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Surfo Technical Report No. 2005-01, Surfo

SURFO Technical Reports

The 2004 technical reports written by undergraduate students participating in the SURFO (Summer Undergraduate Research Fellowships in Oceanography) Program while at the University of Rhode Island.

Regulation Of Vibrio Anguillarum Empa Metalloprotease Expression And Its Role In Virulence, Steven M. Denkin, David R. Nelson

Cell and Molecular Biology Faculty Publications

Atlantic salmon (Salmo salar) were challenged with Vibrio anguillarum strains M93Sm and NB10 and empA null mutants M99 and NB12. Both wild types were virulent when administered by intraperitoneal (i.p.) injection or anal intubation. NB12 was avirulent via either route of infection. M99 virulence was attenuated when delivered by intubation, but fully virulent by i.p. injection. Northern blot analysis revealed empA expression in M93Sm and NB10 cells incubated in mucus, while incubation in Luria-Bertani broth plus 2% NaCl (LB20) induced empA expression only in NB10. Nucleotide differences between M93Sm and NB10 empA sequences were found in regions located …

Carbon Nutrition Of Escherichia Coli In The Mouse Intestine, Dong-Eun Chang, Darren J. Smalley, Don L. Tucker, Mary P. Leatham, Wendy E. Norris, Sarah J. Stevenson, April B. Anderson, Joe E. Grissom, David C. Laux, Paul S. Cohen, Tyrrell Conway

Cell and Molecular Biology Faculty Publications

Whole-genome expression profiling revealed Escherichia coli MG1655 genes induced by growth on mucus, conditions designed to mimic nutrient availability in the mammalian intestine. Most were nutritional genes corresponding to catabolic pathways for nutrients found in mucus. We knocked out several pathways and tested the relative fitness of the mutants for colonization of the mouse intestine in competition with their wild-type parent. We found that only mutations in sugar pathways affected colonization, not phospholipid and amino acid catabolism, not gluconeogenesis, not the tricarboxylic acid cycle, and not the pentose phosphate pathway. Gluconate appeared to be a major carbon source used by …

Inhibitors Of Protein Kinase Signaling Pathways: Emerging Therapies For Cardiovascular Disease, Thomas Force, Keisuke Kuida, Mark Namchuk, Keykavous Parang, John M. Kyriakis

Biomedical and Pharmaceutical Sciences Faculty Publications

Protein kinases are enzymes that covalently modify proteins by attaching phosphate groups (from ATP) to serine, threonine, and/or tyrosine residues. In so doing, the functional properties of the protein kinase’s substrates are modified. Protein kinases transduce signals from the cell membrane into the interior of the cell. Such signals include not only those arising from ligand–receptor interactions but also environmental perturbations such as when the membrane undergoes mechanical deformation (ie, cell stretch or shear stress). Ultimately, the activation of signaling pathways that use protein kinases often culminates in the reprogramming of gene expression through the direct regulation of transcription factors …

A Comparative Evaluation Of The Habitat Value Of Shellfish Aquaculture Gear, Submerged Aquatic Vegetation And A Non-Vegetated Seabed, Joseph Dealteris, Brian D. Kilpatrick, Robert B. Rheault

Fisheries, Animal and Veterinary Sciences Faculty Publications

The habitat value of modified rack and bag, shellfish aquaculture gear (SAG) used for the grow-out phase of the American oyster, Crassostrea virginica, submerged aquatic vegetation (SAV), Zostera marina, and a shallow nonvegetated seabed (NVSB) was comparatively evaluated over a 1-year period in Pt. Judith Pond, a tidal estuary in Southern Rhode Island. Enclosure gear was used to sample the three ecotypes, and organisms (>5 mm) were identified, enumerated, and measured to the nearest millimeter. Abundances of marine organisms and species diversity indices were used as measures of the habitat value of these ecotypes within each season. Environmental …

Glycolytic And Gluconeogenic Growth Of Escherichia Coli O157:H7 (Edl933) And E. Coli K-12 (Mg1655) In The Mouse Intestine, Regina L. Miranda, Tyrrell Conway, Mary P. Leatham, Dong Eun Chang, Wendy E. Norris, James H. Allen, Sarah J. Stevenson, David C. Laux, Paul S. Cohen

