Digital Commons Network^™

The Influence Of The Sensory Environment On Avian Reproductive Success And Human Well-Being, Danielle Marie Ferraro

Master's Theses

Sensory pollutants such as anthropogenic noise and night lighting now expose much of the world to evolutionarily novel sound and night lighting conditions, which can have detrimental effects on humans and wildlife. In my first chapter, we exposed wild Western Bluebird (Sialia mexicana) nestlings to noise, light, and combination (i.e., noise and light) treatments. Nests exposed to noise and light together experienced less predation than control and light-exposed nests, and noise-exposed nests experienced less predation than control nests, yet overall nest success was only higher in noise-exposed nests compared to light-exposed nests. Although exposure to light decreased nestling body condition …

Cal Poly Pier Master Plan, Troy A. Lawson

Master's Theses

The Cal Poly Pier (Pier) Master/Facility Plan (FP) document provides the vision of the future for the Pier, a marine science research facility. The Plan facilitates project development and management of the Pier while meeting university and department research goals. Specifically, the FP document establishes goals and strategies to direct long-term development of the Pier, streamlines agency approval and permit requirements, provides context for pier management, and assists the permitting process for future development as it relates to regulatory permits and programmatic growth on the Cal Poly Pier to help meet goals of the Center for Coastal Marine Sciences (CCMS). …

Assessing Methods For Determining Reference Conditions For Riparian Restoration In Santa Clara County, Claire Mallen

Master's Theses

Valley Water is the primary water wholesaler and flood control agency in Santa Clara County, providing services to 1.9 million residents. The operation and maintenance of infrastructure for water supply and flood control often require work within legally protected natural resources such as riparian ecosystems. Riparian ecosystems are dynamic and diverse ecosystems that provide our society with valuable services such as wildlife habitat, water quality, and recreation. However, the threat of human development on native ecosystems has led to the degradation and loss of 85-98% of riparian ecosystems nationwide. Today, federal, state, and regional laws mitigate further impacts to riparian …

Evaluating Methods To Reduce Humpback Whale (Megaptera Novaeamgliae) Ship Strike Mortality In Nearshore Feeding Habitats Within The San Francisco Bay, Alisa Keenan

Master's Theses

Across our world’s oceans, whales are perpetually stuck and killed by large ships. Sea-based commercial trade is increasing on a global scale; therefore, more large ships are circumnavigating through biologically important whale habitats. This is of grave concern to marine resource managers, especially in the United States where major shipping corridors overlap critical whale habitat. It is feared that in these areas with high whale density, ship strikes are reducing populations of whales to levels below what is sustainable for threatened and endangered species, thereby hindering the recovery of depleted whale populations. Humpback whales, a species that is federally-listed as …

Mosquito Communities And Insect-Specific Viruses In A Heterogenous, Urban Landscape In Puerto Rico, Nicole Scavo

Master's Theses

The goal of my thesis was to investigate the relationships between mosquito diversity, Aedes aegptyi populations, and socioeconomic factors (SEF) in an urban setting and to characterize the virome of Ae. aegypti in San Juan, Puerto Rico. Mosquitoes were collected in three periods during late 2018 and early 2019 and were identified to the species level. Socioeconomic factors were measured using foot surveys and U.S. Census data. Some Ae. aegypti females were processed for sequencing and sent to Quick Biology for RNA sequencing to identify viruses. Results showed a link between SEF and Ae. aegypti abundance as well as between …

Elucidating The Molecular Pathways Involved In The Fitness And Water Stress Response Of Pseudomonas Synxantha 2-79 In The Plant Rhizosphere, Clint Henry D. Pablo

Master's Theses

Pseudomonas synxantha 2-79 is a biocontrol agent that represents beneficial indigenous rhizobacteria that are broadly distributed in the Pacific Northwest, USA and flourish in the rhizosphere of commercially grown wheat under surprisingly arid conditions. The molecular adaptation of 2-79-like bacteria to plants growing in dry soils is poorly understood. We hypothesized that the ability of 2-79 to colonize and persist in the rhizosphere of water-stressed plants is underpinned by the formation of hydrating biofilms and the utilization of root exudates that contain plant-derived osmoprotectants called quaternary ammonium compounds (QACs). We tested this hypothesis by identifying waters stress response pathways in …

