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Impacts Of Plastic Pollution On A Pelagic Marine Mammal, The Northern Elephant Seal, Lauren M. Kashiwabara

University of the Pacific Theses and Dissertations

As plastic pollution increases, top marine predators such as marine mammals are becoming increasingly susceptible to plastic particles and their additives. Plastic particles have been found in gastrointestinal tracts and scat of many marine mammals, and quantifying plastic pollution in those that are pelagic can provide insight into plastic pollution in mesopelagic ecosystems that are just beginning to be analyzed. Adapting well-developed laboratory techniques for microplastic (MP) isolation (i.e. density separation and chemical digestion), I isolated MPs from the scat of the deepest diving pinniped, the northern elephant seal (NES), and found that100% of scat samples (n=11) contained high counts …

Plaster Creek Stewards - Urban Habitat Restoration With Green Team, Jia Luchs, Clare Doss, Rachel Warners, Dave Warners, Deanna Geelhoed

Student Papers and Reports

Plaster Creek, though its watershed is home to many potential stewards in Grand Rapids, is the most polluted creek in West Michigan. The Green Team, a branch of Plaster Creek Stewards, is a group of students that work during the summer with a focus on research, education, and working directly to restore the Plaster Creek Watershed. The Green Team works toward this goal through urban green infrastructure, utilizing native plants to manage stormwater. Two Calvin students, Jia Luchs and Clare Doss, and twenty high school students living in the Plaster Creek watershed were hired by Plaster Creek Stewards this summer …

Urban Insect Biodiversity - Effects Of Native Landscaping, Caedmon Morgret, Dave Warners

Student Papers and Reports

Urban development comes with the cost of destroyed natural habitats. Urban infrastructure flattens entire ecosystems, replacing them with impervious, life-inhibiting constructions.

Alleviating the impacts of urbanization is possible. Green infrastructure mitigates habitat loss by restoring native habitats within urbanized areas. One benefit of green infrastructure is the reestablishment of biodiversity, benefitting plants, animals, and insects alike. Biodiversity creates a healthier habitat and location than urban infrastructure –and lack of biodiversity –does.

To investigate this benefit we performed a pilot study, sampling lawns and curb-cut rain gardens (CCRGs). We compared biodiversity between restored and unrestored urban habitats.

Grassland Bird Responses To Bison And Prescribed Fire Disturbances At Nachusa Grasslands And Kankakee Sands, Antonio Del Valle

Graduate Research Theses & Dissertations

Grazing from native herbivores such as bison (Bison bison), in combination with prescribed fire, are applied to tallgrass prairies by managers to recreate important disturbance patterns in this ecosystem. Bird communities may be indirectly impacted by these disturbances through their direct impact on plants that provides critical breeding habitat for grassland birds. The objectives of this research are to determine the impacts that bison and prescribed fire have on grassland breeding birds in two tallgrass prairie preserves, Kankakee Sands and Nachusa Grasslands. Birds, vegetation structure, and bison activity were surveyed systematically at these two preserves in 2020 and 2021. Prescribed …

Wetland Restoration Efforts Result In Increasing Phylogenetic Diversity, Nicholas T. Foster

Graduate Research Theses & Dissertations

Over the course of ecological restoration efforts, it has been observed that, despite restoration activities, species richness sometimes declines in a given habitat. While this response can be interpreted to mean that restoration activities are ineffective, other measures known as Phylogenetic Diversity Metrics can show that the community is actually becoming more diverse. Utilizing plant inventories collected as transect data from 1992-2021 of five wetland sites under various types of restoration in northern Illinois, a regional wetland community phylogeny was assembled. The community phylogeny was then analyzed for phylogenetic diversity measures through this 30-year period across the five sites. Additionally, …

Microbial Community And Soil Responses To Land Management Practices In Remnant And Restored Tallgrass Prairies, Desirae Marie Klimek

