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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 …

Characterization Of Ovarian Tissue Culture And Investigation Of Embryonic Response To Temperature Stress Using A Shp2 Phosphatase Inhibitor In Ciona Intestinalis, Rose Jacobson

Open Access Dissertations

This dissertation is comprised of two parts, the first is cell culture. In this work I describe the successful primary culture of Ciona intestinalis ovary tissue. Improved cell proliferation in 3D Petri Dish® system over culture treated plastic is shown, as well as the efficacy of using C. intestinalis hemolymph as a media additive. The seeded ovarian cells assemble into multicellular aggregations, which mimic the morphology of in vivo ovaries. It is also important to understand the molecular pathways in which marine organisms handle stress and how these pathways change in high stress situations.

The second is the role of …

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 …

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 …

Development And Characterization Of Nanomaterials To Overcome Pulmonary Epithelial Barriers, Md Golam Jakaria

Open Access Dissertations

With the rapidly growing popularity and sophistication of inhalable therapeutics, there is an increased demand for tailor made inhalable drug-loaded particles capable of efficient delivery to the lungs with optimal therapeutic outcomes. To cope with this formulation demand, a wide variety of novel technologies have emerged. Preparation of particle formulations suitable for inhalation and loaded with biomolecules is also of interest for gene therapy and vaccination applications. Dry powder inhalers (DPI) capable of delivering high dosages of therapeutics have rapidly evolved over the last decade, and nanoparticles have proven to be highly beneficial for controlled and sustained release of therapeutics …

A Local Similarity Function For Katabatic Flows Derived From Field Observations Over Steep- And Shallow-Angled Slopes, Chaoxun Hang, Holly J. Oldroyd, Marco G. Giometto, Eric R. Pardyjak, Marc B. Parlange

Civil & Environmental Engineering Faculty Publications

Katabatic flows are notoriously difficult to model for a variety of reasons. Notably, the assumptions underpinning Monin-Obukhov similarity theory (MOST) are inherently violated by the sloping terrain, causing the traditional flux-gradient relations used in numerical weather prediction models to break down. Focusing on turbulent momentum transport, we show significant flux divergence, further violating MOST assumptions, and that the traditional parameterizations fail even with local scaling for katabatic flow. In response, we propose a modified local-MOST stability-correction function, informed by near-surface turbulence observations collected over two mountainous slopes with inclination angles (α) of α ≈ 7.8° and α ≈ 35.5°. The …

Albumin Protein Coronas Render Nanoparticles Surface Active: Consonant Interactions At Air–Water And At Lipid Monolayer Interfaces, Nasim Ganji, Geoffrey D. Bothun

Chemical, Biomolecular, and Materials Engineering Faculty Publications

Protein coronas are known to alter the physicochemical properties, colloidal stability, and biological fate of nanoparticles. Using human serum albumin (HSA) and polystyrene nanoparticles (NPs) with anionic or cationic surface chemistries, we show that protein coronas also govern the surface activity of PS nanoparticles as well as their interactions with a model red blood cell (RBC) lipid monolayer. The adsorption kinetics of bare nanoparticles (no corona) and nanoparticles with a hard corona (HC) at an air–water interface were well-described theoretically, which revealed that the adsorption energy was greater with the corona due to hydrophobic interactions that were enhanced with protein …

Dominant Entropic Binding Of Perfluoroalkyl Substances (Pfass) To Albumin Protein Revealed By 19f Nmr, Michael Fedorenko, Jessica Alesio, Anatoliy Fedorenko, Angela L. Slitt, Geoffrey D. Bothun

Chemical, Biomolecular, and Materials Engineering Faculty Publications

Mechanistic insight into protein binding by poly- and perfluoroalkyl substances (PFASs) is critical to understanding how PFASs distribute and accumulate within the body and to developing predictive models within and across classes of PFASs. Fluorine nuclear magnetic resonance spectroscopy (¹⁹F NMR) has proven to be a powerful, yet underutilized tool to study PFAS binding; chemical shifts of each fluorine group reflect the local environment along the length of the PFAS molecule. Using bovine serum albumin (BSA), we report dissociation constants, K_d, for four common PFASs well below reported critical micelle concentrations (CMCs) − perfluorooctanoic acid (PFOA), …

Advances In Lipid-Based Nanoparticles For Cancer Chemoimmunotherapy, Tianqi Wang, Yusuke Suita, Saradha Miriyala, Jordan Dean, Nikos Tapinos, Jie Shen

