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The Role Of Climate Change In The Decline Of Narragansett Bay Winter Flounder, Joseph A. Langan

Open Access Dissertations

Winter flounder (Pseudopleuronectes americanus) has historically supported productive commercial and recreational fisheries throughout its range in the northwest Atlantic. As a small flatfish that inhabits estuaries, bays, and the coastal zone, this species is vulnerable to shifting environmental conditions in many of the habitats critical to its life cycle. At the southern edge of the species range, the Southern New England/Mid-Atlantic Bight winter flounder stock entered a steep decline during the 1980s following a period of overfishing. Despite repeated reductions in harvest during the proceeding decades, the population has yet to recover. A decreasing trend in recruitment has …

Microbial Diversity And Community Composition In The Open Ocean And Marine Sediment, Zak Kerrigan

Open Access Dissertations

Over the last fifteen years, there has been a large increase in the literature on microbial community composition in marine sediment (Inagaki et al., 2006, 2015; Biddle et al., 2012; Briggs et al., 2012; Breucker et al., 2013; Lloyd, 2014; Teske et al., 2014; Nunoura et al., 2016; Walsh et al., 2016; Petro et al., 2017; Harrison et al., 2018; Hoshino et al., 2020), and seawater (Quaiser et al., 2011; Hamdan et al., 2013; Walsh et al., 2016; Medina-Silva et al., 2018; Mestre et al., 2018; Quero et al., 2019). As molecular study of these biomes progresses, and the tools …

Marine Microbial Interactions: Diversity And Function Of The Thalassiosira Rotula Phycosphere Community, Olivia Marjorie Ahern

Open Access Dissertations

Interactions between diatoms and bacteria impact global-scale biogeochemical cycling, through regulating the biological pump, impacting productivity of the marine food web, and regulating fluxes of chemicals. The most intimate of these interactions occur in the diatom’s phycosphere, akin to the mammal’s microbiome or rhizosphere. Research into terrestrial systems has shown intimate connections between an organism’s microbiome or rhizosphere and the genetic structure of the host organism’s species. However, little research has been done to elucidate these interactions in the diatom’s phycosphere. The goal of this work is to explore how diatom population structure impacts the phycosphere microbiome, by surveying the …

Evaluating Natural Product Libraries With Emphasis On In Vitro Permeability Workflows, Riley D. Kirk

Open Access Dissertations

New active pharmaceutical ingredients (APIs) continue to be discovered from the natural world. These compounds can be further developed into a range of useful products such as drugs, supplements, or cosmeceuticals. To determine the biological target of the API, the new compounds are evaluated for their biological activity through a combination of in silico, in vitro, and in vivo analyses. These results will determine where the molecular target tissue is located for the API. However, identification of the target is only the beginning of pharmaceutical and cosmeceutical development. A common roadblock in the development of products is the evaluation and …

Characterization Of Impact Pile Driving Signals And Fin Whale Vocalizations At The Block Island Wind Farm Site, Jennifer L. Amaral

Open Access Dissertations

Offshore wind farm development is rapidly expanding and with that comes the need for assessment of the potential short and long term environmental impacts. As a by-product of the construction, operation, and eventual decommissioning of offshore wind farms, sound is generated both in air and underwater through various activities and mechanisms. With the rate of wind farm development continuing to increase worldwide, regulatory agencies, industry, and scientists are attentive to the potential physiological and behavioral effects these sounds might have on marine life living in the surrounding environment. The impact pile driving used to install the wind turbine foundations is …

Optimization Of Riparian Zone Nitrogen Management Through The Development Of Riparian Model, Marzia Tamanna

Open Access Dissertations

This thesis addresses the modeling approach to benefit the riparian zone nutrient management related to water quality in the Northeast and Midwest of USA. Nutrient (primarily Nitrogen (N)) loss from agricultural watersheds through runoff and drainage water continues to be a water quality concern of global importance. Since N is a crucial input for the sustainability of agriculture, the use of N has increased dramatically in recent decades and the excessive nutrient losses have increased too. Like global concern, agriculture (cropland, pasture, managed forest) is an important component of many watersheds of the USA Northeast where N flux to major …

Functional Analysis Of Virulence In Vibrio Coralliilyticus Re22 And Probiotic Mechanisms Of Phaeobacter Inhibens S4, Christian W. Schuttert