Graduate Research Theses & Dissertations

Critical ecosystem functions, such as decomposition and nutrient cycling, are driven by microbial communities within soil. As such, it is important to examine the effect of restoration practices, such as the presence of native grazers and prescribed burning, on these microbes and the soil they inhabit. The Nachusa Grasslands provides a chronosequence of restored tallgrass prairies ranging in restoration age from 5 to 33 years, as well as remnant prairies, and agricultural fields. These sites were sampled seasonally from 2013-2020 and microbial ribosomal RNA genes were surveyed to characterize soil microbial communities and assess how common restoration practices affect these …

Aspergillus Nidulans Septa Are Indispensable For Surviving Cell Wall Stress, Ryland N. Spence, Walker Huso, Harley Edwards, Alexander Doan, Samantha Reese, Steven D. Harris, Ranjan Srivastava, Mark R. Marten

School of Biological Sciences: Faculty Publications

Septation in filamentous fungi is a normal part of development, which involves the formation of cross-hyphal bulkheads, typically containing pores, allowing cytoplasmic streaming between compartments. Based on previous findings regarding septa and cell wall stress, we hypothesized that septa are critical for survival during cell wall stress. To test this hypothesis, we used known Aspergillus nidulans septation-deficient mutants (ΔsepH, Δbud3, Δbud4, and Δrho4) and six antifungal compounds. Three of these compounds (micafungin, Congo red, and calcofluor white) are known cell wall stressors which activate the cell wall integrity signaling pathway (CWIS), while the three others (cycloheximide, miconazole, and 2,3-butanedione monoxime) …

Quantification, Isolation, Characterization, And Biogeography Of Thermoacidophilic Bacteria From Mesophilic Soils, Margaux Karp

Cal Poly Humboldt theses and projects

Many thermoacidophilic bacterial species thrive in hot springs, fumaroles, and geothermally heated soils. These habitats are globally distributed but often small in size and located distantly from similar habitats, and therefore the biogeography of thermoacidophiles may be similar to island biogeography of plants and animals. Little is known about dispersal of thermoacidophiles. In this study I aimed to quantify, isolate, and characterize thermoacidophilic bacteria from non-permissive habitats. I also used genetic approaches to compare these isolates to thermoacidophilic bacteria from permissive habitats to provide insight to their biogeography.

To determine if I could enrich thermoacidophiles from non-permissive habitats, and if …

How Do They Do It? Using Omics Approaches To Explore Metabolic Responses Associated With Hypoxia And Exercise Tolerance In The Deepest Diving Pinniped, Elizabeth R. Piotrowski

University of the Pacific Theses and Dissertations

Marine mammals such as northern elephant seals (NES) routinely experience hypoxemia and ischemia-reperfusion events to many tissues during deep dives with no apparent adverse effects. Adaptations to diving include increased antioxidants and elevated oxygen storage capacity associated with high hemoprotein content in blood and muscle. Despite experiencing decreased oxygen tensions during diving, NES likely rely on the mobilization of large lipids stores and catabolism of fatty acids to provide energy to exercising muscle while diving. To identify potential regulatory mechanisms that may underly hypoxia and exercise tolerance in diving mammals, this study used system-wide approaches to characterize changes in genes …

Beyond Cortisol: Indicators Of Stress And Negative Feedback In Plasma And Blubber Of Marine Mammals, Jessica Avalos

University of the Pacific Theses and Dissertations

Marine mammals play an important role in ecosystem stability. However, anthropogenic activity is compounding pressure on many already vulnerable populations. A potential consequence of anthropogenic disturbance is physiological stress, which can impact metabolism, immunity, and reproduction, especially if it occurs repeatedly. Previous studies on marine mammals have focused on acute stress, but the impacts of repeated stress are poorly understood. Due to its accessibility on land during haul-outs, the northern elephant seal (Mirounga angustirostris) is a good system in which to study the effects of stress in marine mammals. Stress stimulates the release of glucocorticoid hormones, primarily cortisol. Elevated cortisol …