Chemical, Biomolecular, and Materials Engineering Faculty Publications

Nanomedicines have shown great potential in cancer therapy; in particular, the combination of chemotherapy and immunotherapy (namely chemoimmunotherapy) that is revolutionizing cancer treatment. Currently, most nanomedicines for chemoimmunotherapy are still in preclinical and clinical trials. Lipid-based nanoparticles, the most widely used nanomedicine platform in cancer therapy, is a promising delivery platform for chemoimmunotherapy. In this review, we introduce the commonly used immunotherapy agents and discuss the opportunities for chemoimmunotherapy mediated by lipid-based nanoparticles. We summarize the clinical trials involving lipid-based nanoparticles for chemoimmunotherapy. We also highlight different chemoimmunotherapy strategies based on lipid-based nanoparticles such as liposomes, nanodiscs, and lipid-based hybrid …

The Fiber Optic Reel System: A Compact Deployment Solution For Tethered Live-Telemetry Deep-Sea Robots And Sensors, Brennan T. Phillips, Nicholas Chaloux, Russell Shomberg, Adrjana Muñoz-Soto, Jim Owens

Ocean Engineering Faculty Publications

Tethered deep-sea robots and instrument platforms, such as Remotely Operated Vehicles (ROVs) and vertical-profiling or towed instrument arrays, commonly rely on fiber optics for real-time data transmission. Fiber optic tethers used for these applications are either heavily reinforced load-bearing cables used to support lifting and pulling, or bare optical fibers used in non-load bearing applications. Load-bearing tethers directly scale operations for deep-sea robots as the cable diameter, mass, and length typically require heavy winches and large surface support vessels to operate, and also guide the design of the deep-sea robot itself. In an effort to dramatically reduce the physical scale …

Optimization And Assessment Of Phytoplankton Size Class Algorithms For Ocean Color Data On The Northeast U.S. Continental Shelf, Kyle J. Turner, Colleen B. Mouw, Kimberly J.W. Hyde, Ryan Morse, Audrey B. Ciochetto

Graduate School of Oceanography Faculty Publications

The size structure of phytoplankton communities influences important ecological and biogeochemical processes, including the transfer of energy through marine food webs. A variety of algorithms have been developed to estimate phytoplankton size classes (PSCs) from satellite ocean color data. However, many of these algorithms were developed for application to the global ocean, and their performance in more productive, optically complex coastal and continental shelf regions warrants evaluation. In this study, several existing PSC models were applied in the Northeast U.S. continental shelf (NES) region and compared with in situ PSC estimates derived from a local HPLC pigment data set. The …

Surviving Heatwaves: Thermal Experience Predicts Life And Death In A Southern Ocean Diatom, Toby Samuels, Tatiana A. Rynearson, Sinéad Collins

Graduate School of Oceanography Faculty Publications

Extreme environmental fluctuations such as marine heatwaves (MHWs) can have devastating effects on ecosystem health and functioning through rapid population declines and destabilization of trophic interactions. However, recent studies have highlighted that population tolerance to MHWs is variable, with some populations even benefitting from MHWs. A number of factors can explain variation in responses between populations including their genetic variation, previous thermal experience and the cumulative heatwave intensity (°C d) of the heatwave itself. We disentangle the contributions of these factors on population mortality and post-heatwave growth rates by experimentally simulating heatwaves (7.5 or 9.2°C, for up to 9 days) …

Meta-Analysis Of Primary Producer Amino Acid Δ15N Values And Their Influence On Trophic Position Estimation, Matthew D. Ramirez, Alexi C. Besser, Seth D. Newsome, Kelton Mcmahon

Graduate School of Oceanography Faculty Publications

1. Compound-specific stable isotope analysis of individual amino acids (CSIA-AA) has emerged as a transformative approach to estimate consumer trophic positions (TP_CSIA) that are internally indexed to primary producer nitrogen isotope baselines. Central to accurate TP_CSIA estimation is an understanding of beta (β) values—the differences between trophic and source AA δ¹⁵N values in the primary producers at the base of a consumers’ food web. Growing evidence suggests higher taxonomic and tissue-specific β value variability than typically appreciated.
2. This meta-analysis fulfills a pressing need to comprehensively evaluate relevant sources of β value variability and its contribution to …

Open Ocean Particle Flux Variability From Surface To Seafloor, B. B. Cael, Kelsey Bisson, Maureen Conte, Manon T. Duret, Christopher L. Follett, Stephanie A. Henson, Makio C. Honda, Morten H. Inversen, David M. Kart, Richard S. Lampitt, Colleen B. Mouw, Frank Muller-Karger, Corinne A. Pebody, Kenneth L. Smith, David Talmy

