Digital Commons Network^™

Spatial Patterns Of The Humpback Whale (Megaptera Novaeangliae) And Its Summer Habitat In The North Atlantic Ocean, Kathleen J. Vigness-Raposa

Open Access Dissertations

The humpback whale (Megaptera novaeangliae) is found in all oceans of the world, migrating between low-latitude breeding grounds in the winter and high-latitude feeding grounds in the summer. In addition to these broad-scale spatial patterns, individuals in the North Atlantic Ocean exhibit fine-scale site fidelity, with median re-sighting distances of less than 40 km in consecutive years. Because they occur close to coasts and demonstrate a predictable distribution, humpback whales are particularly susceptible to disturbance from human activities. A clear understanding of the geographic pattern of summer sightings, along with the environmental features that characterize areas of concentrated distribution, could …

Structure-Function Studies Of Protein Tyrosine Kinases: Regulation And Substrate Specificity, Kezhen Huang

Open Access Dissertations

Protein tyrosine kinases (PTKs) are a large family of enzymes that play critical roles in signal transduction. Through transferring γ-phosphate group from ATP to protein substrates, PTKs regulate functions of these substrates. Due to the utmost importance in signal transduction, malfunction of PTKs usually leads to severe consequences such as cell transformation. Therefore, how PTKs function becomes a focal question in the field of cancer biology. To build a knowledge base for the investigation of specific functions of PTKs, we focused on two major aspects: regulation and substrate specificity. Two general strategies of regulating PTKs have been observed. In the …

The Role Of Pedagogical Documentation In Developing Young Children's Thinking Processes, Leslie A. Sevey

Open Access Dissertations

This study examines the role of pedagogical documentation on young children's thinking processes. Pedagogical documentation is utilized as part of the Reggio Emilia Approach for several purposes, such as assessment, curriculum planning, and instructional accountability. This study was conducted in a kindergarten classroom that utilizes the Reggio Emilia Approach, at a laboratory school on a college campus. Acting in the role of participant observer I spent nine weeks observing and at times interacting with the students as they engaged in activities involving science kits. I specifically looked at the experiences of the children as they interacted with the pedagogical documentation, …

Characterizing The Advanced Glycation Endproducts Formation Of Proteins And Nucleotides By Methylglyoxal And Glyoxal, Praveen Kumar Pampati

Open Access Dissertations

Advanced glycation endproducts (AGEs) are a heterogeneous group of molecules formed from the nonenzymatic reaction of reducing sugars with free amino groups of proteins, lipids, and nucleic acids. The initial product of this reaction is called a Schiff base, which rearranges itself into an Amadori or glycation product which can further rearrange to AGEs. The reaction is called Maillard reaction and is the basis for all protein glycation studies. AGEs accumulate in tissues and associate with the pathology of various diseases like Diabetes, Alzheimer's disease, renal failure, aging, etc. Methylglyoxal, 3-Deoxyglucosone and glyoxal (oxoaldehydes or α-dicarbonyls) have recently been proposed …

Trophoblasts And Endothelial Cells In Pregnancy-Associated Vascularization, Satyan Kalkunte

Open Access Dissertations

Dysregulated uteroplacental interaction and vascular remodeling are thought to be associated with the molecular events in preeclampsia. Due to the co-onset of maternal symptoms and placental pathology, we hypothesize that serum from preeclampsia patients could provide a "blueprint" of etiologic factors. To substantiate the hypothesis, a novel three dimensional dual cell culture in vitro model, a mimic of the vascular remodeling events during pregnancy, was established. In this model, unlike term trophoblasts, first trimester trophoblasts engage in a dynamic cross-talk and synchronize with the endothelial cells in a capillary network. Mechanistic studies indicate that poor expression of VEGF C and …

The Drift: Rethinking The Affective Dynamics Of Adaptation, John Hodgkins

Open Access Dissertations

The Drift effects a deeper understanding of the dynamic relationship between literature and cinema by articulating an "affective turn" for adaptation studies, a field whose traditional focus has been the critical castigation of filmic adaptations based on canonical plays or novels. Specifically, this project draws on theorists such as Gilles Deleuze, Brian Massumi, and Marco Abel to re-conceive literary and cinematic texts as spatio-temporal engines generating and disseminating affect, and the adaptive process as a drifting of those intensities from one medium to another. By conceptualizing adaptation in this manner, this study steers clear of the chimerical notion of fidelity …

Using Passive Samplers To Measure The Bioavailability And Transport Of Sedimentary Organic Contaminants, Carey L. Friedman

