Digital Commons Network^™

A Dynamic Oyster Reef Bioenergetics Model: Predictions Of Secondary Production Based On Different Restoration Scenarios, Elizabeth Gomez

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

The presence of oyster reefs augments the biomass and abundance of many transient fish and crustacean species. Therefore, restoration of oyster reefs has become an increasingly common practice in coastal areas with the goal of enhancing production of transient fish. However, predicting the effect of oyster restoration on transient fish community biomass remains elusive. To address this challenge, I created a trophic bioenergetic model to understand how energy transfers in an oyster reef and assess the effects of various restoration strategies on transient fish species. The model used a set of functional groups representing organisms commonly found in an oyster …

Denitrifying Bioreactors: A Solution To Groundwater Nitrate Pollution At The Forge River?, Christine Jean Gurdon

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Denitrifying bioreactors are an approach to remediate groundwater contaminated with nitrate. Their popularity as a remediation system has increased due to their unnecessary maintenance, low cost, and longevity. While field trials on their performance have been conducted, few have been completed in a marine coastal environment. In this study, a denitrification wall was designed to be installed and monitored along the shore of a coastal environment, namely, the Forge River, New York. Prior to the design phase, a groundwater plume of elevated nitrate-nitrite concentrations needed to be identified. Groundwater nitrate-nitrite concentrations ranged from 0.01-17.68 mg/L along Riviera Drive, a road …

Advancing Numerical Prediction Of Physical And Biological Processes In Long Island Sound, Ling Liu

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

The occurrence and spread of hypoxia in coastal waters is known to depend strongly on nutrients, primary production, water column structure, wind and tidal mixing. Accurate prediction of the onset, intensity and areal extent of hypoxia remains a challenge. Previous modeling efforts have needed to ‘tune’ vertical mixing or phytoplankton respiration in order to obtain results that agree with field observations of dissolved oxygen (DO). We use a one-dimensional physical model coupled with a biogeochemical model to establish mechanistic links between factors involved in the evolution of seasonal hypoxia in western Long Island Sound. The coupled model includes bacterial dynamics, …

Net N2 Fluxes In Muddy Sediments Of Great Peconic Bay: Rates, Pathways & Controls, Stuart Waugh

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Abstract of the Dissertation NET N2 FLUXES IN MUDDY SEDIMENTS OF GREAT PECONIC BAY: RATES, PATHWAYS & CONTROLS by Stuart Waugh Doctor of Philosophy in Marine and Atmospheric Sciences Stony Brook University 2015 Depending on its form, nitrogen (N) can exert a dominant control on marine productivity and ecosystem structure. Multiple geochemical processes are involved in redox transformations of nitrogen (N) in marine sediments. In coastal benthic environments, a number of abiotic and biological environmental factors control the extent to which these processes are relevant and therefore the outcomes of sedimentary N transformations. This dissertation seeks to quantify rates of …

Radium Isotopes As Tracers Of Pore Water Dynamics In Two Long Island Salt Marsh Systems, Camilo Salazar

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

A study of pore water residence time as traced by short-lived radium (Ra) isotopes (224Ra and 223Ra) was conducted on two marsh systems in the south shore of Long Island, New York. Pore water was collected in July (summer) and November-December (winter) of 2013 at depths of 20 cm and 120 cm over three-station transects from the inner marsh to the marsh edge adjacent to a tidal channel. One of the marsh systems is the Wertheim Nationals Wildlife Refuge (NWR), from which two marshes were sampled; Wertheim 1 (W1), a restored marsh, and Wertheim 2 (W2), non-restored. The second marsh …

Marine Acoustics And Habitat Mapping In The Peconic Estuary, Ny, Michael Patrick White

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

As coastal populations grow, there is an increasing need for better spatial management of the seafloor. Multibeam backscatter data can be a powerful tool for habitat mapping and segmenting large areas of the seabed, based on similar physical characteristics. In order to increase the effectiveness of backscatter data sets, MBES data from the Peconic Estuary, NY, is reprocessed using newly developed software. These mosaics are less noisy compared to prior results. The relationship between grain size and backscatter is found to have a good correlation in the Peconic Estuary and a simple regression is used to predict mean phi size …

