Digital Commons Network^™

Restoring Native Plants Following Invasive Malephora Crocea (Coppery Iceplant, Aizoaceae) Eradication On Anacapa Island, Nathan William Hale

Master's Theses

To avoid unintended complications of invasive species eradication, it is important to understand the potential implications of the techniques used in species eradication efforts. This study aimed to compare how different methods of removing Malephora crocea affect the survivorship of planted seedlings of native perennial plants on Anacapa Island. Employing a randomized complete block design in an M. crocea stand, three removal treatments were tested: 1) hand-pull; 2) spray with herbicide and leave skeletons; and 3) spray and then remove skeletons after 2.5 months. In each treatment, seedlings of three species (Leptosyne gigantea, Frankenia salina, and Grindelia …

Relationship Between Cognitive Functions And Hormones, Daniel C. Miao

Master's Theses

Stress has been implicated by recent research to significantly contribute towards many cognitive and physiological deficiencies. One of the most popular topics of study is the effect of stress on inhibition, the all-or-none decision about an action or inaction. However, only recently have scientists begun investigating neuroendocrine molecules that link stress and inhibitory processing. Participants included San José State University undergraduates (27 male, 63 female, 1 unstated) who were exposed to the Trier Social Stress Test, an established stress task, and who were assessed before and after stress exposure for cortisol levels. Participants were also given a pre- and post-test …

Application Of Query-Based Qualitative Descriptors In Conjunction With Protein Sequence Homology For Prediction Of Residue Solvent Accessibility, Reecha Nepal

Master's Theses

Characterization of relative solvent accessibility (RSA) plays a major role in classifying a given protein residue as being on the surface or buried. This information is useful for studying protein structure and protein-protein interactions, and it is usually the first approach applied in the prediction of 3-dimensional (3D) protein structures.

Various complicated and time-consuming methods, such as machine learning, have been applied in solvent-accessibility predictions. In this thesis, we presented a simple application of linear regression methods using various sequence homology values for each residue as well as query residue qualitative predictors corresponding to each of the 20 amino acids. …

Foraging Behavior, Habitat, Health, And Survival Of Resident And Translocated Hawaiian Monk Seals At Nihoa Island, Hawaii, Tenaya A. Norris

Master's Theses

Translocations aimed at promoting population recovery for threatened and endangered species also can function as forced dispersals. To assess the efficacy of translocating Hawaiian monk seals (Monachus schauinslandi) and examine post-dispersal effects on monk seals, in 2008-2009, 12 weanling seals were translocated from French Frigate Shoals (FFS) to Nihoa Island (NIH). In addition, nine adult and eight weanling resident seals were captured at NIH. Satellite instrument attachment, biological sampling, and morphometry were conducted on seals at capture. Focal video camera drops also were conducted at 45 sites around NIH (< 100 m) in 2010-2011. Translocated and resident weanlings primarily dove to 40-60 m and used sandy-bottomed habitat < 13 km from NIH. In contrast, resident adults had greater variability in foraging behavior and habitat use. There also was a low prevalence of infectious disease in translocated and resident seals, excluding Chlamydophila abortus and enteric bacteria. First-year survival was greater for …

Characterization Of Hydride-Based Silica And Diamond Hydride Stationary Phases, Nima C. Parmar

Master's Theses

Aqueous normal phase chromatography possesses characteristics of both normal phase (NP) and also reverse phase (RP) chromatography. It can retain polar as well as non-polar compounds by carefully selecting the concentration ratio of organic solvent to water in the mobile phase. Silica hydride columns contain only a small percentage of silanol groups which are polar in nature and have an effect on the separation process. Diamond hydride columns consist of a small amount (~2%) of carbon chemically bonded to a silica hydride surface.

This research work characterized both hydride-based silica and diamond hydride stationary phases under isocratic and gradient conditions. …

Experiences Of Coping With Injury In Division I Athletes From Low-To-Middle Socioeconomic Status Backgrounds, Matthew Philip Bejar

Master's Theses

Injuries inevitably occur in any sport at any level. The integrated sport injury model is one of the most extensive frameworks to address the psychological responses to athletic injury. While this model posits that socioeconomic status (SES) influences how an athlete cognitively, emotionally, and behaviorally responds to an injury, no research has substantiated this claim. Low SES individuals experience an exceptional amount of stress, which may complicate how they cope with a negative event. The coping strategies employed by an athlete can have major implications on rehabilitation adherence, recovery time, and psychosocial well-being. The purpose of this study was to …

