Digital Commons Network^™

A Taxonomic Revision And Characterization Of Sciuravus Nitidus And S. Undans (Rodentia; Sciuravidae), Early To Middle Eocene Rodents From The Bridger Formation, Green River Basin, Wyoming, Emily Mazier

Student Presentations

New specimens from the Bridger Formation allow for a critical review of the alpha taxonomy and evolution of the two most abundant species of sciuravid rodents from the Early Eocene of the Green River Basin, Sciuravus nitidus and S. undans. Previously, the two species were considered to be synonymous, based on studies of the upper and/or lower dentitions. Specimens with nearly complete lower dentitions are studied for the first time and they reveal clear distinctions between the two species in the molar crown patterns, incisor shape, and mandible morphology. The key specimen, UM 101638, closely matched the type specimen of …

Genetic Characterization And Dna Barcoding Of The Zoonotic Parasite Gnathostoma, Ryan Pogodzinski

Student Presentations

Zoonotic diseases are transmitted to humans from wildlife and often pose serious health risks. One such disease, gnathostomiasis, is caused by parasitic nematodes in the genus Gnathostoma, commonly transmitted by consumption of infected undercooked freshwater fish. Lately, movement of animals over international borders has increased, leading to emerging zoonotic diseases (2018; CDC – One Health Basics). Human gnathostomiasis is just one example.

This project expands on previous research (Cole et al.) which identified Gnathostoma in invasive eels and imported eels from food markets, using morphological features and DNA sequences of the ribosomal RNA gene array’s ITS-2 (intergenic transcribed spacer-2) region. …

Lifelines Winter 2022, Southern Adventist University

Lifelines - Biology Department Newsletter

The Winter 2022 issue of Lifelines contains articles on student community service, Alumni Spotlight, Department Happenings, and graduates.

Predicting Gene Function Of Unknown Yeast Orfs Through Phylogenetic Comparative Analysis, Lewis Barr

Graduate Research Showcase

Yeast (Saccharomyces cerevisiae) has been an instrumental model system for an extraordinary diverse array of research applications for over a century now. The S. cerevisiae genome was fully sequenced in 1996, and, as a result, 6,753 potential proteins were identified. These putative proteins were established by investigating likely open reading frames within the genome. Over the past few decades, nearly 5,000 open reading frames (ORFs) and their expressed proteins have been described, and the remaining undefined open reading frames are labeled as open reading frames of unknown function (ORFans). To better understand the remaining gaps within the S. …

Patterns Of Natural Variation In Drought Escape And Drought Avoidance In The Common Monkeyflower, Joshua Fitzpatrick

Honors Baccalaureate Theses

Climate change has caused increasing temperatures and drier climates over the past decade. This has especially affected the western coast of North America, bringing even drier and hotter climates. This makes it difficult for plant life to prosper in these areas. One way that plants fight these drought conditions is through drought resistance traits. These drought resistance traits include flowering early and reproducing early before drought conditions onset or increasing the efficiency of water use by tissues and the stomata of the plant. While these traits are both beneficial in fighting drought conditions, they often negatively impact each other. This …

Patterns And Process Of Sandbar Revegetation On The Missouri National Recreational Rive, Amena Begum Ruma

Dissertations and Theses

Decades of flow regulation have reduced sandbar area and recruitment of cottonwood and willow along the Missouri River. Conflicts exist between managing sandbars for habitat (removing vegetation) for threatened sandbar-nesting birds (i.e., Piping Plover) and allowing natural recruitment of early successional riparian woodland (set-aside bars) that may support other species and ecological values. Recent changes in topography, geomorphology, and vegetation were examined on sandbars that have been “set aside” from management within seven reaches of the Missouri National Recreational River (MNRR) in southeastern South Dakota, USA. An existing time series of maps of sandbar landcover, derived from satellite imagery, was …

Final Report Floating Upwelling System Harvest Road Oceans, Robert Michael, Scott Bennett

Fisheries Occasional Publications

A Floating Upwelling System or FLUPSY is a mechanical system for the culture of seed stock during the nursery stage of commercial bivalve production.