Chemical Aging And Cloud Condensation Nuclei Activity Of Biomass Burning Aerosol Proxies In The Presence Of Oh Radicals, Jonathan Hall Slade

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Biomass burning aerosol (BBA) can adversely impact regional and global air quality and represents a significant source of organic aerosol (OA) to the atmosphere that can affect climate. Aerosol particles can alter the transfer of radiation in earth's atmosphere directly by scattering and absorbing radiation or indirectly via cloud formation. Gas-to-particle, also termed heterogeneous, oxidation reactions can significantly alter the particle's physical and chemical properties. In turn, this can lead to the degradation of biomolecular markers for air quality-related aerosol source apportionment studies, the particles' lifetime, and modify the particles' abilities to serve as cloud condensation nuclei (CCN). However, the …

Self-Supported Pani /Wo3 Hybrid Photocatalyst For Dye Remediation, Xicheng Jia

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Polyaniline (PANI), one of the most important conducting polymers, has been studied intensely in recent years for its unique properties. Tungsten trioxide (WO3), on the other hand, is an important functional semiconductor. In this work, a hybrid mat based on PANI and WO3 was synthesized via spin coating and tested as a visible light photocatalyst. A PANI/TiO2 composite photocatalyst was made in the same way and its photocatalytic response was compared to that of PANI/WO3 and of pure WO3, respectively, under visible light for the remediation of methylene blue in water. Furthermore, the effect of salinity on the spontaneous photolysis …

Effect Of Toxicity Of Rdp In Polymer Scaffolds On Fibroblast Cell, Jae Wha Yang

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

The purpose of this thesis is to design substrates with flame retardant and clay to enhance the property of polymer and to study the effect of toxicity of a flame retardant mixed polymer, which had not been conducted in vivo. Therefore the human dermal fibroblast cells, engineered to have green fluorescent membrane (GFFB), were cultured on PS scaffolds with three different conditions: pure PS, PS-Na+-Clay and RDP-Clay. In first part of the study, the polymer samples (PS, PS-Clay and RDP-clay) that would be used as scaffolds were prepared and sterilized to use for cell culture, while testing that sterilization using …

The Dna Damage Response: P53 Regulation Of The Chk1-Suppressed Pathway And Sphingolipid Metabolism, Brittany Carroll

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

The DNA damage response (DDR) is a complex and interconnected signaling network that dictates whether a cell repairs itself and survives or is damaged beyond repair and eliminated; therefore the proteins in this network must be tightly regulated in order to ensure genomic integrity. Conversely, mutational or epigenetic inactivation of DDR components leads to genomic instability, a hallmark of cancer. Indeed there is a high frequency of DDR defects in human cancers of which mutations in the DDR effector and tumor suppressor protein p53 are the best characterized and occur in greater than 50% of all human cancers. Interestingly, a …

Functional Study Of Classical Protein Tyrosine Phosphatases In Mammary Epithelial Cells, Mathangi Ramesh

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Reversible protein tyrosine phosphorylation is critical for the dynamic regulation of protein function and is maintained by the synchronized and complementary activity of Protein Tyrosine Kinases (PTKs) and Protein Tyrosine Phosphatases (PTPs). Although considerable progress has been made in understanding the function of PTKs, the study of PTPs has lagged behind. Some PTPs have been implicated as products of oncogenes or tumor suppressors. Particularly in breast cancers driven by the oncogenic receptor tyrosine kinase ERBB2, there is evidence for PTPs playing diverse regulatory roles, suggesting that systematic analysis of PTP function could yield important insights into this field which could, …

Mechanism Of Type Iii Secretion System-Triggered Killing Of Yersinia In Macrophages, Xiaoying Wang

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

The mammalian immune system has the ability to discriminate between pathogens and innocuous microbes by detecting conserved molecular patterns. In addition to conserved microbial patterns, the mammalian immune system may recognize distinct pathogen-induced processes, the mechanism of which is poorly understood. Pathogenic Yersinia species utilize a type III secretion system (T3SS) to translocate various bacterial effectors into target cells, which aim to modify multiple host signaling pathways. Interestingly, previous studies have shown that the T3SS in Yersinia pseudotuberculosis leads to decreased survival of this bacterium in primary murine macrophages, the mechanism of which is unknown. Here, we use colony forming …

