Digital Commons Network^™

Epitope-Based Vaccination Against Pneumonic Tularemia, Stephen H. Gregory, Stephanie Mott, Jennifer Phung, Jinhee Lee, Leonard Moise, Julie A. Mcmurry, William Martin, Anne S. De Groot

Institute for Immunology and Informatics Faculty Publications

Francisella tularensis, the etiological agent of tularemia, is one of the most infectious bacterial pathogens known. No vaccine is currently approved for public use. Previously, we identified epitopes recognized specifically by T cells obtained from individuals following infection with F. tularensis. Here, we report that a subunit vaccine constructed based upon these epitopes elicited protective immunity in “humanized” HLA class II (DRB1*0401) transgenic mice. Vaccinated mice challenged intratracheally with a lethal dose of F. tularensis (Live Vaccine Strain) exhibited a rapid increase in pro-inflammatory cytokine production and diminished number of organisms in the lungs, and a concurrent increased …

Influence Of Vitamin E On Innate And Humoral Components Of The Immune System Of Pregnant Ewes And Their Lambs, Saritha Anugu

Open Access Master's Theses

The effect of parenteral administration of vitamin E during the pregnancy and lactation period of ewes and their lambs on innate and humoral components of the immune system was investigated in a 3 part study. 1.) Pregnant/Lactating ewes: Fifteen pregnant Dorset sheep were supplemented with vitamin E (30 IU d-α-tocopherol /Kg body weight (BW), E, n=l0) or placebo (emulsified base, P, n=5) from the last trimester of gestation through weaning. Blood and colostrum were analyzed every 2 wk for α-tocopherol, selenium, glutathione peroxidase activity, lysozyme activity, total IgG and IgG antibodies against tetanus toxoid. 2.) Lambs (0-8wks): Lambs born to …

Observer Bias And The Detection Of Low‐Density Populations, Matthew C. Fitzpatrick, Evan L. Preisser, Aaron M. Ellison, Joseph S. Elkinton

Biological Sciences Faculty Publications

Monitoring programs increasingly are used to document the spread of invasive species in the hope of detecting and eradicating low‐density infestations before they become established. However, interobserver variation in the detection and correct identification of low‐density populations of invasive species remains largely unexplored. In this study, we compare the abilities of volunteer and experienced individuals to detect low‐density populations of an actively spreading invasive species, and we explore how interobserver variation can bias estimates of the proportion of sites infested derived from occupancy models that allow for both false negative and false positive (misclassification) errors. We found that experienced individuals …

A Method For Individualizing The Prediction Of Immunogenicity Of Protein Vaccines And Biologic Therapeutics: Individualized T Cell Epitope Measure (Item), Tobias Cohen, Leonard Moise, Matthew Ardito, William Martin, Anne S. De Groot

Institute for Immunology and Informatics Faculty Publications

The promise of pharmacogenomics depends on advancing predictive medicine. To address this need in the area of immunology, we developed the individualized T cell epitope measure (iTEM) tool to estimate an individual's T cell response to a protein antigen based on HLA binding predictions. In this study, we validated prospective iTEM predictions using data from in vitro and in vivo studies. We used a mathematical formula that converts DRB1 allele binding predictions generated by EpiMatrix, an epitope-mapping tool, into an allele-specific scoring system. We then demonstrated that iTEM can be used to define an HLA binding threshold above which immune …

Construction And Sequence Sampling Of Deep-Coverage Large-Insect Bac Libraries For Three Model Lepidopteran Species, Chengcang Wu, Dina Proestou, Dorothy Carter, Erica Nicholson, Filippe Santos, Shaying Zhao, Hong-Bin Zhang, Marian R. Goldsmith

Biological Sciences Faculty Publications

Background: Manduca sexta, Heliothis virescens, and Heliconius erato represent three widely-used insect model species for genomic and fundamental studies in Lepidoptera. Large-insert BAC libraries of these insects are critical resources for many molecular studies, including physical mapping and genome sequencing, but not available to date.