Characterizing Erad And Antioxidant Response In Ixodes Scapularis Ise6 Cells During Borrelia Infection, Latoyia Downs

Master's Theses

Ticks are hematophagous ectoparasites that transmit a multitude of diseases to humans. Borrelia burgdorferi (BB) and Borrelia miyamotoi (BM) are both tick-borne pathogens that cause disease in humans and are transmitted by the black-legged tick (Ixodes scapularis). A byproduct of blood digestion generates reactive oxygen species that are toxic and cause oxidative stress which promotes cellular damage and dysfunction. The endoplasmic reticulum (ER) is especially affected by oxidative stress, resulting in a buildup of improperly folded proteins in the ER lumen called ER stress. To prevent cellular damage, the tick utilizes an antioxidant system to neutralize ROS and mechanisms …

Historical And Contemporary Variables Affecting The Range And Distribution Of Aedes Aegypti, The Yellow Fever Mosquito, In The United States, Nicole Mackey

Master's Theses

Aedes aegypti, the primary mosquito vector of the yellow fever virus, threatens global health by passing on this virus, as well as chikungunya, dengue, and Zika viruses. Through its natural tendency to live in highly urban areas and bite human hosts; understanding the factors that affect the historical and current range of the pest is invaluable (Gubler, 1998). Although these viruses are not normally found in the United States, lack of vaccinations and wide-spread presence of the mosquito could lead to these diseases being reintroduced with potentially devastating effects (Monath, 2001). To determine a partial historical range of A. aegypti …

Development Of An Attenuated Zika Virus By Editing The 5’ Untranslated Region, E. Ashley Thompson

Master's Theses

Zika Virus (ZIKV) is a mosquito-transmitted flavivirus that usually causes no symptoms to mild febrile in humans, and it has been regarded as an insignificant pathogen to public health. However, recent outbreaks of ZIKV infection have revealed that ZIKV can cause severe neurological effects in adults, such as Guillain-Barre Syndrome (GBS), and in infants whose mothers acquired the virus during pregnancy, causing Congenital Zika Syndrome (CZS). Currently, no approved vaccine is available and there is a critical need to develop an effective and safe vaccine. While most vaccine developmental strategies target the viral prM-E protein of ZIKV, we aimed to …

Maturation Spawning And Larviculture Of Atlantic Croaker (Micropogonias Undulatus) At Low Salinity, Edithrose Fairweather

Master's Theses

Atlantic Croaker is a popular baitfish among anglers targeting a variety of gamefish in the Gulf of Mexico. Aquaculture of this species could help meet the demand for Croaker, especially during winter when wild-caught Croaker are unavailable. Currently, Croaker aquaculture involves broodstock maturation, spawning, and larval culture at high salinity. This protocol prevents the direct use of coastal water for culture along the Mississippi Gulf coast where salinity is low. This study examined the feasibility of performing hatchery production of Atlantic Croaker at low salinity.

Culture of Croaker broodstock at 10, 20, and 30 psu during the maturation period was …

An Analysis Of Dredge Efficiency For Surfclam And Ocean Quahog Commercial Dredges, Leanne Poussard

Master's Theses

Between 1997 and 2011, The National Marine Fisheries Service conducted 50 depletion experiments to estimate survey gear efficiency and stock density for Atlantic surfclam (Spisula solidissima) and ocean quahog (Arctica islandica) populations using commercial hydraulic dredges. The Patch Model was formulated to estimate gear efficiency and organism density from the data. The range of efficiencies estimated is substantial, leading to uncertainty in the application of these estimates in stock assessment. Analysis of depletion experiment simulations showed that uncertainty in the estimates of gear efficiency from depletion experiments was reduced by higher numbers of dredge tows per experiment, more tow overlap …

Vegetative Community And Health Assessment Of A Constructed Juncus-Dominated Salt Marsh In The Northern Gulf Of Mexico, Nickolas R. Murphy

Master's Theses

Deer Island is a coastal habitat which provides a buffer from storm and flood damage as well as shore-line stabilization to the mainland of Biloxi, Mississippi. A third of the land has been lost since 1850, largely driven by tropical storm and hurricane impacts as well as sea level rise. The United States Army Corps of Engineers and Mississippi Department of Marine Resources have targeted the shores of the island as sites for restoration using beneficial use dredged material, and two sites of differing age have since been planted with Spartina alterniflora, Juncus roemerianus, Uniola paniculata, S. patens, and Panicum …

