Digital Commons Network^™

Assessing Changes In Freshwater And Marine Food Web Connections Following Restoration On The Penobscot River, Maine, Using Stable Isotope Analysis, Matthew Brewer Ms

Student Scholarship

Oiadromous fish provide ecological subsidies to freshwater and marine food

webs, connecting both ecosystems. A main goal of the Penobscot River Restoration

Project was to increase connectivity between food webs by removing two mainstem

dams, improving fish passage, and reintroducing river herring through stocking.

Oiadromous fish now reach historic spawning habitat that was not accessible for

centuries. As a result, river herring runs in the Penobscot River increased from

2,336 fish in 2009 to over 3 million fish by 2018. To assess food web connectivity in

the Penobscot watershed, I analyzed stable isotopes from samples collected before

(2009-2010) and after …

Evaluating Bat Roost Abundance: A Comparison Of Drone-Acquired Thermal Imagery And Acoustic Estimates With Visual Observations, Karah Jaffe

Electronic Theses and Dissertations

Roosts provide an opportunity to census philopatric populations of bats. Comparing the efficacy of traditional methods with novel methods can provide guidance on the use of new technologies in the field. This project aims to compare the count efficacy of external emergence methodologies, i.e., drone-acquired thermal imagery, acoustic estimates, and visual counts. Surveys were conducted ten nights at two emergence sites and synchronized to compare counts. Acoustic estimates could not be established as there was a weak prediction of the linear relationship between root-mean-square pressure and emergence count; therefore, this method was removed from the comparative analysis. A linear mixed-effects …

Investigating Roles Of 2 Novel Eklf Targets Involved In Erythropoiesis, Rose M. Gott

ETD Archive

Erythrocytes are primarily comprised of the oxygen carrying protein hemoglobin. Genetic mutations causing defects in the proper synthesis of hemoglobin result in various anemias. It is during the last phases of terminal erythroid differentiation that hemoglobin levels rise, making it a focus for therapeutic research. Fetal hemoglobin is comprised of ⍺-globin and gamma globin, then after a change in gene expression called hemoglobin switching which takes place after birth, adult hemoglobin is comprised of ⍺-globin and beta globin. We investigated hemoglobin switching and erythroid terminal differentiation by focusing on the master erythroid transcription factor Erythroid Krüppel-like Factor (EKLF). Data led …

The Roleo F Selectionin Maintaining Mhc Variationi N Mammals: Heterozygotaed Vantage,R Area Llelea Dvantagea Nd Mate Choice, Carol Titterton Ms

Student Scholarship

The major histocompatibility complex (MHC) is the most polymorphic gene

region in jawed vertebrates. Its gene products play a critical role in determining

individual and population fitness by presenting foreign antigens to immune system

cells, thereby initiating immune response to pathogen and parasite infections and

cancer. I surveyed the literature to investigate how selection maintains such

important adaptive diversity in mammalian populations and how MHC diversity

affects individual and population fitness. Balancing selection in the form of either

heterozygote advantage or rare allele advantage has long been proposed as the key

mechanism for maintaining the extreme diversity in MHC gene …

The Role Of Foxd1 In Clear Cell Renal Cell Carcinoma, Kyle H. Bond

Electronic Theses and Dissertations

Renal cell carcinoma (RCC) is the 8^th most common cancer in the United States, with the clear cell variant (ccRCC) being the most prevalent. Over 14,000 people die every year to RCC, with rates continuing to increase with an aging general population. Patients suffering from metastatic RCC (mRCC) have extremely poor prognoses, with a 5-year survival of only 11.2%. Current treatment options include resection of primary lesions, tyrosine kinase inhibition (Sunitinib, Pazopanib), mTOR inhibition (Temsirolimus, Everolimus), and immune checkpoint inhibition (Nivolumab, Atezolizumab). Recent attention has been drawn to inhibition of transcription factors like HIF2α (Belzutifan). There is a need …

Development And Analysis Of Next-Generation Polymeric And Bio-Ceramic Based Orthopedic Scaffolds By Advanced Manufacturing Techniques, Sudeep K. Gummadi

ETD Archive

Gliomas express mutant isocitrate dehydrogenases producing excessive amounts of D 2-hydroxyglutarate (D2HG) and releasing some of it into the environment. The immune surveillance is reduced as a result, however, the mechanisms behind lymphocyte suppression by the D2HG stereoisomer remain unknown. I incubated Jurkat T cells with D2HG at concentrations present within and surrounding gliomas, or its obverse L2HG stereoisomer, and quantified 2HG isomers within washed cells by TSPC derivatization with stable isotope-labeled D2HG and L2HG internal standards, HPLC separation, and mass spectrometry. D2HG was found in quiescent cells in double the amount of L2HG. External D2HG or L2HG increased the …

The Phylogeography And Invasion History Of Jumping Worms On The Hamilton College Campus Inferred Through Populations Genetics, Dylan Morse '22

Biology Theses

Phylogeographic studies are helpful in reconstructing invasion history and population dynamics. Since the first introduction of Amynthas species into the United States in the 1930’s, Amynthas species (invasive jumping worms) have spread throughout the eastern United States and into Canada. Three Amynthas species, Amynthas agrestis, Amynthas tokioensis, and Metaphire hilgendorfi, all affect productivity and nutrient cycling in soil and forested ecosystems. Recent studies have used the COI barcoding region to track invading taxa and elucidate cryptic diversity.