Results: We report the construction and characterization of six large-insert BAC libraries for the three species and sampling sequence analysis of the genomes. The six BAC libraries were constructed with two restriction enzymes, two libraries for each species, and each has an average clone insert size ranging from 152–175 kb. We estimated that …

An Integrated Genetic Linkage Map For Silkworms With Three Parental Combinations And Its Application To The Mapping Of Single Genes And Qtl, Shuai Zhan, Jianhua Huang, Qiuhong Guo, Yunpo Zhao, Weihua Li, Xuexia Miao, Marian R. Goldsmith, Muwang Li, Yongping Huang

Biological Sciences Faculty Publications

Background: Bombyx mori, the domesticated silkworm, is a well-studied model insect with great economic and scientific significance. Although more than 400 mutations have been described in silkworms, most have not been identified, especially those affecting economically-important traits. Simple sequence repeats (SSRs) are effective and economical tools for mapping traits and genetic improvement. The current SSR linkage map is of low density and contains few polymorphisms. The purpose of this work was to develop a dense and informative linkage map that would assist in the preliminary mapping and dissection of quantitative trait loci (QTL) in a variety of silkworm strains. …

Intrusion Of Warm Bering/Chukchi Waters Onto The Shelf In The Western Beaufort Sea, Stephen R. Okkonen, Carin J. Ashjian, Robert G. Campbell, Wieslaw Maslowski, Jaclyn L. Clement-Kinney, Rachel Potter

Graduate School of Oceanography Faculty Publications

Wind‐driven changes in the path of warm Bering/Chukchi waters carried by the Alaska Coastal Current (ACC) through Barrow Canyon during late summer are described from high‐resolution hydrography, acoustic Doppler current profiler–measured currents, and satellite‐measured sea surface temperature imagery acquired from mid‐August to mid‐September 2005–2007 near Barrow, Alaska. Numerical simulations are used to provide a multidecadal context for these observational data. Four generalized wind regimes and associated circulation states are identified. When winds are from the east or east‐southeast, the ACC jet tends to be relatively strong and flows adjacent to the shelf break along the southern flank of Barrow Canyon. …

Eutrophication And The Macroscope, Scott W. Nixon

Graduate School of Oceanography Faculty Publications

It is important to view eutrophication as an increase in the supply of organic matter to an ecosystem rather than as a simple problem of nutrient pollution. This emphasizes that eutrophication is a fundamental change in the energetic base that may propagate through the system in various ways and produce a variety of changes. Some of these changes may be desirable (e.g., increased secondary production) and some may not (e.g., hypoxia). Defining eutrophication in terms of changing nutrient concentrations or chlorophyll levels or species composition confuses symptoms with the underlying phenomenon. While nutrient enrichment is the most common cause of …

The Invasive Colonial Ascidian Didemnum Vexillum On Georges Bank - Ecological Effects And Genetic Identification, Nicole L. Lengyel, Jeremy S. Collie, Page C. Valentine

Graduate School of Oceanography Faculty Publications

Since the discovery of the invasive colonial tunicate Didemnum vexillum Kott, 2002 on Georges Bank in 2002, research has focused on investigating the spread of the tunicate invasion, evaluating its potential impact on the benthic community, identifying it to species level, and determining its region of origin. The percent cover of Didemnum vexillum, measured from bottom photographs, ranges from 0-100% in individual photos and between 0-79% when averaged within photo transects. Individual photos represent an area of the seabed measuring ~ 0.39 m2 while photo transects range from ~ 700-1000 meters in length. Hydroids are the second most abundant …

Nvods And The Development Of Opendap, Peter C. Cornillon, Jennifer Adams, M. Benno Blumenthal, Eric Chassignet, Ethan Davis, Steve Hankin, James Kinter, Roy Mendelssohn, James T. Potemra, Ashwanth Srinivasan, Joseph Sirott