Cell and Molecular Biology Faculty Publications

Escherichia coli EDL933, an O157:H7 strain, is known to colonize the streptomycin-treated CD-1 mouse intestine by growing in intestinal mucus (E. A. Wadolkowski, J. A. Burris, and A. D. O'Brien, Infect. Immun. 58:2438-2445, 1990), but what nutrients and metabolic pathways are employed during colonization has not been determined. In this study, when the wild-type EDL933 strain was fed to mice along with an EDL933 ΔppsA ΔpckA mutant, which is unable to utilize tricarboxylic acid cycle intermediates and gluconeogenic substrates for growth, both strains colonized the mouse intestine equally well. Therefore, EDL933 utilizes a glycolytic substrate(s) for both …

Mechanical Design Of Mussell Byssus: Load Cycle And Strain Rate Dependence, Emily Carrington, John M. Gosline

Biological Sciences Faculty Publications

The ability to produce a strong byssal attachment is one key to the competitive dominance of mussels on many rocky shores. The byssus is composed of numerous extracellular collagenous threads, which in turn can be divided into proximal and distal regions that are distinct in ultrastructure and chemical composition. Our current understanding of the mechanical design of mussel byssus is largely based on quasi-static testing, where a fiber is slowly extended to failure. Mussels in nature, however, inhabit a dynamic environment where repetitive loads can be applied on short time scales. This study evaluates the mechanical properties of the threads …

Allometric Length-Weight Relationships For Benthic Prey Of Aquatic Wildlife In Coastal Marine Habitats, Richard A. Mckinney, Sarah M. Glatt, Scott R. Williams

Natural Resources Science Faculty Publications

We developed models to estimate the soft tissue content of benthic marine invertebrates that are prey for aquatic wildlife. Allometric regression models of tissue wet weight with shell length for 10 species of benthic invertebrates had r² values ranging from 0.29 for hermit crabs Pagurus longicarpus to 0.98 for green crabs Carcinus maenas. As a class, bivalves had the highest r² values (0.84) and crustaceans the lowest (0.48). Energy and nutrient content of soft tissue is also presented for the 10 benthic species. The energy content was lowest in crabs, and ranged within 2.20–4.71 kcal g^-1 dry …

A Split Model For Extraction Of Subpixel Impervious Surface Information, Yeqiao Wang, Xinsheng Zhang

Natural Resources Science Faculty Publications

This paper introduces a Subpixel Proportional Land cover Information Transformation (SPLIT) model to extract proportions of impervious surfaces in urban and suburban areas. High spatial resolution airborne Digital Multispectral Videography (DMSV) data provided subpixel information for Landsat TM data. The SPLIT model employed a Modularized Artificial Neural Network (MANN) to integrate multi-sensor remote sensing data and to extract proportions of impervious surfaces and other types of land cover within TM pixels. Through a control unit, the MANN was able to decompose a complex task into multiple subtasks by using a group of sub-networks. The SPLIT model identified spectral relations between …

Needs Assessment, Creation, And Utilization Of The Coastal Geotoolbox, Arthur Rodriguez

Open Access Master's Theses

Barrier islands are extremely dynamic landforms, and one of the most dynamic aspects of a barrier island is the beach. In an effort to document change in these environments, the National Park Service (NPS) Inventory & Monitoring Program Northeast Coast & Barrier Network (NCBN) have established a set of coastal geomorphology protocols to collect ecological indicator datasets. Two of the most important and readily available sources of data within these protocols are horizontal shoreline locations collected by global positioning systems (GPS), and general beach topography collected by lidar topographic surveys. There are several methods used to quantify the amount of …

Flexible Quota Management Using Virtual Population Units, Jungsam Lee

Open Access Dissertations

Quota management systems such as individual quotas (IQs) and individual transferable quotas (ITQs) are said to provide incentives for individual quota holders to conserve the resource voluntarily since increased stock by an individual fisherman's harvest reduction is shared by all other fishermen. To the extent that this is true if it is because quota holders expect the system to work and to be enforced. However, there is no obvious individual incentive to harvest less than the quota. Voluntary harvest reduction by one resource user is not compensated and this provides incentive for free riding under a traditional quota management system. …