Identification Of Differential Gene Pathways In Microarray Data, Qiao Zhang

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

A gene pathway typically refers to a group of genes and small molecules that work together to control one or more cell functions. In systems biology, pathway analysis is of paramount biological importance, and recent studies revealed that malfunction of gene pathways could induce disease manifestations, such as cancer. Usually, a gene pathway consists of two components: the upstream factors, which are signaling molecules transmitting stimulus from cell surface to nucleus, and the downstream factors, which respond to cell signaling through changes of their expression levels. Although several methods have been reported for analysis of gene pathways, almost all of …

Exploring The Role Of Interferons In Adenovirus Replication And Establishment Of Persistent Infection In Normal Human Cells, Yueting Zheng

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Adenoviruses (Ad) are ubiquitous pathogens that infect a wide range of vertebrates and have been recognized in recent years as significant pathogens in immunocompromised patients. Interferons (IFNs) are cytokines that have pleiotropic effects and play important roles in innate and adaptive immunity. IFNs have broad antiviral properties and function by different mechanisms. IFNs fail to inhibit wild-type Ad replication in established cancer cell lines. In this study, I analyzed the effects of IFNs on Ad replication in normal human cells. The results demonstrated that both IFNα and IFNγ blocked wild-type Ad5 replication in primary human bronchial epithelial cells (NHBEC) and …

Food Waste And Sustainability: Quantifying Food Waste Disposal And Evaluating The Environmental Impacts Of Technologies And Policies, Krista Lee Thyberg

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

There has been growing interest in establishing food waste prevention and recovery programs throughout the United States. An interdisciplinary systems approach to sustainable food waste management was taken to explore three integrated food waste issues: 1. the quantity of residential, commercial and institutional food waste disposed in the U.S.; 2. the environmental impact of food waste treatment technologies; and, 3. approaches for sustainable waste system planning and the development of food waste management policies. The dissertation begins with a review of the history, contributing factors, impacts, and current practices regarding food waste in the U.S. and globally. The amount of …

On Using Risk-Benefit Analysis To Assess And Manage Controversial Research, Daniel Rozell

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Science research in the twenty-first century increasingly results in powerful and rapidly disseminated technologies that raise concerns over technological risk and public safety. A common recommendation for assessing and managing controversial research is to perform a quantitative risk-benefit analysis (RBA) in order to help determine an appropriate course of action. However, these recommendations lack guidelines on how to perform such an assessment. This dissertation lays out a detailed argument why a quantitative RBA should not be used as a basis for making complex policy decisions. Rather, RBA should be regarded as a tool for exploring the impacts of technology on …

Phylogenetic Systematics And Biogeography Of Lemurs From Madagascar, James Paul Herrera

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

The evolutionary mechanisms influencing biodiversity include abiotic and biotic factors, such as climate change, vicariance, ecological adaptation, and competition. I investigated evolutionary mechanisms that may have influenced the diversity of lemurs from Madagascar by testing geographic and ecological hypotheses in a phylogenetic framework. I used total-evidence methods to infer the lemur phylogeny and divergence times of extant and extinct species. I then tested macroevolutionary hypotheses about lemur biogeography based on the phylogeny to shed new light on the causes of lemur diversification. I examined macroevolution and biogeography at four geographic scales: island-wide, regions, localities, and multiple transects within localities. I …

Developing Tools For Cavin-1 Purification And Binding Studies With Caveolin-1, Safa Farjand Siddiqui

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Caveolae are nanoscale invaginations found in the plasma membrane of mammalian cells, and are implicated in numerous essential cellular communication and transport processes. They are characterized by a coat composed of caveolin and cavin proteins. Recent studies of the caveolar coat complex suggest that cavin-1 associates with caveolin-1 during caveolae biogenesis. However, it is not known how this binding occurs. Studies of the spatial and physical interactions between cavin-1 and caveolin-1 can provide valuable insights into the mechanism of caveolae generation. The goal of this study was to test two different fusion tags to purify a sufficient quantity of cavin-1, …

