Physical Sciences and Mathematics Commons^™

Interactive Effects Of Climate Change With Nutrients, Mercury, And Freshwater Acidification On Key Taxa In The North Atlantic Landscape Conservation Cooperative Region, Alfred E. Pinkey, Charles T. Driscoll, David C. Evers, Michael J. Hooper, Jeffrey Horan, Jess W. Jones, Rebecca S. Lazarus, Harold G. Marshall, Andrew Milliken, Barnett A. Rattner, John Schmerfold, Donald W. Sparling

Biological Sciences Faculty Publications

The North Atlantic Landscape Conservation Cooperative LCC (NA LCC) is a public-private partnership that provides information to support conservation decisions that may be affected by global climate change (GCC) and other threats. The NA LCC region extends from southeast Virginia to the Canadian Maritime Provinces. Within this region, the US National Climate Assessment documented increases in air temperature, total precipitation, frequency of heavy precipitation events, and rising sea level, and predicted more drastic changes. Here, we synthesize literature on the effects of GCC interacting with selected contaminant, nutrient, and environmental processes to adversely affect natural resources within this region. Using …

Protein Recycling In Bering Sea Algal Incubations, Eli K. Moore, H. Rodger Harvey, Jessica F. Faux, David R. Goodlett, Brook L. Nunn

OES Faculty Publications

Protein present in phytoplankton represents a large fraction of the organic nitrogen and carbon transported from its synthesis in surface waters to marine sediments. Yet relatively little is known about the longevity of identifiable protein in situ, or the potential modifications to proteins that occur during bloom termination, protein recycling and degradation. To address this knowledge gap, diatom-dominated phytoplankton was collected during the Bering Sea spring blooms of 2009 and 2010, and incubated under darkness in separate shipboard degradation experiments spanning 11 and 53 d, respectively. In each experiment, the protein distribution was monited over time using shotgun proteomics, …

Survey Of The Ectoparasites Of The Invasive Small Indian Mongoose (Herpestes Auropunctatus [Carnivora: Herpestidae]) On St. John, U.S. Virgin Islands, Kelsey L. Townsend, Karen E. Powers

Virginia Journal of Science

In March 2012, live trapping surveys were conducted for invasive small Indian mongoose (Herpestes auropunctatus) on St. John, U.S. Virgin Islands. Forty mongoose were sampled (31%, 9&) for ectoparasites, and cat fleas (Ctenocephalides felis) were discovered on 17 individuals. There was no difference in the number of ectoparasites per mongoose across age classifications (r = 0.109, P = 0.579). However, males had more cat fleas than females, even when mass was taken into account (males are generally heavier). Future behavioral studies may explain these sex differences. Although management suggestions from this research are limited, these …

Predation Thresholds In Marine Microbial Communities Applied To Environments With Low Prey Abundances, Bonnie Bailey

OES Theses and Dissertations

Prokaryotes (Bacteria and Archaea) comprise the largest component of biomass in the world's oceans. Their abundances are controlled by resource availability, viral infections and protist grazing. Many pico- and nano-eukaryotic predators grow almost as quickly as their prey, and greatly increase in numbers as soon as their prey do, leading in tum to depletion in prokaryotes. It is still unclear however, as to what extent microbial predators are able to feed in low prey environments, most prominently in the largest biome on Earth, the deep sea (below l 000 m depth). It has been hypothesized that in low prey environments, …

Predictors Patterns And Processes Of Extinction Risk In Porgies And Seabreams (Family: Sparidae), Mia Theresa B. Conteros

Biological Sciences Theses & Dissertations

A variety of human-induced changes are having profound impacts on the marine environment, and no area on the planet remains unaffected by the detrimental effects of our activities. These stressors can potentially lead to synergistic effects, causing accelerated biodiversity loss and diminished ecosystem functioning. Identification and understanding of the factors that drive species to heightened risk of extinction are important goals in conservation.

The Sparidae are commercially important and ecologically complex marine fishes; global extinction risk assessments using the IUCN Red List of Threatened Species methodology show that 9% (13 species) have increased vulnerability to population declines from intense fishing …

Discretized Agent-Based Model Of Infectious Disease Spread That Uses Contact Probability, Tyrell L. Gardner

Computational Modeling & Simulation Engineering Theses & Dissertations

This study uses contact probability in an agent-based model to simulate the spread of an infectious disease. In order to perform the study, the agent-based model must first be discretized into events. Each agent in the model is given its own infectious disease state machine taken from the Susceptible-Exposed-Infected-Recovered (SEIR) model. The agents move between squares in a grid environment where each square represents a group. Groups have a contact probability as an attribute that is used to predict whether an agent comes in close contact with another agent. The transitions between the states in the SEIR model are easily …

