The Human Lung, Jennifer Alexandra Novak

Master's Theses

Hundreds of interferon effectors comprise the immediate host response to virus infection. One family of interferon stimulated genes is the IFITM (Interferon-Induced Transmembrane) proteins. IFITM3, in particular, has been shown to block virus cell entry of Influenza A Virus, SARS Coronavirus, and West Nile Virus, among others. IFITM3 has also been identified as an essential factor for host protection against Influenza A Virus in mice and humans. However, the mechanism by which IFITM3 functions remains unclear.

IFITM3 may function both intracellularly and extracellularly to block virus infection in the human lung. The extracellular milieu contains microscopic vesicles termed exosomes which …

The Interactive Effects Of Coping Strategies, Gender, And Stress In The Prediction Of Internalizing Symptoms In African American Youth: An Application Of The Specificity Model, Cynthia Pierre

Master's Theses

The current study utilized a specificity framework in the examination of interactions among coping strategies, stressor domains, and participant gender in the prediction of depressive and anxiety symptoms. Participants were 273 African American adolescents (6th - 8th; mean age = 12.9; 58% female). Participants completed measures of universal and culturally-relevant coping strategies in response to a stressor. Stressors were coded by raters across dichotomous domains: interpersonality (interpersonal vs. non-interpersonal), duration (acute vs. chronic), controllability (controllable vs. non-controllable), and sexuality (sexual vs. non-sexual). T-tests were conducted to examine differences in reported coping across stress domains. Inconsistent with predictions, mean differences of …

Testimony, Remhi And Senselessness In Guatemalan Memory, Melissa Jean Boroughs

Master's Theses

This thesis argues that the fragmented form of the Guatemalan collective memory concerning the genocide can be more clearly understood by analyzing and comparing testimonial literature, documentaries, the Truth Commission report, a novel, and works of performance art. All of these works are considered to be artifacts of memory of the Guatemalan genocide, each one offering a different perspective on the past and present of Guatemala.

Spanish Women Remembered In Elena Quiroga's Tristura, Escribo Tu Nombre And A Enferma, Ellen Patricia Brugliera

Master's Theses

The Silenced Women in Spain

Through three novels written by Spanish author, Elena Quiroga (1921-1995), this thesis intends to develop a better comprehension of women's role and identity during the Second Republic in Spain (December, 1931-1936), and under Franco's almost 40 year reign between 1936 and 1975.

Although the Republic sought to initiate change for women via constitutional and legislative reforms, the forms of mobilization occurred under male tutelage, and the Republic's lack of strategy combined with organizational fragmentation led, in some ways, to the immobilization of women. Because the society was in flux, these attempts at reform were also …

Assessing The Effects Of Titanium Dioxide Nanoparticles On Microbial Communities In Stream Sediment Using Artificial Streams And High Throughput Screening, Alexandra Ozaki

Master's Theses

Nano-titanium dioxide (nano-TiO2) is an engineered nanomaterial used in a wide array of commercial products. The production and use of large amounts of nano-TiO2 is resulting in the unintended release to the environment. Nano-TiO2 is known to be cytotoxic due primarily to its ability to generate reactive oxygen species, and negative impacts on a variety of organisms have been demonstrated, but the effects of nano-TiO2 on complex microbial communities under ecologically relevant conditions have rarely been tested. We conducted a controlled manipulative experiment using recirculating model streams dosed with a one-time amendment of 1mg L-1 nano-TiO2 (specifically P25). Within one …

Antibodies To Inhibit Clostridium Difficile Adhesion To Human Gut Epithelial Cell Line, Wonbeom Paik

Master's Theses

Clostridium difficile infection (CDI) is a major hospital-acquired diarrhea that can cause life-threatening complications such as pseudomembranous colitis. CDI is caused by colonization of host with C. difficile, a Gram positive, anaerobic bacterium known to produce toxins that cause disease. Normally, the gut microbiota protects the host from CDI, but disruption of the microbial composition through antibiotic treatment can leave one vulnerable for CDI. To date, no vaccines for preventing CDI are available.

In this study, the potential of antibodies directed against specific surface molecules of C. difficile to block bacterial adherence to host gut epithelial cells was studied, in …

Features Of Copulation And The Copulation Call In Glaucous-Winged Gulls (Larus Glaucescens), Amanda Sandler

Master's Theses

Glaucous-winged gulls (Larus glaucescens) breed along the Pacific Northwest coast where they perform highly stereotypical behavior patterns, including associated vocalizations. Early studies suggested the copulation call functions in maintaining pair bonds. Recent studies, however, challenge the idea that strengthening pair bonds is the only function of this call. I described the spectral and temporal features of the copulation call and investigated whether copulation behaviors varied over the course of the 2012 nesting season. During continuous observations from a blind in daylight hours, I documented the start and stop time for every copulation in a sample area of a nesting colony …

Forest Regeneration On The Osa Peninsula, Costa Rica, Manette E. Sandor

Master's Theses

Woody species diversity of secondary forest has the potential to converge with that found in old growth forest. This study is the first to examine multiple aspects of species and reproductive trait diversity, and their relationship to each other, across a successional chronosequence. Species richness and species diversity increases with increasing age of forest. Diaspore size and diversity as well as fruit size generally increased with increasing age of forest, but fruit size diversity did not. Abundance of animal-dispersed species increased whereas wind-dispersed species decreased in abundance over succession. Insect-pollinated individuals were most abundant overall. Diaspore diversity, pollination diversity, and …