Physical Sciences and Mathematics Commons^™

Identification Of Arabidopsis Gpat9 (At5g60620) As An Essential Gene Involved In Triacylglycerol Biosynthesis, Jay Shockey, Anushobha Regmi, Kimberly Cotton, Neil Adhikari, John Bowse, Philip D. Bates

Faculty Publications

The first step in the biosynthesis of nearly all plant membrane phospholipids and storage triacylglycerols is catalyzed by a glycerol-3-phosphate acyltransferase (GPAT). The requirement for an endoplasmic reticulum (ER)-localized GPAT for both of these critical metabolic pathways was recognized more than 60 years ago. However, identification of the gene(s) encoding this GPAT activity has remained elusive. Here, we present the results of a series of in vivo, in vitro, and in silico experiments in Arabidopsis (Arabidopsis thaliana) designed to assign this essential function to AtGPAT9. This gene has been highly conserved throughout evolution and is …

Elevation Promotes Long-Term Survival Of Pinus Elliottii Var. Densa, A Foundation Species Of The Endangered Pine Rockland Ecosystem In The Florida Keys, Grant L. Harley, Justin T. Maxwell, George T. Raber

Faculty Publications

The pine rockland community in southern Florida, which supports numerous state- and federally listed flora and fauna species, is considered endangered. Without its foundation species, Pinus elliottii var. densa, habitat and species diversity are lost to tropical hardwood hammock. Here, we investigate the landscape factors that contribute to the long-term persistence of pine rocklands on the 2 islands that contain the largest remaining habitat in the Florida Keys: Big Pine Key and No Name Key. Plot-level biophysical data and island-scale remotely sensed vegetation data were collected from pine rockland savannas and examined with multi-dimensional analysis. On both islands, vegetation …

No Reef Is An Island: Integrating Coral Reef Connectivity Data Into The Design Of Regional-Scale Marine Protected Area Networks, Steven R. Schill, George T. Raber, Jason J. Roberts, Eric A. Treml, Jorge Brenner, Patrick N. Halpin

Faculty Publications

We integrated coral reef connectivity data for the Caribbean and Gulf of Mexico into a conservation decision-making framework for designing a regional scale marine protected area (MPA) network that provides insight into ecological and political contexts. We used an ocean circulation model and regional coral reef data to simulate eight spawning events from 2008–2011, applying a maximum 30-day pelagic larval duration and 20% mortality rate. Coral larval dispersal patterns were analyzed between coral reefs across jurisdictional marine zones to identify spatial relationships between larval sources and destinations within countries and territories across the region. We applied our results in Marxan, …

An Integrated Drought Index (Idi) Incorporating Physical And Social Aspects, Rebecca L. Lanier

Master's Theses

The purpose of this research was to determine significant bio-physical (physical and environmental) and social variables that can be integrated into a drought index to predict areas susceptible to drought. Severe drought events are capable of causing millions of dollars in damage. The 1988 drought caused the United States approximately $40 billion in damage. Drought forecasting, modeling, and detection have, therefore, become imperative to understand the social, economic and environmental impacts of droughts, and also to explore how these impacts play a role in the occurrence of a drought. A number of drought indices widely used in the U.S. rely …

The Vascular Flora Of Wayne County, Mississippi, Daniel M. Mcnair

Master's Theses

The vascular flora of Wayne County, Mississippi, was surveyed from 2013–2015, and the species of native and naturalized plants are listed. In total, 1,135 species were identified from field collections, previously collected herbarium specimens, and field observations. These belong to 556 genera and 165 families. Four of these species represent first recorded occurrences in the state of Mississippi: Blyxa aubertii Rich., Gomphrena serrata Pav. ex Moq., Isoetes valida (Engelm.) Clute, and Polypogon interruptus Kunth. GPS coordinates are given for important collection sites representing the diversity of plant communities in the county. All voucher specimens from the survey are deposited in …

A Statistical Model For The Prediction Of Dissolved Oxygen Dynamics And The Potential For Hypoxia In The Mississippi Sound And Bight, Andreas Moshogianis

