Life Sciences Commons^™

Evaluating Alternate Management Strategies For Spotted Seatrout (Cynoscion Nebulosus) In The North-Central Gulf Of Mexico, Nathaniel Wallace Jermain

Master's Theses

Spotted Seatrout (Cynoscion nebulosus) receive considerable fishing pressure as the most popular saltwater target species in the north-central Gulf of Mexico. The potential for alternate management strategies, including stock enhancement and reducing discard mortality, to support the sustainability of the stocks and the desires of stakeholders is unknown. The purpose of this study was to provide an objective evaluation of the efficacy of alternate management strategies for Spotted Seatrout in Louisiana, Mississippi, and Alabama. I used a management strategy evaluation (MSE) to measure the performance of 18 alternate management scenarios relative to control scenarios. Scenarios with a high …

Scl: A Lattice-Based Approach To Infer Three-Dimensional Chromosome Structures From Single-Cell Hi-C Data, Hao Zhu

Master's Theses

In contrast to population-based Hi-C data, single-cell Hi-C data are zero-inflated and do not indicate the frequency of proximate DNA segments. There are a limited number of computational tools that can model the three-dimensional structures of chromosomes based on single-cell Hi-C data.

We developed SCL (Single-Cell Lattice), a computational method to reconstruct three-dimensional (3D) structures of chromosomes based on single-cell Hi-C data. We designed a loss function and a 2D Gaussian function specifically for the characteristics of single-cell Hi-C data. A chromosome is represented as beads-on-a-string and stored in a 3D cubic lattice. Metropolis-Hastings simulation and simulated annealing are used …

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 …

Investigating Diel Periodicity In Export Flux In The Gulf Of Mexico Using A Particulate Imaging System, Justin Edward Blancher

Master's Theses

To estimate the diurnal periodicity in the biological pump, a floating array with a marine snow camera system at 150 m depth was used, and particles were imaged at a 40 second interval for a 24 to 30 hour period at five sites in the Gulf of Mexico in June 2017. Each image was processed to identify and size all the particles within the frame, which was then processed to determine diameter, an estimated volume, and settling speed for each particle. Using these parameters, particle mass was estimated using algebraically rearranged calculations for settling speed. Each hour during the deployment …

The Effects Of Salinity On Zootechnical Performance Of Spotted Seatrout (Cynoscion Nebulosus) In Recirculating Aquaculture Systems, Eric Gigli

Master's Theses

The spotted seatrout (Cynoscion nebulosus) is a euryhaline finfish candidate for marine aquaculture in the northern Gulf of Mexico. Aquaculture of this species currently uses salinities of 25 psu or greater making production challenging in areas where high salinity water is not available. This study aimed to document the effects of salinity on zootechnical performance of spotted seatrout embryos, early larvae, and juveniles in recirculating aquaculture systems to assist with the development of protocols for low salinity culture.

Embryos obtained from a volitional spawn at 29 psu were incubated at three salinities (12.5, 18.75, or 25 psu) until …

Methylation-Specific Differentiation Of Vaginal Epithelial Cells For Forensic Tissue Typing By Bisulfite Conversion And Pyrosequencing, Elise Pood

Master's Theses

The identification of bodily fluids and tissues is often applied to criminal investigations to clarify events that may or may not have taken place. Current forensic techniques can identify blood, saliva, seminal fluid, and spermatozoa, but there is a clear absence of reliable testing to identify vaginal epithelial tissue. Though there are serological tests available for this purpose, tissue-specific methylation markers have recently been investigated as a candidate for the identification of blood, saliva, and spermatozoa.

In this study, tissue-specific methylation markers were analyzed to identify a set of markers for the differentiation of vaginal fluid from blood, saliva, and …

Attenuated Responses To Inflammatory Cytokines In Mouse Embryonic Stem Cells: Biological Implications And The Molecular Basis, Bohan Chen

Master's Theses

Embryonic stem cells (ESCs) have attracted intense interest due to their great potential for regenerative medicine. However, their immune property is an overlooked but a significant issue that needs to be thoroughly investigated not only to resolve the concern for therapeutic applications but also for further understanding the early stage of organismal development. Recent studies demonstrated that ESCs are deficient in innate immune responses to viral/bacterial infections and inflammatory cytokines. Inflammatory conditions generally inhibit cell proliferation, which could be detrimental to ESCs, since cell proliferation is their dedicated task during early embryogenesis. Thus, I hypothesize that the attenuated innate immunity …