Geographic Range Size As A Predictor Of Dispersal-Dependent Behavioral Traits In Two Clades Of A Terrestrial Salamander, Teah Evers

Masters Theses

Animal movement has the potential to affect diverse processes within ecology and evolution including range expansion, gene flow, adaptation, and speciation. Two aspects of animal personality that are germane to dispersal are exploratory and aggressive behavior. These behavioral categories may represent a trade-off such that energy invested in territorial defense leaves little energy for movement and dispersal. The Eastern Red-backed Salamander (Plethodon cinereus) is a wide ranging, dispersal limited, terrestrial salamander with well documented phylogeographic divisions. I examined dispersal-relevant behavioral traits within two clades of P. cinereus with disparate geographic ranges. The Northern Clade (NC) has a range extending from …

Elucidating The Function Of An Evolutionarily Conserved Col2Α1 Isoform During Vertebrate Development, Charles Lantz H. Ingersoll

Master's Theses

ABSTRACT

Formation of skeletal structural elements during vertebrate embryogenesis is largely a

conserved evolutionary process that employs numerous conserved genes and pathways. One

critical gene in this process is the highly conserved vertebrate Type II Collagen alpha 1 (col2α1).

It produces multiple splice isoforms that have different functions and expression patterns during

skeletogenesis. Two of the primary isoforms are of great interest; variant 1, the primary

embryonic isoform, and variant 2, a post embryonic isoform. While the more commonly known

post-embryonic isoform has been well studied over the last 30 years, identification of a unique

role for the evolutionarily conserved …

Twitter: More Than Tweets For Undergraduate Student Researchers, Nathan S. Reyna, Christin Pruett, Mike Morrison, Jennifer Fowler, Sumali Pandey, Lori Hensley

Research, Publications & Creative Work

A vital component of a CURE is feeling a sense of community. While our students often present to each other at the end of the semester, we have struggled with having them interact with a wider audience. A few students may present class results at a regional or national meeting; however, feasibility limits this opportunity to only a handful of students. Twitter has been used as a tool to disseminate scientific findings (1, 2). As a result of COVID-19, scientific societies have used Twitter to provide snapshots of research to be presented at their virtual meetings using “Twitter Posters” (Michael …

Biofilms On Plastic Litter: Community Composition And Activity And The Effects On Ecosystem Processes, Raul F. Lazcano

Master's Theses

The rapid increase of plastic production and disposal has resulted in plastic pollution becoming a global problem. In aquatic ecosystems, plastic litter is a substrate for biofilms, but little research has simultaneously assessed the effects of plastic litter on biofilm activity, community composition, and ecosystem processes. Our objectives were to: (1) measure biofilm activity and community composition on plastic litter relative to a natural surface in an urban river and (2) assess the impact of microplastic pollution on ecosystem metabolism and N2 flux in an oligotrophic lake. For objective (1) we incubated three common plastics with distinct physical and chemical …

Identification Of A Rickettsial Endosymbiont In A Soft Tick Ornithodoros Turicata Americanus, Lichao Liu, Daniel E. Sonenshine, Hameeda Sultana, Girish Neelakanta

Biological Sciences Faculty Publications

Bacterial endosymbionts are abundantly found in both hard and soft ticks. Occidentia massiliensis, a rickettsial endosymbiont, was first identified in the soft tick Ornithodoros sonrai collected from Senegal and later was identified in a hard tick Africaniella transversale. In this study, we noted the presence of Occidentia species, designated as Occidentia-like species, in a soft tick O. turicata americanus. Sequencing and phylogenetic analyses of the two genetic markers, 16S rRNA and groEL confirmed the presence of Occidentia-like species in O. turicata americanus ticks. The Occidentia-like species was noted to be present in all developmental stages …

Development Of Diagnostic Methods And Epidermiology Of Tuberculosis In Free-Ranging Long-Tailed Macaque Macaca Fascicularis And Rhesus Macaque M. Mulatta In Thailand, Suthirote Meesawat