Graduate School of Oceanography Faculty Publications

The National Oceanographic Partnership Program (NOPP) funded a project to develop the foundation for a National Virtual Ocean Data System (NVODS) that has resulted in a robust data access framework for the exchange of oceanographic data (the Open source Project for a Network Data Access Protocol, or OPeNDAP) and a broad community of ocean data providers that remains vigorous and growing five years after NOPP funding ended. The project produced a number of “lessons learned” related to the design and implementation of distributed data systems that can inform other related efforts. These lessons are presented along with a brief overview …

Us Godae: Global Ocean Prediction With The Hybrid Coordinate Ocean Model (Hycom), Eric P. Chassignet, Harley E. Hurlburt, E. Joseph Metzger, Ole Martin Smedstad, James A. Cummings, George R. Halliwell, Rainer Bleck, Remy Baraille, Alan J. Wallcraft, Carlos Lozano, Hendrik L. Tolman, Ashwanth Srinivasan, Steven Hankin, Peter C. Cornillon, Robert Weisberg, Alexander Barth, Ruoying He, Francisco Werner, John Wilkin

Graduate School of Oceanography Faculty Publications

During the past five to ten years, a broad partnership of institutions under NOPP sponsorship has collaborated in developing and demonstrating the performance and application of eddy-resolving, real-time global- and basin-scale ocean prediction systems using the HYbrid Coordinate Ocean Model (HYCOM). The partnership represents a broad spectrum of the oceanographic community, bringing together academia, federal agencies, and industry/commercial entities, and spanning modeling, data assimilation, data management and serving, observational capabilities, and application of HYCOM prediction system outputs. In addition to providing real-time, eddy-resolving global- and basin-scale ocean prediction systems for the US Navy and NOAA, this project also offered an …

Turbulent Supply Of Nutrients To Phytoplankton At The New England Shelf Break Front, Burke Hales, Dave Hebert, John Marra

Graduate School of Oceanography Faculty Publications

We present observations from deployments of a microstructure turbulence instrument (the Towed Microstructure and Auxiliary Sensor Instrument) aboard a pumping profiling vehicle (the Lamont Pumping SeaSoar) towed behind a research vessel at the New England shelf break front in August 2002. From these we determined coincident fine‐scale vertical eddy diffusivity and gradients of nitrate, phosphate, and silicate on several transects spanning the front. We then quantified vertical turbulent nutrient fluxes through the base of the euphotic zone (defined as the 1% light level), the base of the density transition zone, maximum nutrient gradients (the nutriclines), and the depth of maximum …

Oxygen Penetration Deep Into The Sediment Of The South Pacific Gyre, J. P. Fischer, T. G. Ferdelman, Steven D'Hondt, H. Røy, F. Wenzhöfer

Graduate School of Oceanography Faculty Publications

Sediment oxygen concentration profiles and benthic microbial oxygen consumption rates were investigated during an IODP site survey in the South Pacific Gyre. Primary production, particle fluxes and sedimentation rates are extremely low in this ultra-oligotrophic oceanic region. We derived O₂ consumption rates from vertical oxygen profiles in sediments obtained on different spatial scales ex situ (in piston cores and multi cores), and in situ (using a benthic lander equipped with a microelectrode profiler). Along a transect in the area 24 to 46° S and 165 to 117° W, cores from 10 out of 11 sites were oxygenated over their …

Anthropogenic Enhancement Of Egypt's Mediterranean Fishery, Autumn J. Oczkowski, Scott W. Nixon, Stephen L. Granger, Abdel-Fattah M. El-Sayed, Richard A. Mckinney

Graduate School of Oceanography Faculty Publications

The highly productive coastal Mediterranean fishery off the Nile River delta collapsed after the completion of the Aswan High Dam in 1965. But the fishery has been recovering dramatically since the mid-1980s, coincident with large increases in fertilizer application and sewage discharge in Egypt. We use stable isotopes of nitrogen (δ¹⁵N) to demonstrate that 60%–100% of the current fishery production may be from primary production stimulated by nutrients from fertilizer and sewage runoff. Although the establishment of the dam put Egypt in an ideal position to observe the impact of rapid increases in nutrient loading on coastal productivity …