Open Access Dissertations

Infections by pathogenic marine bacteria present a major problem for both the shellfish and finfish aquaculture industries, resulting in severe disease and high mortality. Pathogen infection seriously affect aquaculture production, and cause significant economic loss. Marine pathogens like Vibrio coralliilyticus frequently cause disease in a variety of shellfish. The use of antibiotics in large-scale aquaculture settings leads to the development, and potential transfer, of antibiotic resistance. In order to mitigate this emerging threat, an understanding of pathogenic mechanisms of infection and novel preventative strategies, such as probiotic treatment, is paramount for understanding and preventing future disease.

In manuscript I, “Two …

Mechanisms Of Interaction Between Haemophilus Parainfluenzae And Streptococcus Mitis, Dasith Perera

Open Access Dissertations

The human oral cavity is a complex polymicrobial environment, home to an array of microbes that play roles in health and disease. Oral bacteria have been shown to cause an array of systemic diseases and are particularly concerning to type II diabetics (T2D) with numerous predispositions that exacerbate bacterial infection. In this dissertation, we investigated the serum of healthy subjects and T2D subjects to determine whether we see greater translocation of oral bacteria into the bloodstream of T2D individuals. We didn’t observe any significant enrichment of oral taxa, however we detected the presence of an emerging pathogen, Acinetobacter baumannii that …

Biodiversity And Biogeography Of Protist Communities In Coastal Marine Ecosystems Across Indonesia, Erin Borbee

Open Access Dissertations

Despite a long history of biodiversity and biogeography research in Indonesia we know very little about protist communities across this region. What we do know about protist communities across Indonesia is largely based on visual surveys, which have been proven to vastly underestimate protist diversity. The combination of immense biodiversity, oceanographic significance, and human activity across this region make it an interesting setting for understanding the relative effects of abiotic and biotic drivers of protist community structure. The work presented in this dissertation uses metabarcoding to characterize protist community composition and underwater visual census (UVC) data to characterize fish and …

Molecular Ecology Of Marine Diatoms, Bacteria, And Their Biologically-Active Compounds, Alexa R. Sterling

Open Access Dissertations

This dissertation focuses on the molecular ecology of diatoms in the marine environment as it relates to co-occurring associated bacteria, spatial and temporal gradients of physical and chemical oceanographic parameters, and even biotoxin production. The study sites range from the polar habitat of the Southern Ocean (SO) surrounding the Western Antarctic Peninsula (WAP) to the productive estuary Narragansett Bay (NBay) in Rhode Island, USA. The WAP exhibits a naturally occurring gradient of a dissolved iron (Fe), which is an essential micronutrient that diatoms need for growth. Dissolved Fe is growth-limiting in the offshore area and replete in the nearshore areas. …

Self-Regulated Learning In First-Year Students In An Introductory Biology Course And The Student Experiences And Academic Impacts Of A Campus-Wide Metacognitive Intervention, Holly Joan Swanson

Open Access Dissertations

Post-secondary students often have difficulty with self-regulated learning, particularly in terms of monitoring and accurately assessing their level of understanding and how that is translated into appropriate preparation for their rigorous college/university coursework. With the persistence of academic outcome gaps between marginalized and non-marginalized students in gateway STEM courses and concomitant differences in retention and graduation rates, it is important to understand how self-regulation of learning is developed in students in general, and among different student identities. Interventions and teaching practices need to be cognizant of the unique academic experience of students from different identities if they are to narrow …

Investigating Tolfenamic Acid And Its Analogs As Potential Alzheimer’S Disease Therapeutics, Jaunetta Hill

Open Access Dissertations

Dementia is an umbrella term describing several diseases which cause cognitive impairment, confusion, difficulty completing tasks and social withdrawal. Alzheimer’s disease (AD) is the most common form of dementia, and the incidence is rapidly increasing as the ‘baby boomers’ age. Currently, there is one disease-modifying treatment approved for AD patients, however, its ability to decrease or reverse cognitive decline has yet to be confirmed.

