Life Sciences Commons^™

Annotation Of Non-Model Species’ Genomes, Taiya Jarva

Master's Theses

The innovations in high throughput sequencing technologies in recent decades has allowed unprecedented examination and characterization of the genetic make-up of both model and non-model species, which has led to a surge in the use of genomics in fields which were previously considered unfeasible. These advances have greatly expanded the realm of possibilities in the fields of ecology and conservation. It is now possible to the identification of large cohorts of genetic markers, including single nucleotide polymorphisms (SNPs) and larger structural variants, as well as signatures of selection and local adaptation. Markers can be used to identify species, define population …

Solving The Cable Equation, A Second-Order Time Dependent Pde For Non-Ideal Cables With Action Potentials In The Mammalian Brain Using Kss Methods, Nirmohi Charbe

Master's Theses

In this thesis we shall perform the comparisons of a Krylov Subspace Spectral method with Forward Euler, Backward Euler and Crank-Nicolson to solve the Cable Equation. The Cable Equation measures action potentials in axons in a mammalian brain treated as an ideal cable in the first part of the study. We shall subject this problem to the further assumption of a non-ideal cable. Assume a non-uniform cross section area along the longitudinal axis. At the present time, the effects of torsion, curvature and material capacitance are ignored. There is particular interest to generalize the application of the PDEs including and …

Investigation Of Dead Ocean Quahogs (Arctica Islandica) Shells On The Mid-Atlantic Bight Continental Shelf, Alyssa Leclaire

Master's Theses

Ocean quahogs, Arctica islandica, are a long-lived, widely dispersed, biomass dominate in the Mid-Atlantic; therefore, quahog shells are valuable resources for studying climate change over time. Recently, dead ocean quahog shells were discovered south and inshore of the present biogeographic range of this animal. The presence of ocean quahog shells outside the current range is presumably a consequence of past regressions and transgressions of the Cold Pool, the bottom-trapped, cool body of water that allows boreal animals to live at lower latitudes. Dead ocean quahog shells were collected offshore of the DelMarVa Peninsula then radiocarbon-dated, evaluated for taphonomic condition, …

A Comparison Of Natural, Living, And Hardened Shorelines Ability To Prevent Coastal Erosion And Maintain A Healthy Ecosystem, Gabrielle Spellmann

Master's Theses

It is important to find a suitable method to protect the U.S. Gulf Coast shoreline, since its’ low elevation and the Loop current make it vulnerable to sea level rise. I focused on two manmade methods, hardened, and living shorelines, of coastal protection for when the natural marsh suffers excess erosion rates. Living shorelines are a suite of shoreline conservation and restoration techniques that usually involve some sort of hardened structure that dampens wave energy so that the native vegetation behind it can take root and stabilize the shoreline. This study looked at six different sites, all containing a natural, …

Polycyclic Aromatic Hydrocarbons And The Microbiomes Of Two Benthic Species, Samantha Ells

Master's Theses

The presence of oil has been shown to affect the microbiomes of the water column, sediments, and organisms, both by altering the diversity and the composition of those microbial communities. If the microbiome is altered it may no longer provide benefits to its host organism, impacting its ability to survive. Thus, it is important to understand the effects of large-scale contamination events including the Deepwater Horizon oil spill. This study set out to examine the effects of oil exposure on the microbiome of two benthic species, southern flounder (Paralichthys lethostigma) and eastern oysters (Crassostrea virginica) to further understand the effects …

Determining The Trophic Role Of Red Snapper (Lutjanus Campechanus) In Mississippi State Waters Using Stomach Content And Stable Isotope Analysis, Branden Kohler

Master's Theses

The goal of this study was to determine the diet composition, trophic position and ecological role of red snapper (Lutjanus campechanus) in Mississippi state waters utilizing stable isotopes (δ¹³C and δ¹⁵N) and stomach content analysis. Stable isotope analysis of fish and their prey can provide information on species-specific basal resource utilization, diet composition and trophic position which can improve food web models and inform fisheries management decisions. Particulate organic matter (POM), the presumed base of the food web, red snapper muscle tissue, and red snapper stomach contents were collected from 25 sites in 2016 and …

An Analysis Of Dredge Efficiency For Surfclam And Ocean Quahog Commercial Dredges, Leanne Poussard

Master's Theses

Between 1997 and 2011, The National Marine Fisheries Service conducted 50 depletion experiments to estimate survey gear efficiency and stock density for Atlantic surfclam (Spisula solidissima) and ocean quahog (Arctica islandica) populations using commercial hydraulic dredges. The Patch Model was formulated to estimate gear efficiency and organism density from the data. The range of efficiencies estimated is substantial, leading to uncertainty in the application of these estimates in stock assessment. Analysis of depletion experiment simulations showed that uncertainty in the estimates of gear efficiency from depletion experiments was reduced by higher numbers of dredge tows per experiment, more tow overlap …