Musical Chairs Mortality Functions: Density-Dependent Deaths Caused By Competition For Unguarded Refuges, Jameal F. Samhouri, Richard R. Vance, Graham E. Forrester, Mark A. Steele

Natural Resources Science Faculty Publications

Structural refuges within which prey can escape from predators can be an important limiting resource for the prey. In a manner that resembles the childhood game of musical chairs, many prey species rapidly retreat to shared, unguarded refuges whenever a predator threatens, and only when refuges are relatively abundant do all prey individuals actually escape. The key feature of this process is that the per capita prey mortality rate depends on the ratio of prey individuals to refuges. We introduce a new class of mortality functions with this feature and then demonstrate statistically that they describe field mortality data from …

Evaluation Of Mixed-Effects Modeling Techniques For The Analysis Of Longitudinal Data Collected From Pk-Pd And Efficacy Clinical Trials, Rajesh Narwal

Open Access Dissertations

Linear and non-linear mixed effects modeling techniques are of great importance for the analysis of repeated measure data collected from various pharmacokinetic (PK)-pharmacodynamic (PD) and efficacy clinical trial during drug development. Monte-Carlo simulations were used to evaluate and compare the properties of mixed-model for repeated measure (MMRM) to fixed-effects ANOVA. The methods were compared using three different response profiles, four types of correlation structures (unstructured, compound symmetry, autoregressive and Toeplitz) and three types of missing mechanisms (MCAR (missing completely at random), MAR (missing at random) and MNAR (missing not at random). The MMRM methods adequately controlled type-I error and provided …

A Biochemical Study On The Regulation Of The Src And Fgfr Family Of Protein Tyrosine Kinases, David J. Kemble

Open Access Dissertations

The Src and FGFR family of protein tyrosine kinases (PTKs) are key mammalian enzymes in signal transduction. Regulating their enzymatic activity is imperative and disrupting this regulation can lead to devastating outcomes, including cancer. Our primary focus is to dissect the structure-function relationship that guides the regulation of PTKs. In this study we used site directed mutageneis, bacterial expression, and kinetic analysis to investigate how Src and FGFR PTKS is regulated by Reactive Oxygen Species (ROS) and autophosphorylation. Accumulating evidence suggests that protein tyrosine phosphorylation-based pathways are under the regulation of Reactive Oxygen Species (ROS). Although protein tyrosine phosphatases are …

Assessing Essential Fish Habitat And Connectivity Using Otolith Chemistry And Growth Of Temperate And Tropical Fish, Ivan Mateo

Open Access Dissertations

Many shallow water habitats are vulnerable to loss or deterioration from a variety of processes, including erosion, pollution, and urbanization. Conservation of these 'nursery' habitats protects an important source of young individuals to offshore adult fish populations. The first part of this dissertation investigates whether young-of-the year (YOY) tautog Tautoga onitis, French grunt Haemulon flavolineatum, and schoolmaster Lutjanus apodus from different nursery habitats can be distinguished by chemical signatures in their otoliths. Concentrations of ten elements, as well as stable oxygen (18O) and carbon (13C) isotopes, were determined in otoliths. Chemical signatures differed significantly among fish from different nurseries (MANOVA …

Bio-Optical And Remote Sensing Investigation Of Phytoplankton Community Size Structure, Colleen Beckmann Mouw

Open Access Dissertations

This dissertation examines the optical and ecological role of phytoplankton cell size in the context of chlorophyll concentration and the presence of other optically active constituents. The first study isolates the effect phytoplankton cell size has on varying spectral remote sensing reflectance (Rrs(λ)) through the use of optical and radiative transfer models that are linked in an off-line diagnostic calculation to a global monthly numerical model. Two separate simulations of the optical model were run with cell size-dependent and cell size-independent phytoplankton absorption with all other optical constituents treated identically. The consideration of size-varying phytoplankton absorption resulted in more realistic …

Conservation Genetics Of Association Of Zoos And Aquariums And Wild Matshie's Tree Kangaroo (Dendrolagus Matschiei) From Huon Peninsula, Papua New Guinea, Thomas Joseph Mcgreevy Jr.