Efficacy Of An Audio-Based Biofeedback Intervention To Modify Running Gait In Female Runners 2020, Sarah Rothstein

Master's Theses

Introduction: Gait retraining interventions are used to modify foot strike parameters associated with musculoskeletal injuries. Such interventions may prove beneficial if gait modifications are maintained long-term and provide a physiological performance benefit. Purpose: The primary purpose of this study was to determine whether female recreational runners can use a smartphone decibel app to self-modify gait mechanics associated with injury. The secondary purpose was to determine if such gait modifications are retained beyond the initial training session. The tertiary purpose was to determine if such gait modifications were associated with improved running economy. Methods: The peak vertical ground reaction force (vGRF), …

The Effect Of Attentional Focus Instructions On Single Leg Balance Performance 2020., Cory Monahan

Master's Theses

Balance and postural control exercises are often a part of exercise programs. During exercise programs, movement practitioners can provide instructions to facilitate performance and learning. Instructions can be used to direct attentional focus, which has been found to affect the performance and learning of motor skills, including balance and postural control tasks. However, no known studies to date have investigated the effect of both internal and external attentional focus instructions on static single leg balance performance. The purpose of this study was to investigate the effect of attentional focus instructions on static single leg balance performance as reflected by the …

The Relationship Between Sport Commitment With Off-Season Training Time And Previous In-Season Playing Time In College-Aged Soccer Players 2020., Luke Zuber

Master's Theses

Sport commitment is defined as “…the desire and resolve to continue sport participation” (Scanlan, Carpenter, Schmidt, Simons, & Keeler, 1993, p. 6). Since the first definition, the concept has been further refined to reflect a more multidimensional paradigm. Overall, sport commitment is thought to be comprised of the dimensions of enthusiastic commitment and constrained commitment (Scanlan, Chow, Sousa, Scanlan, & Knifsend, 2016). Those constructs can be broken down further to 12 subconstructs that are represented in the Sport Commitment – 2 (SC; Scanlan, Chow, Sousa, Scanlan, & Knifsend, 2016), in order to evaluate the source and level of an individual’s …

Pismo Clams (Tivela Stultorum) In Califorina: Population Status, Habitat Associations, Reproduction, And Growth, Alexandria R. Marquardt

Master's Theses

Marine shellfish play a vital role in intertidal ecosystems and coastal communities, but many of these fisheries are small-scale and lack the necessary monitoring to ensure long-term sustainability. Effective management often requires information on key demographic parameters, such as population status, reproduction and growth. Pismo clams (Tivela stultorum) are a culturally important and iconic species in California, which supported a thriving commercial and recreational fishery throughout much of the 1900’s. However, Pismo clam populations have declined statewide in recent decades and are attributed to human harvest and predation by California sea otters (Enhydra lutris); However, no …

A Comparison Of Power Variables For Two Loading Methods In Weighted Vertical Jumps 2020, Jonathan Tanguay

Master's Theses

Training exercises to develop muscular strength and power, such as the weighted jump squat, commonly utilize barbells and dumbbells to increase resistance. Strength coaches often measure improvements in peak force, peak power, and rate of force development to determine effectiveness of a training program. The purpose of this study was to determine if equipment selection (barbells vs. dumbbells) affects peak force, peak power, and/or rate of force development in weighted jump squats. Thirteen physically active, college-aged males (age: 21.6 ± 2.0 years, height: 182.8 ± 9.7 cm, body mass: 87.2 ± 9.0 kg, lean mass: 72.3 ± 8.1 kg) performed …

Thermal Ecology Of The Federally Endangered Blunt-Nosed Leopard Lizard, Kathleen N. Ivey

Master's Theses

Recognizing how climate change will impact populations can aid in making decisions about approaches for conservation of endangered species. The Blunt-nosed Leopard Lizard (Gambelia sila) is a federally endangered species that, despite protection, remains in extremely arid, hot areas and may be at risk of extirpation due to climate change. We collected data on the field-active body temperatures, preferred body temperatures, and upper thermal tolerance of G. sila. We then described available thermal habitat using biophysical models, which allowed us to (1) describe patterns in lizard body temperatures, microhabitat temperatures, and lizard microhabitat use, (2) quantify the …