Open Access Dissertations

Polyethylene (PE) sampler uptake was compared to polychaete uptake to assess bioavailability of polychlorinated biphenyls (PCBs) from resuspended sediments in the laboratory. Disequilibrium-corrected PE were found to take up PCBs in nearly a 1:1 ratio with polychaete lipid (r2 = 0.88), demonstrating that PE samplers are good biomimetic tools in laboratory exposure tests. When dissolved concentrations were calculated based on equilibrium partitioning from both PE and lipid, PE were found to overestimate biota exposure by 3.6 times on average. PE samplers and polychaetes demonstrated that resuspension under varying water column redox conditions does not affect bioavailability of residual PCBs. In …

The Development Of Novel Mr Molecular Imaging Agents Towards The Visualization Of Dat, Gregory R. Naumiec

Open Access Dissertations

The facile and definitive diagnosis of disease is paramount in treating patients effectively. The ability to image the body, and more precisely the ability to image the specific site of the ailment, has become a cornerstone in medicine. Currently, most imaging technologies focus on macroscopic physical, physiological, or metabolic changes rather than identifying specific molecular events that are responsible for disease. Magnetic resonance imaging (MRI) is a non-radioactive and high spatial resolution diagnostic technique capable of both anatomical and molecular imaging. Paramagnetic complexes, such as gadolinium, can be used as MRI contrast agents because their unpaired electrons increase the relaxivity …

Free Energy Changes In Water Clusters, Glen L. Holden

Open Access Dissertations

Free energy changes and other thermodynamic properties have been determined for classical TIP4P water clusters for aggregrate sizes 2 ≤ n ≤ 20 using Monte Carlo methods. The pairwise monomer interactions (PMI) are represented by Lennard-Jones and Coulombic potentials and the free energies, enthalpies and entropies are calculated as a function of temperature and cluster size. Temperature dependent heat capacity curves have provided the diagnostic for the observed phase changes in the processes considered. By examining the fine structure in the free energy changes as a function of cluster size, processes n=7 and n=11 have been found to be particularly …

A Polymorphism Near Igf1 Is Associated With Body Composition And Muscle Function In Women From The Health, Aging, And Body Composition Study, Matthew C. Kostek, Joseph M. Devaney, Heather Gordish-Dressman, Tamara B. Harris, Paul D. Thompson, Priscilla M. Clarkson, Theodore J. Angelopoulos, Paul M. Gordon, Niall M. Moyna, Linda S. Pescatello, Paul S. Visich, Robert F. Zoeller, Richard L. Seip, Melissa Garcia, Rongling Li, Joseph M. Zmuda, Matthew J. Delmonico, Alka Kanaya, Eric P. Hoffman

Kinesiology Faculty Publications

Previous studies have reported associations of polymorphisms in the IGF1 gene with phenotypes of body composition (BC). The purpose of this study was to identify phenotypes of BC and physical function that were associated with the IGF1 promoter polymorphism (rs35767, −C1245T). Subjects from the Health, Aging, and Body Composition Study, white males and females (n = 925/836) and black males and females (533/705) aged 70–79 years were genotyped for the polymorphism. Phenotypes of muscle size and function, bone mineral density, and BC were analyzed for associations with this polymorphism. To validate and compare these findings, a cohort of young …

Physiological And Molecular Mechanisms Of Salt Stress Tolerance In Festuca Rubra And Lolium Perenne, Sanalkumar Krishnan

Open Access Dissertations

The present study was conducted to identify the physiological and molecular mechanisms involved in the salt tolerance of Festuca rubra ssp rubra and Lolium perenne. The salt tolerance levels of 36 Festuca accessions and 52 Lolium perenne accessions were evaluated in the greenhouse under 5000, 7500, 10000, 12500 and 15000 ppm NaCl concentrations. The study identified PI 595057 and PI 632525 as salt tolerant and sensitive Festuca rubra accessions. PI 632542, PI 636644 and PI 618999 were found to be the most salt tolerant L. perenne accessions while PI 610932, PI 619002, PI 610924 and PI 632474 were the most …

Farnesoid X Receptor Modulation By Systematic Ligands Of Translocator Protein (18kda), Linnea Elsa Anderson

Open Access Master's Theses

The synthesis of bile acids is the major biological mechanism for cholesterol removal in the human body. Strict regulation of both cholesterol and bile acid levels is necessary to maintain a healthy balance and to prevent health problems. Bile acids are natural ligands for famesoid x receptor (FXR), a nuclear receptor that controls gene expression for multiple proteins involved in maintenance of bile acid homeostasis. Many endogenous and exogenous chemical ligands have been found to activate FXR; chenodeoxycholic acid (CDCA) is the most well characterized endogenous ligand. This study identifies a synthetic indole-acetamide, FGIN-1-27, as a new FXR agonist. FGIN-1-27 …