Effects Of Water Table Depth And Edaphic Characteristics On Plant Diversity In A Southern Mississippi Pitcher Plant Bog, Patrick Kirby

Master's Theses

This study examined the effects that water table depth and soil characteristics have on plant species richness and species composition within pitcher plant bogs across seasons. Eight piezometers were installed at random distances to monitor long-term water table depth and pressure fluctuations along a ~710-meter line transect traversing upland and bog habitats. Vegetation sampling quadrats (n=128) were set up near each piezometer. Cover data and water table depths were collected in spring and late summer. Soil samples collected from each treatment group were used to obtain soil texture and nutrient data. The summer collection period yielded a total gdiversity of …

Gogo: An Improved Algorithm To Measure The Semantic Similarity Between Gene Ontology Terms, Chenguang Zhao

Master's Theses

Measuring the semantic similarity between Gene Ontology (GO) terms is an essential step in functional bioinformatics research. We implemented a software named GOGO for calculating the semantic similarity between GO terms. GOGO has the advantages of both information-content-based and hybrid methods, such as Resnik’s and Wang’s methods. Moreover, GOGO is relatively fast and does not need to calculate information content (IC) from a large gene annotation corpus but still has the advantage of using IC. This is achieved by considering the number of children nodes in the GO directed acyclic graphs when calculating the semantic contribution of an ancestor node …

Coastal Wetland Dynamics Under Sea-Level Rise And Wetland Restoration In The Northern Gulf Of Mexico Using Bayesian Multilevel Models And A Web Tool, Tyler Hardy

Master's Theses

There is currently a lack of modeling framework to predict how relative sea-level rise (SLR), combined with restoration activities, affects landscapes of coastal wetlands with uncertainties accounted for at the entire northern Gulf of Mexico (NGOM). I developed such a modeling framework – Bayesian multi-level models to study the spatial pattern of wetland loss in the NGOM, driven by relative RSLR, vegetation productivity, tidal range, coastal slope, and wave height – all interacting with river-borne sediment availability, indicated by hydrological regimes. These interactions have not been comprehensively investigated before. I further modified this model to assess the efficacy of restoration …

Life-History Characteristics And Fishery Dynamics Of Red Drum (Sciaenops Ocellatus), In The North-Central Gulf Of Mexico, Corbin Bennetts

Master's Theses

Red Drum (Sciaenops ocellatus) are highly targeted recreationally in the Gulf of Mexico, and support a small commercial fishery in Mississippi. Despite their popularity, the stock is assessed using data limited approaches that necessitate accurate life history information. I estimated the year-specific and year-aggregated escapement rates for the Mississippi stock (years 2004 to 2015), which were sensitive to mortality estimation methods; year-aggregated estimates were 6.9 to 28.2 % depending on the method, but temporal patterns were consistent. I then addressed concerns with previously estimated life-history characteristics by describing the sex-specific growth and reproductive dynamics. The three-parameter von Bertalanffy …

Combined Effects Of Dissolved Oxygen And Temperature On Aerobic Respiration And Respiratory Recovery Responses Of The Spioniform Polychaete, Streblospio Gynobranchiata, In Relation To Body Size, Alyssa Bennett

Master's Theses

Elevated surface temperatures exacerbate the threat of hypoxia within coastal ecosystems. These two primary stressors likely interact as they elicit opposing physiological responses from marine organisms. Metabolic depression is typically associated with hypoxia, while metabolic rates increase with temperature. Moreover, physiological effects of combined stressors may not be additive. In light of increasing pressures from hypoxia, elevated ocean temperatures, and other stressors within coastal regions, studies need to examine effects of multiple stressors on physiology of coastal organisms.

Mass-specific aerobic respiration (V_O2) was characterized as a proxy for metabolic cost of Streblospio gynobranchiata, at combined levels of …

Effects Of Temperature On Growth And Molting In Blue Crabs (Callinectes Sapidus) And Lesser Blue Crabs (Callinectes Similis), Abigail Ann Kuhn

Master's Theses

Temperature can exert impacts on many processes in ectotherms. With global temperatures rising due to climate change, many ectothermic species may exhibit changes in growth rates and size at maturity, and these changes can have population-level effects. Predicting responses of species to climate change will require not only knowledge of thermal tolerance limits, but also effects of temperature change on growth rates and other life history parameters. For arthropods that exhibit discontinuous growth (i.e., molting), this includes both intermolt period and growth per molt. Previous laboratory and field experiments suggest that temperature affects both intermolt period (IMP) and growth per …

Environmentally-Driven Variation In The Population Dynamics Of Gulf Menhaden (Brevoortia Patronus), Grant D. Adams