Valorization Of Carrot Processing Waste, Alexandra M. Duval

Master's Theses

Commercial carrot processors produce up to 175,000 tons of carrot waste annually. Carrot Mash (CM) is the term referring to the waste by-product of peeled baby carrot processing. Transportation of carrot processing waste is expensive due to its high- water content (approx. 83-95%). High in bioactive compounds (carotenoids) and dietary fibers, it is expected that its conversion into a value-added by-product is of interest to the carrot processing industry. Hemicellulose-rich plant materials have proven to be a source of oligosaccharides, which are known for their beneficial prebiotic activity. The objectives of this research were to: 1) determine the effect of …

Patterns In Size Distribution And Catch Of Rockfish (Sebastes Spp.) In Fisheries-Independent And Fisheries- Dependent Hook-And-Line Surveys On The Central Coast Of California, Rose Elizabeth Dodgen

Master's Theses

Stock assessments are statistical models which characterize the state of a population of fish. Data for stock assessment models of West Coast nearshore groundfish come largely from fisheries-dependent sources. Incorporating fisheries-independent data would increase data availability. A potential source of fisheries-independent data which is comparable to existing fisheries-dependent data is the California Collaborative Fisheries Research Program (CCFRP), a Marine Protected Area (MPA) monitoring study. We are interested in understanding the context in which CCFRP could be implemented into assessments of nearshore groundfish, specifically rockfish. To investigate this, we used management-relevant metrics to examine three questions concerning the implementation of CCFRP …

Inactivation Of Foodborne Pathogens During Cider Fermentation, In A Cider Model System And Commerical Cider, Kathryn K. Yamada

Master's Theses

Hard cider is an alcoholic drink made from fermented crushed fruit, typically apples. The popularity of this fermented alcoholic beverage has been on the rise within the last decade. Historically, hard cider has been deemed safe due to the presence of ethanol and the low pH. Although there is lack of scientific evidence to prove that hard cider will and can be safe from foodborne pathogens. Escherichia coli O157:H7, Salmonella spp., and Listeria monocytogenes are three predominate foodborne bacterial pathogens of concern in the food and beverage industry. Escherichia coli O157:H7 in particular has been associated with fresh produce and …

Fruit, Flower, And Thorn: A Phenological Study Of 'Wonderful' Pomegranate, Kylie M. Mendonca

Master's Theses

‘Wonderful’ pomegranate flowering and fruiting habits are not well understood. Characterizing any relationship between flowering habit and fruit size and quality could lead to effective cultural practices for producing high-value fruit. Five mature ‘Wonderful’ pomegranate trees were monitored every 5-14 days throughout the 2015 growing season. Newly emerged flowers were tagged and characterized with respect to sex (determined by ovary shape and style length at anthesis), clustering habit, age of wood on which floral buds were borne, and direction of wood growth. More than 1,100 hermaphroditic flowers were identified and ovary/fruit diameter was recorded throughout the season. In addition to …

The Characterization Of Inflammatory Extracellular Vesicles, Barak Balva

Master's Theses

One of the driving factors behind innate immunity is the early response of inflammation. While beneficial in controlling infections, when uncontrolled it can lead to a plethora of disorders. Thus, it is essential to understand the driving factors behind inflammation. a cell's ability to recycle, discard, or transfer proteins is integral for survival and intercellular communication. It has been appreciated that inflammatory components, such as caspase-1, play a huge role in driving protein secretion. Thus, inflammation also plays a role in the distribution of proteins released from cells. These proteins are released via non-conventional secretory pathways, and our lab is …

Zika Virus Inactivates Polyamine Catabolism Via Alternative Splicing To Enhance Infection, Marion Lea Graham

Master's Theses

During viral infection, the virus and host must compete for resources inside the cell. One of these resources is polyamines. Polyamines are small, positively charged molecules that are found in all eukaryotic cells. They play a key role in several cellular functions including growth and proliferation, transcription and translation, and membrane stability. Viruses also rely polyamines for productive replication, utilizing them during DNA/RNa polymerization, nucleic acid packaging, and protein synthesis. in response to a virus infecting a host cell, the host cell will begin to regulate polyamine levels as a way to combat the infection. Polyamine levels are regulated by …

Optimizing Gene Expression Prediction And Omics Integration In Populations Of African Ancestry, Paul Chukwuebuka Okoro