Open Access Dissertations

The Association of Zoos and Aquariums (AZA) Matschie's tree kangaroo (Dendrolagus matschiei) population is at a critical point for assessing long-term viability; they have endured a founder effect and have low mitochondrial DNA (mtDNA) diversity. The mean kinship (MK) strategy is used to preserve their genetic diversity by minimizing the overall kinship of the population; however, the MK strategy has not been evaluated in an AZA population. Wild D. matschiei is listed as endangered and genetically unique populations may warrant management as separate conservation units. My objectives were to: (i) develop molecular markers to facilitate genetic analyses, (ii) assist AZA …

Diet, Feeding Ecology, Trophic Relationships, Morphometric Condition, And Ontogeny For The Sandbar Shark, Carcharhinus Plumbeus, And Smooth Dogfish, Mustelus Canis, Within The Delaware Bay Estuary, William David Mcelroy

Open Access Dissertations

Feeding ecology and condition were examined for sandbar shark, Carcharhinus plumbeus, and smooth dogfish, Mustelus canis, in Delaware Bay. Prey quantity indicated continuous feeding by M. canis, but female sharks had significantly greater quantities of prey than males. Small sharks fed on annelids, isopods, shrimp, bivalves and crabs, and significant shifts occurred in larger sharks to a diet dominated by large crabs with some gastropods and teleosts. Limited monthly shifts were evident. These were likely influenced by changes in prey availability but also by ontogeny in small M. canis. Feeding in C. plumbeus was intermittent, with episodic consumption of large …

Interface Dosimetry For Electronic Brachytherapy Xoft Axxent Intracavitary Breast Balloon Applicators, And, Fluorescence Anisotropy Imaging Of Quantum Dots, James J. Segala

Open Access Dissertations

In this thesis two topics in biological physics are explored. These are presented as manuscripts which have been submitted to scientific journals. The first topic deals with administering radiation therapy to cancer patients using a miniature x-ray source that can be inserted through a catheter into a body cavity at the tumor site. The manuscript investigates how ionizing radiation deposits its energy for the special case where there is additional attenuating material in the path between the radiation source and patient. It was previously speculated that a global correction factor can be applied to account for the attenuating substance. However, …

Economics Of Bluefin Tuna Aquaculture In The United States, Gina Louise Shamshak

Open Access Dissertations

This research presents a bioeconomic framework for assessing the economics of offshore bluefin tuna aquaculture production by developing a dynamic stochastic adaptive bioeconomic model of such an offshore enterprise. The bioeconomic model incorporates the biological constraints of the species, the interaction of relevant economic parameters and constraints, and stochastic sources of risk to solve for the profit maximizing behavior of a farmed bluefin tuna producer. The model identifies the optimal harvest schedule for an offshore bluefin tuna farming facility that maximizes the net present value of the operation under a variety of economic, biological and regulatory conditions. This model is …

Benthic Macrofauna In Narragansett Bay, Rhode Island: An Examination Of Factors Causing Variability In Community Structure, Christopher John Calabretta

Open Access Dissertations

Benthic macrofaunal communities in the upper Narragansett Bay, Rhode Island have been sampled annually since 2000 as part of the Narragansett Bay Benthic Study (NBBS). This work explored the natural and anthropogenic drivers underlying spatial and temporal variability in benthic community structure. Spatial variability in the structure of Narragansett Bay's benthic macrofaunal communities was related to the degree of exposure to anthropogenic stress. Results suggested a progression in the structure of benthic assemblages from early successional stages in the areas of Mt. Hope Bay and Conimicut Point, to an intermediate stage at the mouth of Greenwich Bay and culminating with …

Resistance To Northern Root-Knot Nematode (Meloidygyne Hapla Chitwood) In Lettuce (Lactuca Sativa L.), Parminderjit Kaur