Graduate School of Oceanography Faculty Publications

The sinking of carbon fixed via net primary production (NPP) into the ocean interior is an important part of marine biogeochemical cycles. NPP measurements follow a log-normal probability distribution, meaning NPP variations can be simply described by two parameters despite NPP's complexity. By analyzing a global database of open ocean particle fluxes, we show that this log-normal probability distribution propagates into the variations of near-seafloor fluxes of particulate organic carbon (POC), calcium carbonate, and opal. Deep-sea particle fluxes at subtropical and temperate time-series sites follow the same log-normal probability distribution, strongly suggesting the log-normal description is robust and applies on …

Addressing Urgent Questions For Pfas In The 21st Century, Carla Ng, Ian T. Cousins, Jamie C. Dewitt, Juliane Glüge, Gretta Goldenman, Dorte Herzke, Rainer Lohmann, Mark Miller, Sharyle Patton, Martin Scheringer, Xenia Trier, Zhanyun Wang

Graduate School of Oceanography Faculty Publications

Despite decades of research on per- and polyfluoroalkyl substances (PFAS), fundamental obstacles remain to addressing worldwide contamination by these chemicals and their associated impacts on environmental quality and health. Here, we propose six urgent questions relevant to science, technology, and policy that must be tackled to address the “PFAS problem”: (1) What are the global production volumes of PFAS, and where are PFAS used? (2) Where are the unknown PFAS hotspots in the environment? (3) How can we make measuring PFAS globally accessible? (4) How can we safely manage PFAS-containing waste? (5) How do we understand and describe the health …

Information Requirements Under The Essential-Use Concept: Pfas Case Studies, Juliane Glüge, Rachel London, Ian T. Cousins, Jamie Dewitt, Gretta Goldenman, Dorte Herzke, Rainer Lohmann, Mark Miller, Carla A. Ng, Sharyle Patton, Xenia Trier, Zhanyun Wang, Martin Scheringer

Graduate School of Oceanography Faculty Publications

Per- and polyfluoroalkyl substances (PFAS) are a class of substances for which there are widespread concerns about their extreme persistence in combination with toxic effects. It has been argued that PFAS should only be employed in those uses that are necessary for health or safety or are critical for the functioning of society and where no alternatives are available (“essential-use concept”). Implementing the essential-use concept requires a sufficient understanding of the current uses of PFAS and of the availability, suitability, and hazardous properties of alternatives. To illustrate the information requirements under the essential-use concept, we investigate seven different PFAS uses, …

An Operational Overview Of The Export Processes In The Ocean From Remote Sensing (Exports) Northeast Pacific Field Deployment, Melissa M. Omand, Bethany D. Jenkins, Heather Mcnair, Tatiana A. Rynearson, Et Al

Graduate School of Oceanography Faculty Publications

The goal of the EXport Processes in the Ocean from RemoTe Sensing (EXPORTS) field campaign is to develop a predictive understanding of the export, fate, and carbon cycle impacts of global ocean net primary production. To accomplish this goal, observations of export flux pathways, plankton community composition, food web processes, and optical, physical, and biogeochemical (BGC) properties are needed over a range of ecosystem states. Here we introduce the first EXPORTS field deployment to Ocean Station Papa in the Northeast Pacific Ocean during summer of 2018, providing context for other papers in this special collection. The experiment was conducted with …

Differential Patterns Of Connectivity In Western Pacific Hydrothermal Vent Metapopulations: A Comparison Of Biophysical And Genetic Models, Corinna Breusing, Shannon B. Johnson, Satoshi Mitarai, Roxanne A. Beinart, Verena Tunnicliffe

Graduate School of Oceanography Faculty Publications

Hydrothermal ecosystems face threats from planned deep-seabed mining activities, despite the fact that patterns of realized connectivity among vent-associated populations and communities are still poorly understood. Since populations of vent endemic species depend on larval dispersal to maintain connectivity and resilience to habitat changes, effective conservation strategies for hydrothermal ecosystems should include assessments of metapopulation dynamics. In this study, we combined population genetic methods with biophysical models to assess strength and direction of gene flow within four species of the genus Alviniconcha (A. boucheti, A. kojimai, A. strummeri and A. hessleri) that …

Deep Learning Of Sea Surface Temperature Patterns To Identify Ocean Extremes, J. Xavier Prochaska, Peter C. Cornillon, David M. Reiman