Spatial And Temporal Variability In Net Community Metabolism In The Middle Atlantic Bight, Georges Bank, And Gulf Of Maine: Observations Of Net Heterotrophic Phases In The Highly Productive Coastal Zone, Cory James Staryk

OES Theses and Dissertations

Net community metabolism (NCM), the balance between primary production and community respiration, was measured during two cruises, June 2011 and August 2012, in the Middle Atlantic Bight, Georges Bank and Gulf of Maine. Net heterotrophy was observed in Georges Bank and Gulf of Maine during the June 2011 cruise. During the August 2012 cruise, net heterotrophy was observed in the Middle Atlantic Bight and net autotrophy was observed in Georges Bank and the Gulf of Maine. Dark community respiration increased (DCR) with biomass and temperature. Gross community production (GCP) also increased with Chl a, bicarbonate uptake, and temperature. Net …

A Comprehensive Evaluation Of C25 Highly Branched Isoprenoid Alkenes Of Marine Diatoms As Proxies For Sea Ice Extent In The Arctic Ocean, Tetiana Muniak

OES Theses and Dissertations

Sea Ice extent is one of the major factors regulating carbon cycling and ecosystem function in the modern Arctic Ocean. It is an essential component of climate models and is crucial for the evaluation of various oceanographic processes that influence a particular region. Yet it is also one of the most difficult attributes of the ocean with respect to our ability for its accurate reconstruction from paleo records. The lack of the detailed records prior to satellite information has encouraged the development of new proxy records for the reconstruction of past

sea ice conditions. In recent years, a new monounsaturated …

Density Functional Theory Modeling Of It-Stacking And Electrophilic Donor-Acceptor Interactions With Application To Therapeutic Targeting Of Zinc-Finger Proteins, Patricia Beall Lutz

Chemistry & Biochemistry Theses & Dissertations

Several viruses, including viruses that cause cancer, contain conserved zinc finger (ZF) proteins that are essential for viral reproduction, making them attractive drug targets for cancer and viral treatment. ZFs are small protein domains that have Zn²⁺ tetrahedrally coordinated to at least 2 Cys and His. They form three classes of ZFs depending on the amino acid ligands, CCHH, CCCH, and CCCC. Zn²⁺ is stable towards redox reactions; however, the Cys thiolates are redox active. Oxidation of the Cys thiolates release Zn²⁺, and the ZF loses its tertiary structure and can no longer bind DNA or …

Improving Structural Features Prediction In Protein Structure Modeling, Ashraf Yaseen

Computer Science Theses & Dissertations

Proteins play a vital role in the biological activities of all living species. In nature, a protein folds into a specific and energetically favorable three-dimensional structure which is critical to its biological function. Hence, there has been a great effort by researchers in both experimentally determining and computationally predicting the structures of proteins.

The current experimental methods of protein structure determination are complicated, time-consuming, and expensive. On the other hand, the sequencing of proteins is fast, simple, and relatively less expensive. Thus, the gap between the number of known sequences and the determined structures is growing, and is expected to …

Computational Analysis Of Gene Expression And Connectivity Patterns In The Convoluted Structures Of Mouse Cerebellum, Tao Zeng

Computer Science Theses & Dissertations

One significant difference between evolved mammalian brains and other species is that mammalian brains exhibit increasingly convoluted structures in the cerebral cortex. Groove and ridge shaped structures named gyri and sulci expand surface area of cerebral cortex, making more functions possible. Prior studies using neuroimaging techniques such as dMRI and DTI have revealed that neural fibers are heavily connected to gyri comparing to those connected to sulci, such macro-scale experiments indicates that gyri are involved in large scale information processing while sulci process information locally. However, molecular and cellar level evidences, namely, gene expression pattern and its resulting neuronal connectivity …

Redox Active Motifs In Selenoproteins, Fei Li, Yuliya Pepelyayeva, Elias S. J. Arner, Craig A. Bayse, Sharon Rozovsky

Chemistry & Biochemistry Faculty Publications

Selenoproteins use the rare amino acid selenocysteine (Sec) to act as the first line of defense against oxidants, which are linked to aging, cancer, and neurodegenerative diseases. Many selenoproteins are oxidoreductases in which the reactive Sec is connected to a neighboring Cys and able to form a ring. These Sec-containing redox motifs govern much of the reactivity of selenoproteins. To study their fundamental properties, we have used Se-77 NMR spectroscopy in concert with theoretical calculations to determine the conformational preferences and mobility of representative motifs. This use of Se-77 as a probe enables the direct recording of the properties of …

Phytoplankton In Virginia Lakes And Reservoirs: Part Ii, Harold G. Marshall

Virginia Journal of Science

Phytoplankton composition from 16 Virginia lakes and reservoirs are discussed with emphasis on the dominant taxa, algal bloom producers, and potentially harmful species at these locations. This is a companion study to the more comprehensive publication regarding Virginia freshwater phytoplankton by Marshall (2013).

