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Theses/Dissertations

Old Dominion University

2012

Life Sciences

Articles 1 - 11 of 11

Full-Text Articles in Physical Sciences and Mathematics

Fecal Indicator Bacteria In Knitting Mill Creek With A Comparison Of Methods Used To Enumerate E. Coli, Manju Nagarajan Oct 2012

Fecal Indicator Bacteria In Knitting Mill Creek With A Comparison Of Methods Used To Enumerate E. Coli, Manju Nagarajan

OES Theses and Dissertations

This research seeks to evaluate the impact of an urban, multi-use neighborhood on the bacteriological quality of water in Knitting Mill Creek, a blind arm of the Lafayette River, a sub-estuary of the lower Chesapeake Bay. A principal objective was to determine the effects of rainfall, a surrogate for run-off, on water-column concentrations of fecal-indicator bacteria (FIB). I collected water samples weekly (September 2009-December 2010) and biweekly (January 2010-December 2011) at a storm-sewer outfall and a nearby marina and quantified their E. coli and enterococci concentrations using Colilert-18 and Enterolert, most-probable-number assays. In addition, I took monthly samples for these …

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Thresholds Of Change In Decomposition Rate Along A Dune/Swale Transect On A Virginia Barrier Island, Dominic J. Graziani Oct 2012

Thresholds Of Change In Decomposition Rate Along A Dune/Swale Transect On A Virginia Barrier Island, Dominic J. Graziani

Biological Sciences Theses & Dissertations

Aboveground and belowground decomposition rates were determined along a barrier island dune/swale transect located on the Virginia Coast Reserve-Long Term Ecological Research Site using litterbags and wooden dowels. The objective was to determine the influence of fine scale changes in the environment on decomposition to identify any potential thresholds affecting decomposition rate. Wax myrtle (Morella cerifera L. Small) leaves and dowels of southern yellow pine wood were used as standard substrates to evaluate environmental influences on decay. Aboveground (F=6.494, p < 0.0001) and belowground (F=5.705, p < 0.0001) decay rates (yr-1) showed significant variation among litterbag/dowel locations. Aboveground decay rates (yr-1) ranged from 0.339 (Upper Dune station) …

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A Statistical Model To Determine Multiple Binding Sites Of A Transcription Factor On Dna Using Chip-Seq Data, Rasika Jayatillake Jul 2012

A Statistical Model To Determine Multiple Binding Sites Of A Transcription Factor On Dna Using Chip-Seq Data, Rasika Jayatillake

Mathematics & Statistics Theses & Dissertations

Protein-DNA interaction is vital to many biological processes in cells such as cell division, embryo development and regulating gene expression. Chromatin Immunoprecipitation followed by massively parallel sequencing (ChIP-seq) is a new technology that can reveal protein binding sites in genome with superior accuracy. Although many methods have been proposed to find binding sites for ChIP-seq data, they can find only one binding site within a short region of the genome. In this study we introduce a statistical model to identify multiple binding sites of a transcription factor within a short region of the genome using the ChIP-seq data. Mapped sequence …

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Assessing Movement Of Fish Through Spectral Analysis Of Otolith Life History Scans, Renee Reilly Hoover Jul 2012

Assessing Movement Of Fish Through Spectral Analysis Of Otolith Life History Scans, Renee Reilly Hoover

OES Theses and Dissertations

The ability to accurately measure movement timing across environmental gradients is fundamental for testing hypotheses in marine ecology that deal with ingress, egress, and migration of fish. Timing and patterns of movement have been estimated using life-history scans of the chemical signatures encoded in fish otoliths (ear stones). I provide a quantitative approach to examining life history scan data using spectral analysis, which retrospectively measures the movement timing for individual fish. Sagittal otoliths from juvenile Atlantic croaker (Micropogonias undulates) and adult black sea bass (Centropristis striata) were sampled using laser ablation inductively coupled plasma mass spectrometry …

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De Novo Protein Structure Modeling From Cryoem Data Through A Dynamic Programming Algorithm In The Secondary Structure Topology Graph, Kamal H. Al Nasr Jul 2012

De Novo Protein Structure Modeling From Cryoem Data Through A Dynamic Programming Algorithm In The Secondary Structure Topology Graph, Kamal H. Al Nasr

Computer Science Theses & Dissertations

Proteins are the molecules carry out the vital functions and make more than the half of dry weight in every cell. Protein in nature folds into a unique and energetically favorable 3-Dimensional (3-D) structure which is critical and unique to its biological function. In contrast to other methods for protein structure determination, Electron Cryorricroscopy (CryoEM) is able to produce volumetric maps of proteins that are poorly soluble, large and hard to crystallize. Furthermore, it studies the proteins in their native environment. Unfortunately, the volumetric maps generated by current advances in CryoEM technique produces protein maps at medium resolution about (~5 …

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Identification Of Persistent Long Range Interactions In GA95 And GB95 Through Thermal Unfolding Simulations, Milen Redai Tesfamariam Jul 2012

Identification Of Persistent Long Range Interactions In GA95 And GB95 Through Thermal Unfolding Simulations, Milen Redai Tesfamariam