Master's Theses

Gulf Menhaden (Brevoortia patronus) is an abundant forage fish distributed throughout the Northern Gulf of Mexico (NGOM). Gulf Menhaden support the second largest fishery, by weight, in the United States and represent a key linkage between upper and lower trophic levels. Variation in the population dynamics can, therefore, pose consequences for the ecology and economy in the NGOM. Here we aim to understand variation in the individual and population dynamics of Gulf Menhaden throughout ontogeny and how such variation relates to environmental processes. We utilized a suite of fishery-dependent and –independent, remote sensing, modeled, and in situ data …

Age, Growth, And Reproduction Of Vermilion Snapper (Rhomboplites Aurorubens) In The North-Central Gulf Of Mexico, Trevor Dalton Moncrief

Master's Theses

Vermilion Snapper is a commonly harvested species of reef fish in the northern Gulf of Mexico (GOM). It supports both a large commercial and popular recreational fishery, however knowledge of this fish’s life history is limited spatially. Non-linear curve fitting was used to estimate growth parameters and Akaike information criteria (AIC) was used to determine relative model fit. The 2-parameter von Bertalanffy growth function provided the best model fit and lowest AIC score. Histological examination indicated that Vermilion Snapper are batch spawners with asynchronous oocyte development. Additionally, 17% of Vermilion Snapper in the actively spawning phase containing 24 hour POF’s …

Modern Fair-Weather And Storm Sediment Transport Around Ship Island, Mississippi: Implications For Coastal Habitats And Restoration Efforts, Eve Rettew Eisemann

Master's Theses

The Mississippi – Alabama barrier island chain is experiencing accelerated sea level rise, decreased sediment supply, and frequent hurricane impacts. These three factors drive unprecedented rates of morphology change and ecosystem reduction. All islands in the chain have experienced land loss on the order of hectares per year since records began in the 1840s. In 1969, Hurricane Camille impacted as a Category 5, breaching Ship Island, and significantly reduced viable seagrass habitat. Hurricane Katrina impacted as a Category 3 in 2005, further widening Camille Cut. To better understand the sustainability of these important islands and the ecosystems they support, sediment …

Bloom Or Bust: Retrospective Analysis Of The Giant Jellyfish, Nemopilema Nomurai (Scyphozoa: Rhizostomeae), Ecology In The East Asian Marginal Seas, Naomi Yoder

Master's Theses

The Giant Jellyfish, Nemopilema nomurai, is a large-bodied bloom-forming jellyfish that occurs in the semi-enclosed basins of the East Asian Marginal Seas. N. nomurai has bloomed more frequently in the past 20 years than in any period previously recorded. In Japan, recent N. nomurai blooms were responsible for millions of dollars in lost revenue and equipment damage to commercial fisheries alone. This study statistically analyzed 21 environmental factors in connection with N. nomurai occurrence (using occurrence as a proxy for blooms). Eight factors resulted in a statistically significant or marginally significant (p ≤ 0.10), linear or non-linear relationship with …

Fire And Fuels: Vegetation Change Over Time In The Zuni Mountains, New Mexico, Luke Wylie

Master's Theses

The Zuni Mountains are a region that has been dramatically changed by human interference. Anthropogenically, fire suppression practices have allowed a buildup of fuels and caused a change in the fire-adapted ponderosa pine ecosystem such that the new ecosystem now incorporates many fire-intolerant species. As a result, the low-severity fires that the ecosystem once depended on to regenerate the forest are much reduced, and these low-severity fires are now replaced by crown-level infernos that threaten the forest and nearby towns. In order to combat these effects, land managers are implementing fuel reduction practices and are striving to better understand the …

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 …

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 …

Naturalists’ Perspectives On The Use Of Mobile Technology During A Nature Hike, Aubin Marishka Radzewicz St. Clair

Master's Theses

Naturalists act as our link between scientific knowledge and the public’s understanding of natural history and conservation efforts. In order for them to succeed, they need access to reference materials as well as up-to-date information (Mankin, Warner, & Anderson, 1999). Incorporating mobile technology (i.e. tablets) into naturalists’ endeavors in natural history and environmental education can be used as supportive and educational tools. My project investigated how newly trained naturalists used tablet technology while leading groups of children on nature hikes. I investigated naturalists’ views on the use of mobile technology as a tool during the hikes. My research was guided …

Three-Dimensional Reconstruction Of Marine Clay Nano- And Microstructure By Transmission Electron Microscopy: Analysis Of Fabric And Pore Network, Jessica Rae Gardner Douglas

Master's Theses

Three-dimensional reconstructions of marine fine-grained sediment open a new dimension for studying nano- and microscale organo-clay fabric important to improving and advancing organic matter (OM) sequestration and fluid flow dynamics modeling. I created 3-D reconstructions of clay fabric and pore pathways from serial sections and photographic mosaics obtained using transmission electron microscopy. These reconstructions show aggregations of clay domains, surrounding OM, and pore networks. I examined a Model sample (laboratory consolidated) with 1% OM and a Natural sample (polychaete fecal pellet) with high levels of OM. Three-dimensional reconstructions were segmented into 300 nm cube subsamples to make highly localized qualitative …