Growth And Nitrogen Uptake Kinetics In Cultured Procentrum Donghaiense, Zhangxi Hu, Shunshan Duan, Margaret R. Mulholland

OES Faculty Publications

We compared growth kinetics of Prorocentrum donghaiense cultures on different nitrogen (N) compounds including nitrate, ammonium urea, glutamic acid, dialanine, and cynate. P. donghaiense exhibited standard Monod-type growth kinetics over a range of nitrogen concentrations for all N. Compounds tested. Cultures grown on glu and urea had the highest maximum growth rates. However, cultures grown on cyanate had lower half saturation constants. Nitrogen uptake kinetics were measured in nitrate-deplete and replete batch cultures of P. donghaiense. In nitrate-deplete batch cultures, P. donghaiense exhibited Michaelis-Menten type uptake kinetics for nitrate, ammonium, urea and algal amino acids; uptake was saturated at …

Modeling Stem Cell Population Dynamics, Samiur Arif

Computer Science Theses & Dissertations

Because of the stochastic nature of biological systems, mathematical and computational modeling approaches have become more acceptable to experimentalists and clinicians in recent years as contributing to new understandings of complicated cell mechanisms and tissue physiology. Indeed, even single cell or small tissue samples are complex dynamic systems that adapt to environmental challenges in space and time which is poorly understood. Mathematical models and computer simulations can explain and uncover unknown aspects of cell behavior and tissue functions. Models based on key biological mechanisms can give interesting insights and formulate predictions that cannot be derived from physical experiments or statistical …

Benthic And Planktonic Microalgal Community Structure And Primary Productivity In Lower Chesapeake Bay, Matthew Reginald Semcheski

Biological Sciences Theses & Dissertations

Microalgal populations are trophically important to a variety of micro- and macroheterotrophs in marine and estuarine systems. In Chesapeake Bay, microalgae facilitate the survival and development of ecologically and economically relevant fauna, including shellfish and finfish populations. While regarded as significant components of coastal environments, microphytobenthic communities are historically understudied. In Chesapeake Bay, the importance of phytoplankton to the ecosystem is understood, but the contribution of microphytobenthos remains unclear. This project surveys intertidal microphytobenthic communities, in relation to phytoplankton communities, around lower Chesapeake Bay describing the taxonomic makeup of these populations, coupled with quantification of cell abundance, biomass, and primary …

Comparison Of Two Separation Methods For Biological Particles: Field-Flow Fractionation (Fff) And Sucrose Density Gradients, Cody E. Garrison

OES Theses and Dissertations

Sucrose gradient centrifugation and Field-flow fractionation (FFF) are two different particle separation methods that overcome the problems of similar size microorganisms clumping together during standard filtration methods. FFF separates particles based on size and density via the parabolic velocity profile of laminar flow in a ribbon-like channel. The sucrose method separates particles via centrifugation in a density gradient. Both techniques worked well in separating eukaryotic from prokaryotic microbes, with the preferred method depending on the type and relative abundance of organisms to be separated. Minicells were separated from mother cells in transformed Escherichia coli cultures, heterotrophic flagellates (e.g., Diplonema papillatum …

Determination Of The Ecological Condition Of Benthic Communities Affected By Polycyclic Aromatic Hydrocarbons In The Elizabeth River, Chesapeake Bay, Usa, Adam M. Webb

Biological Sciences Theses & Dissertations

The Southern Branch of the Elizabeth River, a tributary of Chesapeake Bay, has historically been polluted with hydrocarbon based industrial by-products. My study compared benthic community condition from two locations in the Southern Branch: the subtidal region near Money Point, historically affected by pollution of polycyclic aromatic hydrocarbons (PAHs), to a subtidal region near Blows Creek on the opposite shore that is putatively designated as unimpacted by P AH contamination. Samples from both study sites in the Southern Branch were compared to the benthic community condition of samples from the same habitat type designations collected as part of the Chesapeake …

Rums: Research For Undergraduates In Math And Science, David Gauthier

Undergraduate Research Symposium

Chair: Dr. David Gauthier, Department of Biological Sciences

Presenters: Elizabeth Smith, Jessica Vincent, Amarilis Dyer, Amy Johnson, Joseph Brown