Instrumentation Of The Universal Clamp And Modeling In Biochemistry, Jiang Wu

Open Access Dissertations

Instrumentation of the universal clamp. Voltage clamp has been an important method for studying current-voltage relationships across membranes of excitable cells such as neurons and muscles. The conventional voltage clamp amplifiers have been based on analog feedback controls. In this study a prototype digital voltage clamp system has been developed, which uses a digital signal processor (DSP) to implement feedback controls. The development was guided by computer simulation of both analog and digital voltage clamps that interact with a neuron model. Feasibility of the digital voltage clamp was demonstrated by its performance in an experiment comparable to that of an …

Direct Observations Of Along-Isopycnal Upwelling And Diapycnal Velocity At A Shelfbreak Front, John A. Barth, Dave Hebert, Andrew C. Dale, David S. Ullman

Graduate School of Oceanography Faculty Publications

By mapping the three-dimensional density field while simultaneously tracking a subsurface, isopycnal float, direct observations of upwelling along a shelfbreak front were made on the southern flank of Georges Bank. The thermohaline and bio-optical fields were mapped using a towed undulating vehicle, and horizontal velocity was measured with a shipboard acoustic Doppler current profiler. A subsurface isopycnal float capable of measuring diapycnal flow past the float was acoustically tracked from the ship. The float was released near the foot of the shelfbreak front (95–100-m isobath) and moved 15 km seaward as it rose from 80 to 50 m along the …

Analysis Of The Atmospheric Distribution, Sources, And Sinks Of Oxygenated Volatile Organic Chemicals Based On Measurements Over The Pacific During Trace‐P, H. B. Singh, L. J. Salas, R. B. Chatfield, E. Czech, A. Fried, J. Walega, M. J. Evans, B. S. Field, D. J. Jacob, D. Blake, Brian G. Heikes, R. Talbot, G. Sachse, J. H. Crawford, M. A. Avery, S. Sandholm, H. Fuelberg

Graduate School of Oceanography Faculty Publications

Airborne measurements of a large number of oxygenated volatile organic chemicals (OVOC) were carried out in the Pacific troposphere (0.1–12 km) in winter/spring of 2001 (24 February to 10 April). Specifically, these measurements included acetone (CH₃COCH₃), methylethyl ketone (CH₃COC₂H₅, MEK), methanol (CH₃OH), ethanol (C₂H₅OH), acetaldehyde (CH₃CHO), propionaldehyde (C₂H₅CHO), peroxyacylnitrates (PANs) (C_nH_2n+1COO₂NO₂), and organic nitrates (C_nH_2n+1ONO₂). Complementary measurements of formaldehyde (HCHO), …

Uri Undergraduate And Graduate Course Catalog 2004-2005, University Of Rhode Island

URI Course Catalogs Archive

No abstract provided.

Acoustic Sensing For Ocean Research, Bruce M. Howe, James H. Miller

Ocean Engineering Faculty Publications

Ocean observatories have the potential to examine the physical, chemical, biological, and geological parameters and processes of the ocean at time and space scales previously unexplored. Acoustics provides an efficient and cost-effective means by which these parameters and processes can be measured and information can be communicated. Integrated acoustics systems providing navigation and communications and conducting acoustic measurements in support of science applications are, in concept, analogous to the Global Positioning System, but rely on acoustics because the ocean is opaque to electromagnetic waves and transparent to sound. A series of nested systems is envisioned, from small- to regional- to …

Examining The Processes Controlling Water Column Variability In Narragansett Bay: Time Series Data And Numerical Modeling, Deanna L. Bergondo

Open Access Dissertations

Narragansett Bay is an important resource to the state of Rhode Island for recreational and commercial use. Eutrophication of coastal waters and its associated oxygen demand are of increasing concern for Narragansett Bay. This project focused on continuous in situ measurements and three-dimensional model simulations to better understand the physical, biological and chemical processes which occur in the Bay. Measurements of temperature, salinity, dissolved oxygen, pH, chlorophyll and depth were obtained to gain insight into the process that contribute to phytoplankton production and hypoxia in the Bay. Six major hypoxic events were captured during the summers of 2001 and 2002. …

Ecomorphology Of The Temperate Scleractinian Astrangia Poculata: Coral-Macroalgal Interactions In Narragansett Bay, Sean Patrick Grace

Open Access Dissertations

Corals and macroalgae often co-occur on temperate reefs, where macroalgae provide a majority of the bio-complexity and small scleractinian corals occur in low abundance. Macroalgae typically outcompete adjacent organisms for resources such as space, light, and nutrients, and one mechanism for this competitive success is abrasion. This study explores factors that may influence the interactions between corals and macroalgae, in particular macroalgal abrasion, on a temperate reef in Narragansett Bay, Rhode Island. Chapter One examines how exposure, depth and orientation influence the abundance and morphology of the coral Astrangia poculata, as well as the percent cover of macroalgae and other …