Age-Related Tick Infestation Patterns In Springtime Migratory Passerines, Matthew Dunning

Honors Theses

To test the hypothesis that younger migrants are more prone to arrive at stopover sites on the northern coast of the Gulf of Mexico with ticks than adult migrants, 2177 migratory passerines were screened for ticks at Gulf Coast sites in Texas and Louisiana. Fifty eight (2.7%) were infested with ticks with 28 (1.3%) being young birds and 30 (1.4%) being adult birds. The body condition of the birds was assessed to determine if tick infestation had negative consequences and if the severity of consequences varied between ages. I found no relationship of age with the prevalence of a tick …

Bottlenose Dolphin (Tursiops Truncatus) Vocal Responses To Sonar And Spectrally Pink Background Noise, Maria Zapetis

Dissertations

As human populations rise, the level of man-made noise increases globally. Naval sonar and boat traffic are underwater sound sources of particular concern to marine mammal welfare. To better understand the impact of these noise increases on cetaceans, studies can explore animals’ behavioral changes in response to noise. Studies have investigated the ‘dose-response’ relationship between the received sound pressure level of sonar signals and the behavior of cetaceans in the wild, but exposure studies in controlled environments are limited. The studies in this dissertation examined bottlenose dolphin vocal modifications during various experimental noise treatments. Acoustic recordings previously obtained for bottlenose …

The Development Of Socio-Sexual Behavior In Beluga Whales (Delphinapterus Leucas), Malin K. Lilley

Dissertations

The reproductive success of the beluga whale is critical for a species facing extinction in its endangered Cook Inlet, Alaska population. To date, little is known about the mating behavior of these whales in wild populations. On the other hand, observations of beluga whales in human care allow researchers to better understand many aspects of their daily lives and life histories that are difficult to assess in wild populations. Thus far, a catalog of socio-sexual behavior has been established based on observations of belugas; however, the developmental trajectory of socio-sexual behavior is not well-understood. The present study explored how socio-sexual …

Checklist Of The Vascular Flora, Restoration Plans, And Educational Interpretive Signs For A Remnant Prairie At The Lakewood Memorial Cemetery, Hinds County, Mississippi, Olivia Shelton

Honors Theses

A floristic survey was conducted on the eastern margin of the Lakewood Memorial Park Cemetery, located between Jackson and Clinton, Mississippi, near the western edge of the Jackson Prairie ecoregion. From soil map data and preliminary observations of the landform and flora, the eastern part of the cemetery was hypothesized to be remnant prairie now mostly covered by exotic grasses (pasture) and woodland. Plant specimens were collected, identified, and preserved in the herbarium of The University of Southern Mississippi (USMS). The survey yielded 119 species of vascular plants, of which 98 (82%) were native and 21 (18%) were non-native. Indicative …

Characterizing The Central Hemodynamic Response To Orthostasis: Influence Of Sex, Fitness And Body Composition, Benjamin Schreck

Honors Theses

Inter-individual responses to orthostasis (i.e., ability to maintain consciousness in the upright posture) exist. However, few studies provide insight into the potential mechanisms for this variation. The purpose of this thesis project was to explore individual differences (i.e., sex, fitness, and body composition) on the central hemodynamic response to a modified head-up tilt table test (HUT). Fourteen volunteers with an average age of 22±1 years and an average body mass index (BMI) of 8±1 kg/m² underwent assessments of pulse wave analysis, heart rate variability, and perfusion determination via near-infrared spectroscopy over the gastrocnemius muscle while supine, followed by a …

The Acute Effects Of Artificially-Sweetened Beverages On Cardiovascular Health, Adria Mulligan

Honors Theses

Consuming artificially-sweetened beverages instead of sugar-sweetened beverages is becoming increasingly popular among those who want to lose weight, have medical conditions that prohibit intake of sugar, or want to improve overall health. However, little research has been conducted on the repercussions of the intake of these diet drinks, specifically on how they affect the cardiovascular system. The purpose of this study was to examine the acute effects of artificially-sweetened beverages on cardiovascular health. Eight participants with no pre-existing heart conditions underwent two separate appointments, one where they consumed a 12 oz. water and one where they consumed a 12 oz. …