Estimating Sustainable Harvests Of Eastern Oysters, Crassostrea Virginica, Thomas M. Soniat, Nathan Cooper, Eric N. Powell, John M. Klinck, Mahdi Abdelguerfi, Shengru Tu, Roger Mann, Patrick D. Banks

CCPO Publications

Sustainability of a fishery is traditionally and typically considered achieved if the exploited population does not decline in numbers or biomass over time as a result of fishing relative to biological reference point goals. Oysters, however, exhibit atypical population dynamics compared with many other commercial species. The population dynamics often display extreme natural interannual variation in numbers and biomass, and oysters create their own habitat--the reef itself. With the worldwide decline of oyster reef habitat and the oyster fisheries dependent thereon, the maintenance of shell has received renewed attention as essential to population sustainability. We apply a shell budget model …

Diuron From Maui Sugarcane Field Runoff Is Potentially Harmful To Local Coral Reefs, Thomas C. Royer, Patricia A. Tester, Thomas N. Stewart

CCPO Publications

In a grassroots effort to identify stressors influencing the health of Maui’s coral reefs, samples for the pre- and post-emergent herbicide, Diuron, were taken in July–August 2013, prior to, during, and after the passage of Tropical Storm Flossie on the south central coast of Maui, Hawaii. Diuron is routinely used on sugarcane fields adjacent to Hawaiian coastal waters and is a component of the anti-fouling paint used on small boats. It inhibits photosynthesis of terrestrial plants at concentrations as low as 0.1 parts per billion and can be lethal to endosymbiotic dinoflagellates in corals at concentrations less than 3 parts …

Basic Features Of A Cell Electroporation Model: Illustrative Behavior For Two Very Different Pulses, Reuben S. Son, Kyle C. Smith, Thiruvallur R. Gowrishankar, P. Thomas Vernier, James C. Weaver

Bioelectrics Publications

Science increasingly involves complex modeling. Here we describe a model for cell electroporation in which membrane properties are dynamically modified by poration. Spatial scales range from cell membrane thickness (5 nm) to a typical mammalian cell radius (10 μm), and can be used with idealized and experimental pulse waveforms. The model consists of traditional passive components and additional active components representing nonequilibrium processes. Model responses include measurable quantities: transmembrane voltage, membrane electrical conductance, and solute transport rates and amounts for the representative "long" and "short" pulses. The long pulse-1.5 kV/cm, 100 μs-evolves two pore subpopulations with a valley at ~5 …

An Unexpected Particle Oscillation For Electrophoresis In Viscoelastic Fluids Through A Microchannel Constriction, Xinyu Lu, Saurin Patel, Meng Zhang, Sang Woo Joo, Shizhi Qian, Amod Ogale, Xiangchun Xuan

Mechanical & Aerospace Engineering Faculty Publications

Electrophoresis plays an important role in many applications, which, however, has so far been extensively studied in Newtonian fluids only. This work presents the first experimental investigation of particle electrophoresis in viscoelastic polyethylene oxide (PEO) solutions through a microchannel constriction under pure DC electric fields. An oscillatory particle motion is observed in the constriction region, which is distinctly different from the particle behavior in a polymer-free Newtonian fluid. This stream-wise particle oscillation continues until a sufficient number of particles form a chain to pass through the constriction completely. It is speculated that such an unexpected particle oscillating phenomenon is a …

Microfluidic Electrical Sorting Of Particles Based On Shape In A Spiral Microchannel, John Dubose, Xinyu Lu, Saurin Patel, Shizhi Qian, Sang Woo Joo

Mechanical & Aerospace Engineering Faculty Publications

Shape is an intrinsic marker of cell cycle, an important factor for identifying a bioparticle, and also a useful indicator of cell state for disease diagnostics. Therefore, shape can be a specific marker in label-free particle and cell separation for various chemical and biological applications. We demonstrate in this work a continuous-flow electrical sorting of spherical and peanut-shaped particles of similar volumes in an asymmetric double-spiral microchannel. It exploits curvature-induced dielectrophoresis to focus particles to a tight stream in the first spiral without any sheath flow and subsequently displace them to shape-dependent flow paths in the second spiral without any …

Tracing Beta Strands Using Strandtwister From Cryo-Em Density Maps At Medium Resolutions, Dong Si, Jing He

Computer Science Faculty Publications

Major secondary structure elements such as α helices and β sheets can be computationally detected from cryoelectron microscopy (cryo-EM) density maps with medium resolutions of 5–10 A˚ . However, a critical piece of information for modeling atomic structures is missing, because there are no tools to detect β strands from cryo-EM maps at medium resolutions. We propose a method, StrandTwister, to detect the traces of β strands through the analysis of twist, an intrinsic nature of a β sheet. StrandTwister has been tested using 100 β sheets simulated at 10 A˚ resolution and 39 β sheets computationally detected from cryo-EM …