Chulalongkorn University Theses and Dissertations (Chula ETD)

Cross-species infectious disease transmission, especially between humans and wildlife, is increasing during the global warming. Tuberculosis (TB) is an air-borne infectious disease that can be transmitted from humans to non-human primates (NHPs), however, no report of TB prevalence in free ranging NHPs that highly interacted with humans in Thailand was published. Thus, this study was conducted and separated into 3 phases. Phase I, active TB in 1,836 free-ranging macaques including 6 rhesus (Macaca mulatta; Mm), 23 common long-tailed (M. fascicularis fascicularis; Mff), and 3 Burmese long-tailed (M. f. aurea; Mfa) macaque populations throughout Thailand was assesses. Monkeys were captured, anesthetized, …

Chronic Adolescent Stress As A Predictive Factor For The Risk Of Developing Ptsd-Like Symptoms In Adulthood, Grace K. Young

Theses and Dissertations

Post-traumatic stress disorder is a stress and trauma based psychological disorder that is defined by the DSM-IV as an anxiety disorder that affects approximately 7.8% of people in the United States. PTSD is when those who suffer a traumatic event have intense and distressing feelings, emotions, and memories for a prolonged period of time after the event. A prominent feature of PTSD is the impaired ability to properly extinguish a fear response after a dangerous trigger or stressor is no longer present, also known as safety learning. Stressors are threats perceived within the environment that activate a response within the …

Crispr/Cas9 Whole-Genome Screens Identify Genes Critical For Neutral Lipid Metabolism In Macrophages, Rifat Sultana

Electronic Theses and Dissertations

Lipid-laden macrophages contribute to atherosclerotic plaque formation in atherosclerosisrelated heart diseases. Thus, understanding formation and degradation of lipid would help identify therapeutic targets for the treatment of atherosclerosis. In the first chapter of this dissertation, I have explained the current understanding of cholesterol metabolism in macrophages and how mTOR could play a potential role in this process. Additionally, I have described how CRISPR/Cas9 whole-genome screens present an effective tool to identify genes regulating cholesterol metabolism including positive and negative regulators of lipid droplet formation and lipid droplet degradation. In Chapter 2, I have described the results of the CRISPR/Cas9 whole-genome …

Disentangling The Complex Evolutionary History Of Invasive Russian Thistle: Phylogenetic Relationships, The Role Of Hybridization, And Public Engagement, Deva Raj Khanal

Electronic Theses and Dissertations

Invasive species are forces of environmental, economic, and social change with detrimental impacts on ecosystems, commerce, agriculture, and human health. However, we still have a poor understanding of the processes that could be driving invasive potential. Hybridization may contribute to the establishment and spread of invasive lineages, as it may enhance genetic variation and facilitate rapid adaptation. Focusing on Russian thistle (Salsola tragus s.l., family Amaranthaceae) and closely related species, my thesis aims to clarify phylogenetic relationships and investigate how hybridization has shaped the invasion dynamics of these lineages. Known as one of the fastest plant invasions in the United …

Stop, Then Go! Rapid Acceleration Offsets The Costs Of Intermittent Locomotion When Turning In Florida Scrub Lizards, Cheyenne Walker

College of Graduate Studies: Theses & Dissertations

Intermittent locomotion is a commonly used escape strategy with a wide array of potential benefits. Pausing may aid in locating a predator, crypsis, lowering energy costs, and avoiding obstacles. Turning may also benefit from intermittent locomotion by allowing an animal time to assess its surroundings; therefore, decreasing the chances of making a mistake and/or stumbling. Florida scrub lizards live in environments with a variety of obstacles such as turns. The goal of this study is to quantify the locomotor behavior and performance by lizards while navigating a 45° or 90° turn. Lizards were run along both a 45° and 90° …

Species-Specific Interactions In Avian–Bryophyte Dispersal Networks, Matthew Chmielewski, Sarah Eppley