Predicting Slender False Brome (Brachypodium Sylvaticum) Invasion In The Santa Cruz Mountains, California, Janine Ellen Bird

Master's Theses

Early detection of an invasive species facilitates control and eradication. Slender false brome (Brachypodium sylvaticum) was first discovered in the Santa Cruz Mountains of Central California in 2003 as a non-native grass in redwood forests, competing with native vegetation. The current infestation in the Santa Cruz Mountains, estimated to be 300 acres, is concentrated in San Mateo County and could be eradicated. This study sought to determine most likely locations of slender false brome in the Santa Cruz Mountains by assessing environmental attributes of known presence locations using species distribution modeling and Maxent software. The study used 1,320 species presence …

A Study Of Genetic Variability In Larval And Adult Populations Of Dungeness Crab (Cancer Magister), Cairbre Fanslow

Master's Theses

Spatial and temporal genetic variation was assessed using mitochondrial DNA from adult and megalopae of Dungeness crabs, Cancer magister, from Fraser Delta in British Columbia, Washington, Oregon, and California. Megalopae were continuously sampled using light traps in one location, Coos Bay, Oregon, and compared with adults sampled across the species' range. While small-scale spatial and temporal variation were evident, there was no significant fit to the Isolation-by-Distance model when considering adult and larvae populations sampled over a coastal length of ~1700 km (Mantel r = 0.059, p = 0.289). Smaller bays showed higher genetic diversity than larger bays, contrary to …

The Prevalence Of The Uncultivated Bacterium Tm7a In Human Subgingival Plaque, Jamsheed Adrian Ghadiri

Master's Theses

Most bacteria are yet to be cultivated, and some uncultivated bacteria have been associated with human diseases. TM7, an uncultivated candidate division of bacteria, has been recently associated with periodontitis, a disease if left untreated causes tooth degradation and gum decay. A subgroup of TM7, known as TM7a, has been found in both human samples and activated wastewater. TM7a from these two locations are as high as 99.7% similar by 16S rRNA gene sequence analysis, leading researchers to believe both TM7a strains are very similar functionally. TM7a has been extensively studied in activated wastewater. However, little is known of its …

Women In Science, Technology, Engineering, And Mathematics (Stem) Fields: The Importance Of The Need To Belong And Self-Esteem On The Intention To Leave A Job, Jung Eun Lee

Master's Theses

The purpose of the study was to predict individual intentions to leave science, technology, engineering, and mathematics (STEM) field jobs. Psychological predictors were gender, the need to belong, self-esteem, perceived personal discrimination, and perceived group discrimination. We used the Amazon Mechanical Turk to recruit participants and Survey Monkey to conduct an online survey. Participants were 174 men and women who worked or studied in STEM fields. Two-step hierarchical linear regression analyses were performed to analyze the data. As a result, we found that all predictors mentioned above accounted for the variance in the intention to leave a job. Self-esteem and …

Response Of Waterbirds To Salt Pond Enhancements And Island Creation In The San Francisco Bay, Stacy M. Moskal

Master's Theses

Historically, San Francisco Bay supported the largest salt pond complex on the Pacific coast of North America, and these areas have been used by large numbers of migrating and wintering waterbirds for more than a century. In 2003, salt ponds in the South San Francisco Bay were purchased with a goal of restoring 50-90% of the 6100 ha of former salt ponds to replace lost tidal marsh habitats. However, a major challenge for the restoration project has been maintaining the abundance of non-breeding waterbirds in a smaller footprint of managed ponds. Thus, in 2009-2010, Pond SF2 was enhanced with 30 …

Use Of Dna Sequences To Identify Forensically Important Fly Species In The Coastal Region Of Central California (Santa Clara County), Angela T. Nakano

Master's Theses

Forensic entomology has gained prominence in recent years, as improvements in DNA technology and molecular methods have allowed insect and other arthropod evidence to become increasingly useful in criminal and civil investigations. However, comprehensive faunal inventories are still needed, including cataloguing local DNA sequences for forensically significant Diptera. This multi-year fly-trapping study was built upon and expanded a previous survey of these flies in Santa Clara County, including the addition of genetic barcoding data from collected species of flies.