An Investigation Of The Relationship Of Wave Intensity And Byssal Thread Strength Of The Mussel Mytilus Californianus, Felicia M. Miller

Master's Theses

The intertidal zone is a stressful environment with one of the main stressors being the fluctuation of wave energy over time and space. A structural adaptation employed by mussels living within the intertidal zone is byssal threads that aid in attachment while dealing with various levels of wave exposure. The California mussel, Mytilus californianus, lives in extremely wave exposure conditions, which makes it a great study species to assess the relationship between wave intensity and byssal thread strength. In this study, Mytilus californianus were collected from two locations in the Monterey Bay, each with a predicted wave exposed site and …

Chemosensitivity Of Locus Coeruleus Neurons Decreases With Postnatal Development, Yasmeen Samar

Browse all Theses and Dissertations

The locus coeruleus (LC) is a chemosensory area partially responsible for ventilation. Control over ventilation relies on inter-network communication via chemical and electrical synapses and chemosensitivity to CO2/pH. As the LC develops, it’s neural control over ventilation changes. This study investigates the chemosensitivity of the locus coeruleus over the course of development in postnatal rats. We hypothesize that 1) the CO2 sensitivity of LC neurons is highest at birth and declines with development 2) LC neurons are intrinsically chemosensitive and this chemosensitivity does not decrease with development and 3) the presence of gap junctions is highest at the beginning of …

Characterizing Metabolic Changes In Cancer Cells After Treatment With An Extract Created From Walnuts, Codey Y. Huang

Master's Theses

Cancer cells undergo metabolic reprogramming to meet the energy and metabolite demands of constant proliferation. Originally observed as the Warburg Effect, where cancer cells are more glycolytically active, recent research has shown that cancer cells can also utilize oxidative phosphorylation to meet these demands, better known as metabolic flux. Previous work from our lab showed that treatment with a Walnut Extract (WE) induced cell death in MDA-MB-231 and HeLa cells by destabilizing the mitochondrial outer membrane potential, suggesting that the extract may be able to impact oxidative phosphorylation. The aim of the current research was to further characterize the impact …

Covid-19 Impact And The Association Between Sociodemographic, Social Support, Depression, And Anxiety In The Mindful Moms Program, Ashley Nguyen

Undergraduate Research Posters

Background: The Covid-19 Pandemic lockdown resulted in lessened social support and a higher incidence of depressive symptoms in the United States. Low-income families were more likely to have experienced negative impacts on income, access to mental health treatment, stress, and discord within the family, and higher anxiety scores during the pandemic. Minority groups had higher COVID-19 incidence and mortality rates. More than 1 in 5 pregnant women in the United States experience clinically significant depressive symptoms, with marginalized populations carrying a greater burden. Maternal depression is linked to poor maternal and child health outcomes.

Depression scores of pregnant individuals during …

Observing Gravitropism In Brassica Rapa Roots, Trang Ly, Maya O'Callagham, Lan Poeschl, Adil Saeed, George Zorn

Undergraduate Research Posters

The objective of this experiment is to observe the effect of gravitropism on the orientation of Brassica rapa (B. rapa) roots. Specifically, amyloplasts that reside at the bottom of root tips act as gravity sensors. As plants are disturbed from upright orientation, roots automatically grow according to the downward pull of gravity. It is hypothesized that as the angle of rotation increases, the angle of root growth is inversely proportional. Five plants containing four seeds of B. rapa were grown over the course of 10 days. Each plates, aside from the control, were rotated once 90°, 80°, and 270° to …

Cpf1-Based Crispr Genome Editing In The Cyanobacterium N. Punctiforme, Soohan Woo

University of the Pacific Theses and Dissertations

CRISPR systems have been growing in their utility and their application throughout the biological field as researchers continue to grow in their understanding of the relatively novel genome editing technology. However, despite the potential of CRISPR as a genome editing tool, the complexity of applying this technology to a specific organism calls for custom modifications to the system to improve its success rate. In this project, a CRISPR-Cpf1 system that can be effectively employed in the cyanobacterium Nostoc punctiforme was designed, with a focus on the hormogonium development of this species. Multiple plasmids containing the CRISPR system and targeting different …