Culture Of Summer Flounder Paralichthys Dentatus: Environmental And Endocrine Synchronization Of Growth And Settlement In Larvae And Identification Of Stressors In Juveniles, Steven Gavlik

Open Access Dissertations

This dissertation addresses the variability in settlement behavior, growth and development during metamorphosis of summer flounder. There were three objectives: (1) Expand basic knowledge of hormonal and environmental factors that regulate timing of metamorphosis, (2) develop hormonal and environmental techniques that promote synchronization of metamorphic growth and settling behavior in order to eventually reduce cannibalism in juveniles, and (3) identify stressful culture practices and evaluate their long-term effects on growth in juvenile flounder. The first and second objectives were accomplished through manipulations of cortisol and thyroxine and of rearing salinity. Endogenous whole-body cortisol concentrations increased through the late larval stages, …

Predicting Condition Of Small Estuarine Systems Along The United States' Atlantic Coast, Jeffrey W. Hollister

Open Access Dissertations

Anthropogenic activities are known to degrade the ecological condition of estuaries. Also, numerous studies find links between landscape structure and estuarine condition. From these relationships, it is possible to build predictive models of estuarine condition. In this study, I examined issues of data quality, scale, and statistical approach to developing predictive models of estuarine sediment metal concentrations in the Mid-Atlantic region of the United States. I assessed the accuracy of the National Land Cover Dataset (NLCD) at multiple scales by comparing it with reference data from Rhode Island and Massachusetts. Area of developed lands, agriculture, forest and water had acceptable …

Suicide Assessment By Psychiatric Mental Health Nurses: A Phenomenographic Study, John M. Aflague

Open Access Dissertations

Suicide is the eleventh leading cause of mortality in the United States. This study explored suicide assessment by psychiatric nurses. The primary aims of this study were to gain an understanding of nurses' conceptions regarding suicide and suicide assessment, describe the strategies of suicide assessment adopted by psychiatric nurses, and contrast these to contemporary standards and practice guidelines of suicide assessment.

The research design was an inductive descriptive phenomenographic study. The nurse participants consisted of a snowball sample of six psychiatric nurses practicing in two psychiatric settings. The data were collected through participant observations of nurses' assessing patients and semi-structured …

Forensic And Biological Applications Of Vibrational Spectroscopy, Edita Botonjic

Open Access Dissertations

Determination of the age of a bloodstain can be used to establish the time when a crime was committed. As blood ages, deoxyhemoglobin (HbO 2) is converted into methemoglobin (MetHb), which is evident by the color change from red to brown. Fluctuations in temperature will cause blood to age at a non-constant rate. It has been shown that higher temperatures cause deoxyhemoglobin to oxidize more rapidly to methemoglobin. Human blood from vein and capillary vessels was used in this investigation. The samples were prepared by placing blood on various substrates such as gauze and watch glasses. Mid-IR and near-IR spectra …

Survivorship Of A Low-Grade Glioma Brain Tumor, Cynthia A. Bautista

Open Access Dissertations

Due to dramatic improvements in diagnosis, treatment options, and improved survival rates, the experience of cancer is changing. Little is known, however, about which factors facilitate positive adaptation for individuals who survive cancer. Research in the area of brain tumor survivorship is limited and provides minimal understanding of the survivor's experience. The purpose of this study was to describe the survivorship experience of adults who were one to four years posttreatment for a low-grade glioma brain tumor and to explore how family, friends, employers, and health care providers had been helpful in the transition back to life after treatment. Eight …

Potential Use Of Nitrogen-15 To Assess Nitrogen Sources And Fate In Narragansett Bay, Joaquin E. Chaves

Open Access Dissertations

Anthropogenic N inputs have been identified as the main source of N to Narragansett Bay, a relatively well-mixed estuary in the northeast coast of the United States. Despite a well constrained N budget high levels of primary production during the summer months, mostly in the form of sporadic "blooms", cannot be explained in terms of current budget estimates. Inputs from the adjacent Rhode Island Sound have been invoked as a potential source of N to account for the Bay's summer production. The dissolved inorganic nitrogen (DIN) from the Rhode Island Sound and the anthropogenic N entering the estuary through the …