Remote Siting And Plant Cost Of A Sofc Power Plant Fed By A Mihb In An Extended Deployable Coast Guard Ice Breaker, Elizabeth Newton

Open Access Master's Theses

In today's world two of the biggest issues are the environment and the economy. Solid Oxide Fuel Cells (SOFC) with a Metal Hydride bed is the most effective and environmentally friendly source of power. The use of hydrogen as a fuel source cuts down on the use of gasoline/diesel and the carbon emissions are little to none. The United States Coast Guard is interested in the idea of implementing a more environmentally and economically friendly system on their cutters.

Methods used to develop this thesis were based upon the USCGC HEALY (WAGB-20), the Coast Guard's largest ship, was used as …

In-Situ Feeding In The Northern Krill, Meganyctiphanes Norvegica: A Dna Analysis Of Gut Contents, Alison Cleary

Open Access Master's Theses

The northern krill, Meganyctiphanes norvegica, is an important member of North Atlantic shelf ecosystems, serving both as prey for whales, fish and seabirds, and as a predator on phytoplankton and other zooplankton. However, understanding in-situ krill feeding is technically challenging; incubations may not be representative of krill feeding in-situ, while biomarkers and microscopic examination of gut contents suffer from limited prey type resolution and have a limited range of detectible prey. Analyzing DNA in gut contents may offer insight into M norvegica feeding in-situ unobtainable using other methodologies. The major technical difficulty in using DNA as a marker …

Global Behavior Of Difference Equations, Ann M. Brett

Open Access Dissertations

In my first manuscript, I investigate the global stability character of the equilibrium points and the period-two solutions of [special characters omitted] with positive parameters and nonnegative initial conditions. I show that every solution of the equation in the title converges to either the zero equilibrium, the positive equilibrium or the period-two solution, for all values of parameters outside of a specific set defined in the paper. In the case when the equilibrium points and period-two solution coexist I give a precise description of the basins of attraction of all points. My results give an affirmative answer to Conjecture 9.5.6 …

Antagonism Of Bacterial Cell To Cell Signalling By Metabolites Of Marine Gram-Positive Bacteria, Margaret E. Teasdale

Open Access Dissertations

A form of communication in bacteria called quorum sensing (QS) regulates both microbial biofilm development and pathogenesis. QS is a process by which bacteria take a census of their numbers and regulate specific phenotypic expression using small signaling molecules called autoinducers. Interference with QS has been identified as a potentially novel therapeutic approach to the treatment of bacterial infections. This attenuation of the bacterial community prevents the successful establishment of an infection. The second chapter discusses the isolation of causative agents of bioluminescence inhibition in Vibrio harveyi. Bioassay-guided fractionation lead to the isolation of two arylethylamides from isolate C42, a …

Drug Safety Issues Focusing On Liver And Pancreas Toxicity, Thamir M. Alshammari

Open Access Dissertations

Background: Medications benefit people with diseases and medical conditions, improving many patients' lives and in some cases significantly increasing their quality of life. Despite these great benefits, medications can lead to serious adverse effects. Adverse drug reactions (ADRs) are the 4^th leading cause of death, greater than major killers including pulmonary diseases, diabetes and automobile death. Not all medication groups have the same incidence in inducing diseases. Anti-infective agents - including antibacterial agents- are the most likely to induce diseases followed by cardiovascular agents and antineoplastic agents.

Objectives: Drug safety is a very important issue in patient …

The Regulation And Processing Of The Empa Metalloprotease Of Vibrio Anguillarum, Maureen Varina

Open Access Dissertations

Vibrio anguillarum is the causative agent of vibriosis, a systemic disease of fish characterized by a hemorrhagic septicemia that results in high mortalities. EmpA has been identified as a virulence factor during infection of the GI tract of juvenile Atlantic salmon. EmpA activity is dependent on successful secretion and processing of the nascent protein to an active mature protease. This study was conducted to identify and characterize the gene(s) involved in the processing mechanism of the EmpA protein. Pro-EmpA is secreted out of the cell and is activated by the cleavage of a ∼10-kDa propeptide. It has been hypothesized that …

Physiology And Behavior Of The Jumbo Squid Dosidicus Gigas, Lloyd A. Trueblood

Open Access Dissertations

Dosidicus gigas is a large, epipelagic squid known to vertically migrate, spending night on the surface, and descending during the day into the oxygen minimum layer (OML). This dissertation seeks to examine physiological and behavioral adaptations of D. gigas to the environment in which it dwells. Life in the open ocean is unique in that there is little physical refuge. In order to capture prey in this environment, many pelagic fishes engage at high relative swimming speeds attempting to strike before being detected. This requires high metabolic rates and increasing anaerobic potential with increasing body size to overcome drag. I …