Open Access Dissertations

The present study was undertaken to identify lettuce gel' plasm having resistance to M. hapla. Approximately 500 Lactuca accessions were evaluated in the greenhouse for resistance to M. hapla. Six week old seedlings were inoculated with M. hapla at 5,000 eggs per plant. Twelve weeks after inoculation data were recorded on root galling and fresh root weight. The accessions with a root galling score of two or less were considered resistant to M. hapla and were screened in a second trial. Two L. sativa accessions (PI 508476 and PI 419140) and three wild Lactuca accessions, L. saligna PI 281876, L. …

A Validation Study Of The Misbehaviors Questionnaire, Racheal Taki Reavy

Open Access Dissertations

This study examined the validity of the Misbehaviors Questionnaire (MBQ), a revision of the Self Report Delinquency scale, which aims to diagnose conduct disorder (CD) and to serve as a valid measure for assessing misbehaviors. The MBQ further assesses whether each misbehavior involved the use of alcohol or marijuana, allowing for comparisons of substance-related clusters of misbehaviors. Participants were 190 incarcerated adolescents (85.8% male; average age 17 years) at a juvenile correctional facility in the Northeast. While incarcerated, they were asked about substance use and misbehaviors in the three months prior to incarceration, as well as parental, peer, and demographic …

Adolescent Gender Differences In Risk Of Alcohol Use, Jessica E. Nargiso

Open Access Dissertations

A significant amount of research has examined the complex set of ecological factors that are associated with alcohol use and abuse during adolescence. Much of this research has focused exclusively on males or failed to report differences by gender. Shifting trends towards earlier age of onset and earlier development of problems among girls highlights the need to explore these factors in both adolescent males and females. Three hundred and seventy middle school students completed self-report assessments of several ecological domains of risk (e.g., peer, family management, community) at two different time points (beginning of sixth grade, end of seventh grade). …

The Use Of Cnidarian Nematocysts By The Aeolidian Nudibranch Cratena Pilata, Sarah Fogg-Matarese

Open Access Dissertations

Nudibranchs feed on anemones and hydroid polyps. The ingested cnidarian nematocysts are stored in cerata, dorsal extensions of the gut, and used to defend against predatation. Specialized smooth muscle sacs in the cerata, the cnidosacs, contain modified epithelial cells, the cnidophages, that hold the nematocysts. Light microscopic and behavioral studies indicate that, upon adequate stimulation, the cnidosac and cerata contract, opening the ceras tip and releasing the stored nematocysts. Ultra-thin sections revealed that the smooth muscle cells of the ceras encompass a network of caveolae and that synaptic terminals containing dense-cored and clear vesicles impinge on the muscles of the …

Exploration Of The Quality Of Three Measures For Assessing State Anxiety In Hospitalized Cardiac Patients, Kari A. Radford

Open Access Dissertations

For many years it has been documented that cardiac patients in the acute care setting experience episodic elevations in anxiety which often have a significant, negative physiological impact. The purpose of this exploratory study was to test three state anxiety short-form scales (NEWTEN - a newly created scale, Anxiety Scale - AS, and SAI-6 - short form of Spielberger's State Anxiety Inventory-SAI) for measuring state anxiety in hospitalized cardiac patients. Criteria-related validity was used to correlate each state anxiety scale with Spielberger's SAI, which is considered the gold standard and has yielded high levels of validity and reliability. The study …

Therapeutic Treatments For Children With Recurrent Abdominal Pain: A Multiple Baseline Pilot Study, Christine Barrett Sieberg

Open Access Dissertations

Chronic pain in children is a significant problem affecting about 15-20% of children (Goodman & McGrath, 1991), yet it is a neglected area in pediatric research and clinical service. Recurrent Abdominal Pain (RAP) is an example of chronic pain in children and one of the most common complaints of childhood and is associated with many adverse outcomes. Research has also identified parental anxiety and depression as potent risk factors for RAP (Garber et al., 1990). Despite the high prevalence rates of RAP, only 12 intervention studies from 1974-2006 have been conducted in this area (Spirito & Kazak, 2006). The primary …