Chemistry & Biochemistry Theses & Dissertations

For over five decades, different experiments have been performed to research how proteins attain their native three dimensional structures. However, the folding problem continues to be a puzzle in modern science. The design of two proteins that have maximal sequence identity but different folds and functions is one method that is being used to study the relationship between protein structure and amino acid sequence. In particular, mutant proteins of Streptococcus protein G, GA and GB, have 95% sequence identity and a 3a helix fold and β4/a fold, respectively. Molecular dynamics simulations of GA95 …

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Population Structure And Connectivity Of An Important Pelagic Forage Fish In The Antarctic Ecosystem, Pleuragramma Antarcticum In Relation To Large Scale Circulation, Jason W. Ferguson Jul 2012

Population Structure And Connectivity Of An Important Pelagic Forage Fish In The Antarctic Ecosystem, Pleuragramma Antarcticum In Relation To Large Scale Circulation, Jason W. Ferguson

OES Theses and Dissertations

Ocean circulation has been identified as a major process controlling the distribution of biological material in marine systems. Large-scale transport by the Antarctic Circumpolar Current (ACC), the Ross and Weddell Gyres, and the Antarctic Coastal Current can promote spatially complex population structure in the Southern Ocean through advection. Antarctic silverfish (Pleuragramma antarcticum), a pelagic, neutrally buoyant notothenioid fish species, are distributed around the shelf systems of Antarctica and are considered an important species rivaling krill as prey for many birds, seals, whales, and other fish. We asked whether silverfish are distributed in independent, discrete populations along the shelf systems of …

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Design Of In Vivo Assays For Study Of Transport, Biocompatibility And Toxicity Of Nanoparticles, Kerry Jean Lee Apr 2012

Design Of In Vivo Assays For Study Of Transport, Biocompatibility And Toxicity Of Nanoparticles, Kerry Jean Lee

Theses and Dissertations in Biomedical Sciences

This dissertation focuses on the design of new in vivo assays for study of transport, biocompatibility and toxicity of nanoparticles (NPs) in zebrafish embryos. We synthesized and purified spherical silver (Ag) NPs with diameters, ranging from 12 to 95 nm, that are stable (non-aggregated) in egg-water media. We developed new imaging approaches to characterize the sizes of single Ag NPs in zebrafish embryos at nanometer resolution by measuring their size-dependent plasmonic spectra and scattering intensity using dark-field optical microscopy and spectroscopy (DFOMS). We used single Ag NPs because they exhibit the high quantum yield (QY) of Rayleigh scattering and resist …

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Modeling The Dispersion Of Eastern Oyster Larvae (Crassostrea Virginica) And Its Effects On The Movement Of Disease Resistant Genes In The Delaware Bay Estuary, Diego A. Narvaez Apr 2012

Modeling The Dispersion Of Eastern Oyster Larvae (Crassostrea Virginica) And Its Effects On The Movement Of Disease Resistant Genes In The Delaware Bay Estuary, Diego A. Narvaez

OES Theses and Dissertations

This study combines several models to address two primary research questions. How does the interaction of larval biology and environmental variability determine the spatial distribution of oyster larvae in Delaware Bay? What is the role of larval dispersion in the transference of disease-resistant genes? The particle-tracking module in the Regional Ocean Modeling System (ROMS) was converted into an Individual-Based model representing Eastern oyster larvae that has growth and vertical migration. Exchange of larvae between natural oyster reefs was estimated and used in an Individual-Based genetic model that simulates the genetic structure of eastern oysters. Particles were released from a number …

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Grazing On Synechococcus Spp. By The Red-Tide Dinoflagellate Karenia Brevis: Implications For Bloom Dynamics In The Gulf Of Mexico, Leo A. Procise Jan 2012

Grazing On Synechococcus Spp. By The Red-Tide Dinoflagellate Karenia Brevis: Implications For Bloom Dynamics In The Gulf Of Mexico, Leo A. Procise

OES Theses and Dissertations

Karenia brevis, the toxic dinoflagellate responsible for massive red tides in the Gulf of Mexico (GOM), causes fish kills, shellfish poisoning, and acute respiratory irritation in humans. Bloom initiation and maintenance have been linked to the physical environment as well as various nutrient input mechanisms. To date, efforts to quantify nitrogen (N) sources fueling K. brevis blooms in the GOM have not included mixotrophic grazing although many dinoflagellates, including K. brevis, are known to be capable of mixotrophy. This dissertation reports field and laboratory results demonstrating that natural bloom populations and K. brevisisolates from the West Florida …

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Eukaryotic Microbes In The Deep Sea: Abundance, Diversity, And The Effect Of Pressure, Danielle Morgan-Smith Jan 2012

Eukaryotic Microbes In The Deep Sea: Abundance, Diversity, And The Effect Of Pressure, Danielle Morgan-Smith

OES Theses and Dissertations

The dark ocean is vast, high in pressure, cold, and scarce in resources, but has been shown to support a diverse and active microbial community wherever it is studied. Such studies, however, are scarce due to the difficulty of sampling at such depths, and are difficult to interpret due to compounding effects of pressure and temperature on physiology. Protists, functionally defined as the microbial portion of the domain Eukarya, are particularly neglected in studies of deep-sea microbiology. Here, I present three studies on microbial eukaryotes in the deep sea: first, a study of the abundance of microbial eukaryotes in the …

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