Reproductive Phase Determination In Male Meagre (Argyrosomus Regius, Sciaenidae): Testis Development And Histologic Corroboration Of A Gross Anatomical Scale, Nuno Prista, Leonel Gordo, Jose L. Costa, Maria J. Costa, Cynthia M. Jones

OES Faculty Publications

Reproductive stage determination of male gonads has received sparse attention in fish biology literature with few studies detailing the building of gross anatomical-and histologic scales. The meagre (Argyrosomus regius) is one of the world's largest sciaenids and supports a significant regional fishery in European and North African waters whose reproductive patterns are yet to be fully investigated. In the present study, we derive a macroscopic grading system for meagre testis using semi-quantitative graphs that feature the testis variability along the species size range and time of the year. We then describe the histological stages and reproductive phases of …

Krill, Climate, And Contrasting Future Scenarios For Arctic And Antarctic Fisheries, Margaret M. Mcbride, Padmini Dalpadado, Kenneth F. Drinkwater, Olav Rune Godø, Alistair J. Hobday, Anne B. Hollowed, Trond Kristiansen, Eugene J. Murphy, Patrick H. Ressler, Sam Subbey, Eileen E. Hofmann, Harald Loeng

CCPO Publications

Arctic and Antarcticmarine systems have incommon high latitudes, large seasonal changes in light levels, cold air and sea temperatures, and sea ice. In other ways, however, they are strikingly different, including their: age, extent, geological structure, ice stability, and foodweb structure. Both regions contain very rapidly warming areas and climate impacts have been reported, as have dramatic future projections. However, the combined effects of a changing climate on oceanographic processes and foodweb dynamics are likely to influence their future fisheries in very different ways. Differences in the life-history strategies of the key zooplankton species (Antarctic krill in the Southern Ocean …

Emergence Of Algal Blooms: The Effects Of Short-Term Variability In Water Quality On Phytoplankton Abundance, Diversity, And Community Composition In A Tidal Estuary, Todd A. Egerton, Ryan E. Morse, Harold G. Marshall, Margaret R. Mulholland

OES Faculty Publications

Algal blooms are dynamic phenomena, often attributed to environmental parameters that vary on short timescales (e.g., hours to days). Phytoplankton monitoring programs are largely designed to examine long-term trends and interannual variability. In order to better understand and evaluate the relationships between water quality variables and the genesis of algal blooms, daily samples were collected over a 34 day period in the eutrophic Lafayette River, a tidal tributary within Chesapeake Bay's estuarine complex, during spring 2006. During this period two distinct algal blooms occurred; the first was a cryptomonad bloom and this was followed by a bloom of the mixotrophic …

Lack Of Equivalence In The Elemental And Stable Isotope Chemistry Within The Sagittal Otolith Pair Of The Summer Flounder, Paralichthys Dentatus, Antranik Kajajian, Jason J. Schaffler, Cynthia M. Jones

OES Faculty Publications

In fish that are not bilaterally symmetrical, the left and right sagittae are often not symmetrical, exhibiting divergent growth patterns and mass, and may have differences in chemical composition. We investigated this in the asymmetrical summer flounder Paralichthys dentatus, collected from different nursery habitats along the US east coast. Significant differences were detected in otolith mass, δ¹³C, δ¹⁸O, Li:Ca, Mg:Ca, and Sr:Ca, and overall chemical signatures. These results refute the hypothesis of left-right equivalence that is prevalent for bilaterally symmetrical fishes. We tested whether a specific side was better suited for classification. The best models …

A Coupled Geochemical And Biogeochemical Approach To Characterize The Bioreactivity Of Dissolved Organic Matter From A Headwater Stream, Rachel L. Sleighter, Rose M. Cory, Louis A. Kaplan, Hussain A.N. Abdulla, Patrick G. Hatcher

Chemistry & Biochemistry Faculty Publications

The bioreactivity or susceptibility of dissolved organic matter (DOM) to microbial degradation in streams and rivers is of critical importance to global change studies, but a comprehensive understanding of DOM bioreactivity has been elusive due, in part, to the stunningly diverse assemblages of organic molecules within DOM. We approach this problem by employing a range of techniques to characterize DOM as it flows through biofilm reactors: dissolved organic carbon (DOC) concentrations, excitation emission matrix spectroscopy (EEMs), and ultrahigh resolution mass spectrometry. The EEMs and mass spectral data were analyzed using a combination of multivariate statistical approaches. We found that 45% …