Master's Theses

Hypoxia events occur when dissolved oxygen concentrations fall below the minimum threshold (dissolved oxygen concentrations < 2 mg O₂ L^-1) necessary to avoid respiratory distress among aquatic organisms. In the Mississippi Sound and Bight, hypoxia is most prevalent from late-spring through late summer. Since hypoxia events can have dramatic effects on coastal fisheries, the spatial and temporal magnitude of hypoxia presents a clear threat to the productive fisheries in the northern Gulf of Mexico. Long-term hydrographic data were collected from eight sampling stations on a monthly basis from January 2009 to December 2011 along a cross-shelf transect from the mouth of …

Supporting Data For The Characterization Of Pna-Dna Four-Way Junctions, Douglas Van Iverson Ii, Crystal C. Serrano, Ann Marie Brahan, Arik Shams, Filbert Totsingan, Anthony J. Bell Jr.

Faculty Publications

Holliday or DNA four-way junctions (4WJs) are cruciform/bent structures composed of four DNA duplexes. 4WJs are key intermediates in homologous genetic recombination and double-strand break repair. To investigate 4WJs in vitro, junctions are assembled using four asymmetric DNA strands. The presence of four asymmetric strands about the junction branch point eliminates branch migration, and effectively immobilizes the resulting 4WJ. The purpose of these experiments is to show that immobile 4WJs composed of DNA and peptide nucleic acids (PNAs) can be distinguished from contaminating labile nucleic acid structures. These data compare the electrophoretic mobility of hybrid PNA–DNA junctions vs. …

Identities And Motives Of Naturalist Development Program Attendees And Their Relation To Professional Careers, Jennifer A. Mraz

Dissertations

In recent years, there has been much concern over the decline of biologists who actually identify themselves to be naturalists, which negatively impacts the field of conservation and the study of biology as a whole. This could result in a decrease in individuals who participate in naturalist-like activities, such as informal environmental education and environmental volunteerism. The purpose of my study was to determine what discourse identities were held by naturalist development program participants, how these discourse identities related to their volunteer motives in environmental settings, and how discourse identity related to professional careers. I defined identity through the lens …

Hybrid Aryl-Ether-Ketone And Hyperbranched Epoxy Networks, John Misasi

Dissertations

In this dissertation, relationships between chemical structures, cure kinetics and network architectures are correlated to bulk mechanical properties for novel, hybrid epoxy-amine networks. The work is split into two primary sections: the first is the synthesis and characterization of multifunctional glassy networks based on aryl-ether-ketone diamine curatives, while the second is based on the synthesis and characterization of hyperbranched epoxy polymers and their resulting networks.

Three aryl-ether-ketone (AEK) diamines of increasing molecular weights were synthesized and used to cure 4,4’-tetraglycidylether of diaminodiphenylmethane (TGDDM); the resulting networks were compared to 4,4’-diaminodiphenyl sulfone cured TGDDM. Architectural differences were created by varying cure …

Olfactory Enrichment In California Sea Lions (Zalophus Californianus), Mystera M. Samuelson

Dissertations

In the wild, California sea lions (Zalophus californianus) are exposed to a wide array of sensory information at all times. However, it is impossible for captive environments to provide this level of complexity. Therefore unique procedures and practices are necessary for the maintenance of physiological and psychological health in captive animals (Wells, 2009). This project aims to explore the behavioral effect of scent added to the environment, with the goal of improving the welfare of captive sea lions by introducing two scent types: 1.) Natural scents, found in their native environment, and 2.) Non-natural scents, not found in …

Macrobenthic Communities In The Northern Gulf Of Mexico Hypoxic Zone: Testing The Pearson-Rosenberg Model, Shivakumar Shivarudrappa

Dissertations

The Pearson and Rosenberg (P-R) conceptual model of macrobenthic succession was used to assess the impact of hypoxia (dissolved oxygen [DO] ≤ 2 mg/L) on the macrobenthic community on the continental shelf of northern Gulf of Mexico for the first time. The model uses a stress-response relationship between environmental parameters and the macrobenthic community to determine the ecological condition of the benthic habitat. The ecological significance of dissolved oxygen in a benthic habitat is well understood. In addition, the annual recurrence of bottom-water hypoxia on the Louisiana/Texas shelf during summer months is well documented.