Flies from the families Calliphoridae, Sarcophagidae, and Muscidae were trapped in meat-baited traps set in a variety of locations throughout the …

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 …

Genetic And Biochemical Analyses Of Streptomyces Coelicolor Ftsz, Sepf, And Other Possible Ftsz-Interacting Proteins, Allen M. Kotun

Electronic Theses and Dissertations

For various bacteria, an assortment of proteins, many of which are nonessential for division, bind the C-terminal tip of FtsZ to help stabilize the Z-ring and tether it to the cytoplasmic membrane. S. coelicolor produces aerial hyphae that contain numerous, evenly-spaced Z-rings that jointly constrict to form a chain of spores. Our understanding of this developmental process is complicated by the lack of known FtsZ-interacting proteins. To date, only two proteins, SsgA and SsgB, have been found to aid in Z-ring localization. For this study, the 399 amino acid FtsZ, multiple FtsZ C-terminal tip variants, and four putative FtsZ-associated proteins …

Mass Spectrometric Analysis Of Oxidized Eicosapentaenoic Acid Sodium Salt, Kelsey D. Jordan, Rita K. Upmacis

Faculty Papers and Publications

Eicosapentaenoic acid (EPA) is an omega-3 polyunsaturated fatty acid (PUFA) with 20 carbon atoms and 5 carbon-carbon double bonds. Mammalian cells cannot synthesize long chain PUFAs such as EPA de novo, and, thus, the most effective way to enrich cells in EPA is by dietary intake of fish oils. EPA supplementation causes an increase in its concentration in plasma lipids and in cell membrane phospholipids. Many beneficial effects of EPA supplementation have been noted, including (1) the potential to sensitize cancerous tumors towards chemotherapy, (2) the promotion of cardiovascular health, and (3) the alleviation of some mental disorders, but results …

Student Library And Technology Engagement Survey Summary Report: 2012, M. Sara Lowe, Char Booth

Library Staff Publications and Research

Based on a framework established by two prior investigations of local academic communities to inform library operations the CCL Student Library & Technology Engagement Survey was designed to explore: how Claremont Colleges students use, perceive, and understand CCL and its services; academic information technologies; and information literacy skills.

Student Library And Technology Engagement Survey, M. Sara Lowe, Char Booth

Library Staff Publications and Research

This survey was designed to understand how Claremont Colleges students use, perceive, and understand the Claremont Colleges Library, academic information technologies, and Information literacy skills. It was developed by Sara Lowe and Char Booth based on a survey Char Booth created and administered with the Council of Chief Librarians of California Community Colleges.

Reinforcing, Subjective, And Cognitive Effects Of Methamphetamine During D-Amphetamine Maintenance, Erika Pike

Theses and Dissertations--Psychology

Translational research suggests that agonist replacement may be a viable treatment approach for managing methamphetamine dependence. This study sought to determine the effects of d-amphetamine maintenance on methamphetamine self-administration in stimulant using participants. A cognitive battery was used to determine the performance effects of methamphetamine alone and during d-amphetamine maintenance. During each maintenance condition, participants first sampled a dose of intranasal methamphetamine then had the opportunity to respond on a progressive ratio task to earn portions of the sampled dose. Subject-rated drug-effect and physiological measures were completed prior to and after sampling methamphetamine. Methamphetamine was self-administered as function …

Examining The Interaction Of Neonatal Alcohol And Hypoxia In Vitro, Megan L. Carter

Theses and Dissertations--Psychology

Exposure to ethanol (ETOH) during fetal development results in a range of cognitive/behavioral deficits. There are differences in sensitivity to the effects of ETOH that could be explained by other factors, such as hypoxia. Similar mechanisms of damage underlie both ETOH, more specifically ETOH withdrawal, and hypoxia. Based on this overlap, it was hypothesized that sub threshold levels of these insults may interact to produce increased damage in sensitive brain regions. This study used a rodent organotypic hippocampal slice culture model to investigate the interaction of hypoxia and ETOH withdrawal and to determine possible developmental differences in the sensitivity to …

Forgiving Warriors: Does Outgroup Threat Reduce Ingroup Aggression Among Males?, David Chester

Theses and Dissertations--Psychology

In order to defend against outgroups, males and females respond to outgroup threat with different strategies. Specifically, males have been shown to respond to outgroup threat with increased ingroup solidarity and cooperation which is likely reflective of their ancestral role as warriors. What remains unknown is whether this cooperative warrior mindset among males not only increases ingroup prosociality, but also decreases ingroup aggression. Aggression against ingroup members under outgroup threat would likely disadvantage the ingroup by reducing the ingroup’s collective formidability. Further, prosocial motivations inhibit aggression. As such, I hypothesized that sex and outgroup threat would interact such that males, …