Biology Faculty Publications and Presentations

Studies from seed plants have shown that animal dispersal fundamentally alters the success of plant dispersal, shaping community composition through time. Our understanding of this phenomenon in spore plants is comparatively limited. Though little is known about species-specific dispersal relationships between passerine birds and bryophytes, birds are particularly attractive as a potential bryophyte dispersal vector given their highly vagile nature as well as their association with bryophytes when foraging and building nests. We captured birds in Gifford Pinchot National Forest to sample their legs and tails for bryophyte propagules. We found 24 bryophyte species across 34 bird species. We examined …

Phylogenetics And Genetic Variation Of Heligmosomoides Thomomyos In Western Pocket Gophers (Thomomys Spp.), Malorri R. Hughes, Alexandra A. Gibson, Emily R. Wolfe, Cecily D. Bronson, Deborah A. Duffield

Biology Faculty Publications and Presentations

The host specificities and systematics of North American Heligmosomoides species remain particularly uncertain. The primary aim of this study was to verify that a species described previously based only on morphology, H. thomomyos, from pocket gopher (Rodentia: Geomyidae) hosts in Oregon represented a monophyletic lineage. In order to address this aspect, as well as to further understand relationships and geographic patterns, we carried out phylogenetic, genetic diversity, and population dynamic analyses using partial 18S rRNA and COI mtDNA sequences of Heligmosomoides specimens. Phylogenetic analyses suggested that there are likely multiple Heligmosomoides species present in these hosts. This was supported by …

Impact Of Orthophosphate As A Corrosion Inhibitor And Chloramine Disinfectant On Drinking Water Biofilm Communities, Mitchell Cooke

Theses and Dissertations (Comprehensive)

A drinking water distribution system (DWDS) must maintain conditions within quality standards which assure the effective and safe transport of finished drinking water from treatment plants to the household tap. Although safe to drink, finished water is not sterile, and may contain hundreds of microorganisms in a single milliliter. These microorganisms are present from the source waters, such as lakes, rivers and aquifers, and have passed through early treatment steps. Final treatment steps, such as the maintenance of disinfectant residuals, are used to further minimize viable cells present and focus on the reduction of harmful organisms. Microbial cells entering the …

Design And Validation Of Artificial Feeders To Study Feeding Preferences And Growth Of Hematophagous Juvenile Sea Lamprey (Petromyzon Marinus), Gracie Li-Ting-Wai

Theses and Dissertations (Comprehensive)

The parasitic and invasive land-locked sea lamprey Petromyzon marinus populations contributed to the collapse of the Great Lakes fisheries in the mid-1900s, while native anadromous populations are currently under threat and require conservation efforts for protection. Despite the increasing concern for both populations of this species, the juvenile stage of the sea lamprey’s life cycle has not been well studied. This is due, in part, to ethical concerns raised around holding live host fish with juveniles and the lack of an alternative feeding method to maintain these juveniles in the laboratory. The feeder should be designed to minimize fouling of …

In Vivo Activity Of Metal Complexes Containing 1,10-Phenanthroline And 3,6,9-Trioxaundecanedioate Ligands Against Pseudomonas Aeruginosa Infection In Galleria Mellonella Larvae, Megan O'Shaughnessy, Magdalena Piatek, Pauraic Mccarron, Malachy Mccann, Michael Devereux, Kevin Kavanagh, Orla L. Howe

Articles

Drug-resistant Pseudomonas aeruginosa is rapidly developing resulting in a serious global threat. Immunocompromised patients are specifically at risk, especially those with cystic fibrosis (CF). Novel metal complexes incorporating 1,10-phenanthroline (phen) ligands have previously demonstrated antibacterial and anti-biofilm effects against resistant P. aeruginosa from CF patients in vitro. Herein, we present the in vivo efficacy of {[Cu(3,6,9-tdda)(phen)₂]·₃H₂O·EtOH}_n (Cu-tdda-phen), {[Mn(3,6,9-tdda)(phen)₂]·₃H₂O·EtOH}_n (Mn-tdda-phen) and [Ag₂(3,6,9-tdda)(phen)₄]·EtOH (Ag-tdda-phen) (tddaH₂ = 3,6,9-trioxaundecanedioic acid). Individual treatments of these metal-tdda-phen complexes and in combination with the established antibiotic gentamicin were …