Individual, Organizational, And Contextual Determinants Of Realized Strategy In Not-For-Profit Organizations, Henry T. Ulrich

Open Access Dissertations

This study addresses organizational direction form the perspective of organizational strategy. It explores the factors that influence realized strategy and especially the degree to which realized strategy is deliberate or emergent. A model is offered that proposes both direct and indirect factors as determinants of realized strategy. Specific direct and indirect factors are hypothesized and the relationships are statistically examined. The sample is composed of twenty nonprofit organizations with a primary base of operations in southern New England. Data was collected for multiple respondents within each organization representing the various levels of management. Most participating organizations were mid-sized, social service …

Preparation Of Optically Pure Anti-Diolepoxides Of 2-Fluorobenzo[A]-Pyrene And Their Dna Adducts, Tianle Yang

Open Access Dissertations

Benzo[a]pyrene (BP) is a prototypical PAH and undergoes metabolic activation in vivo to highly mutagenic/carcinogenic diol epoxide derivatives (BPDE) that bind to DNA, ultimately initiating sequence-specific mutations. Structural studies indicate that BPDE-modified DNA exist in three major conformations: base-displacement, minor-groove, and classical intercalation. The relative conformeric ratios of these structures are known to vary depending on the modified base and the base sequences surrounding the lesion site. Our long-term research goal is to investigate the sequence dependent conformational heterogeneity of BP-DNA adducts with 19F NMR technique, which then requires preparation of (+)-and (−)-anti-2-fluorobenzo[a]pyrene diol epoxides (2-FBPDE) as 19F NMR probes. …

The Economic Consequences Of Fish Habitat Conservation And Management, Harold Frank Upton

Open Access Dissertations

Economic considerations can play a critical role in decisions regarding habitat alteration and protection. Yet the Essential Fish Habitat provisions of the Magnuson-Stevens Act are silent on the role of economic analysis in efforts to identify and protect marine fish habitat. On the federal level, actions taken to amend Fishery Management Plans (FMPs) or implement other regulations governing these fisheries must meet the requirements of Federal Laws and regulations, many of which address economic concerns. Perhaps of greater importance is the consideration of changes in social welfare associated with habitat management alternatives. Economic analysis can provide decision makers with information …

Victim Empathy As A Function Of Attachment Style, Sex, Self-Esteem And Type Of Victimization, Molly Ann Hedrick

Open Access Master's Theses

The conceptualization of adult attachment styles corresponding internal working models is a useful frame when considering empathetic responses to victims. This study explored empathy for fictional victims of several types of traumas, including date and stranger rape, as a function of ideal and actual attachment style, self-esteem, and rape victim-perpetrator association. Forty male and 157 female undergraduates at a large state university completed a questionnaire packet consisting of demographic information, a self-esteem scale, an actual and an ideal relationship style measure, and a philosophies of human nature scale utilized to measure related attachment dimensions. They then read 10 trauma scenarios …

Extent And Composition Of Open Coastal Sandplain Plant Communities Of The Cape Cod National Seashore, Evan L. Gwilliam

Open Access Master's Theses

Coastal sandplain heathlands and grasslands of the northeastern United States are globally rare habitat types that support a unique assemblage of plants and animals. This habitat is rapidly disappearing due to plant succession following cessation of land use, and coastal processes. I used interpretation of historical maps, aerial photography, GIS, and analysis of field data to examine vegetation dynamics and the impact of historic land use and coastal processes on the current extent and composition of coastal sandplain plant communities found within the Cape Cod National Seashore (CCNS). Currently, one third (244 ha) of the coastal heathland and grassland habitat …

Enhancement Of Carbamzepine Solubility Using Selected Water Soluble Polymers And A Solid Dispersion Technique, Sameer Late

Open Access Master's Theses

With the recent advent of combinatorial chemistry and high throughput screening of potentially therapeutic agents, the number of poorly soluble drug candidate has risen sharply and the formulation of poorly soluble compounds for oral delivery now presents one of the most frequent and greatest challenge to formulation scientists in the pharmaceutical industry. There are certain drugs for which solubility has presented a challenge to the development of a suitable formulation for oral administration. And one of these drugs is carbamazepine. In the literature, solid dispersions have shown tremendous potential for improving drug solubility and dissolution.

In this study the main …