The Roles Of Sox2 And Canonical Wnt Signaling Pathway In Fate Specification Of Tailbud Bipotential Stem Cells, Yu-Jung Tseng

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

During vertebrate development, formation of the head -to-tail body axis is shaped by a group of unspecified cells at the caudal region of the embryo. The undifferentiated tail bud stem cells are capable of adopting mesodermal or neural cell fates as the embryo develops, but the mechanism of this patterning process remains largely unknown. Our previous studies confirm that Wnt signaling is required in tail bud stem cells to repress the neural transcription factor sox2 and induce mesodermal fate. However, it is unclear if sox2 repression at the cell-autonomous level is the critical factor required for Wnt mediated mesoderm induction. …

Comparative Morphology Of Primate Distal Phalanges: Implications For Early Primate Evolution And The Origins Of The Primate Nail, Stephanie A. Maiolino

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Human manual dexterity is strongly enhanced by the presence of flattened nails associated with well-developed apical pads. However, the presence of nails is not unique to humans; it is one of the few traits that unite all living primates. Further, the form of the keratinous structure (nail, claw, etc.) on the ends of primate digits is often considered to be a diagnostic trait of major primate clades; strepsirrhines (lemurs, lorises, and galagos) possess a grooming claw (a specialized nail or claw used to scratch and clean the fur around the head and neck) on each second pedal digit; tarsiers possess …

Bmp-2 Gene Delivery Using Electrospun Collagen/Plla Scaffold With Surface Adsorbed Transfection Complexes For Bone Formation, Xia Zhao

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Bone tissue engineering provides an alternative to bone grafting. Our laboratory previously developed two different types of electrospun scaffolds for bone tissue engineering, including a DNA containing PLGA/PELA scaffold for delivering genes and a collagen/PLLA scaffold for delivering cells. For this dissertation research, we firstly fabricated a DNA containing PLGA/PELA electrospun scaffold using the same method as previously developed, with the intent of delivering osteogenic growth factor genes for bone regeneration. However, the scaffold shrunk severely after being submerged into aqueous environment and failed to achieve high transfection efficiency in vitro. Subsequently, we used the collagen/PLLA scaffold (originally developed for …

Characterization Of Bacterial Multi-Component Regulatory Systems: Nitric Oxide, Quorum Sensing And, Takahiro B. Ueno

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Bacterial quorum sensing (QS) is an essential cell-to-cell communication system used by bacteria. Bacteria produce and detect small signaling molecules called autoinducers (AIs) to assess their surrounding bacterial population. Once the AI concentration reaches a threshold, the entire bacterial population undertakes a coordinated change in gene expression patterns. Thus, QS enables bacteria to orchestrate population-wide changes in behavior appropriate for different growth phases or environmental conditions. QS is widely spread among bacteria and regulates a wide array of biological functions that are critical for their survival. Controlled manipulation of QS may provide the means for the design of more selective …

Design, Synthesis, And Biological Evaluation Of Novel Taxoid-Based Small-Molecule Theranostic Pet/Spect Imaging Agents And Nano-Scale Asymmetric Bow-Tie Dendrimer Drug Conjugates Towards Tumor-Targeted Chemotherapy, Tao Wang

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Cancer remains the second leading cause of death in the United States. Traditional chemotherapy relies on highly potent cytotoxic agents, such as paclitaxel and docetaxel, to kill rapidly dividing cancer cells. But these drugs usually cause undesired side-effects due to lack of tumor-selectivity, and decreased efficacy against MDR cancer cell lines. Accordingly, newer generation taxoids were designed and evaluated showing several orders of magnitude greater potency than paclitaxel and docetaxel. Over the past decade, significant advancement has been made on the development of newer generation taxoids based on SAR study. As a selected example of second generation taxoid, SB-T-1214 was …

Getting To Know Siblings Of Youth With Autism Spectrum Disorder: A Model Of Risk And Resilience, Megan Elissa Tudor

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Therapy and support programs for siblings of youth with autism spectrum disorders (ASD) are on the rise, indicating a growing demand for specialized sibling services. However, current research findings remain unclear as to what exactly the needs of siblings might be and why those needs might be present. The current dissertation aims to identify what particular risk factors may lead to problematic outcomes that warrant clinical services (e.g. | emotional, behavioral, or social problems), while concurrently, examining resilience factors that may lead to positive functioning in these areas. A comprehensive family systems model was created drawing from literature related to …