The Puzzle Of Problem-Solving Efficacy: Understanding Anxiety Among Urban Children Coping With Asthma-Related And Life Stress, Kara Klein Murdock, Carolyn Greene, Sue K. Adams, William Hartmann, Sally Bittinger, Kelly Will

Human Development and Family Science Faculty Publications

Children with asthma living in urban environments are at risk for experiencing anxiety by virtue of both social context and health-related stressors. Although the use of active coping strategies is generally associated with more optimal psychosocial functioning, there is evidence that active coping is less helpful in response to uncontrollable or severe stress. Expectations that one can fix a problem that is uncontrollable or insurmountable may create distress. Problem-solving efficacy was examined as a moderator of the association between stress and anxiety among children residing in inner-city neighborhoods. It was hypothesized that children's perceptions of high problem-solving efficacy would exacerbate …

Red Algae Lose Key Mitochondrial Genes In Response To Becoming Parasitic, Lillian Hancock, Lynda Goff, Christopher E. Lane

Biological Sciences Faculty Publications

Red algal parasites are unusual because the vast majority of them parasitize species with which they share a recent common ancestor. This strategy has earned them the name “adelphoparasites,” from the Greek, adelpho, meaning “kin.” Intracellular adelphoparasites are very rare in nature, yet have independently evolved hundreds of times among the floridiophyte red algae. Much is known about the life history and infection cycle of these parasites but nearly nothing in known about their genomes. We sequenced the mitochondrial genomes of the free-living Gracilariopsis andersonii and its closely related parasite Gracilariophila oryzoides to determine what effect a parasitic lifestyle has …

Shark Scavenging Behavior In The Presence Of Competition, Shannon P. Gerry, Andrea J. Scott

Biological Sciences Faculty Publications

The distribution of organisms within a community can often be determined by the degree of plasticity or degree of specialization of resource acquisition. Resource acquisition is often based on the morphology of an organism, behavior, or a combination of both. Performance tests of feeding can identify the possible interactions that allow one species to better exploit a prey item. Scavenging behaviors in the presence or absence of a competitor were investigated by quantifying prey selection in a trophic generalist, spiny dogfish Squalus acanthias, and a trophic specialist, smooth-hounds Mustelus canis, in order to determine if each shark scavenged …

Critical Oxygen Levels And Metabolic Suppression In Oceanic Oxygen Minimum Zones, Brad A. Seibel

Biological Sciences Faculty Publications

The survival of oceanic organisms in oxygen minimum zones (OMZs) depends on their total oxygen demand and the capacities for oxygen extraction and transport, anaerobic ATP production and metabolic suppression. Anaerobic metabolism and metabolic suppression are required for daytime forays into the most extreme OMZs. Critical oxygen partial pressures are, within a range, evolved to match the minimum oxygen level to which a species is exposed. This fact demands that low oxygen habitats be defined by the biological response to low oxygen rather than by some arbitrary oxygen concentration. A broad comparative analysis of oxygen tolerance facilitates the identification of …

Spatial And Temporal Variation In Otolith Chemistry For Tautog (Tautoga Onitis) In Narragansett Bay And Rhode Island Coastal Ponds, Ivan Mateo, Edward G. Durbin, David A. Bengtson, Richard Kingsley, Peter K. Swart, Daisy Durant

Fisheries, Animal and Veterinary Sciences Faculty Publications

The elemental composition of otoliths may provide valuable information for establishing connectivity between fish nursery grounds and adult fish populations. Concentrations of Rb, Mg, Ca, Mn, Sr, Na, K, Sr, Pb, and Ba were determined by using solution-based inductively coupled plasma mass spectrometry in otoliths of young-of-the year tautog (Tautoga onitis) captured in nursery areas along the Rhode Island coast during two consecutive years. Stable oxygen (δ¹⁸O) and carbon (δ¹³C) isotopic ratios in young-of-the year otoliths were also analyzed with isotope ratio mass spectrometry. Chemical signatures differed significantly among the distinct nurseries within Narragansett …

Tracking The Oxidative Kinetics Of Carbohydrates, Amino Acids And Fatty Acids In The House Sparrow Using Exhaled 13Co2, Marshall D. Mccue, O. Sivan, Scott R. Mcwilliams, B. Pinshow