The etiology of AD is unknown, however, there are two forms of AD associated with onset age. Early-onset AD (EOAD) is considered genetic and accounts for less than 5% of AD cases worldwide. Typically, EOAD is …

Probing Interactions Of Single-Walled Carbon Nanotubes At The Nano-Bio Interface, Mitchell Gravely

Open Access Dissertations

Non-covalent hybrids of single-stranded DNA and single-walled carbon nanotubes (DNA-SWCNTs) have demonstrated applications in biomedical imaging and sensing due to their enhanced biocompatibility and photostable, environmentally-responsive near-infrared (NIR) fluorescence. Significant progress has been made in developing robust biological probes based on the sensitive optical properties of SWCNTs, however biological environments introduce complex and dynamic conditions that interact with, and ultimately modulate, their intrinsic properties. These fundamental interactions within biological settings can determine whether a nanomaterial is biocompatible and robust, or cytotoxic and disruptive to biological processes. Thus, a mechanistic understanding of such interactions and their effect on cellular function is …

Feeling Good: Happiness And Health In Dutch Older Adults, Joshua Ray Tanzer

Open Access Dissertations

Statement of the problem: Positive psychology research has sought to identify cost efficient and intuitive ways to increase subjective happiness, with broad implications to personal health and overall quality of life (Lee Duckworth, Steen, & Seligman, 2005; Rashid, 2009; Seligman, 2008; Seligman, Ernst, Gillham, Reivich, & Linkins, 2009; Seligman, Rashid, & Parks, 2006). A complication in this research has been conflicting findings in the longitudinal stability of happiness (Easterlin, 2006). This analysis examines age related changes in happiness and physiological immune responsiveness to clarify the implications of positive health interventions.

Methods: Pretest-posttest structural equation modeling is employed to examine longitudinal …

Nurse Practitioners’ Experiences Working With Patients Living With Morbid Obesity, Sharon A. Mclimans

Open Access Dissertations

Morbid obesity is recognized as a complex chronic medical disease which has been increasing at an alarming rate in the U.S. The etiologies of this disease involve a complex interplay of genetics, physiological, psychological, behavioral, socioeconomic, and environmental factors. Serious medical consequences are associated with morbid obesity including diabetes, hyperlipidemia, hypertension, cardiovascular disease, and increasing the risk of certain cancers. Research has shown individuals with morbid obesity have higher incidence of depression and are subjected to stigmatizing and biases across society including health care professionals. The monumental cost of health care associated with morbid obesity places enormous burden on our …

Quantifying And Compensating For P300 Variations In Amyotrophic Lateral Sclerosis, Alyssa Hillary Zisk

Open Access Dissertations

P300-based brain–computer interface (BCI) systems enable people with neuromuscular disabilities, including amyotrophic lateral sclerosis (ALS), to communicate and to control their environments using brain activity. However, BCI systems have not yet fulfilled their promise as reliable communication systems for all who need them. Despite continued work on improving BCIs for end users, people with ALS can experience both reduced performance overall compared to neurotypical users and significant day to day variations in BCI performance and event-related potential (ERP) characteristics.

The P300 response, which the P300 speller is based on, is also known to exhibit trial-to-trial latency variability. The importance of …

True Crime, Women, And Sensationalized Representations In The Italian American Imaginary, Francesca Borrione

Open Access Dissertations

This dissertation explores American true crime literary and visual narratives and focuses on historical cases involving Italian American women and the cross-cultural relations between Italy and the United States from the late-nineteenth century to the beginning of the twenty-first century. I investigate the influence of true crime narratives on the popular imagination, with attention to the construction of ethnicity, class, and gender. The focus on Italian American women functions as a case study to discuss the impact and persistence of racialized assumptions and cultural stereotypes in American literature and cinema and explores the resistance of women to the dominant narrative. …

Fantasizing Reproduction: The Biologization Of The Desire For Progress In Victorian Literature, Xinqiang Chang

Open Access Dissertations

The preoccupation with reproduction in Victorian literature has, by and large, received little critical attention. This dissertation seeks to contribute to Victorian scholarship and examines the representations of reproduction in Victorian literature in relation to the contemporaneous desire for progress. Adopting a historiographical approach, this dissertation analyzes five Victorian novels: Charlotte Brontë’s Jane Eyre, George Eliot’s Middlemarch, George Du Maurier’s Trilby, Thomas Hardy’s Jude the Obscure, and Sarah Grand’s The Heavenly Twins. In this dissertation, I demonstrate the different ways in which these Victorian novelists explored, accommodated, and concretized the Victorian desire for and pursuit …