Scalable End-To-End Data I/O Over Enterprise And Data-Center Networks, Yufei Ren

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Data-intensive applications in commercial cloud and scientific computing demand ultra-high-speed end-to-end data access capability between data storage and computing locations. Meanwhile, advancements in hardware systems continuously change the landscape of data centers’ core capabilities, i.e. | computing, networking, and storage. The two trends expose new research and development challenges and opportunities to bring the bare-metal capacity and performance of state-of-the-art hardware to the rising needs for high performance by applications. Simply deploying and tuning existing software and services on state-of-the-art platforms does not necessarily ensure expected performance due to the overhead on data-copy in OS kernel functions and conservative network …

Educated Birth: Beliefs Vs. Outcomes, Lauren Presley

Human Nutrition and Hospitality Management Undergraduate Honors Theses

“Our infant mortality rate is a national embarrassment.”¹ The words seem shocking and harsh across the headline of a 2014 Washington Post article. The thought of America not only not being the best at something, but falling upsettingly behind, is a foreign concept to many who view America as a nation inferior to none. However, the statistics on infant mortality rate tell the stark truth that of 26 “wealthy” countries, the U.S. ranks last, with a sobering 6.1 deaths per 1,000 live infant births.²

Part of the Healthy People 2020 Objectives is to reduce the rate of infant …

The Use Of Lasers For Direct Pulp Capping, Takashi Komabayashi, Arata Ebihara, Akira Aoki

Dental Medicine Faculty Publications

Direct pulp capping helps extend the life of a diseased tooth by maintaining tooth vitality. Nowadays, lasers are more frequently used during direct pulp capping in the clinic, but their use has not been previously reviewed. This review presents the basic properties of currently available lasers, scientific evidence on the effects of laser application on direct pulp capping, and future directions for this technology. An extensive literature search was conducted in various databases for articles published up to January 2015. Original in vitro, in vivo, and clinical studies, reviews, and book chapters published in English were included. Various laser systems …

Research Notes Lower Prairie Creek Project Redwood National Park, Susie Van Kirk

Susie Van Kirk Papers

Project Description: to conduct Phase 1 of a narrative history project for the Lower Prairie Creek Watershed, funded by Save the Redwoods League. Phase1 of this project will be to compile reference materials, sources, conduct scoping with NPS staff and other local stakeholders to develop historical research themes that will be needed for a future narrative history of the Lower Prairie Creek Watershed. It will result in a detailed chapter outline to be submitted to NPS.

Using Precision Agriculture Field Data To Evaluate Combine Harvesting Efficiency, Justin Carroll

Agricultural Education, Communications and Technology Undergraduate Honors Theses

Soybean crops must be harvested during a limited time period using expensive combines and associated equipment. Maximizing combine field efficiency, the ratio of the actual harvesting capacity to theoretical harvesting capacity, is an important objective of machinery managers. Spatial and temporal yield data from a 2012 CaseIH 8120 Axial-Flow combine equipped with a 30-foot MacDon D-65 Draper header and the Case-IH Advanced Farming System (AFS) yield monitoring system were used to examine field efficiency when harvesting soybean in three Arkansas Delta irrigated soybean fields during the 2015 season. Time efficiencies (TE) in the three fields ranged from 72.9 to 85.8% …

Estimating The Water Quality Condition Of River And Lake Water In The Midwestern United States From Its Spectral Characteristics, Jing Tan

Open Access Dissertations

This study focuses on developing/calibrating remote sensing algorithms for water quality retrieval in Midwestern rivers and lakes. In the first part of this study, the spectral measurements collected using a hand-held spectrometer as well as water quality observations for the Wabash River and its tributary the Tippecanoe River in Indiana were used to develop empirical models for the retrieval of chlorophyll (chl) and total suspended solids (TSS). A method for removing sky and sun glint from field spectra for turbid inland waters was developed and tested. Empirical models were then developed using a subset of the field measurements with the …