The P-R model illustrates the decreasing …

Hydrogen Bond-Mediated Structural Order In Hydroxylated Bis-Mpa Dendritic Polymers: Experimental And Molecular Dynamics Simulation Study, Maliha N. Syed

Dissertations

Dendritic architectures are echoed throughout nature. While the significance of these pervasive patterns is not entirely clear, connections between their structures and physical properties are fascinating to contemplate. Particular interest has been paid to a family of synthetically manufactured and commercially available dendritic polymers based on 2,2-bis(hydroxymethyl) propionic acid (bis-MPA) as a monomer. Composed of two hydroxyls and a carboxyl group, bis-MPA based structures hydrogen bond (H-bond) profusely. Given the high concentration and unique spatial orientation of end-groups, as well as the multitude of carbonyl, ester, and ether interior H-bond acceptors, a set of distinct H-bond organizations may be observed …

Asymmetric Synthesis Of Cα-Methyl-Γ- And Δ-Amino Acids From A Common Synthon And Evaluation Of Thionyl Chloride Assisted Peptide Esterifications, Emily Rose Vogel

Dissertations

C^α-methyl-γ- and δ-unnatural amino acids (UAAs) are important class of biomolecules used extensively as structural scaffolds, peptidomimetics, and in the development of pharmaceuticals. Due to steric congestion surrounding the quaternary center, asymmetric preparation of α,α-disubstituted UAAs are synthetically challenging. Herein, two methods for the synthesis of chiral synthons to prepare C^α-methyl-γ- and -δ-UAAs are reported. A crucial step in both strategies includes an enzymatic hydrolysis of prochiral malonic esters with pig liver esterase (PLE). The first method utilizes the Meyer Schuster rearrangement to prepare α,β-unsaturated diesters synthons, but the preparation of the precursor propargyl alcohol decomposes …

Recreation Ecology Of Colorado Fourteeners: An Assessment Of Trail Usage And Impacts, James C. Ewing

Master's Theses

The popularity of climbing Colorado’s 14,000 ft. peaks, or “Fourteeners”, has risen dramatically in recent years, raising important sustainability and management questions. Moreover, groups managing the peaks operate with major capital constraints so their efforts need to be informed, prioritized, and efficient. This paper gauges the dynamics of trail usage, explanatory variables, and recreational impacts across all 58 Fourteeners, and details evaluation adjustments that minimize error and produce results in-step with the resource management framework. Relative to a baseline study completed in 2005, substantial changes occurred in trail usage and impact dynamics. The greatest changes were concentrated on peaks previously …

Development Of Dual-Cure Hybrid Polybenzoxazine Thermosets, Jananee Narayanan Sivakami

Dissertations

Polybenzoxazines are potential high performance thermoset replacements for traditional phenolic resins that can undergo an autocatalytic, thermally initiated ring - opening polymerization, and possess superior processing advantages including excellent shelf-life stability, zero volatile loss and limited volumetric shrinkage. The simplistic monomer synthesis and availability of a wide variety of inexpensive starting materials allows enormous molecular design flexibility for accessing a wide range of tailorable material properties for targeted applications. Despite the fact, once fully cured, benzoxazines are difficult to handle due to their inherent brittleness, leaving a very little scope for any modifications. The motivation of this dissertation is directed …

An Enantiodivergent Synthesis Of CΑ-Methyl Nipecotic Acid Analogues From δ-Lactam Derivatives Obtained Through A Highly Stereoselective Cyclization Strategy, Souvik Banerjee, Emily R. Vogel, Daniel Hinton, Michael Sterling, Douglas S. Masterson

Faculty Publications

A stereoselective and enantiodivergent strategy for the construction of δ-lactams is described. The strategy utilizes chiral malonic esters prepared from enantiomerically enriched mono esters of disubstituted malonic acid. A cyclization occurs with the selective displacement of a substituted benzyl alcohol as the leaving group. The resulting δ-lactams are then converted into nipecotic acid analogues using straightforward transformations. The resulting nipecotic acid analogues proved capable organocatalysts in Mannich reactions.