This study investigates populations of Amynthas species on the Hamilton College campus. Using the COI barcoding region to conduct a …

Simulating Polistes Dominulus Nest-Building Heuristics With Deterministic And Markovian Properties, Benjamin Pottinger

Undergraduate Honors Theses

European Paper Wasps (Polistes dominula) are social insects that build round, symmetrical nests. Current models indicate that these wasps develop colonies by following simple heuristics based on nest stimuli. Computer simulations can model wasp behavior to imitate natural nest building. This research investigated various building heuristics through a novel Markov-based simulation. The simulation used a hexagonal grid to build cells based on the building rule supplied to the agent. Nest data was compared with natural data and through visual inspection. Larger nests were found to be less compact for the rules simulated.

Anxiety And Immunity: Affecting The Body And The Mind, Katelynn Dobbs

Theses/Capstones/Creative Projects

Speculations have been made within the scientific community that there is a link between the underlying mechanisms that impact anxiety disorders and immune system disorders. While many correlations between these disorders have been observed through various immune system disorder studies, this subject is still severely under-explored. In order to examine the potential relationship between anxiety disorders and immune system disorders, a survey was conducted and distributed among the student population at the University of Nebraska at Omaha. This survey collected data by asking a variety of questions that pertained to anxiety and immune system disorders diagnoses within the student population …

Aeromonas Phage Research And The Public Health Impact Of Antibiotics In Aquaculture Workers, Madelyn Merchant

Honors Projects

One of the most common fish diseases in aquaculture is Aeromonas infection. The most common way to treat this infection is through antibiotics. The bacteria in the fish can become antibiotic-resistant and perpetuate the disease. The diseases in fish create a huge financial loss and the industry loses $6 billion per year due to diseases in fish. An alternative to antibiotics is bacteriophage which causes less environmental degradation and is better for human gut flora. In aquaculture there have been examples of aquaculture workers becoming sick from the water in aquaculture ponds as well as from people eating the fish. …

Bci Validation: Yfiler Plus Kit Validation, Chloe Koon

Honors Projects

In order to have access and use the Combined DNA Index System (CODIS), it is required by the Federal Bureau of Investigation's Quality Assurance Standards (FBI-QAS) for Forensic DNA Units to complete comprehensive validation studies on all equipment, materials, and methods used in the process of DNA analysis. This study continues validation previous done within the Ohio Bureau of Criminal Investigation (BCI). YFiler Plus is a DNA amplification kit that is used in cases where it is most useful to examine only male DNA profile(s) within a sample by amplifying loci only on the Y-Chromosome. Components of this study include …

A Multi-Spatial Analysis Of Land Use Effects On Freshwater Mussels In The Upper Cuyahoga River And Tinkers Creek, Tamar Atwell

ETD Archive

Mussels are considered one indicator of good water quality in rivers, but over the past 20 years mussel populations have continued to decline, while water quality improves. According to the Ohio Environmental Protection Agency (OEPA), water quality in the Cuyahoga River is now within safe levels for all parameters. However, what are safe levels for humans may not be safe for mussels. An analysis of freshwater mussel populations in two similarly sized watersheds, the Upper Cuyahoga River and Tinkers Creek was conducted. Correlations of mussel abundance and diversity were assessed by multivariate GIS/remote sensing tools to contrast water flow rates, …

Analysis Of Invasive Aedes Japonicus Populations And Bloodmeals In Rural, Suburban, And Urban Land-Use Conditions, Matthew Oberholtzer Ms

Student Scholarship

Adult female mosquitoes were collected at six sites with differing land-use and

livestock characteristics to characterize populations and bloodmeal habits of the invasive

vector mosquito species, Aedes japonicus in Southern Maine. Mosquitoes were collected

and DNA was extracted for PCR amplification of cytochrome C oxidase I (COi)

mitochondrial DNA for barcoding analysis of vertebrate bloodmeals. A total of 7460

adult female mosquitoes were collected, with 444 being Ae. japonicus (5.6%). This

indicates an established breeding population of Ae. japonicus in Southern Maine. The

rural site adjacent to livestock had the highest yield of total mosquitoes as well as the

catch …

Alewife (Alosa Pseudoharengus) Contributions To Lake Phosphorus Budgets: Implications For Management, Meg "Rue" Farley Thurrell Ms

Student Scholarship

As human-made dams are removed and fish passage at dams is improved in

support of restoration efforts, anadromous alewives (Alosa pseudoharengus) gain

access to historic spawning grounds. As they migrate to spawn, adult alewives import

marine derived nutrients to lakes and impoundments. Young of year alewives (juveniles)

export nutrients as they emigrate to the sea. These nutrients support primary

production and are incorporated into freshwater food webs. However, many lakes in

New England are mesotrophic or eutrophic. Additional nutrients, specifically

phosphorus (P), may exacerbate water quality issues. To examine these issues, I

compared outputs ofan alewife nutrient and population model …

Functional Analysis Of Stn1 Winged-Helix (Wh) Domains, Anna Bazell

Senior Theses

CST (CTC1-STN1-TEN1) is a heterotrimeric RPA-like protein complex that preferentially binds to single-stranded DNA (ssDNA). CST is conserved from yeast to humans and has been found to play a role in telomere maintenance, DNA replication, and DNA repair. Mutations in CST, specifically in the subunits of CTC1 and STN1, have been implicated in the development of the genetic diseases Coats plus and dyskeratosis congenita. Despite the known functions of CST, the mechanistic relationship between its structure and function has yet to be characterized, particularly with respect to its protein-protein interactions and DNA binding. An X-ray crystallography structure of CST revealed …

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 …

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 …

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 …

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 …

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 …

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 …

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 …

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 …

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 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 …

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 …

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 …

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 …

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 …