Graduate School of Oceanography Faculty Publications

We performed an out-of-distribution (OOD) analysis of ∼12,000,000 semi-independent 128 × 128 pixel² sea surface temperature (SST) regions, which we define as cutouts, from all nighttime granules in the MODIS R2019 Level-2 public dataset to discover the most complex or extreme phenomena at the ocean’s surface. Our algorithm (ULMO) is a probabilistic autoencoder (PAE), which combines two deep learning modules: (1) an autoencoder, trained on ∼150,000 random cutouts from 2010, to represent any input cutout with a 512-dimensional latent vector akin to a (non-linear) Empirical Orthogonal Function (EOF) analysis; and (2) a normalizing flow, which maps the autoencoder’s latent …

Photoperiod Decelerates The Advance Of Spring Phenology Of Six Deciduous Tree Species Under Climate Warming, Lin Meng, Yuyu Zhou, Lianhong Gu, Andrew D. Richardson, Josep Peñuelas, Yongshuo Fu, Yeqiao Wang, Ghasserm R. Asrar, Hans G. De Boeck, Jiafu Mao, Yongguang Zhang, Zhousen Wang

Natural Resources Science Faculty Publications

Vegetation phenology in spring has substantially advanced under climate warming, consequently shifting the seasonality of ecosystem process and altering biosphere–atmosphere feedbacks. However, whether and to what extent photoperiod (i.e., daylength) affects the phenological advancement is unclear, leading to large uncertainties in projecting future phenological changes. Here we examined the photoperiod effect on spring phenology at a regional scale using in situ observation of six deciduous tree species from the Pan European Phenological Network during 1980–2016. We disentangled the photoperiod effect from the temperature effect (i.e., forcing and chilling) by utilizing the unique topography of the northern Alps of Europe (i.e., …

Seasonal And Interspecific Variation In Frugivory By A Mixed Resident-Migrant Overwintering Songbird Community, Wales A. Carter, Scott F. Pearson, Adam D. Smith, Scott R. Mcwilliams, Douglas J. Levey

Natural Resources Science Faculty Publications

Many temperate passerine bird species switch from diets of mostly invertebrates in the spring and summer to diets that include fruit and seeds in the fall and winter. However, relatively few studies have quantified diet composition or the extent of seasonal shifts during the non-breeding period, particularly among species and across communities with both residents and migrants. We measured carbon and nitrogen stable isotope values in food items (fruits, C₃ and C₄seeds, and insects from various trophic levels and plant communities) and in multiple tissues (feathers and plasma/whole blood) from 11 species of songbirds wintering in the …

Investigating Long-Term Physical, Chemical And Biological Changes In Narragansett Bay Using Bayesian Multivariate Dynamic Linear Models, Jacob P. Strock

Open Access Master's Theses

Within the past 50 years, Narragansett Bay has undergone major physical and chemical changes including climate-induced warming and policy-driven reductions in anthropogenic nutrient pollution. These long-term changes have the capacity to transform the ecological function of Narragansett Bay, but may also represent a case study for global oceanic changes. Despite its importance, the long-term response of ecosystems to climatological change remains uncertain, as well as the consistency of biological interactions with the environment over time. I explore these uncertainties here using Bayesian dynamic linear models (DLMs) to investigate the Narragansett Bay Long-Term Plankton Time Series. In a first stage, DLMs …

Real-World Utilization And Expenditure Of Top-Down And Step-Up Therapy In Inflammatory Bowel Disease, Kanya K. Shah

Open Access Master's Theses

Introduction:

Inflammatory bowel disease (IBD) describes gastrointestinal inflammatory diseases Crohn’s disease (CD) and ulcerative colitis (UC). The inflammation associated with CD can penetrate deep layers of gastrointestinal tissue anywhere along the gastrointestinal tract. Pharmaceutical therapy options for CD include aminosalicylates, corticosteroids, antimicrobials, immunomodulators, and biologics. The step-up (SU) treatment strategy for CD begins with anti-inflammatory agents (aminosalicylates, corticosteroids, and antimicrobials), and progresses to immunomodulators and biologics if disease control is not achieved. Conversely, with top-down (TD) therapy strategy, patients initiate CD medication treatment with immunomodulators and biologics and use anti-inflammatory agents as second-line options. Presently, limited evidence exists characterizing the …

Identifying Novel Isotopic Tracers Of Marine Primary Producers To Study Food Web Carbon Cycles, Angela Stahl