Land-Use And Ant Biodiversity In California’S Central Valley, Laura L. Navarro

University of the Pacific Theses and Dissertations

The growing human population results in growing demand for land allocated to urban development and agricultural production (Godfray et al. 2010; Tilman et al. 2011; McDonnell and Hahs 2013; Alexander et al. 2015; Erlwein and Pauleit 2021). Changes to land allocation associated with agricultural and urban development will increasingly alter terrestrial ecosystems impacting biodiversity (Ricketts et al. 2001; McDonald et al. 2008). Ants are an ideal organism for monitoring changes in biodiversity related to land-use change due to their ubiquitous nature, high diversity, and their role as bioindicators. The goal of this study was to assess the diversity of the …

The Plight Of Western Rivers, W. Howard Brandenburg

Natural Resources Journal

My oil paintings weave a narrative about the human species. I am interested in the space where our proliferation infringes upon ecosystem function. I am fascinated in what makes our species so successful and what that success means for the balance of nature. My paintings often target concepts around environmental transformations attributed to human activities and economies. Visual art provides me the latitude and freedom to explore and communicate these concepts, using a visual language which conveys disparate perspectives; universally and individualistically.

This duality is what I strive for in my work; producing an image that not only speaks a …

Impaired Β-Cell Neogenesis In A Mouse Model Of Metabolic Syndrome, Modhi Abdullah Alshammari

Browse all Theses and Dissertations

Pancreatic islet β-cell plays an essential role in insulin release and hence glucose homeostasis. The maintenance of glucose homeostasis depends on β-cell ability to cope with enough insulin to fulfill metabolic and physiological demands. Adequate insulin release is the result of highly complex and dynamic interplays between acute changes in β- cell electrical activity, exocytosis and chronic adaptations in cellular function, volume, mass and proliferation. All of this appears modulated, to some extent, by the functional presence of Slc12a2 symporters, also known as Na+K+2Cl– cotransporter-1 (Nkcc1), which accumulates intracellular Cl– above its electrochemical equilibrium. Recent studies from our laboratory showed …

Evaluating Energy-Based Trait Shifts And Population Level Impacts Of Big Brown Bats (Eptesicus Fuscus) With Long-Term Exposure To Pseudogymnoascus Destructans, Molly C. Simonis

Browse all Theses and Dissertations

Disturbances in environment can lead to a wide range of host physiological responses. These responses can either allow hosts to adjust to new conditions in their environment or can reduce their survival, and can subsequently cause host traits to shift. Small mammals are particularly vulnerable to stochastic disturbances, like a pathogen introduction, because of their high energy demands. Studies examining host responses to pathogens often focus on species highly susceptible to infection that typically have high mortality rates, leading to a gap in understanding the responses of less susceptible species. My dissertation evaluates the energy balance of Eptesicus fuscus (big …

Genomic Instability At A Polypurine/Polypyrimidine Repeat Sequence, Nathen S. Zavada

Browse all Theses and Dissertations

Microsatellite repeat sequences have been shown to induce replication stalling, fork collapse, double-strand breaks (DSBs), and possibly stimulate break-induced replication. In this study we use a dual-fluorescent HeLa model that is designed to monitor recombination at an ectopic site through use of flow cytometry and inverse PCR with a microsatellite in the lagging strand for DNA synthesis. To test the stability of the 78 bp polypurine/pyrimidine repeat from the PDK1 locus, we subjected cells to replication stress drugs designed to induce DSBs and measure break-induced replication (BIR). The study revealed that polypurine repeat cells undergo endogenous stress contributing to instability …

Erk3 And Dgkζ Interact To Modulate Cell Motility In Lung Cancer Cells, Amanda Myers