Natural Resources Science Faculty Publications

Clinicians commonly measure the ¹³CO₂ in exhaled breath samples following administration of a metabolic tracer (breath testing) to diagnose certain infections and metabolic disorders. We believe that breath testing can become a powerful tool to investigate novel questions about the influence of ecological and physiological factors on the oxidative fates of exogenous nutrients. Here we examined several predictions regarding the oxidative kinetics of specific carbohydrates, amino acids and fatty acids in a dietary generalist, the house sparrow (Passer domesticus). After administering postprandial birds with 20 mg of one of seven ¹³C-labeled tracers, we measured rates …

Emerging Vaccine Informatics, Yongqun He, Rino Rappuoli, Anne S. De Groot, Robert T. Chen

Institute for Immunology and Informatics Faculty Publications

Vaccine informatics is an emerging research area that focuses on development and applications of bioinformatics methods that can be used to facilitate every aspect of the preclinical, clinical, and postlicensure vaccine enterprises. Many immunoinformatics algorithms and resources have been developed to predict T- and B-cell immune epitopes for epitope vaccine development and protective immunity analysis. Vaccine protein candidates are predictable in silico from genome sequences using reverse vaccinology. Systematic transcriptomics and proteomics gene expression analyses facilitate rational vaccine design and identification of gene responses that are correlates of protection in vivo. Mathematical simulations have been used to model host-pathogen interactions …

Seasonal Distribution Of Dissolved Inorganic Carbon And Net Community Production On The Bering Sea Shelf, J. T. Mathis, J. N. Cross, N. R. Bates, S. Bradley Moran, M. W. Lomas, C. W. Mordy, P. J. Stabeno

Graduate School of Oceanography Faculty Publications

In order to assess the current state of net community production (NCP) in the southeastern Bering Sea, we measured the spatio-temporal distribution and controls on dissolved inorganic carbon (DIC) concentrations in spring and summer of 2008 across six shelf domains defined by differing biogeochemical characteristics. DIC concentrations were tightly coupled to salinity in spring and ranged from ~1900 μmoles kg⁻¹ over the inner shelf to ~2400 μmoles kg⁻¹ in the deeper waters of the Bering Sea. In summer, DIC concentrations were lower due to dilution from sea ice melt, terrestrial inputs, and primary production. Concentrations were found to …

Pah Mineralization And Bacterial Organotolerance In Surface Sediments Of The Charleston Harbor Estuary, Michael T. Montgomery, Thomas J. Boyd, Christopher L. Osburn, David C. Smith

Graduate School of Oceanography Faculty Publications

Semi-volatile organic compounds (SVOCs) in estuarine waters can adversely affect biota but watershed sources can be difficult to identify because these compounds are transient. Natural bacterial assemblages may respond to chronic, episodic exposure to SVOCs through selection of more organotolerant bacterial communities. We measured bacterial production, organotolerance and polycyclic aromatic hydrocarbon (PAH) mineralization in Charleston Harbor and compared surface sediment from stations near a known, permitted SVOC outfall (pulp mill effluent) to that from more pristine stations. Naphthalene additions inhibited an average of 77% of bacterial metabolism in sediments from the more pristine site (Wando River). Production in sediments nearest …

Toward Linking Ocean Models To Fish Population Dynamics, Lawrence J. Buckley, Lauren B. Buckley

Graduate School of Oceanography Faculty Publications

We discuss Lehodey et al.’s (2009) approach to linking ocean models to population dynamics of large marine predators, consider its benefits and limitations, and outline alternative approaches. We advocate a middle ground between Lehodey et al.’s pragmatic, phenomenological approach and the detailed mechanistic approach common to most individual based models. These models should capture the essence of critical processes controlling recruitment and dynamic density-dependent and environmental effects.

Coastal New England Pilot Study To Determine Fossil And Biogenic Formaldehyde Source Contributions Using Radiocarbon, Haiwei Shen, Brian G. Heikes, John T. Merrill, Ann P. Mcnichol, Li Xu

Graduate School of Oceanography Faculty Publications

Compound specific radiocarbon analyses of atmospheric formaldehyde are reported as fraction modern (Fm) for a limited number of winter and summer air samples collected in coastal southern New England in 2007. The 11 of 13 samples with Fm < 0.2 were collected under the influence of the semipermanent Bermuda high‐pressure system with transport from the Washington, D. C., to New York City urban corridor. The two samples with Fm > 0.2 (max ∼ 0.35) were collected on days with strong northwesterly flow and the least urban impact. The Fm data were combined with VOC observations from the Rhode Island Department of Environmental Management, estimates of oxygenated VOC (OVOC), and back trajectories to interpret the relative contributions of biogenic and fossil carbon sources. It is argued that CH₂O sources were dominated …