Open Access Master's Theses

Eukaryotic microalgae play critical roles in global biogeochemical cycling, the efficacy of the biological pump, and the structure and function of most marine food webs. Compound-specific isotope analysis of amino acids (CSIA-AA) couples molecular-level biomarkers with stable isotope analyses to track the contribution of primary producers to food webs. Previous work has developed δ13CAA fingerprints for major groups of primary producers but categorized all marine algae together despite their vast taxonomic and ecological diversity. This work characterizes the δ13CAA fingerprints of four major groups of eukaryotic microalgae — diatoms, dinoflagellates, raphidophytes, and prasinophytes — in controlled cultures, and quantifies the …

Data Dimensionality Reduction Through Cluster Trees And Manifold Learning, Ali Amani

Open Access Master's Theses

Dimensionality reduction algorithms are a commonly used solution to create a visual summary of high dimensional data in a way that makes identification of patterns and trends easier. Algorithms that are used to visualize data as 2 or 3 dimensional plots are popular options, even more so due to clustering and manifold learning. There already exist many tools, both linear and nonlinear, that are used in visualizing high dimensional data, three of the most popular being PCA, t-SNE and UMAP. PCA has low memory requirements and is efficient in low dimensions, t-SNE captures much of the local structure of high …

Understanding The Public Perception Of Selective Breeding Practices In Rhode Island Oyster Aquaculture, Nathan M. Brown

Open Access Master's Theses

Selective breeding is a common practice within oyster aquaculture and is used to improve growth rates as well as reduce the negative impacts of water temperature rise, ocean acidification and disease among oysters. What is lesser understood is the public perception of the use of selective breeding in oyster aquaculture. A total of 81 Rhode Island residents responded online concerning how they perceived selective breeding in Rhode Island as well as what types of oysters they preferred. Multiple 5-point Likert scale questions and discrete choice experiments were used to better understand these perceptions. A majority of those who responded view …

The Initial Response Of The United States’ Textile Recycling Industry To The Covid-19 Pandemic, Rosemary Leger

Open Access Master's Theses

The fashion industry is cited as a major contributor to global pollution. The urgent need for a reversal of climate change has led the textile and apparel industry to assess what opportunities exist to convert to greener, less damaging solutions. The recycling of existing textiles and textile waste into yarns and fabrics would reduce the need for raw materials as well as divert millions of tons of textile waste from landfill. Just as these advancements are being made and consumers are beginning to invest in more responsible textile products, the COVID-19 pandemic occurs, and global markets come to a halt. …

Reclaiming Black And Indigenous Ecologies On Block Island Through Oral History And Ethnography, Adrian Cato

Open Access Master's Theses

Public memory on Block Island largely ignores Black and Indigenous labor, life, and legacy. Reclaiming the past and present narratives of Black and Indigenous peoples on Block Island challenges historical erasure; their experiences can then become a meaningful part of the collective public memory of the region. Black and Indigenous women are a key aspect of erased and reclaimed memory, often tasked with maintaining place for their families over generations, upholding their connection to their land and their history - depended upon to maintain and pass down tradition. Developing new memory worlds would mean recognizing the contributions of Black-Indigenous peoples, …

Several Factors And Their Role In Control Of Lepidoptera Populations, Alex K. Baranowski

Open Access Master's Theses

A number of factors influence Lepidoptera populations. The larvae are at the mercy of their environment, susceptible to the effects of poor food quality, and highly vulnerable to predation. In this thesis I present three manuscripts dealing with a small snapshot of what dynamics are at play in the control of Lepidoptera numbers.

Host quality is a cornerstone of developmental success, with host suitability to the herbivore in question being affected by the plant’s nutritional profile and its defenses against herbivory. Plant genotype influences plant suitability to herbivores; domesticated plants selected for properties such as high fruit yield are demonstrably …

Environmental Drivers Of Phytoplankton Growth And Grazing Mortality, Mikayla Cote

Open Access Master's Theses

In an effort to better understand what factors govern phytoplankton growth (μ, d^-1) and mortality due to herbivorous protist grazing (g, d^-1) in different biogeographic regions of the oceans, I analyzed data from 401 dilution experiments performed over a decade by the Menden-Deuer laboratory. Measurements were made in the North Atlantic, North Pacific, West Antarctic, Narragansett Bay, and along the Northeast U.S. Shelf. Experiments were performed over temperatures that ranged from -1.5 to 27.4 °C, salinity from 14.1 to 36.5, photosynthetically active radiation (PAR) from 0.24 to 60.0 mol/m^2.s chlorophyll a (chl a) …