The Correlation Between Physical Activity And Grade Point Average, Asia Mccoy

Honors Theses

The correlation between grade point average (GPA) and physical activity has typically been researched in adolescents, but not a lot of research has focused on traditional college students. Previous research in adolescents has shown mixed outcomes, but there is still evidence that a positive correlation exists between physical activity and GPA. It is also believed that adolescents who are physically active tend to have better academic outcomes than their non-active counterparts as they mature. The primary purpose of our study was to examine the correlation between GPA and physical activity in students attending the College of Education and Human Sciences …

The Importance Of Rnd-Type Efflux Pumps In The Interactions Of Pseudomonas Aeruginosa With 4-Methoxybenzaldehyde, Sanchirmaa Namjilsuren

Honors Theses

Pseudomonas aeruginosa is a common hospital-acquired pathogen and is often associated with high mortality rates due to the development of multidrug-resistance. Antimicrobial plant-derived (phyto-) aldehydes present a promising alternative to antibiotics due to their broad-spectrum antimicrobial activity and low propensity to trigger resistance. However, two main problems preclude the widespread application of these compounds: chemical instability and low antimicrobial efficacy. The ongoing collaboration between the Mavrodi and Patton labs at USM has recently addressed the problem of chemical instability by incorporating plant aldehydes into polymer materials called Pro-Antimicrobial Networks via Degradable Acetals (PANDAs). Thus, this study aimed to address the …

Transformation Of Model Organisms With Munc13-1 For Subcloning And Protein Harvesting, Grace Dittmar

Honors Theses

Exocytosis is the process by which cells release various molecules into the extracellular space. This mechanism is accomplished by membrane fusion, in which the membrane of the transport vesicle and that of the cell itself fuse to create one continuous membrane, allowing the release of the molecules inside the vesicle. A family of proteins, known as SNARE proteins, is responsible for facilitating membrane fusion. SNARE proteins form a complex between the vesicle membrane and the plasma membrane. For various cells, such as mast cells and neurons, exocytosis is essential to carry out their vital functions. Various accessory proteins are known …

Fate Of Ingested Rna In The Two-Spotted Spider Mite, Obrie D. Scarbrough

Honors Theses

RNA interference, or RNAi, is a gene regulation mechanism that uses small noncoding RNAs (sRNAs) to silence the expression of certain genes. The application of RNAi has been extended to insect pest control. The two-spotted spider mite Tetranychus urticae is a persistent agricultural pest that tends to develop pesticide resistance at an alarming rate, making it a perfect candidate for RNAi technology development. It was hypothesized that unique sRNAs could be isolated from RNA soaked spider mites, and new synthetic RNAs could be synthesized to elicit greater knockdown than was achieved in previous studies. To perform this research, a small …

The Impact Of Oxygen On The Intracellular Survival Of Listeria Monocytogenes, Amber N. Coats

Honors Theses

Listeria monocytogenes is an intracellular pathogen that is responsible for the foodborne disease listeriosis. In order to invade host cells and establish an infection, this pathogen must travel through the gastrointestinal tract where it is exposed to a variety of stressors, including low pH, bile, and variations in oxygen concentrations. These stressors necessitate this organism’s ability to sense and respond to its environment. Previous research has shown that bacteria use two-component systems to sense and regulate genes needed for improved survival in stressful environmental conditions. The goal of this study was to determine if the expression of the putative oxygen …

Cloning, Expression, And Purification Of Fadk And Its Application In Coa-Rna Capture, Jon-Michael L. Stork

Honors Theses

Coenzyme A (CoA) is an important enzyme cofactor involved in acyl transfer reactions. Recently, CoA and its various thioesters were found to exist at the 5’ end of RNA molecules. Although the function of these molecules is still unknown due to difficulties in their isolation, their existence at the 5’ RNA end reveals potentially novel biological roles of RNA. We are exploiting the broad substrate tolerance of the medium chain fatty acid-coenzyme A ligase (FadK), hypothesizing that this enzyme will accept biotinylated medium chain fatty acid substrates, creating biotin-tagged CoA-RNA. This modified CoA-RNA can later be captured using streptavidin affinity …

The Incorporation Of Lipids Into The Cellular Membrane Of Salmonella, Betsy H. Redfern