Social Justice And Evolutionary Biology: A Natural Fit, David I. Upegui

Open Access Dissertations

This dissertation is an extended prescription for the inclusion of social justice in high school biology (HSB) curricula. Chapter 1 is context: a review of social injustice (mainly racism) in the US, and the specious scientific justifications for it. Chapter 2 explores how three veteran teachers introduce social justice in HSB classes. A case-study, semi-constructed interview-based approach is used. Chapter 3, the culmination of these ideas, adduces a practical curriculum module that provides the theory, lessons and activities for HSB student exploration the inferior science used to sustain racial inequities. The dissertation thus reviews the moral imperatives for introducing social …

Anti-Inflammatory Effects Of Polyphenol-Enriched Extracts, Chang Liu

Open Access Dissertations

Our laboratory initiated a comprehensive research program to investigate the phytochemical composition and biological effects of several botanical based natural products including pomegranate (Punica granatum), red maple (Acer rubrum), polyphenol-enriched maple (Acer saccharum) syrup extract, and various phytocannabinoids (Cannabis sp.). We hypothesize that these bioactive natural products can exert beneficial biological effects via their antioxidant and anti-inflammatory effects.

In Manuscript 1-4, we identified a series of phytochemicals from botanical extracts including pomegranate, red maple, phenolic-enriched maple syrup extract (MSX) and evaluated their biological activities for potential cosmeceutical and/or dermatological applications. In …

Functional Consequences Of Apoptosis Gene Diversification In Eastern Oyster Immunity, Erin Michele Witkop

Open Access Dissertations

The eastern oyster is an ecologically and economically important filter feeding bivalve mollusc endemic to the east coast of the United States. Outbreaks of disease, such as Dermo disease caused by the parasite Perkinsus marinus, threaten natural oyster populations, and oysters have evolved a complex innate immune system containing large, expanded gene families to combat the diverse array of pathogens in their environment. Apoptosis, or programmed cell death, is a critical immune response to Dermo disease involving a series of expanded gene families, including the Inhibitor of Apoptosis (IAP) family of apoptosis regulatory molecules. The goal of this research is …

Salt Marsh Management: Monitoring Threats And Implementing Climate Adaptation Initiatives, Danielle C. Perry

Open Access Dissertations

Salt marshes serve as important coastal resources both economically and environmentally and are particularly susceptible to the negative implications of climate change. As climate change impacts become more prevalent, it is important to understand how salt marshes will respond. Two climate change impacts on salt marshes are macroalgae inundation and accelerated relative sea-level rise (hereafter referred to as SLR). Due to warming temperatures and sea level rise, salt marshes can be inundated by macroalgae through tidal movement, and the impacts of this excess macroalgal accumulation are poorly understood. Sea level rise also has negative implications on salt marsh by leading …

Nitrogen-Removing Wastewater Treatment Systems: Microbial Communities And Greenhouse Gas Emissions, Sara Katherine Wigginton

Open Access Dissertations

Wastewater is a major source of anthropogenic nitrogen (N) pollution that causes groundwater contamination and eutrophication in coastal ecosystems. The negative effects of excess N from wastewater on human and environmental health have led the United States Environmental Protection Agency (USEPA) and many state and local agencies to set maximum N concentrations for treated wastewater before it can be discharged to ground and surface water bodies. Wastewater treatment systems that include biological nitrogen removal (BNR) can help meet these standards by promoting microbial N removal in centralized wastewater treatment plants (WTP) as well as decentralized, onsite wastewater treatment systems (OWTS; …

Determining Impacts Of Iron Limitation On Diatom Chloroplast Metabolism And Physiology, Kristofer Gomes

Open Access Dissertations

Within the marine ecosystem, phytoplankton such as diatoms experience regions of nutrient limitation including macronutrients such as nitrogen, silica, and phosphate. In regions with high concentration of these nutrients but low chlorophyll a concentrations (HNLCs), phytoplankton are limited for micronutrients such as iron (Fe) an element that serves as a co-factor in proteins involved in cellular redox reactions. Of particular interest for diatoms is the Fe requirement of cellular processes localized to the chloroplast. These Fe requirements are in multiple metabolic pathways such as light reactions of photosynthesis that generate the necessary energy and reducing power necessary for anabolic processes …