Browse all Theses and Dissertations

Extracellular-regulated kinase 3 (ERK3) is overexpressed in a variety of cancers, including lung cancer. This atypical mitogen-activated protein kinase (MAPK) has a unique structure which includes a C34 domain and C-terminus and about which relatively little is known. ERK3 has been demonstrated to promote cell migration and metastasis in multiple cancer types. A yeast two-hybrid assay using ERK3 as bait indicated Diacylglycerol kinase ζ (DGKζ) is a binding partner. DGKζ is an isoform in the DGK family, all the members of which phosphorylate the lipid diacylglycerol (DAG) to generate phosphatidic acid (PA). DGKζ was shown to promote migration in mouse …

Exploring The Host Range, Impacts, And Distribution Of Black Rot Disease On Alliaria Petiolata, Gabriela Ivette Harney-Davila

Browse all Theses and Dissertations

Garlic mustard is an invasive Eurasian biennial spreading in deciduous forests of North America. Garlic mustard plants in Ohio can be infected with a strain of Xanthomonas campestris, the causal agent of black rot disease in brassicas. I examined variation in susceptibility to X. campestris among garlic mustard populations, several native wild species, and agricultural crop varieties. Twenty-four garlic mustard populations were universally susceptible to X. campestris, though disease severity varied. Cardamine concatenata and Cardamine diphylla were susceptible but can phenologically escape infection in the field. Of the 14 agricultural crops tested, three cultivars (Raphanus sativus, Brassica rapa var. Rapa …

The Impact Of Sentiment And Misinformation Cycling Through The Social Media Platform, Twitter, During The Initial Phase Of The Covid-19 Vaccine Rollout, Emily Grace Burwell

Browse all Theses and Dissertations

This study assesses the underlying topics, sentiment, and types of information regarding COVID-19 vaccines on Twitter during the initiation of the vaccine rollout. Tweets about the COVID-19 vaccine were collected and the relevant tweets were then filtered out using a relevancy classifier. Latent Dirichlet Allocation (LDA) was used to uncover topics of discussion within the relevant tweets. The NRC lexicon was used to assess positive and negative sentiment within tweets. The type of information (information, misinformation, opinion, or question) in tweets was evaluated. The relevancy classifier resulted in a dataset of 210,657 relevant tweets. Eight topics provided the best representation …

Gene Vectors With Fluorescence Tracking Capabilities, Sophia Despina Angelopoulos

Browse all Theses and Dissertations

This project focuses on the optimization of benzothiazole-based chromophores to utilize them as fluorescent tags functionalized onto stimuli-responsive, or “smart,” polymers as non-viral gene delivery vectors for gene therapy applications. Blue-fluorescent emissive chromophores will allow tracking capabilities for the transfection pathway of the vector to be monitored as it delivers the DNA payload within intercellular space. The most appropriate chromophore must be covalently bound to a free amine within the vector, which is accomplished through NAS chemistry from fluorophenyl-benzothiazoles (F-BTZ-CBz) derivatives to amidated hyperbranched poly(ethyleneimine)(HPEI-IBAm0.61). HPEI is considered to be a synthetic polycation, which promotes tunable solubility through characteristics of …

The Role Of Son In Chromatin-Mediated Gene Expression, Melissa Jordan Ward

Browse all Theses and Dissertations

Gene expression in mammalian cells requires complex nuclear choreography, and there is increasing evidence that spatiotemporal organization of chromatin and nuclear compartments plays an important role in gene expression. In this dissertation, I examined the function of SON, a splicing factor with a known role in nuclear organization, in chromatin-mediated gene expression. SON association with a transcriptionally inactive U2OS 2-6-3 reporter gene array provided a useful model to study SON’s chromatin dynamics. I demonstrated that SON associates with the inactive but not the activated array, and that SON’s RNA binding domains are not necessary for that association. Second, I discovered …

Modeling Als-Associated Matrin-3 Toxicity In Yeast, Widad El-Zein

Browse all Theses and Dissertations

ALS is a neurodegenerative disease characterized by degeneration of upper and lower motor neurons in the brain and spinal cord leading to progressive paralysis and ultimately death. Perturbations in RNA metabolism and RNA binding proteins have emerged as underlying defects in ALS pathogenesis. Matrin-3 is a multifunctional RNA binding protein that has been linked to familial and sporadic ALS. Matrin-3 is normally found in the nucleus, but mutations in the gene cause mislocalization of the protein from the nucleus into the cytoplasm of neuronal cells where it forms protein aggregates. In this study, we show that over-expressing human MATR3 in …