Structural Characterization Of A Newly Identified Component Of Α-Carboxysomes: The Aaa+ Domain Protein Csocbbq, Markus Sutter, Evan W. Roberts, Raul C. Gonzalez, Cassandra Bates, Salma Dawoud, Kimberly Landry, Gordon C. Cannon, Sabine Heinhorst, Cheryl A. Kerfeld

Faculty Publications

Carboxysomes are bacterial microcompartments that enhance carbon fixation by concentrating ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) and its substrate CO₂ within a proteinaceous shell. They are found in all cyanobacteria, some purple photoautotrophs and many chemoautotrophic bacteria. Carboxysomes consist of a protein shell that encapsulates several hundred molecules of RuBisCO and contain carbonic anhydrase and other accessory proteins. Genes coding for carboxysome shell components and the encapsulated proteins are typically found together in an operon. The α-carboxysome operon is embedded in a cluster of additional, conserved genes that are presumably related to its function. In many chemoautotrophs, products of the expanded carboxysome …

Abundance, Stable Isotopic Composition, And Export Fluxes Of Doc, Poc, And Dic From The Lower Mississippi River During 2006-2008, Yihua Cai, Laodong Guo, Xuri Wang, George Aiken

Faculty Publications

Sources, abundance, isotopic compositions, and export fluxes of dissolved inorganic carbon (DIC), dissolved and colloidal organic carbon (DOC and COC), and particulate organic carbon (POC), and their response to hydrologic regimes were examined through monthly sampling from the Lower Mississippi River during 2006–2008. DIC was the most abundant carbon species, followed by POC and DOC. Concentration and δ¹³C of DIC decreased with increasing river discharge, while those of DOC remained fairly stable. COC comprised 61 ± 3% of the bulk DOC with similar δ¹³C abundances but higher percentages of hydrophobic organic acids than DOC, suggesting its …

Preparation And Preliminary Dielectric Characterization Of Structured C60-Thiol-Ene Polymer Nanocomposites Assembled Using The Thiol-Ene Click Reaction, Hanaa Mohammed Ahmed, Amber Danielle Windham, Maryam M. Al-Ejji, Noora H. Al-Qahtani, Mohammad K. Hassan, Kenneth A. Mauritz, Randy K. Buchanan, J. Paige Buchanan

Faculty Publications

Fullerene-containing materials have the ability to store and release electrical energy. Therefore, fullerenes may ultimately find use in high-voltage equipment devices or as super capacitors for high electric energy storage due to this ease of manipulating their excellent dielectric properties and their high volume resistivity. A series of structured fullerene (C₆₀) polymer nanocomposites were assembled using the thiol-ene click reaction, between alkyl thiols and allyl functionalized C₆₀ derivatives. The resulting high-density C₆₀-urethane-thiol-ene (C₆₀-Thiol-Ene) networks possessed excellent mechanical properties. These novel networks were characterized using standard techniques, including infrared spectroscopy (FTIR), differential scanning calorimetry …

Force-Enhanced Atomic Refinement: Structural Modeling With Interatomic Forces In A Reverse Monte Carlo Approach Applied To Amorphous Si And Sio2, A. Pandey, Parthapratim Biswas, D. A. Drabold

Faculty Publications

We introduce a structural modeling technique, called force-enhanced atomic refinement (FEAR). The technique incorporates interatomic forces in reverse Monte Carlo (RMC) simulations for structural refinement by fitting experimental diffraction data using the conventional RMC algorithm, and minimizes the total energy and forces from an interatomic potential. We illustrate the usefulness of the approach by studying a−SiO₂ and a−Si. The structural and electronic properties of the FEAR models agree well with experimental neutron and x-ray diffraction data and the results obtained from previous molecular dynamics simulations of a−SiO₂ and a−Si. We have shown that the method is more efficient …