Honors Theses

Salmonella is a gram negative, facultative anaerobic food borne pathogen and is the leading cause of deaths related to food borne illnesses. In order to establish an infection successfully, Salmonella must be able to survive in the presence of various stressors that it encounters, namely changes in pH, oxygen availability, osmolarity and bile. Previous research has shown that exposure to bile causes a shift in fatty acid composition in the cell membrane of the enteric bacterium Enterococcus faecalis. Thus, this led to the hypothesis that Salmonella incorporates fatty acids into its cellular membrane following exposure to bile and thereby protects …

The Dna Damage Response Gene Ddr48 Regulates Sterol Synthesis Genes To Confer Antifungal Resistance To The Pathogenic Fungus Histoplasma Capsulatum, Gabriella Reyes

Honors Theses

Histoplasma capsulatum is a dimorphic fungal pathogen that is endemic to the Ohio, Missouri, and Mississippi river valley regions. The fungus grows as a mold at environmental temperatures (25C) and transforms into a unicellular yeast upon inhalation by a mammalian host (37C). The mold to yeast shift is required for pathogenicity in host organisms, where the potentially fatal disease, histoplasmosis, can present. This study aims to characterize the DNA damage response protein DDR48 and the role that it plays in combating cellular stressors in H. capsulatum. We found that DDR48 is expressed strongly in the mold phase but expressed only …

Algal-Mediated Priming Effects On The Ecological Stoichiometry Of Leaf Litter Decomposition: A Meta-Analysis, Halvor M. Halvorson, Steven N. Francoeur, Robert H. Findlay, Kevin A. Kuehn

Faculty Publications

In aquatic settings, periphytic algae exude labile carbon (C) that can significantly suppress or stimulate heterotrophic decomposition of recalcitrant C via priming effects. The magnitude and direction of priming effects may depend on the availability and stoichiometry of nutrients like nitrogen (N) and phosphorus (P), which can constrain algal and heterotrophic activity; in turn, priming may affect heterotrophic acquisition not only of recalcitrant C, but also N and P. In this study, we conducted a meta-analysis of algal-mediated priming across leaf litter decomposition experiments to investigate (1) bottom-up controls on priming intensity by dissolved N and P concentrations, and (2) …

In Situ Observations Of Fish Larvae Encased Within A Pelagic Gelatinous Matrix, Adam T. Greer, Luciano M. Chiaverano, James G. Ditty, Frank J. Hernandez

Faculty Publications

The degree to which marine fish larvae aggregate (i.e. patchiness) is predominantly determined by the physical oceanographic environment. Biological traits, however, can also influence spatial distributions and have adaptive value for larvae (e.g. favorable transport or reducing predation mortality). Although several fish families are known to release eggs within a gelatinous matrix, hatched larvae have not been found inside this type of structure. We present observations of hatched, preflexion yolk-sac larvae encased within a pelagic gelatinous matrix (mass). Two different masses (40-60 mm in length) containing free swimming, elongate larvae were imaged in the northern Gulf of Mexico (nGOM) near …

Age And Growth Of Gray Triggerfish (Balistes Capriscus) From A North-Central Gulf Of Mexico Artifical Reef Zone, Amanda E. Jefferson, Robert J. Allman, Ashley E. Pacicco, James S. Franks, Frank J. Hernandez, Mark A. Albins, Sean P. Powers, Robert L. Shipp, J. Marcus Drymon

Faculty Publications

The overexploitation of many traditionally targeted reef fishes such as red snapper (Lutjanus campechanus, Poey 1860), alongside the implementation of increasingly restrictive management measures on those species, has led to increased targeting of conventionally discarded Gulf of Mexico gray triggerfish (Balistes capriscus, Gmelin 1789) commercially and recreationally. The goal of this study was to assess age and growth of gray triggerfish from the Alabama Artificial Reef Zone in the north-central Gulf of Mexico. Gray triggerfish (n = 1135) were collected predominantly from artificial habitat during 1999 – 2017. Specimens were sexed macroscopically and ages were assigned …

Too Much Workplace Sitting: A Brief Historical Perspective, Raymond Jones, Daniel P. Credeur, Stephanie M. Mccoy