Master's Theses

Popular transcriptome imputation methods such as PrediXcan and FUSIon use parametric linear assumptions, and thus are unable to flexibly model the complex genetic architecture of the transcriptome. Although non-linear modeling has been shown to improve imputation performance, replicability and potential cross-population differences have not been adequately studied. Therefore, to optimize imputation performance across global populations, we used the non-linear machine learning (ML) models random forest (RF), support vector regression (SVR), and K nearest neighbor (KNN) to build transcriptome imputation models, and evaluated their performance in comparison to elastic net (EN). We trained gene expression prediction models using genotype and blood …

Characterization Of Caspase 1 Substrate Specificity Utilizing Luminescent Reporter Constructs, Nicholas Rohlfes

Master's Theses

Inflammation is the bodies first response to defend itself against foreign pathogens and damage. Cellular sensors are constantly monitoring the body and checking for homeostatic disruption. Microbial pathogens and tissue damage are sensed by pattern recognition receptors (PRRs), which sense pathogen associated molecular patterns and damage associated molecular patterns, termed PAMPs and DAMPs respectively. Within the family of PRRs are sensors that can induce the formation of the multi-protein complex termed the inflammasome following activation. the inflammasome complex is a molecular platform for which caspase 1, a cysteine protease, is incorporated and is responsible for the maturation of pro-inflammatory cytokines …

Reducing Reperfusion Injury In An Adult Rat Stroke Model With St-115 Treatment, Morgan Rae Lenz

Master's Theses

The restoration of blood flow to ischemic cerebral tissue can result in reperfusion injury, and blocking reperfusion injury can significantly aid in recovery of ischemic tissue. Bradykinin has been shown to exhibit protective effects, but does not reach protective levels during reperfusion due to inactivation by aminopeptidase P2 (APP2). Therefore, inhibiting APP2 during reperfusion is a potential therapeutic strategy to aid in the reduction of reperfusion injury, leading to the development of ST-115, an APP2 inhibitor. It was hypothesized that administration of ST-115 during ischemic stroke, and just prior to reperfusion, will result in reduced neurological injury and increased functional …

Paleoenvironmental Implications Of Small-Animal Fossils From The Black Mountain Turtle Layer And Associated Layers, Eocene Of Wyoming, Jeremy Mclarty

Master's Theses

The Bridger Formation is an Early Middle Eocene deposit in southwestern Wyoming that preserves a rich record of life from North America. Some horizons within the Bridger Formation contain abundant fossil turtle shells, but turtle skulls are rarely found. Previous research focused on one of these fossil-rich horizons, the Black Mountain turtle layer, to develop a model for the abundance and taphonomic condition of the fossil turtles. The proposed model begins with a limestone layer deposited in a lake. Then, an influx of fine-grained volcanic ash (forming the Black Mountain turtle layer) was rapidly deposited into this lake likely causing …

Investigating The Nightime Departures Of Glaucous-Winged Gulls (Larus Glaucescens) And The Role Of Social Facilitation, Devon Leigh Mcclain

Master's Theses

Daytime behaviors and occupancy patterns of Glaucous-winged Gulls (Larus glaucescens) have been described and can be mathematically predicted based on environmental factors. However, little is known about the nighttime behaviors of Glaucous-winged Gulls. I used trail cameras to study the daytime and nighttime colony occupancy patterns of Glaucous-winged Gulls on a breeding colony on Protection Island, Washington, USA. Early in the breeding season gulls desert the colony en masse during nighttime even after some gulls have initiated clutches. Using acoustic recording units to identify an acoustic cue that signals the onset of the coordinated nightly departures from the colony, I …

Using Crispr-Cas9 As A Restriction Enzyme, Zack Crawley

Master's Theses

Restriction digests are a commonly utilized process for cleaving DNA at specific, but relatively common sites. Restriction enzymes have widespread use in DNA manipulation. CRISPR/Cas9 is a recently identified endonuclease which utilizes a customizable guide sequence to recognize and cut specific ~20 bp sites located in a DNA sequence. This preliminary research aimed to exploit the potential benefit of DNA restriction using the CRISPR/Cas9 procedure through alterations of different components involved in that system. We sought to refine existing CRISPR/Cas9 protocols and make a budget friendly, user-selectable CRISPR/Cas9 restriction digest protocol. The motivation for this research was to simplify and …