Sculpting The Band Gap: A Computational Approach, Kiran Prasai, Parthapratim Biswas, D.A. Drabold

Faculty Publications

Materials with optimized band gap are needed in many specialized applications. In this work, we demonstrate that Hellmann-Feynman forces associated with the gap states can be used to find atomic coordinates that yield desired electronic density of states. Using tight-binding models, we show that this approach may be used to arrive at electronically designed models of amorphous silicon and carbon. We provide a simple recipe to include a priori electronic information in the formation of computer models of materials, and prove that this information may have profound structural consequences. The models are validated with plane-wave density functional calculations.

Relativistic Elastic Differential Cross Sections For Equal Mass Nuclei, Charles M. Werneth, Khin M. Maung, W.P. Ford

Faculty Publications

The effects of relativistic kinematics are studied for nuclear collisions of equal mass nuclei. It is found that the relativistic and non-relativistic elastic scattering amplitudes are nearly indistinguishable, and, hence, the relativistic and non-relativistic differential cross sections become indistinguishable. These results are explained by analyzing the Lippmann–Schwinger equation with the first order optical potential that was employed in the calculation.

A Generalized Force-Modified Potential Energy Surface For Mechanochemical Simulations, Gopinath Subramanian, Nithin Mathew, Jeff Leiding

Faculty Publications

We describe the modifications that a spatially varying external load produces on a Born-Oppenheimer potential energy surface (PES) by calculating static quantities of interest. The effects of the external loads are exemplified using electronic structure calculations (at the HF/6-31G- level) of two different molecules: ethane and hexahydro-1,3,5-trinitro-s-triazine (RDX). The calculated transition states and Hessian matrices of stationary points show that spatially varying external loads shift the stationary points and modify the curvature of the PES, thereby affecting the harmonic transition rates by altering both the energy barrier as well as the prefactor. The harmonic spectra of both molecules are blueshifted …

Differential Effects Of Munc18s On Multiple Degranulation-Relevant Trans-Snare Complexes, Hao Xu, Matthew Grant Arnold, Sushmitha Vijay Kumar

Faculty Publications

Mast cell exocytosis, which includes compound degranulation and vesicle-associated piecemeal degranulation, requires multiple Q- and R- SNAREs. It is not clear how these SNAREs pair to form functional trans-SNARE complexes and how these trans-SNARE complexes are selectively regulated for fusion. Here we undertake a comprehensive examination of the capacity of two Q-SNARE subcomplexes (syntaxin3/SNAP-23 and syntaxin4/SNAP-23) to form fusogenic trans-SNARE complexes with each of the four granule-borne R-SNAREs (VAMP2, 3, 7, 8). We report the identification of at least six distinct trans-SNARE complexes under enhanced tethering conditions: i) VAMP2/syntaxin3/SNAP-23, ii) VAMP2/syntaxin4/SNAP-23, iii) VAMP3/syntaxin3/SNAP-23, iv) VAMP3/syntaxin4/SNAP-23, v) VAMP8/syntaxin3/SNAP-23, and vi) VAMP8/syntaxin4/SNAP-23. …

Indirect Evidence For Substantial Damping Of Low-Mode Internal Tides In The Open Ocean, Joseph K. Ansong, Brian K. Arbic, Maarten C. Buijsman, James G. Richman, Jay F. Shriver, Alan J. Wallcraft

Faculty Publications

A global high-resolution ocean circulation model forced by atmospheric fields and the M₂ tidal constituent is used to explore plausible scenarios for the damping of low-mode internal tides. The plausibility of different damping scenarios is tested by comparing the modeled barotropic tides with TPXO8, a highly accurate satellite-altimetry-constrained tide model, and by comparing the modeled coherent baroclinic tide amplitudes against along-track altimetry. Five scenarios are tested: (1) a topographic internal wave drag, argued here to represent the breaking of unresolved high vertical modes, applied to the bottom flow (default configuration), (2) a wave drag applied to the barotropic flow, …