Modulation Of Receptor Interacting Protein Kinase 1 (Ripk1) Signaling During Dengue Virus Infection, Darshika Jeewanthi Udawatte

Open Access Dissertations

Dengue virus (DENV) infection is the most prevalent arthropod-borne virus disease. There are estimated 100 million symptomatic cases of dengue disease per year worldwide. A lack of effective antiviral therapies or vaccines makes DENV infections a major global health concern. Therefore, understanding the viral and host factors contributing to the disease pathogenesis is critical. DENV has been shown to effectively counteract host innate immune mechanisms. In particular, DENV protease, NS3 has emerged as an inhibitor of host cellular signaling by targeting crucial host proteins. Here we identified RIPK1 as a novel target of DENV NS3. RIPK1 is a central mediator …

The Frequent Flyer’S Guide To Migration: How Songbird Metabolism And Oxidative Status Respond To Endurance Flight And Diet Quality, Kristen J. Demoranville

Open Access Dissertations

Migratory songbirds are among the best high-performance endurance athletes on the planet and during their annual peregrinations they are particularly vulnerable to oxidative damage because they maintain relatively high metabolic rates at rest, they are able to fly for long durations while operating at 9 times their resting metabolic rate, and they rely on fats to fuel this exercise which increases reactive oxygen species (ROS) formation. The concept of evolutionary economic design of physiological systems considers such phenotypic flexibility in metabolic and antioxidant responses adaptive in that it allows birds to match the capacity of key physiological systems to prevailing …

Design And Validation Of Smart Fabric Sensors Based On Semiconductive Polymer Composites, Arar Alkhader

Open Access Dissertations

Smart Fabric Sensors (SFSs) have recently gained much interest as they are convenient as a long-term wearable as well as for their simplicity, lightweight, low manufacturing cost, high sensitivity, and flexibility. Semiconductive polymer composites SCPCs can be used as smart fabrics to create force or pressure sensors based on the piezoresistive effect, however, their wider application is limited due to their narrow sensing range, hysteresis and output drift issues as well as due to the lack of literature studying their voltage response related errors especially under high impact forces. In this Doctoral research, eight proposed designs of a smart fabric …

Regulating Quiescence And Division In Escherichia Coli, Eric Charles Dibiasio

Open Access Dissertations

The decision for a bacterium to grow and divide may seem like a simple process, but in reality, there are many factors that influence and regulate this choice. Bacteria have been known to respond to many environmental signals or cues that represent either favorable or non-favorable growth conditions, as well as cues, secreted from other bacteria or, in the case of a pathogen, the host. It is not uncommon for bacteria that find their environment unfavorable, to alter their growth, and in some cases, even enter into a type of non-proliferative state, which we term, dormancy. Bacterial dormancy has many …

Function And Variability Of Metabolic Networks, Keith Dufault-Thompson

Open Access Dissertations

The study of bacterial growth has highlighted the importance of metabolism in how microorganisms have evolved and how they survive in different conditions. The introduction of next-generation sequencing methods has allowed for the study of metabolism in new ways by predicting metabolic phenotypes based on gene annotations. The development of GEnome-scale models (GEMs) of metabolism from these annotations has provided another method to investigate microbial metabolism. An overview of GEM development and simulation methods is provided in Appendix I.

In Manuscript I, a GEM was developed for the psychrotolerant, piezotolerant, deep-sea bacteria Shewanella piezotolerans WP3. Despite the broad differences in …

The Biogeography Of Antarctic Marine Diatoms And Their Response To Varied Iron Concentrations, Laura Z. Holland

Open Access Dissertations

Diatoms are a group of highly diverse photosynthetic eukaryotes that account for about 40% of oceanic primary production. In large areas of the ocean deemed high nitrate, low chlorophyll (HNLC) regions, dissolved macronutrient (nitrogen, phosphorus, silica) concentrations are high in the surface but diatom biomass is consistently low. The Southern Ocean (SO) is the largest of these environments, and when exogenous Fe is supplied to this region, large diatoms blooms and subsequent carbon export are promoted. As such, SO diatoms are major players in the global carbon cycle and were the focus of this dissertation. This work sought to determine …