Faculty Publications

Sedentary behavior is a risk factor for the development of chronic diseases, especially those of cardiovascular and metabolic origins. Prolonged sitting is one of the most common sedentary behaviors among adults. Individuals sit for hours every day for several reasons, including work and or physical limitations. Historical accounts regarding the negative health effects of prolonged sitting began with early epidemiological studies, which sparked a breakout of research examining this behavior in the workplace setting. Understanding the risks associated with prolonged workplace sitting is important when considering workplace interventions, such as sit-stand workstations. These interventions appear to be beneficial in reducing …

Sex-Specific Growth And Reproductive Dynamics Of Red Drum In The Northern Gulf Of Mexico, Corbin F. Bennetts, Robert T. Leaf, Nancy J. Brown-Peterson

Faculty Publications

The Red Drum Sciaenops ocellatus stock is heavily targeted in the Gulf of Mexico (GOM) by recreational fishers and supports a small commercial fishery in Mississippi. Despite their popularity, little recent work has been done to describe their life history. In this work, we describe sex‐specific growth and reproductive dynamics of Red Drum collected from the northern GOM from September 2016 through October 2017. We evaluated seven candidate growth models and found that the three‐parameter von Bertalanffy growth function (VBGF) was the best candidate length‐at‐age model. No significant difference in growth between sexes was observed with the three‐parameter VBGF, despite …

Importance Of Weak Trophic Interactions In The Structure Of The Food Web In La Paz Bay, Southern Gulf Of California: A Topological Approach, Andrés F. Navia, Sergio R. Maciel-Zapata, Adrián F. González-Acosta, Robert T. Leaf, Victor H. Cruz-Escalona

Faculty Publications

Here, we describe the trophic structure of the La Paz Bay, Baja California Sur, Mexico, and evaluate the role of weak trophic interactions in the ecosystem using a suite of topological indices. We used information derived from published and unpublished stomach contents analysis studies from the region to construct an unweighted and directional trophic network (comprising 250 nodes and 1528 associated interactions) to assess the impact of predators in three scenarios. Each scenario simulated the removal of weak interactions corresponding to removal of those nodes with trophic contributions less than 5%, 10%, and 15%. In each removal scenario, the nodes …

The Strength Of Migratory Connectivity For Birds En Route To Breeding Through The Gulf Of Mexico, Emily B. Cohen, Clark R. Rushing, Frank R. Moore, Michael T. Hallworth, Jeffrey A. Hostetler, Mariamar Gutierrez Ramirez, Peter P. Marra

Faculty Publications

The strength of migratory connectivity is a measure of the cohesion of populations among phases of the annual cycle, including breeding, migration, and wintering. Many Nearctic‐Neotropical species have strong migratory connectivity between breeding and wintering phases of the annual cycle. It is less clear if this strength persists during migration when multiple endogenous and exogenous factors may decrease the cohesion of populations among routes or through time along the same routes. We sampled three bird species, American redstart Setophaga ruticilla, ovenbird Seiurus aurocapilla, and wood thrush Hylocichla mustelina, during spring migration through the Gulf of Mexico region …

The Role Of Temperature In Affecting Carry-Over Effects And Larval Competition In The Globally Invasive Mosquito Aedes Albopictus, Nnaemeka F. Ezeakacha, Donald Yee

Faculty Publications

Background

Ectotherms, like mosquitoes, have evolved specific responses to variation in environmental conditions like temperature, and these responses could confer a fitness benefit or cost when carried-over to different life stages. However, effects of temperature on animals with complex life-cycles often only focus on part of their life-cycle, or only consider how single aspects of life-history may carry over to new stages. Herein we investigated how temperature affects intraspecific larval competition and carry-over effects from larval to adult stages in the widespread invasive Asian tiger mosquito Aedes albopictus.

Methods

For larval competition, larvae were reared at three densities (10, …

Predicting Protein Residue-Residue Contacts Using Random Forests And Deep Networks, Joseph Luttrell Iv, Tong Liu, Chaoyang Zhang, Zheng Wang

Faculty Publications

Background: The ability to predict which pairs of amino acid residues in a protein are in contact with each other offers many advantages for various areas of research that focus on proteins. For example, contact prediction can be used to reduce the computational complexity of predicting the structure of proteins and even to help identify functionally important regions of proteins. These predictions are becoming especially important given the relatively low number of experimentally determined protein structures compared to the amount of available protein sequence data.

Results: Here we have developed and benchmarked a set of machine learning methods …