Inhibition Of Staphylococcus Aureus Biofilm By Variovorax Paradoxus, Esther Gomez

University of the Pacific Theses and Dissertations

Staphylococcus aureus is one of the leading causes of fatal nosocomial infections. Often, S. aureus can grow as a biofilm which protects the population from the surrounding environment. Strains of S. aureus are resistant to virtually all known antibiotics on the market. Variovorax paradoxus is a soil microbe with many unusual metabolic activities. It has been previously observed that, V. paradoxus can inhibit the growth of S. aureus when in co-culture. In this work we report on inhibition of S. aureus biofilm formation by V. paradoxus due to a suspected inhibitory soluble factor.

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 …

The Bgs 13 Mutant Of Pichia Pastoris And Its Effect On Structural Changes Of The Reporter Protein B-Lactogolbulin, Bushra Irshad

University of the Pacific Theses and Dissertations

Pichia pastoris, a methylotrophic yeast, is an ideal host for recombinant protein expression. It has the capability of performing many eukaryotic post-translational modifications and grows to high cell densities. However, P. pastoris’s secretion properties are not always efficient, and its secretory pathway mechanisms have not been thoroughly elucidated. A previously identified mutant strain, bgs13, was found to efficiently secrete most recombinant proteins tested, raising the possibility that this bgs13 mutant is a universal super secreter and understanding its secretion process is needed. In this study, we used a reporter protein, ?-lactoglobulin (b-LG), to perform structural analysis and comparisons of protein …

The Transcription Factor Nfe2l2a Is Required For Development Of Hematopoietic Stem Cells In The Zebrafish Embryo, Sivam Bhatt, Teerth Patel, Madeleine Seputro, Anubhav Thapaliya, Erich Damm

Undergraduate Research Posters

Hematopoietic Stem Cells (HSCs) are the self-renewing population of cells that generate all erythrocytes and leukocytes over the lifetime of a vertebrate organism. HSCs are also the therapeutic units of curative bone marrow transplants used in the treatment of blood malignancies and in gene therapy for genetic blood disorders. In all vertebrate embryos, HSCs originate from the floor of the embryonic dorsal aorta during the endothelial to hematopoietic transition. Nascent HSCs will bud into the blood vessel and be carried to maturation sites by the embryonic blood flow. Despite the curative potential of HSC transplants in blood disorders, this approach …

Astrocyte Elevated Gene-1 (Aeg-1) Deletion Selectively Enhances The Antinociceptive Effects Of Morphine, Apurva Puli, Shivani Patel, Bryan Mckiver, Eda Köseli, Devanand Sarkar Ph.D., M. Imad Damaj Ph.D.

Undergraduate Research Posters

Background: Opioids are a class of drugs that are utilized in clinical settings to alleviate acute and chronic pain, but can often lead to development of tolerance, addiction and overdose following prolonged usage. Opioids such as morphine function by activating endogenous µ opioid receptors, which are located in various tissues throughout the body. Astrocyte Elevated Gene-1 (AEG-1) is a multifunctional protein that regulates inflammation, myeloid cell activity and lipid metabolism. Studies have shown interactions and overlaps in cellular signaling between the inflammatory/immune responses and the endogenous opioid system which could suggest a role for AEG-1 in opioids effects. Our goal …

A Participatory Group Process To Collect And Disseminate Covid-19 Needs Assessment Data, Areebah Ahmed

Undergraduate Research Posters

The Richmond, VA COVID-19 Needs Assessment Survey (RVA CoNA) was created in March 2020 to identify behaviors and needs related to COVID-19 in Richmond area adults ages 18 and over. Results are being used to inform support, strategic efforts, and educational outreach of local community organizations. The purpose of this study is to (1) summarize the process used to develop the RVA CoNA, (2) summarize preliminary survey results from a second phase of data collection as well as initial feedback from community partners, and (3) summarize initial conclusions and results dissemination strategies.Community partners and researchers at Virginia Commonwealth University jointly …