Chesapeake Bay Nitrogen Fluxes Derived From A Land-Estuarine Ocean Biogeochemical Modeling System: Model Description, Evaluation, And Nitrogen Budgets, Yang Feng, Marjorie A.M. Friedrichs, John Wilkin, Hanqin Tian, Qichun Yang, Eileen E. Hofmann, Jerry D. Wiggert, Raleigh R. Hood

Faculty Publications

The Chesapeake Bay plays an important role in transforming riverine nutrients before they are exported to the adjacent continental shelf. Although the mean nitrogen budget of the Chesapeake Bay has been previously estimated from observations, uncertainties associated with interannually varying hydrological conditions remain. In this study, a land-estuarine-ocean biogeochemical modeling system is developed to quantify Chesapeake riverine nitrogen inputs, within-estuary nitrogen transformation processes and the ultimate export of nitrogen to the coastal ocean. Model skill was evaluated using extensive in situ and satellite-derived data, and a simulation using environmental conditions for 2001–2005 was conducted to quantify the Chesapeake Bay nitrogen …

Human Impacts On Fire In De Soto National Forest, Mississippi, U.S.A., Charles Raymond White

Master's Theses

Fire is a common occurrence in the longleaf pine (Pinus palustris) forests of the Southeast United States. Prescribed fire is used to manage these threatened ecosystems, but information regarding historical fire activity is unknown. My goals were to determine the historical fire regimes in De Soto National Forest (DSNF), southern Mississippi, and determine the influence of climate and land use history on fire activity at two study sites: Fern Gulley Ridge (FGR) and Death Scar Valley (DSV). The composite mean fire interval during the prescribed burning period (1980–2013) was 3.4 years. During settlements periods, fire intervals at FGR …

Lorentz Invariant Spacelike Surfaces Of Constant Mean Curvature In Anti-De Sitter 3-Space, Jamie Patrick Lambert

Master's Theses

In this thesis, I studied Lorentz invariant spacelike surfaces with constant mean curvature H = c in the anti-de Sitter 3-space H³₁(−c²) of constant curvature −c². In particular, I construct Lorentz invariant spacelike surfaces of constant mean curvature c and maximal Lorentz invariant spacelike surfaces in H³₁(−c²). I also studied the limit behavior of those constant mean curvature c surfaces in H³₁(−c²). It turns out that they approach a maximal catenoid in Minkowski 3-space E³₁ as c → …

The Distribution Of Dissolved Barium Along The U.S. Geotraces North Atlantic Transect: Impact Of Biogeochemical Processes, Circulation And Phase Association, Karen Renee Grissom

Master's Theses

During the last four decades, since the completion of the GEOSECS program, there has been a growing interest in the biogeochemical cycle of barium (Ba) due to its potential as a proxy for interpreting the geologic record. The typical barium distribution exhibits removal in the upper water column and regeneration at depth, consistent with its classification as a bio-intermediate element and similar to the nutrient-like profiles of silicic acid and alkalinity. To better constrain the uses of Ba, trace element clean samples were collected during the North Atlantic US GEOTRACES cruises.

The cycling of barium in the North Atlantic region …

Habitat Selection Of Gulf-Strain Striped Bass, Morone Saxatilis: Relationships To Dynamic Abiotic Environmental Characteristics Within The Biloxi River, Mississippi, Jennifer Lynne Green

Master's Theses

The purpose of this project was to provide insights about the short- and long-term patterns of habitat selection of Gulf-strain Striped Bass, Morone saxatilis, based on spatially and seasonally variable abiotic environmental characteristics (water temperature, dissolved oxygen (DO), salinity, specific conductivity, and pH) in the Biloxi River, MS system. Juvenile hatchery-reared and feral adult Gulf-strain Striped Bass were acoustically-tagged and continuously monitored via active and passive telemetry from November 2012 – June 2014. Each month the available abiotic environmental characteristics of 40 random locations within the Biloxi River, along with sub-habitat conditions occupied by acoustically-tagged Gulf-strain Striped Bass, were …