Soil Organic Carbon Accumulation In Restored Native Prairies Over Time, Samrin Shahnaz

Honors Program Theses

With the recent focus on the causes and effects of climate change, the relationship between agriculture and climate change has become an important concern. Conventional farming maximizes crop production at the expense of ecosystem services like soil carbon storage. As the human population grows, it is vital to develop practices that balance crop production and ecosystem services.

We investigated organic carbon accumulation in restored prairie soil over the course of a decade. Our goal was to determine how organic carbon levels and soil bulk density changed over time, and how that change was influenced by species diversity and soil depth. …

The Role Of Rad51 In Trichomonas Vaginalis, Dominique Hall

University of the Pacific Theses and Dissertations

Drug resistance to the current treatments on the market is on the rise, therefore there is strong interest in understanding what could be causing the resistance, how resistance could be spreading through the population, and finding some possible new drug targets. One protein of interest is Radiation Sensitive Protein 51 (Rad51). It is a protein that is involved in homologous recombination as well as other processes such as DNA damage repair. While Trichomonas vaginalis traditionally has been known to replicate via binary fission, a modified form of closed mitosis, there is some evidence that meiosis, or at least some form …

Investigating The Genetic Diversity Of Immune Genes In Non-Native Populations Of American Bullfrogs (Rana Catesbeiana), Luisa Nereyda Segovia

Cal Poly Humboldt theses and projects

The American Bullfrog (Rana catesbeiana) is a highly invasive species that has successfully colonized habitats around the world. The genetic variability of immune genes within invasive populations, like that of bullfrogs, may contribute to how resistant a population is to pathogens. The objective of this project was to characterize the genetic diversity of an immune gene in invasive bullfrog populations in California to better understand how persistent these populations might be over time. To characterize immune gene variability, I isolated exon 2 of the Major Histocompatibility Complex (MHC) Class II Beta chain gene and a neutral mitochondrial marker, …

Degradation And Nitrogen Cycling In The Context Of Biodiversity-Ecosystem Function Relationships In The Inquiline Bacterial Community Of Darlingtonia Californica, Megan Teigen

Cal Poly Humboldt theses and projects

Biodiversity-ecosystem function (BEF) research aims to explain how species and their environments interact with each other. Microbial communities engage in vital biogeochemical pathways in a variety of natural ecosystems, and yet there are large knowledge gaps about the specific metabolic pathways in which they are involved. Degradation specifically contributes to nitrogen cycling globally through the breakdown of large organic nitrogen compounds into small inorganic nitrogen that is necessary for the survival of many other organisms. In this study, I focused on the degradative function of the inquiline microbial communities found within the carnivorous pitcher plant, Darlingtonia californica. Darlingtonia grows in …

Regulation Of Ppp1r15a (Gadd34) And Ppp1r15b (Crep) Mrna Expression And Localization In The Unfolded Protein Response, Krithika Giresh

University of the Pacific Theses and Dissertations

The failure to balance protein synthesis, folding, and degradation in the endoplasmic reticulum (ER) leads to the accumulation of unfolded proteins, leading to ER stress. Cells respond to this stress by activating a response signaling pathway known as the Unfolded Protein Response (UPR). One of the branches of the UPR induces the phosphorylation of eIF2α (Eukaryotic Initiation Factor 2) to attenuate global protein synthesis, allowing for a chance to clear misfolded and unfolded proteins. This phosphorylation of eIF2α is opposed by a phosphatase, containing a catalytic subunit, Protein Phosphatase 1, and a scaffolding protein, either GADD34 or CReP. Inhibition of …